Query 002503
Match_columns 914
No_of_seqs 409 out of 1748
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 01:16:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002503.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002503hhsearch_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 2E-62 4.3E-67 550.6 21.3 351 43-432 120-479 (687)
2 PRK10829 ribonuclease D; Provi 100.0 2.3E-49 4.9E-54 442.1 31.2 288 108-437 2-290 (373)
3 COG0349 Rnd Ribonuclease D [Tr 100.0 3.3E-45 7.1E-50 401.1 26.1 286 112-438 1-287 (361)
4 TIGR01388 rnd ribonuclease D. 100.0 4E-44 8.7E-49 400.4 31.1 286 111-438 1-287 (367)
5 cd06129 RNaseD_like DEDDy 3'-5 100.0 1.1E-29 2.4E-34 253.0 16.7 157 118-274 2-161 (161)
6 cd06146 mut-7_like_exo DEDDy 3 100.0 9.8E-29 2.1E-33 254.0 18.2 165 109-273 1-192 (193)
7 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 8.5E-27 1.8E-31 232.7 17.9 162 112-273 1-169 (170)
8 cd06148 Egl_like_exo DEDDy 3'- 99.9 6.3E-27 1.4E-31 241.1 14.6 159 121-280 3-181 (197)
9 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 1.2E-25 2.7E-30 222.1 17.5 169 109-277 1-176 (176)
10 cd06142 RNaseD_exo DEDDy 3'-5' 99.8 4.4E-19 9.6E-24 176.8 20.6 172 118-299 2-174 (178)
11 cd06147 Rrp6p_like_exo DEDDy 3 99.8 2E-18 4.3E-23 176.5 20.3 176 106-281 2-177 (192)
12 smart00474 35EXOc 3'-5' exonuc 99.8 5.4E-18 1.2E-22 166.2 18.8 166 110-276 2-171 (172)
13 PRK05755 DNA polymerase I; Pro 99.7 8.8E-16 1.9E-20 189.6 31.5 173 106-280 293-473 (880)
14 PRK14975 bifunctional 3'-5' ex 99.7 3.2E-15 6.8E-20 176.3 23.2 142 108-279 2-147 (553)
15 cd09018 DEDDy_polA_RNaseD_like 99.6 3.7E-15 8.1E-20 144.2 14.4 143 130-273 1-149 (150)
16 cd00007 35EXOc 3'-5' exonuclea 99.6 6.3E-15 1.4E-19 141.8 14.7 146 130-275 2-154 (155)
17 cd06140 DNA_polA_I_Bacillus_li 99.6 5.1E-14 1.1E-18 141.3 16.7 152 128-280 3-160 (178)
18 cd06139 DNA_polA_I_Ecoli_like_ 99.4 6.4E-12 1.4E-16 126.8 17.2 151 126-278 3-172 (193)
19 KOG4373 Predicted 3'-5' exonuc 99.4 2.4E-13 5.2E-18 147.8 5.2 149 497-712 104-252 (319)
20 KOG2207 Predicted 3'-5' exonuc 99.3 5.9E-12 1.3E-16 145.3 7.3 172 106-277 389-586 (617)
21 COG0749 PolA DNA polymerase I 99.2 2.8E-09 6.1E-14 125.3 25.0 169 110-280 4-184 (593)
22 TIGR00593 pola DNA polymerase 99.2 1.4E-08 3E-13 125.8 30.2 166 109-280 304-481 (887)
23 PF00570 HRDC: HRDC domain Blo 98.9 1.5E-09 3.2E-14 93.5 5.9 68 343-426 1-68 (68)
24 smart00341 HRDC Helicase and R 98.9 6E-09 1.3E-13 92.3 7.8 76 341-432 2-77 (81)
25 cd06128 DNA_polA_exo DEDDy 3'- 98.7 3.2E-07 7E-12 90.1 15.0 126 144-273 17-150 (151)
26 KOG4373 Predicted 3'-5' exonuc 97.7 7.9E-05 1.7E-09 82.3 7.4 127 143-269 145-281 (319)
27 cd06125 DnaQ_like_exo DnaQ-lik 97.6 0.00029 6.3E-09 65.3 9.5 73 131-213 1-83 (96)
28 TIGR01389 recQ ATP-dependent D 97.3 0.00049 1.1E-08 82.6 7.5 70 343-428 521-590 (591)
29 PRK06310 DNA polymerase III su 96.1 0.085 1.8E-06 57.3 13.3 132 125-276 4-174 (250)
30 PRK06063 DNA polymerase III su 95.8 0.18 3.9E-06 56.6 14.9 92 171-281 86-184 (313)
31 PRK07740 hypothetical protein; 95.7 0.2 4.3E-06 54.3 14.1 92 171-281 133-231 (244)
32 PRK06807 DNA polymerase III su 95.6 0.16 3.5E-06 57.0 13.3 89 171-279 80-175 (313)
33 KOG2405 Predicted 3'-5' exonuc 95.3 0.0091 2E-07 67.4 2.4 125 148-275 214-360 (458)
34 cd06144 REX4_like DEDDh 3'-5' 95.3 0.1 2.2E-06 52.2 9.5 81 170-269 68-151 (152)
35 PRK08517 DNA polymerase III su 95.2 0.33 7.2E-06 53.1 13.8 133 125-278 65-233 (257)
36 TIGR01298 RNaseT ribonuclease 95.1 0.58 1.3E-05 49.1 14.8 85 182-282 106-198 (200)
37 PRK07883 hypothetical protein; 95.1 0.21 4.5E-06 60.3 12.8 138 123-281 10-187 (557)
38 cd06131 DNA_pol_III_epsilon_Ec 95.0 0.39 8.6E-06 48.0 12.9 86 170-272 72-166 (167)
39 TIGR01405 polC_Gram_pos DNA po 95.0 0.32 6.9E-06 63.5 14.8 135 126-281 188-360 (1213)
40 PF14239 RRXRR: RRXRR protein 94.9 0.01 2.2E-07 61.3 1.0 48 511-558 1-48 (176)
41 cd06149 ISG20 DEDDh 3'-5' exon 94.7 0.28 6E-06 49.5 10.8 83 170-269 68-156 (157)
42 PRK05168 ribonuclease T; Provi 94.6 0.97 2.1E-05 47.8 15.1 148 118-281 7-206 (211)
43 cd06145 REX1_like DEDDh 3'-5' 94.6 0.38 8.2E-06 48.1 11.3 80 172-269 68-149 (150)
44 PRK07942 DNA polymerase III su 94.5 0.64 1.4E-05 50.0 13.5 82 182-280 94-184 (232)
45 PRK11057 ATP-dependent DNA hel 94.4 0.075 1.6E-06 64.5 7.2 73 343-431 532-604 (607)
46 cd06127 DEDDh DEDDh 3'-5' exon 94.3 0.63 1.4E-05 44.6 11.9 82 170-269 70-158 (159)
47 TIGR00573 dnaq exonuclease, DN 94.1 0.54 1.2E-05 49.8 11.8 92 171-279 79-180 (217)
48 TIGR01406 dnaQ_proteo DNA poly 94.0 0.63 1.4E-05 49.8 12.3 87 171-274 74-170 (225)
49 PRK09145 DNA polymerase III su 93.9 1.2 2.7E-05 46.4 14.0 135 118-273 19-198 (202)
50 cd05160 DEDDy_DNA_polB_exo DED 93.9 0.82 1.8E-05 47.2 12.5 99 170-269 67-198 (199)
51 PF13482 RNase_H_2: RNase_H su 93.8 0.15 3.2E-06 50.8 6.6 141 131-272 1-163 (164)
52 PRK05601 DNA polymerase III su 93.7 0.88 1.9E-05 52.4 13.2 136 125-272 43-245 (377)
53 PRK05711 DNA polymerase III su 93.6 0.81 1.8E-05 49.7 12.2 87 172-275 79-175 (240)
54 smart00479 EXOIII exonuclease 93.4 1.3 2.8E-05 43.8 12.5 89 170-276 71-167 (169)
55 PRK06309 DNA polymerase III su 93.3 1.2 2.6E-05 47.8 12.8 88 172-277 72-167 (232)
56 COG2176 PolC DNA polymerase II 93.1 0.23 5.1E-06 63.1 8.1 135 126-281 419-591 (1444)
57 cd06130 DNA_pol_III_epsilon_li 92.9 2.1 4.6E-05 42.0 13.1 80 170-269 68-154 (156)
58 KOG2249 3'-5' exonuclease [Rep 92.8 0.9 1.9E-05 49.9 10.9 131 129-279 106-269 (280)
59 cd06137 DEDDh_RNase DEDDh 3'-5 92.7 0.33 7.2E-06 49.0 7.2 61 172-237 76-141 (161)
60 PRK07246 bifunctional ATP-depe 92.5 1.4 3E-05 55.8 13.8 91 171-280 78-174 (820)
61 TIGR01407 dinG_rel DnaQ family 92.3 1.7 3.7E-05 55.1 14.4 91 171-280 72-169 (850)
62 KOG2405 Predicted 3'-5' exonuc 91.9 0.015 3.2E-07 65.8 -3.8 120 144-264 73-215 (458)
63 PRK09146 DNA polymerase III su 91.7 3.4 7.3E-05 44.8 13.9 86 172-276 122-227 (239)
64 cd06136 TREX1_2 DEDDh 3'-5' ex 91.4 2.5 5.4E-05 43.4 12.0 79 172-269 87-174 (177)
65 cd05780 DNA_polB_Kod1_like_exo 90.5 2.7 5.9E-05 43.8 11.4 102 170-272 60-195 (195)
66 PLN03137 ATP-dependent DNA hel 90.3 0.6 1.3E-05 60.2 7.5 71 344-430 1029-1101(1195)
67 PRK08074 bifunctional ATP-depe 90.3 3.6 7.8E-05 52.8 14.4 91 171-280 76-173 (928)
68 cd06143 PAN2_exo DEDDh 3'-5' e 90.3 0.68 1.5E-05 48.1 6.6 77 173-269 95-173 (174)
69 PRK00448 polC DNA polymerase I 88.9 2.5 5.5E-05 56.3 11.7 84 181-281 499-589 (1437)
70 PF13391 HNH_2: HNH endonuclea 86.5 0.37 8E-06 41.0 1.5 48 574-621 1-59 (66)
71 PF06147 DUF968: Protein of un 86.3 0.49 1.1E-05 50.0 2.6 67 564-639 119-186 (200)
72 cd06134 RNaseT DEDDh 3'-5' exo 86.2 4.4 9.5E-05 42.1 9.5 77 182-274 103-187 (189)
73 PF01844 HNH: HNH endonuclease 84.4 0.4 8.7E-06 38.1 0.7 41 574-621 1-45 (47)
74 cd00085 HNHc HNH nucleases; HN 81.3 0.49 1.1E-05 38.1 0.1 41 572-619 12-55 (57)
75 COG0514 RecQ Superfamily II DN 79.0 2.5 5.5E-05 51.4 5.0 49 343-391 517-565 (590)
76 cd05785 DNA_polB_like2_exo Unc 78.3 20 0.00044 38.0 11.1 139 128-269 9-206 (207)
77 PRK09182 DNA polymerase III su 78.0 32 0.0007 38.6 13.0 83 171-272 112-197 (294)
78 PRK06195 DNA polymerase III su 73.7 18 0.00039 40.6 9.7 88 171-278 72-166 (309)
79 smart00507 HNHc HNH nucleases. 72.6 1.7 3.8E-05 34.2 1.0 40 572-618 11-52 (52)
80 cd05779 DNA_polB_epsilon_exo D 71.9 41 0.00089 35.8 11.3 89 179-270 88-204 (204)
81 cd05781 DNA_polB_B3_exo DEDDy 69.6 73 0.0016 33.3 12.4 141 129-271 4-187 (188)
82 COG3183 Predicted restriction 66.5 2.9 6.3E-05 45.9 1.4 48 572-623 196-254 (272)
83 cd05783 DNA_polB_B1_exo DEDDy 66.3 84 0.0018 33.3 12.3 97 169-270 76-202 (204)
84 COG3359 Predicted exonuclease 62.2 1.2E+02 0.0026 33.7 12.4 150 129-279 99-272 (278)
85 COG0847 DnaQ DNA polymerase II 61.5 1E+02 0.0022 32.8 12.0 132 128-275 13-181 (243)
86 KOG1275 PAB-dependent poly(A) 59.5 5.1 0.00011 50.4 1.8 84 176-280 1009-1095(1118)
87 PRK11779 sbcB exonuclease I; P 58.5 35 0.00076 40.9 8.5 87 172-275 84-197 (476)
88 PRK07247 DNA polymerase III su 56.2 41 0.00088 35.5 7.7 85 170-275 75-168 (195)
89 PRK11295 hypothetical protein; 54.9 7.2 0.00016 38.0 1.7 62 564-637 17-84 (113)
90 cd05782 DNA_polB_like1_exo Unc 54.4 1.2E+02 0.0026 32.2 10.9 127 141-270 47-207 (208)
91 PRK07983 exodeoxyribonuclease 52.7 61 0.0013 34.8 8.5 77 182-274 75-152 (219)
92 PRK05766 rps14P 30S ribosomal 51.2 6.7 0.00014 33.2 0.7 25 571-595 14-41 (52)
93 PRK08061 rpsN 30S ribosomal pr 51.1 7.7 0.00017 33.9 1.1 28 568-595 18-46 (61)
94 PF11408 Helicase_Sgs1: Sgs1 R 51.0 32 0.0007 31.7 5.1 46 346-391 8-53 (80)
95 KOG2248 3'-5' exonuclease [Rep 50.6 41 0.00088 39.3 7.1 83 171-271 285-370 (380)
96 PRK07748 sporulation inhibitor 49.4 91 0.002 32.8 9.0 90 169-275 82-179 (207)
97 PF04161 Arv1: Arv1-like famil 48.1 5.9 0.00013 42.1 -0.1 37 573-624 2-38 (208)
98 PF09281 Taq-exonuc: Taq polym 46.2 72 0.0016 32.1 7.0 69 189-276 70-138 (138)
99 COG0199 RpsN Ribosomal protein 43.1 9.5 0.00021 33.4 0.5 17 570-586 20-36 (61)
100 cd06133 ERI-1_3'hExo_like DEDD 40.1 1.6E+02 0.0035 29.2 8.9 86 170-272 79-175 (176)
101 cd06138 ExoI_N N-terminal DEDD 39.1 1E+02 0.0022 31.8 7.3 65 171-236 74-165 (183)
102 PF00253 Ribosomal_S14: Riboso 38.3 13 0.00028 31.6 0.6 20 568-587 13-32 (55)
103 PF09706 Cas_CXXC_CXXC: CRISPR 35.0 22 0.00047 31.7 1.4 52 568-619 2-60 (69)
104 KOG3506 40S ribosomal protein 34.4 13 0.00028 31.9 -0.1 25 572-596 19-46 (56)
105 cd05784 DNA_polB_II_exo DEDDy 34.2 62 0.0013 34.1 4.9 62 207-270 123-193 (193)
106 COG4855 Uncharacterized protei 33.8 19 0.0004 32.2 0.8 45 570-619 22-72 (76)
107 COG1403 McrA Restriction endon 29.1 16 0.00035 34.9 -0.4 48 568-623 66-115 (146)
108 PRK05762 DNA polymerase II; Re 28.5 5.2E+02 0.011 33.1 12.5 91 179-272 218-348 (786)
109 cd05777 DNA_polB_delta_exo DED 27.9 87 0.0019 33.5 4.9 67 207-273 153-224 (230)
110 PF08662 eIF2A: Eukaryotic tra 26.6 79 0.0017 33.0 4.2 51 508-559 102-158 (194)
111 PTZ00218 40S ribosomal protein 22.3 41 0.00088 28.9 0.9 26 571-596 16-44 (54)
112 PRK10291 glyoxalase I; Provisi 22.0 68 0.0015 30.3 2.4 25 510-538 104-128 (129)
113 PHA03093 EEV glycoprotein; Pro 21.5 1.1E+02 0.0024 32.3 4.0 31 7-37 41-71 (185)
114 KOG3657 Mitochondrial DNA poly 20.9 2.7E+02 0.0059 35.8 7.6 98 182-280 242-387 (1075)
115 PF04981 NMD3: NMD3 family ; 20.1 38 0.00081 36.7 0.3 45 574-621 1-46 (236)
116 PF02002 TFIIE_alpha: TFIIE al 20.1 77 0.0017 29.8 2.3 37 693-731 2-50 (105)
117 PRK09685 DNA-binding transcrip 20.0 1.8E+02 0.0039 31.8 5.5 50 686-737 194-243 (302)
No 1
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-62 Score=550.58 Aligned_cols=351 Identities=39% Similarity=0.617 Sum_probs=307.9
Q ss_pred cCCCCCccccccccCCCCCCCCCccCCC---CC-----CCCCCCcHHHHHhccCCCCCCcccCCC-CCCCCCCCCeEEec
Q 002503 43 LQSEPKPQHNFKRVLADNSYSPFKHANK---EK-----SSGSHPYELEITALLENPRPEFDFSNV-DLDLQRSDSFVWVE 113 (914)
Q Consensus 43 ~~~~~kPQ~~F~~~~~dn~~~pf~p~~~---~~-----~~~~hPY~~Ei~~~~~~p~~~~~~~~~-~~~p~~~~~~~~Id 113 (914)
..++.|||+.|..++ ||+..||.|.+. +. ..+.|||+||+.++. .++.+++...+ ...|.+.+++.||+
T Consensus 120 ~~~l~kpq~~f~~~i-dn~~~pf~~~~~~~vEr~e~~~~~~~hpye~e~~~f~-~~~~~le~~~~~~~~~le~T~~~~I~ 197 (687)
T KOG2206|consen 120 TMNLLKPQVRFVEGI-DNLHHPFCSMLASEVERLEDRPREVQHPYEDEERHFR-QIDKQLEEGEPRKSSPLEITPKVWIC 197 (687)
T ss_pred cccccchHHHHhhcc-ccccCCchhhhhhhhhchhhcchhccCcchhhhhhhc-ccchhhhcccccCCCcccccCceeee
Confidence 557999999999875 999999999864 22 247899999999984 45555544332 34566778899999
Q ss_pred CHHHHHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEeCCceEEEeCCCccchhhhHHHhhcCCCCeEEEechhHhH
Q 002503 114 TKSQLNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKVFHGSDNDV 193 (914)
Q Consensus 114 T~e~L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~~yLID~laL~d~l~~L~elLaDp~IvKV~Hgak~Dl 193 (914)
|..+|.++.+.+....++|+|+|+|++++|.|++|||||+|++++||||++.+++.++.|+++|+||+|+|||||++.|+
T Consensus 198 t~~el~~l~~~l~~~~Efavdlehhsyrsf~gltclmqISTr~ed~iIDt~~l~~~i~~l~e~fsdp~ivkvfhgaD~di 277 (687)
T KOG2206|consen 198 TLGELEALPEILDSVIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKLRDHIGILNEVFSDPGIVKVFHGADTDI 277 (687)
T ss_pred chHHHHHHHHHHhhhhhhhhhccccchhhhcCceeEEEeeccchhheehhHHHHHHHHHhhhhccCCCeEEEEecCccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCcCeEeehhhHHHHcCCCCCCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHHHHHHHHHH
Q 002503 194 MWLQRDFHIYVVNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLV 273 (914)
Q Consensus 194 ~~LqrdfGI~~~nlFDTqlAAyLLg~~~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~ 273 (914)
.||||+||||++|+|||..|+++||.+.+||++|++.|||+..+|.+|++|||+|||+++|+.||+.|+|||++||+.|+
T Consensus 278 iwlqrdfgiyvvnLfdt~~a~r~L~~~r~sL~~ll~~~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr 357 (687)
T KOG2206|consen 278 IWLQRDFGIYVVNLFDTIQASRLLGLPRPSLAYLLECVCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLR 357 (687)
T ss_pred hhhhccceEEEEechhhHHHHHHhCCCcccHHHHHHHHHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCCCCCCCcchHHHHHHHhhhhhhhhhhhhhccccCCCcccchhhHHHHhhcCCCCCCCCCHHHHHHHHHHHHH
Q 002503 274 AELKQQGNENSYCPDDKFNFVLEASRRSNTVCLQVYTKEIESYPGEAAASSIFFRLLNGQGGVSSISSVTQDLVRRLCAW 353 (914)
Q Consensus 274 ~eL~e~g~~~~~~~~~~~~~v~e~~~~s~~~~l~~Y~k~~~~~pg~~~~~~~~~r~l~~~~~~~~~~~~~l~vlr~L~~W 353 (914)
.+|.+.+.... -.+.++..+|...|.++.++..+ ++.++. . ..+++.+|+.+|++|++|
T Consensus 358 ~el~~~a~~~~-----------~~~~~~~d~c~~~~~k~~~~~~s---y~~v~~-~------q~~ln~~q~~~l~~L~~w 416 (687)
T KOG2206|consen 358 KELKRLAKGRA-----------VTYSESRDMCTNGYKKKTFCTKS---YLEVED-I------QSRLNSSQLDVLRALLRW 416 (687)
T ss_pred HHHHHHhcccc-----------cccchhhhhhhcceecccCCCcc---hHhHHH-H------HhccchhHHHHHHHHHHH
Confidence 99988763221 12236678999999998875432 222221 1 123678999999999999
Q ss_pred HHHHHHHhCCCcCcccChHHHHHHHHhCCCCHHHHHHHHhhcCCcccccccCCCCCCCChhhcccHHHHHHHHHHHhhh
Q 002503 354 RDLMARVHDESLRFVLSDQAIIALANKAPANRTDVYTTIAQADSDVDCLNLSSSLPSPSPVVCSHLDDVERQVCNNVEN 432 (914)
Q Consensus 354 RD~~AR~~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~i~~~d~~~~~~~l~~~~~~~sp~Vr~hl~eL~~lI~~a~~~ 432 (914)
||.+||.+|||++|||||++|++||+.+|.+..+|++++. +.+|+|++|+++++.||+.+...
T Consensus 417 Rd~iARaeDES~~yVlpN~~ll~l~e~~P~~v~gl~~~ln----------------~~~p~vkq~~~~~~~ii~~a~~~ 479 (687)
T KOG2206|consen 417 RDFIARAEDESVHYVLPNDQLLKLAEERPDTVDGLLGGLN----------------RLSPLVKQNVMDFLYIIRSAGRG 479 (687)
T ss_pred HHHHHhhccCCCceecccHHHHHHHHHCCccHHHHHHhcc----------------CCCHHHHHHHHHHHHHHHHHhhh
Confidence 9999999999999999999999999999999999998752 35699999999999999988766
No 2
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=2.3e-49 Score=442.08 Aligned_cols=288 Identities=24% Similarity=0.331 Sum_probs=255.1
Q ss_pred CeEEecCHHHHHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEeCCceEEEeCCCccchhhhHHHhhcCCCCeEEEe
Q 002503 108 SFVWVETKSQLNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKVFH 187 (914)
Q Consensus 108 ~~~~IdT~e~L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~~yLID~laL~d~l~~L~elLaDp~IvKV~H 187 (914)
.|.+|+|+++|.++++.+..++++||||||++.++|++.+|||||++++.+|+||++++. .+..|+++|+|++|+||||
T Consensus 2 ~~~~I~t~~~L~~~~~~l~~~~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~~~-d~~~L~~ll~~~~ivKV~H 80 (373)
T PRK10829 2 NYQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGIT-DWSPFKALLRDPQVTKFLH 80 (373)
T ss_pred CcEEeCCHHHHHHHHHHHhcCCeEEEecccccCccCCCceeEEEEecCCceEEEecCCcc-chHHHHHHHcCCCeEEEEe
Confidence 478999999999999999999999999999999999999999999999999999999885 4789999999999999999
Q ss_pred chhHhHHHHHHhcCCCcCeEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHHH
Q 002503 188 GSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLL 266 (914)
Q Consensus 188 gak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL 266 (914)
++++|+.+|++++|+.+.++|||++||++||.+ +.||+.|+++|||++++|++|++||+.||||++|+.||+.||+||+
T Consensus 81 ~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~ 160 (373)
T PRK10829 81 AGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLL 160 (373)
T ss_pred ChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999987 7999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCCCCCCCcchHHHHHHHhhhhhhhhhhhhhccccCCCcccchhhHHHHhhcCCCCCCCCCHHHHHH
Q 002503 267 YIAKCLVAELKQQGNENSYCPDDKFNFVLEASRRSNTVCLQVYTKEIESYPGEAAASSIFFRLLNGQGGVSSISSVTQDL 346 (914)
Q Consensus 267 ~Lyd~L~~eL~e~g~~~~~~~~~~~~~v~e~~~~s~~~~l~~Y~k~~~~~pg~~~~~~~~~r~l~~~~~~~~~~~~~l~v 346 (914)
.||+.|.++|.+.| +++|+.|+|+.. |..... ...|+ ..|+++++. +.++++++++
T Consensus 161 ~l~~~L~~~L~~~g---------~~~w~~ee~~~l---~~~~~~---~~~~~------~~~~~ik~~---~~L~~~~lav 216 (373)
T PRK10829 161 PIAAKLMAETEAAG---------WLPAALDECRLL---CQRRQE---VLAPE------EAYRDITNA---WQLRTRQLAC 216 (373)
T ss_pred HHHHHHHHHHHHcC---------cHHHHHHHHHHH---Hhcccc---CCChH------HHHHHhccc---cCCCHHHHHH
Confidence 99999999999887 788999999753 221110 11121 247788764 3567999999
Q ss_pred HHHHHHHHHHHHHHhCCCcCcccChHHHHHHHHhCCCCHHHHHHHHhhcCCcccccccCCCCCCCChhhcccHHHHHHHH
Q 002503 347 VRRLCAWRDLMARVHDESLRFVLSDQAIIALANKAPANRTDVYTTIAQADSDVDCLNLSSSLPSPSPVVCSHLDDVERQV 426 (914)
Q Consensus 347 lr~L~~WRD~~AR~~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~i~~~d~~~~~~~l~~~~~~~sp~Vr~hl~eL~~lI 426 (914)
+++|++|||.+||.+|+|++|||+|+.|++||+++|++.++|.+. . + ....++.|.++|+.+|
T Consensus 217 l~~L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~--~-------------~--~~~~~r~~g~~ll~~i 279 (373)
T PRK10829 217 LQLLADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSL--G-------------L--SGSEIRFHGKTLLALV 279 (373)
T ss_pred HHHHHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhc--c-------------C--ChHhHHhhHHHHHHHH
Confidence 999999999999999999999999999999999999999998873 1 1 1357888998899999
Q ss_pred HHHhhhhhHHH
Q 002503 427 CNNVENLDDIL 437 (914)
Q Consensus 427 ~~a~~~~ddif 437 (914)
+.+....++-+
T Consensus 280 ~~a~~~~~~~~ 290 (373)
T PRK10829 280 AKAQALPEEAL 290 (373)
T ss_pred HHHhcCCHhhC
Confidence 98876655443
No 3
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-45 Score=401.11 Aligned_cols=286 Identities=29% Similarity=0.349 Sum_probs=250.0
Q ss_pred ecCHHHHHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEeCCceEEEeCCCccchhhhHHHhhcCCCCeEEEechhH
Q 002503 112 VETKSQLNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKVFHGSDN 191 (914)
Q Consensus 112 IdT~e~L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~~yLID~laL~d~l~~L~elLaDp~IvKV~Hgak~ 191 (914)
|++.+.++.++..+.+.+.|||||||++.++|++.+|||||+.+++.++||++.....+..|..+|.|++|+||||++++
T Consensus 1 i~~~~~l~~~~~~~~~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~~lIdpl~~~~d~~~l~~Ll~d~~v~KIfHaa~~ 80 (361)
T COG0349 1 ITTGDLLAAACALLRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEGASLIDPLAGILDLPPLVALLADPNVVKIFHAARF 80 (361)
T ss_pred CCchhHHHHHHHHhcCCCceEEecccccccccCCceEEEEEecCCCceEecccccccccchHHHHhcCCceeeeeccccc
Confidence 46778899999999999999999999999999999999999999899999998854567899999999999999999999
Q ss_pred hHHHHHHhcCCCcCeEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHHHHHHH
Q 002503 192 DVMWLQRDFHIYVVNLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIAK 270 (914)
Q Consensus 192 Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd 270 (914)
|+.+|++.||+.|.++|||++|+.++|++ ++||+.|+++++|++++|++|.+||..||||++|++||+.||.||+.||+
T Consensus 81 DL~~l~~~~g~~p~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~ 160 (361)
T COG0349 81 DLEVLLNLFGLLPTPLFDTQIAAKLAGFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYD 160 (361)
T ss_pred cHHHHHHhcCCCCCchhHHHHHHHHhCCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999988 99999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCCCCCCCcchHHHHHHHhhhhhhhhhhhhhccccCCCcccchhhHHHHhhcCCCCCCCCCHHHHHHHHHH
Q 002503 271 CLVAELKQQGNENSYCPDDKFNFVLEASRRSNTVCLQVYTKEIESYPGEAAASSIFFRLLNGQGGVSSISSVTQDLVRRL 350 (914)
Q Consensus 271 ~L~~eL~e~g~~~~~~~~~~~~~v~e~~~~s~~~~l~~Y~k~~~~~pg~~~~~~~~~r~l~~~~~~~~~~~~~l~vlr~L 350 (914)
.|.++|.+.| ++.|+.++|+..... .+ .....+ ..|+.+++ .+...+.++++++.|
T Consensus 161 ~L~~~L~~~~---------r~~~a~~ef~~l~~r---~~----~~~~~~-----~~w~~i~~---a~~~~p~~la~l~~L 216 (361)
T COG0349 161 KLTEELAREG---------RLEWAEDEFRLLPTR---RT----YKVLPE-----DAWREIKI---AHSLDPRELAVLREL 216 (361)
T ss_pred HHHHHHHHcC---------chHHHHHHHHHhhhc---cc----cccChH-----hHHHHhhh---hhcCChHHHHHHHHH
Confidence 9999999887 778999887643211 01 111111 24666654 345678999999999
Q ss_pred HHHHHHHHHHhCCCcCcccChHHHHHHHHhCCCCHHHHHHHHhhcCCcccccccCCCCCCCChhhcccHHHHHHHHHHHh
Q 002503 351 CAWRDLMARVHDESLRFVLSDQAIIALANKAPANRTDVYTTIAQADSDVDCLNLSSSLPSPSPVVCSHLDDVERQVCNNV 430 (914)
Q Consensus 351 ~~WRD~~AR~~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~i~~~d~~~~~~~l~~~~~~~sp~Vr~hl~eL~~lI~~a~ 430 (914)
++|||.+||.+|.+++|||+|+.|+++|+..|++..++.+.- .. ...++.|...++.+|.++.
