Query 003416
Match_columns 821
No_of_seqs 492 out of 1973
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 23:01:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003416.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003416hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2206 Exosome 3'-5' exoribon 100.0 4.1E-73 8.9E-78 630.4 24.5 390 2-427 87-481 (687)
2 PRK10829 ribonuclease D; Provi 100.0 2.8E-61 6.1E-66 530.4 33.8 347 129-492 2-372 (373)
3 COG0349 Rnd Ribonuclease D [Tr 100.0 3.3E-58 7.1E-63 497.5 28.5 343 133-492 1-361 (361)
4 TIGR01388 rnd ribonuclease D. 100.0 8.9E-56 1.9E-60 486.8 32.3 344 132-493 1-367 (367)
5 cd06129 RNaseD_like DEDDy 3'-5 100.0 6.4E-30 1.4E-34 250.9 18.0 156 139-295 2-160 (161)
6 cd06146 mut-7_like_exo DEDDy 3 100.0 2.5E-29 5.5E-34 254.6 18.7 166 130-295 1-192 (193)
7 cd06141 WRN_exo DEDDy 3'-5' ex 100.0 3.3E-27 7.2E-32 231.8 18.3 162 133-295 1-169 (170)
8 cd06148 Egl_like_exo DEDDy 3'- 99.9 1.6E-27 3.4E-32 241.9 15.1 159 142-301 3-180 (197)
9 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 1.7E-26 3.8E-31 224.1 17.9 170 130-299 1-176 (176)
10 cd06142 RNaseD_exo DEDDy 3'-5' 99.8 2.3E-19 5E-24 175.8 20.1 162 139-302 2-164 (178)
11 cd06147 Rrp6p_like_exo DEDDy 3 99.8 6E-19 1.3E-23 177.5 21.4 176 126-302 1-176 (192)
12 smart00474 35EXOc 3'-5' exonuc 99.8 1.6E-18 3.6E-23 166.7 20.1 167 130-298 1-171 (172)
13 PRK05755 DNA polymerase I; Pro 99.7 2.3E-16 4.9E-21 191.9 28.1 173 127-301 293-472 (880)
14 cd00007 35EXOc 3'-5' exonuclea 99.7 8.5E-16 1.8E-20 145.2 15.7 147 151-297 2-154 (155)
15 PRK14975 bifunctional 3'-5' ex 99.7 9.9E-16 2.1E-20 177.9 18.0 142 129-301 2-147 (553)
16 cd09018 DEDDy_polA_RNaseD_like 99.7 1E-15 2.2E-20 145.6 14.5 143 151-295 1-149 (150)
17 cd06140 DNA_polA_I_Bacillus_li 99.6 6.1E-15 1.3E-19 145.5 15.8 152 149-302 3-160 (178)
18 cd06139 DNA_polA_I_Ecoli_like_ 99.5 8.5E-13 1.8E-17 130.9 17.4 152 147-300 3-172 (193)
19 PF00570 HRDC: HRDC domain Blo 99.5 9.8E-14 2.1E-18 117.7 7.0 68 352-419 1-68 (68)
20 smart00341 HRDC Helicase and R 99.4 4.5E-13 9.7E-18 117.0 9.8 78 350-427 2-79 (81)
21 KOG2207 Predicted 3'-5' exonuc 99.4 3.8E-13 8.1E-18 153.4 9.7 174 126-299 388-586 (617)
22 COG0749 PolA DNA polymerase I 99.3 7.3E-11 1.6E-15 136.7 19.0 170 130-301 3-183 (593)
23 TIGR00593 pola DNA polymerase 99.3 1.1E-09 2.3E-14 133.7 26.7 167 129-301 303-480 (887)
24 cd06128 DNA_polA_exo DEDDy 3'- 98.9 6.6E-08 1.4E-12 93.4 15.1 128 165-295 17-150 (151)
25 TIGR01389 recQ ATP-dependent D 98.7 4E-08 8.7E-13 115.3 8.9 71 351-421 520-590 (591)
26 PRK11057 ATP-dependent DNA hel 98.1 5.5E-06 1.2E-10 98.1 9.3 74 351-424 531-604 (607)
27 PLN03137 ATP-dependent DNA hel 97.9 1.9E-05 4.2E-10 98.0 8.8 72 352-423 1028-1101(1195)
28 cd06125 DnaQ_like_exo DnaQ-lik 97.9 8E-05 1.7E-09 68.1 9.1 73 152-235 1-83 (96)
29 KOG4373 Predicted 3'-5' exonuc 97.8 5.3E-05 1.2E-09 82.6 7.4 127 164-291 145-281 (319)
30 COG0514 RecQ Superfamily II DN 97.6 0.00011 2.4E-09 86.4 7.3 72 352-423 517-588 (590)
31 PRK06063 DNA polymerase III su 96.6 0.055 1.2E-06 59.8 15.5 135 149-302 15-183 (313)
32 TIGR01298 RNaseT ribonuclease 96.5 0.076 1.6E-06 54.9 14.8 85 203-303 105-197 (200)
33 PRK07942 DNA polymerase III su 96.4 0.093 2E-06 55.5 15.1 137 147-301 4-183 (232)
34 PRK06310 DNA polymerase III su 96.3 0.071 1.5E-06 57.1 14.1 133 146-298 4-174 (250)
35 PRK05168 ribonuclease T; Provi 96.2 0.16 3.6E-06 52.8 15.5 149 138-302 6-205 (211)
36 cd06137 DEDDh_RNase DEDDh 3'-5 96.1 0.052 1.1E-06 54.0 11.1 79 195-291 77-160 (161)
37 PRK07740 hypothetical protein; 96.1 0.15 3.2E-06 54.4 15.0 89 195-302 135-230 (244)
38 PRK06807 DNA polymerase III su 96.1 0.1 2.2E-06 57.8 14.2 130 149-300 8-174 (313)
39 PRK05711 DNA polymerase III su 96.1 0.089 1.9E-06 56.2 13.2 86 195-297 80-175 (240)
40 KOG2405 Predicted 3'-5' exonuc 96.1 0.0037 8E-08 69.8 2.8 127 168-297 213-360 (458)
41 cd06131 DNA_pol_III_epsilon_Ec 96.0 0.14 3E-06 50.4 13.5 84 194-294 74-166 (167)
42 cd06149 ISG20 DEDDh 3'-5' exon 95.9 0.064 1.4E-06 53.3 10.5 82 193-291 69-156 (157)
43 TIGR01406 dnaQ_proteo DNA poly 95.9 0.13 2.8E-06 54.3 13.3 86 194-296 75-170 (225)
44 PF13482 RNase_H_2: RNase_H su 95.8 0.033 7.2E-07 54.5 8.0 141 152-294 1-163 (164)
45 cd06144 REX4_like DEDDh 3'-5' 95.8 0.046 9.9E-07 53.8 8.8 80 193-291 69-151 (152)
46 PRK05601 DNA polymerase III su 95.7 0.16 3.4E-06 57.5 13.7 137 146-294 43-245 (377)
47 TIGR01405 polC_Gram_pos DNA po 95.6 0.17 3.7E-06 65.0 15.2 135 147-302 188-359 (1213)
48 TIGR00573 dnaq exonuclease, DN 95.6 0.15 3.3E-06 53.1 12.4 135 146-300 4-179 (217)
49 PRK07883 hypothetical protein; 95.3 0.23 5E-06 59.1 14.2 137 145-302 11-186 (557)
50 PRK08517 DNA polymerase III su 95.2 0.46 1E-05 51.3 14.8 133 146-299 65-232 (257)
51 cd06145 REX1_like DEDDh 3'-5' 95.2 0.18 3.9E-06 49.7 10.7 80 194-291 68-149 (150)
52 PRK07246 bifunctional ATP-depe 94.9 0.44 9.6E-06 59.2 15.3 133 148-302 6-174 (820)
53 cd06134 RNaseT DEDDh 3'-5' exo 94.8 0.77 1.7E-05 47.0 14.5 77 204-296 103-187 (189)
54 KOG2405 Predicted 3'-5' exonuc 94.7 0.0012 2.7E-08 73.4 -6.4 121 165-286 73-215 (458)
55 cd06127 DEDDh DEDDh 3'-5' exon 94.7 0.64 1.4E-05 43.8 12.6 81 193-291 71-158 (159)
56 PRK09145 DNA polymerase III su 94.6 1.1 2.3E-05 46.2 15.0 136 139-295 19-198 (202)
57 PRK09146 DNA polymerase III su 94.5 0.9 2E-05 48.5 14.5 79 204-299 130-228 (239)
58 COG2176 PolC DNA polymerase II 94.5 0.17 3.7E-06 63.6 10.1 136 146-302 418-590 (1444)
59 cd06136 TREX1_2 DEDDh 3'-5' ex 94.4 0.63 1.4E-05 47.1 12.7 80 194-292 87-175 (177)
60 smart00479 EXOIII exonuclease 94.4 0.71 1.5E-05 44.8 12.6 88 194-299 73-168 (169)
61 cd05160 DEDDy_DNA_polB_exo DED 94.4 0.77 1.7E-05 46.7 13.3 99 192-291 67-198 (199)
62 PRK06309 DNA polymerase III su 94.4 0.81 1.7E-05 48.4 13.9 130 150-299 3-167 (232)
63 TIGR01407 dinG_rel DnaQ family 94.1 0.82 1.8E-05 57.0 15.3 91 193-302 72-169 (850)
64 KOG2249 3'-5' exonuclease [Rep 94.1 0.43 9.2E-06 51.7 11.0 132 150-301 106-269 (280)
65 cd06130 DNA_pol_III_epsilon_li 94.0 1.4 2.9E-05 42.6 13.6 78 194-291 70-154 (156)
66 PRK00448 polC DNA polymerase I 93.0 0.66 1.4E-05 60.7 12.2 83 203-302 499-588 (1437)
67 PRK08074 bifunctional ATP-depe 92.8 1.7 3.8E-05 54.8 15.1 91 193-302 76-173 (928)
68 PF11408 Helicase_Sgs1: Sgs1 R 92.7 0.42 9.2E-06 43.2 7.0 67 354-420 7-75 (80)
69 cd06143 PAN2_exo DEDDh 3'-5' e 92.4 0.26 5.7E-06 50.4 6.0 77 195-291 95-173 (174)
70 cd05780 DNA_polB_Kod1_like_exo 92.3 2.3 5E-05 43.6 12.8 102 191-293 59-194 (195)
71 PRK07983 exodeoxyribonuclease 89.6 6.9 0.00015 41.4 13.6 78 203-296 74-152 (219)
72 PRK09182 DNA polymerase III su 86.3 9.9 0.00021 42.1 12.8 82 194-294 113-197 (294)
73 cd05784 DNA_polB_II_exo DEDDy 84.7 7.4 0.00016 40.3 10.3 62 229-292 123-193 (193)
74 PRK11779 sbcB exonuclease I; P 84.6 23 0.0005 41.9 15.4 87 194-297 84-197 (476)
75 COG0847 DnaQ DNA polymerase II 84.6 19 0.00042 37.7 13.6 133 149-297 13-181 (243)
76 PRK06195 DNA polymerase III su 84.1 7 0.00015 43.2 10.4 86 194-299 73-165 (309)
77 PRK07247 DNA polymerase III su 83.5 24 0.00052 36.7 13.5 84 193-297 76-168 (195)
78 cd05785 DNA_polB_like2_exo Unc 82.3 10 0.00022 39.7 10.2 140 149-291 9-206 (207)
79 cd05781 DNA_polB_B3_exo DEDDy 79.3 42 0.00092 34.5 13.4 142 150-293 4-187 (188)
80 KOG1275 PAB-dependent poly(A) 78.4 1.2 2.5E-05 55.2 1.9 91 198-317 1009-1102(1118)
81 PF09281 Taq-exonuc: Taq polym 77.3 8.4 0.00018 38.0 7.1 69 212-298 70-138 (138)
82 cd06133 ERI-1_3'hExo_like DEDD 77.2 56 0.0012 32.0 13.2 85 194-294 81-175 (176)
83 cd05782 DNA_polB_like1_exo Unc 69.5 59 0.0013 34.0 11.7 129 161-292 46-207 (208)
84 cd05783 DNA_polB_B1_exo DEDDy 67.8 1.4E+02 0.0031 31.2 14.1 97 191-292 76-202 (204)
85 KOG3657 Mitochondrial DNA poly 66.9 13 0.00027 46.3 6.8 97 204-301 242-386 (1075)
86 COG3359 Predicted exonuclease 63.7 1.5E+02 0.0033 32.6 13.3 149 150-300 99-271 (278)
87 cd05779 DNA_polB_epsilon_exo D 62.8 1.2E+02 0.0027 31.8 12.5 96 194-292 79-204 (204)
88 KOG2248 3'-5' exonuclease [Rep 56.6 39 0.00085 38.9 8.1 84 192-293 284-370 (380)
89 cd06138 ExoI_N N-terminal DEDD 51.6 62 0.0014 32.8 8.0 80 194-290 75-181 (183)
90 PRK07748 sporulation inhibitor 48.1 1.2E+02 0.0027 31.3 9.6 88 193-297 84-179 (207)
91 PRK05762 DNA polymerase II; Re 38.0 3.3E+02 0.0071 34.4 12.8 98 194-294 209-348 (786)
92 cd05777 DNA_polB_delta_exo DED 28.4 80 0.0017 33.3 4.6 67 229-295 153-224 (230)
93 cd06135 Orn DEDDh 3'-5' exonuc 25.4 2.9E+02 0.0063 27.8 7.9 30 203-232 94-127 (173)
94 COG1460 Uncharacterized protei 24.9 91 0.002 30.3 3.8 46 378-423 66-112 (114)
95 PF03874 RNA_pol_Rpb4: RNA pol 24.4 2E+02 0.0043 27.1 6.0 46 376-421 69-115 (117)
96 PRK06722 exonuclease; Provisio 23.7 2.9E+02 0.0063 30.7 8.0 84 194-295 83-178 (281)
97 PF04857 CAF1: CAF1 family rib 22.9 1.4E+02 0.0031 32.1 5.4 54 201-254 147-215 (262)
98 PRK05359 oligoribonuclease; Pr 22.3 8.5E+02 0.018 24.9 13.3 37 205-241 100-143 (181)
99 PRK14981 DNA-directed RNA poly 21.7 1.2E+02 0.0026 29.0 4.0 45 378-422 65-110 (112)
100 PRK02925 glucuronate isomerase 21.4 2E+02 0.0043 34.3 6.4 74 394-477 104-184 (466)
101 cd05778 DNA_polB_zeta_exo inac 21.0 1E+02 0.0022 32.8 3.7 63 229-291 162-230 (231)
No 1
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.1e-73 Score=630.37 Aligned_cols=390 Identities=46% Similarity=0.740 Sum_probs=355.9
Q ss_pred CcchhHhhhhhccCCCCCCCCCCceeeecccccCCCCCCCCCCCceeeeecccccccCCCCCCCCCcccccCCCCCCCCC
Q 003416 2 DVSFDEFSKARGENGEGDGNEGGFQLVYGKNKKKGDIVGGSAPASVKVKDRKEKSKVPFHVPTITKPQEEYKIVVNNANQ 81 (821)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~i~kPQ~~F~~~vdNs~~ 81 (821)
|.++|||+++|..|-+.... ++-+. -..|+++| ..+|.|||+.|+.+|||+++
T Consensus 87 d~~lDe~k~~~k~e~~~~~s-----------------~~~r~--------fsGKa~sp--~~~l~kpq~~f~~~idn~~~ 139 (687)
T KOG2206|consen 87 DHLLDELKRARKSESRGSPS-----------------EYDRE--------FSGKAKSP--TMNLLKPQVRFVEGIDNLHH 139 (687)
T ss_pred cchHHHHHhhhhccccCChh-----------------hhhhh--------ccccccCc--cccccchHHHHhhccccccC
Confidence 67899999999886442210 00000 00356667 88999999999999999999
Q ss_pred CCccccc---cccCCCCC-CCCCCC-ccccccccccccCCCCCCCCCCCCCCCcEEecCHHHHHHHHHHHhcCCeeEEEe
Q 003416 82 PFQHVWL---QKSEDSGR-FIHPLD-NLSVLDFVDKDIGDVEAVKPPSLEQTPFKLVEEVKDLKELAAKLKSVDEFAVDL 156 (821)
Q Consensus 82 pf~~~~~---~~~~~~~~-~~hPye-~~~~~~~~~~~~~~~~p~~~~~l~~t~~~lIdT~e~L~~lle~L~~a~~IAVDt 156 (821)
||.|.+. ++.+++.+ +.|||+ .+.++.+++.+++..+|.++.+++.|++.||.+..+|.++.+.|....++|||+
T Consensus 140 pf~~~~~~~vEr~e~~~~~~~hpye~e~~~f~~~~~~le~~~~~~~~~le~T~~~~I~t~~el~~l~~~l~~~~Efavdl 219 (687)
T KOG2206|consen 140 PFCSMLASEVERLEDRPREVQHPYEDEERHFRQIDKQLEEGEPRKSSPLEITPKVWICTLGELEALPEILDSVIEFAVDL 219 (687)
T ss_pred CchhhhhhhhhchhhcchhccCcchhhhhhhcccchhhhcccccCCCcccccCceeeechHHHHHHHHHHhhhhhhhhhc
Confidence 9999998 88888887 999999 588899999999999999999999999999999999999999999999999999
Q ss_pred eecccccCCCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCceEEEecchhcHHHHHHHhCCCcCccchhHHHH
Q 003416 157 EHNQYRSFLGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQAS 236 (821)
Q Consensus 157 E~~~~rty~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~nlFDTqLAA 236 (821)
|||.+++|.|.+|||||+|++++||||++.++..+. +|+++|.||+|+||+||+..|+.||+++|||+++|+|||..|+
T Consensus 220 ehhsyrsf~gltclmqISTr~ed~iIDt~~l~~~i~-~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvnLfdt~~a~ 298 (687)
T KOG2206|consen 220 EHHSYRSFLGLTCLMQISTRTEDFIIDTFKLRDHIG-ILNEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVNLFDTIQAS 298 (687)
T ss_pred cccchhhhcCceeEEEeeccchhheehhHHHHHHHH-HhhhhccCCCeEEEEecCccchhhhhccceEEEEechhhHHHH
Confidence 999999999999999999999999999999987776 8999999999999999999999999999999999999999999
Q ss_pred HhhCCCCCcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHhcCCCCCCCCCChHHHHH
Q 003416 237 RVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMPKESENSDTPLTEVY 316 (821)
Q Consensus 237 yLLg~~~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee~G~~~~~~~~~l~ev~ 316 (821)
++||.++++|++|++.|||+..+|.+|++||++|||+++|+.||..|+|||++||+.|+.+|.+.+. ++ . -++
T Consensus 299 r~L~~~r~sL~~ll~~~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~---~~-~---~~~ 371 (687)
T KOG2206|consen 299 RLLGLPRPSLAYLLECVCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAK---GR-A---VTY 371 (687)
T ss_pred HHhCCCcccHHHHHHHHHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhc---cc-c---ccc
Confidence 9999999999999999999999999999999999999999999999999999999999999887652 11 1 234
Q ss_pred HHHHHHHHHHHhhccCChhhHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccCHHHHHHHHHhCCCCHHH
Q 003416 317 KRSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAK 396 (821)
Q Consensus 317 ~rs~e~~l~~yek~~~~e~~~~~i~~l~~~~l~~~qlavlraL~aWRD~iAR~~Dep~~~VL~D~~LleLA~~~P~t~~e 396 (821)
.+++++|...|.+++++...|+.++.+..+ ++..|+.+|++|++|||.+||.+|+|++|||||++|++||+.+|.+.+.
T Consensus 372 ~~~~d~c~~~~~k~~~~~~sy~~v~~~q~~-ln~~q~~~l~~L~~wRd~iARaeDES~~yVlpN~~ll~l~e~~P~~v~g 450 (687)
T KOG2206|consen 372 SESRDMCTNGYKKKTFCTKSYLEVEDIQSR-LNSSQLDVLRALLRWRDFIARAEDESVHYVLPNDQLLKLAEERPDTVDG 450 (687)
T ss_pred chhhhhhhcceecccCCCcchHhHHHHHhc-cchhHHHHHHHHHHHHHHHHhhccCCCceecccHHHHHHHHHCCccHHH
Confidence 478899999999999999999999887654 9999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcCChhHHHHhHHHHHHHHHHhHhccc
Q 003416 397 LRRLLKSKHSYIERYMGPVLSIIKNSMQNAA 427 (821)
Q Consensus 397 L~~l~g~~~~~vrr~g~eIL~iI~~a~~~~~ 427 (821)
|.+++...+++++++..+++.+|+.|+....
T Consensus 451 l~~~ln~~~p~vkq~~~~~~~ii~~a~~~~l 481 (687)
T KOG2206|consen 451 LLGGLNRLSPLVKQNVMDFLYIIRSAGRGFL 481 (687)
T ss_pred HHHhccCCCHHHHHHHHHHHHHHHHHhhhhh
Confidence 9999999999999999999999999988764
No 2
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=2.8e-61 Score=530.39 Aligned_cols=347 Identities=19% Similarity=0.275 Sum_probs=309.2
Q ss_pred CcEEecCHHHHHHHHHHHhcCCeeEEEeeecccccCCCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCceEEE
Q 003416 129 PFKLVEEVKDLKELAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVM 208 (821)
Q Consensus 129 ~~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~ 208 (821)
.|.+|+|+++|.++|+.+..++.|||||||++.++|++++|||||++++.+||||++++. ++ ..|+++|+|++|+||+
T Consensus 2 ~~~~I~t~~~L~~~~~~l~~~~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~~~-d~-~~L~~ll~~~~ivKV~ 79 (373)
T PRK10829 2 NYQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGIT-DW-SPFKALLRDPQVTKFL 79 (373)
T ss_pred CcEEeCCHHHHHHHHHHHhcCCeEEEecccccCccCCCceeEEEEecCCceEEEecCCcc-ch-HHHHHHHcCCCeEEEE
Confidence 478999999999999999999999999999999999999999999999999999999885 44 4699999999999999
Q ss_pred ecchhcHHHHHHHhCCCcCccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhHHH
Q 003416 209 HGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYL 287 (821)
Q Consensus 209 H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yL 287 (821)
|++++|+.+|++.+|+.+.++||||+|+++||.+ ++||+.|+++|||++++|+++++||+.||||++|+.||+.||+||
T Consensus 80 H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L 159 (373)
T PRK10829 80 HAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYL 159 (373)
T ss_pred eChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999988 799999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhhccCChhhHHHHhcccCCCCCHHHHHHHHHHHHHHHHHH
Q 003416 288 LYIYDIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIA 367 (821)
Q Consensus 288 L~Lyd~L~~eLee~G~~~~~~~~~l~ev~~rs~e~~l~~yek~~~~e~~~~~i~~l~~~~l~~~qlavlraL~aWRD~iA 367 (821)
+.||+.|..+|.+.| +.+|+.+.|... |.... ....++..|.++++. +.++++|++++++|++|||++|
T Consensus 160 ~~l~~~L~~~L~~~g-----~~~w~~ee~~~l---~~~~~-~~~~~~~~~~~ik~~--~~L~~~~lavl~~L~~WRe~~A 228 (373)
T PRK10829 160 LPIAAKLMAETEAAG-----WLPAALDECRLL---CQRRQ-EVLAPEEAYRDITNA--WQLRTRQLACLQLLADWRLRKA 228 (373)
T ss_pred HHHHHHHHHHHHHcC-----cHHHHHHHHHHH---Hhccc-cCCChHHHHHHhccc--cCCCHHHHHHHHHHHHHHHHHH
Confidence 999999999999876 357888777542 32211 123345678898773 6789999999999999999999
Q ss_pred HHcCCCCccccCHHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHhHhcccch--------------HHHH
Q 003416 368 RADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNAANF--------------EVIA 433 (821)
Q Consensus 368 R~~Dep~~~VL~D~~LleLA~~~P~t~~eL~~l~g~~~~~vrr~g~eIL~iI~~a~~~~~~~--------------~al~ 433 (821)
|++|+|++|||+|++|++||+++|++.++|.++ ++.+..+++||++|+++|+++.+.+++. .++.
