Query 020975
Match_columns 319
No_of_seqs 225 out of 1424
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 06:37:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020975.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020975hhsearch_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 5.1E-35 1.1E-39 277.1 14.7 248 27-296 2-283 (373)
2 COG0349 Rnd Ribonuclease D [Tr 100.0 3.2E-33 6.8E-38 258.7 12.5 248 32-300 2-283 (361)
3 TIGR01388 rnd ribonuclease D. 100.0 3.3E-32 7.1E-37 259.0 14.6 245 30-296 1-279 (367)
4 cd06148 Egl_like_exo DEDDy 3'- 100.0 1.5E-29 3.3E-34 221.5 18.5 181 46-228 7-189 (197)
5 cd06129 RNaseD_like DEDDy 3'-5 100.0 8.1E-28 1.8E-32 204.1 13.6 156 37-213 2-160 (161)
6 cd06146 mut-7_like_exo DEDDy 3 100.0 1.7E-27 3.6E-32 207.9 15.5 175 28-213 1-192 (193)
7 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 2.8E-26 6.1E-31 195.9 15.6 170 28-217 1-176 (176)
8 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 2.4E-26 5.2E-31 196.5 13.8 164 32-213 2-169 (170)
9 PRK05755 DNA polymerase I; Pro 99.9 8.8E-24 1.9E-28 221.7 12.3 228 26-271 294-528 (880)
10 COG0749 PolA DNA polymerase I 99.9 4.5E-24 9.7E-29 209.3 6.0 225 31-271 6-239 (593)
11 KOG2206 Exosome 3'-5' exoribon 99.9 1.5E-23 3.4E-28 201.1 7.2 249 26-296 191-477 (687)
12 cd06142 RNaseD_exo DEDDy 3'-5' 99.9 2.4E-21 5.1E-26 166.2 16.4 163 46-228 9-172 (178)
13 cd06140 DNA_polA_I_Bacillus_li 99.9 9.6E-21 2.1E-25 162.8 15.1 171 49-235 3-176 (178)
14 TIGR00593 pola DNA polymerase 99.8 2.8E-20 6E-25 193.6 11.2 222 28-272 304-536 (887)
15 smart00474 35EXOc 3'-5' exonuc 99.8 3E-19 6.5E-24 151.4 14.3 168 29-217 2-172 (172)
16 cd06147 Rrp6p_like_exo DEDDy 3 99.8 1E-18 2.2E-23 152.4 16.0 173 25-219 2-175 (192)
17 cd06139 DNA_polA_I_Ecoli_like_ 99.8 2.5E-18 5.4E-23 149.1 16.2 177 47-235 3-191 (193)
18 PRK14975 bifunctional 3'-5' ex 99.8 4.6E-20 9.9E-25 184.6 5.0 199 27-272 2-219 (553)
19 cd00007 35EXOc 3'-5' exonuclea 99.7 8.4E-17 1.8E-21 133.8 15.0 152 51-216 2-155 (155)
20 cd09018 DEDDy_polA_RNaseD_like 99.7 7.8E-17 1.7E-21 134.0 13.8 146 51-213 1-149 (150)
21 cd06128 DNA_polA_exo DEDDy 3'- 99.3 1.5E-10 3.2E-15 96.8 14.5 132 64-213 17-150 (151)
22 KOG2207 Predicted 3'-5' exonuc 99.3 4.6E-12 1E-16 123.3 5.0 181 25-217 389-586 (617)
23 KOG2405 Predicted 3'-5' exonuc 98.1 2E-07 4.4E-12 86.7 -2.1 149 54-204 63-215 (458)
24 KOG2405 Predicted 3'-5' exonuc 98.1 2.6E-06 5.7E-11 79.4 3.2 164 64-235 210-376 (458)
25 KOG4373 Predicted 3'-5' exonuc 97.8 4.6E-05 9.9E-10 70.2 7.1 129 64-209 146-281 (319)
26 cd06125 DnaQ_like_exo DnaQ-lik 97.8 0.00011 2.5E-09 56.6 8.0 72 52-134 1-83 (96)
27 PRK07740 hypothetical protein; 97.5 0.0026 5.6E-08 57.6 13.4 98 90-223 131-233 (244)
28 PRK06063 DNA polymerase III su 97.4 0.002 4.3E-08 60.5 12.3 138 49-222 15-185 (313)
29 PRK07942 DNA polymerase III su 97.2 0.011 2.4E-07 53.0 13.6 136 48-217 5-181 (232)
30 cd06144 REX4_like DEDDh 3'-5' 97.1 0.0041 8.8E-08 52.0 9.5 67 90-168 67-133 (152)
31 cd06149 ISG20 DEDDh 3'-5' exon 97.0 0.0036 7.9E-08 52.7 8.4 67 90-169 67-137 (157)
32 TIGR01298 RNaseT ribonuclease 97.0 0.024 5.3E-07 49.6 13.8 86 103-223 106-199 (200)
33 PRK07246 bifunctional ATP-depe 97.0 0.01 2.2E-07 62.7 13.1 135 48-220 6-174 (820)
34 cd06137 DEDDh_RNase DEDDh 3'-5 96.9 0.0094 2E-07 50.3 10.1 66 92-168 75-140 (161)
35 PRK06310 DNA polymerase III su 96.9 0.021 4.5E-07 51.9 12.9 136 46-217 4-175 (250)
36 PRK06309 DNA polymerase III su 96.9 0.041 8.9E-07 49.3 14.5 142 50-226 3-176 (232)
37 TIGR00573 dnaq exonuclease, DN 96.9 0.017 3.6E-07 51.3 11.7 142 46-219 4-180 (217)
38 TIGR01405 polC_Gram_pos DNA po 96.9 0.014 3.1E-07 63.7 13.3 139 47-221 188-360 (1213)
39 cd06145 REX1_like DEDDh 3'-5' 96.8 0.016 3.6E-07 48.3 10.6 65 90-168 65-129 (150)
40 PRK07883 hypothetical protein; 96.7 0.024 5.3E-07 57.3 13.0 141 46-220 12-186 (557)
41 PRK08517 DNA polymerase III su 96.7 0.059 1.3E-06 49.1 14.1 133 46-217 65-232 (257)
42 PRK06807 DNA polymerase III su 96.6 0.042 9.2E-07 51.6 12.9 91 90-217 78-173 (313)
43 PRK06195 DNA polymerase III su 96.6 0.089 1.9E-06 49.3 14.9 100 90-226 70-174 (309)
44 PRK09146 DNA polymerase III su 96.6 0.078 1.7E-06 47.8 13.8 143 46-217 44-228 (239)
45 COG2176 PolC DNA polymerase II 96.6 0.0086 1.9E-07 63.7 8.5 140 46-223 418-593 (1444)
46 PRK05711 DNA polymerase III su 96.5 0.084 1.8E-06 47.6 13.7 90 90-214 76-174 (240)
47 cd06131 DNA_pol_III_epsilon_Ec 96.5 0.06 1.3E-06 45.3 11.9 88 90-212 71-166 (167)
48 PRK05601 DNA polymerase III su 96.4 0.074 1.6E-06 50.7 13.2 143 46-212 43-245 (377)
49 PRK05168 ribonuclease T; Provi 96.4 0.17 3.7E-06 44.6 14.9 86 102-222 114-207 (211)
50 TIGR01406 dnaQ_proteo DNA poly 96.4 0.073 1.6E-06 47.5 12.6 90 90-214 72-170 (225)
51 KOG2249 3'-5' exonuclease [Rep 96.4 0.031 6.7E-07 50.4 9.8 136 50-219 106-269 (280)
52 cd06130 DNA_pol_III_epsilon_li 96.2 0.11 2.4E-06 43.0 12.0 66 90-167 67-137 (156)
53 cd05160 DEDDy_DNA_polB_exo DED 96.2 0.12 2.5E-06 44.9 12.5 102 89-209 65-198 (199)
54 cd05780 DNA_polB_Kod1_like_exo 96.1 0.15 3.3E-06 44.3 12.9 144 50-211 4-194 (195)
55 TIGR01407 dinG_rel DnaQ family 96.1 0.072 1.6E-06 56.8 12.4 93 90-218 70-167 (850)
56 smart00479 EXOIII exonuclease 96.0 0.17 3.7E-06 42.1 12.3 92 90-217 70-168 (169)
57 PRK08074 bifunctional ATP-depe 96.0 0.077 1.7E-06 57.1 12.2 93 90-218 74-171 (928)
58 cd06136 TREX1_2 DEDDh 3'-5' ex 95.9 0.17 3.6E-06 43.4 11.9 63 92-168 86-157 (177)
59 PRK09145 DNA polymerase III su 95.8 0.32 6.8E-06 42.5 13.6 136 47-213 27-198 (202)
60 cd06127 DEDDh DEDDh 3'-5' exon 95.2 0.26 5.6E-06 40.1 10.3 50 90-141 69-123 (159)
61 PRK00448 polC DNA polymerase I 95.1 0.13 2.7E-06 57.4 10.0 96 91-222 490-590 (1437)
