Query 020417
Match_columns 326
No_of_seqs 215 out of 1310
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 09:34:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020417.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020417hhsearch_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 5.5E-44 1.2E-48 377.6 10.9 208 73-309 371-593 (1444)
2 KOG0542 Predicted exonuclease 100.0 3.2E-42 6.9E-47 316.8 13.7 192 112-315 53-257 (280)
3 PTZ00315 2'-phosphotransferase 100.0 5E-38 1.1E-42 320.1 22.0 209 109-325 50-280 (582)
4 PRK07748 sporulation inhibitor 100.0 8.8E-37 1.9E-41 277.1 17.3 170 116-308 5-186 (207)
5 PRK06722 exonuclease; Provisio 100.0 2.1E-34 4.6E-39 273.3 19.1 165 115-300 5-179 (281)
6 TIGR01405 polC_Gram_pos DNA po 100.0 1.1E-33 2.4E-38 309.6 18.2 207 71-306 137-359 (1213)
7 cd06133 ERI-1_3'hExo_like DEDD 100.0 8.8E-32 1.9E-36 234.6 17.7 164 117-299 1-176 (176)
8 PRK06195 DNA polymerase III su 100.0 7.1E-31 1.5E-35 252.3 18.4 160 116-303 2-165 (309)
9 smart00479 EXOIII exonuclease 100.0 3.4E-30 7.3E-35 222.2 18.8 160 116-302 1-167 (169)
10 cd06130 DNA_pol_III_epsilon_li 100.0 2.2E-30 4.8E-35 222.0 17.1 151 117-296 1-155 (156)
11 PRK00448 polC DNA polymerase I 100.0 6.5E-31 1.4E-35 291.1 17.5 207 71-306 367-588 (1437)
12 TIGR01406 dnaQ_proteo DNA poly 100.0 2.4E-30 5.2E-35 238.6 18.2 165 116-305 1-175 (225)
13 PRK06807 DNA polymerase III su 100.0 3.6E-30 7.8E-35 248.1 19.0 162 112-302 4-172 (313)
14 COG5018 KapD Inhibitor of the 100.0 9.4E-32 2E-36 235.1 6.8 176 115-306 4-189 (210)
15 PRK05711 DNA polymerase III su 100.0 5.4E-30 1.2E-34 238.6 18.4 167 116-308 5-182 (240)
16 cd06131 DNA_pol_III_epsilon_Ec 100.0 8.1E-30 1.8E-34 221.9 18.1 156 117-298 1-166 (167)
17 PRK08517 DNA polymerase III su 100.0 9.3E-30 2E-34 239.1 18.4 158 115-302 68-231 (257)
18 PRK07247 DNA polymerase III su 100.0 4.1E-29 8.8E-34 226.0 18.3 161 113-306 3-173 (195)
19 PRK07740 hypothetical protein; 100.0 4.6E-29 9.9E-34 232.6 18.5 166 111-304 53-228 (244)
20 TIGR00573 dnaq exonuclease, DN 100.0 1.6E-28 3.4E-33 224.7 19.0 169 115-306 7-181 (217)
21 PRK06063 DNA polymerase III su 100.0 8.6E-29 1.9E-33 238.5 16.9 159 115-302 15-179 (313)
22 PRK07942 DNA polymerase III su 100.0 2.6E-28 5.7E-33 225.8 17.9 169 115-303 6-181 (232)
23 PRK09145 DNA polymerase III su 100.0 2.6E-28 5.6E-33 220.6 16.8 159 115-301 29-200 (202)
24 PRK09146 DNA polymerase III su 100.0 4E-28 8.6E-33 225.9 18.1 166 111-303 41-228 (239)
25 PRK05168 ribonuclease T; Provi 100.0 5.9E-28 1.3E-32 220.4 17.3 173 115-302 17-201 (211)
26 PRK06310 DNA polymerase III su 100.0 1.3E-27 2.7E-32 223.6 18.5 162 115-302 7-174 (250)
27 PRK07246 bifunctional ATP-depe 100.0 7.5E-28 1.6E-32 257.2 19.1 161 115-304 7-172 (820)
28 PRK07883 hypothetical protein; 100.0 8.5E-28 1.8E-32 247.3 18.4 163 115-303 15-183 (557)
29 PRK06309 DNA polymerase III su 100.0 1.4E-27 2.9E-32 220.8 17.2 158 115-302 2-166 (232)
30 PRK08074 bifunctional ATP-depe 99.9 3.1E-27 6.6E-32 255.5 19.1 161 115-303 3-170 (928)
31 cd06134 RNaseT DEDDh 3'-5' exo 99.9 4.8E-27 1E-31 210.8 17.2 171 116-301 6-188 (189)
32 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 2.3E-27 4.9E-32 210.8 14.1 154 117-297 1-176 (177)
33 TIGR01298 RNaseT ribonuclease 99.9 1.7E-26 3.6E-31 209.2 16.9 172 116-302 9-192 (200)
34 TIGR01407 dinG_rel DnaQ family 99.9 2.1E-26 4.6E-31 247.0 18.9 159 116-302 1-165 (850)
35 PRK05601 DNA polymerase III su 99.9 6.7E-26 1.4E-30 221.0 18.5 164 115-304 46-251 (377)
36 cd06127 DEDDh DEDDh 3'-5' exon 99.9 7.4E-26 1.6E-30 190.5 15.2 151 118-295 1-158 (159)
37 PRK07983 exodeoxyribonuclease 99.9 8.9E-26 1.9E-30 207.6 17.1 145 117-301 2-153 (219)
38 cd06138 ExoI_N N-terminal DEDD 99.9 2.1E-25 4.5E-30 198.9 14.6 159 118-295 1-182 (183)
39 cd06135 Orn DEDDh 3'-5' exonuc 99.9 7.9E-25 1.7E-29 193.8 14.7 161 117-300 1-170 (173)
40 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 1.5E-25 3.3E-30 196.1 9.0 144 118-296 1-161 (161)
41 COG0847 DnaQ DNA polymerase II 99.9 5.1E-24 1.1E-28 196.4 17.2 161 115-301 13-181 (243)
42 cd06145 REX1_like DEDDh 3'-5' 99.9 1.4E-24 3E-29 188.2 10.5 139 118-295 1-149 (150)
43 cd06144 REX4_like DEDDh 3'-5' 99.9 2E-24 4.3E-29 187.2 9.9 146 118-296 1-152 (152)
44 PF00929 RNase_T: Exonuclease; 99.9 4.2E-26 9.1E-31 192.2 -0.7 157 118-295 1-164 (164)
45 cd06149 ISG20 DEDDh 3'-5' exon 99.9 6.8E-24 1.5E-28 185.3 9.4 142 118-296 1-157 (157)
46 PRK09182 DNA polymerase III su 99.9 2.1E-22 4.6E-27 192.7 14.5 156 115-303 37-202 (294)
47 PRK05359 oligoribonuclease; Pr 99.9 1.6E-21 3.5E-26 174.4 15.3 162 115-301 3-174 (181)
48 PRK11779 sbcB exonuclease I; P 99.8 2.2E-19 4.8E-24 181.6 19.4 168 115-301 6-197 (476)
49 cd05160 DEDDy_DNA_polB_exo DED 99.0 5.3E-09 1.2E-13 93.6 11.9 129 118-276 2-161 (199)
50 PHA02570 dexA exonuclease; Pro 98.9 1.3E-08 2.9E-13 93.5 12.6 162 118-296 4-193 (220)
51 cd06143 PAN2_exo DEDDh 3'-5' e 98.7 1.1E-07 2.3E-12 85.1 11.7 121 140-295 46-173 (174)
52 KOG2249 3'-5' exonuclease [Rep 98.7 3.1E-07 6.7E-12 86.4 12.6 152 112-300 102-264 (280)
53 cd06125 DnaQ_like_exo DnaQ-lik 98.6 2E-07 4.4E-12 75.0 9.1 49 192-251 35-83 (96)
54 COG2925 SbcB Exonuclease I [DN 98.3 7E-06 1.5E-10 80.9 12.2 164 115-298 9-197 (475)
55 cd05782 DNA_polB_like1_exo Unc 98.2 7.5E-05 1.6E-09 68.4 15.4 78 185-277 78-170 (208)
56 COG1949 Orn Oligoribonuclease 98.1 1.8E-05 3.9E-10 70.0 9.3 156 114-297 5-173 (184)
57 KOG0304 mRNA deadenylase subun 98.1 2.8E-05 6E-10 71.6 10.8 158 126-300 62-237 (239)
58 KOG3242 Oligoribonuclease (3'- 98.0 2.3E-05 4.9E-10 70.0 8.6 157 115-298 26-195 (208)
59 cd05780 DNA_polB_Kod1_like_exo 98.0 0.00016 3.5E-09 65.2 13.4 121 116-277 4-156 (195)
60 cd05781 DNA_polB_B3_exo DEDDy 97.9 0.00013 2.8E-09 65.8 11.6 112 116-276 4-144 (188)
61 PF13482 RNase_H_2: RNase_H su 97.9 7E-05 1.5E-09 64.7 8.6 110 118-278 1-117 (164)
62 PF10108 DNA_pol_B_exo2: Predi 97.9 0.00072 1.6E-08 62.3 15.6 106 185-305 37-176 (209)
63 KOG2248 3'-5' exonuclease [Rep 97.8 5.8E-05 1.3E-09 75.1 8.1 154 115-305 216-378 (380)
64 PF04857 CAF1: CAF1 family rib 97.3 0.003 6.4E-08 59.7 12.1 170 116-297 23-262 (262)
65 PRK05755 DNA polymerase I; Pro 97.3 0.0016 3.4E-08 71.4 11.1 93 187-301 357-468 (880)
66 cd05779 DNA_polB_epsilon_exo D 97.0 0.013 2.8E-07 53.7 12.3 82 182-276 70-168 (204)
67 TIGR03491 RecB family nuclease 97.0 0.0073 1.6E-07 61.5 11.8 122 115-278 284-411 (457)
68 cd06139 DNA_polA_I_Ecoli_like_ 96.8 0.0052 1.1E-07 53.8 7.9 101 181-302 48-170 (193)
69 cd05777 DNA_polB_delta_exo DED 96.7 0.067 1.5E-06 49.4 14.7 126 116-275 8-181 (230)
70 cd05783 DNA_polB_B1_exo DEDDy 96.6 0.034 7.4E-07 50.8 12.2 79 183-275 71-169 (204)
71 COG5228 POP2 mRNA deadenylase 96.0 0.011 2.4E-07 54.9 5.4 151 126-297 80-248 (299)
72 smart00486 POLBc DNA polymeras 96.0 0.22 4.7E-06 49.4 14.7 129 116-275 4-177 (471)
73 cd05785 DNA_polB_like2_exo Unc 95.6 0.14 3.1E-06 46.8 10.9 85 182-277 55-169 (207)
74 cd05784 DNA_polB_II_exo DEDDy 95.6 0.12 2.7E-06 46.8 10.3 121 116-274 4-150 (193)
75 PRK05762 DNA polymerase II; Re 95.4 0.34 7.3E-06 52.8 14.7 107 179-298 197-348 (786)
76 cd05778 DNA_polB_zeta_exo inac 95.2 0.76 1.7E-05 42.7 14.4 165 116-301 5-222 (231)
77 KOG4793 Three prime repair exo 95.0 0.15 3.3E-06 48.8 9.2 170 111-298 8-214 (318)
78 PF13017 Maelstrom: piRNA path 94.9 0.11 2.4E-06 47.9 7.9 167 128-309 10-204 (213)
79 PTZ00166 DNA polymerase delta 94.6 0.47 1E-05 53.4 13.2 154 116-299 265-483 (1054)
80 COG3359 Predicted exonuclease 93.7 0.5 1.1E-05 44.9 9.4 61 214-278 158-220 (278)
81 PF03104 DNA_pol_B_exo1: DNA p 91.0 1.2 2.7E-05 42.1 8.7 92 116-237 158-264 (325)
82 cd05776 DNA_polB_alpha_exo ina 90.1 3.1 6.7E-05 38.6 10.3 131 126-275 21-185 (234)
83 cd00007 35EXOc 3'-5' exonuclea 89.4 3.1 6.8E-05 34.2 8.9 67 186-273 40-106 (155)
84 PHA02528 43 DNA polymerase; Pr 89.4 6.6 0.00014 43.7 13.6 103 182-297 175-323 (881)
85 TIGR00592 pol2 DNA polymerase 88.5 10 0.00022 43.5 14.7 138 116-273 505-678 (1172)
86 KOG1798 DNA polymerase epsilon 87.4 2.4 5.2E-05 49.0 8.6 149 116-299 247-451 (2173)
87 PHA03036 DNA polymerase; Provi 82.7 18 0.00038 40.9 12.6 173 116-309 161-399 (1004)
88 smart00474 35EXOc 3'-5' exonuc 81.9 20 0.00044 29.9 10.4 90 189-300 64-169 (172)
89 PHA02524 43A DNA polymerase su 80.5 18 0.00039 37.8 11.1 82 178-272 173-282 (498)
90 PRK10829 ribonuclease D; Provi 76.0 17 0.00036 36.5 9.1 75 215-300 78-168 (373)
91 cd06146 mut-7_like_exo DEDDy 3 75.9 13 0.00027 33.4 7.6 83 215-299 86-192 (193)
92 KOG4793 Three prime repair exo 74.6 3.2 7E-05 40.0 3.5 150 126-299 130-288 (318)
93 COG0349 Rnd Ribonuclease D [Tr 73.1 24 0.00052 35.3 9.3 75 215-300 74-164 (361)
94 PF01612 DNA_pol_A_exo1: 3'-5' 72.7 6.7 0.00014 33.2 4.8 91 188-300 65-173 (176)
95 COG0417 PolB DNA polymerase el 67.3 40 0.00087 37.1 10.3 83 179-275 205-306 (792)
96 cd06129 RNaseD_like DEDDy 3'-5 66.4 41 0.00089 28.9 8.4 74 215-299 71-160 (161)
97 smart00481 POLIIIAc DNA polyme 66.3 2.6 5.7E-05 31.0 0.7 34 70-104 31-64 (67)
98 cd06141 WRN_exo DEDDy 3'-5' ex 63.4 35 0.00076 29.3 7.4 75 215-299 77-169 (170)
99 TIGR00593 pola DNA polymerase 62.5 20 0.00044 39.9 7.0 95 185-301 363-476 (887)
100 TIGR01388 rnd ribonuclease D. 56.5 88 0.0019 31.1 9.8 75 214-299 73-163 (367)
101 PRK05761 DNA polymerase I; Rev 53.3 42 0.00092 36.9 7.5 100 183-295 208-334 (787)
102 KOG1275 PAB-dependent poly(A) 49.0 5.3 0.00012 44.2 -0.2 75 213-301 1015-1091(1118)
103 cd06140 DNA_polA_I_Bacillus_li 43.6 1.6E+02 0.0035 25.1 8.4 68 188-276 44-112 (178)
104 cd06142 RNaseD_exo DEDDy 3'-5' 42.4 2.1E+02 0.0046 24.2 9.6 90 188-300 52-158 (178)
105 TIGR03447 mycothiol_MshC cyste 36.6 2E+02 0.0043 29.4 8.8 91 184-305 59-149 (411)
106 PRK12418 cysteinyl-tRNA synthe 35.1 1.9E+02 0.0042 29.2 8.4 91 184-305 32-122 (384)
107 PF11079 YqhG: Bacterial prote 30.0 31 0.00067 33.1 1.7 74 112-200 116-196 (260)
108 PRK07279 dnaE DNA polymerase I 23.9 33 0.00071 39.0 0.8 35 69-104 33-67 (1034)
109 PHA03308 transcriptional regul 23.3 69 0.0015 35.2 2.9 14 185-198 1358-1371(1463)
110 PLN02946 cysteine-tRNA ligase 22.0 5.5E+02 0.012 27.3 9.3 91 184-305 103-193 (557)
111 PRK06920 dnaE DNA polymerase I 22.0 30 0.00064 39.6 -0.0 35 69-104 34-68 (1107)
112 PRK14535 cysS cysteinyl-tRNA s 20.1 5.7E+02 0.012 28.1 9.0 91 184-305 271-361 (699)
113 COG0386 BtuE Glutathione perox 20.0 49 0.0011 29.5 0.9 28 135-168 132-159 (162)
No 1
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.5e-44 Score=377.56 Aligned_cols=208 Identities=18% Similarity=0.230 Sum_probs=190.3
Q ss_pred cccCCccccCccchhhhhhcCCCcceeeechh---h----hcccCCCCC--CeEEEEEeccC------CceeeeeEEEEE
Q 020417 73 YFTQGKCTMMDDVMHLEKFNHDISRDLQVDAA---A----FQHKCSQDL--DFFLVLDLEGK------IEILEFPVLMID 137 (326)
Q Consensus 73 ~~dhg~~q~~~~a~~~~~~~~~~~~~~~v~~~---~----~~~~~~~~~--~~~vVfDlETT------~EIIEIgAVkvD 137 (326)
-|||||||+||+++++++ ++++|.+||+|++ | +.|+.++.+ .+|||||+||| ++|||||||||
T Consensus 371 ITDh~~VqafP~~y~~ak-K~giK~IyG~EanlvdD~vpiv~N~~d~~l~datyVVfDiETTGLs~~~d~iIE~aAvKi- 448 (1444)
T COG2176 371 ITDHGVVQAFPEAYKAAK-KYGIKAIYGLEANLVDDGVPIVYNPDDQKLDDATYVVFDIETTGLSPVYDEIIEIAAVKI- 448 (1444)
T ss_pred EecCcchhhchHHHHhhh-hcCceEEEeeeeeeccCCCceecCccccccccccEEEEEeecCCcCcccchhhhheeeee-
Confidence 499999999999999998 5899999999997 3 338888887 47999999999 99999999999
Q ss_pred cCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEE
Q 020417 138 AKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFAT 217 (326)
Q Consensus 138 ~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ 217 (326)
++|+++|+|+.||+|.. +||.++++|| ||||+||.+|+++++||++|.+|+++++ .|||
T Consensus 449 -kng~iId~f~~Fi~P~~----pl~~~~telT---gITdeml~~a~~i~~vL~kf~~~~~d~I-------------lVAH 507 (1444)
T COG2176 449 -KNGRIIDKFQFFIKPGR----PLSATITELT---GITDEMLENAPEIEEVLEKFREFIGDSI-------------LVAH 507 (1444)
T ss_pred -eCCcchHHHHHhcCCCC----cCchhhhhcc---ccCHHHHcCCccHHHHHHHHHHHhcCcE-------------EEec
Confidence 89999999999999998 5999999998 9999999999999999999999999985 4699
Q ss_pred cCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHH
Q 020417 218 CGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQR 297 (326)
Q Consensus 218 ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ 297 (326)
|++||++ ||+.++.+.|+.. +-+++||+..+.+.++|..+ +++|+.+++.||+.++ +||||++||++||+||..
T Consensus 508 NasFD~g-Fl~~~~~k~~~~~--~~~pvIDTL~lar~L~P~~k--sh~Lg~l~kk~~v~le-~hHRA~yDaeat~~vf~~ 581 (1444)
T COG2176 508 NASFDMG-FLNTNYEKYGLEP--LTNPVIDTLELARALNPEFK--SHRLGTLCKKLGVELE-RHHRADYDAEATAKVFFV 581 (1444)
T ss_pred cCccchh-HHHHHHHHhCCcc--ccCchhhHHHHHHHhChhhh--hcchHHHHHHhCccHH-HhhhhhhhHHHHHHHHHH
Confidence 9999999 9999999988875 56899999999999998887 9999999999999994 899999999999999999
Q ss_pred HHHcCCcccccc
Q 020417 298 MLADGARVQITA 309 (326)
Q Consensus 298 ll~~g~~~~it~ 309 (326)
|+++.....|+.
T Consensus 582 f~~~~ke~Gi~~ 593 (1444)
T COG2176 582 FLKDLKEKGITN 593 (1444)
T ss_pred HHHHHHHhchhh
Confidence 988765555543
No 2
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=3.2e-42 Score=316.81 Aligned_cols=192 Identities=34% Similarity=0.689 Sum_probs=174.8
Q ss_pred CCCCeEEEEEeccC----------CceeeeeEEEEEcC-CCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHh
Q 020417 112 QDLDFFLVLDLEGK----------IEILEFPVLMIDAK-TMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHD 180 (326)
Q Consensus 112 ~~~~~~vVfDlETT----------~EIIEIgAVkvD~k-~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~ 180 (326)
|+|++++++|+|+| .||||++||.+|.. +++|.++||+||+|..+| ++|+||++|| ||.|++|+
T Consensus 53 q~fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np--~LS~fC~~lT---gI~Q~tVD 127 (280)
T KOG0542|consen 53 QPFDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENP--RLSDFCTSLT---GIQQETVD 127 (280)
T ss_pred CccceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCc--hHHHHHHHhh---CchHhhhc
Confidence 78999999999999 79999999966554 454445999999999998 8999999998 99999999
Q ss_pred CCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCc
Q 020417 181 TALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRK 260 (326)
Q Consensus 181 ~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~ 260 (326)
.||+|.+|+.+|..|+....+..+ +++++||+||+||++.||..+|++++|..|.|+++|||+++.|+.+|....
T Consensus 128 ~a~~f~~vl~~f~~Wlr~~~~~~k-----~~~~Afvtdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~ 202 (280)
T KOG0542|consen 128 EAPTFPQVLSEFDSWLRKDSLGDK-----NGKFAFVTDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPA 202 (280)
T ss_pred cCCCHHHHHHHHHHHHHHhhcccc-----cCceEEEeCchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCcc
Confidence 999999999999999998876432 368999999999999999999999999999999999999999999998743
Q ss_pred CCCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCccccc--cccCCCC
Q 020417 261 SEATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGARVQIT--ARRNPDS 315 (326)
Q Consensus 261 ~~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~~~it--~~~~~~~ 315 (326)
..+++.|++++|++++|+.|+|+|||+|+|+|+++|+.+|+.++|+ ..+.+++
T Consensus 203 --~t~it~mLe~~gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~~~In~~~~~~~~q 257 (280)
T KOG0542|consen 203 --PTNITGMLEHYGLQFEGRAHSGIDDARNIARIAQKMIRDGAEFRINELCDLWERQ 257 (280)
T ss_pred --ccCHHHHHHHhCCcccCCcccCchhHHHHHHHHHHHHhCCcEEEechhhhhcccC
Confidence 7899999999999999999999999999999999999999999999 5555544
No 3
>PTZ00315 2'-phosphotransferase; Provisional
Probab=100.00 E-value=5e-38 Score=320.10 Aligned_cols=209 Identities=31% Similarity=0.478 Sum_probs=175.6
Q ss_pred cCCCCCCeEEEEEeccC---------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHH
Q 020417 109 KCSQDLDFFLVLDLEGK---------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWH 179 (326)
Q Consensus 109 ~~~~~~~~~vVfDlETT---------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V 179 (326)
...|+|++||||||||| +||||||||+||.++|+|+++|++||||...| +|+++|++|| |||++||
T Consensus 50 ~~~q~~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p--~Ls~fct~LT---GITqe~V 124 (582)
T PTZ00315 50 IAPQPFDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNP--VLSRFCTELT---GITQSMV 124 (582)
T ss_pred cccCCCCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCC--CCChhHhhhc---CcCHHHH
Confidence 35689999999999999 69999999999988999999999999999866 6999999997 9999999
Q ss_pred hCCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhC-CCCCCCCccHhhHHHHHHh-hcC
Q 020417 180 DTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQ-IKLPPYFMEWINLKDVFYN-FYK 257 (326)
Q Consensus 180 ~~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~g-i~~p~~~~~~iDl~~l~~~-~~~ 257 (326)
++||+|++|+++|.+|+++..+.+. ..+.+++|+|||+||++.||..+|+.++ ...|..+..|+|++..+.. +++
T Consensus 125 ~~Ap~F~eVl~ef~~fL~~~~~~e~---~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p 201 (582)
T PTZ00315 125 SRADPFPVVYCEALQFLAEAGLGDA---PPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFG 201 (582)
T ss_pred hcCCCHHHHHHHHHHHHhccccccc---cccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCc
Confidence 9999999999999999998753211 1245689999999999769999998543 2344456789999766544 344
Q ss_pred CC---------cCCCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCccccccccCCCC--CCCcccccCC
Q 020417 258 PR---------KSEATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGARVQITARRNPDS--RNVQYLFEDR 325 (326)
Q Consensus 258 ~~---------~~~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~~~it~~~~~~~--~~~~~~~~~~ 325 (326)
.. ....++|.+|++.+||+++|++|||+|||++||+|+.+|+++|+.+.+|....|.. +.+.|.=.++
T Consensus 202 ~~~~~~~~~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~~~~t~~~~~~~~~~~~~~~~~~~ 280 (582)
T PTZ00315 202 NGSGCGGGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTFDTAPFRRWHAPTEASLPA 280 (582)
T ss_pred cccccccccccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCCEEEecCCCChhhhccccccccccc
Confidence 21 11368999999999999999999999999999999999999999999999999987 4666655443
No 4
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=100.00 E-value=8.8e-37 Score=277.12 Aligned_cols=170 Identities=20% Similarity=0.369 Sum_probs=151.2
Q ss_pred eEEEEEeccC------------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCC
Q 020417 116 FFLVLDLEGK------------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTAL 183 (326)
Q Consensus 116 ~~vVfDlETT------------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap 183 (326)
+|||||+||| +||||||||+++ +|+++++|++||||...+ +|+++++++| |||++||++||
T Consensus 5 ~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~--~~~i~~~f~~lV~P~~~~--~i~~~~~~lt---GIt~~~l~~ap 77 (207)
T PRK07748 5 QFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVV--GCEVEDTFSSYVKPKTFP--SLTERCKSFL---GITQEDVDKGI 77 (207)
T ss_pred eEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEe--cCcChhhhcceECCCccC--ccChhhhhhc---CcCHHHHccCC
Confidence 6999999998 489999999995 678999999999999854 5999999996 99999999999
Q ss_pred CHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCC
Q 020417 184 PFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEA 263 (326)
Q Consensus 184 ~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~ 263 (326)
+|++|+++|.+|+++. ..+++||++||++ ||.++|+++|++.| +.+.|+|+..+++.+++... .
T Consensus 78 ~~~evl~~f~~~~~~~------------~~~iv~~~~fD~~-fL~~~~~~~~~~~~-~~~~~~dl~~~~~~~~~~~~--~ 141 (207)
T PRK07748 78 SFEELVEKLAEYDKRC------------KPTIVTWGNMDMK-VLKHNCEKAGVPFP-FKGQCRDLSLEYKKFFGERN--Q 141 (207)
T ss_pred CHHHHHHHHHHHhCcC------------CeEEEEECHHHHH-HHHHHHHHcCCCCc-ccccceeHHHHHHHHhCcCC--C
Confidence 9999999999999863 2467899999999 99999999999877 35789999999888877653 7
Q ss_pred CCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCccccc
Q 020417 264 TGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGARVQIT 308 (326)
Q Consensus 264 ~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~~~it 308 (326)
++|++++++|||+..++||||++||++||+||.+|+++++.+...
T Consensus 142 ~~L~~~~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~~~ 186 (207)
T PRK07748 142 TGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVEKDKEYLVKP 186 (207)
T ss_pred CCHHHHHHHcCCCCCCCCcChHHHHHHHHHHHHHHHhCcceeecC
Confidence 899999999999987889999999999999999999988765543
No 5
>PRK06722 exonuclease; Provisional
Probab=100.00 E-value=2.1e-34 Score=273.28 Aligned_cols=165 Identities=19% Similarity=0.365 Sum_probs=143.6
Q ss_pred CeEEEEEeccC---------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCH
Q 020417 115 DFFLVLDLEGK---------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPF 185 (326)
Q Consensus 115 ~~~vVfDlETT---------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f 185 (326)
+.|||||+||| ++|||||||+|+..+++++++|++||||.. +|+++|+++| |||++||++||+|
T Consensus 5 ~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~----~I~~~i~~LT---GIT~emV~~AP~f 77 (281)
T PRK06722 5 THFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGA----RLTRHTTKLT---GITKKDLIGVEKF 77 (281)
T ss_pred CEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCC----cCCHhHhhhc---CCCHHHHcCCCCH
Confidence 68999999998 699999999996433489999999999997 5999999996 9999999999999
Q ss_pred HHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCC-CccHhhHHHHHHhhcCCCcCCCC
Q 020417 186 KEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPY-FMEWINLKDVFYNFYKPRKSEAT 264 (326)
Q Consensus 186 ~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~-~~~~iDl~~l~~~~~~~~~~~~~ 264 (326)
++|+++|.+|+++. ..||||+.||++ ||.++|+++|++.|.+ ...|+|+.+++...++....+.+
T Consensus 78 ~eVl~ef~~fig~~-------------~lvahna~FD~~-FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~ 143 (281)
T PRK06722 78 PQIIEKFIQFIGED-------------SIFVTWGKEDYR-FLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTP 143 (281)
T ss_pred HHHHHHHHHHHCCC-------------cEEEEEeHHHHH-HHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCC
Confidence 99999999999865 357999999999 9999999999987743 24689999877655543211257
Q ss_pred CHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHH
Q 020417 265 GMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLA 300 (326)
Q Consensus 265 ~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~ 300 (326)
+|+++++++||+.+|++|||++||++||+|+.+|++
T Consensus 144 sL~~l~~~lgL~~~g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 144 SLQSAVEQLGLIWEGKQHRALADAENTANILLKAYS 179 (281)
T ss_pred CHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHhc
Confidence 899999999999888999999999999999999984
No 6
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=100.00 E-value=1.1e-33 Score=309.59 Aligned_cols=207 Identities=16% Similarity=0.237 Sum_probs=181.8
Q ss_pred cccccCCccccCccchhhhhhcCCCcceeeechh---h----hcccCCCCC---CeEEEEEeccC------CceeeeeEE
Q 020417 71 CLYFTQGKCTMMDDVMHLEKFNHDISRDLQVDAA---A----FQHKCSQDL---DFFLVLDLEGK------IEILEFPVL 134 (326)
Q Consensus 71 ~~~~dhg~~q~~~~a~~~~~~~~~~~~~~~v~~~---~----~~~~~~~~~---~~~vVfDlETT------~EIIEIgAV 134 (326)
---|||+++|+||+++++.+ +.++++++|||.+ + +.|..++++ .+|||||+||| ++|||||||
T Consensus 137 iAITDH~~~~~~~~~~~~~~-~~~ikvI~GvE~~~~~d~~~~v~n~~~~~l~~~~~~VVfDiETTGL~~~~d~IIEIGAV 215 (1213)
T TIGR01405 137 IAITDHGVVQAFPEAYKAAK-KDGIKIIYGMEANLVDDRVPIVYNPDDQKLLDDATYVVFDIETTGLSPQYDEIIEFGAV 215 (1213)
T ss_pred EEEecCCCccCHHHHHHHHH-hcCCEEEEEEEEEeecccchhhcCccccccccCCcEEEEEeEecCCCCCCCeEEEEEEE
Confidence 34599999999999999887 5689999999996 2 346677776 37999999999 899999999
Q ss_pred EEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHHHHHHHHhCcccccccCCCCcceE
Q 020417 135 MIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAA 214 (326)
Q Consensus 135 kvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~ 214 (326)
+++ +|+++++|++||+|.. +|+++++++| |||++||++||++++|+++|.+|+++. +.
T Consensus 216 kv~--~g~iid~f~~~V~P~~----~I~~~~~~lt---GIT~e~L~~ap~~~evl~~f~~fl~~~-------------iL 273 (1213)
T TIGR01405 216 KVK--NGRIIDKFQFFIKPHE----PLSAFVTELT---GITQDMLENAPEIEEVLEKFKEFFKDS-------------IL 273 (1213)
T ss_pred EEE--CCeEEEEEEEEECCCC----CCCHHHHHHh---CCCHHHHhCCCCHHHHHHHHHHHhCCC-------------eE
Confidence 995 6899999999999997 4999999996 999999999999999999999999875 45
Q ss_pred EEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHH
Q 020417 215 FATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNRQVPMFGSHHLGIDDTKNITRV 294 (326)
Q Consensus 215 ~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I 294 (326)
++||+.||++ ||+++++++|++. +.+.++|+..+++.+++..+ .++|++++++||++.+ ++|||++||++|++|
T Consensus 274 VaHNa~FD~~-fL~~~~~r~g~~~--~~~~~IDTl~lar~l~p~~k--~~kL~~Lak~lgi~~~-~~HrAl~DA~aTa~I 347 (1213)
T TIGR01405 274 VAHNASFDIG-FLNTNFEKVGLEP--LENPVIDTLELARALNPEYK--SHRLGNICKKLGVDLD-DHHRADYDAEATAKV 347 (1213)
T ss_pred EEEChHHHHH-HHHHHHHHcCCCc--cCCCEeEHHHHHHHHhccCC--CCCHHHHHHHcCCCCC-CCcCHHHHHHHHHHH
Confidence 6999999999 9999999999863 34689999999998887665 8999999999999986 499999999999999
Q ss_pred HHHHHHcCCccc
Q 020417 295 LQRMLADGARVQ 306 (326)
Q Consensus 295 ~~~ll~~g~~~~ 306 (326)
+.+|+++.....