T Consensus 229 r~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~-~~~~~~~r~~g~~ll~~i~~a~~~~~~~~P~~~~~~~~~~~~~~~~ 307 (373)
T PRK10829 229 RERDLAVNFVVREEHLWQVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALVAKAQALPEEALPPPVLNLIDMPGYRKAF 307 (373)
T ss_pred HHhCCCcceecChHHHHHHHHhCCCCHHHHHhc-cCChHhHHhhHHHHHHHHHHHhcCCHhhCCCCCCCcccChhHHHHH
Confidence 999999999999999999999999999999999 8888899999999999999998765553 3444
Q ss_pred HHH---HHHHHhhhcccchhhccCchhhccccCC-----CCCCCc-cccccccccCCCcchhhhccCC
Q 003416 434 QKL---KEERMEVASEETEVLVLDTSSNLKIPNV-----GRESVD-GVDALVGTTMPHPPAYTQLKQE 492 (821)
Q Consensus 434 elL---lk~~~e~~~va~~~lia~~~dl~~ia~~-----~~~~v~-al~gwr~~~fg~~~~a~~l~~g 492 (821)
+.| ...+|+++||+ +.+|++..+|++|+.+ +....| .|+|||+++|| +...++..|
T Consensus 308 ~~l~~~v~~~a~~~~i~-~ellas~~~l~~l~~~~~~~~~~~~~p~~l~GWR~e~~g--~~l~~~l~~ 372 (373)
T PRK10829 308 KAIKALIQEVSETHGLS-AELLASRRQINQLLNWHWKLKPQNGLPELISGWRGELLA--EALTEILQE 372 (373)
T ss_pred HHHHHHHHHHHHHhCCC-HHHhCCHHHHHHHHHhhcccCCccCCchHhhhhhHHHHH--HHHHHHHhc
Confidence 444 89999999999 9999999999999973 232334 89999999999 888887765
No 3
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-58 Score=497.54 Aligned_cols=343 Identities=23% Similarity=0.324 Sum_probs=307.6
Q ss_pred ecCHHHHHHHHHHHhcCCeeEEEeeecccccCCCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCceEEEecch
Q 003416 133 VEEVKDLKELAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGAD 212 (821)
Q Consensus 133 IdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H~aK 212 (821)
|++.+.++.+|..+..++.|||||||+++++|++.+|||||+.++.+++||++....++ +.|..+|.|++|+||||+++
T Consensus 1 i~~~~~l~~~~~~~~~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~~lIdpl~~~~d~-~~l~~Ll~d~~v~KIfHaa~ 79 (361)
T COG0349 1 ITTGDLLAAACALLRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEGASLIDPLAGILDL-PPLVALLADPNVVKIFHAAR 79 (361)
T ss_pred CCchhHHHHHHHHhcCCCceEEecccccccccCCceEEEEEecCCCceEeccccccccc-chHHHHhcCCceeeeecccc
Confidence 46778899999999999999999999999999999999999999999999999854345 45889999999999999999
Q ss_pred hcHHHHHHHhCCCcCccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhHHHHHHH
Q 003416 213 RDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 213 ~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Ly 291 (821)
+|+.+|++.||+.|.++|||++|++++|++ ++||+.||++++|++++|++|.+||+.||||++|++||+.||.||+.||
T Consensus 80 ~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~ 159 (361)
T COG0349 80 FDLEVLLNLFGLLPTPLFDTQIAAKLAGFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLY 159 (361)
T ss_pred ccHHHHHHhcCCCCCchhHHHHHHHHhCCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999998 8999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhhccCChhhHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHcC
Q 003416 292 DIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADD 371 (821)
Q Consensus 292 d~L~~eLee~G~~~~~~~~~l~ev~~rs~e~~l~~yek~~~~e~~~~~i~~l~~~~l~~~qlavlraL~aWRD~iAR~~D 371 (821)
+.|.++|.+.| +..|..++|.... .+.+ ....++.+|.++.. .+.+++.+++++++|++||+++||++|
T Consensus 160 ~~L~~~L~~~~-----r~~~a~~ef~~l~---~r~~-~~~~~~~~w~~i~~--a~~~~p~~la~l~~La~wRe~~Ar~rd 228 (361)
T COG0349 160 DKLTEELAREG-----RLEWAEDEFRLLP---TRRT-YKVLPEDAWREIKI--AHSLDPRELAVLRELAAWREREARERD 228 (361)
T ss_pred HHHHHHHHHcC-----chHHHHHHHHHhh---hccc-cccChHhHHHHhhh--hhcCChHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999876 4567777654321 1111 23466788988875 578999999999999999999999999
Q ss_pred CCCccccCHHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHhHhcccch--------------HHHHHHH-
Q 003416 372 ESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNAANF--------------EVIAQKL- 436 (821)
Q Consensus 372 ep~~~VL~D~~LleLA~~~P~t~~eL~~l~g~~~~~vrr~g~eIL~iI~~a~~~~~~~--------------~al~elL- 436 (821)
+|++||++|+.|+++|+.+|++..+|..+..... ..+.++..|+.+|.++++.|.+. .++.+.|
T Consensus 229 ~~~~~vl~de~i~~~a~~~P~~~~~l~~l~~~~~-~~~~~~~~l~~~~~~a~~~p~~~~p~~~~~~~~~p~~~~~~~~lk 307 (361)
T COG0349 229 LARNFVLKDEALWELARYTPKNLKELDALGLIPK-ERRRHGKLLLALLANALASPESDLPPPPGRLAPPPGYKAALKALK 307 (361)
T ss_pred cccccccchhHHHHHHHhCCCCHHHHHhccCCcc-cchhhhHHHHHHHHHHHhCchhhCCCCCcccCCChhHHHHHHHHH
Confidence 9999999999999999999999999999976655 77899999999999999887766 3555655
Q ss_pred --HHHHHhhhcccchhhccCchhhccccCCCCCCCccccccccccCCCcchhhhccCC
Q 003416 437 --KEERMEVASEETEVLVLDTSSNLKIPNVGRESVDGVDALVGTTMPHPPAYTQLKQE 492 (821)
Q Consensus 437 --lk~~~e~~~va~~~lia~~~dl~~ia~~~~~~v~al~gwr~~~fg~~~~a~~l~~g 492 (821)
++.+++..||+ +++||+. +|++|+.+....+.++.|||+++|| ++++.|++|
T Consensus 308 ~l~~~~s~~~gv~-~e~las~-~l~~l~~~~~~~~~~l~gWr~e~~~--~~l~~ll~~ 361 (361)
T COG0349 308 ALLKSVSEKHGVA-AELLASR-DLERLLAWGDDRPEALRGWRRELFG--EILLALLEG 361 (361)
T ss_pred HHHHHhhhhcCCc-HHHhccH-HHHHHHHccCCChHHHHHHHHHHhH--HHHHHHhcC
Confidence 89999999999 9999999 9999999976678899999999999 998888765
No 4
>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=100.00 E-value=8.9e-56 Score=486.84 Aligned_cols=344 Identities=22% Similarity=0.280 Sum_probs=304.5
Q ss_pred EecCHHHHHHHHHHHhcCCeeEEEeeecccccCCCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCceEEEecc
Q 003416 132 LVEEVKDLKELAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGA 211 (821)
Q Consensus 132 lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H~a 211 (821)
||+|+++|.++|+.|...++|||||||++.++|++++|||||++++.+||||++++. ++ +.|+++|+|++|.||+|++
T Consensus 1 ~I~t~~~l~~~~~~l~~~~~ia~DtE~~~~~~y~~~l~LiQia~~~~~~liD~~~~~-~~-~~L~~lL~d~~i~KV~h~~ 78 (367)
T TIGR01388 1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVII-DW-SPLKELLRDESVVKVLHAA 78 (367)
T ss_pred CcCCHHHHHHHHHHHhcCCEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCcc-cH-HHHHHHHCCCCceEEEeec
Confidence 589999999999999999999999999999999999999999999999999999874 44 4689999999999999999
Q ss_pred hhcHHHHHHHhCCCcCccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhHHHHHH
Q 003416 212 DRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYI 290 (821)
Q Consensus 212 K~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~L 290 (821)
++|+.+|++.+++.+.++|||++|+|+||++ ++||+.|+++|||+.++|+.+.+||..|||+.+|+.||+.||+||+.|
T Consensus 79 k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L 158 (367)
T TIGR01388 79 SEDLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPL 158 (367)
T ss_pred HHHHHHHHHHhCCCCCCcccHHHHHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 9999999888888888999999999999997 689999999999999999989999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhhccCChhhHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHc
Q 003416 291 YDIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEKELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARAD 370 (821)
Q Consensus 291 yd~L~~eLee~G~~~~~~~~~l~ev~~rs~e~~l~~yek~~~~e~~~~~i~~l~~~~l~~~qlavlraL~aWRD~iAR~~ 370 (821)
|+.|..+|.+.| +..|+.+.|.... ... .....++..|.++++. +.|++++++++++|++|||.+||++
T Consensus 159 ~~~L~~~L~~~g-----~~~w~~ee~~~l~---~~~-~~~~~~~~~~~~i~~~--~~l~~~~l~~l~~L~~wRe~~A~~~ 227 (367)
T TIGR01388 159 YAKLMERLEESG-----RLAWLEEECTLLT---DRR-TYVVNPEDAWRDIKNA--WQLRPQQLAVLQALAAWREREARER 227 (367)
T ss_pred HHHHHHHHHHcC-----cHHHHHHHHHHHh---ccc-cCCCChHHHHHHhccc--ccCCHHHHHHHHHHHHHHHHHHHHc
Confidence 999999999876 3578887765432 111 1122345678888763 6789999999999999999999999
Q ss_pred CCCCccccCHHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHhHhcccch--------------HHHHHHH
Q 003416 371 DESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNAANF--------------EVIAQKL 436 (821)
Q Consensus 371 Dep~~~VL~D~~LleLA~~~P~t~~eL~~l~g~~~~~vrr~g~eIL~iI~~a~~~~~~~--------------~al~elL 436 (821)
|+|+++||+|+.|++||+++|+|.++|.++ ++.+..+++|+++|+++|+++.+.+++. .++.+.|
T Consensus 228 d~p~~~il~d~~l~~lA~~~P~~~~~l~~~-~~~~~~~r~~~~~l~~~i~~a~~~~~~~~P~~~~~~~~~~~~~~~~~~l 306 (367)
T TIGR01388 228 DLPRNFVLKEEALWELARQAPGNLTELASL-GPKGSEIRKHGDTLLALVKTALALPEDALPQAPLNLMPPPGYKALFKLL 306 (367)
T ss_pred CCCcceeeCHHHHHHHHHhCCCCHHHHHhc-cCChHHHHhhHHHHHHHHHHHhhCCHhhCCCCCCCCCCChhHHHHHHHH
Confidence 999999999999999999999999999999 8888999999999999999998765544 3455555
Q ss_pred ---HHHHHhhhcccchhhccCchhhccccCC----CCCCCc-cccccccccCCCcchhhhccCCC
Q 003416 437 ---KEERMEVASEETEVLVLDTSSNLKIPNV----GRESVD-GVDALVGTTMPHPPAYTQLKQEP 493 (821)
Q Consensus 437 ---lk~~~e~~~va~~~lia~~~dl~~ia~~----~~~~v~-al~gwr~~~fg~~~~a~~l~~g~ 493 (821)
.+.+|+++||+ +.+|++..+|++|+.+ ...+.| .|+|||++ || .+++.++.|+
T Consensus 307 ~~~~~~~a~~~~i~-~~~l~~~~~l~~l~~~~~~~~~~~~~~~~~gWR~~-~~--~~~~~~~~~~ 367 (367)
T TIGR01388 307 KVLVKDVSETLGLA-SELLASRRQLEQLLAWGWKLKPNALPPLLQGWRRE-LG--EEALKNLLSE 367 (367)
T ss_pred HHHHHHHHHHhCCC-HHHcCCHHHHHHHHHhhcccccccccHHHHhhHHH-HH--HHHHHHhcCC
Confidence 89999999999 9999999999999975 223455 89999999 88 8888888874
No 5
>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=99.97 E-value=6.4e-30 Score=250.88 Aligned_cols=156 Identities=34% Similarity=0.509 Sum_probs=146.3
Q ss_pred HHHHHHHHh-cCCeeEEEeeecccccCCCcEEEEEEEeC-CceEEEecCCcchhhhHHHHHhhcCCCceEEEecchhcHH
Q 003416 139 LKELAAKLK-SVDEFAVDLEHNQYRSFLGLTCLMQISTR-TEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIV 216 (821)
Q Consensus 139 L~~lle~L~-~a~~IAVDtE~~~~rty~g~LcLIQISt~-~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H~aK~DL~ 216 (821)
|+++|+.|. ....||+|+||.+..++.+++|+|||+++ +.+||||+..++. ..+.|+++|+|++|+||+|+++.|+.
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~-~~~~L~~lL~d~~i~Kvg~~~k~D~~ 80 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSV-DWQGLKMLLENPSIVKALHGIEGDLW 80 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCcc-CHHHHHHHhCCCCEEEEEeccHHHHH
Confidence 678999999 99999999999998888999999999999 8999999988753 34568999999999999999999999
Q ss_pred HHHHHhCCCcCccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhHHHHHHHHHHH
Q 003416 217 WLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 295 (821)
Q Consensus 217 ~L~rd~GI~~~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~ 295 (821)
.|++.+|+.+.++|||++|+|+++++ +.||+.|+++|+|+.++|..+.+||..|||+++|+.||+.||++++.||+.|+
T Consensus 81 ~L~~~~gi~~~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 81 KLLRDFGEKLQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHcCCCcccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99888999999999999999999986 78999999999999999999999999999999999999999999999999986
No 6
>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=99.96 E-value=2.5e-29 Score=254.56 Aligned_cols=166 Identities=24% Similarity=0.361 Sum_probs=150.6
Q ss_pred cEEecCHHHHHHHHHH--HhcCCeeEEEeeecccccC--CCcEEEEEEEeCCceEEEecCCcc----hhhhHHHHHhhcC
Q 003416 130 FKLVEEVKDLKELAAK--LKSVDEFAVDLEHNQYRSF--LGLTCLMQISTRTEDFVVDTLKLR----VQVGPYLREVFKD 201 (821)
Q Consensus 130 ~~lIdT~e~L~~lle~--L~~a~~IAVDtE~~~~rty--~g~LcLIQISt~~~~yLID~Lal~----~~L~~~L~eLLeD 201 (821)
+.+|++++++.+++.. +.....||+|+||.+...+ .+++|||||++.+.+||||+..++ ..+.+.|+++|+|
T Consensus 1 ~~~i~~~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~ll~d 80 (193)
T cd06146 1 IHIVDSEEELEALLLALSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKRLFED 80 (193)
T ss_pred CeEecCHHHHHHHHHHHhhccCCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHHHhCC
Confidence 4689999999999999 8999999999999877654 689999999999999999998765 2356679999999
Q ss_pred CCceEEEecchhcHHHHHHHhCCC------cCccchhHHHHHhhCC------------CCCcHHHHHHHHcCCCCccccc
Q 003416 202 PTKKKVMHGADRDIVWLQRDFGIY------LCNMFDTGQASRVLKL------------ERNSLEYLLHHFCGVNANKEYQ 263 (821)
Q Consensus 202 p~IvKV~H~aK~DL~~L~rd~GI~------~~nlFDTqLAAyLLg~------------~~~SLa~LvekyLgv~LdK~~Q 263 (821)
|+|+||+|++++|+.+|++++|+. +.++|||+.+++.+.. ...||+.|++++||+.++|..|
T Consensus 81 ~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~q 160 (193)
T cd06146 81 PDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQ 160 (193)
T ss_pred CCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCcccc
Confidence 999999999999999999999974 5789999998886652 2589999999999999999999
Q ss_pred cccccCCCCCHHHHHHHHHhhHHHHHHHHHHH
Q 003416 264 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 295 (821)
Q Consensus 264 ~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~ 295 (821)
++||..|||+++|+.|||.||++++.||+.|.
T Consensus 161 ~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 161 CSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999875
No 7
>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=99.95 E-value=3.3e-27 Score=231.85 Aligned_cols=162 Identities=23% Similarity=0.348 Sum_probs=149.2
Q ss_pred ecCHHHHHHHHHHHh-cCCeeEEEeeeccccc--CCCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCceEEEe
Q 003416 133 VEEVKDLKELAAKLK-SVDEFAVDLEHNQYRS--FLGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMH 209 (821)
Q Consensus 133 IdT~e~L~~lle~L~-~a~~IAVDtE~~~~rt--y~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H 209 (821)
+++...+..+++.+. ....||+|+||.+..+ +.+.+|+|||++.+.+||||+..+. .+.+.|+++|++++|.||+|
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~-~~~~~l~~ll~~~~i~kv~~ 79 (170)
T cd06141 1 TDSAQDAEEAVKELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMD-KLPPSLKQLLEDPSILKVGV 79 (170)
T ss_pred CCCHHHHHHHHHHHhcCCCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhh-cccHHHHHHhcCCCeeEEEe
Confidence 357788999999998 9999999999998766 7899999999999999999998763 45567999999999999999
Q ss_pred cchhcHHHHHHHhCCCcCccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCc--cccccccccCCCCCHHHHHHHHHhhH
Q 003416 210 GADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNAN--KEYQNADWRVRPLPDEMLRYAREDTH 285 (821)
Q Consensus 210 ~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~Ld--K~~Q~SDW~~RPLs~eql~YAA~DA~ 285 (821)
+++.|+..|.+.+|+.+.++|||++|+|++++. ..||+.|+..|+|..++ |..+.+||..|||+++|+.||+.||+
T Consensus 80 ~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~ 159 (170)
T cd06141 80 GIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAY 159 (170)
T ss_pred eeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHH
Confidence 999999999889999999999999999999986 47999999999999998 78899999999999999999999999
Q ss_pred HHHHHHHHHH
Q 003416 286 YLLYIYDIMK 295 (821)
Q Consensus 286 yLL~Lyd~L~ 295 (821)
+++.||+.|.
T Consensus 160 ~~~~l~~~l~ 169 (170)
T cd06141 160 ASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHh
Confidence 9999999875
No 8
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.95 E-value=1.6e-27 Score=241.95 Aligned_cols=159 Identities=31% Similarity=0.406 Sum_probs=142.3
Q ss_pred HHHHHhcCCeeEEEeeecccccCCCcEEEEEEEeC-CceEEEecCCcch-hhhHHHHHhhcCCCceEEEecchhcHHHHH
Q 003416 142 LAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQISTR-TEDFVVDTLKLRV-QVGPYLREVFKDPTKKKVMHGADRDIVWLQ 219 (821)
Q Consensus 142 lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt~-~~~yLID~Lal~~-~L~~~L~eLLeDp~IvKV~H~aK~DL~~L~ 219 (821)
.++.|.....||||+|+.+... ++.+|||||++. +.+||||+..++. .+...|+++|++++|+||+|+++.|+.+|+
T Consensus 3 ~~~~l~~~~~i~~D~E~~~~~~-~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~ 81 (197)
T cd06148 3 AIIHLKKQKVIGLDCEGVNLGR-KGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALY 81 (197)
T ss_pred hhhhhhhCCEEEEEcccccCCC-CCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHH
Confidence 4567888999999999987766 689999999999 9999999988752 244678999999999999999999999998
Q ss_pred HHhCCCcCccchhHHHHHhhCCC---------CCcHHHHHHHHcCCCCcc--------ccccccccCCCCCHHHHHHHHH
Q 003416 220 RDFGIYLCNMFDTGQASRVLKLE---------RNSLEYLLHHFCGVNANK--------EYQNADWRVRPLPDEMLRYARE 282 (821)
Q Consensus 220 rd~GI~~~nlFDTqLAAyLLg~~---------~~SLa~LvekyLgv~LdK--------~~Q~SDW~~RPLs~eql~YAA~ 282 (821)
+.+|+.+.++|||++|+|+|++. ..||+.|+++|+++.++| ..+.+||..|||+++|+.||+.
T Consensus 82 ~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~ 161 (197)
T cd06148 82 HQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAAL 161 (197)
T ss_pred HhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHH
Confidence 89999999999999999999864 269999999999999865 4578999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHhcC
Q 003416 283 DTHYLLYIYDIMKIKLSSM 301 (821)
Q Consensus 283 DA~yLL~Lyd~L~~eLee~ 301 (821)
||+||+.||+.|...|.+.
T Consensus 162 Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 162 DVLCLLPLYYAMLDALISK 180 (197)
T ss_pred HHHhHHHHHHHHHHHhhhh
Confidence 9999999999999999864
No 9
>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=99.94 E-value=1.7e-26 Score=224.11 Aligned_cols=170 Identities=33% Similarity=0.548 Sum_probs=153.9
Q ss_pred cEEecCHHHHHHHHHHHhcCCeeEEEeeeccccc--CCCcEEEEEEEeCCceEEEecCCcchh-hhHHHHHhhcCCCceE
Q 003416 130 FKLVEEVKDLKELAAKLKSVDEFAVDLEHNQYRS--FLGLTCLMQISTRTEDFVVDTLKLRVQ-VGPYLREVFKDPTKKK 206 (821)
Q Consensus 130 ~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rt--y~g~LcLIQISt~~~~yLID~Lal~~~-L~~~L~eLLeDp~IvK 206 (821)
|++|+|.+++.+++..+.....+|+|+|+.+... +.+.+++||+++.+.+|++++...... +...|+++|+|++|.|
T Consensus 1 y~~v~~~~~l~~~~~~l~~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i~k 80 (176)
T PF01612_consen 1 YQIVDTEEELEEAIKKLKNAKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPNIIK 80 (176)
T ss_dssp SEEEHSHHHHHHHHHHHTTTSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTTSEE
T ss_pred CEecCCHHHHHHHHHHHcCCCeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCCccE
Confidence 6899999999999999999999999999998776 678899999999999999998776543 4567999999999999
Q ss_pred EEecchhcHHHHHHHhCCCcCccchhHHHHHhhCCCC-CcHHHHHHHHcC-CCCcccccccccc-CCCCCHHHHHHHHHh
Q 003416 207 VMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLER-NSLEYLLHHFCG-VNANKEYQNADWR-VRPLPDEMLRYARED 283 (821)
Q Consensus 207 V~H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~~-~SLa~LvekyLg-v~LdK~~Q~SDW~-~RPLs~eql~YAA~D 283 (821)
|+|++++|+.+|++.+|+.+.++|||++|++++++.. +||+.|+.+|+| ..++|..+.++|. .+||+++|+.||+.|
T Consensus 81 v~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D 160 (176)
T PF01612_consen 81 VGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQD 160 (176)
T ss_dssp EESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHH
T ss_pred EEEEEechHHHHHHHhccccCCccchhhhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHH
Confidence 9999999999998889999999999999999999985 999999999999 7778889999999 899999999999999
Q ss_pred hHHHHHHHHHHHHHHh
Q 003416 284 THYLLYIYDIMKIKLS 299 (821)
Q Consensus 284 A~yLL~Lyd~L~~eLe 299 (821)
|++++.||+.|.++|+
T Consensus 161 ~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 161 AVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHTHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHhhC
Confidence 9999999999999884
No 10
>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=99.83 E-value=2.3e-19 Score=175.83 Aligned_cols=162 Identities=39% Similarity=0.593 Sum_probs=137.1
Q ss_pred HHHHHHHHhcCCeeEEEeeecccccCCCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCceEEEecchhcHHHH
Q 003416 139 LKELAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWL 218 (821)
Q Consensus 139 L~~lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H~aK~DL~~L 218 (821)
|.++++.+.....+++|+|+....++.+.++++||++.+.+|+||+... ...+.|+++|+|+++.||+|+++.|+..|
T Consensus 2 ~~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~i~l~~~~~~~~i~~~~~--~~~~~l~~ll~~~~i~kv~~d~K~~~~~L 79 (178)
T cd06142 2 LEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI--GDLSPLKELLADPNIVKVFHAAREDLELL 79 (178)
T ss_pred HHHHHHHHhcCCeEEEECCccCCCcCCCceEEEEEeeCCCEEEEeCCCc--ccHHHHHHHHcCCCceEEEeccHHHHHHH
Confidence 3455555555668999999877666678999999999855899985432 23345889999999999999999999999
Q ss_pred HHHhCCCcCccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHH
Q 003416 219 QRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 297 (821)
Q Consensus 219 ~rd~GI~~~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 297 (821)
++.+|+...++|||++|+|+|++. .++|..|+++|++..+.+....++|..+||+.+|+.||+.|+.+++.||+.|.++
T Consensus 80 ~~~~gi~~~~~~D~~laayLl~p~~~~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~ 159 (178)
T cd06142 80 KRDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEE 159 (178)
T ss_pred HHHcCCCCCCcccHHHHHHHhCCCccccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 877799855689999999999996 5799999999999886665577899999999999999999999999999999999
Q ss_pred HhcCC
Q 003416 298 LSSMP 302 (821)
Q Consensus 298 Lee~G 302 (821)
|.+.+
T Consensus 160 L~e~~ 164 (178)
T cd06142 160 LEEEG 164 (178)
T ss_pred HHHcC
Confidence 99764
No 11
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=99.82 E-value=6e-19 Score=177.52 Aligned_cols=176 Identities=62% Similarity=1.079 Sum_probs=146.5
Q ss_pred CCCCcEEecCHHHHHHHHHHHhcCCeeEEEeeecccccCCCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCce
Q 003416 126 EQTPFKLVEEVKDLKELAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKK 205 (821)
Q Consensus 126 ~~t~~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~Iv 205 (821)
++++|.||++.+++..+++.+.....+++++|...+.++.+.++++|+++.+++|+|+++... ...+.|+++|+++++.
T Consensus 1 ~~~~~~~i~~~~~l~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~l~~~-~~~~~L~~~L~~~~i~ 79 (192)
T cd06147 1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLR-DDMHILNEVFTDPNIL 79 (192)
T ss_pred CCCCcEEECCHHHHHHHHHHHhcCCeEEEEeEecCCccCCCceEEEEEecCCCcEEEEecccc-cchHHHHHHhcCCCce
Confidence 357899997778888877777656689999988777777889999999988778888743322 1223588999999999
Q ss_pred EEEecchhcHHHHHHHhCCCcCccchhHHHHHhhCCCCCcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhH
Q 003416 206 KVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTH 285 (821)
Q Consensus 206 KV~H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~ 285 (821)
||+|++|.++.+|.+.+|+.+.++|||++|+|+|+++.++|..|+++|++..+.|..+.++|..+||..+|..||+.++.
T Consensus 80 kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~~~~l~~l~~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~ 159 (192)
T cd06147 80 KVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTH 159 (192)
T ss_pred EEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCCcccHHHHHHHHhCCCcchhhhccccccCCCCHHHHHHHHhhHH
Confidence 99999999999995478998877799999999999965699999999998875454566779888988999999999999
Q ss_pred HHHHHHHHHHHHHhcCC
Q 003416 286 YLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 286 yLL~Lyd~L~~eLee~G 302 (821)
+++.|++.|..+|+++.
T Consensus 160 ~l~~L~~~L~~~L~e~~ 176 (192)
T cd06147 160 YLLYIYDRLRNELLERA 176 (192)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 99999999999998764
No 12
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.81 E-value=1.6e-18 Score=166.75 Aligned_cols=167 Identities=38% Similarity=0.555 Sum_probs=138.3
Q ss_pred cEEecCHHHHHHHHHHHh-cCCeeEEEeeecccccCCCcEEEEEEEeCC-ceEEEecCCcchhhhHHHHHhhcCCCceEE
Q 003416 130 FKLVEEVKDLKELAAKLK-SVDEFAVDLEHNQYRSFLGLTCLMQISTRT-EDFVVDTLKLRVQVGPYLREVFKDPTKKKV 207 (821)
Q Consensus 130 ~~lIdT~e~L~~lle~L~-~a~~IAVDtE~~~~rty~g~LcLIQISt~~-~~yLID~Lal~~~L~~~L~eLLeDp~IvKV 207 (821)
+.+|++.+++..+++.+. ....+++|+|+.....+.+.++++|+++.+ .+|+++..... .....|.++|+++.+.||
T Consensus 1 ~~~i~~~~~~~~~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~~-~~~~~l~~~l~~~~~~kv 79 (172)
T smart00474 1 VRVVTDSETLEELLEKLRAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALG-DDLEILKDLLEDETITKV 79 (172)
T ss_pred CEEecCHHHHHHHHHHHHhcCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccch-hhHHHHHHHhcCCCceEE
Confidence 357888888888777776 566999999988777678899999999644 45655443222 223458899999999999
Q ss_pred EecchhcHHHHHHHhCCCcCccchhHHHHHhhCCC-C-CcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhH
Q 003416 208 MHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-R-NSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTH 285 (821)
Q Consensus 208 ~H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~-~-~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~ 285 (821)
+|+++.|+.+|++ +|+.+.++|||++|+|+|++. . ++|+.|+..|++..+++..+..+|..+|+...|+.||+.||+
T Consensus 80 ~~d~k~~~~~L~~-~gi~~~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~ 158 (172)
T smart00474 80 GHNAKFDLHVLAR-FGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGARPLSEEQLQYAAEDAD 158 (172)
T ss_pred EechHHHHHHHHH-CCCcccchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCcccCccccccCCCCHHHHHHHHHHHH
Confidence 9999999999965 999988899999999999985 3 799999999999886654455689878989999999999999
Q ss_pred HHHHHHHHHHHHH
Q 003416 286 YLLYIYDIMKIKL 298 (821)
Q Consensus 286 yLL~Lyd~L~~eL 298 (821)
+++.||+.|.++|
T Consensus 159 ~~~~L~~~l~~~l 171 (172)
T smart00474 159 ALLRLYEKLEKEL 171 (172)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999998876
No 13
>PRK05755 DNA polymerase I; Provisional
Probab=99.75 E-value=2.3e-16 Score=191.90 Aligned_cols=173 Identities=24% Similarity=0.292 Sum_probs=144.2
Q ss_pred CCCcEEecCHHHHHHHHHHHhcCCeeEEEeeecccccCCCcEEEEEEEeCCc-eEEEecCCcchhhhHHHHHhhcCCCce
Q 003416 127 QTPFKLVEEVKDLKELAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQISTRTE-DFVVDTLKLRVQVGPYLREVFKDPTKK 205 (821)
Q Consensus 127 ~t~~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt~~~-~yLID~Lal~~~L~~~L~eLLeDp~Iv 205 (821)
...|.+|++.++|..+++.+.....+++|+|+.+.++|.+.+|+||+++.++ .|+|++..+.....+.|.++|+++.+.
