Query 006352
Match_columns 649
No_of_seqs 275 out of 1834
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 22:02:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006352.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006352hhsearch_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 1.7E-46 3.6E-51 409.2 20.2 248 1-257 236-483 (687)
2 PRK10829 ribonuclease D; Provi 100.0 3.4E-45 7.4E-50 392.0 26.6 241 1-255 46-287 (373)
3 COG0349 Rnd Ribonuclease D [Tr 100.0 2.3E-41 4.9E-46 357.7 23.5 242 1-255 41-283 (361)
4 TIGR01388 rnd ribonuclease D. 100.0 2.1E-40 4.6E-45 354.5 26.4 241 1-255 42-283 (367)
5 cd06129 RNaseD_like DEDDy 3'-5 99.9 1.5E-23 3.2E-28 199.7 13.6 122 1-123 37-160 (161)
6 cd06148 Egl_like_exo DEDDy 3'- 99.9 9E-23 1.9E-27 201.0 11.2 129 1-129 33-180 (197)
7 cd06146 mut-7_like_exo DEDDy 3 99.9 2E-22 4.4E-27 198.2 13.1 123 1-123 48-192 (193)
8 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 1.4E-21 3E-26 186.0 13.6 122 1-123 44-169 (170)
9 PF01612 DNA_pol_A_exo1: 3'-5' 99.8 1.6E-19 3.4E-24 169.6 11.0 127 1-127 46-176 (176)
10 cd06142 RNaseD_exo DEDDy 3'-5' 99.7 1.7E-16 3.8E-21 150.4 15.6 128 1-130 36-164 (178)
11 cd06147 Rrp6p_like_exo DEDDy 3 99.6 3.8E-14 8.1E-19 138.4 13.8 128 2-130 49-176 (192)
12 smart00474 35EXOc 3'-5' exonuc 99.6 5E-14 1.1E-18 131.0 13.6 119 6-126 51-171 (172)
13 PF00570 HRDC: HRDC domain Blo 99.5 1.3E-14 2.9E-19 119.4 7.0 68 180-247 1-68 (68)
14 smart00341 HRDC Helicase and R 99.5 1E-13 2.2E-18 117.3 9.6 77 178-254 2-78 (81)
15 cd00007 35EXOc 3'-5' exonuclea 99.5 6.2E-13 1.4E-17 121.4 11.8 105 21-125 44-154 (155)
16 cd09018 DEDDy_polA_RNaseD_like 99.4 7.9E-13 1.7E-17 121.6 11.8 120 2-123 24-149 (150)
17 cd06140 DNA_polA_I_Bacillus_li 99.4 3.1E-12 6.7E-17 122.2 12.1 127 2-130 28-160 (178)
18 PRK05755 DNA polymerase I; Pro 99.3 2.2E-10 4.7E-15 135.9 21.2 127 2-130 340-473 (880)
19 PRK14975 bifunctional 3'-5' ex 99.2 1.5E-10 3.3E-15 130.9 17.9 81 48-129 63-147 (553)
20 cd06139 DNA_polA_I_Ecoli_like_ 99.0 3.5E-09 7.5E-14 101.6 13.7 106 21-128 57-172 (193)
21 KOG2207 Predicted 3'-5' exonuc 98.9 3.8E-09 8.3E-14 118.3 9.1 126 1-126 438-585 (617)
22 TIGR01389 recQ ATP-dependent D 98.9 4.2E-09 9.1E-14 119.6 8.6 75 174-249 516-590 (591)
23 TIGR00593 pola DNA polymerase 98.8 2.5E-07 5.4E-12 110.2 22.8 108 21-129 368-480 (887)
24 cd06128 DNA_polA_exo DEDDy 3'- 98.6 3.1E-07 6.8E-12 85.9 12.3 117 2-123 26-150 (151)
25 COG0749 PolA DNA polymerase I 98.6 2.4E-07 5.3E-12 105.2 11.0 108 21-130 68-184 (593)
26 PRK11057 ATP-dependent DNA hel 98.5 2.2E-07 4.8E-12 106.4 8.7 75 178-252 530-604 (607)
27 PLN03137 ATP-dependent DNA hel 98.3 9.3E-07 2E-11 106.5 8.6 73 180-252 1028-1102(1195)
28 COG0514 RecQ Superfamily II DN 98.0 9.3E-06 2E-10 92.7 7.2 72 180-251 517-588 (590)
29 KOG4373 Predicted 3'-5' exonuc 97.6 0.00013 2.9E-09 77.6 8.0 114 5-119 159-281 (319)
30 KOG2405 Predicted 3'-5' exonuc 95.8 0.0051 1.1E-07 67.1 2.2 121 1-124 218-359 (458)
31 PF11408 Helicase_Sgs1: Sgs1 R 93.7 0.21 4.6E-06 43.9 6.6 66 182-247 7-74 (80)
32 cd06143 PAN2_exo DEDDh 3'-5' e 92.2 0.31 6.8E-06 48.5 6.2 79 23-119 95-173 (174)
33 PRK06063 DNA polymerase III su 92.1 1.2 2.6E-05 47.9 11.0 91 21-130 86-183 (313)
34 cd06137 DEDDh_RNase DEDDh 3'-5 91.3 0.55 1.2E-05 45.2 6.7 80 22-119 76-160 (161)
35 cd06144 REX4_like DEDDh 3'-5' 90.7 0.36 7.9E-06 46.0 4.8 80 21-119 69-151 (152)
36 PRK05711 DNA polymerase III su 90.7 1.7 3.8E-05 45.1 10.1 87 22-125 79-175 (240)
37 TIGR01406 dnaQ_proteo DNA poly 90.6 1.4 3E-05 45.2 9.1 87 21-124 74-170 (225)
38 cd06131 DNA_pol_III_epsilon_Ec 90.4 1.5 3.2E-05 41.8 8.6 85 21-122 73-166 (167)
39 KOG2405 Predicted 3'-5' exonuc 90.0 0.044 9.6E-07 60.1 -2.3 110 4-114 84-215 (458)
40 cd06145 REX1_like DEDDh 3'-5' 89.9 0.87 1.9E-05 43.5 6.6 81 21-119 67-149 (150)
41 PRK07740 hypothetical protein; 89.7 4.5 9.7E-05 42.0 12.1 90 22-130 134-230 (244)
42 PRK07942 DNA polymerase III su 89.7 2.2 4.7E-05 43.9 9.7 81 31-128 93-182 (232)
43 TIGR01298 RNaseT ribonuclease 89.3 3.1 6.7E-05 41.7 10.3 84 32-131 106-197 (200)
44 PRK05168 ribonuclease T; Provi 88.5 5.4 0.00012 40.3 11.5 84 31-130 114-205 (211)
45 PRK06310 DNA polymerase III su 88.0 3.8 8.3E-05 42.6 10.2 87 22-126 80-174 (250)
46 cd06127 DEDDh DEDDh 3'-5' exon 87.6 4 8.6E-05 37.0 9.1 81 21-119 71-158 (159)
47 PRK06807 DNA polymerase III su 87.5 4 8.7E-05 44.0 10.3 88 21-128 80-174 (313)
48 COG2176 PolC DNA polymerase II 87.5 2.2 4.8E-05 53.0 9.1 91 21-130 493-590 (1444)
49 cd06125 DnaQ_like_exo DnaQ-lik 87.4 1.4 3E-05 39.1 5.7 41 23-63 35-83 (96)
50 PRK08517 DNA polymerase III su 87.2 5.3 0.00011 41.9 10.8 88 21-127 139-232 (257)
51 cd06134 RNaseT DEDDh 3'-5' exo 87.0 6.1 0.00013 39.2 10.6 77 32-124 103-187 (189)
52 cd06149 ISG20 DEDDh 3'-5' exon 86.9 1.7 3.6E-05 41.9 6.5 82 21-119 69-156 (157)
53 smart00479 EXOIII exonuclease 86.0 4.3 9.3E-05 38.0 8.6 89 21-127 72-168 (169)
54 PRK07246 bifunctional ATP-depe 85.5 6.1 0.00013 47.9 11.6 91 21-130 78-174 (820)
55 TIGR00573 dnaq exonuclease, DN 85.3 4.6 0.0001 40.8 8.9 91 21-128 79-179 (217)
56 TIGR01405 polC_Gram_pos DNA po 84.5 3.2 6.9E-05 52.4 8.8 91 21-130 262-359 (1213)
57 cd06130 DNA_pol_III_epsilon_li 84.4 7 0.00015 36.4 9.2 79 21-119 69-154 (156)
58 PRK06309 DNA polymerase III su 81.4 10 0.00022 38.9 9.7 88 22-127 72-167 (232)
59 PRK06195 DNA polymerase III su 80.8 14 0.00031 39.6 10.9 88 21-128 72-166 (309)
60 TIGR01407 dinG_rel DnaQ family 80.7 12 0.00027 45.4 11.6 91 21-130 72-169 (850)
61 PRK07883 hypothetical protein; 79.4 14 0.00029 43.1 10.9 90 22-130 88-186 (557)
62 KOG2249 3'-5' exonuclease [Rep 78.5 3.4 7.4E-05 43.9 5.2 88 23-129 178-269 (280)
63 PF13482 RNase_H_2: RNase_H su 77.3 1.5 3.3E-05 41.4 2.1 97 25-122 52-163 (164)
64 cd05160 DEDDy_DNA_polB_exo DED 77.2 11 0.00023 37.1 8.0 98 21-119 68-198 (199)
65 PRK05601 DNA polymerase III su 76.9 17 0.00037 40.5 10.2 96 20-122 116-245 (377)
66 cd06136 TREX1_2 DEDDh 3'-5' ex 76.9 8.1 0.00017 37.9 7.1 79 22-119 87-174 (177)
67 PRK08074 bifunctional ATP-depe 76.5 19 0.00041 44.4 11.5 91 21-130 76-173 (928)
68 KOG1275 PAB-dependent poly(A) 75.5 1.4 3.1E-05 53.2 1.6 87 25-130 1008-1095(1118)
69 KOG3657 Mitochondrial DNA poly 72.8 7.7 0.00017 46.9 6.6 97 32-129 242-386 (1075)
70 cd05780 DNA_polB_Kod1_like_exo 67.5 19 0.00041 35.8 7.3 100 21-121 61-194 (195)
71 PRK00448 polC DNA polymerase I 66.5 32 0.00069 44.6 10.6 90 22-130 492-588 (1437)
72 PRK09146 DNA polymerase III su 64.8 66 0.0014 33.4 10.9 86 23-127 123-228 (239)
73 PRK09145 DNA polymerase III su 60.1 78 0.0017 31.5 10.1 84 21-123 103-198 (202)
74 PRK07748 sporulation inhibitor 59.7 89 0.0019 31.3 10.5 88 21-125 84-179 (207)
75 PF09281 Taq-exonuc: Taq polym 56.2 33 0.00072 33.2 6.2 69 40-126 70-138 (138)
76 PRK07247 DNA polymerase III su 55.9 84 0.0018 31.7 9.6 85 21-126 76-169 (195)
77 PRK07983 exodeoxyribonuclease 54.7 65 0.0014 33.1 8.7 78 31-124 74-152 (219)
78 PRK11779 sbcB exonuclease I; P 46.3 1.3E+02 0.0028 34.7 10.2 87 22-125 84-197 (476)
79 cd06133 ERI-1_3'hExo_like DEDD 44.1 1.7E+02 0.0037 27.6 9.2 86 21-122 80-175 (176)
80 cd06138 ExoI_N N-terminal DEDD 38.0 1.3E+02 0.0027 29.6 7.5 80 22-118 75-181 (183)
81 COG0847 DnaQ DNA polymerase II 37.2 2.5E+02 0.0054 28.4 9.7 88 22-125 87-181 (243)
82 PRK14981 DNA-directed RNA poly 35.2 49 0.0011 30.7 3.9 46 206-251 65-111 (112)
83 cd05784 DNA_polB_II_exo DEDDy 33.5 63 0.0014 32.5 4.6 96 22-120 57-193 (193)
84 PF03874 RNA_pol_Rpb4: RNA pol 32.0 1.2E+02 0.0026 27.6 5.9 45 206-250 71-116 (117)
85 PF09862 DUF2089: Protein of u 31.3 90 0.002 29.4 4.9 50 220-269 50-103 (113)
86 cd05782 DNA_polB_like1_exo Unc 30.5 1.9E+02 0.004 29.4 7.5 97 21-120 83-207 (208)
87 PRK09182 DNA polymerase III su 30.1 2.8E+02 0.0061 29.9 9.1 82 22-122 113-197 (294)
88 COG1460 Uncharacterized protei 29.2 79 0.0017 29.9 4.1 47 206-252 66-113 (114)
89 COG2906 Bfd Bacterioferritin-a 28.2 1.6E+02 0.0034 25.3 5.3 42 206-247 9-52 (63)
90 cd05777 DNA_polB_delta_exo DED 27.1 94 0.002 31.7 4.7 67 57-123 153-224 (230)
91 TIGR01388 rnd ribonuclease D. 25.2 1.5E+02 0.0032 32.9 6.1 42 176-217 295-336 (367)
92 PRK06722 exonuclease; Provisio 25.1 3.4E+02 0.0073 29.3 8.5 85 21-123 82-178 (281)
93 cd05778 DNA_polB_zeta_exo inac 23.8 87 0.0019 32.2 3.8 63 57-119 162-230 (231)
94 PF10108 DNA_pol_B_exo2: Predi 21.5 7.7E+02 0.017 25.6 10.0 100 21-123 42-170 (209)
95 cd05779 DNA_polB_epsilon_exo D 21.2 1.4E+02 0.003 30.4 4.6 97 21-120 78-204 (204)
96 cd05776 DNA_polB_alpha_exo ina 21.2 1.1E+02 0.0023 31.6 3.8 93 28-122 96-226 (234)
97 cd05785 DNA_polB_like2_exo Unc 20.1 1.8E+02 0.004 29.5 5.2 95 22-119 64-206 (207)
No 1
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-46 Score=409.15 Aligned_cols=248 Identities=50% Similarity=0.836 Sum_probs=229.7
Q ss_pred CCCCCceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCCCCcHHHHHHH
Q 006352 1 MSLRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLERNSLEYLLHH 80 (649)
Q Consensus 1 IST~~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~~~sLa~LVe~ 80 (649)
|||++++||||++.+..+++ .|.++|.||.|+||+|++..|+.||+++|||+++|+|||..|+++||.++++|++|++.
T Consensus 236 ISTr~ed~iIDt~~l~~~i~-~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvnLfdt~~a~r~L~~~r~sL~~ll~~ 314 (687)
T KOG2206|consen 236 ISTRTEDFIIDTFKLRDHIG-ILNEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVNLFDTIQASRLLGLPRPSLAYLLEC 314 (687)
T ss_pred eeccchhheehhHHHHHHHH-HhhhhccCCCeEEEEecCccchhhhhccceEEEEechhhHHHHHHhCCCcccHHHHHHH
Confidence 89999999999999998885 89999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhhhcc
Q 006352 81 FCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEKELL 160 (649)
Q Consensus 81 ~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~gr~~e~~~~wL~Ev~k~s~e~~l~ly~ke~~ 160 (649)
|+|+..+|.+|+.||++|||+.+|+.||..|+|||+.||+.|+..|.+.+. +. .. .+.++++.|...|.++..
T Consensus 315 ~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~---~~-~~---~~~~~~d~c~~~~~k~~~ 387 (687)
T KOG2206|consen 315 VCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAK---GR-AV---TYSESRDMCTNGYKKKTF 387 (687)
T ss_pred HHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhc---cc-cc---ccchhhhhhhcceecccC
Confidence 999999999999999999999999999999999999999999988887652 11 11 233567889999988888
Q ss_pred ChhHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhH
Q 006352 161 SENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYM 240 (649)
Q Consensus 161 ~e~~y~~i~g~~~~~L~~~qlaVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrryG 240 (649)
....|+.+..++. .++..|+.+|++|++||+.+||+.|++++|||+|+.|+.||..+|.+...|.++....+++++++.
T Consensus 388 ~~~sy~~v~~~q~-~ln~~q~~~l~~L~~wRd~iARaeDES~~yVlpN~~ll~l~e~~P~~v~gl~~~ln~~~p~vkq~~ 466 (687)
T KOG2206|consen 388 CTKSYLEVEDIQS-RLNSSQLDVLRALLRWRDFIARAEDESVHYVLPNDQLLKLAEERPDTVDGLLGGLNRLSPLVKQNV 466 (687)
T ss_pred CCcchHhHHHHHh-ccchhHHHHHHHHHHHHHHHHhhccCCCceecccHHHHHHHHHCCccHHHHHHhccCCCHHHHHHH
Confidence 8888999988754 499999999999999999999999999999999999999999999999999999888899999999
Q ss_pred HHHHHHHHHHHhccccH
Q 006352 241 GPVLSIIKNSMQNAANF 257 (649)
Q Consensus 241 deIL~iI~~ale~~~~~ 257 (649)
..++.+|+.++.+...+
T Consensus 467 ~~~~~ii~~a~~~~l~~ 483 (687)
T KOG2206|consen 467 MDFLYIIRSAGRGFLLQ 483 (687)
T ss_pred HHHHHHHHHHhhhhhhh
Confidence 99999999999986544
No 2
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=3.4e-45 Score=391.99 Aligned_cols=241 Identities=21% Similarity=0.308 Sum_probs=218.7
Q ss_pred CCCCCceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC-CCcHHHHHH
Q 006352 1 MSLRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLH 79 (649)
Q Consensus 1 IST~~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~-~~sLa~LVe 79 (649)
|+|.+.+||||++++. ++ ..|+++|+|++|+||+|+|++|+.+|++.+|+.|.++||||+|+++||.+ .+||+.|++
T Consensus 46 l~~~~~~~LiD~l~~~-d~-~~L~~ll~~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~~~gl~~Lv~ 123 (373)
T PRK10829 46 LYDGEQLSLIDPLGIT-DW-SPFKALLRDPQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVE 123 (373)
T ss_pred EecCCceEEEecCCcc-ch-HHHHHHHcCCCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCccccHHHHHH
Confidence 5788999999999986 46 56999999999999999999999999999999999999999999999987 699999999
Q ss_pred HHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhhhc
Q 006352 80 HFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEKEL 159 (649)
Q Consensus 80 ~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~gr~~e~~~~wL~Ev~k~s~e~~l~ly~ke~ 159 (649)
++||++++|.++++||+.||||++|+.|||.||+||+.||+.|.++|.+.|+ .+|+.|+|... |.... ...