T Consensus 348 ~~~ll~~l~~~~ 359 (1213)
T TIGR01405 348 FKVMVEQLKEKG 359 (1213)
T ss_pred HHHHHHHHHHcC
Confidence 999987654333
No 7
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=100.00 E-value=8.8e-32 Score=234.60 Aligned_cols=164 Identities=35% Similarity=0.677 Sum_probs=143.2
Q ss_pred EEEEEeccC-----------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCH
Q 020417 117 FLVLDLEGK-----------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPF 185 (326)
Q Consensus 117 ~vVfDlETT-----------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f 185 (326)
|||||+||| ++|||||||++|..+++++++|+++|||...+ .++++++++| |||+++++++|+|
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~--~i~~~~~~i~---gIt~e~l~~~~~~ 75 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINP--KLSDFCTELT---GITQEDVDNAPSF 75 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCC--chhHHHHHhc---CcCHHHHhcCCCH
Confidence 799999999 28999999999875556899999999999743 5999999985 9999999999999
Q ss_pred HHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCC-CCCCCccHhhHHHHHHhhcCCCcCCCC
Q 020417 186 KEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIK-LPPYFMEWINLKDVFYNFYKPRKSEAT 264 (326)
Q Consensus 186 ~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~-~p~~~~~~iDl~~l~~~~~~~~~~~~~ 264 (326)
++|+++|.+|+++.. +..++||+.||.+ +|.+++.+.+.. .++....|+|++.+++..++..+ .+
T Consensus 76 ~~vl~~~~~~l~~~~-----------~~~~v~~~~~d~~-~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~--~~ 141 (176)
T cd06133 76 PEVLKEFLEWLGKNG-----------KYAFVTWGDWDLK-DLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKK--RT 141 (176)
T ss_pred HHHHHHHHHHHHhCC-----------CeEEEeecHhhHH-HHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCC--CC
Confidence 999999999998751 2467999999999 777787777664 35567899999999999887753 89
Q ss_pred CHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHH
Q 020417 265 GMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRML 299 (326)
Q Consensus 265 ~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll 299 (326)
+|.+++++||++.++++|+|++||++||+|+++|+
T Consensus 142 ~L~~l~~~~gi~~~~~~H~Al~DA~~~a~l~~~~~ 176 (176)
T cd06133 142 GLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176 (176)
T ss_pred CHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHhC
Confidence 99999999999998789999999999999999884
No 8
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=7.1e-31 Score=252.28 Aligned_cols=160 Identities=15% Similarity=0.283 Sum_probs=143.8
Q ss_pred eEEEEEeccC----CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHH
Q 020417 116 FFLVLDLEGK----IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQ 191 (326)
Q Consensus 116 ~~vVfDlETT----~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~ 191 (326)
.|||||+||| ++|||||||+++ +|+++++|++||||... .++++++++ ||||++||+++|+|.+|+++
T Consensus 2 ~~vviD~ETTg~~~d~IieIgav~v~--~g~i~~~f~~lv~P~~~---~~~~~~~~I---hGIT~e~v~~ap~f~ev~~~ 73 (309)
T PRK06195 2 NFVAIDFETANEKRNSPCSIGIVVVK--DGEIVEKVHYLIKPKEM---RFMPINIGI---HGIRPHMVEDELEFDKIWEK 73 (309)
T ss_pred cEEEEEEeCCCCCCCceEEEEEEEEE--CCEEEEEEEEEECCCCC---CCChhheec---cCcCHHHHhCCCCHHHHHHH
Confidence 5999999999 899999999994 78999999999999862 478888887 59999999999999999999
Q ss_pred HHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHH
Q 020417 192 FEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMK 271 (326)
Q Consensus 192 F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k 271 (326)
|.+|+++. .+|+||++||++ ||+++|++++++.|. +.|+|+..+++.+++..+ +++|.++++
T Consensus 74 ~~~fl~~~-------------~lVaHNa~FD~~-fL~~~~~r~~~~~~~--~~~idT~~lar~l~~~~~--~~~L~~L~~ 135 (309)
T PRK06195 74 IKHYFNNN-------------LVIAHNASFDIS-VLRKTLELYNIPMPS--FEYICTMKLAKNFYSNID--NARLNTVNN 135 (309)
T ss_pred HHHHhCCC-------------EEEEECcHHHHH-HHHHHHHHhCCCCCC--CCEEEHHHHHHHHcCCCC--cCCHHHHHH
Confidence 99999865 467999999999 999999999998774 589999999999887754 899999999
Q ss_pred hcCCCCCCCCCChHHHHHHHHHHHHHHHHcCC
Q 020417 272 NRQVPMFGSHHLGIDDTKNITRVLQRMLADGA 303 (326)
Q Consensus 272 ~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~ 303 (326)
+||+++ .+|+|++||++||+|+..|+++..
T Consensus 136 ~~gi~~--~~H~Al~DA~ata~l~~~l~~~~~ 165 (309)
T PRK06195 136 FLGYEF--KHHDALADAMACSNILLNISKELN 165 (309)
T ss_pred HcCCCC--cccCCHHHHHHHHHHHHHHHHHhc
Confidence 999985 589999999999999999987654
No 9
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.97 E-value=3.4e-30 Score=222.22 Aligned_cols=160 Identities=21% Similarity=0.331 Sum_probs=142.7
Q ss_pred eEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHH
Q 020417 116 FFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVI 189 (326)
Q Consensus 116 ~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl 189 (326)
+||+||+||| ++|||||||++|. ++++++|+.+|+|.. +|+++++++| ||+++++.+++++.+|+
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~--~~~~~~f~~~v~p~~----~i~~~~~~~~---Git~~~l~~~~~~~~~~ 71 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDG--GRIIVVFDTYVKPDR----PITDYATEIH---GITPEMLDDAPTFEEVL 71 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEEC--CEeEEEEEEEECCCC----CCCHHHHHHh---CCCHHHHhCCCCHHHHH
Confidence 4899999999 6899999999974 568899999999965 5999999986 99999999999999999
Q ss_pred HHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHH
Q 020417 190 QQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMG 268 (326)
Q Consensus 190 ~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~ 268 (326)
.+|.+|+++. .+++||+ +||+. ||++++.+.|+..|. ...|+|+..+++..++.. ..+|.+
T Consensus 72 ~~~~~~l~~~-------------~~v~~n~~~fD~~-~L~~~~~~~~~~~~~-~~~~iD~~~~~~~~~~~~---~~~L~~ 133 (169)
T smart00479 72 EELLEFLKGK-------------ILVAGNALNFDLR-FLKLEHPRLGIKDPP-KNPVIDTLKLARALNPGR---KYSLKK 133 (169)
T ss_pred HHHHHHhcCC-------------EEEEeCCHHHhHH-HHHHHHHHhCCCCCc-CCCeeEHHHHHHHHCCCC---CCCHHH
Confidence 9999999865 3578998 99999 999999999998774 356999999988877654 799999
Q ss_pred HHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcC
Q 020417 269 MMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADG 302 (326)
Q Consensus 269 l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g 302 (326)
+++.||++..+++|+|++||++|++|+.+|++.+
T Consensus 134 l~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 134 LAERLGLEVIGRAHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred HHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHHh
Confidence 9999999987767999999999999999998654
No 10
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.97 E-value=2.2e-30 Score=221.95 Aligned_cols=151 Identities=15% Similarity=0.244 Sum_probs=137.5
Q ss_pred EEEEEeccC----CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHHH
Q 020417 117 FLVLDLEGK----IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQF 192 (326)
Q Consensus 117 ~vVfDlETT----~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~F 192 (326)
||+||+||| ++|||||||+++ +|+++++|+.+|+|.. +++++++++| |||++++.++++|++|+++|
T Consensus 1 ~v~~D~Ettg~~~~~ii~ig~v~~~--~~~~~~~~~~~i~p~~----~~~~~~~~i~---GIt~e~l~~~~~~~~v~~~l 71 (156)
T cd06130 1 FVAIDFETANADRASACSIGLVKVR--DGQIVDTFYTLIRPPT----RFDPFNIAIH---GITPEDVADAPTFPEVWPEI 71 (156)
T ss_pred CEEEEEeCCCCCCCceEEEEEEEEE--CCEEEEEEEEEeCcCC----CCChhhcccc---CcCHHHHhcCCCHHHHHHHH
Confidence 699999999 899999999995 6899999999999998 4899999885 99999999999999999999
Q ss_pred HHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHh
Q 020417 193 EAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKN 272 (326)
Q Consensus 193 ~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~ 272 (326)
.+|+++. ..++||++||++ ||++++++.|+..+. ..|+|+..+++..++..+ .++|.+++++
T Consensus 72 ~~~l~~~-------------~lv~hn~~fD~~-~l~~~~~~~g~~~~~--~~~idt~~~~~~~~~~~~--~~~L~~l~~~ 133 (156)
T cd06130 72 KPFLGGS-------------LVVAHNASFDRS-VLRAALEAYGLPPPP--YQYLCTVRLARRVWPLLP--NHKLNTVAEH 133 (156)
T ss_pred HHHhCCC-------------EEEEeChHHhHH-HHHHHHHHcCCCCCC--CCEEEHHHHHHHHhccCC--CCCHHHHHHH
Confidence 9999864 467899999999 999999999998764 589999999998887654 8999999999
Q ss_pred cCCCCCCCCCChHHHHHHHHHHHH
Q 020417 273 RQVPMFGSHHLGIDDTKNITRVLQ 296 (326)
Q Consensus 273 lgI~~~g~hHrAldDA~~tA~I~~ 296 (326)
||++.. +|+|++||++||+|+.
T Consensus 134 ~g~~~~--~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 134 LGIELN--HHDALEDARACAEILL 155 (156)
T ss_pred cCCCcc--CcCchHHHHHHHHHHh
Confidence 999985 8999999999999884
No 11
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.97 E-value=6.5e-31 Score=291.06 Aligned_cols=207 Identities=18% Similarity=0.227 Sum_probs=179.4
Q ss_pred cccccCCccccCccchhhhhhcCCCcceeeechh---h----hcccCCCCC--CeEEEEEeccC------CceeeeeEEE
Q 020417 71 CLYFTQGKCTMMDDVMHLEKFNHDISRDLQVDAA---A----FQHKCSQDL--DFFLVLDLEGK------IEILEFPVLM 135 (326)
Q Consensus 71 ~~~~dhg~~q~~~~a~~~~~~~~~~~~~~~v~~~---~----~~~~~~~~~--~~~vVfDlETT------~EIIEIgAVk 135 (326)
---||||+||+||+++++.+ +.+++++||||.+ + +.+...+.+ ..|||||+||| ++|||||||+
T Consensus 367 IAITDH~~v~~~p~a~~~~k-~~gikvI~GvE~~~~~~~~~iv~~~~~~~L~~~~~VVfDLETTGL~~~~deIIEIgAV~ 445 (1437)
T PRK00448 367 IAITDHGVVQAFPEAYNAAK-KAGIKVIYGVEANLVDDGVPIVYNEVDRDLKDATYVVFDVETTGLSAVYDEIIEIGAVK 445 (1437)
T ss_pred EEEecCCCCcCHHHHHHHHH-hcCCceEeeeeEEEeccceeEEecCCchhhccCcEEEEEhhhcCCCCchhhhheeeeEE
Confidence 34599999999999999887 5689999999996 1 124444555 47999999999 8999999999
Q ss_pred EEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHHHHHHHHhCcccccccCCCCcceEE
Q 020417 136 IDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAF 215 (326)
Q Consensus 136 vD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~ 215 (326)
+ ++|+++++|++||+|.. +++++++++| |||++||.+++++++|+++|.+|+++. +++
T Consensus 446 V--~~G~iie~F~~~V~P~~----~I~~~~~~LT---GIT~e~L~~aps~~EaL~~f~~figg~-------------vLV 503 (1437)
T PRK00448 446 I--KNGEIIDKFEFFIKPGH----PLSAFTTELT---GITDDMVKDAPSIEEVLPKFKEFCGDS-------------ILV 503 (1437)
T ss_pred E--eCCeEeeeEEEEECCCC----CCCHHHHHHh---CCCHHHHcCCCCHHHHHHHHHHHhCCC-------------EEE
Confidence 9 47899999999999997 4999999996 999999999999999999999999875 467
Q ss_pred EEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHH
Q 020417 216 ATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVL 295 (326)
Q Consensus 216 a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~ 295 (326)
+||+.||++ ||++++++.|++.+ .+.++|+.++++.+++..+ +++|++++++||++.+ .||||++||.+||+|+
T Consensus 504 AHNa~FD~~-fL~~~l~rlgl~~l--~~~~IDTLelar~l~p~~k--~~kL~~LAk~lGL~~~-~~HrAl~DA~aTa~lf 577 (1437)
T PRK00448 504 AHNASFDVG-FINTNYEKLGLEKI--KNPVIDTLELSRFLYPELK--SHRLNTLAKKFGVELE-HHHRADYDAEATAYLL 577 (1437)
T ss_pred EeCccccHH-HHHHHHHHcCCccc--cccceeHHHHHHHHcCccc--cccHHHHHHHcCCCCC-CCcChHHHHHHHHHHH
Confidence 999999999 99999999998653 4689999999988877654 8999999999999986 5799999999999999
Q ss_pred HHHHHcCCccc
Q 020417 296 QRMLADGARVQ 306 (326)
Q Consensus 296 ~~ll~~g~~~~ 306 (326)
.+|+++.....
T Consensus 578 ~~ll~~l~~~g 588 (1437)
T PRK00448 578 IKFLKDLKEKG 588 (1437)
T ss_pred HHHHHHHHHcC
Confidence 99987654333
No 12
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.97 E-value=2.4e-30 Score=238.57 Aligned_cols=165 Identities=15% Similarity=0.160 Sum_probs=140.7
Q ss_pred eEEEEEeccC-------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHH
Q 020417 116 FFLVLDLEGK-------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEV 188 (326)
Q Consensus 116 ~~vVfDlETT-------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eV 188 (326)
.+||||+||| ++|||||||+++. ...+.++|+.||+|.. .|++.++++ ||||++||+++|+|++|
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~-~~~~~~~f~~~i~P~~----~i~~~a~~v---hGIt~e~l~~~p~f~ev 72 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVN-RMLTGDNFHVYVNPER----DMPAEAAKV---HGITDEFLADKPKFKEI 72 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEEC-CcEecceEEEEECcCC----CCCHHHHhc---cCCCHHHHhCCCCHHHH
Confidence 4899999999 5899999999853 2334579999999987 499999998 59999999999999999
Q ss_pred HHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCC--CCCccHhhHHHHHHhhcCCCcCCCCCH
Q 020417 189 IQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLP--PYFMEWINLKDVFYNFYKPRKSEATGM 266 (326)
Q Consensus 189 l~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p--~~~~~~iDl~~l~~~~~~~~~~~~~~L 266 (326)
+++|.+|+++.. .++||++||++ ||+.++++.|...+ ..++.|+|+..+++..++.. +++|
T Consensus 73 ~~~f~~fi~~~~-------------lVaHNa~FD~~-fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~---~~~L 135 (225)
T TIGR01406 73 ADEFLDFIGGSE-------------LVIHNAAFDVG-FLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQ---RNSL 135 (225)
T ss_pred HHHHHHHhCCCE-------------EEEEecHHHHH-HHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCC---CCCH
Confidence 999999998763 46899999999 99999999995332 22468999999999888765 7899
Q ss_pred HHHHHhcCCCCCCC-CCChHHHHHHHHHHHHHHHHcCCcc
Q 020417 267 MGMMKNRQVPMFGS-HHLGIDDTKNITRVLQRMLADGARV 305 (326)
Q Consensus 267 ~~l~k~lgI~~~g~-hHrAldDA~~tA~I~~~ll~~g~~~ 305 (326)
++++++|||+..+. +|+|++||+++|+|+.+|......+
T Consensus 136 ~~L~~~~gi~~~~r~~H~Al~DA~~~a~v~~~l~~~~~~~ 175 (225)
T TIGR01406 136 DALCKRFKVDNSHRTLHGALLDAHLLAEVYLALTGGQESL 175 (225)
T ss_pred HHHHHhcCCCCCCCCCcCHHHHHHHHHHHHHHHHcCCcch
Confidence 99999999997653 6999999999999999998655433
No 13
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=3.6e-30 Score=248.08 Aligned_cols=162 Identities=19% Similarity=0.250 Sum_probs=146.0
Q ss_pred CCC-CeEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCC
Q 020417 112 QDL-DFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALP 184 (326)
Q Consensus 112 ~~~-~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~ 184 (326)
|++ ++|||||+||| ++|||||||+++ +|+++++|+.+|+|.. +|+++++++| |||++||.++|+
T Consensus 4 ~~~~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~--~g~i~~~f~~lVkP~~----~I~~~a~~ih---GIT~e~l~~~~~ 74 (313)
T PRK06807 4 ISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYR--NHELVDQFVSYVNPER----PIPDRITSLT---GITNYRVSDAPT 74 (313)
T ss_pred cCCCCCEEEEEEECCCCCCCCCeEEEEEEEEEE--CCEEEEEEEEEECcCC----CCCHhhhccC---CCCHHHHhCCCC
Confidence 443 78999999999 799999999996 7899999999999998 4999999885 999999999999
Q ss_pred HHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCC
Q 020417 185 FKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEAT 264 (326)
Q Consensus 185 f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~ 264 (326)
|++|+++|.+|+++. ..|+||++||++ ||.++|.+.|++.+. +.++|+..+++.+++..+ .+
T Consensus 75 ~~evl~~f~~fl~~~-------------~lVaHNa~FD~~-fL~~~~~~~gl~~~~--~~~iDtl~la~~~~~~~~--~~ 136 (313)
T PRK06807 75 IEEVLPLFLAFLHTN-------------VIVAHNASFDMR-FLKSNVNMLGLPEPK--NKVIDTVFLAKKYMKHAP--NH 136 (313)
T ss_pred HHHHHHHHHHHHcCC-------------eEEEEcHHHHHH-HHHHHHHHcCCCCCC--CCEeeHHHHHHHHhCCCC--CC
Confidence 999999999999875 457999999999 999999999997663 579999999988887654 78
Q ss_pred CHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcC
Q 020417 265 GMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADG 302 (326)
Q Consensus 265 ~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g 302 (326)
+|++++++||++. ++|||++||.+|++|+.+++...
T Consensus 137 kL~~L~~~lgi~~--~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 137 KLETLKRMLGIRL--SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred CHHHHHHHcCCCC--CCcChHHHHHHHHHHHHHHHHhh
Confidence 9999999999997 68999999999999999998654
No 14
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.97 E-value=9.4e-32 Score=235.13 Aligned_cols=176 Identities=24% Similarity=0.397 Sum_probs=157.5
Q ss_pred CeEEEEEeccC----------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCC
Q 020417 115 DFFLVLDLEGK----------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALP 184 (326)
Q Consensus 115 ~~~vVfDlETT----------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~ 184 (326)
..++|+|+|+| .|||||+|.+|+.-+.+++|+|++||||...| .++.+|..|| ||+|..|++||-
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P--~Lt~~Ckslt---~I~Q~~VD~api 78 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFP--KLTKRCKSLT---KITQKQVDEAPI 78 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCc--hHHHHHHHhh---hhhhhhccccch
Confidence 46899999998 89999999999887889999999999999988 8999999998 999999999999
Q ss_pred HHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCC
Q 020417 185 FKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEAT 264 (326)
Q Consensus 185 f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~ 264 (326)
|..|+++|..|+..+.- ....+|++||++|++ .|.++|..+++..-++--+++|++..|..+++... ..
T Consensus 79 fs~v~E~f~r~L~~h~P--------r~~~~wa~wG~~Dm~-~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr--~t 147 (210)
T COG5018 79 FSMVFEDFIRKLNEHDP--------RKNSTWATWGNMDMK-VLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPR--LT 147 (210)
T ss_pred HHHHHHHHHHHHHhcCc--------ccCCccccccchhHH-HHHHHHHhcCCCCccccCccchHHHHHHHHhcCCc--cc
Confidence 99999999999998741 234479999999999 88899999998844445689999999999998874 69
Q ss_pred CHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCccc
Q 020417 265 GMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGARVQ 306 (326)
Q Consensus 265 ~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~~~ 306 (326)
+|+.+++++|..++|+||||||||+++++|+..+..+...+.
T Consensus 148 gln~ale~~G~sf~G~~HraldDArn~~rl~klv~~~~~~~e 189 (210)
T COG5018 148 GLNKALEEYGDSFTGTHHRALDDARNAYRLFKLVEQDKQYLE 189 (210)
T ss_pred cHHHHHHHhccccCCchhhhHHHHHHHHHHHHHHcchhhhcc
Confidence 999999999999999999999999999999999887665543
No 15
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=5.4e-30 Score=238.56 Aligned_cols=167 Identities=13% Similarity=0.198 Sum_probs=144.1
Q ss_pred eEEEEEeccC-------CceeeeeEEEEEcCCCeEE-eEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHH
Q 020417 116 FFLVLDLEGK-------IEILEFPVLMIDAKTMAFV-DLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKE 187 (326)
Q Consensus 116 ~~vVfDlETT-------~EIIEIgAVkvD~k~geii-d~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~e 187 (326)
.|||||+||| ++|||||||+++ ++.++ ++|+.||+|.. +|++.++++ ||||++||.++|+|+|
T Consensus 5 r~vvlDtETTGldp~~~drIIEIGaV~v~--~~~~~~~~f~~~i~P~~----~i~~~a~~V---HGIT~e~l~~~p~f~e 75 (240)
T PRK05711 5 RQIVLDTETTGLNQREGHRIIEIGAVELI--NRRLTGRNFHVYIKPDR----LVDPEALAV---HGITDEFLADKPTFAE 75 (240)
T ss_pred eEEEEEeeCCCcCCCCCCeEEEEEEEEEE--CCEEeccEEEEEECcCC----cCCHHHhhh---cCCCHHHHcCCCCHHH
Confidence 6999999999 489999999995 55554 68999999987 499999988 5999999999999999
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCC--CccHhhHHHHHHhhcCCCcCCCCC
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPY--FMEWINLKDVFYNFYKPRKSEATG 265 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~--~~~~iDl~~l~~~~~~~~~~~~~~ 265 (326)
|+++|.+|+++.. .++||+.||++ ||+.++++.|..+|.. +..++|+..+.+..++.. +++
T Consensus 76 v~~~f~~fi~~~~-------------lVaHNa~FD~~-fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~---~~~ 138 (240)
T PRK05711 76 VADEFLDFIRGAE-------------LIIHNAPFDIG-FMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGK---RNS 138 (240)
T ss_pred HHHHHHHHhCCCE-------------EEEEccHHhHH-HHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCC---CCC
Confidence 9999999998764 46899999999 9999999998666532 357999999999888764 689
Q ss_pred HHHHHHhcCCCCCC-CCCChHHHHHHHHHHHHHHHHcCCccccc
Q 020417 266 MMGMMKNRQVPMFG-SHHLGIDDTKNITRVLQRMLADGARVQIT 308 (326)
Q Consensus 266 L~~l~k~lgI~~~g-~hHrAldDA~~tA~I~~~ll~~g~~~~it 308 (326)
|++++++|||+..+ +.|+|+.||++||+|+.+|......+.+.
T Consensus 139 L~aL~~~~gi~~~~r~~H~AL~DA~~~A~v~~~l~~~~~~l~~~ 182 (240)
T PRK05711 139 LDALCKRYGIDNSHRTLHGALLDAEILAEVYLAMTGGQTSLGFA 182 (240)
T ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCcccccccc
Confidence 99999999998754 36999999999999999998776655553
No 16
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=99.97 E-value=8.1e-30 Score=221.95 Aligned_cols=156 Identities=13% Similarity=0.178 Sum_probs=135.6
Q ss_pred EEEEEeccC-------CceeeeeEEEEEcCCCeE-EeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHH
Q 020417 117 FLVLDLEGK-------IEILEFPVLMIDAKTMAF-VDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEV 188 (326)
Q Consensus 117 ~vVfDlETT-------~EIIEIgAVkvD~k~gei-id~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eV 188 (326)
||+||+||| ++|||||||+++ ++.+ .+.|+.+|+|.. .++++++++| |||+++++++|++++|
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~--~~~~~~~~~~~~v~P~~----~i~~~~~~ih---GIt~e~l~~~~~~~~v 71 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELI--NRRLTGNTFHVYINPER----DIPEEAFKVH---GITDEFLADKPKFAEI 71 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEE--CCcEeccEEEEEECCCC----CCCHHHHHHh---CCCHHHHhcCCCHHHH
Confidence 699999999 489999999996 3444 468999999997 4999999985 9999999999999999
Q ss_pred HHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCC-CCccHhhHHHHHHhhcCCCcCCCCCHH
Q 020417 189 IQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPP-YFMEWINLKDVFYNFYKPRKSEATGMM 267 (326)
Q Consensus 189 l~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~-~~~~~iDl~~l~~~~~~~~~~~~~~L~ 267 (326)
+++|.+|+++. ..++||++||++ ||.+++++.|+..+. ....|+|+..+++..++.. .++|+
T Consensus 72 ~~~l~~~l~~~-------------~lv~hn~~fD~~-~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~---~~~L~ 134 (167)
T cd06131 72 ADEFLDFIRGA-------------ELVIHNASFDVG-FLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGK---PNSLD 134 (167)
T ss_pred HHHHHHHHCCC-------------eEEEeChHHhHH-HHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCC---CCCHH
Confidence 99999999875 356899999999 999999998876443 2368999999988877654 68999
Q ss_pred HHHHhcCCCCCC-CCCChHHHHHHHHHHHHHH
Q 020417 268 GMMKNRQVPMFG-SHHLGIDDTKNITRVLQRM 298 (326)
Q Consensus 268 ~l~k~lgI~~~g-~hHrAldDA~~tA~I~~~l 298 (326)
+++++||++.++ ++|+|++||++||+|+.+|
T Consensus 135 ~l~~~~~i~~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 135 ALCKRFGIDNSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred HHHHHCCCCCCCCCCCChHHHHHHHHHHHHHh
Confidence 999999999864 4799999999999999876
No 17
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=9.3e-30 Score=239.11 Aligned_cols=158 Identities=17% Similarity=0.222 Sum_probs=141.4
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEV 188 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eV 188 (326)
..|||||+||| ++|||||||+++ +|+++++|+++|+|.. ++++++++| ||+++|+++||++.+|
T Consensus 68 ~~~vv~DiETTG~~~~~~~IIEIGAv~v~--~g~i~~~f~~~v~p~~-----ip~~~~~it---GIt~e~l~~ap~~~ev 137 (257)
T PRK08517 68 QVFCFVDIETNGSKPKKHQIIEIGAVKVK--NGEIIDRFESFVKAKE-----VPEYITELT---GITYEDLENAPSLKEV 137 (257)
T ss_pred CCEEEEEEeCCCCCCCCCeEEEEEEEEEE--CCEEEEEEEEEECCCC-----CChhhhhhc---CcCHHHHcCCCCHHHH
Confidence 46999999999 699999999995 7899999999999963 889999985 9999999999999999
Q ss_pred HHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHH
Q 020417 189 IQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMG 268 (326)
Q Consensus 189 l~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~ 268 (326)
+++|.+|+++. +.++||++||.+ ||.+++++.|.... .+.++|+.++++..++.. +++|++
T Consensus 138 l~~f~~fl~~~-------------v~VaHNa~FD~~-fL~~~l~r~g~~~~--~~~~ldtl~la~~~~~~~---~~~L~~ 198 (257)
T PRK08517 138 LEEFRLFLGDS-------------VFVAHNVNFDYN-FISRSLEEIGLGPL--LNRKLCTIDLAKRTIESP---RYGLSF 198 (257)
T ss_pred HHHHHHHHCCC-------------eEEEECHHHHHH-HHHHHHHHcCCCCC--CCCcEehHHHHHHHccCC---CCCHHH
Confidence 99999999865 457899999999 99999999988753 568899999988877654 799999
Q ss_pred HHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcC
Q 020417 269 MMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADG 302 (326)
Q Consensus 269 l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g 302 (326)
+++++|++.+ ++|||++||.+|++|+..++...
T Consensus 199 L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 199 LKELLGIEIE-VHHRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred HHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHh
Confidence 9999999975 78999999999999999998654
No 18
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=4.1e-29 Score=226.04 Aligned_cols=161 Identities=17% Similarity=0.223 Sum_probs=131.2
Q ss_pred CCCeEEEEEeccC-----CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHH
Q 020417 113 DLDFFLVLDLEGK-----IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKE 187 (326)
Q Consensus 113 ~~~~~vVfDlETT-----~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~e 187 (326)
.+++|||||+||| ++|||||||+++ +|+++++|++||+|.. +++++++++| |||++||++||+|.+
T Consensus 3 ~~~~~vvlD~EtTGl~~~~eIIeIgaV~v~--~g~~~~~f~~lv~P~~----~i~~~~~~lh---GIt~~~v~~ap~~~e 73 (195)
T PRK07247 3 RLETYIAFDLEFNTVNGVSHIIQVSAVKYD--DHKEVDSFDSYVYTDV----PLQSFINGLT---GITADKIADAPKVEE 73 (195)
T ss_pred cCCeEEEEEeeCCCCCCCCeEEEEEEEEEE--CCEEEEEEEEEECCCC----CCCccceecC---CCCHHHHhCCCCHHH
Confidence 4578999999999 799999999995 6888999999999987 4999999985 999999999999999
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEEcCc-ccHHHHHHHHHHHhCCCCCCCCccHhhHHHHH-H-hh--cCCCcCC
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGN-WDLKTKVPDQCKVSQIKLPPYFMEWINLKDVF-Y-NF--YKPRKSE 262 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~-fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~-~-~~--~~~~~~~ 262 (326)
|+++|.+|+++.. .++||+. ||++ ||.+ .|+..+. ..++|+.+.. . .. ++.. .
T Consensus 74 vl~~f~~f~~~~~-------------lVaHNa~~fD~~-fL~~----~g~~~~~--~~~idt~~~~~~~~~~~~~~~--~ 131 (195)
T PRK07247 74 VLAAFKEFVGELP-------------LIGYNAQKSDLP-ILAE----NGLDLSD--QYQVDLYDEAFERRSSDLNGI--A 131 (195)
T ss_pred HHHHHHHHHCCCe-------------EEEEeCcHhHHH-HHHH----cCCCcCC--CceeehHHHHHHhhccccCCC--C
Confidence 9999999998764 4689997 8999 9854 4665432 2345654322 1 11 2322 2
Q ss_pred CCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCccc
Q 020417 263 ATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGARVQ 306 (326)
Q Consensus 263 ~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~~~ 306 (326)
+++|.+++++||++. .+|||++||++||.|+.+|++.+....
T Consensus 132 ~~~L~~La~~~gi~~--~~HrAl~DA~~ta~v~~~ll~~~~~~~ 173 (195)
T PRK07247 132 NLKLQTVADFLGIKG--RGHNSLEDARMTARVYESFLESDQNKE 173 (195)
T ss_pred CCCHHHHHHhcCCCC--CCcCCHHHHHHHHHHHHHHHhhccchh
Confidence 799999999999984 589999999999999999998765544
No 19
>PRK07740 hypothetical protein; Provisional
Probab=99.96 E-value=4.6e-29 Score=232.60 Aligned_cols=166 Identities=19% Similarity=0.190 Sum_probs=142.3
Q ss_pred CCCC--CeEEEEEeccC-------CceeeeeEEEEEcCCCeE-EeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHh
Q 020417 111 SQDL--DFFLVLDLEGK-------IEILEFPVLMIDAKTMAF-VDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHD 180 (326)
Q Consensus 111 ~~~~--~~~vVfDlETT-------~EIIEIgAVkvD~k~gei-id~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~ 180 (326)
.+++ ..|||||+||| +||||||||+++ ++++ .++|+++|+|.. +|+++++++| |||+++|+
T Consensus 53 ~~~~~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~--~~~i~~~~f~~lv~P~~----~i~~~~~~lt---GIt~e~l~ 123 (244)
T PRK07740 53 DIPLTDLPFVVFDLETTGFSPQQGDEILSIGAVKTK--GGEVETDTFYSLVKPKR----PIPEHILELT---GITAEDVA 123 (244)
T ss_pred CCCccCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEE--CCEEEEEEEEEEeCcCC----CCChhheecc---CCCHHHHh
Confidence 4565 36999999999 589999999996 5676 899999999997 4999999986 99999999
Q ss_pred CCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCc
Q 020417 181 TALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRK 260 (326)
Q Consensus 181 ~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~ 260 (326)
+||+|+||+.+|.+|+++. ..++||+.||.+ ||..++.+... .| +...|+|+..+++.+++..+
T Consensus 124 ~ap~~~evl~~f~~fi~~~-------------~lVahna~fD~~-fL~~~~~~~~~-~~-~~~~~iDt~~l~r~l~~~~~ 187 (244)
T PRK07740 124 FAPPLAEVLHRFYAFIGAG-------------VLVAHHAGHDKA-FLRHALWRTYR-QP-FTHRLIDTMFLTKLLAHERD 187 (244)
T ss_pred CCCCHHHHHHHHHHHhCCC-------------EEEEeCHHHHHH-HHHHHHHHhcC-CC-cCCCeechHHHHHHHcCCCC
Confidence 9999999999999999875 456899999999 99998866532 22 34689999999988877654
Q ss_pred CCCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCc
Q 020417 261 SEATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGAR 304 (326)
Q Consensus 261 ~~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~ 304 (326)
.++|++++++||++.++ +|+|++||++||+|+.+++.....
T Consensus 188 --~~sL~~l~~~~gi~~~~-~H~Al~Da~ata~l~~~ll~~~~~ 228 (244)
T PRK07740 188 --FPTLDDALAYYGIPIPR-RHHALGDALMTAKLWAILLVEAQQ 228 (244)
T ss_pred --CCCHHHHHHHCCcCCCC-CCCcHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999875 688999999999999999876443
No 20
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.96 E-value=1.6e-28 Score=224.69 Aligned_cols=169 Identities=14% Similarity=0.121 Sum_probs=140.5
Q ss_pred CeEEEEEeccC-----CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHH
Q 020417 115 DFFLVLDLEGK-----IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVI 189 (326)
Q Consensus 115 ~~~vVfDlETT-----~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl 189 (326)
..|||||+||| ..|||||||+++. ++.++++|+++|+|.. +++++++++| |||++||.++|+|++|+
T Consensus 7 ~~fvv~D~ETTGl~~~~~IIeIgav~v~~-~~~~~~~f~~li~P~~----~i~~~a~~ih---GIt~e~l~~~p~~~ev~ 78 (217)
T TIGR00573 7 DTETTGDNETTGLYAGHDIIEIGAVEIIN-RRITGNKFHTYIKPDR----PIDPDAIKIH---GITDDMLKDKPDFKEIA 78 (217)
T ss_pred cCEEEEEecCCCCCCCCCEEEEEEEEEEC-CCEeeeEEEEEECcCC----CCCHHHHhhc---CCCHHHHcCCCCHHHHH
Confidence 47999999999 3499999999753 4567799999999997 4999999885 99999999999999999
Q ss_pred HHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHH
Q 020417 190 QQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGM 269 (326)
Q Consensus 190 ~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l 269 (326)
++|.+|+++. .+++||+.||++ ||.+++++.+...+ ....|+|+..+++.+++..+..+++|.++
T Consensus 79 ~~~~~~~~~~-------------~lVaHNa~FD~~-fL~~~~~r~~~~~~-~~~~~~dtl~l~~~~~~~~~~~~~~L~~l 143 (217)
T TIGR00573 79 EDFADYIRGA-------------ELVIHNASFDVG-FLNYEFSKLYKVEP-KTNDVIDTTDTLQYARPEFPGKRNTLDAL 143 (217)
T ss_pred HHHHHHhCCC-------------EEEEeccHHHHH-HHHHHHHHhcCCCC-CccceecHHHHHHHHHHhCCCCCCCHHHH
Confidence 9999999764 467999999999 99999998765433 23578898887776655432236899999
Q ss_pred HHhcCCCCCC-CCCChHHHHHHHHHHHHHHHHcCCccc
Q 020417 270 MKNRQVPMFG-SHHLGIDDTKNITRVLQRMLADGARVQ 306 (326)
Q Consensus 270 ~k~lgI~~~g-~hHrAldDA~~tA~I~~~ll~~g~~~~ 306 (326)
+++||++... ..|+|++||++|++|+.+|+.......
