Query 006313
Match_columns 651
No_of_seqs 286 out of 1850
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 21:28:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006313.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006313hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10829 ribonuclease D; Provi 100.0 4.8E-46 1E-50 398.8 26.6 243 1-257 44-287 (373)
2 KOG2206 Exosome 3'-5' exoribon 100.0 2.2E-46 4.7E-51 408.3 20.0 250 1-259 234-483 (687)
3 COG0349 Rnd Ribonuclease D [Tr 100.0 2.1E-42 4.6E-47 365.6 24.0 244 1-257 39-283 (361)
4 TIGR01388 rnd ribonuclease D. 100.0 2.1E-41 4.5E-46 362.5 26.2 243 1-257 40-283 (367)
5 cd06129 RNaseD_like DEDDy 3'-5 99.9 7.3E-25 1.6E-29 208.7 13.4 124 1-125 35-160 (161)
6 cd06146 mut-7_like_exo DEDDy 3 99.9 9.5E-24 2E-28 207.7 13.0 125 1-125 46-192 (193)
7 cd06148 Egl_like_exo DEDDy 3'- 99.9 8.1E-24 1.8E-28 208.5 11.2 131 1-131 31-180 (197)
8 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 6.4E-23 1.4E-27 195.3 13.5 124 1-125 42-169 (170)
9 PF01612 DNA_pol_A_exo1: 3'-5' 99.8 1.4E-20 3.1E-25 176.8 11.8 129 1-129 44-176 (176)
10 cd06142 RNaseD_exo DEDDy 3'-5' 99.7 2.7E-17 5.8E-22 156.1 15.5 130 1-132 34-164 (178)
11 smart00474 35EXOc 3'-5' exonuc 99.6 8.3E-15 1.8E-19 136.4 13.5 126 1-128 43-171 (172)
12 cd06147 Rrp6p_like_exo DEDDy 3 99.6 9.9E-15 2.1E-19 142.5 13.5 131 1-132 46-176 (192)
13 PF00570 HRDC: HRDC domain Blo 99.5 1.6E-14 3.6E-19 118.9 7.1 68 182-249 1-68 (68)
14 cd00007 35EXOc 3'-5' exonuclea 99.5 7.8E-14 1.7E-18 127.4 11.6 127 1-127 22-154 (155)
15 cd09018 DEDDy_polA_RNaseD_like 99.5 1.2E-13 2.5E-18 127.3 11.6 123 1-125 21-149 (150)
16 smart00341 HRDC Helicase and R 99.5 1.1E-13 2.4E-18 117.2 9.6 78 180-257 2-79 (81)
17 cd06140 DNA_polA_I_Bacillus_li 99.4 1E-12 2.2E-17 125.7 12.0 130 1-132 25-160 (178)
18 PRK05755 DNA polymerase I; Pro 99.3 8.1E-11 1.8E-15 139.6 21.2 130 1-132 337-473 (880)
19 PRK14975 bifunctional 3'-5' ex 99.3 4E-11 8.7E-16 135.7 17.4 103 1-131 41-147 (553)
20 cd06139 DNA_polA_I_Ecoli_like_ 99.1 7.9E-10 1.7E-14 106.1 13.2 128 1-130 27-172 (193)
21 KOG2207 Predicted 3'-5' exonuc 99.0 5.4E-10 1.2E-14 125.0 7.5 129 1-129 436-586 (617)
22 TIGR01389 recQ ATP-dependent D 98.9 4.5E-09 9.7E-14 119.5 8.6 75 176-251 516-590 (591)
23 TIGR00593 pola DNA polymerase 98.8 3E-07 6.5E-12 109.6 21.8 109 23-132 368-481 (887)
24 cd06128 DNA_polA_exo DEDDy 3'- 98.6 3.2E-07 6.9E-12 85.9 11.9 118 3-125 25-150 (151)
25 COG0749 PolA DNA polymerase I 98.6 1.7E-07 3.6E-12 106.5 10.9 110 21-132 66-184 (593)
26 PRK11057 ATP-dependent DNA hel 98.5 2.3E-07 5.1E-12 106.3 8.9 75 180-254 530-604 (607)
27 PLN03137 ATP-dependent DNA hel 98.3 8.9E-07 1.9E-11 106.7 8.6 73 182-254 1028-1102(1195)
28 KOG4373 Predicted 3'-5' exonuc 98.3 1.7E-06 3.6E-11 91.8 7.5 120 1-121 152-281 (319)
29 COG0514 RecQ Superfamily II DN 98.0 7.7E-06 1.7E-10 93.5 7.2 72 182-253 517-588 (590)
30 KOG2405 Predicted 3'-5' exonuc 96.3 0.00081 1.8E-08 73.1 -0.6 123 1-126 216-359 (458)
31 PF11408 Helicase_Sgs1: Sgs1 R 94.3 0.14 3E-06 45.1 6.6 66 185-250 8-75 (80)
32 cd06143 PAN2_exo DEDDh 3'-5' e 93.5 0.16 3.5E-06 50.6 6.1 79 25-121 95-173 (174)
33 KOG2405 Predicted 3'-5' exonuc 92.8 0.005 1.1E-07 67.2 -5.9 115 1-116 79-215 (458)
34 cd06125 DnaQ_like_exo DnaQ-lik 92.4 0.3 6.5E-06 43.4 5.7 41 25-65 35-83 (96)
35 TIGR01298 RNaseT ribonuclease 91.7 1.3 2.9E-05 44.3 10.2 86 33-134 105-198 (200)
36 TIGR01406 dnaQ_proteo DNA poly 91.7 0.84 1.8E-05 46.7 8.8 86 24-126 75-170 (225)
37 PRK05711 DNA polymerase III su 91.7 0.77 1.7E-05 47.7 8.6 87 24-127 79-175 (240)
38 PRK06063 DNA polymerase III su 91.5 0.85 1.8E-05 49.1 9.0 91 23-132 86-183 (313)
39 cd06145 REX1_like DEDDh 3'-5' 91.4 0.51 1.1E-05 45.1 6.5 81 23-121 67-149 (150)
40 cd06137 DEDDh_RNase DEDDh 3'-5 91.3 0.55 1.2E-05 45.3 6.6 80 24-121 76-160 (161)
41 cd06131 DNA_pol_III_epsilon_Ec 91.0 1.3 2.7E-05 42.2 8.7 84 24-124 74-166 (167)
42 PRK05168 ribonuclease T; Provi 90.7 2.7 5.8E-05 42.5 11.2 85 33-133 114-206 (211)
43 cd06144 REX4_like DEDDh 3'-5' 89.9 0.35 7.5E-06 46.1 3.9 80 23-121 69-151 (152)
44 PRK07740 hypothetical protein; 89.7 3.5 7.7E-05 42.7 11.3 90 24-132 134-230 (244)
45 PRK07942 DNA polymerase III su 89.1 1.6 3.4E-05 44.9 8.1 83 33-132 93-184 (232)
46 cd06134 RNaseT DEDDh 3'-5' exo 89.0 3.7 8E-05 40.7 10.5 77 34-126 103-187 (189)
47 COG2176 PolC DNA polymerase II 88.8 1.7 3.8E-05 53.9 9.4 91 23-132 493-590 (1444)
48 cd06149 ISG20 DEDDh 3'-5' exon 88.2 1.1 2.4E-05 43.2 6.1 82 23-121 69-156 (157)
49 TIGR00573 dnaq exonuclease, DN 87.2 2.8 6.1E-05 42.4 8.5 90 24-130 80-179 (217)
50 cd06127 DEDDh DEDDh 3'-5' exon 86.9 2.7 5.8E-05 38.2 7.5 81 23-121 71-158 (159)
51 smart00479 EXOIII exonuclease 86.6 3.6 7.9E-05 38.5 8.4 89 23-129 72-168 (169)
52 TIGR01405 polC_Gram_pos DNA po 85.2 2.5 5.5E-05 53.2 8.4 91 23-132 262-359 (1213)
53 PRK06807 DNA polymerase III su 85.2 5.5 0.00012 43.1 9.9 87 24-130 81-174 (313)
54 cd06130 DNA_pol_III_epsilon_li 84.8 6.3 0.00014 36.7 9.0 79 23-121 69-154 (156)
55 KOG2249 3'-5' exonuclease [Rep 84.7 1.5 3.2E-05 46.5 5.2 88 25-131 178-269 (280)
56 PRK08517 DNA polymerase III su 84.5 4.4 9.6E-05 42.5 8.7 87 24-129 140-232 (257)
57 PRK06310 DNA polymerase III su 84.3 6.4 0.00014 41.0 9.7 87 24-128 80-174 (250)
58 PRK07246 bifunctional ATP-depe 82.5 5.4 0.00012 48.5 9.4 91 23-132 78-174 (820)
59 cd06136 TREX1_2 DEDDh 3'-5' ex 81.2 6.1 0.00013 38.7 7.7 80 24-122 87-175 (177)
60 PRK06195 DNA polymerase III su 80.6 13 0.00028 39.9 10.5 87 24-130 73-166 (309)
61 PRK06309 DNA polymerase III su 80.6 9.2 0.0002 39.2 9.1 88 24-129 72-167 (232)
62 cd05160 DEDDy_DNA_polB_exo DED 80.0 10 0.00022 37.3 8.8 98 23-121 68-198 (199)
63 PF13482 RNase_H_2: RNase_H su 79.2 1.5 3.2E-05 41.5 2.7 97 27-124 52-163 (164)
64 PRK07883 hypothetical protein; 77.5 8.6 0.00019 44.7 8.6 90 24-132 88-186 (557)
65 TIGR01407 dinG_rel DnaQ family 77.1 11 0.00023 45.9 9.6 91 23-132 72-169 (850)
66 KOG1275 PAB-dependent poly(A) 75.5 1.5 3.2E-05 53.0 1.7 86 28-132 1009-1095(1118)
67 cd05780 DNA_polB_Kod1_like_exo 75.3 12 0.00026 37.2 7.9 100 23-123 61-194 (195)
68 PRK05601 DNA polymerase III su 73.3 20 0.00044 40.0 9.6 95 23-124 117-245 (377)
69 PRK08074 bifunctional ATP-depe 72.2 23 0.00049 43.7 10.8 91 23-132 76-173 (928)
70 KOG3657 Mitochondrial DNA poly 71.4 9.5 0.00021 46.2 6.9 96 34-130 242-385 (1075)
71 PF09281 Taq-exonuc: Taq polym 68.5 20 0.00044 34.6 7.2 69 42-128 70-138 (138)
72 PRK00448 polC DNA polymerase I 67.5 21 0.00046 46.1 9.3 89 25-132 493-588 (1437)
73 PRK07983 exodeoxyribonuclease 58.3 52 0.0011 33.8 8.7 78 33-126 74-152 (219)
74 PRK07247 DNA polymerase III su 57.9 59 0.0013 32.8 8.9 84 23-127 76-168 (195)
75 PRK09146 DNA polymerase III su 57.0 37 0.0008 35.3 7.4 86 25-129 123-228 (239)
76 PRK07748 sporulation inhibitor 56.5 68 0.0015 32.2 9.1 88 23-127 84-179 (207)
77 PRK09145 DNA polymerase III su 54.4 92 0.002 31.0 9.6 83 24-125 104-198 (202)
78 PRK11779 sbcB exonuclease I; P 49.6 63 0.0014 37.2 8.4 87 24-127 84-197 (476)
79 COG0847 DnaQ DNA polymerase II 45.9 1.5E+02 0.0032 30.0 9.7 88 24-127 87-181 (243)
80 cd06133 ERI-1_3'hExo_like DEDD 43.2 1.3E+02 0.0028 28.4 8.3 86 23-124 80-175 (176)
81 cd05784 DNA_polB_II_exo DEDDy 38.5 56 0.0012 32.9 5.2 62 59-122 123-193 (193)
82 cd06138 ExoI_N N-terminal DEDD 38.0 1E+02 0.0022 30.2 6.9 80 24-120 75-181 (183)
83 cd05777 DNA_polB_delta_exo DED 37.5 55 0.0012 33.4 5.1 67 59-125 153-224 (230)
84 cd05782 DNA_polB_like1_exo Unc 33.2 1.7E+02 0.0036 29.8 7.6 97 23-122 83-207 (208)
85 PRK09182 DNA polymerase III su 31.3 2.2E+02 0.0047 30.7 8.5 82 24-124 113-197 (294)
86 PF09862 DUF2089: Protein of u 30.7 95 0.0021 29.3 5.0 50 222-271 50-103 (113)
87 cd05778 DNA_polB_zeta_exo inac 30.6 60 0.0013 33.4 4.1 63 59-121 162-230 (231)
88 COG2906 Bfd Bacterioferritin-a 30.5 1.4E+02 0.003 25.6 5.3 43 208-250 9-53 (63)
89 PF03874 RNA_pol_Rpb4: RNA pol 28.5 1.5E+02 0.0032 27.0 5.8 45 208-252 71-116 (117)
90 KOG2248 3'-5' exonuclease [Rep 27.9 53 0.0012 36.8 3.3 85 21-123 283-370 (380)
91 PF10108 DNA_pol_B_exo2: Predi 27.5 5E+02 0.011 26.9 10.0 100 23-125 42-170 (209)
92 COG1460 Uncharacterized protei 27.3 87 0.0019 29.6 4.1 47 208-254 66-113 (114)
93 cd05785 DNA_polB_like2_exo Unc 27.3 1.4E+02 0.003 30.4 5.9 61 59-121 136-206 (207)
94 PRK14981 DNA-directed RNA poly 26.0 84 0.0018 29.2 3.8 46 208-253 65-111 (112)
95 cd05776 DNA_polB_alpha_exo ina 25.3 74 0.0016 32.7 3.6 93 30-124 96-226 (234)
96 cd05779 DNA_polB_epsilon_exo D 25.0 1.2E+02 0.0025 31.0 4.9 96 24-122 79-204 (204)
97 TIGR00592 pol2 DNA polymerase 22.9 2.8E+02 0.006 35.6 8.5 94 31-125 599-723 (1172)
98 TIGR01388 rnd ribonuclease D. 22.2 1.8E+02 0.0039 32.2 6.1 42 178-219 295-336 (367)
99 PF04857 CAF1: CAF1 family rib 20.3 1.4E+02 0.003 31.2 4.5 53 31-83 147-214 (262)
No 1
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=4.8e-46 Score=398.76 Aligned_cols=243 Identities=21% Similarity=0.318 Sum_probs=221.5
Q ss_pred CeeeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC-CCcHHHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYL 79 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~-~~gL~~L 79 (651)
|||++++.+||||++++. ++ ..|+++|+|++|+||+|+|++|+.+|++.+|+.|.++|||++|+++||.+ ++||+.|
T Consensus 44 iQl~~~~~~~LiD~l~~~-d~-~~L~~ll~~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~~~gl~~L 121 (373)
T PRK10829 44 IQLYDGEQLSLIDPLGIT-DW-SPFKALLRDPQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASM 121 (373)
T ss_pred EEEecCCceEEEecCCcc-ch-HHHHHHHcCCCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCccccHHHH
Confidence 799999999999999986 46 46999999999999999999999999999999999999999999999987 6999999
Q ss_pred HHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhh
Q 006313 80 LHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEK 159 (651)
Q Consensus 80 Ve~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~Gr~~e~~~~wL~Ev~k~s~e~~l~ly~k 159 (651)
+++|||++++|.++++||+.||||++|+.|||.||+||+.||+.|..+|.+.|+ .+|+.|+|... |.... .
T Consensus 122 v~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~-----~~w~~ee~~~l---~~~~~-~ 192 (373)
T PRK10829 122 VEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGW-----LPAALDECRLL---CQRRQ-E 192 (373)
T ss_pred HHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc-----HHHHHHHHHHH---Hhccc-c
Confidence 999999999999999999999999999999999999999999999999998874 57998888643 22111 1
Q ss_pred hccChhHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHH
Q 006313 160 ELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIE 239 (651)
Q Consensus 160 e~~~e~~y~ri~g~~~~~L~~~qlaVL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~ 239 (651)
...++..|+++++. +.|+++|++|+++|+.|||++|+++|+|+++||+|+.|++||+++|+|.++|.++ |+.+..++
T Consensus 193 ~~~~~~~~~~ik~~--~~L~~~~lavl~~L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~-~~~~~~~r 269 (373)
T PRK10829 193 VLAPEEAYRDITNA--WQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSL-GLSGSEIR 269 (373)
T ss_pred CCChHHHHHHhccc--cCCCHHHHHHHHHHHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhc-cCChHhHH
Confidence 23456779999874 7899999999999999999999999999999999999999999999999999999 89888899
Q ss_pred HhHHHHHHHHHHHHhccc
Q 006313 240 RYMGPVLSIIKNSMQNAA 257 (651)
Q Consensus 240 r~G~eIL~iI~~Ale~~~ 257 (651)
+||++|+++|+++.+.|+
T Consensus 270 ~~g~~ll~~i~~a~~~~~ 287 (373)
T PRK10829 270 FHGKTLLALVAKAQALPE 287 (373)
T ss_pred hhHHHHHHHHHHHhcCCH
Confidence 999999999999987664
No 2
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-46 Score=408.35 Aligned_cols=250 Identities=52% Similarity=0.846 Sum_probs=231.8
Q ss_pred CeeeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCCCCcHHHHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLERNSLEYLL 80 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~~~gL~~LV 80 (651)
|||+|+.+.||||++.+.++++ .|+++|.||.|+||+|++..|+.||+++|||+++++|||..|+++||.++++|.+|.