T Consensus 217 a~wRe~~Ar~rd~~~~~vl~de~i~~~a~~~P~~~~~l~~l~--------------~~---~~~~~~~~~~l~~~~~~a~ 279 (361)
T COG0349 217 AAWREREARERDLARNFVLKDEALWELARYTPKNLKELDALG--------------LI---PKERRRHGKLLLALLANAL 279 (361)
T ss_pred HHHHHHHHHHhccccccccchhHHHHHHHhCCCCHHHHHhcc--------------CC---cccchhhhHHHHHHHHHHH
Confidence 999999999999999999999999999999999999998731 11 1278899999999999998
Q ss_pred hhhhHHHH
Q 002503 431 ENLDDILL 438 (914)
Q Consensus 431 ~~~ddif~ 438 (914)
+..++-++
T Consensus 280 ~~p~~~~p 287 (361)
T COG0349 280 ASPESDLP 287 (361)
T ss_pred hCchhhCC
Confidence 88765443
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=4e-44 Score=400.35 Aligned_cols=286 Identities=27% Similarity=0.382 Sum_probs=251.4
Q ss_pred EecCHHHHHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEeCCceEEEeCCCccchhhhHHHhhcCCCCeEEEechh
Q 002503 111 WVETKSQLNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKVFHGSD 190 (914)
Q Consensus 111 ~IdT~e~L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~~yLID~laL~d~l~~L~elLaDp~IvKV~Hgak 190 (914)
||+|.++|..+++.+..+++|||||||++.++|++.+|||||++++.+|+||++++. .+..|+++|+|++|.||+|+++
T Consensus 1 ~I~t~~~l~~~~~~l~~~~~ia~DtE~~~~~~y~~~l~LiQia~~~~~~liD~~~~~-~~~~L~~lL~d~~i~KV~h~~k 79 (367)
T TIGR01388 1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVII-DWSPLKELLRDESVVKVLHAAS 79 (367)
T ss_pred CcCCHHHHHHHHHHHhcCCEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCcc-cHHHHHHHHCCCCceEEEeecH
Confidence 589999999999999999999999999999999999999999999999999999874 5789999999999999999999
Q ss_pred HhHHHHHHhcCCCcCeEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHHHHHH
Q 002503 191 NDVMWLQRDFHIYVVNLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 191 ~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~Ly 269 (914)
+|+.+|++.+|+.+.++|||++|+|+||++ +.||+.|+++|||+.++|+.+.+||..|||+++|+.||+.||+||+.||
T Consensus 80 ~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~ 159 (367)
T TIGR01388 80 EDLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLY 159 (367)
T ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 999999888888888999999999999986 6899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCCCCCCCcchHHHHHHHhhhhhhhhhhhhhccccCCCcccchhhHHHHhhcCCCCCCCCCHHHHHHHHH
Q 002503 270 KCLVAELKQQGNENSYCPDDKFNFVLEASRRSNTVCLQVYTKEIESYPGEAAASSIFFRLLNGQGGVSSISSVTQDLVRR 349 (914)
Q Consensus 270 d~L~~eL~e~g~~~~~~~~~~~~~v~e~~~~s~~~~l~~Y~k~~~~~pg~~~~~~~~~r~l~~~~~~~~~~~~~l~vlr~ 349 (914)
+.|.++|++.| +..|+.++|...... ..|. ..| ...|+++++.+ .+++++++++++
T Consensus 160 ~~L~~~L~~~g---------~~~w~~ee~~~l~~~--~~~~----~~~------~~~~~~i~~~~---~l~~~~l~~l~~ 215 (367)
T TIGR01388 160 AKLMERLEESG---------RLAWLEEECTLLTDR--RTYV----VNP------EDAWRDIKNAW---QLRPQQLAVLQA 215 (367)
T ss_pred HHHHHHHHHcC---------cHHHHHHHHHHHhcc--ccCC----CCh------HHHHHHhcccc---cCCHHHHHHHHH
Confidence 99999999886 788999998753221 1111 111 12477777643 567999999999
Q ss_pred HHHHHHHHHHHhCCCcCcccChHHHHHHHHhCCCCHHHHHHHHhhcCCcccccccCCCCCCCChhhcccHHHHHHHHHHH
Q 002503 350 LCAWRDLMARVHDESLRFVLSDQAIIALANKAPANRTDVYTTIAQADSDVDCLNLSSSLPSPSPVVCSHLDDVERQVCNN 429 (914)
Q Consensus 350 L~~WRD~~AR~~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~i~~~d~~~~~~~l~~~~~~~sp~Vr~hl~eL~~lI~~a 429 (914)
|++|||.+||+.|+|++|||+|+.|++||++.|+|.++|.++ . -....++.|.++|+.+|+++
T Consensus 216 L~~wRe~~A~~~d~p~~~il~d~~l~~lA~~~P~~~~~l~~~-~----------------~~~~~~r~~~~~l~~~i~~a 278 (367)
T TIGR01388 216 LAAWREREARERDLPRNFVLKEEALWELARQAPGNLTELASL-G----------------PKGSEIRKHGDTLLALVKTA 278 (367)
T ss_pred HHHHHHHHHHHcCCCcceeeCHHHHHHHHHhCCCCHHHHHhc-c----------------CChHHHHhhHHHHHHHHHHH
Confidence 999999999999999999999999999999999999998763 1 12357899999999999998
Q ss_pred hhhhhHHHH
Q 002503 430 VENLDDILL 438 (914)
Q Consensus 430 ~~~~ddif~ 438 (914)
....++.++
T Consensus 279 ~~~~~~~~P 287 (367)
T TIGR01388 279 LALPEDALP 287 (367)
T ss_pred hhCCHhhCC
Confidence 876555433
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=1.1e-29 Score=253.01 Aligned_cols=157 Identities=33% Similarity=0.462 Sum_probs=147.8
Q ss_pred HHHHHHHHh-ccCcceEEEeecccCCCCCcEEEEEEEeC-CceEEEeCCCccchhhhHHHhhcCCCCeEEEechhHhHHH
Q 002503 118 LNELANALS-KEFFFAVDTEQHSLRSFLGFTALIQISTE-KEDYLVDTIALHDEISILQPFFADPGVCKVFHGSDNDVMW 195 (914)
Q Consensus 118 L~~lle~L~-~a~~IAVDtE~~s~rsy~g~lcLLQLSt~-~~~yLID~laL~d~l~~L~elLaDp~IvKV~Hgak~Dl~~ 195 (914)
|+++++.|. ..++||+|+||.+..++.+.+|+|||+++ +.+||||+..+...+..|+++|+|++|+||+|+++.|+..
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~~~~~L~~lL~d~~i~Kvg~~~k~D~~~ 81 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDLWK 81 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCccCHHHHHHHhCCCCEEEEEeccHHHHHH
Confidence 678899999 99999999999998888999999999999 8899999988765678899999999999999999999999
Q ss_pred HHHhcCCCcCeEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHHHHHHHHHHH
Q 002503 196 LQRDFHIYVVNLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVA 274 (914)
Q Consensus 196 LqrdfGI~~~nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~ 274 (914)
|++++|+.+.++|||++|++++|++ +.||+.|+++|+|+.++|..|++||..||||++|+.||+.||++++.||+.|++
T Consensus 82 L~~~~gi~~~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 82 LLRDFGEKLQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLRN 161 (161)
T ss_pred HHHHcCCCcccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 9888999999999999999999986 679999999999999999999999999999999999999999999999999863
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=9.8e-29 Score=253.98 Aligned_cols=165 Identities=30% Similarity=0.379 Sum_probs=149.4
Q ss_pred eEEecCHHHHHHHHHH--HhccCcceEEEeecccCCC--CCcEEEEEEEeCCceEEEeCCCcc-----chhhhHHHhhcC
Q 002503 109 FVWVETKSQLNELANA--LSKEFFFAVDTEQHSLRSF--LGFTALIQISTEKEDYLVDTIALH-----DEISILQPFFAD 179 (914)
Q Consensus 109 ~~~IdT~e~L~~lle~--L~~a~~IAVDtE~~s~rsy--~g~lcLLQLSt~~~~yLID~laL~-----d~l~~L~elLaD 179 (914)
+.+|+|++++.+++.. +....+||+|+||.....+ .+.+|+|||++.+.+|+||+..+. .....|+++|+|
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 8899999999999876654 689999999999999999988764 234579999999
Q ss_pred CCCeEEEechhHhHHHHHHhcCCC------cCeEeehhhHHHHcCC------------CCCCHHHHHHHHcCCcCCcccc
Q 002503 180 PGVCKVFHGSDNDVMWLQRDFHIY------VVNLFDTAKACEVLSK------------PQKSLAYLLETYCGVATNKFLQ 241 (914)
Q Consensus 180 p~IvKV~Hgak~Dl~~LqrdfGI~------~~nlFDTqlAAyLLg~------------~~~SLa~Lle~yLgv~ldK~~q 241 (914)
|+|+||+||+++|+.+|+++||+. +.++|||+.+++.++. ...||+.|+++++|+.++|..|
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 999999999999999999999984 5799999998887652 3679999999999999999999
Q ss_pred cccccCCCCCHHHHHHHHHchHHHHHHHHHHH
Q 002503 242 REDWRQRPLPAEMLQYAQTDAHYLLYIAKCLV 273 (914)
Q Consensus 242 ~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~ 273 (914)
++||+.||||++|+.|||.||++++.||+.|.
T Consensus 161 ~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 161 CSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999985
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=8.5e-27 Score=232.73 Aligned_cols=162 Identities=28% Similarity=0.333 Sum_probs=149.9
Q ss_pred ecCHHHHHHHHHHHh-ccCcceEEEeecccCC--CCCcEEEEEEEeCCceEEEeCCCccchhhhHHHhhcCCCCeEEEec
Q 002503 112 VETKSQLNELANALS-KEFFFAVDTEQHSLRS--FLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKVFHG 188 (914)
Q Consensus 112 IdT~e~L~~lle~L~-~a~~IAVDtE~~s~rs--y~g~lcLLQLSt~~~~yLID~laL~d~l~~L~elLaDp~IvKV~Hg 188 (914)
++++.+++.+++.+. ....||+|+||....+ +.+.+|+|||++++.+|+||+..+......|.++|++++|.||+|+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~~~~~~l~~ll~~~~i~kv~~~ 80 (170)
T cd06141 1 TDSAQDAEEAVKELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVG 80 (170)
T ss_pred CCCHHHHHHHHHHHhcCCCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhhcccHHHHHHhcCCCeeEEEee
Confidence 357888999999998 9999999999987765 7889999999999999999988876667789999999999999999
Q ss_pred hhHhHHHHHHhcCCCcCeEeehhhHHHHcCCC--CCCHHHHHHHHcCCcCC--cccccccccCCCCCHHHHHHHHHchHH
Q 002503 189 SDNDVMWLQRDFHIYVVNLFDTAKACEVLSKP--QKSLAYLLETYCGVATN--KFLQREDWRQRPLPAEMLQYAQTDAHY 264 (914)
Q Consensus 189 ak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~--~~SLa~Lle~yLgv~ld--K~~q~sDWr~RPLseeql~YAa~Da~y 264 (914)
++.|+..|.+.+|+.+.++|||++|++++++. ..||+.|++.|+|..++ |..|.+||..|||+++|+.|||.||++
T Consensus 81 ~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~ 160 (170)
T cd06141 81 IKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYA 160 (170)
T ss_pred eHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHH
Confidence 99999999889999999999999999999985 47999999999999998 788999999999999999999999999
Q ss_pred HHHHHHHHH
Q 002503 265 LLYIAKCLV 273 (914)
Q Consensus 265 LL~Lyd~L~ 273 (914)
++.||+.|.
T Consensus 161 ~~~l~~~l~ 169 (170)
T cd06141 161 SLELYRKLL 169 (170)
T ss_pred HHHHHHHHh
Confidence 999999885
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=99.94 E-value=6.3e-27 Score=241.08 Aligned_cols=159 Identities=28% Similarity=0.333 Sum_probs=143.0
Q ss_pred HHHHHhccCcceEEEeecccCCCCCcEEEEEEEeC-CceEEEeCCCcc--chhhhHHHhhcCCCCeEEEechhHhHHHHH
Q 002503 121 LANALSKEFFFAVDTEQHSLRSFLGFTALIQISTE-KEDYLVDTIALH--DEISILQPFFADPGVCKVFHGSDNDVMWLQ 197 (914)
Q Consensus 121 lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~-~~~yLID~laL~--d~l~~L~elLaDp~IvKV~Hgak~Dl~~Lq 197 (914)
.++.|.++++||||+|+.+... +|.+|||||++. +.+||||+.++. .....|+++|+|++|.||+|+++.|+.+|+
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 4577888999999999987766 689999999999 899999998875 246789999999999999999999999998
Q ss_pred HhcCCCcCeEeehhhHHHHcCCC---------CCCHHHHHHHHcCCcCCc--------ccccccccCCCCCHHHHHHHHH
Q 002503 198 RDFHIYVVNLFDTAKACEVLSKP---------QKSLAYLLETYCGVATNK--------FLQREDWRQRPLPAEMLQYAQT 260 (914)
Q Consensus 198 rdfGI~~~nlFDTqlAAyLLg~~---------~~SLa~Lle~yLgv~ldK--------~~q~sDWr~RPLseeql~YAa~ 260 (914)
+.+|+.+.++|||++|+++|++. ..||+.++++|+|+.++| ..+.+||..||||++|+.|||.
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 89999999999999999999753 269999999999998864 4678999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHcC
Q 002503 261 DAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 261 Da~yLL~Lyd~L~~eL~e~g 280 (914)
||+||+.||+.|..+|.+..
T Consensus 162 Dv~~Ll~l~~~l~~~l~~~~ 181 (197)
T cd06148 162 DVLCLLPLYYAMLDALISKF 181 (197)
T ss_pred HHHhHHHHHHHHHHHhhhhH
Confidence 99999999999999998753
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=99.93 E-value=1.2e-25 Score=222.08 Aligned_cols=169 Identities=35% Similarity=0.518 Sum_probs=153.4
Q ss_pred eEEecCHHHHHHHHHHHhccCcceEEEeecccCC--CCCcEEEEEEEeCCceEEEeCCCccc--hhhhHHHhhcCCCCeE
Q 002503 109 FVWVETKSQLNELANALSKEFFFAVDTEQHSLRS--FLGFTALIQISTEKEDYLVDTIALHD--EISILQPFFADPGVCK 184 (914)
Q Consensus 109 ~~~IdT~e~L~~lle~L~~a~~IAVDtE~~s~rs--y~g~lcLLQLSt~~~~yLID~laL~d--~l~~L~elLaDp~IvK 184 (914)
|++|+|.+++.++++.+...+.+|+|+|+.+... +.+.++++|+++++..|+++...... .+..|+++|+||+|.|
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 6789999999999999999999999999998776 67789999999998899999877665 3688999999999999
Q ss_pred EEechhHhHHHHHHhcCCCcCeEeehhhHHHHcCCCC-CCHHHHHHHHcC-CcCCccccccccc-CCCCCHHHHHHHHHc
Q 002503 185 VFHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKPQ-KSLAYLLETYCG-VATNKFLQREDWR-QRPLPAEMLQYAQTD 261 (914)
Q Consensus 185 V~Hgak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~~-~SLa~Lle~yLg-v~ldK~~q~sDWr-~RPLseeql~YAa~D 261 (914)
|+|++++|+.+|.+.+|+.+.++|||++|+++++... +||+.|+.+|+| ..++|..+.++|. .|||+++|+.||+.|
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 9999999999998889999999999999999999875 999999999999 7778899999999 899999999999999
Q ss_pred hHHHHHHHHHHHHHHH
Q 002503 262 AHYLLYIAKCLVAELK 277 (914)
Q Consensus 262 a~yLL~Lyd~L~~eL~ 277 (914)
|.+++.||+.|.++|+
T Consensus 161 ~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 161 AVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHTHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHhhC
Confidence 9999999999998874
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=4.4e-19 Score=176.82 Aligned_cols=172 Identities=40% Similarity=0.599 Sum_probs=143.6
Q ss_pred HHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEeCCceEEEeCCCccchhhhHHHhhcCCCCeEEEechhHhHHHHH
Q 002503 118 LNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKVFHGSDNDVMWLQ 197 (914)
Q Consensus 118 L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~~yLID~laL~d~l~~L~elLaDp~IvKV~Hgak~Dl~~Lq 197 (914)
|.++++.+...+.+++|+|+.+..++.+.++++||++.+..|+||+... .....|+++|+|+++.||+|+++.|+.+|+
T Consensus 2 ~~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~i~l~~~~~~~~i~~~~~-~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~ 80 (178)
T cd06142 2 LEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI-GDLSPLKELLADPNIVKVFHAAREDLELLK 80 (178)
T ss_pred HHHHHHHHhcCCeEEEECCccCCCcCCCceEEEEEeeCCCEEEEeCCCc-ccHHHHHHHHcCCCceEEEeccHHHHHHHH
Confidence 4455655555668999998876666678999999999855889885433 345568899999999999999999999998
Q ss_pred HhcCCCcCeEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHHHHHHHHHHHHH
Q 002503 198 RDFHIYVVNLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAEL 276 (914)
Q Consensus 198 rdfGI~~~nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL 276 (914)
+.+|+...++|||++|+|+|++. ..+|..|+++|+|..+.+....++|..||++.+++.||+.|+.+++.|++.|.++|
T Consensus 81 ~~~gi~~~~~~D~~laayLl~p~~~~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L 160 (178)
T cd06142 81 RDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEEL 160 (178)
T ss_pred HHcCCCCCCcccHHHHHHHhCCCccccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 77799866789999999999985 57999999999998866655778999999999999999999999999999999999
Q ss_pred HHcCCCCCCCCcchHHHHHHHhh
Q 002503 277 KQQGNENSYCPDDKFNFVLEASR 299 (914)
Q Consensus 277 ~e~g~~~~~~~~~~~~~v~e~~~ 299 (914)
++.+ ....+.++|+
T Consensus 161 ~e~~---------l~~L~~~~~~ 174 (178)
T cd06142 161 EEEG---------RLEWAEEECE 174 (178)
T ss_pred HHcC---------cHHHHHHHHH
Confidence 9886 3455666653
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=99.80 E-value=2e-18 Score=176.54 Aligned_cols=176 Identities=53% Similarity=0.924 Sum_probs=147.2
Q ss_pred CCCeEEecCHHHHHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEeCCceEEEeCCCccchhhhHHHhhcCCCCeEE
Q 002503 106 SDSFVWVETKSQLNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKV 185 (914)
Q Consensus 106 ~~~~~~IdT~e~L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~~yLID~laL~d~l~~L~elLaDp~IvKV 185 (914)
.+++.||++.+++..+++.+...+.+++|+|...+.++.+.++++|++++++.|+||.+........|.++|+++++.||
T Consensus 2 ~~~~~~i~~~~~l~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~l~~~~~~~~L~~~L~~~~i~kv 81 (192)
T cd06147 2 ETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILKV 81 (192)
T ss_pred CCCcEEECCHHHHHHHHHHHhcCCeEEEEeEecCCccCCCceEEEEEecCCCcEEEEecccccchHHHHHHhcCCCceEE
Confidence 56789997778888877777555689999987766677789999999988777888743333334568899999999999
Q ss_pred EechhHhHHHHHHhcCCCcCeEeehhhHHHHcCCCCCCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHH
Q 002503 186 FHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYL 265 (914)
Q Consensus 186 ~Hgak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yL 265 (914)
+|+++.|+.+|.+.+|+.+.++|||++|+|+|++...+|+.|+++|++..++|..+.+||..+||+.++..||+.++.++
T Consensus 82 ~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~~~~l~~l~~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l 161 (192)
T cd06147 82 FHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYL 161 (192)
T ss_pred EechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCCcccHHHHHHHHhCCCcchhhhccccccCCCCHHHHHHHHhhHHHH
Confidence 99999999999547899887779999999999985469999999999987445456677988898999999999999999
Q ss_pred HHHHHHHHHHHHHcCC
Q 002503 266 LYIAKCLVAELKQQGN 281 (914)
Q Consensus 266 L~Lyd~L~~eL~e~g~ 281 (914)
+.|++.|..+|+++.+
T Consensus 162 ~~L~~~L~~~L~e~~~ 177 (192)
T cd06147 162 LYIYDRLRNELLERAN 177 (192)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 9999999999998763
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=99.79 E-value=5.4e-18 Score=166.15 Aligned_cols=166 Identities=39% Similarity=0.501 Sum_probs=137.9
Q ss_pred EEecCHHHHHHHHHHHh-ccCcceEEEeecccCCCCCcEEEEEEEeCC-ceEEEeCCCccchhhhHHHhhcCCCCeEEEe
Q 002503 110 VWVETKSQLNELANALS-KEFFFAVDTEQHSLRSFLGFTALIQISTEK-EDYLVDTIALHDEISILQPFFADPGVCKVFH 187 (914)
Q Consensus 110 ~~IdT~e~L~~lle~L~-~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~-~~yLID~laL~d~l~~L~elLaDp~IvKV~H 187 (914)
.+|++.+++..+++.+. ....+++|+|+.....+.+.++++|+++.+ ..|+++.......+..|.++|+++++.||+|
T Consensus 2 ~~i~~~~~~~~~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~kv~~ 81 (172)
T smart00474 2 RVVTDSETLEELLEKLRAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGH 81 (172)
T ss_pred EEecCHHHHHHHHHHHHhcCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccchhhHHHHHHHhcCCCceEEEe
Confidence 57888888888777776 566899999987777677899999999644 4565554323223456889999999999999
Q ss_pred chhHhHHHHHHhcCCCcCeEeehhhHHHHcCCC-C-CCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHH
Q 002503 188 GSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKP-Q-KSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYL 265 (914)
Q Consensus 188 gak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~-~-~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yL 265 (914)
+++.|+.+|++ +|+.+.++|||++|+|+|++. . .+|+.+++.|+|..+++..+..+|..+|+.++|+.||+.|+.++
T Consensus 82 d~k~~~~~L~~-~gi~~~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~ 160 (172)
T smart00474 82 NAKFDLHVLAR-FGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGARPLSEEQLQYAAEDADAL 160 (172)
T ss_pred chHHHHHHHHH-CCCcccchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCcccCccccccCCCCHHHHHHHHHHHHHH
Confidence 99999999965 999988889999999999874 2 79999999999988765555568988899999999999999999
Q ss_pred HHHHHHHHHHH
Q 002503 266 LYIAKCLVAEL 276 (914)
Q Consensus 266 L~Lyd~L~~eL 276 (914)
+.|++.|.++|
T Consensus 161 ~~L~~~l~~~l 171 (172)
T smart00474 161 LRLYEKLEKEL 171 (172)
T ss_pred HHHHHHHHHHh
Confidence 99999998876
No 13
>PRK05755 DNA polymerase I; Provisional
Probab=99.74 E-value=8.8e-16 Score=189.63 Aligned_cols=173 Identities=24% Similarity=0.293 Sum_probs=144.9
Q ss_pred CCCeEEecCHHHHHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEeCCc-eEEEeCCCcc-chhhhHHHhhcCCCCe
Q 002503 106 SDSFVWVETKSQLNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEKE-DYLVDTIALH-DEISILQPFFADPGVC 183 (914)
Q Consensus 106 ~~~~~~IdT~e~L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~-~yLID~laL~-d~l~~L~elLaDp~Iv 183 (914)
+..|.+|++.++|.++++.+.....+|+|+|+.+.++|.+.++++|+++.++ .++|++..+. ..+..|.++|+|+.+.
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 3457889999999999999988899999999999999999999999999876 7888763332 3567889999999999
Q ss_pred EEEechhHhHHHHHHhcCCCc-CeEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCccc----ccccccCCCCCHHHHHH
Q 002503 184 KVFHGSDNDVMWLQRDFHIYV-VNLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFL----QREDWRQRPLPAEMLQY 257 (914)
Q Consensus 184 KV~Hgak~Dl~~LqrdfGI~~-~nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~----q~sDWr~RPLseeql~Y 257 (914)
||+|++++|+.+|. .+|+.+ .++|||++|++++++. .+||+.|+++|+|+++.... ...+|..+|+ +.+..|
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 579876 5799999999999986 38999999999998742100 1233444577 579999
Q ss_pred HHHchHHHHHHHHHHHHHHHHcC
Q 002503 258 AQTDAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 258 Aa~Da~yLL~Lyd~L~~eL~e~g 280 (914)
|+.||.+++.||..|.++|.+.+
T Consensus 451 Aa~Dv~~~~~L~~~L~~~L~~~~ 473 (880)
T PRK05755 451 AAEDADVTLRLHEVLKPKLLEEP 473 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999999998763
No 14
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.67 E-value=3.2e-15 Score=176.33 Aligned_cols=142 Identities=24% Similarity=0.180 Sum_probs=127.1
Q ss_pred CeEEecCHHHHHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEeCCceEEEeCCCccchhhhHHHhhcCCCCeEEEe
Q 002503 108 SFVWVETKSQLNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKVFH 187 (914)
Q Consensus 108 ~~~~IdT~e~L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~~yLID~laL~d~l~~L~elLaDp~IvKV~H 187 (914)
.+.+|++.++|..++..+...+.+++|+|+.+.++ .+|++|++.++..|+||+++. |.++
T Consensus 2 ~~~~I~~~~~l~~~~~~l~~~~~~a~DtEf~r~~t---~l~liQ~~~~~~~~liDpl~~------l~~~----------- 61 (553)
T PRK14975 2 DMKVILAPEELGAALERLSPAGVVAGDTETTGDDA---AAAAAQEGEEEPRWVWASTAA------LYPR----------- 61 (553)
T ss_pred CceEEeccchhHHHHHHhccCCceeCCccccCCcc---hhheeeecCCCceEEECchHH------hHHH-----------
Confidence 36789999999999999999999999999998777 899999999889999998652 2221
Q ss_pred chhHhHHHHHHhcCCCcCeEeehhhHHHHcCCC----CCCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchH
Q 002503 188 GSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKP----QKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAH 263 (914)
Q Consensus 188 gak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~----~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~ 263 (914)
| ..+|+.+.++|||++|+|+||.+ +.+|+.|+.+|+++.++|..+.+||. ||++++|+.||+.|+.