T Consensus 144 ~~~~gl~~~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 144 CKRYEITNSHRALHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred HHHcCCCCCCcccCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 9999998642 479999999999999999988764443
No 21
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.96 E-value=8.6e-29 Score=238.50 Aligned_cols=159 Identities=14% Similarity=0.148 Sum_probs=139.5
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEV 188 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eV 188 (326)
..|||||+||| ++|||||||++|. +|+++++|+++|+|... +..+.+ ||||++||.++|+|+++
T Consensus 15 ~~fvvlD~ETTGl~p~~d~IIeIgav~v~~-~g~i~~~~~~lv~P~~~------~~~~~I---hGIt~e~l~~ap~f~ev 84 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQARIISLAVLGLDA-DGNVEQSVVTLLNPGVD------PGPTHV---HGLTAEMLEGQPQFADI 84 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEEC-CceeeeEEEEEECcCCC------CCCeec---CCCCHHHHhCCCCHHHH
Confidence 57999999999 6999999999984 78999999999999873 233455 69999999999999999
Q ss_pred HHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHH
Q 020417 189 IQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMG 268 (326)
Q Consensus 189 l~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~ 268 (326)
+++|.+|+++. .+++||++||++ ||.+++++.|+..|. +.|+|+..+.+.+++..+ +++|.+
T Consensus 85 ~~~l~~~l~~~-------------~lVaHNa~FD~~-fL~~~~~r~g~~~~~--~~~ldTl~lar~~~~~~~--~~kL~~ 146 (313)
T PRK06063 85 AGEVAELLRGR-------------TLVAHNVAFDYS-FLAAEAERAGAELPV--DQVMCTVELARRLGLGLP--NLRLET 146 (313)
T ss_pred HHHHHHHcCCC-------------EEEEeCHHHHHH-HHHHHHHHcCCCCCC--CCEEehHHHHHHhccCCC--CCCHHH
Confidence 99999999865 467999999999 999999999998763 578999999888765544 899999
Q ss_pred HHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcC
Q 020417 269 MMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADG 302 (326)
Q Consensus 269 l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g 302 (326)
++++||++.. ++|+|++||++||+|+.++++..
T Consensus 147 l~~~~gi~~~-~~H~Al~DA~ata~l~~~ll~~~ 179 (313)
T PRK06063 147 LAAHWGVPQQ-RPHDALDDARVLAGILRPSLERA 179 (313)
T ss_pred HHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHH
Confidence 9999999974 78999999999999999987653
No 22
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.96 E-value=2.6e-28 Score=225.78 Aligned_cols=169 Identities=14% Similarity=0.103 Sum_probs=140.9
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhC-CCCHHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDT-ALPFKE 187 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~-Ap~f~e 187 (326)
..|||||+||| ++|||||+|++|. +|+++++|+.+|+|.. +|+++++++| |||++|+.+ ++++.+
T Consensus 6 ~~~vv~D~ETTGl~p~~d~Iieig~v~v~~-~g~~~~~~~~lv~P~~----~i~~~a~~Ih---GIt~e~l~~~g~~~~~ 77 (232)
T PRK07942 6 GPLAAFDLETTGVDPETARIVTAALVVVDA-DGEVVESREWLADPGV----EIPEEASAVH---GITTEYARAHGRPAAE 77 (232)
T ss_pred CcEEEEEeccCCCCCCCCeeEEEEEEEEeC-CCccccceEEEECCCC----CCCHHHHHHh---CCCHHHHHhhCCCHHH
Confidence 46999999999 7899999999973 6889999999999987 4999999985 999999975 889999
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHH
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMM 267 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~ 267 (326)
|+++|.+++.+... ....+++||++||++ ||.+++++.|+..+ ....++|+..+.+.+.+.++ ++++|+
T Consensus 78 vl~e~~~~l~~~~~--------~~~~lVahNa~FD~~-fL~~~~~r~~~~~~-~~~~~iDt~~l~~~~~~~~~-~~~~L~ 146 (232)
T PRK07942 78 VLAEIADALREAWA--------RGVPVVVFNAPYDLT-VLDRELRRHGLPSL-VPGPVIDPYVIDKAVDRYRK-GKRTLT 146 (232)
T ss_pred HHHHHHHHHHHHhh--------cCCEEEEeCcHhhHH-HHHHHHHHcCCCCc-cCCcEeeHHHHHhhhhcccC-CCCCHH
Confidence 99999999965311 124678999999999 99999999997643 22467898877766554332 368999
Q ss_pred HHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCC
Q 020417 268 GMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGA 303 (326)
Q Consensus 268 ~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~ 303 (326)
+++++||++.+ ++|+|++||.+|++|+.+|++...
T Consensus 147 ~l~~~~gi~~~-~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 147 ALCEHYGVRLD-NAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred HHHHHcCCCCC-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 99999999986 589999999999999999987544
No 23
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=2.6e-28 Score=220.56 Aligned_cols=159 Identities=16% Similarity=0.237 Sum_probs=133.0
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEE--eEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFV--DLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFK 186 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geii--d~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~ 186 (326)
+.|||||+||| ++|||||||++|. ++++ ++|+.+|+|.. .++++++++| |||+++|+++|+++
T Consensus 29 ~~~vviD~ETTGl~~~~d~IieIgaV~~~~--~~~~~~~~f~~~i~p~~----~i~~~~~~ih---GIt~~~l~~~~~~~ 99 (202)
T PRK09145 29 DEWVALDCETTGLDPRRAEIVSIAAVKIRG--NRILTSERLELLVRPPQ----SLSAESIKIH---RLRHQDLEDGLSEE 99 (202)
T ss_pred CCEEEEEeECCCCCCCCCceEEEEEEEEEC--CEEeecCceEEEECCCC----CCCHhHhhhc---CcCHHHHhcCCCHH
Confidence 57999999999 7999999999974 4544 68999999996 4999999985 99999999999999
Q ss_pred HHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHH-hCCCCCCCCccHhhHHHHHHhh----cCCCcC
Q 020417 187 EVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKV-SQIKLPPYFMEWINLKDVFYNF----YKPRKS 261 (326)
Q Consensus 187 eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~-~gi~~p~~~~~~iDl~~l~~~~----~~~~~~ 261 (326)
+|+++|.+|+++. ..++||+.||+. ||.+++++ .+.++| ..++|+..++... ++.. .
T Consensus 100 ~vl~~~~~~i~~~-------------~lv~hn~~fD~~-fL~~~~~~~~~~~~~---~~~id~~~l~~~~~~~~~~~~-~ 161 (202)
T PRK09145 100 EALRQLLAFIGNR-------------PLVGYYLEFDVA-MLNRYVRPLLGIPLP---NPLIEVSALYYDKKERHLPDA-Y 161 (202)
T ss_pred HHHHHHHHHHcCC-------------eEEEeCHHHHHH-HHHHHHHHhcCCCCC---CCeeeHHHHHHHHhhccCCCc-c
Confidence 9999999999865 356899999999 99999986 466654 4688988776432 1211 1
Q ss_pred CCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHc
Q 020417 262 EATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLAD 301 (326)
Q Consensus 262 ~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~ 301 (326)
.+++|++++++||++.. .+|+|++||++||+|+.+|++.
T Consensus 162 ~~~~L~~l~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~ 200 (202)
T PRK09145 162 IDLRFDAILKHLDLPVL-GRHDALNDAIMAALIFLRLRKG 200 (202)
T ss_pred cCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHhc
Confidence 26899999999999985 5799999999999999999754
No 24
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=4e-28 Score=225.85 Aligned_cols=166 Identities=13% Similarity=0.154 Sum_probs=139.7
Q ss_pred CCCC--CeEEEEEeccC------CceeeeeEEEEEcCCCeE--EeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHh
Q 020417 111 SQDL--DFFLVLDLEGK------IEILEFPVLMIDAKTMAF--VDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHD 180 (326)
Q Consensus 111 ~~~~--~~~vVfDlETT------~EIIEIgAVkvD~k~gei--id~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~ 180 (326)
++++ ..|||||+||| ++|||||||+++ ++++ .++|+.+|+|.. +|++.++++ ||||+++|.
T Consensus 41 ~~~~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~--~~~i~~~~~~~~li~P~~----~i~~~~~~I---hGIt~e~l~ 111 (239)
T PRK09146 41 DTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFT--LQRIRCRQARHWVVKPRR----PLEEESVVI---HGITHSELQ 111 (239)
T ss_pred CCCcccCCEEEEEeECCCCCCCCCcEEEEEEEEEE--CCeEeecceEEEEECCCC----CCChhhhhh---cCCCHHHHh
Confidence 4554 47999999999 799999999995 4665 479999999998 499998887 599999999
Q ss_pred CCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHh-CCCCCCCCccHhhHHHHHHhhcCCC
Q 020417 181 TALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVS-QIKLPPYFMEWINLKDVFYNFYKPR 259 (326)
Q Consensus 181 ~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~-gi~~p~~~~~~iDl~~l~~~~~~~~ 259 (326)
+||+|++|+++|.+|+++. ..++||+.||++ ||++++++. +..++ +.|+|+..+++.+++..
T Consensus 112 ~ap~~~evl~~l~~~~~~~-------------~lVaHna~FD~~-fL~~~l~~~~~~~~~---~~~iDTl~Lar~l~~~~ 174 (239)
T PRK09146 112 DAPDLERILDELLEALAGK-------------VVVVHYRRIERD-FLDQALRNRIGEGIE---FPVIDTMEIEARIQRKQ 174 (239)
T ss_pred CCCCHHHHHHHHHHHhCCC-------------EEEEECHHHHHH-HHHHHHHHhcCCCCC---CceechHHHHHHHcccc
Confidence 9999999999999999765 457999999999 999999875 33432 47899999988765432
Q ss_pred --------c---CCCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCC
Q 020417 260 --------K---SEATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGA 303 (326)
Q Consensus 260 --------~---~~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~ 303 (326)
+ ..+++|++++++|||+.. ++|+|++||.+||+||..++....
T Consensus 175 ~~~~~~~~~~~~~~~~~L~~l~~~~gl~~~-~~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 175 AGGLWNRLKGKKPESIRLADSRLRYGLPAY-SPHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred cccccchhccCCCCCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHHc
Confidence 0 136899999999999964 689999999999999999987653
No 25
>PRK05168 ribonuclease T; Provisional
Probab=99.96 E-value=5.9e-28 Score=220.39 Aligned_cols=173 Identities=13% Similarity=0.104 Sum_probs=139.1
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEc-CCCeE--EeEEeecccCCcCCCCCcChhhhcccccCCCCHHH-HhCCCC
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDA-KTMAF--VDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVW-HDTALP 184 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~-k~gei--id~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~-V~~Ap~ 184 (326)
.+|||||+||| ++|||||||+|.. ++|.+ +++|+++|+|.... +|+++++++| |||+++ ++++++
T Consensus 17 ~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~--~i~~~~~~ih---GIt~e~~~~~~~~ 91 (211)
T PRK05168 17 FLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGA--NLEPEALAFN---GIDPDNPLRGAVS 91 (211)
T ss_pred CceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCC--CCCHHHHhhc---CCCchhhhhcCCC
Confidence 47999999999 7999999999842 24653 58999999995322 5999999985 999875 899999
Q ss_pred HHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCC-CccHhhHHHHHHhhcCCCcCCC
Q 020417 185 FKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPY-FMEWINLKDVFYNFYKPRKSEA 263 (326)
Q Consensus 185 f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~-~~~~iDl~~l~~~~~~~~~~~~ 263 (326)
+++++.+|.+|+.+..... .......++||++||++ ||.+++++.|+...++ ...++|+..+++.+++ .
T Consensus 92 ~~~~l~~~~~~l~~~~~~~----~~~~~~lVaHNa~FD~~-fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~-----~ 161 (211)
T PRK05168 92 EKEALHEIFKMVRKGIKAS----GCNRAILVAHNAHFDLS-FLMAAAERAGLKRNPFHPFSTFDTATLSGLALG-----Q 161 (211)
T ss_pred hHHHHHHHHHHHHHHHHhc----ccCCceEEEeccHHhHH-HHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC-----C
Confidence 9999999999997532100 00124678999999999 9999999999753222 2368999999988765 3
Q ss_pred CCHHHHHHhcCCCCCC-CCCChHHHHHHHHHHHHHHHHcC
Q 020417 264 TGMMGMMKNRQVPMFG-SHHLGIDDTKNITRVLQRMLADG 302 (326)
Q Consensus 264 ~~L~~l~k~lgI~~~g-~hHrAldDA~~tA~I~~~ll~~g 302 (326)
.+|+++++++|+++++ ++|+|++||.+||+|+.+|+++.
T Consensus 162 ~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 162 TVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred CCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 5799999999999753 58999999999999999998764
No 26
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.3e-27 Score=223.65 Aligned_cols=162 Identities=12% Similarity=0.160 Sum_probs=141.3
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEV 188 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eV 188 (326)
..||+||+||| ++|||||+|+++. ++++++|+.+|+|.. +|++..+++ ||||++||+++|+|.+|
T Consensus 7 ~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~--~~~~~~~~~li~P~~----~I~~~a~~i---hgIt~e~v~~~p~~~ev 77 (250)
T PRK06310 7 TEFVCLDCETTGLDVKKDRIIEFAAIRFTF--DEVIDSVEFLINPER----VVSAESQRI---HHISDAMLRDKPKIAEV 77 (250)
T ss_pred CcEEEEEEeCCCCCCCCCeEEEEEEEEEEC--CeEEEEEEEEECcCC----CCCHhhhhc---cCcCHHHHhCCCCHHHH
Confidence 46999999999 6999999999964 578899999999998 499988887 59999999999999999
Q ss_pred HHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHH
Q 020417 189 IQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMG 268 (326)
Q Consensus 189 l~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~ 268 (326)
+++|.+|+++. .++++||++||+. ||.++|.+.|++.+.....++|+..+++.+ +... +++|..
T Consensus 78 ~~~~~~fl~~~------------~~lvghn~~FD~~-~L~~~~~r~g~~~~~~~~~~iDtl~lar~~-~~~~--~~~L~~ 141 (250)
T PRK06310 78 FPQIKGFFKEG------------DYIVGHSVGFDLQ-VLSQESERIGETFLSKHYYIIDTLRLAKEY-GDSP--NNSLEA 141 (250)
T ss_pred HHHHHHHhCCC------------CEEEEECHHHHHH-HHHHHHHHcCCCccccCCcEEehHHHHHhc-ccCC--CCCHHH
Confidence 99999999763 2567899999999 999999999998764336899999998764 4332 789999
Q ss_pred HHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcC
Q 020417 269 MMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADG 302 (326)
Q Consensus 269 l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g 302 (326)
+++++|++.. .+|||++||.+|++|+..++++.
T Consensus 142 l~~~~g~~~~-~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 142 LAVHFNVPYD-GNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred HHHHCCCCCC-CCcChHHHHHHHHHHHHHHHHhc
Confidence 9999999986 58999999999999999998654
No 27
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=7.5e-28 Score=257.17 Aligned_cols=161 Identities=14% Similarity=0.230 Sum_probs=145.4
Q ss_pred CeEEEEEeccC-----CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHH
Q 020417 115 DFFLVLDLEGK-----IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVI 189 (326)
Q Consensus 115 ~~~vVfDlETT-----~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl 189 (326)
..|||||+||| ++|||||||++ ++|+++++|+++|+|.. +|+++++++| |||++||++||+|+||+
T Consensus 7 ~~~vvvD~ETTGl~~~d~IIeIgaV~v--~~g~i~~~f~~lv~P~~----~i~~~~~~lt---GIt~e~l~~ap~~~ev~ 77 (820)
T PRK07246 7 RKYAVVDLEATGAGPNASIIQVGIVII--EGGEIIDSYTTDVNPHE----PLDEHIKHLT---GITDQQLAQAPDFSQVA 77 (820)
T ss_pred CCEEEEEEecCCcCCCCeEEEEEEEEE--ECCEEEEEEEEEeCcCC----CCCHhHhhcC---CCCHHHHhcCCCHHHHH
Confidence 57999999999 79999999999 57899999999999987 4999999996 99999999999999999
Q ss_pred HHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHH
Q 020417 190 QQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGM 269 (326)
Q Consensus 190 ~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l 269 (326)
++|.+|+++. ..++||++||++ ||.+++.+.|++++ +.++|+..+.+.+++... +++|+++
T Consensus 78 ~~~~~~l~~~-------------~lVaHN~~FD~~-fL~~~~~~~g~~~~---~~~iDT~~la~~~~p~~~--~~~L~~L 138 (820)
T PRK07246 78 RHIYDLIEDC-------------IFVAHNVKFDAN-LLAEALFLEGYELR---TPRVDTVELAQVFFPTLE--KYSLSHL 138 (820)
T ss_pred HHHHHHhCCC-------------EEEEECcHHHHH-HHHHHHHHcCCCCC---CCceeHHHHHHHHhCCCC--CCCHHHH
Confidence 9999999875 457999999999 99999988888764 578999999998888764 8999999
Q ss_pred HHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCc
Q 020417 270 MKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGAR 304 (326)
Q Consensus 270 ~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~ 304 (326)
+++||++.+ ++|+|++||++||+|+.+|+++...
T Consensus 139 ~~~lgl~~~-~~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 139 SRELNIDLA-DAHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred HHHcCCCCC-CCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 999999975 6899999999999999999876543
No 28
>PRK07883 hypothetical protein; Validated
Probab=99.95 E-value=8.5e-28 Score=247.29 Aligned_cols=163 Identities=16% Similarity=0.189 Sum_probs=144.7
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEV 188 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eV 188 (326)
..|||||+||| ++|||||||+++ +|+++++|+++|+|.. +|+++++++| |||++||.++|+|.+|
T Consensus 15 ~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~--~g~iv~~f~~lV~P~~----~i~~~~~~it---GIt~e~l~~ap~~~ev 85 (557)
T PRK07883 15 VTFVVVDLETTGGSPAGDAITEIGAVKVR--GGEVLGEFATLVNPGR----PIPPFITVLT---GITTAMVAGAPPIEEV 85 (557)
T ss_pred CCEEEEEEecCCCCCCCCeEEEEEEEEEE--CCEEEEEEEEEECCCC----CCChhHHhhc---CCCHHHHhCCCCHHHH
Confidence 47999999999 799999999995 6899999999999987 4999999985 9999999999999999
Q ss_pred HHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHH
Q 020417 189 IQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMG 268 (326)
Q Consensus 189 l~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~ 268 (326)
+.+|.+|+++. ..++||++||+. ||..+|+++|+++|. +.|+|+..+++.+++.....+++|.+
T Consensus 86 l~~f~~fl~~~-------------~lVaHNa~FD~~-fL~~~~~r~g~~~~~--~~~iDTl~lar~l~~~~~~~~~~L~~ 149 (557)
T PRK07883 86 LPAFLEFARGA-------------VLVAHNAPFDIG-FLRAAAARCGYPWPG--PPVLCTVRLARRVLPRDEAPNVRLST 149 (557)
T ss_pred HHHHHHHhcCC-------------EEEEeCcHHHHH-HHHHHHHHcCCCCCC--CCcEecHHHHHHhcccCCCCCCCHHH
Confidence 99999999864 456899999999 999999999998763 57899999998887632224899999
Q ss_pred HHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCC
Q 020417 269 MMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGA 303 (326)
Q Consensus 269 l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~ 303 (326)
+++++|++.+ ++|+|++||++|++|+.+++....
T Consensus 150 L~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 150 LARLFGATTT-PTHRALDDARATVDVLHGLIERLG 183 (557)
T ss_pred HHHHCCcccC-CCCCHHHHHHHHHHHHHHHHHHHH
Confidence 9999999975 589999999999999999976543
No 29
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.4e-27 Score=220.82 Aligned_cols=158 Identities=16% Similarity=0.198 Sum_probs=137.4
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEV 188 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eV 188 (326)
..+||||+||| ++|||||++ | +++.+.|+++|+|.. +|++.++++ ||||++||+++|+|.+|
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIeig~v--~---~~~~~~f~~lv~P~~----~I~~~a~~I---hGIt~e~v~~~p~f~ev 69 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAAY--N---GVTSESFQTLVNPEI----PIPAEASKI---HGITTDEVADAPKFPEA 69 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEE--c---CccccEEEEEeCCCC----CCChhHHhh---cCCCHHHHhCCCCHHHH
Confidence 36999999999 699999995 3 245678999999998 499999887 59999999999999999
Q ss_pred HHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHH
Q 020417 189 IQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMM 267 (326)
Q Consensus 189 l~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~ 267 (326)
+++|.+|+++. ...++||+ +||+. ||.+++++.|+..+. +.++|+..+++.+++... +++|.
T Consensus 70 ~~~~~~fi~~~------------~~lVaHN~~~FD~~-~L~~e~~r~g~~~~~--~~~iDt~~l~~~~~~~~~--~~~L~ 132 (232)
T PRK06309 70 YQKFIEFCGTD------------NILVAHNNDAFDFP-LLRKECRRHGLEPPT--LRTIDSLKWAQKYRPDLP--KHNLQ 132 (232)
T ss_pred HHHHHHHHcCC------------CEEEEeCCHHHHHH-HHHHHHHHcCCCCCC--CcEEeHHHHHHHHcCCCC--CCCHH
Confidence 99999999754 24678994 89999 999999999998764 689999999988776543 78999
Q ss_pred HHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcC
Q 020417 268 GMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADG 302 (326)
Q Consensus 268 ~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g 302 (326)
+++++||++. +++|+|++||.+|++|+.+|+++.
T Consensus 133 ~l~~~~~~~~-~~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 133 YLRQVYGFEE-NQAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred HHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHH
Confidence 9999999996 468999999999999999998654
No 30
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=3.1e-27 Score=255.53 Aligned_cols=161 Identities=14% Similarity=0.191 Sum_probs=145.8
Q ss_pred CeEEEEEeccC-------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHH
Q 020417 115 DFFLVLDLEGK-------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKE 187 (326)
Q Consensus 115 ~~~vVfDlETT-------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~e 187 (326)
+.|||||+||| ++|||||||++ ++|+++++|+++|||.. +|+++++++| |||++||++||+|++
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v--~~~~i~~~f~~~v~P~~----~i~~~~~~lt---GIt~~~l~~ap~f~e 73 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVV--EDGEILERFSSFVNPER----PIPPFITELT---GISEEMVKQAPLFED 73 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEE--ECCEEEEEEEEEECcCC----CCCHHHhhcC---CCCHHHHhcCCCHHH
Confidence 56999999999 58999999999 47999999999999987 4999999996 999999999999999
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHH
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMM 267 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~ 267 (326)
|+++|.+|+++. ..++||++||++ ||++++.+.|++.+ .+.++|+.++.+.+++... +++|.
T Consensus 74 v~~~l~~~l~~~-------------~~VaHN~~FD~~-fL~~~~~~~g~~~~--~~~~iDt~~la~~~~p~~~--~~~L~ 135 (928)
T PRK08074 74 VAPEIVELLEGA-------------YFVAHNVHFDLN-FLNEELERAGYTEI--HCPKLDTVELARILLPTAE--SYKLR 135 (928)
T ss_pred HHHHHHHHhCCC-------------eEEEEChHHHHH-HHHHHHHHcCCCCC--CCCeeeHHHHHHHhcCCCC--CCCHH
Confidence 999999999875 457999999999 99999999998754 3689999999998888764 89999
Q ss_pred HHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCC
Q 020417 268 GMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGA 303 (326)
Q Consensus 268 ~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~ 303 (326)
+++++||++.+ ++|+|++||++||+|+.+|+.+..
T Consensus 136 ~l~~~l~i~~~-~~H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 136 DLSEELGLEHD-QPHRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred HHHHhCCCCCC-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 99999999974 789999999999999999987543
No 31
>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=99.95 E-value=4.8e-27 Score=210.85 Aligned_cols=171 Identities=14% Similarity=0.125 Sum_probs=135.5
Q ss_pred eEEEEEeccC------CceeeeeEEEEEc-CCCe--EEeEEeecccCCcCCCCCcChhhhcccccCCCCHHH-HhCCCCH
Q 020417 116 FFLVLDLEGK------IEILEFPVLMIDA-KTMA--FVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVW-HDTALPF 185 (326)
Q Consensus 116 ~~vVfDlETT------~EIIEIgAVkvD~-k~ge--iid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~-V~~Ap~f 185 (326)
.+||||+||| ++|||||||+|+. ++|. ++++|+++|+|.... +|++.++++| |||+++ +.+++..
T Consensus 6 ~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~--~i~~~~~~ih---GIt~~~~~~~~~~~ 80 (189)
T cd06134 6 LPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGA--NLDPAALEFN---GIDPFHPFRFAVDE 80 (189)
T ss_pred eeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCC--CCCHHHHhhc---CCCchhhhccccch
Confidence 3799999999 7999999999952 2454 468999999994211 4999999985 999886 7899999
Q ss_pred HHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCC-CCCCCccHhhHHHHHHhhcCCCcCCCC
Q 020417 186 KEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIK-LPPYFMEWINLKDVFYNFYKPRKSEAT 264 (326)
Q Consensus 186 ~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~-~p~~~~~~iDl~~l~~~~~~~~~~~~~ 264 (326)
.+++++|.+|+.+.... .+..+...++||++||++ ||+++++++|+. .+.....++|+..+.+.+++ ..
T Consensus 81 ~~~~~~~~~~l~~~~~~----~~~~~~~lVaHna~FD~~-fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~-----~~ 150 (189)
T cd06134 81 KEALKEIFKPIRKALKA----QGCTRAILVGHNAHFDLG-FLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG-----QT 150 (189)
T ss_pred HHHHHHHHHHHHHHHhh----cccCCCeEEEecchhhHH-HHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC-----CC
Confidence 99999988888753200 000124678999999999 999999999984 32212468999999888765 45
Q ss_pred CHHHHHHhcCCCCC-CCCCChHHHHHHHHHHHHHHHHc
Q 020417 265 GMMGMMKNRQVPMF-GSHHLGIDDTKNITRVLQRMLAD 301 (326)
Q Consensus 265 ~L~~l~k~lgI~~~-g~hHrAldDA~~tA~I~~~ll~~ 301 (326)
+|++++++|||+++ .++|+|++||++||+||.+|+++
T Consensus 151 ~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 151 VLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred cHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 79999999999974 46899999999999999999864
No 32
>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=99.95 E-value=2.3e-27 Score=210.76 Aligned_cols=154 Identities=16% Similarity=0.197 Sum_probs=126.8
Q ss_pred EEEEEeccC-------CceeeeeEEEEEcCCC------------eEEeEEeecccCCcCCCCCcChhhhcccccCCCCHH
Q 020417 117 FLVLDLEGK-------IEILEFPVLMIDAKTM------------AFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRV 177 (326)
Q Consensus 117 ~vVfDlETT-------~EIIEIgAVkvD~k~g------------eiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e 177 (326)
|||||+||| ++|||||||+|+. ++ +++++|+++|||.. +|++.++++| |||++
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~-~~~~~~~~~~~~~~~~~~~~~~lv~P~~----~I~~~a~~Ih---GIt~e 72 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHR-DHLLNTSRDKPALPRVLDKLSLCFNPGR----AISPGASEIT---GLSND 72 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEec-ccccccccccccccceeeeeeEEeCCCC----cCChhHHHHh---CcCHH
Confidence 799999999 6999999999964 21 36789999999997 4999999985 99999
Q ss_pred HHhCCCCHHH-HHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhh
Q 020417 178 WHDTALPFKE-VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNF 255 (326)
Q Consensus 178 ~V~~Ap~f~e-Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~ 255 (326)
|+.++|+|++ +++.|.+|++... ...+.++||+ +||++ ||++++++.|+.++ ..+.++|+..+++.+
T Consensus 73 ~l~~~~~~~~~~~~~l~~f~~~~~---------~~~~lVaHNa~~FD~~-fL~~~~~r~~~~~~-~~~~~iDtl~l~r~~ 141 (177)
T cd06136 73 LLEHKAPFDSDTANLIKLFLRRQP---------KPICLVAHNGNRFDFP-ILRSELERLGTKLP-DDILCVDSLPAFREL 141 (177)
T ss_pred HHhcCCCccHHHHHHHHHHHHhcC---------CCCEEEEcCCcccCHH-HHHHHHHHcCCCCC-CCCEEEEeHHHHhhh
Confidence 9999999874 5666777775421 0125789998 89999 99999999999876 345778999888875
Q ss_pred cCCCcCCCCCHHHHHHh-cCCCCCCCCCChHHHHHHHHHHHHH
Q 020417 256 YKPRKSEATGMMGMMKN-RQVPMFGSHHLGIDDTKNITRVLQR 297 (326)
Q Consensus 256 ~~~~~~~~~~L~~l~k~-lgI~~~g~hHrAldDA~~tA~I~~~ 297 (326)
.+ +|++++++ ||++.. ++|||++||.+|++|+.+
T Consensus 142 ~~-------~L~~l~~~~~~~~~~-~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 142 DQ-------SLGSLYKRLFGQEPK-NSHTAEGDVLALLKCALH 176 (177)
T ss_pred Hh-------hHHHHHHHHhCCCcc-cccchHHHHHHHHHHHhh
Confidence 42 79999885 899975 689999999999999864
No 33
>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=99.94 E-value=1.7e-26 Score=209.24 Aligned_cols=172 Identities=14% Similarity=0.109 Sum_probs=136.1
Q ss_pred eEEEEEeccC------CceeeeeEEEEEc-CCCeEE--eEEeecccCCcCCCCCcChhhhcccccCCCCHH-HHhCCCCH
Q 020417 116 FFLVLDLEGK------IEILEFPVLMIDA-KTMAFV--DLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRV-WHDTALPF 185 (326)
Q Consensus 116 ~~vVfDlETT------~EIIEIgAVkvD~-k~geii--d~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e-~V~~Ap~f 185 (326)
.+||||+||| ++|||||||+|.. .+|++. ++|+++|+|.... +|++.+.++| |||++ |+.+++++
T Consensus 9 ~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~--~i~~~a~~ih---GIt~~~~~~~~~~~ 83 (200)
T TIGR01298 9 LPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGA--NIQPEALEFT---GIDLDHPLRGAVSE 83 (200)
T ss_pred eeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCC--CCCHHHHHcc---CCChhhhhhcCcch
Confidence 6999999999 6999999999842 256663 6899999985211 5999998885 99975 79999999
Q ss_pred HHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCC-CccHhhHHHHHHhhcCCCcCCCC
Q 020417 186 KEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPY-FMEWINLKDVFYNFYKPRKSEAT 264 (326)
Q Consensus 186 ~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~-~~~~iDl~~l~~~~~~~~~~~~~ 264 (326)
.+++++|.+|+.+...-. .......++||++||++ ||++++++.|+....+ ...++|+..+.+..++ ..
T Consensus 84 ~~~~~~~~~~l~~~~~~~----~~~~~~lVaHNa~FD~~-fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~-----~~ 153 (200)
T TIGR01298 84 YEALHEIFKVVRKAMKAS----GCQRAILVGHNANFDLG-FLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG-----QT 153 (200)
T ss_pred HHHHHHHHHHHHHHHHhc----ccCCCEEEEECchhhHH-HHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC-----cc
Confidence 999999999985432100 00124678999999999 9999999998753111 2468999999887764 45
Q ss_pred CHHHHHHhcCCCCC-CCCCChHHHHHHHHHHHHHHHHcC
Q 020417 265 GMMGMMKNRQVPMF-GSHHLGIDDTKNITRVLQRMLADG 302 (326)
Q Consensus 265 ~L~~l~k~lgI~~~-g~hHrAldDA~~tA~I~~~ll~~g 302 (326)
+|++++++||++.+ .++|||++||.+||+|+.+|+.+.
T Consensus 154 ~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 154 VLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred cHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHH
Confidence 79999999999964 368999999999999999998654
No 34
>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=99.94 E-value=2.1e-26 Score=247.03 Aligned_cols=159 Identities=18% Similarity=0.209 Sum_probs=143.4
Q ss_pred eEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHH
Q 020417 116 FFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVI 189 (326)
Q Consensus 116 ~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl 189 (326)
.|||||+||| ++|||||||+++ +|+++++|+++|+|.. +|+++++++| |||++||++||.|++|+
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~--~~~i~~~f~~~v~P~~----~i~~~~~~lt---GIt~e~l~~ap~~~ev~ 71 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVE--DGEIVDTFHTDVNPNE----PIPPFIQELT---GISDNMLQQAPYFSQVA 71 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEE--CCEEEEEEEEEeCCCC----CCChhhhhhc---CcCHHHHhCCCCHHHHH
Confidence 4999999999 799999999994 7899999999999997 4999999996 99999999999999999
Q ss_pred HHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHH
Q 020417 190 QQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGM 269 (326)
Q Consensus 190 ~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l 269 (326)
++|.+|+++. ..++||++||++ ||.+++++.|++.. .+.++|+..+.+.+++..+ +++|.++
T Consensus 72 ~~l~~~l~~~-------------~~VahN~~fD~~-fL~~~~~~~g~~~~--~~~~iDt~~l~~~~~p~~~--~~~L~~l 133 (850)
T TIGR01407 72 QEIYDLLEDG-------------IFVAHNVHFDLN-FLAKALKDCGYEPL--PKPRIDTVELAQIFFPTEE--SYQLSEL 133 (850)
T ss_pred HHHHHHhCCC-------------EEEEeCcHHHHH-HHHHHHHHcCCCCC--CCCeEeHHHHHHHhcCCCC--CCCHHHH
Confidence 9999999765 457899999999 99999999998743 3678999999998888764 8999999
Q ss_pred HHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcC
Q 020417 270 MKNRQVPMFGSHHLGIDDTKNITRVLQRMLADG 302 (326)
Q Consensus 270 ~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g 302 (326)
+++||++.+ ++|+|++||++||+|+.+|+.+.