T Consensus 293 ~~~~~~I~~~~~L~~~l~~l~~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~v~ 372 (880)
T PRK05755 293 EEDYETILDEEELEAWLAKLKAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPAIK 372 (880)
T ss_pred CCceEEeCCHHHHHHHHHHhhccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCCCc
Confidence 3467899999999999999998899999999999999999999999999876 788876333212345688999999999
Q ss_pred EEEecchhcHHHHHHHhCCCc-CccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCcccc----ccccccCCCCCHHHHHH
Q 003416 206 KVMHGADRDIVWLQRDFGIYL-CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEY----QNADWRVRPLPDEMLRY 279 (821)
Q Consensus 206 KV~H~aK~DL~~L~rd~GI~~-~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~----Q~SDW~~RPLs~eql~Y 279 (821)
||+||+++|+.+|+ .+|+.+ .++|||++|+|+|+++ .++|+.|+++|+|+.+.... ...+|..+|+ +.+..|
T Consensus 373 kV~HNakfDl~~L~-~~gi~~~~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~pl-e~~~~Y 450 (880)
T PRK05755 373 KVGQNLKYDLHVLA-RYGIELRGIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDL-EEAAEY 450 (880)
T ss_pred EEEeccHhHHHHHH-hCCCCcCCCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchHHhcCCCCCccccCH-HHHHHH
Confidence 99999999999996 478876 5699999999999987 49999999999998742110 1233445577 579999
Q ss_pred HHHhhHHHHHHHHHHHHHHhcC
Q 003416 280 AREDTHYLLYIYDIMKIKLSSM 301 (821)
Q Consensus 280 AA~DA~yLL~Lyd~L~~eLee~ 301 (821)
|+.||.+++.||..|..+|.+.
T Consensus 451 Aa~Dv~~~~~L~~~L~~~L~~~ 472 (880)
T PRK05755 451 AAEDADVTLRLHEVLKPKLLEE 472 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999865
No 14
>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=99.68 E-value=8.5e-16 Score=145.18 Aligned_cols=147 Identities=31% Similarity=0.316 Sum_probs=114.7
Q ss_pred eeEEEeeecccccCCCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCceEEEecchhcHHHHHHHhCCCcCccc
Q 003416 151 EFAVDLEHNQYRSFLGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMF 230 (821)
Q Consensus 151 ~IAVDtE~~~~rty~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~nlF 230 (821)
.+++|+|+.+...+.+.++++|+++.++.++|........+.+.|.++|+++.+.||+|++++|+.+|.+.+...+.++|
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~ 81 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIF 81 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcc
Confidence 57899998776666789999999987435555322111234455889999999999999999999999655444456789
Q ss_pred hhHHHHHhhCCC--CCcHHHHHHHHcCCCCcccccccccc----CCCCCHHHHHHHHHhhHHHHHHHHHHHHH
Q 003416 231 DTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADWR----VRPLPDEMLRYAREDTHYLLYIYDIMKIK 297 (821)
Q Consensus 231 DTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~SDW~----~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 297 (821)
||++|+|+|++. .++|+.|+++|++..+.+..+..+|. .+|++..|..||+.|+.+++.|++.|..+
T Consensus 82 D~~~~ayll~~~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 82 DTMLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred cHHHHHHHhCCCCCcCCHHHHHHHHcCCCCccHHHHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 999999999985 47999999999998754423344442 57888999999999999999999998765
No 15
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.67 E-value=9.9e-16 Score=177.89 Aligned_cols=142 Identities=20% Similarity=0.191 Sum_probs=127.4
Q ss_pred CcEEecCHHHHHHHHHHHhcCCeeEEEeeecccccCCCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCceEEE
Q 003416 129 PFKLVEEVKDLKELAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVM 208 (821)
Q Consensus 129 ~~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~ 208 (821)
.+.+|++.++|..+|..+...+.+++|||+++.++ .+||+|++.++..|+||+++. +. ++
T Consensus 2 ~~~~I~~~~~l~~~~~~l~~~~~~a~DtEf~r~~t---~l~liQ~~~~~~~~liDpl~~---l~----~~---------- 61 (553)
T PRK14975 2 DMKVILAPEELGAALERLSPAGVVAGDTETTGDDA---AAAAAQEGEEEPRWVWASTAA---LY----PR---------- 61 (553)
T ss_pred CceEEeccchhHHHHHHhccCCceeCCccccCCcc---hhheeeecCCCceEEECchHH---hH----HH----------
Confidence 46789999999999999999999999999998877 899999999999999998753 22 11
Q ss_pred ecchhcHHHHHHHhCCCcCccchhHHHHHhhCCC----CCcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhh
Q 003416 209 HGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE----RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDT 284 (821)
Q Consensus 209 H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~----~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA 284 (821)
| ..+|+.+.++||||+|+|+|+.+ +++|+.|+.+|+++.++|..+.+||. ||++++|+.||+.|+
T Consensus 62 ---------L-~~~Gv~~~~~fDT~LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~~sdw~-rpls~~q~~YAa~Dv 130 (553)
T PRK14975 62 ---------L-LAAGVRVERCHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALS-DPPDEEQLLYAAADA 130 (553)
T ss_pred ---------H-HHCCCccCCCchHHHHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChhhhcccc-ccchHHHHHHHHHHh
Confidence 4 34698888899999999999985 68999999999999999988899996 999999999999999
Q ss_pred HHHHHHHHHHHHHHhcC
Q 003416 285 HYLLYIYDIMKIKLSSM 301 (821)
Q Consensus 285 ~yLL~Lyd~L~~eLee~ 301 (821)
.|++.||..|..+|.+.
T Consensus 131 ~~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 131 DVLLELYAVLADQLNRI 147 (553)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 99999999999999865
No 16
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.67 E-value=1e-15 Score=145.64 Aligned_cols=143 Identities=24% Similarity=0.223 Sum_probs=113.7
Q ss_pred eeEEEeeecccccCCCcEEEEEEEeCCc-eEEEecCCcchhhhHHHHHhhcCCCceEEEecchhcHHHHHHHhCCCcC-c
Q 003416 151 EFAVDLEHNQYRSFLGLTCLMQISTRTE-DFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLC-N 228 (821)
Q Consensus 151 ~IAVDtE~~~~rty~g~LcLIQISt~~~-~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~-n 228 (821)
.+++|+|+.++.++.+.+|++||++.++ +|+|++..... ....|.++|+|+++.||+|++|.|+.+|. ..|+... +
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~~~-~~~~l~~~l~~~~~~kv~~d~K~~~~~L~-~~~~~~~~~ 78 (150)
T cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHDYL-ALELLKPLLEDEKALKVGQNLKYDRGILL-NYFIELRGI 78 (150)
T ss_pred CEEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCccc-CHHHHHHHhcCCCCceeeecHHHHHHHHH-HcCCccCCc
Confidence 3789998877776678999999998754 78887432110 13458899999999999999999999995 4566554 5
Q ss_pred cchhHHHHHhhCCC--CCcHHHHHHHHcCCCCccccccc--cccCCCCCHHHHHHHHHhhHHHHHHHHHHH
Q 003416 229 MFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNA--DWRVRPLPDEMLRYAREDTHYLLYIYDIMK 295 (821)
Q Consensus 229 lFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~S--DW~~RPLs~eql~YAA~DA~yLL~Lyd~L~ 295 (821)
+|||++|+|+|++. +.+|+.|+++|++..+.+..+.. .|..+++..+|+.||+.|+.+++.||+.|.
T Consensus 79 ~~D~~laayLl~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 79 AFDTMLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred chhHHHHHHHhCCCCCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 89999999999985 57999999999998854422222 386688889999999999999999999874
No 17
>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=99.63 E-value=6.1e-15 Score=145.52 Aligned_cols=152 Identities=18% Similarity=0.129 Sum_probs=122.7
Q ss_pred CCeeEEEeeecccccCCCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCceEEEecchhcHHHHHHHhCCCcCc
Q 003416 149 VDEFAVDLEHNQYRSFLGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCN 228 (821)
Q Consensus 149 a~~IAVDtE~~~~rty~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~n 228 (821)
...++||+|+.+..++.+++|+++|+..+.+|+|++.. .......|+++|+++++.||+|++|.|++.|. .+|+.+.+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~~~~~i~~~~-~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~~~~ 80 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGGGAYYIPLEL-ALLDLAALKEWLEDEKIPKVGHDAKRAYVALK-RHGIELAG 80 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCCcEEEEeccc-hHHHHHHHHHHHhCCCCceeccchhHHHHHHH-HCCCcCCC
Confidence 45689999999888888999999999877778887421 10122458899999999999999999999994 58987754
Q ss_pred -cchhHHHHHhhCCCC--CcHHHHHHHHcCCCCcccccccccc---CCCCCHHHHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 229 -MFDTGQASRVLKLER--NSLEYLLHHFCGVNANKEYQNADWR---VRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 229 -lFDTqLAAyLLg~~~--~SLa~LvekyLgv~LdK~~Q~SDW~---~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
+|||++|+|+|++.. ++|..|+.+|++..+.+..+..+|. .++..+.+..|++.|+.+++.||+.|..+|++.+
T Consensus 81 ~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~ 160 (178)
T cd06140 81 VAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEENE 160 (178)
T ss_pred cchhHHHHHHHcCCCCCCCCHHHHHHHHcCCCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 799999999999973 8999999999998865533344452 2444577889999999999999999999998653
No 18
>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=99.49 E-value=8.5e-13 Score=130.90 Aligned_cols=152 Identities=26% Similarity=0.351 Sum_probs=119.3
Q ss_pred hcCCeeEEEeeecccccCCCcEEEEEEEeCCc-eEEEecCC------cc-hhhhHHHHHhhcCCCceEEEecchhcHHHH
Q 003416 147 KSVDEFAVDLEHNQYRSFLGLTCLMQISTRTE-DFVVDTLK------LR-VQVGPYLREVFKDPTKKKVMHGADRDIVWL 218 (821)
Q Consensus 147 ~~a~~IAVDtE~~~~rty~g~LcLIQISt~~~-~yLID~La------l~-~~L~~~L~eLLeDp~IvKV~H~aK~DL~~L 218 (821)
.+...+++|+|..++.++.+.++.++++.... .|+|+... +. ..+...|..+|++..+.+|+|++++|+.+|
T Consensus 3 ~~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l 82 (193)
T cd06139 3 EKAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVL 82 (193)
T ss_pred ccCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHHH
Confidence 35678999999988888888999999998754 66665321 11 123344788899988899999999999999
Q ss_pred HHHhCCCcC-ccchhHHHHHhhCCC--CCcHHHHHHHHcCCCC-------ccccccccccCCCCCHHHHHHHHHhhHHHH
Q 003416 219 QRDFGIYLC-NMFDTGQASRVLKLE--RNSLEYLLHHFCGVNA-------NKEYQNADWRVRPLPDEMLRYAREDTHYLL 288 (821)
Q Consensus 219 ~rd~GI~~~-nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~L-------dK~~Q~SDW~~RPLs~eql~YAA~DA~yLL 288 (821)
. .+|+.+. .+|||++++|+|++. .++|..|+++|++... .|+.+..+|...|+ ..+..||+.|+.+++
T Consensus 83 ~-~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~ 160 (193)
T cd06139 83 A-NHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADITL 160 (193)
T ss_pred H-HCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHHHHHHHHH
Confidence 4 5788765 489999999999985 5899999999998762 12233455655555 668999999999999
Q ss_pred HHHHHHHHHHhc
Q 003416 289 YIYDIMKIKLSS 300 (821)
Q Consensus 289 ~Lyd~L~~eLee 300 (821)
.|+..|..+|.+
T Consensus 161 ~l~~~l~~~l~~ 172 (193)
T cd06139 161 RLYELLKPKLKE 172 (193)
T ss_pred HHHHHHHHHHhh
Confidence 999999999975
No 19
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=99.46 E-value=9.8e-14 Score=117.71 Aligned_cols=68 Identities=35% Similarity=0.586 Sum_probs=62.4
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCccccCHHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHH
Q 003416 352 QLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSII 419 (821)
Q Consensus 352 qlavlraL~aWRD~iAR~~Dep~~~VL~D~~LleLA~~~P~t~~eL~~l~g~~~~~vrr~g~eIL~iI 419 (821)
|++++++|++||+++|++.|+|+++||+|.+|.+||..+|+|.++|.++.|+....+++||++|+++|
T Consensus 1 q~~~~~~L~~~R~~~A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i~g~~~~~~~~~g~~il~~I 68 (68)
T PF00570_consen 1 QLALLKALKEWREELAREEDVPPYRILSDEALLEIAKRLPTSIEELLQIPGMGKRKVRKYGDEILEII 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTSTTCGHHHHHHCHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHccCCCHHHHHHHHHHHHhhC
Confidence 68899999999999999999999999999999999999999999999999999999999999999987
No 20
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=99.44 E-value=4.5e-13 Score=116.96 Aligned_cols=78 Identities=32% Similarity=0.532 Sum_probs=74.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCccccCHHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHhHhccc
Q 003416 350 AQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNAA 427 (821)
Q Consensus 350 ~~qlavlraL~aWRD~iAR~~Dep~~~VL~D~~LleLA~~~P~t~~eL~~l~g~~~~~vrr~g~eIL~iI~~a~~~~~ 427 (821)
+.+++++++|+.||+.+|++.|+|+++||+|.+|++||..+|+|..+|.++.+.....+++|+..|+++|+++.+.+.
T Consensus 2 ~~~~~~~~~L~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~~~~~~~~g~~~~~~i~~~~~~~~ 79 (81)
T smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSPS 79 (81)
T ss_pred hHHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHhccc
Confidence 578999999999999999999999999999999999999999999999999999999999999999999999887654
No 21
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.42 E-value=3.8e-13 Score=153.37 Aligned_cols=174 Identities=21% Similarity=0.270 Sum_probs=138.2
Q ss_pred CCCCcEEecCHHHHHHHH-HHHhcC-CeeEEEeeeccc-ccCCCcEEEEEEEeCCceEEEecCCcch---h-hhHHHHHh
Q 003416 126 EQTPFKLVEEVKDLKELA-AKLKSV-DEFAVDLEHNQY-RSFLGLTCLMQISTRTEDFVVDTLKLRV---Q-VGPYLREV 198 (821)
Q Consensus 126 ~~t~~~lIdT~e~L~~ll-e~L~~a-~~IAVDtE~~~~-rty~g~LcLIQISt~~~~yLID~Lal~~---~-L~~~L~eL 198 (821)
-.+.+.+|+++.+|..++ +.|... -+|++|.||..+ .....++|+|||++.+.+||||.+++.. + +.-.+..+
T Consensus 388 ~~~~i~~V~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~i 467 (617)
T KOG2207|consen 388 WVESIGMVGNEKELRDLLLESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQI 467 (617)
T ss_pred cccceeeeCCHHHHHHHHHHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHH
Confidence 345789999999999988 345444 789999999887 3446789999999999999999887643 1 33457789
Q ss_pred hcCCCceEEEecchhcHHHHHH-----HhCCCc---Ccc-chhHHHHHhhCC-------C--CCcHHHHHHHHcCCCCcc
Q 003416 199 FKDPTKKKVMHGADRDIVWLQR-----DFGIYL---CNM-FDTGQASRVLKL-------E--RNSLEYLLHHFCGVNANK 260 (821)
Q Consensus 199 LeDp~IvKV~H~aK~DL~~L~r-----d~GI~~---~nl-FDTqLAAyLLg~-------~--~~SLa~LvekyLgv~LdK 260 (821)
|+++.|+||+.+..+|++.|++ .+...+ .++ .++-++-.+.+. . ..+|++|...++|..++|
T Consensus 468 f~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnK 547 (617)
T KOG2207|consen 468 FESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNK 547 (617)
T ss_pred ccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhccc
Confidence 9999999999999999999975 233322 222 234444444332 1 478999999999999999
Q ss_pred ccccccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHh
Q 003416 261 EYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 299 (821)
Q Consensus 261 ~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLe 299 (821)
..|.++|..|||...|+.||+.|++.+..+|..+.....
T Consensus 548 teqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 548 TEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred ccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 999999999999999999999999999999998765443
No 22
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.30 E-value=7.3e-11 Score=136.69 Aligned_cols=170 Identities=21% Similarity=0.244 Sum_probs=132.7
Q ss_pred cEEecCHHHHHHHHHHHhcCCeeEEEeeecccccCCCcEEEEEEEeCCceEEEecCC--cchhhhHHHHHhhcCCCceEE
Q 003416 130 FKLVEEVKDLKELAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQISTRTEDFVVDTLK--LRVQVGPYLREVFKDPTKKKV 207 (821)
Q Consensus 130 ~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt~~~~yLID~La--l~~~L~~~L~eLLeDp~IvKV 207 (821)
+..|.+.+.+..++..+.....+++|+|+.+..++...++.+.++..+++++|.... ........|++||+++.+.||
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~a~~~et~~l~~~~~~lvg~s~~~~~~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~kv 82 (593)
T COG0749 3 YGTITDLAVLNAWLTKLNAAANIAFDTETDGLDPHGADLVGLSVASEEEAAYIPLLHGPEQLNVLAALKPLLEDEGIKKV 82 (593)
T ss_pred chhhhHHHHHHHHHHHHhhcccceeeccccccCcccCCeeEEEeeccccceeEeeccchhhhhhHHHHHHHhhCcccchh
Confidence 445666777888888777666699999999998888888888888776655554332 112345679999999999999
Q ss_pred EecchhcHHHHHHHhCCCcCccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCc-------cccccccccCCCCCHHHHH
Q 003416 208 MHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNAN-------KEYQNADWRVRPLPDEMLR 278 (821)
Q Consensus 208 ~H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~Ld-------K~~Q~SDW~~RPLs~eql~ 278 (821)
+|++|.|.+.|+ .+|+..+..||||+|+|+++++ .+++..|+++|++.+.- |+.+.-+....++ +....
T Consensus 83 ~~~~K~d~~~l~-~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~-~~~~~ 160 (593)
T COG0749 83 GQNLKYDYKVLA-NLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKL-EKATE 160 (593)
T ss_pred ccccchhHHHHH-HcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchH-HHHHH
Confidence 999999999995 5786546699999999999987 59999999999987652 3333333333344 56789
Q ss_pred HHHHhhHHHHHHHHHHHHHHhcC
Q 003416 279 YAREDTHYLLYIYDIMKIKLSSM 301 (821)
Q Consensus 279 YAA~DA~yLL~Lyd~L~~eLee~ 301 (821)
|++.|+..+++||..|..+|.+.
T Consensus 161 y~a~~a~~~~~L~~~l~~~l~~~ 183 (593)
T COG0749 161 YAAEDADATLRLESILEPELLKT 183 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhh
Confidence 99999999999999999888765
No 23
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.25 E-value=1.1e-09 Score=133.73 Aligned_cols=167 Identities=18% Similarity=0.116 Sum_probs=120.9
Q ss_pred CcEEecCHHHHHHHHHHHhcCCeeEEEeeecccccCCCcEEEEEEEeCC-c-eEEEecCC---cc-hhhhHHHHHhhcCC
Q 003416 129 PFKLVEEVKDLKELAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQISTRT-E-DFVVDTLK---LR-VQVGPYLREVFKDP 202 (821)
Q Consensus 129 ~~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt~~-~-~yLID~La---l~-~~L~~~L~eLLeDp 202 (821)
.+..|.+.+.+..+++. .....+++ .++..+...+..+.+++.+ . .|+|+... +. ......|+++|+|+
T Consensus 303 ~~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~ 377 (887)
T TIGR00593 303 CAKESEEAAPLANPAEK-AEVGGFVL----ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLNE 377 (887)
T ss_pred cceEeCCHHHHHHHHHh-CcCCeEEE----cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhCC
Confidence 35567777888887765 44456777 3344456778888899864 3 56654210 11 12234588999999
Q ss_pred CceEEEecchhcHHHHHHHhCCCcCc-cchhHHHHHhhCCC-CCcHHHHHHHHcCCCCcccccccccc--CCCCC-HHHH
Q 003416 203 TKKKVMHGADRDIVWLQRDFGIYLCN-MFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWR--VRPLP-DEML 277 (821)
Q Consensus 203 ~IvKV~H~aK~DL~~L~rd~GI~~~n-lFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~SDW~--~RPLs-~eql 277 (821)
.+.||+||+|+|+.+|. .+|+.+.+ +||||+|+|+|+++ .++|+.|+.+|++..+........|. ...++ +.+.
T Consensus 378 ~~~~v~~n~K~d~~~l~-~~gi~~~~~~~Dt~la~yll~~~~~~~l~~la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~ 456 (887)
T TIGR00593 378 QIKKIGHDAKFLMHLLK-REGIELGGVIFDTMLAAYLLDPAQVSTLDTLARRYLVEELILDEKIGGKLAKFAFPPLEEAT 456 (887)
T ss_pred CCcEEEeeHHHHHHHHH-hCCCCCCCcchhHHHHHHHcCCCCCCCHHHHHHHHcCcccccHHHhccCCCCcccccHHHHH
Confidence 99999999999999994 68998865 89999999999986 57999999999997643311111111 11232 5578
Q ss_pred HHHHHhhHHHHHHHHHHHHHHhcC
Q 003416 278 RYAREDTHYLLYIYDIMKIKLSSM 301 (821)
Q Consensus 278 ~YAA~DA~yLL~Lyd~L~~eLee~ 301 (821)
.||+.|+.++++||..|..+|.+.
T Consensus 457 ~ya~~d~~~~~~L~~~l~~~l~~~ 480 (887)
T TIGR00593 457 EYLARRAAATKRLAEELLKELDEN 480 (887)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhc
Confidence 999999999999999999999853
No 24
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=98.85 E-value=6.6e-08 Score=93.44 Aligned_cols=128 Identities=18% Similarity=0.121 Sum_probs=88.5
Q ss_pred CCcEEEEEEEeCCceEEEecCCcchhhhHHHHHhhcCCCceEEEecchhcHHHHHHHhCCCcCc-cchhHHHHHhhCCC-
Q 003416 165 LGLTCLMQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCN-MFDTGQASRVLKLE- 242 (821)
Q Consensus 165 ~g~LcLIQISt~~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~n-lFDTqLAAyLLg~~- 242 (821)
...+..+.+++.++.|+|++-. ... ...|+++|++..+.||+|++|.++.+| +.+|+.+.+ +|||++|+|||++.
T Consensus 17 ~~~~~glal~~~~~~~yi~~~~-~~~-~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~~LAaYLL~p~~ 93 (151)
T cd06128 17 SANLVGLAFAIEGVAAYIPVAH-DYA-LELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDTMLEAYLLDPVA 93 (151)
T ss_pred cCcEEEEEEEcCCCeEEEeCCC-CcC-HHHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhHHHHHHHcCCCC
Confidence 4567778888776677775211 001 234788999999999999999999999 568998765 69999999999996
Q ss_pred C-CcHHHHHHHHcCCCCccccccccccC--CCC-CHHHHHHHHHhhHHHHHHHHHHH
Q 003416 243 R-NSLEYLLHHFCGVNANKEYQNADWRV--RPL-PDEMLRYAREDTHYLLYIYDIMK 295 (821)
Q Consensus 243 ~-~SLa~LvekyLgv~LdK~~Q~SDW~~--RPL-s~eql~YAA~DA~yLL~Lyd~L~ 295 (821)
+ .+|..|+++|++..+-...+...+.. .++ ......|++..+.+++.|++.|.
T Consensus 94 ~~~~l~~la~~yl~~~~~~~~~~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 94 GRHDMDSLAERWLKEKTITFEEIAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CCCCHHHHHHHHcCCCCccHHHHcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3 69999999998876211000111110 011 12223478888888888888764
No 25
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=98.68 E-value=4e-08 Score=115.33 Aligned_cols=71 Identities=23% Similarity=0.313 Sum_probs=67.7
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCCCccccCHHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHH
Q 003416 351 QQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKN 421 (821)
Q Consensus 351 ~qlavlraL~aWRD~iAR~~Dep~~~VL~D~~LleLA~~~P~t~~eL~~l~g~~~~~vrr~g~eIL~iI~~ 421 (821)
.+.++|++|++||+++|++.|+|+++||+|.+|++||+.+|+|.++|.++.|++...+++||+.|+++|+.