T Consensus 234 mqISTr~ed~iIDt~~l~~~i~-~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvnLfdt~~a~r~L~~~r~sL~~ll 312 (687)
T KOG2206|consen 234 MQISTRTEDFIIDTFKLRDHIG-ILNEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVNLFDTIQASRLLGLPRPSLAYLL 312 (687)
T ss_pred EEeeccchhheehhHHHHHHHH-HhhhhccCCCeEEEEecCccchhhhhccceEEEEechhhHHHHHHhCCCcccHHHHH
Confidence 7999999999999999998886 899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhhh
Q 006313 81 HHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEKE 160 (651)
Q Consensus 81 e~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~Gr~~e~~~~wL~Ev~k~s~e~~l~ly~ke 160 (651)
+.|+|+..+|.+|+.||++|||+.+|+.||..|++||+.||+.|+..|.+.+. +. . -++.++++.|...|.++
T Consensus 313 ~~~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~---~~-~---~~~~~~~d~c~~~~~k~ 385 (687)
T KOG2206|consen 313 ECVCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAK---GR-A---VTYSESRDMCTNGYKKK 385 (687)
T ss_pred HHHHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhc---cc-c---cccchhhhhhhcceecc
Confidence 99999999999999999999999999999999999999999999998887662 11 1 12335678899999888
Q ss_pred ccChhHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHHH
Q 006313 161 LLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIER 240 (651)
Q Consensus 161 ~~~e~~y~ri~g~~~~~L~~~qlaVL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~r 240 (651)
......|+.+..++. .++..|+.+|++|++||+.+||+.|+++.|||+|+.|+.||+.+|.+...|.++....++.+++
T Consensus 386 ~~~~~sy~~v~~~q~-~ln~~q~~~l~~L~~wRd~iARaeDES~~yVlpN~~ll~l~e~~P~~v~gl~~~ln~~~p~vkq 464 (687)
T KOG2206|consen 386 TFCTKSYLEVEDIQS-RLNSSQLDVLRALLRWRDFIARAEDESVHYVLPNDQLLKLAEERPDTVDGLLGGLNRLSPLVKQ 464 (687)
T ss_pred cCCCcchHhHHHHHh-ccchhHHHHHHHHHHHHHHHHhhccCCCceecccHHHHHHHHHCCccHHHHHHhccCCCHHHHH
Confidence 888888999888754 4999999999999999999999999999999999999999999999999999998888999999
Q ss_pred hHHHHHHHHHHHHhccccH
Q 006313 241 YMGPVLSIIKNSMQNAANF 259 (651)
Q Consensus 241 ~G~eIL~iI~~Ale~~~~~ 259 (651)
+...++.+|+.+++....+
T Consensus 465 ~~~~~~~ii~~a~~~~l~~ 483 (687)
T KOG2206|consen 465 NVMDFLYIIRSAGRGFLLQ 483 (687)
T ss_pred HHHHHHHHHHHHhhhhhhh
Confidence 9999999999999977655
No 3
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-42 Score=365.56 Aligned_cols=244 Identities=27% Similarity=0.401 Sum_probs=219.1
Q ss_pred CeeeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC-CCcHHHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYL 79 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~-~~gL~~L 79 (651)
|||+.++.+++||++....++ +.|..+|.|++|+||||++.+|+.+|++.||+.|.++|||+||+.++|.+ ++||+.|
T Consensus 39 IQi~~~e~~~lIdpl~~~~d~-~~l~~Ll~d~~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~~~gl~~L 117 (361)
T COG0349 39 IQISDGEGASLIDPLAGILDL-PPLVALLADPNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGTSHGLADL 117 (361)
T ss_pred EEEecCCCceEeccccccccc-chHHHHhcCCceeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHhCCcccccHHHH
Confidence 799999999999999954456 45999999999999999999999999999999999999999999999997 8999999
Q ss_pred HHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhh
Q 006313 80 LHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEK 159 (651)
Q Consensus 80 Ve~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~Gr~~e~~~~wL~Ev~k~s~e~~l~ly~k 159 (651)
|++++|++++|++|.|||+.||||++|++||+.||.||+.||+.|.++|.+.|+ ..|+.++|.-.. .+.+ .
T Consensus 118 v~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r-----~~~a~~ef~~l~---~r~~-~ 188 (361)
T COG0349 118 VEELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGR-----LEWAEDEFRLLP---TRRT-Y 188 (361)
T ss_pred HHHHhCCcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc-----hHHHHHHHHHhh---hccc-c
Confidence 999999999999999999999999999999999999999999999999998874 477777664321 1100 2
Q ss_pred hccChhHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHH
Q 006313 160 ELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIE 239 (651)
Q Consensus 160 e~~~e~~y~ri~g~~~~~L~~~qlaVL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~ 239 (651)
...++..|+++.. .+.+++.++++++.|++||++.||.+|+|+++|++|+.|+++|+++|++..+|..+..+.+ ..+
T Consensus 189 ~~~~~~~w~~i~~--a~~~~p~~la~l~~La~wRe~~Ar~rd~~~~~vl~de~i~~~a~~~P~~~~~l~~l~~~~~-~~~ 265 (361)
T COG0349 189 KVLPEDAWREIKI--AHSLDPRELAVLRELAAWREREARERDLARNFVLKDEALWELARYTPKNLKELDALGLIPK-ERR 265 (361)
T ss_pred ccChHhHHHHhhh--hhcCChHHHHHHHHHHHHHHHHHHHhccccccccchhHHHHHHHhCCCCHHHHHhccCCcc-cch
Confidence 2356788998876 5889999999999999999999999999999999999999999999999999999876555 677
Q ss_pred HhHHHHHHHHHHHHhccc
Q 006313 240 RYMGPVLSIIKNSMQNAA 257 (651)
Q Consensus 240 r~G~eIL~iI~~Ale~~~ 257 (651)
.++..|+.+|.++++.|.
T Consensus 266 ~~~~~l~~~~~~a~~~p~ 283 (361)
T COG0349 266 RHGKLLLALLANALASPE 283 (361)
T ss_pred hhhHHHHHHHHHHHhCch
Confidence 899999999999998875
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-41 Score=362.52 Aligned_cols=243 Identities=27% Similarity=0.378 Sum_probs=218.7
Q ss_pred CeeeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC-CCcHHHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYL 79 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~-~~gL~~L 79 (651)
|||+|++.+||||++.+. ++ ..|+++|+|++|.||+|++++|+.+|++.+++.+.++|||++|+|+|+++ .+||..|
T Consensus 40 iQia~~~~~~liD~~~~~-~~-~~L~~lL~d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~~~l~~L 117 (367)
T TIGR01388 40 IQVADGEQLALIDPLVII-DW-SPLKELLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKL 117 (367)
T ss_pred EEEeeCCeEEEEeCCCcc-cH-HHHHHHHCCCCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCCCccHHHH
Confidence 799999999999999884 46 46999999999999999999999999888888888999999999999986 5899999
Q ss_pred HHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCCCChHHHHHHHHHHHHHHHHhh
Q 006313 80 LHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMPKESENSDTPLTEVYKRSYDVCRQLYEK 159 (651)
Q Consensus 80 Ve~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~Gr~~e~~~~wL~Ev~k~s~e~~l~ly~k 159 (651)
+++|||++++|++++++|..|||+.+|+.||+.||+||+.||+.|..+|.+.|+ ..|+.++|.... ... ..
T Consensus 118 v~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~-----~~w~~ee~~~l~---~~~-~~ 188 (367)
T TIGR01388 118 VQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGR-----LAWLEEECTLLT---DRR-TY 188 (367)
T ss_pred HHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc-----HHHHHHHHHHHh---ccc-cC
Confidence 999999999999999999999999999999999999999999999999998873 578888776432 111 11
Q ss_pred hccChhHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHH
Q 006313 160 ELLSENSYLHIYGLQGAGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIE 239 (651)
Q Consensus 160 e~~~e~~y~ri~g~~~~~L~~~qlaVL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~ 239 (651)
...++..|+++++. +.|++++++++++|++|||.+|+++|+|+++||+|+.|++||+++|+|..+|.++ |+....++
T Consensus 189 ~~~~~~~~~~i~~~--~~l~~~~l~~l~~L~~wRe~~A~~~d~p~~~il~d~~l~~lA~~~P~~~~~l~~~-~~~~~~~r 265 (367)
T TIGR01388 189 VVNPEDAWRDIKNA--WQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEALWELARQAPGNLTELASL-GPKGSEIR 265 (367)
T ss_pred CCChHHHHHHhccc--ccCCHHHHHHHHHHHHHHHHHHHHcCCCcceeeCHHHHHHHHHhCCCCHHHHHhc-cCChHHHH
Confidence 23456679999874 7899999999999999999999999999999999999999999999999999999 88888899
Q ss_pred HhHHHHHHHHHHHHhccc
Q 006313 240 RYMGPVLSIIKNSMQNAA 257 (651)
Q Consensus 240 r~G~eIL~iI~~Ale~~~ 257 (651)
+||++|+++|+.+.+.|+
T Consensus 266 ~~~~~l~~~i~~a~~~~~ 283 (367)
T TIGR01388 266 KHGDTLLALVKTALALPE 283 (367)
T ss_pred hhHHHHHHHHHHHhhCCH
Confidence 999999999999988664
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=99.92 E-value=7.3e-25 Score=208.74 Aligned_cols=124 Identities=35% Similarity=0.533 Sum_probs=116.5
Q ss_pred CeeeeC-CccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC-CCcHHH
Q 006313 1 MQISTR-TEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEY 78 (651)
Q Consensus 1 IQIAT~-~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~-~~gL~~ 78 (651)
|||+|+ +.|||||+..++. ....|+++|+|++|+||+|++++|+..|++++|+.+.++|||++|++++++. +.||+.
T Consensus 35 iQl~~~~~~~~l~d~~~~~~-~~~~L~~lL~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll~~~~~~~L~~ 113 (161)
T cd06129 35 IQLCVSEEKCYLFDPLSLSV-DWQGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLKGLPERWSLAS 113 (161)
T ss_pred EEEEECCCCEEEEecccCcc-CHHHHHHHhCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHhCCCCCchHHH
Confidence 799999 9999999998864 3457999999999999999999999999888999999999999999999986 689999
Q ss_pred HHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006313 79 LLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 125 (651)
Q Consensus 79 LVe~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 125 (651)
|+++|||+.++|..+++||..|||+++|+.|||.||+|++.||+.|+
T Consensus 114 l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 114 LVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999875
No 6
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.90 E-value=9.5e-24 Score=207.75 Aligned_cols=125 Identities=27% Similarity=0.444 Sum_probs=113.7
Q ss_pred CeeeeCCccEEEecCCccc----hhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCC------cCceehHHHHHHHhC
Q 006313 1 MQISTRTEDFVVDTLKLRV----QVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIY------LCNMFDTGQASRVLK 70 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~----dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~------p~nlFDTqLAA~lLg 70 (651)
|||+|.+.+||||+..++. .+.+.|+++|+||+|+||+|++++|+.+|+++||+. +.++|||+.+++.+.
T Consensus 46 iQiat~~~~~lid~~~~~~~~~~~~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~ 125 (193)
T cd06146 46 LQLATEDEVFLLDLLALENLESEDWDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQ 125 (193)
T ss_pred EEEecCCCEEEEEchhccccchHHHHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHh
Confidence 7999999999999998862 355679999999999999999999999999999974 579999998888654
Q ss_pred C------------CCCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006313 71 L------------ERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 125 (651)
Q Consensus 71 ~------------~~~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 125 (651)
. ...||+.|++++||+.++|..+++||..||||++|+.|||.||++++.||+.|.
T Consensus 126 ~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 126 KSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred hccccccccccCcccCCHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 2 258999999999999999999999999999999999999999999999999875
No 7
>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=99.90 E-value=8.1e-24 Score=208.50 Aligned_cols=131 Identities=33% Similarity=0.429 Sum_probs=118.7
Q ss_pred CeeeeC-CccEEEecCCccc-hhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC------
Q 006313 1 MQISTR-TEDFVVDTLKLRV-QVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE------ 72 (651)
Q Consensus 1 IQIAT~-~~~~LID~laL~~-dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~------ 72 (651)
|||+|. +.+||||++.++. .+...|+++|+|++|.||+|++++|+.+|++.+|+.+.++|||++|+++|++.
T Consensus 31 iQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~ 110 (197)
T cd06148 31 VQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFN 110 (197)
T ss_pred EEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCcc
Confidence 799999 9999999999863 23457999999999999999999999999889999999999999999999763
Q ss_pred ---CCcHHHHHHHHcCCCCCc--------ccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcC
Q 006313 73 ---RNSLEYLLHHFCGVNANK--------EYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSM 131 (651)
Q Consensus 73 ---~~gL~~LVe~yLGv~LdK--------~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~ 131 (651)
..||..++++|+|+.++| ..+.+||..|||+++|+.|||.||+||+.||+.|...|.+.
T Consensus 111 ~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 111 PDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred ccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 269999999999999875 46789999999999999999999999999999999999864
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=99.89 E-value=6.4e-23 Score=195.31 Aligned_cols=124 Identities=26% Similarity=0.426 Sum_probs=116.1
Q ss_pred CeeeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC--CCcHHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE--RNSLEY 78 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~--~~gL~~ 78 (651)
|||+|++.|||||+..+. .+++.|+++|++++|.||+|+++.|+..|.+.+|+.+.++|||++|++++++. ..||..
T Consensus 42 iQl~~~~~~~l~~~~~~~-~~~~~l~~ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~ 120 (170)
T cd06141 42 LQLATESRCLLFQLAHMD-KLPPSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLAR 120 (170)
T ss_pred EEEecCCcEEEEEhhhhh-cccHHHHHHhcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHH
Confidence 799999999999999974 45567999999999999999999999999889999999999999999999985 479999
Q ss_pred HHHHHcCCCCC--cccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006313 79 LLHHFCGVNAN--KEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 125 (651)
Q Consensus 79 LVe~yLGv~Ld--K~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 125 (651)
|+..|||.+++ |..+++||..|||+++|+.|||.||++++.||+.|.
T Consensus 121 l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 121 LVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999 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=99.84 E-value=1.4e-20 Score=176.77 Aligned_cols=129 Identities=36% Similarity=0.600 Sum_probs=116.5
Q ss_pred CeeeeCCccEEEecCCccch-hhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCCC-CcHHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQ-VGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLER-NSLEY 78 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~d-L~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~~-~gL~~ 78 (651)
|||++.+.+|++|+...... +...|+++|+|++|.||+|++++|+.+|++.+|+.+.++|||+++++++++.+ +||..
T Consensus 44 iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~~~L~~ 123 (176)
T PF01612_consen 44 IQLATGEGCYIIDPIDLGDNWILDALKELLEDPNIIKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRSYSLKD 123 (176)
T ss_dssp EEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTTSEEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTTSSHHH
T ss_pred EEEecCCCceeeeeccccccchHHHHHHHHhCCCccEEEEEEechHHHHHHHhccccCCccchhhhhhcccccccccHHH
Confidence 69999999999999988753 34679999999999999999999999998889999999999999999999876 99999
Q ss_pred HHHHHcC-CCCCcccccccCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006313 79 LLHHFCG-VNANKEYQNADWR-VRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 129 (651)
Q Consensus 79 LVe~yLG-v~LdK~~q~SDW~-~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~ 129 (651)
|+.+|+| ..++|..+.++|. .+||+++|+.|||.||++++.||+.|..+|+
T Consensus 124 L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 124 LAEEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred HHHHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 9999999 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=99.75 E-value=2.7e-17 Score=156.08 Aligned_cols=130 Identities=41% Similarity=0.606 Sum_probs=114.4
Q ss_pred CeeeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC-CCcHHHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYL 79 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~-~~gL~~L 79 (651)
|||++.+.+|+||+..+ . ..+.|+++|+|+++.||+|+++.|+..|++.+|+...++|||++|+|+|++. ..+|..|
T Consensus 34 i~l~~~~~~~~i~~~~~-~-~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl~p~~~~~l~~l 111 (178)
T cd06142 34 IQISTGGEVYLIDPLAI-G-DLSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLLGLGDSVGLAAL 111 (178)
T ss_pred EEEeeCCCEEEEeCCCc-c-cHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHhCCCccccHHHH
Confidence 58898866999986643 2 3356899999999999999999999999777799966789999999999995 4799999
Q ss_pred HHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 80 LHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 80 Ve~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
++.|++..+.+....++|..+||+.+|+.||+.||++++.|++.|..+|.+.+
T Consensus 112 ~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~ 164 (178)
T cd06142 112 VEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEG 164 (178)
T ss_pred HHHHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Confidence 99999998766667899999999999999999999999999999999999876
No 11
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.61 E-value=8.3e-15 Score=136.39 Aligned_cols=126 Identities=39% Similarity=0.571 Sum_probs=104.9
Q ss_pred CeeeeCC-ccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC-C-CcHH
Q 006313 1 MQISTRT-EDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-R-NSLE 77 (651)
Q Consensus 1 IQIAT~~-~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~-~-~gL~ 77 (651)
|||++.+ .+||++..... .....|+++|+++.+.||+|+++.|+.+|+ .+|+.+.++|||++|+|+|.+. . .+|.
T Consensus 43 l~l~~~~~~~~i~~~~~~~-~~~~~l~~~l~~~~~~kv~~d~k~~~~~L~-~~gi~~~~~~D~~laayll~p~~~~~~l~ 120 (172)
T smart00474 43 IQISVTGEGAFIIDPLALG-DDLEILKDLLEDETITKVGHNAKFDLHVLA-RFGIELENIFDTMLAAYLLLGGPSKHGLA 120 (172)
T ss_pred EEEeEcCCceEEEEeccch-hhHHHHHHHhcCCCceEEEechHHHHHHHH-HCCCcccchhHHHHHHHHHcCCCCcCCHH
Confidence 5788544 56666554332 222458999999999999999999999996 4999988889999999999875 2 7999
Q ss_pred HHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q 006313 78 YLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKL 128 (651)
Q Consensus 78 ~LVe~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L 128 (651)
.++..|++..+++..+.++|..+|+...|+.||+.||++++.|++.|.++|
T Consensus 121 ~l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 121 TLLKEYLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred HHHHHHhCCCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999876655567998899999999999999999999999998876
No 12
>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=99.60 E-value=9.9e-15 Score=142.52 Aligned_cols=131 Identities=65% Similarity=1.133 Sum_probs=110.3
Q ss_pred CeeeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCCCCcHHHHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLERNSLEYLL 80 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~~~gL~~LV 80 (651)
|||++++.+|+||++.....+ ..|+++|+++++.||+|+++.++.+|.+.+|+.+.++|||++|+|+|++...+|..|+
T Consensus 46 l~l~~~~~~~~i~~l~~~~~~-~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~~~~l~~l~ 124 (192)
T cd06147 46 MQISTREEDYIVDTLKLRDDM-HILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLL 124 (192)
T ss_pred EEEecCCCcEEEEecccccch-HHHHHHhcCCCceEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCCcccHHHHH
Confidence 578887778888853332222 3588999999999999999999999954889988777999999999998546999999
Q ss_pred HHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 81 HHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 81 e~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
++||+..+.|..+.++|..+||..+|..|++.++.+++.|++.|..+|+++.