T Consensus 134 ~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~ 165 (850)
T TIGR01407 134 SEALGLTHE-NPHRADSDAQATAELLLLLFEKM 165 (850)
T ss_pred HHHCCCCCC-CCCChHHHHHHHHHHHHHHHHHH
Confidence 999999985 68999999999999999997653
No 35
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=6.7e-26 Score=221.00 Aligned_cols=164 Identities=10% Similarity=0.105 Sum_probs=135.5
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEV 188 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eV 188 (326)
..|||||+||| ++|||||||+++. +|+++++|+++|||... +.++ .+ ||||++||.+||+|++|
T Consensus 46 ~~fVvlDiETTGLdp~~drIIeIgAV~i~~-~g~ive~f~tLVnP~~~----~~p~--~L---HGIT~e~La~AP~f~eV 115 (377)
T PRK05601 46 APFVAVSIQTSGIHPSTSRLITIDAVTLTA-DGEEVEHFHAVLNPGED----PGPF--HL---HGLSAEEFAQGKRFSQI 115 (377)
T ss_pred CCEEEEEEECCCCCCCCCeEEEEEEEEEEc-CCEEEEEEEEEECcCCC----CCCc--cc---cCCCHHHHhcCCCHHHH
Confidence 36999999999 8999999999964 78999999999999983 3232 45 69999999999999999
Q ss_pred HHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCC-------------------------CCCCCc
Q 020417 189 IQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIK-------------------------LPPYFM 243 (326)
Q Consensus 189 l~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~-------------------------~p~~~~ 243 (326)
+++|.+|+++.+ +++||+.||++ ||..++++.+.. ..+..+
T Consensus 116 l~el~~fL~g~v-------------LVaHNA~FD~~-FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~ 181 (377)
T PRK05601 116 LKPLDRLIDGRT-------------LILHNAPRTWG-FIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPV 181 (377)
T ss_pred HHHHHHHhCCCE-------------EEEECcHHHHH-HHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCC
Confidence 999999998764 56999999999 999998775221 111236
Q ss_pred cHhhHHHHHHhhcCCCcCCCCCHHHHHHhcCCCCC---------CCCCChH--HHHHHHHHHHHHHHHcCCc
Q 020417 244 EWINLKDVFYNFYKPRKSEATGMMGMMKNRQVPMF---------GSHHLGI--DDTKNITRVLQRMLADGAR 304 (326)
Q Consensus 244 ~~iDl~~l~~~~~~~~~~~~~~L~~l~k~lgI~~~---------g~hHrAl--dDA~~tA~I~~~ll~~g~~ 304 (326)
.|+|+..+.+.+++..+ +++|.+++++|||+.. ...|+|+ +||+.+++|+.++.+.+..
T Consensus 182 ~~iDTL~LARrl~p~l~--~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~~~l 251 (377)
T PRK05601 182 VIVDTLATARRQGVALD--DIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRASGPL 251 (377)
T ss_pred CEEEhHHHHHHHcCCCC--CCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhccCCc
Confidence 89999999999887765 8999999999999871 2458888 7999999999987544433
No 36
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=99.94 E-value=7.4e-26 Score=190.54 Aligned_cols=151 Identities=19% Similarity=0.280 Sum_probs=133.9
Q ss_pred EEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHH
Q 020417 118 LVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQ 191 (326)
Q Consensus 118 vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~ 191 (326)
|++|+||| ++|||||+|+++. ++++++.|+.+|+|.. .+++++++++ ||+++++.+++++++++.+
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~-~~~~~~~~~~~i~p~~----~~~~~~~~~~---gi~~~~~~~~~~~~~~~~~ 72 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDG-GIEIVERFETLVNPGR----PIPPEATAIH---GITDEMLADAPPFEEVLPE 72 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEEC-CcChhhhhheeeCcCC----cCCHhheecc---CCCHHHHhcCCCHHHHHHH
Confidence 68999999 8999999999985 4788999999999998 4888988885 9999999999999999999
Q ss_pred HHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHH-H
Q 020417 192 FEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGM-M 270 (326)
Q Consensus 192 F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l-~ 270 (326)
|.+|+.+. ..++||+.||.. ||.+.+.++|... ....|+|+..+++.+++..+ ..++..+ +
T Consensus 73 ~~~~l~~~-------------~~v~~n~~fD~~-~l~~~~~~~~~~~--~~~~~iDt~~~~~~~~~~~~--~~~l~~~~~ 134 (159)
T cd06127 73 FLEFLGGR-------------VLVAHNASFDLR-FLNRELRRLGGPP--LPNPWIDTLRLARRLLPGLR--SHRLGLLLA 134 (159)
T ss_pred HHHHHCCC-------------EEEEeCcHhhHH-HHHHHHHHhCCCC--CCCCeeEHHHHHHHHcCCCC--cCchHHHHH
Confidence 99999863 467899999999 9999999998333 45789999999999888765 7889988 8
Q ss_pred HhcCCCCCCCCCChHHHHHHHHHHH
Q 020417 271 KNRQVPMFGSHHLGIDDTKNITRVL 295 (326)
Q Consensus 271 k~lgI~~~g~hHrAldDA~~tA~I~ 295 (326)
+.+|++. +++|+|++||.+|++|+
T Consensus 135 ~~~~~~~-~~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 135 ERYGIPL-EGAHRALADALATAELL 158 (159)
T ss_pred HHcCCCC-CCCCCcHHHHHHHHHHh
Confidence 9999986 57999999999999987
No 37
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.94 E-value=8.9e-26 Score=207.63 Aligned_cols=145 Identities=17% Similarity=0.211 Sum_probs=126.3
Q ss_pred EEEEEeccC---CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHHHH
Q 020417 117 FLVLDLEGK---IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQFE 193 (326)
Q Consensus 117 ~vVfDlETT---~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~F~ 193 (326)
++|||+||| .+|||||+|+| ++|+++++|+++|+|.. +|++.++++ ||||++||.++|+|++|+++|
T Consensus 2 ~~vlD~ETTGl~~~IieIg~v~v--~~~~i~~~~~~lv~P~~----~i~~~~~~i---hgIt~e~v~~ap~~~ev~~~~- 71 (219)
T PRK07983 2 LRVIDTETCGLQGGIVEIASVDV--IDGKIVNPMSHLVRPDR----PISPQAMAI---HRITEAMVADKPWIEDVIPHY- 71 (219)
T ss_pred eEEEEEECCCCCCCCEEEEEEEE--ECCEEEEEEEEEECcCC----CCCHHHhhc---CCCCHHHHcCCCCHHHHHHHH-
Confidence 799999999 58999999999 57899999999999998 499999988 599999999999999999985
Q ss_pred HHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHhc
Q 020417 194 AWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNR 273 (326)
Q Consensus 194 ~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~l 273 (326)
+++ .++++||++||.+ ||+. ....|+|+.++++.+++.. .++|..+++++
T Consensus 72 --~~~-------------~~lVaHNa~FD~~-~L~~-----------~~~~~idTl~lar~l~p~~---~~~l~~L~~~~ 121 (219)
T PRK07983 72 --YGS-------------EWYVAHNASFDRR-VLPE-----------MPGEWICTMKLARRLWPGI---KYSNMALYKSR 121 (219)
T ss_pred --cCC-------------CEEEEeCcHhhHH-HHhC-----------cCCCcEeHHHHHHHHccCC---CCCHHHHHHHc
Confidence 333 3578999999999 9852 1257999999999988875 58999999999
Q ss_pred CCCCC----CCCCChHHHHHHHHHHHHHHHHc
Q 020417 274 QVPMF----GSHHLGIDDTKNITRVLQRMLAD 301 (326)
Q Consensus 274 gI~~~----g~hHrAldDA~~tA~I~~~ll~~ 301 (326)
|++.. .++|||++||.+||.|+++|++.
T Consensus 122 ~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 122 KLNVQTPPGLHHHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred CCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 98642 46999999999999999999864
No 38
>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=99.93 E-value=2.1e-25 Score=198.90 Aligned_cols=159 Identities=13% Similarity=0.067 Sum_probs=124.4
Q ss_pred EEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhC-CCCHHHHHH
Q 020417 118 LVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDT-ALPFKEVIQ 190 (326)
Q Consensus 118 vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~-Ap~f~eVl~ 190 (326)
++||+||| ++|||||||+++. ++.++++|+.+|+|.... .+++...++ ||||++||.+ +|++.++++
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~-~~~~~~~~~~~v~p~~~~--~~~~~a~~i---hGIt~e~l~~~~~~~~~~l~ 74 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDE-NFNEIEPFNIFCRLPPDV--LPSPEALIV---TGITPQQLLKEGLSEYEFIA 74 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECC-CCCCccceeEEEeCCCCC--CCCHHHHHH---hCCCHHHHHhcCCCHHHHHH
Confidence 58999999 7999999999974 556779999999997521 367777777 5999999999 999999999
Q ss_pred HHHHHHHhCcccccccCCCCcceEEEEc-CcccHHHHHHHHHHHhCCCCCCC----CccHhhHHHHHHhhc---CC----
Q 020417 191 QFEAWLIQHHLWEKGRGGHLKRAAFATC-GNWDLKTKVPDQCKVSQIKLPPY----FMEWINLKDVFYNFY---KP---- 258 (326)
Q Consensus 191 ~F~~fl~~~~Lv~~~~~~~~~~~~~a~n-g~fDl~~fL~~~~~~~gi~~p~~----~~~~iDl~~l~~~~~---~~---- 258 (326)
+|.+|+++.. .+.++|| .+||++ ||++++.+.+...+.+ .+.++|+..+.+..+ +.
T Consensus 75 ~~~~~~~~~~-----------~~lVahn~~~FD~~-fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~ 142 (183)
T cd06138 75 KIHRLFNTPG-----------TCIVGYNNIRFDDE-FLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVW 142 (183)
T ss_pred HHHHHHccCC-----------CcEEeeCchhhHHH-HHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccC
Confidence 9999997421 2456887 689999 9999999998764321 134567666655432 21
Q ss_pred C----cCCCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHH
Q 020417 259 R----KSEATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVL 295 (326)
Q Consensus 259 ~----~~~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~ 295 (326)
. ...+++|++++++||++. .++|||++||++||+|+
T Consensus 143 ~~~~~~~~~~~L~~l~~~~gi~~-~~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 143 PKNDDGKPSFKLEDLAQANGIEH-SNAHDALSDVEATIALA 182 (183)
T ss_pred ccccCCCcchhHHHHHHHCCCCc-cccccHHHHHHHHHHHh
Confidence 0 012688999999999997 47899999999999886
No 39
>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=99.92 E-value=7.9e-25 Score=193.80 Aligned_cols=161 Identities=11% Similarity=0.090 Sum_probs=121.9
Q ss_pred EEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHH
Q 020417 117 FLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQ 190 (326)
Q Consensus 117 ~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~ 190 (326)
+|+||+||| ++|||||||++|...+++.++|+.+|+|.....+.+++++.+++..+||+++|++++|++++|++
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl~ 80 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEA 80 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHHH
Confidence 589999999 79999999999865568889999999998721012345555553234999999999999999999
Q ss_pred HHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhH---HHHHHhhcCCCcCCCCCHH
Q 020417 191 QFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINL---KDVFYNFYKPRKSEATGMM 267 (326)
Q Consensus 191 ~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl---~~l~~~~~~~~~~~~~~L~ 267 (326)
+|.+|+++..-. ....+++||++||+. ||++++++.|.. +.+..+|+ .++.+.+++..+ +
T Consensus 81 ~~~~f~~~~~~~-------~~~~lvgh~~~FD~~-fL~~~~~~~~~~---~~~~~~D~~~l~~l~~~l~p~~~--~---- 143 (173)
T cd06135 81 ELLEFIKKYVPK-------GKSPLAGNSVHQDRR-FLDKYMPELEEY---LHYRILDVSSIKELARRWYPEIY--R---- 143 (173)
T ss_pred HHHHHHHHhcCC-------CCCceeecchhhCHH-HHHHHHHHHhcc---CCcchhhHHHHHHHHHHhCcHhh--h----
Confidence 999999874200 112345566799999 999999988732 34567887 456666665432 1
Q ss_pred HHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHH
Q 020417 268 GMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLA 300 (326)
Q Consensus 268 ~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~ 300 (326)
++++. +..|||++||.+++.++..+++
T Consensus 144 -----~~~~~-~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 144 -----KAPKK-KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred -----cCCCC-CCCcchHHHHHHHHHHHHHHHH
Confidence 56764 4689999999999999998875
No 40
>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=99.92 E-value=1.5e-25 Score=196.06 Aligned_cols=144 Identities=13% Similarity=0.110 Sum_probs=119.6
Q ss_pred EEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCH------
Q 020417 118 LVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPF------ 185 (326)
Q Consensus 118 vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f------ 185 (326)
||||+||| ++|||||||++ ++|+++ |++||+|.. +|+++++++| |||++||++||++
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v--~~g~i~--~~~~v~P~~----~i~~~~~~i~---GIt~~~l~~a~~~~~~~~~ 69 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDV--LTGEVL--IDSLVRPSV----RVTDWRTRFS---GVTPADLEEAAKAGKTIFG 69 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEc--CCCeEE--EeccccCCC----CCCccceecc---CCCHHHHhhhhhcCCcccc
Confidence 68999998 79999999999 688886 999999987 4999999985 9999999999864
Q ss_pred -HHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcC-CC
Q 020417 186 -KEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKS-EA 263 (326)
Q Consensus 186 -~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~-~~ 263 (326)
++|+++|.+|+++. ...++||+.||++ ||+.. .+.|+|+..+++.+++.... .+
T Consensus 70 ~~~~~~~~~~~i~~~------------~vlVgHn~~fD~~-fL~~~-----------~~~~iDT~~l~~~~~~~~~~~~~ 125 (161)
T cd06137 70 WEAARAALWKFIDPD------------TILVGHSLQNDLD-ALRMI-----------HTRVVDTAILTREAVKGPLAKRQ 125 (161)
T ss_pred HHHHHHHHHHhcCCC------------cEEEeccHHHHHH-HHhCc-----------CCCeeEehhhhhhccCCCcCCCC
Confidence 58999999999862 2456899999999 99631 24789999999987765310 27
Q ss_pred CCHHHHHHh-cCCCCC--CCCCChHHHHHHHHHHHH
Q 020417 264 TGMMGMMKN-RQVPMF--GSHHLGIDDTKNITRVLQ 296 (326)
Q Consensus 264 ~~L~~l~k~-lgI~~~--g~hHrAldDA~~tA~I~~ 296 (326)
++|++++++ ||++.. ..+|+|++||++|++|++
T Consensus 126 ~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 126 WSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREVVL 161 (161)
T ss_pred ccHHHHHHHHCCchhcCCCCCCCcHHHHHHHHHHhC
Confidence 999999987 798763 357999999999999873
No 41
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.92 E-value=5.1e-24 Score=196.38 Aligned_cols=161 Identities=17% Similarity=0.199 Sum_probs=142.6
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEEeE-EeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDL-FHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKE 187 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~-F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~e 187 (326)
..++|||+||| ++|||||||.+ .++++++. |+.+|+|.. +|++++.+++ ||+.+||.++|.|.+
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~--~~~~i~~~~~~~~v~P~~----~i~~~~~~i~---git~e~l~~~p~~~~ 83 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTL--EDGRIVERSFHTLVNPER----PIPPEIFKIH---GITDEMLADAPKFAE 83 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEE--ECCeeecceeEEEECCCC----CCChhhhhhc---CCCHHHHhcCCCHHH
Confidence 47999999999 89999999999 57888865 999999955 4999999985 999999999999999
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHH
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMM 267 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~ 267 (326)
++++|.+|+++. ...++||+.||+. ||..++.+.+...+ ...++|+..+.+..++... .++|+
T Consensus 84 v~~~~~~~i~~~------------~~~Vahna~fD~~-fl~~~~~~~~~~~~--~~~~~~t~~~~r~~~~~~~--~~~L~ 146 (243)
T COG0847 84 VLPEFLDFIGGL------------RLLVAHNAAFDVG-FLRVESERLGIEIP--GDPVLDTLALARRHFPGFD--RSSLD 146 (243)
T ss_pred HHHHHHHHHCCC------------CeEEEEchhhcHH-HHHHHHHHcCCCcc--cCceehHHHHHHHHcCCCc--cchHH
Confidence 999999999983 2467999999999 99999999999876 4678999999998888733 89999
Q ss_pred HHHHhcCCCCC-CCCCChHHHHHHHHHHHHHHHHc
Q 020417 268 GMMKNRQVPMF-GSHHLGIDDTKNITRVLQRMLAD 301 (326)
Q Consensus 268 ~l~k~lgI~~~-g~hHrAldDA~~tA~I~~~ll~~ 301 (326)
.+++++|++.. .++|+|+.||.++|.++..+...
T Consensus 147 ~l~~~~gi~~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 147 ALAERLGIDRNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred HHHHHcCCCcCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 99999999953 35799999999999999999874
No 42
>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=99.91 E-value=1.4e-24 Score=188.19 Aligned_cols=139 Identities=14% Similarity=0.167 Sum_probs=116.2
Q ss_pred EEEEeccC-----CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCC-CHHHHHHH
Q 020417 118 LVLDLEGK-----IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTAL-PFKEVIQQ 191 (326)
Q Consensus 118 vVfDlETT-----~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap-~f~eVl~~ 191 (326)
|++|.||| +||+||++|++ +|++ .|++||+|.. +++++++++| |||++||.+|| +|++|+++
T Consensus 1 ~~iD~E~~g~~~g~ei~~i~~v~~---~~~~--~f~~lv~P~~----~i~~~~t~it---GIt~~~l~~a~~~~~~v~~~ 68 (150)
T cd06145 1 FALDCEMCYTTDGLELTRVTVVDE---NGKV--VLDELVKPDG----EIVDYNTRFS---GITEEMLENVTTTLEDVQKK 68 (150)
T ss_pred CEEeeeeeeecCCCEEEEEEEEeC---CCCE--EEEEeECCCC----ccchhccCcC---CCCHHHhccCCCCHHHHHHH
Confidence 58999998 79999999976 4555 4999999997 4999999986 99999999995 99999999
Q ss_pred HHHHHH-hCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHH
Q 020417 192 FEAWLI-QHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMM 270 (326)
Q Consensus 192 F~~fl~-~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~ 270 (326)
|.+|++ +. .+++||++||++ ||+.. .++++|+..+++..++..+ +++|++++
T Consensus 69 ~~~fl~~~~-------------vlVgHn~~fD~~-fL~~~-----------~~~~iDT~~l~r~~~~~~~--~~~L~~L~ 121 (150)
T cd06145 69 LLSLISPDT-------------ILVGHSLENDLK-ALKLI-----------HPRVIDTAILFPHPRGPPY--KPSLKNLA 121 (150)
T ss_pred HHHHhCCCC-------------EEEEcChHHHHH-Hhhcc-----------CCCEEEcHHhccccCCCCC--ChhHHHHH
Confidence 999997 43 457899999999 99631 2468999999887666554 78999999
Q ss_pred Hhc-CCCCC--CCCCChHHHHHHHHHHH
Q 020417 271 KNR-QVPMF--GSHHLGIDDTKNITRVL 295 (326)
Q Consensus 271 k~l-gI~~~--g~hHrAldDA~~tA~I~ 295 (326)
++| |+... +.+|||++||++|++|+
T Consensus 122 ~~~~~~~i~~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 122 KKYLGRDIQQGEGGHDSVEDARAALELV 149 (150)
T ss_pred HHHCCcceeCCCCCCCcHHHHHHHHHHh
Confidence 887 54432 46899999999999987
No 43
>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=99.91 E-value=2e-24 Score=187.19 Aligned_cols=146 Identities=15% Similarity=0.175 Sum_probs=113.0
Q ss_pred EEEEeccC-----CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHHH
Q 020417 118 LVLDLEGK-----IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQF 192 (326)
Q Consensus 118 vVfDlETT-----~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~F 192 (326)
||||+||| ++++||++|.+...+|+++ |++||+|.. .++++++++| |||++||++||+|.+++++|
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~--~~~~v~P~~----~i~~~~~~ih---GIt~~~v~~a~~~~~~~~~l 71 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVV--YDTYVKPQE----PVTDYRTAVS---GIRPEHLKDAPDFEEVQKKV 71 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEE--EEEEECCCC----CCCcccccCC---CCCHHHHcCCCCHHHHHHHH
Confidence 68999999 3588888764422356654 999999987 4999999985 99999999999999999999
Q ss_pred HHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHh
Q 020417 193 EAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKN 272 (326)
Q Consensus 193 ~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~ 272 (326)
.+|+++. ..++||+.||++ ||. +..|. +.++|+..+........ ..+++|.+++++
T Consensus 72 ~~~l~~~-------------vlVgHn~~fD~~-~L~-------~~~~~--~~~~dt~~l~~~~~~~~-~~~~sL~~l~~~ 127 (152)
T cd06144 72 AELLKGR-------------ILVGHALKNDLK-VLK-------LDHPK--KLIRDTSKYKPLRKTAK-GKSPSLKKLAKQ 127 (152)
T ss_pred HHHhCCC-------------EEEEcCcHHHHH-Hhc-------CcCCC--ccEEEeEEeeccccccC-CCChhHHHHHHH
Confidence 9999875 456899999999 995 23332 35667655432221110 138999999997
Q ss_pred -cCCCCCCCCCChHHHHHHHHHHHH
Q 020417 273 -RQVPMFGSHHLGIDDTKNITRVLQ 296 (326)
Q Consensus 273 -lgI~~~g~hHrAldDA~~tA~I~~ 296 (326)
+|++..+.+|||++||++|++|++
T Consensus 128 ~lgi~~~~~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 128 LLGLDIQEGEHSSVEDARAAMRLYR 152 (152)
T ss_pred HcCcccCCCCcCcHHHHHHHHHHhC
Confidence 699875568999999999999874
No 44
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=99.91 E-value=4.2e-26 Score=192.19 Aligned_cols=157 Identities=19% Similarity=0.324 Sum_probs=124.5
Q ss_pred EEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHH
Q 020417 118 LVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQ 191 (326)
Q Consensus 118 vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~ 191 (326)
||||+||| ++|||||+|+++....+++++|++||+|...+ .++++++++| |||++++.+++++.+++++
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~--~i~~~~~~~~---gIt~~~l~~~~~~~~~~~~ 75 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPP--KISPWATKVH---GITQEDLEDAPSFEEALDE 75 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHC--SSEHHHHHHH---HHCHHHHHCHCEHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccc--cCCHHHeeec---CCcccccccCCcHHHHHHh
Confidence 79999999 79999999999874445889999999999843 6999999996 9999999999999999999
Q ss_pred HHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHh-CCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHH
Q 020417 192 FEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVS-QIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMM 270 (326)
Q Consensus 192 F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~-gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~ 270 (326)
|.+|+.+.. ..+.||+.||.+ ++...+.+. +...| ....++|+..+.+..++... .++|+.++
T Consensus 76 ~~~~~~~~~------------~~v~~n~~fd~~-~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~--~~~l~~l~ 139 (164)
T PF00929_consen 76 FEEFLKKND------------ILVGHNASFDIG-FLRREDKRFLGKPIP-KPNPFIDTLELARALFPNRK--KYSLDDLA 139 (164)
T ss_dssp HHHHHHHHT------------EEEETTCCHEEE-SSHHHHHHHHHHHHH-HHHHECEEEEEHHHHHHHHH--HHSHHHHH
T ss_pred hhhhhhccc------------ccccccccchhh-HHHHhhhhccccccc-ccchhhhhhHHHHHHhhccc--cCCHHHHH
Confidence 999998532 345678899999 998888776 44333 11234443333333222222 46899999
Q ss_pred HhcCCCCCCCCCChHHHHHHHHHHH
Q 020417 271 KNRQVPMFGSHHLGIDDTKNITRVL 295 (326)
Q Consensus 271 k~lgI~~~g~hHrAldDA~~tA~I~ 295 (326)
++||++..+.+|+|++||++|++||
T Consensus 140 ~~~~~~~~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 140 EYFGIPFDGTAHDALDDARATAELF 164 (164)
T ss_dssp HHTTSSSTSTTTSHHHHHHHHHHHH
T ss_pred HHcCCCCCCCCcChHHHHHHHhCcC
Confidence 9999998877899999999999986
No 45
>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=99.90 E-value=6.8e-24 Score=185.30 Aligned_cols=142 Identities=13% Similarity=0.183 Sum_probs=113.4
Q ss_pred EEEEeccC--------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHH
Q 020417 118 LVLDLEGK--------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVI 189 (326)
Q Consensus 118 vVfDlETT--------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl 189 (326)
||||+||| ++|++|++|.+ +|+++ |++||||.. +|+++++++| ||+++||++||++++|+
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~---~g~~~--~~~lv~P~~----~i~~~~~~i~---GIt~~~l~~a~~~~~v~ 68 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNY---HGDVL--YDKYIRPEG----PVTDYRTRWS---GIRRQHLVNATPFAVAQ 68 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeC---CCCEE--EEEeECCCC----ccCccceECC---CCCHHHHhcCCCHHHHH
Confidence 68999999 46777777764 67776 999999997 4999999985 99999999999999999
Q ss_pred HHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHH--HHhh--cCCCcCCCCC
Q 020417 190 QQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDV--FYNF--YKPRKSEATG 265 (326)
Q Consensus 190 ~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l--~~~~--~~~~~~~~~~ 265 (326)
++|.+|+++. ..|+||..||++ ||+.. .+. +.++|+..+ ++.. ++..+ +++
T Consensus 69 ~~l~~~l~~~-------------vlV~Hn~~~D~~-~l~~~-------~~~--~~~~Dt~~l~~~~~~~~~p~~~--~~~ 123 (157)
T cd06149 69 KEILKILKGK-------------VVVGHAIHNDFK-ALKYF-------HPK--HMTRDTSTIPLLNRKAGFPENC--RVS 123 (157)
T ss_pred HHHHHHcCCC-------------EEEEeCcHHHHH-Hhccc-------CCC--cCEEECcccccchhhcCCcccC--Chh
Confidence 9999999875 456999999999 99633 221 346676544 3333 44433 799
Q ss_pred HHHHHHhc---CCCCCCCCCChHHHHHHHHHHHH
Q 020417 266 MMGMMKNR---QVPMFGSHHLGIDDTKNITRVLQ 296 (326)
Q Consensus 266 L~~l~k~l---gI~~~g~hHrAldDA~~tA~I~~ 296 (326)
|.+++++| +++..++.|||+.||++|+++|+
T Consensus 124 L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 124 LKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred HHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 99999999 67754567999999999999873
No 46
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=2.1e-22 Score=192.68 Aligned_cols=156 Identities=17% Similarity=0.144 Sum_probs=117.4
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcC-CC---eEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCC
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAK-TM---AFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALP 184 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k-~g---eiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~ 184 (326)
..+||||+||| ++|||||+|+++.. +| +++++|+.+|+|.. +|++.++++| |||++||.+++.
T Consensus 37 ~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~----~I~~~~t~Ih---GIt~e~v~~~~~ 109 (294)
T PRK09182 37 RLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSR----PIPPEITRLT---GITDEMVAGQTI 109 (294)
T ss_pred CeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCC----CCCHHHHHhc---CCCHHHHhcCCC
Confidence 67999999999 79999999999631 34 45789999999997 4999999985 999999999997
Q ss_pred HHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCC
Q 020417 185 FKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEAT 264 (326)
Q Consensus 185 f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~ 264 (326)
..+++. +|++.. .++|+||+.||++ ||.+.+....- ..|.++........... .++
T Consensus 110 ~~~~l~---~fl~~~------------~vlVAHNA~FD~~-fL~~~~~~~~~------~~~~ct~~~i~~~~~~~--~~~ 165 (294)
T PRK09182 110 DPAAVD---ALIAPA------------DLIIAHNAGFDRP-FLERFSPVFAT------KPWACSVSEIDWSARGF--EGT 165 (294)
T ss_pred cHHHHH---HHhcCC------------CEEEEeCHHHHHH-HHHHHHHhccC------CcccccHHHHhhccccC--CCC
Confidence 665554 445442 2568999999999 99887654321 12333332222111222 379
Q ss_pred CHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCC
Q 020417 265 GMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGA 303 (326)
Q Consensus 265 ~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~ 303 (326)
+|.+++++|| .. .++|||++||.+|++|+..++....
T Consensus 166 kL~~La~~~g-~~-~~aHrAl~Da~Ata~ll~~~l~~~~ 202 (294)
T PRK09182 166 KLGYLAGQAG-FF-HEGHRAVDDCQALLELLARPLPETG 202 (294)
T ss_pred CHHHHHHHcC-CC-CCCcChHHHHHHHHHHHHHHHhhcC
Confidence 9999999999 43 3689999999999999998776544
No 47
>PRK05359 oligoribonuclease; Provisional
Probab=99.87 E-value=1.6e-21 Score=174.36 Aligned_cols=162 Identities=12% Similarity=0.054 Sum_probs=123.0
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEE-eEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFV-DLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKE 187 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geii-d~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~e 187 (326)
+.|||||+||| ++|||||||++|. +++++ +.|+.+|+|.......+++++++++|++||++++++++|++++
T Consensus 3 ~~~vvlD~ETTGLdp~~d~IieIgaV~~~~-~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~e 81 (181)
T PRK05359 3 DNLIWIDLEMTGLDPERDRIIEIATIVTDA-DLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEAE 81 (181)
T ss_pred CcEEEEEeecCCCCCCCCeEEEEEEEEEcC-CceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHHH
Confidence 57999999999 8999999999974 44555 6799999997620003577888876667999999999999999
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhH--H-HHHHhhcCCCcCCCC
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINL--K-DVFYNFYKPRKSEAT 264 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl--~-~l~~~~~~~~~~~~~ 264 (326)
|+++|++|+++..+.. ....+.++..||++ ||++.+.+.+..+ .++++|+ . ++.+.++|..
T Consensus 82 ~~~~~l~fl~~~~~~~-------~~~l~g~~v~FD~~-FL~~~~~~~~~~l---~~~~~Dv~tl~~l~r~~~P~~----- 145 (181)
T PRK05359 82 AEAQTLEFLKQWVPAG-------KSPLCGNSIGQDRR-FLARYMPELEAYF---HYRNLDVSTLKELARRWKPEI----- 145 (181)
T ss_pred HHHHHHHHHHHhcCCC-------CCceeecchhhCHH-HHHHHHHHhcccC---CCcccchhHHHHHHHHhChhh-----
Confidence 9999999998764311 12334456699999 9999998877654 3567774 3 5666665531
Q ss_pred CHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHc
Q 020417 265 GMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLAD 301 (326)
Q Consensus 265 ~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~ 301 (326)
.++++.. ..|||++||+.+.+.+..+.+.
T Consensus 146 -------~~~~~~~-~~HRal~D~~~s~~~~~~~~~~ 174 (181)
T PRK05359 146 -------LNGFKKQ-GTHRALADIRESIAELKYYREH 174 (181)
T ss_pred -------hhCCCCc-CCcccHHHHHHHHHHHHHHHHH
Confidence 3577765 4699999999999988877653
No 48
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.83 E-value=2.2e-19 Score=181.64 Aligned_cols=168 Identities=11% Similarity=0.014 Sum_probs=124.0
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCC-eEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhC-CCCHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTM-AFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDT-ALPFK 186 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~g-eiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~-Ap~f~ 186 (326)
.+|||+|+||| ++|||||||++|. ++ .+.+.|+.+|+|.... .+++....+ ||||++||.+ +.+..
T Consensus 6 ~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~-~~~~i~e~~~~~~~P~~~~--lp~p~a~~I---hGIT~e~l~~~g~~e~ 79 (476)
T PRK11779 6 PTFLWHDYETFGANPALDRPAQFAGIRTDA-DLNIIGEPLVFYCKPADDY--LPSPEAVLI---TGITPQEALEKGLPEA 79 (476)
T ss_pred CcEEEEEEECCCCCCCCCeeEEEEEEEEeC-CCceecceeEEEEcCCcCc--CCCHHHHHH---hCCCHHHHHhcCCCHH
Confidence 46999999999 8999999999985 44 4457899999998621 245666666 5999999954 55799
Q ss_pred HHHHHHHHHHHhCcccccccCCCCcceEEEEc-CcccHHHHHHHHHHHhCCCC-------CCCCccHhhHHHHHHhhcCC
Q 020417 187 EVIQQFEAWLIQHHLWEKGRGGHLKRAAFATC-GNWDLKTKVPDQCKVSQIKL-------PPYFMEWINLKDVFYNFYKP 258 (326)
Q Consensus 187 eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~n-g~fDl~~fL~~~~~~~gi~~-------p~~~~~~iDl~~l~~~~~~~ 258 (326)
+++++|.+|+... ..++++|| .+||.. ||+.++.+..+.. +.....++|+..++..+.+.
T Consensus 80 e~~~~i~~~l~~~-----------~~~lVGhNni~FD~e-flr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~ 147 (476)
T PRK11779 80 EFAARIHAEFSQP-----------GTCILGYNNIRFDDE-VTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPE 147 (476)
T ss_pred HHHHHHHHHHhcC-----------CCEEEEeCchhhcHH-HHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccc
Confidence 9999999999621 13567786 589999 9999987665431 00012445555544332211
Q ss_pred C--------cCCCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHc
Q 020417 259 R--------KSEATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLAD 301 (326)
Q Consensus 259 ~--------~~~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~ 301 (326)
. ...+++|+++++++||+. +++|+|+.||++|++|+..+.+.