T Consensus 62 --------L-~~~Gv~~~~~fDT~LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~~sdw~-rpls~~q~~YAa~Dv~ 131 (553)
T PRK14975 62 --------L-LAAGVRVERCHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALS-DPPDEEQLLYAAADAD 131 (553)
T ss_pred --------H-HHCCCccCCCchHHHHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChhhhcccc-ccchHHHHHHHHHHhH
Confidence 4 35699888899999999999974 68999999999999999988899996 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHc
Q 002503 264 YLLYIAKCLVAELKQQ 279 (914)
Q Consensus 264 yLL~Lyd~L~~eL~e~ 279 (914)
|++.||..|.++|++.
T Consensus 132 ~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 132 VLLELYAVLADQLNRI 147 (553)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999999876
No 15
>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=99.63 E-value=3.7e-15 Score=144.20 Aligned_cols=143 Identities=28% Similarity=0.302 Sum_probs=113.8
Q ss_pred cceEEEeecccCCCCCcEEEEEEEeCCc-eEEEeCCCccchhhhHHHhhcCCCCeEEEechhHhHHHHHHhcCCCc-CeE
Q 002503 130 FFAVDTEQHSLRSFLGFTALIQISTEKE-DYLVDTIALHDEISILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYV-VNL 207 (914)
Q Consensus 130 ~IAVDtE~~s~rsy~g~lcLLQLSt~~~-~yLID~laL~d~l~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~-~nl 207 (914)
++++|+|+.+..++.+.++++||+++++ .|+|+.....-....|.++|+|+++.||+|+++.|+.+|. ..|+.. .++
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L~-~~~~~~~~~~ 79 (150)
T cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILL-NYFIELRGIA 79 (150)
T ss_pred CEEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCcccCHHHHHHHhcCCCCceeeecHHHHHHHHH-HcCCccCCcc
Confidence 4789998877666678999999998744 7888743211124568899999999999999999999995 556655 468
Q ss_pred eehhhHHHHcCCC--CCCHHHHHHHHcCCcCCccccc--ccccCCCCCHHHHHHHHHchHHHHHHHHHHH
Q 002503 208 FDTAKACEVLSKP--QKSLAYLLETYCGVATNKFLQR--EDWRQRPLPAEMLQYAQTDAHYLLYIAKCLV 273 (914)
Q Consensus 208 FDTqlAAyLLg~~--~~SLa~Lle~yLgv~ldK~~q~--sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~ 273 (914)
|||++|+|+|++. ..+|+.|+++|++..+.+..+. ..|..+|++.+|+.||+.|+.+++.|++.|.
T Consensus 80 ~D~~laayLl~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 80 FDTMLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred hhHHHHHHHhCCCCCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999984 4799999999999885441212 2386688899999999999999999998874
No 16
>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=99.62 E-value=6.3e-15 Score=141.81 Aligned_cols=146 Identities=32% Similarity=0.360 Sum_probs=114.2
Q ss_pred cceEEEeecccCCCCCcEEEEEEEeCCceEEEe-CCCccchhhhHHHhhcCCCCeEEEechhHhHHHHHHhcCCCcCeEe
Q 002503 130 FFAVDTEQHSLRSFLGFTALIQISTEKEDYLVD-TIALHDEISILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVVNLF 208 (914)
Q Consensus 130 ~IAVDtE~~s~rsy~g~lcLLQLSt~~~~yLID-~laL~d~l~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~nlF 208 (914)
.+++|+|+.....+.+.++++|+++.++.++|+ ..........|.++|+++.+.||+|+++.|+.+|.+.++..+.++|
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 578999887666667899999999864355553 2211234455889999999999999999999999654444456789
Q ss_pred ehhhHHHHcCCC--CCCHHHHHHHHcCCcCCcccccccc----cCCCCCHHHHHHHHHchHHHHHHHHHHHHH
Q 002503 209 DTAKACEVLSKP--QKSLAYLLETYCGVATNKFLQREDW----RQRPLPAEMLQYAQTDAHYLLYIAKCLVAE 275 (914)
Q Consensus 209 DTqlAAyLLg~~--~~SLa~Lle~yLgv~ldK~~q~sDW----r~RPLseeql~YAa~Da~yLL~Lyd~L~~e 275 (914)
||++|+|+|++. ..+|+.|+++|++..+.+..+..+| ..+|++.++..||+.|+.+++.|++.|.++
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 999999999984 4799999999999875442233444 258889999999999999999999998765
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=99.57 E-value=5.1e-14 Score=141.34 Aligned_cols=152 Identities=17% Similarity=0.090 Sum_probs=122.7
Q ss_pred cCcceEEEeecccCCCCCcEEEEEEEeCCceEEEeCCCccchhhhHHHhhcCCCCeEEEechhHhHHHHHHhcCCCcC-e
Q 002503 128 EFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVV-N 206 (914)
Q Consensus 128 a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~~yLID~laL~d~l~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~-n 206 (914)
...++||+|..+..++.+.++.++|+++++.|+|+..........|.++|+|+++.||+|++|.|++.| ..+|+.+. .
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~~~~~ 81 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGGGAYYIPLELALLDLAALKEWLEDEKIPKVGHDAKRAYVAL-KRHGIELAGV 81 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCCcEEEEeccchHHHHHHHHHHHhCCCCceeccchhHHHHHH-HHCCCcCCCc
Confidence 356889999988777889999999998767778873221013345889999999999999999999999 46899875 5
Q ss_pred EeehhhHHHHcCCC--CCCHHHHHHHHcCCcCCccccccccc---CCCCCHHHHHHHHHchHHHHHHHHHHHHHHHHcC
Q 002503 207 LFDTAKACEVLSKP--QKSLAYLLETYCGVATNKFLQREDWR---QRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 207 lFDTqlAAyLLg~~--~~SLa~Lle~yLgv~ldK~~q~sDWr---~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~g 280 (914)
+|||++|+|+|++. ++++..|+.+|+++++.+..+..+|. .++..+.+..|++.|+.+++.|++.|.++|++.+
T Consensus 82 ~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~ 160 (178)
T cd06140 82 AFDTMLAAYLLDPTRSSYDLADLAKRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEENE 160 (178)
T ss_pred chhHHHHHHHcCCCCCCCCHHHHHHHHcCCCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 79999999999986 37999999999998865433344441 3455677899999999999999999999998764
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=99.41 E-value=6.4e-12 Score=126.81 Aligned_cols=151 Identities=28% Similarity=0.327 Sum_probs=119.3
Q ss_pred hccCcceEEEeecccCCCCCcEEEEEEEeCCc-eEEEeCCC--------ccchhhhHHHhhcCCCCeEEEechhHhHHHH
Q 002503 126 SKEFFFAVDTEQHSLRSFLGFTALIQISTEKE-DYLVDTIA--------LHDEISILQPFFADPGVCKVFHGSDNDVMWL 196 (914)
Q Consensus 126 ~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~-~yLID~la--------L~d~l~~L~elLaDp~IvKV~Hgak~Dl~~L 196 (914)
.+.+.+|+|+|..+..++.+.++.++++..++ .++|+... ....+..|.++|++..+.+|+|++++|+.+|
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 34677999999888777788999999998754 66665321 1123445888999988899999999999999
Q ss_pred HHhcCCCcC-eEeehhhHHHHcCCC--CCCHHHHHHHHcCCcC-------CcccccccccCCCCCHHHHHHHHHchHHHH
Q 002503 197 QRDFHIYVV-NLFDTAKACEVLSKP--QKSLAYLLETYCGVAT-------NKFLQREDWRQRPLPAEMLQYAQTDAHYLL 266 (914)
Q Consensus 197 qrdfGI~~~-nlFDTqlAAyLLg~~--~~SLa~Lle~yLgv~l-------dK~~q~sDWr~RPLseeql~YAa~Da~yLL 266 (914)
+..|+.+. .+|||++|+|++++. ..+|..++++|+|... .|+.+..+|...|+ ..+..||+.|+.+++
T Consensus 83 -~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~ 160 (193)
T cd06139 83 -ANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADITL 160 (193)
T ss_pred -HHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHHHHHHHHH
Confidence 56788865 589999999999984 5799999999998762 12234455654455 668999999999999
Q ss_pred HHHHHHHHHHHH
Q 002503 267 YIAKCLVAELKQ 278 (914)
Q Consensus 267 ~Lyd~L~~eL~e 278 (914)
.|+..|.++|.+
T Consensus 161 ~l~~~l~~~l~~ 172 (193)
T cd06139 161 RLYELLKPKLKE 172 (193)
T ss_pred HHHHHHHHHHhh
Confidence 999999999976
No 19
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=99.39 E-value=2.4e-13 Score=147.79 Aligned_cols=149 Identities=21% Similarity=0.246 Sum_probs=120.5
Q ss_pred HhhhccCCCCcccceeEEeCCCceeeeecCccccceecccchhhccCCCceEEeecccCCCCCccccchhccccCCceEE
Q 002503 497 FVQKFSCKSPVYHNCRIYANDGRLLCYCDRKKLEWYLTRDLAKLVEDNPPAIMLLFEPKGRPEDEGNEFYIQSKKNICVS 576 (914)
Q Consensus 497 f~~k~~~k~p~Y~NC~l~apdG~lLc~cd~kKa~WYl~k~La~~v~e~P~~IrL~FeP~gr~~~~~~~yY~~~k~N~CVv 576 (914)
-....+++.++|+||+..++||...|.|+++++.||+++| +|+|. | +.+++-.++|.|++
T Consensus 104 ~~~~d~~a~~~~~~~~~~~~~s~~~~~~~~~e~~~~~d~~--------------~~~P~--~----~~lqlcV~en~C~I 163 (319)
T KOG4373|consen 104 GYGSDARASPYIDNSLEIADDSDPPFVCYRREAQPYLDMG--------------RSDPP--P----DTLQLCVGENRCLI 163 (319)
T ss_pred ccccccccccccccccccccccCCcceeeccccccccccc--------------ccCCC--c----chhhhhhcccceee
Confidence 3445677899999999999999999999999999999999 77776 2 67999999999999
Q ss_pred cCCCCcccccccccchhhhcchhhhhccCCcceeecchhhHHhHHHhHHHHHHHHHHHhCCCccccccccccccccCCCC
Q 002503 577 CGEGNHYLRYRIIPSCYRIHFPEQLKSHRSHDIVLLCVDCHEVAHAAAEKYKKQISAEFGIPLFIHKVADSRKAEARPGF 656 (914)
Q Consensus 577 CG~~~~~~R~~vVP~~YR~hfP~~~KsH~ShDvllLC~~CH~~~~~~~~~~k~~la~~~~~pl~~~~~~~~~~~~~~~~~ 656 (914)
| .+++...||++|| || |++| +||.+..-.+.-.++....+++++++-.
T Consensus 164 ~----ql~~~~~IP~~LR-~f---l~D~----------~~~~vgv~~d~D~~KL~r~~hql~I~~~-------------- 211 (319)
T KOG4373|consen 164 I----QLIHCKRIPHELR-SF---LEDP----------DHTFVGVWNDQDAGKLERKEHQLEIGEL-------------- 211 (319)
T ss_pred E----EeeccccchHHHH-Hh---hcCC----------CceEEeccccccHHHHhhhhhcccHHhh--------------
Confidence 9 9999999999999 88 7776 6888888888888887788999998521
Q ss_pred cccccccccCCChHHHHHHHHHHHhcCCCCCHhHHHHHHHHHHHHhCCccCCHHHH
Q 002503 657 SASITNFEAGVSPLQLRTAAMALLHHGPTMPSNRREELRRIVMRYYGGREISQEDL 712 (914)
Q Consensus 657 ~~~~~~~~~~v~~~~vrsaa~aLl~~~~~~P~~r~eeL~~~i~~~~~~~~~t~~~l 712 (914)
.-+|-.+.-.+. ..||-.+++++.+.-..|++..-..+..+
T Consensus 212 -------------~dlr~~~~d~~g--~~~~~~s~e~i~~~~~~~~~~~v~l~~~i 252 (319)
T KOG4373|consen 212 -------------EDLRLLVNDSLG--GSMPNDSFEEIVSETLGYYGKDVRLDKEI 252 (319)
T ss_pred -------------hhHHhhcchhhc--cCccCccHHHHHHHHhhccccccccChhc
Confidence 123333333232 38999999999999999987655544443
No 20
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.26 E-value=5.9e-12 Score=145.31 Aligned_cols=172 Identities=26% Similarity=0.313 Sum_probs=135.1
Q ss_pred CCCeEEecCHHHHHHHH-HHHhcc-CcceEEEeeccc-CCCCCcEEEEEEEeCCceEEEeCCCccch----h-hhHHHhh
Q 002503 106 SDSFVWVETKSQLNELA-NALSKE-FFFAVDTEQHSL-RSFLGFTALIQISTEKEDYLVDTIALHDE----I-SILQPFF 177 (914)
Q Consensus 106 ~~~~~~IdT~e~L~~ll-e~L~~a-~~IAVDtE~~s~-rsy~g~lcLLQLSt~~~~yLID~laL~d~----l-~~L~elL 177 (914)
...+.+|+++.+|..++ +.+.+. -.||+|.||... ......+|++||++.+.+||||..++... + ..+..+|
T Consensus 389 ~~~i~~V~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~if 468 (617)
T KOG2207|consen 389 VESIGMVGNEKELRDLLLESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQIF 468 (617)
T ss_pred ccceeeeCCHHHHHHHHHHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHHc
Confidence 45688999999999887 455555 679999999765 33456799999999999999999886422 2 2456799
Q ss_pred cCCCCeEEEechhHhHHHHHHh-----cCCCc---CeE-eehhhHHHHcC-------C--CCCCHHHHHHHHcCCcCCcc
Q 002503 178 ADPGVCKVFHGSDNDVMWLQRD-----FHIYV---VNL-FDTAKACEVLS-------K--PQKSLAYLLETYCGVATNKF 239 (914)
Q Consensus 178 aDp~IvKV~Hgak~Dl~~Lqrd-----fGI~~---~nl-FDTqlAAyLLg-------~--~~~SLa~Lle~yLgv~ldK~ 239 (914)
++++|.|||.+..+|+..|++. +.+.+ .++ -++.++..+.+ . ...+|+.|....+|..++|.
T Consensus 469 ~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKt 548 (617)
T KOG2207|consen 469 ESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNKT 548 (617)
T ss_pred cCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhcccc
Confidence 9999999999999999999742 22222 122 23334443332 1 25689999999999999999
Q ss_pred cccccccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHH
Q 002503 240 LQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELK 277 (914)
Q Consensus 240 ~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~ 277 (914)
.|+++|-.|||...|+.||+.|++.+..+|..+.....
T Consensus 549 eqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 549 EQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred cccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 99999999999999999999999999999999876544
No 21
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.19 E-value=2.8e-09 Score=125.27 Aligned_cols=169 Identities=23% Similarity=0.224 Sum_probs=129.6
Q ss_pred EEecCHHHHHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEeCCceEEEeCCC---ccchhhhHHHhhcCCCCeEEE
Q 002503 110 VWVETKSQLNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEKEDYLVDTIA---LHDEISILQPFFADPGVCKVF 186 (914)
Q Consensus 110 ~~IdT~e~L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~~~yLID~la---L~d~l~~L~elLaDp~IvKV~ 186 (914)
..+.+.+.+..|+..+.....+|+|+|..+.++..+.+..+.++..+..++|.... .-+....|++||+|+.+.||+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~a~~~et~~l~~~~~~lvg~s~~~~~~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~kv~ 83 (593)
T COG0749 4 GTITDLAVLNAWLTKLNAAANIAFDTETDGLDPHGADLVGLSVASEEEAAYIPLLHGPEQLNVLAALKPLLEDEGIKKVG 83 (593)
T ss_pred hhhhHHHHHHHHHHHHhhcccceeeccccccCcccCCeeEEEeeccccceeEeeccchhhhhhHHHHHHHhhCcccchhc
Confidence 34566777888888877666699999999988877777777777666555554322 223678899999999999999
Q ss_pred echhHhHHHHHHhcCCCcCeEeehhhHHHHcCCC--CCCHHHHHHHHcCCcCC-------cccccccccCCCCCHHHHHH
Q 002503 187 HGSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKP--QKSLAYLLETYCGVATN-------KFLQREDWRQRPLPAEMLQY 257 (914)
Q Consensus 187 Hgak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~--~~SLa~Lle~yLgv~ld-------K~~q~sDWr~RPLseeql~Y 257 (914)
|++|.|.+.|+ .+|+.....|||++|+|+|+++ .+++..|+++|++.+.- |+.+.-+...-++ +....|
T Consensus 84 ~~~K~d~~~l~-~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~-~~~~~y 161 (593)
T COG0749 84 QNLKYDYKVLA-NLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKL-EKATEY 161 (593)
T ss_pred cccchhHHHHH-HcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchH-HHHHHH
Confidence 99999999995 6886546799999999999976 58999999999987652 3333222211222 556899
Q ss_pred HHHchHHHHHHHHHHHHHHHHcC
Q 002503 258 AQTDAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 258 Aa~Da~yLL~Lyd~L~~eL~e~g 280 (914)
++.|+..+++|+..|..+|.+..
T Consensus 162 ~a~~a~~~~~L~~~l~~~l~~~~ 184 (593)
T COG0749 162 AAEDADATLRLESILEPELLKTP 184 (593)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhh
Confidence 99999999999999998887654
No 22
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.16 E-value=1.4e-08 Score=125.82 Aligned_cols=166 Identities=17% Similarity=0.053 Sum_probs=120.4
Q ss_pred eEEecCHHHHHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEeCC-c-eEEEeCC-----CccchhhhHHHhhcCCC
Q 002503 109 FVWVETKSQLNELANALSKEFFFAVDTEQHSLRSFLGFTALIQISTEK-E-DYLVDTI-----ALHDEISILQPFFADPG 181 (914)
Q Consensus 109 ~~~IdT~e~L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~~-~-~yLID~l-----aL~d~l~~L~elLaDp~ 181 (914)
+..|.+.+++..+++. ...+.+++ .+...+...+..+.+++.+ . .|+|+.. ........|.++|+|+.
T Consensus 304 ~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~ 378 (887)
T TIGR00593 304 AKESEEAAPLANPAEK-AEVGGFVL----ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLNEQ 378 (887)
T ss_pred ceEeCCHHHHHHHHHh-CcCCeEEE----cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhCCC
Confidence 5567677888887765 44446666 3344455677788888864 3 5666421 11223456889999999
Q ss_pred CeEEEechhHhHHHHHHhcCCCcC-eEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCcccccccc--cCCCCC-HHHHH
Q 002503 182 VCKVFHGSDNDVMWLQRDFHIYVV-NLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFLQREDW--RQRPLP-AEMLQ 256 (914)
Q Consensus 182 IvKV~Hgak~Dl~~LqrdfGI~~~-nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~q~sDW--r~RPLs-eeql~ 256 (914)
+.||+|++++|+.+| ..+|+.+. .+|||++|+|+|++. .++|..|+.+|++..+.+......| ....++ +.+..
T Consensus 379 ~~~v~~n~K~d~~~l-~~~gi~~~~~~~Dt~la~yll~~~~~~~l~~la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 457 (887)
T TIGR00593 379 IKKIGHDAKFLMHLL-KREGIELGGVIFDTMLAAYLLDPAQVSTLDTLARRYLVEELILDEKIGGKLAKFAFPPLEEATE 457 (887)
T ss_pred CcEEEeeHHHHHHHH-HhCCCCCCCcchhHHHHHHHcCCCCCCCHHHHHHHHcCcccccHHHhccCCCCcccccHHHHHH
Confidence 999999999999999 56899875 589999999999974 5799999999999764321111111 111333 55789
Q ss_pred HHHHchHHHHHHHHHHHHHHHHcC
Q 002503 257 YAQTDAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 257 YAa~Da~yLL~Lyd~L~~eL~e~g 280 (914)
||+.|+.+++.||..|..+|.+.+
T Consensus 458 ya~~d~~~~~~L~~~l~~~l~~~~ 481 (887)
T TIGR00593 458 YLARRAAATKRLAEELLKELDENK 481 (887)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcc
Confidence 999999999999999999998654
No 23
>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=98.93 E-value=1.5e-09 Score=93.51 Aligned_cols=68 Identities=22% Similarity=0.336 Sum_probs=56.0
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCcCcccChHHHHHHHHhCCCCHHHHHHHHhhcCCcccccccCCCCCCCChhhcccHHHH
Q 002503 343 TQDLVRRLCAWRDLMARVHDESLRFVLSDQAIIALANKAPANRTDVYTTIAQADSDVDCLNLSSSLPSPSPVVCSHLDDV 422 (914)
Q Consensus 343 ~l~vlr~L~~WRD~~AR~~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~i~~~d~~~~~~~l~~~~~~~sp~Vr~hl~eL 422 (914)
|++++++|++||+.+|+..|.|+.+||+|.+|.+||+..|+|.++|.++- + -....++.|.++|
T Consensus 1 q~~~~~~L~~~R~~~A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i~----------g------~~~~~~~~~g~~i 64 (68)
T PF00570_consen 1 QLALLKALKEWREELAREEDVPPYRILSDEALLEIAKRLPTSIEELLQIP----------G------MGKRKVRKYGDEI 64 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTST----------T------CGHHHHHHCHHHH
T ss_pred CHHHHHHHHHHHHHHHHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHcc----------C------CCHHHHHHHHHHH
Confidence 57899999999999999999999999999999999999999999998741 1 1235789999999
Q ss_pred HHHH
Q 002503 423 ERQV 426 (914)
Q Consensus 423 ~~lI 426 (914)
+++|
T Consensus 65 l~~I 68 (68)
T PF00570_consen 65 LEII 68 (68)
T ss_dssp HHHH
T ss_pred HhhC
Confidence 9886
No 24
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=98.87 E-value=6e-09 Score=92.34 Aligned_cols=76 Identities=25% Similarity=0.342 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCCcCcccChHHHHHHHHhCCCCHHHHHHHHhhcCCcccccccCCCCCCCChhhcccHH
Q 002503 341 SVTQDLVRRLCAWRDLMARVHDESLRFVLSDQAIIALANKAPANRTDVYTTIAQADSDVDCLNLSSSLPSPSPVVCSHLD 420 (914)
Q Consensus 341 ~~~l~vlr~L~~WRD~~AR~~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~i~~~d~~~~~~~l~~~~~~~sp~Vr~hl~ 420 (914)
+.+++++++|+.||+.+|++.|.|+++||+|.+|++||...|+|..+|.+.- + -....++.+..
T Consensus 2 ~~~~~~~~~L~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~----------g------~~~~~~~~~g~ 65 (81)
T smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAID----------G------VGEEKARRYGK 65 (81)
T ss_pred hHHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCC----------C------CCHHHHHHHHH
Confidence 3578999999999999999999999999999999999999999999888731 1 12357888999
Q ss_pred HHHHHHHHHhhh
Q 002503 421 DVERQVCNNVEN 432 (914)
Q Consensus 421 eL~~lI~~a~~~ 432 (914)
.++.+|+++...
T Consensus 66 ~~~~~i~~~~~~ 77 (81)
T smart00341 66 DLLAVIQEASDS 77 (81)
T ss_pred HHHHHHHHHHhc
Confidence 999999987654
No 25
>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=98.71 E-value=3.2e-07 Score=90.10 Aligned_cols=126 Identities=17% Similarity=0.124 Sum_probs=87.3
Q ss_pred CCcEEEEEEEeCCceEEEeCCCccchhhhHHHhhcCCCCeEEEechhHhHHHHHHhcCCCcC-eEeehhhHHHHcCCC-C
Q 002503 144 LGFTALIQISTEKEDYLVDTIALHDEISILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVV-NLFDTAKACEVLSKP-Q 221 (914)
Q Consensus 144 ~g~lcLLQLSt~~~~yLID~laL~d~l~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~-nlFDTqlAAyLLg~~-~ 221 (914)
.+.+..+.+++.++.|+|+... ......|.++|+|+++.|++|++|.++.+| +..|+.+. .+|||++|+|||++. .
T Consensus 17 ~~~~~glal~~~~~~~yi~~~~-~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~~LAaYLL~p~~~ 94 (151)
T cd06128 17 SANLVGLAFAIEGVAAYIPVAH-DYALELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDTMLEAYLLDPVAG 94 (151)
T ss_pred cCcEEEEEEEcCCCeEEEeCCC-CcCHHHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhHHHHHHHcCCCCC
Confidence 4556667777765677775211 002456889999999999999999999999 67899876 469999999999985 2
Q ss_pred -CCHHHHHHHHcCCc-CC-cccccccccC--CCC-CHHHHHHHHHchHHHHHHHHHHH
Q 002503 222 -KSLAYLLETYCGVA-TN-KFLQREDWRQ--RPL-PAEMLQYAQTDAHYLLYIAKCLV 273 (914)
Q Consensus 222 -~SLa~Lle~yLgv~-ld-K~~q~sDWr~--RPL-seeql~YAa~Da~yLL~Lyd~L~ 273 (914)
.++..|+++|++.. +. .. ...+.. .++ ..+...|++..+.++..|++.|.
T Consensus 95 ~~~l~~la~~yl~~~~~~~~~--~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 95 RHDMDSLAERWLKEKTITFEE--IAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CCCHHHHHHHHcCCCCccHHH--HcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 59999999999876 32 10 100000 012 12233477777888888888764
No 26
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=97.69 E-value=7.9e-05 Score=82.26 Aligned_cols=127 Identities=20% Similarity=0.216 Sum_probs=99.1
Q ss_pred CCCcEEEEEEEeC-CceEEEeCCCccchhhhHHHhhcCCCCeEEEechhHhHHHHHH-hcCCCcCeEeehhhH-HHHcCC
Q 002503 143 FLGFTALIQISTE-KEDYLVDTIALHDEISILQPFFADPGVCKVFHGSDNDVMWLQR-DFHIYVVNLFDTAKA-CEVLSK 219 (914)
Q Consensus 143 y~g~lcLLQLSt~-~~~yLID~laL~d~l~~L~elLaDp~IvKV~Hgak~Dl~~Lqr-dfGI~~~nlFDTqlA-AyLLg~ 219 (914)
+.|....+||+.+ ..++||..+.-......|+-+|+|++.++|+-+.++|...|.| .+++.|..+.|+..- .-.+|.
T Consensus 145 ~~P~~~~lqlcV~en~C~I~ql~~~~~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g~ 224 (319)
T KOG4373|consen 145 SDPPPDTLQLCVGENRCLIIQLIHCKRIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLGG 224 (319)
T ss_pred cCCCcchhhhhhcccceeeEEeeccccchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhhcc
Confidence 3455778999998 4577775444334567888899999999999999999999988 899999888888743 234443
Q ss_pred --CCCCHHHHHHHHc---C--CcCCcccccccccCCCCCHHHHHHHHHchHHHHHHH
Q 002503 220 --PQKSLAYLLETYC---G--VATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 220 --~~~SLa~Lle~yL---g--v~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~Ly 269 (914)
+..+...|+...+ | +.+++.-+.+||...||+.+|+.||+-||+....|+
T Consensus 225 ~~~~~s~e~i~~~~~~~~~~~v~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 225 SMPNDSFEEIVSETLGYYGKDVRLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred CccCccHHHHHHHHhhccccccccChhcccccceeeeccHHHHHHHHhHHHHHHHHH
Confidence 2345555555544 4 556778899999999999999999999999999998
No 27
>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=97.64 E-value=0.00029 Score=65.29 Aligned_cols=73 Identities=22% Similarity=0.229 Sum_probs=56.7
Q ss_pred ceEEEeecccCCCCCcEEEEEEEeC--CceEEEeCCCccchhhhHHHhhcCCC-CeEEEechhHhHHHHHHhcCC---C-
Q 002503 131 FAVDTEQHSLRSFLGFTALIQISTE--KEDYLVDTIALHDEISILQPFFADPG-VCKVFHGSDNDVMWLQRDFHI---Y- 203 (914)
Q Consensus 131 IAVDtE~~s~rsy~g~lcLLQLSt~--~~~yLID~laL~d~l~~L~elLaDp~-IvKV~Hgak~Dl~~LqrdfGI---~- 203 (914)
+++|+|+.+.+++...++++|+... +..|++| +.+++.+.. .+.|+|++..|+..|.+.+.. .