62 PF13482 RNase_H_2: RNase_H su 95.0 0.49 1.1E-05 39.5 11.5 146 52-212 1-163 (164)
63 cd06143 PAN2_exo DEDDh 3'-5' e 95.0 0.07 1.5E-06 45.6 6.2 81 92-209 93-173 (174)
64 PRK07247 DNA polymerase III su 94.3 1.2 2.7E-05 38.7 12.6 94 90-217 74-170 (195)
65 PRK09182 DNA polymerase III su 94.1 1.4 3E-05 41.1 13.2 103 92-231 112-216 (294)
66 PF09281 Taq-exonuc: Taq polym 94.0 0.16 3.6E-06 40.8 5.8 71 108-216 68-138 (138)
67 cd05785 DNA_polB_like2_exo Unc 93.4 2.1 4.6E-05 37.6 12.5 145 49-209 9-206 (207)
68 cd06134 RNaseT DEDDh 3'-5' exo 92.3 1.3 2.8E-05 38.3 9.5 78 103-215 103-188 (189)
69 cd05781 DNA_polB_B3_exo DEDDy 91.9 7.6 0.00016 33.5 14.3 144 50-212 4-188 (188)
70 KOG3657 Mitochondrial DNA poly 90.7 0.75 1.6E-05 47.8 7.1 105 103-218 242-385 (1075)
71 PRK11779 sbcB exonuclease I; P 90.0 4.5 9.8E-05 40.2 11.8 98 91-215 82-197 (476)
72 PRK07983 exodeoxyribonuclease 89.9 3 6.6E-05 37.0 9.6 80 103-216 75-154 (219)
73 cd05784 DNA_polB_II_exo DEDDy 89.8 4.2 9.1E-05 35.3 10.3 49 151-210 139-193 (193)
74 PF10108 DNA_pol_B_exo2: Predi 87.7 6.2 0.00013 34.8 9.9 107 89-214 39-171 (209)
75 cd05782 DNA_polB_like1_exo Unc 86.0 15 0.00033 32.2 11.6 129 63-210 49-207 (208)
76 cd05783 DNA_polB_B1_exo DEDDy 84.9 23 0.00051 30.9 12.2 105 89-210 75-202 (204)
77 cd06133 ERI-1_3'hExo_like DEDD 84.9 21 0.00046 29.6 12.1 90 90-212 78-175 (176)
78 KOG2248 3'-5' exonuclease [Rep 83.9 7.3 0.00016 37.6 9.1 89 92-214 285-373 (380)
79 PRK06722 exonuclease; Provisio 83.6 37 0.0008 31.4 13.9 91 90-213 80-178 (281)
80 COG0847 DnaQ DNA polymerase II 82.2 36 0.00077 30.2 12.8 134 49-215 13-181 (243)
81 smart00341 HRDC Helicase and R 75.8 0.49 1.1E-05 34.6 -1.3 54 243-296 12-75 (81)
82 PRK07748 sporulation inhibitor 74.4 28 0.0006 30.3 9.2 92 90-215 82-179 (207)
83 PHA02528 43 DNA polymerase; Pr 71.7 75 0.0016 34.3 13.1 50 151-211 272-323 (881)
84 PRK05762 DNA polymerase II; Re 70.7 68 0.0015 34.1 12.6 104 89-211 205-347 (786)
85 PRK05359 oligoribonuclease; Pr 70.4 43 0.00094 28.6 9.3 40 91-130 83-130 (181)
86 KOG1275 PAB-dependent poly(A) 68.2 2.6 5.6E-05 44.4 1.3 88 97-221 1009-1096(1118)
87 PF00570 HRDC: HRDC domain Blo 64.4 0.3 6.5E-06 34.5 -4.6 48 245-292 11-68 (68)
88 cd06138 ExoI_N N-terminal DEDD 57.0 34 0.00074 29.1 6.2 29 91-119 73-102 (183)
89 cd02394 vigilin_like_KH K homo 55.8 4.7 0.0001 27.7 0.5 41 273-313 7-47 (62)
90 cd05777 DNA_polB_delta_exo DED 41.7 33 0.00072 30.4 3.8 54 151-213 168-224 (230)
91 cd02396 PCBP_like_KH K homolog 30.2 23 0.00049 24.7 0.7 37 275-311 9-47 (65)
92 KOG1798 DNA polymerase epsilon 28.9 3.8E+02 0.0083 30.9 9.6 153 48-213 245-451 (2173)
93 cd05779 DNA_polB_epsilon_exo D 27.1 67 0.0014 28.1 3.2 103 89-209 75-203 (204)
94 cd06135 Orn DEDDh 3'-5' exonuc 25.0 84 0.0018 26.4 3.4 30 90-119 78-111 (173)
95 PF13014 KH_3: KH domain 24.9 33 0.00072 21.6 0.7 27 277-303 2-28 (43)
No 1
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=5.1e-35 Score=277.09 Aligned_cols=248 Identities=23% Similarity=0.298 Sum_probs=211.6
Q ss_pred CeEEeCCcccchHHhhhccccCCCeEEEEeeecCCC-CCCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceE
Q 020975 27 PIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITK 105 (319)
Q Consensus 27 ~~~~I~t~~~L~~~~l~~~l~~~~~ia~D~E~~~~~-~~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i~K 105 (319)
.|.+|+|.++|.+ +++. +...+.+|||||+.+.. +++++|+|||++++++|+||+..+.+ +..|+++|+|++|.|
T Consensus 2 ~~~~I~t~~~L~~-~~~~-l~~~~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~~~d--~~~L~~ll~~~~ivK 77 (373)
T PRK10829 2 NYQMITTDDALAS-VCEA-ARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITD--WSPFKALLRDPQVTK 77 (373)
T ss_pred CcEEeCCHHHHHH-HHHH-HhcCCeEEEecccccCccCCCceeEEEEecCCceEEEecCCccc--hHHHHHHHcCCCeEE
Confidence 4789999999998 9988 88899999999998775 78899999999988999999987743 688999999999999
Q ss_pred EEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCC
Q 020975 106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFW 185 (319)
Q Consensus 106 V~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w 185 (319)
|+|++++|+..|++.+|+.+.++||||+|+.+++.+. .+||+.|++ +|||++++| +.. .++|
T Consensus 78 V~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~--------~~gl~~Lv~--~~lgv~ldK-~~~-------~sDW 139 (373)
T PRK10829 78 FLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPL--------SCGFASMVE--EYTGVTLDK-SES-------RTDW 139 (373)
T ss_pred EEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCc--------cccHHHHHH--HHhCCccCc-ccc-------cCCC
Confidence 9999999999998889999999999999999998642 268999999 999999985 332 2599
Q ss_pred ccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchHHHHHhhcc-c-cc---c------c-c------cCCCc------
Q 020975 186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGAL-Y-CR---C------F-C------INEND------ 241 (319)
Q Consensus 186 ~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~~l~~~~e~-~-~~---v------l-~------me~~g------ 241 (319)
..|||+++|+.|||.||.+++.||+.|.++|++.|.++++.+... . .+ . . . +.+.+
T Consensus 140 ~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~ik~~~~L~~~~lavl~~ 219 (373)
T PRK10829 140 LARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQL 219 (373)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHhccccCCChHHHHHHhccccCCCHHHHHHHHH
Confidence 999999999999999999999999999999999998887654321 1 00 0 0 1 12222
Q ss_pred cCCCCCCCCCCCcccccCccChHHHHHhhccCCCCcc---------hhhccccchHHHHHHhcc
Q 020975 242 YVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG---------RIIGRRGSSILAIKESCN 296 (319)
Q Consensus 242 ~~d~~~l~a~~~~l~~~~~~~~~~i~~~ag~~~~~~~---------~~~~~~~~~~~~~~~~~~ 296 (319)
...||+..|+..|.+++++..++.++++|..+|.+.. +.++++|..|+.+++.|.