T Consensus 520 ~~~~l~~~L~~wR~~~A~~~~~p~~~If~d~~L~~ia~~~P~~~~~l~~i~gv~~~k~~~~G~~~l~~i~~ 590 (591)
T TIGR01389 520 VDNALFEALRELRKEQADEQNVPPYVIFSDSTLREMAEKRPATLNALLKIKGVGQNKLDRYGEAFLEVIRE 590 (591)
T ss_pred cHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhCCCCCCHHHHHHHHHHHHHHHHh
Confidence 34499999999999999999999999999999999999999999999999999999999999999999975
No 26
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=98.15 E-value=5.5e-06 Score=98.13 Aligned_cols=74 Identities=26% Similarity=0.387 Sum_probs=70.2
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCCCccccCHHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHhHh
Q 003416 351 QQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQ 424 (821)
Q Consensus 351 ~qlavlraL~aWRD~iAR~~Dep~~~VL~D~~LleLA~~~P~t~~eL~~l~g~~~~~vrr~g~eIL~iI~~a~~ 424 (821)
.+..+|.+|..||.++|++.++|++.||+|.+|.+||+.+|+|.++|.++.|++..++.+||..++++|+...+
T Consensus 531 ~~~~l~~~Lr~~R~~~a~~~~~~~~~if~d~tL~~ia~~~P~t~~~l~~i~Gvg~~K~~~yg~~~l~~i~~~~~ 604 (607)
T PRK11057 531 YDRKLFAKLRKLRKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGKPFMALIRAHVD 604 (607)
T ss_pred chHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45679999999999999999999999999999999999999999999999999999999999999999988754
No 27
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=97.94 E-value=1.9e-05 Score=97.96 Aligned_cols=72 Identities=19% Similarity=0.313 Sum_probs=67.7
Q ss_pred HHHHHHHHHHHHHHHHHH--cCCCCccccCHHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHhH
Q 003416 352 QLAVVAGLCEWRDVIARA--DDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSM 423 (821)
Q Consensus 352 qlavlraL~aWRD~iAR~--~Dep~~~VL~D~~LleLA~~~P~t~~eL~~l~g~~~~~vrr~g~eIL~iI~~a~ 423 (821)
+..+|.+|.+||.++|++ +++|++.||+|.+|.+||..+|+|.++|.++.|++..++.+||..+|++|+..+
T Consensus 1028 d~~Lfe~Lr~lR~elA~e~~~~vppyvIFsD~TL~eIA~~~P~T~~eLl~I~GVG~~KlekYG~~fL~vI~~~~ 1101 (1195)
T PLN03137 1028 SAILYTALRKLRTALVKEAGDGVMAYHIFGNATLQQISKRIPRTKEELLEINGLGKAKVSKYGDRLLETIESTI 1101 (1195)
T ss_pred cHHHHHHHHHHHHHHHHhhhcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCccHHHHHHHHHHHHHHHHHHH
Confidence 346899999999999999 699999999999999999999999999999999999999999999999997654
No 28
>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=97.85 E-value=8e-05 Score=68.06 Aligned_cols=73 Identities=18% Similarity=0.236 Sum_probs=55.2
Q ss_pred eEEEeeecccccCCCcEEEEEEEeC--CceEEEecCCcchhhhHHHHHhhcCCC-ceEEEecchhcHHHHHHHhCC----
Q 003416 152 FAVDLEHNQYRSFLGLTCLMQISTR--TEDFVVDTLKLRVQVGPYLREVFKDPT-KKKVMHGADRDIVWLQRDFGI---- 224 (821)
Q Consensus 152 IAVDtE~~~~rty~g~LcLIQISt~--~~~yLID~Lal~~~L~~~L~eLLeDp~-IvKV~H~aK~DL~~L~rd~GI---- 224 (821)
+++|+|+.+.+++...+|++|++.. +..|++| +.+++.+.. .++|+|++..|+..|.+.+..
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~~~-----------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~ 69 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAVID-----------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLK 69 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEEeh-----------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCC
Confidence 5799999999999999999999876 4567766 446676655 678999999999887655432
Q ss_pred ---CcCccchhHHH
Q 003416 225 ---YLCNMFDTGQA 235 (821)
Q Consensus 225 ---~~~nlFDTqLA 235 (821)
...+++||+.+
T Consensus 70 ~p~~~~~~lDT~~l 83 (96)
T cd06125 70 YPLLAGSWIDTIKL 83 (96)
T ss_pred CCCcCCcEEEehHH
Confidence 12346777755
No 29
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=97.76 E-value=5.3e-05 Score=82.65 Aligned_cols=127 Identities=21% Similarity=0.256 Sum_probs=97.6
Q ss_pred CCCcEEEEEEEeC-CceEEEecCCcchhhhHHHHHhhcCCCceEEEecchhcHHHHHH-HhCCCcCccchhHHHH-HhhC
Q 003416 164 FLGLTCLMQISTR-TEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQR-DFGIYLCNMFDTGQAS-RVLK 240 (821)
Q Consensus 164 y~g~LcLIQISt~-~~~yLID~Lal~~~L~~~L~eLLeDp~IvKV~H~aK~DL~~L~r-d~GI~~~nlFDTqLAA-yLLg 240 (821)
+.+....+||+.. ..++||...... .+...|+.+|+|++..+|+-+.++|...|.+ .+++.+..+.|+..-+ -.||
T Consensus 145 ~~P~~~~lqlcV~en~C~I~ql~~~~-~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g 223 (319)
T KOG4373|consen 145 SDPPPDTLQLCVGENRCLIIQLIHCK-RIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLG 223 (319)
T ss_pred cCCCcchhhhhhcccceeeEEeeccc-cchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhhc
Confidence 3456788999998 567777544332 3556788899999999999999999988877 8888887777776432 3455
Q ss_pred CC--CCcHHHHHHH---HcC--CCCccccccccccCCCCCHHHHHHHHHhhHHHHHHH
Q 003416 241 LE--RNSLEYLLHH---FCG--VNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 241 ~~--~~SLa~Lvek---yLg--v~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Ly 291 (821)
.. .-+...|+.. +.| +.+++.-+.+||...||+.+|+.||+.||+....||
T Consensus 224 ~~~~~~s~e~i~~~~~~~~~~~v~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 224 GSMPNDSFEEIVSETLGYYGKDVRLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred cCccCccHHHHHHHHhhccccccccChhcccccceeeeccHHHHHHHHhHHHHHHHHH
Confidence 42 2444555554 444 566777899999999999999999999999999998
No 30
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=97.59 E-value=0.00011 Score=86.42 Aligned_cols=72 Identities=24% Similarity=0.311 Sum_probs=68.4
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCccccCHHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHhH
Q 003416 352 QLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSM 423 (821)
Q Consensus 352 qlavlraL~aWRD~iAR~~Dep~~~VL~D~~LleLA~~~P~t~~eL~~l~g~~~~~vrr~g~eIL~iI~~a~ 423 (821)
...+|.+|..||-++|++.|+||+.||+|.+|.++|+.+|.+..+|..+.|++...+.+||..+++.|.+..
T Consensus 517 ~~~lf~~lr~~r~~~a~~~~vp~~vif~d~tl~~ma~~~p~~~~~~~~i~gvg~~k~~~yg~~fl~~i~~~~ 588 (590)
T COG0514 517 DRDLFERLRALRKEIADEENVPPYVVFSDATLKEMAEKQPQSADELLSINGVGEAKLERYGQAFLAVIQAHA 588 (590)
T ss_pred cHHHHHHHHHHHHHhhhhhcCCceEEecchHHHHHHHHcCCCHHHHHHhcCCcccchhhccHHHHHHHHHhc
Confidence 556999999999999999999999999999999999999999999999999999999999999999998754
No 31
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.58 E-value=0.055 Score=59.83 Aligned_cols=135 Identities=19% Similarity=0.160 Sum_probs=86.8
Q ss_pred CCeeEEEeeecccccCCCcEEEEEEEe--CC-c-----eEEEecCC------c---c----------hhhhHHHHHhhcC
Q 003416 149 VDEFAVDLEHNQYRSFLGLTCLMQIST--RT-E-----DFVVDTLK------L---R----------VQVGPYLREVFKD 201 (821)
Q Consensus 149 a~~IAVDtE~~~~rty~g~LcLIQISt--~~-~-----~yLID~La------l---~----------~~L~~~L~eLLeD 201 (821)
..+++||+|+.+.......+|-|.+.. .+ . ..+|.|-. + . .++...|..++.+
T Consensus 15 ~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~l~~ 94 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRG 94 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHHHHcCC
Confidence 468999999998876555554333221 11 1 13444311 1 0 0122345556654
Q ss_pred CCceEEEecchhcHHHHHHHh---CCCc--CccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCccccccccccCCCCCH
Q 003416 202 PTKKKVMHGADRDIVWLQRDF---GIYL--CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADWRVRPLPD 274 (821)
Q Consensus 202 p~IvKV~H~aK~DL~~L~rd~---GI~~--~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~ 274 (821)
-+.|.|++.+|+.+|.+.+ |+.+ ..++||+..++.+.++ .+.|..|+++ +|+.....
T Consensus 95 --~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~-~gi~~~~~------------- 158 (313)
T PRK06063 95 --RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAH-WGVPQQRP------------- 158 (313)
T ss_pred --CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHH-cCCCCCCC-------------
Confidence 3579999999999987543 4432 3478999888877653 7899999976 46543211
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 275 EMLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 275 eql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
.-|..||..+..|+..|..++.+.+
T Consensus 159 ---H~Al~DA~ata~l~~~ll~~~~~~~ 183 (313)
T PRK06063 159 ---HDALDDARVLAGILRPSLERARERD 183 (313)
T ss_pred ---CCcHHHHHHHHHHHHHHHHHHHhcC
Confidence 2277899999999999988887654
No 32
>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=96.47 E-value=0.076 Score=54.86 Aligned_cols=85 Identities=15% Similarity=0.104 Sum_probs=60.3
Q ss_pred CceEEEecchhcHHHHHHH---hCCCc-----CccchhHHHHHhhCCCCCcHHHHHHHHcCCCCccccccccccCCCCCH
Q 003416 203 TKKKVMHGADRDIVWLQRD---FGIYL-----CNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPD 274 (821)
Q Consensus 203 ~IvKV~H~aK~DL~~L~rd---~GI~~-----~nlFDTqLAAyLLg~~~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~ 274 (821)
.-+-|+|++.+|+.+|.+. +|... ..++||...++.+. +..+|..|++.| |+... .
T Consensus 105 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~-~~~~L~~l~~~~-gi~~~--------------~ 168 (200)
T TIGR01298 105 RAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAY-GQTVLAKACQAA-GXDFD--------------S 168 (200)
T ss_pred CCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHc-CcccHHHHHHHc-CCCcc--------------c
Confidence 3467999999999998643 34321 23789998887654 346899988864 55431 1
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHHHhcCCC
Q 003416 275 EMLRYAREDTHYLLYIYDIMKIKLSSMPK 303 (821)
Q Consensus 275 eql~YAA~DA~yLL~Lyd~L~~eLee~G~ 303 (821)
.+..-|..||..+..|+..|..++.+.+.
T Consensus 169 ~~~H~Al~Da~ata~lf~~l~~~~~~~~~ 197 (200)
T TIGR01298 169 TQAHSALYDTEKTAELFCEIVNRWKRLGG 197 (200)
T ss_pred cchhhhHHhHHHHHHHHHHHHHHHHHccC
Confidence 12334788999999999999999987663
No 33
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.38 E-value=0.093 Score=55.48 Aligned_cols=137 Identities=15% Similarity=0.173 Sum_probs=83.6
Q ss_pred hcCCeeEEEeeecccccCCCcEEE---EEEEe-CC----ceEEEecCC-c----------ch-hh-------hHHHHHh-
Q 003416 147 KSVDEFAVDLEHNQYRSFLGLTCL---MQIST-RT----EDFVVDTLK-L----------RV-QV-------GPYLREV- 198 (821)
Q Consensus 147 ~~a~~IAVDtE~~~~rty~g~LcL---IQISt-~~----~~yLID~La-l----------~~-~L-------~~~L~eL- 198 (821)
.....++||+|+.+..+....++- +.+.. +. ..++|+|-. + .. .+ .+.|.++
T Consensus 4 ~~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~ 83 (232)
T PRK07942 4 HPGPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEIA 83 (232)
T ss_pred ccCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHHH
Confidence 345789999999998765555432 22221 11 235676521 1 00 01 1122222
Q ss_pred ------hcCCCceEEEecchhcHHHHHHHh---CCC---cCccchhHHHHHhhCC---CCCcHHHHHHHHcCCCCccccc
Q 003416 199 ------FKDPTKKKVMHGADRDIVWLQRDF---GIY---LCNMFDTGQASRVLKL---ERNSLEYLLHHFCGVNANKEYQ 263 (821)
Q Consensus 199 ------LeDp~IvKV~H~aK~DL~~L~rd~---GI~---~~nlFDTqLAAyLLg~---~~~SLa~LvekyLgv~LdK~~Q 263 (821)
+.. ..+.|+|++.+|+.+|.+.+ |+. ..+++||...++.+.. ++++|..|++. +|+.....
T Consensus 84 ~~l~~~~~~-~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~-~gi~~~~a-- 159 (232)
T PRK07942 84 DALREAWAR-GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEH-YGVRLDNA-- 159 (232)
T ss_pred HHHHHHhhc-CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHH-cCCCCCCC--
Confidence 222 34569999999998886543 432 2357899988775543 36899999977 46654321
Q ss_pred cccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHhcC
Q 003416 264 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSM 301 (821)
Q Consensus 264 ~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee~ 301 (821)
.-|..||..+..|+..|..++.+.
T Consensus 160 --------------H~Al~Da~ata~l~~~l~~~~~~l 183 (232)
T PRK07942 160 --------------HEATADALAAARVAWALARRFPEL 183 (232)
T ss_pred --------------CChHHHHHHHHHHHHHHHHHHHHh
Confidence 127789999999999987766533
No 34
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.33 E-value=0.071 Score=57.05 Aligned_cols=133 Identities=20% Similarity=0.250 Sum_probs=82.6
Q ss_pred HhcCCeeEEEeeecccccCCCcEEEEEEEe----CC-----ceEEEecCC-c----------ch----------hhhHHH
Q 003416 146 LKSVDEFAVDLEHNQYRSFLGLTCLMQIST----RT-----EDFVVDTLK-L----------RV----------QVGPYL 195 (821)
Q Consensus 146 L~~a~~IAVDtE~~~~rty~g~LcLIQISt----~~-----~~yLID~La-l----------~~----------~L~~~L 195 (821)
|+....+.||+|+.+.......+ |||+. .+ ...+|.|-. + .. ++.+.+
T Consensus 4 l~~~~~v~~D~ETTGl~~~~d~I--IEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~ 81 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDVKKDRI--IEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQI 81 (250)
T ss_pred ccCCcEEEEEEeCCCCCCCCCeE--EEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHH
Confidence 44568999999999876544333 44432 11 123454321 0 00 122234
Q ss_pred HHhhcCCCceEEEecchhcHHHHHHHh---CCCc----CccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCccccccccc
Q 003416 196 REVFKDPTKKKVMHGADRDIVWLQRDF---GIYL----CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADW 267 (821)
Q Consensus 196 ~eLLeDp~IvKV~H~aK~DL~~L~rd~---GI~~----~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~SDW 267 (821)
..++.+. -..|+|++.+|+.+|.+.+ |+.. ..++||+..++.++.. .++|..|++.| |+.....
T Consensus 82 ~~fl~~~-~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~-g~~~~~a------ 153 (250)
T PRK06310 82 KGFFKEG-DYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHF-NVPYDGN------ 153 (250)
T ss_pred HHHhCCC-CEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHC-CCCCCCC------
Confidence 4555543 4579999999999886533 4432 3489999888876543 68999998775 6543211
Q ss_pred cCCCCCHHHHHHHHHhhHHHHHHHHHHHHHH
Q 003416 268 RVRPLPDEMLRYAREDTHYLLYIYDIMKIKL 298 (821)
Q Consensus 268 ~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL 298 (821)
.=|..||..+..|+..|..++
T Consensus 154 ----------H~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 154 ----------HRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred ----------cChHHHHHHHHHHHHHHHHhc
Confidence 227889999999988876443
No 35
>PRK05168 ribonuclease T; Provisional
Probab=96.18 E-value=0.16 Score=52.82 Aligned_cols=149 Identities=17% Similarity=0.220 Sum_probs=89.4
Q ss_pred HHHHHHHHHhcCCeeEEEeeecccccCCCcE---EEEEEEeC--C-----c--eEEEecC---Ccc----------hh--
Q 003416 138 DLKELAAKLKSVDEFAVDLEHNQYRSFLGLT---CLMQISTR--T-----E--DFVVDTL---KLR----------VQ-- 190 (821)
Q Consensus 138 ~L~~lle~L~~a~~IAVDtE~~~~rty~g~L---cLIQISt~--~-----~--~yLID~L---al~----------~~-- 190 (821)
++.-+-..+....+++||+|+.+.......+ +.+.+... + . ..+|.|. .+. .+
T Consensus 6 ~~~~~~~~~~~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~ 85 (211)
T PRK05168 6 DLNPLKDRFRGFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNP 85 (211)
T ss_pred ccchHHHHhcCCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhh
Confidence 3455556777888999999999887655443 22222211 1 1 1345541 110 01
Q ss_pred ------hhHHHHH---hhc----C---CCceEEEecchhcHHHHHHH---hCCC-----cCccchhHHHHHhhCCCCCcH
Q 003416 191 ------VGPYLRE---VFK----D---PTKKKVMHGADRDIVWLQRD---FGIY-----LCNMFDTGQASRVLKLERNSL 246 (821)
Q Consensus 191 ------L~~~L~e---LLe----D---p~IvKV~H~aK~DL~~L~rd---~GI~-----~~nlFDTqLAAyLLg~~~~SL 246 (821)
..+.+.+ ++. + ...+.|+|++.+|+..|.+. +|+. +..++||...++.+. +..+|
T Consensus 86 ~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~-~~~~L 164 (211)
T PRK05168 86 LRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLAL-GQTVL 164 (211)
T ss_pred hhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHc-CCCCH
Confidence 1111222 221 1 24578999999999887643 4442 124789987776553 34689
Q ss_pred HHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 247 EYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 247 a~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
..++++| |+.+... . ..-|..||..+..||..|..++.+.+
T Consensus 165 ~~l~~~~-gl~~~~~-~-------------~H~Al~DA~ata~l~~~l~~~~~~~~ 205 (211)
T PRK05168 165 AKACQAA-GIEFDNK-E-------------AHSALYDTEKTAELFCEIVNRWKRLG 205 (211)
T ss_pred HHHHHHC-CCCCCCC-C-------------CCChHHHHHHHHHHHHHHHHHHHHcc
Confidence 9988864 6543211 1 12278899999999999999988765
No 36
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=96.14 E-value=0.052 Score=53.97 Aligned_cols=79 Identities=19% Similarity=0.129 Sum_probs=54.2
Q ss_pred HHHhhcCCCceEEEecchhcHHHHHHHhCCCcCccchhHHHHHhhCC-----CCCcHHHHHHHHcCCCCccccccccccC
Q 003416 195 LREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKL-----ERNSLEYLLHHFCGVNANKEYQNADWRV 269 (821)
Q Consensus 195 L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~-----~~~SLa~LvekyLgv~LdK~~Q~SDW~~ 269 (821)
|..++.+ ..+-|+|++.+|+.+|.. ....+.||...++.+.+ .+++|..|+++|+|..+...+..-
T Consensus 77 ~~~~i~~-~~vlVgHn~~fD~~fL~~----~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H---- 147 (161)
T cd06137 77 LWKFIDP-DTILVGHSLQNDLDALRM----IHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGH---- 147 (161)
T ss_pred HHHhcCC-CcEEEeccHHHHHHHHhC----cCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCCC----
Confidence 4455554 245799999999999953 23458899988876554 358999999999997664311111
Q ss_pred CCCCHHHHHHHHHhhHHHHHHH
Q 003416 270 RPLPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 270 RPLs~eql~YAA~DA~yLL~Ly 291 (821)
+ |..||..+..||
T Consensus 148 ~---------A~~DA~at~~l~ 160 (161)
T cd06137 148 D---------SLEDALAAREVV 160 (161)
T ss_pred C---------cHHHHHHHHHHh
Confidence 1 557777777765
No 37
>PRK07740 hypothetical protein; Provisional
Probab=96.09 E-value=0.15 Score=54.44 Aligned_cols=89 Identities=17% Similarity=0.194 Sum_probs=63.9
Q ss_pred HHHhhcCCCceEEEecchhcHHHHHHH----hCCCc-CccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCccccccccc
Q 003416 195 LREVFKDPTKKKVMHGADRDIVWLQRD----FGIYL-CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADW 267 (821)
Q Consensus 195 L~eLLeDp~IvKV~H~aK~DL~~L~rd----~GI~~-~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~SDW 267 (821)
|..++.+ -..|+|++..|+.+|.+. ++... ..++||+..++.+.+. .++|..|+.. +|+.....
T Consensus 135 f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~-~gi~~~~~------ 205 (244)
T PRK07740 135 FYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAY-YGIPIPRR------ 205 (244)
T ss_pred HHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHH-CCcCCCCC------
Confidence 3344443 357899999999887543 23333 3589999888877654 6899999864 67655321
Q ss_pred cCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 268 RVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 268 ~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
.-|..||..+..|+..+..++.+.|
T Consensus 206 ----------H~Al~Da~ata~l~~~ll~~~~~~~ 230 (244)
T PRK07740 206 ----------HHALGDALMTAKLWAILLVEAQQRG 230 (244)
T ss_pred ----------CCcHHHHHHHHHHHHHHHHHHHHcC
Confidence 1277899999999999999888765
No 38
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.09 E-value=0.1 Score=57.84 Aligned_cols=130 Identities=18% Similarity=0.237 Sum_probs=80.8
Q ss_pred CCeeEEEeeecccccCCCcEEEEEEEe---CCc------eEEEecCC-----------cch----------hhhHHHHHh
Q 003416 149 VDEFAVDLEHNQYRSFLGLTCLMQIST---RTE------DFVVDTLK-----------LRV----------QVGPYLREV 198 (821)
Q Consensus 149 a~~IAVDtE~~~~rty~g~LcLIQISt---~~~------~yLID~La-----------l~~----------~L~~~L~eL 198 (821)
..++++|+|+.+..+..+. +|||+. .+. ..+|.|-. +.. ++.+.|..+
T Consensus 8 ~~~Vv~DlETTGl~p~~~e--IIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f~~f 85 (313)
T PRK06807 8 LDYVVIDFETTGFNPYNDK--IIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAF 85 (313)
T ss_pred CCEEEEEEECCCCCCCCCe--EEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHHHHH
Confidence 3689999999887665444 455543 111 12333210 000 122334455
Q ss_pred hcCCCceEEEecchhcHHHHHHHh---CCC-c-CccchhHHHHHhhCC--CCCcHHHHHHHHcCCCCccccccccccCCC
Q 003416 199 FKDPTKKKVMHGADRDIVWLQRDF---GIY-L-CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNADWRVRP 271 (821)
Q Consensus 199 LeDp~IvKV~H~aK~DL~~L~rd~---GI~-~-~nlFDTqLAAyLLg~--~~~SLa~LvekyLgv~LdK~~Q~SDW~~RP 271 (821)
+.+ .+ -|+|++.+|+.+|.+.+ |+. + ..++||+..++.+.+ +.++|..|++. +|+.. + .
T Consensus 86 l~~-~~-lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~-lgi~~-~---~------- 151 (313)
T PRK06807 86 LHT-NV-IVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRM-LGIRL-S---S------- 151 (313)
T ss_pred HcC-Ce-EEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHH-cCCCC-C---C-------
Confidence 554 33 48999999999997654 442 2 348899987765544 36899999865 56543 1 1
Q ss_pred CCHHHHHHHHHhhHHHHHHHHHHHHHHhc
Q 003416 272 LPDEMLRYAREDTHYLLYIYDIMKIKLSS 300 (821)
Q Consensus 272 Ls~eql~YAA~DA~yLL~Lyd~L~~eLee 300 (821)
.=|..||.++..||..|...+..
T Consensus 152 ------H~Al~DA~~ta~l~~~l~~~~~~ 174 (313)
T PRK06807 152 ------HNAFDDCITCAAVYQKCASIEEE 174 (313)
T ss_pred ------cChHHHHHHHHHHHHHHHHhhhh
Confidence 22778999999999998877743
No 39
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.07 E-value=0.089 Score=56.18 Aligned_cols=86 Identities=27% Similarity=0.394 Sum_probs=58.4
Q ss_pred HHHhhcCCCceEEEecchhcHHHHHHHh---CCC------cCccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCcccccc
Q 003416 195 LREVFKDPTKKKVMHGADRDIVWLQRDF---GIY------LCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQN 264 (821)
Q Consensus 195 L~eLLeDp~IvKV~H~aK~DL~~L~rd~---GI~------~~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~ 264 (821)
|.+++.+. ..|+|++.+|+..|.+.+ |.. .+.++||...++.+-++ +++|..|+++| |+...
T Consensus 80 f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~~~~-gi~~~----- 151 (240)
T PRK05711 80 FLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRY-GIDNS----- 151 (240)
T ss_pred HHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHHHHC-CCCCC-----
Confidence 44555543 358999999998886543 321 14588999888766555 68999999876 54321
Q ss_pred ccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHH
Q 003416 265 ADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 297 (821)
Q Consensus 265 SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 297 (821)
.|.+ .=|..||..+..||..|...
T Consensus 152 ----~r~~-----H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 152 ----HRTL-----HGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred ----CCCC-----CCHHHHHHHHHHHHHHHHCc
Confidence 1111 23788999999999887643
No 40
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.06 E-value=0.0037 Score=69.79 Aligned_cols=127 Identities=22% Similarity=0.257 Sum_probs=85.6
Q ss_pred EEEEEEEeCCceEEEecCCcchh-hhHHHHHhhcCCCceEEEecchhcHHHHHHHhCCCcCccchhHHHHHhhCCC----
Q 003416 168 TCLMQISTRTEDFVVDTLKLRVQ-VGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE---- 242 (821)
Q Consensus 168 LcLIQISt~~~~yLID~Lal~~~-L~~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~---- 242 (821)
+.+|+|+++...|++|.+.-+.- +..-.+..++...+ |. +++.++..+...|++.+.+++|||+|..++.+.
T Consensus 213 ~~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~sLve~~e~gr 289 (458)
T KOG2405|consen 213 ATYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIASSLVEPSEYGR 289 (458)
T ss_pred hhhhhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHHHHhhhHHhcc
Confidence 34589999999999996543211 11223455655443 45 999999999999999999999999999987642
Q ss_pred CCcHHHHHH--------HHcCCCCc------cc-c-ccccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHH
Q 003416 243 RNSLEYLLH--------HFCGVNAN------KE-Y-QNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 297 (821)
Q Consensus 243 ~~SLa~Lve--------kyLgv~Ld------K~-~-Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 297 (821)
++....++- .|++.... +. . ....|.+||.++.+..-+..||++|+.+++.|.+.
T Consensus 290 r~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a~ 360 (458)
T KOG2405|consen 290 RHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVAV 360 (458)
T ss_pred cCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhhh
Confidence 222222211 12222111 11 1 22369999999999999999999999988666543
No 41
>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=96.03 E-value=0.14 Score=50.44 Aligned_cols=84 Identities=25% Similarity=0.386 Sum_probs=56.1
Q ss_pred HHHHhhcCCCceEEEecchhcHHHHHHHh---CCC-----cCccchhHHHHHhhCC-CCCcHHHHHHHHcCCCCcccccc
Q 003416 194 YLREVFKDPTKKKVMHGADRDIVWLQRDF---GIY-----LCNMFDTGQASRVLKL-ERNSLEYLLHHFCGVNANKEYQN 264 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~aK~DL~~L~rd~---GI~-----~~nlFDTqLAAyLLg~-~~~SLa~LvekyLgv~LdK~~Q~ 264 (821)
.|..++.+ . ..|+|++.+|+.+|.+.+ |+. ...++||+..++.+.+ ..++|..|+++| |+.....