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~~~----------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~~ 70 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAVID----------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLKY 70 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEEeh----------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCCC
Confidence 5899999999999999999999876 4567776 556777765 678999999999888755432 1
Q ss_pred ---cCeEeehhhH
Q 002503 204 ---VVNLFDTAKA 213 (914)
Q Consensus 204 ---~~nlFDTqlA 213 (914)
....+||+.+
T Consensus 71 p~~~~~~lDT~~l 83 (96)
T cd06125 71 PLLAGSWIDTIKL 83 (96)
T ss_pred CCcCCcEEEehHH
Confidence 2457888875
No 28
>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=97.26 E-value=0.00049 Score=82.64 Aligned_cols=70 Identities=14% Similarity=0.121 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCcCcccChHHHHHHHHhCCCCHHHHHHHHhhcCCcccccccCCCCCCCChhhcccHHHH
Q 002503 343 TQDLVRRLCAWRDLMARVHDESLRFVLSDQAIIALANKAPANRTDVYTTIAQADSDVDCLNLSSSLPSPSPVVCSHLDDV 422 (914)
Q Consensus 343 ~l~vlr~L~~WRD~~AR~~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~i~~~d~~~~~~~l~~~~~~~sp~Vr~hl~eL 422 (914)
..++|++|.+||+++|++.|.|+.+|++|..|++||+.+|+|.++|.+.- ++ ...-++.+.+++
T Consensus 521 ~~~l~~~L~~wR~~~A~~~~~p~~~If~d~~L~~ia~~~P~~~~~l~~i~----------gv------~~~k~~~~G~~~ 584 (591)
T TIGR01389 521 DNALFEALRELRKEQADEQNVPPYVIFSDSTLREMAEKRPATLNALLKIK----------GV------GQNKLDRYGEAF 584 (591)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhCCC----------CC------CHHHHHHHHHHH
Confidence 34999999999999999999999999999999999999999999888620 11 124577888888
Q ss_pred HHHHHH
Q 002503 423 ERQVCN 428 (914)
Q Consensus 423 ~~lI~~ 428 (914)
+.+|+.
T Consensus 585 l~~i~~ 590 (591)
T TIGR01389 585 LEVIRE 590 (591)
T ss_pred HHHHHh
Confidence 888863
No 29
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.07 E-value=0.085 Score=57.28 Aligned_cols=132 Identities=19% Similarity=0.260 Sum_probs=83.0
Q ss_pred HhccCcceEEEeecccCCCCCcEEEEEEEe----CC-----ceEEEeCCC-c-------c--------------chhhhH
Q 002503 125 LSKEFFFAVDTEQHSLRSFLGFTALIQIST----EK-----EDYLVDTIA-L-------H--------------DEISIL 173 (914)
Q Consensus 125 L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt----~~-----~~yLID~la-L-------~--------------d~l~~L 173 (914)
|++...+.+|+|..+...-... +|||+. .+ ...+|.|-. + . +.+..+
T Consensus 4 l~~~~~v~~D~ETTGl~~~~d~--IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~ 81 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDVKKDR--IIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQI 81 (250)
T ss_pred ccCCcEEEEEEeCCCCCCCCCe--EEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHH
Confidence 4456789999999887654333 233332 11 123454311 1 0 122344
Q ss_pred HHhhcCCCCeEEEechhHhHHHHHHh---cCCCc----CeEeehhhHHHHcCC-CCCCHHHHHHHHcCCcCCcccccccc
Q 002503 174 QPFFADPGVCKVFHGSDNDVMWLQRD---FHIYV----VNLFDTAKACEVLSK-PQKSLAYLLETYCGVATNKFLQREDW 245 (914)
Q Consensus 174 ~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~~----~nlFDTqlAAyLLg~-~~~SLa~Lle~yLgv~ldK~~q~sDW 245 (914)
.+++.+.. .-|+|++.+|+.+|.+. .|+.. ..++||+..++.++. +.++|+.|++.| |+.....
T Consensus 82 ~~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~-g~~~~~a------ 153 (250)
T PRK06310 82 KGFFKEGD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHF-NVPYDGN------ 153 (250)
T ss_pred HHHhCCCC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHC-CCCCCCC------
Confidence 55555433 56999999999998644 35432 358999988888764 468999998775 6654322
Q ss_pred cCCCCCHHHHHHHHHchHHHHHHHHHHHHHH
Q 002503 246 RQRPLPAEMLQYAQTDAHYLLYIAKCLVAEL 276 (914)
Q Consensus 246 r~RPLseeql~YAa~Da~yLL~Lyd~L~~eL 276 (914)
.-|..||..+..++..|...+
T Consensus 154 ----------H~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 154 ----------HRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred ----------cChHHHHHHHHHHHHHHHHhc
Confidence 227789999999988876543
No 30
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=95.84 E-value=0.18 Score=56.63 Aligned_cols=92 Identities=17% Similarity=0.140 Sum_probs=67.0
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHh---cCCCc--CeEeehhhHHHHcCC--CCCCHHHHHHHHcCCcCCcccccc
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRD---FHIYV--VNLFDTAKACEVLSK--PQKSLAYLLETYCGVATNKFLQRE 243 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~~--~nlFDTqlAAyLLg~--~~~SLa~Lle~yLgv~ldK~~q~s 243 (914)
..|.+++.+ -+-|.|++.+|+.+|.+. +|+.. ...+||+..++.+.+ +.++|+.|++. +|+.....
T Consensus 86 ~~l~~~l~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~-~gi~~~~~---- 158 (313)
T PRK06063 86 GEVAELLRG--RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAH-WGVPQQRP---- 158 (313)
T ss_pred HHHHHHcCC--CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHH-cCCCCCCC----
Confidence 455556654 356899999999999754 35442 358999988887754 47899999975 57654322
Q ss_pred cccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHHHcCC
Q 002503 244 DWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQGN 281 (914)
Q Consensus 244 DWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~g~ 281 (914)
+-|..||..+..|+..+.+++.+.+.
T Consensus 159 ------------H~Al~DA~ata~l~~~ll~~~~~~~~ 184 (313)
T PRK06063 159 ------------HDALDDARVLAGILRPSLERARERDV 184 (313)
T ss_pred ------------CCcHHHHHHHHHHHHHHHHHHHhcCC
Confidence 22778999999999999888887763
No 31
>PRK07740 hypothetical protein; Provisional
Probab=95.69 E-value=0.2 Score=54.26 Aligned_cols=92 Identities=21% Similarity=0.196 Sum_probs=66.2
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHh----cCCCc-CeEeehhhHHHHcCCC--CCCHHHHHHHHcCCcCCcccccc
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRD----FHIYV-VNLFDTAKACEVLSKP--QKSLAYLLETYCGVATNKFLQRE 243 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~Lqrd----fGI~~-~nlFDTqlAAyLLg~~--~~SLa~Lle~yLgv~ldK~~q~s 243 (914)
..|.+++.+ -.-|+|++..|..+|.+. ++... ..++||+..++.+.+. .++|..|+.. +|+..+..+
T Consensus 133 ~~f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~-~gi~~~~~H--- 206 (244)
T PRK07740 133 HRFYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAY-YGIPIPRRH--- 206 (244)
T ss_pred HHHHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHH-CCcCCCCCC---
Confidence 344444443 356899999999988543 33333 4689999988877653 6899999864 677654222
Q ss_pred cccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHHHcCC
Q 002503 244 DWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQGN 281 (914)
Q Consensus 244 DWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~g~ 281 (914)
-|..||..+..|+..+..++.+.|.
T Consensus 207 -------------~Al~Da~ata~l~~~ll~~~~~~~~ 231 (244)
T PRK07740 207 -------------HALGDALMTAKLWAILLVEAQQRGI 231 (244)
T ss_pred -------------CcHHHHHHHHHHHHHHHHHHHHcCC
Confidence 2678999999999999999988774
No 32
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=95.58 E-value=0.16 Score=57.03 Aligned_cols=89 Identities=17% Similarity=0.177 Sum_probs=61.5
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHhc---CCC-c-CeEeehhhHHHHcCC--CCCCHHHHHHHHcCCcCCcccccc
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRDF---HIY-V-VNLFDTAKACEVLSK--PQKSLAYLLETYCGVATNKFLQRE 243 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~Lqrdf---GI~-~-~nlFDTqlAAyLLg~--~~~SLa~Lle~yLgv~ldK~~q~s 243 (914)
..|.+++.+ .+ -|+|++.+|+..|.+.+ |+. + ..++||+..+..+.+ +.++|..|++. +|+.. +.
T Consensus 80 ~~f~~fl~~-~~-lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~-lgi~~-~~---- 151 (313)
T PRK06807 80 PLFLAFLHT-NV-IVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRM-LGIRL-SS---- 151 (313)
T ss_pred HHHHHHHcC-Ce-EEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHH-cCCCC-CC----
Confidence 344455544 33 48999999999997654 543 2 358999987765543 46799999865 56554 21
Q ss_pred cccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHHHc
Q 002503 244 DWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQ 279 (914)
Q Consensus 244 DWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~ 279 (914)
+=|..||.++..||..+.......
T Consensus 152 ------------H~Al~DA~~ta~l~~~l~~~~~~~ 175 (313)
T PRK06807 152 ------------HNAFDDCITCAAVYQKCASIEEEA 175 (313)
T ss_pred ------------cChHHHHHHHHHHHHHHHHhhhhc
Confidence 227789999999999988877533
No 33
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=95.35 E-value=0.0091 Score=67.44 Aligned_cols=125 Identities=19% Similarity=0.190 Sum_probs=82.8
Q ss_pred EEEEEEeCCceEEEeCCCc--cchhhhHHHhhcCCCCeEEEechhHhHHHHHHhcCCCcCeEeehhhHHHHcCCCC----
Q 002503 148 ALIQISTEKEDYLVDTIAL--HDEISILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKPQ---- 221 (914)
Q Consensus 148 cLLQLSt~~~~yLID~laL--~d~l~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~~---- 221 (914)
.+|+|+++.+.|++|.+.- .-..+-.+..++...+ |. |+..++..|...|++.+.+++|||+|..++.+..
T Consensus 214 ~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~sLve~~e~grr 290 (458)
T KOG2405|consen 214 TYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIASSLVEPSEYGRR 290 (458)
T ss_pred hhhhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHHHHhhhHHhccc
Confidence 3488999888999986542 1111212344554333 45 9999999998889999999999999999886421
Q ss_pred CCHHHHH------H--HHcCCcCC------c-ccc-cccccCCCCCHHHHHHHHHchHHHHHHHHHHHHH
Q 002503 222 KSLAYLL------E--TYCGVATN------K-FLQ-REDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAE 275 (914)
Q Consensus 222 ~SLa~Ll------e--~yLgv~ld------K-~~q-~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~e 275 (914)
+....++ . .|++.... + -.+ .-.|..||.++.+..-+..|++.|+.+++.+.+.
T Consensus 291 ~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a~ 360 (458)
T KOG2405|consen 291 HPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVAV 360 (458)
T ss_pred CCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhhh
Confidence 1111111 1 12222111 1 112 2369999999999999999999999987666544
No 34
>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=95.32 E-value=0.1 Score=52.17 Aligned_cols=81 Identities=17% Similarity=0.093 Sum_probs=54.8
Q ss_pred hhhHHHhhcCCCCeEEEechhHhHHHHHHhcCCCcCeEeehhhHHHHcC---CCCCCHHHHHHHHcCCcCCccccccccc
Q 002503 170 ISILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLS---KPQKSLAYLLETYCGVATNKFLQREDWR 246 (914)
Q Consensus 170 l~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg---~~~~SLa~Lle~yLgv~ldK~~q~sDWr 246 (914)
+..|.+++.+ .+ -|+|++.+|+.+|. .+.....++||.....+.. ...++|+.|+++|+|+.+....
T Consensus 68 ~~~l~~~l~~-~v-lVgHn~~fD~~~L~--~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~------ 137 (152)
T cd06144 68 QKKVAELLKG-RI-LVGHALKNDLKVLK--LDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGE------ 137 (152)
T ss_pred HHHHHHHhCC-CE-EEEcCcHHHHHHhc--CcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCC------
Confidence 4456667765 44 49999999999994 3333346889876444433 2478999999999998764211
Q ss_pred CCCCCHHHHHHHHHchHHHHHHH
Q 002503 247 QRPLPAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 247 ~RPLseeql~YAa~Da~yLL~Ly 269 (914)
.-|..||..+..||
T Consensus 138 ---------H~Al~DA~at~~l~ 151 (152)
T cd06144 138 ---------HSSVEDARAAMRLY 151 (152)
T ss_pred ---------cCcHHHHHHHHHHh
Confidence 11567888777776
No 35
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=95.18 E-value=0.33 Score=53.10 Aligned_cols=133 Identities=20% Similarity=0.261 Sum_probs=83.1
Q ss_pred HhccCcceEEEeecccCCCCCcEEEEEEEe----CCc-----eEEEeCCCc---------------------cchhhhHH
Q 002503 125 LSKEFFFAVDTEQHSLRSFLGFTALIQIST----EKE-----DYLVDTIAL---------------------HDEISILQ 174 (914)
Q Consensus 125 L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt----~~~-----~yLID~laL---------------------~d~l~~L~ 174 (914)
+.+...+++|+|+.+.....+. +++|+. .+. ..+|.+..+ .+.+..|.
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 4556788999999877655443 333332 111 124433111 11344555
Q ss_pred HhhcCCCCeEEEechhHhHHHHHH---hcCCCc--CeEeehhhHHH-HcCCCCCCHHHHHHHHcCCcCCcccccccccCC
Q 002503 175 PFFADPGVCKVFHGSDNDVMWLQR---DFHIYV--VNLFDTAKACE-VLSKPQKSLAYLLETYCGVATNKFLQREDWRQR 248 (914)
Q Consensus 175 elLaDp~IvKV~Hgak~Dl~~Lqr---dfGI~~--~nlFDTqlAAy-LLg~~~~SLa~Lle~yLgv~ldK~~q~sDWr~R 248 (914)
+++.+ . +.|+|++.+|..+|.+ .+|+.. ...+||.-.+. ++..+.++|++|++ ++|+.....+
T Consensus 143 ~fl~~-~-v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~~-~lgi~~~~~H-------- 211 (257)
T PRK08517 143 LFLGD-S-VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKE-LLGIEIEVHH-------- 211 (257)
T ss_pred HHHCC-C-eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHHH-HcCcCCCCCC--------
Confidence 56654 3 4689999999999864 345543 35778875554 44445789999987 5676653222
Q ss_pred CCCHHHHHHHHHchHHHHHHHHHHHHHHHH
Q 002503 249 PLPAEMLQYAQTDAHYLLYIAKCLVAELKQ 278 (914)
Q Consensus 249 PLseeql~YAa~Da~yLL~Lyd~L~~eL~e 278 (914)
-|..||..+..|+..+..++..
T Consensus 212 --------rAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 212 --------RAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred --------ChHHHHHHHHHHHHHHHHHhHH
Confidence 2678999999999998877753
No 36
>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=95.09 E-value=0.58 Score=49.10 Aligned_cols=85 Identities=20% Similarity=0.124 Sum_probs=61.3
Q ss_pred CeEEEechhHhHHHHHHh---cCCC-----cCeEeehhhHHHHcCCCCCCHHHHHHHHcCCcCCcccccccccCCCCCHH
Q 002503 182 VCKVFHGSDNDVMWLQRD---FHIY-----VVNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQREDWRQRPLPAE 253 (914)
Q Consensus 182 IvKV~Hgak~Dl~~Lqrd---fGI~-----~~nlFDTqlAAyLLg~~~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLsee 253 (914)
-+-|+|++.+|+.+|.+. +|+. ...++||...++.+. +..+|+.+++.| |+..+. .
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~-~~~~L~~l~~~~-gi~~~~--------------~ 169 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAY-GQTVLAKACQAA-GXDFDS--------------T 169 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHc-CcccHHHHHHHc-CCCccc--------------c
Confidence 357999999999998643 3432 124799998887664 356899988864 654321 1
Q ss_pred HHHHHHHchHHHHHHHHHHHHHHHHcCCC
Q 002503 254 MLQYAQTDAHYLLYIAKCLVAELKQQGNE 282 (914)
Q Consensus 254 ql~YAa~Da~yLL~Lyd~L~~eL~e~g~~ 282 (914)
+..-|..||..+..|+..|..++.+.+.+
T Consensus 170 ~~H~Al~Da~ata~lf~~l~~~~~~~~~~ 198 (200)
T TIGR01298 170 QAHSALYDTEKTAELFCEIVNRWKRLGGW 198 (200)
T ss_pred chhhhHHhHHHHHHHHHHHHHHHHHccCC
Confidence 22447789999999999999999888753
No 37
>PRK07883 hypothetical protein; Validated
Probab=95.06 E-value=0.21 Score=60.35 Aligned_cols=138 Identities=20% Similarity=0.180 Sum_probs=88.6
Q ss_pred HHHhccCcceEEEeecccCCCCCcEEEEEEEe----CCc-----eEEEeCCC-----------cc-----------chhh
Q 002503 123 NALSKEFFFAVDTEQHSLRSFLGFTALIQIST----EKE-----DYLVDTIA-----------LH-----------DEIS 171 (914)
Q Consensus 123 e~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt----~~~-----~yLID~la-----------L~-----------d~l~ 171 (914)
..+.+...++||+|+.+.++....+ ++|+. .+. ..+|.|-. +. +.+.
T Consensus 10 ~~~~~~~~Vv~D~ETTGl~p~~~~I--IEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~ 87 (557)
T PRK07883 10 TPLRDVTFVVVDLETTGGSPAGDAI--TEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLP 87 (557)
T ss_pred CCCcCCCEEEEEEecCCCCCCCCeE--EEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHH
Confidence 4455678899999998776544333 33332 111 23454311 11 1233
Q ss_pred hHHHhhcCCCCeEEEechhHhHHHHHHh---cCCCc--CeEeehhhHHHH-cC---CCCCCHHHHHHHHcCCcCCccccc
Q 002503 172 ILQPFFADPGVCKVFHGSDNDVMWLQRD---FHIYV--VNLFDTAKACEV-LS---KPQKSLAYLLETYCGVATNKFLQR 242 (914)
Q Consensus 172 ~L~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~~--~nlFDTqlAAyL-Lg---~~~~SLa~Lle~yLgv~ldK~~q~ 242 (914)
.|.+++.+ .+-|+|++.+|+.+|.+. +|+.. ...+||+.-+.- +. ...++|+.|++ ++|+.....
T Consensus 88 ~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~-~~gi~~~~~--- 161 (557)
T PRK07883 88 AFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLAR-LFGATTTPT--- 161 (557)
T ss_pred HHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHH-HCCcccCCC---
Confidence 44555654 356899999999998754 46554 357899876654 32 34789999987 567765322
Q ss_pred ccccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHHHcCC
Q 002503 243 EDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQGN 281 (914)
Q Consensus 243 sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~g~ 281 (914)
+-|..||.++..|+..+..++.+.|.
T Consensus 162 -------------H~Al~DA~ata~l~~~l~~~~~~~~~ 187 (557)
T PRK07883 162 -------------HRALDDARATVDVLHGLIERLGNLGV 187 (557)
T ss_pred -------------CCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 23789999999999999999987663
No 38
>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=95.03 E-value=0.39 Score=47.99 Aligned_cols=86 Identities=21% Similarity=0.206 Sum_probs=57.1
Q ss_pred hhhHHHhhcCCCCeEEEechhHhHHHHHHhc---CCC-----cCeEeehhhHHHHcCC-CCCCHHHHHHHHcCCcCCccc
Q 002503 170 ISILQPFFADPGVCKVFHGSDNDVMWLQRDF---HIY-----VVNLFDTAKACEVLSK-PQKSLAYLLETYCGVATNKFL 240 (914)
Q Consensus 170 l~~L~elLaDp~IvKV~Hgak~Dl~~Lqrdf---GI~-----~~nlFDTqlAAyLLg~-~~~SLa~Lle~yLgv~ldK~~ 240 (914)
+..|.+++.+ . ..|+|++.+|+.+|.+.+ |+. ...++||+..++.+.. ...+|+.++++| |+..+..
T Consensus 72 ~~~l~~~l~~-~-~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~-~i~~~~~- 147 (167)
T cd06131 72 ADEFLDFIRG-A-ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRF-GIDNSHR- 147 (167)
T ss_pred HHHHHHHHCC-C-eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHC-CCCCCCC-
Confidence 3455566655 3 358999999999986543 332 2358999977766553 467999999886 6543211
Q ss_pred ccccccCCCCCHHHHHHHHHchHHHHHHHHHH
Q 002503 241 QREDWRQRPLPAEMLQYAQTDAHYLLYIAKCL 272 (914)
Q Consensus 241 q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L 272 (914)
...-|..||..+..|+..|
T Consensus 148 -------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 148 -------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred -------------CCCChHHHHHHHHHHHHHh
Confidence 1123778999998888655
No 39
>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=94.95 E-value=0.32 Score=63.50 Aligned_cols=135 Identities=19% Similarity=0.297 Sum_probs=91.9
Q ss_pred hccCcceEEEeecccCCCCCcEEEEEEEe----CCc-----eEEEeCCC----------------------ccchhhhHH
Q 002503 126 SKEFFFAVDTEQHSLRSFLGFTALIQIST----EKE-----DYLVDTIA----------------------LHDEISILQ 174 (914)
Q Consensus 126 ~~a~~IAVDtE~~s~rsy~g~lcLLQLSt----~~~-----~yLID~la----------------------L~d~l~~L~ 174 (914)
.....+++|+|+.+..+....+ ++|+. .+. ..+|.|.. +.+.+..+.
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 5668899999998876654443 33332 111 12343311 112344555
Q ss_pred HhhcCCCCeEEEechhHhHHHHHHh---cCCCc--CeEeehhhHHHHcCC--CCCCHHHHHHHHcCCcCCcccccccccC
Q 002503 175 PFFADPGVCKVFHGSDNDVMWLQRD---FHIYV--VNLFDTAKACEVLSK--PQKSLAYLLETYCGVATNKFLQREDWRQ 247 (914)
Q Consensus 175 elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~~--~nlFDTqlAAyLLg~--~~~SLa~Lle~yLgv~ldK~~q~sDWr~ 247 (914)
+++.+ -+-|.|++.+|+..|.+. +|+.. ..++||...++.+.+ ..++|+.|++++ |+....
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 66654 356899999999988643 46542 468999998888764 478999999874 776532
Q ss_pred CCCCHHHHHHHHHchHHHHHHHHHHHHHHHHcCC
Q 002503 248 RPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQGN 281 (914)
Q Consensus 248 RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~g~ 281 (914)
.+.|..||..+..|+..|.+++.+.+.
T Consensus 334 -------~HrAl~DA~aTa~I~~~ll~~l~~~~i 360 (1213)
T TIGR01405 334 -------HHRADYDAEATAKVFKVMVEQLKEKGI 360 (1213)
T ss_pred -------CcCHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 144889999999999999999988764
No 40
>PF14239 RRXRR: RRXRR protein
Probab=94.88 E-value=0.01 Score=61.25 Aligned_cols=48 Identities=27% Similarity=0.423 Sum_probs=45.1
Q ss_pred eeEEeCCCceeeeecCccccceecccchhhccCCCceEEeecccCCCC
Q 002503 511 CRIYANDGRLLCYCDRKKLEWYLTRDLAKLVEDNPPAIMLLFEPKGRP 558 (914)
Q Consensus 511 C~l~apdG~lLc~cd~kKa~WYl~k~La~~v~e~P~~IrL~FeP~gr~ 558 (914)
.+++|+||++|--|...+|...|++|-|.++.-.||||+|+.+|++..
T Consensus 1 VfVld~~gkPLmP~~p~rAR~LLk~GkA~V~r~~PFtI~L~~~~~~~~ 48 (176)
T PF14239_consen 1 VFVLDKNGKPLMPCHPARARKLLKQGKAKVVRRYPFTIQLKYEPSGSY 48 (176)
T ss_pred CeEECCCCCcCCCCCHHHHHHHHHCCCEEEEecCCeEEEEEeccCCCc
Confidence 378999999999999999999999999999999999999999988665
No 41
>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=94.70 E-value=0.28 Score=49.52 Aligned_cols=83 Identities=16% Similarity=-0.065 Sum_probs=52.4
Q ss_pred hhhHHHhhcCCCCeEEEechhHhHHHHHHhcCCCcCeEeehhh---HHHHcCC---CCCCHHHHHHHHcCCcCCcccccc
Q 002503 170 ISILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVVNLFDTAK---ACEVLSK---PQKSLAYLLETYCGVATNKFLQRE 243 (914)
Q Consensus 170 l~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~nlFDTql---AAyLLg~---~~~SLa~Lle~yLgv~ldK~~q~s 243 (914)
+..|.+++.+ -+-|+|++.+|+.+|... .....+.||.. +.+..++ ..++|..|+++|++..+...++.-
T Consensus 68 ~~~l~~~l~~--~vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H 143 (157)
T cd06149 68 QKEILKILKG--KVVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGH 143 (157)
T ss_pred HHHHHHHcCC--CEEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCc
Confidence 3455566653 457999999999999422 22235778854 3333333 358999999999876654322211
Q ss_pred cccCCCCCHHHHHHHHHchHHHHHHH
Q 002503 244 DWRQRPLPAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 244 DWr~RPLseeql~YAa~Da~yLL~Ly 269 (914)
| |..||.....||
T Consensus 144 ----~---------Al~DA~at~~l~ 156 (157)
T cd06149 144 ----S---------SVEDARATMELY 156 (157)
T ss_pred ----C---------cHHHHHHHHHHh
Confidence 2 556777777766
No 42
>PRK05168 ribonuclease T; Provisional
Probab=94.61 E-value=0.97 Score=47.84 Aligned_cols=148 Identities=18% Similarity=0.181 Sum_probs=90.0
Q ss_pred HHHHHHHHhccCcceEEEeecccCCCCCcE---EEEEEEeC--C-----c--eEEEeCC---Cc----------c-ch--
Q 002503 118 LNELANALSKEFFFAVDTEQHSLRSFLGFT---ALIQISTE--K-----E--DYLVDTI---AL----------H-DE-- 169 (914)
Q Consensus 118 L~~lle~L~~a~~IAVDtE~~s~rsy~g~l---cLLQLSt~--~-----~--~yLID~l---aL----------~-d~-- 169 (914)
++-+-..+.....+++|+|..+.......+ +.+.+... + . ..+|.|. .+ . +.
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~ 86 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPL 86 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhh
Confidence 455566777888999999998776654443 23333211 1 1 2355541 11 0 10
Q ss_pred ---------hhhHHHhhcC-------CCCeEEEechhHhHHHHHH---hcCCC-----cCeEeehhhHHHHcCCCCCCHH
Q 002503 170 ---------ISILQPFFAD-------PGVCKVFHGSDNDVMWLQR---DFHIY-----VVNLFDTAKACEVLSKPQKSLA 225 (914)
Q Consensus 170 ---------l~~L~elLaD-------p~IvKV~Hgak~Dl~~Lqr---dfGI~-----~~nlFDTqlAAyLLg~~~~SLa 225 (914)
+..+.+++.+ ...+-|+|++.+|+..|.+ .+|+. ...++||...++.+. +..+|.
T Consensus 87 ~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~-~~~~L~ 165 (211)
T PRK05168 87 RGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLAL-GQTVLA 165 (211)
T ss_pred hcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHc-CCCCHH
Confidence 1112222221 2456799999999988764 34542 124899987776653 346899
Q ss_pred HHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHHHcCC
Q 002503 226 YLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQGN 281 (914)
Q Consensus 226 ~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~g~ 281 (914)
.+++.| |+.++... ..-|..||..+..|+..|.+++.+.|.