T Consensus 220 L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~~~~~~~~r~~g~~ll~~i~~a~ 283 (373)
T PRK10829 220 LADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQ 283 (373)
T ss_pred HHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhccCChHhHHhhHHHHHHHHHHHh
Confidence 3389999999999999999999999999999996544 577889999999999985
No 2
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.2e-33 Score=258.66 Aligned_cols=248 Identities=21% Similarity=0.257 Sum_probs=206.2
Q ss_pred CCcccchHHhhhccccCCCeEEEEeeecCCC-CCCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEeeh
Q 020975 32 TNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDC 110 (319)
Q Consensus 32 ~t~~~L~~~~l~~~l~~~~~ia~D~E~~~~~-~~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV~hd~ 110 (319)
++.+.+++ ++.. ....+.|++|||+.+.. +++++|+||++.++++++||+..... -...|..+|.|++|.||+|.+
T Consensus 2 ~~~~~l~~-~~~~-~~~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~~lIdpl~~~~-d~~~l~~Ll~d~~v~KIfHaa 78 (361)
T COG0349 2 TTGDLLAA-ACAL-LRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEGASLIDPLAGIL-DLPPLVALLADPNVVKIFHAA 78 (361)
T ss_pred CchhHHHH-HHHH-hcCCCceEEecccccccccCCceEEEEEecCCCceEeccccccc-ccchHHHHhcCCceeeeeccc
Confidence 34455665 7766 67788999999998875 89999999999987799999987422 267788899999999999999
Q ss_pred hhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCC
Q 020975 111 KRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPL 190 (319)
Q Consensus 111 k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL 190 (319)
++|+.+|++.+|+.+.++|||++|+.+++.+. + +||++|++ +++|++++| ++. .++|..|||
T Consensus 79 ~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~-~-------~gl~~Lv~--~ll~v~ldK-~~q-------~SDW~~RPL 140 (361)
T COG0349 79 RFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGT-S-------HGLADLVE--ELLGVELDK-SEQ-------RSDWLARPL 140 (361)
T ss_pred cccHHHHHHhcCCCCCchhHHHHHHHHhCCcc-c-------ccHHHHHH--HHhCCcccc-ccc-------ccccccCCC
Confidence 99999999889999999999999999998863 2 78999999 999999985 332 259999999
Q ss_pred CHHHHHHHHhhhhHHHHHHHHHHHHHhhhchHHHHHhhcc--ccc-ccccCC-Cc--------------------cCCCC
Q 020975 191 TELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGAL--YCR-CFCINE-ND--------------------YVDWP 246 (319)
Q Consensus 191 ~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~~l~~~~e~--~~~-vl~me~-~g--------------------~~d~~ 246 (319)
|++|++|||.||.|++.||..|.++|.+.|.+.+..+... +.+ ....+. .+ ...||
T Consensus 141 s~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~~l~~r~~~~~~~~~~w~~i~~a~~~~p~~la~l~~La~wR 220 (361)
T COG0349 141 SEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFRLLPTRRTYKVLPEDAWREIKIAHSLDPRELAVLRELAAWR 220 (361)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHhhhccccccChHhHHHHhhhhhcCChHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999888776432 222 111110 00 23899
Q ss_pred CCCCCCCcccccCccChHHHHHhhccCCCC---------cchhhccccchHHHHHHhcchhhh
Q 020975 247 PLPPVPDYLIVEGDVPEEEILSILDVPPGK---------MGRIIGRRGSSILAIKESCNAEIL 300 (319)
Q Consensus 247 ~l~a~~~~l~~~~~~~~~~i~~~ag~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~ 300 (319)
+..|+.++++++.+..++.|+++|.++|.. .+...+.+|..++.+++.+.+.-.
T Consensus 221 e~~Ar~rd~~~~~vl~de~i~~~a~~~P~~~~~l~~l~~~~~~~~~~~~~l~~~~~~a~~~p~ 283 (361)
T COG0349 221 EREARERDLARNFVLKDEALWELARYTPKNLKELDALGLIPKERRRHGKLLLALLANALASPE 283 (361)
T ss_pred HHHHHHhccccccccchhHHHHHHHhCCCCHHHHHhccCCcccchhhhHHHHHHHHHHHhCch
Confidence 999999999999999999999999999942 235778999999999988865444
No 3
>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=99.98 E-value=3.3e-32 Score=258.98 Aligned_cols=245 Identities=21% Similarity=0.273 Sum_probs=204.9
Q ss_pred EeCCcccchHHhhhccccCCCeEEEEeeecCCC-CCCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEe
Q 020975 30 IVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIH 108 (319)
Q Consensus 30 ~I~t~~~L~~~~l~~~l~~~~~ia~D~E~~~~~-~~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV~h 108 (319)
+|+|.++|.+ +++. +...+++|||||+.+.. +++++|+|||++++.+|+||+.... .+..|+++|+|+++.||+|
T Consensus 1 ~I~t~~~l~~-~~~~-l~~~~~ia~DtE~~~~~~y~~~l~LiQia~~~~~~liD~~~~~--~~~~L~~lL~d~~i~KV~h 76 (367)
T TIGR01388 1 WITTDDELAT-VCEA-VRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVII--DWSPLKELLRDESVVKVLH 76 (367)
T ss_pred CcCCHHHHHH-HHHH-HhcCCEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCcc--cHHHHHHHHCCCCceEEEe
Confidence 3788899997 9988 78889999999998775 7889999999999999999998764 3788999999999999999
Q ss_pred ehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccC
Q 020975 109 DCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYR 188 (319)
Q Consensus 109 d~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~r 188 (319)
|+|+|+++|.+.+|+.++++||||+|+|+++++. .+||+.|++ +|||++++| +. ..++|..|
T Consensus 77 ~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~--------~~~l~~Lv~--~~Lg~~l~K-~~-------~~sdW~~r 138 (367)
T TIGR01388 77 AASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGM--------SMGYAKLVQ--EVLGVELDK-SE-------SRTDWLAR 138 (367)
T ss_pred ecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCC--------CccHHHHHH--HHcCCCCCc-cc-------ccccCCCC
Confidence 9999999997666777688999999999999853 258999999 999998873 22 12589999
Q ss_pred CCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchHHHHHhhcc-c-ccc-c---------------ccCCCc------cCC
Q 020975 189 PLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGAL-Y-CRC-F---------------CINEND------YVD 244 (319)
Q Consensus 189 pL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~~l~~~~e~-~-~~v-l---------------~me~~g------~~d 244 (319)
||+.+|+.|||.||.+++.||+.|.++|++.|.+.++.+... . ... . .+.+.+ ...
T Consensus 139 PL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~i~~~~~l~~~~l~~l~~L~~ 218 (367)
T TIGR01388 139 PLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAA 218 (367)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHhccccCCCChHHHHHHhcccccCCHHHHHHHHHHHH
Confidence 999999999999999999999999999999998877554211 1 110 0 112222 248
Q ss_pred CCCCCCCCCcccccCccChHHHHHhhccCCCCcc---------hhhccccchHHHHHHhcc
Q 020975 245 WPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG---------RIIGRRGSSILAIKESCN 296 (319)
Q Consensus 245 ~~~l~a~~~~l~~~~~~~~~~i~~~ag~~~~~~~---------~~~~~~~~~~~~~~~~~~ 296 (319)
||+..|+..|.+++++..++.++++|..+|.+.. ..++++|.+|+.+++.+.
T Consensus 219 wRe~~A~~~d~p~~~il~d~~l~~lA~~~P~~~~~l~~~~~~~~~~r~~~~~l~~~i~~a~ 279 (367)
T TIGR01388 219 WREREARERDLPRNFVLKEEALWELARQAPGNLTELASLGPKGSEIRKHGDTLLALVKTAL 279 (367)
T ss_pred HHHHHHHHcCCCcceeeCHHHHHHHHHhCCCCHHHHHhccCChHHHHhhHHHHHHHHHHHh
Confidence 9999999999999999999999999999996544 577889999999999985
No 4
>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=99.97 E-value=1.5e-29 Score=221.54 Aligned_cols=181 Identities=49% Similarity=0.724 Sum_probs=150.2
Q ss_pred ccCCCeEEEEeeecCCCCCCcEEEEEEEeC-CceEEEEccCCCh-hhHHHHHHHHcCCCceEEEeehhhhHHHHHHHcCC
Q 020975 46 SERQLVIGFDCEGVDLCRHGSLCIMQLAFP-DAIYLVDAIQGGE-TVVKACKPALESSYITKVIHDCKRDSEALYFQFGI 123 (319)
Q Consensus 46 l~~~~~ia~D~E~~~~~~~g~l~~lqls~~-~~~~~id~~~l~~-~~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi 123 (319)
+.+++.+|||+|+.+.+..|++|++||++. +++|+||+..++. .+...|+++|+++++.||+||+|+|+..|++.+|+
T Consensus 7 l~~~~~i~~D~E~~~~~~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi 86 (197)
T cd06148 7 LKKQKVIGLDCEGVNLGRKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGI 86 (197)
T ss_pred hhhCCEEEEEcccccCCCCCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHHhcCc
Confidence 667899999999988877899999999998 9999999998762 35688999999999999999999999999778999
Q ss_pred ccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhh
Q 020975 124 KLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVR 203 (319)
Q Consensus 124 ~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~ 203 (319)
.+.++|||++|+|++++..+.........||+.+++ +|++.+++++...+..++...++|..|||+++|+.|||.||+
T Consensus 87 ~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~--~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~ 164 (197)
T cd06148 87 KLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLD--KYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVL 164 (197)
T ss_pred cccceeeHHHHHHHHHHHhcCCccccccccHHHHHH--HhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHH
Confidence 998999999999999986431011112368999999 999998864333222223345699999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhchHHHHHhh
Q 020975 204 FLPYIYHNMMKKLNQQSLWYLAVRG 228 (319)
Q Consensus 204 ~ll~L~~~L~~~L~~~~~~~l~~~~ 228 (319)
+++.|++.|...|.+.....+|.+.