T Consensus 148 ~i~~P~~~~g~~s~rLe~L~~~~gI~~-~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 148 GINWPENEDGLPSFKLEHLTKANGIEH-ENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred cccCcccccCCCCCcHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHh
Confidence 0 013799999999999997 47899999999999999988755
No 49
>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=98.98 E-value=5.3e-09 Score=93.65 Aligned_cols=129 Identities=13% Similarity=0.009 Sum_probs=95.1
Q ss_pred EEEEeccC----------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHH
Q 020417 118 LVLDLEGK----------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKE 187 (326)
Q Consensus 118 vVfDlETT----------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~e 187 (326)
++||+||| ++||+||++.. .+|+.. .+....++.. .. . .||++.+|..+++..+
T Consensus 2 ~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~--~~g~~~-~~~~~~~~~~-------~~---~---~~i~~~~v~~~~~E~~ 65 (199)
T cd05160 2 LSFDIETTPPVGGPEPDRDPIICITYADS--FDGVKV-VFLLKTSTVG-------DD---I---EFIDGIEVEYFADEKE 65 (199)
T ss_pred ccEEEeecCCCCCcCCCCCCEEEEEEEEe--eCCcee-eEEEeecccC-------Cc---C---CCCCCceEEEeCCHHH
Confidence 68999997 79999999886 355533 2322222222 11 1 1577888999999999
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCC-CC-------------------CccHh
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLP-PY-------------------FMEWI 246 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p-~~-------------------~~~~i 246 (326)
+|.+|.+++++.. -..++.||+ +||+. ||.+.++++|++.. .. -..++
T Consensus 66 lL~~f~~~i~~~d----------pdiivg~N~~~FD~~-~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~ 134 (199)
T cd05160 66 LLKRFFDIIREYD----------PDILTGYNIDDFDLP-YLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVF 134 (199)
T ss_pred HHHHHHHHHHhcC----------CCEEEEeccCCCcHH-HHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEee
Confidence 9999999998752 135678899 89999 99999999998761 00 12478
Q ss_pred hHHHHHHhhcCCCcCCCCCHHHHHHhcCCC
Q 020417 247 NLKDVFYNFYKPRKSEATGMMGMMKNRQVP 276 (326)
Q Consensus 247 Dl~~l~~~~~~~~~~~~~~L~~l~k~lgI~ 276 (326)
|+..+++..++.. +++|++++++++..
T Consensus 135 D~~~~~r~~~~l~---sy~L~~v~~~~l~~ 161 (199)
T cd05160 135 DLLAAYKRDFKLK---SYTLDAVAEELLGE 161 (199)
T ss_pred ehHHHHHHhcCcc---cCCHHHHHHHHhCC
Confidence 9998888877633 89999999988765
No 50
>PHA02570 dexA exonuclease; Provisional
Probab=98.93 E-value=1.3e-08 Score=93.53 Aligned_cols=162 Identities=14% Similarity=0.129 Sum_probs=100.5
Q ss_pred EEEEeccC-----CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhc--cc-----ccCCCCHH-----HH-
Q 020417 118 LVLDLEGK-----IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEG--KY-----GKFGVDRV-----WH- 179 (326)
Q Consensus 118 vVfDlETT-----~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~--LT-----gi~GIt~e-----~V- 179 (326)
+++|+||. .-||+||||.+|...| ++.+|+++|.....- ++....++ .+ -.|+..|. .+
T Consensus 4 lMIDlETmG~~p~AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~--k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~ 80 (220)
T PHA02570 4 FIIDFETFGNTPDGAVIDLAVIAFEHDPH-NPPTFEELVSRGRRI--KFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLK 80 (220)
T ss_pred EEEEeeccCCCCCceEEEEEEEEecCCCC-ccccHHHHhhccccc--ccchhhccCCCccCchHHHHHHhCCHHHHHhcc
Confidence 79999997 8999999999998555 789999999743210 12111111 00 00121111 11
Q ss_pred --hCCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHh----C--CCCCCCCccHhhHHH
Q 020417 180 --DTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVS----Q--IKLPPYFMEWINLKD 250 (326)
Q Consensus 180 --~~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~----g--i~~p~~~~~~iDl~~ 250 (326)
.+..++.+++.+|.+||..+.. ......+-.|| +||.. .|...+++. + ++.|+.|+.--|+|.
T Consensus 81 ~s~~~~~l~~al~~F~~fi~~~~~-------~~~~~~vWgnG~sFD~~-IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT 152 (220)
T PHA02570 81 PSDEDVSTYEGHKKFFEYLEANGV-------DPWKSQGWCRGNSFDFP-ILVDVIRDIHNTRDTFKLEPVKFWNQRDVRT 152 (220)
T ss_pred CCCccccHHHHHHHHHHHHHHcCC-------CccceeEecCCCccCHH-HHHHHHHHHhcccCcCcCCCeeecCccchHH
Confidence 1357899999999999997631 01122333454 89999 999999988 7 678877777788888
Q ss_pred HHHhhcCCCcCCCCCHHHHHHhcCCCCCC-CCCChHHHHHHHHHHHH
Q 020417 251 VFYNFYKPRKSEATGMMGMMKNRQVPMFG-SHHLGIDDTKNITRVLQ 296 (326)
Q Consensus 251 l~~~~~~~~~~~~~~L~~l~k~lgI~~~g-~hHrAldDA~~tA~I~~ 296 (326)
+....+..+ ++...--.-| .++| .+|+|+.||..=|..+.
T Consensus 153 ~ie~~~l~r-----~~~~cp~~~g-~l~gfv~H~sihDcakd~lml~ 193 (220)
T PHA02570 153 AIEATLLTR-----GMTTCPLPKG-TLDGFVAHDSIHDCAKDILMLI 193 (220)
T ss_pred HHhhhhccC-----CcccCCCcCc-cccchhhcccHHHHHHHHHHHH
Confidence 765432222 1111000011 1133 58999999988764444
No 51
>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=98.75 E-value=1.1e-07 Score=85.10 Aligned_cols=121 Identities=10% Similarity=0.085 Sum_probs=91.2
Q ss_pred CCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCC------CHHHHHHHHHHHHHhCcccccccCCCCcce
Q 020417 140 TMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTAL------PFKEVIQQFEAWLIQHHLWEKGRGGHLKRA 213 (326)
Q Consensus 140 ~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap------~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~ 213 (326)
+|+++ +..||+|.. +|..|.|+.+ |||.++++++. ++++|-.++.+++... ..
T Consensus 46 ~g~vl--lD~~VkP~~----~V~DYrT~~S---GIt~~~L~~a~~~~~~~t~~~v~~~l~~li~~~------------tI 104 (174)
T cd06143 46 EGVPF--IDDYISTTE----PVVDYLTRFS---GIKPGDLDPKTSSKNLTTLKSAYLKLRLLVDLG------------CI 104 (174)
T ss_pred CCCEE--EeeeECCCC----CccCcCcccc---ccCHHHcCccccccccCCHHHHHHHHHHHcCCC------------CE
Confidence 66665 788999987 4999999987 99999999875 6899999998888532 23
Q ss_pred EEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHh-cCCCCCCCCCChHHHHHHHH
Q 020417 214 AFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKN-RQVPMFGSHHLGIDDTKNIT 292 (326)
Q Consensus 214 ~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~-lgI~~~g~hHrAldDA~~tA 292 (326)
++.|.-..|++ . .++..|. ...+|+..+|+. +.. ...+|..+++. ||.......|+.+.||+++.
T Consensus 105 LVGHsL~nDL~-a-------L~l~hp~--~~viDTa~l~~~--~~~--r~~sLk~La~~~L~~~IQ~~~HdSvEDArAam 170 (174)
T cd06143 105 FVGHGLAKDFR-V-------INIQVPK--EQVIDTVELFHL--PGQ--RKLSLRFLAWYLLGEKIQSETHDSIEDARTAL 170 (174)
T ss_pred EEeccchhHHH-H-------hcCcCCC--cceEEcHHhccC--CCC--CChhHHHHHHHHcCCcccCCCcCcHHHHHHHH
Confidence 45566677877 4 4666653 367899877653 222 26899999765 57776545799999999999
Q ss_pred HHH
Q 020417 293 RVL 295 (326)
Q Consensus 293 ~I~ 295 (326)
+++
T Consensus 171 ~Ly 173 (174)
T cd06143 171 KLY 173 (174)
T ss_pred HHh
Confidence 876
No 52
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.67 E-value=3.1e-07 Score=86.45 Aligned_cols=152 Identities=13% Similarity=0.221 Sum_probs=106.6
Q ss_pred CCCCeEEEEEeccC--------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCC
Q 020417 112 QDLDFFLVLDLEGK--------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTAL 183 (326)
Q Consensus 112 ~~~~~~vVfDlETT--------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap 183 (326)
.++..+|++|-|.- +..--+. +|| ..|.|+ |+.||+|.. ++..|-|..+ ||+.+.+.+|.
T Consensus 102 ~~~~r~vAmDCEMVG~Gp~G~~s~lARvS--IVN-~~G~Vv--yDkyVkP~~----~VtDyRT~vS---GIrpehm~~A~ 169 (280)
T KOG2249|consen 102 GSLTRVVAMDCEMVGVGPDGRESLLARVS--IVN-YHGHVV--YDKYVKPTE----PVTDYRTRVS---GIRPEHMRDAM 169 (280)
T ss_pred cccceEEEEeeeEeccCCCccceeeeEEE--Eee-ccCcEe--eeeecCCCc----ccccceeeec---ccCHHHhccCc
Confidence 34557999999975 3232333 345 378887 899999998 4999999987 99999999999
Q ss_pred CHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHH--HHhhcCCCcC
Q 020417 184 PFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDV--FYNFYKPRKS 261 (326)
Q Consensus 184 ~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l--~~~~~~~~~~ 261 (326)
+|+.|=.+..++|.+.+|| .|--..|+. .| ++..|. ...-|+... +...+...
T Consensus 170 pf~~aQ~ev~klL~gRIlV-------------GHaLhnDl~-~L-------~l~hp~--s~iRDTs~~~pl~k~~~~~-- 224 (280)
T KOG2249|consen 170 PFKVAQKEVLKLLKGRILV-------------GHALHNDLQ-AL-------KLEHPR--SMIRDTSKYPPLMKLLSKK-- 224 (280)
T ss_pred cHHHHHHHHHHHHhCCEEe-------------ccccccHHH-HH-------hhhCch--hhhcccccCchHHHHhhcc--
Confidence 9999999999999987655 343345665 44 444442 122233221 22222332
Q ss_pred CCCCHHHHHH-hcCCCCCCCCCChHHHHHHHHHHHHHHHH
Q 020417 262 EATGMMGMMK-NRQVPMFGSHHLGIDDTKNITRVLQRMLA 300 (326)
Q Consensus 262 ~~~~L~~l~k-~lgI~~~g~hHrAldDA~~tA~I~~~ll~ 300 (326)
...+|..|.+ .||++...-.|+.+.||++|.+++.++-.
T Consensus 225 ~tpSLK~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~~vk~ 264 (280)
T KOG2249|consen 225 ATPSLKKLTEALLGKDIQVGEHSSVEDARATMELYKRVKV 264 (280)
T ss_pred CCccHHHHHHHHhchhhhccccCcHHHHHHHHHHHHHHHH
Confidence 2788998866 45877643359999999999999987753
No 53
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=98.63 E-value=2e-07 Score=75.05 Aligned_cols=49 Identities=20% Similarity=0.373 Sum_probs=39.8
Q ss_pred HHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHH
Q 020417 192 FEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDV 251 (326)
Q Consensus 192 F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l 251 (326)
|.+|+++... ...++||++||+. ||.++|+++|++.|.....++|++.+
T Consensus 35 f~~~l~~~~~----------~v~V~hn~~fD~~-fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 35 LKDILRDKPL----------AILVGHNGSFDLP-FLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHHHHhhCCC----------CEEEEeCcHHhHH-HHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 8888887521 2467788899999 99999999999988666789998765
No 54
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.31 E-value=7e-06 Score=80.91 Aligned_cols=164 Identities=13% Similarity=0.053 Sum_probs=115.3
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHH-hCCCCHHH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWH-DTALPFKE 187 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V-~~Ap~f~e 187 (326)
-+|.+.|.||. +++-||++|+-|..=..|.+--..|++|... -+|.--.-| |||||.... +++.+-.+
T Consensus 9 ~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdD---yLP~P~a~L--ITGITPQ~~~~~G~~E~~ 83 (475)
T COG2925 9 PTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADD---YLPQPGAVL--ITGITPQEAREKGINEAA 83 (475)
T ss_pred CcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccc---cCCCCCcee--eecCCHHHHHhcCCChHH
Confidence 46999999997 9999999999987333344568889999873 344322223 469998877 57888888
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEE-cCcccHHHHHHHHHHHhCCCCCCCC------ccHhhHHHHHHhhcCCCc
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFAT-CGNWDLKTKVPDQCKVSQIKLPPYF------MEWINLKDVFYNFYKPRK 260 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~-ng~fDl~~fL~~~~~~~gi~~p~~~------~~~iDl~~l~~~~~~~~~ 260 (326)
...++.+-+... ..+++.. +..||=. +.+..+-|+=+++ |. |.-.|+.++.+..|..+.
T Consensus 84 F~~~I~~~ls~P-----------~Tcv~GYNniRFDDE-vtRy~fyRNF~DP--Ya~sWqngNSRWDLLD~~RacyALRP 149 (475)
T COG2925 84 FAARIHAELTQP-----------NTCVLGYNNIRFDDE-VTRYIFYRNFYDP--YAWSWQNGNSRWDLLDVVRACYALRP 149 (475)
T ss_pred HHHHHHHHhCCC-----------CeeeecccccccchH-HHHHHHHHhcCch--hhhhhcCCCchhHHHHHHHHHHhcCc
Confidence 888887766543 1234444 4589966 7777776665542 22 334677777666654332
Q ss_pred C-----------CCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHH
Q 020417 261 S-----------EATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRM 298 (326)
Q Consensus 261 ~-----------~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~l 298 (326)
+ .+.+|+.+.+.-||+. +++|.|+.|+++|..+.+.+
T Consensus 150 eGI~Wp~n~dG~pSFkLEhLt~ANgieH-~nAHdAmsDVyATIamAklv 197 (475)
T COG2925 150 EGINWPENDDGLPSFKLEHLTKANGIEH-SNAHDAMSDVYATIAMAKLV 197 (475)
T ss_pred ccCCCCcCCCCCcchhhHHHhhcccccc-chhhHHHHHHHHHHHHHHHH
Confidence 1 3789999999999997 58999999999998766644
No 55
>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=98.18 E-value=7.5e-05 Score=68.37 Aligned_cols=78 Identities=18% Similarity=0.296 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCCCc--------------cHhhHH
Q 020417 185 FKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPYFM--------------EWINLK 249 (326)
Q Consensus 185 f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~--------------~~iDl~ 249 (326)
-.+.|.+|.+++++.. ..++.+|| +||+. +|..-+..+|++.|.++. ..+|+.
T Consensus 78 E~elL~~F~~~i~~~~-----------p~lv~yNg~~FDlP-~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~ 145 (208)
T cd05782 78 EKELLEDFFQLIEKKN-----------PRLVSFNGRGFDLP-VLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLM 145 (208)
T ss_pred HHHHHHHHHHHHHHhC-----------CEEEecCCCcCCHH-HHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHH
Confidence 3788999999998742 23455677 79999 999999999998774331 278988
Q ss_pred HHHHhhcCCCcCCCCCHHHHHHhcCCCC
Q 020417 250 DVFYNFYKPRKSEATGMMGMMKNRQVPM 277 (326)
Q Consensus 250 ~l~~~~~~~~~~~~~~L~~l~k~lgI~~ 277 (326)
.+++.. +.. .+++|+++++.+|++-
T Consensus 146 ~~~~~~-~~~--~~~~L~~va~~lG~~~ 170 (208)
T cd05782 146 DLLAFY-GAR--ARASLDLLAKLLGIPG 170 (208)
T ss_pred HHHhcc-Ccc--CCCCHHHHHHHhCCCC
Confidence 887653 222 2899999999999964
No 56
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.11 E-value=1.8e-05 Score=70.01 Aligned_cols=156 Identities=12% Similarity=0.130 Sum_probs=103.2
Q ss_pred CCeEEEEEeccC------CceeeeeEEEEEcCCCeEEeE-Eeeccc-C-CcCCCCCcChhhhcccccCCCCHHHHhCCCC
Q 020417 114 LDFFLVLDLEGK------IEILEFPVLMIDAKTMAFVDL-FHRFVR-P-SKMSEQHINKYIEGKYGKFGVDRVWHDTALP 184 (326)
Q Consensus 114 ~~~~vVfDlETT------~EIIEIgAVkvD~k~geiid~-F~~fVr-P-~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~ 184 (326)
.+++|=+|+|.| +.||||++++-|. +..++.+ +..-|. | +... ...+++++..|..|+++.--....+
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIEiA~iVTD~-~Lnilaegp~~~Ihq~~e~L~--~Mdew~~~~H~~sGL~~rV~~S~~t 81 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIEIATIVTDA-NLNILAEGPVIAIHQSDEQLA--KMDEWNTETHGRSGLTERVKASTVT 81 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEEEEEEEecC-cccccccCceEEEeCCHHHHH--HHHHHHHHccccccHHHHHHHhhcc
Confidence 468999999999 9999999999986 7666643 222232 2 2211 3567787776667888887789999
Q ss_pred HHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCCCccHhhH---HHHHHhhcCCCc
Q 020417 185 FKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPYFMEWINL---KDVFYNFYKPRK 260 (326)
Q Consensus 185 f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~~~iDl---~~l~~~~~~~~~ 260 (326)
..+|-.+.++|++..+--+ ..-+|.|+ .-|.+ ||.+..-+..- .+.++++|+ +++.++..|.-
T Consensus 82 ~~~aE~~~l~flkkwvp~~--------~spicGNSI~qDRr-Fl~r~MP~Le~---yfHYR~lDVSTlKELa~RW~P~i- 148 (184)
T COG1949 82 EAEAEAQTLDFLKKWVPKG--------VSPICGNSIAQDRR-FLFRYMPKLEA---YFHYRYLDVSTLKELARRWNPEI- 148 (184)
T ss_pred HHHHHHHHHHHHHHhCCCC--------CCCCccchhhHHHH-HHHHHhhhHHH---HhhhHhhhHHHHHHHHHhhCcHh-
Confidence 9999999999999875321 12234443 45888 88776643211 123577774 55666655432
Q ss_pred CCCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHH
Q 020417 261 SEATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQR 297 (326)
Q Consensus 261 ~~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ 297 (326)
..| +-.+..|+|++|.+--..=++.
T Consensus 149 -----------~~~-~~K~~~H~Al~DI~ESI~EL~~ 173 (184)
T COG1949 149 -----------LAG-FKKGGTHRALDDIRESIAELRY 173 (184)
T ss_pred -----------hhc-cccccchhHHHHHHHHHHHHHH
Confidence 123 2246789999998865444443
No 57
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=98.10 E-value=2.8e-05 Score=71.59 Aligned_cols=158 Identities=13% Similarity=0.097 Sum_probs=104.9
Q ss_pred CceeeeeEEEEEcCCCeEEe----EEeeccc---CCcCCCCCcChhhhcccccCCCCHHHHh-CCCCHHHHHHHHHHHHH
Q 020417 126 IEILEFPVLMIDAKTMAFVD----LFHRFVR---PSKMSEQHINKYIEGKYGKFGVDRVWHD-TALPFKEVIQQFEAWLI 197 (326)
Q Consensus 126 ~EIIEIgAVkvD~k~geiid----~F~~fVr---P~~~p~~~Is~~it~LTgi~GIt~e~V~-~Ap~f~eVl~~F~~fl~ 197 (326)
-++||+|....|. +|++-+ +|+.-.+ +.... -++...++....||+-+... .+...++ |-+-+-
T Consensus 62 lklIQlGlTlsd~-~Gn~p~~g~~tWqfNF~dF~~~~D~---~a~~SIElLr~~Gidf~K~~e~GI~~~~----F~ellm 133 (239)
T KOG0304|consen 62 LKLIQLGLTLSDE-KGNLPDCGTDTWQFNFSDFNLEKDM---YAQDSIELLRRSGIDFEKHREEGIDIEE----FAELLM 133 (239)
T ss_pred hhhhheeeeeecc-CCCCCCCCCceeEEecccCCchhhc---cchhhHHHHHHcCcCHHHHHHcCCCHHH----HHHHHH
Confidence 5899999999996 677665 5554443 32211 22222234345799988774 6666664 444444
Q ss_pred hCcccccccCCCCcceEEEE-cCcccHHHHHHHHHHHhCCCCC---------CCCccHhhHHHHHHhhcCCCcCCCCCHH
Q 020417 198 QHHLWEKGRGGHLKRAAFAT-CGNWDLKTKVPDQCKVSQIKLP---------PYFMEWINLKDVFYNFYKPRKSEATGMM 267 (326)
Q Consensus 198 ~~~Lv~~~~~~~~~~~~~a~-ng~fDl~~fL~~~~~~~gi~~p---------~~~~~~iDl~~l~~~~~~~~~~~~~~L~ 267 (326)
...++. ..++.|+| ++.+|.+ +|-+-.....++.. .++..+.|++.+++..-+.. ...+|+
T Consensus 134 ~sg~v~------~~~V~WvTFhs~YDfg-YLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~--l~~GL~ 204 (239)
T KOG0304|consen 134 TSGLVL------DENVTWVTFHSGYDFG-YLLKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLS--LKGGLQ 204 (239)
T ss_pred Hhhhhc------cCceEEEEeeccchHH-HHHHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhh--hhcCHH
Confidence 444432 23678887 6899999 77666544444321 12335667777765542211 268999
Q ss_pred HHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHH
Q 020417 268 GMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLA 300 (326)
Q Consensus 268 ~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~ 300 (326)
.+++.||++-.|..|.|=.|+..||.+|.+|.+
T Consensus 205 ~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 205 RLADLLGLKRVGIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred HHHHHhCCCeeecccccCcHHHHHHHHHHHHHh
Confidence 999999999889999999999999999999865
No 58
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.04 E-value=2.3e-05 Score=70.03 Aligned_cols=157 Identities=16% Similarity=0.240 Sum_probs=107.9
Q ss_pred CeEEEEEeccC------CceeeeeEEEEEcCCCeE-EeEEeeccc-CCc-CCCCCcChhhhcccccCCCCHHHHhCCCCH
Q 020417 115 DFFLVLDLEGK------IEILEFPVLMIDAKTMAF-VDLFHRFVR-PSK-MSEQHINKYIEGKYGKFGVDRVWHDTALPF 185 (326)
Q Consensus 115 ~~~vVfDlETT------~EIIEIgAVkvD~k~gei-id~F~~fVr-P~~-~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f 185 (326)
..+|=+|+|.| +.||||++++-|. +... .+-+...|+ |.. .. ..+++|.+--|.-|+|..-+....++
T Consensus 26 q~lVWiD~EMTGLdvekd~i~EiacIITD~-dL~~~~egpd~vI~~~~evld--~MneWc~ehhg~SGLt~kv~~S~~tl 102 (208)
T KOG3242|consen 26 QPLVWIDCEMTGLDVEKDRIIEIACIITDG-DLNPVAEGPDLVIHQPKEVLD--KMNEWCIEHHGNSGLTEKVLASKITL 102 (208)
T ss_pred CceEEEeeeccccccccceeEEEEEEEecC-CccccccCccchhcCCHHHHH--HHHHHHHHhccchhHHHHHHHhhccH
Confidence 56899999999 9999999999876 4443 345777776 332 21 47788888877789999999999999
Q ss_pred HHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCCCccHhh---HHHHHHhhcCCCcC
Q 020417 186 KEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPYFMEWIN---LKDVFYNFYKPRKS 261 (326)
Q Consensus 186 ~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~~~iD---l~~l~~~~~~~~~~ 261 (326)
+||-.++++|++.+.. ++ .+.++.|+ --|.. ||.+..-..---+ ....+| ++++.++++|..+
T Consensus 103 ~~aEnevl~yikk~ip--~~------~~~laGNSV~~Drl-Fl~k~mPk~~~~l---hyrivDVStIkeL~~Rw~P~~~- 169 (208)
T KOG3242|consen 103 ADAENEVLEYIKKHIP--KG------KCPLAGNSVYMDRL-FLKKYMPKLIKHL---HYRIVDVSTIKELARRWYPDIK- 169 (208)
T ss_pred HHHHHHHHHHHHHhCC--CC------CCCccCcchhhHHH-HHHHHhHHHHHhc---ceeeeeHHHHHHHHHHhCchhh-
Confidence 9999999999999864 21 23344443 36777 8887764322111 245666 4667788877642
Q ss_pred CCCCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHH
Q 020417 262 EATGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRM 298 (326)
Q Consensus 262 ~~~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~l 298 (326)
.+. |-....|||+||.+--..=++..
T Consensus 170 ----------~~a-PkK~~~HrAldDI~ESI~ELq~Y 195 (208)
T KOG3242|consen 170 ----------ARA-PKKKATHRALDDIRESIKELQYY 195 (208)
T ss_pred ----------ccC-cccccccchHHHHHHHHHHHHHH
Confidence 111 11234699999988755444433
No 59
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=97.98 E-value=0.00016 Score=65.17 Aligned_cols=121 Identities=12% Similarity=0.104 Sum_probs=80.4
Q ss_pred eEEEEEeccC----------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCH
Q 020417 116 FFLVLDLEGK----------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPF 185 (326)
Q Consensus 116 ~~vVfDlETT----------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f 185 (326)
..+.||+||| ++||.||.+.. ..++++ .+ ++.. . +++ ..-.+-
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~--~~~~~~-~~----~~~~-----~-~~v--------------~~~~~E 56 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADE--GGNKVI-TW----KKFD-----L-PFV--------------EVVKTE 56 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecC--CCceEE-Ee----cCCC-----C-CeE--------------EEeCCH
Confidence 3789999996 89999998653 122222 11 1111 1 111 112344
Q ss_pred HHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCC--------------------Ccc
Q 020417 186 KEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPY--------------------FME 244 (326)
Q Consensus 186 ~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~--------------------~~~ 244 (326)
.+.|.+|.+++.... ..+++.+|+ +||+. +|..-|.++|++.+.- -..
T Consensus 57 ~~lL~~F~~~i~~~d----------pdiivgyN~~~FD~p-yL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~ 125 (195)
T cd05780 57 KEMIKRFIEIVKEKD----------PDVIYTYNGDNFDFP-YLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRI 125 (195)
T ss_pred HHHHHHHHHHHHHcC----------CCEEEecCCCCCcHH-HHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeE
Confidence 789999999998742 134556776 69999 9999999999985520 013
Q ss_pred HhhHHHHHHhhcCCCcCCCCCHHHHHH-hcCCCC
Q 020417 245 WINLKDVFYNFYKPRKSEATGMMGMMK-NRQVPM 277 (326)
Q Consensus 245 ~iDl~~l~~~~~~~~~~~~~~L~~l~k-~lgI~~ 277 (326)
.+|+..+++..+... +++|+++++ .||.+-
T Consensus 126 ~lDl~~~~~~~~~l~---sy~L~~v~~~~Lg~~k 156 (195)
T cd05780 126 HVDLYPVARRTLNLT---RYTLERVYEELFGIEK 156 (195)
T ss_pred EEeHHHHHHhhCCCC---cCcHHHHHHHHhCCCC
Confidence 688888887765543 899999977 667753
No 60
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=97.93 E-value=0.00013 Score=65.79 Aligned_cols=112 Identities=13% Similarity=0.071 Sum_probs=77.5
Q ss_pred eEEEEEeccC----------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCH
Q 020417 116 FFLVLDLEGK----------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPF 185 (326)
Q Consensus 116 ~~vVfDlETT----------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f 185 (326)
..+.||+||+ +.||.||++.. +|.+. . ++ ....+-
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~---~g~~~----------~-----~~-----------------~~~~~E 48 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATS---NGDVE----------F-----IL-----------------AEGLDD 48 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeC---CCCEE----------E-----EE-----------------ecCCCH
Confidence 4789999997 68999998654 33210 0 10 012356
Q ss_pred HHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCC--C----------------ccHh
Q 020417 186 KEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPY--F----------------MEWI 246 (326)
Q Consensus 186 ~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~--~----------------~~~i 246 (326)
.+.|.+|.+++....- .+++-.|+ +||+. +|..-|+++|+..+.. . ...+
T Consensus 49 ~~lL~~F~~~i~~~dP----------d~i~gyN~~~FDlp-yl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~i 117 (188)
T cd05781 49 RKIIREFVKYVKEYDP----------DIIVGYNSNAFDWP-YLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNV 117 (188)
T ss_pred HHHHHHHHHHHHHcCC----------CEEEecCCCcCcHH-HHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEE
Confidence 7899999999998631 23333465 69999 9999999999876411 0 0167
Q ss_pred hHHHHHHhhcCCCcCCCCCHHHHHHhcCCC
Q 020417 247 NLKDVFYNFYKPRKSEATGMMGMMKNRQVP 276 (326)
Q Consensus 247 Dl~~l~~~~~~~~~~~~~~L~~l~k~lgI~ 276 (326)
|+-.+.+...... +++|++++++||+.
T Consensus 118 Dl~~~~~~~~~l~---~y~L~~Va~~Lg~~ 144 (188)
T cd05781 118 DLYDFAEEIPEVK---VKTLENVAEYLGVM 144 (188)
T ss_pred EhHHHHHhhCCCC---CCCHHHHHHHHCCC
Confidence 8888877765433 89999999999974
No 61
>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=97.87 E-value=7e-05 Score=64.70 Aligned_cols=110 Identities=17% Similarity=0.194 Sum_probs=58.2
Q ss_pred EEEEeccC------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHH
Q 020417 118 LVLDLEGK------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQ 191 (326)
Q Consensus 118 vVfDlETT------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~ 191 (326)
|+||+||| +.|+-||++.+|...... |..+.-... .-++++.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~---~~~~~~~~~----------------------------~ee~~~~~ 49 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIIT---FIQWFAEDP----------------------------DEEEIILE 49 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE----EEEE-GGGH----------------------------HHHHHHHH
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEE---eeHhhccCc----------------------------HHHHHHHH
Confidence 68999999 789999999886422211 222221111 12334444
Q ss_pred HHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHH
Q 020417 192 FEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMM 270 (326)
Q Consensus 192 F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~ 270 (326)
+.+++.+.. .++++|| +||+. +|++-+.+.+++. ...++|+...++.... .+++|.+++
T Consensus 50 ~~~~l~~~~------------~iv~yng~~FD~p-~L~~~~~~~~~~~---~~~~iDl~~~~~~~~~----~~~~Lk~ve 109 (164)
T PF13482_consen 50 FFELLDEAD------------NIVTYNGKNFDIP-FLKRRAKRYGLPP---PFNHIDLLKIIKKHFL----ESYSLKNVE 109 (164)
T ss_dssp --HHHHTT--------------EEESSTTTTHHH-HHHHHH-HHHH-----GGGEEEHHHHHT-TTS----CCTT--SHH
T ss_pred HHHHHhcCC------------eEEEEeCcccCHH-HHHHHHHHcCCCc---ccchhhHHHHHHhccC----CCCCHHHHh
Confidence 447776653 3456675 89999 9999998888775 3578999988875433 278999999
Q ss_pred HhcCCCCC
Q 020417 271 KNRQVPMF 278 (326)
Q Consensus 271 k~lgI~~~ 278 (326)
+.+|+...
T Consensus 110 ~~lg~~~~ 117 (164)
T PF13482_consen 110 KFLGIERR 117 (164)
T ss_dssp H-------
T ss_pred hhcccccc
Confidence 99999753
No 62
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=97.87 E-value=0.00072 Score=62.32 Aligned_cols=106 Identities=18% Similarity=0.201 Sum_probs=77.7
Q ss_pred HHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCCCc---------------cHhhH
Q 020417 185 FKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPYFM---------------EWINL 248 (326)
Q Consensus 185 f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~---------------~~iDl 248 (326)
-.+.+.+|.+++++.. ...+.+|| .||+- +|...+-.+|++.|.+++ ..+||
T Consensus 37 E~~lL~~F~~~~~~~~-----------p~LVs~NG~~FDlP-~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DL 104 (209)
T PF10108_consen 37 EKELLQDFFDLVEKYN-----------PQLVSFNGRGFDLP-VLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDL 104 (209)
T ss_pred HHHHHHHHHHHHHhCC-----------CeEEecCCccCCHH-HHHHHHHHhCCCCchhhhcCCCCccccccccCcccccH
Confidence 6788999999998753 23455676 79999 999999999999886442 35888
Q ss_pred HHHHHhhcCCCcCCCCCHHHHHHhcCCCCCCCCC------------------ChHHHHHHHHHHHHHHHHcCCcc
Q 020417 249 KDVFYNFYKPRKSEATGMMGMMKNRQVPMFGSHH------------------LGIDDTKNITRVLQRMLADGARV 305 (326)
Q Consensus 249 ~~l~~~~~~~~~~~~~~L~~l~k~lgI~~~g~hH------------------rAldDA~~tA~I~~~ll~~g~~~ 305 (326)
.+++.. ++.+ ...+|+.+|.-+|||-...-+ --..|+.+|+.|+.++......+
T Consensus 105 md~l~~-~g~~--~~~sLd~la~~lgiPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~~G~l 176 (209)
T PF10108_consen 105 MDLLSF-YGAK--ARTSLDELAALLGIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELLRGRL 176 (209)
T ss_pred HHHHhc-cCcc--ccCCHHHHHHHcCCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence 888665 3433 289999999999998531111 11468999999999986544333
No 63
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=97.82 E-value=5.8e-05 Score=75.11 Aligned_cols=154 Identities=14% Similarity=0.181 Sum_probs=108.6
Q ss_pred CeEEEEEeccC-----CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHh-CCCCHHHH
Q 020417 115 DFFLVLDLEGK-----IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHD-TALPFKEV 188 (326)
Q Consensus 115 ~~~vVfDlETT-----~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~-~Ap~f~eV 188 (326)
.+.+++|-|.- -|+..+++|=+ ++++ -+..||+|.. +|-.|.|..+ |||+++++ ...++++|
T Consensus 216 ~~i~AlDCEm~~te~g~el~RVt~VD~---~~~v--i~D~fVkP~~----~VvDy~T~~S---GIT~~~~e~~t~tl~dv 283 (380)
T KOG2248|consen 216 PNIFALDCEMVVTENGLELTRVTAVDR---DGKV--ILDTFVKPNK----PVVDYNTRYS---GITEEDLENSTITLEDV 283 (380)
T ss_pred CCeEEEEeeeeeeccceeeEEeeeeec---cCcE--EeEEeecCCC----cccccccccc---cccHHHHhcCccCHHHH
Confidence 46899999964 67888888654 6676 4788999998 4889988875 99999997 55678888
Q ss_pred HHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHH
Q 020417 189 IQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMG 268 (326)
Q Consensus 189 l~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~ 268 (326)
=.++..|+.... +.+.|--+-|++ -|+- . ...+||+.-+|..-.+. .+...+|..