T Consensus 125 ~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~~ 176 (192)
T cd06147 125 QKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERA 176 (192)
T ss_pred HHHhCCCcchhhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHhc
Confidence 9999987545455677988898999999999999999999999999998765
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=99.53 E-value=1.6e-14 Score=118.90 Aligned_cols=68 Identities=35% Similarity=0.586 Sum_probs=62.4
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHHHhHHHHHHHH
Q 006313 182 QLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSII 249 (651)
Q Consensus 182 qlaVL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~r~G~eIL~iI 249 (651)
|++++++|+.||+++|++.|+||++||+|.+|.+||+++|+|.++|.++.|++...+++||++|+++|
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
>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=99.52 E-value=7.8e-14 Score=127.45 Aligned_cols=127 Identities=31% Similarity=0.346 Sum_probs=97.8
Q ss_pred CeeeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC--CCcHHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE--RNSLEY 78 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~--~~gL~~ 78 (651)
|||++.+.+++|........+.+.|+++|+++.+.||+|+++.|+.+|...+...+.++|||++|+|+|++. .++|+.
T Consensus 22 ~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ayll~~~~~~~~l~~ 101 (155)
T cd00007 22 IQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDD 101 (155)
T ss_pred EEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCcCCHHH
Confidence 588886435555422211123355889999999999999999999999655544556799999999999985 379999
Q ss_pred HHHHHcCCCCCcccccccCC----CCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006313 79 LLHHFCGVNANKEYQNADWR----VRPLPDEMLRYAREDTHYLLYIYDIMKIK 127 (651)
Q Consensus 79 LVe~yLGv~LdK~~q~SDW~----~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~ 127 (651)
|+++|++..+.+..+..+|. .+|++..|..||+.|+.+++.|++.|..+
T Consensus 102 l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 102 LAKEYLGIELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred HHHHHcCCCCccHHHHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 99999998854422334442 58889999999999999999999998765
No 15
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.51 E-value=1.2e-13 Score=127.26 Aligned_cols=123 Identities=24% Similarity=0.253 Sum_probs=97.3
Q ss_pred CeeeeCCc-cEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCc-CceehHHHHHHHhCCC--CCcH
Q 006313 1 MQISTRTE-DFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYL-CNMFDTGQASRVLKLE--RNSL 76 (651)
Q Consensus 1 IQIAT~~~-~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p-~nlFDTqLAA~lLg~~--~~gL 76 (651)
|||++++. +|+||+....... ..|+++|+|+++.||+|+++.|+.+|. ..|+.. .++|||++|+|+|++. +.+|
T Consensus 21 l~l~~~~~~~~~i~~~~~~~~~-~~l~~~l~~~~~~kv~~d~K~~~~~L~-~~~~~~~~~~~D~~laayLl~p~~~~~~l 98 (150)
T cd09018 21 IQLAIEPGVAALIPVAHDYLAL-ELLKPLLEDEKALKVGQNLKYDRGILL-NYFIELRGIAFDTMLEAYILNSVAGRWDM 98 (150)
T ss_pred EEEEcCCCcEEEEEcCCcccCH-HHHHHHhcCCCCceeeecHHHHHHHHH-HcCCccCCcchhHHHHHHHhCCCCCCCCH
Confidence 58888744 8888854321112 458899999999999999999999994 556554 4689999999999984 4799
Q ss_pred HHHHHHHcCCCCCc-cc-ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006313 77 EYLLHHFCGVNANK-EY-QNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 125 (651)
Q Consensus 77 ~~LVe~yLGv~LdK-~~-q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 125 (651)
..|+.+||+.++.+ .. ....|..+|++.+|+.||+.|+.+++.|++.|.
T Consensus 99 ~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 99 DSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred HHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999998544 21 112386688899999999999999999998864
No 16
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=99.49 E-value=1.1e-13 Score=117.17 Aligned_cols=78 Identities=32% Similarity=0.532 Sum_probs=74.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHHHhHHHHHHHHHHHHhccc
Q 006313 180 AQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQNAA 257 (651)
Q Consensus 180 ~~qlaVL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~r~G~eIL~iI~~Ale~~~ 257 (651)
+.++++|++|+.||+.+|++.|+|+++||+|.+|++||+++|+|..+|..+.|++...+++||..|+.+|+.+.+.+.
T Consensus 2 ~~~~~~~~~L~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~~~~~~~~g~~~~~~i~~~~~~~~ 79 (81)
T smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSPS 79 (81)
T ss_pred hHHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHhccc
Confidence 578999999999999999999999999999999999999999999999999999999999999999999999887653
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=99.43 E-value=1e-12 Score=125.67 Aligned_cols=130 Identities=18% Similarity=0.160 Sum_probs=103.3
Q ss_pred CeeeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcC-ceehHHHHHHHhCCCC--CcHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLC-NMFDTGQASRVLKLER--NSLE 77 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~-nlFDTqLAA~lLg~~~--~gL~ 77 (651)
|+|++++.+|+|++-.. ......|+++|+|+++.||+|+++.|++.| ..+|+.+. .+|||++|+|+|++.. ++|.
T Consensus 25 i~l~~~~~~~~i~~~~~-~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~~~~~~fDt~laaYLL~p~~~~~~l~ 102 (178)
T cd06140 25 LALANGGGAYYIPLELA-LLDLAALKEWLEDEKIPKVGHDAKRAYVAL-KRHGIELAGVAFDTMLAAYLLDPTRSSYDLA 102 (178)
T ss_pred EEEEeCCcEEEEeccch-HHHHHHHHHHHhCCCCceeccchhHHHHHH-HHCCCcCCCcchhHHHHHHHcCCCCCCCCHH
Confidence 47777777888874321 011245889999999999999999999999 56898875 5799999999999963 8999
Q ss_pred HHHHHHcCCCCCcccccccCC---CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 78 YLLHHFCGVNANKEYQNADWR---VRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 78 ~LVe~yLGv~LdK~~q~SDW~---~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
.|+.+|+++++.+..+...|. .++....+..|++.||.+++.|++.|..+|.+.+
T Consensus 103 ~l~~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~ 160 (178)
T cd06140 103 DLAKRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEENE 160 (178)
T ss_pred HHHHHHcCCCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 999999999875533344452 2454677889999999999999999999998754
No 18
>PRK05755 DNA polymerase I; Provisional
Probab=99.32 E-value=8.1e-11 Score=139.57 Aligned_cols=130 Identities=26% Similarity=0.319 Sum_probs=103.6
Q ss_pred CeeeeCCc-cEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCc-CceehHHHHHHHhCCCC-CcHH
Q 006313 1 MQISTRTE-DFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYL-CNMFDTGQASRVLKLER-NSLE 77 (651)
Q Consensus 1 IQIAT~~~-~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p-~nlFDTqLAA~lLg~~~-~gL~ 77 (651)
|||++.+. +|+||+..+.....+.|+++|+|+.+.||+|++++|+.+|+ .+|+.+ .++|||++|+++|+++. ++|+
T Consensus 337 i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~v~kV~HNakfDl~~L~-~~gi~~~~~~~DT~iAa~Ll~~~~~~~L~ 415 (880)
T PRK05755 337 LSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPAIKKVGQNLKYDLHVLA-RYGIELRGIAFDTMLASYLLDPGRRHGLD 415 (880)
T ss_pred EEEEeCCCcEEEEecccccHHHHHHHHHHHhCCCCcEEEeccHhHHHHHH-hCCCCcCCCcccHHHHHHHcCCCCCCCHH
Confidence 57887766 88888744321223568999999999999999999999995 578875 57999999999999864 8999
Q ss_pred HHHHHHcCCCCCccc----ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 78 YLLHHFCGVNANKEY----QNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 78 ~LVe~yLGv~LdK~~----q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
.|+++|+|+++.... ...+|..+|+ +.+..||+.||.+++.||..|..+|.+.+
T Consensus 416 ~L~~~ylg~~~~~~~~~~gk~~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~ 473 (880)
T PRK05755 416 SLAERYLGHKTISFEEVAGKQLTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEP 473 (880)
T ss_pred HHHHHHhCCCccchHHhcCCCCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 999999998852110 1233444577 57999999999999999999999998753
No 19
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.31 E-value=4e-11 Score=135.66 Aligned_cols=103 Identities=23% Similarity=0.236 Sum_probs=90.3
Q ss_pred CeeeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC----CCcH
Q 006313 1 MQISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE----RNSL 76 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~----~~gL 76 (651)
||+++++.+||||++.. +.+ + | ..+|+.+.++|||++|+|+|+++ .++|
T Consensus 41 iQ~~~~~~~~liDpl~~---l~~----~-------------------L-~~~Gv~~~~~fDT~LAa~lL~~~~~~~~~~l 93 (553)
T PRK14975 41 AQEGEEEPRWVWASTAA---LYP----R-------------------L-LAAGVRVERCHDLMLASQLLLGSEGRAGSSL 93 (553)
T ss_pred eeecCCCceEEECchHH---hHH----H-------------------H-HHCCCccCCCchHHHHHHHcCCCCCcCCCCH
Confidence 58888889999998752 221 1 4 45699888899999999999984 5899
Q ss_pred HHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcC
Q 006313 77 EYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSM 131 (651)
Q Consensus 77 ~~LVe~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~ 131 (651)
..++..||++.++|..+.++|. |||++.|+.||+.||.|++.||..|..+|.+.
T Consensus 94 ~~la~~~l~~~l~k~~~~sdw~-rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 94 SAAAARALGEGLDKPPQTSALS-DPPDEEQLLYAAADADVLLELYAVLADQLNRI 147 (553)
T ss_pred HHHHHHHhCCCCCChhhhcccc-ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence 9999999999999988899996 99999999999999999999999999999875
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=99.12 E-value=7.9e-10 Score=106.13 Aligned_cols=128 Identities=27% Similarity=0.391 Sum_probs=97.2
Q ss_pred CeeeeCCc-cEEEecCC------ccc-hhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcC-ceehHHHHHHHhCC
Q 006313 1 MQISTRTE-DFVVDTLK------LRV-QVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLC-NMFDTGQASRVLKL 71 (651)
Q Consensus 1 IQIAT~~~-~~LID~la------L~~-dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~-nlFDTqLAA~lLg~ 71 (651)
|+|+..+. .|+|++.. +.. .+...|..+|++..+.+|+|+++.|+.+| +.+|+.+. .+|||++++|+|++
T Consensus 27 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l-~~~gi~~~~~~~Dt~l~a~ll~p 105 (193)
T cd06139 27 ISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVL-ANHGIELRGPAFDTMLASYLLNP 105 (193)
T ss_pred EEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHHH-HHCCCCCCCCcccHHHHHHHhCC
Confidence 45665543 66665432 111 12234888999988899999999999999 56788765 58999999999998
Q ss_pred C--CCcHHHHHHHHcCCCC-------CcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhc
Q 006313 72 E--RNSLEYLLHHFCGVNA-------NKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSS 130 (651)
Q Consensus 72 ~--~~gL~~LVe~yLGv~L-------dK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e 130 (651)
. .++|..++++|++..+ .|..+..+|...|+ ..+..||+.|+.+++.|+..|..+|.+
T Consensus 106 ~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 106 GRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred CCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 5 4799999999998763 12233455654555 668999999999999999999999975
No 21
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.00 E-value=5.4e-10 Score=125.04 Aligned_cols=129 Identities=23% Similarity=0.300 Sum_probs=103.5
Q ss_pred CeeeeCCccEEEecCCccch----hhHHHHHhhcCCCceEEEeeccccHHHHHH-----hhCCCc---Ccee-hHHHHHH
Q 006313 1 MQISTRTEDFVVDTLKLRVQ----VGPYLREVFKDPTKKKVMHGADRDIVWLQR-----DFGIYL---CNMF-DTGQASR 67 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~d----L~~~L~~lLeDp~I~KV~H~ak~DL~~L~r-----dfGI~p---~nlF-DTqLAA~ 67 (651)
|||++.+++||||+.++... +.-.+..||+++.|.||+.+..+|++.+.+ .+++.+ .+++ ++.++..
T Consensus 436 lQif~~~~v~Lidc~~l~~~~se~w~~~~s~if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~ 515 (617)
T KOG2207|consen 436 LQIFFKDCVYLIDCVKLENLASEIWHLLLSQIFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAEN 515 (617)
T ss_pred HHHHhcCeEEEeehHHhhhchHHHHHHHHHHHccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHH
Confidence 69999999999999987532 234577899999999999999999999964 333332 2333 3344544
Q ss_pred HhCC-------C--CCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006313 68 VLKL-------E--RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 129 (651)
Q Consensus 68 lLg~-------~--~~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~ 129 (651)
+.+. . ..+|..|...++|..++|..|++||..|||...|+.|||.|++.+..+|..+.....
T Consensus 516 ~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 516 VIDLPLSIENLNEATKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred HhcccchhhhhcchhhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 4332 1 378999999999999999999999999999999999999999999999998766443
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=98.86 E-value=4.5e-09 Score=119.46 Aligned_cols=75 Identities=21% Similarity=0.310 Sum_probs=69.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHHHhHHHHHHHHHH
Q 006313 176 AGLNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKN 251 (651)
Q Consensus 176 ~~L~~~qlaVL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~r~G~eIL~iI~~ 251 (651)
+.+.. +.++|++|++||+++|++.|+|+++||+|.+|++||+.+|+|.++|.++.|++..++++||++|+++|+.
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=98.81 E-value=3e-07 Score=109.58 Aligned_cols=109 Identities=17% Similarity=0.105 Sum_probs=86.8
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcC-ceehHHHHHHHhCCC-CCcHHHHHHHHcCCCCCcccccccCC--
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLC-NMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWR-- 98 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~-nlFDTqLAA~lLg~~-~~gL~~LVe~yLGv~LdK~~q~SDW~-- 98 (651)
..|+++|+|+.+.||+|++++|+.+| ..+|+.+. .+|||++|+|+|++. .++|..|+.+||+.++.+......|.
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 35889999999999999999999999 57999875 589999999999985 47999999999997754322111111
Q ss_pred CCCCC-HHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 99 VRPLP-DEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 99 ~RPLS-~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
...++ +.+..||+.||.+++.||..|..+|.+.+
T Consensus 447 ~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~ 481 (887)
T TIGR00593 447 FAFPPLEEATEYLARRAAATKRLAEELLKELDENK 481 (887)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 11232 45678999999999999999999998543
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=98.63 E-value=3.2e-07 Score=85.89 Aligned_cols=118 Identities=20% Similarity=0.202 Sum_probs=81.8
Q ss_pred eeeCCccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCc-eehHHHHHHHhCCC-C-CcHHHH
Q 006313 3 ISTRTEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCN-MFDTGQASRVLKLE-R-NSLEYL 79 (651)
Q Consensus 3 IAT~~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~n-lFDTqLAA~lLg~~-~-~gL~~L 79 (651)
|++.+.+|+|++-. .... ..|+++|+|..+.|++|+.|.++.+| ..+|+...+ +|||+||+|+|++. . .+|..|
T Consensus 25 l~~~~~~~yi~~~~-~~~~-~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~~LAaYLL~p~~~~~~l~~l 101 (151)
T cd06128 25 FAIEGVAAYIPVAH-DYAL-ELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDTMLEAYLLDPVAGRHDMDSL 101 (151)
T ss_pred EEcCCCeEEEeCCC-CcCH-HHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhHHHHHHHcCCCCCCCCHHHH
Confidence 34554567775211 0012 35889999999999999999999999 678998764 69999999999995 2 699999
Q ss_pred HHHHcCCC-CC-cccccccCCC--CCC-CHHHHHHHHHhHHHHHHHHHHHH
Q 006313 80 LHHFCGVN-AN-KEYQNADWRV--RPL-PDEMLRYAREDTHYLLYIYDIMK 125 (651)
Q Consensus 80 Ve~yLGv~-Ld-K~~q~SDW~~--RPL-S~eQl~YAA~DV~yLl~Lyd~L~ 125 (651)
+.+||+.. +. .. ...+.. .++ ......|++..+.+++.|++.|.
T Consensus 102 a~~yl~~~~~~~~~--~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 102 AERWLKEKTITFEE--IAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred HHHHcCCCCccHHH--HcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 99999877 32 11 111110 011 12233488888888888888764
No 25
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=98.61 E-value=1.7e-07 Score=106.54 Aligned_cols=110 Identities=26% Similarity=0.296 Sum_probs=89.9
Q ss_pred hhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC--CCcHHHHHHHHcCCCCC-------cc
Q 006313 21 VGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNAN-------KE 91 (651)
Q Consensus 21 L~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~--~~gL~~LVe~yLGv~Ld-------K~ 91 (651)
....|++||+|+.+.||+|+.+.|.+.| ..+|+.++..|||++|+|+|+++ .++++.|+++|++.+.- |+
T Consensus 66 ~~~~l~~~l~~~~~~kv~~~~K~d~~~l-~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg 144 (593)
T COG0749 66 VLAALKPLLEDEGIKKVGQNLKYDYKVL-ANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKG 144 (593)
T ss_pred hHHHHHHHhhCcccchhccccchhHHHH-HHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccc
Confidence 3367999999999999999999999999 67886656899999999999986 49999999999998763 33
Q ss_pred cccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 92 YQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 92 ~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
.+.-++..-++ .....|++.||..+++|+..|..+|.+..