T Consensus 124 ~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~-----~~w~~ee~~~l---~~~~~-~~~ 194 (373)
T PRK10829 124 EYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGW-----LPAALDECRLL---CQRRQ-EVL 194 (373)
T ss_pred HHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc-----HHHHHHHHHHH---Hhccc-cCC
Confidence 9999999999999999999999999999999999999999999999998873 58998888643 22111 123
Q ss_pred cChhHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHHh
Q 006352 160 LSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERY 239 (649)
Q Consensus 160 ~~e~~y~~i~g~~~~~L~~~qlaVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrry 239 (649)
.++..|+++++. +.|+++|++||++|+.|||++|+++|+|+++||+|+.|++||+++|+|.++|.++ ++....+++|
T Consensus 195 ~~~~~~~~ik~~--~~L~~~~lavl~~L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~-~~~~~~~r~~ 271 (373)
T PRK10829 195 APEEAYRDITNA--WQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSL-GLSGSEIRFH 271 (373)
T ss_pred ChHHHHHHhccc--cCCCHHHHHHHHHHHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhc-cCChHhHHhh
Confidence 456779999874 7899999999999999999999999999999999999999999999999999999 8888889999
Q ss_pred HHHHHHHHHHHHhccc
Q 006352 240 MGPVLSIIKNSMQNAA 255 (649)
Q Consensus 240 GdeIL~iI~~ale~~~ 255 (649)
|++|+++|+++.+.++
T Consensus 272 g~~ll~~i~~a~~~~~ 287 (373)
T PRK10829 272 GKTLLALVAKAQALPE 287 (373)
T ss_pred HHHHHHHHHHHhcCCH
Confidence 9999999999987654
No 3
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-41 Score=357.66 Aligned_cols=242 Identities=26% Similarity=0.388 Sum_probs=215.8
Q ss_pred CCCCCceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC-CCcHHHHHH
Q 006352 1 MSLRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLH 79 (649)
Q Consensus 1 IST~~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~-~~sLa~LVe 79 (649)
|++++.+++||++....++ +.|..+|.|++|+||||++.+|+.+|++.||+.|.++|||+||+.++|.+ ++||+.||+
T Consensus 41 i~~~e~~~lIdpl~~~~d~-~~l~~Ll~d~~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~~~gl~~Lv~ 119 (361)
T COG0349 41 ISDGEGASLIDPLAGILDL-PPLVALLADPNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGTSHGLADLVE 119 (361)
T ss_pred EecCCCceEeccccccccc-chHHHHhcCCceeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHhCCcccccHHHHHH
Confidence 5677889999999953355 56999999999999999999999999999999999999999999999998 899999999
Q ss_pred HHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhhhc
Q 006352 80 HFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEKEL 159 (649)
Q Consensus 80 ~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~gr~~e~~~~wL~Ev~k~s~e~~l~ly~ke~ 159 (649)
+++|++++|++|.+||++||||++|+.||+.||.||+.||+.|.++|.+.| +..|+.++|.... .+. ....
T Consensus 120 ~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~-----r~~~a~~ef~~l~---~r~-~~~~ 190 (361)
T COG0349 120 ELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREG-----RLEWAEDEFRLLP---TRR-TYKV 190 (361)
T ss_pred HHhCCcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-----chHHHHHHHHHhh---hcc-cccc
Confidence 999999999999999999999999999999999999999999999999887 3578877664321 110 0233
Q ss_pred cChhHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHHh
Q 006352 160 LSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERY 239 (649)
Q Consensus 160 ~~e~~y~~i~g~~~~~L~~~qlaVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrry 239 (649)
.++..|+++.. .+.+++.++++++.|++||+++||.+|+|+++|++|+.|+++|+++|++..+|..+..+.+ ..+.+
T Consensus 191 ~~~~~w~~i~~--a~~~~p~~la~l~~La~wRe~~Ar~rd~~~~~vl~de~i~~~a~~~P~~~~~l~~l~~~~~-~~~~~ 267 (361)
T COG0349 191 LPEDAWREIKI--AHSLDPRELAVLRELAAWREREARERDLARNFVLKDEALWELARYTPKNLKELDALGLIPK-ERRRH 267 (361)
T ss_pred ChHhHHHHhhh--hhcCChHHHHHHHHHHHHHHHHHHHhccccccccchhHHHHHHHhCCCCHHHHHhccCCcc-cchhh
Confidence 66788998876 5899999999999999999999999999999999999999999999999999999865545 67889
Q ss_pred HHHHHHHHHHHHhccc
Q 006352 240 MGPVLSIIKNSMQNAA 255 (649)
Q Consensus 240 GdeIL~iI~~ale~~~ 255 (649)
+..|+.+|+++++.|+
T Consensus 268 ~~~l~~~~~~a~~~p~ 283 (361)
T COG0349 268 GKLLLALLANALASPE 283 (361)
T ss_pred hHHHHHHHHHHHhCch
Confidence 9999999999998875
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=2.1e-40 Score=354.52 Aligned_cols=241 Identities=27% Similarity=0.362 Sum_probs=216.2
Q ss_pred CCCCCceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC-CCcHHHHHH
Q 006352 1 MSLRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLH 79 (649)
Q Consensus 1 IST~~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~-~~sLa~LVe 79 (649)
|+|.+.+||||++++. ++ ..|+++|+|++|.||+|++++|+.+|++.+++.+.++|||++|+|+|+++ .+||..|++
T Consensus 42 ia~~~~~~liD~~~~~-~~-~~L~~lL~d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~~~l~~Lv~ 119 (367)
T TIGR01388 42 VADGEQLALIDPLVII-DW-SPLKELLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQ 119 (367)
T ss_pred EeeCCeEEEEeCCCcc-cH-HHHHHHHCCCCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCCCccHHHHHH
Confidence 5899999999999884 56 57999999999999999999999999888888889999999999999986 689999999
Q ss_pred HHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhhhc
Q 006352 80 HFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEKEL 159 (649)
Q Consensus 80 ~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~gr~~e~~~~wL~Ev~k~s~e~~l~ly~ke~ 159 (649)
+|||++++|+++++||..|||+.+|+.||+.||+||+.||+.|..+|.+.| +..|+.++|.... ... ....
T Consensus 120 ~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g-----~~~w~~ee~~~l~---~~~-~~~~ 190 (367)
T TIGR01388 120 EVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESG-----RLAWLEEECTLLT---DRR-TYVV 190 (367)
T ss_pred HHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-----cHHHHHHHHHHHh---ccc-cCCC
Confidence 999999999999999999999999999999999999999999999999877 3578888775432 111 1123
Q ss_pred cChhHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHHh
Q 006352 160 LSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERY 239 (649)
Q Consensus 160 ~~e~~y~~i~g~~~~~L~~~qlaVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrry 239 (649)
.++..|+++++. +.|++++++|+++|++|||.+||++|+|+++||+|+.|++||+++|+|..+|.++ ++....+++|
T Consensus 191 ~~~~~~~~i~~~--~~l~~~~l~~l~~L~~wRe~~A~~~d~p~~~il~d~~l~~lA~~~P~~~~~l~~~-~~~~~~~r~~ 267 (367)
T TIGR01388 191 NPEDAWRDIKNA--WQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEALWELARQAPGNLTELASL-GPKGSEIRKH 267 (367)
T ss_pred ChHHHHHHhccc--ccCCHHHHHHHHHHHHHHHHHHHHcCCCcceeeCHHHHHHHHHhCCCCHHHHHhc-cCChHHHHhh
Confidence 456679999874 7899999999999999999999999999999999999999999999999999999 8888889999
Q ss_pred HHHHHHHHHHHHhccc
Q 006352 240 MGPVLSIIKNSMQNAA 255 (649)
Q Consensus 240 GdeIL~iI~~ale~~~ 255 (649)
|++|+++|+++++.++
T Consensus 268 ~~~l~~~i~~a~~~~~ 283 (367)
T TIGR01388 268 GDTLLALVKTALALPE 283 (367)
T ss_pred HHHHHHHHHHHhhCCH
Confidence 9999999999987664
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=99.90 E-value=1.5e-23 Score=199.67 Aligned_cols=122 Identities=34% Similarity=0.542 Sum_probs=113.9
Q ss_pred CCCC-CceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC-CCcHHHHH
Q 006352 1 MSLR-TEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLL 78 (649)
Q Consensus 1 IST~-~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~-~~sLa~LV 78 (649)
|+|. +.+||||+..++.. ...|+++|+|++|.||+|++++|+..|++++|+.+.++|||++|++++++. ..||+.|+
T Consensus 37 l~~~~~~~~l~d~~~~~~~-~~~L~~lL~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll~~~~~~~L~~l~ 115 (161)
T cd06129 37 LCVSEEKCYLFDPLSLSVD-WQGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLKGLPERWSLASLV 115 (161)
T ss_pred EEECCCCEEEEecccCccC-HHHHHHHhCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHhCCCCCchHHHHH
Confidence 5788 99999999998633 357999999999999999999999999888999999999999999999986 68999999
Q ss_pred HHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006352 79 HHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 123 (649)
Q Consensus 79 e~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 123 (649)
++|+|+.++|..+++||..||||++|+.|||.||+|++.||+.|+
T Consensus 116 ~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 116 EHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred HHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999875
No 6
>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=99.88 E-value=9e-23 Score=200.99 Aligned_cols=129 Identities=31% Similarity=0.411 Sum_probs=116.3
Q ss_pred CCCC-CceEEEeCCCcch-hhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC--------
Q 006352 1 MSLR-TEDFVVDTLKLRV-QVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-------- 70 (649)
Q Consensus 1 IST~-~~~yLID~Lal~~-~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~-------- 70 (649)
|||. +.+||||++.+.. .+...|+++|++++|.||+|++++|+.+|++.+|+.+.++|||++|+++|++.
T Consensus 33 ia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~ 112 (197)
T cd06148 33 IATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPD 112 (197)
T ss_pred EeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCcccc
Confidence 6888 9999999999862 23357899999999999999999999999889999999999999999999753
Q ss_pred -CCcHHHHHHHHcCCCCCc--------ccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcC
Q 006352 71 -RNSLEYLLHHFCGVNANK--------EYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSM 129 (649)
Q Consensus 71 -~~sLa~LVe~~LGv~LdK--------~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~ 129 (649)
..||..++++|+|+.++| ..+.+||..||||++|+.|||.||+||+.||+.|...|.+.
T Consensus 113 ~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 113 RVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred ccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 269999999999999875 46789999999999999999999999999999999999864
No 7
>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=99.88 E-value=2e-22 Score=198.21 Aligned_cols=123 Identities=26% Similarity=0.426 Sum_probs=111.0
Q ss_pred CCCCCceEEEeCCCcch----hhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCC------ccccchHHHHHHHhCC-
Q 006352 1 MSLRTEDFVVDTLKLRV----QVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIY------LCNMFDTGQASRVLKL- 69 (649)
Q Consensus 1 IST~~~~yLID~Lal~~----~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~------p~nvFDTqIAA~LLg~- 69 (649)
|||.+.+||||+..++. .+.+.|+++|+||+|.||+|++++|+.+|+++||+. +.++|||+.+++.+..
T Consensus 48 iat~~~~~lid~~~~~~~~~~~~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~ 127 (193)
T cd06146 48 LATEDEVFLLDLLALENLESEDWDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKS 127 (193)
T ss_pred EecCCCEEEEEchhccccchHHHHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhc
Confidence 68999999999998861 354679999999999999999999999999999974 6799999988876542
Q ss_pred -----------CCCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006352 70 -----------ERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 123 (649)
Q Consensus 70 -----------~~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 123 (649)
...||+.|++++||+.++|..|+|||..||||++|+.|||.||+|++.||+.|.
T Consensus 128 ~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 128 DMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred cccccccccCcccCCHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 258999999999999999999999999999999999999999999999999875
No 8
>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=99.87 E-value=1.4e-21 Score=185.99 Aligned_cols=122 Identities=25% Similarity=0.408 Sum_probs=113.4
Q ss_pred CCCCCceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC--CCcHHHHH
Q 006352 1 MSLRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE--RNSLEYLL 78 (649)
Q Consensus 1 IST~~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~--~~sLa~LV 78 (649)
|||.+.+||||+..+. .+.+.|+++|++++|.||+|+++.|+..|.+.+|+.+.++|||++|++++++. ..||..|+
T Consensus 44 l~~~~~~~l~~~~~~~-~~~~~l~~ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~ 122 (170)
T cd06141 44 LATESRCLLFQLAHMD-KLPPSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLV 122 (170)
T ss_pred EecCCcEEEEEhhhhh-cccHHHHHHhcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHH
Confidence 6899999999999974 35567999999999999999999999999889999999999999999999985 47999999
Q ss_pred HHHcCCCCC--cccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006352 79 HHFCGVNAN--KEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 123 (649)
Q Consensus 79 e~~LGv~Ld--K~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 123 (649)
..++|.+++ |..+++||..|||+++|+.|||.||++++.||+.|.
T Consensus 123 ~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 123 EEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999 788999999999999999999999999999999875
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=99.80 E-value=1.6e-19 Score=169.61 Aligned_cols=127 Identities=35% Similarity=0.586 Sum_probs=112.9
Q ss_pred CCCCCceEEEeCCCcchh-hhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCCC-CcHHHHH
Q 006352 1 MSLRTEDFVVDTLKLRVQ-VGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLER-NSLEYLL 78 (649)
Q Consensus 1 IST~~~~yLID~Lal~~~-L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~~-~sLa~LV 78 (649)
|++.+.+|++|+...... +...|+++|+|++|.||+|++++|+.+|++.+|+.+.++|||+++++++++.. +||..|+
T Consensus 46 ~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~~~L~~L~ 125 (176)
T PF01612_consen 46 LATGEGCYIIDPIDLGDNWILDALKELLEDPNIIKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRSYSLKDLA 125 (176)
T ss_dssp EEESCEEEEECGTTSTTTTHHHHHHHHHTTTTSEEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTTSSHHHHH
T ss_pred EecCCCceeeeeccccccchHHHHHHHHhCCCccEEEEEEechHHHHHHHhccccCCccchhhhhhcccccccccHHHHH
Confidence 356788899999988753 23679999999999999999999999998889999999999999999999875 9999999
Q ss_pred HHHcC-CCCCcccccccCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006352 79 HHFCG-VNANKEYQNADWR-VRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 127 (649)
Q Consensus 79 e~~LG-v~LdK~~q~SDW~-~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~ 127 (649)
.+++| ..++|..+.++|. .+||+++|+.|||.||++++.||+.|..+|+
T Consensus 126 ~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 126 EEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred HHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 99999 7888899999999 8999999999999999999999999999874
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=99.71 E-value=1.7e-16 Score=150.38 Aligned_cols=128 Identities=39% Similarity=0.588 Sum_probs=110.8
Q ss_pred CCCCCceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC-CCcHHHHHH
Q 006352 1 MSLRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLH 79 (649)
Q Consensus 1 IST~~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~-~~sLa~LVe 79 (649)
|+|.+.+|+||+..+ . ..+.|+++|+|+.+.||+|+++.|+..|.+.+|+...++|||++|+|+|++. ..+|..|++
T Consensus 36 l~~~~~~~~i~~~~~-~-~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl~p~~~~~l~~l~~ 113 (178)
T cd06142 36 ISTGGEVYLIDPLAI-G-DLSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLLGLGDSVGLAALVE 113 (178)
T ss_pred EeeCCCEEEEeCCCc-c-cHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHhCCCccccHHHHHH
Confidence 355555889986543 2 2255889999999999999999999999777799966789999999999995 479999999
Q ss_pred HHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 80 HFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 80 ~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
.|++..+.+....++|..+||+..|+.||+.||.+++.|++.|..+|.+.+
T Consensus 114 ~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~ 164 (178)
T cd06142 114 ELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEG 164 (178)
T ss_pred HHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Confidence 999998766667799999999999999999999999999999999999765
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=99.56 E-value=3.8e-14 Score=138.36 Aligned_cols=128 Identities=63% Similarity=1.121 Sum_probs=106.6
Q ss_pred CCCCceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCCCCcHHHHHHHH
Q 006352 2 SLRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLERNSLEYLLHHF 81 (649)
Q Consensus 2 ST~~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~~~sLa~LVe~~ 81 (649)
++.+.+|+||++.....+ +.|+++|+++++.||+|+++.++.+|.+.+|+.+.++|||++|+|+|++...+|..|+++|
T Consensus 49 ~~~~~~~~i~~l~~~~~~-~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~~~~l~~l~~~y 127 (192)
T cd06147 49 STREEDYIVDTLKLRDDM-HILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKY 127 (192)
T ss_pred ecCCCcEEEEecccccch-HHHHHHhcCCCceEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCCcccHHHHHHHH
Confidence 455567888753332222 4588999999999999999999999954889988877999999999998546999999999
Q ss_pred cCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 82 CGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 82 LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
|+..+.|..+.++|..+||+.+|..|++.++.+++.|++.|..+|+++.
T Consensus 128 l~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~~ 176 (192)
T cd06147 128 CNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERA 176 (192)
T ss_pred hCCCcchhhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHhc
Confidence 9987545456677988898999999999999999999999999998754
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=99.56 E-value=5e-14 Score=131.05 Aligned_cols=119 Identities=39% Similarity=0.576 Sum_probs=100.2
Q ss_pred ceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC-C-CcHHHHHHHHcC
Q 006352 6 EDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-R-NSLEYLLHHFCG 83 (649)
Q Consensus 6 ~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~-~-~sLa~LVe~~LG 83 (649)
.+|+++..... .....|+++|+++.+.||+|+++.|+.+|+ .+|+.+.++|||++|+|+|++. . .+|..++..|++
T Consensus 51 ~~~i~~~~~~~-~~~~~l~~~l~~~~~~kv~~d~k~~~~~L~-~~gi~~~~~~D~~laayll~p~~~~~~l~~l~~~~l~ 128 (172)
T smart00474 51 GAFIIDPLALG-DDLEILKDLLEDETITKVGHNAKFDLHVLA-RFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLG 128 (172)
T ss_pred ceEEEEeccch-hhHHHHHHHhcCCCceEEEechHHHHHHHH-HCCCcccchhHHHHHHHHHcCCCCcCCHHHHHHHHhC
Confidence 55665554332 212458899999999999999999999996 4999988889999999999875 2 799999999999
Q ss_pred CCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q 006352 84 VNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKL 126 (649)
Q Consensus 84 v~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL 126 (649)
..+++..+.++|..+|+...|+.||+.||++++.|++.|..+|
T Consensus 129 ~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 129 VELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred CCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9876655567998899999999999999999999999998876
No 13
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=99.54 E-value=1.3e-14 Score=119.41 Aligned_cols=68 Identities=35% Similarity=0.586 Sum_probs=62.3
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHH
Q 006352 180 QLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSII 247 (649)
Q Consensus 180 qlaVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrryGdeIL~iI 247 (649)
|+++|++|+.||+++|++.|+||++||+|.+|.+||+++|+|.++|.+|.|++...+++||++|+++|
T Consensus 1 q~~~~~~L~~~R~~~A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i~g~~~~~~~~~g~~il~~I 68 (68)
T PF00570_consen 1 QLALLKALKEWREELAREEDVPPYRILSDEALLEIAKRLPTSIEELLQIPGMGKRKVRKYGDEILEII 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTSTTCGHHHHHHCHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHccCCCHHHHHHHHHHHHhhC
Confidence 67899999999999999999999999999999999999999999999999999999999999999987
No 14
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=99.50 E-value=1e-13 Score=117.32 Aligned_cols=77 Identities=32% Similarity=0.534 Sum_probs=73.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHHHhcc
Q 006352 178 AQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNA 254 (649)
Q Consensus 178 ~~qlaVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrryGdeIL~iI~~ale~~ 254 (649)
+.++++|++|+.||+.+|++.|+|+++||+|.+|++||+++|+|..+|..+.|++...+++||..|+.+|+.+.+.+
T Consensus 2 ~~~~~~~~~L~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~~~~~~~~g~~~~~~i~~~~~~~ 78 (81)
T smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSP 78 (81)
T ss_pred hHHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 57899999999999999999999999999999999999999999999999999998999999999999999988765
No 15
>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=99.45 E-value=6.2e-13 Score=121.40 Aligned_cols=105 Identities=34% Similarity=0.431 Sum_probs=87.7
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC--CCcHHHHHHHHcCCCCCcccccccCC--
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADWR-- 96 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~--~~sLa~LVe~~LGv~LdK~~q~SDW~-- 96 (649)
+.|+++|+++.+.||+|++++|+.+|...+...+.++|||++|+|+|++. .++|+.|+++|++..+.+..+..+|.