T Consensus 74 ~l~~~l~~-~-~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~-~i~~~~~--- 147 (167)
T cd06131 74 EFLDFIRG-A-ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRF-GIDNSHR--- 147 (167)
T ss_pred HHHHHHCC-C-eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHC-CCCCCCC---
Confidence 45556655 2 358999999999886543 331 2347999977766554 368999999886 5443210
Q ss_pred ccccCCCCCHHHHHHHHHhhHHHHHHHHHH
Q 003416 265 ADWRVRPLPDEMLRYAREDTHYLLYIYDIM 294 (821)
Q Consensus 265 SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L 294 (821)
...-|..||..+..||..|
T Consensus 148 -----------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 148 -----------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred -----------CCCChHHHHHHHHHHHHHh
Confidence 1133788999998888665
No 42
>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=95.89 E-value=0.064 Score=53.30 Aligned_cols=82 Identities=21% Similarity=0.136 Sum_probs=52.2
Q ss_pred HHHHHhhcCCCceEEEecchhcHHHHHHHhCCCcCccchhHH---HHHhhCCC---CCcHHHHHHHHcCCCCcccccccc
Q 003416 193 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQ---ASRVLKLE---RNSLEYLLHHFCGVNANKEYQNAD 266 (821)
Q Consensus 193 ~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~nlFDTqL---AAyLLg~~---~~SLa~LvekyLgv~LdK~~Q~SD 266 (821)
+.|.+++.+ -+-|+|++++|+.+|... ....++.||.. +.+..+++ .++|..|+++|++..+...++..
T Consensus 69 ~~l~~~l~~--~vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H- 143 (157)
T cd06149 69 KEILKILKG--KVVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGH- 143 (157)
T ss_pred HHHHHHcCC--CEEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCc-
Confidence 345566654 467999999999998432 22234678854 22222222 58999999999876554322211
Q ss_pred ccCCCCCHHHHHHHHHhhHHHHHHH
Q 003416 267 WRVRPLPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 267 W~~RPLs~eql~YAA~DA~yLL~Ly 291 (821)
| |..||..+..||
T Consensus 144 ---~---------Al~DA~at~~l~ 156 (157)
T cd06149 144 ---S---------SVEDARATMELY 156 (157)
T ss_pred ---C---------cHHHHHHHHHHh
Confidence 2 567888887776
No 43
>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=95.88 E-value=0.13 Score=54.26 Aligned_cols=86 Identities=28% Similarity=0.350 Sum_probs=59.0
Q ss_pred HHHHhhcCCCceEEEecchhcHHHHHHH---hCC--C-c---CccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCccccc
Q 003416 194 YLREVFKDPTKKKVMHGADRDIVWLQRD---FGI--Y-L---CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQ 263 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~aK~DL~~L~rd---~GI--~-~---~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q 263 (821)
.|.+++.+ ...|.|++.+|+.+|.+. +|. . + +.++||+..++.+-++ +++|..|+++| |+...
T Consensus 75 ~f~~fi~~--~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~-gi~~~---- 147 (225)
T TIGR01406 75 EFLDFIGG--SELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRF-KVDNS---- 147 (225)
T ss_pred HHHHHhCC--CEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhc-CCCCC----
Confidence 34456654 345899999999998654 342 2 1 4589999888766555 68999999986 54321
Q ss_pred cccccCCCCCHHHHHHHHHhhHHHHHHHHHHHH
Q 003416 264 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKI 296 (821)
Q Consensus 264 ~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~ 296 (821)
.|.. .=|..||..+..||..|..
T Consensus 148 -----~r~~-----H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 148 -----HRTL-----HGALLDAHLLAEVYLALTG 170 (225)
T ss_pred -----CCCC-----cCHHHHHHHHHHHHHHHHc
Confidence 1111 2278999999999988754
No 44
>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=95.80 E-value=0.033 Score=54.55 Aligned_cols=141 Identities=16% Similarity=0.218 Sum_probs=73.6
Q ss_pred eEEEeeecccccCCCcEEEEEEEeC--Cc-eEEEecCCcchh----hhHHHHHhhcCCCceEEEecchhcHHHHHHHh--
Q 003416 152 FAVDLEHNQYRSFLGLTCLMQISTR--TE-DFVVDTLKLRVQ----VGPYLREVFKDPTKKKVMHGADRDIVWLQRDF-- 222 (821)
Q Consensus 152 IAVDtE~~~~rty~g~LcLIQISt~--~~-~yLID~Lal~~~----L~~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~-- 222 (821)
+.+|+|+.+..+..+.+.++.+... +. .+++........ +...+ .++.....+.++|+..+|+..|.+.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~-~~l~~~~~iv~yng~~FD~p~L~~~~~~ 79 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFF-ELLDEADNIVTYNGKNFDIPFLKRRAKR 79 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH---HHHHTT--EEESSTTTTHHHHHHHHH-H
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHH-HHHhcCCeEEEEeCcccCHHHHHHHHHH
Confidence 4689999987665666777777752 32 223332222211 22222 45666667767777889999987655
Q ss_pred -CCC-cCccchhHHHHHhhCCCCCcHHHHHHHHcCCCCcc----ccc----ccccc---CCCCCHHHHHHHHHhhHHHHH
Q 003416 223 -GIY-LCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANK----EYQ----NADWR---VRPLPDEMLRYAREDTHYLLY 289 (821)
Q Consensus 223 -GI~-~~nlFDTqLAAyLLg~~~~SLa~LvekyLgv~LdK----~~Q----~SDW~---~RPLs~eql~YAA~DA~yLL~ 289 (821)
++. ..+.+|++..++-....+++|..|... +|+.-.. +.+ ...|. .....+.++.|...|+..+..
T Consensus 80 ~~~~~~~~~iDl~~~~~~~~~~~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~Dv~~~~~ 158 (164)
T PF13482_consen 80 YGLPPPFNHIDLLKIIKKHFLESYSLKNVEKF-LGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNEDDVRATRR 158 (164)
T ss_dssp HHH--GGGEEEHHHHHT-TTSCCTT--SHHH------------HHHHHHHHHH---TTGGTS--HHHHHHHHHHHHHHHH
T ss_pred cCCCcccchhhHHHHHHhccCCCCCHHHHhhh-cccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 222 355889998876444466788888766 6655431 111 01121 123448899999999999999
Q ss_pred HHHHH
Q 003416 290 IYDIM 294 (821)
Q Consensus 290 Lyd~L 294 (821)
||+.|
T Consensus 159 L~~~l 163 (164)
T PF13482_consen 159 LYEWL 163 (164)
T ss_dssp HHHHH
T ss_pred HHHHh
Confidence 99876
No 45
>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=95.76 E-value=0.046 Score=53.77 Aligned_cols=80 Identities=20% Similarity=0.208 Sum_probs=54.5
Q ss_pred HHHHHhhcCCCceEEEecchhcHHHHHHHhCCCcCccchhHHHHHhhCC---CCCcHHHHHHHHcCCCCccccccccccC
Q 003416 193 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKL---ERNSLEYLLHHFCGVNANKEYQNADWRV 269 (821)
Q Consensus 193 ~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~---~~~SLa~LvekyLgv~LdK~~Q~SDW~~ 269 (821)
+.|..++.+ . +.|+|++.+|+.+|. .......++||.....+... ..++|+.|+++|+|+.+....
T Consensus 69 ~~l~~~l~~-~-vlVgHn~~fD~~~L~--~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~------- 137 (152)
T cd06144 69 KKVAELLKG-R-ILVGHALKNDLKVLK--LDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGE------- 137 (152)
T ss_pred HHHHHHhCC-C-EEEEcCcHHHHHHhc--CcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCC-------
Confidence 345567765 4 459999999999994 33333457888765444432 368999999999997654211
Q ss_pred CCCCHHHHHHHHHhhHHHHHHH
Q 003416 270 RPLPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 270 RPLs~eql~YAA~DA~yLL~Ly 291 (821)
.-|..||..+..||
T Consensus 138 --------H~Al~DA~at~~l~ 151 (152)
T cd06144 138 --------HSSVEDARAAMRLY 151 (152)
T ss_pred --------cCcHHHHHHHHHHh
Confidence 11667888888876
No 46
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=95.70 E-value=0.16 Score=57.55 Aligned_cols=137 Identities=18% Similarity=0.223 Sum_probs=83.4
Q ss_pred HhcCCeeEEEeeecccccCCCcEEEEEEEe---C-C------ceEEEecCC------cc-------------hhhhHHHH
Q 003416 146 LKSVDEFAVDLEHNQYRSFLGLTCLMQIST---R-T------EDFVVDTLK------LR-------------VQVGPYLR 196 (821)
Q Consensus 146 L~~a~~IAVDtE~~~~rty~g~LcLIQISt---~-~------~~yLID~La------l~-------------~~L~~~L~ 196 (821)
+....+++||+|+.++.+... ++|+|+. . + ...+|.|-. +. .++.+.|.
T Consensus 43 ~~~~~fVvlDiETTGLdp~~d--rIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~ 120 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTS--RLITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLD 120 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCC--eEEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHH
Confidence 445689999999999877654 4444431 1 1 123454321 10 02334455
Q ss_pred HhhcCCCceEEEecchhcHHHHHHHh-------------------------------CCCc-CccchhHHHHHhhCCC--
Q 003416 197 EVFKDPTKKKVMHGADRDIVWLQRDF-------------------------------GIYL-CNMFDTGQASRVLKLE-- 242 (821)
Q Consensus 197 eLLeDp~IvKV~H~aK~DL~~L~rd~-------------------------------GI~~-~nlFDTqLAAyLLg~~-- 242 (821)
+++.+ .+.|+|++.+|+..|...+ ++.+ ..++||.-.++.+.+.
T Consensus 121 ~fL~g--~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~ 198 (377)
T PRK05601 121 RLIDG--RTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALD 198 (377)
T ss_pred HHhCC--CEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCC
Confidence 66765 3579999999999886543 1122 2489999999888764
Q ss_pred CCcHHHHHHHHcCCCCccc---cccccccCCCCCHHHHHHHHHhhHHHHHHHHHH
Q 003416 243 RNSLEYLLHHFCGVNANKE---YQNADWRVRPLPDEMLRYAREDTHYLLYIYDIM 294 (821)
Q Consensus 243 ~~SLa~LvekyLgv~LdK~---~Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L 294 (821)
.+.|..|+++ +|+..+-. .++.+ +| .. ..+.+|+..|..||..+
T Consensus 199 ~~rL~~La~~-lGi~~p~~~A~~~Ra~---~p--~~--~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 199 DIRIRGVAHT-LGLDAPAAEASVERAQ---VP--HR--QLCREETLLVARLYFAL 245 (377)
T ss_pred CCCHHHHHHH-hCCCCCchhhhhhhhc---CC--hh--hhhhHHHHHHHHHHHHh
Confidence 7999999987 46654311 01111 11 11 12447999999998765
No 47
>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=95.61 E-value=0.17 Score=64.99 Aligned_cols=135 Identities=20% Similarity=0.287 Sum_probs=90.8
Q ss_pred hcCCeeEEEeeecccccCCCcEEEEEEEe---CCc------eEEEecCC-----------cc----------hhhhHHHH
Q 003416 147 KSVDEFAVDLEHNQYRSFLGLTCLMQIST---RTE------DFVVDTLK-----------LR----------VQVGPYLR 196 (821)
Q Consensus 147 ~~a~~IAVDtE~~~~rty~g~LcLIQISt---~~~------~yLID~La-----------l~----------~~L~~~L~ 196 (821)
....+|.+|+|+.+..+....+ |+|+. .+. ..+|.|.. +. .++.+.|.
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~I--IEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~ 265 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEI--IEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFK 265 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeE--EEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHH
Confidence 5678999999999887655544 33332 111 12333311 00 01233455
Q ss_pred HhhcCCCceEEEecchhcHHHHHHH---hCCCc--CccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCccccccccccC
Q 003416 197 EVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADWRV 269 (821)
Q Consensus 197 eLLeDp~IvKV~H~aK~DL~~L~rd---~GI~~--~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~SDW~~ 269 (821)
+++.+ -+.|.|++.+|+..|.+. +|+.+ ..++||+..++.+.++ .++|..|++++ |+.+..
T Consensus 266 ~fl~~--~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~l-gi~~~~--------- 333 (1213)
T TIGR01405 266 EFFKD--SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKKL-GVDLDD--------- 333 (1213)
T ss_pred HHhCC--CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHHc-CCCCCC---------
Confidence 66655 356899999999888643 45532 4589999998887654 79999999874 765532
Q ss_pred CCCCHHHHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 270 RPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 270 RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
...|..||..+..||..|..++.+.+
T Consensus 334 -------~HrAl~DA~aTa~I~~~ll~~l~~~~ 359 (1213)
T TIGR01405 334 -------HHRADYDAEATAKVFKVMVEQLKEKG 359 (1213)
T ss_pred -------CcCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 13488999999999999998887654
No 48
>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=95.59 E-value=0.15 Score=53.09 Aligned_cols=135 Identities=19% Similarity=0.249 Sum_probs=80.9
Q ss_pred HhcCCeeEEEeeecccccCCCcEEEEEEEe----CCc------eEEEecCC-c----------c-------h---hhhHH
Q 003416 146 LKSVDEFAVDLEHNQYRSFLGLTCLMQIST----RTE------DFVVDTLK-L----------R-------V---QVGPY 194 (821)
Q Consensus 146 L~~a~~IAVDtE~~~~rty~g~LcLIQISt----~~~------~yLID~La-l----------~-------~---~L~~~ 194 (821)
|....++.+|+|+.+..+... +|+|+. ... ..+|.|.. + . . ++.+.
T Consensus 4 l~~~~fvv~D~ETTGl~~~~~---IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~ 80 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAGHD---IIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80 (217)
T ss_pred EEecCEEEEEecCCCCCCCCC---EEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHH
Confidence 455689999999998776444 333332 111 13444321 0 0 0 12233
Q ss_pred HHHhhcCCCceEEEecchhcHHHHHHHhC---CC-c--CccchhHHHHHhhC---C-CCCcHHHHHHHHcCCCCcccccc
Q 003416 195 LREVFKDPTKKKVMHGADRDIVWLQRDFG---IY-L--CNMFDTGQASRVLK---L-ERNSLEYLLHHFCGVNANKEYQN 264 (821)
Q Consensus 195 L~eLLeDp~IvKV~H~aK~DL~~L~rd~G---I~-~--~nlFDTqLAAyLLg---~-~~~SLa~LvekyLgv~LdK~~Q~ 264 (821)
|..++.+ -..|+|++.+|+.+|.+.+. .. + ..++||...++.+. + .+++|..|++.| |+....
T Consensus 81 ~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~-gl~~~~---- 153 (217)
T TIGR00573 81 FADYIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRY-EITNSH---- 153 (217)
T ss_pred HHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHc-CCCCCC----
Confidence 4555554 35689999999999976543 11 1 34779876555432 2 257899998775 543210
Q ss_pred ccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHhc
Q 003416 265 ADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSS 300 (821)
Q Consensus 265 SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee 300 (821)
| ...=|..||.++..|+..|..+..+
T Consensus 154 -----~-----~~H~Al~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 154 -----R-----ALHGALADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred -----c-----ccCCHHHHHHHHHHHHHHHHhcchh
Confidence 0 0122789999999999998766543
No 49
>PRK07883 hypothetical protein; Validated
Probab=95.33 E-value=0.23 Score=59.07 Aligned_cols=137 Identities=20% Similarity=0.170 Sum_probs=86.9
Q ss_pred HHhcCCeeEEEeeecccccCCCcEEEEEEEe----CCc-----eEEEecCC-----------cch----------hhhHH
Q 003416 145 KLKSVDEFAVDLEHNQYRSFLGLTCLMQIST----RTE-----DFVVDTLK-----------LRV----------QVGPY 194 (821)
Q Consensus 145 ~L~~a~~IAVDtE~~~~rty~g~LcLIQISt----~~~-----~yLID~La-----------l~~----------~L~~~ 194 (821)
.+.....|.||+|+.+..+....+ |+|+. .+. ..+|.|-. +.. .....
T Consensus 11 ~~~~~~~Vv~D~ETTGl~p~~~~I--IEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~ 88 (557)
T PRK07883 11 PLRDVTFVVVDLETTGGSPAGDAI--TEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPA 88 (557)
T ss_pred CCcCCCEEEEEEecCCCCCCCCeE--EEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 455678999999999876654443 33332 111 23444421 110 11223
Q ss_pred HHHhhcCCCceEEEecchhcHHHHHHH---hCCCc--CccchhHHHHHhhCC----CCCcHHHHHHHHcCCCCccccccc
Q 003416 195 LREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL----ERNSLEYLLHHFCGVNANKEYQNA 265 (821)
Q Consensus 195 L~eLLeDp~IvKV~H~aK~DL~~L~rd---~GI~~--~nlFDTqLAAyLLg~----~~~SLa~LvekyLgv~LdK~~Q~S 265 (821)
|..++.+ .+.|+|++.+|+.+|.+. +|+.. ..++||+..++.+-+ ..++|..|++ ++|+.....
T Consensus 89 f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~-~~gi~~~~~---- 161 (557)
T PRK07883 89 FLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLAR-LFGATTTPT---- 161 (557)
T ss_pred HHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHH-HCCcccCCC----
Confidence 4455654 456899999999988654 45544 347899876654332 3689999987 567654211
Q ss_pred cccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 266 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 266 DW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
.-|..||.++..|+..|..++.+.+
T Consensus 162 ------------H~Al~DA~ata~l~~~l~~~~~~~~ 186 (557)
T PRK07883 162 ------------HRALDDARATVDVLHGLIERLGNLG 186 (557)
T ss_pred ------------CCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 2388999999999999988887544
No 50
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=95.22 E-value=0.46 Score=51.30 Aligned_cols=133 Identities=20% Similarity=0.234 Sum_probs=82.2
Q ss_pred HhcCCeeEEEeeecccccCCCcEEEEEEEe----CCc-----eEEEecCCcc----------h----------hhhHHHH
Q 003416 146 LKSVDEFAVDLEHNQYRSFLGLTCLMQIST----RTE-----DFVVDTLKLR----------V----------QVGPYLR 196 (821)
Q Consensus 146 L~~a~~IAVDtE~~~~rty~g~LcLIQISt----~~~-----~yLID~Lal~----------~----------~L~~~L~ 196 (821)
+....++.||+|+.+.....+. +|+|+. ... ..+|.+..+. . .+...|.
T Consensus 65 ~~~~~~vv~DiETTG~~~~~~~--IIEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f~ 142 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKKHQ--IIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFR 142 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCCCe--EEEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHHH
Confidence 4567889999999987765544 334332 111 1234332110 0 1223455
Q ss_pred HhhcCCCceEEEecchhcHHHHHH---HhCCCc--CccchhHHHHH-hhCCCCCcHHHHHHHHcCCCCccccccccccCC
Q 003416 197 EVFKDPTKKKVMHGADRDIVWLQR---DFGIYL--CNMFDTGQASR-VLKLERNSLEYLLHHFCGVNANKEYQNADWRVR 270 (821)
Q Consensus 197 eLLeDp~IvKV~H~aK~DL~~L~r---d~GI~~--~nlFDTqLAAy-LLg~~~~SLa~LvekyLgv~LdK~~Q~SDW~~R 270 (821)
.++.+ -+.|+|++.+|..+|.+ .+|..+ ...+||+-.+. ++...+++|++|++ ++|+.....
T Consensus 143 ~fl~~--~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~~-~lgi~~~~~--------- 210 (257)
T PRK08517 143 LFLGD--SVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKE-LLGIEIEVH--------- 210 (257)
T ss_pred HHHCC--CeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHHH-HcCcCCCCC---------
Confidence 56655 35789999999999864 344432 34778875554 44445789999987 457654311
Q ss_pred CCCHHHHHHHHHhhHHHHHHHHHHHHHHh
Q 003416 271 PLPDEMLRYAREDTHYLLYIYDIMKIKLS 299 (821)
Q Consensus 271 PLs~eql~YAA~DA~yLL~Lyd~L~~eLe 299 (821)
.=|..||..+..|+..+..++.
T Consensus 211 -------HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 211 -------HRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred -------CChHHHHHHHHHHHHHHHHHhH
Confidence 1277899999999998877764
No 51
>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=95.18 E-value=0.18 Score=49.70 Aligned_cols=80 Identities=19% Similarity=0.163 Sum_probs=53.6
Q ss_pred HHHHhhcCCCceEEEecchhcHHHHHHHhCCCcCccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCccccccccccCCC
Q 003416 194 YLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADWRVRP 271 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~SDW~~RP 271 (821)
.+.+++. +..+.|+|++.+|+.+|.. . ...++||...++.+... +++|..|+++|++..+...... -|
T Consensus 68 ~~~~fl~-~~~vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~----H~- 137 (150)
T cd06145 68 KLLSLIS-PDTILVGHSLENDLKALKL-I---HPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGG----HD- 137 (150)
T ss_pred HHHHHhC-CCCEEEEcChHHHHHHhhc-c---CCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCC----CC-
Confidence 4555664 2356799999999999953 2 24489999777654332 5899999999988654321111 12
Q ss_pred CCHHHHHHHHHhhHHHHHHH
Q 003416 272 LPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 272 Ls~eql~YAA~DA~yLL~Ly 291 (821)
|..||..+..||
T Consensus 138 --------Al~DA~~t~~l~ 149 (150)
T cd06145 138 --------SVEDARAALELV 149 (150)
T ss_pred --------cHHHHHHHHHHh
Confidence 567888887776
No 52
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=94.89 E-value=0.44 Score=59.22 Aligned_cols=133 Identities=20% Similarity=0.171 Sum_probs=86.1
Q ss_pred cCCeeEEEeeecccccCCCcEEEEEEEeC---Cc------eEEEecCC-----------cch----------hhhHHHHH
Q 003416 148 SVDEFAVDLEHNQYRSFLGLTCLMQISTR---TE------DFVVDTLK-----------LRV----------QVGPYLRE 197 (821)
Q Consensus 148 ~a~~IAVDtE~~~~rty~g~LcLIQISt~---~~------~yLID~La-----------l~~----------~L~~~L~e 197 (821)
...+++||+|+.+.... . .+|||+.- ++ ..+|.|-. +.. ++.+.|.+
T Consensus 6 ~~~~vvvD~ETTGl~~~-d--~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~ 82 (820)
T PRK07246 6 LRKYAVVDLEATGAGPN-A--SIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYD 82 (820)
T ss_pred CCCEEEEEEecCCcCCC-C--eEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHH
Confidence 35789999999987642 3 45565531 11 12343311 000 12234555
Q ss_pred hhcCCCceEEEecchhcHHHHHHHh---CCCc-CccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCccccccccccCCC
Q 003416 198 VFKDPTKKKVMHGADRDIVWLQRDF---GIYL-CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADWRVRP 271 (821)
Q Consensus 198 LLeDp~IvKV~H~aK~DL~~L~rd~---GI~~-~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~SDW~~RP 271 (821)
++.+ .+.|+|++.+|+..|.+.+ |+.+ .+.+||...++.+-+. +++|..|++. +|+.....
T Consensus 83 ~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~-lgl~~~~~---------- 149 (820)
T PRK07246 83 LIED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRE-LNIDLADA---------- 149 (820)
T ss_pred HhCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHH-cCCCCCCC----------
Confidence 6665 4579999999999986543 4443 4578999888766543 7999999986 57654311
Q ss_pred CCHHHHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 272 LPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 272 Ls~eql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
.-|..||..+..|+..|..++...+
T Consensus 150 ------H~Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 150 ------HTAIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred ------CCHHHHHHHHHHHHHHHHHHHhhcC
Confidence 1277899999999999988887543
No 53
>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=94.81 E-value=0.77 Score=46.98 Aligned_cols=77 Identities=18% Similarity=0.105 Sum_probs=52.9
Q ss_pred ceEEEecchhcHHHHHH---HhCCC-----cCccchhHHHHHhhCCCCCcHHHHHHHHcCCCCccccccccccCCCCCHH
Q 003416 204 KKKVMHGADRDIVWLQR---DFGIY-----LCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDE 275 (821)
Q Consensus 204 IvKV~H~aK~DL~~L~r---d~GI~-----~~nlFDTqLAAyLLg~~~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~e 275 (821)
.+.|+|++.+|+..|.+ .+|+. +..++||...++.+.+ ...|..++++| |+..+. .+
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~-~~~L~~l~~~~-gi~~~~-~~------------ 167 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG-QTVLAKACQAA-GIEFDN-KE------------ 167 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC-CCcHHHHHHHC-CCCCCC-CC------------
Confidence 46899999999988864 34541 2347999988876643 56899988864 654321 11
Q ss_pred HHHHHHHhhHHHHHHHHHHHH
Q 003416 276 MLRYAREDTHYLLYIYDIMKI 296 (821)
Q Consensus 276 ql~YAA~DA~yLL~Lyd~L~~ 296 (821)
..=|..||..+..|+..|.+
T Consensus 168 -~H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 168 -AHSALYDTQKTAELFCKIVN 187 (189)
T ss_pred -CcChHHHHHHHHHHHHHHHH
Confidence 12277899999899887754
No 54
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=94.71 E-value=0.0012 Score=73.39 Aligned_cols=121 Identities=26% Similarity=0.405 Sum_probs=88.0
Q ss_pred CCcEEEEEEEeCCceEEEecCCcchh-hhHHHHHhhcCCCceEEEecchhcHHHHHHHhCCCcCccchhHHHHHhhCC--
Q 003416 165 LGLTCLMQISTRTEDFVVDTLKLRVQ-VGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKL-- 241 (821)
Q Consensus 165 ~g~LcLIQISt~~~~yLID~Lal~~~-L~~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~-- 241 (821)
.+++|.+|+++.-..|++|++.++.. +...+..+++|..|.||.|+|..-+.++.+.|||...++|||++|.-+-..