T Consensus 145 ~~~~~~~~~~~-~~~~~y~a~~a~~~~~L~~~l~~~l~~~~ 184 (593)
T COG0749 145 KKQLTFADVKL-EKATEYAAEDADATLRLESILEPELLKTP 184 (593)
T ss_pred cccCccccchH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 33333333344 55689999999999999999998887643
No 26
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=98.51 E-value=2.3e-07 Score=106.30 Aligned_cols=75 Identities=25% Similarity=0.380 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHHHhHHHHHHHHHHHHh
Q 006313 180 AQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQ 254 (651)
Q Consensus 180 ~~qlaVL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~r~G~eIL~iI~~Ale 254 (651)
..+..+|.+|..||.++|++.++|++.||+|.+|.+||+.+|+|.++|.+|.|++..++++||.+|+++|+.+.+
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 346789999999999999999999999999999999999999999999999999999999999999999998754
No 27
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=98.35 E-value=8.9e-07 Score=106.68 Aligned_cols=73 Identities=19% Similarity=0.312 Sum_probs=68.8
Q ss_pred HHHHHHHHHHHHHHHHHH--cCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHHHhHHHHHHHHHHHHh
Q 006313 182 QLAVVAGLCEWRDVIARA--DDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSMQ 254 (651)
Q Consensus 182 qlaVL~~L~~WRe~iAr~--~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~r~G~eIL~iI~~Ale 254 (651)
+..+|.+|..||.++|++ .++|++.||+|.+|.+||+.+|+|.++|.+|.|++..++++||.++|++|+..+.
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 457999999999999999 6999999999999999999999999999999999999999999999999987554
No 28
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=98.27 E-value=1.7e-06 Score=91.78 Aligned_cols=120 Identities=23% Similarity=0.290 Sum_probs=97.7
Q ss_pred CeeeeC-CccEEEecCCccchhhHHHHHhhcCCCceEEEeeccccHHHHHH-hhCCCcCceehHHHHH-HHhCCC--CCc
Q 006313 1 MQISTR-TEDFVVDTLKLRVQVGPYLREVFKDPTKKKVMHGADRDIVWLQR-DFGIYLCNMFDTGQAS-RVLKLE--RNS 75 (651)
Q Consensus 1 IQIAT~-~~~~LID~laL~~dL~~~L~~lLeDp~I~KV~H~ak~DL~~L~r-dfGI~p~nlFDTqLAA-~lLg~~--~~g 75 (651)
+||+.+ +.|+||...... .++..|+-+|+|++.++|+-..++|...|.+ .|++.+..+.|+..-+ -.+|.. .-+
T Consensus 152 lqlcV~en~C~I~ql~~~~-~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g~~~~~~s 230 (319)
T KOG4373|consen 152 LQLCVGENRCLIIQLIHCK-RIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLGGSMPNDS 230 (319)
T ss_pred hhhhhcccceeeEEeeccc-cchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhhccCccCcc
Confidence 699988 889999777665 3667799999999999999999999988877 8999888888887433 356552 245
Q ss_pred HHHHHHHHc---C--CCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006313 76 LEYLLHHFC---G--VNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 76 L~~LVe~yL---G--v~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Ly 121 (651)
...|+..++ | +.+++.-+.+||+..||+.+|+.||+.||+....|+
T Consensus 231 ~e~i~~~~~~~~~~~v~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 231 FEEIVSETLGYYGKDVRLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred HHHHHHHHhhccccccccChhcccccceeeeccHHHHHHHHhHHHHHHHHH
Confidence 555665554 4 556777899999999999999999999999999998
No 29
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=98.04 E-value=7.7e-06 Score=93.45 Aligned_cols=72 Identities=24% Similarity=0.311 Sum_probs=69.0
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHHHhHHHHHHHHHHHH
Q 006313 182 QLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIERYMGPVLSIIKNSM 253 (651)
Q Consensus 182 qlaVL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~r~G~eIL~iI~~Al 253 (651)
...+|.+|..||.++|.+.|+||+.|++|.+|.++|+.+|.+..+|..+.|++..++.+||..++++|.+..
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 567999999999999999999999999999999999999999999999999999999999999999998764
No 30
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.32 E-value=0.00081 Score=73.10 Aligned_cols=123 Identities=23% Similarity=0.271 Sum_probs=85.4
Q ss_pred CeeeeCCccEEEecCCccch-hhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC----CCc
Q 006313 1 MQISTRTEDFVVDTLKLRVQ-VGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE----RNS 75 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~d-L~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~----~~g 75 (651)
+|||+..++||+|.+.-+.- +-.-.+..|+...+ |. ++..++..++..|++.+.+++|||+|..++.+. ++.
T Consensus 216 m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~sLve~~e~grr~p 292 (458)
T KOG2405|consen 216 MNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIASSLVEPSEYGRRHP 292 (458)
T ss_pred hhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHHHHhhhHHhcccCC
Confidence 58999999999998874422 11224566766554 44 999999999999999999999999999887642 122
Q ss_pred HHHHHH--------HHcCCCCC------cc--cccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHH
Q 006313 76 LEYLLH--------HFCGVNAN------KE--YQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKI 126 (651)
Q Consensus 76 L~~LVe--------~yLGv~Ld------K~--~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~ 126 (651)
...++- .|++.... +. .....|..||.+.....-+..||+.|+.++..|..
T Consensus 293 ~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a 359 (458)
T KOG2405|consen 293 TSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVA 359 (458)
T ss_pred ccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhh
Confidence 222111 12222111 11 12246999999999999999999999997766543
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=94.34 E-value=0.14 Score=45.06 Aligned_cols=66 Identities=17% Similarity=0.260 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHhCCCCHHHHHhhhCCChhHHHH--hHHHHHHHHH
Q 006313 185 VVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQLPTTAAKLRRLLKSKHSYIER--YMGPVLSIIK 250 (651)
Q Consensus 185 VL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~~P~S~eeL~~i~G~~~~~v~r--~G~eIL~iI~ 250 (651)
.+..|.+-|-.++.+.|.|..-.|+|..|..||...|.|..++..|.|......++ |-...|-.++
T Consensus 8 aY~~Lr~~~~~~~~~~n~p~~~f~sd~~LKk~A~~LP~te~eF~~l~g~~~~~~~kFkyFK~tl~~Lr 75 (80)
T PF11408_consen 8 AYEKLREISINLSNRMNPPNDNFMSDTILKKMATKLPTTEEEFSKLVGINEQQRKKFKYFKDTLMRLR 75 (80)
T ss_dssp HHHHHHHHHHHHHHSSSS--S-SS-HHHHHHHHHH---SHHHHGGGS---HHHHHHGGGTHHHHHHHH
T ss_pred HHHHHHHHHHHHhhccCCCccccCCHHHHHHHHHHCCCCHHHHHHhcCCcHHHHHHHHHHHHHHHHHH
Confidence 47788999999999999999888999999999999999999999999987766553 5555444443
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=93.45 E-value=0.16 Score=50.57 Aligned_cols=79 Identities=23% Similarity=0.217 Sum_probs=53.4
Q ss_pred HHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCCCCcHHHHHHHHcCCCCCcccccccCCCCCCCH
Q 006313 25 LREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPD 104 (651)
Q Consensus 25 L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~~~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS~ 104 (651)
|+.++ ++..+.|+|+..+|+.+|. +-..-..+.||.+.-..-.....+|..|+.+|||.++..+.
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 44554 4566889999999999993 22122479999753221111258999999999999885321
Q ss_pred HHHHHHHHhHHHHHHHH
Q 006313 105 EMLRYAREDTHYLLYIY 121 (651)
Q Consensus 105 eQl~YAA~DV~yLl~Ly 121 (651)
.-..+||.+.+.||
T Consensus 160 ---HdSvEDArAam~Ly 173 (174)
T cd06143 160 ---HDSIEDARTALKLY 173 (174)
T ss_pred ---cCcHHHHHHHHHHh
Confidence 11357888888887
No 33
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=92.80 E-value=0.005 Score=67.16 Aligned_cols=115 Identities=25% Similarity=0.415 Sum_probs=85.0
Q ss_pred CeeeeCCccEEEecCCccch-hhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHh-CC--C----
Q 006313 1 MQISTRTEDFVVDTLKLRVQ-VGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVL-KL--E---- 72 (651)
Q Consensus 1 IQIAT~~~~~LID~laL~~d-L~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lL-g~--~---- 72 (651)
+|++|.-.+||+|++.++.. ....+..+++|..|.|+.|+|..-..++.+.|||...++|||++|--+- +. +
T Consensus 79 ~q~~~~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~q~~d~~q~~~e~g~~~~ 158 (458)
T KOG2405|consen 79 LQVATNCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVADVLQFSMETGGYLP 158 (458)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhhhhhhhhhhcccccccCC
Confidence 47778888899999988753 3456888999999999999999999999999999999999999976542 21 1
Q ss_pred C--CcH-HHHHHHHcCCCCC------cc-----cccccCCCCCCCHHHHHHHHHhHHH
Q 006313 73 R--NSL-EYLLHHFCGVNAN------KE-----YQNADWRVRPLPDEMLRYAREDTHY 116 (651)
Q Consensus 73 ~--~gL-~~LVe~yLGv~Ld------K~-----~q~SDW~~RPLS~eQl~YAA~DV~y 116 (651)
. ..+ ..|++++ .+-+. |. ...-.|-.||.++.-+.-.+..+.|
T Consensus 159 n~~~~~q~sl~kh~-~~a~k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 159 NCITTLQESLIKHL-QVAPKYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred ccccchHHHHHHHH-HhcccHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 1 223 4455533 33221 21 2345699999999888877777777
No 34
>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=92.40 E-value=0.3 Score=43.36 Aligned_cols=41 Identities=20% Similarity=0.267 Sum_probs=29.3
Q ss_pred HHHhhcCCC-ceEEEeeccccHHHHHHhhCC-------CcCceehHHHH
Q 006313 25 LREVFKDPT-KKKVMHGADRDIVWLQRDFGI-------YLCNMFDTGQA 65 (651)
Q Consensus 25 L~~lLeDp~-I~KV~H~ak~DL~~L~rdfGI-------~p~nlFDTqLA 65 (651)
|.+++.+.. ..+|+|++..|+..|.+.+.. .....+||+.+
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 567787766 678999999999887655432 23457888855
No 35
>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=91.74 E-value=1.3 Score=44.33 Aligned_cols=86 Identities=15% Similarity=0.072 Sum_probs=61.6
Q ss_pred CceEEEeeccccHHHHHHh---hCCC-----cCceehHHHHHHHhCCCCCcHHHHHHHHcCCCCCcccccccCCCCCCCH
Q 006313 33 TKKKVMHGADRDIVWLQRD---FGIY-----LCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPD 104 (651)
Q Consensus 33 ~I~KV~H~ak~DL~~L~rd---fGI~-----p~nlFDTqLAA~lLg~~~~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS~ 104 (651)
..+.|+|++..|+.+|... +|+. +..++||...++.+.+ ..+|..+++.| |+... .
T Consensus 105 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~-~~~L~~l~~~~-gi~~~--------------~ 168 (200)
T TIGR01298 105 RAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG-QTVLAKACQAA-GXDFD--------------S 168 (200)
T ss_pred CCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC-cccHHHHHHHc-CCCcc--------------c
Confidence 3468999999999888643 3432 1247999977776543 46799988764 65432 1
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHhcCCCC
Q 006313 105 EMLRYAREDTHYLLYIYDIMKIKLSSMPKE 134 (651)
Q Consensus 105 eQl~YAA~DV~yLl~Lyd~L~~~L~e~Gr~ 134 (651)
.+..-|..||..+..|+..|..++.+.+.|
T Consensus 169 ~~~H~Al~Da~ata~lf~~l~~~~~~~~~~ 198 (200)
T TIGR01298 169 TQAHSALYDTEKTAELFCEIVNRWKRLGGW 198 (200)
T ss_pred cchhhhHHhHHHHHHHHHHHHHHHHHccCC
Confidence 234558899999999999999999887743
No 36
>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=91.72 E-value=0.84 Score=46.73 Aligned_cols=86 Identities=29% Similarity=0.377 Sum_probs=59.7
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHh---hC--CC-c---CceehHHHHHHHhCCC-CCcHHHHHHHHcCCCCCcccc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRD---FG--IY-L---CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQ 93 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rd---fG--I~-p---~nlFDTqLAA~lLg~~-~~gL~~LVe~yLGv~LdK~~q 93 (651)
.|..++.+. ..|.|++.+|+.+|.+. +| +. + ..++||...++.+-++ +++|..|+++| |+...
T Consensus 75 ~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~-gi~~~---- 147 (225)
T TIGR01406 75 EFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRF-KVDNS---- 147 (225)
T ss_pred HHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhc-CCCCC----
Confidence 455677653 46899999999988644 34 22 1 4689999877765544 58999999886 55432
Q ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHH
Q 006313 94 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKI 126 (651)
Q Consensus 94 ~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~ 126 (651)
.|. ..-|..||..+..||..|..
T Consensus 148 -----~r~-----~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 148 -----HRT-----LHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred -----CCC-----CcCHHHHHHHHHHHHHHHHc
Confidence 111 23478899999999988654
No 37
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=91.66 E-value=0.77 Score=47.69 Aligned_cols=87 Identities=28% Similarity=0.403 Sum_probs=59.4
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHhh---C--CC----cCceehHHHHHHHhCCC-CCcHHHHHHHHcCCCCCcccc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRDF---G--IY----LCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQ 93 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rdf---G--I~----p~nlFDTqLAA~lLg~~-~~gL~~LVe~yLGv~LdK~~q 93 (651)
.|..++.+. ..|+|++.+|+.+|.+.+ | +. .+.++||...++.+-++ +++|..|+++| |+...
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 355666553 468999999998886443 3 21 14589998777766544 58999999875 65432
Q ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006313 94 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 127 (651)
Q Consensus 94 ~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~ 127 (651)
.|. ..-|..||..+..||..|...
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 234788999999999887644
No 38
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=91.51 E-value=0.85 Score=49.05 Aligned_cols=91 Identities=23% Similarity=0.208 Sum_probs=66.1
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHhh---CCCc--CceehHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRDF---GIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 95 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rdf---GI~p--~nlFDTqLAA~lLg~--~~~gL~~LVe~yLGv~LdK~~q~S 95 (651)
..|..++.+ .+.|.|++.+|+.+|.+.+ |+.. ..++||+..++.+.+ ..+.|..|+++ +|+....
T Consensus 86 ~~l~~~l~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~-~gi~~~~----- 157 (313)
T PRK06063 86 GEVAELLRG--RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAH-WGVPQQR----- 157 (313)
T ss_pred HHHHHHcCC--CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHH-cCCCCCC-----
Confidence 346667765 3678999999999986543 4432 358999987776654 36899999975 5765421
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 96 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 96 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
..-|..||.++..|+..|..++.+.+
T Consensus 158 -----------~H~Al~DA~ata~l~~~ll~~~~~~~ 183 (313)
T PRK06063 158 -----------PHDALDDARVLAGILRPSLERARERD 183 (313)
T ss_pred -----------CCCcHHHHHHHHHHHHHHHHHHHhcC
Confidence 13477899999999999988888765
No 39
>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=91.45 E-value=0.51 Score=45.07 Aligned_cols=81 Identities=17% Similarity=0.096 Sum_probs=54.5
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccccCCCC
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNADWRVR 100 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~--~~~gL~~LVe~yLGv~LdK~~q~SDW~~R 100 (651)
+.|.+++.+ ..+.|+|++..|+.+|.. + ...++||...++.+.. .+++|..|++.|++..+.....
T Consensus 67 ~~~~~fl~~-~~vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~------- 134 (150)
T cd06145 67 KKLLSLISP-DTILVGHSLENDLKALKL-I---HPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEG------- 134 (150)
T ss_pred HHHHHHhCC-CCEEEEcChHHHHHHhhc-c---CCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCC-------
Confidence 456677752 346899999999999943 2 2458999876664332 2589999999999866532100
Q ss_pred CCCHHHHHHHHHhHHHHHHHH
Q 006313 101 PLPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 101 PLS~eQl~YAA~DV~yLl~Ly 121 (651)
..-|..||..+..||
T Consensus 135 ------~H~Al~DA~~t~~l~ 149 (150)
T cd06145 135 ------GHDSVEDARAALELV 149 (150)
T ss_pred ------CCCcHHHHHHHHHHh
Confidence 122557777777765
No 40
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=91.31 E-value=0.55 Score=45.28 Aligned_cols=80 Identities=19% Similarity=0.111 Sum_probs=54.9
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCC-----CCCcHHHHHHHHcCCCCCcccccccCC
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKL-----ERNSLEYLLHHFCGVNANKEYQNADWR 98 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~-----~~~gL~~LVe~yLGv~LdK~~q~SDW~ 98 (651)
.|..++.+. .+.|+|++..|+.+|.. ....++||...++.+.+ .+++|..|+..|+|+++......
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 456666542 46799999999999943 23468999977776543 35899999999999776431111
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHH
Q 006313 99 VRPLPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 99 ~RPLS~eQl~YAA~DV~yLl~Ly 121 (651)
.-|..||..+..||
T Consensus 147 ---------H~A~~DA~at~~l~ 160 (161)
T cd06137 147 ---------HDSLEDALAAREVV 160 (161)
T ss_pred ---------CCcHHHHHHHHHHh
Confidence 22556777776665
No 41
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=90.97 E-value=1.3 Score=42.22 Aligned_cols=84 Identities=25% Similarity=0.385 Sum_probs=56.9
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHhh---CCC-----cCceehHHHHHHHhCC-CCCcHHHHHHHHcCCCCCccccc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRDF---GIY-----LCNMFDTGQASRVLKL-ERNSLEYLLHHFCGVNANKEYQN 94 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rdf---GI~-----p~nlFDTqLAA~lLg~-~~~gL~~LVe~yLGv~LdK~~q~ 94 (651)
.|..++.+. ..|+|++..|+.+|.+.+ |+. +..++||+..++.+.+ ...+|..++++| |+....
T Consensus 74 ~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~-~i~~~~---- 146 (167)
T cd06131 74 EFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRF-GIDNSH---- 146 (167)
T ss_pred HHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHC-CCCCCC----
Confidence 456677653 468999999998886543 332 2458999876665544 357999999886 554321
Q ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 006313 95 ADWRVRPLPDEMLRYAREDTHYLLYIYDIM 124 (651)
Q Consensus 95 SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L 124 (651)
....-|..||.++..|+..|
T Consensus 147 ----------~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 147 ----------RTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred ----------CCCCChHHHHHHHHHHHHHh
Confidence 11244788999998888665
No 42
>PRK05168 ribonuclease T; Provisional
Probab=90.71 E-value=2.7 Score=42.55 Aligned_cols=85 Identities=18% Similarity=0.143 Sum_probs=59.7
Q ss_pred CceEEEeeccccHHHHHH---hhCCC-----cCceehHHHHHHHhCCCCCcHHHHHHHHcCCCCCcccccccCCCCCCCH
Q 006313 33 TKKKVMHGADRDIVWLQR---DFGIY-----LCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPD 104 (651)
Q Consensus 33 ~I~KV~H~ak~DL~~L~r---dfGI~-----p~nlFDTqLAA~lLg~~~~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS~ 104 (651)
..+.|+|++..|+.+|.+ .+|+. +..++||...++.+.. ...|..++.. +|+.+...