T Consensus 44 ~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ayll~~~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~ 123 (155)
T cd00007 44 EALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQIYGKGAK 123 (155)
T ss_pred HHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCcCCHHHHHHHHcCCCCccHHHHhcCCCC
Confidence 45889999999999999999999999655544566799999999999985 37999999999998854422334442
Q ss_pred --CCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006352 97 --VRPLPDEMLRYAREDTHYLLYIYDIMKIK 125 (649)
Q Consensus 97 --~RPLS~eQl~YAA~DV~yLl~Lyd~L~~q 125 (649)
.+|++..|..||+.|+.+++.|++.|..+
T Consensus 124 ~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 124 TFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred ccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 58889999999999999999999998765
No 16
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.44 E-value=7.9e-13 Score=121.64 Aligned_cols=120 Identities=23% Similarity=0.215 Sum_probs=93.6
Q ss_pred CCCCc-eEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCc-cccchHHHHHHHhCCC--CCcHHHH
Q 006352 2 SLRTE-DFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYL-CNMFDTGQASRVLKLE--RNSLEYL 77 (649)
Q Consensus 2 ST~~~-~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p-~nvFDTqIAA~LLg~~--~~sLa~L 77 (649)
++.+. +|+||+....... ..|+++|+|+++.||+|+++.|+.+| ...|+.. .++|||++|+|+|++. ..+|..|
T Consensus 24 ~~~~~~~~~i~~~~~~~~~-~~l~~~l~~~~~~kv~~d~K~~~~~L-~~~~~~~~~~~~D~~laayLl~p~~~~~~l~~l 101 (150)
T cd09018 24 AIEPGVAALIPVAHDYLAL-ELLKPLLEDEKALKVGQNLKYDRGIL-LNYFIELRGIAFDTMLEAYILNSVAGRWDMDSL 101 (150)
T ss_pred EcCCCcEEEEEcCCcccCH-HHHHHHhcCCCCceeeecHHHHHHHH-HHcCCccCCcchhHHHHHHHhCCCCCCCCHHHH
Confidence 44433 7888754311022 45889999999999999999999999 4556554 5689999999999984 4799999
Q ss_pred HHHHcCCCCCccccc--ccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006352 78 LHHFCGVNANKEYQN--ADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 123 (649)
Q Consensus 78 Ve~~LGv~LdK~~q~--SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 123 (649)
+.+||+..+.+..+. ..|..++++.+|+.||+.|+.+++.|++.|.
T Consensus 102 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 102 VERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred HHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999985441211 2386688899999999999999999998864
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=99.38 E-value=3.1e-12 Score=122.23 Aligned_cols=127 Identities=19% Similarity=0.165 Sum_probs=99.7
Q ss_pred CCCCceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCcc-ccchHHHHHHHhCCCC--CcHHHHH
Q 006352 2 SLRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLC-NMFDTGQASRVLKLER--NSLEYLL 78 (649)
Q Consensus 2 ST~~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~-nvFDTqIAA~LLg~~~--~sLa~LV 78 (649)
++.+.+|+||+....... ..|+++|+|+++.||+|+++.|++.| ..+|+.+. .+|||++|+|+|++.. ++|..++
T Consensus 28 ~~~~~~~~i~~~~~~~~~-~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~~~~~~fDt~laaYLL~p~~~~~~l~~l~ 105 (178)
T cd06140 28 ANGGGAYYIPLELALLDL-AALKEWLEDEKIPKVGHDAKRAYVAL-KRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLA 105 (178)
T ss_pred EeCCcEEEEeccchHHHH-HHHHHHHhCCCCceeccchhHHHHHH-HHCCCcCCCcchhHHHHHHHcCCCCCCCCHHHHH
Confidence 344567788743210112 45889999999999999999999999 56898775 5799999999999963 7999999
Q ss_pred HHHcCCCCCcccccccCC---CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 79 HHFCGVNANKEYQNADWR---VRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 79 e~~LGv~LdK~~q~SDW~---~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
.+|+++++.+..+...|. .++....+..|++.|+.+++.|++.|..+|.+.+
T Consensus 106 ~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~ 160 (178)
T cd06140 106 KRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEENE 160 (178)
T ss_pred HHHcCCCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 999999876533344452 2454677889999999999999999999998654
No 18
>PRK05755 DNA polymerase I; Provisional
Probab=99.27 E-value=2.2e-10 Score=135.92 Aligned_cols=127 Identities=27% Similarity=0.321 Sum_probs=99.7
Q ss_pred CCCCc-eEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCc-cccchHHHHHHHhCCCC-CcHHHHH
Q 006352 2 SLRTE-DFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYL-CNMFDTGQASRVLKLER-NSLEYLL 78 (649)
Q Consensus 2 ST~~~-~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p-~nvFDTqIAA~LLg~~~-~sLa~LV 78 (649)
++.+. +|+||+..+.....+.|+++|+++.+.||+|++++|+.+|+ .+|+.+ .++|||++|+++|++.. ++|..|+
T Consensus 340 s~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~v~kV~HNakfDl~~L~-~~gi~~~~~~~DT~iAa~Ll~~~~~~~L~~L~ 418 (880)
T PRK05755 340 AVEPGEAAYIPLDQLDREVLAALKPLLEDPAIKKVGQNLKYDLHVLA-RYGIELRGIAFDTMLASYLLDPGRRHGLDSLA 418 (880)
T ss_pred EeCCCcEEEEecccccHHHHHHHHHHHhCCCCcEEEeccHhHHHHHH-hCCCCcCCCcccHHHHHHHcCCCCCCCHHHHH
Confidence 34444 78888744321223568999999999999999999999995 578875 57999999999999863 8999999
Q ss_pred HHHcCCCCCccc----ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 79 HHFCGVNANKEY----QNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 79 e~~LGv~LdK~~----q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
++|+|+++.... ...+|..+|+ +.+..||+.||.+++.||..|..+|.+.+
T Consensus 419 ~~ylg~~~~~~~~~~gk~~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~ 473 (880)
T PRK05755 419 ERYLGHKTISFEEVAGKQLTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEP 473 (880)
T ss_pred HHHhCCCccchHHhcCCCCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 999998852110 1233445577 57999999999999999999999998753
No 19
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.25 E-value=1.5e-10 Score=130.87 Aligned_cols=81 Identities=25% Similarity=0.262 Sum_probs=75.6
Q ss_pred HHhCCCccccchHHHHHHHhCCC----CCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006352 48 RDFGIYLCNMFDTGQASRVLKLE----RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 123 (649)
Q Consensus 48 rd~GI~p~nvFDTqIAA~LLg~~----~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 123 (649)
..+|+.+.++||||+|+|+|+.+ .++|..++.+|+++.++|..+++||. |||+++|+.||+.||.||+.||..|.
T Consensus 63 ~~~Gv~~~~~fDT~LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~~sdw~-rpls~~q~~YAa~Dv~~l~~L~~~L~ 141 (553)
T PRK14975 63 LAAGVRVERCHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALS-DPPDEEQLLYAAADADVLLELYAVLA 141 (553)
T ss_pred HHCCCccCCCchHHHHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChhhhcccc-ccchHHHHHHHHHHhHHHHHHHHHHH
Confidence 56799998999999999999984 58999999999999999988899996 99999999999999999999999999
Q ss_pred HHHhcC
Q 006352 124 IKLSSM 129 (649)
Q Consensus 124 ~qL~e~ 129 (649)
.+|.+.
T Consensus 142 ~qL~~~ 147 (553)
T PRK14975 142 DQLNRI 147 (553)
T ss_pred HHHHhh
Confidence 999875
No 20
>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=99.03 E-value=3.5e-09 Score=101.65 Aligned_cols=106 Identities=31% Similarity=0.449 Sum_probs=87.6
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHhCCCcc-ccchHHHHHHHhCCC--CCcHHHHHHHHcCCCC-------Cccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLC-NMFDTGQASRVLKLE--RNSLEYLLHHFCGVNA-------NKEY 90 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~-nvFDTqIAA~LLg~~--~~sLa~LVe~~LGv~L-------dK~~ 90 (649)
..|..+|++..+.+|+|++++|+.+| +.+|+.+. .+|||++++|+|++. .++|..++++|++..+ .|+.
T Consensus 57 ~~l~~~l~~~~~~~v~hn~k~d~~~l-~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~ 135 (193)
T cd06139 57 AALKPLLEDPSIKKVGQNLKFDLHVL-ANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGK 135 (193)
T ss_pred HHHHHHHhCCCCcEEeeccHHHHHHH-HHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCc
Confidence 34888999988899999999999999 56888765 589999999999985 4799999999998763 1223
Q ss_pred ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhc
Q 006352 91 QNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSS 128 (649)
Q Consensus 91 q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e 128 (649)
+..+|...|+ ..+..||+.|+.+++.|+..|..+|.+
T Consensus 136 ~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 136 KQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred CcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3455655555 668999999999999999999999975
No 21
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.89 E-value=3.8e-09 Score=118.29 Aligned_cols=126 Identities=22% Similarity=0.307 Sum_probs=100.3
Q ss_pred CCCCCceEEEeCCCcch---h-hhHHHHHhhcCCCceEEEEechhhHHHHHH-----HhCCCc---cccch-HHHHHHHh
Q 006352 1 MSLRTEDFVVDTLKLRV---Q-VGPYLREVFKDPTKKKVMHGADRDIVWLQR-----DFGIYL---CNMFD-TGQASRVL 67 (649)
Q Consensus 1 IST~~~~yLID~Lal~~---~-L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~r-----d~GI~p---~nvFD-TqIAA~LL 67 (649)
|++.+++||||+.++.. + +.-.+..+|+++.|.||+.+..+|++.|++ .+++.+ .++++ +.++..+.
T Consensus 438 if~~~~v~Lidc~~l~~~~se~w~~~~s~if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~ 517 (617)
T KOG2207|consen 438 IFFKDCVYLIDCVKLENLASEIWHLLLSQIFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVI 517 (617)
T ss_pred HHhcCeEEEeehHHhhhchHHHHHHHHHHHccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHh
Confidence 57889999999999864 2 223466899999999999999999999975 333332 33443 34454443
Q ss_pred CC-------C--CCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q 006352 68 KL-------E--RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKL 126 (649)
Q Consensus 68 g~-------~--~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL 126 (649)
+. . ..+|++|...++|..++|..|+++|..|||...|+.||+.|++.+..+|..+....
T Consensus 518 ~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv 585 (617)
T KOG2207|consen 518 DLPLSIENLNEATKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVV 585 (617)
T ss_pred cccchhhhhcchhhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhc
Confidence 32 1 37899999999999999999999999999999999999999999999999866544
No 22
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=98.87 E-value=4.2e-09 Score=119.62 Aligned_cols=75 Identities=21% Similarity=0.310 Sum_probs=69.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHH
Q 006352 174 AGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKN 249 (649)
Q Consensus 174 ~~L~~~qlaVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrryGdeIL~iI~~ 249 (649)
+.+.. +.++|++|++||+++|++.|+|+++||+|.+|++||+.+|+|.++|.++.|++...+++||++|+++|+.
T Consensus 516 ~~~~~-~~~l~~~L~~wR~~~A~~~~~p~~~If~d~~L~~ia~~~P~~~~~l~~i~gv~~~k~~~~G~~~l~~i~~ 590 (591)
T TIGR01389 516 LSVGV-DNALFEALRELRKEQADEQNVPPYVIFSDSTLREMAEKRPATLNALLKIKGVGQNKLDRYGEAFLEVIRE 590 (591)
T ss_pred ccccc-HHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhCCCCCCHHHHHHHHHHHHHHHHh
Confidence 34444 4499999999999999999999999999999999999999999999999999999999999999999975
No 23
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.85 E-value=2.5e-07 Score=110.19 Aligned_cols=108 Identities=18% Similarity=0.107 Sum_probs=86.3
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHhCCCcc-ccchHHHHHHHhCCC-CCcHHHHHHHHcCCCCCcccccccCC--
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLC-NMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWR-- 96 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~-nvFDTqIAA~LLg~~-~~sLa~LVe~~LGv~LdK~~q~SDW~-- 96 (649)
..|+++|+|+.+.||+|++++|+.+| ..+|+.+. .+|||++|+|+|++. .++|..|+.+|++.++.+......|.
T Consensus 368 ~~l~~~l~~~~~~~v~~n~K~d~~~l-~~~gi~~~~~~~Dt~la~yll~~~~~~~l~~la~~yl~~~~~~~~~~~~~~~~ 446 (887)
T TIGR00593 368 DKFARWLLNEQIKKIGHDAKFLMHLL-KREGIELGGVIFDTMLAAYLLDPAQVSTLDTLARRYLVEELILDEKIGGKLAK 446 (887)
T ss_pred HHHHHHHhCCCCcEEEeeHHHHHHHH-HhCCCCCCCcchhHHHHHHHcCCCCCCCHHHHHHHHcCcccccHHHhccCCCC
Confidence 45889999999999999999999999 67999875 589999999999985 47999999999997754322111111
Q ss_pred CCCCC-HHHHHHHHHhHHHHHHHHHHHHHHHhcC
Q 006352 97 VRPLP-DEMLRYAREDTHYLLYIYDIMKIKLSSM 129 (649)
Q Consensus 97 ~RPLS-~eQl~YAA~DV~yLl~Lyd~L~~qL~e~ 129 (649)
...++ +.+..||+.||.+++.||..|..+|.+.
T Consensus 447 ~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~~~ 480 (887)
T TIGR00593 447 FAFPPLEEATEYLARRAAATKRLAEELLKELDEN 480 (887)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 11232 4567899999999999999999999854
No 24
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=98.65 E-value=3.1e-07 Score=85.90 Aligned_cols=117 Identities=21% Similarity=0.211 Sum_probs=81.0
Q ss_pred CCCCceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccc-cchHHHHHHHhCCC-C-CcHHHHH
Q 006352 2 SLRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCN-MFDTGQASRVLKLE-R-NSLEYLL 78 (649)
Q Consensus 2 ST~~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~n-vFDTqIAA~LLg~~-~-~sLa~LV 78 (649)
++.+.+|+|++-. .... ..|+++|+|..+.|++|+.|.++.+| +.+|+.+.+ +|||+||+|+|++. . .+|..|+
T Consensus 26 ~~~~~~~yi~~~~-~~~~-~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~~LAaYLL~p~~~~~~l~~la 102 (151)
T cd06128 26 AIEGVAAYIPVAH-DYAL-ELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDTMLEAYLLDPVAGRHDMDSLA 102 (151)
T ss_pred EcCCCeEEEeCCC-CcCH-HHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhHHHHHHHcCCCCCCCCHHHHH
Confidence 3444567775211 0012 35889999999999999999999999 788998764 69999999999995 2 6999999
Q ss_pred HHHcCCC-CC-cccccccCCC--CCC-CHHHHHHHHHhHHHHHHHHHHHH
Q 006352 79 HHFCGVN-AN-KEYQNADWRV--RPL-PDEMLRYAREDTHYLLYIYDIMK 123 (649)
Q Consensus 79 e~~LGv~-Ld-K~~q~SDW~~--RPL-S~eQl~YAA~DV~yLl~Lyd~L~ 123 (649)
.+|++.. +. .. ...+.. .++ ......|++..+.+++.|++.|.
T Consensus 103 ~~yl~~~~~~~~~--~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 103 ERWLKEKTITFEE--IAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred HHHcCCCCccHHH--HcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 9999877 32 10 111110 011 12223478888888888888764
No 25
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=98.58 E-value=2.4e-07 Score=105.17 Aligned_cols=108 Identities=26% Similarity=0.304 Sum_probs=89.1
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC--CCcHHHHHHHHcCCCCC-------cccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNAN-------KEYQ 91 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~--~~sLa~LVe~~LGv~Ld-------K~~q 91 (649)
..|++||+|+.+.||+|+++.|.+.| ..+|+.++..||||+|+|+++++ .+++..|+.+|++.++- |+.+
T Consensus 68 ~~l~~~l~~~~~~kv~~~~K~d~~~l-~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~ 146 (593)
T COG0749 68 AALKPLLEDEGIKKVGQNLKYDYKVL-ANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKK 146 (593)
T ss_pred HHHHHHhhCcccchhccccchhHHHH-HHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccc
Confidence 67999999999999999999999999 67886656799999999999986 58999999999998763 3333
Q ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 92 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 92 ~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
.-++..-++ .....|++.|+..++.|+..|..+|.+..
T Consensus 147 ~~~~~~~~~-~~~~~y~a~~a~~~~~L~~~l~~~l~~~~ 184 (593)
T COG0749 147 QLTFADVKL-EKATEYAAEDADATLRLESILEPELLKTP 184 (593)
T ss_pred cCccccchH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 333333333 45689999999999999999998887643
No 26
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=98.51 E-value=2.2e-07 Score=106.45 Aligned_cols=75 Identities=25% Similarity=0.380 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHHHh
Q 006352 178 AQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQ 252 (649)
Q Consensus 178 ~~qlaVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrryGdeIL~iI~~ale 252 (649)
..+..+|.+|..||.++|++.++|++.||+|.+|.+||+.+|+|.++|.+|.|++..++++||++|+++|+.+.+
T Consensus 530 ~~~~~l~~~Lr~~R~~~a~~~~~~~~~if~d~tL~~ia~~~P~t~~~l~~i~Gvg~~K~~~yg~~~l~~i~~~~~ 604 (607)
T PRK11057 530 NYDRKLFAKLRKLRKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGKPFMALIRAHVD 604 (607)
T ss_pred cchHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 345789999999999999999999999999999999999999999999999999999999999999999998764
No 27
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=98.34 E-value=9.3e-07 Score=106.51 Aligned_cols=73 Identities=19% Similarity=0.312 Sum_probs=69.0
Q ss_pred HHHHHHHHHHHHHHHHHH--cCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHHHh
Q 006352 180 QLAVVAGLCEWRDVIARA--DDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQ 252 (649)
Q Consensus 180 qlaVL~aL~~WRe~iAR~--~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrryGdeIL~iI~~ale 252 (649)
+..+|.+|..||.++|++ +++|++.||+|.+|.+||+.+|+|.++|.+|.|++..++++||+++|++|+..+.