T Consensus 73 ~~~l~~~q~~~~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~q~~d~~q~~~e 152 (458)
T KOG2405|consen 73 HGKLCWLQVATNCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVADVLQFSME 152 (458)
T ss_pred cCcchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhhhhhhhhhhccc
Confidence 46999999999888899998776542 445677899999999999999999999999999999999999997544221
Q ss_pred -C----C--CcH-HHHHHHHcCCCCc------cc-----cccccccCCCCCHHHHHHHHHhhHH
Q 003416 242 -E----R--NSL-EYLLHHFCGVNAN------KE-----YQNADWRVRPLPDEMLRYAREDTHY 286 (821)
Q Consensus 242 -~----~--~SL-a~LvekyLgv~Ld------K~-----~Q~SDW~~RPLs~eql~YAA~DA~y 286 (821)
| . ..+ ..|.+++ .+.+. |. .....|-+||.++..+.--+..+.|
T Consensus 153 ~g~~~~n~~~~~q~sl~kh~-~~a~k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 153 TGGYLPNCITTLQESLIKHL-QVAPKYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred ccccCCccccchHHHHHHHH-HhcccHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 1 1 123 3444433 22221 11 1345699999998887776666666
No 55
>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=94.65 E-value=0.64 Score=43.80 Aligned_cols=81 Identities=22% Similarity=0.178 Sum_probs=53.5
Q ss_pred HHHHHhhcCCCceEEEecchhcHHHHHHHhC-----CCcCccchhHHHHHhhC-CC-CCcHHHHHHHHcCCCCccccccc
Q 003416 193 PYLREVFKDPTKKKVMHGADRDIVWLQRDFG-----IYLCNMFDTGQASRVLK-LE-RNSLEYLLHHFCGVNANKEYQNA 265 (821)
Q Consensus 193 ~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~G-----I~~~nlFDTqLAAyLLg-~~-~~SLa~LvekyLgv~LdK~~Q~S 265 (821)
..+..++.+ ...|+|++.+|..+|.+.+. ......+||+..+..+. .. .+++..+...+++....
T Consensus 71 ~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~------ 142 (159)
T cd06127 71 PEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE------ 142 (159)
T ss_pred HHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC------
Confidence 345567766 56799999999999876543 23355899997665443 33 57788775555554321
Q ss_pred cccCCCCCHHHHHHHHHhhHHHHHHH
Q 003416 266 DWRVRPLPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 266 DW~~RPLs~eql~YAA~DA~yLL~Ly 291 (821)
...-|..||..+..||
T Consensus 143 ----------~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 143 ----------GAHRALADALATAELL 158 (159)
T ss_pred ----------CCCCcHHHHHHHHHHh
Confidence 1233778888888776
No 56
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=94.59 E-value=1.1 Score=46.18 Aligned_cols=136 Identities=16% Similarity=0.129 Sum_probs=78.6
Q ss_pred HHHHHHHHhcCCeeEEEeeecccccCCCcEEEEEEEe---C-C-----c--eEEEecCC--------c---c-------h
Q 003416 139 LKELAAKLKSVDEFAVDLEHNQYRSFLGLTCLMQIST---R-T-----E--DFVVDTLK--------L---R-------V 189 (821)
Q Consensus 139 L~~lle~L~~a~~IAVDtE~~~~rty~g~LcLIQISt---~-~-----~--~yLID~La--------l---~-------~ 189 (821)
+..+.+.......|.||+|+.+.......+ |+|+. . + . .++|.|.. + . .
T Consensus 19 ~~~~~~~~~~~~~vviD~ETTGl~~~~d~I--ieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~ 96 (202)
T PRK09145 19 YAFLFEPPPPDEWVALDCETTGLDPRRAEI--VSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGL 96 (202)
T ss_pred HHHHhcCCCCCCEEEEEeECCCCCCCCCce--EEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCC
Confidence 344444445568899999999876654444 33332 1 1 1 13444421 0 0 0
Q ss_pred ---hhhHHHHHhhcCCCceEEEecchhcHHHHHHHh----CCCc-CccchhHHHHH--hh-C-C---CCCcHHHHHHHHc
Q 003416 190 ---QVGPYLREVFKDPTKKKVMHGADRDIVWLQRDF----GIYL-CNMFDTGQASR--VL-K-L---ERNSLEYLLHHFC 254 (821)
Q Consensus 190 ---~L~~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~----GI~~-~nlFDTqLAAy--LL-g-~---~~~SLa~LvekyL 254 (821)
+....|..++.+ ...|+|++.+|+..|.+.+ |..+ ...+|+.-..+ .. . + .+++|+.|++.|
T Consensus 97 ~~~~vl~~~~~~i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~- 173 (202)
T PRK09145 97 SEEEALRQLLAFIGN--RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHL- 173 (202)
T ss_pred CHHHHHHHHHHHHcC--CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHc-
Confidence 122334455654 3578999999999886543 4433 34778864332 11 1 1 158999999765
Q ss_pred CCCCccccccccccCCCCCHHHHHHHHHhhHHHHHHHHHHH
Q 003416 255 GVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 295 (821)
Q Consensus 255 gv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~ 295 (821)
|+..... .=|..||..+..||..|.
T Consensus 174 gi~~~~~----------------H~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 174 DLPVLGR----------------HDALNDAIMAALIFLRLR 198 (202)
T ss_pred CCCCCCC----------------CCcHHHHHHHHHHHHHHH
Confidence 6544211 127789999999998764
No 57
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=94.47 E-value=0.9 Score=48.51 Aligned_cols=79 Identities=16% Similarity=0.074 Sum_probs=52.8
Q ss_pred ceEEEecchhcHHHHHHHh----CCCc-CccchhHHHHHhhCC---------------CCCcHHHHHHHHcCCCCccccc
Q 003416 204 KKKVMHGADRDIVWLQRDF----GIYL-CNMFDTGQASRVLKL---------------ERNSLEYLLHHFCGVNANKEYQ 263 (821)
Q Consensus 204 IvKV~H~aK~DL~~L~rd~----GI~~-~nlFDTqLAAyLLg~---------------~~~SLa~LvekyLgv~LdK~~Q 263 (821)
-+-|+|++.+|+.+|.+.+ +..+ ..++||+..++.+-+ ..+.|..|+++| |+....
T Consensus 130 ~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~-gl~~~~--- 205 (239)
T PRK09146 130 KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRY-GLPAYS--- 205 (239)
T ss_pred CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHc-CCCCCC---
Confidence 3578999999999986542 3333 358899987764321 246788888764 543211
Q ss_pred cccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHh
Q 003416 264 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 299 (821)
Q Consensus 264 ~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLe 299 (821)
..-|..||..+..|+..+..++-
T Consensus 206 -------------~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 206 -------------PHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred -------------CCCcHHHHHHHHHHHHHHHHHHc
Confidence 12277899999999888766653
No 58
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=94.46 E-value=0.17 Score=63.63 Aligned_cols=136 Identities=21% Similarity=0.259 Sum_probs=96.7
Q ss_pred HhcCCeeEEEeeecccccCCCcEEEEEEEeC---C------ceEEEecCC-----------cch----------hhhHHH
Q 003416 146 LKSVDEFAVDLEHNQYRSFLGLTCLMQISTR---T------EDFVVDTLK-----------LRV----------QVGPYL 195 (821)
Q Consensus 146 L~~a~~IAVDtE~~~~rty~g~LcLIQISt~---~------~~yLID~La-----------l~~----------~L~~~L 195 (821)
|..+.+|.+|+|+.++.+.+.. +|||+.- . ..++|+|-. +.+ ...+.+
T Consensus 418 l~datyVVfDiETTGLs~~~d~--iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf 495 (1444)
T COG2176 418 LDDATYVVFDIETTGLSPVYDE--IIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKF 495 (1444)
T ss_pred cccccEEEEEeecCCcCcccch--hhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHH
Confidence 5567899999999998766554 4555542 1 123444321 100 133456
Q ss_pred HHhhcCCCceEEEecchhcHHHHHHH---hCCCc--CccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCcccccccccc
Q 003416 196 REVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADWR 268 (821)
Q Consensus 196 ~eLLeDp~IvKV~H~aK~DL~~L~rd---~GI~~--~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~SDW~ 268 (821)
++++.| -+-|.||+.+|+-.|+.. +|+.+ .++.||.-.|+.|++. +|+|..|+++| ++.+
T Consensus 496 ~~~~~d--~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~-~v~l---------- 562 (1444)
T COG2176 496 REFIGD--SILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKKL-GVEL---------- 562 (1444)
T ss_pred HHHhcC--cEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHHh-CccH----------
Confidence 778876 357999999999888654 55555 5699999999999986 79999999886 4433
Q ss_pred CCCCCHHHHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 269 VRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 269 ~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
++..-|-.|+.++.+|+-.+.+.|.++|
T Consensus 563 ------e~hHRA~yDaeat~~vf~~f~~~~ke~G 590 (1444)
T COG2176 563 ------ERHHRADYDAEATAKVFFVFLKDLKEKG 590 (1444)
T ss_pred ------HHhhhhhhhHHHHHHHHHHHHHHHHHhc
Confidence 2344467799999999999999999876
No 59
>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=94.45 E-value=0.63 Score=47.07 Aligned_cols=80 Identities=23% Similarity=0.192 Sum_probs=54.3
Q ss_pred HHHHhhcC--CCceEEEecc-hhcHHHHHHH---hCCCc---CccchhHHHHHhhCCCCCcHHHHHHHHcCCCCcccccc
Q 003416 194 YLREVFKD--PTKKKVMHGA-DRDIVWLQRD---FGIYL---CNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQN 264 (821)
Q Consensus 194 ~L~eLLeD--p~IvKV~H~a-K~DL~~L~rd---~GI~~---~nlFDTqLAAyLLg~~~~SLa~LvekyLgv~LdK~~Q~ 264 (821)
.|..++.. ...+-|+||+ .+|+..|.+. +|+.+ ..++||+..++.+.+ +|..|+++++|+.....
T Consensus 87 ~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~---~L~~l~~~~~~~~~~~~--- 160 (177)
T cd06136 87 LIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ---SLGSLYKRLFGQEPKNS--- 160 (177)
T ss_pred HHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh---hHHHHHHHHhCCCcccc---
Confidence 44445442 2457899998 8999988654 34433 225799988876654 89999998888765321
Q ss_pred ccccCCCCCHHHHHHHHHhhHHHHHHHH
Q 003416 265 ADWRVRPLPDEMLRYAREDTHYLLYIYD 292 (821)
Q Consensus 265 SDW~~RPLs~eql~YAA~DA~yLL~Lyd 292 (821)
.-|..||..+..++.
T Consensus 161 -------------H~A~~Da~at~~v~~ 175 (177)
T cd06136 161 -------------HTAEGDVLALLKCAL 175 (177)
T ss_pred -------------cchHHHHHHHHHHHh
Confidence 227788888877653
No 60
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=94.42 E-value=0.71 Score=44.80 Aligned_cols=88 Identities=22% Similarity=0.221 Sum_probs=59.4
Q ss_pred HHHHhhcCCCceEEEecc-hhcHHHHHHH---hCCCc---CccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCccccccc
Q 003416 194 YLREVFKDPTKKKVMHGA-DRDIVWLQRD---FGIYL---CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNA 265 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~a-K~DL~~L~rd---~GI~~---~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~S 265 (821)
.|..++.+ . ..|+|++ .+|+.+|.+. +|+.. ..++||+..++.+... .++|..|++.|. +.....
T Consensus 73 ~~~~~l~~-~-~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~L~~l~~~~~-~~~~~~---- 145 (169)
T smart00479 73 ELLEFLKG-K-ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGRKYSLKKLAERLG-LEVIGR---- 145 (169)
T ss_pred HHHHHhcC-C-EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCCCCCHHHHHHHCC-CCCCCC----
Confidence 45566655 3 3467777 9999988653 33322 2378998877765543 789999998763 322100
Q ss_pred cccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHh
Q 003416 266 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 299 (821)
Q Consensus 266 DW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLe 299 (821)
...|..||..+..||..|..++.
T Consensus 146 -----------~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 146 -----------AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred -----------CcCcHHHHHHHHHHHHHHHHHhh
Confidence 24588999999999999877653
No 61
>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=94.42 E-value=0.77 Score=46.65 Aligned_cols=99 Identities=22% Similarity=0.265 Sum_probs=62.8
Q ss_pred hHHHHHhhc--CCCceEEEecc-hhcHHHHHH---HhCCCc------------------------CccchhHHHHHhh-C
Q 003416 192 GPYLREVFK--DPTKKKVMHGA-DRDIVWLQR---DFGIYL------------------------CNMFDTGQASRVL-K 240 (821)
Q Consensus 192 ~~~L~eLLe--Dp~IvKV~H~a-K~DL~~L~r---d~GI~~------------------------~nlFDTqLAAyLL-g 240 (821)
...+..++. ||.+ -|+|+. .+|+..|.. .+|+.+ ..++|+...++-. .
T Consensus 67 L~~f~~~i~~~dpdi-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~ 145 (199)
T cd05160 67 LKRFFDIIREYDPDI-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK 145 (199)
T ss_pred HHHHHHHHHhcCCCE-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcC
Confidence 334445554 4554 689999 789988754 345444 1267988777643 3
Q ss_pred CCCCcHHHHHHHHcCCCCcc--ccccccccCCCCCHHHHHHHHHhhHHHHHHH
Q 003416 241 LERNSLEYLLHHFCGVNANK--EYQNADWRVRPLPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 241 ~~~~SLa~LvekyLgv~LdK--~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Ly 291 (821)
..+++|..+++++++..-.. .....+|....-....++|...||..++.|+
T Consensus 146 l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 146 LKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred cccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 34799999999999864221 1122222111122568999999999998886
No 62
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=94.40 E-value=0.81 Score=48.37 Aligned_cols=130 Identities=17% Similarity=0.201 Sum_probs=79.9
Q ss_pred CeeEEEeeecccccCCCcEEEEEEEeC----Cc--eEEEecCC-----------cch----------hhhHHHHHhhcCC
Q 003416 150 DEFAVDLEHNQYRSFLGLTCLMQISTR----TE--DFVVDTLK-----------LRV----------QVGPYLREVFKDP 202 (821)
Q Consensus 150 ~~IAVDtE~~~~rty~g~LcLIQISt~----~~--~yLID~La-----------l~~----------~L~~~L~eLLeDp 202 (821)
..+.+|+|+.+...-... +|+|+.- .. ..+|.|-. +.+ +..+.+.+++.+
T Consensus 3 ~~vv~D~ETTGl~~~~d~--IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~~- 79 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDR--IIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGT- 79 (232)
T ss_pred cEEEEEeeCCCCCCCCCE--EEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHcC-
Confidence 468899999987654444 3444431 11 23455421 000 111234445543
Q ss_pred CceEEEec-chhcHHHHHHH---hCCCc--CccchhHHHHHhhCC--CCCcHHHHHHHHcCCCCccccccccccCCCCCH
Q 003416 203 TKKKVMHG-ADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNADWRVRPLPD 274 (821)
Q Consensus 203 ~IvKV~H~-aK~DL~~L~rd---~GI~~--~nlFDTqLAAyLLg~--~~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~ 274 (821)
....|+|| +.+|+..|.+. +|+.. ..++||+-.++.+.+ +.++|..|++.| |+.....
T Consensus 80 ~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~-~~~~~~a------------- 145 (232)
T PRK06309 80 DNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVY-GFEENQA------------- 145 (232)
T ss_pred CCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHHHHc-CCCCCCC-------------
Confidence 35679999 58999988654 34432 358899888776654 368999998776 5443211
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHHHh
Q 003416 275 EMLRYAREDTHYLLYIYDIMKIKLS 299 (821)
Q Consensus 275 eql~YAA~DA~yLL~Lyd~L~~eLe 299 (821)
.-|..||.++..|+..|..++.
T Consensus 146 ---H~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 146 ---HRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred ---CCcHHHHHHHHHHHHHHHHHHH
Confidence 1277899999999998876653
No 63
>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=94.14 E-value=0.82 Score=57.03 Aligned_cols=91 Identities=16% Similarity=0.193 Sum_probs=64.7
Q ss_pred HHHHHhhcCCCceEEEecchhcHHHHHHH---hCCC--cCccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCccccccc
Q 003416 193 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIY--LCNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNA 265 (821)
Q Consensus 193 ~~L~eLLeDp~IvKV~H~aK~DL~~L~rd---~GI~--~~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~S 265 (821)
+.|.+++.+ -+.|+|++.+|+.+|.+. .|+. ....+||+..++.+.+. +++|.+|++. +|+..+..
T Consensus 72 ~~l~~~l~~--~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~-~gi~~~~~---- 144 (850)
T TIGR01407 72 QEIYDLLED--GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEA-LGLTHENP---- 144 (850)
T ss_pred HHHHHHhCC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHH-CCCCCCCC----
Confidence 344556654 357999999999998653 4544 34589999888776543 6899999887 46654321
Q ss_pred cccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 266 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 266 DW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
.=|..||..+..|+..|..++.+..
T Consensus 145 ------------H~Al~DA~ata~l~~~l~~~~~~l~ 169 (850)
T TIGR01407 145 ------------HRADSDAQATAELLLLLFEKMEKLP 169 (850)
T ss_pred ------------CChHHHHHHHHHHHHHHHHHHHhcC
Confidence 2277899999999999888877543
No 64
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=94.12 E-value=0.43 Score=51.75 Aligned_cols=132 Identities=17% Similarity=0.174 Sum_probs=84.1
Q ss_pred CeeEEEeeecccccC--CCcEEEEEEEeCCceEEEecCC---------------cch-h------h---hHHHHHhhcCC
Q 003416 150 DEFAVDLEHNQYRSF--LGLTCLMQISTRTEDFVVDTLK---------------LRV-Q------V---GPYLREVFKDP 202 (821)
Q Consensus 150 ~~IAVDtE~~~~rty--~g~LcLIQISt~~~~yLID~La---------------l~~-~------L---~~~L~eLLeDp 202 (821)
.+||+|+|..+..+- ...++-+.|-...+..++|..- ++. + + -..+.++|..
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL~g- 184 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLLKG- 184 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHHHhC-
Confidence 689999999876542 2233444454445556666321 110 0 1 1123356765
Q ss_pred CceEEEecchhcHHHHHHHhCCCcCc-cchhHHHHHhh---CCC-CCcHHHHHHHHcCCCCccccccccccCCCCCHHHH
Q 003416 203 TKKKVMHGADRDIVWLQRDFGIYLCN-MFDTGQASRVL---KLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEML 277 (821)
Q Consensus 203 ~IvKV~H~aK~DL~~L~rd~GI~~~n-lFDTqLAAyLL---g~~-~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql 277 (821)
-+.|+|+...|+..|+-. .|.. +-||.----|+ ... ..||..|.+.+||.++.-+...
T Consensus 185 -RIlVGHaLhnDl~~L~l~---hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHs------------- 247 (280)
T KOG2249|consen 185 -RILVGHALHNDLQALKLE---HPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHS------------- 247 (280)
T ss_pred -CEEeccccccHHHHHhhh---CchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccccC-------------
Confidence 456999999999999533 2332 66886443232 323 6899999999999887544432
Q ss_pred HHHHHhhHHHHHHHHHHHHHHhcC
Q 003416 278 RYAREDTHYLLYIYDIMKIKLSSM 301 (821)
Q Consensus 278 ~YAA~DA~yLL~Lyd~L~~eLee~ 301 (821)
..+||.....||...+.+-++.
T Consensus 248 --SvEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 248 --SVEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred --cHHHHHHHHHHHHHHHHHHHHH
Confidence 2479999999999988776643
No 65
>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=94.03 E-value=1.4 Score=42.60 Aligned_cols=78 Identities=21% Similarity=0.186 Sum_probs=52.7
Q ss_pred HHHHhhcCCCceEEEecchhcHHHHHHHh---CCCc--CccchhHHHHHhhCC--CCCcHHHHHHHHcCCCCcccccccc
Q 003416 194 YLREVFKDPTKKKVMHGADRDIVWLQRDF---GIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNAD 266 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~aK~DL~~L~rd~---GI~~--~nlFDTqLAAyLLg~--~~~SLa~LvekyLgv~LdK~~Q~SD 266 (821)
.|..++.+ ...|+|++.+|..+|.+.+ |+.. ...+||+..+..+-. ..++|..|++. +|+..+ .
T Consensus 70 ~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~~~-~g~~~~-~----- 140 (156)
T cd06130 70 EIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEH-LGIELN-H----- 140 (156)
T ss_pred HHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHHHH-cCCCcc-C-----
Confidence 45566765 4579999999999986543 5443 348899877665433 36899999986 465443 1
Q ss_pred ccCCCCCHHHHHHHHHhhHHHHHHH
Q 003416 267 WRVRPLPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 267 W~~RPLs~eql~YAA~DA~yLL~Ly 291 (821)
.=|..||..+..|+
T Consensus 141 -----------H~Al~Da~~ta~l~ 154 (156)
T cd06130 141 -----------HDALEDARACAEIL 154 (156)
T ss_pred -----------cCchHHHHHHHHHH
Confidence 12567777777765
No 66
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=93.04 E-value=0.66 Score=60.73 Aligned_cols=83 Identities=23% Similarity=0.258 Sum_probs=62.3
Q ss_pred CceEEEecchhcHHHHH---HHhCCC-c-CccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCccccccccccCCCCCHH
Q 003416 203 TKKKVMHGADRDIVWLQ---RDFGIY-L-CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDE 275 (821)
Q Consensus 203 ~IvKV~H~aK~DL~~L~---rd~GI~-~-~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~e 275 (821)
....|.|++.+|+..|. +.+|+. + ...+||+..++.+.+. .++|..|+++ +|+.+...
T Consensus 499 g~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~-lGL~~~~~-------------- 563 (1437)
T PRK00448 499 DSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKK-FGVELEHH-------------- 563 (1437)
T ss_pred CCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHH-cCCCCCCC--------------
Confidence 46789999999997764 345553 2 4588999888877654 6899999986 46654321
Q ss_pred HHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 276 MLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 276 ql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
.-|..||..+..|+..|..++.+.|
T Consensus 564 --HrAl~DA~aTa~lf~~ll~~l~~~g 588 (1437)
T PRK00448 564 --HRADYDAEATAYLLIKFLKDLKEKG 588 (1437)
T ss_pred --cChHHHHHHHHHHHHHHHHHHHHcC
Confidence 3488999999999999998887654
No 67
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=92.77 E-value=1.7 Score=54.78 Aligned_cols=91 Identities=22% Similarity=0.328 Sum_probs=64.8
Q ss_pred HHHHHhhcCCCceEEEecchhcHHHHHHH---hCCCc--CccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCccccccc
Q 003416 193 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNA 265 (821)
Q Consensus 193 ~~L~eLLeDp~IvKV~H~aK~DL~~L~rd---~GI~~--~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~S 265 (821)
+.|..++.+ ...|+|++.+|+.+|.+. .|+.+ ..++||+-.++.+-+. .++|.+|++.+ |+..+..
T Consensus 76 ~~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~l-~i~~~~~---- 148 (928)
T PRK08074 76 PEIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEEL-GLEHDQP---- 148 (928)
T ss_pred HHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHhC-CCCCCCC----
Confidence 345556654 456999999999998653 34433 3588999887776553 68999998874 6543311
Q ss_pred cccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHhcCC
Q 003416 266 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 302 (821)
Q Consensus 266 DW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLee~G 302 (821)
.=|..||..+..|+..|..++...+
T Consensus 149 ------------H~Al~DA~ata~l~~~l~~~~~~l~ 173 (928)
T PRK08074 149 ------------HRADSDAEVTAELFLQLLNKLERLP 173 (928)
T ss_pred ------------CChHHHHHHHHHHHHHHHHHHHhcC
Confidence 1277899999999999988887543
No 68
>PF11408 Helicase_Sgs1: Sgs1 RecQ helicase; InterPro: IPR022758 RecQ helicases unwind DNA in an ATP-dependent manner. Sgs1 has a HRDC (helicase and RNaseD C-terminal) domain which modulates the helicase function via auxiliary contacts to DNA []. The proteins matching this entry are restricted to fungi (Saccharomycetaceae). ; PDB: 1D8B_A.
Probab=92.65 E-value=0.42 Score=43.20 Aligned_cols=67 Identities=16% Similarity=0.262 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHHHHcCCCCccccCHHHHHHHHHhCCCCHHHHHhhhcCChhHHH--HhHHHHHHHHH
Q 003416 354 AVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIE--RYMGPVLSIIK 420 (821)
Q Consensus 354 avlraL~aWRD~iAR~~Dep~~~VL~D~~LleLA~~~P~t~~eL~~l~g~~~~~vr--r~g~eIL~iI~ 420 (821)
..+..|.+-|-.++.+.+-|..-.|+|.+|.+||..+|+|.+++.++.|......+ .|-...+-.++
T Consensus 7 ~aY~~Lr~~~~~~~~~~n~p~~~f~sd~~LKk~A~~LP~te~eF~~l~g~~~~~~~kFkyFK~tl~~Lr 75 (80)
T PF11408_consen 7 SAYEKLREISINLSNRMNPPNDNFMSDTILKKMATKLPTTEEEFSKLVGINEQQRKKFKYFKDTLMRLR 75 (80)
T ss_dssp HHHHHHHHHHHHHHHSSSS--S-SS-HHHHHHHHHH---SHHHHGGGS---HHHHHHGGGTHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhccCCCccccCCHHHHHHHHHHCCCCHHHHHHhcCCcHHHHHHHHHHHHHHHHHH
Confidence 35778888899999999999999999999999999999999999999998877755 45555554444
No 69
>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=92.37 E-value=0.26 Score=50.44 Aligned_cols=77 Identities=25% Similarity=0.226 Sum_probs=53.1
Q ss_pred HHHhhcCCCceEEEecchhcHHHHHHHhCCC-c-CccchhHHHHHhhCCCCCcHHHHHHHHcCCCCccccccccccCCCC
Q 003416 195 LREVFKDPTKKKVMHGADRDIVWLQRDFGIY-L-CNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPL 272 (821)
Q Consensus 195 L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~-~-~nlFDTqLAAyLLg~~~~SLa~LvekyLgv~LdK~~Q~SDW~~RPL 272 (821)
|..++ ++..+.|+|+...|+.+|. +. | ..+.||.+....-.....+|..|+++|||..+..+. .