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 34442 1258999866665533 3678888876 46554211
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHhcCCC
Q 006313 105 EMLRYAREDTHYLLYIYDIMKIKLSSMPK 133 (651)
Q Consensus 105 eQl~YAA~DV~yLl~Lyd~L~~~L~e~Gr 133 (651)
...-|..||..+..|+..|..++.+.+.
T Consensus 179 -~~H~Al~DA~ata~l~~~l~~~~~~~~~ 206 (211)
T PRK05168 179 -EAHSALYDTEKTAELFCEIVNRWKRLGG 206 (211)
T ss_pred -CCCChHHHHHHHHHHHHHHHHHHHHccC
Confidence 1133788999999999999999987763
No 43
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=89.89 E-value=0.35 Score=46.12 Aligned_cols=80 Identities=20% Similarity=0.208 Sum_probs=55.1
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCC---CCCcHHHHHHHHcCCCCCcccccccCCC
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKL---ERNSLEYLLHHFCGVNANKEYQNADWRV 99 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~---~~~gL~~LVe~yLGv~LdK~~q~SDW~~ 99 (651)
+.|..++.+ . +.|+|++..|+.+|. .......++||.....+... ..++|+.|++.|+|+.+....
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 469999999999994 33333468888754333322 358999999999998764211
Q ss_pred CCCCHHHHHHHHHhHHHHHHHH
Q 006313 100 RPLPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 100 RPLS~eQl~YAA~DV~yLl~Ly 121 (651)
.-|..||..+..||
T Consensus 138 --------H~Al~DA~at~~l~ 151 (152)
T cd06144 138 --------HSSVEDARAAMRLY 151 (152)
T ss_pred --------cCcHHHHHHHHHHh
Confidence 22667888887776
No 44
>PRK07740 hypothetical protein; Provisional
Probab=89.69 E-value=3.5 Score=42.74 Aligned_cols=90 Identities=17% Similarity=0.212 Sum_probs=65.4
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHh----hCCCc-CceehHHHHHHHhCCC--CCcHHHHHHHHcCCCCCccccccc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRD----FGIYL-CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNAD 96 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rd----fGI~p-~nlFDTqLAA~lLg~~--~~gL~~LVe~yLGv~LdK~~q~SD 96 (651)
.|..++.+ -+.|+|++..|+.+|.+. ++... ..++||+..++.+.+. .++|..++. ++|+.+...
T Consensus 134 ~f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~-~~gi~~~~~----- 205 (244)
T PRK07740 134 RFYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALA-YYGIPIPRR----- 205 (244)
T ss_pred HHHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHH-HCCcCCCCC-----
Confidence 34455554 367899999999887542 23333 4699999888876653 589999985 467765421
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 97 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 97 W~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
.-|..||.++..|+..|..++.+.|
T Consensus 206 -----------H~Al~Da~ata~l~~~ll~~~~~~~ 230 (244)
T PRK07740 206 -----------HHALGDALMTAKLWAILLVEAQQRG 230 (244)
T ss_pred -----------CCcHHHHHHHHHHHHHHHHHHHHcC
Confidence 2377899999999999999988766
No 45
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=89.05 E-value=1.6 Score=44.91 Aligned_cols=83 Identities=17% Similarity=0.199 Sum_probs=58.8
Q ss_pred CceEEEeeccccHHHHHHh---hCCC---cCceehHHHHHHHhCC---CCCcHHHHHHHHcCCCCCcccccccCCCCCCC
Q 006313 33 TKKKVMHGADRDIVWLQRD---FGIY---LCNMFDTGQASRVLKL---ERNSLEYLLHHFCGVNANKEYQNADWRVRPLP 103 (651)
Q Consensus 33 ~I~KV~H~ak~DL~~L~rd---fGI~---p~nlFDTqLAA~lLg~---~~~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS 103 (651)
..+.|+|++.+|+.+|.+. +|+. ..+++||...++.+.. ++++|..|+++ +|+.+...
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 3466999999999888554 3433 2468999987765432 35899999877 57665421
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 104 DEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 104 ~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
.-|..||..+..|+..|..++.+.+
T Consensus 160 ----H~Al~Da~ata~l~~~l~~~~~~l~ 184 (232)
T PRK07942 160 ----HEATADALAAARVAWALARRFPELA 184 (232)
T ss_pred ----CChHHHHHHHHHHHHHHHHHHHHhh
Confidence 2377899999999999887666443
No 46
>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=88.97 E-value=3.7 Score=40.72 Aligned_cols=77 Identities=18% Similarity=0.115 Sum_probs=53.0
Q ss_pred ceEEEeeccccHHHHHH---hhCCC-----cCceehHHHHHHHhCCCCCcHHHHHHHHcCCCCCcccccccCCCCCCCHH
Q 006313 34 KKKVMHGADRDIVWLQR---DFGIY-----LCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDE 105 (651)
Q Consensus 34 I~KV~H~ak~DL~~L~r---dfGI~-----p~nlFDTqLAA~lLg~~~~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS~e 105 (651)
.+.|+|++..|+.+|++ .+|+. +..++||...++.+.+ ...|..++.. +|+.++. .
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~-~~~L~~l~~~-~gi~~~~--------------~ 166 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG-QTVLAKACQA-AGIEFDN--------------K 166 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC-CCcHHHHHHH-CCCCCCC--------------C
Confidence 46899999999988864 35551 2358999977766543 4689988876 4665421 0
Q ss_pred HHHHHHHhHHHHHHHHHHHHH
Q 006313 106 MLRYAREDTHYLLYIYDIMKI 126 (651)
Q Consensus 106 Ql~YAA~DV~yLl~Lyd~L~~ 126 (651)
...-|..||..+..|+..|.+
T Consensus 167 ~~H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 167 EAHSALYDTQKTAELFCKIVN 187 (189)
T ss_pred CCcChHHHHHHHHHHHHHHHH
Confidence 123377899999888887654
No 47
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=88.80 E-value=1.7 Score=53.86 Aligned_cols=91 Identities=24% Similarity=0.283 Sum_probs=72.4
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHh---hCCCc--CceehHHHHHHHhCCC--CCcHHHHHHHHcCCCCCcccccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNA 95 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rd---fGI~p--~nlFDTqLAA~lLg~~--~~gL~~LVe~yLGv~LdK~~q~S 95 (651)
+.+++|+.|. +-|.|++..|+..|+.. +++.+ .+++||.-.|+.|.+. +++|..|+.+| |+.+
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 4578898874 67999999999888654 55655 4799999999999875 69999999876 4443
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 96 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 96 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
++..-|-.|+.++..|+..+.+.|.++|
T Consensus 563 ---------e~hHRA~yDaeat~~vf~~f~~~~ke~G 590 (1444)
T COG2176 563 ---------ERHHRADYDAEATAKVFFVFLKDLKEKG 590 (1444)
T ss_pred ---------HHhhhhhhhHHHHHHHHHHHHHHHHHhc
Confidence 3455677799999999999999888876
No 48
>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=88.22 E-value=1.1 Score=43.17 Aligned_cols=82 Identities=21% Similarity=0.125 Sum_probs=52.8
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHH---HHHHhCC---CCCcHHHHHHHHcCCCCCccccccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQ---ASRVLKL---ERNSLEYLLHHFCGVNANKEYQNAD 96 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqL---AA~lLg~---~~~gL~~LVe~yLGv~LdK~~q~SD 96 (651)
+.|..++.+ .+.|+|++.+|+.+|... ..+..+.||.. +.+..+. ..++|..|+++|++..+....+.
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 468999999999998422 22335778853 2233222 24899999999997766432211
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHH
Q 006313 97 WRVRPLPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 97 W~~RPLS~eQl~YAA~DV~yLl~Ly 121 (651)
.-|..||.+...||
T Consensus 143 -----------H~Al~DA~at~~l~ 156 (157)
T cd06149 143 -----------HSSVEDARATMELY 156 (157)
T ss_pred -----------cCcHHHHHHHHHHh
Confidence 22556777777776
No 49
>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=87.17 E-value=2.8 Score=42.40 Aligned_cols=90 Identities=21% Similarity=0.321 Sum_probs=59.7
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHhhC---CC---cCceehHHHHHHHhC---C-CCCcHHHHHHHHcCCCCCcccc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRDFG---IY---LCNMFDTGQASRVLK---L-ERNSLEYLLHHFCGVNANKEYQ 93 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rdfG---I~---p~nlFDTqLAA~lLg---~-~~~gL~~LVe~yLGv~LdK~~q 93 (651)
.|..++.+ ...|+|++.+|+.+|.+.+. .. ...++||...++.+. + .+++|..|++.| |+....
T Consensus 80 ~~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~-gl~~~~--- 153 (217)
T TIGR00573 80 DFADYIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRY-EITNSH--- 153 (217)
T ss_pred HHHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHc-CCCCCC---
Confidence 45666655 35789999999999976542 21 135789876555432 2 257899998775 654220
Q ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhc
Q 006313 94 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSS 130 (651)
Q Consensus 94 ~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e 130 (651)
....-|..||.++..|+..|..+...
T Consensus 154 -----------~~~H~Al~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 154 -----------RALHGALADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred -----------cccCCHHHHHHHHHHHHHHHHhcchh
Confidence 01233788999999999988776554
No 50
>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=86.93 E-value=2.7 Score=38.20 Aligned_cols=81 Identities=22% Similarity=0.184 Sum_probs=54.7
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHhhC-----CCcCceehHHHHHHH-hCCC-CCcHHHHHHHHcCCCCCcccccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRDFG-----IYLCNMFDTGQASRV-LKLE-RNSLEYLLHHFCGVNANKEYQNA 95 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfG-----I~p~nlFDTqLAA~l-Lg~~-~~gL~~LVe~yLGv~LdK~~q~S 95 (651)
..|..++.+ ...|+|++..|..+|.+.+. ......+||+..+.. ++.. ..++..+...+++....
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 346667776 57899999999999866543 334579999866554 4433 47787775556665432
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006313 96 DWRVRPLPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 96 DW~~RPLS~eQl~YAA~DV~yLl~Ly 121 (651)
+..-|..||.++..||
T Consensus 143 ----------~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 143 ----------GAHRALADALATAELL 158 (159)
T ss_pred ----------CCCCcHHHHHHHHHHh
Confidence 2244778888888775
No 51
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=86.57 E-value=3.6 Score=38.49 Aligned_cols=89 Identities=22% Similarity=0.246 Sum_probs=60.3
Q ss_pred HHHHHhhcCCCceEEEeec-cccHHHHHHh---hCCCc---CceehHHHHHHHhCCC-CCcHHHHHHHHcCCCCCccccc
Q 006313 23 PYLREVFKDPTKKKVMHGA-DRDIVWLQRD---FGIYL---CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQN 94 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~a-k~DL~~L~rd---fGI~p---~nlFDTqLAA~lLg~~-~~gL~~LVe~yLGv~LdK~~q~ 94 (651)
..|..++.+. ..|+|++ ..|+.+|.+. +|+.. ...+||...++.+... ..+|..|++.| |+.....
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 3466777653 3567777 9999988653 33332 2479998777655433 68999999775 4333210
Q ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006313 95 ADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 129 (651)
Q Consensus 95 SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~ 129 (651)
...|..||..+..|+..|..++.
T Consensus 146 ------------~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 146 ------------AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred ------------CcCcHHHHHHHHHHHHHHHHHhh
Confidence 25688999999999998876653
No 52
>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=85.19 E-value=2.5 Score=53.23 Aligned_cols=91 Identities=24% Similarity=0.314 Sum_probs=69.0
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHh---hCCCc--CceehHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 95 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rd---fGI~p--~nlFDTqLAA~lLg~--~~~gL~~LVe~yLGv~LdK~~q~S 95 (651)
+.|..++.+ .+.|.|++..|+.+|.+. +|+.+ ..++||...++.+.+ ..++|..|+++ +|+.+..
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 346677765 367899999999888643 45542 468999988887764 36999999987 4776532
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 96 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 96 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
...|..||.++..|+..|..++.+.+
T Consensus 334 -----------~HrAl~DA~aTa~I~~~ll~~l~~~~ 359 (1213)
T TIGR01405 334 -----------HHRADYDAEATAKVFKVMVEQLKEKG 359 (1213)
T ss_pred -----------CcCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 25688999999999999998887654
No 53
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=85.17 E-value=5.5 Score=43.06 Aligned_cols=87 Identities=17% Similarity=0.152 Sum_probs=61.0
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHhh---CCC--cCceehHHHHHHHhCC--CCCcHHHHHHHHcCCCCCccccccc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRDF---GIY--LCNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNAD 96 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rdf---GI~--p~nlFDTqLAA~lLg~--~~~gL~~LVe~yLGv~LdK~~q~SD 96 (651)
.|..++.+. ..|+|++..|+.+|.+.+ |+. ...++||+..++.+.+ ..++|..|++. +|+.. +
T Consensus 81 ~f~~fl~~~--~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~-lgi~~-~------ 150 (313)
T PRK06807 81 LFLAFLHTN--VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRM-LGIRL-S------ 150 (313)
T ss_pred HHHHHHcCC--eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHH-cCCCC-C------
Confidence 455566553 358999999999987644 442 2358999976665443 35899999854 56554 1
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhc
Q 006313 97 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSS 130 (651)
Q Consensus 97 W~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e 130 (651)
..-|..||.++..||..|...+..
T Consensus 151 ----------~H~Al~DA~~ta~l~~~l~~~~~~ 174 (313)
T PRK06807 151 ----------SHNAFDDCITCAAVYQKCASIEEE 174 (313)
T ss_pred ----------CcChHHHHHHHHHHHHHHHHhhhh
Confidence 133778999999999998887743
No 54
>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=84.76 E-value=6.3 Score=36.70 Aligned_cols=79 Identities=22% Similarity=0.215 Sum_probs=53.8
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHhh---CCC--cCceehHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRDF---GIY--LCNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 95 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rdf---GI~--p~nlFDTqLAA~lLg~--~~~gL~~LVe~yLGv~LdK~~q~S 95 (651)
..|..++.+ ...|+|++..|..+|.+.+ |+. ....+||+..+..+-+ ..++|..|++. +|+... .
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 346677766 4679999999999886543 544 3468999876665433 35899999986 566543 1
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006313 96 DWRVRPLPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 96 DW~~RPLS~eQl~YAA~DV~yLl~Ly 121 (651)
.-|..||..+..|+
T Consensus 141 ------------H~Al~Da~~ta~l~ 154 (156)
T cd06130 141 ------------HDALEDARACAEIL 154 (156)
T ss_pred ------------cCchHHHHHHHHHH
Confidence 22567777777765
No 55
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=84.68 E-value=1.5 Score=46.53 Aligned_cols=88 Identities=17% Similarity=0.226 Sum_probs=62.0
Q ss_pred HHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHh---CC-CCCcHHHHHHHHcCCCCCcccccccCCCC
Q 006313 25 LREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVL---KL-ERNSLEYLLHHFCGVNANKEYQNADWRVR 100 (651)
Q Consensus 25 L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lL---g~-~~~gL~~LVe~yLGv~LdK~~q~SDW~~R 100 (651)
...||.+ .+.|+|+..+|+..|+-.+- -.-+-||.-.--|. .. ...||..|.+.+||+++--++..+
T Consensus 178 v~klL~g--RIlVGHaLhnDl~~L~l~hp--~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHsS----- 248 (280)
T KOG2249|consen 178 VLKLLKG--RILVGHALHNDLQALKLEHP--RSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHSS----- 248 (280)
T ss_pred HHHHHhC--CEEeccccccHHHHHhhhCc--hhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccccCc-----
Confidence 4457755 46799999999999964432 12366886433332 22 258999999999999986555333
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHHHHHHhcC
Q 006313 101 PLPDEMLRYAREDTHYLLYIYDIMKIKLSSM 131 (651)
Q Consensus 101 PLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~ 131 (651)
.+||.+...||.....+.++.
T Consensus 249 ----------vEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 249 ----------VEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred ----------HHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999887766643
No 56
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=84.54 E-value=4.4 Score=42.54 Aligned_cols=87 Identities=20% Similarity=0.260 Sum_probs=60.8
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHH---hhCCCc--CceehHHHHHH-HhCCCCCcHHHHHHHHcCCCCCcccccccC
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQR---DFGIYL--CNMFDTGQASR-VLKLERNSLEYLLHHFCGVNANKEYQNADW 97 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~r---dfGI~p--~nlFDTqLAA~-lLg~~~~gL~~LVe~yLGv~LdK~~q~SDW 97 (651)
.|..++.+. +.|+|++..|..+|.+ .+|+.+ ...+||.-.++ ++...+++|+.|++ ++|++...
T Consensus 140 ~f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~~-~lgi~~~~------- 209 (257)
T PRK08517 140 EFRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKE-LLGIEIEV------- 209 (257)
T ss_pred HHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHHH-HcCcCCCC-------
Confidence 466677653 5789999999988854 344432 35788875444 45445789999987 56766532
Q ss_pred CCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006313 98 RVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 129 (651)
Q Consensus 98 ~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~ 129 (651)
..-|..||.++..|+..+..++.
T Consensus 210 ---------~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 210 ---------HHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred ---------CCChHHHHHHHHHHHHHHHHHhH
Confidence 13377899999999998887764
No 57
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=84.31 E-value=6.4 Score=40.97 Aligned_cols=87 Identities=22% Similarity=0.265 Sum_probs=60.7
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHh---hCCCc----CceehHHHHHHHhCCC-CCcHHHHHHHHcCCCCCcccccc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL----CNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNA 95 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rd---fGI~p----~nlFDTqLAA~lLg~~-~~gL~~LVe~yLGv~LdK~~q~S 95 (651)
.|..++.+. -..|+|++.+|+.+|.+. +|+.. ..++||+-.++.++.. .++|..|++.| |+.+..