T Consensus 1028 d~~Lfe~Lr~lR~elA~e~~~~vppyvIFsD~TL~eIA~~~P~T~~eLl~I~GVG~~KlekYG~~fL~vI~~~~~ 1102 (1195)
T PLN03137 1028 SAILYTALRKLRTALVKEAGDGVMAYHIFGNATLQQISKRIPRTKEELLEINGLGKAKVSKYGDRLLETIESTIN 1102 (1195)
T ss_pred cHHHHHHHHHHHHHHHHhhhcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCccHHHHHHHHHHHHHHHHHHHH
Confidence 456999999999999999 6999999999999999999999999999999999999999999999999987654
No 28
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=98.01 E-value=9.3e-06 Score=92.74 Aligned_cols=72 Identities=24% Similarity=0.311 Sum_probs=68.9
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHHhHHHHHHHHHHHH
Q 006352 180 QLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSM 251 (649)
Q Consensus 180 qlaVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrryGdeIL~iI~~al 251 (649)
...+|.+|..||.++|++.|+||+.|++|.+|.++|..+|.+..+|..+.|++..++.+||..++++|....
T Consensus 517 ~~~lf~~lr~~r~~~a~~~~vp~~vif~d~tl~~ma~~~p~~~~~~~~i~gvg~~k~~~yg~~fl~~i~~~~ 588 (590)
T COG0514 517 DRDLFERLRALRKEIADEENVPPYVVFSDATLKEMAEKQPQSADELLSINGVGEAKLERYGQAFLAVIQAHA 588 (590)
T ss_pred cHHHHHHHHHHHHHhhhhhcCCceEEecchHHHHHHHHcCCCHHHHHHhcCCcccchhhccHHHHHHHHHhc
Confidence 566999999999999999999999999999999999999999999999999999999999999999998764
No 29
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=97.64 E-value=0.00013 Score=77.63 Aligned_cols=114 Identities=23% Similarity=0.292 Sum_probs=86.9
Q ss_pred CceEEEeCCCcchhhhHHHHHhhcCCCceEEEEechhhHHHHHH-HhCCCccccchHHH-HHHHhCCC--CCcHHHHHHH
Q 006352 5 TEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQR-DFGIYLCNMFDTGQ-ASRVLKLE--RNSLEYLLHH 80 (649)
Q Consensus 5 ~~~yLID~Lal~~~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~r-d~GI~p~nvFDTqI-AA~LLg~~--~~sLa~LVe~ 80 (649)
+.|+||-..... .+...|+.+|+|++...|+-+.++|..-|.+ .+++.+..+.|+.. +.-.+|.. .-+...|+..
T Consensus 159 n~C~I~ql~~~~-~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g~~~~~~s~e~i~~~ 237 (319)
T KOG4373|consen 159 NRCLIIQLIHCK-RIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLGGSMPNDSFEEIVSE 237 (319)
T ss_pred cceeeEEeeccc-cchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhhccCccCccHHHHHHH
Confidence 456666444332 2555688999999999999999999988877 88888888888863 33345552 2445555555
Q ss_pred Hc---C--CCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006352 81 FC---G--VNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 81 ~L---G--v~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Ly 119 (649)
++ | +.+++.-+.+||+..||+.+|+.||+.||+....|+
T Consensus 238 ~~~~~~~~v~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 238 TLGYYGKDVRLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred HhhccccccccChhcccccceeeeccHHHHHHHHhHHHHHHHHH
Confidence 44 4 556677789999999999999999999999999998
No 30
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=95.76 E-value=0.0051 Score=67.10 Aligned_cols=121 Identities=21% Similarity=0.260 Sum_probs=82.0
Q ss_pred CCCCCceEEEeCCCcchh-hhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC----CCcHH
Q 006352 1 MSLRTEDFVVDTLKLRVQ-VGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE----RNSLE 75 (649)
Q Consensus 1 IST~~~~yLID~Lal~~~-L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~----~~sLa 75 (649)
||+.+..||+|.+.-+.- +-.-.+..|+...+ |. ++..+...|...|++.+.+++|||+|..++.+. ++...
T Consensus 218 ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~sLve~~e~grr~p~~ 294 (458)
T KOG2405|consen 218 IADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIASSLVEPSEYGRRHPTS 294 (458)
T ss_pred hcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHHHHhhhHHhcccCCcc
Confidence 688899999998875421 11124556665544 44 999999999999999999999999999887542 11111
Q ss_pred HHHH--------HHcCCCC------Cccc--ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHH
Q 006352 76 YLLH--------HFCGVNA------NKEY--QNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKI 124 (649)
Q Consensus 76 ~LVe--------~~LGv~L------dK~~--q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~ 124 (649)
.++- .|++... .+.. ....|..||.+..+..-+..||+.|+.+++.|.+
T Consensus 295 ~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a 359 (458)
T KOG2405|consen 295 ILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVA 359 (458)
T ss_pred ceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhh
Confidence 1111 1111111 1111 2246999999999999999999999997766544
No 31
>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=93.75 E-value=0.21 Score=43.94 Aligned_cols=66 Identities=17% Similarity=0.252 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHhCCCCHHHHHhhhcCChhHHHH--hHHHHHHHH
Q 006352 182 AVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIER--YMGPVLSII 247 (649)
Q Consensus 182 aVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~~P~S~~eL~~i~g~~~~~vrr--yGdeIL~iI 247 (649)
..+..|.+-|-.++.+.|.|..-.|+|.+|..||...|+|..++..+.|......++ |-...|-.+
T Consensus 7 ~aY~~Lr~~~~~~~~~~n~p~~~f~sd~~LKk~A~~LP~te~eF~~l~g~~~~~~~kFkyFK~tl~~L 74 (80)
T PF11408_consen 7 SAYEKLREISINLSNRMNPPNDNFMSDTILKKMATKLPTTEEEFSKLVGINEQQRKKFKYFKDTLMRL 74 (80)
T ss_dssp HHHHHHHHHHHHHHHSSSS--S-SS-HHHHHHHHHH---SHHHHGGGS---HHHHHHGGGTHHHHHHH
T ss_pred HHHHHHHHHHHHHhhccCCCccccCCHHHHHHHHHHCCCCHHHHHHhcCCcHHHHHHHHHHHHHHHHH
Confidence 356778889999999999998888899999999999999999999999887766553 444444333
No 32
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=92.21 E-value=0.31 Score=48.53 Aligned_cols=79 Identities=23% Similarity=0.217 Sum_probs=53.5
Q ss_pred HHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCCCCcHHHHHHHHcCCCCCcccccccCCCCCCCH
Q 006352 23 LREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPD 102 (649)
Q Consensus 23 Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~ 102 (649)
|+.++ ++..+-|+|+...|+.+|. +-..-..++||.+.-..-.....+|..|+.+|||..+..+.
T Consensus 95 l~~li-~~~tILVGHsL~nDL~aL~--l~hp~~~viDTa~l~~~~~~r~~sLk~La~~~L~~~IQ~~~------------ 159 (174)
T cd06143 95 LRLLV-DLGCIFVGHGLAKDFRVIN--IQVPKEQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSET------------ 159 (174)
T ss_pred HHHHc-CCCCEEEeccchhHHHHhc--CcCCCcceEEcHHhccCCCCCChhHHHHHHHHcCCcccCCC------------
Confidence 55555 4556789999999999993 22222479999743222111258999999999999885321
Q ss_pred HHHHHHHHhHHHHHHHH
Q 006352 103 EMLRYAREDTHYLLYIY 119 (649)
Q Consensus 103 eQl~YAA~DV~yLl~Ly 119 (649)
.-..+||.+.+.||
T Consensus 160 ---HdSvEDArAam~Ly 173 (174)
T cd06143 160 ---HDSIEDARTALKLY 173 (174)
T ss_pred ---cCcHHHHHHHHHHh
Confidence 11357888888887
No 33
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=92.14 E-value=1.2 Score=47.91 Aligned_cols=91 Identities=23% Similarity=0.215 Sum_probs=65.8
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHh---CCCc--cccchHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDF---GIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~---GI~p--~nvFDTqIAA~LLg~--~~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
..|..++.+ -.-|.|++.+|+.+|.+.+ |+.. ..++||+..++.+.+ ..+.|..|+++ +|+.....
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 346667765 3568999999999986543 4432 358999987776654 36899999875 57654221
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
.-|..||.++..|+..|..++.+.+
T Consensus 159 ------------H~Al~DA~ata~l~~~ll~~~~~~~ 183 (313)
T PRK06063 159 ------------HDALDDARVLAGILRPSLERARERD 183 (313)
T ss_pred ------------CCcHHHHHHHHHHHHHHHHHHHhcC
Confidence 3377899999999999988887655
No 34
>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=91.33 E-value=0.55 Score=45.24 Aligned_cols=80 Identities=19% Similarity=0.111 Sum_probs=54.7
Q ss_pred HHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCC-----CCCcHHHHHHHHcCCCCCcccccccCC
Q 006352 22 YLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKL-----ERNSLEYLLHHFCGVNANKEYQNADWR 96 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~-----~~~sLa~LVe~~LGv~LdK~~q~SDW~ 96 (649)
.|..++.+. .+-|+|++..|+.+|.. ....++||...++.+.+ ..++|..|+.+|+|+.+......
T Consensus 76 ~~~~~i~~~-~vlVgHn~~fD~~fL~~----~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~---- 146 (161)
T cd06137 76 ALWKFIDPD-TILVGHSLQNDLDALRM----IHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEG---- 146 (161)
T ss_pred HHHHhcCCC-cEEEeccHHHHHHHHhC----cCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCC----
Confidence 466666542 35689999999999943 23468999877776543 35899999999999776431111
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHH
Q 006352 97 VRPLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 97 ~RPLS~eQl~YAA~DV~yLl~Ly 119 (649)
.-|..||..+..||
T Consensus 147 ---------H~A~~DA~at~~l~ 160 (161)
T cd06137 147 ---------HDSLEDALAAREVV 160 (161)
T ss_pred ---------CCcHHHHHHHHHHh
Confidence 12456777766665
No 35
>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=90.75 E-value=0.36 Score=45.96 Aligned_cols=80 Identities=20% Similarity=0.208 Sum_probs=54.9
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCC---CCCcHHHHHHHHcCCCCCcccccccCCC
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKL---ERNSLEYLLHHFCGVNANKEYQNADWRV 97 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~---~~~sLa~LVe~~LGv~LdK~~q~SDW~~ 97 (649)
+.|..++.+ . .-|+|++.+|+.+|. .+.....++||.....+... ..++|..|+++++|+.+....
T Consensus 69 ~~l~~~l~~-~-vlVgHn~~fD~~~L~--~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~------- 137 (152)
T cd06144 69 KKVAELLKG-R-ILVGHALKNDLKVLK--LDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGE------- 137 (152)
T ss_pred HHHHHHhCC-C-EEEEcCcHHHHHHhc--CcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCC-------
Confidence 457778876 4 458999999999994 33333467888654333322 368999999999998764211
Q ss_pred CCCCHHHHHHHHHhHHHHHHHH
Q 006352 98 RPLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 98 RPLS~eQl~YAA~DV~yLl~Ly 119 (649)
.-|..||..+..||
T Consensus 138 --------H~Al~DA~at~~l~ 151 (152)
T cd06144 138 --------HSSVEDARAAMRLY 151 (152)
T ss_pred --------cCcHHHHHHHHHHh
Confidence 22567888887776
No 36
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=90.69 E-value=1.7 Score=45.09 Aligned_cols=87 Identities=25% Similarity=0.359 Sum_probs=58.7
Q ss_pred HHHHhhcCCCceEEEEechhhHHHHHHH---hCC--C----ccccchHHHHHHHhCCC-CCcHHHHHHHHcCCCCCcccc
Q 006352 22 YLREVFKDPTKKKVMHGADRDIVWLQRD---FGI--Y----LCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQ 91 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~GI--~----p~nvFDTqIAA~LLg~~-~~sLa~LVe~~LGv~LdK~~q 91 (649)
.|..++.+. ..|+|++.+|+..|.+. +|. . .+.++||...++.+-++ .++|..|+++| |+...
T Consensus 79 ~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~~~~-gi~~~---- 151 (240)
T PRK05711 79 EFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRY-GIDNS---- 151 (240)
T ss_pred HHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHHHHC-CCCCC----
Confidence 455666553 35899999999888654 332 1 14589998777765443 57999999875 65432
Q ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006352 92 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 125 (649)
Q Consensus 92 ~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~q 125 (649)
.|. ..-|..||..+..||..|...
T Consensus 152 -----~r~-----~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 152 -----HRT-----LHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred -----CCC-----CCCHHHHHHHHHHHHHHHHCc
Confidence 111 133778999999999887643
No 37
>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=90.63 E-value=1.4 Score=45.17 Aligned_cols=87 Identities=29% Similarity=0.380 Sum_probs=59.5
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHH---hC--CC-c---cccchHHHHHHHhCCC-CCcHHHHHHHHcCCCCCccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FG--IY-L---CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEY 90 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~G--I~-p---~nvFDTqIAA~LLg~~-~~sLa~LVe~~LGv~LdK~~ 90 (649)
..|..++.+. ..|.|++.+|+.+|.+. +| +. + ..++||...++.+-++ .++|..|+++| |+....
T Consensus 74 ~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~-gi~~~~-- 148 (225)
T TIGR01406 74 DEFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRF-KVDNSH-- 148 (225)
T ss_pred HHHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhc-CCCCCC--
Confidence 3466677653 45899999999988654 45 22 1 4689998877755443 68999999885 554321
Q ss_pred ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHH
Q 006352 91 QNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKI 124 (649)
Q Consensus 91 q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~ 124 (649)
|. ..-|..||..+..||..|..
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 13378899999999987654
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=90.38 E-value=1.5 Score=41.78 Aligned_cols=85 Identities=25% Similarity=0.378 Sum_probs=57.2
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHh---CCC-----ccccchHHHHHHHhCC-CCCcHHHHHHHHcCCCCCcccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDF---GIY-----LCNMFDTGQASRVLKL-ERNSLEYLLHHFCGVNANKEYQ 91 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~---GI~-----p~nvFDTqIAA~LLg~-~~~sLa~LVe~~LGv~LdK~~q 91 (649)
..|..++.+. ..|+|++.+|+.+|.+.+ |+. +..++||+..++.+.+ ...+|..++++| |+..+..
T Consensus 73 ~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~-~i~~~~~-- 147 (167)
T cd06131 73 DEFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRF-GIDNSHR-- 147 (167)
T ss_pred HHHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHC-CCCCCCC--
Confidence 3466677653 358999999998886543 332 2458999876665543 357999999885 6544211
Q ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 006352 92 NADWRVRPLPDEMLRYAREDTHYLLYIYDIM 122 (649)
Q Consensus 92 ~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L 122 (649)
...-|..||.++..|+..|
T Consensus 148 ------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 148 ------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred ------------CCCChHHHHHHHHHHHHHh
Confidence 1244788999998888654
No 39
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=90.05 E-value=0.044 Score=60.06 Aligned_cols=110 Identities=23% Similarity=0.357 Sum_probs=78.5
Q ss_pred CCceEEEeCCCcch-hhhHHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHh-CC--C----C--Cc
Q 006352 4 RTEDFVVDTLKLRV-QVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVL-KL--E----R--NS 73 (649)
Q Consensus 4 ~~~~yLID~Lal~~-~L~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LL-g~--~----~--~s 73 (649)
.-..||+|.+.++. .....+..+++|..|.|+.|+|..-..|+...|||...++|||++|-.+- ++ + + ..
T Consensus 84 ~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~q~~d~~q~~~e~g~~~~n~~~~ 163 (458)
T KOG2405|consen 84 NCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVADVLQFSMETGGYLPNCITT 163 (458)
T ss_pred HHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhhhhhhhhhhcccccccCCccccc
Confidence 33457778777754 23355788999999999999999999999999999999999999976542 21 1 1 23
Q ss_pred HH-HHHHHHcCCCCC------cc-----cccccCCCCCCCHHHHHHHHHhHHH
Q 006352 74 LE-YLLHHFCGVNAN------KE-----YQNADWRVRPLPDEMLRYAREDTHY 114 (649)
Q Consensus 74 La-~LVe~~LGv~Ld------K~-----~q~SDW~~RPLS~eQl~YAA~DV~y 114 (649)
++ .|+. .|.+.+. |. ...-.|-.||.++.-+.-.+..+.|
T Consensus 164 ~q~sl~k-h~~~a~k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 164 LQESLIK-HLQVAPKYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred hHHHHHH-HHHhcccHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 43 4444 4443332 21 1346699999999888887777777
No 40
>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=89.92 E-value=0.87 Score=43.50 Aligned_cols=81 Identities=17% Similarity=0.116 Sum_probs=54.2
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccccCCCC
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNADWRVR 98 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~--~~~sLa~LVe~~LGv~LdK~~q~SDW~~R 98 (649)
+.|.+++.. ...-|+|++.+|+.+|.. + ...++||...++.+.. .+++|..|+++|++..+......
T Consensus 67 ~~~~~fl~~-~~vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~------ 135 (150)
T cd06145 67 KKLLSLISP-DTILVGHSLENDLKALKL-I---HPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGG------ 135 (150)
T ss_pred HHHHHHhCC-CCEEEEcChHHHHHHhhc-c---CCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCC------
Confidence 457777752 346799999999999943 2 2458999876654332 25899999999998665321111
Q ss_pred CCCHHHHHHHHHhHHHHHHHH
Q 006352 99 PLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 99 PLS~eQl~YAA~DV~yLl~Ly 119 (649)
.-|..||..+..||
T Consensus 136 -------H~Al~DA~~t~~l~ 149 (150)
T cd06145 136 -------HDSVEDARAALELV 149 (150)
T ss_pred -------CCcHHHHHHHHHHh
Confidence 22556777777765
No 41
>PRK07740 hypothetical protein; Provisional
Probab=89.72 E-value=4.5 Score=41.96 Aligned_cols=90 Identities=17% Similarity=0.185 Sum_probs=65.3
Q ss_pred HHHHhhcCCCceEEEEechhhHHHHHHH----hCCCc-cccchHHHHHHHhCCC--CCcHHHHHHHHcCCCCCccccccc
Q 006352 22 YLREVFKDPTKKKVMHGADRDIVWLQRD----FGIYL-CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNAD 94 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~ak~DL~~L~rd----~GI~p-~nvFDTqIAA~LLg~~--~~sLa~LVe~~LGv~LdK~~q~SD 94 (649)
.|..++.+ -.-|+|++..|+.+|.+. ++... ..++||+..++.+.+. .++|..++.. +|+.+...