T Consensus 95 l~~li-~~~tILVGHsL~nDL~aL~----l~hp~~~viDTa~l~~~~~~r~~sLk~La~~~L~~~IQ~~~--H------- 160 (174)
T cd06143 95 LRLLV-DLGCIFVGHGLAKDFRVIN----IQVPKEQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSET--H------- 160 (174)
T ss_pred HHHHc-CCCCEEEeccchhHHHHhc----CcCCCcceEEcHHhccCCCCCChhHHHHHHHHcCCcccCCC--c-------
Confidence 44444 5566789999999999993 32 2 358999754322111258999999999998875321 1
Q ss_pred CHHHHHHHHHhhHHHHHHH
Q 003416 273 PDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 273 s~eql~YAA~DA~yLL~Ly 291 (821)
-..+||.+.+.||
T Consensus 161 ------dSvEDArAam~Ly 173 (174)
T cd06143 161 ------DSIEDARTALKLY 173 (174)
T ss_pred ------CcHHHHHHHHHHh
Confidence 1357888888888
No 70
>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=92.25 E-value=2.3 Score=43.60 Aligned_cols=102 Identities=24% Similarity=0.353 Sum_probs=65.6
Q ss_pred hhHHHHHhhcC--CCceEEEecc-hhcHHHHHHH---hCCCc------------------------CccchhHHHHH-hh
Q 003416 191 VGPYLREVFKD--PTKKKVMHGA-DRDIVWLQRD---FGIYL------------------------CNMFDTGQASR-VL 239 (821)
Q Consensus 191 L~~~L~eLLeD--p~IvKV~H~a-K~DL~~L~rd---~GI~~------------------------~nlFDTqLAAy-LL 239 (821)
+...+..++.. |.+ .|+||. .+|+..|... +|+.. ..++|++..++ .+
T Consensus 59 lL~~F~~~i~~~dpdi-ivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~ 137 (195)
T cd05780 59 MIKRFIEIVKEKDPDV-IYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTL 137 (195)
T ss_pred HHHHHHHHHHHcCCCE-EEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhC
Confidence 33344455554 765 588987 5799887643 34431 12678877665 34
Q ss_pred CCCCCcHHHHHHHHcCCCCcc--cccccc-ccCCCCCHHHHHHHHHhhHHHHHHHHH
Q 003416 240 KLERNSLEYLLHHFCGVNANK--EYQNAD-WRVRPLPDEMLRYAREDTHYLLYIYDI 293 (821)
Q Consensus 240 g~~~~SLa~LvekyLgv~LdK--~~Q~SD-W~~RPLs~eql~YAA~DA~yLL~Lyd~ 293 (821)
...+++|..+++++||..... ..+... |...+--...++|+..||..++.|...
T Consensus 138 ~l~sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~ 194 (195)
T cd05780 138 NLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKE 194 (195)
T ss_pred CCCcCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhh
Confidence 556899999999999975321 112222 333323366899999999999998765
No 71
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=89.63 E-value=6.9 Score=41.37 Aligned_cols=78 Identities=17% Similarity=-0.070 Sum_probs=53.0
Q ss_pred CceEEEecchhcHHHHHHHhCCCcCccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHH
Q 003416 203 TKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAR 281 (821)
Q Consensus 203 ~IvKV~H~aK~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA 281 (821)
.-+-|+||+.+|+..|.. + ....+||+-.++.+-+. .+++..|++. +++..+.... ....=|.
T Consensus 74 ~~~lVaHNa~FD~~~L~~-~---~~~~idTl~lar~l~p~~~~~l~~L~~~-~~l~~~~~~~-----------~~aHrAl 137 (219)
T PRK07983 74 SEWYVAHNASFDRRVLPE-M---PGEWICTMKLARRLWPGIKYSNMALYKS-RKLNVQTPPG-----------LHHHRAL 137 (219)
T ss_pred CCEEEEeCcHhhHHHHhC-c---CCCcEeHHHHHHHHccCCCCCHHHHHHH-cCCCCCCCCC-----------CCCCcHH
Confidence 346799999999999842 2 24688999888866654 6889888865 4544311000 0123378
Q ss_pred HhhHHHHHHHHHHHH
Q 003416 282 EDTHYLLYIYDIMKI 296 (821)
Q Consensus 282 ~DA~yLL~Lyd~L~~ 296 (821)
.||..+..|+..|..
T Consensus 138 ~Da~ata~ll~~l~~ 152 (219)
T PRK07983 138 YDCYITAALLIDIMN 152 (219)
T ss_pred HHHHHHHHHHHHHHH
Confidence 899999999887753
No 72
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=86.29 E-value=9.9 Score=42.05 Aligned_cols=82 Identities=17% Similarity=0.098 Sum_probs=50.9
Q ss_pred HHHHhhcCCCceEEEecchhcHHHHHHHhCCCc-CccchhHHHHHh--hCCCCCcHHHHHHHHcCCCCccccccccccCC
Q 003416 194 YLREVFKDPTKKKVMHGADRDIVWLQRDFGIYL-CNMFDTGQASRV--LKLERNSLEYLLHHFCGVNANKEYQNADWRVR 270 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~-~nlFDTqLAAyL--Lg~~~~SLa~LvekyLgv~LdK~~Q~SDW~~R 270 (821)
.+..++.+ .-+.|.||+.+|+.+|.+.+.-.. ..+.+|+..... .++++++|.+|+..| |... .
T Consensus 113 ~l~~fl~~-~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~~~-g~~~----~------- 179 (294)
T PRK09182 113 AVDALIAP-ADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLAGQA-GFFH----E------- 179 (294)
T ss_pred HHHHHhcC-CCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHHHHc-CCCC----C-------
Confidence 45566665 346799999999999965432111 234555543322 234578999999875 3210 1
Q ss_pred CCCHHHHHHHHHhhHHHHHHHHHH
Q 003416 271 PLPDEMLRYAREDTHYLLYIYDIM 294 (821)
Q Consensus 271 PLs~eql~YAA~DA~yLL~Lyd~L 294 (821)
..=|..||.+++.|+..+
T Consensus 180 ------aHrAl~Da~Ata~ll~~~ 197 (294)
T PRK09182 180 ------GHRAVDDCQALLELLARP 197 (294)
T ss_pred ------CcChHHHHHHHHHHHHHH
Confidence 122788999998887754
No 73
>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=84.70 E-value=7.4 Score=40.34 Aligned_cols=62 Identities=19% Similarity=0.272 Sum_probs=40.8
Q ss_pred cchhHHHHH--hhCCCCCcHHHHHHHHcCCCCcc-cc-----c-cccccCCCCCHHHHHHHHHhhHHHHHHHH
Q 003416 229 MFDTGQASR--VLKLERNSLEYLLHHFCGVNANK-EY-----Q-NADWRVRPLPDEMLRYAREDTHYLLYIYD 292 (821)
Q Consensus 229 lFDTqLAAy--LLg~~~~SLa~LvekyLgv~LdK-~~-----Q-~SDW~~RPLs~eql~YAA~DA~yLL~Lyd 292 (821)
++|+....+ .+...+++|.++++++||..-.. .. . ..-|...+ ...++|+..||..+++|++
T Consensus 123 ~~D~~~~~k~~~~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 123 VLDGIDALKTATYHFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred EEEhHHHHHHccCCCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 668765543 34456899999999999863211 10 0 11233333 5689999999999999873
No 74
>PRK11779 sbcB exonuclease I; Provisional
Probab=84.64 E-value=23 Score=41.89 Aligned_cols=87 Identities=18% Similarity=0.118 Sum_probs=53.3
Q ss_pred HHHHhhcCCCceEEEec-chhcHHHHHHHhCCC--------------cCccchhHHHHHhhC------------CCCCcH
Q 003416 194 YLREVFKDPTKKKVMHG-ADRDIVWLQRDFGIY--------------LCNMFDTGQASRVLK------------LERNSL 246 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~-aK~DL~~L~rd~GI~--------------~~nlFDTqLAAyLLg------------~~~~SL 246 (821)
.+..+|..+..+.|+|+ +.+|...+...+... ...++||..+++.+. ..++.|
T Consensus 84 ~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rL 163 (476)
T PRK11779 84 RIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKL 163 (476)
T ss_pred HHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcH
Confidence 34455654556679997 689998875543111 012446666666542 235889
Q ss_pred HHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHH
Q 003416 247 EYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 297 (821)
Q Consensus 247 a~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 297 (821)
+.|+..+ |+.... ..=|..||..+..|+..|..+
T Consensus 164 e~L~~~~-gI~~~~----------------AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 164 EHLTKAN-GIEHEN----------------AHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHHHHc-CCCCCC----------------CCCcHHHHHHHHHHHHHHHHh
Confidence 9999875 544321 122678888888888877654
No 75
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=84.64 E-value=19 Score=37.68 Aligned_cols=133 Identities=19% Similarity=0.202 Sum_probs=81.6
Q ss_pred CCeeEEEeeecccccCCCcEE---EEEEEeC---Cc--eEEEecCC-cc--------------------hhhhHHHHHhh
Q 003416 149 VDEFAVDLEHNQYRSFLGLTC---LMQISTR---TE--DFVVDTLK-LR--------------------VQVGPYLREVF 199 (821)
Q Consensus 149 a~~IAVDtE~~~~rty~g~Lc---LIQISt~---~~--~yLID~La-l~--------------------~~L~~~L~eLL 199 (821)
...+.||+|+.+.......++ .+.+... .. ..+|.|-. +. ..+.+.+..++
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~i 92 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDFI 92 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 467999999998876444433 2333333 11 13454411 00 01222333455
Q ss_pred cCCCceEEEecchhcHHHHHHHh---CCCc--CccchhHHHHHhhCCC--CCcHHHHHHHHcCCCCccccccccccCCCC
Q 003416 200 KDPTKKKVMHGADRDIVWLQRDF---GIYL--CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADWRVRPL 272 (821)
Q Consensus 200 eDp~IvKV~H~aK~DL~~L~rd~---GI~~--~nlFDTqLAAyLLg~~--~~SLa~LvekyLgv~LdK~~Q~SDW~~RPL 272 (821)
.+. -.-|.|++..|+..|...+ +..+ ..+.||...++...++ .++|..|+. .+|+... ....
T Consensus 93 ~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~-~~~~-------- 161 (243)
T COG0847 93 GGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRN-PFHP-------- 161 (243)
T ss_pred CCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHH-HcCCCcC-CcCC--------
Confidence 543 5679999999999886433 3332 3477999888876665 789999998 6676633 1111
Q ss_pred CHHHHHHHHHhhHHHHHHHHHHHHH
Q 003416 273 PDEMLRYAREDTHYLLYIYDIMKIK 297 (821)
Q Consensus 273 s~eql~YAA~DA~yLL~Lyd~L~~e 297 (821)
.=|..|+..+..+|..+...
T Consensus 162 -----H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 162 -----HRALFDALALAELFLLLQTG 181 (243)
T ss_pred -----cchHHHHHHHHHHHHHHHhc
Confidence 12778999999998887664
No 76
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=84.08 E-value=7 Score=43.19 Aligned_cols=86 Identities=16% Similarity=0.181 Sum_probs=58.8
Q ss_pred HHHHhhcCCCceEEEecchhcHHHHHHH---hCCCc--CccchhHHHHHhhCC--CCCcHHHHHHHHcCCCCcccccccc
Q 003416 194 YLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNAD 266 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~aK~DL~~L~rd---~GI~~--~nlFDTqLAAyLLg~--~~~SLa~LvekyLgv~LdK~~Q~SD 266 (821)
.|.+++.+ -+.|.|++.+|+.+|.+. +++.. ..++||+..++.+-+ ..++|..|++.| |+..+
T Consensus 73 ~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~~-gi~~~------- 142 (309)
T PRK06195 73 KIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFL-GYEFK------- 142 (309)
T ss_pred HHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHHc-CCCCc-------
Confidence 34455543 467999999999888643 34433 348899876665433 368999998875 54321
Q ss_pred ccCCCCCHHHHHHHHHhhHHHHHHHHHHHHHHh
Q 003416 267 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 299 (821)
Q Consensus 267 W~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eLe 299 (821)
-.-|..||..+..|+..|..++.
T Consensus 143 ----------~H~Al~DA~ata~l~~~l~~~~~ 165 (309)
T PRK06195 143 ----------HHDALADAMACSNILLNISKELN 165 (309)
T ss_pred ----------ccCCHHHHHHHHHHHHHHHHHhc
Confidence 12377899999999888877665
No 77
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=83.53 E-value=24 Score=36.68 Aligned_cols=84 Identities=15% Similarity=0.190 Sum_probs=52.2
Q ss_pred HHHHHhhcCCCceEEEecch-hcHHHHHHHhCCCcCc--cchhH---HHHHhh---CCCCCcHHHHHHHHcCCCCccccc
Q 003416 193 PYLREVFKDPTKKKVMHGAD-RDIVWLQRDFGIYLCN--MFDTG---QASRVL---KLERNSLEYLLHHFCGVNANKEYQ 263 (821)
Q Consensus 193 ~~L~eLLeDp~IvKV~H~aK-~DL~~L~rd~GI~~~n--lFDTq---LAAyLL---g~~~~SLa~LvekyLgv~LdK~~Q 263 (821)
+.|..++.+. ..|+|++. +|+.+|. ..|+.+.+ .+||. .+.+.. +...++|..|++. +|+...
T Consensus 76 ~~f~~f~~~~--~lVaHNa~~fD~~fL~-~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~-~gi~~~---- 147 (195)
T PRK07247 76 AAFKEFVGEL--PLIGYNAQKSDLPILA-ENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADF-LGIKGR---- 147 (195)
T ss_pred HHHHHHHCCC--eEEEEeCcHhHHHHHH-HcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHh-cCCCCC----
Confidence 3455666553 46899995 8999995 56765533 34554 222221 1236899999886 465421
Q ss_pred cccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHH
Q 003416 264 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 297 (821)
Q Consensus 264 ~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 297 (821)
. .=|..||..+..||..|...
T Consensus 148 ~-------------HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 148 G-------------HNSLEDARMTARVYESFLES 168 (195)
T ss_pred C-------------cCCHHHHHHHHHHHHHHHhh
Confidence 1 12678999999999877443
No 78
>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=82.25 E-value=10 Score=39.70 Aligned_cols=140 Identities=20% Similarity=0.300 Sum_probs=77.4
Q ss_pred CCeeEEEeeeccccc-C-----CCcEEEEEEEeCC--c-eEEEec-CCcchhhhHHHHHhhc--CCCceEEEecc-hhcH
Q 003416 149 VDEFAVDLEHNQYRS-F-----LGLTCLMQISTRT--E-DFVVDT-LKLRVQVGPYLREVFK--DPTKKKVMHGA-DRDI 215 (821)
Q Consensus 149 a~~IAVDtE~~~~rt-y-----~g~LcLIQISt~~--~-~yLID~-Lal~~~L~~~L~eLLe--Dp~IvKV~H~a-K~DL 215 (821)
-..+++|+|...... + ...-+++||+... . ..++.. ..-...+...+..++. ||.| .|+||. .+|+
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdi-i~g~N~~~FD~ 87 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPDV-IEGHNIFRFDL 87 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccCCCCHHHHHHHHHHHHHHhCCCE-EeccCCcccCH
Confidence 357899999865432 2 2234678888742 1 112211 1111123333334443 5764 478887 7899
Q ss_pred HHHHH---HhCCCc--------------------------------CccchhHHHHHhh-----CCCCCcHHHHHHHH--
Q 003416 216 VWLQR---DFGIYL--------------------------------CNMFDTGQASRVL-----KLERNSLEYLLHHF-- 253 (821)
Q Consensus 216 ~~L~r---d~GI~~--------------------------------~nlFDTqLAAyLL-----g~~~~SLa~Lveky-- 253 (821)
..|.. .+|+.. .-++|++.+.+-. ...+++|..+++.+
T Consensus 88 pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~ 167 (207)
T cd05785 88 PYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGL 167 (207)
T ss_pred HHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHhcc
Confidence 77653 244432 1137888766632 23468999999986
Q ss_pred cCC-CC--ccccccccccCCCCCHHHHHHHHHhhHHHHHHH
Q 003416 254 CGV-NA--NKEYQNADWRVRPLPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 254 Lgv-~L--dK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Ly 291 (821)
++. +. +...=..-|...+ +..++|+..||..++.|+
T Consensus 168 ~~~~k~d~~~~~I~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 168 ASPDRTYIDGRQIAEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred cCCCcCCCCHHHHHHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 232 11 1111011244332 678999999999988875
No 79
>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=79.34 E-value=42 Score=34.50 Aligned_cols=142 Identities=17% Similarity=0.166 Sum_probs=78.1
Q ss_pred CeeEEEeeecccccC----CCcEEEEEEEeCCc-eEEEec-CCcchhhhHHHHHhhc--CCCceEEEecc-hhcHHHHHH
Q 003416 150 DEFAVDLEHNQYRSF----LGLTCLMQISTRTE-DFVVDT-LKLRVQVGPYLREVFK--DPTKKKVMHGA-DRDIVWLQR 220 (821)
Q Consensus 150 ~~IAVDtE~~~~rty----~g~LcLIQISt~~~-~yLID~-Lal~~~L~~~L~eLLe--Dp~IvKV~H~a-K~DL~~L~r 220 (821)
..+++|+|......+ ...+..|.++..++ ..++-. ..-...+...+..++. ||.++ ++||. .+|+..|..
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~i-~gyN~~~FDlpyl~~ 82 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDII-VGYNSNAFDWPYLVE 82 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCEE-EecCCCcCcHHHHHH
Confidence 468999999743222 23444555554332 233311 1111133334445544 56654 57775 688877643
Q ss_pred ---HhCCCcC----------------------ccchhHHHHH-hhCCCCCcHHHHHHHHcCCC--Cccc----ccc-ccc
Q 003416 221 ---DFGIYLC----------------------NMFDTGQASR-VLKLERNSLEYLLHHFCGVN--ANKE----YQN-ADW 267 (821)
Q Consensus 221 ---d~GI~~~----------------------nlFDTqLAAy-LLg~~~~SLa~LvekyLgv~--LdK~----~Q~-SDW 267 (821)
.+|+.+. -.+|+....+ ....++++|..+++ +||.. .+|. ++. .-|
T Consensus 83 Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l~~y~L~~Va~-~Lg~~k~~~k~~~~~~~i~~~~ 161 (188)
T cd05781 83 RARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEVKVKTLENVAE-YLGVMKKSERVLIEWYRIYEYW 161 (188)
T ss_pred HHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCCCCCCCHHHHHH-HHCCCccccccCCCHHHHHHHH
Confidence 3454321 1567665544 33445799999987 58863 2221 111 124
Q ss_pred cCCCCCHHHHHHHHHhhHHHHHHHHH
Q 003416 268 RVRPLPDEMLRYAREDTHYLLYIYDI 293 (821)
Q Consensus 268 ~~RPLs~eql~YAA~DA~yLL~Lyd~ 293 (821)
...--......|+..|+..++.||..
T Consensus 162 ~~~~~~~~l~~Y~~~D~~~t~~l~~~ 187 (188)
T cd05781 162 DDEKKRDILLKYNRDDARSTYGLAEK 187 (188)
T ss_pred cCcccHHHHHHHHHHHHHHHHHHHhh
Confidence 43212367899999999999999875
No 80
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=78.38 E-value=1.2 Score=55.18 Aligned_cols=91 Identities=22% Similarity=0.183 Sum_probs=64.0
Q ss_pred hhcCCCceEEEecchhcHHHHHHHhCCCc--CccchhHHHHHhhCCC-CCcHHHHHHHHcCCCCccccccccccCCCCCH
Q 003416 198 VFKDPTKKKVMHGADRDIVWLQRDFGIYL--CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPD 274 (821)
Q Consensus 198 LLeDp~IvKV~H~aK~DL~~L~rd~GI~~--~nlFDTqLAAyLLg~~-~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~ 274 (821)
+|-+-.++.|+||...|...+ +|.+ ..++||.+. ++++.+ ..+|.+|+..+||.++.-.. .
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvI----Ni~Vp~~QiiDTv~l-f~~~s~R~LSLrfLa~~lLg~~IQ~~~--H--------- 1072 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVI----NIHVPEEQIIDTVTL-FRLGSQRMLSLRFLAWELLGETIQMEA--H--------- 1072 (1118)
T ss_pred HHHHcCcEEEcccccccceEE----EEecChhhheeeeEE-EecccccEEEHHHHHHHHhcchhhccc--c---------
Confidence 566889999999999998776 3443 339998754 334444 48999999999998763221 1
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHHHhcCCCCCCCCCChHHHHHH
Q 003416 275 EMLRYAREDTHYLLYIYDIMKIKLSSMPKESENSDTPLTEVYK 317 (821)
Q Consensus 275 eql~YAA~DA~yLL~Lyd~L~~eLee~G~~~~~~~~~l~ev~~ 317 (821)
-..+||++.|.||++.. +|+++| .+.++++
T Consensus 1073 ----DSIeDA~taLkLYk~Yl-~lkeq~--------~~~~~l~ 1102 (1118)
T KOG1275|consen 1073 ----DSIEDARTALKLYKKYL-KLKEQG--------KLESELR 1102 (1118)
T ss_pred ----ccHHHHHHHHHHHHHHH-HHHHhh--------HHHHHHH
Confidence 14589999999999864 355543 5666554
No 81
>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase []. ; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 4DF4_A 3T3F_A 1QSY_A 3OJS_A 3PO5_A 3OJU_A 1QTM_A 1QSS_A 3PY8_A 4DFJ_A ....
Probab=77.32 E-value=8.4 Score=38.04 Aligned_cols=69 Identities=13% Similarity=0.125 Sum_probs=40.8
Q ss_pred hhcHHHHHHHhCCCcCccchhHHHHHhhCCCCCcHHHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhHHHHHHH
Q 003416 212 DRDIVWLQRDFGIYLCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 212 K~DL~~L~rd~GI~~~nlFDTqLAAyLLg~~~~SLa~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Ly 291 (821)
-.|+..+...-|+.+.+--|-++.||||++.......++++|++ .+|... |+..+....+|+
T Consensus 70 AK~LAv~a~~~G~~v~PGDDPlLlAYLlDPsNt~p~~varRY~~---------~~W~~d---------A~~RA~~t~~L~ 131 (138)
T PF09281_consen 70 AKDLAVHALREGVVVEPGDDPLLLAYLLDPSNTNPEGVARRYLG---------GEWPED---------AATRALATARLL 131 (138)
T ss_dssp HHHHHHHHHHTT----B---HHHHHHHH-TT--SHHHHHHHH-T---------S---SS---------HHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCcccCCCCCcchhhhhcCccCCChHHHHHHhcC---------CCCCcc---------HHHHHHHHHHHH
Confidence 44555544568988888889999999999988899999999987 356432 556666667777
Q ss_pred HHHHHHH
Q 003416 292 DIMKIKL 298 (821)
Q Consensus 292 d~L~~eL 298 (821)
..|..+|
T Consensus 132 ~~L~prL 138 (138)
T PF09281_consen 132 RALPPRL 138 (138)
T ss_dssp HHHHHHT
T ss_pred HHhhhcC
Confidence 7776654
No 82
>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=77.20 E-value=56 Score=32.00 Aligned_cols=85 Identities=16% Similarity=0.173 Sum_probs=50.6
Q ss_pred HHHHhhcCCCceEEEecchhcHHHHHH---HhCC-----CcCccchhHHHHHh-hCCC-CCcHHHHHHHHcCCCCccccc
Q 003416 194 YLREVFKDPTKKKVMHGADRDIVWLQR---DFGI-----YLCNMFDTGQASRV-LKLE-RNSLEYLLHHFCGVNANKEYQ 263 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~aK~DL~~L~r---d~GI-----~~~nlFDTqLAAyL-Lg~~-~~SLa~LvekyLgv~LdK~~Q 263 (821)
.|..++.+..-..+.|....|...|.+ .++. .....+|++..+.. .+.. .++|..|++.| |+....
T Consensus 81 ~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~~-gi~~~~--- 156 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYL-GLEFEG--- 156 (176)
T ss_pred HHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHHC-CCCCCC---
Confidence 455677663113445556888654432 2333 22458899866554 4433 78999998654 655431
Q ss_pred cccccCCCCCHHHHHHHHHhhHHHHHHHHHH
Q 003416 264 NADWRVRPLPDEMLRYAREDTHYLLYIYDIM 294 (821)
Q Consensus 264 ~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L 294 (821)
...-|..||..+..|+..|
T Consensus 157 ------------~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 157 ------------RHHRGLDDARNIARILKRL 175 (176)
T ss_pred ------------CCcCcHHHHHHHHHHHHHh
Confidence 1123778999998888765
No 83
>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=69.49 E-value=59 Score=34.02 Aligned_cols=129 Identities=15% Similarity=0.082 Sum_probs=73.7
Q ss_pred cccCCCcEEEEEEEe---CCceEEE-ecCCc-chhhhHHHHHhhcCCCceEEEecc-hhcHHHHHHH---hCCCcC----
Q 003416 161 YRSFLGLTCLMQIST---RTEDFVV-DTLKL-RVQVGPYLREVFKDPTKKKVMHGA-DRDIVWLQRD---FGIYLC---- 227 (821)
Q Consensus 161 ~rty~g~LcLIQISt---~~~~yLI-D~Lal-~~~L~~~L~eLLeDp~IvKV~H~a-K~DL~~L~rd---~GI~~~---- 227 (821)
.....+++++|.+.. .+..+.+ ..... ...+...+..++.+-..+.|+||. .+|+..|... +|+.+.
T Consensus 46 l~~~~~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~ 125 (208)
T cd05782 46 LPLPFHKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFD 125 (208)
T ss_pred CccccCceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccC
Confidence 344556777777766 3333333 11111 113434444555542224588887 7899887643 455321
Q ss_pred --------------ccchhHHHHHhhCC-CCCcHHHHHHHHcCCCCccc----cc-cccccCCCCCHHHHHHHHHhhHHH
Q 003416 228 --------------NMFDTGQASRVLKL-ERNSLEYLLHHFCGVNANKE----YQ-NADWRVRPLPDEMLRYAREDTHYL 287 (821)
Q Consensus 228 --------------nlFDTqLAAyLLg~-~~~SLa~LvekyLgv~LdK~----~Q-~SDW~~RPLs~eql~YAA~DA~yL 287 (821)
..+|++....-.+. ...+|..+++ +||+. .|. .+ ..-|....+ .+..+|+..||..+
T Consensus 126 ~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~L~~va~-~lG~~-~K~d~~G~~v~~~y~~g~~-~~I~~Yc~~Dv~~t 202 (208)
T cd05782 126 LGNKDWNYRNRYSERHLDLMDLLAFYGARARASLDLLAK-LLGIP-GKMDVDGSQVWELYAEGKL-DEIAEYCETDVLNT 202 (208)
T ss_pred cccchhhccCcCCCCcccHHHHHhccCccCCCCHHHHHH-HhCCC-CCcCCCHHHHHHHHHcCCh-HHHHHHHHHHHHHH
Confidence 15788876554433 3689999875 67762 221 11 122444343 66889999999999
Q ss_pred HHHHH
Q 003416 288 LYIYD 292 (821)
Q Consensus 288 L~Lyd 292 (821)
..||.
T Consensus 203 ~~l~l 207 (208)
T cd05782 203 YLLYL 207 (208)
T ss_pred HHHHh
Confidence 88874
No 84
>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=67.77 E-value=1.4e+02 Score=31.20 Aligned_cols=97 Identities=14% Similarity=0.114 Sum_probs=57.8
Q ss_pred hhHHHHHhhcCCCceEEEecc-hhcHHHHHH---HhCCC--------------c--CccchhHHHHH--h-----h--CC
Q 003416 191 VGPYLREVFKDPTKKKVMHGA-DRDIVWLQR---DFGIY--------------L--CNMFDTGQASR--V-----L--KL 241 (821)
Q Consensus 191 L~~~L~eLLeDp~IvKV~H~a-K~DL~~L~r---d~GI~--------------~--~nlFDTqLAAy--L-----L--g~ 241 (821)
+...+..++.+.. ..|++|. .+|+..|.. .+|+. + .-.+|++.... . . ..