T Consensus 80 ~~~~fl~~~-~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~-g~~~~~----- 152 (250)
T PRK06310 80 QIKGFFKEG-DYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHF-NVPYDG----- 152 (250)
T ss_pred HHHHHhCCC-CEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHC-CCCCCC-----
Confidence 455666553 367999999999888643 34432 4589999877776543 58999998765 665432
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q 006313 96 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKL 128 (651)
Q Consensus 96 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L 128 (651)
..-|..||.++..|+..|..++
T Consensus 153 -----------aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 153 -----------NHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred -----------CcChHHHHHHHHHHHHHHHHhc
Confidence 1337789999999988876543
No 58
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=82.51 E-value=5.4 Score=48.45 Aligned_cols=91 Identities=21% Similarity=0.186 Sum_probs=66.2
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHh---hCCCc-CceehHHHHHHHhCC--CCCcHHHHHHHHcCCCCCccccccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL-CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNAD 96 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rd---fGI~p-~nlFDTqLAA~lLg~--~~~gL~~LVe~yLGv~LdK~~q~SD 96 (651)
+.|..++.+ .+.|+|++..|+.+|.+. .|+.+ .+.+||...++.+-+ .+++|..|++. +|+....
T Consensus 78 ~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~-lgl~~~~------ 148 (820)
T PRK07246 78 RHIYDLIED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRE-LNIDLAD------ 148 (820)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHH-cCCCCCC------
Confidence 345667765 457999999999998654 35543 468999977776544 36999999975 6766432
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 97 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 97 W~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
..-|..||.++..|+..|..++...+
T Consensus 149 ----------~H~Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 149 ----------AHTAIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred ----------CCCHHHHHHHHHHHHHHHHHHHhhcC
Confidence 13377899999999999988887654
No 59
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=81.17 E-value=6.1 Score=38.72 Aligned_cols=80 Identities=23% Similarity=0.183 Sum_probs=54.7
Q ss_pred HHHHhhcC--CCceEEEeec-cccHHHHHHh---hCCCc---CceehHHHHHHHhCCCCCcHHHHHHHHcCCCCCccccc
Q 006313 24 YLREVFKD--PTKKKVMHGA-DRDIVWLQRD---FGIYL---CNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQN 94 (651)
Q Consensus 24 ~L~~lLeD--p~I~KV~H~a-k~DL~~L~rd---fGI~p---~nlFDTqLAA~lLg~~~~gL~~LVe~yLGv~LdK~~q~ 94 (651)
.|..++.. ...+.|+|++ ..|+.+|.+. +|+.+ ..++||...++.+.+ +|+.|+.+++|+....
T Consensus 87 ~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~---~L~~l~~~~~~~~~~~---- 159 (177)
T cd06136 87 LIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ---SLGSLYKRLFGQEPKN---- 159 (177)
T ss_pred HHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh---hHHHHHHHHhCCCccc----
Confidence 35555543 2357899998 8999888543 34443 235799877776554 8999999888877542
Q ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 006313 95 ADWRVRPLPDEMLRYAREDTHYLLYIYD 122 (651)
Q Consensus 95 SDW~~RPLS~eQl~YAA~DV~yLl~Lyd 122 (651)
..-|..||..+..++.
T Consensus 160 ------------~H~A~~Da~at~~v~~ 175 (177)
T cd06136 160 ------------SHTAEGDVLALLKCAL 175 (177)
T ss_pred ------------ccchHHHHHHHHHHHh
Confidence 2347788888877653
No 60
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=80.60 E-value=13 Score=39.90 Aligned_cols=87 Identities=17% Similarity=0.187 Sum_probs=59.9
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHh---hCCCc--CceehHHHHHHHhCC--CCCcHHHHHHHHcCCCCCccccccc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNAD 96 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rd---fGI~p--~nlFDTqLAA~lLg~--~~~gL~~LVe~yLGv~LdK~~q~SD 96 (651)
.|..++.+ -+.|+|++.+|+.+|.+. +++.. ...+||+..++.+-+ ..++|..|++.| |+...
T Consensus 73 ~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~~-gi~~~------- 142 (309)
T PRK06195 73 KIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFL-GYEFK------- 142 (309)
T ss_pred HHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHHc-CCCCc-------
Confidence 45566654 467999999999888543 34443 358999866654433 368999998875 54321
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhc
Q 006313 97 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSS 130 (651)
Q Consensus 97 W~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e 130 (651)
..-|..||..+..|+..|..++..
T Consensus 143 ----------~H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 143 ----------HHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred ----------ccCCHHHHHHHHHHHHHHHHHhcc
Confidence 144778999999998888776653
No 61
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=80.60 E-value=9.2 Score=39.21 Aligned_cols=88 Identities=19% Similarity=0.264 Sum_probs=60.4
Q ss_pred HHHHhhcCCCceEEEee-ccccHHHHHHh---hCCCc--CceehHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006313 24 YLREVFKDPTKKKVMHG-ADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 95 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~-ak~DL~~L~rd---fGI~p--~nlFDTqLAA~lLg~--~~~gL~~LVe~yLGv~LdK~~q~S 95 (651)
.|..++.+ ....|+|+ +..|+.+|.+. +|+.. ...+||+-.++.+.+ ..++|..|+..| |+....
T Consensus 72 ~~~~fi~~-~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~-~~~~~~----- 144 (232)
T PRK06309 72 KFIEFCGT-DNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVY-GFEENQ----- 144 (232)
T ss_pred HHHHHHcC-CCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHHHHc-CCCCCC-----
Confidence 34555643 34678999 48999888643 34432 368999877776644 368999998776 554322
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006313 96 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 129 (651)
Q Consensus 96 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~ 129 (651)
..-|..||.++..|+..|..++.
T Consensus 145 -----------aH~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 145 -----------AHRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred -----------CCCcHHHHHHHHHHHHHHHHHHH
Confidence 13377899999999998876653
No 62
>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=80.04 E-value=10 Score=37.30 Aligned_cols=98 Identities=21% Similarity=0.277 Sum_probs=63.4
Q ss_pred HHHHHhhcC--CCceEEEeec-cccHHHHHH---hhCCCc-----------------------C-ceehHHHHHHHh-CC
Q 006313 23 PYLREVFKD--PTKKKVMHGA-DRDIVWLQR---DFGIYL-----------------------C-NMFDTGQASRVL-KL 71 (651)
Q Consensus 23 ~~L~~lLeD--p~I~KV~H~a-k~DL~~L~r---dfGI~p-----------------------~-nlFDTqLAA~lL-g~ 71 (651)
..|..++.+ |. +.|+|+. ..|+..|.. .+|+.. . .++|+...++.. ..
T Consensus 68 ~~f~~~i~~~dpd-iivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~l 146 (199)
T cd05160 68 KRFFDIIREYDPD-ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFKL 146 (199)
T ss_pred HHHHHHHHhcCCC-EEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcCc
Confidence 345566654 55 4789999 789987754 345444 1 368998776643 34
Q ss_pred CCCcHHHHHHHHcCCCCCc--ccccccCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006313 72 ERNSLEYLLHHFCGVNANK--EYQNADWRVRPLPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 72 ~~~gL~~LVe~yLGv~LdK--~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Ly 121 (651)
..++|..+++++|+..-.. .....+|....--...++|...||...+.|+
T Consensus 147 ~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 147 KSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred ccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 5699999999999864321 1122222111122568999999999998875
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=79.25 E-value=1.5 Score=41.52 Aligned_cols=97 Identities=20% Similarity=0.303 Sum_probs=55.8
Q ss_pred HhhcCCCceEEEeeccccHHHHHHhh---CCC-cCceehHHHHHHHhCCCCCcHHHHHHHHcCCCCCc-c---cc----c
Q 006313 27 EVFKDPTKKKVMHGADRDIVWLQRDF---GIY-LCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANK-E---YQ----N 94 (651)
Q Consensus 27 ~lLeDp~I~KV~H~ak~DL~~L~rdf---GI~-p~nlFDTqLAA~lLg~~~~gL~~LVe~yLGv~LdK-~---~q----~ 94 (651)
.++.........|+..+|+.+|.+.+ ++. +.+.+|++..++-....+++|..|... +|+.-.. . .. .
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 45666666666777788999987665 333 457899998776444456788888776 6665431 1 10 1
Q ss_pred ccCCC---CCCCHHHHHHHHHhHHHHHHHHHHH
Q 006313 95 ADWRV---RPLPDEMLRYAREDTHYLLYIYDIM 124 (651)
Q Consensus 95 SDW~~---RPLS~eQl~YAA~DV~yLl~Lyd~L 124 (651)
..|.. ....+..+.|...||..+..|++.|
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 12211 2344889999999999999999876
No 64
>PRK07883 hypothetical protein; Validated
Probab=77.50 E-value=8.6 Score=44.75 Aligned_cols=90 Identities=20% Similarity=0.177 Sum_probs=63.8
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHh---hCCCc--CceehHHHHHH-HhC---CCCCcHHHHHHHHcCCCCCccccc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASR-VLK---LERNSLEYLLHHFCGVNANKEYQN 94 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rd---fGI~p--~nlFDTqLAA~-lLg---~~~~gL~~LVe~yLGv~LdK~~q~ 94 (651)
.|..++.+ .+.|+|++..|+.+|... +|+.. ...+||+..++ ++. ...++|..|++ ++|+....
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 45566665 457899999999888643 45544 35789986555 343 23589999986 56776532
Q ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 95 ADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 95 SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
..-|..||.++..|+..|..++.+.+
T Consensus 161 ------------~H~Al~DA~ata~l~~~l~~~~~~~~ 186 (557)
T PRK07883 161 ------------THRALDDARATVDVLHGLIERLGNLG 186 (557)
T ss_pred ------------CCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 14478899999999999988887554
No 65
>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=77.08 E-value=11 Score=45.94 Aligned_cols=91 Identities=18% Similarity=0.207 Sum_probs=65.5
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHh---hCCC--cCceehHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIY--LCNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 95 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rd---fGI~--p~nlFDTqLAA~lLg~--~~~gL~~LVe~yLGv~LdK~~q~S 95 (651)
+.|..++.+ .+.|+|++..|+.+|.+. +|+. +...+||...++.+.+ ..++|.+|++. +|+..+..
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 345567654 357999999999988653 4554 3568999977776644 36899999877 57665321
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 96 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 96 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
.-|..||.++..|+..|..++....
T Consensus 145 ------------H~Al~DA~ata~l~~~l~~~~~~l~ 169 (850)
T TIGR01407 145 ------------HRADSDAQATAELLLLLFEKMEKLP 169 (850)
T ss_pred ------------CChHHHHHHHHHHHHHHHHHHHhcC
Confidence 3377899999999999988887644
No 66
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=75.52 E-value=1.5 Score=53.02 Aligned_cols=86 Identities=22% Similarity=0.182 Sum_probs=61.2
Q ss_pred hhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCCC-CcHHHHHHHHcCCCCCcccccccCCCCCCCHHH
Q 006313 28 VFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLER-NSLEYLLHHFCGVNANKEYQNADWRVRPLPDEM 106 (651)
Q Consensus 28 lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~~-~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS~eQ 106 (651)
+|-+-.++.|+|+...|..++. .-+....++||.+. .+++.++ .+|..|+-++||.++--+.
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvIN--i~Vp~~QiiDTv~l-f~~~s~R~LSLrfLa~~lLg~~IQ~~~-------------- 1071 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVIN--IHVPEEQIIDTVTL-FRLGSQRMLSLRFLAWELLGETIQMEA-------------- 1071 (1118)
T ss_pred HHHHcCcEEEcccccccceEEE--EecChhhheeeeEE-EecccccEEEHHHHHHHHhcchhhccc--------------
Confidence 5667889999999999988762 22333359999743 2345544 7999999999998873221
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 107 LRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 107 l~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
.-..+||++.+.||++.. +|+++|
T Consensus 1072 -HDSIeDA~taLkLYk~Yl-~lkeq~ 1095 (1118)
T KOG1275|consen 1072 -HDSIEDARTALKLYKKYL-KLKEQG 1095 (1118)
T ss_pred -cccHHHHHHHHHHHHHHH-HHHHhh
Confidence 123689999999999844 477655
No 67
>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=75.27 E-value=12 Score=37.16 Aligned_cols=100 Identities=24% Similarity=0.370 Sum_probs=65.2
Q ss_pred HHHHHhhcC--CCceEEEeec-cccHHHHHHh---hCCCc------------------------CceehHHHHHH-HhCC
Q 006313 23 PYLREVFKD--PTKKKVMHGA-DRDIVWLQRD---FGIYL------------------------CNMFDTGQASR-VLKL 71 (651)
Q Consensus 23 ~~L~~lLeD--p~I~KV~H~a-k~DL~~L~rd---fGI~p------------------------~nlFDTqLAA~-lLg~ 71 (651)
..|..++.. |.+ .|+|+. ..|+..|..+ +|+.. ...+|+...++ .+..
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 345556654 774 678886 5799877543 34431 12789886665 3555
Q ss_pred CCCcHHHHHHHHcCCCCCc--cccccc-CCCCCCCHHHHHHHHHhHHHHHHHHHH
Q 006313 72 ERNSLEYLLHHFCGVNANK--EYQNAD-WRVRPLPDEMLRYAREDTHYLLYIYDI 123 (651)
Q Consensus 72 ~~~gL~~LVe~yLGv~LdK--~~q~SD-W~~RPLS~eQl~YAA~DV~yLl~Lyd~ 123 (651)
..++|..+++++||..... ..+... |...+--...++|+..||..++.|...
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 6799999999999986321 112222 333323366899999999999988764
No 68
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=73.31 E-value=20 Score=39.98 Aligned_cols=95 Identities=18% Similarity=0.241 Sum_probs=60.2
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHhh------------------------------C-CCc-CceehHHHHHHHhC
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRDF------------------------------G-IYL-CNMFDTGQASRVLK 70 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rdf------------------------------G-I~p-~nlFDTqLAA~lLg 70 (651)
+.|..++.+ .+.|+|++.+|+.+|...+ | +.. ..++||.-.++.+.
T Consensus 117 ~el~~fL~g--~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~ 194 (377)
T PRK05601 117 KPLDRLIDG--RTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQG 194 (377)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHc
Confidence 456677765 3679999999999886543 1 122 35899998888776
Q ss_pred CC--CCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 006313 71 LE--RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIM 124 (651)
Q Consensus 71 ~~--~~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L 124 (651)
+. .+.|..|+.+ +|+..+-. ..+.= .+-.+..+ .+..|+..|..||..+
T Consensus 195 p~l~~~rL~~La~~-lGi~~p~~-~A~~~-Ra~~p~~~--l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 195 VALDDIRIRGVAHT-LGLDAPAA-EASVE-RAQVPHRQ--LCREETLLVARLYFAL 245 (377)
T ss_pred CCCCCCCHHHHHHH-hCCCCCch-hhhhh-hhcCChhh--hhhHHHHHHHHHHHHh
Confidence 53 6999999987 57665321 00000 01111222 2446899999998775
No 69
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=72.24 E-value=23 Score=43.75 Aligned_cols=91 Identities=23% Similarity=0.328 Sum_probs=65.1
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHh---hCCCc--CceehHHHHHHHhCC--CCCcHHHHHHHHcCCCCCcccccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL--CNMFDTGQASRVLKL--ERNSLEYLLHHFCGVNANKEYQNA 95 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rd---fGI~p--~nlFDTqLAA~lLg~--~~~gL~~LVe~yLGv~LdK~~q~S 95 (651)
+.|..++.+ .+.|+|++.+|+.+|.+. .|+.+ ..++||.-.++.+-+ ..++|..|++. +|+..+..
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 346667765 467999999999998653 35443 468999877776544 36899999986 46554321
Q ss_pred cCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 96 DWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 96 DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
.-|..||.++..|+..|..++....
T Consensus 149 ------------H~Al~DA~ata~l~~~l~~~~~~l~ 173 (928)
T PRK08074 149 ------------HRADSDAEVTAELFLQLLNKLERLP 173 (928)
T ss_pred ------------CChHHHHHHHHHHHHHHHHHHHhcC
Confidence 3367899999999999988887654
No 70
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=71.37 E-value=9.5 Score=46.19 Aligned_cols=96 Identities=15% Similarity=0.172 Sum_probs=66.0
Q ss_pred ceEEEeeccccHHHHHHhhCCCcC--ceehHHHHHH----Hh----------------------------------CCC-
Q 006313 34 KKKVMHGADRDIVWLQRDFGIYLC--NMFDTGQASR----VL----------------------------------KLE- 72 (651)
Q Consensus 34 I~KV~H~ak~DL~~L~rdfGI~p~--nlFDTqLAA~----lL----------------------------------g~~- 72 (651)
-+.|+|+..+|...++..|.|.-. ...|||-... ++ +..