T Consensus 134 ~f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~-~gi~~~~~----- 205 (244)
T PRK07740 134 RFYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAY-YGIPIPRR----- 205 (244)
T ss_pred HHHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHH-CCcCCCCC-----
Confidence 45555554 357899999999887543 33333 4699999888776553 6899999864 68766421
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 95 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 95 W~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
.-|..||..+..|+..|..++.+.+
T Consensus 206 -----------H~Al~Da~ata~l~~~ll~~~~~~~ 230 (244)
T PRK07740 206 -----------HHALGDALMTAKLWAILLVEAQQRG 230 (244)
T ss_pred -----------CCcHHHHHHHHHHHHHHHHHHHHcC
Confidence 2267899999999999999888765
No 42
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=89.69 E-value=2.2 Score=43.85 Aligned_cols=81 Identities=17% Similarity=0.191 Sum_probs=57.5
Q ss_pred CceEEEEechhhHHHHHHH---hCCC---ccccchHHHHHHHhCC---CCCcHHHHHHHHcCCCCCcccccccCCCCCCC
Q 006352 31 TKKKVMHGADRDIVWLQRD---FGIY---LCNMFDTGQASRVLKL---ERNSLEYLLHHFCGVNANKEYQNADWRVRPLP 101 (649)
Q Consensus 31 ~I~KV~H~ak~DL~~L~rd---~GI~---p~nvFDTqIAA~LLg~---~~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS 101 (649)
..+.|.|++.+|+.+|.+. +|+. ..+++||...++.+.. +.++|..|+++ +|+.....
T Consensus 93 ~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~-~gi~~~~a------------ 159 (232)
T PRK07942 93 GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEH-YGVRLDNA------------ 159 (232)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHH-cCCCCCCC------------
Confidence 3456999999999888654 3432 2468999887765432 35789999877 57765422
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHhc
Q 006352 102 DEMLRYAREDTHYLLYIYDIMKIKLSS 128 (649)
Q Consensus 102 ~eQl~YAA~DV~yLl~Lyd~L~~qL~e 128 (649)
.-|..||..+..|+..|..++.+
T Consensus 160 ----H~Al~Da~ata~l~~~l~~~~~~ 182 (232)
T PRK07942 160 ----HEATADALAAARVAWALARRFPE 182 (232)
T ss_pred ----CChHHHHHHHHHHHHHHHHHHHH
Confidence 23778999999999988776653
No 43
>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=89.32 E-value=3.1 Score=41.71 Aligned_cols=84 Identities=15% Similarity=0.102 Sum_probs=59.9
Q ss_pred ceEEEEechhhHHHHHHH---hCCC-----ccccchHHHHHHHhCCCCCcHHHHHHHHcCCCCCcccccccCCCCCCCHH
Q 006352 32 KKKVMHGADRDIVWLQRD---FGIY-----LCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDE 103 (649)
Q Consensus 32 I~KV~H~ak~DL~~L~rd---~GI~-----p~nvFDTqIAA~LLg~~~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~e 103 (649)
-.-|+|++.+|+.+|... +|.. +..++||...++.+.+ ..+|..++++ +|+... ..
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~-~~~L~~l~~~-~gi~~~--------------~~ 169 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG-QTVLAKACQA-AGXDFD--------------ST 169 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC-cccHHHHHHH-cCCCcc--------------cc
Confidence 457999999999888643 3432 1237999877766543 4679988876 465532 11
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHhcCCC
Q 006352 104 MLRYAREDTHYLLYIYDIMKIKLSSMPK 131 (649)
Q Consensus 104 Ql~YAA~DV~yLl~Lyd~L~~qL~e~gr 131 (649)
+..-|..||..+..|+..|..++.+.+.
T Consensus 170 ~~H~Al~Da~ata~lf~~l~~~~~~~~~ 197 (200)
T TIGR01298 170 QAHSALYDTEKTAELFCEIVNRWKRLGG 197 (200)
T ss_pred chhhhHHhHHHHHHHHHHHHHHHHHccC
Confidence 3355788999999999999999987763
No 44
>PRK05168 ribonuclease T; Provisional
Probab=88.53 E-value=5.4 Score=40.32 Aligned_cols=84 Identities=18% Similarity=0.149 Sum_probs=58.8
Q ss_pred CceEEEEechhhHHHHHH---HhCCC-----ccccchHHHHHHHhCCCCCcHHHHHHHHcCCCCCcccccccCCCCCCCH
Q 006352 31 TKKKVMHGADRDIVWLQR---DFGIY-----LCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPD 102 (649)
Q Consensus 31 ~I~KV~H~ak~DL~~L~r---d~GI~-----p~nvFDTqIAA~LLg~~~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~ 102 (649)
....|+|++.+|+..|.+ .+|+. +..++||...++.+.. ..+|..++++ +|+.++..
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~-~~~L~~l~~~-~gl~~~~~------------- 178 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG-QTVLAKACQA-AGIEFDNK------------- 178 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC-CCCHHHHHHH-CCCCCCCC-------------
Confidence 457899999999988754 34542 1247999866665533 3678888876 46654311
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 103 EMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 103 eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
...-|..||..+..|+..|..++.+.+
T Consensus 179 -~~H~Al~DA~ata~l~~~l~~~~~~~~ 205 (211)
T PRK05168 179 -EAHSALYDTEKTAELFCEIVNRWKRLG 205 (211)
T ss_pred -CCCChHHHHHHHHHHHHHHHHHHHHcc
Confidence 113377899999999999999998766
No 45
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=88.00 E-value=3.8 Score=42.62 Aligned_cols=87 Identities=22% Similarity=0.280 Sum_probs=60.3
Q ss_pred HHHHhhcCCCceEEEEechhhHHHHHHH---hCCCc----cccchHHHHHHHhCCC-CCcHHHHHHHHcCCCCCcccccc
Q 006352 22 YLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL----CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~GI~p----~nvFDTqIAA~LLg~~-~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
.|..++.+. -..|+|++.+|+.+|.+. .|+.. ..++||+..++.++.. .++|..|++.| |+.+...
T Consensus 80 ~~~~fl~~~-~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~-g~~~~~a---- 153 (250)
T PRK06310 80 QIKGFFKEG-DYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHF-NVPYDGN---- 153 (250)
T ss_pred HHHHHhCCC-CEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHC-CCCCCCC----
Confidence 455666553 357899999999888653 34432 3589999877776543 58999998765 6654321
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKL 126 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL 126 (649)
.-|..||.++..|+..|..++
T Consensus 154 ------------H~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 154 ------------HRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred ------------cChHHHHHHHHHHHHHHHHhc
Confidence 337789999999888876543
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=87.61 E-value=4 Score=37.04 Aligned_cols=81 Identities=22% Similarity=0.184 Sum_probs=54.4
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHhC-----CCccccchHHHHHHH-hCCC-CCcHHHHHHHHcCCCCCcccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDFG-----IYLCNMFDTGQASRV-LKLE-RNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~G-----I~p~nvFDTqIAA~L-Lg~~-~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
..|..++.+ ...|+|++..|..+|.+.+. ......+||+..+.. ++.. ..++..+...+++....
T Consensus 71 ~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~------ 142 (159)
T cd06127 71 PEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE------ 142 (159)
T ss_pred HHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC------
Confidence 456677776 56799999999999866543 334579999866554 4332 46777775556665432
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Ly 119 (649)
+..-|..||.++..||
T Consensus 143 ----------~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 143 ----------GAHRALADALATAELL 158 (159)
T ss_pred ----------CCCCcHHHHHHHHHHh
Confidence 1234778888888775
No 47
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=87.49 E-value=4 Score=44.05 Aligned_cols=88 Identities=18% Similarity=0.179 Sum_probs=61.4
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHh---CCC--ccccchHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDF---GIY--LCNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~---GI~--p~nvFDTqIAA~LLg~--~~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
+.|..++.+. .-|+|++.+|+.+|.+.+ |+. ...++||+..++.+.+ ..++|..|+++ +|+.. +
T Consensus 80 ~~f~~fl~~~--~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~-lgi~~-~----- 150 (313)
T PRK06807 80 PLFLAFLHTN--VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRM-LGIRL-S----- 150 (313)
T ss_pred HHHHHHHcCC--eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHH-cCCCC-C-----
Confidence 3466666553 348999999999997654 442 2358999876665443 35899999754 56554 1
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhc
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSS 128 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e 128 (649)
..-|..||.++..||..|...+..
T Consensus 151 -----------~H~Al~DA~~ta~l~~~l~~~~~~ 174 (313)
T PRK06807 151 -----------SHNAFDDCITCAAVYQKCASIEEE 174 (313)
T ss_pred -----------CcChHHHHHHHHHHHHHHHHhhhh
Confidence 133778999999999998877743
No 48
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=87.49 E-value=2.2 Score=52.97 Aligned_cols=91 Identities=24% Similarity=0.283 Sum_probs=72.0
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHH---hCCCc--cccchHHHHHHHhCCC--CCcHHHHHHHHcCCCCCcccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~GI~p--~nvFDTqIAA~LLg~~--~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
..+++|+.|. +-|.|++.+|+..|+.. +|+.+ .+++||.-.|+.|.+. +++|..|+.+| |+.+
T Consensus 493 ~kf~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~-~v~l------- 562 (1444)
T COG2176 493 EKFREFIGDS--ILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKKL-GVEL------- 562 (1444)
T ss_pred HHHHHHhcCc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHHh-CccH-------
Confidence 4688898873 56899999999888654 55655 4799999999999875 79999999875 4443
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
++..-|--|+.++..|+..+.+.|.++|
T Consensus 563 ---------e~hHRA~yDaeat~~vf~~f~~~~ke~G 590 (1444)
T COG2176 563 ---------ERHHRADYDAEATAKVFFVFLKDLKEKG 590 (1444)
T ss_pred ---------HHhhhhhhhHHHHHHHHHHHHHHHHHhc
Confidence 3445567799999999999999888876
No 49
>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=87.42 E-value=1.4 Score=39.12 Aligned_cols=41 Identities=20% Similarity=0.267 Sum_probs=29.2
Q ss_pred HHHhhcCCC-ceEEEEechhhHHHHHHHhCC-------CccccchHHHH
Q 006352 23 LREVFKDPT-KKKVMHGADRDIVWLQRDFGI-------YLCNMFDTGQA 63 (649)
Q Consensus 23 Lk~lLeDp~-I~KV~H~ak~DL~~L~rd~GI-------~p~nvFDTqIA 63 (649)
|.+++.+.. ..+|+|++..|+..|.+.+.. ...+.+||+.+
T Consensus 35 f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 35 LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 667887766 678999999999887655432 12457888755
No 50
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=87.19 E-value=5.3 Score=41.94 Aligned_cols=88 Identities=19% Similarity=0.264 Sum_probs=61.1
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHH---HhCCCc--cccchHHHHHH-HhCCCCCcHHHHHHHHcCCCCCccccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQR---DFGIYL--CNMFDTGQASR-VLKLERNSLEYLLHHFCGVNANKEYQNAD 94 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~r---d~GI~p--~nvFDTqIAA~-LLg~~~~sLa~LVe~~LGv~LdK~~q~SD 94 (649)
..|..++.+. ..|.|++.+|+.+|.+ .+|+.+ ...+||.-.++ ++...+++|+.|++ ++|+.....
T Consensus 139 ~~f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~~-~lgi~~~~~----- 210 (257)
T PRK08517 139 EEFRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKE-LLGIEIEVH----- 210 (257)
T ss_pred HHHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHHH-HcCcCCCCC-----
Confidence 4566777653 5789999999988854 445432 35788875444 44445789999987 567765321
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006352 95 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 127 (649)
Q Consensus 95 W~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~ 127 (649)
.-|..||.++..|+..+..++.
T Consensus 211 -----------HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 211 -----------HRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred -----------CChHHHHHHHHHHHHHHHHHhH
Confidence 2367899999999988877664
No 51
>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=87.04 E-value=6.1 Score=39.18 Aligned_cols=77 Identities=18% Similarity=0.115 Sum_probs=52.5
Q ss_pred ceEEEEechhhHHHHHH---HhCCC-----ccccchHHHHHHHhCCCCCcHHHHHHHHcCCCCCcccccccCCCCCCCHH
Q 006352 32 KKKVMHGADRDIVWLQR---DFGIY-----LCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDE 103 (649)
Q Consensus 32 I~KV~H~ak~DL~~L~r---d~GI~-----p~nvFDTqIAA~LLg~~~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~e 103 (649)
..-|+|++.+|+..|++ .+|+. +..++||...++.+.+ ...|..++.+ +|+.++..
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~-~~~L~~l~~~-~gi~~~~~-------------- 166 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG-QTVLAKACQA-AGIEFDNK-------------- 166 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC-CCcHHHHHHH-CCCCCCCC--------------
Confidence 46799999999988864 35551 2357999877766543 4678888876 47654210
Q ss_pred HHHHHHHhHHHHHHHHHHHHH
Q 006352 104 MLRYAREDTHYLLYIYDIMKI 124 (649)
Q Consensus 104 Ql~YAA~DV~yLl~Lyd~L~~ 124 (649)
...-|..||..+..|+..|.+
T Consensus 167 ~~H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 167 EAHSALYDTQKTAELFCKIVN 187 (189)
T ss_pred CCcChHHHHHHHHHHHHHHHH
Confidence 113367889988888877654
No 52
>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=86.94 E-value=1.7 Score=41.92 Aligned_cols=82 Identities=21% Similarity=0.125 Sum_probs=52.5
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHH---HHHHhCC---CCCcHHHHHHHHcCCCCCccccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQ---ASRVLKL---ERNSLEYLLHHFCGVNANKEYQNAD 94 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqI---AA~LLg~---~~~sLa~LVe~~LGv~LdK~~q~SD 94 (649)
+.|..++.+ .+-|+|++.+|+.+|... ..+.++.||.. +.+..+. ..++|..|+++|++..+...++.
T Consensus 69 ~~l~~~l~~--~vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~-- 142 (157)
T cd06149 69 KEILKILKG--KVVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQG-- 142 (157)
T ss_pred HHHHHHcCC--CEEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCC--
Confidence 456677754 467999999999999432 22335778753 2222222 25899999999997766432211
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHH
Q 006352 95 WRVRPLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 95 W~~RPLS~eQl~YAA~DV~yLl~Ly 119 (649)
.-|..||.+...||
T Consensus 143 -----------H~Al~DA~at~~l~ 156 (157)
T cd06149 143 -----------HSSVEDARATMELY 156 (157)
T ss_pred -----------cCcHHHHHHHHHHh
Confidence 12456777777766
No 53
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=86.00 E-value=4.3 Score=37.97 Aligned_cols=89 Identities=22% Similarity=0.246 Sum_probs=60.3
Q ss_pred HHHHHhhcCCCceEEEEec-hhhHHHHHHH---hCCCc---cccchHHHHHHHhCCC-CCcHHHHHHHHcCCCCCccccc
Q 006352 21 PYLREVFKDPTKKKVMHGA-DRDIVWLQRD---FGIYL---CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQN 92 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~a-k~DL~~L~rd---~GI~p---~nvFDTqIAA~LLg~~-~~sLa~LVe~~LGv~LdK~~q~ 92 (649)
..|..++.+. ..|+|++ .+|+.+|.+. +|+.. ...+||+..++.+... ..+|..|++.| |+.....
T Consensus 72 ~~~~~~l~~~--~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~L~~l~~~~-~~~~~~~--- 145 (169)
T smart00479 72 EELLEFLKGK--ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGRKYSLKKLAERL-GLEVIGR--- 145 (169)
T ss_pred HHHHHHhcCC--EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCCCCCHHHHHHHC-CCCCCCC---
Confidence 4567777653 3567777 9999988653 34322 2379998776655433 68999999775 4433210
Q ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006352 93 ADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 127 (649)
Q Consensus 93 SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~ 127 (649)
...|..||..+..|+..|..++.
T Consensus 146 ------------~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 146 ------------AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred ------------CcCcHHHHHHHHHHHHHHHHHhh
Confidence 25688999999999998876653
No 54
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=85.53 E-value=6.1 Score=47.95 Aligned_cols=91 Identities=21% Similarity=0.212 Sum_probs=65.9
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHh---CCCc-cccchHHHHHHHhCC--CCCcHHHHHHHHcCCCCCccccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDF---GIYL-CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNAD 94 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~---GI~p-~nvFDTqIAA~LLg~--~~~sLa~LVe~~LGv~LdK~~q~SD 94 (649)
+.|.+++.+ ...|+|++.+|+..|.+.+ |+.+ .+.+||...++.+-+ ..++|..|++. +|+.....
T Consensus 78 ~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~-lgl~~~~~----- 149 (820)
T PRK07246 78 RHIYDLIED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRE-LNIDLADA----- 149 (820)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHH-cCCCCCCC-----
Confidence 446667765 4579999999999986543 5443 468999877766544 36899999976 67765321
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 95 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 95 W~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
.-|..||..+..|+..|..++...+
T Consensus 150 -----------H~Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 150 -----------HTAIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred -----------CCHHHHHHHHHHHHHHHHHHHhhcC
Confidence 2377899999999999988887644
No 55
>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=85.25 E-value=4.6 Score=40.81 Aligned_cols=91 Identities=21% Similarity=0.316 Sum_probs=59.6
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHhC---CC---ccccchHHHHHHHhC---C-CCCcHHHHHHHHcCCCCCccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDFG---IY---LCNMFDTGQASRVLK---L-ERNSLEYLLHHFCGVNANKEY 90 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~G---I~---p~nvFDTqIAA~LLg---~-~~~sLa~LVe~~LGv~LdK~~ 90 (649)
..|..++.+ -..|+|++.+|+.+|.+.+. .. ...++||...++.+. + ..++|..|+++| |+.....
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 346667655 35689999999999976542 21 235789876555432 1 257899998775 6543200
Q ss_pred ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhc
Q 006352 91 QNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSS 128 (649)
Q Consensus 91 q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e 128 (649)
...=|..||.++..|+..|..++..
T Consensus 155 -------------~~H~Al~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 155 -------------ALHGALADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred -------------ccCCHHHHHHHHHHHHHHHHhcchh
Confidence 1123778999999999988766543
No 56
>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=84.48 E-value=3.2 Score=52.35 Aligned_cols=91 Identities=24% Similarity=0.314 Sum_probs=69.0
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHH---hCCCc--cccchHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~GI~p--~nvFDTqIAA~LLg~--~~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
+.|..++.+ ...|.|++.+|+.+|.+. +|+.+ ..++||+..++.+.+ ..++|..|+.+ +|+.+..
T Consensus 262 ~~f~~fl~~--~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~-lgi~~~~----- 333 (1213)
T TIGR01405 262 EKFKEFFKD--SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKK-LGVDLDD----- 333 (1213)
T ss_pred HHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHH-cCCCCCC-----
Confidence 456777765 356899999999888643 46542 468999988887754 36899999987 4776542
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
...|..||..+..|+..|..++.+.+
T Consensus 334 -----------~HrAl~DA~aTa~I~~~ll~~l~~~~ 359 (1213)
T TIGR01405 334 -----------HHRADYDAEATAKVFKVMVEQLKEKG 359 (1213)
T ss_pred -----------CcCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 25588999999999999998887654
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=84.44 E-value=7 Score=36.37 Aligned_cols=79 Identities=22% Similarity=0.215 Sum_probs=53.7
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHHh---CCC--ccccchHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRDF---GIY--LCNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~---GI~--p~nvFDTqIAA~LLg~--~~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
..|..++.+ ...|+|++.+|+.+|.+.+ |+. ....+||+..+..+-+ ..++|..|++. +|+..+ .