T Consensus 76 lL~~F~~~i~~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~ 154 (204)
T cd05783 76 LIREAFKIISEYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKY 154 (204)
T ss_pred HHHHHHHHHhcCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcccc
Confidence 4444556666654 4566765 679977653 35655 1 12467765422 1 1 12
Q ss_pred CCCcHHHHHHHHcCCC-CccccccccccCCCCCHHHHHHHHHhhHHHHHHHH
Q 003416 242 ERNSLEYLLHHFCGVN-ANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYD 292 (821)
Q Consensus 242 ~~~SLa~LvekyLgv~-LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd 292 (821)
.+++|..+++.+||.. ++-..+. |.. =..+.+.|+..||..++.|..
T Consensus 155 ~~~~L~~Va~~~lg~~K~~~~~~i--~~~--~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 155 REYTLDAVAKALLGEGKVELEKNI--SEL--NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccCcHHHHHHHhcCCCcccCCchh--hhh--cHHHHHHhhHHHHHHHHHHhc
Confidence 4789999999999863 1111111 211 126678999999999888753
No 85
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=66.88 E-value=13 Score=46.30 Aligned_cols=97 Identities=14% Similarity=0.154 Sum_probs=67.3
Q ss_pred ceEEEecchhcHHHHHHHhCCCcCc--cchhHHHHHh----hCC--------------------------------C---
Q 003416 204 KKKVMHGADRDIVWLQRDFGIYLCN--MFDTGQASRV----LKL--------------------------------E--- 242 (821)
Q Consensus 204 IvKV~H~aK~DL~~L~rd~GI~~~n--lFDTqLAAyL----Lg~--------------------------------~--- 242 (821)
-+.|+||..+|..-+...|.|.-.. ..|||-.+.. +.. +
T Consensus 242 ~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~~pWL~~SS 321 (1075)
T KOG3657|consen 242 QLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDYDNPWLGRSS 321 (1075)
T ss_pred ceEEeccccchHHHHHHHHhccccceeeeechhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhhhhhhhhhhh
Confidence 5679999999999888888876543 5699865331 110 0
Q ss_pred CCcHHHHHHHHcCCC-CccccccccccCCCCC------HHHHHHHHHhhHHHHHHHHHHHHHHhcC
Q 003416 243 RNSLEYLLHHFCGVN-ANKEYQNADWRVRPLP------DEMLRYAREDTHYLLYIYDIMKIKLSSM 301 (821)
Q Consensus 243 ~~SLa~LvekyLgv~-LdK~~Q~SDW~~RPLs------~eql~YAA~DA~yLL~Lyd~L~~eLee~ 301 (821)
-.||.++.+.+||+. ++|..+ .++..-++. .+.+.|+|.|++.+.+||..+.....+.
T Consensus 322 ~NSL~dVhk~~c~~~~LdKt~R-d~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fler 386 (1075)
T KOG3657|consen 322 LNSLVDVHKFHCGIDALDKTPR-DSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLER 386 (1075)
T ss_pred hHHHHHHHHhhCCCCccccchH-HhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHh
Confidence 146777788899988 777543 122222221 3457899999999999999998887664
No 86
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=63.72 E-value=1.5e+02 Score=32.63 Aligned_cols=149 Identities=22% Similarity=0.228 Sum_probs=87.7
Q ss_pred CeeEEEeeecccccCCCcEEEEEEEeC-CceEEEe---cCCcchhhhHHHHHhhcCC--CceEEEecchhcHHHHHH---
Q 003416 150 DEFAVDLEHNQYRSFLGLTCLMQISTR-TEDFVVD---TLKLRVQVGPYLREVFKDP--TKKKVMHGADRDIVWLQR--- 220 (821)
Q Consensus 150 ~~IAVDtE~~~~rty~g~LcLIQISt~-~~~yLID---~Lal~~~L~~~L~eLLeDp--~IvKV~H~aK~DL~~L~r--- 220 (821)
..+-+|+|+.++......+.++..+.. +..+.|- .-+...+. ..|..++.++ +++.-+-|..+|+..++|
T Consensus 99 ~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~~Vrq~~lp~p~~E~-avle~fl~~~~~~~lvsfNGkaFD~PfikR~v~ 177 (278)
T COG3359 99 DVAFFDIETTGLDRAGNTITLVGGARGVDDTMHVRQHFLPAPEEEV-AVLENFLHDPDFNMLVSFNGKAFDIPFIKRMVR 177 (278)
T ss_pred ceEEEeeeccccCCCCCeEEEEEEEEccCceEEEEeecCCCcchhh-HHHHHHhcCCCcceEEEecCcccCcHHHHHHHh
Confidence 477899999998773344445555543 2334332 11222122 2355555555 344556777899988862
Q ss_pred H-hCCCc-CccchhHHHHHhhCC---CCCcHHHHHHHHcCCCCcc---cc----ccccccCCC---CCHHHHHHHHHhhH
Q 003416 221 D-FGIYL-CNMFDTGQASRVLKL---ERNSLEYLLHHFCGVNANK---EY----QNADWRVRP---LPDEMLRYAREDTH 285 (821)
Q Consensus 221 d-~GI~~-~nlFDTqLAAyLLg~---~~~SLa~LvekyLgv~LdK---~~----Q~SDW~~RP---Ls~eql~YAA~DA~ 285 (821)
+ +-..+ ..-||++..++-|.- .+.+|..+-+ +||++-.- ++ -.-.|.+-+ |-+..+.|-..|+.
T Consensus 178 ~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr-~LGi~R~edtdG~~~p~lyr~~~~~~dp~ll~~l~~hN~eDvl 256 (278)
T COG3359 178 DRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVER-ILGIRREEDTDGYDGPELYRLYRRYGDPGLLDGLVLHNREDVL 256 (278)
T ss_pred cccccCccccchhhhhhhhhhhhccCCCCChhhHHH-HhCccccccCCCcchHHHHHHHHHcCCHHHHHHHHHccHHHHH
Confidence 1 23333 347999999998773 3678887555 99975321 11 011243221 11445677788888
Q ss_pred HHHHHHHHHHHHHhc
Q 003416 286 YLLYIYDIMKIKLSS 300 (821)
Q Consensus 286 yLL~Lyd~L~~eLee 300 (821)
-|..||..+...+.+
T Consensus 257 nL~~i~~h~~~~i~~ 271 (278)
T COG3359 257 NLPTIIKHVSKKILE 271 (278)
T ss_pred hHHHHHHHHHHHHHH
Confidence 888888888777653
No 87
>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=62.77 E-value=1.2e+02 Score=31.78 Aligned_cols=96 Identities=16% Similarity=0.136 Sum_probs=58.2
Q ss_pred HHHHhhc--CCCceEEEecc-hhcHHHHHH---HhCCCcC------------------ccchhHHHHH---hhCCCCCcH
Q 003416 194 YLREVFK--DPTKKKVMHGA-DRDIVWLQR---DFGIYLC------------------NMFDTGQASR---VLKLERNSL 246 (821)
Q Consensus 194 ~L~eLLe--Dp~IvKV~H~a-K~DL~~L~r---d~GI~~~------------------nlFDTqLAAy---LLg~~~~SL 246 (821)
.+..++. +|.++ +++|. .+|+..|.. .+|+.+. -.+|++.... .+..+.++|
T Consensus 79 ~f~~~i~~~~Pd~i-~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysL 157 (204)
T cd05779 79 RFFEHIREVKPHII-VTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGL 157 (204)
T ss_pred HHHHHHHHhCCCEE-EecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccH
Confidence 3444444 46664 55554 778877653 2444321 0456665443 344457899
Q ss_pred HHHHHHHcCCCCcc-cc-c-cccccCCCCCHHHHHHHHHhhHHHHHHHH
Q 003416 247 EYLLHHFCGVNANK-EY-Q-NADWRVRPLPDEMLRYAREDTHYLLYIYD 292 (821)
Q Consensus 247 a~LvekyLgv~LdK-~~-Q-~SDW~~RPLs~eql~YAA~DA~yLL~Lyd 292 (821)
..+++.+||..-.. .. . ..-|...+ ...++|+..||..++.||.
T Consensus 158 d~Va~~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 158 KAVTKAKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred HHHHHHHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 99999999963211 10 0 01354443 5789999999999999983
No 88
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=56.59 E-value=39 Score=38.94 Aligned_cols=84 Identities=18% Similarity=0.133 Sum_probs=53.3
Q ss_pred hHHHHHhhcCCCceEEEecchhcHHHHHHHhCCCcCccchhHHHH-HhhCC-C-CCcHHHHHHHHcCCCCcccccccccc
Q 003416 192 GPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQAS-RVLKL-E-RNSLEYLLHHFCGVNANKEYQNADWR 268 (821)
Q Consensus 192 ~~~L~eLLeDp~IvKV~H~aK~DL~~L~rd~GI~~~nlFDTqLAA-yLLg~-~-~~SLa~LvekyLgv~LdK~~Q~SDW~ 268 (821)
...|.. |-+++-+-|+|+.-.|+..|...| ..+.||.+.- +-.++ + ..+|..|++.|||..+.-+....
T Consensus 284 q~~l~~-~~~~~TILVGHSLenDL~aLKl~H----~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~H--- 355 (380)
T KOG2248|consen 284 QKELLE-LISKNTILVGHSLENDLKALKLDH----PSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGGH--- 355 (380)
T ss_pred HHHHHh-hcCcCcEEEeechhhHHHHHhhhC----CceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCCC---
Confidence 344556 445666779999999999995433 3466888332 22331 3 46799999999997664111101
Q ss_pred CCCCCHHHHHHHHHhhHHHHHHHHH
Q 003416 269 VRPLPDEMLRYAREDTHYLLYIYDI 293 (821)
Q Consensus 269 ~RPLs~eql~YAA~DA~yLL~Lyd~ 293 (821)
-..+||...+.|...
T Consensus 356 ----------dS~eDA~acm~Lv~~ 370 (380)
T KOG2248|consen 356 ----------DSVEDALACMKLVKL 370 (380)
T ss_pred ----------ccHHHHHHHHHHHHH
Confidence 145778777777654
No 89
>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=51.64 E-value=62 Score=32.80 Aligned_cols=80 Identities=18% Similarity=0.112 Sum_probs=45.5
Q ss_pred HHHHhhcCCCceEEEec-chhcHHHHHHHh---CCCc--------CccchhHHHHHhh---CC------------CCCcH
Q 003416 194 YLREVFKDPTKKKVMHG-ADRDIVWLQRDF---GIYL--------CNMFDTGQASRVL---KL------------ERNSL 246 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~-aK~DL~~L~rd~---GI~~--------~nlFDTqLAAyLL---g~------------~~~SL 246 (821)
.+..++..+..+-|+|+ +.+|+..|.+.+ ++.+ ...+||.-.++++ .+ ..++|
T Consensus 75 ~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L 154 (183)
T cd06138 75 KIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKL 154 (183)
T ss_pred HHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhH
Confidence 34455654444568886 799999986543 2211 1245776544432 11 25779
Q ss_pred HHHHHHHcCCCCccccccccccCCCCCHHHHHHHHHhhHHHHHH
Q 003416 247 EYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYI 290 (821)
Q Consensus 247 a~LvekyLgv~LdK~~Q~SDW~~RPLs~eql~YAA~DA~yLL~L 290 (821)
+.|+++ +|+... ...-|..||..+..|
T Consensus 155 ~~l~~~-~gi~~~----------------~~H~Al~Da~~ta~l 181 (183)
T cd06138 155 EDLAQA-NGIEHS----------------NAHDALSDVEATIAL 181 (183)
T ss_pred HHHHHH-CCCCcc----------------ccccHHHHHHHHHHH
Confidence 999976 465431 112366777766554
No 90
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=48.09 E-value=1.2e+02 Score=31.35 Aligned_cols=88 Identities=14% Similarity=0.157 Sum_probs=54.6
Q ss_pred HHHHHhhcCCCceEEEecchhcHHHHHHH---hCCCc---CccchhHHHHHhh-CC-CCCcHHHHHHHHcCCCCcccccc
Q 003416 193 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL---CNMFDTGQASRVL-KL-ERNSLEYLLHHFCGVNANKEYQN 264 (821)
Q Consensus 193 ~~L~eLLeDp~IvKV~H~aK~DL~~L~rd---~GI~~---~nlFDTqLAAyLL-g~-~~~SLa~LvekyLgv~LdK~~Q~ 264 (821)
+.|..++.+...+ |+|.+..|+..|.+. +|+.. ..+.|++.....+ +. ..++|..++++| |+.... +
T Consensus 84 ~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~-gi~~~~--~- 158 (207)
T PRK07748 84 EKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEEY-GKEGTG--K- 158 (207)
T ss_pred HHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHHHc-CCCCCC--C-
Confidence 3455667653333 446678999888654 35432 2367777665433 32 258999988764 543210 0
Q ss_pred ccccCCCCCHHHHHHHHHhhHHHHHHHHHHHHH
Q 003416 265 ADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 297 (821)
Q Consensus 265 SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 297 (821)
..-|..||..+..|+..|...
T Consensus 159 ------------~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 159 ------------HHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred ------------CcChHHHHHHHHHHHHHHHhC
Confidence 123788999999999988765
No 91
>PRK05762 DNA polymerase II; Reviewed
Probab=38.04 E-value=3.3e+02 Score=34.35 Aligned_cols=98 Identities=20% Similarity=0.276 Sum_probs=60.2
Q ss_pred HHHHhhc--CCCceEEEecc-hhcHHHHHHH---hCCCc-------------------------Cc--cchhHHHHHhh-
Q 003416 194 YLREVFK--DPTKKKVMHGA-DRDIVWLQRD---FGIYL-------------------------CN--MFDTGQASRVL- 239 (821)
Q Consensus 194 ~L~eLLe--Dp~IvKV~H~a-K~DL~~L~rd---~GI~~-------------------------~n--lFDTqLAAyLL- 239 (821)
.|..++. ||+|+ ++||. .+|+..|... +|+.+ .+ ++|+....+-.
T Consensus 209 ~F~~~i~~~DPDII-vGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~ 287 (786)
T PRK05762 209 KFNAWFAEHDPDVI-IGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSAT 287 (786)
T ss_pred HHHHHHHhcCCCEE-EEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhh
Confidence 3334443 57764 78886 5799777532 34421 01 45777665532
Q ss_pred -CCCCCcHHHHHHHHcCCCCcc--c----ccc-ccccCCCCCHHHHHHHHHhhHHHHHHHHHH
Q 003416 240 -KLERNSLEYLLHHFCGVNANK--E----YQN-ADWRVRPLPDEMLRYAREDTHYLLYIYDIM 294 (821)
Q Consensus 240 -g~~~~SLa~LvekyLgv~LdK--~----~Q~-SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L 294 (821)
...+++|..+++++||..-.. . .+. .-|... .....+|...|+..++.|+..+
T Consensus 288 ~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 288 WVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred ccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 445799999999999854211 0 111 113211 1567899999999999999843
No 92
>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=28.36 E-value=80 Score=33.30 Aligned_cols=67 Identities=24% Similarity=0.240 Sum_probs=44.6
Q ss_pred cchhHHHHH-hhCCCCCcHHHHHHHHcCCCCcc-c-ccccc-ccCCCCC-HHHHHHHHHhhHHHHHHHHHHH
Q 003416 229 MFDTGQASR-VLKLERNSLEYLLHHFCGVNANK-E-YQNAD-WRVRPLP-DEMLRYAREDTHYLLYIYDIMK 295 (821)
Q Consensus 229 lFDTqLAAy-LLg~~~~SLa~LvekyLgv~LdK-~-~Q~SD-W~~RPLs-~eql~YAA~DA~yLL~Lyd~L~ 295 (821)
++|+..... .....+++|..+++++||..-.. . ..... |...|-. ...++|...||.+.++|+..|.
T Consensus 153 ~iD~~~~~~~~~kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 153 QFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred eeeHHHHHHHhcCcccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 557776654 23445799999999999964321 1 12222 3333321 4689999999999999998874
No 93
>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=25.42 E-value=2.9e+02 Score=27.78 Aligned_cols=30 Identities=17% Similarity=0.255 Sum_probs=20.5
Q ss_pred CceEEEecchhcHHHHHHHh---CCCcCc-cchh
Q 003416 203 TKKKVMHGADRDIVWLQRDF---GIYLCN-MFDT 232 (821)
Q Consensus 203 ~IvKV~H~aK~DL~~L~rd~---GI~~~n-lFDT 232 (821)
..+-|+|++.+|+.+|.+.+ |....+ ..||
T Consensus 94 ~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~ 127 (173)
T cd06135 94 KSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDV 127 (173)
T ss_pred CCceeecchhhCHHHHHHHHHHHhccCCcchhhH
Confidence 46778999999999986544 433332 5676
No 94
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.87 E-value=91 Score=30.34 Aligned_cols=46 Identities=20% Similarity=0.413 Sum_probs=36.1
Q ss_pred cCHHHHHHHHHhCCCCHHHHHhhhcCCh-hHHHHhHHHHHHHHHHhH
Q 003416 378 LPNRTLIEIAKQLPTTAAKLRRLLKSKH-SYIERYMGPVLSIIKNSM 423 (821)
Q Consensus 378 L~D~~LleLA~~~P~t~~eL~~l~g~~~-~~vrr~g~eIL~iI~~a~ 423 (821)
|+....+.||--+|+|.++|..|...-. ......++.|+++|.+..
T Consensus 66 ~~e~~avkIadI~P~t~~ElRsIla~e~~~~s~E~l~~Ildiv~Ky~ 112 (114)
T COG1460 66 MSEKIAVKIADIMPRTPDELRSILAKERVMLSDEELDKILDIVDKYR 112 (114)
T ss_pred ccHHHHHHHHHhCCCCHHHHHHHHHHccCCCCHHHHHHHHHHHHHHh
Confidence 6889999999999999999998864322 223477889999988754
No 95
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=24.37 E-value=2e+02 Score=27.06 Aligned_cols=46 Identities=24% Similarity=0.457 Sum_probs=33.9
Q ss_pred cccCHHHHHHHHHhCCCCHHHHHhhhcCCh-hHHHHhHHHHHHHHHH
Q 003416 376 YVLPNRTLIEIAKQLPTTAAKLRRLLKSKH-SYIERYMGPVLSIIKN 421 (821)
Q Consensus 376 ~VL~D~~LleLA~~~P~t~~eL~~l~g~~~-~~vrr~g~eIL~iI~~ 421 (821)
+-|....++.|+..+|++..++..|..... .+-....+.||++|.+
T Consensus 69 ~~L~~~E~~qi~Nl~P~~~~El~~ii~~~~~r~~ee~l~~iL~~v~~ 115 (117)
T PF03874_consen 69 FGLTEFEILQIINLRPTTAVELRAIIESLESRFSEEDLEEILDLVSK 115 (117)
T ss_dssp STS-HHHHHHHHHH--SSHHHHHHHSTTGTTTSTHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHhcCCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHH
Confidence 338999999999999999999999875544 3345778888888875
No 96
>PRK06722 exonuclease; Provisional
Probab=23.69 E-value=2.9e+02 Score=30.67 Aligned_cols=84 Identities=12% Similarity=0.053 Sum_probs=49.2
Q ss_pred HHHHhhcCCCceEEEecchhcHHHHHHH---hCCCcC-----ccchhHHHHH-hhC---CCCCcHHHHHHHHcCCCCccc
Q 003416 194 YLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYLC-----NMFDTGQASR-VLK---LERNSLEYLLHHFCGVNANKE 261 (821)
Q Consensus 194 ~L~eLLeDp~IvKV~H~aK~DL~~L~rd---~GI~~~-----nlFDTqLAAy-LLg---~~~~SLa~LvekyLgv~LdK~ 261 (821)
.|..++.+. . -|.|++.+|+..|.+. +|+... ..+|++-.++ +.. ...++|..|++.| |+....
T Consensus 83 ef~~fig~~-~-lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~l-gL~~~g- 158 (281)
T PRK06722 83 KFIQFIGED-S-IFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQL-GLIWEG- 158 (281)
T ss_pred HHHHHHCCC-c-EEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHC-CCCCCC-
Confidence 344566543 2 3567789999888764 344321 1367764332 221 1247899998875 544321
Q ss_pred cccccccCCCCCHHHHHHHHHhhHHHHHHHHHHH
Q 003416 262 YQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 295 (821)
Q Consensus 262 ~Q~SDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~ 295 (821)
+. .=|..||..+..|+..|.
T Consensus 159 -~~-------------HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 159 -KQ-------------HRALADAENTANILLKAY 178 (281)
T ss_pred -CC-------------cCcHHHHHHHHHHHHHHh
Confidence 11 126678888888887775
No 97
>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=22.92 E-value=1.4e+02 Score=32.13 Aligned_cols=54 Identities=20% Similarity=0.184 Sum_probs=38.9
Q ss_pred CCCceEEEecchhcHHHHHHHhCCC---------------cCccchhHHHHHhhCCCCCcHHHHHHHHc
Q 003416 201 DPTKKKVMHGADRDIVWLQRDFGIY---------------LCNMFDTGQASRVLKLERNSLEYLLHHFC 254 (821)
Q Consensus 201 Dp~IvKV~H~aK~DL~~L~rd~GI~---------------~~nlFDTqLAAyLLg~~~~SLa~LvekyL 254 (821)
+.++..|+|++-.|+..|++.|--. ...++||-+.+..+.....+|..|...+.
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~~~~L~~l~~~l~ 215 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECPGKSTSLQELAEELG 215 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS-SSHHHHHHHTT
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhccccccCHHHHHHHhC
Confidence 3458899999999998876543222 13478999999888755789999988753
No 98
>PRK05359 oligoribonuclease; Provisional
Probab=22.31 E-value=8.5e+02 Score=24.90 Aligned_cols=37 Identities=22% Similarity=0.197 Sum_probs=22.6
Q ss_pred eEEEecchhcHHHHHHHh---CCCcC-ccch--hH-HHHHhhCC
Q 003416 205 KKVMHGADRDIVWLQRDF---GIYLC-NMFD--TG-QASRVLKL 241 (821)
Q Consensus 205 vKV~H~aK~DL~~L~rd~---GI~~~-nlFD--Tq-LAAyLLg~ 241 (821)
.-|+|++.+|+.+|.+.+ +..+. .+.| |. ..++.+.+
T Consensus 100 ~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~P 143 (181)
T PRK05359 100 PLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWKP 143 (181)
T ss_pred ceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhCh
Confidence 348899999998887654 44443 3556 33 34444444
No 99
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=21.65 E-value=1.2e+02 Score=29.03 Aligned_cols=45 Identities=24% Similarity=0.434 Sum_probs=36.0
Q ss_pred cCHHHHHHHHHhCCCCHHHHHhhhcCC-hhHHHHhHHHHHHHHHHh
Q 003416 378 LPNRTLIEIAKQLPTTAAKLRRLLKSK-HSYIERYMGPVLSIIKNS 422 (821)
Q Consensus 378 L~D~~LleLA~~~P~t~~eL~~l~g~~-~~~vrr~g~eIL~iI~~a 422 (821)
|+....+.||.-+|.|.+++..+.... ..+-...+++||++|.+.
T Consensus 65 l~e~~a~~I~nL~P~~~dElrai~~~~~~~~~~e~l~~ILd~l~k~ 110 (112)
T PRK14981 65 MKEKTAVKIADILPETRDELRAIFAKERYTLSPEELDEILDIVKKY 110 (112)
T ss_pred CCHHHHHHHHhcCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHh
Confidence 688899999999999999999987544 223457788888888764
No 100
>PRK02925 glucuronate isomerase; Reviewed
Probab=21.41 E-value=2e+02 Score=34.27 Aligned_cols=74 Identities=11% Similarity=0.040 Sum_probs=50.4
Q ss_pred HHHHHhhhcCChhHHHHhHHHHHHHHHHhHhcccchHHHHHHHHHHHHhhhcccchhhccCchh-hccc------cCCCC
Q 003416 394 AAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNAANFEVIAQKLKEERMEVASEETEVLVLDTSS-NLKI------PNVGR 466 (821)
Q Consensus 394 ~~eL~~l~g~~~~~vrr~g~eIL~iI~~a~~~~~~~~al~elLlk~~~e~~~va~~~lia~~~d-l~~i------a~~~~ 466 (821)
.-+|.+..|+....-.+++++|++.+.+.++.++ +--+...++.+|. +|+|++| ++.+ |++..
T Consensus 104 hlELkr~FGi~~~l~~~nA~~Iwd~~n~~L~~p~-------f~~r~Ll~~~nVe---~icTTDDP~DdL~~H~~l~~d~~ 173 (466)
T PRK02925 104 HLELRRVFGITELLSPETADEIWDEINELLATPE-------FRPRALIERFNVE---VICTTDDPLDDLEYHKAIAEDGS 173 (466)
T ss_pred HHHHHHHcCCCCCCChhhHHHHHHHHHHHHCCCC-------CCHHHHHHHCCce---EEEecCCCCccHHHHHHHHhcCC
Confidence 3468888887666556899999999988888765 2235555667776 5777766 5544 44333
Q ss_pred CCCcccccccc
Q 003416 467 ESVDGVDALVG 477 (821)
Q Consensus 467 ~~v~al~gwr~ 477 (821)
=++.-+..||-
T Consensus 174 f~~~VlPtfRP 184 (466)
T PRK02925 174 FDGRVLPTFRP 184 (466)
T ss_pred CCceEecCcCC
Confidence 36667778885
No 101
>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=20.97 E-value=1e+02 Score=32.76 Aligned_cols=63 Identities=17% Similarity=0.179 Sum_probs=42.8
Q ss_pred cchhHHHHH-hhCCCCCcHHHHHHHHcCCCCcc--cccccccc-C-CC-CCHHHHHHHHHhhHHHHHHH
Q 003416 229 MFDTGQASR-VLKLERNSLEYLLHHFCGVNANK--EYQNADWR-V-RP-LPDEMLRYAREDTHYLLYIY 291 (821)
Q Consensus 229 lFDTqLAAy-LLg~~~~SLa~LvekyLgv~LdK--~~Q~SDW~-~-RP-Ls~eql~YAA~DA~yLL~Ly 291 (821)
++|+....+ -+...+++|..++.++||...+. ....++|- . .+ --...+.|...||...++|.
T Consensus 162 ~lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 162 ILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred EeEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 678875554 45566899999999999986542 12445552 1 11 12557889999999888774
Done!