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 467999999999988888887754 3679984321 11 000
Q ss_pred CCcHHHHHHHHcCCC-CCcccccccCCCCCCC------HHHHHHHHHhHHHHHHHHHHHHHHHhc
Q 006313 73 RNSLEYLLHHFCGVN-ANKEYQNADWRVRPLP------DEMLRYAREDTHYLLYIYDIMKIKLSS 130 (651)
Q Consensus 73 ~~gL~~LVe~yLGv~-LdK~~q~SDW~~RPLS------~eQl~YAA~DV~yLl~Lyd~L~~~L~e 130 (651)
-.||.++.+.+||++ |+|.... +|-.-++. .+.+.|+|.||+....+|..+.....+
T Consensus 322 ~NSL~dVhk~~c~~~~LdKt~Rd-~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fle 385 (1075)
T KOG3657|consen 322 LNSLVDVHKFHCGIDALDKTPRD-SFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLE 385 (1075)
T ss_pred hHHHHHHHHhhCCCCccccchHH-hhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHH
Confidence 146777888899988 8875422 22222221 445789999999999999998876554
No 71
>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=68.54 E-value=20 Score=34.61 Aligned_cols=69 Identities=13% Similarity=0.106 Sum_probs=40.7
Q ss_pred cccHHHHHHhhCCCcCceehHHHHHHHhCCCCCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006313 42 DRDIVWLQRDFGIYLCNMFDTGQASRVLKLERNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 42 k~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~~~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Ly 121 (651)
..|+..+...-|+.+.+--|-++.||+|++.......++++|+|- +|... |+..+....+|+
T Consensus 70 AK~LAv~a~~~G~~v~PGDDPlLlAYLlDPsNt~p~~varRY~~~---------~W~~d---------A~~RA~~t~~L~ 131 (138)
T PF09281_consen 70 AKDLAVHALREGVVVEPGDDPLLLAYLLDPSNTNPEGVARRYLGG---------EWPED---------AATRALATARLL 131 (138)
T ss_dssp HHHHHHHHHHTT----B---HHHHHHHH-TT--SHHHHHHHH-TS------------SS---------HHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCcccCCCCCcchhhhhcCccCCChHHHHHHhcCC---------CCCcc---------HHHHHHHHHHHH
Confidence 456666657788888888899999999999989999999999883 45422 455566666677
Q ss_pred HHHHHHH
Q 006313 122 DIMKIKL 128 (651)
Q Consensus 122 d~L~~~L 128 (651)
+.|..+|
T Consensus 132 ~~L~prL 138 (138)
T PF09281_consen 132 RALPPRL 138 (138)
T ss_dssp HHHHHHT
T ss_pred HHhhhcC
Confidence 7766553
No 72
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=67.46 E-value=21 Score=46.09 Aligned_cols=89 Identities=22% Similarity=0.247 Sum_probs=65.2
Q ss_pred HHHhhcCCCceEEEeeccccHHHHH---HhhCCC--cCceehHHHHHHHhCCC--CCcHHHHHHHHcCCCCCcccccccC
Q 006313 25 LREVFKDPTKKKVMHGADRDIVWLQ---RDFGIY--LCNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNADW 97 (651)
Q Consensus 25 L~~lLeDp~I~KV~H~ak~DL~~L~---rdfGI~--p~nlFDTqLAA~lLg~~--~~gL~~LVe~yLGv~LdK~~q~SDW 97 (651)
+..++. ....|.|.+..|+.+|. +.+|+. ....+||+..++.+.+. .++|..|+++ +|+.+...
T Consensus 493 f~~fig--g~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~-lGL~~~~~------ 563 (1437)
T PRK00448 493 FKEFCG--DSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKK-FGVELEHH------ 563 (1437)
T ss_pred HHHHhC--CCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHH-cCCCCCCC------
Confidence 444454 35789999999997763 345664 24689999888876543 6899999986 57665421
Q ss_pred CCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHhcCC
Q 006313 98 RVRPLPDEMLRYAREDTHYLLYIYDIMKIKLSSMP 132 (651)
Q Consensus 98 ~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~e~G 132 (651)
.-|..||.++..|+..|..++.+.|
T Consensus 564 ----------HrAl~DA~aTa~lf~~ll~~l~~~g 588 (1437)
T PRK00448 564 ----------HRADYDAEATAYLLIKFLKDLKEKG 588 (1437)
T ss_pred ----------cChHHHHHHHHHHHHHHHHHHHHcC
Confidence 4588899999999999998887654
No 73
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=58.32 E-value=52 Score=33.78 Aligned_cols=78 Identities=17% Similarity=-0.063 Sum_probs=52.9
Q ss_pred CceEEEeeccccHHHHHHhhCCCcCceehHHHHHHHhCCC-CCcHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHH
Q 006313 33 TKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASRVLKLE-RNSLEYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAR 111 (651)
Q Consensus 33 ~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~lLg~~-~~gL~~LVe~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA 111 (651)
..+.|+|++.+|..+|. .+ ....+||.-.++.+-+. .+++..|+.. +|+..... + .....-|.
T Consensus 74 ~~~lVaHNa~FD~~~L~-~~---~~~~idTl~lar~l~p~~~~~l~~L~~~-~~l~~~~~-----~------~~~aHrAl 137 (219)
T PRK07983 74 SEWYVAHNASFDRRVLP-EM---PGEWICTMKLARRLWPGIKYSNMALYKS-RKLNVQTP-----P------GLHHHRAL 137 (219)
T ss_pred CCEEEEeCcHhhHHHHh-Cc---CCCcEeHHHHHHHHccCCCCCHHHHHHH-cCCCCCCC-----C------CCCCCcHH
Confidence 34789999999999983 22 34689999888766553 5889888865 45443110 0 01234588
Q ss_pred HhHHHHHHHHHHHHH
Q 006313 112 EDTHYLLYIYDIMKI 126 (651)
Q Consensus 112 ~DV~yLl~Lyd~L~~ 126 (651)
.||..+..|+..|..
T Consensus 138 ~Da~ata~ll~~l~~ 152 (219)
T PRK07983 138 YDCYITAALLIDIMN 152 (219)
T ss_pred HHHHHHHHHHHHHHH
Confidence 899999998887653
No 74
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=57.95 E-value=59 Score=32.81 Aligned_cols=84 Identities=15% Similarity=0.169 Sum_probs=52.9
Q ss_pred HHHHHhhcCCCceEEEeecc-ccHHHHHHhhCCCcCc--eehHH---HHHHHh---CCCCCcHHHHHHHHcCCCCCcccc
Q 006313 23 PYLREVFKDPTKKKVMHGAD-RDIVWLQRDFGIYLCN--MFDTG---QASRVL---KLERNSLEYLLHHFCGVNANKEYQ 93 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak-~DL~~L~rdfGI~p~n--lFDTq---LAA~lL---g~~~~gL~~LVe~yLGv~LdK~~q 93 (651)
+.|..++.+. ..|+|++. .|+.+| ...|+.+.+ .+||. .+.+.. +...++|..|++. +|+...
T Consensus 76 ~~f~~f~~~~--~lVaHNa~~fD~~fL-~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~-~gi~~~---- 147 (195)
T PRK07247 76 AAFKEFVGEL--PLIGYNAQKSDLPIL-AENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADF-LGIKGR---- 147 (195)
T ss_pred HHHHHHHCCC--eEEEEeCcHhHHHHH-HHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHh-cCCCCC----
Confidence 3466777654 47899996 799999 456765443 34553 222221 1235899999875 566421
Q ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006313 94 NADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 127 (651)
Q Consensus 94 ~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~ 127 (651)
..-|..||.++..||..|...
T Consensus 148 -------------~HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 148 -------------GHNSLEDARMTARVYESFLES 168 (195)
T ss_pred -------------CcCCHHHHHHHHHHHHHHHhh
Confidence 123668899999988876543
No 75
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=57.00 E-value=37 Score=35.28 Aligned_cols=86 Identities=17% Similarity=0.069 Sum_probs=56.1
Q ss_pred HHHhhcCCCceEEEeeccccHHHHHHhh----CCCc-CceehHHHHHHHhCC---------------CCCcHHHHHHHHc
Q 006313 25 LREVFKDPTKKKVMHGADRDIVWLQRDF----GIYL-CNMFDTGQASRVLKL---------------ERNSLEYLLHHFC 84 (651)
Q Consensus 25 L~~lLeDp~I~KV~H~ak~DL~~L~rdf----GI~p-~nlFDTqLAA~lLg~---------------~~~gL~~LVe~yL 84 (651)
|..++.+ .+.|+|++..|..+|.+.+ +..+ ..++||+..++.+-+ ..+.|..++.. +
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 3578999999999886542 3333 468999976654311 23678888876 4
Q ss_pred CCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 006313 85 GVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIKLS 129 (651)
Q Consensus 85 Gv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~L~ 129 (651)
|+... ...-|..||.++..|+..+..++-
T Consensus 200 gl~~~----------------~~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 200 GLPAY----------------SPHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred CCCCC----------------CCCCcHHHHHHHHHHHHHHHHHHc
Confidence 54432 113477899999999888776663
No 76
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=56.53 E-value=68 Score=32.16 Aligned_cols=88 Identities=14% Similarity=0.124 Sum_probs=55.8
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHHh---hCCCc---CceehHHHHHHH-hCC-CCCcHHHHHHHHcCCCCCccccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQRD---FGIYL---CNMFDTGQASRV-LKL-ERNSLEYLLHHFCGVNANKEYQN 94 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~rd---fGI~p---~nlFDTqLAA~l-Lg~-~~~gL~~LVe~yLGv~LdK~~q~ 94 (651)
..|..++.+.... |+|.+..|+..|.+. +|+.. ...+|++..... .+. ..++|..+++. +|+....
T Consensus 84 ~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~-~gi~~~~---- 157 (207)
T PRK07748 84 EKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEE-YGKEGTG---- 157 (207)
T ss_pred HHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHHH-cCCCCCC----
Confidence 3567778763333 445578999888654 35442 246778765543 332 24899998876 4554311
Q ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006313 95 ADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 127 (651)
Q Consensus 95 SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~ 127 (651)
...-|..||.++..|+..|...
T Consensus 158 -----------~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 158 -----------KHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred -----------CCcChHHHHHHHHHHHHHHHhC
Confidence 1134788999999999887765
No 77
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=54.40 E-value=92 Score=31.00 Aligned_cols=83 Identities=16% Similarity=0.124 Sum_probs=53.2
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHhh----CCCc-CceehHHHHHH-HhC---C---CCCcHHHHHHHHcCCCCCcc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRDF----GIYL-CNMFDTGQASR-VLK---L---ERNSLEYLLHHFCGVNANKE 91 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rdf----GI~p-~nlFDTqLAA~-lLg---~---~~~gL~~LVe~yLGv~LdK~ 91 (651)
.|..++.+ .+.|+|++..|+.+|.+.+ +... ...+|+.-..+ ... + ..++|+.+++.| |+.....
T Consensus 104 ~~~~~i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~-gi~~~~~ 180 (202)
T PRK09145 104 QLLAFIGN--RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHL-DLPVLGR 180 (202)
T ss_pred HHHHHHcC--CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHc-CCCCCCC
Confidence 45566664 3578999999998886443 4443 35789863322 111 1 148999999664 6654221
Q ss_pred cccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006313 92 YQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 125 (651)
Q Consensus 92 ~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 125 (651)
.-|..||.++..||..|.
T Consensus 181 ----------------H~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 181 ----------------HDALNDAIMAALIFLRLR 198 (202)
T ss_pred ----------------CCcHHHHHHHHHHHHHHH
Confidence 236788999988888764
No 78
>PRK11779 sbcB exonuclease I; Provisional
Probab=49.62 E-value=63 Score=37.20 Aligned_cols=87 Identities=18% Similarity=0.107 Sum_probs=51.5
Q ss_pred HHHHhhcCCCceEEEee-ccccHHHHHHhhCCC-----------cC---ceehHHHHHHHhC------------CCCCcH
Q 006313 24 YLREVFKDPTKKKVMHG-ADRDIVWLQRDFGIY-----------LC---NMFDTGQASRVLK------------LERNSL 76 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~-ak~DL~~L~rdfGI~-----------p~---nlFDTqLAA~lLg------------~~~~gL 76 (651)
.+..+|..+..+.|+|+ +.+|..++...+... .. .++|+.-+++.+. ...+.|
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 35556654556688996 689998875443111 01 2345554444432 234889
Q ss_pred HHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006313 77 EYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 127 (651)
Q Consensus 77 ~~LVe~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~ 127 (651)
+.|+..+ |+.... ..-|..||..+..|+..|..+
T Consensus 164 e~L~~~~-gI~~~~----------------AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 164 EHLTKAN-GIEHEN----------------AHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHHHHc-CCCCCC----------------CCCcHHHHHHHHHHHHHHHHh
Confidence 9999875 554321 133667888888777776654
No 79
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=45.86 E-value=1.5e+02 Score=30.04 Aligned_cols=88 Identities=22% Similarity=0.226 Sum_probs=60.8
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHhh---CCCc--CceehHHHHHHHhCCC--CCcHHHHHHHHcCCCCCccccccc
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRDF---GIYL--CNMFDTGQASRVLKLE--RNSLEYLLHHFCGVNANKEYQNAD 96 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rdf---GI~p--~nlFDTqLAA~lLg~~--~~gL~~LVe~yLGv~LdK~~q~SD 96 (651)
.+..++.+. -..|.|++..|+..|...+ +..+ ..+.||...++...++ ..+|..|+. .+|+.... ...
T Consensus 87 ~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~~-~~~-- 161 (243)
T COG0847 87 EFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRNP-FHP-- 161 (243)
T ss_pred HHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHH-HcCCCcCC-cCC--
Confidence 344566554 4679999999998885433 3332 4578998777765554 689999998 67777431 110
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q 006313 97 WRVRPLPDEMLRYAREDTHYLLYIYDIMKIK 127 (651)
Q Consensus 97 W~~RPLS~eQl~YAA~DV~yLl~Lyd~L~~~ 127 (651)
.-|..|+..+..+|..+...
T Consensus 162 -----------H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 162 -----------HRALFDALALAELFLLLQTG 181 (243)
T ss_pred -----------cchHHHHHHHHHHHHHHHhc
Confidence 23778999999988887764
No 80
>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=43.20 E-value=1.3e+02 Score=28.42 Aligned_cols=86 Identities=16% Similarity=0.162 Sum_probs=52.6
Q ss_pred HHHHHhhcCCCceEEEeeccccHHHHHH---hhCC-----CcCceehHHHHHH-HhCCC-CCcHHHHHHHHcCCCCCccc
Q 006313 23 PYLREVFKDPTKKKVMHGADRDIVWLQR---DFGI-----YLCNMFDTGQASR-VLKLE-RNSLEYLLHHFCGVNANKEY 92 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~ak~DL~~L~r---dfGI-----~p~nlFDTqLAA~-lLg~~-~~gL~~LVe~yLGv~LdK~~ 92 (651)
..|..++.+.....+.|....|...+.. .++. .....+|++..+. +.+.. ..+|..++.. +|+....
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 3466777764113445556888755432 3333 2346899986555 44443 6899999855 4766531
Q ss_pred ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 006313 93 QNADWRVRPLPDEMLRYAREDTHYLLYIYDIM 124 (651)
Q Consensus 93 q~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L 124 (651)
+..-|..||.++..|+..|
T Consensus 157 -------------~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 157 -------------RHHRGLDDARNIARILKRL 175 (176)
T ss_pred -------------CCcCcHHHHHHHHHHHHHh
Confidence 1234678999998887765
No 81
>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=38.48 E-value=56 Score=32.88 Aligned_cols=62 Identities=19% Similarity=0.252 Sum_probs=40.9
Q ss_pred eehHHHHHH--HhCCCCCcHHHHHHHHcCCCCCc-cc-----cc-ccCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 006313 59 MFDTGQASR--VLKLERNSLEYLLHHFCGVNANK-EY-----QN-ADWRVRPLPDEMLRYAREDTHYLLYIYD 122 (651)
Q Consensus 59 lFDTqLAA~--lLg~~~~gL~~LVe~yLGv~LdK-~~-----q~-SDW~~RPLS~eQl~YAA~DV~yLl~Lyd 122 (651)
++|+..... .+...+++|..+++++||..-.. .. .. .-|...+ ...++|+..||...++|++
T Consensus 123 ~~D~~~~~k~~~~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 123 VLDGIDALKTATYHFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred EEEhHHHHHHccCCCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 678765543 24455799999999999964221 10 11 1133333 5689999999999998863
No 82
>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=38.02 E-value=1e+02 Score=30.24 Aligned_cols=80 Identities=19% Similarity=0.129 Sum_probs=46.3
Q ss_pred HHHHhhcCCCceEEEee-ccccHHHHHHhh---CCCc--------CceehHHHHHHH---hCC------------CCCcH
Q 006313 24 YLREVFKDPTKKKVMHG-ADRDIVWLQRDF---GIYL--------CNMFDTGQASRV---LKL------------ERNSL 76 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~-ak~DL~~L~rdf---GI~p--------~nlFDTqLAA~l---Lg~------------~~~gL 76 (651)
.|..++..+..+.|+|+ +..|+.+|.+.+ ++.+ ...+||.-.+++ +.+ ..++|
T Consensus 75 ~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L 154 (183)
T cd06138 75 KIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKL 154 (183)
T ss_pred HHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhH
Confidence 35556654444568886 789999986543 3321 124677644432 211 24779
Q ss_pred HHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHH
Q 006313 77 EYLLHHFCGVNANKEYQNADWRVRPLPDEMLRYAREDTHYLLYI 120 (651)
Q Consensus 77 ~~LVe~yLGv~LdK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~L 120 (651)
+.|+++ +|+... +..-|..||..+..|
T Consensus 155 ~~l~~~-~gi~~~----------------~~H~Al~Da~~ta~l 181 (183)
T cd06138 155 EDLAQA-NGIEHS----------------NAHDALSDVEATIAL 181 (183)
T ss_pred HHHHHH-CCCCcc----------------ccccHHHHHHHHHHH
Confidence 999976 465542 224466777766554
No 83
>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=37.49 E-value=55 Score=33.40 Aligned_cols=67 Identities=24% Similarity=0.245 Sum_probs=44.2
Q ss_pred eehHHHHHHH-hCCCCCcHHHHHHHHcCCCCCc-c-ccccc-CCCCCCC-HHHHHHHHHhHHHHHHHHHHHH
Q 006313 59 MFDTGQASRV-LKLERNSLEYLLHHFCGVNANK-E-YQNAD-WRVRPLP-DEMLRYAREDTHYLLYIYDIMK 125 (651)
Q Consensus 59 lFDTqLAA~l-Lg~~~~gL~~LVe~yLGv~LdK-~-~q~SD-W~~RPLS-~eQl~YAA~DV~yLl~Lyd~L~ 125 (651)
++|+...+.- .....++|..+++++||..... . ..... |...|-. ...++|+..||...+.|+..|.