T Consensus 69 ~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~~~-~g~~~~-~---- 140 (156)
T cd06130 69 PEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEH-LGIELN-H---- 140 (156)
T ss_pred HHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHHHH-cCCCcc-C----
Confidence 456777776 4678999999999886543 544 3458999866655433 36899999886 566553 1
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Ly 119 (649)
.-|..||..+..|+
T Consensus 141 ------------H~Al~Da~~ta~l~ 154 (156)
T cd06130 141 ------------HDALEDARACAEIL 154 (156)
T ss_pred ------------cCchHHHHHHHHHH
Confidence 22556777777665
No 58
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=81.41 E-value=10 Score=38.90 Aligned_cols=88 Identities=19% Similarity=0.268 Sum_probs=60.0
Q ss_pred HHHHhhcCCCceEEEEe-chhhHHHHHHH---hCCCc--cccchHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006352 22 YLREVFKDPTKKKVMHG-ADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~-ak~DL~~L~rd---~GI~p--~nvFDTqIAA~LLg~--~~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
.|.+++.+ ...-|+|+ +.+|+..|.+. +|+.. ...+||+-.++.+.+ ..++|..|+..| |+.....
T Consensus 72 ~~~~fi~~-~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~-~~~~~~a---- 145 (232)
T PRK06309 72 KFIEFCGT-DNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVY-GFEENQA---- 145 (232)
T ss_pred HHHHHHcC-CCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHHHHc-CCCCCCC----
Confidence 35556643 34568999 58999888643 44432 368999877776644 358999988776 6554321
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 127 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~ 127 (649)
.-|..||.++..|+..|..++.
T Consensus 146 ------------H~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 146 ------------HRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred ------------CCcHHHHHHHHHHHHHHHHHHH
Confidence 2377899999999988776653
No 59
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=80.78 E-value=14 Score=39.56 Aligned_cols=88 Identities=17% Similarity=0.183 Sum_probs=59.7
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHH---hCCCc--cccchHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~GI~p--~nvFDTqIAA~LLg~--~~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
..|.+++.+ -.-|.|++.+|+.+|.+. +++.. ...+||+..++.+-+ ..++|..|+++| |+..+
T Consensus 72 ~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~~-gi~~~------ 142 (309)
T PRK06195 72 EKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFL-GYEFK------ 142 (309)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHHc-CCCCc------
Confidence 345666654 457899999999888543 44433 358999866654433 368999998874 54321
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhc
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSS 128 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e 128 (649)
..-|..||..+..|+..|..++..
T Consensus 143 -----------~H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 143 -----------HHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred -----------ccCCHHHHHHHHHHHHHHHHHhcc
Confidence 144778999999998887776653
No 60
>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=80.72 E-value=12 Score=45.38 Aligned_cols=91 Identities=16% Similarity=0.193 Sum_probs=65.0
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHH---hCCC--ccccchHHHHHHHhCCC--CCcHHHHHHHHcCCCCCcccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIY--LCNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~GI~--p~nvFDTqIAA~LLg~~--~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
..|.+++.+ ...|+|++.+|+.+|.+. +|+. +...+||...++.+-+. .++|..|+++ +|+..+..
T Consensus 72 ~~l~~~l~~--~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~-~gi~~~~~---- 144 (850)
T TIGR01407 72 QEIYDLLED--GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEA-LGLTHENP---- 144 (850)
T ss_pred HHHHHHhCC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHH-CCCCCCCC----
Confidence 346667754 347999999999988653 4554 35689998777766443 6899999877 57665322
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
.-|..||.++..|+..|..++.+..
T Consensus 145 ------------H~Al~DA~ata~l~~~l~~~~~~l~ 169 (850)
T TIGR01407 145 ------------HRADSDAQATAELLLLLFEKMEKLP 169 (850)
T ss_pred ------------CChHHHHHHHHHHHHHHHHHHHhcC
Confidence 2367889999999888888877543
No 61
>PRK07883 hypothetical protein; Validated
Probab=79.35 E-value=14 Score=43.11 Aligned_cols=90 Identities=20% Similarity=0.177 Sum_probs=63.5
Q ss_pred HHHHhhcCCCceEEEEechhhHHHHHHH---hCCCc--cccchHHHHHH-HhC---CCCCcHHHHHHHHcCCCCCccccc
Q 006352 22 YLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASR-VLK---LERNSLEYLLHHFCGVNANKEYQN 92 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~GI~p--~nvFDTqIAA~-LLg---~~~~sLa~LVe~~LGv~LdK~~q~ 92 (649)
.|..++.+ ..-|.|++.+|+.+|... +|+.. ...+||+.-++ ++. ...++|..|++ ++|+....
T Consensus 88 ~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~-~~gi~~~~---- 160 (557)
T PRK07883 88 AFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLAR-LFGATTTP---- 160 (557)
T ss_pred HHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHH-HCCcccCC----
Confidence 45666764 356899999999888653 45543 35899986554 343 23689999986 57876532
Q ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 93 ADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 93 SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
..-|..||.++..|+..|..++.+.+
T Consensus 161 ------------~H~Al~DA~ata~l~~~l~~~~~~~~ 186 (557)
T PRK07883 161 ------------THRALDDARATVDVLHGLIERLGNLG 186 (557)
T ss_pred ------------CCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 13478899999999999888886544
No 62
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=78.54 E-value=3.4 Score=43.88 Aligned_cols=88 Identities=17% Similarity=0.226 Sum_probs=61.6
Q ss_pred HHHhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHh---CC-CCCcHHHHHHHHcCCCCCcccccccCCCC
Q 006352 23 LREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVL---KL-ERNSLEYLLHHFCGVNANKEYQNADWRVR 98 (649)
Q Consensus 23 Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LL---g~-~~~sLa~LVe~~LGv~LdK~~q~SDW~~R 98 (649)
...||.. -+.|+|+...|+..|+..+- -.-+-||.----|. .. ...||..|.+.+||+++.-++..
T Consensus 178 v~klL~g--RIlVGHaLhnDl~~L~l~hp--~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHs------ 247 (280)
T KOG2249|consen 178 VLKLLKG--RILVGHALHNDLQALKLEHP--RSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHS------ 247 (280)
T ss_pred HHHHHhC--CEEeccccccHHHHHhhhCc--hhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccccC------
Confidence 4456654 45699999999999964442 12356776433232 22 26899999999999998655533
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHHHHHHhcC
Q 006352 99 PLPDEMLRYAREDTHYLLYIYDIMKIKLSSM 129 (649)
Q Consensus 99 PLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~ 129 (649)
..+||.....||.....+.++.
T Consensus 248 ---------SvEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 248 ---------SVEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred ---------cHHHHHHHHHHHHHHHHHHHHH
Confidence 2479999999999887766643
No 63
>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=77.30 E-value=1.5 Score=41.41 Aligned_cols=97 Identities=20% Similarity=0.303 Sum_probs=55.3
Q ss_pred HhhcCCCceEEEEechhhHHHHHHHh---CCC-ccccchHHHHHHHhCCCCCcHHHHHHHHcCCCCCcc----cc----c
Q 006352 25 EVFKDPTKKKVMHGADRDIVWLQRDF---GIY-LCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKE----YQ----N 92 (649)
Q Consensus 25 ~lLeDp~I~KV~H~ak~DL~~L~rd~---GI~-p~nvFDTqIAA~LLg~~~~sLa~LVe~~LGv~LdK~----~q----~ 92 (649)
.++.........|+..+|+.+|.+.+ ++. +.+.+|++..++-....+++|..|... +|+.-... .. -
T Consensus 52 ~~l~~~~~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~~~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~ 130 (164)
T PF13482_consen 52 ELLDEADNIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFLESYSLKNVEKF-LGIERRDDDISGSESVKLY 130 (164)
T ss_dssp HHHHTT--EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TTSCCTT--SHHH------------HHHHHHHHH
T ss_pred HHHhcCCeEEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhccCCCCCHHHHhhh-cccccccCCCCHHHHHHHH
Confidence 45666666666677789999987765 333 457899998776444456788887766 66655311 10 0
Q ss_pred ccCCC---CCCCHHHHHHHHHhHHHHHHHHHHH
Q 006352 93 ADWRV---RPLPDEMLRYAREDTHYLLYIYDIM 122 (649)
Q Consensus 93 SDW~~---RPLS~eQl~YAA~DV~yLl~Lyd~L 122 (649)
..|.. ...-+..+.|...||..+..|++.|
T Consensus 131 ~~~~~~~~~~~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 131 KEYLETGDPEALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp H---TTGGTS--HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 11211 2345889999999999999999876
No 64
>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=77.15 E-value=11 Score=37.12 Aligned_cols=98 Identities=21% Similarity=0.297 Sum_probs=63.2
Q ss_pred HHHHHhhcC--CCceEEEEec-hhhHHHHHH---HhCCCc-----------------------c-ccchHHHHHHH-hCC
Q 006352 21 PYLREVFKD--PTKKKVMHGA-DRDIVWLQR---DFGIYL-----------------------C-NMFDTGQASRV-LKL 69 (649)
Q Consensus 21 ~~Lk~lLeD--p~I~KV~H~a-k~DL~~L~r---d~GI~p-----------------------~-nvFDTqIAA~L-Lg~ 69 (649)
..|..++.+ |.+ -|+|+. .+|+..|.. .+|+.+ + .++|+...++- ...
T Consensus 68 ~~f~~~i~~~dpdi-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~l 146 (199)
T cd05160 68 KRFFDIIREYDPDI-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFKL 146 (199)
T ss_pred HHHHHHHHhcCCCE-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcCc
Confidence 445666654 554 689999 789977754 345544 1 26898876664 334
Q ss_pred CCCcHHHHHHHHcCCCCCc--ccccccCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006352 70 ERNSLEYLLHHFCGVNANK--EYQNADWRVRPLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 70 ~~~sLa~LVe~~LGv~LdK--~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Ly 119 (649)
..++|..+++++++..-.. .....+|....--...++|...||...+.|+
T Consensus 147 ~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 147 KSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred ccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 5799999999999864321 1122222111122568999999999998875
No 65
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=76.94 E-value=17 Score=40.50 Aligned_cols=96 Identities=19% Similarity=0.237 Sum_probs=60.7
Q ss_pred hHHHHHhhcCCCceEEEEechhhHHHHHHHh------------------------------C-CCc-cccchHHHHHHHh
Q 006352 20 GPYLREVFKDPTKKKVMHGADRDIVWLQRDF------------------------------G-IYL-CNMFDTGQASRVL 67 (649)
Q Consensus 20 ~~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~------------------------------G-I~p-~nvFDTqIAA~LL 67 (649)
.+.|..++.+ .+.|+|++.+|+.+|...+ | +.. ..++||...++.+
T Consensus 116 l~el~~fL~g--~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl 193 (377)
T PRK05601 116 LKPLDRLIDG--RTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQ 193 (377)
T ss_pred HHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHH
Confidence 3456777765 3578999999999886543 1 122 3489999888877
Q ss_pred CCC--CCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 006352 68 KLE--RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIM 122 (649)
Q Consensus 68 g~~--~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L 122 (649)
.+. .+.|..|+++ +|+..+-. ..+.- .+-.+..++ +..|+..|..||..+
T Consensus 194 ~p~l~~~rL~~La~~-lGi~~p~~-~A~~~-Ra~~p~~~l--~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 194 GVALDDIRIRGVAHT-LGLDAPAA-EASVE-RAQVPHRQL--CREETLLVARLYFAL 245 (377)
T ss_pred cCCCCCCCHHHHHHH-hCCCCCch-hhhhh-hhcCChhhh--hhHHHHHHHHHHHHh
Confidence 653 6999999987 57765311 00000 011112222 446999999998765
No 66
>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=76.90 E-value=8.1 Score=37.86 Aligned_cols=79 Identities=23% Similarity=0.212 Sum_probs=53.8
Q ss_pred HHHHhhcC--CCceEEEEec-hhhHHHHHHH---hCCCc---cccchHHHHHHHhCCCCCcHHHHHHHHcCCCCCccccc
Q 006352 22 YLREVFKD--PTKKKVMHGA-DRDIVWLQRD---FGIYL---CNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQN 92 (649)
Q Consensus 22 ~Lk~lLeD--p~I~KV~H~a-k~DL~~L~rd---~GI~p---~nvFDTqIAA~LLg~~~~sLa~LVe~~LGv~LdK~~q~ 92 (649)
.|..++.. ....-|+|++ .+|+..|.+. +|+.+ ..++||...++.+.+ +|..|+.+++|+.....
T Consensus 87 ~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~---~L~~l~~~~~~~~~~~~--- 160 (177)
T cd06136 87 LIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ---SLGSLYKRLFGQEPKNS--- 160 (177)
T ss_pred HHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh---hHHHHHHHHhCCCcccc---
Confidence 35555543 2356899998 8999888653 35443 235799877776554 89999998888776422
Q ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006352 93 ADWRVRPLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 93 SDW~~RPLS~eQl~YAA~DV~yLl~Ly 119 (649)
.-|..||..+..++
T Consensus 161 -------------H~A~~Da~at~~v~ 174 (177)
T cd06136 161 -------------HTAEGDVLALLKCA 174 (177)
T ss_pred -------------cchHHHHHHHHHHH
Confidence 33677888877665
No 67
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=76.54 E-value=19 Score=44.39 Aligned_cols=91 Identities=23% Similarity=0.328 Sum_probs=64.7
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHH---hCCCc--cccchHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 93 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~GI~p--~nvFDTqIAA~LLg~--~~~sLa~LVe~~LGv~LdK~~q~S 93 (649)
+.|..++.+ ...|.|++.+|+.+|.+. .|+.+ ...+||.-.++.+-+ ..++|..|++. +|+..+..
T Consensus 76 ~~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~-l~i~~~~~---- 148 (928)
T PRK08074 76 PEIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEE-LGLEHDQP---- 148 (928)
T ss_pred HHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHh-CCCCCCCC----
Confidence 456667764 456999999999998653 45443 468999877776544 36899999887 46654321
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 94 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 94 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
.-|..||.++..|+..|..++.+..
T Consensus 149 ------------H~Al~DA~ata~l~~~l~~~~~~l~ 173 (928)
T PRK08074 149 ------------HRADSDAEVTAELFLQLLNKLERLP 173 (928)
T ss_pred ------------CChHHHHHHHHHHHHHHHHHHHhcC
Confidence 2367789999999998888887543
No 68
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=75.50 E-value=1.4 Score=53.19 Aligned_cols=87 Identities=21% Similarity=0.162 Sum_probs=61.9
Q ss_pred HhhcCCCceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC-CCcHHHHHHHHcCCCCCcccccccCCCCCCCHH
Q 006352 25 EVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDE 103 (649)
Q Consensus 25 ~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~-~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~e 103 (649)
.+|-+-.++-|+|+...|..++ ...+....++||-+. .+++.+ ..+|..|+-++||.++.-+.
T Consensus 1008 ~~Li~~GviFVGHGL~nDFrvI--Ni~Vp~~QiiDTv~l-f~~~s~R~LSLrfLa~~lLg~~IQ~~~------------- 1071 (1118)
T KOG1275|consen 1008 RLLIQRGVIFVGHGLQNDFRVI--NIHVPEEQIIDTVTL-FRLGSQRMLSLRFLAWELLGETIQMEA------------- 1071 (1118)
T ss_pred HHHHHcCcEEEcccccccceEE--EEecChhhheeeeEE-EecccccEEEHHHHHHHHhcchhhccc-------------
Confidence 3667888999999999998776 233333459998643 234444 47999999999998874221
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 104 MLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 104 Ql~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
.-..+||++.+.||+... +|++++
T Consensus 1072 --HDSIeDA~taLkLYk~Yl-~lkeq~ 1095 (1118)
T KOG1275|consen 1072 --HDSIEDARTALKLYKKYL-KLKEQG 1095 (1118)
T ss_pred --cccHHHHHHHHHHHHHHH-HHHHhh
Confidence 114589999999999854 476654
No 69
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=72.82 E-value=7.7 Score=46.89 Aligned_cols=97 Identities=14% Similarity=0.168 Sum_probs=67.2
Q ss_pred ceEEEEechhhHHHHHHHhCCCcc--ccchHHHHH---H-HhC----------------------C------------C-
Q 006352 32 KKKVMHGADRDIVWLQRDFGIYLC--NMFDTGQAS---R-VLK----------------------L------------E- 70 (649)
Q Consensus 32 I~KV~H~ak~DL~~L~rd~GI~p~--nvFDTqIAA---~-LLg----------------------~------------~- 70 (649)
-..|+|+..+|...++..|.|.-. ...|||-.. + ++. + .
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 456999999999999889998754 367988431 1 110 0 0
Q ss_pred CCcHHHHHHHHcCCC-CCcccccccCCCCCCC------HHHHHHHHHhHHHHHHHHHHHHHHHhcC
Q 006352 71 RNSLEYLLHHFCGVN-ANKEYQNADWRVRPLP------DEMLRYAREDTHYLLYIYDIMKIKLSSM 129 (649)
Q Consensus 71 ~~sLa~LVe~~LGv~-LdK~~q~SDW~~RPLS------~eQl~YAA~DV~yLl~Lyd~L~~qL~e~ 129 (649)
-.||.++...+||++ ++|..+ .+|-.-++. .+.+.|+|.||+....+|..+.....+.
T Consensus 322 ~NSL~dVhk~~c~~~~LdKt~R-d~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fler 386 (1075)
T KOG3657|consen 322 LNSLVDVHKFHCGIDALDKTPR-DSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLER 386 (1075)
T ss_pred hHHHHHHHHhhCCCCccccchH-HhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHh
Confidence 146777888899988 887542 233222222 3457899999999999999988776653
No 70
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=67.52 E-value=19 Score=35.76 Aligned_cols=100 Identities=24% Similarity=0.366 Sum_probs=64.9
Q ss_pred HHHHHhhcC--CCceEEEEec-hhhHHHHHHH---hCCCc------------------------cccchHHHHHH-HhCC
Q 006352 21 PYLREVFKD--PTKKKVMHGA-DRDIVWLQRD---FGIYL------------------------CNMFDTGQASR-VLKL 69 (649)
Q Consensus 21 ~~Lk~lLeD--p~I~KV~H~a-k~DL~~L~rd---~GI~p------------------------~nvFDTqIAA~-LLg~ 69 (649)
..|..++.. |.+ -|+|+. .+|+..|..+ +|+.. ...+|+...++ .+..
T Consensus 61 ~~F~~~i~~~dpdi-ivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~l 139 (195)
T cd05780 61 KRFIEIVKEKDPDV-IYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNL 139 (195)
T ss_pred HHHHHHHHHcCCCE-EEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCCC
Confidence 445566654 775 578886 5799777643 34431 12788876655 3555
Q ss_pred CCCcHHHHHHHHcCCCCCcc--ccccc-CCCCCCCHHHHHHHHHhHHHHHHHHHH
Q 006352 70 ERNSLEYLLHHFCGVNANKE--YQNAD-WRVRPLPDEMLRYAREDTHYLLYIYDI 121 (649)
Q Consensus 70 ~~~sLa~LVe~~LGv~LdK~--~q~SD-W~~RPLS~eQl~YAA~DV~yLl~Lyd~ 121 (649)
..++|..+++++||.....- .+... |...+--...++|+..||..++.|...