T Consensus 165 ~Ll~l~~~l~~~l~~~~~~~~~~~~ 189 (197)
T cd06148 165 CLLPLYYAMLDALISKFLKAVFKYL 189 (197)
T ss_pred hHHHHHHHHHHHhhhhHHHHHHHHh
Confidence 9999999999999988766666543
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=99.95 E-value=8.1e-28 Score=204.10 Aligned_cols=156 Identities=31% Similarity=0.347 Sum_probs=135.4
Q ss_pred chHHhhhcccc-CCCeEEEEeeecCCC-CCCcEEEEEEEeC-CceEEEEccCCChhhHHHHHHHHcCCCceEEEeehhhh
Q 020975 37 LPAEFLEPSSE-RQLVIGFDCEGVDLC-RHGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRD 113 (319)
Q Consensus 37 L~~~~l~~~l~-~~~~ia~D~E~~~~~-~~g~l~~lqls~~-~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~d 113 (319)
+++ +++. +. ..+.+|||+||.+.. +.+++|++||+++ +.+|+||+..++. ....|+++|+|+++.||+||+|.|
T Consensus 2 l~~-~~~~-l~~~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~-~~~~L~~lL~d~~i~Kvg~~~k~D 78 (161)
T cd06129 2 LSS-LCED-LSMDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSV-DWQGLKMLLENPSIVKALHGIEGD 78 (161)
T ss_pred HHH-HHHH-HhcCCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCcc-CHHHHHHHhCCCCEEEEEeccHHH
Confidence 344 6666 66 889999999999775 6789999999998 9999999987653 467899999999999999999999
Q ss_pred HHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHH
Q 020975 114 SEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTEL 193 (319)
Q Consensus 114 ~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~ 193 (319)
+..|.+.+|+.+.++|||++++|++++.. ..||+++++ +|+|..++| ... .++|..|||+++
T Consensus 79 ~~~L~~~~gi~~~~~~D~~~aa~ll~~~~--------~~~L~~l~~--~~lg~~l~K-~~~-------~s~W~~rpLt~~ 140 (161)
T cd06129 79 LWKLLRDFGEKLQRLFDTTIAANLKGLPE--------RWSLASLVE--HFLGKTLDK-SIS-------CADWSYRPLTED 140 (161)
T ss_pred HHHHHHHcCCCcccHhHHHHHHHHhCCCC--------CchHHHHHH--HHhCCCCCc-cce-------eccCCCCCCCHH
Confidence 99997669999988999999999999752 258999999 999998874 221 259999999999
Q ss_pred HHHHHHhhhhHHHHHHHHHH
Q 020975 194 MVRAAADDVRFLPYIYHNMM 213 (319)
Q Consensus 194 ~~~YAa~Da~~ll~L~~~L~ 213 (319)
|+.|||.||++++.||+.|+
T Consensus 141 qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 141 QKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999885
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=99.95 E-value=1.7e-27 Score=207.94 Aligned_cols=175 Identities=26% Similarity=0.313 Sum_probs=143.8
Q ss_pred eEEeCCcccchHHhhhcc-ccCCCeEEEEeeecCCC---CCCcEEEEEEEeCCceEEEEccCCC----hhhHHHHHHHHc
Q 020975 28 IHIVTNASQLPAEFLEPS-SERQLVIGFDCEGVDLC---RHGSLCIMQLAFPDAIYLVDAIQGG----ETVVKACKPALE 99 (319)
Q Consensus 28 ~~~I~t~~~L~~~~l~~~-l~~~~~ia~D~E~~~~~---~~g~l~~lqls~~~~~~~id~~~l~----~~~~~~L~~lLe 99 (319)
+++|+|++++.+ ++... +.....+|||+||.+.. ..+++++||||+++.+|+||+..++ +.+...|+++|+
T Consensus 1 ~~~i~~~~el~~-~~~~~~l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~ll~ 79 (193)
T cd06146 1 IHIVDSEEELEA-LLLALSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKRLFE 79 (193)
T ss_pred CeEecCHHHHHH-HHHHHhhccCCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHHHhC
Confidence 478999999997 87653 56789999999998653 2689999999999999999998765 234567999999
Q ss_pred CCCceEEEeehhhhHHHHHHHcCCc------cccEEechhHHhhhhhhcC-CC--CCCCCcccHHhhhcCCcccCCccch
Q 020975 100 SSYITKVIHDCKRDSEALYFQFGIK------LHNVVDTQIAYSLIEEQEG-RK--RSPDDYISFVGLLADPRYCGISYQE 170 (319)
Q Consensus 100 ~~~i~KV~hd~k~d~~~L~~~~gi~------l~~vfDt~lAayLL~~~~~-~~--~L~~~~~sL~~L~~~~~~lg~~l~~ 170 (319)
|++|.||||++++|+..|++.+|+. +.+++||+.+++.+..... .. .......||++|++ ++||.+++|
T Consensus 80 d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~--~~lg~~l~K 157 (193)
T cd06146 80 DPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQ--EVLGKPLDK 157 (193)
T ss_pred CCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHH--HHhCCCcCc
Confidence 9999999999999999998889874 5789999998887764211 00 01113479999999 999999885
Q ss_pred hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHH
Q 020975 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (319)
Q Consensus 171 k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~ 213 (319)
..+ .++|..|||+++|+.|||.||++++.||+.|.
T Consensus 158 ~~q--------~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 158 SEQ--------CSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred ccc--------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 322 25999999999999999999999999999985
No 7
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=99.94 E-value=2.8e-26 Score=195.88 Aligned_cols=170 Identities=31% Similarity=0.465 Sum_probs=144.6
Q ss_pred eEEeCCcccchHHhhhccccCCCeEEEEeeecCCC---CCCcEEEEEEEeCCceEEEEccCCChh-hHHHHHHHHcCCCc
Q 020975 28 IHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC---RHGSLCIMQLAFPDAIYLVDAIQGGET-VVKACKPALESSYI 103 (319)
Q Consensus 28 ~~~I~t~~~L~~~~l~~~l~~~~~ia~D~E~~~~~---~~g~l~~lqls~~~~~~~id~~~l~~~-~~~~L~~lLe~~~i 103 (319)
|++|+|.+++.+ ++.. +...+.+|||+||.+.. ....++++|+++.+.+|++++...... +...|+++|+|+++
T Consensus 1 y~~v~~~~~l~~-~~~~-l~~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i 78 (176)
T PF01612_consen 1 YQIVDTEEELEE-AIKK-LKNAKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPNI 78 (176)
T ss_dssp SEEEHSHHHHHH-HHHH-HTTTSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTTS
T ss_pred CEecCCHHHHHH-HHHH-HcCCCeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCCc
Confidence 678999999998 9987 78889999999999874 367899999999988999988776542 57889999999999
Q ss_pred eEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccC-CccchhHHHHHHhcCCC
Q 020975 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCG-ISYQEKEEVRVLLRQDP 182 (319)
Q Consensus 104 ~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg-~~l~~k~~~~~~~~~~~ 182 (319)
.||+||+++|..+|.+.+|+.+.+++|||+++|++++..+ +||++|+. .|+| ...+ ++ ...
T Consensus 79 ~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~--------~~L~~L~~--~~l~~~~~~-~~-------~~~ 140 (176)
T PF01612_consen 79 IKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRS--------YSLKDLAE--EYLGNIDLD-KK-------EQM 140 (176)
T ss_dssp EEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTT--------SSHHHHHH--HHHSEEE-G-HC-------CTT
T ss_pred cEEEEEEechHHHHHHHhccccCCccchhhhhhccccccc--------ccHHHHHH--HHhhhccCc-HH-------Hhh
Confidence 9999999999999986699999999999999999998642 58999999 9999 4443 21 223
Q ss_pred CCCc-cCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 020975 183 QFWT-YRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (319)
Q Consensus 183 ~~w~-~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (319)
.+|. .+|++++++.|||.||+++++||+.|.++|+
T Consensus 141 ~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 141 SDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp SSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred ccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 5899 8999999999999999999999999999885
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=99.94 E-value=2.4e-26 Score=196.50 Aligned_cols=164 Identities=23% Similarity=0.285 Sum_probs=139.2
Q ss_pred CCcccchHHhhhcccc-CCCeEEEEeeecCCC---CCCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEE
Q 020975 32 TNASQLPAEFLEPSSE-RQLVIGFDCEGVDLC---RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVI 107 (319)
Q Consensus 32 ~t~~~L~~~~l~~~l~-~~~~ia~D~E~~~~~---~~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV~ 107 (319)
++..++++ +++. +. ....+|||+||.+.. ..+++++||||+++++|+||+..+. .+...|+++|+++++.||+
T Consensus 2 ~~~~~~~~-~~~~-~~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~-~~~~~l~~ll~~~~i~kv~ 78 (170)
T cd06141 2 DSAQDAEE-AVKE-LLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMD-KLPPSLKQLLEDPSILKVG 78 (170)
T ss_pred CCHHHHHH-HHHH-HhcCCCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhh-cccHHHHHHhcCCCeeEEE
Confidence 35566776 7776 66 889999999998763 4789999999999999999998763 3567799999999999999
Q ss_pred eehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCcc
Q 020975 108 HDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTY 187 (319)
Q Consensus 108 hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~ 187 (319)
||+|+|+..|.+.+|+.+.++|||++++|++++..+. .||+++++ .|+|.++.+.+.. ..++|..