T Consensus 284 q~~l~~~~~~~T------------ILVGHSLenDL~-aLKl-------~----H~~ViDTa~lf~~~~g~-~~~k~sLk~ 338 (380)
T KOG2248|consen 284 QKELLELISKNT------------ILVGHSLENDLK-ALKL-------D----HPSVIDTAVLFKHPTGP-YPFKSSLKN 338 (380)
T ss_pred HHHHHhhcCcCc------------EEEeechhhHHH-HHhh-------h----CCceeeeeEEEecCCCC-ccchHHHHH
Confidence 889999886542 334455577888 5532 2 24678988665533231 012456888
Q ss_pred HHHhc-CCCCC-C-CCCChHHHHHHHHHHHHHHHHcCCcc
Q 020417 269 MMKNR-QVPMF-G-SHHLGIDDTKNITRVLQRMLADGARV 305 (326)
Q Consensus 269 l~k~l-gI~~~-g-~hHrAldDA~~tA~I~~~ll~~g~~~ 305 (326)
+++.+ |.... | ..|....||.++.+++...+..+..+
T Consensus 339 L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv~~k~~~~~~~ 378 (380)
T KOG2248|consen 339 LAKSYLGKLIQEGVGGHDSVEDALACMKLVKLKIKNSESQ 378 (380)
T ss_pred HHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHhccccc
Confidence 87654 43322 2 35999999999999999877766544
No 64
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=97.34 E-value=0.003 Score=59.68 Aligned_cols=170 Identities=15% Similarity=0.118 Sum_probs=96.3
Q ss_pred eEEEEEeccC---------------------------CceeeeeEEEEEcCCCeEE-----eEEeecccCCcCCCCCcCh
Q 020417 116 FFLVLDLEGK---------------------------IEILEFPVLMIDAKTMAFV-----DLFHRFVRPSKMSEQHINK 163 (326)
Q Consensus 116 ~~vVfDlETT---------------------------~EIIEIgAVkvD~k~geii-----d~F~~fVrP~~~p~~~Is~ 163 (326)
.||.||+|.| -.|||+|...+..++++.. ..|.-++-|.... -.+.
T Consensus 23 ~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~--~~~~ 100 (262)
T PF04857_consen 23 DFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRD--FSQA 100 (262)
T ss_dssp SEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTC--EEEH
T ss_pred CEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccc--eecc
Confidence 4999999986 5899999999932466653 3444443443310 1111
Q ss_pred hhhcccccCCCCHHHH-hCCCCHHHHHHH--HHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCC
Q 020417 164 YIEGKYGKFGVDRVWH-DTALPFKEVIQQ--FEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPP 240 (326)
Q Consensus 164 ~it~LTgi~GIt~e~V-~~Ap~f~eVl~~--F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~ 240 (326)
...+....+|++=+.+ .++.++...-++ ..+.++-..++..- ......+|.||+-+|+. +|-+.+- | ++|.
T Consensus 101 ~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~--~~~~~p~Vghn~~~Dl~-~l~~~f~--~-~LP~ 174 (262)
T PF04857_consen 101 SSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDAL--KSSKKPIVGHNGLYDLM-YLYKKFI--G-PLPE 174 (262)
T ss_dssp HHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHC--HCC-SEEEESSTHHHHH-HHHHHHT--T-S--S
T ss_pred hhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHh--hccCCcEEEeChHhHHH-HHHHHhc--C-CCCC
Confidence 1111112367775544 566666554431 11445444444210 01225678899999999 7776653 3 6664
Q ss_pred CC-----------ccHhhHHHHHHhhcCCCcCCCCCHHHHHHhcCCCC-----------------------CCC-CCChH
Q 020417 241 YF-----------MEWINLKDVFYNFYKPRKSEATGMMGMMKNRQVPM-----------------------FGS-HHLGI 285 (326)
Q Consensus 241 ~~-----------~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~lgI~~-----------------------~g~-hHrAl 285 (326)
-. ...+|++-+....- . ...+|+.+.+.+++.. .+. .|.|=
T Consensus 175 t~~eF~~~~~~~FP~i~DtK~la~~~~--~--~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAG 250 (262)
T PF04857_consen 175 TLEEFKELLRELFPRIYDTKYLAEECP--G--KSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAG 250 (262)
T ss_dssp SHHHHHHHHHHHSSSEEEHHHHHTSTT--T--S-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHH
T ss_pred CHHHHHHHHHHHCcccccHHHHHHhcc--c--cccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcc
Confidence 22 22345554443221 1 2679999999999764 344 89999
Q ss_pred HHHHHHHHHHHH
Q 020417 286 DDTKNITRVLQR 297 (326)
Q Consensus 286 dDA~~tA~I~~~ 297 (326)
.||..|+.+|.+
T Consensus 251 yDA~mTg~~F~~ 262 (262)
T PF04857_consen 251 YDAYMTGCVFIK 262 (262)
T ss_dssp HHHHHHHHHHHH
T ss_pred hHHHHHHHHHcC
Confidence 999999999864
No 65
>PRK05755 DNA polymerase I; Provisional
Probab=97.29 E-value=0.0016 Score=71.41 Aligned_cols=93 Identities=13% Similarity=0.104 Sum_probs=69.9
Q ss_pred HHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCH
Q 020417 187 EVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGM 266 (326)
Q Consensus 187 eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L 266 (326)
++++.|.+|+++... ..++||+.||+. +|.+ .|+.++ ..|+|++-....+.+.. .++|
T Consensus 357 ~~l~~l~~~L~d~~v-----------~kV~HNakfDl~-~L~~----~gi~~~---~~~~DT~iAa~Ll~~~~---~~~L 414 (880)
T PRK05755 357 EVLAALKPLLEDPAI-----------KKVGQNLKYDLH-VLAR----YGIELR---GIAFDTMLASYLLDPGR---RHGL 414 (880)
T ss_pred HHHHHHHHHHhCCCC-----------cEEEeccHhHHH-HHHh----CCCCcC---CCcccHHHHHHHcCCCC---CCCH
Confidence 678889999987542 357899999999 8863 487764 47899987766554443 4899
Q ss_pred HHHHHhc-CCCC------------------CCCCCChHHHHHHHHHHHHHHHHc
Q 020417 267 MGMMKNR-QVPM------------------FGSHHLGIDDTKNITRVLQRMLAD 301 (326)
Q Consensus 267 ~~l~k~l-gI~~------------------~g~hHrAldDA~~tA~I~~~ll~~ 301 (326)
+++++.| |+.. +...|.|..|+..+.+|+.+|.+.
T Consensus 415 ~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 415 DSLAERYLGHKTISFEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred HHHHHHHhCCCccchHHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999887 5542 112478999999999999998764
No 66
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=97.00 E-value=0.013 Score=53.71 Aligned_cols=82 Identities=12% Similarity=0.090 Sum_probs=57.1
Q ss_pred CCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCC----CCc----------cHh
Q 020417 182 ALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPP----YFM----------EWI 246 (326)
Q Consensus 182 Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~----~~~----------~~i 246 (326)
-.+-.+.|.+|.+|+.+..- .+++..|+ +||+. +|.+-|+++|+.... ... -.+
T Consensus 70 ~~~E~~lL~~f~~~i~~~~P----------d~i~gyN~~~FD~p-yl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~i 138 (204)
T cd05779 70 EPDEKALLQRFFEHIREVKP----------HIIVTYNGDFFDWP-FVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHM 138 (204)
T ss_pred CCCHHHHHHHHHHHHHHhCC----------CEEEecCccccCHH-HHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEE
Confidence 46788999999999998631 23334465 79999 999999999987541 000 157
Q ss_pred hHHHHHHhh-cCCCcCCCCCHHHHHHh-cCCC
Q 020417 247 NLKDVFYNF-YKPRKSEATGMMGMMKN-RQVP 276 (326)
Q Consensus 247 Dl~~l~~~~-~~~~~~~~~~L~~l~k~-lgI~ 276 (326)
|+-.+++.. +... ++++|++++++ ||..
T Consensus 139 Dl~~~~~~~~~l~~--~sysLd~Va~~~Lg~~ 168 (204)
T cd05779 139 DCFRWVKRDSYLPQ--GSQGLKAVTKAKLGYD 168 (204)
T ss_pred EhHHHHHHhhcCCC--CCccHHHHHHHHhCCC
Confidence 887777653 2222 28999999995 8874
No 67
>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=96.99 E-value=0.0073 Score=61.50 Aligned_cols=122 Identities=11% Similarity=0.052 Sum_probs=81.3
Q ss_pred CeEEEEEeccC---CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHH
Q 020417 115 DFFLVLDLEGK---IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQ 191 (326)
Q Consensus 115 ~~~vVfDlETT---~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~ 191 (326)
...+.|||||+ .-.-.+|++..+ +|+..++|+.|..... ..-.+++.+
T Consensus 284 ~~~~ffDiEt~P~~~~~yL~G~~~~~--~~~~~~~~~~fla~~~---------------------------~~E~~~~~~ 334 (457)
T TIGR03491 284 PGELIFDIESDPDENLDYLHGFLVVD--KGQENEKYRPFLAEDP---------------------------NTEELAWQQ 334 (457)
T ss_pred CccEEEEecCCCCCCCceEEEEEEec--CCCCCcceeeeecCCc---------------------------hHHHHHHHH
Confidence 34689999999 557889987653 3332223433322111 124568899
Q ss_pred HHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCC---CCCccHhhHHHHHHhhcCCCcCCCCCHHH
Q 020417 192 FEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLP---PYFMEWINLKDVFYNFYKPRKSEATGMMG 268 (326)
Q Consensus 192 F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p---~~~~~~iDl~~l~~~~~~~~~~~~~~L~~ 268 (326)
|.+|+.... ...++|++.+... .|++-+.++|.... .+...++|+..+.+..+-.. .++++|++
T Consensus 335 f~~~l~~~~-----------~~~i~hY~~~e~~-~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p-~~sysLK~ 401 (457)
T TIGR03491 335 FLQLLQSYP-----------DAPIYHYGETEKD-SLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILP-IESYSLKS 401 (457)
T ss_pred HHHHHHHCC-----------CCeEEeeCHHHHH-HHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECC-CCCCCHHH
Confidence 999998752 2356787788877 99999999887632 12236788887766443221 14899999
Q ss_pred HHHhcCCCCC
Q 020417 269 MMKNRQVPMF 278 (326)
Q Consensus 269 l~k~lgI~~~ 278 (326)
++..+|....
T Consensus 402 v~~~lg~~~~ 411 (457)
T TIGR03491 402 IARWLGFEWR 411 (457)
T ss_pred HHHHhCcccC
Confidence 9999999764
No 68
>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=96.81 E-value=0.0052 Score=53.84 Aligned_cols=101 Identities=14% Similarity=0.115 Sum_probs=71.1
Q ss_pred CCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCc
Q 020417 181 TALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRK 260 (326)
Q Consensus 181 ~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~ 260 (326)
+++.+++++++|.+|+++.. ...++||+.||+. +|. +.|+.++ ..++|+..+...+.+...
T Consensus 48 ~~~~~~~~~~~l~~~l~~~~-----------~~~v~hn~k~d~~-~l~----~~gi~~~---~~~~Dt~l~a~ll~p~~~ 108 (193)
T cd06139 48 EQLPREEVLAALKPLLEDPS-----------IKKVGQNLKFDLH-VLA----NHGIELR---GPAFDTMLASYLLNPGRR 108 (193)
T ss_pred cCCCHHHHHHHHHHHHhCCC-----------CcEEeeccHHHHH-HHH----HCCCCCC---CCcccHHHHHHHhCCCCC
Confidence 45578889999999998652 1357899999998 874 4677754 467999887766655442
Q ss_pred CCCCCHHHHHHhc-CCCC----------------C-----CCCCChHHHHHHHHHHHHHHHHcC
Q 020417 261 SEATGMMGMMKNR-QVPM----------------F-----GSHHLGIDDTKNITRVLQRMLADG 302 (326)
Q Consensus 261 ~~~~~L~~l~k~l-gI~~----------------~-----g~hHrAldDA~~tA~I~~~ll~~g 302 (326)
..+|+++++.| |... + ...|.|..||..+.+++..|...-
T Consensus 109 --~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l 170 (193)
T cd06139 109 --RHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKL 170 (193)
T ss_pred --CCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46999998875 3320 0 012358888999999988886543
No 69
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=96.68 E-value=0.067 Score=49.42 Aligned_cols=126 Identities=13% Similarity=0.100 Sum_probs=78.2
Q ss_pred eEEEEEeccC-----------CceeeeeEEEEEcCCCe--EEeEEeec-ccCCcCCCCCcChhhhcccccCCCCHHHHhC
Q 020417 116 FFLVLDLEGK-----------IEILEFPVLMIDAKTMA--FVDLFHRF-VRPSKMSEQHINKYIEGKYGKFGVDRVWHDT 181 (326)
Q Consensus 116 ~~vVfDlETT-----------~EIIEIgAVkvD~k~ge--iid~F~~f-VrP~~~p~~~Is~~it~LTgi~GIt~e~V~~ 181 (326)
..+.||+||+ ++||.|+.+.-. +|. ...+ .-| +++.. + ++ ...|..
T Consensus 8 ~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~--~~~~~~~~~-~~~~l~~~~-~---~~-------------~~~v~~ 67 (230)
T cd05777 8 RILSFDIECAGRKGVFPEPEKDPVIQIANVVTR--QGEGEPFIR-NIFTLKTCA-P---IV-------------GAQVFS 67 (230)
T ss_pred eEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEe--CCCCCCcee-EEEEeCCCC-C---CC-------------CCEEEE
Confidence 4899999996 899999998642 332 1111 111 22221 1 21 111223
Q ss_pred CCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCC-C--------------C---
Q 020417 182 ALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPP-Y--------------F--- 242 (326)
Q Consensus 182 Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~-~--------------~--- 242 (326)
-.+-.+.|.+|.+++.... -.+++.+|+ +||+. +|.+-|++.|++.-. + +
T Consensus 68 ~~~E~eLL~~f~~~i~~~D----------PDii~GyN~~~FDl~-yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~ 136 (230)
T cd05777 68 FETEEELLLAWRDFVQEVD----------PDIITGYNICNFDLP-YLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSK 136 (230)
T ss_pred ECCHHHHHHHHHHHHHhcC----------CCEEEEecCCCCCHH-HHHHHHHHhCCccccccccccCCceeEeCCccccc
Confidence 3577889999999998753 135666786 79999 998888888876210 0 0
Q ss_pred --------------ccHhhHHHHHHhhcCCCcCCCCCHHHHHHh-cCC
Q 020417 243 --------------MEWINLKDVFYNFYKPRKSEATGMMGMMKN-RQV 275 (326)
Q Consensus 243 --------------~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~-lgI 275 (326)
.-.+|+-.+++..+.. .+++|++++++ ||.
T Consensus 137 ~~g~~~~~~~~i~GR~~iD~~~~~~~~~kl---~sy~L~~Va~~~Lg~ 181 (230)
T cd05777 137 QMGTRETKEINIEGRIQFDLLQVIQRDYKL---RSYSLNSVSAHFLGE 181 (230)
T ss_pred ccccccceEEEEcCEEeeeHHHHHHHhcCc---ccCcHHHHHHHHhCC
Confidence 1135666666655443 38999999884 453
No 70
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=96.64 E-value=0.034 Score=50.83 Aligned_cols=79 Identities=20% Similarity=0.176 Sum_probs=53.6
Q ss_pred CCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCC---CCCC---------CccHhhHH
Q 020417 183 LPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIK---LPPY---------FMEWINLK 249 (326)
Q Consensus 183 p~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~---~p~~---------~~~~iDl~ 249 (326)
..-.+.|.+|.+|+.+.. .++..|+ +||+. +|.+-|+++|+. .|.. ....+|+.
T Consensus 71 ~~E~~lL~~F~~~i~~~~------------~iig~N~~~FDlp-yl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~ 137 (204)
T cd05783 71 DSEKELIREAFKIISEYP------------IVLTFNGDNFDLP-YLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLY 137 (204)
T ss_pred CCHHHHHHHHHHHHhcCC------------EEEEeCCCCcCHH-HHHHHHHHhCCChhhCceeecCCceeccCcEEeECH
Confidence 578899999999998652 3344465 79999 999999999987 2211 12357776
Q ss_pred HHHHh-h-----cCCCcCCCCCHHHHHHhc-CC
Q 020417 250 DVFYN-F-----YKPRKSEATGMMGMMKNR-QV 275 (326)
Q Consensus 250 ~l~~~-~-----~~~~~~~~~~L~~l~k~l-gI 275 (326)
..+.. . ++. +..+++|+++++++ |.
T Consensus 138 ~~~~~~~~~~~~~~~-~~~~~~L~~Va~~~lg~ 169 (204)
T cd05783 138 KFFSNRAIQVYAFGN-KYREYTLDAVAKALLGE 169 (204)
T ss_pred HHhhccchhhhhhcc-ccccCcHHHHHHHhcCC
Confidence 65442 1 111 11389999999966 44
No 71
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=96.04 E-value=0.011 Score=54.94 Aligned_cols=151 Identities=16% Similarity=0.167 Sum_probs=97.7
Q ss_pred CceeeeeEEEEEcCCCe-EE----eEEeecccCCcCCCCCcChhhhcccccCCCCHHHHh-CCCCHHHHHHHHHHHHHhC
Q 020417 126 IEILEFPVLMIDAKTMA-FV----DLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHD-TALPFKEVIQQFEAWLIQH 199 (326)
Q Consensus 126 ~EIIEIgAVkvD~k~ge-ii----d~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~-~Ap~f~eVl~~F~~fl~~~ 199 (326)
=+||++|...-|. +|. -. =.|..-.+|+..- ..+...+|..+-||+=+..+ -+... .+|-+.+-+.
T Consensus 80 LkiIQlGlsLSDe-~GN~P~~~sTWQFNF~F~l~~dm---ya~ESieLL~ksgIdFkkHe~~GI~v----~eF~elLm~S 151 (299)
T COG5228 80 LKIIQLGLSLSDE-NGNKPNGPSTWQFNFEFDLKKDM---YATESIELLRKSGIDFKKHENLGIDV----FEFSELLMDS 151 (299)
T ss_pred hhhhheeeeeccc-cCCCCCCCceeEEEEEecchhhh---cchHHHHHHHHcCCChhhHhhcCCCH----HHHHHHHhcc
Confidence 4899999999886 443 22 2466666676632 22332234335677766653 23322 3577777787
Q ss_pred cccccccCCCCcceEEEE-cCcccHHHHHHHHHHHhCCCCCC-----------CCccHhhHHHHHHhhcCCCcCCCCCHH
Q 020417 200 HLWEKGRGGHLKRAAFAT-CGNWDLKTKVPDQCKVSQIKLPP-----------YFMEWINLKDVFYNFYKPRKSEATGMM 267 (326)
Q Consensus 200 ~Lv~~~~~~~~~~~~~a~-ng~fDl~~fL~~~~~~~gi~~p~-----------~~~~~iDl~~l~~~~~~~~~~~~~~L~ 267 (326)
.||-. ..+.|++ ++.+|++ +|-+... +.++|. ++..+.|++-++...... +.+|.
T Consensus 152 GLvm~------e~VtWitfHsaYDfg-yLikilt--~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~~~----~KglQ 218 (299)
T COG5228 152 GLVMD------ESVTWITFHSAYDFG-YLIKILT--NDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNN----SKGLQ 218 (299)
T ss_pred Cceec------cceEEEEeecchhHH-HHHHHHh--cCCCCccHHHHHHHHHHHCccccchHHHHHhhhhh----hhHHH
Confidence 76643 3577887 6889999 7766543 344442 122345565555544333 46899
Q ss_pred HHHHhcCCCCCCCCCChHHHHHHHHHHHHH
Q 020417 268 GMMKNRQVPMFGSHHLGIDDTKNITRVLQR 297 (326)
Q Consensus 268 ~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ 297 (326)
+....+++...|..|.|-.||..||+.+-+
T Consensus 219 ei~ndlql~r~g~QhQagsdaLlTa~~ff~ 248 (299)
T COG5228 219 EIKNDLQLQRSGQQHQAGSDALLTADEFFL 248 (299)
T ss_pred HhcCcHhhhccchhhhccchhhhhhHHhcc
Confidence 999999998889999999999999987753
No 72
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=95.96 E-value=0.22 Score=49.39 Aligned_cols=129 Identities=17% Similarity=0.117 Sum_probs=78.7
Q ss_pred eEEEEEeccC-------------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCC
Q 020417 116 FFLVLDLEGK-------------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTA 182 (326)
Q Consensus 116 ~~vVfDlETT-------------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~A 182 (326)
..++||+||+ ++||.|+.+.-+...............+.. .+. | ..+..-
T Consensus 4 ~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~----~~~----------~---~~~~~~ 66 (471)
T smart00486 4 KILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCK----EID----------G---VEVYEF 66 (471)
T ss_pred eEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcC----CCC----------C---CeEEec
Confidence 4789999995 589999987764321111111111122222 111 1 112222
Q ss_pred CCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCC----------C----------
Q 020417 183 LPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPP----------Y---------- 241 (326)
Q Consensus 183 p~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~----------~---------- 241 (326)
..-.+.|.+|.+++....- .+++.||+ +||+. +|...+...++.... .
T Consensus 67 ~~E~~lL~~f~~~i~~~dp----------dii~g~N~~~FD~~-~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~ 135 (471)
T smart00486 67 NNEKELLKAFLEFIKKYDP----------DIIYGHNISNFDLP-YIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSK 135 (471)
T ss_pred CCHHHHHHHHHHHHHHhCC----------CEEEeecCCCCCHH-HHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccc
Confidence 2677899999999987631 35677887 59999 898888777664321 0
Q ss_pred -----------CccHhhHHHHHHhhcCCCcCCCCCHHHHHHhcCC
Q 020417 242 -----------FMEWINLKDVFYNFYKPRKSEATGMMGMMKNRQV 275 (326)
Q Consensus 242 -----------~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~lgI 275 (326)
..-.+|+..+++..+.. .+++|+++++++.-
T Consensus 136 ~~~~~~~~~~~g~~~~Dl~~~~~~~~kl---~~~~L~~va~~~l~ 177 (471)
T smart00486 136 SFGKTIKVKIKGRLVIDLYNLYKNKLKL---PSYKLDTVAEYLLG 177 (471)
T ss_pred cccccceeEeccEEEEEhHHHHHHHhCc---ccCCHHHHHHHHhC
Confidence 01346777777776653 38999999886543
No 73
>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=95.62 E-value=0.14 Score=46.85 Aligned_cols=85 Identities=14% Similarity=0.149 Sum_probs=59.5
Q ss_pred CCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCC-------------C------
Q 020417 182 ALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPP-------------Y------ 241 (326)
Q Consensus 182 Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~-------------~------ 241 (326)
..+-.++|.+|.+++.... -.+++.+|+ +||+. +|.+.|+++|++.+. +
T Consensus 55 ~~~E~~lL~~f~~~i~~~d----------Pdii~g~N~~~FD~p-yl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~ 123 (207)
T cd05785 55 DAAEKELLEELVAIIRERD----------PDVIEGHNIFRFDLP-YLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERL 123 (207)
T ss_pred CCCHHHHHHHHHHHHHHhC----------CCEEeccCCcccCHH-HHHHHHHHhCCCcccccCCCcceEeeccccccccc
Confidence 4678899999999999852 124456777 89999 999999999988641 0
Q ss_pred ----C-----ccHhhHHHHHHhhcC-CCcCCCCCHHHHHHhcCCCC
Q 020417 242 ----F-----MEWINLKDVFYNFYK-PRKSEATGMMGMMKNRQVPM 277 (326)
Q Consensus 242 ----~-----~~~iDl~~l~~~~~~-~~~~~~~~L~~l~k~lgI~~ 277 (326)
. ...+|+..+++.+-. ..+..+++|+++++++|+..
T Consensus 124 ~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~~ 169 (207)
T cd05785 124 IDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLAS 169 (207)
T ss_pred cccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHhcccC
Confidence 0 112687777664211 11123899999999998744
No 74
>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=95.59 E-value=0.12 Score=46.78 Aligned_cols=121 Identities=13% Similarity=0.065 Sum_probs=75.2
Q ss_pred eEEEEEeccC--CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHHHH
Q 020417 116 FFLVLDLEGK--IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQFE 193 (326)
Q Consensus 116 ~~vVfDlETT--~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~F~ 193 (326)
..+.||+||+ .+|+-||- .|.+...++ .+=.+.. .. |. .+.--++-.+.|..|.
T Consensus 4 ~~~~fDIE~~~~~~i~~i~~--~~~~~~~i~----~~~~~~~-----~~----------~~---~v~~~~~E~~lL~~f~ 59 (193)
T cd05784 4 KVVSLDIETSMDGELYSIGL--YGEGQERVL----MVGDPED-----DA----------PD---NIEWFADEKSLLLALI 59 (193)
T ss_pred cEEEEEeecCCCCCEEEEEe--ecCCCCEEE----EECCCCC-----CC----------CC---EEEEECCHHHHHHHHH
Confidence 3789999998 67888886 333333322 1111111 10 00 0122246678899999
Q ss_pred HHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCC----------------------CccHhhHHH
Q 020417 194 AWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPY----------------------FMEWINLKD 250 (326)
Q Consensus 194 ~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~----------------------~~~~iDl~~ 250 (326)
+++....- .+++.+|+ .||+. +|.+-|+++|++.+.- ..-.+|+..
T Consensus 60 ~~i~~~dP----------Dvi~g~N~~~FD~~-yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~ 128 (193)
T cd05784 60 AWFAQYDP----------DIIIGWNVINFDLR-LLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGID 128 (193)
T ss_pred HHHHhhCC----------CEEEECCCcCcCHH-HHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHH
Confidence 99987631 34566776 79999 9999999998875300 011567776
Q ss_pred HHHh-hcCCCcCCCCCHHHHHHhcC
Q 020417 251 VFYN-FYKPRKSEATGMMGMMKNRQ 274 (326)
Q Consensus 251 l~~~-~~~~~~~~~~~L~~l~k~lg 274 (326)
+.+. .+.. .+++|+++++++.
T Consensus 129 ~~k~~~~kl---~sy~L~~Va~~~L 150 (193)
T cd05784 129 ALKTATYHF---ESFSLENVAQELL 150 (193)
T ss_pred HHHHccCCC---CcCCHHHHHHHHh
Confidence 6654 3433 3899999999553
No 75
>PRK05762 DNA polymerase II; Reviewed
Probab=95.42 E-value=0.34 Score=52.82 Aligned_cols=107 Identities=13% Similarity=0.173 Sum_probs=71.2
Q ss_pred HhCCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCC-------------CCC--
Q 020417 179 HDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLP-------------PYF-- 242 (326)
Q Consensus 179 V~~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p-------------~~~-- 242 (326)
|..-++-.+.|..|.+|+.... -.+++.+|+ +||+. +|.+-|+.+|+++. ...
T Consensus 197 v~~~~sE~~LL~~F~~~i~~~D----------PDIIvGyNi~~FDlp-yL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~ 265 (786)
T PRK05762 197 LEYVADEKALLEKFNAWFAEHD----------PDVIIGWNVVQFDLR-LLQERAERYGIPLRLGRDGSELEWREHPFRSG 265 (786)
T ss_pred EEEcCCHHHHHHHHHHHHHhcC----------CCEEEEeCCCCCcHH-HHHHHHHHhCCCcccCcCCCccccccCCCCCC
Confidence 3344577889999999998863 135566675 69999 99999999998742 000
Q ss_pred --------ccHhhHHHHHHhhcCCCcCCCCCHHHHHHhcCCCCCCCCC---C------------------hHHHHHHHHH
Q 020417 243 --------MEWINLKDVFYNFYKPRKSEATGMMGMMKNRQVPMFGSHH---L------------------GIDDTKNITR 293 (326)
Q Consensus 243 --------~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~lgI~~~g~hH---r------------------AldDA~~tA~ 293 (326)
.-.+|+..+.+...... .+++|+++++++..+-...++ + .+.||..+.+
T Consensus 266 ~~~~~i~GRv~lDl~~~~k~~~~~l--~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~ 343 (786)
T PRK05762 266 YGFASVPGRLVLDGIDALKSATWVF--DSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTR 343 (786)
T ss_pred cceEEEeeEEEEEHHHHHHHhhccC--CCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence 01567777776654222 389999999987654211111 1 3678888888
Q ss_pred HHHHH
Q 020417 294 VLQRM 298 (326)
Q Consensus 294 I~~~l 298 (326)
|+.++
T Consensus 344 L~~kl 348 (786)
T PRK05762 344 IFEKT 348 (786)
T ss_pred HHHHh
Confidence 87744
No 76
>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=95.18 E-value=0.76 Score=42.66 Aligned_cols=165 Identities=8% Similarity=-0.063 Sum_probs=96.4
Q ss_pred eEEEEEeccC-----------CceeeeeEEEEEcCCCeEE---eEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhC
Q 020417 116 FFLVLDLEGK-----------IEILEFPVLMIDAKTMAFV---DLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDT 181 (326)
Q Consensus 116 ~~vVfDlETT-----------~EIIEIgAVkvD~k~geii---d~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~ 181 (326)
+.+.||+|+. +.|+.|..++-+....... ...--++.+...+ .... ... ..+....|.-
T Consensus 5 ~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~-~~~---~~~~~~~v~~ 77 (231)
T cd05778 5 TILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSN---ASNG-RIR---SGLSGIPVEV 77 (231)
T ss_pred EEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccch---hhhh-ccc---cCCCCCeEEE
Confidence 4788999985 8999999986532111111 1112333333311 1100 000 1333445566
Q ss_pred CCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCC-----C---------------
Q 020417 182 ALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLP-----P--------------- 240 (326)
Q Consensus 182 Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p-----~--------------- 240 (326)
-++-.+.|.+|.+|+.... -.++..+|. +||+. +|.+-|+..++..- +
T Consensus 78 ~~~E~~LL~~f~~~i~~~D----------PDii~GyNi~~fd~~-YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~ 146 (231)
T cd05778 78 VESELELFEELIDLVRRFD----------PDILSGYEIQRSSWG-YLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDE 146 (231)
T ss_pred eCCHHHHHHHHHHHHHHhC----------CCEEEEeccccCcHH-HHHHHHHHhCCcchhhhccCCCCCCcccccccccc
Confidence 7788899999999998763 135556675 79999 88887877766421 0
Q ss_pred CC-----------ccHhhHHHHHHhhcCCCcCCCCCHHHHHH-hcCCCCCCCCCChHHHH------HHHHHHHHHHHHc
Q 020417 241 YF-----------MEWINLKDVFYNFYKPRKSEATGMMGMMK-NRQVPMFGSHHLGIDDT------KNITRVLQRMLAD 301 (326)
Q Consensus 241 ~~-----------~~~iDl~~l~~~~~~~~~~~~~~L~~l~k-~lgI~~~g~hHrAldDA------~~tA~I~~~ll~~ 301 (326)
+. .-.+|+-.+++..+... +++|+++++ .||-..+.-++..+.+. ....+++...+++
T Consensus 147 ~g~~~~~~~~i~GRi~lD~~~~~r~~~kl~---sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d 222 (231)
T cd05778 147 WGYTHTSGIKIVGRHILNVWRLMRSELALT---NYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKR 222 (231)
T ss_pred cccccCCceEEeeEEEeEhHHHHHHHcCcc---cCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHH
Confidence 00 01245666666555443 899999998 55665443456666665 2455666666554
No 77
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=95.04 E-value=0.15 Score=48.81 Aligned_cols=170 Identities=16% Similarity=0.191 Sum_probs=100.5
Q ss_pred CCC-CCeEEEEEeccC------CceeeeeEEE-----EEcC------C-------CeEEeEEeecccCCcCCCCCcChhh
Q 020417 111 SQD-LDFFLVLDLEGK------IEILEFPVLM-----IDAK------T-------MAFVDLFHRFVRPSKMSEQHINKYI 165 (326)
Q Consensus 111 ~~~-~~~~vVfDlETT------~EIIEIgAVk-----vD~k------~-------geiid~F~~fVrP~~~p~~~Is~~i 165 (326)
+++ +.+|+++|+|+| .+|-|+...- ++.+ + -.+.++-+-++.|.. ...+.-
T Consensus 8 e~pr~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~----v~~p~a 83 (318)
T KOG4793|consen 8 EVPRLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVP----VTRPIA 83 (318)
T ss_pred cCCceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcC----CcChhh
Confidence 345 689999999999 6666654322 2221 1 134456666777765 255556
Q ss_pred hcccccCCCCHHHH--hCCCCHHH-HHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCC
Q 020417 166 EGKYGKFGVDRVWH--DTALPFKE-VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPY 241 (326)
Q Consensus 166 t~LTgi~GIt~e~V--~~Ap~f~e-Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~ 241 (326)
++.| |.++.-+ ..---|+. +.+-+..|+.+.. ...+.|+||| .||+- .|.++.+..|+..|.-
T Consensus 84 eeit---gls~~~~~l~rr~~~D~dla~LL~afls~lp---------~p~CLVaHng~~~dfp-il~qela~lg~~lpq~ 150 (318)
T KOG4793|consen 84 EEIT---GLSQPFLALQRRLAFDKDLAKLLTAFLSRLP---------TPGCLVAHNGNEYDFP-ILAQELAGLGYSLPQD 150 (318)
T ss_pred hhhc---ccccHHHHHHHHhhhhHHHHHHHHHHHhcCC---------CCceEEeecCCccccH-HHHHHHHhcCccchhh
Confidence 6665 7888543 23333444 4456677776542 1247788998 59998 9999999999998742
Q ss_pred CccHhhHHHHHHhhcC-----CC--cCCCCCHHHHHH-hcCCCCCCCCCChHHHHHHHHHHHHHH
Q 020417 242 FMEWINLKDVFYNFYK-----PR--KSEATGMMGMMK-NRQVPMFGSHHLGIDDTKNITRVLQRM 298 (326)
Q Consensus 242 ~~~~iDl~~l~~~~~~-----~~--~~~~~~L~~l~k-~lgI~~~g~hHrAldDA~~tA~I~~~l 298 (326)
...+|....+..+-. .+ +...++|..+-. +++-.....-|.+..|...+.-+++..