T Consensus 140 ~sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~ 194 (195)
T cd05780 140 TRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKE 194 (195)
T ss_pred CcCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhh
Confidence 67999999999999863211 11222 333322366899999999999988764
No 71
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=66.54 E-value=32 Score=44.56 Aligned_cols=90 Identities=22% Similarity=0.236 Sum_probs=65.4
Q ss_pred HHHHhhcCCCceEEEEechhhHHHHH---HHhCCC--ccccchHHHHHHHhCCC--CCcHHHHHHHHcCCCCCccccccc
Q 006352 22 YLREVFKDPTKKKVMHGADRDIVWLQ---RDFGIY--LCNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNAD 94 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~ak~DL~~L~---rd~GI~--p~nvFDTqIAA~LLg~~--~~sLa~LVe~~LGv~LdK~~q~SD 94 (649)
.|..++. ....|.|.+.+|+..|. +.+|+. ....+||+..++.+.+. .++|..|+++ +|+.+...
T Consensus 492 ~f~~fig--g~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~-lGL~~~~~----- 563 (1437)
T PRK00448 492 KFKEFCG--DSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKK-FGVELEHH----- 563 (1437)
T ss_pred HHHHHhC--CCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHH-cCCCCCCC-----
Confidence 3444554 35779999999997763 345663 24689999888776543 6899999986 57665421
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006352 95 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 130 (649)
Q Consensus 95 W~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~e~g 130 (649)
.-|..||.++..|+..|..++.+.+
T Consensus 564 -----------HrAl~DA~aTa~lf~~ll~~l~~~g 588 (1437)
T PRK00448 564 -----------HRADYDAEATAYLLIKFLKDLKEKG 588 (1437)
T ss_pred -----------cChHHHHHHHHHHHHHHHHHHHHcC
Confidence 4578899999999999998887554
No 72
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=64.82 E-value=66 Score=33.43 Aligned_cols=86 Identities=17% Similarity=0.074 Sum_probs=55.6
Q ss_pred HHHhhcCCCceEEEEechhhHHHHHHHh----CCCc-cccchHHHHHHHhCC---------------CCCcHHHHHHHHc
Q 006352 23 LREVFKDPTKKKVMHGADRDIVWLQRDF----GIYL-CNMFDTGQASRVLKL---------------ERNSLEYLLHHFC 82 (649)
Q Consensus 23 Lk~lLeDp~I~KV~H~ak~DL~~L~rd~----GI~p-~nvFDTqIAA~LLg~---------------~~~sLa~LVe~~L 82 (649)
|..++.+ -.-|+|++..|+.+|.+.+ +..+ ..++||+..++.+-+ ..+.|..++.+ +
T Consensus 123 l~~~~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~-~ 199 (239)
T PRK09146 123 LLEALAG--KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLR-Y 199 (239)
T ss_pred HHHHhCC--CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHH-c
Confidence 4444443 3568999999999886542 3333 468999876654311 23678888876 4
Q ss_pred CCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006352 83 GVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 127 (649)
Q Consensus 83 Gv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL~ 127 (649)
|+.... ..-|..||..+..|+..+..++-
T Consensus 200 gl~~~~----------------~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 200 GLPAYS----------------PHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred CCCCCC----------------CCCcHHHHHHHHHHHHHHHHHHc
Confidence 554321 13377899999988887776653
No 73
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=60.09 E-value=78 Score=31.51 Aligned_cols=84 Identities=15% Similarity=0.110 Sum_probs=53.2
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHH----hCCCc-cccchHHHHHH-Hh--C-C---CCCcHHHHHHHHcCCCCCc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRD----FGIYL-CNMFDTGQASR-VL--K-L---ERNSLEYLLHHFCGVNANK 88 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd----~GI~p-~nvFDTqIAA~-LL--g-~---~~~sLa~LVe~~LGv~LdK 88 (649)
..|..++.+ ...|+|++.+|+..|.+. ++..+ ...+|+.-..+ .. . + ..++|..+++. +|+....
T Consensus 103 ~~~~~~i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~ 179 (202)
T PRK09145 103 RQLLAFIGN--RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKH-LDLPVLG 179 (202)
T ss_pred HHHHHHHcC--CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHH-cCCCCCC
Confidence 345666664 356899999999888654 34433 35788863321 11 1 1 14799999966 4765532
Q ss_pred ccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006352 89 EYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 123 (649)
Q Consensus 89 ~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 123 (649)
. .-|..||.++..||..|.
T Consensus 180 ~----------------H~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 180 R----------------HDALNDAIMAALIFLRLR 198 (202)
T ss_pred C----------------CCcHHHHHHHHHHHHHHH
Confidence 1 226788998888888764
No 74
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=59.73 E-value=89 Score=31.33 Aligned_cols=88 Identities=14% Similarity=0.124 Sum_probs=55.9
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHH---hCCCc---cccchHHHHHHHh-CC-CCCcHHHHHHHHcCCCCCccccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL---CNMFDTGQASRVL-KL-ERNSLEYLLHHFCGVNANKEYQN 92 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~GI~p---~nvFDTqIAA~LL-g~-~~~sLa~LVe~~LGv~LdK~~q~ 92 (649)
..|..++.+... .|+|.+..|+..|.+. +|+.. ...+|++.....+ +. ..++|..++++ +|+....
T Consensus 84 ~~f~~~~~~~~~-~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~-~gi~~~~---- 157 (207)
T PRK07748 84 EKLAEYDKRCKP-TIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEE-YGKEGTG---- 157 (207)
T ss_pred HHHHHHhCcCCe-EEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHHH-cCCCCCC----
Confidence 457777776333 3456689999888654 35432 3467787655433 32 25899998876 4554321
Q ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006352 93 ADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 125 (649)
Q Consensus 93 SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~q 125 (649)
...-|..||.++..|+..|...
T Consensus 158 -----------~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 158 -----------KHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred -----------CCcChHHHHHHHHHHHHHHHhC
Confidence 1134778999999998887755
No 75
>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=56.18 E-value=33 Score=33.18 Aligned_cols=69 Identities=13% Similarity=0.125 Sum_probs=40.2
Q ss_pred hhhHHHHHHHhCCCccccchHHHHHHHhCCCCCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006352 40 DRDIVWLQRDFGIYLCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 40 k~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Ly 119 (649)
..|+..+...-|+.+.+--|-++.+|||.+.+.....++.+|+| .+|... |+..+.....|+
T Consensus 70 AK~LAv~a~~~G~~v~PGDDPlLlAYLlDPsNt~p~~varRY~~---------~~W~~d---------A~~RA~~t~~L~ 131 (138)
T PF09281_consen 70 AKDLAVHALREGVVVEPGDDPLLLAYLLDPSNTNPEGVARRYLG---------GEWPED---------AATRALATARLL 131 (138)
T ss_dssp HHHHHHHHHHTT----B---HHHHHHHH-TT--SHHHHHHHH-T---------S---SS---------HHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCcccCCCCCcchhhhhcCccCCChHHHHHHhcC---------CCCCcc---------HHHHHHHHHHHH
Confidence 56777766788988888889999999999998899999999988 345322 344555555666
Q ss_pred HHHHHHH
Q 006352 120 DIMKIKL 126 (649)
Q Consensus 120 d~L~~qL 126 (649)
..|..+|
T Consensus 132 ~~L~prL 138 (138)
T PF09281_consen 132 RALPPRL 138 (138)
T ss_dssp HHHHHHT
T ss_pred HHhhhcC
Confidence 6665543
No 76
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=55.93 E-value=84 Score=31.69 Aligned_cols=85 Identities=15% Similarity=0.166 Sum_probs=53.2
Q ss_pred HHHHHhhcCCCceEEEEech-hhHHHHHHHhCCCccc--cchHH---HHHHHh---CCCCCcHHHHHHHHcCCCCCcccc
Q 006352 21 PYLREVFKDPTKKKVMHGAD-RDIVWLQRDFGIYLCN--MFDTG---QASRVL---KLERNSLEYLLHHFCGVNANKEYQ 91 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak-~DL~~L~rd~GI~p~n--vFDTq---IAA~LL---g~~~~sLa~LVe~~LGv~LdK~~q 91 (649)
..|..++.+. ..|+|++. +|+.+| ...|+.+.+ .+||. .+.+.. +...++|..|+++ +|+... .
T Consensus 76 ~~f~~f~~~~--~lVaHNa~~fD~~fL-~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~-~gi~~~-~-- 148 (195)
T PRK07247 76 AAFKEFVGEL--PLIGYNAQKSDLPIL-AENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADF-LGIKGR-G-- 148 (195)
T ss_pred HHHHHHHCCC--eEEEEeCcHhHHHHH-HHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHh-cCCCCC-C--
Confidence 4566777654 46899996 899999 556765443 34543 222221 1235899999875 566531 1
Q ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q 006352 92 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKL 126 (649)
Q Consensus 92 ~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~qL 126 (649)
.-|..||..+..||..|...-
T Consensus 149 --------------HrAl~DA~~ta~v~~~ll~~~ 169 (195)
T PRK07247 149 --------------HNSLEDARMTARVYESFLESD 169 (195)
T ss_pred --------------cCCHHHHHHHHHHHHHHHhhc
Confidence 226678999988888765433
No 77
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=54.72 E-value=65 Score=33.08 Aligned_cols=78 Identities=17% Similarity=-0.054 Sum_probs=52.2
Q ss_pred CceEEEEechhhHHHHHHHhCCCccccchHHHHHHHhCCC-CCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHH
Q 006352 31 TKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAR 109 (649)
Q Consensus 31 ~I~KV~H~ak~DL~~L~rd~GI~p~nvFDTqIAA~LLg~~-~~sLa~LVe~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA 109 (649)
.-.-|+|++.+|+..|. .+ ....+||.-.++.+-+. .+++..|+.. +|+..+... . ....-|.
T Consensus 74 ~~~lVaHNa~FD~~~L~-~~---~~~~idTl~lar~l~p~~~~~l~~L~~~-~~l~~~~~~-~----------~~aHrAl 137 (219)
T PRK07983 74 SEWYVAHNASFDRRVLP-EM---PGEWICTMKLARRLWPGIKYSNMALYKS-RKLNVQTPP-G----------LHHHRAL 137 (219)
T ss_pred CCEEEEeCcHhhHHHHh-Cc---CCCcEeHHHHHHHHccCCCCCHHHHHHH-cCCCCCCCC-C----------CCCCcHH
Confidence 34679999999999983 22 34689999888766553 5888888765 565432100 0 0124478
Q ss_pred HhHHHHHHHHHHHHH
Q 006352 110 EDTHYLLYIYDIMKI 124 (649)
Q Consensus 110 ~DV~yLl~Lyd~L~~ 124 (649)
.||..+..|+..|..
T Consensus 138 ~Da~ata~ll~~l~~ 152 (219)
T PRK07983 138 YDCYITAALLIDIMN 152 (219)
T ss_pred HHHHHHHHHHHHHHH
Confidence 899999888877653
No 78
>PRK11779 sbcB exonuclease I; Provisional
Probab=46.35 E-value=1.3e+02 Score=34.69 Aligned_cols=87 Identities=18% Similarity=0.123 Sum_probs=51.0
Q ss_pred HHHHhhcCCCceEEEEe-chhhHHHHHHHhCCC--------------ccccchHHHHHHHhC------------CCCCcH
Q 006352 22 YLREVFKDPTKKKVMHG-ADRDIVWLQRDFGIY--------------LCNMFDTGQASRVLK------------LERNSL 74 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~-ak~DL~~L~rd~GI~--------------p~nvFDTqIAA~LLg------------~~~~sL 74 (649)
.+..+|..+..+.|+|+ ..+|..+|+..+... ...++|+.-+++.+. ...+.|
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 45556654555678996 689998875543111 012345555555432 234889
Q ss_pred HHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006352 75 EYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 125 (649)
Q Consensus 75 a~LVe~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~q 125 (649)
+.|+.++ |+..... .-|..||..+..|+..|..+
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 9998875 6554211 22566777777777766644
No 79
>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=44.13 E-value=1.7e+02 Score=27.62 Aligned_cols=86 Identities=16% Similarity=0.162 Sum_probs=52.7
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHH---HhCC-----CccccchHHHHHH-HhCC-CCCcHHHHHHHHcCCCCCccc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQR---DFGI-----YLCNMFDTGQASR-VLKL-ERNSLEYLLHHFCGVNANKEY 90 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~r---d~GI-----~p~nvFDTqIAA~-LLg~-~~~sLa~LVe~~LGv~LdK~~ 90 (649)
..|..++.+..-..+.|....|...+.. .++. .....+|++..+. +.+. ..++|..++.. +|+....
T Consensus 80 ~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~-- 156 (176)
T cd06133 80 KEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEY-LGLEFEG-- 156 (176)
T ss_pred HHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHH-CCCCCCC--
Confidence 4566788764113455666888755433 3333 2346899986555 4444 36899999865 5766541
Q ss_pred ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 006352 91 QNADWRVRPLPDEMLRYAREDTHYLLYIYDIM 122 (649)
Q Consensus 91 q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L 122 (649)
+..-|..||.++..|+..|
T Consensus 157 -------------~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 157 -------------RHHRGLDDARNIARILKRL 175 (176)
T ss_pred -------------CCcCcHHHHHHHHHHHHHh
Confidence 1134677899888887764
No 80
>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=38.01 E-value=1.3e+02 Score=29.61 Aligned_cols=80 Identities=19% Similarity=0.129 Sum_probs=46.3
Q ss_pred HHHHhhcCCCceEEEEe-chhhHHHHHHHh---CCCc--------cccchHHHHHHH---hCC------------CCCcH
Q 006352 22 YLREVFKDPTKKKVMHG-ADRDIVWLQRDF---GIYL--------CNMFDTGQASRV---LKL------------ERNSL 74 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~-ak~DL~~L~rd~---GI~p--------~nvFDTqIAA~L---Lg~------------~~~sL 74 (649)
.|..++..+...-|+|+ +.+|+..|.+.+ ++.+ ...+||.-.+++ +.+ ..++|
T Consensus 75 ~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L 154 (183)
T cd06138 75 KIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKL 154 (183)
T ss_pred HHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhH
Confidence 45566654444568886 799999886543 3321 124677644433 211 24779
Q ss_pred HHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHH
Q 006352 75 EYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYI 118 (649)
Q Consensus 75 a~LVe~~LGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~L 118 (649)
..|+++ +|+... +..-|..||..+..|
T Consensus 155 ~~l~~~-~gi~~~----------------~~H~Al~Da~~ta~l 181 (183)
T cd06138 155 EDLAQA-NGIEHS----------------NAHDALSDVEATIAL 181 (183)
T ss_pred HHHHHH-CCCCcc----------------ccccHHHHHHHHHHH
Confidence 999876 566542 124466777766554
No 81
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=37.20 E-value=2.5e+02 Score=28.39 Aligned_cols=88 Identities=22% Similarity=0.226 Sum_probs=60.3
Q ss_pred HHHHhhcCCCceEEEEechhhHHHHHHHh---CCCc--cccchHHHHHHHhCCC--CCcHHHHHHHHcCCCCCccccccc
Q 006352 22 YLREVFKDPTKKKVMHGADRDIVWLQRDF---GIYL--CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNAD 94 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~---GI~p--~nvFDTqIAA~LLg~~--~~sLa~LVe~~LGv~LdK~~q~SD 94 (649)
.+..++.+. -.-|.|++..|+..|...+ +..+ ..+.||...++...++ ..+|..|+. .+|+... ....
T Consensus 87 ~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~-~~~~-- 161 (243)
T COG0847 87 EFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRN-PFHP-- 161 (243)
T ss_pred HHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHH-HcCCCcC-CcCC--
Confidence 345566553 4679999999998885433 3332 4578998777765554 689999998 6787743 1111
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006352 95 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 125 (649)
Q Consensus 95 W~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~q 125 (649)
.-|..|+..+..+|..+...
T Consensus 162 -----------H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 162 -----------HRALFDALALAELFLLLQTG 181 (243)
T ss_pred -----------cchHHHHHHHHHHHHHHHhc
Confidence 23778999999988887764
No 82
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=35.21 E-value=49 Score=30.73 Aligned_cols=46 Identities=24% Similarity=0.412 Sum_probs=37.1
Q ss_pred cChHHHHHHHHhCCCCHHHHHhhhcCC-hhHHHHhHHHHHHHHHHHH
Q 006352 206 LPNRTLIEIAKQLPTTAAKLRRLLKSK-HSYIERYMGPVLSIIKNSM 251 (649)
Q Consensus 206 LsD~~LleIA~~~P~S~~eL~~i~g~~-~~~vrryGdeIL~iI~~al 251 (649)
|+....+.||--+|.|.++++.+...- ........++||++|..++
T Consensus 65 l~e~~a~~I~nL~P~~~dElrai~~~~~~~~~~e~l~~ILd~l~k~~ 111 (112)
T PRK14981 65 MKEKTAVKIADILPETRDELRAIFAKERYTLSPEELDEILDIVKKYR 111 (112)
T ss_pred CCHHHHHHHHhcCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHhh
Confidence 588889999999999999999986443 2334678899999998764
No 83
>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=33.49 E-value=63 Score=32.52 Aligned_cols=96 Identities=23% Similarity=0.273 Sum_probs=58.2
Q ss_pred HHHHhhc--CCCceEEEEec-hhhHHHHHHH---hCCCc-------------------------c-ccchHHHHHH--Hh
Q 006352 22 YLREVFK--DPTKKKVMHGA-DRDIVWLQRD---FGIYL-------------------------C-NMFDTGQASR--VL 67 (649)
Q Consensus 22 ~Lk~lLe--Dp~I~KV~H~a-k~DL~~L~rd---~GI~p-------------------------~-nvFDTqIAA~--LL 67 (649)
.|..++. ||.| -++|+. .+|+..|..+ +|+.+ + -++|+....+ .+
T Consensus 57 ~f~~~i~~~dPDv-i~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~ 135 (193)
T cd05784 57 ALIAWFAQYDPDI-IIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATY 135 (193)
T ss_pred HHHHHHHhhCCCE-EEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccC
Confidence 3444553 4564 467776 5688776543 34432 0 1678765443 24
Q ss_pred CCCCCcHHHHHHHHcCCCCCc-cc-----cc-ccCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 006352 68 KLERNSLEYLLHHFCGVNANK-EY-----QN-ADWRVRPLPDEMLRYAREDTHYLLYIYD 120 (649)
Q Consensus 68 g~~~~sLa~LVe~~LGv~LdK-~~-----q~-SDW~~RPLS~eQl~YAA~DV~yLl~Lyd 120 (649)
...+++|..+++++||..-.. .. .. .-|...+ ...++|+..||...++|++
T Consensus 136 kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 136 HFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred CCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 455799999999999964221 10 01 1133333 5689999999999998863
No 84
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=32.04 E-value=1.2e+02 Score=27.57 Aligned_cols=45 Identities=24% Similarity=0.440 Sum_probs=33.7
Q ss_pred cChHHHHHHHHhCCCCHHHHHhhhcCCh-hHHHHhHHHHHHHHHHH
Q 006352 206 LPNRTLIEIAKQLPTTAAKLRRLLKSKH-SYIERYMGPVLSIIKNS 250 (649)
Q Consensus 206 LsD~~LleIA~~~P~S~~eL~~i~g~~~-~~vrryGdeIL~iI~~a 250 (649)
|....++.|+-.+|++..++..|..... ++-....+.||++|...