T Consensus 166 ~l~~~~-gl~~~~~~--------------~H~Al~DA~ata~l~~~l~~~~~~~~~ 206 (211)
T PRK05168 166 KACQAA-GIEFDNKE--------------AHSALYDTEKTAELFCEIVNRWKRLGG 206 (211)
T ss_pred HHHHHC-CCCCCCCC--------------CCChHHHHHHHHHHHHHHHHHHHHccC
Confidence 988864 66542111 122778999999999999999988774
No 43
>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=94.56 E-value=0.38 Score=48.14 Aligned_cols=80 Identities=23% Similarity=0.169 Sum_probs=52.5
Q ss_pred hHHHhhcCCCCeEEEechhHhHHHHHHhcCCCcCeEeehhhHHHHcCC--CCCCHHHHHHHHcCCcCCcccccccccCCC
Q 002503 172 ILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLSK--PQKSLAYLLETYCGVATNKFLQREDWRQRP 249 (914)
Q Consensus 172 ~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~--~~~SLa~Lle~yLgv~ldK~~q~sDWr~RP 249 (914)
.+.+++. +.-+-|+|++.+|+.+|.. . ...++||...++.+.. .+++|..|+++|++..+...... -|
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 4455564 2345699999999999942 2 2458999977665432 25799999999998654321111 12
Q ss_pred CCHHHHHHHHHchHHHHHHH
Q 002503 250 LPAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 250 Lseeql~YAa~Da~yLL~Ly 269 (914)
|..||..+..||
T Consensus 138 --------Al~DA~~t~~l~ 149 (150)
T cd06145 138 --------SVEDARAALELV 149 (150)
T ss_pred --------cHHHHHHHHHHh
Confidence 556777777665
No 44
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=94.48 E-value=0.64 Score=49.96 Aligned_cols=82 Identities=20% Similarity=0.170 Sum_probs=58.9
Q ss_pred CeEEEechhHhHHHHHHh---cCCC---cCeEeehhhHHHHcCC---CCCCHHHHHHHHcCCcCCcccccccccCCCCCH
Q 002503 182 VCKVFHGSDNDVMWLQRD---FHIY---VVNLFDTAKACEVLSK---PQKSLAYLLETYCGVATNKFLQREDWRQRPLPA 252 (914)
Q Consensus 182 IvKV~Hgak~Dl~~Lqrd---fGI~---~~nlFDTqlAAyLLg~---~~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLse 252 (914)
.+-|+|++.+|+.+|.+. +|+. ...++||...++.+.. ++++|..|++. +|+.....+
T Consensus 94 ~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~-~gi~~~~aH------------ 160 (232)
T PRK07942 94 VPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEH-YGVRLDNAH------------ 160 (232)
T ss_pred CEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHH-cCCCCCCCC------------
Confidence 455999999999988654 3443 2468999987765532 36789999877 477654322
Q ss_pred HHHHHHHHchHHHHHHHHHHHHHHHHcC
Q 002503 253 EMLQYAQTDAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 253 eql~YAa~Da~yLL~Lyd~L~~eL~e~g 280 (914)
-|..||..+..|+..|.+++.+.+
T Consensus 161 ----~Al~Da~ata~l~~~l~~~~~~l~ 184 (232)
T PRK07942 161 ----EATADALAAARVAWALARRFPELA 184 (232)
T ss_pred ----ChHHHHHHHHHHHHHHHHHHHHhh
Confidence 277899999999999887776443
No 45
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=94.44 E-value=0.075 Score=64.53 Aligned_cols=73 Identities=14% Similarity=0.199 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCcCcccChHHHHHHHHhCCCCHHHHHHHHhhcCCcccccccCCCCCCCChhhcccHHHH
Q 002503 343 TQDLVRRLCAWRDLMARVHDESLRFVLSDQAIIALANKAPANRTDVYTTIAQADSDVDCLNLSSSLPSPSPVVCSHLDDV 422 (914)
Q Consensus 343 ~l~vlr~L~~WRD~~AR~~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~i~~~d~~~~~~~l~~~~~~~sp~Vr~hl~eL 422 (914)
...++.+|-.||.++|++.+.|+.-|++|..|.+||+.+|+|.+++.+.- +. ...-+..+..++
T Consensus 532 ~~~l~~~Lr~~R~~~a~~~~~~~~~if~d~tL~~ia~~~P~t~~~l~~i~----------Gv------g~~K~~~yg~~~ 595 (607)
T PRK11057 532 DRKLFAKLRKLRKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVN----------GV------GQRKLERFGKPF 595 (607)
T ss_pred hHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHcCCC----------CC------CHHHHHHHHHHH
Confidence 45789999999999999999999999999999999999999999988621 10 123467788888
Q ss_pred HHHHHHHhh
Q 002503 423 ERQVCNNVE 431 (914)
Q Consensus 423 ~~lI~~a~~ 431 (914)
+.+|.+...
T Consensus 596 l~~i~~~~~ 604 (607)
T PRK11057 596 MALIRAHVD 604 (607)
T ss_pred HHHHHHHHh
Confidence 888886543
No 46
>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=94.31 E-value=0.63 Score=44.64 Aligned_cols=82 Identities=20% Similarity=0.225 Sum_probs=54.2
Q ss_pred hhhHHHhhcCCCCeEEEechhHhHHHHHHhcC-----CCcCeEeehhhHHHHc-CC-CCCCHHHHHHHHcCCcCCccccc
Q 002503 170 ISILQPFFADPGVCKVFHGSDNDVMWLQRDFH-----IYVVNLFDTAKACEVL-SK-PQKSLAYLLETYCGVATNKFLQR 242 (914)
Q Consensus 170 l~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfG-----I~~~nlFDTqlAAyLL-g~-~~~SLa~Lle~yLgv~ldK~~q~ 242 (914)
+..+..++.+ ...|+|++.+|..+|.+.+. ......+||+..+..+ +. ...++..+...++|....+
T Consensus 70 ~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~---- 143 (159)
T cd06127 70 LPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEG---- 143 (159)
T ss_pred HHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCCC----
Confidence 4556667765 56799999999999976543 2345789998766544 33 2567877755566653321
Q ss_pred ccccCCCCCHHHHHHHHHchHHHHHHH
Q 002503 243 EDWRQRPLPAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 243 sDWr~RPLseeql~YAa~Da~yLL~Ly 269 (914)
..-|..||.++..|+
T Consensus 144 ------------~H~Al~Da~~t~~l~ 158 (159)
T cd06127 144 ------------AHRALADALATAELL 158 (159)
T ss_pred ------------CCCcHHHHHHHHHHh
Confidence 123778888887775
No 47
>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=94.06 E-value=0.54 Score=49.84 Aligned_cols=92 Identities=17% Similarity=0.220 Sum_probs=59.8
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHhcC---CC-c--CeEeehhhHHHHcC---C-CCCCHHHHHHHHcCCcCCccc
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRDFH---IY-V--VNLFDTAKACEVLS---K-PQKSLAYLLETYCGVATNKFL 240 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfG---I~-~--~nlFDTqlAAyLLg---~-~~~SLa~Lle~yLgv~ldK~~ 240 (914)
..|.+++.+ -.-|+|++.+|+.+|.+.+. .. + ..++||...++.+. . .+.+|..|++.| |+.....
T Consensus 79 ~~~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~-gl~~~~~- 154 (217)
T TIGR00573 79 EDFADYIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRY-EITNSHR- 154 (217)
T ss_pred HHHHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHc-CCCCCCc-
Confidence 345555544 34689999999999976643 21 1 35789886555432 1 356899998775 6543200
Q ss_pred ccccccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHHHc
Q 002503 241 QREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQ 279 (914)
Q Consensus 241 q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~ 279 (914)
. ..=|..||.++..|+..|..+..+.
T Consensus 155 ~-------------~H~Al~DA~~ta~l~~~l~~~~~~~ 180 (217)
T TIGR00573 155 A-------------LHGALADAFILAKLYLVMTGKQTKY 180 (217)
T ss_pred c-------------cCCHHHHHHHHHHHHHHHHhcchhh
Confidence 0 1227789999999999987765543
No 48
>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=94.03 E-value=0.63 Score=49.85 Aligned_cols=87 Identities=23% Similarity=0.240 Sum_probs=58.7
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHh---cCC--C-c---CeEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCccc
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRD---FHI--Y-V---VNLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFL 240 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI--~-~---~nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~ 240 (914)
..|.+++.+ ..-|+|++.+|+.+|.+. +|. . + ..++||...++.+-+. .++|..|+++| |+....
T Consensus 74 ~~f~~fi~~--~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~-gi~~~~-- 148 (225)
T TIGR01406 74 DEFLDFIGG--SELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRF-KVDNSH-- 148 (225)
T ss_pred HHHHHHhCC--CEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhc-CCCCCC--
Confidence 344555654 235899999999998744 452 2 1 4689999877765443 68999999886 554321
Q ss_pred ccccccCCCCCHHHHHHHHHchHHHHHHHHHHHH
Q 002503 241 QREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVA 274 (914)
Q Consensus 241 q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~ 274 (914)
|. ..=|..||..+..||..|..
T Consensus 149 -------r~-----~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 149 -------RT-----LHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred -------CC-----CcCHHHHHHHHHHHHHHHHc
Confidence 11 12277899999999987754
No 49
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=93.92 E-value=1.2 Score=46.42 Aligned_cols=135 Identities=17% Similarity=0.079 Sum_probs=78.3
Q ss_pred HHHHHHHHhccCcceEEEeecccCCCCCcEEEEEEEe----CCc-------eEEEeCCC--------c------------
Q 002503 118 LNELANALSKEFFFAVDTEQHSLRSFLGFTALIQIST----EKE-------DYLVDTIA--------L------------ 166 (914)
Q Consensus 118 L~~lle~L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt----~~~-------~yLID~la--------L------------ 166 (914)
+..+.+.......++||+|..+.......+ ++|+. ++. .++|.+.. +
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 334444444567899999998776544443 33331 111 23454321 0
Q ss_pred --cchhhhHHHhhcCCCCeEEEechhHhHHHHHHh----cCCCc-CeEeehhhHHH--Hc-C----CCCCCHHHHHHHHc
Q 002503 167 --HDEISILQPFFADPGVCKVFHGSDNDVMWLQRD----FHIYV-VNLFDTAKACE--VL-S----KPQKSLAYLLETYC 232 (914)
Q Consensus 167 --~d~l~~L~elLaDp~IvKV~Hgak~Dl~~Lqrd----fGI~~-~nlFDTqlAAy--LL-g----~~~~SLa~Lle~yL 232 (914)
.+.+..|..++.+ ...|+|++.+|...|.+. +|..+ ...+||.-..+ .. . ..+++|+.+++.|
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 1123455556654 346899999999998654 34443 35789864321 11 1 1257999999764
Q ss_pred CCcCCcccccccccCCCCCHHHHHHHHHchHHHHHHHHHHH
Q 002503 233 GVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLV 273 (914)
Q Consensus 233 gv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~ 273 (914)
|+.....+ =|..||..+..||..|.
T Consensus 174 gi~~~~~H----------------~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 174 DLPVLGRH----------------DALNDAIMAALIFLRLR 198 (202)
T ss_pred CCCCCCCC----------------CcHHHHHHHHHHHHHHH
Confidence 66543221 16689998888887764
No 50
>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=93.89 E-value=0.82 Score=47.20 Aligned_cols=99 Identities=21% Similarity=0.179 Sum_probs=63.9
Q ss_pred hhhHHHhhc--CCCCeEEEech-hHhHHHHHH---hcCCCc-----------------------C-eEeehhhHHHHcC-
Q 002503 170 ISILQPFFA--DPGVCKVFHGS-DNDVMWLQR---DFHIYV-----------------------V-NLFDTAKACEVLS- 218 (914)
Q Consensus 170 l~~L~elLa--Dp~IvKV~Hga-k~Dl~~Lqr---dfGI~~-----------------------~-nlFDTqlAAyLLg- 218 (914)
+..+.+++. ||.+ -|+|+. .+|+..|.. .+|+.. + .++|+...++-..
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 344444554 3665 489998 689988763 355544 1 3789987776443
Q ss_pred CCCCCHHHHHHHHcCCcCCc--ccccccccCCCCCHHHHHHHHHchHHHHHHH
Q 002503 219 KPQKSLAYLLETYCGVATNK--FLQREDWRQRPLPAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 219 ~~~~SLa~Lle~yLgv~ldK--~~q~sDWr~RPLseeql~YAa~Da~yLL~Ly 269 (914)
.++++|..+++.+++..-.. .....+|....-....++|...||...+.|+
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 45789999999999864321 1122222111223678999999999998875
No 51
>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=93.77 E-value=0.15 Score=50.81 Aligned_cols=141 Identities=18% Similarity=0.192 Sum_probs=73.8
Q ss_pred ceEEEeecccCCCCCcEEEEEEEe--CCc-eEEEeCCCcc-chhhhHH---HhhcCCCCeEEEechhHhHHHHHHhc---
Q 002503 131 FAVDTEQHSLRSFLGFTALIQIST--EKE-DYLVDTIALH-DEISILQ---PFFADPGVCKVFHGSDNDVMWLQRDF--- 200 (914)
Q Consensus 131 IAVDtE~~s~rsy~g~lcLLQLSt--~~~-~yLID~laL~-d~l~~L~---elLaDp~IvKV~Hgak~Dl~~Lqrdf--- 200 (914)
+.+|+|+.+..+..+.+.++.+.. ++. .+++....-. +.-..+. ..+.+...+.++||..+|+..|.+.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~l~~~~~iv~yng~~FD~p~L~~~~~~~ 80 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFFELLDEADNIVTYNGKNFDIPFLKRRAKRY 80 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH--HHHHTT--EEESSTTTTHHHHHHHHH-HH
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHHHHHhcCCeEEEEeCcccCHHHHHHHHHHc
Confidence 468999987665556666777764 232 2233322111 1111222 45666677777888899999997655
Q ss_pred CCC-cCeEeehhhHHHHcCCCCCCHHHHHHHHcCCcCC-cc---cc----cccccC---CCCCHHHHHHHHHchHHHHHH
Q 002503 201 HIY-VVNLFDTAKACEVLSKPQKSLAYLLETYCGVATN-KF---LQ----REDWRQ---RPLPAEMLQYAQTDAHYLLYI 268 (914)
Q Consensus 201 GI~-~~nlFDTqlAAyLLg~~~~SLa~Lle~yLgv~ld-K~---~q----~sDWr~---RPLseeql~YAa~Da~yLL~L 268 (914)
++. ..+.+|++..++-...++.+|..+... +|+.-. +. .+ ...|.. +...++++.|...|+..+.+|
T Consensus 81 ~~~~~~~~iDl~~~~~~~~~~~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~Dv~~~~~L 159 (164)
T PF13482_consen 81 GLPPPFNHIDLLKIIKKHFLESYSLKNVEKF-LGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNEDDVRATRRL 159 (164)
T ss_dssp HH--GGGEEEHHHHHT-TTSCCTT--SHHH------------HHHHHHHHHH---TTGGTS--HHHHHHHHHHHHHHHHH
T ss_pred CCCcccchhhHHHHHHhccCCCCCHHHHhhh-cccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 333 457899998876555566788887666 676543 11 10 011211 235588999999999999999
Q ss_pred HHHH
Q 002503 269 AKCL 272 (914)
Q Consensus 269 yd~L 272 (914)
++.|
T Consensus 160 ~~~l 163 (164)
T PF13482_consen 160 YEWL 163 (164)
T ss_dssp HHHH
T ss_pred HHHh
Confidence 9876
No 52
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=93.68 E-value=0.88 Score=52.37 Aligned_cols=136 Identities=15% Similarity=0.197 Sum_probs=83.8
Q ss_pred HhccCcceEEEeecccCCCCCcEEEEEEEe-----CC---c--eEEEeCCC------c--------------cchhhhHH
Q 002503 125 LSKEFFFAVDTEQHSLRSFLGFTALIQIST-----EK---E--DYLVDTIA------L--------------HDEISILQ 174 (914)
Q Consensus 125 L~~a~~IAVDtE~~s~rsy~g~lcLLQLSt-----~~---~--~yLID~la------L--------------~d~l~~L~ 174 (914)
+.+...++||+|..+++..... +|+|+. .. . ..+|.+-. + .+.+..|.
T Consensus 43 ~~~~~fVvlDiETTGLdp~~dr--IIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~ 120 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTSR--LITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLD 120 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCCe--EEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHH
Confidence 4456889999999888765543 333321 11 1 22554311 1 12345566
Q ss_pred HhhcCCCCeEEEechhHhHHHHHHhc-------------------------------CCCc-CeEeehhhHHHHcCC--C
Q 002503 175 PFFADPGVCKVFHGSDNDVMWLQRDF-------------------------------HIYV-VNLFDTAKACEVLSK--P 220 (914)
Q Consensus 175 elLaDp~IvKV~Hgak~Dl~~Lqrdf-------------------------------GI~~-~nlFDTqlAAyLLg~--~ 220 (914)
+++.+ .+.|+|++.+|+..|.+.+ ++.. ..++||...++.+.+ +
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 66764 3569999999999886543 1222 358999998888875 4
Q ss_pred CCCHHHHHHHHcCCcCCcc---cccccccCCCCCHHHHHHHHHchHHHHHHHHHH
Q 002503 221 QKSLAYLLETYCGVATNKF---LQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCL 272 (914)
Q Consensus 221 ~~SLa~Lle~yLgv~ldK~---~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L 272 (914)
.+.|..|+++ +|+..+.. .++++ + +.. ..+.+|+..|..||..+
T Consensus 199 ~~rL~~La~~-lGi~~p~~~A~~~Ra~---~--p~~--~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 199 DIRIRGVAHT-LGLDAPAAEASVERAQ---V--PHR--QLCREETLLVARLYFAL 245 (377)
T ss_pred CCCHHHHHHH-hCCCCCchhhhhhhhc---C--Chh--hhhhHHHHHHHHHHHHh
Confidence 7999999987 47665321 11211 1 111 12457999999998776
No 53
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=93.58 E-value=0.81 Score=49.68 Aligned_cols=87 Identities=18% Similarity=0.233 Sum_probs=57.5
Q ss_pred hHHHhhcCCCCeEEEechhHhHHHHHHh---cCCC------cCeEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCcccc
Q 002503 172 ILQPFFADPGVCKVFHGSDNDVMWLQRD---FHIY------VVNLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFLQ 241 (914)
Q Consensus 172 ~L~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~------~~nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~q 241 (914)
.|.+++.+. ..|+|++.+|+..|.+. +|.. ...++||...++.+-++ .++|..|+++| |+....
T Consensus 79 ~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~~~~-gi~~~~--- 152 (240)
T PRK05711 79 EFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRY-GIDNSH--- 152 (240)
T ss_pred HHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHHHHC-CCCCCC---
Confidence 444555542 35899999999988654 3322 14589999877766443 67999999876 653221
Q ss_pred cccccCCCCCHHHHHHHHHchHHHHHHHHHHHHH
Q 002503 242 REDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAE 275 (914)
Q Consensus 242 ~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~e 275 (914)
|. ..=|..||..+..+|-.|...
T Consensus 153 ------r~-----~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 153 ------RT-----LHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred ------CC-----CCCHHHHHHHHHHHHHHHHCc
Confidence 11 122778999999998777543
No 54
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=93.41 E-value=1.3 Score=43.76 Aligned_cols=89 Identities=25% Similarity=0.230 Sum_probs=59.8
Q ss_pred hhhHHHhhcCCCCeEEEech-hHhHHHHHHh---cCCCc---CeEeehhhHHHHcCC-CCCCHHHHHHHHcCCcCCcccc
Q 002503 170 ISILQPFFADPGVCKVFHGS-DNDVMWLQRD---FHIYV---VNLFDTAKACEVLSK-PQKSLAYLLETYCGVATNKFLQ 241 (914)
Q Consensus 170 l~~L~elLaDp~IvKV~Hga-k~Dl~~Lqrd---fGI~~---~nlFDTqlAAyLLg~-~~~SLa~Lle~yLgv~ldK~~q 241 (914)
+..|..++.+. . .|+|++ .+|+.+|.+. +|+.. ...+||...++.+.. ...+|..|++.| |+.....
T Consensus 71 ~~~~~~~l~~~-~-~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~L~~l~~~~-~~~~~~~-- 145 (169)
T smart00479 71 LEELLEFLKGK-I-LVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGRKYSLKKLAERL-GLEVIGR-- 145 (169)
T ss_pred HHHHHHHhcCC-E-EEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCCCCCHHHHHHHC-CCCCCCC--
Confidence 45566677553 3 456666 9999998653 44432 247999877776543 378999999776 4332111
Q ss_pred cccccCCCCCHHHHHHHHHchHHHHHHHHHHHHHH
Q 002503 242 REDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAEL 276 (914)
Q Consensus 242 ~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL 276 (914)
...|..||..+..|+..+.+++
T Consensus 146 -------------~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 146 -------------AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred -------------CcCcHHHHHHHHHHHHHHHHHh
Confidence 2458899999999999887665
No 55
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=93.26 E-value=1.2 Score=47.80 Aligned_cols=88 Identities=23% Similarity=0.291 Sum_probs=60.9
Q ss_pred hHHHhhcCCCCeEEEec-hhHhHHHHHHh---cCCCc--CeEeehhhHHHHcCC--CCCCHHHHHHHHcCCcCCcccccc
Q 002503 172 ILQPFFADPGVCKVFHG-SDNDVMWLQRD---FHIYV--VNLFDTAKACEVLSK--PQKSLAYLLETYCGVATNKFLQRE 243 (914)
Q Consensus 172 ~L~elLaDp~IvKV~Hg-ak~Dl~~Lqrd---fGI~~--~nlFDTqlAAyLLg~--~~~SLa~Lle~yLgv~ldK~~q~s 243 (914)
.+.+++.+ .-.-|+|+ +.+|+..|.+. .|+.. ...+||+-.+..+.+ +.++|..|++.| |+.....+
T Consensus 72 ~~~~fi~~-~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~-~~~~~~aH--- 146 (232)
T PRK06309 72 KFIEFCGT-DNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVY-GFEENQAH--- 146 (232)
T ss_pred HHHHHHcC-CCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHHHHc-CCCCCCCC---
Confidence 44445543 34568999 48999998754 45442 368999888776643 468999998776 65443222
Q ss_pred cccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHH
Q 002503 244 DWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELK 277 (914)
Q Consensus 244 DWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~ 277 (914)
-|..||.++..|+..|..++.
T Consensus 147 -------------~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 147 -------------RALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred -------------CcHHHHHHHHHHHHHHHHHHH
Confidence 277899999999999877664
No 56
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=93.13 E-value=0.23 Score=63.11 Aligned_cols=135 Identities=19% Similarity=0.289 Sum_probs=94.9
Q ss_pred hccCcceEEEeecccCCCCCcEEEEEEEeC-----C----ceEEEeCCC--------c--------------cchhhhHH
Q 002503 126 SKEFFFAVDTEQHSLRSFLGFTALIQISTE-----K----EDYLVDTIA--------L--------------HDEISILQ 174 (914)
Q Consensus 126 ~~a~~IAVDtE~~s~rsy~g~lcLLQLSt~-----~----~~yLID~la--------L--------------~d~l~~L~ 174 (914)
..+..+.+|+|..++.+.+.. +|||+.. . ..++|+|-. + ...+..+.
T Consensus 419 ~datyVVfDiETTGLs~~~d~--iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf~ 496 (1444)
T COG2176 419 DDATYVVFDIETTGLSPVYDE--IIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKFR 496 (1444)
T ss_pred ccccEEEEEeecCCcCcccch--hhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHHH
Confidence 345678889998777654443 3555431 1 123443311 1 12455667
Q ss_pred HhhcCCCCeEEEechhHhHHHHHHh---cCCCc--CeEeehhhHHHHcCCC--CCCHHHHHHHHcCCcCCcccccccccC
Q 002503 175 PFFADPGVCKVFHGSDNDVMWLQRD---FHIYV--VNLFDTAKACEVLSKP--QKSLAYLLETYCGVATNKFLQREDWRQ 247 (914)
Q Consensus 175 elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~~--~nlFDTqlAAyLLg~~--~~SLa~Lle~yLgv~ldK~~q~sDWr~ 247 (914)
+++.|. +-|.|++.+|+-.|... +|+.+ .++.||.-.|+.|++. +++|..|+++| |+.+
T Consensus 497 ~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~-~v~l----------- 562 (1444)
T COG2176 497 EFIGDS--ILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKKL-GVEL----------- 562 (1444)
T ss_pred HHhcCc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHHh-CccH-----------
Confidence 778763 45999999999888643 56665 4799999999999975 89999999886 4443
Q ss_pred CCCCHHHHHHHHHchHHHHHHHHHHHHHHHHcCC
Q 002503 248 RPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQGN 281 (914)
Q Consensus 248 RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~g~ 281 (914)
+...-|--|+..+-+++..+.+.|++.|.
T Consensus 563 -----e~hHRA~yDaeat~~vf~~f~~~~ke~Gi 591 (1444)
T COG2176 563 -----ERHHRADYDAEATAKVFFVFLKDLKEKGI 591 (1444)
T ss_pred -----HHhhhhhhhHHHHHHHHHHHHHHHHHhch
Confidence 34555778999999999999999999984
No 57
>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=92.91 E-value=2.1 Score=41.97 Aligned_cols=80 Identities=20% Similarity=0.211 Sum_probs=53.9
Q ss_pred hhhHHHhhcCCCCeEEEechhHhHHHHHHh---cCCCc--CeEeehhhHHHHcCC--CCCCHHHHHHHHcCCcCCccccc
Q 002503 170 ISILQPFFADPGVCKVFHGSDNDVMWLQRD---FHIYV--VNLFDTAKACEVLSK--PQKSLAYLLETYCGVATNKFLQR 242 (914)
Q Consensus 170 l~~L~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~~--~nlFDTqlAAyLLg~--~~~SLa~Lle~yLgv~ldK~~q~ 242 (914)
+..|..++.+ ..-|+|++.+|..+|.+. +|+.. ...+||+..+..+-. +..+|+.|++. +|+..+ .+
T Consensus 68 ~~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~~~-~g~~~~-~H-- 141 (156)
T cd06130 68 WPEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEH-LGIELN-HH-- 141 (156)
T ss_pred HHHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHHHH-cCCCcc-Cc--
Confidence 3456666765 356999999999998654 35543 468999877655432 46899999986 566543 22
Q ss_pred ccccCCCCCHHHHHHHHHchHHHHHHH
Q 002503 243 EDWRQRPLPAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 243 sDWr~RPLseeql~YAa~Da~yLL~Ly 269 (914)
+ |..||..+..|+
T Consensus 142 -----~---------Al~Da~~ta~l~ 154 (156)
T cd06130 142 -----D---------ALEDARACAEIL 154 (156)
T ss_pred -----C---------chHHHHHHHHHH
Confidence 2 556777776665
No 58
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=92.75 E-value=0.9 Score=49.87 Aligned_cols=131 Identities=20% Similarity=0.123 Sum_probs=82.4
Q ss_pred CcceEEEeecccCCC--CCcEEEEEEEeCCceEEEeCCC-----c----------c-----c------hhhhHHHhhcCC
Q 002503 129 FFFAVDTEQHSLRSF--LGFTALIQISTEKEDYLVDTIA-----L----------H-----D------EISILQPFFADP 180 (914)
Q Consensus 129 ~~IAVDtE~~s~rsy--~g~lcLLQLSt~~~~yLID~la-----L----------~-----d------~l~~L~elLaDp 180 (914)
..||+|+|..+..+- ...++-+.|-...+..++|..- + + + .-....++|.+
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 689999999865432 1223334443333445555211 1 1 0 11233456654
Q ss_pred CCeEEEechhHhHHHHHHhcCCCcC-eEeehhhHHHH---cCC-CCCCHHHHHHHHcCCcCCcccccccccCCCCCHHHH
Q 002503 181 GVCKVFHGSDNDVMWLQRDFHIYVV-NLFDTAKACEV---LSK-PQKSLAYLLETYCGVATNKFLQREDWRQRPLPAEML 255 (914)
Q Consensus 181 ~IvKV~Hgak~Dl~~LqrdfGI~~~-nlFDTqlAAyL---Lg~-~~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql 255 (914)
.+.|+|+...|+..|+-++ +. -+-||..---| +.. ...||..|.+.+||.++.-++..
T Consensus 185 -RIlVGHaLhnDl~~L~l~h---p~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHs------------- 247 (280)
T KOG2249|consen 185 -RILVGHALHNDLQALKLEH---PRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHS------------- 247 (280)
T ss_pred -CEEeccccccHHHHHhhhC---chhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccccC-------------
Confidence 4569999999999996433 33 46688754323 222 36799999999999888655433
Q ss_pred HHHHHchHHHHHHHHHHHHHHHHc
Q 002503 256 QYAQTDAHYLLYIAKCLVAELKQQ 279 (914)
Q Consensus 256 ~YAa~Da~yLL~Lyd~L~~eL~e~ 279 (914)
..+|+.....||..++.+-++.
T Consensus 248 --SvEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 248 --SVEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred --cHHHHHHHHHHHHHHHHHHHHH
Confidence 3479999999999987766543
No 59
>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=92.70 E-value=0.33 Score=49.00 Aligned_cols=61 Identities=26% Similarity=0.195 Sum_probs=44.7
Q ss_pred hHHHhhcCCCCeEEEechhHhHHHHHHhcCCCcCeEeehhhHHHHcCC-----CCCCHHHHHHHHcCCcCC
Q 002503 172 ILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLSK-----PQKSLAYLLETYCGVATN 237 (914)
Q Consensus 172 ~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~-----~~~SLa~Lle~yLgv~ld 237 (914)
.|.+++.+. -+-|+|++.+|+.+|.. ....+.||...+..+.+ ++++|..|+++|+|..+.