T Consensus 79 ~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~-------~~l~~l~~--~~l~~~~~k~k~~------~~s~W~~ 143 (170)
T cd06141 79 VGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKL-------VSLARLVE--EVLGLPLSKPKKV------RCSNWEA 143 (170)
T ss_pred eeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCC-------ccHHHHHH--HHcCcccCCCCCc------ccCCCCC
Confidence 9999999999778999998899999999999985322 48999999 9999988731111 1269999
Q ss_pred CCCCHHHHHHHHhhhhHHHHHHHHHH
Q 020975 188 RPLTELMVRAAADDVRFLPYIYHNMM 213 (319)
Q Consensus 188 rpL~~~~~~YAa~Da~~ll~L~~~L~ 213 (319)
|||+++|+.|||.||++++.||+.|.
T Consensus 144 rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 144 RPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999885
No 9
>PRK05755 DNA polymerase I; Provisional
Probab=99.90 E-value=8.8e-24 Score=221.66 Aligned_cols=228 Identities=23% Similarity=0.208 Sum_probs=192.9
Q ss_pred cCeEEeCCcccchHHhhhccccCCCeEEEEeeecCCC-CCCcEEEEEEEeCCc-eEEEEccCCChhhHHHHHHHHcCCCc
Q 020975 26 VPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDA-IYLVDAIQGGETVVKACKPALESSYI 103 (319)
Q Consensus 26 ~~~~~I~t~~~L~~~~l~~~l~~~~~ia~D~E~~~~~-~~g~l~~lqls~~~~-~~~id~~~l~~~~~~~L~~lLe~~~i 103 (319)
..|.+|++.+++.+ +++. +.....++||+|+.++. +.++++++|+++.++ +++||+..+....+..|+++|+++.+
T Consensus 294 ~~~~~I~~~~~L~~-~l~~-l~~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~v 371 (880)
T PRK05755 294 EDYETILDEEELEA-WLAK-LKAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPAI 371 (880)
T ss_pred CceEEeCCHHHHHH-HHHH-hhccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCCC
Confidence 45778989999997 9887 67788999999999885 788999999998644 88887644332457889999999999
Q ss_pred eEEEeehhhhHHHHHHHcCCcc-ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCC
Q 020975 104 TKVIHDCKRDSEALYFQFGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDP 182 (319)
Q Consensus 104 ~KV~hd~k~d~~~L~~~~gi~l-~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~ 182 (319)
.||+||+++|+.+|. .+|+.+ +++||||+|+|+++++.+ +||+++++ +|+|.++....+ ++++ .
T Consensus 372 ~kV~HNakfDl~~L~-~~gi~~~~~~~DT~iAa~Ll~~~~~--------~~L~~L~~--~ylg~~~~~~~~---~~gk-~ 436 (880)
T PRK05755 372 KKVGQNLKYDLHVLA-RYGIELRGIAFDTMLASYLLDPGRR--------HGLDSLAE--RYLGHKTISFEE---VAGK-Q 436 (880)
T ss_pred cEEEeccHhHHHHHH-hCCCCcCCCcccHHHHHHHcCCCCC--------CCHHHHHH--HHhCCCccchHH---hcCC-C
Confidence 999999999999996 689987 569999999999998641 58999999 999877532222 1222 2
Q ss_pred CCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhh-chHHHHHhhccc-cccc-ccCCCc-cCCCCCCCCCCCccccc
Q 020975 183 QFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ-SLWYLAVRGALY-CRCF-CINEND-YVDWPPLPPVPDYLIVE 258 (319)
Q Consensus 183 ~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~-~~~~l~~~~e~~-~~vl-~me~~g-~~d~~~l~a~~~~l~~~ 258 (319)
.+|..+|+ +.+..||+.|+.++++|+..|.++|.+. +++.++.++|+| .+++ .||.+| .+|...+.++...+..+
T Consensus 437 ~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l~~l~~eiE~p~~~~l~~me~~Gi~vD~~~~~~~~~~~~~~ 515 (880)
T PRK05755 437 LTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEPGLLELYEEIELPLVPVLARMERNGIKVDREYLKELSAELAQR 515 (880)
T ss_pred CCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhhchHHHHHHHHHhcCeEeCHHHHHHHHHHHHHH
Confidence 35666676 5788999999999999999999999876 899999999999 8888 999999 99999999999999999
Q ss_pred CccChHHHHHhhc
Q 020975 259 GDVPEEEILSILD 271 (319)
Q Consensus 259 ~~~~~~~i~~~ag 271 (319)
+...++++++++|
T Consensus 516 ~~~l~~~~~~~~g 528 (880)
T PRK05755 516 LAELEQEIYELAG 528 (880)
T ss_pred HHHHHHHHHHHhC
Confidence 9999999999998
No 10
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.89 E-value=4.5e-24 Score=209.28 Aligned_cols=225 Identities=24% Similarity=0.218 Sum_probs=181.0
Q ss_pred eCCcccchHHhhhccccCCCeEEEEeeecCCC-CCCcEEEEEEEeCCceEEEEccC--CChhhHHHHHHHHcCCCceEEE
Q 020975 31 VTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQ--GGETVVKACKPALESSYITKVI 107 (319)
Q Consensus 31 I~t~~~L~~~~l~~~l~~~~~ia~D~E~~~~~-~~g~l~~lqls~~~~~~~id~~~--l~~~~~~~L~~lLe~~~i~KV~ 107 (319)
+.+...+.. |+.. ......+++|+|+.+++ ..+.+++++++...+++|++... ..-.....|++||+++.+.|++
T Consensus 6 ~~~~~~~~~-~~~~-~~~~~~~a~~~et~~l~~~~~~lvg~s~~~~~~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~kv~ 83 (593)
T COG0749 6 ITDLAVLNA-WLTK-LNAAANIAFDTETDGLDPHGADLVGLSVASEEEAAYIPLLHGPEQLNVLAALKPLLEDEGIKKVG 83 (593)
T ss_pred hhHHHHHHH-HHHH-HhhcccceeeccccccCcccCCeeEEEeeccccceeEeeccchhhhhhHHHHHHHhhCcccchhc
Confidence 444455554 6655 33344499999999887 68899999999876777775544 1223578999999999999999
Q ss_pred eehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCC--CCC
Q 020975 108 HDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDP--QFW 185 (319)
Q Consensus 108 hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~--~~w 185 (319)
||.|+|.++|. .+|+..+..||||+|+|+++|+.++ +++++|+. +|++.+....+.+. +++. .++
T Consensus 84 ~~~K~d~~~l~-~~Gi~~~~~~DtmlasYll~~~~~~-------~~~~~l~~--r~l~~~~~~~~~i~---~kg~~~~~~ 150 (593)
T COG0749 84 QNLKYDYKVLA-NLGIEPGVAFDTMLASYLLNPGAGA-------HNLDDLAK--RYLGLETITFEDIA---GKGKKQLTF 150 (593)
T ss_pred cccchhHHHHH-HcCCcccchHHHHHHHhccCcCcCc-------CCHHHHHH--HhcCCccchhHHhh---ccccccCcc
Confidence 99999999995 7896545689999999999998655 46899999 99987765443322 2221 234
Q ss_pred ccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhc-hHHHHHhhccc-cccc-ccCCCc-cCCCCCCCCCCCcccccCcc
Q 020975 186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS-LWYLAVRGALY-CRCF-CINEND-YVDWPPLPPVPDYLIVEGDV 261 (319)
Q Consensus 186 ~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~-~~~l~~~~e~~-~~vl-~me~~g-~~d~~~l~a~~~~l~~~~~~ 261 (319)
...++ .....|+|.||+++++|+..|.+++.+.. +.++|.++||| ++|| .||.+| .+|...|..++.++..++..
T Consensus 151 ~~~~~-~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L~~l~~~iE~Pl~~VLa~ME~~Gi~vD~~~L~~l~~el~~~l~~ 229 (593)
T COG0749 151 ADVKL-EKATEYAAEDADATLRLESILEPELLKTPVLLELYEEIEMPLVRVLARMERNGIKVDVQYLKELSKELGCELAE 229 (593)
T ss_pred ccchH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHhccHHHHHHHhHhcCceecHHHHHHHHHHHHHHHHH
Confidence 33333 55689999999999999999998887755 69999999999 9999 999999 99999999999999999999
Q ss_pred ChHHHHHhhc
Q 020975 262 PEEEILSILD 271 (319)
Q Consensus 262 ~~~~i~~~ag 271 (319)
.+++||++||
T Consensus 230 le~eiy~laG 239 (593)
T COG0749 230 LEEEIYELAG 239 (593)
T ss_pred HHHHHHHHhc
Confidence 9999999999
No 11
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=1.5e-23 Score=201.06 Aligned_cols=249 Identities=22% Similarity=0.305 Sum_probs=203.0
Q ss_pred cCeEEeCCcccchHHhhhccccCCCeEEEEeeecCCC-CCCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCce
Q 020975 26 VPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYIT 104 (319)
Q Consensus 26 ~~~~~I~t~~~L~~~~l~~~l~~~~~ia~D~E~~~~~-~~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i~ 104 (319)
+++.+|++..+|.+ +.+. +.....+|+|+|+.+.. +.|-.|++||+|..+.|+||.+.+.+ .+..|+++|.||++.