T Consensus 151 -lvcvdslpa~~ald~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~ 214 (318)
T KOG4793|consen 151 -LVCVDSLPALNALDRANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFR 214 (318)
T ss_pred -hcCcchhHHHHHHhhhcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHH
Confidence 223454444333211 00 112566666533 333311223588888887777766644
No 78
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=94.92 E-value=0.11 Score=47.89 Aligned_cols=167 Identities=10% Similarity=0.122 Sum_probs=91.0
Q ss_pred eeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChh-hh----cccccCCCCHHHHhCCC-CHHHHHHHHHHHHHhCcc
Q 020417 128 ILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKY-IE----GKYGKFGVDRVWHDTAL-PFKEVIQQFEAWLIQHHL 201 (326)
Q Consensus 128 IIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~-it----~LTgi~GIt~e~V~~Ap-~f~eVl~~F~~fl~~~~L 201 (326)
.+|||++++..++| |++.||++|+|...| +.-. -. +-| |+|..+-...+. .+..++.++..|++....
T Consensus 10 PaEiai~~fSL~~G-I~~~~H~~I~Pg~~p---~G~~~~a~~hs~~t--H~ip~~~~~~~~~d~~~l~~~l~~fl~~~~~ 83 (213)
T PF13017_consen 10 PAEIAICKFSLKEG-IIDSFHTFINPGQIP---LGYRYDAQHHSDET--HQIPIPPNALGESDYSELYNELLNFLKPNKG 83 (213)
T ss_pred eEEEEEEEEecCCc-cchhhhcccCCCCCC---cHHHHHHHHhhhhh--cCCCCCCcccccCCHHHHHHHHHHHhhhcCC
Confidence 58999999999887 999999999999743 3211 11 112 555554344444 699999999999988631
Q ss_pred cccccCCCCcceEEEEcCcccHHH-HHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCC----CcC-CCCCHHHHH----H
Q 020417 202 WEKGRGGHLKRAAFATCGNWDLKT-KVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKP----RKS-EATGMMGMM----K 271 (326)
Q Consensus 202 v~~~~~~~~~~~~~a~ng~fDl~~-fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~----~~~-~~~~L~~l~----k 271 (326)
+.....+++.-.....-+ +|+.-+...+.... ....++..++-.++.. ... ...-..... .
T Consensus 84 ------~~~~~~i~~~~~~~~~V~~cl~~La~~a~~~~~---~~v~~~~~lf~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 154 (213)
T PF13017_consen 84 ------GEKMPPIFTKRDQIPRVQSCLKWLAKKAGEDND---FKVYDFEYLFFDLKNEKVDYRWDRQDFPSKTIADALFP 154 (213)
T ss_pred ------CCCcceEEEeHhHHHHHHHHHHHHHHhcCCCcc---eEeecHHHHHHHHHHHHhhcccccccCchHHHHHHHcc
Confidence 122344554433333322 55555555555432 1223333333222211 000 011111111 1
Q ss_pred ----h--cCCC------CCCCCCChHHHHHHHHHHHHHHHHcCCcccccc
Q 020417 272 ----N--RQVP------MFGSHHLGIDDTKNITRVLQRMLADGARVQITA 309 (326)
Q Consensus 272 ----~--lgI~------~~g~hHrAldDA~~tA~I~~~ll~~g~~~~it~ 309 (326)
. -|+. .+...+.|+..+...|..+...+.....++++.
T Consensus 155 ~~~~~y~~~~~C~~He~~d~~~~Ca~s~v~r~ay~i~d~~c~~~~i~~~p 204 (213)
T PF13017_consen 155 KDFFEYSSNIRCDFHEEIDRSKYCALSTVKRWAYTISDYMCRDLGIKLIP 204 (213)
T ss_pred chhhhccCCCceeecccCCCcccchhHHHHHHHHHHHHHHHHhcCccccC
Confidence 1 1221 122368889999999988777765555555544
No 79
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=94.59 E-value=0.47 Score=53.39 Aligned_cols=154 Identities=13% Similarity=0.069 Sum_probs=90.7
Q ss_pred eEEEEEeccC------------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCC
Q 020417 116 FFLVLDLEGK------------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTAL 183 (326)
Q Consensus 116 ~~vVfDlETT------------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap 183 (326)
..+.|||||. ++||+|+.+.. .+|.-.+.+...|=.-. .|. .|....|..-.
T Consensus 265 rilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~--~~g~~~~~~~r~vftl~--------~c~------~i~g~~V~~f~ 328 (1054)
T PTZ00166 265 RILSFDIECIKLKGLGFPEAENDPVIQISSVVT--NQGDEEEPLTKFIFTLK--------ECA------SIAGANVLSFE 328 (1054)
T ss_pred EEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEe--eCCCccCCcceEEEecC--------ccc------cCCCceEEEeC
Confidence 4899999985 79999999865 24432211211110000 010 11112233446
Q ss_pred CHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCC-CC--------------------C
Q 020417 184 PFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKL-PP--------------------Y 241 (326)
Q Consensus 184 ~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~-p~--------------------~ 241 (326)
+-.+.|..|.+|+.... -.+++.+|. +||+. +|..-|+..|+.. +. +
T Consensus 329 sE~eLL~~f~~~I~~~D----------PDII~GYNi~~FDlp-YL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~ 397 (1054)
T PTZ00166 329 TEKELLLAWAEFVIAVD----------PDFLTGYNIINFDLP-YLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQM 397 (1054)
T ss_pred CHHHHHHHHHHHHHhcC----------CCEEEecCCcCCcHH-HHHHHHHHhCCCchhhcCcccCCCccccccccccccc
Confidence 78889999999998753 145666776 69999 8888888877651 10 0
Q ss_pred C-----------ccHhhHHHHHHhhcCCCcCCCCCHHHHHHhc-CCCCCCCCCC-------------------hHHHHHH
Q 020417 242 F-----------MEWINLKDVFYNFYKPRKSEATGMMGMMKNR-QVPMFGSHHL-------------------GIDDTKN 290 (326)
Q Consensus 242 ~-----------~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~l-gI~~~g~hHr-------------------AldDA~~ 290 (326)
- .-.+|+-.+++..+.. .+++|++++.++ |..-+.-+|. .+.||..
T Consensus 398 g~~~~~~~~i~GR~~iDl~~~~~~~~kl---~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L 474 (1054)
T PTZ00166 398 GTRESKEINIEGRIQFDVMDLIRRDYKL---KSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAIL 474 (1054)
T ss_pred cccccceeEeeeEEEEEHHHHHHHhcCc---CcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHH
Confidence 0 0235666666665543 389999999954 5432111221 2467777
Q ss_pred HHHHHHHHH
Q 020417 291 ITRVLQRML 299 (326)
Q Consensus 291 tA~I~~~ll 299 (326)
+.+|+.+|.
T Consensus 475 ~~~L~~kl~ 483 (1054)
T PTZ00166 475 PLRLLDKLL 483 (1054)
T ss_pred HHHHHHHHh
Confidence 777777663
No 80
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=93.71 E-value=0.5 Score=44.88 Aligned_cols=61 Identities=10% Similarity=0.100 Sum_probs=40.0
Q ss_pred EEEE-cC-cccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHhcCCCCC
Q 020417 214 AFAT-CG-NWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNRQVPMF 278 (326)
Q Consensus 214 ~~a~-ng-~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~lgI~~~ 278 (326)
.+|+ || .||.- |+++ +.+..+++.. -+..+|+..-.+++.... ..+.+|.++-+.+|+.-+
T Consensus 158 ~lvsfNGkaFD~P-fikR-~v~~~~el~l-~~~H~DL~h~~RRlwk~~-l~~c~Lk~VEr~LGi~R~ 220 (278)
T COG3359 158 MLVSFNGKAFDIP-FIKR-MVRDRLELSL-EFGHFDLYHPSRRLWKHL-LPRCGLKTVERILGIRRE 220 (278)
T ss_pred eEEEecCcccCcH-HHHH-HHhcccccCc-cccchhhhhhhhhhhhcc-CCCCChhhHHHHhCcccc
Confidence 3455 65 79999 9995 6555565432 246788765555543322 237899999999999643
No 81
>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=91.02 E-value=1.2 Score=42.11 Aligned_cols=92 Identities=15% Similarity=0.075 Sum_probs=60.0
Q ss_pred eEEEEEeccC-----------CceeeeeEEEEEcCCCe---EEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhC
Q 020417 116 FFLVLDLEGK-----------IEILEFPVLMIDAKTMA---FVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDT 181 (326)
Q Consensus 116 ~~vVfDlETT-----------~EIIEIgAVkvD~k~ge---iid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~ 181 (326)
..+.||+||. ++|+.|+.+.-+ +|. ..+.+-++..+.. ... ...|.-
T Consensus 158 ~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~--~~~~~~~~~~~~~~~~~~~-----~~~------------~~~v~~ 218 (325)
T PF03104_consen 158 RILSFDIETYSNDGKFPDPEKDEIIMISYVVYR--NGSSEPYRRKVFTLGSCDS-----IED------------NVEVIY 218 (325)
T ss_dssp EEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEE--TTEEETTEEEEEECSCSCC-----TTC------------TTEEEE
T ss_pred ceeEEEEEEccccCCCCCCCCCeEEEEEEEEEe--ccccCCCceEEEEecCCCC-----CCC------------CcEEEE
Confidence 5999999997 579999988763 221 1122333333332 110 112333
Q ss_pred CCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCC
Q 020417 182 ALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIK 237 (326)
Q Consensus 182 Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~ 237 (326)
-++-.+.|..|.+++.... -.+++.+|+ +||+. +|.+-|+..|++
T Consensus 219 ~~~E~~lL~~f~~~i~~~d----------PDii~GyN~~~fD~~-yl~~R~~~l~~~ 264 (325)
T PF03104_consen 219 FDSEKELLEAFLDIIQEYD----------PDIITGYNIDGFDLP-YLIERAKKLGID 264 (325)
T ss_dssp ESSHHHHHHHHHHHHHHHS-----------SEEEESSTTTTHHH-HHHHHHHHTTTC
T ss_pred ECCHHHHHHHHHHHHHhcC----------CcEEEEecccCCCHH-HHHHHHHHhCcc
Confidence 4577889999999998753 135666776 69999 998888888654
No 82
>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=90.14 E-value=3.1 Score=38.62 Aligned_cols=131 Identities=11% Similarity=0.003 Sum_probs=82.1
Q ss_pred CceeeeeEEEEEcC--C-----CeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCCHHHHHHHHHHHHHh
Q 020417 126 IEILEFPVLMIDAK--T-----MAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQFEAWLIQ 198 (326)
Q Consensus 126 ~EIIEIgAVkvD~k--~-----geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~f~eVl~~F~~fl~~ 198 (326)
+||+-|.++....- + ......+-++++|.... ..+....+.- ......|.--..-.+.|..|.+++..
T Consensus 21 ~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~--~~~~~~~~~~---~~~~~~v~~~~~E~~LL~~f~~~i~~ 95 (234)
T cd05776 21 NEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRS--PPPDLFEKNA---KKKKTKVRIFENERALLNFFLAKLQK 95 (234)
T ss_pred chhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCC--CCCchHHHHH---HhcCCcEEEeCCHHHHHHHHHHHHhh
Confidence 89999999875210 1 11123556677887631 1122222211 12223356677888999999999987
Q ss_pred CcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCC------------CCC-------------CccHhhHHHHH
Q 020417 199 HHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKL------------PPY-------------FMEWINLKDVF 252 (326)
Q Consensus 199 ~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~------------p~~-------------~~~~iDl~~l~ 252 (326)
.. -.+++.||. +||+. +|..-++..|++. |.. -.-.+|+...+
T Consensus 96 ~D----------PDiivG~Ni~~fdl~-~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~~ 164 (234)
T cd05776 96 ID----------PDVLVGHDLEGFDLD-VLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLSA 164 (234)
T ss_pred cC----------CCEEEeeccCCCCHH-HHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHHHH
Confidence 53 146677886 89999 8888888877752 100 01156777777
Q ss_pred HhhcCCCcCCCCCHHHHHH-hcCC
Q 020417 253 YNFYKPRKSEATGMMGMMK-NRQV 275 (326)
Q Consensus 253 ~~~~~~~~~~~~~L~~l~k-~lgI 275 (326)
+.++.. .+++|+++++ .||.
T Consensus 165 k~~~~~---~sY~L~~va~~~Lg~ 185 (234)
T cd05776 165 KELIRC---KSYDLTELSQQVLGI 185 (234)
T ss_pred HHHhCC---CCCChHHHHHHHhCc
Confidence 776553 3899999998 6676
No 83
>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=89.36 E-value=3.1 Score=34.21 Aligned_cols=67 Identities=13% Similarity=0.182 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCC
Q 020417 186 KEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATG 265 (326)
Q Consensus 186 ~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~ 265 (326)
.++++.|.+|+++... ..++||+.+|+. +|. ..++..+ ..++|+..+...+.+... .++
T Consensus 40 ~~~~~~l~~~l~~~~~-----------~~v~~~~k~d~~-~L~----~~~~~~~---~~~~D~~~~ayll~~~~~--~~~ 98 (155)
T cd00007 40 EEDLEALKELLEDEDI-----------TKVGHDAKFDLV-VLA----RDGIELP---GNIFDTMLAAYLLNPGEG--SHS 98 (155)
T ss_pred HHHHHHHHHHHcCCCC-----------cEEeccHHHHHH-HHH----HCCCCCC---CCcccHHHHHHHhCCCCC--cCC
Confidence 5677788889886531 246889999988 774 3454443 357898877666555442 469
Q ss_pred HHHHHHhc
Q 020417 266 MMGMMKNR 273 (326)
Q Consensus 266 L~~l~k~l 273 (326)
|+++++.|
T Consensus 99 l~~l~~~~ 106 (155)
T cd00007 99 LDDLAKEY 106 (155)
T ss_pred HHHHHHHH
Confidence 99998887
No 84
>PHA02528 43 DNA polymerase; Provisional
Probab=89.35 E-value=6.6 Score=43.66 Aligned_cols=103 Identities=10% Similarity=0.089 Sum_probs=63.3
Q ss_pred CCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHH-hCCCC----CCCC-------------
Q 020417 182 ALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKV-SQIKL----PPYF------------- 242 (326)
Q Consensus 182 Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~-~gi~~----p~~~------------- 242 (326)
-++-.+.|.+|.+|+....- .+++..|+ +||+. +|.+-|++ .|... .++-
T Consensus 175 ~~sE~eLL~~F~~~i~~~DP----------DII~GyNi~~FDlp-YL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~ 243 (881)
T PHA02528 175 FDTEREMLLEYINFWEENTP----------VIFTGWNVELFDVP-YIINRIKNILGEKTAKRLSPWGKVKERTIENMYGR 243 (881)
T ss_pred cCCHHHHHHHHHHHHHHhCC----------cEEEecCCccCCHH-HHHHHHHHHcCcccccccccccccccccccccccc
Confidence 45778999999999987531 24444565 79999 88777764 46441 1000
Q ss_pred ---------ccHhhHHHHHHhh-cCCCcCCCCCHHHHHHh-cCCCCCCCC----------------CChHHHHHHHHHHH
Q 020417 243 ---------MEWINLKDVFYNF-YKPRKSEATGMMGMMKN-RQVPMFGSH----------------HLGIDDTKNITRVL 295 (326)
Q Consensus 243 ---------~~~iDl~~l~~~~-~~~~~~~~~~L~~l~k~-lgI~~~g~h----------------HrAldDA~~tA~I~ 295 (326)
.-.+|+..+++.+ +... .+++|++++++ ||..-.... +=.+.||+.+.+|+
T Consensus 244 ~~~~~~i~GRv~lD~~dl~k~~~~~~l--~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~ 321 (881)
T PHA02528 244 EEIAYDISGISILDYLDLYKKFTFTNQ--PSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLD 321 (881)
T ss_pred cceeEEEcceEEEeHHHHHHHhhhccc--ccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence 0134555666653 2122 38999999995 786432110 11356888888888
Q ss_pred HH
Q 020417 296 QR 297 (326)
Q Consensus 296 ~~ 297 (326)
.+
T Consensus 322 ~k 323 (881)
T PHA02528 322 DK 323 (881)
T ss_pred HH
Confidence 77
No 85
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.48 E-value=10 Score=43.49 Aligned_cols=138 Identities=12% Similarity=0.043 Sum_probs=86.8
Q ss_pred eEEEEEec--cC------CceeeeeEEEEEcCC-----Ce--EEeEEeecccCCcCCCCCcChhhh-cccccCCCCHHHH
Q 020417 116 FFLVLDLE--GK------IEILEFPVLMIDAKT-----MA--FVDLFHRFVRPSKMSEQHINKYIE-GKYGKFGVDRVWH 179 (326)
Q Consensus 116 ~~vVfDlE--TT------~EIIEIgAVkvD~k~-----ge--iid~F~~fVrP~~~p~~~Is~~it-~LTgi~GIt~e~V 179 (326)
.++|+||- +. ++||.|..+..+.-+ ++ ....|...++|... .+|.... .. .|+-...|
T Consensus 505 Pl~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~---~~p~~~~~~~---~~~~~~~L 578 (1172)
T TIGR00592 505 PLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDC---SFPLDLKGEF---PGKKPSLV 578 (1172)
T ss_pred CeEEEEeeeEEecCccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCC---CCCchhhhhh---hccCCcEE
Confidence 37777776 43 899999888763200 11 12345556667321 1222211 22 25555667
Q ss_pred hCCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCC----------CC--------
Q 020417 180 DTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKL----------PP-------- 240 (326)
Q Consensus 180 ~~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~----------p~-------- 240 (326)
..-..-.+.+..|++++.... -...++||+ +||+. +|-.-|.+.+++. +.
T Consensus 579 ~~~~sEr~lL~~fl~~~~~~D----------PDii~g~n~~qfdlk-vl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~ 647 (1172)
T TIGR00592 579 EDLATERALIKKFMAKVKKID----------PDEIVGHDYQQRALK-VLANRINDLKIPTWSKIGRLRRSPKFGRRFGER 647 (1172)
T ss_pred EEecCHHHHHHHHHHHHHhcC----------CCEEEEEcccCccHH-HHHHHHHHcCCCcccccCccccCCCccccccce
Confidence 777888999999999998542 135667886 79999 7777787777753 00
Q ss_pred C-CccHhhHHHHHHhhcCCCcCCCCCHHHHHHhc
Q 020417 241 Y-FMEWINLKDVFYNFYKPRKSEATGMMGMMKNR 273 (326)
Q Consensus 241 ~-~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~l 273 (326)
+ -.-.+|+...++..+... +++|+++++++
T Consensus 648 ~~Grl~~D~~~~~k~~~~~~---sy~L~~v~~~~ 678 (1172)
T TIGR00592 648 TCGRMICDVEISAKELIRCK---SYDLSELVQQI 678 (1172)
T ss_pred ECCEEEEEHHHHHHHHhCcC---CCCHHHHHHHH
Confidence 0 012467777777776543 89999998855
No 86
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=87.37 E-value=2.4 Score=49.02 Aligned_cols=149 Identities=16% Similarity=0.206 Sum_probs=87.6
Q ss_pred eEEEEEeccC-----------CceeeeeEEEEEcCCCeEE----------eEEeecccCCcCCCCCcChhhhcccccCCC
Q 020417 116 FFLVLDLEGK-----------IEILEFPVLMIDAKTMAFV----------DLFHRFVRPSKMSEQHINKYIEGKYGKFGV 174 (326)
Q Consensus 116 ~~vVfDlETT-----------~EIIEIgAVkvD~k~geii----------d~F~~fVrP~~~p~~~Is~~it~LTgi~GI 174 (326)
..++||+||| |+|.=|.- +||. .|-.+ +-|+---||+. .-+|+
T Consensus 247 ~VlAFDIETtKlPLKFPDae~DqIMMISY-MiDG-qGfLItNREiVs~DIedfEYTPKpE~-----eG~F~--------- 310 (2173)
T KOG1798|consen 247 RVLAFDIETTKLPLKFPDAESDQIMMISY-MIDG-QGFLITNREIVSEDIEDFEYTPKPEY-----EGPFC--------- 310 (2173)
T ss_pred eEEEEeeecccCCCCCCCcccceEEEEEE-EecC-ceEEEechhhhccchhhcccCCcccc-----ccceE---------
Confidence 5899999999 78887764 5676 33322 23443334443 12222
Q ss_pred CHHHHhCCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEE-cCc-ccHHHHHHHHHHHhCCCCCC-----------C
Q 020417 175 DRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFAT-CGN-WDLKTKVPDQCKVSQIKLPP-----------Y 241 (326)
Q Consensus 175 t~e~V~~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~-ng~-fDl~~fL~~~~~~~gi~~p~-----------~ 241 (326)
|-+.+.-...|++|.+-+++. ..-+++| ||+ ||.- |+.+-+..+|+++-. |
T Consensus 311 ----v~Ne~dEv~Ll~RfFeHiq~~-----------kP~iivTyNGDFFDWP-Fve~Ra~~hGi~m~eEiGF~~D~~gEy 374 (2173)
T KOG1798|consen 311 ----VFNEPDEVGLLQRFFEHIQEV-----------KPTIIVTYNGDFFDWP-FVEARAKIHGISMNEEIGFRRDSQGEY 374 (2173)
T ss_pred ----EecCCcHHHHHHHHHHHHHhc-----------CCcEEEEecCccccch-hhHHHHHhcCCCcchhcCceecccccc
Confidence 234556678899999888764 2345565 786 8998 999999999987431 1
Q ss_pred CccHhhHHHHHHh-----hcCCCcCCCCCHHHHHH-hcCC---CC----------CCCCC---ChHHHHHHHHHHHHHHH
Q 020417 242 FMEWINLKDVFYN-----FYKPRKSEATGMMGMMK-NRQV---PM----------FGSHH---LGIDDTKNITRVLQRML 299 (326)
Q Consensus 242 ~~~~iDl~~l~~~-----~~~~~~~~~~~L~~l~k-~lgI---~~----------~g~hH---rAldDA~~tA~I~~~ll 299 (326)
-.+++.-.+.|+- ++|. ++.+|..+.+ .||- ++ +..+| -.+.||-+|=.++++.+
T Consensus 375 ks~~c~HmDcfrWVKRDSYLPq---GSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYV 451 (2173)
T KOG1798|consen 375 KSPFCIHMDCFRWVKRDSYLPQ---GSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYV 451 (2173)
T ss_pred cccceeehhhhhhhhhcccCCC---cccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHh
Confidence 1122222222221 1222 3777877654 3342 11 11123 34789999988877764
No 87
>PHA03036 DNA polymerase; Provisional
Probab=82.68 E-value=18 Score=40.86 Aligned_cols=173 Identities=16% Similarity=0.167 Sum_probs=98.0
Q ss_pred eEEEEEeccC----------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChh-hhcccccCCCC---HHHHhC
Q 020417 116 FFLVLDLEGK----------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKY-IEGKYGKFGVD---RVWHDT 181 (326)
Q Consensus 116 ~~vVfDlETT----------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~-it~LTgi~GIt---~e~V~~ 181 (326)
.|+.||+|+. +-|++|....+|. .|. +.--++++....++...... ....+.+-.|. -..+-.
T Consensus 161 ~~lsfDIEC~~~g~FPs~~~~pvshIs~~~~~~-~~~--~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 237 (1004)
T PHA03036 161 SYLFLDIECHFDKKFPSVFINPVSHISCCYIDL-SGK--EKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDYSKELI 237 (1004)
T ss_pred eeEEEEEEeccCCCCCCcccCcceEEEEEEEec-CCC--eeEEEEeccccccccccccceeeeeeccccccccCCceeee
Confidence 6999999986 8899999877875 443 22234566543211001000 00000000111 111111
Q ss_pred CCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCC---CCC--------------C---
Q 020417 182 ALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQI---KLP--------------P--- 240 (326)
Q Consensus 182 Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi---~~p--------------~--- 240 (326)
-.+-.+ +-+|.+++..... .+++--|| +||+. .|..-++..+. .++ +
T Consensus 238 ~~sE~~-ml~~~~~i~~~d~----------D~i~~yNg~nFD~~-Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~ 305 (1004)
T PHA03036 238 LCSEIV-LLRIAKKLLELEF----------DYVVTFNGHNFDLR-YISNRLELLTGEKIIFRSPDGKETVHLCIYERNLS 305 (1004)
T ss_pred cCCHHH-HHHHHHHHHhcCC----------CEEEeccCCCcchH-HHHHHHHHhccCceeeccCCCcccccceeeccccc
Confidence 133333 5578888876532 34544576 79999 77666655422 100 0
Q ss_pred ------------------CCccHhhHHHHHHhhcCCCcCCCCCHHHHHHh-cCC------------CCCCCCCChHHHHH
Q 020417 241 ------------------YFMEWINLKDVFYNFYKPRKSEATGMMGMMKN-RQV------------PMFGSHHLGIDDTK 289 (326)
Q Consensus 241 ------------------~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~-lgI------------~~~g~hHrAldDA~ 289 (326)
.-.-++|+-.+.+.-+... +++|+++.+. ||. .+.|. --.|+.
T Consensus 306 s~~~~gg~~~~t~~i~~~~G~i~fDLy~~i~k~~~L~---sYkL~~Vsk~~f~~~~~~~~~~~~~~~~~g~---~~~~~~ 379 (1004)
T PHA03036 306 SHKGVGGVANTTYHINNNNGTIFFDLYTFIQKTEKLD---SYKLDSISKNAFNCNAKVLSENNNEVTFIGD---NTTDAK 379 (1004)
T ss_pred cccccCccccceEEecccCCeEEEEhHHHHhhhcCcc---cccHHHHHHHhhccceeeeecCCceeEEccC---cccccc
Confidence 0012567777777666554 8999999998 322 11111 134899
Q ss_pred HHHHHHHHHHHcCCcccccc
Q 020417 290 NITRVLQRMLADGARVQITA 309 (326)
Q Consensus 290 ~tA~I~~~ll~~g~~~~it~ 309 (326)
+.++||...+.-|....|.+
T Consensus 380 ~~~~~f~~vl~t~ny~~i~~ 399 (1004)
T PHA03036 380 GKASIFSEVLSTGNYVTIND 399 (1004)
T ss_pred cchhhhhhhhcccceeeecc
Confidence 99999999999998888877
No 88
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=81.93 E-value=20 Score=29.86 Aligned_cols=90 Identities=12% Similarity=0.193 Sum_probs=54.0
Q ss_pred HHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHH
Q 020417 189 IQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMG 268 (326)
Q Consensus 189 l~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~ 268 (326)
++.+.+|+.+.. -..++||..+|+. +|. +.|+..+ .++|+.-.+..+.+... ..+|..
T Consensus 64 ~~~l~~~l~~~~-----------~~kv~~d~k~~~~-~L~----~~gi~~~----~~~D~~laayll~p~~~--~~~l~~ 121 (172)
T smart00474 64 LEILKDLLEDET-----------ITKVGHNAKFDLH-VLA----RFGIELE----NIFDTMLAAYLLLGGPS--KHGLAT 121 (172)
T ss_pred HHHHHHHhcCCC-----------ceEEEechHHHHH-HHH----HCCCccc----chhHHHHHHHHHcCCCC--cCCHHH
Confidence 455667776542 1346788898988 774 3688764 24898766554444432 369999
Q ss_pred HHHhc-CCCCCC---C--------CC----ChHHHHHHHHHHHHHHHH
Q 020417 269 MMKNR-QVPMFG---S--------HH----LGIDDTKNITRVLQRMLA 300 (326)
Q Consensus 269 l~k~l-gI~~~g---~--------hH----rAldDA~~tA~I~~~ll~ 300 (326)
+++.| |...+. . .. -|..||..+.++...|.+
T Consensus 122 l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~ 169 (172)
T smart00474 122 LLKEYLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEK 169 (172)
T ss_pred HHHHHhCCCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 98776 655321 0 00 145556666666665543
No 89
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=80.49 E-value=18 Score=37.77 Aligned_cols=82 Identities=12% Similarity=0.149 Sum_probs=52.5
Q ss_pred HHhCCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHH-HhCCCC----CCCC---------
Q 020417 178 WHDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCK-VSQIKL----PPYF--------- 242 (326)
Q Consensus 178 ~V~~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~-~~gi~~----p~~~--------- 242 (326)
.+..-++-.+.|.+|.+|+.+.. -.++...|+ +||+. +|.+-|+ ..|+.. .++-
T Consensus 173 ~v~~f~sE~eLL~~F~~~i~~~D----------PDIItGYNi~nFDlP-YL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~ 241 (498)
T PHA02524 173 VYMPFEDEVDLLLNYIQLWKANT----------PDLVFGWNSEGFDIP-YIITRITNILGEKAANQLSPYGKITSKTITN 241 (498)
T ss_pred EEEEeCCHHHHHHHHHHHHHHhC----------CCEEEeCCCcccCHH-HHHHHHHHHhCCcccccccccccccccccee
Confidence 44566788999999999998852 134445565 79999 7777775 467641 1110
Q ss_pred ------------ccHhhHHHHHHhh-cCCCcCCCCCHHHHHHh
Q 020417 243 ------------MEWINLKDVFYNF-YKPRKSEATGMMGMMKN 272 (326)
Q Consensus 243 ------------~~~iDl~~l~~~~-~~~~~~~~~~L~~l~k~ 272 (326)
.-.+|+..+++.. +... .+++|++++++
T Consensus 242 ~~G~~~~~~I~GRv~iDl~~l~kk~s~~~l--~sYsL~~Vs~~ 282 (498)
T PHA02524 242 LYGEKIIYKIHGIALMDYMDVFKKFSFTPM--PDYKLGNVGYR 282 (498)
T ss_pred ecCceeEEEEeeEEEeEHHHHHHHhhhccC--CCCCHHHHHHH
Confidence 0135666777764 2222 38999999763
No 90
>PRK10829 ribonuclease D; Provisional
Probab=76.01 E-value=17 Score=36.53 Aligned_cols=75 Identities=16% Similarity=0.167 Sum_probs=52.0
Q ss_pred EEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHh-cCCCCCCCC------------
Q 020417 215 FATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKN-RQVPMFGSH------------ 281 (326)
Q Consensus 215 ~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~-lgI~~~g~h------------ 281 (326)
|.|.+.+|+. +|.+ ..|+.. ..++||+-.+. +.+... +.||..+++. +|+.++..+
T Consensus 78 V~H~~~~Dl~-~l~~---~~g~~p----~~~fDTqiaa~-~lg~~~--~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~ 146 (373)
T PRK10829 78 FLHAGSEDLE-VFLN---AFGELP----QPLIDTQILAA-FCGRPL--SCGFASMVEEYTGVTLDKSESRTDWLARPLSE 146 (373)
T ss_pred EEeChHhHHH-HHHH---HcCCCc----CCeeeHHHHHH-HcCCCc--cccHHHHHHHHhCCccCcccccCCCCCCCCCH
Confidence 5799999999 7754 347643 36789966544 445442 6899998764 588654221
Q ss_pred ---CChHHHHHHHHHHHHHHHH
Q 020417 282 ---HLGIDDTKNITRVLQRMLA 300 (326)
Q Consensus 282 ---HrAldDA~~tA~I~~~ll~ 300 (326)
+=|..|+..+..|+.+|.+
T Consensus 147 ~ql~YAa~Dv~~L~~l~~~L~~ 168 (373)
T PRK10829 147 RQCEYAAADVFYLLPIAAKLMA 168 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3378999999988888754
No 91
>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=75.91 E-value=13 Score=33.44 Aligned_cols=83 Identities=14% Similarity=0.157 Sum_probs=53.3
Q ss_pred EEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCC--------cCCCCCHHHHHHhc-CCCCCCC-----
Q 020417 215 FATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPR--------KSEATGMMGMMKNR-QVPMFGS----- 280 (326)
Q Consensus 215 ~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~--------~~~~~~L~~l~k~l-gI~~~g~----- 280 (326)
+.|+...|+. +|.+.+...+-. +.....++|+..++..+.... .....+|..+++.+ |.++...
T Consensus 86 Vg~~~~~D~~-~L~~~~~~~~~~-~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~q~Sd 163 (193)
T cd06146 86 LGFGFKQDLK-ALSASYPALKCM-FERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQCSN 163 (193)
T ss_pred EEechHHHHH-HHHHhcCccccc-cccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCcccccCC
Confidence 5688899999 887655322100 001247899988877543221 01368999998865 5443211
Q ss_pred ----------CCChHHHHHHHHHHHHHHH
Q 020417 281 ----------HHLGIDDTKNITRVLQRML 299 (326)
Q Consensus 281 ----------hHrAldDA~~tA~I~~~ll 299 (326)
-+-|..||..+..|+.+|.
T Consensus 164 W~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 164 WERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 2458899999999999885
No 92
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=74.62 E-value=3.2 Score=40.00 Aligned_cols=150 Identities=8% Similarity=0.005 Sum_probs=91.8
Q ss_pred CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCC--CHHHHHHHHHHHHHhCcccc
Q 020417 126 IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTAL--PFKEVIQQFEAWLIQHHLWE 203 (326)
Q Consensus 126 ~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap--~f~eVl~~F~~fl~~~~Lv~ 203 (326)
..+++|-+.-+ ..+ =...|+.+|+|... +.+ ..+. -++.|+..++ .-++-..-|..+.+...