T Consensus 76 ~~~~~i~~~-~vlVgHn~~fD~~fL~~----~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~ 141 (161)
T cd06137 76 ALWKFIDPD-TILVGHSLQNDLDALRM----IHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQ 141 (161)
T ss_pred HHHHhcCCC-cEEEeccHHHHHHHHhC----cCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhc
Confidence 344555542 34699999999999942 23457899988876653 368999999999997764
No 60
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=92.52 E-value=1.4 Score=55.81 Aligned_cols=91 Identities=16% Similarity=0.069 Sum_probs=65.6
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHh---cCCCc-CeEeehhhHHHHcCC--CCCCHHHHHHHHcCCcCCccccccc
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRD---FHIYV-VNLFDTAKACEVLSK--PQKSLAYLLETYCGVATNKFLQRED 244 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~~-~nlFDTqlAAyLLg~--~~~SLa~Lle~yLgv~ldK~~q~sD 244 (914)
..|.+++.+ -+-|+|++.+|+..|.+. .|..+ ...+||...+..+-+ ++++|..|++. +|+.....+
T Consensus 78 ~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~-lgl~~~~~H---- 150 (820)
T PRK07246 78 RHIYDLIED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRE-LNIDLADAH---- 150 (820)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHH-cCCCCCCCC----
Confidence 344556654 446999999999999754 35543 457999987776544 47899999976 576653222
Q ss_pred ccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHHHcC
Q 002503 245 WRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 245 Wr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~g 280 (914)
-|..||..+..|+..|.+++.+.+
T Consensus 151 ------------~Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 151 ------------TAIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred ------------CHHHHHHHHHHHHHHHHHHHhhcC
Confidence 277899999999999988887654
No 61
>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=92.33 E-value=1.7 Score=55.08 Aligned_cols=91 Identities=16% Similarity=0.133 Sum_probs=65.6
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHh---cCCC--cCeEeehhhHHHHcCC--CCCCHHHHHHHHcCCcCCcccccc
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRD---FHIY--VVNLFDTAKACEVLSK--PQKSLAYLLETYCGVATNKFLQRE 243 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~--~~nlFDTqlAAyLLg~--~~~SLa~Lle~yLgv~ldK~~q~s 243 (914)
..|.+++.+ -+-|+|++.+|+.+|.+. .|+. ....+||...+..+.+ ++++|.+|++. +|+..+..+
T Consensus 72 ~~l~~~l~~--~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~-~gi~~~~~H--- 145 (850)
T TIGR01407 72 QEIYDLLED--GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEA-LGLTHENPH--- 145 (850)
T ss_pred HHHHHHhCC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHH-CCCCCCCCC---
Confidence 344556654 346999999999999753 4554 3468999987777654 37899999887 576654322
Q ss_pred cccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHHHcC
Q 002503 244 DWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 244 DWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~g 280 (914)
-|..||..+..|+..|.+++.+.+
T Consensus 146 -------------~Al~DA~ata~l~~~l~~~~~~l~ 169 (850)
T TIGR01407 146 -------------RADSDAQATAELLLLLFEKMEKLP 169 (850)
T ss_pred -------------ChHHHHHHHHHHHHHHHHHHHhcC
Confidence 277899999999999988887644
No 62
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=91.93 E-value=0.015 Score=65.79 Aligned_cols=120 Identities=28% Similarity=0.313 Sum_probs=85.4
Q ss_pred CCcEEEEEEEeCCceEEEeCCCccc--hhhhHHHhhcCCCCeEEEechhHhHHHHHHhcCCCcCeEeehhhHHHHcC-C-
Q 002503 144 LGFTALIQISTEKEDYLVDTIALHD--EISILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLS-K- 219 (914)
Q Consensus 144 ~g~lcLLQLSt~~~~yLID~laL~d--~l~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg-~- 219 (914)
.|.+|.+|+++.-..|++|.+.+.. .-.-+.-+++|..|.||.|++..-...+.+.|||...++|||++|--+-. .
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 3589999999887789998766542 23467779999999999999999999998899999999999999754421 1
Q ss_pred -----C--CCCHHH-HHHHHcCCcCC------c-----ccccccccCCCCCHHHHHHHHHchHH
Q 002503 220 -----P--QKSLAY-LLETYCGVATN------K-----FLQREDWRQRPLPAEMLQYAQTDAHY 264 (914)
Q Consensus 220 -----~--~~SLa~-Lle~yLgv~ld------K-----~~q~sDWr~RPLseeql~YAa~Da~y 264 (914)
+ ...++. |.+ .+.+.+. | .....-|-+||.++..+.-.+..+.|
T Consensus 153 ~g~~~~n~~~~~q~sl~k-h~~~a~k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 153 TGGYLPNCITTLQESLIK-HLQVAPKYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred ccccCCccccchHHHHHH-HHHhcccHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 1 122333 444 3333221 1 12345599999998887776666666
No 63
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=91.74 E-value=3.4 Score=44.84 Aligned_cols=86 Identities=19% Similarity=0.098 Sum_probs=55.9
Q ss_pred hHHHhhcCCCCeEEEechhHhHHHHHHh----cCCCc-CeEeehhhHHHHcCC---------------CCCCHHHHHHHH
Q 002503 172 ILQPFFADPGVCKVFHGSDNDVMWLQRD----FHIYV-VNLFDTAKACEVLSK---------------PQKSLAYLLETY 231 (914)
Q Consensus 172 ~L~elLaDp~IvKV~Hgak~Dl~~Lqrd----fGI~~-~nlFDTqlAAyLLg~---------------~~~SLa~Lle~y 231 (914)
.|.+++.+ -+-|+|++..|+.+|.+. .|..+ ..++||+..++.+-+ +.++|..++.+|
T Consensus 122 ~l~~~~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~ 199 (239)
T PRK09146 122 ELLEALAG--KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRY 199 (239)
T ss_pred HHHHHhCC--CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHc
Confidence 33344433 356899999999998654 23333 368999987765411 346788888764
Q ss_pred cCCcCCcccccccccCCCCCHHHHHHHHHchHHHHHHHHHHHHHH
Q 002503 232 CGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAEL 276 (914)
Q Consensus 232 Lgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL 276 (914)
|+..... .-|..||..+..|+..+..++
T Consensus 200 -gl~~~~~----------------H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 200 -GLPAYSP----------------HHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred -CCCCCCC----------------CCcHHHHHHHHHHHHHHHHHH
Confidence 5543211 227789999988888876665
No 64
>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=91.41 E-value=2.5 Score=43.43 Aligned_cols=79 Identities=23% Similarity=0.277 Sum_probs=54.1
Q ss_pred hHHHhhcC--CCCeEEEech-hHhHHHHHHh---cCCCc---CeEeehhhHHHHcCCCCCCHHHHHHHHcCCcCCccccc
Q 002503 172 ILQPFFAD--PGVCKVFHGS-DNDVMWLQRD---FHIYV---VNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQR 242 (914)
Q Consensus 172 ~L~elLaD--p~IvKV~Hga-k~Dl~~Lqrd---fGI~~---~nlFDTqlAAyLLg~~~~SLa~Lle~yLgv~ldK~~q~ 242 (914)
.|.+++.. ...+-|+|++ .+|+..|.+. +|+.+ ..++||...++.+.+ +|+.|+++++|+.....+
T Consensus 87 ~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~---~L~~l~~~~~~~~~~~~H-- 161 (177)
T cd06136 87 LIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ---SLGSLYKRLFGQEPKNSH-- 161 (177)
T ss_pred HHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh---hHHHHHHHHhCCCccccc--
Confidence 44445442 2356799998 7999988644 45443 245799988877654 899999998887654322
Q ss_pred ccccCCCCCHHHHHHHHHchHHHHHHH
Q 002503 243 EDWRQRPLPAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 243 sDWr~RPLseeql~YAa~Da~yLL~Ly 269 (914)
-|..||..+..++
T Consensus 162 --------------~A~~Da~at~~v~ 174 (177)
T cd06136 162 --------------TAEGDVLALLKCA 174 (177)
T ss_pred --------------chHHHHHHHHHHH
Confidence 2778888777665
No 65
>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=90.53 E-value=2.7 Score=43.77 Aligned_cols=102 Identities=19% Similarity=0.253 Sum_probs=67.0
Q ss_pred hhhHHHhhcC--CCCeEEEechh-HhHHHHHHh---cCCCc------------------------CeEeehhhHHHH-cC
Q 002503 170 ISILQPFFAD--PGVCKVFHGSD-NDVMWLQRD---FHIYV------------------------VNLFDTAKACEV-LS 218 (914)
Q Consensus 170 l~~L~elLaD--p~IvKV~Hgak-~Dl~~Lqrd---fGI~~------------------------~nlFDTqlAAyL-Lg 218 (914)
+..+..++.. |.++ |+|+.. +|+..|... +|+.. ...+|++..++- ++
T Consensus 60 L~~F~~~i~~~dpdii-vgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~ 138 (195)
T cd05780 60 IKRFIEIVKEKDPDVI-YTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLN 138 (195)
T ss_pred HHHHHHHHHHcCCCEE-EecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCC
Confidence 4444455554 7764 788864 799887643 44431 127898876653 45
Q ss_pred CCCCCHHHHHHHHcCCcCCc-c-cccc-cccCCCCCHHHHHHHHHchHHHHHHHHHH
Q 002503 219 KPQKSLAYLLETYCGVATNK-F-LQRE-DWRQRPLPAEMLQYAQTDAHYLLYIAKCL 272 (914)
Q Consensus 219 ~~~~SLa~Lle~yLgv~ldK-~-~q~s-DWr~RPLseeql~YAa~Da~yLL~Lyd~L 272 (914)
.++++|..+++++||..... . .+.. -|...+--...++|+..||...++|...|
T Consensus 139 l~sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 139 LTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred CCcCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 66899999999999975321 1 1112 24444344778999999999999987653
No 66
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=90.34 E-value=0.6 Score=60.21 Aligned_cols=71 Identities=10% Similarity=0.159 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHHHHHH--hCCCcCcccChHHHHHHHHhCCCCHHHHHHHHhhcCCcccccccCCCCCCCChhhcccHHH
Q 002503 344 QDLVRRLCAWRDLMARV--HDESLRFVLSDQAIIALANKAPANRTDVYTTIAQADSDVDCLNLSSSLPSPSPVVCSHLDD 421 (914)
Q Consensus 344 l~vlr~L~~WRD~~AR~--~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~i~~~d~~~~~~~l~~~~~~~sp~Vr~hl~e 421 (914)
-.++.+|-.||.++|++ ++.|+.-|++|..|.+||+..|+|..+|.+.- |. ...-+..+..+
T Consensus 1029 ~~Lfe~Lr~lR~elA~e~~~~vppyvIFsD~TL~eIA~~~P~T~~eLl~I~----------GV------G~~KlekYG~~ 1092 (1195)
T PLN03137 1029 AILYTALRKLRTALVKEAGDGVMAYHIFGNATLQQISKRIPRTKEELLEIN----------GL------GKAKVSKYGDR 1092 (1195)
T ss_pred HHHHHHHHHHHHHHHHhhhcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCC----------Cc------cHHHHHHHHHH
Confidence 36899999999999999 69999999999999999999999999988731 10 12346677777
Q ss_pred HHHHHHHHh
Q 002503 422 VERQVCNNV 430 (914)
Q Consensus 422 L~~lI~~a~ 430 (914)
++.+|.+-+
T Consensus 1093 fL~vI~~~~ 1101 (1195)
T PLN03137 1093 LLETIESTI 1101 (1195)
T ss_pred HHHHHHHHH
Confidence 888877543
No 67
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=90.30 E-value=3.6 Score=52.83 Aligned_cols=91 Identities=18% Similarity=0.150 Sum_probs=65.5
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHh---cCCCc--CeEeehhhHHHHcCC--CCCCHHHHHHHHcCCcCCcccccc
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRD---FHIYV--VNLFDTAKACEVLSK--PQKSLAYLLETYCGVATNKFLQRE 243 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~~--~nlFDTqlAAyLLg~--~~~SLa~Lle~yLgv~ldK~~q~s 243 (914)
..|..++.+ ..-|+|++.+|..+|.+. .|+.. ..++||.-.+..+-+ .+++|..|++. +|+..+..+
T Consensus 76 ~~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~-l~i~~~~~H--- 149 (928)
T PRK08074 76 PEIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEE-LGLEHDQPH--- 149 (928)
T ss_pred HHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHh-CCCCCCCCC---
Confidence 445556654 356999999999999753 45543 468999887777654 37899999887 466543222
Q ss_pred cccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHHHcC
Q 002503 244 DWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 244 DWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e~g 280 (914)
-|..||.....|+..|.+++.+.+
T Consensus 150 -------------~Al~DA~ata~l~~~l~~~~~~l~ 173 (928)
T PRK08074 150 -------------RADSDAEVTAELFLQLLNKLERLP 173 (928)
T ss_pred -------------ChHHHHHHHHHHHHHHHHHHHhcC
Confidence 277899999999999988887654
No 68
>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=90.28 E-value=0.68 Score=48.09 Aligned_cols=77 Identities=23% Similarity=0.217 Sum_probs=52.7
Q ss_pred HHHhhcCCCCeEEEechhHhHHHHHHhcCCC-c-CeEeehhhHHHHcCCCCCCHHHHHHHHcCCcCCcccccccccCCCC
Q 002503 173 LQPFFADPGVCKVFHGSDNDVMWLQRDFHIY-V-VNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQREDWRQRPL 250 (914)
Q Consensus 173 L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~-~-~nlFDTqlAAyLLg~~~~SLa~Lle~yLgv~ldK~~q~sDWr~RPL 250 (914)
|..++ ++..+-|+|+...|+.+| ++. + ..+.||.+.-..-.....||..|+++|||.++..+.- |
T Consensus 95 l~~li-~~~tILVGHsL~nDL~aL----~l~hp~~~viDTa~l~~~~~~r~~sLk~La~~~L~~~IQ~~~H--d------ 161 (174)
T cd06143 95 LRLLV-DLGCIFVGHGLAKDFRVI----NIQVPKEQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSETH--D------ 161 (174)
T ss_pred HHHHc-CCCCEEEeccchhHHHHh----cCcCCCcceEEcHHhccCCCCCChhHHHHHHHHcCCcccCCCc--C------
Confidence 44444 455667999999999998 343 2 3789997532221122579999999999988753211 1
Q ss_pred CHHHHHHHHHchHHHHHHH
Q 002503 251 PAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 251 seeql~YAa~Da~yLL~Ly 269 (914)
..+||.+.+.||
T Consensus 162 -------SvEDArAam~Ly 173 (174)
T cd06143 162 -------SIEDARTALKLY 173 (174)
T ss_pred -------cHHHHHHHHHHh
Confidence 347888888887
No 69
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=88.86 E-value=2.5 Score=56.34 Aligned_cols=84 Identities=21% Similarity=0.278 Sum_probs=63.8
Q ss_pred CCeEEEechhHhHHHHH---HhcCCC-c-CeEeehhhHHHHcCC--CCCCHHHHHHHHcCCcCCcccccccccCCCCCHH
Q 002503 181 GVCKVFHGSDNDVMWLQ---RDFHIY-V-VNLFDTAKACEVLSK--PQKSLAYLLETYCGVATNKFLQREDWRQRPLPAE 253 (914)
Q Consensus 181 ~IvKV~Hgak~Dl~~Lq---rdfGI~-~-~nlFDTqlAAyLLg~--~~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLsee 253 (914)
....|.|++.+|+..|. +.+|+. + ...+||...++.+.+ ..++|..|+++ +|+.....
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 35679999999997764 345664 2 468999988887764 37899999986 47655422
Q ss_pred HHHHHHHchHHHHHHHHHHHHHHHHcCC
Q 002503 254 MLQYAQTDAHYLLYIAKCLVAELKQQGN 281 (914)
Q Consensus 254 ql~YAa~Da~yLL~Lyd~L~~eL~e~g~ 281 (914)
+-|..||..+..|+..|.+++.+.|.
T Consensus 564 --HrAl~DA~aTa~lf~~ll~~l~~~gi 589 (1437)
T PRK00448 564 --HRADYDAEATAYLLIKFLKDLKEKGI 589 (1437)
T ss_pred --cChHHHHHHHHHHHHHHHHHHHHcCC
Confidence 34788999999999999999987764
No 70
>PF13391 HNH_2: HNH endonuclease
Probab=86.47 E-value=0.37 Score=41.01 Aligned_cols=48 Identities=19% Similarity=0.210 Sum_probs=35.9
Q ss_pred eEEcCCCC-----cccccccccchhhhcchhhhhc------cCCcceeecchhhHHhHH
Q 002503 574 CVSCGEGN-----HYLRYRIIPSCYRIHFPEQLKS------HRSHDIVLLCVDCHEVAH 621 (914)
Q Consensus 574 CVvCG~~~-----~~~R~~vVP~~YR~hfP~~~Ks------H~ShDvllLC~~CH~~~~ 621 (914)
||+||..+ .+--.||+|..........-.. -...-.++||.++|..-.
T Consensus 1 C~itg~~~~~~~~~~eaaHI~P~s~~~~~~~~~~~~~~~~~~~~~Ngl~L~~~lH~~fd 59 (66)
T PF13391_consen 1 CVITGIRDPSPWELLEAAHIVPFSLGSWWMNNWFGEYANDWISPSNGLLLRPDLHKLFD 59 (66)
T ss_pred CcCCcCCcCCCCCcEEEEEcccCccCCCchhhhhhhhhccCCCccEEEEcCHhHHHHHC
Confidence 99999999 6666999999886555542110 056789999999998644
No 71
>PF06147 DUF968: Protein of unknown function (DUF968); InterPro: IPR010373 This is a family of uncharacterised prophage proteins that are also found in bacteria and humans.
Probab=86.26 E-value=0.49 Score=50.04 Aligned_cols=67 Identities=25% Similarity=0.352 Sum_probs=43.5
Q ss_pred chhc-cccCCceEEcCCCCcccccccccchhhhcchhhhhccCCcceeecchhhHHhHHHhHHHHHHHHHHHhCCCc
Q 002503 564 EFYI-QSKKNICVSCGEGNHYLRYRIIPSCYRIHFPEQLKSHRSHDIVLLCVDCHEVAHAAAEKYKKQISAEFGIPL 639 (914)
Q Consensus 564 ~yY~-~~k~N~CVvCG~~~~~~R~~vVP~~YR~hfP~~~KsH~ShDvllLC~~CH~~~~~~~~~~k~~la~~~~~pl 639 (914)
+.|+ -.+.-.||+||+...=+ ||||++--++.- -.|..+-++.||..||.-.+. +. ....++|++-.
T Consensus 119 ~~yl~~v~~~~C~iCGk~~~d~-hH~iG~g~~~~~----~~~~d~~~ipLCr~hH~e~H~-g~---~~Fe~ky~~~~ 186 (200)
T PF06147_consen 119 EKYLYWVKSRPCVICGKPPADI-HHIIGMGRGRMG----IKHHDLFVIPLCREHHRELHR-GR---KAFEQKYGIQG 186 (200)
T ss_pred HHHHhhhccCccccCCCCcccc-ceeeccccCccc----cccCCCeehhccHHHHHHHhC-CH---HHHHHHhCCch
Confidence 3444 36999999999754322 344665422211 166778899999999998777 33 55667776643
No 72
>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=86.17 E-value=4.4 Score=42.12 Aligned_cols=77 Identities=21% Similarity=0.144 Sum_probs=53.0
Q ss_pred CeEEEechhHhHHHHHH---hcCCC-----cCeEeehhhHHHHcCCCCCCHHHHHHHHcCCcCCcccccccccCCCCCHH
Q 002503 182 VCKVFHGSDNDVMWLQR---DFHIY-----VVNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQREDWRQRPLPAE 253 (914)
Q Consensus 182 IvKV~Hgak~Dl~~Lqr---dfGI~-----~~nlFDTqlAAyLLg~~~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLsee 253 (914)
.+-|+|++.+|+..|.+ .+|+. ...++||...+..+. ++.+|+.++++| |+..+. .+
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~-~~~~L~~l~~~~-gi~~~~-~~------------ 167 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAY-GQTVLAKACQAA-GIEFDN-KE------------ 167 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHh-CCCcHHHHHHHC-CCCCCC-CC------------
Confidence 45799999999988864 35551 235799998887664 356899988864 665421 11
Q ss_pred HHHHHHHchHHHHHHHHHHHH
Q 002503 254 MLQYAQTDAHYLLYIAKCLVA 274 (914)
Q Consensus 254 ql~YAa~Da~yLL~Lyd~L~~ 274 (914)
..=|..||..+..|+..|.+
T Consensus 168 -~H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 168 -AHSALYDTQKTAELFCKIVN 187 (189)
T ss_pred -CcChHHHHHHHHHHHHHHHH
Confidence 12267889888888887754
No 73
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=84.43 E-value=0.4 Score=38.10 Aligned_cols=41 Identities=29% Similarity=0.617 Sum_probs=25.7
Q ss_pred eEEcCCCC----cccccccccchhhhcchhhhhccCCcceeecchhhHHhHH
Q 002503 574 CVSCGEGN----HYLRYRIIPSCYRIHFPEQLKSHRSHDIVLLCVDCHEVAH 621 (914)
Q Consensus 574 CVvCG~~~----~~~R~~vVP~~YR~hfP~~~KsH~ShDvllLC~~CH~~~~ 621 (914)
|.+||... .+.-++|+|..- --...-....+||..||..-+
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~-------gg~~~~~Nl~~lC~~Ch~~k~ 45 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSK-------GGKNDLENLILLCPSCHRKKH 45 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTT-------T---STTTEEEEEHHHHHHHH
T ss_pred CCCCCCcCccCcceEeECcCchhc-------CCCCCHHHHHHHhHHHHHHhc
Confidence 88899984 556799999763 223346789999999998543
No 74
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=81.29 E-value=0.49 Score=38.13 Aligned_cols=41 Identities=29% Similarity=0.567 Sum_probs=33.1
Q ss_pred CceEEcCC---CCcccccccccchhhhcchhhhhccCCcceeecchhhHHh
Q 002503 572 NICVSCGE---GNHYLRYRIIPSCYRIHFPEQLKSHRSHDIVLLCVDCHEV 619 (914)
Q Consensus 572 N~CVvCG~---~~~~~R~~vVP~~YR~hfP~~~KsH~ShDvllLC~~CH~~ 619 (914)
..|.+||. ...+.-++|+|... -....-...+++|..||..
T Consensus 12 ~~C~~c~~~~~~~~~~v~Hi~p~~~-------~~~~~~~Nl~~~c~~ch~~ 55 (57)
T cd00085 12 GLCPYCGKPGGTEGLEVDHIIPLSD-------GGNNDLDNLVLLCRKCHRK 55 (57)
T ss_pred CcCccCCCcCCCCCceEEeecchhh-------CCCCchHHhHHHHHHHhhc
Confidence 68999998 57788899999765 2345566789999999974
No 75
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=79.01 E-value=2.5 Score=51.41 Aligned_cols=49 Identities=27% Similarity=0.387 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCcCcccChHHHHHHHHhCCCCHHHHHHH
Q 002503 343 TQDLVRRLCAWRDLMARVHDESLRFVLSDQAIIALANKAPANRTDVYTT 391 (914)
Q Consensus 343 ~l~vlr~L~~WRD~~AR~~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~ 391 (914)
...++.+|..||-++|+++|.||.-|++|..|.++|+.+|.+..++...
T Consensus 517 ~~~lf~~lr~~r~~~a~~~~vp~~vif~d~tl~~ma~~~p~~~~~~~~i 565 (590)
T COG0514 517 DRDLFERLRALRKEIADEENVPPYVVFSDATLKEMAEKQPQSADELLSI 565 (590)
T ss_pred cHHHHHHHHHHHHHhhhhhcCCceEEecchHHHHHHHHcCCCHHHHHHh
Confidence 3468999999999999999999999999999999999999999999873
No 76
>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=78.34 E-value=20 Score=37.99 Aligned_cols=139 Identities=22% Similarity=0.284 Sum_probs=77.8
Q ss_pred cCcceEEEeecccCC-C-----CCcEEEEEEEeCCc---eEEEeC--CCccchhhhHHHhhc--CCCCeEEEech-hHhH
Q 002503 128 EFFFAVDTEQHSLRS-F-----LGFTALIQISTEKE---DYLVDT--IALHDEISILQPFFA--DPGVCKVFHGS-DNDV 193 (914)
Q Consensus 128 a~~IAVDtE~~s~rs-y-----~g~lcLLQLSt~~~---~yLID~--laL~d~l~~L~elLa--Dp~IvKV~Hga-k~Dl 193 (914)
-..+++|+|..+... + ...-..+||+.... ..++.. ..-++.+..+..++. ||.|+ |+|+. .+|+
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdii-~g~N~~~FD~ 87 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPDVI-EGHNIFRFDL 87 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccCCCCHHHHHHHHHHHHHHhCCCEE-eccCCcccCH
Confidence 367899999865432 2 12246788876421 112211 111123333444443 47754 67776 6898
Q ss_pred HHHHH---hcCCCc--------------------------------CeEeehhhHHHHc-----CCCCCCHHHHHHHH--
Q 002503 194 MWLQR---DFHIYV--------------------------------VNLFDTAKACEVL-----SKPQKSLAYLLETY-- 231 (914)
Q Consensus 194 ~~Lqr---dfGI~~--------------------------------~nlFDTqlAAyLL-----g~~~~SLa~Lle~y-- 231 (914)
..|.+ .+|+.. .-++|++.+..-. ..++++|..+++.+
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 77652 244432 1237998766532 23578999999986
Q ss_pred cCCc-C--CcccccccccCCCCCHHHHHHHHHchHHHHHHH
Q 002503 232 CGVA-T--NKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIA 269 (914)
Q Consensus 232 Lgv~-l--dK~~q~sDWr~RPLseeql~YAa~Da~yLL~Ly 269 (914)
++.. . +...-..-|...+ +..++|...||..++.|+
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 2321 1 1111111254442 678999999999888875
No 77
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=77.98 E-value=32 Score=38.63 Aligned_cols=83 Identities=16% Similarity=0.110 Sum_probs=51.0
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHhcCCCc-CeEeehhhHHHH--cCCCCCCHHHHHHHHcCCcCCcccccccccC
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYV-VNLFDTAKACEV--LSKPQKSLAYLLETYCGVATNKFLQREDWRQ 247 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~-~nlFDTqlAAyL--Lg~~~~SLa~Lle~yLgv~ldK~~q~sDWr~ 247 (914)
..+..++.+. -+-|.|++.+|..+|.+.+.-.. ....+|+..... .+.++++|.+|+..| |... .
T Consensus 112 ~~l~~fl~~~-~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~~~-g~~~----~------ 179 (294)
T PRK09182 112 AAVDALIAPA-DLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLAGQA-GFFH----E------ 179 (294)
T ss_pred HHHHHHhcCC-CEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHHHHc-CCCC----C------
Confidence 4556666653 35699999999999965432111 234555543322 234578999999875 4211 1
Q ss_pred CCCCHHHHHHHHHchHHHHHHHHHH
Q 002503 248 RPLPAEMLQYAQTDAHYLLYIAKCL 272 (914)
Q Consensus 248 RPLseeql~YAa~Da~yLL~Lyd~L 272 (914)
..-|..|+.++..|+..+
T Consensus 180 -------aHrAl~Da~Ata~ll~~~ 197 (294)
T PRK09182 180 -------GHRAVDDCQALLELLARP 197 (294)
T ss_pred -------CcChHHHHHHHHHHHHHH
Confidence 123778999998877644
No 78
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=73.75 E-value=18 Score=40.59 Aligned_cols=88 Identities=17% Similarity=0.178 Sum_probs=59.6
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHh---cCCCc--CeEeehhhHHHHcC--CCCCCHHHHHHHHcCCcCCcccccc
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRD---FHIYV--VNLFDTAKACEVLS--KPQKSLAYLLETYCGVATNKFLQRE 243 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~~--~nlFDTqlAAyLLg--~~~~SLa~Lle~yLgv~ldK~~q~s 243 (914)
..|.+++.+ -+-|+|++.+|+..|.+. +|+.. ...+||+..++-+- .+.++|..|++.| |+..+ .