T Consensus 191 T~~~~I~t~~el~~-l~~~-l~~~~Efavdlehhsyrsf~gltclmqISTr~ed~iIDt~~l~~-~i~~l~e~fsdp~iv 267 (687)
T KOG2206|consen 191 TPKVWICTLGELEA-LPEI-LDSVIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKLRD-HIGILNEVFSDPGIV 267 (687)
T ss_pred cCceeeechHHHHH-HHHH-HhhhhhhhhhccccchhhhcCceeEEEeeccchhheehhHHHHH-HHHHhhhhccCCCeE
Confidence 34788999999997 8876 77788999999998885 78999999999998999999987754 466899999999999
Q ss_pred EEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCC
Q 020975 105 KVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQF 184 (319)
Q Consensus 105 KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~ 184 (319)
||+|++..|+.||++.|||.+.++|||..|+.+|+-++ .||+.|.+ .|+|+..+++.+. .+
T Consensus 268 kvfhgaD~diiwlqrdfgiyvvnLfdt~~a~r~L~~~r---------~sL~~ll~--~~~~v~~nk~yql--------ad 328 (687)
T KOG2206|consen 268 KVFHGADTDIIWLQRDFGIYVVNLFDTIQASRLLGLPR---------PSLAYLLE--CVCGVLTNKKYQL--------AD 328 (687)
T ss_pred EEEecCccchhhhhccceEEEEechhhHHHHHHhCCCc---------ccHHHHHH--HHHhhhhhhhhhh--------ch
Confidence 99999999999999999999999999999999998753 58999999 9999877754442 38
Q ss_pred CccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhc--hHHHHH---hhccc---ccc---------c----ccCCCc--
Q 020975 185 WTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS--LWYLAV---RGALY---CRC---------F----CINEND-- 241 (319)
Q Consensus 185 w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~--~~~l~~---~~e~~---~~v---------l----~me~~g-- 241 (319)
|+.|||+++++.||-.|++|++.+|+.|+..|.+.+ ..-.+. +++.. .++ + ..+...
T Consensus 329 wR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~~~~~~~~~~~d~c~~~~~k~~~~~~sy~~v~~~q~~ln~~q~~ 408 (687)
T KOG2206|consen 329 WRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAKGRAVTYSESRDMCTNGYKKKTFCTKSYLEVEDIQSRLNSSQLD 408 (687)
T ss_pred hccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhcccccccchhhhhhhcceecccCCCcchHhHHHHHhccchhHHH
Confidence 999999999999999999999999999998887754 111111 11110 011 1 111111
Q ss_pred ----cCCCCCCCCCCCcccccCccChHHHHHhhccCCCCcc----------hhhccccchHHHHHHhcc
Q 020975 242 ----YVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG----------RIIGRRGSSILAIKESCN 296 (319)
Q Consensus 242 ----~~d~~~l~a~~~~l~~~~~~~~~~i~~~ag~~~~~~~----------~~~~~~~~~~~~~~~~~~ 296 (319)
+..||...|++.+.+...+.+...+..+|..+|...+ ..++++.-+++.|++.+-
T Consensus 409 ~l~~L~~wRd~iARaeDES~~yVlpN~~ll~l~e~~P~~v~gl~~~ln~~~p~vkq~~~~~~~ii~~a~ 477 (687)
T KOG2206|consen 409 VLRALLRWRDFIARAEDESVHYVLPNDQLLKLAEERPDTVDGLLGGLNRLSPLVKQNVMDFLYIIRSAG 477 (687)
T ss_pred HHHHHHHHHHHHHhhccCCCceecccHHHHHHHHHCCccHHHHHHhccCCCHHHHHHHHHHHHHHHHHh
Confidence 4599999999999999999999999999999995443 466777778888887763
No 12
>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=99.87 E-value=2.4e-21 Score=166.16 Aligned_cols=163 Identities=29% Similarity=0.418 Sum_probs=134.5
Q ss_pred ccCCCeEEEEeeecCCC-CCCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEeehhhhHHHHHHHcCCc
Q 020975 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIK 124 (319)
Q Consensus 46 l~~~~~ia~D~E~~~~~-~~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~ 124 (319)
+...+.+++|+|+.+.. ..++++++++++++++|+||+... .....|+++|+|+++.||+||+|+|.+.|.+.+|+.
T Consensus 9 l~~~~~l~~~~e~~~~~~~~~~~~~i~l~~~~~~~~i~~~~~--~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~ 86 (178)
T cd06142 9 LASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI--GDLSPLKELLADPNIVKVFHAAREDLELLKRDFGIL 86 (178)
T ss_pred HhcCCeEEEECCccCCCcCCCceEEEEEeeCCCEEEEeCCCc--ccHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCC
Confidence 44456899999876554 478999999998855899975533 256678999999999999999999999997556998
Q ss_pred cccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhH
Q 020975 125 LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRF 204 (319)
Q Consensus 125 l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ 204 (319)
.+++|||++|+|+++|..+ .+++++++ +|++..+.+ .... .+|..+|++..+..|++.||.+
T Consensus 87 ~~~~~D~~laayLl~p~~~--------~~l~~l~~--~~l~~~~~~-~~~~-------~~w~~~~l~~~~~~yaa~~a~~ 148 (178)
T cd06142 87 PQNLFDTQIAARLLGLGDS--------VGLAALVE--ELLGVELDK-GEQR-------SDWSKRPLTDEQLEYAALDVRY 148 (178)
T ss_pred CCCcccHHHHHHHhCCCcc--------ccHHHHHH--HHhCCCCCc-cccc-------ccCCCCCCCHHHHHHHHHhHHH
Confidence 5568999999999999632 47999999 999987542 2111 3788899999999999999999
Q ss_pred HHHHHHHHHHHHhhhchHHHHHhh
Q 020975 205 LPYIYHNMMKKLNQQSLWYLAVRG 228 (319)
Q Consensus 205 ll~L~~~L~~~L~~~~~~~l~~~~ 228 (319)
+++|++.|.++|++.|+++++.+.