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 4577655542 3345799999999999965321 1 12222 3323321 4579999999999999988765
No 84
>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=33.17 E-value=1.7e+02 Score=29.75 Aligned_cols=97 Identities=19% Similarity=0.192 Sum_probs=59.6
Q ss_pred HHHHHhhcCCCceEEEeec-cccHHHHHHh---hCCCcC------------------ceehHHHHHHHhCC-CCCcHHHH
Q 006313 23 PYLREVFKDPTKKKVMHGA-DRDIVWLQRD---FGIYLC------------------NMFDTGQASRVLKL-ERNSLEYL 79 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~a-k~DL~~L~rd---fGI~p~------------------nlFDTqLAA~lLg~-~~~gL~~L 79 (651)
..|..++.+-.-..|+|+. ..|+..|..+ +|+... ..+|++......+. ...+|..+
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 3455566542224578877 7899888653 455311 16788866554443 46899998
Q ss_pred HHHHcCCCCCccc----c-cccCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 006313 80 LHHFCGVNANKEY----Q-NADWRVRPLPDEMLRYAREDTHYLLYIYD 122 (651)
Q Consensus 80 Ve~yLGv~LdK~~----q-~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd 122 (651)
++ +||+. .|.. + ..-|..-.+ ....+|+..||..+..||-
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 67763 2211 1 122443333 6689999999999988873
No 85
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=31.34 E-value=2.2e+02 Score=30.72 Aligned_cols=82 Identities=17% Similarity=0.082 Sum_probs=50.4
Q ss_pred HHHHhhcCCCceEEEeeccccHHHHHHhhCCCc-CceehHHHHHHH--hCCCCCcHHHHHHHHcCCCCCcccccccCCCC
Q 006313 24 YLREVFKDPTKKKVMHGADRDIVWLQRDFGIYL-CNMFDTGQASRV--LKLERNSLEYLLHHFCGVNANKEYQNADWRVR 100 (651)
Q Consensus 24 ~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p-~nlFDTqLAA~l--Lg~~~~gL~~LVe~yLGv~LdK~~q~SDW~~R 100 (651)
.|..++.+. -+.|.|++.+|+.+|.+.+.-.. ....+++..... .+...++|.+|+..| |.. |
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 466677663 46789999999999965432211 234445432222 233468999999865 421 1
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHH
Q 006313 101 PLPDEMLRYAREDTHYLLYIYDIM 124 (651)
Q Consensus 101 PLS~eQl~YAA~DV~yLl~Lyd~L 124 (651)
...-|..||.++..|+..+
T Consensus 179 -----~aHrAl~Da~Ata~ll~~~ 197 (294)
T PRK09182 179 -----EGHRAVDDCQALLELLARP 197 (294)
T ss_pred -----CCcChHHHHHHHHHHHHHH
Confidence 1134788999998877643
No 86
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=30.70 E-value=95 Score=29.27 Aligned_cols=50 Identities=8% Similarity=0.143 Sum_probs=36.4
Q ss_pred CCHHHHHhhhCCChhHHHHhHHHHHHHHHH----HHhccccHHHHHHHHHHHhh
Q 006313 222 TTAAKLRRLLKSKHSYIERYMGPVLSIIKN----SMQNAANFEVIAQKLKEERM 271 (651)
Q Consensus 222 ~S~eeL~~i~G~~~~~v~r~G~eIL~iI~~----Ale~~~~~e~~~~~~k~~~~ 271 (651)
.++.++.+..|+..+.++.+.+.|++.|.- ..........++.+|.+|.+
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 577888888899999999999999998875 23333445566667766643
No 87
>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=30.55 E-value=60 Score=33.39 Aligned_cols=63 Identities=17% Similarity=0.175 Sum_probs=42.4
Q ss_pred eehHHHHHH-HhCCCCCcHHHHHHHHcCCCCCc--ccccccCCC--CC-CCHHHHHHHHHhHHHHHHHH
Q 006313 59 MFDTGQASR-VLKLERNSLEYLLHHFCGVNANK--EYQNADWRV--RP-LPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 59 lFDTqLAA~-lLg~~~~gL~~LVe~yLGv~LdK--~~q~SDW~~--RP-LS~eQl~YAA~DV~yLl~Ly 121 (651)
++|+.-.++ .+....++|..++.++||...+. ..+.+.|-. .+ --..-+.|...||...+.|.
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 567764444 34556799999999999987553 224556621 11 22557899999999888774
No 88
>COG2906 Bfd Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]
Probab=30.52 E-value=1.4e+02 Score=25.61 Aligned_cols=43 Identities=23% Similarity=0.165 Sum_probs=32.6
Q ss_pred cchhHHHHHHHhCCCCHHHHHhhhCCChh--HHHHhHHHHHHHHH
Q 006313 208 LPNRTLIEIAKQLPTTAAKLRRLLKSKHS--YIERYMGPVLSIIK 250 (651)
Q Consensus 208 LsD~~LleIAk~~P~S~eeL~~i~G~~~~--~v~r~G~eIL~iI~ 250 (651)
++|+.|.+.+..-|+|.++|.+..|.+.. +-.+...+||....
T Consensus 9 VtD~~Ir~av~~g~tt~~el~~~~gvGs~CGkC~~~Arevl~e~~ 53 (63)
T COG2906 9 VTDKQIREAVAQGATTLKELRRFTGVGSQCGKCVRAAREVLEEAL 53 (63)
T ss_pred ccHHHHHHHHHHcCCCHHHHHHHcCcccchHHHHHHHHHHHHHHH
Confidence 57999999999999999999999888653 33455555554433
No 89
>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=28.45 E-value=1.5e+02 Score=26.97 Aligned_cols=45 Identities=24% Similarity=0.440 Sum_probs=33.5
Q ss_pred cchhHHHHHHHhCCCCHHHHHhhhCCCh-hHHHHhHHHHHHHHHHH
Q 006313 208 LPNRTLIEIAKQLPTTAAKLRRLLKSKH-SYIERYMGPVLSIIKNS 252 (651)
Q Consensus 208 LsD~~LleIAk~~P~S~eeL~~i~G~~~-~~v~r~G~eIL~iI~~A 252 (651)
|....++.|+-.+|+|..++..|...-. +.-....+.||++|.+.
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 8999999999999999999999865433 34456788888888763
No 90
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=27.90 E-value=53 Score=36.80 Aligned_cols=85 Identities=19% Similarity=0.170 Sum_probs=53.8
Q ss_pred hhHHHHHhhcCCCceEEEeeccccHHHHHHhhCCCcCceehHHHHHH-HhCC-C-CCcHHHHHHHHcCCCCCcccccccC
Q 006313 21 VGPYLREVFKDPTKKKVMHGADRDIVWLQRDFGIYLCNMFDTGQASR-VLKL-E-RNSLEYLLHHFCGVNANKEYQNADW 97 (651)
Q Consensus 21 L~~~L~~lLeDp~I~KV~H~ak~DL~~L~rdfGI~p~nlFDTqLAA~-lLg~-~-~~gL~~LVe~yLGv~LdK~~q~SDW 97 (651)
+...|..|+ +++.+-|+|+...||.+|+..| ..+.||.+.-. -.++ . ..+|..|++.|||..+.-+...
T Consensus 283 vq~~l~~~~-~~~TILVGHSLenDL~aLKl~H----~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~--- 354 (380)
T KOG2248|consen 283 VQKELLELI-SKNTILVGHSLENDLKALKLDH----PSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGG--- 354 (380)
T ss_pred HHHHHHhhc-CcCcEEEeechhhHHHHHhhhC----CceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCC---
Confidence 444566644 5566789999999999996433 34778873222 2332 2 3679999999999877511100
Q ss_pred CCCCCCHHHHHHHHHhHHHHHHHHHH
Q 006313 98 RVRPLPDEMLRYAREDTHYLLYIYDI 123 (651)
Q Consensus 98 ~~RPLS~eQl~YAA~DV~yLl~Lyd~ 123 (651)
.-...|+...+.|...
T Consensus 355 ----------HdS~eDA~acm~Lv~~ 370 (380)
T KOG2248|consen 355 ----------HDSVEDALACMKLVKL 370 (380)
T ss_pred ----------CccHHHHHHHHHHHHH
Confidence 1145677777776554
No 91
>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=27.45 E-value=5e+02 Score=26.92 Aligned_cols=100 Identities=19% Similarity=0.204 Sum_probs=60.8
Q ss_pred HHHHHhhcCCCceEEEeec-cccHHHHHH---hhCCCcCc-------------------eehHHHHHHHhCCC-CCcHHH
Q 006313 23 PYLREVFKDPTKKKVMHGA-DRDIVWLQR---DFGIYLCN-------------------MFDTGQASRVLKLE-RNSLEY 78 (651)
Q Consensus 23 ~~L~~lLeDp~I~KV~H~a-k~DL~~L~r---dfGI~p~n-------------------lFDTqLAA~lLg~~-~~gL~~ 78 (651)
..|..+++.....-|.|+. ..|+..|.+ .+|+.+.. -+||+-.-..-|.. ..+|..
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 4466677654555688886 679988754 36666433 25666443333322 478887
Q ss_pred HHHHHcCCCCCccc----c-cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006313 79 LLHHFCGVNANKEY----Q-NADWRVRPLPDEMLRYAREDTHYLLYIYDIMK 125 (651)
Q Consensus 79 LVe~yLGv~LdK~~----q-~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 125 (651)
|+ ..||+.- |.. + ..-|..-.+ ++-..|+-.||..+..||-.+.
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 76 5678764 421 1 111333333 6678999999999999886643
No 92
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.32 E-value=87 Score=29.64 Aligned_cols=47 Identities=19% Similarity=0.398 Sum_probs=36.9
Q ss_pred cchhHHHHHHHhCCCCHHHHHhhhCCC-hhHHHHhHHHHHHHHHHHHh
Q 006313 208 LPNRTLIEIAKQLPTTAAKLRRLLKSK-HSYIERYMGPVLSIIKNSMQ 254 (651)
Q Consensus 208 LsD~~LleIAk~~P~S~eeL~~i~G~~-~~~v~r~G~eIL~iI~~Ale 254 (651)
++......||--+|+|..+|+.|.-.- ........+.|+++|.++..
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 588889999999999999999986332 22234678999999988653
No 93
>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=27.28 E-value=1.4e+02 Score=30.36 Aligned_cols=61 Identities=21% Similarity=0.330 Sum_probs=36.8
Q ss_pred eehHHHHHHHh-----CCCCCcHHHHHHHH--cCCC-C--CcccccccCCCCCCCHHHHHHHHHhHHHHHHHH
Q 006313 59 MFDTGQASRVL-----KLERNSLEYLLHHF--CGVN-A--NKEYQNADWRVRPLPDEMLRYAREDTHYLLYIY 121 (651)
Q Consensus 59 lFDTqLAA~lL-----g~~~~gL~~LVe~y--LGv~-L--dK~~q~SDW~~RPLS~eQl~YAA~DV~yLl~Ly 121 (651)
++|+..+.... ....++|..+++++ ++.. . +...=..-|...+ ...++|+..||..++.|+
T Consensus 136 ~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~~~~k~d~~~~~I~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 136 VIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLASPDRTYIDGRQIAEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred EEEcHHHHHhhcccccCCCCCCHHHHHHHhcccCCCcCCCCHHHHHHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 37988765532 22368999999986 3321 1 1100011243332 678999999999888875
No 94
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=26.04 E-value=84 Score=29.19 Aligned_cols=46 Identities=24% Similarity=0.412 Sum_probs=36.5
Q ss_pred cchhHHHHHHHhCCCCHHHHHhhhCCC-hhHHHHhHHHHHHHHHHHH
Q 006313 208 LPNRTLIEIAKQLPTTAAKLRRLLKSK-HSYIERYMGPVLSIIKNSM 253 (651)
Q Consensus 208 LsD~~LleIAk~~P~S~eeL~~i~G~~-~~~v~r~G~eIL~iI~~Al 253 (651)
|+....+.||--+|.|.++++.+...- ........++||++|..+.
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 2234567889999988753
No 95
>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=25.34 E-value=74 Score=32.71 Aligned_cols=93 Identities=16% Similarity=0.162 Sum_probs=57.9
Q ss_pred cCCCceEEEeec-cccHHHHHHh---hCCC---------------------------c-C-ceehHHHHHHH-hCCCCCc
Q 006313 30 KDPTKKKVMHGA-DRDIVWLQRD---FGIY---------------------------L-C-NMFDTGQASRV-LKLERNS 75 (651)
Q Consensus 30 eDp~I~KV~H~a-k~DL~~L~rd---fGI~---------------------------p-~-nlFDTqLAA~l-Lg~~~~g 75 (651)
.||+| .|+|+. ..|+..|..+ +|+. . + -++|+...++- +....++
T Consensus 96 ~DPDi-ivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~~k~~~~~~sY~ 174 (234)
T cd05776 96 IDPDV-LVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLSAKELIRCKSYD 174 (234)
T ss_pred cCCCE-EEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHHHHHHHhCCCCCC
Confidence 57885 579998 7788766432 2221 1 1 15788877763 3445799
Q ss_pred HHHHHHHHcCCCCCc-cc-ccc-cCCC-CCCCHHHHHHHHHhHHHHHHHHHHH
Q 006313 76 LEYLLHHFCGVNANK-EY-QNA-DWRV-RPLPDEMLRYAREDTHYLLYIYDIM 124 (651)
Q Consensus 76 L~~LVe~yLGv~LdK-~~-q~S-DW~~-RPLS~eQl~YAA~DV~yLl~Lyd~L 124 (651)
|.++++++||.+-.. .. ... -|.. ..+ ..-++|...||.+.+.|...|
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 11 111 2332 111 445888999999999887764
No 96
>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=25.01 E-value=1.2e+02 Score=30.97 Aligned_cols=96 Identities=16% Similarity=0.115 Sum_probs=58.1
Q ss_pred HHHHhhc--CCCceEEEee-ccccHHHHHH---hhCCCcC------------------ceehHHHHHH---HhCCCCCcH
Q 006313 24 YLREVFK--DPTKKKVMHG-ADRDIVWLQR---DFGIYLC------------------NMFDTGQASR---VLKLERNSL 76 (651)
Q Consensus 24 ~L~~lLe--Dp~I~KV~H~-ak~DL~~L~r---dfGI~p~------------------nlFDTqLAA~---lLg~~~~gL 76 (651)
.|..++. ||.++ ++|+ ..+|+..|.. .+|+.+. ..+|+.-... .+....++|
T Consensus 79 ~f~~~i~~~~Pd~i-~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysL 157 (204)
T cd05779 79 RFFEHIREVKPHII-VTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGL 157 (204)
T ss_pred HHHHHHHHhCCCEE-EecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccH
Confidence 3445554 46654 4554 4789877643 2343321 1467765443 344456899
Q ss_pred HHHHHHHcCCCCCcc-c-c-cccCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 006313 77 EYLLHHFCGVNANKE-Y-Q-NADWRVRPLPDEMLRYAREDTHYLLYIYD 122 (651)
Q Consensus 77 ~~LVe~yLGv~LdK~-~-q-~SDW~~RPLS~eQl~YAA~DV~yLl~Lyd 122 (651)
..+++++||..-..- . . ..-|...+ ..-++|+..||...+.||.
T Consensus 158 d~Va~~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 158 KAVTKAKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred HHHHHHHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 999999999742211 0 0 01354443 5689999999999999873
No 97
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.91 E-value=2.8e+02 Score=35.63 Aligned_cols=94 Identities=15% Similarity=0.200 Sum_probs=58.2
Q ss_pred CCCceEEEeec-cccHHHHHHhh---CCC---------------------cC--ceehHHHHHH-HhCCCCCcHHHHHHH
Q 006313 31 DPTKKKVMHGA-DRDIVWLQRDF---GIY---------------------LC--NMFDTGQASR-VLKLERNSLEYLLHH 82 (651)
Q Consensus 31 Dp~I~KV~H~a-k~DL~~L~rdf---GI~---------------------p~--nlFDTqLAA~-lLg~~~~gL~~LVe~ 82 (651)
||.+.. +|+. ..|+..|..+. ++. .. -++|+...+. .+....++|..|+.+
T Consensus 599 DPDii~-g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~~~~sy~L~~v~~~ 677 (1172)
T TIGR00592 599 DPDEIV-GHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELIRCKSYDLSELVQQ 677 (1172)
T ss_pred CCCEEE-EEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHHhCcCCCCHHHHHHH
Confidence 888654 5555 66887764422 111 11 3789987766 455567999999999
Q ss_pred HcCCCCCc-c-cccc-cCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 006313 83 FCGVNANK-E-YQNA-DWRVRPLPDEMLRYAREDTHYLLYIYDIMK 125 (651)
Q Consensus 83 yLGv~LdK-~-~q~S-DW~~RPLS~eQl~YAA~DV~yLl~Lyd~L~ 125 (651)
+||.+-.. . .... -|.....-..-+.|...||.+++.|...|.
T Consensus 678 ~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l~ 723 (1172)
T TIGR00592 678 ILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCELN 723 (1172)
T ss_pred HhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99963211 0 0011 132211124568899999999998877654
No 98
>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=22.24 E-value=1.8e+02 Score=32.16 Aligned_cols=42 Identities=10% Similarity=-0.046 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHcCCCCccccchhHHHHHHHh
Q 006313 178 LNAQQLAVVAGLCEWRDVIARADDESTGYVLPNRTLIEIAKQ 219 (651)
Q Consensus 178 L~~~qlaVL~~L~~WRe~iAr~~DiPp~~VLsD~~LleIAk~ 219 (651)
..+....+++.|..+...+|.+.|+|+..|++.+.|..|+..
T Consensus 295 ~~~~~~~~~~~l~~~~~~~a~~~~i~~~~l~~~~~l~~l~~~ 336 (367)
T TIGR01388 295 PPPGYKALFKLLKVLVKDVSETLGLASELLASRRQLEQLLAW 336 (367)
T ss_pred CChhHHHHHHHHHHHHHHHHHHhCCCHHHcCCHHHHHHHHHh
Confidence 345667899999999999999999999999999999999975
No 99
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=20.28 E-value=1.4e+02 Score=31.22 Aligned_cols=53 Identities=21% Similarity=0.200 Sum_probs=38.3
Q ss_pred CCCceEEEeeccccHHHHHHhhCCC---------------cCceehHHHHHHHhCCCCCcHHHHHHHH
Q 006313 31 DPTKKKVMHGADRDIVWLQRDFGIY---------------LCNMFDTGQASRVLKLERNSLEYLLHHF 83 (651)
Q Consensus 31 Dp~I~KV~H~ak~DL~~L~rdfGI~---------------p~nlFDTqLAA~lLg~~~~gL~~LVe~y 83 (651)
+.++++|+|++-.|+..|++.|--. .+.++||.+.+..+.....+|+.|.+.+
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~~~~L~~l~~~l 214 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECPGKSTSLQELAEEL 214 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS-SSHHHHHHHT
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhccccccCHHHHHHHh
Confidence 4458999999999997766543221 1458999988887765568999998775
Done!