T Consensus 72 ~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~~-gi~~~-~---- 143 (309)
T PRK06195 72 EKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFL-GYEFK-H---- 143 (309)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHHc-CCCCc-c----
Confidence 345555543 456999999999888643 45443 35899987665443 3478999998875 54321 1
Q ss_pred cccCCCCCHHHHHHHHHchHHHHHHHHHHHHHHHH
Q 002503 244 DWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAELKQ 278 (914)
Q Consensus 244 DWr~RPLseeql~YAa~Da~yLL~Lyd~L~~eL~e 278 (914)
+-|..||..+..|+..|..++..
T Consensus 144 ------------H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 144 ------------HDALADAMACSNILLNISKELNS 166 (309)
T ss_pred ------------cCCHHHHHHHHHHHHHHHHHhcc
Confidence 33778999999998888776644
No 79
>smart00507 HNHc HNH nucleases.
Probab=72.60 E-value=1.7 Score=34.19 Aligned_cols=40 Identities=30% Similarity=0.604 Sum_probs=30.6
Q ss_pred CceEEcCCCCc--ccccccccchhhhcchhhhhccCCcceeecchhhHH
Q 002503 572 NICVSCGEGNH--YLRYRIIPSCYRIHFPEQLKSHRSHDIVLLCVDCHE 618 (914)
Q Consensus 572 N~CVvCG~~~~--~~R~~vVP~~YR~hfP~~~KsH~ShDvllLC~~CH~ 618 (914)
..|..||..-. +.-++|+|..= . .+..-...++||..||.
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p~~~--~-----~~~~~~Nl~~~c~~ch~ 52 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIPLSD--G-----GNDDLDNLVLLCPKCHI 52 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCChhc--C-----CCCChHhCeecChhhCc
Confidence 79999999885 78899999521 1 23455578999999994
No 80
>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=71.86 E-value=41 Score=35.75 Aligned_cols=89 Identities=15% Similarity=0.107 Sum_probs=56.5
Q ss_pred CCCCeEEEec-hhHhHHHHHH---hcCCCcC------------------eEeehhhHHH---HcCCCCCCHHHHHHHHcC
Q 002503 179 DPGVCKVFHG-SDNDVMWLQR---DFHIYVV------------------NLFDTAKACE---VLSKPQKSLAYLLETYCG 233 (914)
Q Consensus 179 Dp~IvKV~Hg-ak~Dl~~Lqr---dfGI~~~------------------nlFDTqlAAy---LLg~~~~SLa~Lle~yLg 233 (914)
||.++ ++++ ..+|+..|.. .+|+.+. ..+|++.... .+..+.++|..+++.+||
T Consensus 88 ~Pd~i-~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysLd~Va~~~Lg 166 (204)
T cd05779 88 KPHII-VTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLKAVTKAKLG 166 (204)
T ss_pred CCCEE-EecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccHHHHHHHHhC
Confidence 46665 4555 4688877653 2444321 1467776544 344457899999999999
Q ss_pred CcCCc-cc-c-cccccCCCCCHHHHHHHHHchHHHHHHHH
Q 002503 234 VATNK-FL-Q-REDWRQRPLPAEMLQYAQTDAHYLLYIAK 270 (914)
Q Consensus 234 v~ldK-~~-q-~sDWr~RPLseeql~YAa~Da~yLL~Lyd 270 (914)
..-.. .. . ..-|...+ +..++|...||...+.||.
T Consensus 167 ~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 167 YDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred CCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 74211 10 0 11355444 6789999999999999873
No 81
>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=69.57 E-value=73 Score=33.25 Aligned_cols=141 Identities=20% Similarity=0.166 Sum_probs=78.7
Q ss_pred CcceEEEeecccCCC----CCcEEEEEEEeCCc-eEEEeC--CCccchhhhHHHhhc--CCCCeEEEech-hHhHHHHHH
Q 002503 129 FFFAVDTEQHSLRSF----LGFTALIQISTEKE-DYLVDT--IALHDEISILQPFFA--DPGVCKVFHGS-DNDVMWLQR 198 (914)
Q Consensus 129 ~~IAVDtE~~s~rsy----~g~lcLLQLSt~~~-~yLID~--laL~d~l~~L~elLa--Dp~IvKV~Hga-k~Dl~~Lqr 198 (914)
..+++|+|..+...+ ...+..|.++..++ ..++-. ..-.+.+..+..++. ||.++ ++++. .+|+..|..
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 468999998743322 12344444444322 233321 111123344444443 46654 56664 578877652
Q ss_pred ---hcCCCcC----------------------eEeehhhHHHH-cCCCCCCHHHHHHHHcCCc--CCcc----ccc-ccc
Q 002503 199 ---DFHIYVV----------------------NLFDTAKACEV-LSKPQKSLAYLLETYCGVA--TNKF----LQR-EDW 245 (914)
Q Consensus 199 ---dfGI~~~----------------------nlFDTqlAAyL-Lg~~~~SLa~Lle~yLgv~--ldK~----~q~-sDW 245 (914)
.+|+.+. -.+|+.....- ...++++|..+++ +||.. .+|. .+. .-|
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 3554321 16788766543 3356899999987 68863 2221 111 125
Q ss_pred cCCCCCHHHHHHHHHchHHHHHHHHH
Q 002503 246 RQRPLPAEMLQYAQTDAHYLLYIAKC 271 (914)
Q Consensus 246 r~RPLseeql~YAa~Da~yLL~Lyd~ 271 (914)
...--..+.+.|...|+..++.|+..
T Consensus 162 ~~~~~~~~l~~Y~~~D~~~t~~l~~~ 187 (188)
T cd05781 162 DDEKKRDILLKYNRDDARSTYGLAEK 187 (188)
T ss_pred cCcccHHHHHHHHHHHHHHHHHHHhh
Confidence 43213478899999999999999865
No 82
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=66.46 E-value=2.9 Score=45.90 Aligned_cols=48 Identities=23% Similarity=0.569 Sum_probs=32.5
Q ss_pred CceEEcCCC---------Ccccc-ccccc-chhhhcchhhhhccCCcceeecchhhHHhHHHh
Q 002503 572 NICVSCGEG---------NHYLR-YRIIP-SCYRIHFPEQLKSHRSHDIVLLCVDCHEVAHAA 623 (914)
Q Consensus 572 N~CVvCG~~---------~~~~R-~~vVP-~~YR~hfP~~~KsH~ShDvllLC~~CH~~~~~~ 623 (914)
-.|-|||-+ ..||- ||++| +++-+-.+.. .--|..+||+.||..-|.+
T Consensus 196 ~vC~vC~fdF~k~YGe~gKgyIeVHH~~piae~e~~~~vn----p~tDL~plCpNCH~mvHrr 254 (272)
T COG3183 196 TVCDVCEFDFQKKYGEIGKGYIEVHHKIPIAEFEGEYHVN----PLTDLAPLCPNCHKMVHRR 254 (272)
T ss_pred ceeeecCccHHHHhhhhccCeEEEeeccchhhhcCccccC----chhhhhhcCccHHHHHhcc
Confidence 469999864 46776 89999 3332222222 2359999999999988765
No 83
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=66.30 E-value=84 Score=33.34 Aligned_cols=97 Identities=13% Similarity=0.038 Sum_probs=59.0
Q ss_pred hhhhHHHhhcCCCCeEEEech-hHhHHHHHH---hcCCC----------------cCeEeehhhHHH-------Hc--CC
Q 002503 169 EISILQPFFADPGVCKVFHGS-DNDVMWLQR---DFHIY----------------VVNLFDTAKACE-------VL--SK 219 (914)
Q Consensus 169 ~l~~L~elLaDp~IvKV~Hga-k~Dl~~Lqr---dfGI~----------------~~nlFDTqlAAy-------LL--g~ 219 (914)
.+..+..++.+..+ -|+++. .+|+..|.. .+|+. -...+|++.... .. ..
T Consensus 76 lL~~F~~~i~~~~~-iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~ 154 (204)
T cd05783 76 LIREAFKIISEYPI-VLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKY 154 (204)
T ss_pred HHHHHHHHHhcCCE-EEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcccc
Confidence 34455556666544 456654 589988763 35655 123578866432 12 22
Q ss_pred CCCCHHHHHHHHcCCcC-CcccccccccCCCCCHHHHHHHHHchHHHHHHHH
Q 002503 220 PQKSLAYLLETYCGVAT-NKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIAK 270 (914)
Q Consensus 220 ~~~SLa~Lle~yLgv~l-dK~~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd 270 (914)
++++|..+++.++|..- +-..+ -|.. =.++.+.|...||...+.|..
T Consensus 155 ~~~~L~~Va~~~lg~~K~~~~~~--i~~~--~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 155 REYTLDAVAKALLGEGKVELEKN--ISEL--NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccCcHHHHHHHhcCCCcccCCch--hhhh--cHHHHHHhhHHHHHHHHHHhc
Confidence 57899999999999632 11111 1222 126789999999998888753
No 84
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=62.22 E-value=1.2e+02 Score=33.71 Aligned_cols=150 Identities=20% Similarity=0.249 Sum_probs=91.9
Q ss_pred CcceEEEeecccCCCCCcEEEEEEEeCC-ceEEEe---CCCccchhhhHHHhhcCC--CCeEEEechhHhHHHHHH---h
Q 002503 129 FFFAVDTEQHSLRSFLGFTALIQISTEK-EDYLVD---TIALHDEISILQPFFADP--GVCKVFHGSDNDVMWLQR---D 199 (914)
Q Consensus 129 ~~IAVDtE~~s~rsy~g~lcLLQLSt~~-~~yLID---~laL~d~l~~L~elLaDp--~IvKV~Hgak~Dl~~Lqr---d 199 (914)
...-+|+|..++..-...+.++..+... ....|- ..+.......|..++.++ +++.-+-|..+|+-.++| +
T Consensus 99 ~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~~Vrq~~lp~p~~E~avle~fl~~~~~~~lvsfNGkaFD~PfikR~v~~ 178 (278)
T COG3359 99 DVAFFDIETTGLDRAGNTITLVGGARGVDDTMHVRQHFLPAPEEEVAVLENFLHDPDFNMLVSFNGKAFDIPFIKRMVRD 178 (278)
T ss_pred ceEEEeeeccccCCCCCeEEEEEEEEccCceEEEEeecCCCcchhhHHHHHHhcCCCcceEEEecCcccCcHHHHHHHhc
Confidence 3677999998887733334444444432 233331 122222334566677776 345567788899998872 2
Q ss_pred -cCCCc-CeEeehhhHHHHcCC---CCCCHHHHHHHHcCCcCCc---cc----ccccccCCC---CCHHHHHHHHHchHH
Q 002503 200 -FHIYV-VNLFDTAKACEVLSK---PQKSLAYLLETYCGVATNK---FL----QREDWRQRP---LPAEMLQYAQTDAHY 264 (914)
Q Consensus 200 -fGI~~-~nlFDTqlAAyLLg~---~~~SLa~Lle~yLgv~ldK---~~----q~sDWr~RP---Lseeql~YAa~Da~y 264 (914)
+.+.+ ..-||++.+++-|.. +..+|..+ ++++|+.=.- ++ -.-.|+.-+ +-.-.+.|-..|+.-
T Consensus 179 ~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~V-Er~LGi~R~edtdG~~~p~lyr~~~~~~dp~ll~~l~~hN~eDvln 257 (278)
T COG3359 179 RLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTV-ERILGIRREEDTDGYDGPELYRLYRRYGDPGLLDGLVLHNREDVLN 257 (278)
T ss_pred ccccCccccchhhhhhhhhhhhccCCCCChhhH-HHHhCccccccCCCcchHHHHHHHHHcCCHHHHHHHHHccHHHHHh
Confidence 33333 357999999998873 36678764 5599975321 11 111243322 224467788899999
Q ss_pred HHHHHHHHHHHHHHc
Q 002503 265 LLYIAKCLVAELKQQ 279 (914)
Q Consensus 265 LL~Lyd~L~~eL~e~ 279 (914)
|..|+..+...+.+.
T Consensus 258 L~~i~~h~~~~i~~~ 272 (278)
T COG3359 258 LPTIIKHVSKKILED 272 (278)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999998877654
No 85
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=61.46 E-value=1e+02 Score=32.81 Aligned_cols=132 Identities=20% Similarity=0.171 Sum_probs=80.2
Q ss_pred cCcceEEEeecccCCCCCcE---EEEEEEeCC---c--eEEEeCCC-cc---------------------chhhhHHHhh
Q 002503 128 EFFFAVDTEQHSLRSFLGFT---ALIQISTEK---E--DYLVDTIA-LH---------------------DEISILQPFF 177 (914)
Q Consensus 128 a~~IAVDtE~~s~rsy~g~l---cLLQLSt~~---~--~yLID~la-L~---------------------d~l~~L~elL 177 (914)
...+.||+|..+.+.....+ +.+.+..+. . ..++.|-. +. +....+.+++
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 46789999998876533332 334444331 1 13555411 00 1122333444
Q ss_pred cCCCCeEEEechhHhHHHHHHh---cCCCc--CeEeehhhHHHHcCCC--CCCHHHHHHHHcCCcCCcccccccccCCCC
Q 002503 178 ADPGVCKVFHGSDNDVMWLQRD---FHIYV--VNLFDTAKACEVLSKP--QKSLAYLLETYCGVATNKFLQREDWRQRPL 250 (914)
Q Consensus 178 aDp~IvKV~Hgak~Dl~~Lqrd---fGI~~--~nlFDTqlAAyLLg~~--~~SLa~Lle~yLgv~ldK~~q~sDWr~RPL 250 (914)
.+. -.-|.|++..|+..|... ++..+ ..+.||.-.++...++ ..+|..|+. .+|+... ....
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 443 456999999999998644 34443 3577999887776554 789999998 6677643 1111
Q ss_pred CHHHHHHHHHchHHHHHHHHHHHHH
Q 002503 251 PAEMLQYAQTDAHYLLYIAKCLVAE 275 (914)
Q Consensus 251 seeql~YAa~Da~yLL~Lyd~L~~e 275 (914)
.=|..|+..+..+|..+...
T Consensus 162 -----H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 162 -----HRALFDALALAELFLLLQTG 181 (243)
T ss_pred -----cchHHHHHHHHHHHHHHHhc
Confidence 22778888888888877663
No 86
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=59.49 E-value=5.1 Score=50.43 Aligned_cols=84 Identities=30% Similarity=0.304 Sum_probs=60.9
Q ss_pred hhcCCCCeEEEechhHhHHHHHHhcCCCcC--eEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCcccccccccCCCCCH
Q 002503 176 FFADPGVCKVFHGSDNDVMWLQRDFHIYVV--NLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFLQREDWRQRPLPA 252 (914)
Q Consensus 176 lLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~--nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLse 252 (914)
+|-+-.++.|+||...|...+ ++.|. -++||.+. .++|.. ..||.+|+..+||.++.-..- |
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvI----Ni~Vp~~QiiDTv~l-f~~~s~R~LSLrfLa~~lLg~~IQ~~~H--D-------- 1073 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVI----NIHVPEEQIIDTVTL-FRLGSQRMLSLRFLAWELLGETIQMEAH--D-------- 1073 (1118)
T ss_pred HHHHcCcEEEcccccccceEE----EEecChhhheeeeEE-EecccccEEEHHHHHHHHhcchhhcccc--c--------
Confidence 567788999999999998665 55553 39999763 233443 579999999999987632221 1
Q ss_pred HHHHHHHHchHHHHHHHHHHHHHHHHcC
Q 002503 253 EMLQYAQTDAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 253 eql~YAa~Da~yLL~Lyd~L~~eL~e~g 280 (914)
..+||++.|.||++-. +|+++|
T Consensus 1074 -----SIeDA~taLkLYk~Yl-~lkeq~ 1095 (1118)
T KOG1275|consen 1074 -----SIEDARTALKLYKKYL-KLKEQG 1095 (1118)
T ss_pred -----cHHHHHHHHHHHHHHH-HHHHhh
Confidence 4579999999999864 466665
No 87
>PRK11779 sbcB exonuclease I; Provisional
Probab=58.51 E-value=35 Score=40.95 Aligned_cols=87 Identities=22% Similarity=0.253 Sum_probs=54.8
Q ss_pred hHHHhhcCCCCeEEEec-hhHhHHHHHHhcCCC--------------cCeEeehhhHHHHc------------CCCCCCH
Q 002503 172 ILQPFFADPGVCKVFHG-SDNDVMWLQRDFHIY--------------VVNLFDTAKACEVL------------SKPQKSL 224 (914)
Q Consensus 172 ~L~elLaDp~IvKV~Hg-ak~Dl~~LqrdfGI~--------------~~nlFDTqlAAyLL------------g~~~~SL 224 (914)
.+..+|..+..+-|+|+ +.+|...|.+.+... ...++||..+++.+ |.++++|
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 44556654555678996 689998875543111 01245666666654 2346889
Q ss_pred HHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHHHHHHHHHHHH
Q 002503 225 AYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAE 275 (914)
Q Consensus 225 a~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~e 275 (914)
+.|++.| |+..... .-|..||..+..|+..|+++
T Consensus 164 e~L~~~~-gI~~~~A----------------HdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 164 EHLTKAN-GIEHENA----------------HDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHHHHc-CCCCCCC----------------CCcHHHHHHHHHHHHHHHHh
Confidence 9999875 6543211 22678999999998887643
No 88
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=56.24 E-value=41 Score=35.53 Aligned_cols=85 Identities=9% Similarity=0.080 Sum_probs=53.1
Q ss_pred hhhHHHhhcCCCCeEEEechh-HhHHHHHHhcCCCcCe--Eeehh---hHHHHc---CCCCCCHHHHHHHHcCCcCCccc
Q 002503 170 ISILQPFFADPGVCKVFHGSD-NDVMWLQRDFHIYVVN--LFDTA---KACEVL---SKPQKSLAYLLETYCGVATNKFL 240 (914)
Q Consensus 170 l~~L~elLaDp~IvKV~Hgak-~Dl~~LqrdfGI~~~n--lFDTq---lAAyLL---g~~~~SLa~Lle~yLgv~ldK~~ 240 (914)
+..|..++.+. ..|+|++. +|+.+|. ..|+.+.+ ..||. .+.... +...++|..|++. +|+.. ..
T Consensus 75 l~~f~~f~~~~--~lVaHNa~~fD~~fL~-~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~-~gi~~-~~- 148 (195)
T PRK07247 75 LAAFKEFVGEL--PLIGYNAQKSDLPILA-ENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADF-LGIKG-RG- 148 (195)
T ss_pred HHHHHHHHCCC--eEEEEeCcHhHHHHHH-HcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHh-cCCCC-CC-
Confidence 34555666543 36899986 7999994 56766432 34554 222221 2246899999885 56642 11
Q ss_pred ccccccCCCCCHHHHHHHHHchHHHHHHHHHHHHH
Q 002503 241 QREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAE 275 (914)
Q Consensus 241 q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~e 275 (914)
.-|..||..+..|+..|...
T Consensus 149 ---------------HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 149 ---------------HNSLEDARMTARVYESFLES 168 (195)
T ss_pred ---------------cCCHHHHHHHHHHHHHHHhh
Confidence 12668999998888877443
No 89
>PRK11295 hypothetical protein; Provisional
Probab=54.88 E-value=7.2 Score=38.03 Aligned_cols=62 Identities=23% Similarity=0.363 Sum_probs=35.3
Q ss_pred chhccccCCceEEcCCC------CcccccccccchhhhcchhhhhccCCcceeecchhhHHhHHHhHHHHHHHHHHHhCC
Q 002503 564 EFYIQSKKNICVSCGEG------NHYLRYRIIPSCYRIHFPEQLKSHRSHDIVLLCVDCHEVAHAAAEKYKKQISAEFGI 637 (914)
Q Consensus 564 ~yY~~~k~N~CVvCG~~------~~~~R~~vVP~~YR~hfP~~~KsH~ShDvllLC~~CH~~~~~~~~~~k~~la~~~~~ 637 (914)
..|+....-.|+.||+. ..++=+||+|+-- --|. -..-.-+||..||..-+ -|+..+..++.
T Consensus 17 ~~~L~r~p~lC~~Cgr~~~~a~~~a~vVDHIip~~~--gd~~-----D~sNLQ~LC~~CHn~kh-----~R~~~~~~~~~ 84 (113)
T PRK11295 17 EKALKLYPWVCGRCSREFVYSNLRELTVHHIDHDHD--NNPE-----DGSNWELLCLYCHDHEH-----SKYTEADQYGS 84 (113)
T ss_pred HHHHHHCcchhhhhcChhccCCCCCceeeccCCCCC--CCCC-----chhHHHHHhHHHHhHHH-----hhHHHhhhccc
Confidence 45666444479999997 1223455555311 0000 12237799999999743 34556665554
No 90
>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=54.41 E-value=1.2e+02 Score=32.23 Aligned_cols=127 Identities=14% Similarity=0.065 Sum_probs=72.5
Q ss_pred CCCCCcEEEEEEEe---CCceEEEeCCCc---cchhhhHHHhhcCCCCeEEEech-hHhHHHHHHh---cCCCcC-----
Q 002503 141 RSFLGFTALIQIST---EKEDYLVDTIAL---HDEISILQPFFADPGVCKVFHGS-DNDVMWLQRD---FHIYVV----- 205 (914)
Q Consensus 141 rsy~g~lcLLQLSt---~~~~yLID~laL---~d~l~~L~elLaDp~IvKV~Hga-k~Dl~~Lqrd---fGI~~~----- 205 (914)
+...+.+.+|.+.. .+..+.+-.... .+.+..+..++.+..-+-|+|+. .+|+..|.+. +|+.+.
T Consensus 47 ~~~~~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~ 126 (208)
T cd05782 47 PLPFHKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDL 126 (208)
T ss_pred ccccCceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCc
Confidence 34445666666665 233332311111 12344444455542224478876 5899888643 555321
Q ss_pred -------------eEeehhhHHHHcCC-CCCCHHHHHHHHcCCcCCccc----c-cccccCCCCCHHHHHHHHHchHHHH
Q 002503 206 -------------NLFDTAKACEVLSK-PQKSLAYLLETYCGVATNKFL----Q-REDWRQRPLPAEMLQYAQTDAHYLL 266 (914)
Q Consensus 206 -------------nlFDTqlAAyLLg~-~~~SLa~Lle~yLgv~ldK~~----q-~sDWr~RPLseeql~YAa~Da~yLL 266 (914)
..+|++.+..-.+. ...+|..+++ +||+. .|.. + ..-|.... -++..+|...||..+.
T Consensus 127 ~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~L~~va~-~lG~~-~K~d~~G~~v~~~y~~g~-~~~I~~Yc~~Dv~~t~ 203 (208)
T cd05782 127 GNKDWNYRNRYSERHLDLMDLLAFYGARARASLDLLAK-LLGIP-GKMDVDGSQVWELYAEGK-LDEIAEYCETDVLNTY 203 (208)
T ss_pred ccchhhccCcCCCCcccHHHHHhccCccCCCCHHHHHH-HhCCC-CCcCCCHHHHHHHHHcCC-hHHHHHHHHHHHHHHH
Confidence 16788877655443 4789998875 67872 2211 1 12255444 4678999999999998
Q ss_pred HHHH
Q 002503 267 YIAK 270 (914)
Q Consensus 267 ~Lyd 270 (914)
.||-
T Consensus 204 ~l~l 207 (208)
T cd05782 204 LLYL 207 (208)
T ss_pred HHHh
Confidence 8873
No 91
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=52.67 E-value=61 Score=34.82 Aligned_cols=77 Identities=14% Similarity=-0.057 Sum_probs=52.0
Q ss_pred CeEEEechhHhHHHHHHhcCCCcCeEeehhhHHHHcCCC-CCCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHH
Q 002503 182 VCKVFHGSDNDVMWLQRDFHIYVVNLFDTAKACEVLSKP-QKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQT 260 (914)
Q Consensus 182 IvKV~Hgak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~-~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~ 260 (914)
-.-|+|++.+|...|. .+ ....+||...|+.+-+. .+++..|.+. +|+..+.... ....-|..
T Consensus 75 ~~lVaHNa~FD~~~L~-~~---~~~~idTl~lar~l~p~~~~~l~~L~~~-~~l~~~~~~~-----------~~aHrAl~ 138 (219)
T PRK07983 75 EWYVAHNASFDRRVLP-EM---PGEWICTMKLARRLWPGIKYSNMALYKS-RKLNVQTPPG-----------LHHHRALY 138 (219)
T ss_pred CEEEEeCcHhhHHHHh-Cc---CCCcEeHHHHHHHHccCCCCCHHHHHHH-cCCCCCCCCC-----------CCCCcHHH
Confidence 4569999999999984 32 24679999888766543 6889888865 4654321000 01234788
Q ss_pred chHHHHHHHHHHHH
Q 002503 261 DAHYLLYIAKCLVA 274 (914)
Q Consensus 261 Da~yLL~Lyd~L~~ 274 (914)
||..+..|+..|.+
T Consensus 139 Da~ata~ll~~l~~ 152 (219)
T PRK07983 139 DCYITAALLIDIMN 152 (219)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999888877753
No 92
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=51.25 E-value=6.7 Score=33.22 Aligned_cols=25 Identities=24% Similarity=0.626 Sum_probs=18.4
Q ss_pred CCceEEcCCCCcccccc---cccchhhh
Q 002503 571 KNICVSCGEGNHYLRYR---IIPSCYRI 595 (914)
Q Consensus 571 ~N~CVvCG~~~~~~R~~---vVP~~YR~ 595 (914)
.|.|++||...+++|+. +=..++|.
T Consensus 14 ~nrC~~~Gr~rgvirkf~l~lcR~~FRe 41 (52)
T PRK05766 14 ARECQRCGRKQGLIRKYGLYLCRQCFRE 41 (52)
T ss_pred CceeecCCCCceeHHhhCCcccHHHHHH
Confidence 49999999999999953 33444443
No 93
>PRK08061 rpsN 30S ribosomal protein S14; Reviewed
Probab=51.05 E-value=7.7 Score=33.94 Aligned_cols=28 Identities=21% Similarity=0.443 Sum_probs=20.0
Q ss_pred cccCCceEEcCCCCcccccc-cccchhhh
Q 002503 568 QSKKNICVSCGEGNHYLRYR-IIPSCYRI 595 (914)
Q Consensus 568 ~~k~N~CVvCG~~~~~~R~~-vVP~~YR~ 595 (914)
+--.|.|++||...+++|+. +=..++|.
T Consensus 18 ~r~~nRC~~tGR~rgvir~fgl~R~~FRe 46 (61)
T PRK08061 18 VRAYTRCERCGRPHSVYRKFGLCRICFRE 46 (61)
T ss_pred cccceeeecCCCCcceeccCCccHHHHHH
Confidence 33469999999999999954 33344444
No 94
>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=51.04 E-value=32 Score=31.69 Aligned_cols=46 Identities=13% Similarity=0.119 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHhCCCcCcccChHHHHHHHHhCCCCHHHHHHH
Q 002503 346 LVRRLCAWRDLMARVHDESLRFVLSDQAIIALANKAPANRTDVYTT 391 (914)
Q Consensus 346 vlr~L~~WRD~~AR~~Des~~~VL~d~~Ll~LA~~~P~s~~eL~~~ 391 (914)
.+.+|-+-|-.++.+.+-|..-.|||..|-+||..+|+|.+++...
T Consensus 8 aY~~Lr~~~~~~~~~~n~p~~~f~sd~~LKk~A~~LP~te~eF~~l 53 (80)
T PF11408_consen 8 AYEKLREISINLSNRMNPPNDNFMSDTILKKMATKLPTTEEEFSKL 53 (80)
T ss_dssp HHHHHHHHHHHHHHSSSS--S-SS-HHHHHHHHHH---SHHHHGGG
T ss_pred HHHHHHHHHHHHhhccCCCccccCCHHHHHHHHHHCCCCHHHHHHh
Confidence 4567777788899999999988999999999999999999988764
No 95
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=50.63 E-value=41 Score=39.31 Aligned_cols=83 Identities=24% Similarity=0.232 Sum_probs=51.7
Q ss_pred hhHHHhhcCCCCeEEEechhHhHHHHHHhcCCCcCeEeehhhHH-HHcCC-C-CCCHHHHHHHHcCCcCCcccccccccC
Q 002503 171 SILQPFFADPGVCKVFHGSDNDVMWLQRDFHIYVVNLFDTAKAC-EVLSK-P-QKSLAYLLETYCGVATNKFLQREDWRQ 247 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hgak~Dl~~LqrdfGI~~~nlFDTqlAA-yLLg~-~-~~SLa~Lle~yLgv~ldK~~q~sDWr~ 247 (914)
..|..+ -+++-+-|||+...|+..|...+ ..+.||.+.- +-.|. + ..+|.+|++.|+|..+.-.....|
T Consensus 285 ~~l~~~-~~~~TILVGHSLenDL~aLKl~H----~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~Hd--- 356 (380)
T KOG2248|consen 285 KELLEL-ISKNTILVGHSLENDLKALKLDH----PSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGGHD--- 356 (380)
T ss_pred HHHHhh-cCcCcEEEeechhhHHHHHhhhC----CceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCCCc---
Confidence 345554 45566679999999999995433 3467888422 22231 3 457999999999977651111111
Q ss_pred CCCCHHHHHHHHHchHHHHHHHHH
Q 002503 248 RPLPAEMLQYAQTDAHYLLYIAKC 271 (914)
Q Consensus 248 RPLseeql~YAa~Da~yLL~Lyd~ 271 (914)
...||...+.|...