T Consensus 149 l~~L~~~l~~~L~e~~l~~L~~~~ 172 (178)
T cd06142 149 LLPLYEKLKEELEEEGRLEWAEEE 172 (178)
T ss_pred HHHHHHHHHHHHHHcCcHHHHHHH
Confidence 999999999999999999998753
No 13
>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=99.86 E-value=9.6e-21 Score=162.78 Aligned_cols=171 Identities=22% Similarity=0.211 Sum_probs=135.3
Q ss_pred CCeEEEEeeecCCC-CCCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEeehhhhHHHHHHHcCCccc-
Q 020975 49 QLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLH- 126 (319)
Q Consensus 49 ~~~ia~D~E~~~~~-~~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~- 126 (319)
...+++++|+.+.+ ..+++++++++.++++|+|++... ......|+++|+++++.|++||+|++++.|. .+|+.+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~~~~~i~~~~~-~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~~~~ 80 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGGGAYYIPLELA-LLDLAALKEWLEDEKIPKVGHDAKRAYVALK-RHGIELAG 80 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCCcEEEEeccch-HHHHHHHHHHHhCCCCceeccchhHHHHHHH-HCCCcCCC
Confidence 35678899987765 578999999998767888864321 0134568899999999999999999999995 7999884
Q ss_pred cEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHH
Q 020975 127 NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLP 206 (319)
Q Consensus 127 ~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll 206 (319)
.+||||+|+||++|+.++ +++++++. +|++.++.+..+. ++++ ..+. ++....+..|++.++.+++
T Consensus 81 ~~fDt~laaYLL~p~~~~-------~~l~~l~~--~yl~~~~~~~~~~---~~~~-~~~~-~~~~~~~~~y~~~~a~~l~ 146 (178)
T cd06140 81 VAFDTMLAAYLLDPTRSS-------YDLADLAK--RYLGRELPSDEEV---YGKG-AKFA-VPDEEVLAEHLARKAAAIA 146 (178)
T ss_pred cchhHHHHHHHcCCCCCC-------CCHHHHHH--HHcCCCCcchHHh---cCCC-CCcc-cCCHHHHHHHHHHHHHHHH
Confidence 579999999999997533 47899999 9999876532221 1221 1132 3435667899999999999
Q ss_pred HHHHHHHHHHhhhchHHHHHhhccc-cccc
Q 020975 207 YIYHNMMKKLNQQSLWYLAVRGALY-CRCF 235 (319)
Q Consensus 207 ~L~~~L~~~L~~~~~~~l~~~~e~~-~~vl 235 (319)
+|++.|.++|++++++++|.++||| ++||
T Consensus 147 ~l~~~l~~~L~~~~l~~L~~~iE~PL~~VL 176 (178)
T cd06140 147 RLAPKLEEELEENEQLELYYEVELPLAEVL 176 (178)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHhhHHHHh
Confidence 9999999999999999999999999 8887
No 14
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.82 E-value=2.8e-20 Score=193.59 Aligned_cols=222 Identities=18% Similarity=0.078 Sum_probs=172.7
Q ss_pred eEEeCCcccchHHhhhccccCCCeEEEEeeecCCC-CCCcEEEEEEEeCC--ceEEEEccC---CC-hhhHHHHHHHHcC
Q 020975 28 IHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPD--AIYLVDAIQ---GG-ETVVKACKPALES 100 (319)
Q Consensus 28 ~~~I~t~~~L~~~~l~~~l~~~~~ia~D~E~~~~~-~~g~l~~lqls~~~--~~~~id~~~---l~-~~~~~~L~~lLe~ 100 (319)
+..+.+.+++.+ +++. ...+.+++ .+.. ..+.++++++++.. ..||++... +. ..+...|+++|++
T Consensus 304 ~~~~~~~~~~~~-~~~~--~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 376 (887)
T TIGR00593 304 AKESEEAAPLAN-PAEK--AEVGGFVL----ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLN 376 (887)
T ss_pred ceEeCCHHHHHH-HHHh--CcCCeEEE----cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhC
Confidence 455656666775 6643 23446777 2333 46789999999853 477775321 11 2345669999999
Q ss_pred CCceEEEeehhhhHHHHHHHcCCccc-cEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhc
Q 020975 101 SYITKVIHDCKRDSEALYFQFGIKLH-NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLR 179 (319)
Q Consensus 101 ~~i~KV~hd~k~d~~~L~~~~gi~l~-~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~ 179 (319)
+.+.||+||+|+|+++|. .+|+.+. .+||||+|+||++++.+ .+|++++. +|++.......+. .+
T Consensus 377 ~~~~~v~~n~K~d~~~l~-~~gi~~~~~~~Dt~la~yll~~~~~--------~~l~~la~--~yl~~~~~~~~~~---~~ 442 (887)
T TIGR00593 377 EQIKKIGHDAKFLMHLLK-REGIELGGVIFDTMLAAYLLDPAQV--------STLDTLAR--RYLVEELILDEKI---GG 442 (887)
T ss_pred CCCcEEEeeHHHHHHHHH-hCCCCCCCcchhHHHHHHHcCCCCC--------CCHHHHHH--HHcCcccccHHHh---cc
Confidence 999999999999999995 7999985 58999999999998632 47899999 9998764422221 12
Q ss_pred CCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchHHHHHhhccc-cccc-ccCCCc-cCCCCCCCCCCCccc
Q 020975 180 QDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALY-CRCF-CINEND-YVDWPPLPPVPDYLI 256 (319)
Q Consensus 180 ~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~~l~~~~e~~-~~vl-~me~~g-~~d~~~l~a~~~~l~ 256 (319)
++ ..|...| .+.+..||+.||.++++|+..|.++|++.+++.+|.++||| ++|| .||.+| .+|...+.++..++.
T Consensus 443 ~~-~~~~~~~-~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~l~~l~~~iE~pl~~vLa~ME~~Gi~vD~~~l~~~~~~~~ 520 (887)
T TIGR00593 443 KL-AKFAFPP-LEEATEYLARRAAATKRLAEELLKELDENKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQELSQEFG 520 (887)
T ss_pred CC-CCccccc-HHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHhCCEEeCHHHHHHHHHHHH
Confidence 21 2233222 25567899999999999999999999999999999999999 9999 999999 999999999999999
Q ss_pred ccCccChHHHHHhhcc
Q 020975 257 VEGDVPEEEILSILDV 272 (319)
Q Consensus 257 ~~~~~~~~~i~~~ag~ 272 (319)
.++...+++|++++|.
T Consensus 521 ~~l~~le~~i~~~~g~ 536 (887)
T TIGR00593 521 EEIADLEEEIYELAGE 536 (887)
T ss_pred HHHHHHHHHHHHHhCC
Confidence 9999999999999993
No 15
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.82 E-value=3e-19 Score=151.35 Aligned_cols=168 Identities=29% Similarity=0.442 Sum_probs=130.8
Q ss_pred EEeCCcccchHHhhhcccc-CCCeEEEEeeecCCC-CCCcEEEEEEEeCC-ceEEEEccCCChhhHHHHHHHHcCCCceE
Q 020975 29 HIVTNASQLPAEFLEPSSE-RQLVIGFDCEGVDLC-RHGSLCIMQLAFPD-AIYLVDAIQGGETVVKACKPALESSYITK 105 (319)
Q Consensus 29 ~~I~t~~~L~~~~l~~~l~-~~~~ia~D~E~~~~~-~~g~l~~lqls~~~-~~~~id~~~l~~~~~~~L~~lLe~~~i~K 105 (319)
.+|++.+++.+ +++. +. ....+++|+|+.+.. ..+++++++++..+ .+|+++... ....+..|+++|+++.+.|
T Consensus 2 ~~i~~~~~~~~-~~~~-~~~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~-~~~~~~~l~~~l~~~~~~k 78 (172)
T smart00474 2 RVVTDSETLEE-LLEK-LRAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLA-LGDDLEILKDLLEDETITK 78 (172)
T ss_pred EEecCHHHHHH-HHHH-HHhcCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEecc-chhhHHHHHHHhcCCCceE
Confidence 46777777776 7755 44 456899999886654 47899999999754 445443322 2223566899999999999
Q ss_pred EEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCC
Q 020975 106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFW 185 (319)
Q Consensus 106 V~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w 185 (319)
|+||+|+|.+.|. .+|+.+.++||||+|+|+++|..+. .+|+.++. .|++..+++ . .++ .+|
T Consensus 79 v~~d~k~~~~~L~-~~gi~~~~~~D~~laayll~p~~~~-------~~l~~l~~--~~l~~~~~~--~----~~~--~~~ 140 (172)
T smart00474 79 VGHNAKFDLHVLA-RFGIELENIFDTMLAAYLLLGGPSK-------HGLATLLK--EYLGVELDK--E----EQK--SDW 140 (172)
T ss_pred EEechHHHHHHHH-HCCCcccchhHHHHHHHHHcCCCCc-------CCHHHHHH--HHhCCCCCc--c----cCc--ccc
Confidence 9999999999996 5999998789999999999986432 47899999 999876542 1 111 278
Q ss_pred ccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 020975 186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (319)
Q Consensus 186 ~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (319)
..+|+...+..||+.||.++++|++.|.++|.
T Consensus 141 ~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l~ 172 (172)
T smart00474 141 GARPLSEEQLQYAAEDADALLRLYEKLEKELE 172 (172)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 77888999999999999999999999998873
No 16
>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=99.81 E-value=1e-18 Score=152.39 Aligned_cols=173 Identities=26% Similarity=0.407 Sum_probs=136.0
Q ss_pred ccCeEEeCCcccchHHhhhccccCCCeEEEEeeecCCC-CCCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCc
Q 020975 25 VVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYI 103 (319)
Q Consensus 25 ~~~~~~I~t~~~L~~~~l~~~l~~~~~ia~D~E~~~~~-~~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i 103 (319)
+++|.+|++.+++.. |++. +...+.+++++++.+.. +.+++++++++.++++|+|++... ......|+++|+++++
T Consensus 2 ~~~~~~i~~~~~l~~-~~~~-l~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~l~~-~~~~~~L~~~L~~~~i 78 (192)
T cd06147 2 ETPLTFVDTEEKLEE-LVEK-LKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKL-RDDMHILNEVFTDPNI 78 (192)
T ss_pred CCCcEEECCHHHHHH-HHHH-HhcCCeEEEEeEecCCccCCCceEEEEEecCCCcEEEEeccc-ccchHHHHHHhcCCCc
Confidence 567889966676775 7754 44456899999875543 468899999998766888864222 2235568899999999
Q ss_pred eEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCC
Q 020975 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQ 183 (319)
Q Consensus 104 ~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~ 183 (319)
.|++||+|.+++.|.+.+|+.+.++||||+|+|||+|+ + .+++.+++ +|++..+. +.. ...