T Consensus 130 ~~dfpil~qel--a~l-g~~lpq~lvcvdsl-----pa~-~ald----~a~s~~tr~~~~~~~~l~~If~ry~~q~e--- 193 (318)
T KOG4793|consen 130 EYDFPILAQEL--AGL-GYSLPQDLVCVDSL-----PAL-NALD----RANSMVTRPEVRRMYSLGSIFLRYVEQRE--- 193 (318)
T ss_pred ccccHHHHHHH--Hhc-CccchhhhcCcchh-----HHH-HHHh----hhcCcccCCCCCcccccchHHHhhhcccC---
Confidence 56666666544 112 13678889999874 322 1221 1445554333 44445567777887631
Q ss_pred cccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHH------hhcCCCcCCCCCHHHHHHhcCCC
Q 020417 204 KGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFY------NFYKPRKSEATGMMGMMKNRQVP 276 (326)
Q Consensus 204 ~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~------~~~~~~~~~~~~L~~l~k~lgI~ 276 (326)
+. ..+..-+.+++ .|+.. |..++.-|.+-+.++ .|.-++.+|. ..+|..+ ..+++..++.++...
T Consensus 194 pp---a~~~~e~d~~~l~~~fq-f~~~ellR~~deqa~---pw~~ir~l~~~~~~a~~~~P~p~-~vs~le~Lat~~~~~ 265 (318)
T KOG4793|consen 194 PP---AGHVAEGDVNGLLFIFQ-FRINELLRWSDEQAR---PWLLIRPLYLARENAKSVEPTPK-LVSSLEALATYYSLT 265 (318)
T ss_pred CC---cceeeecccchhHHHHH-HHHHHHHhhHhhcCC---CcccccchhhhhhhccccCCCCc-cchhHHHHHHHhhcC
Confidence 11 11223334454 46766 888888777665543 4655555552 1223111 367889999999887
Q ss_pred CCCCCCChHHHHHHHHHHHHHHH
Q 020417 277 MFGSHHLGIDDTKNITRVLQRML 299 (326)
Q Consensus 277 ~~g~hHrAldDA~~tA~I~~~ll 299 (326)
-++.+|||+.|...+.++++++-
T Consensus 266 p~l~ahra~~Dv~~~~k~~q~~~ 288 (318)
T KOG4793|consen 266 PELDAHRALSDVLLLSKVFQKLT 288 (318)
T ss_pred cccchhhhccccchhhhHHHHhh
Confidence 78889999999999999999874
No 93
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=73.09 E-value=24 Score=35.34 Aligned_cols=75 Identities=8% Similarity=0.125 Sum_probs=52.2
Q ss_pred EEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHhc-CCCCCCCCC-----------
Q 020417 215 FATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNR-QVPMFGSHH----------- 282 (326)
Q Consensus 215 ~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~l-gI~~~g~hH----------- 282 (326)
+.|.++||+. +|.+.+ |+... ..+|++-. ..+.+... +++|.+|++.+ |+.++..+-
T Consensus 74 IfHaa~~DL~-~l~~~~---g~~p~----plfdTqiA-a~l~g~~~--~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~ 142 (361)
T COG0349 74 IFHAARFDLE-VLLNLF---GLLPT----PLFDTQIA-AKLAGFGT--SHGLADLVEELLGVELDKSEQRSDWLARPLSE 142 (361)
T ss_pred eeccccccHH-HHHHhc---CCCCC----chhHHHHH-HHHhCCcc--cccHHHHHHHHhCCcccccccccccccCCCCH
Confidence 6799999999 665444 55443 56888755 44445543 89999998765 887753321
Q ss_pred ----ChHHHHHHHHHHHHHHHH
Q 020417 283 ----LGIDDTKNITRVLQRMLA 300 (326)
Q Consensus 283 ----rAldDA~~tA~I~~~ll~ 300 (326)
-|..|+..+..|..+|.+
T Consensus 143 ~Ql~YAa~DV~yL~~l~~~L~~ 164 (361)
T COG0349 143 AQLEYAAADVEYLLPLYDKLTE 164 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 267899999888887754
No 94
>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=72.65 E-value=6.7 Score=33.25 Aligned_cols=91 Identities=10% Similarity=0.175 Sum_probs=58.3
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHH
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMM 267 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~ 267 (326)
+++.+.+++++... .-+.||+.||+. +|.+. .|+... .++|+ .+...+.+... .++|+
T Consensus 65 ~~~~l~~ll~~~~i-----------~kv~~n~~~D~~-~L~~~---~~i~~~----~~~D~-~l~~~~l~~~~--~~~L~ 122 (176)
T PF01612_consen 65 ILDALKELLEDPNI-----------IKVGHNAKFDLK-WLYRS---FGIDLK----NVFDT-MLAAYLLDPTR--SYSLK 122 (176)
T ss_dssp HHHHHHHHHTTTTS-----------EEEESSHHHHHH-HHHHH---HTS--S----SEEEH-HHHHHHTTTST--TSSHH
T ss_pred hHHHHHHHHhCCCc-----------cEEEEEEechHH-HHHHH---hccccC----Cccch-hhhhhcccccc--cccHH
Confidence 56667777776532 346789999999 87655 677653 56788 55555555442 48999
Q ss_pred HHHHhc-C-CCC--C---CCCC--C---------hHHHHHHHHHHHHHHHH
Q 020417 268 GMMKNR-Q-VPM--F---GSHH--L---------GIDDTKNITRVLQRMLA 300 (326)
Q Consensus 268 ~l~k~l-g-I~~--~---g~hH--r---------AldDA~~tA~I~~~ll~ 300 (326)
++++.+ | ++. + ++.. + |-.||..+.+|+.+|..
T Consensus 123 ~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~ 173 (176)
T PF01612_consen 123 DLAEEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKP 173 (176)
T ss_dssp HHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHH
T ss_pred HHHHHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 997655 6 322 1 1122 2 55689999998888764
No 95
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=67.31 E-value=40 Score=37.07 Aligned_cols=83 Identities=10% Similarity=0.113 Sum_probs=57.7
Q ss_pred HhCCCCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCc-ccHHHHHHHHHHHhCCCCC-------------CC---
Q 020417 179 HDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGN-WDLKTKVPDQCKVSQIKLP-------------PY--- 241 (326)
Q Consensus 179 V~~Ap~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~-fDl~~fL~~~~~~~gi~~p-------------~~--- 241 (326)
|....+-.+.+.+|.+|+.... ...++..|+. ||+. +|..-+.+.|++.. .+
T Consensus 205 v~~~~~e~e~l~~~~~~i~~~d----------PdVIvgyn~~~fd~p-yl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~ 273 (792)
T COG0417 205 VEVVISEAELLERFVELIREYD----------PDVIVGYNGDNFDWP-YLAERAERLGIPLRLGRDGSELRVRKSGFSSQ 273 (792)
T ss_pred eEEecCHHHHHHHHHHHHHhcC----------CCEEEeccCCcCChH-HHHHHHHHhCCCccccccccccceeecccccc
Confidence 4555567889999999998763 2456667875 9999 99999999998865 00
Q ss_pred -CccHhhHHHHHH-hhcCCCcCCCCCHHHHHHhcCC
Q 020417 242 -FMEWINLKDVFY-NFYKPRKSEATGMMGMMKNRQV 275 (326)
Q Consensus 242 -~~~~iDl~~l~~-~~~~~~~~~~~~L~~l~k~lgI 275 (326)
-.-.+|+-..++ ..+... .++|..+++.+..
T Consensus 274 ~Gr~~iDl~~~~~~~~~~~~---~ysl~~v~~~~l~ 306 (792)
T COG0417 274 VGRLHIDLYPALRRRPLNLK---SYSLEAVSEALLG 306 (792)
T ss_pred cceEEEecHHHHhhhhcccc---cccHHHHHHHhcc
Confidence 113467766666 233333 7899988776654
No 96
>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=66.36 E-value=41 Score=28.93 Aligned_cols=74 Identities=8% Similarity=-0.088 Sum_probs=49.4
Q ss_pred EEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHhc-CCCCCC--------------
Q 020417 215 FATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNR-QVPMFG-------------- 279 (326)
Q Consensus 215 ~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~l-gI~~~g-------------- 279 (326)
+.|+...|+. .|.+ ..|+... ..+|+...+..+ +... +.+|..+++.+ |+.++.
T Consensus 71 vg~~~k~D~~-~L~~---~~gi~~~----~~~D~~~aa~ll-~~~~--~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~ 139 (161)
T cd06129 71 ALHGIEGDLW-KLLR---DFGEKLQ----RLFDTTIAANLK-GLPE--RWSLASLVEHFLGKTLDKSISCADWSYRPLTE 139 (161)
T ss_pred EEeccHHHHH-HHHH---HcCCCcc----cHhHHHHHHHHh-CCCC--CchHHHHHHHHhCCCCCccceeccCCCCCCCH
Confidence 5678888887 6643 2566542 458998765543 3322 56999998875 765421
Q ss_pred -CCCChHHHHHHHHHHHHHHH
Q 020417 280 -SHHLGIDDTKNITRVLQRML 299 (326)
Q Consensus 280 -~hHrAldDA~~tA~I~~~ll 299 (326)
+-+-|..||..+..|+.+|.
T Consensus 140 ~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 140 DQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 12557889999988888774
No 97
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=66.32 E-value=2.6 Score=30.96 Aligned_cols=34 Identities=12% Similarity=0.051 Sum_probs=27.6
Q ss_pred ccccccCCccccCccchhhhhhcCCCcceeeechh
Q 020417 70 MCLYFTQGKCTMMDDVMHLEKFNHDISRDLQVDAA 104 (326)
Q Consensus 70 ~~~~~dhg~~q~~~~a~~~~~~~~~~~~~~~v~~~ 104 (326)
....|||+.+++++++..+.+ +.+++++.|+|.+
T Consensus 31 ~v~iTDh~~~~~~~~~~~~~~-~~gi~~i~G~E~~ 64 (67)
T smart00481 31 AIAITDHGNLFGAVEFYKAAK-KAGIKPIIGLEAN 64 (67)
T ss_pred EEEEeeCCcccCHHHHHHHHH-HcCCeEEEEEEEE
Confidence 344699999999999887766 4689999999864
No 98
>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=63.42 E-value=35 Score=29.27 Aligned_cols=75 Identities=12% Similarity=0.131 Sum_probs=50.7
Q ss_pred EEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHhc-CCCCC--C------------
Q 020417 215 FATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNR-QVPMF--G------------ 279 (326)
Q Consensus 215 ~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~l-gI~~~--g------------ 279 (326)
+.|+...|+. .|.+ ..|+... ..+|+..++..+-+... ..+|.++++.+ |+... .
T Consensus 77 v~~~~k~D~~-~L~~---~~g~~~~----~~~Dl~~aa~ll~~~~~--~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpL 146 (170)
T cd06141 77 VGVGIKGDAR-KLAR---DFGIEVR----GVVDLSHLAKRVGPRRK--LVSLARLVEEVLGLPLSKPKKVRCSNWEARPL 146 (170)
T ss_pred EEeeeHHHHH-HHHh---HcCCCCC----CeeeHHHHHHHhCCCcC--CccHHHHHHHHcCcccCCCCCcccCCCCCCCC
Confidence 5688889988 7643 4476643 34899887766544322 46999998886 66543 1
Q ss_pred ---CCCChHHHHHHHHHHHHHHH
Q 020417 280 ---SHHLGIDDTKNITRVLQRML 299 (326)
Q Consensus 280 ---~hHrAldDA~~tA~I~~~ll 299 (326)
+-|-|..||..+.+|+.+|.
T Consensus 147 t~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 147 SKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHh
Confidence 11447888988888888774
No 99
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.46 E-value=20 Score=39.93 Aligned_cols=95 Identities=9% Similarity=0.135 Sum_probs=61.7
Q ss_pred HHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCC
Q 020417 185 FKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEAT 264 (326)
Q Consensus 185 f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~ 264 (326)
.+.++..|.+|+++... ..++||+.||+. +|. ++|+.++. .+.|+.-....+-+.. ..
T Consensus 363 ~~~~~~~l~~~l~~~~~-----------~~v~~n~K~d~~-~l~----~~gi~~~~---~~~Dt~la~yll~~~~---~~ 420 (887)
T TIGR00593 363 TILTDDKFARWLLNEQI-----------KKIGHDAKFLMH-LLK----REGIELGG---VIFDTMLAAYLLDPAQ---VS 420 (887)
T ss_pred hHHHHHHHHHHHhCCCC-----------cEEEeeHHHHHH-HHH----hCCCCCCC---cchhHHHHHHHcCCCC---CC
Confidence 55677788888887532 257899999998 774 67887753 4678876544443333 45
Q ss_pred CHHHHHHhc-CCCC---C---CC------------CCChHHHHHHHHHHHHHHHHc
Q 020417 265 GMMGMMKNR-QVPM---F---GS------------HHLGIDDTKNITRVLQRMLAD 301 (326)
Q Consensus 265 ~L~~l~k~l-gI~~---~---g~------------hHrAldDA~~tA~I~~~ll~~ 301 (326)
+|+++++.| +... + |. ...|..||..|.+++..|...
T Consensus 421 ~l~~la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~ 476 (887)
T TIGR00593 421 TLDTLARRYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKE 476 (887)
T ss_pred CHHHHHHHHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 899997765 3210 0 10 013667888888888877654
No 100
>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=56.48 E-value=88 Score=31.12 Aligned_cols=75 Identities=12% Similarity=0.099 Sum_probs=47.2
Q ss_pred EEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHhc-CCCCCCCC------CC---
Q 020417 214 AFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNR-QVPMFGSH------HL--- 283 (326)
Q Consensus 214 ~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~l-gI~~~g~h------Hr--- 283 (326)
-+.|++..|+. +|.+ .+...| ..++|+.-... +++... ..+|..+++.| |+.++..+ .+
T Consensus 73 KV~h~~k~Dl~-~L~~----~~~~~~---~~~fDtqlAa~-lL~~~~--~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~ 141 (367)
T TIGR01388 73 KVLHAASEDLE-VFLN----LFGELP---QPLFDTQIAAA-FCGFGM--SMGYAKLVQEVLGVELDKSESRTDWLARPLT 141 (367)
T ss_pred EEEeecHHHHH-HHHH----HhCCCC---CCcccHHHHHH-HhCCCC--CccHHHHHHHHcCCCCCcccccccCCCCCCC
Confidence 36788999988 7743 333343 35688876543 334332 57999998765 77653211 22
Q ss_pred ------hHHHHHHHHHHHHHHH
Q 020417 284 ------GIDDTKNITRVLQRML 299 (326)
Q Consensus 284 ------AldDA~~tA~I~~~ll 299 (326)
|..||..+..+...|.
T Consensus 142 ~~q~~YAa~Dv~~L~~L~~~L~ 163 (367)
T TIGR01388 142 DAQLEYAAADVTYLLPLYAKLM 163 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 7778888888777764
No 101
>PRK05761 DNA polymerase I; Reviewed
Probab=53.32 E-value=42 Score=36.93 Aligned_cols=100 Identities=14% Similarity=0.138 Sum_probs=62.6
Q ss_pred CCHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcC-cccHHHHHHHHHHHhCCCCCCCCcc------HhhHHHHHHhh
Q 020417 183 LPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG-NWDLKTKVPDQCKVSQIKLPPYFME------WINLKDVFYNF 255 (326)
Q Consensus 183 p~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~~------~iDl~~l~~~~ 255 (326)
++-.+.|.+|.+|+.+.. ..+.-|+ +||+. +|.+-|+++|++...+... .+|+-..+...
T Consensus 208 ~~E~eLL~~f~~~i~~~d------------Pdi~yN~~~FDlP-YL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~ 274 (787)
T PRK05761 208 DSEKELLAELFDIILEYP------------PVVTFNGDNFDLP-YLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNK 274 (787)
T ss_pred CCHHHHHHHHHHHHHhcC------------CEEEEcCCcchHH-HHHHHHHHhCCCchhcccccCCCceEEechhheeec
Confidence 678999999999999874 2234576 69999 9999999999875421111 15554443211
Q ss_pred ----c---CCCcCCCCCHHHHHH-hcCCCCCCC------------CCChHHHHHHHHHHH
Q 020417 256 ----Y---KPRKSEATGMMGMMK-NRQVPMFGS------------HHLGIDDTKNITRVL 295 (326)
Q Consensus 256 ----~---~~~~~~~~~L~~l~k-~lgI~~~g~------------hHrAldDA~~tA~I~ 295 (326)
| +..+...++|+++++ .||..-..- ..=.+.||..+.+|.
T Consensus 275 ~~~~y~~~~~~~~~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 275 AVRSYAFYGKYRHREARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ceeeeeccceeecccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 1 111112689999988 667642111 112478888888874
No 102
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=49.02 E-value=5.3 Score=44.19 Aligned_cols=75 Identities=16% Similarity=0.223 Sum_probs=53.0
Q ss_pred eEEEEcC-cccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHHHHHHhc-CCCCCCCCCChHHHHHH
Q 020417 213 AAFATCG-NWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNR-QVPMFGSHHLGIDDTKN 290 (326)
Q Consensus 213 ~~~a~ng-~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~~l~k~l-gI~~~g~hHrAldDA~~ 290 (326)
++||.+| +-|.+ ..++-.|. .+.+|+..+|.. +..+ ..+|.-++.++ |.......|+.+.||+.
T Consensus 1015 viFVGHGL~nDFr--------vINi~Vp~--~QiiDTv~lf~~--~s~R--~LSLrfLa~~lLg~~IQ~~~HDSIeDA~t 1080 (1118)
T KOG1275|consen 1015 VIFVGHGLQNDFR--------VINIHVPE--EQIIDTVTLFRL--GSQR--MLSLRFLAWELLGETIQMEAHDSIEDART 1080 (1118)
T ss_pred cEEEcccccccce--------EEEEecCh--hhheeeeEEEec--cccc--EEEHHHHHHHHhcchhhccccccHHHHHH
Confidence 5677655 55655 44676664 578898877653 3322 67888887765 66655458999999999
Q ss_pred HHHHHHHHHHc
Q 020417 291 ITRVLQRMLAD 301 (326)
Q Consensus 291 tA~I~~~ll~~ 301 (326)
+.+++.+.++.
T Consensus 1081 aLkLYk~Yl~l 1091 (1118)
T KOG1275|consen 1081 ALKLYKKYLKL 1091 (1118)
T ss_pred HHHHHHHHHHH
Confidence 99999987654
No 103
>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=43.63 E-value=1.6e+02 Score=25.07 Aligned_cols=68 Identities=12% Similarity=0.119 Sum_probs=41.6
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCCCCHH
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMM 267 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L~ 267 (326)
+.+.|.+|+.+... ..++||+.+|+. +| .+.|+..+ ..+.|+.-...-+-+... .+++.
T Consensus 44 ~~~~l~~~l~~~~~-----------~ki~~d~K~~~~-~l----~~~gi~~~---~~~fDt~laaYLL~p~~~--~~~l~ 102 (178)
T cd06140 44 DLAALKEWLEDEKI-----------PKVGHDAKRAYV-AL----KRHGIELA---GVAFDTMLAAYLLDPTRS--SYDLA 102 (178)
T ss_pred HHHHHHHHHhCCCC-----------ceeccchhHHHH-HH----HHCCCcCC---CcchhHHHHHHHcCCCCC--CCCHH
Confidence 45557777776431 245677777766 54 46788875 246888765444433332 36999
Q ss_pred HHHHhc-CCC
Q 020417 268 GMMKNR-QVP 276 (326)
Q Consensus 268 ~l~k~l-gI~ 276 (326)
++++.| |..
T Consensus 103 ~l~~~yl~~~ 112 (178)
T cd06140 103 DLAKRYLGRE 112 (178)
T ss_pred HHHHHHcCCC
Confidence 997765 554
No 104
>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=42.36 E-value=2.1e+02 Score=24.16 Aligned_cols=90 Identities=9% Similarity=0.152 Sum_probs=51.5
Q ss_pred HHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHh-CCCCCCCCccHhhHHHHHHhhcCCCcCCCCCH
Q 020417 188 VIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVS-QIKLPPYFMEWINLKDVFYNFYKPRKSEATGM 266 (326)
Q Consensus 188 Vl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~-gi~~p~~~~~~iDl~~l~~~~~~~~~~~~~~L 266 (326)
+.+.|.+|+.+... ..++|+..+|+. .|. +. |+. + +..+|+.-. ..+++... ..+|
T Consensus 52 ~~~~l~~ll~~~~i-----------~kv~~d~K~~~~-~L~----~~~gi~-~---~~~~D~~la-ayLl~p~~--~~~l 108 (178)
T cd06142 52 DLSPLKELLADPNI-----------VKVFHAAREDLE-LLK----RDFGIL-P---QNLFDTQIA-ARLLGLGD--SVGL 108 (178)
T ss_pred cHHHHHHHHcCCCc-----------eEEEeccHHHHH-HHH----HHcCCC-C---CCcccHHHH-HHHhCCCc--cccH
Confidence 34446667765421 245778887877 654 33 776 3 346888644 33334322 4599
Q ss_pred HHHHHhc-CCCCC-----CC---C-------CChHHHHHHHHHHHHHHHH
Q 020417 267 MGMMKNR-QVPMF-----GS---H-------HLGIDDTKNITRVLQRMLA 300 (326)
Q Consensus 267 ~~l~k~l-gI~~~-----g~---h-------HrAldDA~~tA~I~~~ll~ 300 (326)
.++++.+ |+... +. . +-+..||..+.++...|..
T Consensus 109 ~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~ 158 (178)
T cd06142 109 AALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKE 158 (178)
T ss_pred HHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHH
Confidence 9998864 66521 11 0 0255667777777776643
No 105
>TIGR03447 mycothiol_MshC cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase. Members of this protein family are MshC, l-cysteine:1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, an enzyme that uses ATP to ligate a Cys residue to a mycothiol precursor molecule, in the second to last step in mycothiol biosynthesis. This enzyme shows considerable homology to Cys--tRNA ligases, and many instances are misannotated as such. Mycothiol is found in Mycobacterium tuberculosis, Corynebacterium glutamicum, Streptomyces coelicolor, and various other members of the Actinobacteria. Mycothiol is an analog to glutathione.
Probab=36.61 E-value=2e+02 Score=29.37 Aligned_cols=91 Identities=10% Similarity=0.056 Sum_probs=55.8
Q ss_pred CHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCC
Q 020417 184 PFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEA 263 (326)
Q Consensus 184 ~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~ 263 (326)
-..|++.+++++.+. .+.+++|.. |+.+-|...++..|+... ++. +-+..
T Consensus 59 V~~Dvl~R~lr~~G~-------------~V~fV~nit-D~dDKIi~~A~~~g~t~~----ela---~~y~~--------- 108 (411)
T TIGR03447 59 LTFDLVNRVWRDAGH-------------RVHYVQNVT-DVDDPLFERAERDGVDWR----ELG---TSQID--------- 108 (411)
T ss_pred HHHHHHHHHHHhcCC-------------ceEEeeCCC-chhHHHHHHHHHcCCCHH----HHH---HHHHH---------
Confidence 356788888877643 356777765 666677788888887642 222 22221
Q ss_pred CCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCcc
Q 020417 264 TGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGARV 305 (326)
Q Consensus 264 ~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~~ 305 (326)
.....++.|||......-|+-+....+.+++++|++.|..-
T Consensus 109 -~f~~d~~~Lni~~~d~~~RaTe~i~~ii~~i~~L~~kG~aY 149 (411)
T TIGR03447 109 -LFREDMEALRVLPPRDYIGAVESIDEVIEMVEKLLAAGAAY 149 (411)
T ss_pred -HHHHHHHHcCCCCCCcccCCCCCHHHHHHHHHHHHHCCCEE
Confidence 23445667776421233445555677888889998887654
No 106
>PRK12418 cysteinyl-tRNA synthetase; Provisional
Probab=35.09 E-value=1.9e+02 Score=29.17 Aligned_cols=91 Identities=8% Similarity=0.042 Sum_probs=54.6
Q ss_pred CHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCC
Q 020417 184 PFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEA 263 (326)
Q Consensus 184 ~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~ 263 (326)
-..+++.+++++.+. .+.+|+|.. |+.+-+...+++.|+... ++. +-+..
T Consensus 32 V~~Dvl~R~lr~~G~-------------~V~~V~nit-D~ddKIi~~A~~~G~~~~----e~a---~~~~~--------- 81 (384)
T PRK12418 32 LAFDLVNRVWRDAGH-------------DVHYVQNVT-DVDDPLLERAARDGVDWR----DLA---EREIA--------- 81 (384)
T ss_pred HHHHHHHHHHHHcCC-------------ceEEEEecC-CcchHHHHHHHHcCCCHH----HHH---HHHHH---------
Confidence 356788888887643 356777765 555567778888888742 222 22111
Q ss_pred CCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCcc
Q 020417 264 TGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGARV 305 (326)
Q Consensus 264 ~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~~ 305 (326)
...+.++.|||......-|+-+....+..++++|++.|..-
T Consensus 82 -~f~~d~~~Lni~~~~~~~raTe~i~~~~~~i~~L~~kG~aY 122 (384)
T PRK12418 82 -LFREDMEALRVLPPRDYVGAVESIPEVVELVEKLLASGAAY 122 (384)
T ss_pred -HHHHHHHHhCCCCCCccccCCCCHHHHHHHHHHHHHCCCEE
Confidence 23445567776211123344444667778889998887654
No 107
>PF11079 YqhG: Bacterial protein YqhG of unknown function; InterPro: IPR024562 This family of putative proteins appears to be restricted to Firmicutes. Their function is not known.
Probab=29.95 E-value=31 Score=33.06 Aligned_cols=74 Identities=19% Similarity=0.268 Sum_probs=53.3
Q ss_pred CCCCeEEEEEeccC-------CceeeeeEEEEEcCCCeEEeEEeecccCCcCCCCCcChhhhcccccCCCCHHHHhCCCC
Q 020417 112 QDLDFFLVLDLEGK-------IEILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALP 184 (326)
Q Consensus 112 ~~~~~~vVfDlETT-------~EIIEIgAVkvD~k~geiid~F~~fVrP~~~p~~~Is~~it~LTgi~GIt~e~V~~Ap~ 184 (326)
.++...+.+.+--. +++..+|.-++ +|++++.|+..+...... ++||++|--++ ...+
T Consensus 116 ~pL~PWL~vN~KVsy~cD~KkDel~SlGi~Li---~G~ive~F~~~L~~~~Lt-pkiPdy~ftls-----------p~i~ 180 (260)
T PF11079_consen 116 TPLTPWLGVNVKVSYQCDRKKDELLSLGINLI---SGQIVENFHERLQGRQLT-PKIPDYCFTLS-----------PIIK 180 (260)
T ss_pred ccccceeEEeEEEEEeeccchHHHhhheeecc---CCcchhhHHHHHhcCCCC-CCCCcceeecC-----------CcCC
Confidence 44555555444322 99999998776 899999999999886643 38988875553 2236
Q ss_pred HHHHHHHHHHHHHhCc
Q 020417 185 FKEVIQQFEAWLIQHH 200 (326)
Q Consensus 185 f~eVl~~F~~fl~~~~ 200 (326)
.++++.++.+++.+..
T Consensus 181 ~~sa~~rlE~~l~~~l 196 (260)
T PF11079_consen 181 PKSALKRLEQYLEQYL 196 (260)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 7889999988887753
No 108
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=23.92 E-value=33 Score=38.99 Aligned_cols=35 Identities=3% Similarity=-0.059 Sum_probs=29.6
Q ss_pred cccccccCCccccCccchhhhhhcCCCcceeeechh
Q 020417 69 PMCLYFTQGKCTMMDDVMHLEKFNHDISRDLQVDAA 104 (326)
Q Consensus 69 ~~~~~~dhg~~q~~~~a~~~~~~~~~~~~~~~v~~~ 104 (326)
|-.--||||++.+.++-+.+.+ ++++|+++|+|.+
T Consensus 33 ~alAlTD~~~m~Ga~~F~~~a~-~~gIkPIiG~e~~ 67 (1034)
T PRK07279 33 QTIGIMDKDNLYGAYHFIEGAQ-KNGLQPILGLELN 67 (1034)
T ss_pred CEEEEEcCCccccHHHHHHHHH-HcCCcEEEEEEEE
Confidence 3445699999999999988888 6799999999974
No 109
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=23.31 E-value=69 Score=35.23 Aligned_cols=14 Identities=14% Similarity=0.249 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHHHh
Q 020417 185 FKEVIQQFEAWLIQ 198 (326)
Q Consensus 185 f~eVl~~F~~fl~~ 198 (326)
-+||+.-+.+|.-+
T Consensus 1358 pqevlriisdyypd 1371 (1463)
T PHA03308 1358 PQEVLRIISDYYPD 1371 (1463)
T ss_pred hHHHHHHHhhhCCC
Confidence 34555555555443
No 110
>PLN02946 cysteine-tRNA ligase
Probab=22.05 E-value=5.5e+02 Score=27.34 Aligned_cols=91 Identities=12% Similarity=0.108 Sum_probs=56.7
Q ss_pred CHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCC
Q 020417 184 PFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEA 263 (326)
Q Consensus 184 ~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~ 263 (326)
-+-|++.+++++.+- .+.+|.|.. |+...|...++..|+.. .++.+-+..
T Consensus 103 V~~Dvl~R~Lr~~Gy-------------~V~~V~niT-DiDDKIi~~A~~~g~~~-------~ela~~y~~--------- 152 (557)
T PLN02946 103 VTFDVLYRYLKHLGY-------------EVRYVRNFT-DVDDKIIARANELGEDP-------ISLSRRYCE--------- 152 (557)
T ss_pred HHHHHHHHHHHhcCC-------------cEEEEECCC-CccCHHHHHHHHcCCCH-------HHHHHHHHH---------
Confidence 466788888886643 356788764 44445666777777653 222222222
Q ss_pred CCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCcc
Q 020417 264 TGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGARV 305 (326)
Q Consensus 264 ~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~~ 305 (326)
.....++.|||......-++-+-...+..++++|++.|..-
T Consensus 153 -~f~~d~~~LnI~~p~~~pratehi~~ii~~i~~Li~kG~aY 193 (557)
T PLN02946 153 -EFLSDMAYLHCLPPSVEPRVSDHIPQIIDMIKQILDNGCAY 193 (557)
T ss_pred -HHHHHHHHCCCCCCCeecCcchhHHHHHHHHHHHHHCCCEE
Confidence 13345667887533334567677778888899999887654
No 111
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=22.04 E-value=30 Score=39.63 Aligned_cols=35 Identities=11% Similarity=-0.024 Sum_probs=29.7
Q ss_pred cccccccCCccccCccchhhhhhcCCCcceeeechh
Q 020417 69 PMCLYFTQGKCTMMDDVMHLEKFNHDISRDLQVDAA 104 (326)
Q Consensus 69 ~~~~~~dhg~~q~~~~a~~~~~~~~~~~~~~~v~~~ 104 (326)
|----||||++.+.++-+.+.+ ++++|+++|+|.+
T Consensus 34 ~alAlTDh~~m~Ga~~F~~~a~-~~gIkPIiG~e~~ 68 (1107)
T PRK06920 34 SSLAITDENVMYGVIPFYKACK-KHGIHPIIGLTAS 68 (1107)
T ss_pred CEEEEEeCChHhHHHHHHHHHH-HcCCCEeeeeEEE
Confidence 3345699999999999888887 5799999999986
No 112
>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional
Probab=20.11 E-value=5.7e+02 Score=28.10 Aligned_cols=91 Identities=9% Similarity=0.067 Sum_probs=55.4
Q ss_pred CHHHHHHHHHHHHHhCcccccccCCCCcceEEEEcCcccHHHHHHHHHHHhCCCCCCCCccHhhHHHHHHhhcCCCcCCC
Q 020417 184 PFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEA 263 (326)
Q Consensus 184 ~f~eVl~~F~~fl~~~~Lv~~~~~~~~~~~~~a~ng~fDl~~fL~~~~~~~gi~~p~~~~~~iDl~~l~~~~~~~~~~~~ 263 (326)
-+.+|+.+++++.+- .+.+|.|.. |+..-+...++..|+.+ .++.+-+..
T Consensus 271 V~~DVL~R~Lr~~Gy-------------~V~fV~NiT-D~DDKII~~A~e~G~sp-------~ela~~y~~--------- 320 (699)
T PRK14535 271 VVFDMIARWLRECGY-------------PLTYVRNIT-DIDDKIIARAAENGETI-------GELTARFIQ--------- 320 (699)
T ss_pred HHHHHHHHHHHHcCC-------------ceEEEeCCc-ccchHHHHHHHHcCCCH-------HHHHHHHHH---------
Confidence 356788888887542 356787765 55556667777888764 233332222
Q ss_pred CCHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHcCCcc
Q 020417 264 TGMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGARV 305 (326)
Q Consensus 264 ~~L~~l~k~lgI~~~g~hHrAldDA~~tA~I~~~ll~~g~~~ 305 (326)
.....++.|||......=+|-+-...+..++++|++.|..-
T Consensus 321 -~F~~d~~~LnI~~p~~~praTeHI~~ii~lI~~LidkG~AY 361 (699)
T PRK14535 321 -AMHEDADALGVLRPDIEPKATENIPQMIAMIETLIQNGKAY 361 (699)
T ss_pred -HHHHHHHHcCCCCCcEeeCccchHHHHHHHHHHHHHCCCEE
Confidence 23455677887543223344455666777888898877544
No 113
>COG0386 BtuE Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones]
Probab=20.01 E-value=49 Score=29.50 Aligned_cols=28 Identities=25% Similarity=0.357 Sum_probs=21.7
Q ss_pred EEEcCCCeEEeEEeecccCCcCCCCCcChhhhcc
Q 020417 135 MIDAKTMAFVDLFHRFVRPSKMSEQHINKYIEGK 168 (326)
Q Consensus 135 kvD~k~geiid~F~~fVrP~~~p~~~Is~~it~L 168 (326)
+|| ++|+|+.+|+.-.+|.. +...|+++
T Consensus 132 Lvd-r~G~VV~Rf~p~t~P~d-----~~~~Ie~l 159 (162)
T COG0386 132 LVD-RDGNVVKRFSPKTKPED-----IELAIEKL 159 (162)
T ss_pred EEc-CCCcEEEeeCCCCChhh-----HHHHHHHH
Confidence 467 69999999999999987 33456554
Done!