T Consensus 357 ----------S~eDA~acm~Lv~~ 370 (380)
T KOG2248|consen 357 ----------SVEDALACMKLVKL 370 (380)
T ss_pred ----------cHHHHHHHHHHHHH
Confidence 45677777666543
No 96
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=49.42 E-value=91 Score=32.81 Aligned_cols=90 Identities=16% Similarity=0.090 Sum_probs=56.1
Q ss_pred hhhhHHHhhcCCCCeEEEechhHhHHHHHHh---cCCCc---CeEeehhhHHHHc-CC-CCCCHHHHHHHHcCCcCCccc
Q 002503 169 EISILQPFFADPGVCKVFHGSDNDVMWLQRD---FHIYV---VNLFDTAKACEVL-SK-PQKSLAYLLETYCGVATNKFL 240 (914)
Q Consensus 169 ~l~~L~elLaDp~IvKV~Hgak~Dl~~Lqrd---fGI~~---~nlFDTqlAAyLL-g~-~~~SLa~Lle~yLgv~ldK~~ 240 (914)
.+..|.+++.+.... |+|.+..|+..|.+. +|+.. ...+|++.....+ +. ..++|..+++.| |+....
T Consensus 82 vl~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~-gi~~~~-- 157 (207)
T PRK07748 82 LVEKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEEY-GKEGTG-- 157 (207)
T ss_pred HHHHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHHHc-CCCCCC--
Confidence 345566677663334 345568999988754 45542 3467887655433 32 357999988764 554211
Q ss_pred ccccccCCCCCHHHHHHHHHchHHHHHHHHHHHHH
Q 002503 241 QREDWRQRPLPAEMLQYAQTDAHYLLYIAKCLVAE 275 (914)
Q Consensus 241 q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L~~e 275 (914)
+ -.-|..||..+..|+..|..+
T Consensus 158 ~-------------~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 158 K-------------HHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred C-------------CcChHHHHHHHHHHHHHHHhC
Confidence 1 122778999999998887655
No 97
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=48.11 E-value=5.9 Score=42.13 Aligned_cols=37 Identities=32% Similarity=0.637 Sum_probs=28.8
Q ss_pred ceEEcCCCCcccccccccchhhhcchhhhhccCCcceeecchhhHHhHHHhH
Q 002503 573 ICVSCGEGNHYLRYRIIPSCYRIHFPEQLKSHRSHDIVLLCVDCHEVAHAAA 624 (914)
Q Consensus 573 ~CVvCG~~~~~~R~~vVP~~YR~hfP~~~KsH~ShDvllLC~~CH~~~~~~~ 624 (914)
+||-||.. ||+-||+|=|. +--|--|+.||+.+.+|-
T Consensus 2 iCIeCg~~--------v~~Ly~~Ys~~-------~irLt~C~~C~~vaDkYi 38 (208)
T PF04161_consen 2 ICIECGHP--------VKSLYRQYSPG-------NIRLTKCPNCGKVADKYI 38 (208)
T ss_pred EeccCCCc--------chhhhhccCCC-------cEEEeeccccCCccccee
Confidence 79999964 77889998333 345788999999888773
No 98
>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=46.19 E-value=72 Score=32.09 Aligned_cols=69 Identities=16% Similarity=0.125 Sum_probs=38.1
Q ss_pred hhHhHHHHHHhcCCCcCeEeehhhHHHHcCCCCCCHHHHHHHHcCCcCCcccccccccCCCCCHHHHHHHHHchHHHHHH
Q 002503 189 SDNDVMWLQRDFHIYVVNLFDTAKACEVLSKPQKSLAYLLETYCGVATNKFLQREDWRQRPLPAEMLQYAQTDAHYLLYI 268 (914)
Q Consensus 189 ak~Dl~~LqrdfGI~~~nlFDTqlAAyLLg~~~~SLa~Lle~yLgv~ldK~~q~sDWr~RPLseeql~YAa~Da~yLL~L 268 (914)
+|....++ ..-|+.+.+=-|-++.||||++.....+.++++|+| .+|... |+..+...-+|
T Consensus 70 AK~LAv~a-~~~G~~v~PGDDPlLlAYLlDPsNt~p~~varRY~~---------~~W~~d---------A~~RA~~t~~L 130 (138)
T PF09281_consen 70 AKDLAVHA-LREGVVVEPGDDPLLLAYLLDPSNTNPEGVARRYLG---------GEWPED---------AATRALATARL 130 (138)
T ss_dssp HHHHHHHH-HHTT----B---HHHHHHHH-TT--SHHHHHHHH-T---------S---SS---------HHHHHHHHHHH
T ss_pred HHHHHHHH-HhcCcccCCCCCcchhhhhcCccCCChHHHHHHhcC---------CCCCcc---------HHHHHHHHHHH
Confidence 44444555 467888877779999999999988889999999987 356422 44555555666
Q ss_pred HHHHHHHH
Q 002503 269 AKCLVAEL 276 (914)
Q Consensus 269 yd~L~~eL 276 (914)
+..|..+|
T Consensus 131 ~~~L~prL 138 (138)
T PF09281_consen 131 LRALPPRL 138 (138)
T ss_dssp HHHHHHHT
T ss_pred HHHhhhcC
Confidence 66665543
No 99
>COG0199 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=43.12 E-value=9.5 Score=33.38 Aligned_cols=17 Identities=29% Similarity=0.636 Sum_probs=15.3
Q ss_pred cCCceEEcCCCCccccc
Q 002503 570 KKNICVSCGEGNHYLRY 586 (914)
Q Consensus 570 k~N~CVvCG~~~~~~R~ 586 (914)
..|.|++||....|+|+
T Consensus 20 ~~nRC~~cGRprg~~Rk 36 (61)
T COG0199 20 GRNRCRRCGRPRGVIRK 36 (61)
T ss_pred ccccccccCCCccchhh
Confidence 45999999999999997
No 100
>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=40.07 E-value=1.6e+02 Score=29.22 Aligned_cols=86 Identities=19% Similarity=0.195 Sum_probs=51.3
Q ss_pred hhhHHHhhcCC-CCeEEEechhHhHHHHHH---hcCC-----CcCeEeehhhHHH-HcCC-CCCCHHHHHHHHcCCcCCc
Q 002503 170 ISILQPFFADP-GVCKVFHGSDNDVMWLQR---DFHI-----YVVNLFDTAKACE-VLSK-PQKSLAYLLETYCGVATNK 238 (914)
Q Consensus 170 l~~L~elLaDp-~IvKV~Hgak~Dl~~Lqr---dfGI-----~~~nlFDTqlAAy-LLg~-~~~SLa~Lle~yLgv~ldK 238 (914)
+..|.+++.+. ...-|.| +..|...+.+ .++. .....+||+..+. +.+. ...+|..+++. +|+....
T Consensus 79 l~~~~~~l~~~~~~~~v~~-~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~ 156 (176)
T cd06133 79 LKEFLEWLGKNGKYAFVTW-GDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEY-LGLEFEG 156 (176)
T ss_pred HHHHHHHHHhCCCeEEEee-cHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHH-CCCCCCC
Confidence 45566677664 1333444 5777654332 2333 2346899996655 4444 37899999865 4766541
Q ss_pred ccccccccCCCCCHHHHHHHHHchHHHHHHHHHH
Q 002503 239 FLQREDWRQRPLPAEMLQYAQTDAHYLLYIAKCL 272 (914)
Q Consensus 239 ~~q~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L 272 (914)
+ ..-|..||..+..|+..|
T Consensus 157 --~-------------~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 157 --R-------------HHRGLDDARNIARILKRL 175 (176)
T ss_pred --C-------------CcCcHHHHHHHHHHHHHh
Confidence 1 122667888888887665
No 101
>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=39.07 E-value=1e+02 Score=31.76 Aligned_cols=65 Identities=22% Similarity=0.290 Sum_probs=37.6
Q ss_pred hhHHHhhcCCCCeEEEec-hhHhHHHHHHhc---CCCc--------CeEeehhhHHHHc---------------CCCCCC
Q 002503 171 SILQPFFADPGVCKVFHG-SDNDVMWLQRDF---HIYV--------VNLFDTAKACEVL---------------SKPQKS 223 (914)
Q Consensus 171 ~~L~elLaDp~IvKV~Hg-ak~Dl~~Lqrdf---GI~~--------~nlFDTqlAAyLL---------------g~~~~S 223 (914)
..+.+++.++...-|+|+ +.+|+..|.+.+ |+.+ ...+||.-.++++ +...++
T Consensus 74 ~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~ 153 (183)
T cd06138 74 AKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFK 153 (183)
T ss_pred HHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchh
Confidence 344455654443458886 789999987543 3311 1235777444332 123577
Q ss_pred HHHHHHHHcCCcC
Q 002503 224 LAYLLETYCGVAT 236 (914)
Q Consensus 224 La~Lle~yLgv~l 236 (914)
|+.|+++ +|+..
T Consensus 154 L~~l~~~-~gi~~ 165 (183)
T cd06138 154 LEDLAQA-NGIEH 165 (183)
T ss_pred HHHHHHH-CCCCc
Confidence 9999976 46554
No 102
>PF00253 Ribosomal_S14: Ribosomal protein S14p/S29e; InterPro: IPR001209 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. S14 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S14 is known to be required for the assembly of 30S particles and may also be responsible for determining the conformation of 16S rRNA at the A site. It belongs to a family of ribosomal proteins [, ] that include, bacterial, algal and plant chloroplast, yeast mitochondrial, cyanelle and archael, Methanococcus vannielii S14's, as well as yeast mitochondrial MRP2, yeast YS29A/B and mammalian S29.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_N 2XZM_N 1S1H_N 3IZ6_N 2YKR_N 2QBB_N 3I1Z_N 3OAQ_N 3R8O_N 2Z4K_N ....
Probab=38.32 E-value=13 Score=31.61 Aligned_cols=20 Identities=30% Similarity=0.373 Sum_probs=17.0
Q ss_pred cccCCceEEcCCCCcccccc
Q 002503 568 QSKKNICVSCGEGNHYLRYR 587 (914)
Q Consensus 568 ~~k~N~CVvCG~~~~~~R~~ 587 (914)
+.-.|.|++||...+++|+.
T Consensus 13 ~r~~nrC~~tGR~rgv~r~f 32 (55)
T PF00253_consen 13 TRIKNRCVITGRSRGVIRKF 32 (55)
T ss_dssp TGSCSSBSSSCSSSSBETTT
T ss_pred CCCCeecccCCCceeeeccc
Confidence 34569999999999999965
No 103
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=34.99 E-value=22 Score=31.66 Aligned_cols=52 Identities=19% Similarity=0.264 Sum_probs=31.3
Q ss_pred cccCCceEEcCCCCcccccccccchhhhcchhhh-----hccCC--cceeecchhhHHh
Q 002503 568 QSKKNICVSCGEGNHYLRYRIIPSCYRIHFPEQL-----KSHRS--HDIVLLCVDCHEV 619 (914)
Q Consensus 568 ~~k~N~CVvCG~~~~~~R~~vVP~~YR~hfP~~~-----KsH~S--hDvllLC~~CH~~ 619 (914)
+.+...|+.||++..+.-+.-.=-.+|..||..- .+|-. -.-+.+|+.|--+
T Consensus 2 ~k~~~~C~~Cg~r~~~~~k~~~~~~~~t~fpl~g~~~~~~N~fwn~~~~~~iCp~C~~i 60 (69)
T PF09706_consen 2 SKKKYNCIFCGERPSKKKKGKLSFFNDTGFPLSGSNGRKPNFFWNFNNDADICPICELI 60 (69)
T ss_pred CCCCCcCcCCCCcccccccchhhhhhhccccccccCCCcccccccCcCCCccCHHHHHH
Confidence 3567899999987555444333333466665442 22221 2568899999654
No 104
>KOG3506 consensus 40S ribosomal protein S29 [Translation, ribosomal structure and biogenesis]
Probab=34.38 E-value=13 Score=31.89 Aligned_cols=25 Identities=20% Similarity=0.561 Sum_probs=20.3
Q ss_pred CceEEcCCCCccccc---ccccchhhhc
Q 002503 572 NICVSCGEGNHYLRY---RIIPSCYRIH 596 (914)
Q Consensus 572 N~CVvCG~~~~~~R~---~vVP~~YR~h 596 (914)
-.|+||+...++||| +|-+.++|.+
T Consensus 19 rsC~vCsn~~gLIrKYGL~vcr~cfr~~ 46 (56)
T KOG3506|consen 19 RSCRVCSNRHGLIRKYGLNVCRQCFREY 46 (56)
T ss_pred cceeeeccchhHHHHhhhHHhHHHHHhh
Confidence 579999999999998 6666666653
No 105
>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=34.16 E-value=62 Score=34.10 Aligned_cols=62 Identities=15% Similarity=0.154 Sum_probs=42.2
Q ss_pred EeehhhHHH--HcCCCCCCHHHHHHHHcCCcCCc-cc-----c-cccccCCCCCHHHHHHHHHchHHHHHHHH
Q 002503 207 LFDTAKACE--VLSKPQKSLAYLLETYCGVATNK-FL-----Q-REDWRQRPLPAEMLQYAQTDAHYLLYIAK 270 (914)
Q Consensus 207 lFDTqlAAy--LLg~~~~SLa~Lle~yLgv~ldK-~~-----q-~sDWr~RPLseeql~YAa~Da~yLL~Lyd 270 (914)
++|+..... .....+++|.++++++||..-.. .. . ..-|...+ ..+++|+..||...++|++
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 788876554 34556899999999999964221 10 0 11244333 5789999999999998863
No 106
>COG4855 Uncharacterized protein conserved in archaea [Function unknown]
Probab=33.80 E-value=19 Score=32.15 Aligned_cols=45 Identities=40% Similarity=0.880 Sum_probs=26.7
Q ss_pred cCCceEEcCCC---Ccccccccccchhhhc--chh-hhhccCCcceeecchhhHHh
Q 002503 570 KKNICVSCGEG---NHYLRYRIIPSCYRIH--FPE-QLKSHRSHDIVLLCVDCHEV 619 (914)
Q Consensus 570 k~N~CVvCG~~---~~~~R~~vVP~~YR~h--fP~-~~KsH~ShDvllLC~~CH~~ 619 (914)
-..+|.|||.+ ++++|-.. | .+--- ||. .+|.|.. -.||+.||+.
T Consensus 22 AV~iCIVCG~GlC~EHli~eE~-p-~w~G~YP~p~k~~K~~lp---RilC~~C~~a 72 (76)
T COG4855 22 AVGICIVCGMGLCMEHLIREET-P-MWGGGYPFPAKKLKKTLP---RILCVECHEA 72 (76)
T ss_pred cEEEEEEeCchHHHHHHHhhhc-c-cccCCCCCcchhhhccCC---ceeeHHHHHH
Confidence 45799999986 56666332 1 01111 222 2555554 5799999984
No 107
>COG1403 McrA Restriction endonuclease [Defense mechanisms]
Probab=29.11 E-value=16 Score=34.93 Aligned_cols=48 Identities=19% Similarity=0.415 Sum_probs=36.0
Q ss_pred cccCCceEEcCCCC-cccccccccchhhhcchhhhhccCCc-ceeecchhhHHhHHHh
Q 002503 568 QSKKNICVSCGEGN-HYLRYRIIPSCYRIHFPEQLKSHRSH-DIVLLCVDCHEVAHAA 623 (914)
Q Consensus 568 ~~k~N~CVvCG~~~-~~~R~~vVP~~YR~hfP~~~KsH~Sh-DvllLC~~CH~~~~~~ 623 (914)
.-..-.|..||... .....+|||... --+.+. .+..||..||......
T Consensus 66 ~~d~~~c~~c~~~~~~~~~dHiip~~~--------g~~~~~~Nl~~lc~~c~~~k~~~ 115 (146)
T COG1403 66 LRDNGLCQYCGSVGTDLEVDHIVPLSR--------GGASAWENLETLCERCHNKKGSR 115 (146)
T ss_pred ccccccccccCCcCCCCceeeEeeccc--------CCcchHHHHHHHHHhhccccccc
Confidence 33448999999995 778899999887 223333 8899999999855544
No 108
>PRK05762 DNA polymerase II; Reviewed
Probab=28.54 E-value=5.2e+02 Score=33.14 Aligned_cols=91 Identities=18% Similarity=0.174 Sum_probs=58.5
Q ss_pred CCCCeEEEech-hHhHHHHHHh---cCCCc-------------------------C--eEeehhhHHHHc--CCCCCCHH
Q 002503 179 DPGVCKVFHGS-DNDVMWLQRD---FHIYV-------------------------V--NLFDTAKACEVL--SKPQKSLA 225 (914)
Q Consensus 179 Dp~IvKV~Hga-k~Dl~~Lqrd---fGI~~-------------------------~--nlFDTqlAAyLL--g~~~~SLa 225 (914)
||+|+ ++|+. .+|+..|.+. +|+.. . -++|+.....-. ..++++|.
T Consensus 218 DPDII-vGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~l~sysL~ 296 (786)
T PRK05762 218 DPDVI-IGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSLE 296 (786)
T ss_pred CCCEE-EEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhccCCCCCHH
Confidence 57765 78875 4788777632 44421 0 267888776543 34688999
Q ss_pred HHHHHHcCCcCCc--c----cc-cccccCCCCCHHHHHHHHHchHHHHHHHHHH
Q 002503 226 YLLETYCGVATNK--F----LQ-REDWRQRPLPAEMLQYAQTDAHYLLYIAKCL 272 (914)
Q Consensus 226 ~Lle~yLgv~ldK--~----~q-~sDWr~RPLseeql~YAa~Da~yLL~Lyd~L 272 (914)
.++++++|..... . .+ ..-|... .+..++|...|+...+.|+..+
T Consensus 297 ~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 297 YVSQRLLGEGKAIDDPYDRMDEIDRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HHHHHHhCCCeeccCccccHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999854211 0 00 0113221 2568899999999999999843
No 109
>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=27.95 E-value=87 Score=33.53 Aligned_cols=67 Identities=18% Similarity=0.163 Sum_probs=45.7
Q ss_pred EeehhhHHHH-cCCCCCCHHHHHHHHcCCcCCc-c-ccccc-ccCCCCC-HHHHHHHHHchHHHHHHHHHHH
Q 002503 207 LFDTAKACEV-LSKPQKSLAYLLETYCGVATNK-F-LQRED-WRQRPLP-AEMLQYAQTDAHYLLYIAKCLV 273 (914)
Q Consensus 207 lFDTqlAAyL-Lg~~~~SLa~Lle~yLgv~ldK-~-~q~sD-Wr~RPLs-eeql~YAa~Da~yLL~Lyd~L~ 273 (914)
++|+..++.- ...++++|.++++++||..... . ....+ |+..|-. ...++|...||...++|+..|.
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 5677766543 3446899999999999964321 1 11122 4334432 4689999999999999998874
No 110
>PF08662 eIF2A: Eukaryotic translation initiation factor eIF2A; InterPro: IPR013979 This entry contains beta propellor domains found in eukaryotic translation initiation factors and TolB domain-containing proteins.
Probab=26.57 E-value=79 Score=32.96 Aligned_cols=51 Identities=24% Similarity=0.348 Sum_probs=36.4
Q ss_pred ccceeEEeCCCceeeeecCccc-----cceecccchhhc-cCCCceEEeecccCCCCC
Q 002503 508 YHNCRIYANDGRLLCYCDRKKL-----EWYLTRDLAKLV-EDNPPAIMLLFEPKGRPE 559 (914)
Q Consensus 508 Y~NC~l~apdG~lLc~cd~kKa-----~WYl~k~La~~v-~e~P~~IrL~FeP~gr~~ 559 (914)
+-|+...+|+|++|+++..... =|-+++ .-.+. .+.+-+..+-|.|.||--
T Consensus 102 ~~n~i~wsP~G~~l~~~g~~n~~G~l~~wd~~~-~~~i~~~~~~~~t~~~WsPdGr~~ 158 (194)
T PF08662_consen 102 PRNTISWSPDGRFLVLAGFGNLNGDLEFWDVRK-KKKISTFEHSDATDVEWSPDGRYL 158 (194)
T ss_pred CceEEEECCCCCEEEEEEccCCCcEEEEEECCC-CEEeeccccCcEEEEEEcCCCCEE
Confidence 4589999999999999987654 355542 22222 245678899999998863
No 111
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=22.29 E-value=41 Score=28.91 Aligned_cols=26 Identities=19% Similarity=0.556 Sum_probs=19.4
Q ss_pred CCceEEcCCCCcccccc---cccchhhhc
Q 002503 571 KNICVSCGEGNHYLRYR---IIPSCYRIH 596 (914)
Q Consensus 571 ~N~CVvCG~~~~~~R~~---vVP~~YR~h 596 (914)
...|.|||....+||+. +=..|+|.+
T Consensus 16 sr~C~vCg~~~gliRkygL~~CRqCFRe~ 44 (54)
T PTZ00218 16 SRQCRVCSNRHGLIRKYGLNVCRQCFREN 44 (54)
T ss_pred CCeeecCCCcchhhhhcCcchhhHHHHHh
Confidence 37999999999999964 444555543
No 112
>PRK10291 glyoxalase I; Provisional
Probab=21.95 E-value=68 Score=30.25 Aligned_cols=25 Identities=20% Similarity=0.183 Sum_probs=21.2
Q ss_pred ceeEEeCCCceeeeecCccccceecccch
Q 002503 510 NCRIYANDGRLLCYCDRKKLEWYLTRDLA 538 (914)
Q Consensus 510 NC~l~apdG~lLc~cd~kKa~WYl~k~La 538 (914)
-|++.+|||..+.-+..+++ .+|||
T Consensus 104 ~~~i~DPdG~~iel~~~~~~----~~~~~ 128 (129)
T PRK10291 104 IAFVEDPDGYKIELIEEKDA----GRGLG 128 (129)
T ss_pred EEEEECCCCCEEEEEEcccc----ccccC
Confidence 47899999999999998865 67776
No 113
>PHA03093 EEV glycoprotein; Provisional
Probab=21.53 E-value=1.1e+02 Score=32.30 Aligned_cols=31 Identities=32% Similarity=0.395 Sum_probs=24.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhhccCC
Q 002503 7 IKIAITIASLAAISILFTRQQRRRRKLNQCP 37 (914)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 (914)
+-|+|+|.||+||+++++-|+..=+.++.++
T Consensus 41 isiiiSIlsL~~i~~~LAlqln~Ck~~~e~~ 71 (185)
T PHA03093 41 ISIIISILSLIAITATLALQLNKCKSANESA 71 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 4578899999999999999988866664444
No 114
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=20.95 E-value=2.7e+02 Score=35.79 Aligned_cols=98 Identities=15% Similarity=0.178 Sum_probs=67.0
Q ss_pred CeEEEechhHhHHHHHHhcCCCcC--eEeehhhHH---H-----------------------------------HcCCC-
Q 002503 182 VCKVFHGSDNDVMWLQRDFHIYVV--NLFDTAKAC---E-----------------------------------VLSKP- 220 (914)
Q Consensus 182 IvKV~Hgak~Dl~~LqrdfGI~~~--nlFDTqlAA---y-----------------------------------LLg~~- 220 (914)
-+.|+|+..+|-..+...|.|.-. ...|||-.. + -|+..
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 566999999999999788887653 366998332 1 01111
Q ss_pred CCCHHHHHHHHcCCc-CCcccccccccCCCCC------HHHHHHHHHchHHHHHHHHHHHHHHHHcC
Q 002503 221 QKSLAYLLETYCGVA-TNKFLQREDWRQRPLP------AEMLQYAQTDAHYLLYIAKCLVAELKQQG 280 (914)
Q Consensus 221 ~~SLa~Lle~yLgv~-ldK~~q~sDWr~RPLs------eeql~YAa~Da~yLL~Lyd~L~~eL~e~g 280 (914)
-.||.++.+.+||++ ++|... .++-.-++. .+.+.|.|.|+....++|..+-....++.
T Consensus 322 ~NSL~dVhk~~c~~~~LdKt~R-d~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Flerc 387 (1075)
T KOG3657|consen 322 LNSLVDVHKFHCGIDALDKTPR-DSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLERC 387 (1075)
T ss_pred hHHHHHHHHhhCCCCccccchH-HhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHhC
Confidence 246778888899988 666431 122111111 34689999999999999999988877764
No 115
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=20.12 E-value=38 Score=36.70 Aligned_cols=45 Identities=24% Similarity=0.493 Sum_probs=34.0
Q ss_pred eEEcCCCCcccccccccchhhhcchhh-hhccCCcceeecchhhHHhHH
Q 002503 574 CVSCGEGNHYLRYRIIPSCYRIHFPEQ-LKSHRSHDIVLLCVDCHEVAH 621 (914)
Q Consensus 574 CVvCG~~~~~~R~~vVP~~YR~hfP~~-~KsH~ShDvllLC~~CH~~~~ 621 (914)
|+.||....-+=.++=|.||++.+|.. +..+. .+..|+.|.....
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i---~v~~C~~Cg~~~~ 46 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRI---EVTICPKCGRYRI 46 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCcc---CceECCCCCCEEC
Confidence 999999666555689999999999875 33333 5778999987543
No 116
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=20.09 E-value=77 Score=29.76 Aligned_cols=37 Identities=35% Similarity=0.702 Sum_probs=20.8
Q ss_pred HHHHHHHHHhCC------------ccCCHHHHHHHHHcCCChHHHhhhhhh
Q 002503 693 ELRRIVMRYYGG------------REISQEDLERALLVGMSPRERRRHAKK 731 (914)
Q Consensus 693 eL~~~i~~~~~~------------~~~t~~~l~~a~~~~~~p~~~~~~~~~ 731 (914)
.++.+++.|||. .++++|+|.+. +||++.+=|+..-+
T Consensus 2 L~~~v~r~~yg~~~~~Il~~L~~~~~l~de~la~~--~~l~~~~vRkiL~~ 50 (105)
T PF02002_consen 2 LLKEVVRAFYGEEAVRILDALLRKGELTDEDLAKK--LGLKPKEVRKILYK 50 (105)
T ss_dssp ----HHHTTS-STTHHHHHHHHHH--B-HHHHHHT--T-S-HHHHHHHHHH
T ss_pred hHHHHHHHHcCchHHHHHHHHHHcCCcCHHHHHHH--hCCCHHHHHHHHHH
Confidence 345566666653 67999999888 99999998876654
No 117
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=20.00 E-value=1.8e+02 Score=31.77 Aligned_cols=50 Identities=14% Similarity=0.166 Sum_probs=38.5
Q ss_pred CCHhHHHHHHHHHHHHhCCccCCHHHHHHHHHcCCChHHHhhhhhhccCccc
Q 002503 686 MPSNRREELRRIVMRYYGGREISQEDLERALLVGMSPRERRRHAKKRGLSLK 737 (914)
Q Consensus 686 ~P~~r~eeL~~~i~~~~~~~~~t~~~l~~a~~~~~~p~~~~~~~~~~~~~~~ 737 (914)
.+..+...+...|.++|...++|.++|-++ +|||++-=.|+-|+-|.++.
T Consensus 194 ~~~~~l~~~~~~I~~~l~~~~ls~~~lA~~--~giS~r~L~r~Fk~~G~T~~ 243 (302)
T PRK09685 194 RRERQFQKVVALIDQSIQEEILRPEWIAGE--LGISVRSLYRLFAEQGLVVA 243 (302)
T ss_pred ccHHHHHHHHHHHHHhcCCCCCCHHHHHHH--HCCCHHHHHHHHHHcCCCHH
Confidence 345667788899999998888999999766 99999776555555677654
Done!