T Consensus 71 L~~~E~~qi~Nl~P~~~~El~~ii~~~~~r~~ee~l~~iL~~v~~~ 116 (117)
T PF03874_consen 71 LTEFEILQIINLRPTTAVELRAIIESLESRFSEEDLEEILDLVSKY 116 (117)
T ss_dssp S-HHHHHHHHHH--SSHHHHHHHSTTGTTTSTHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHhcCCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHh
Confidence 8999999999999999999999865443 33456788888888764
No 85
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=31.27 E-value=90 Score=29.42 Aligned_cols=50 Identities=8% Similarity=0.143 Sum_probs=35.7
Q ss_pred CCHHHHHhhhcCChhHHHHhHHHHHHHHHH----HHhccccHHHHHHHHHHHhH
Q 006352 220 TTAAKLRRLLKSKHSYIERYMGPVLSIIKN----SMQNAANFEVIAQKLKEERM 269 (649)
Q Consensus 220 ~S~~eL~~i~g~~~~~vrryGdeIL~iI~~----ale~~~~~e~~~~~~k~~~~ 269 (649)
-++.++.+..|+..+.++.+.+.|++.|.- ..........+++++.+|.+
T Consensus 50 GnlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~GeI 103 (113)
T PF09862_consen 50 GNLKEMEKELGISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGEI 103 (113)
T ss_pred CCHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCCC
Confidence 567777778888899999999999988865 23333445566677776643
No 86
>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=30.54 E-value=1.9e+02 Score=29.39 Aligned_cols=97 Identities=19% Similarity=0.192 Sum_probs=60.0
Q ss_pred HHHHHhhcCCCceEEEEec-hhhHHHHHHH---hCCCcc------------------ccchHHHHHHHhCC-CCCcHHHH
Q 006352 21 PYLREVFKDPTKKKVMHGA-DRDIVWLQRD---FGIYLC------------------NMFDTGQASRVLKL-ERNSLEYL 77 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~a-k~DL~~L~rd---~GI~p~------------------nvFDTqIAA~LLg~-~~~sLa~L 77 (649)
..|..++.+-.-.-|+|+. .+|+..|..+ +|+.+. ..+|++......+. ..++|..+
T Consensus 83 ~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~L~~v 162 (208)
T cd05782 83 EDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARARASLDLL 162 (208)
T ss_pred HHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCccCCCCHHHH
Confidence 4566666642224578877 8899887653 455311 16788876554433 46899988
Q ss_pred HHHHcCCCCCccc----c-cccCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 006352 78 LHHFCGVNANKEY----Q-NADWRVRPLPDEMLRYAREDTHYLLYIYD 120 (649)
Q Consensus 78 Ve~~LGv~LdK~~----q-~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd 120 (649)
++ +||+. .|.. + ..-|..-.+ ....+|+..||..+..||-
T Consensus 163 a~-~lG~~-~K~d~~G~~v~~~y~~g~~-~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 163 AK-LLGIP-GKMDVDGSQVWELYAEGKL-DEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred HH-HhCCC-CCcCCCHHHHHHHHHcCCh-HHHHHHHHHHHHHHHHHHh
Confidence 75 67773 2311 1 122444333 6688999999999888873
No 87
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=30.11 E-value=2.8e+02 Score=29.85 Aligned_cols=82 Identities=17% Similarity=0.082 Sum_probs=50.1
Q ss_pred HHHHhhcCCCceEEEEechhhHHHHHHHhCCCc-cccchHHHHHHH--hCCCCCcHHHHHHHHcCCCCCcccccccCCCC
Q 006352 22 YLREVFKDPTKKKVMHGADRDIVWLQRDFGIYL-CNMFDTGQASRV--LKLERNSLEYLLHHFCGVNANKEYQNADWRVR 98 (649)
Q Consensus 22 ~Lk~lLeDp~I~KV~H~ak~DL~~L~rd~GI~p-~nvFDTqIAA~L--Lg~~~~sLa~LVe~~LGv~LdK~~q~SDW~~R 98 (649)
.+..++.+. -.-|.|++.+|+.+|.+.+.-.. ....+++..... .+...++|..|+.+| |.. |
T Consensus 113 ~l~~fl~~~-~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~~~-g~~---------~--- 178 (294)
T PRK09182 113 AVDALIAPA-DLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLAGQA-GFF---------H--- 178 (294)
T ss_pred HHHHHhcCC-CEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHHHHc-CCC---------C---
Confidence 466677653 35689999999999965432111 234555533222 233468999999864 421 1
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHH
Q 006352 99 PLPDEMLRYAREDTHYLLYIYDIM 122 (649)
Q Consensus 99 PLS~eQl~YAA~DV~yLl~Lyd~L 122 (649)
...-|..||.++..|+..+
T Consensus 179 -----~aHrAl~Da~Ata~ll~~~ 197 (294)
T PRK09182 179 -----EGHRAVDDCQALLELLARP 197 (294)
T ss_pred -----CCcChHHHHHHHHHHHHHH
Confidence 1133778999998876643
No 88
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.23 E-value=79 Score=29.89 Aligned_cols=47 Identities=19% Similarity=0.398 Sum_probs=37.1
Q ss_pred cChHHHHHHHHhCCCCHHHHHhhhcCC-hhHHHHhHHHHHHHHHHHHh
Q 006352 206 LPNRTLIEIAKQLPTTAAKLRRLLKSK-HSYIERYMGPVLSIIKNSMQ 252 (649)
Q Consensus 206 LsD~~LleIA~~~P~S~~eL~~i~g~~-~~~vrryGdeIL~iI~~ale 252 (649)
++......||--+|+|.++|+.|.-.- ........+.|+++|..++.
T Consensus 66 ~~e~~avkIadI~P~t~~ElRsIla~e~~~~s~E~l~~Ildiv~Ky~~ 113 (114)
T COG1460 66 MSEKIAVKIADIMPRTPDELRSILAKERVMLSDEELDKILDIVDKYRE 113 (114)
T ss_pred ccHHHHHHHHHhCCCCHHHHHHHHHHccCCCCHHHHHHHHHHHHHHhc
Confidence 688899999999999999999885322 22245688999999988764
No 89
>COG2906 Bfd Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]
Probab=28.19 E-value=1.6e+02 Score=25.26 Aligned_cols=42 Identities=24% Similarity=0.187 Sum_probs=32.2
Q ss_pred cChHHHHHHHHhCCCCHHHHHhhhcCCh--hHHHHhHHHHHHHH
Q 006352 206 LPNRTLIEIAKQLPTTAAKLRRLLKSKH--SYIERYMGPVLSII 247 (649)
Q Consensus 206 LsD~~LleIA~~~P~S~~eL~~i~g~~~--~~vrryGdeIL~iI 247 (649)
++|+.|.+.+..-|+|.++|.+..|.+. ..-.+...+||.-.
T Consensus 9 VtD~~Ir~av~~g~tt~~el~~~~gvGs~CGkC~~~Arevl~e~ 52 (63)
T COG2906 9 VTDKQIREAVAQGATTLKELRRFTGVGSQCGKCVRAAREVLEEA 52 (63)
T ss_pred ccHHHHHHHHHHcCCCHHHHHHHcCcccchHHHHHHHHHHHHHH
Confidence 5799999999999999999999988775 33445555555433
No 90
>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=27.12 E-value=94 Score=31.74 Aligned_cols=67 Identities=24% Similarity=0.240 Sum_probs=43.3
Q ss_pred cchHHHHHH-HhCCCCCcHHHHHHHHcCCCCCc-c-ccccc-CCCCCCC-HHHHHHHHHhHHHHHHHHHHHH
Q 006352 57 MFDTGQASR-VLKLERNSLEYLLHHFCGVNANK-E-YQNAD-WRVRPLP-DEMLRYAREDTHYLLYIYDIMK 123 (649)
Q Consensus 57 vFDTqIAA~-LLg~~~~sLa~LVe~~LGv~LdK-~-~q~SD-W~~RPLS-~eQl~YAA~DV~yLl~Lyd~L~ 123 (649)
++|+...+. ......++|..+++++||..... . ..... |...|-. ...++|+..||...+.|+..|.
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 346655443 23345799999999999965321 1 12222 3333321 4579999999999999988765
No 91
>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=25.20 E-value=1.5e+02 Score=32.87 Aligned_cols=42 Identities=10% Similarity=-0.046 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHcCCCCccccChHHHHHHHHh
Q 006352 176 LNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQ 217 (649)
Q Consensus 176 L~~~qlaVL~aL~~WRe~iAR~~D~Pp~~VLsD~~LleIA~~ 217 (649)
..+....+++.|..+...+|.+.|+|+..|++.+.|..|+..
T Consensus 295 ~~~~~~~~~~~l~~~~~~~a~~~~i~~~~l~~~~~l~~l~~~ 336 (367)
T TIGR01388 295 PPPGYKALFKLLKVLVKDVSETLGLASELLASRRQLEQLLAW 336 (367)
T ss_pred CChhHHHHHHHHHHHHHHHHHHhCCCHHHcCCHHHHHHHHHh
Confidence 345667899999999999999999999999999999999975
No 92
>PRK06722 exonuclease; Provisional
Probab=25.07 E-value=3.4e+02 Score=29.27 Aligned_cols=85 Identities=12% Similarity=0.045 Sum_probs=51.4
Q ss_pred HHHHHhhcCCCceEEEEechhhHHHHHHH---hCCCcc-----ccchHHHHHH-HhC---CCCCcHHHHHHHHcCCCCCc
Q 006352 21 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYLC-----NMFDTGQASR-VLK---LERNSLEYLLHHFCGVNANK 88 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~ak~DL~~L~rd---~GI~p~-----nvFDTqIAA~-LLg---~~~~sLa~LVe~~LGv~LdK 88 (649)
..|..++.+.. -|.|.+..|+..|.+. +|+... ..+|++-.++ ++. ...++|..|++.+ |+....
T Consensus 82 ~ef~~fig~~~--lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~l-gL~~~g 158 (281)
T PRK06722 82 EKFIQFIGEDS--IFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQL-GLIWEG 158 (281)
T ss_pred HHHHHHHCCCc--EEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHC-CCCCCC
Confidence 34667776532 3677789999888764 454322 2367764332 221 1246899998774 655321
Q ss_pred ccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006352 89 EYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 123 (649)
Q Consensus 89 ~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 123 (649)
. ..-|..||.++..|+..|.
T Consensus 159 ~---------------~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 159 K---------------QHRALADAENTANILLKAY 178 (281)
T ss_pred C---------------CcCcHHHHHHHHHHHHHHh
Confidence 1 1236678888888887766
No 93
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=23.75 E-value=87 Score=32.24 Aligned_cols=63 Identities=17% Similarity=0.160 Sum_probs=41.1
Q ss_pred cchHHHHHH-HhCCCCCcHHHHHHHHcCCCCCcc--cccccCC-C-CC-CCHHHHHHHHHhHHHHHHHH
Q 006352 57 MFDTGQASR-VLKLERNSLEYLLHHFCGVNANKE--YQNADWR-V-RP-LPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 57 vFDTqIAA~-LLg~~~~sLa~LVe~~LGv~LdK~--~q~SDW~-~-RP-LS~eQl~YAA~DV~yLl~Ly 119 (649)
++|+...++ .+....++|..++.++||...+.- .+.+.|- . .+ --..-+.|...||...+.|.
T Consensus 162 ~lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 162 ILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred EeEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 456654433 345557999999999999875432 2445552 1 11 12456889999998888764
No 94
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=21.50 E-value=7.7e+02 Score=25.58 Aligned_cols=100 Identities=19% Similarity=0.204 Sum_probs=61.1
Q ss_pred HHHHHhhcCCCceEEEEec-hhhHHHHHH---HhCCCccc-------------------cchHHHHHHHhCCC-CCcHHH
Q 006352 21 PYLREVFKDPTKKKVMHGA-DRDIVWLQR---DFGIYLCN-------------------MFDTGQASRVLKLE-RNSLEY 76 (649)
Q Consensus 21 ~~Lk~lLeDp~I~KV~H~a-k~DL~~L~r---d~GI~p~n-------------------vFDTqIAA~LLg~~-~~sLa~ 76 (649)
..|+.+++...-.-|.|+. .+|+..|.+ .+|+.+.. -+||+-....-|.. ..+|..
T Consensus 42 ~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~~~sLd~ 121 (209)
T PF10108_consen 42 QDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKARTSLDE 121 (209)
T ss_pred HHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccccCCHHH
Confidence 4566777654545688886 779988754 36766433 25666443333322 467776
Q ss_pred HHHHHcCCCCCccc----c-cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006352 77 LLHHFCGVNANKEY----Q-NADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 123 (649)
Q Consensus 77 LVe~~LGv~LdK~~----q-~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 123 (649)
|+ ..||+.- |.. + ..-|..-.+ ++-..|+..||..+..||-.+.
T Consensus 122 la-~~lgiPg-K~~idGs~V~~~y~~g~i-~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 122 LA-ALLGIPG-KDDIDGSQVAELYQEGDI-DEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred HH-HHcCCCC-CCCCCHHHHHHHHHcCCH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 65 5678764 421 1 111333333 5678999999999999886644
No 95
>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=21.23 E-value=1.4e+02 Score=30.44 Aligned_cols=97 Identities=15% Similarity=0.115 Sum_probs=58.8
Q ss_pred HHHHHhhc--CCCceEEEEec-hhhHHHHHH---HhCCCcc------------------ccchHHHHHH---HhCCCCCc
Q 006352 21 PYLREVFK--DPTKKKVMHGA-DRDIVWLQR---DFGIYLC------------------NMFDTGQASR---VLKLERNS 73 (649)
Q Consensus 21 ~~Lk~lLe--Dp~I~KV~H~a-k~DL~~L~r---d~GI~p~------------------nvFDTqIAA~---LLg~~~~s 73 (649)
..|..++. ||.+. ++|+. .+|+..|.. .+|+.+. ..+|+.-... .+....++
T Consensus 78 ~~f~~~i~~~~Pd~i-~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sys 156 (204)
T cd05779 78 QRFFEHIREVKPHII-VTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQG 156 (204)
T ss_pred HHHHHHHHHhCCCEE-EecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCcc
Confidence 34555554 46654 55554 788877653 3444321 1467664433 34445789
Q ss_pred HHHHHHHHcCCCCCcc-c-c-cccCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 006352 74 LEYLLHHFCGVNANKE-Y-Q-NADWRVRPLPDEMLRYAREDTHYLLYIYD 120 (649)
Q Consensus 74 La~LVe~~LGv~LdK~-~-q-~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd 120 (649)
|..+++++||..-..- . . ..-|...+ ..-.+|+..||...+.||.
T Consensus 157 Ld~Va~~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 157 LKAVTKAKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred HHHHHHHHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 9999999999742111 0 0 01354444 5689999999999998873
No 96
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=21.22 E-value=1.1e+02 Score=31.60 Aligned_cols=93 Identities=16% Similarity=0.165 Sum_probs=57.4
Q ss_pred cCCCceEEEEec-hhhHHHHHHH---hCCC---------------------------c-c-ccchHHHHHHH-hCCCCCc
Q 006352 28 KDPTKKKVMHGA-DRDIVWLQRD---FGIY---------------------------L-C-NMFDTGQASRV-LKLERNS 73 (649)
Q Consensus 28 eDp~I~KV~H~a-k~DL~~L~rd---~GI~---------------------------p-~-nvFDTqIAA~L-Lg~~~~s 73 (649)
.||+|. |+|+. .+|+..|..+ +|+. . + -++|+...++- +....++
T Consensus 96 ~DPDii-vG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~~k~~~~~~sY~ 174 (234)
T cd05776 96 IDPDVL-VGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLSAKELIRCKSYD 174 (234)
T ss_pred cCCCEE-EeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHHHHHHHhCCCCCC
Confidence 578864 89998 7788766432 2221 0 1 15677766653 3445799
Q ss_pred HHHHHHHHcCCCCCc-cc-cc-ccCCC-CCCCHHHHHHHHHhHHHHHHHHHHH
Q 006352 74 LEYLLHHFCGVNANK-EY-QN-ADWRV-RPLPDEMLRYAREDTHYLLYIYDIM 122 (649)
Q Consensus 74 La~LVe~~LGv~LdK-~~-q~-SDW~~-RPLS~eQl~YAA~DV~yLl~Lyd~L 122 (649)
|..+++++||.+-.. .. .. .-|.. ..+ ..-++|...||.+.+.|...|
T Consensus 175 L~~va~~~Lg~~k~di~~~~i~~~~~~~~~l-~~l~~y~~~Da~l~~~L~~kl 226 (234)
T cd05776 175 LTELSQQVLGIERQDIDPEEILNMYNDSESL-LKLLEHTEKDAYLILQLMFKL 226 (234)
T ss_pred hHHHHHHHhCcCcccCCHHHHHHHHhCHHHH-HHHHHHHHHHHHHHHHHHHHH
Confidence 999999999973211 11 11 12332 111 345788899999998887764
No 97
>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=20.08 E-value=1.8e+02 Score=29.45 Aligned_cols=95 Identities=23% Similarity=0.361 Sum_probs=55.2
Q ss_pred HHHHhhc--CCCceEEEEec-hhhHHHHHH---HhCCCcc-------------------------------c-cchHHHH
Q 006352 22 YLREVFK--DPTKKKVMHGA-DRDIVWLQR---DFGIYLC-------------------------------N-MFDTGQA 63 (649)
Q Consensus 22 ~Lk~lLe--Dp~I~KV~H~a-k~DL~~L~r---d~GI~p~-------------------------------n-vFDTqIA 63 (649)
.|..++. ||.| .|+|+. .+|+..|.. .+|+... . ++|+..+
T Consensus 64 ~f~~~i~~~dPdi-i~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~ 142 (207)
T cd05785 64 ELVAIIRERDPDV-IEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFL 142 (207)
T ss_pred HHHHHHHHhCCCE-EeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHH
Confidence 3445553 4664 467777 789977653 2444320 1 3788776
Q ss_pred HHHh-----CCCCCcHHHHHHHH--cCCC-C--CcccccccCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006352 64 SRVL-----KLERNSLEYLLHHF--CGVN-A--NKEYQNADWRVRPLPDEMLRYAREDTHYLLYIY 119 (649)
Q Consensus 64 A~LL-----g~~~~sLa~LVe~~--LGv~-L--dK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Ly 119 (649)
.... ....++|..+++++ ++.. . +-..=..-|...+ ....+|+..||..++.|+
T Consensus 143 ~~~~~~~~~~l~sysL~~Va~~~g~~~~~k~d~~~~~I~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 143 VQLFDVSSRDLPSYGLKAVAKHFGLASPDRTYIDGRQIAEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred HHhhcccccCCCCCCHHHHHHHhcccCCCcCCCCHHHHHHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 5532 22368999999986 2321 1 1100011243332 678999999999888774
Done!