T Consensus 79 ~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~-~--------~~l~~l~~--~yl~~~~~-k~~-------~~~ 139 (192)
T cd06147 79 LKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-R--------HSLAYLLQ--KYCNVDAD-KKY-------QLA 139 (192)
T ss_pred eEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCC-c--------ccHHHHHH--HHhCCCcc-hhh-------hcc
Confidence 99999999999999547899987669999999999996 3 26899999 99987643 211 113
Q ss_pred CCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhh
Q 020975 184 FWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ 219 (319)
Q Consensus 184 ~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~ 219 (319)
+|..+|+..++..|++.+|.++++|++.|.++|+++
T Consensus 140 ~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~ 175 (192)
T cd06147 140 DWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLER 175 (192)
T ss_pred ccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 587778888899999999999999999999999874
No 17
>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=99.79 E-value=2.5e-18 Score=149.14 Aligned_cols=177 Identities=26% Similarity=0.274 Sum_probs=134.9
Q ss_pred cCCCeEEEEeeecCCC-CCCcEEEEEEEeCC-ceEEEEccCC------C-hhhHHHHHHHHcCCCceEEEeehhhhHHHH
Q 020975 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAFPD-AIYLVDAIQG------G-ETVVKACKPALESSYITKVIHDCKRDSEAL 117 (319)
Q Consensus 47 ~~~~~ia~D~E~~~~~-~~g~l~~lqls~~~-~~~~id~~~l------~-~~~~~~L~~lLe~~~i~KV~hd~k~d~~~L 117 (319)
.+.+.+++|+|+.+.. ..+++++++++..+ ..+++++... . ..++..|+++|++..+.+|+||+|+|+.+|
T Consensus 3 ~~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l 82 (193)
T cd06139 3 EKAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVL 82 (193)
T ss_pred ccCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHHH
Confidence 3567899999987765 57889999999864 4777764321 1 234566889999988899999999999999
Q ss_pred HHHcCCccc-cEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHH
Q 020975 118 YFQFGIKLH-NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVR 196 (319)
Q Consensus 118 ~~~~gi~l~-~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~ 196 (319)
. .+|+.+. .++||++++|+++|+..+ .+|+++++ +|++......++... .+.+..+|...|+ ..+..
T Consensus 83 ~-~~gi~~~~~~~Dt~l~a~ll~p~~~~-------~~l~~l~~--~~l~~~~~~~~~~~~-k~~~~~~~~~~~~-~~~~~ 150 (193)
T cd06139 83 A-NHGIELRGPAFDTMLASYLLNPGRRR-------HGLDDLAE--RYLGHKTISFEDLVG-KGKKQITFDQVPL-EKAAE 150 (193)
T ss_pred H-HCCCCCCCCcccHHHHHHHhCCCCCC-------CCHHHHHH--HHhCCCCccHHHHcC-CCcCcCCccccCH-HHHHH
Confidence 5 7898874 589999999999996422 47899999 999865321122110 0111234544444 56788
Q ss_pred HHHhhhhHHHHHHHHHHHHHhh-hchHHHHHhhccc-cccc
Q 020975 197 AAADDVRFLPYIYHNMMKKLNQ-QSLWYLAVRGALY-CRCF 235 (319)
Q Consensus 197 YAa~Da~~ll~L~~~L~~~L~~-~~~~~l~~~~e~~-~~vl 235 (319)
||+.|+.++++|++.|.++|++ .+++++|.++||| .+||
T Consensus 151 ya~~d~~~~~~l~~~l~~~l~~~~~~~~l~~~iE~Pl~~vL 191 (193)
T cd06139 151 YAAEDADITLRLYELLKPKLKEEPGLLELYEEIEMPLIPVL 191 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhccHHHHh
Confidence 9999999999999999999998 8999999999999 8876
No 18
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.79 E-value=4.6e-20 Score=184.63 Aligned_cols=199 Identities=18% Similarity=0.124 Sum_probs=166.1
Q ss_pred CeEEeCCcccchHHhhhccccCCCeEEEEeeecCCCCCCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEE
Q 020975 27 PIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKV 106 (319)
Q Consensus 27 ~~~~I~t~~~L~~~~l~~~l~~~~~ia~D~E~~~~~~~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV 106 (319)
.+.+|++.+++.. ++.. +...+.+++|+|+..... .++++|++..+..|+||+... +. ++
T Consensus 2 ~~~~I~~~~~l~~-~~~~-l~~~~~~a~DtEf~r~~t--~l~liQ~~~~~~~~liDpl~~----l~---~~--------- 61 (553)
T PRK14975 2 DMKVILAPEELGA-ALER-LSPAGVVAGDTETTGDDA--AAAAAQEGEEEPRWVWASTAA----LY---PR--------- 61 (553)
T ss_pred CceEEeccchhHH-HHHH-hccCCceeCCccccCCcc--hhheeeecCCCceEEECchHH----hH---HH---------
Confidence 4678999999997 9987 788999999999875433 799999998889999987531 11 11
Q ss_pred EeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCc
Q 020975 107 IHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWT 186 (319)
Q Consensus 107 ~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~ 186 (319)
| ..+|+.+.++||||+|+|+|+++.+.. .+|++.++. .|+++.+++..+ + ++|.
T Consensus 62 ----------L-~~~Gv~~~~~fDT~LAa~lL~~~~~~~-----~~~l~~la~--~~l~~~l~k~~~-~-------sdw~ 115 (553)
T PRK14975 62 ----------L-LAAGVRVERCHDLMLASQLLLGSEGRA-----GSSLSAAAA--RALGEGLDKPPQ-T-------SALS 115 (553)
T ss_pred ----------H-HHCCCccCCCchHHHHHHHcCCCCCcC-----CCCHHHHHH--HHhCCCCCChhh-h-------cccc
Confidence 4 367999888999999999999864311 258999999 999998874332 2 3796
Q ss_pred cCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhh------chHHHHHhhccc-cccc-ccCCCc-cCCCCCCCCCCCccc-
Q 020975 187 YRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ------SLWYLAVRGALY-CRCF-CINEND-YVDWPPLPPVPDYLI- 256 (319)
Q Consensus 187 ~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~------~~~~l~~~~e~~-~~vl-~me~~g-~~d~~~l~a~~~~l~- 256 (319)
+|+++.+..||+.|+.+++.||..|.++|++. |+..++.++||| .+++ .||.+| .+|...+.++..++.
T Consensus 116 -rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~~~~~~~g~l~ll~~~E~~~~~~l~~me~~Gi~~D~~~~~~~~~~~~~ 194 (553)
T PRK14975 116 -DPPDEEQLLYAAADADVLLELYAVLADQLNRIAAAAHPGRLRLLAAAESAGALAAAEMELAGLPWDTDVHEALLAELLG 194 (553)
T ss_pred -ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHhhHHHHHHHHHHhCeEeCHHHHHHHHHHHhc
Confidence 99999999999999999999999999999987 899999999999 8888 999999 999999888877777
Q ss_pred ---------ccCccChHHHHHhhcc
Q 020975 257 ---------VEGDVPEEEILSILDV 272 (319)
Q Consensus 257 ---------~~~~~~~~~i~~~ag~ 272 (319)
.++..++++|++++|.
T Consensus 195 ~~~~~~~~~~~~~~l~~~i~~~~g~ 219 (553)
T PRK14975 195 PRPAAGGRPARLAELAAEIREALGR 219 (553)
T ss_pred ccccccchHHHHHHHHHHHHHHhCC
Confidence 5677999999999984
No 19
>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=99.73 E-value=8.4e-17 Score=133.81 Aligned_cols=152 Identities=32% Similarity=0.378 Sum_probs=113.8
Q ss_pred eEEEEeeecCCC-CCCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEeehhhhHHHHHHHcCCcc-ccE
Q 020975 51 VIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKL-HNV 128 (319)
Q Consensus 51 ~ia~D~E~~~~~-~~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l-~~v 128 (319)
.+++|+|+.+.. ..++++++|+++++++++++.......+...|+++|+++.+.||+||+|+|+..|. ..++.. +++
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~-~~~~~~~~~~ 80 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLA-RDGIELPGNI 80 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHH-HCCCCCCCCc
Confidence 578999876654 47899999999864466664322113456678999999999999999999999996 556544 578
Q ss_pred EechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHH
Q 020975 129 VDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYI 208 (319)
Q Consensus 129 fDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L 208 (319)
|||++|+|+++|...+ .+|+++++ +|++..+.+.++.. +.+. .|..++++..+..|++.|+.++++|
T Consensus 81 ~D~~~~ayll~~~~~~-------~~l~~l~~--~~l~~~~~~~~~~~---~~~~-~~~~~~~~~~~~~y~~~da~~~~~l 147 (155)
T cd00007 81 FDTMLAAYLLNPGEGS-------HSLDDLAK--EYLGIELDKDEQIY---GKGA-KTFARPLSEELLEYAAEDADALLRL 147 (155)
T ss_pred ccHHHHHHHhCCCCCc-------CCHHHHHH--HHcCCCCccHHHHh---cCCC-CccccCCHHHHHHHHHHhHHHHHHH
Confidence 9999999999996422 47999999 99987754212221 1111 1334777899999999999999999
Q ss_pred HHHHHHHH
Q 020975 209 YHNMMKKL 216 (319)
Q Consensus 209 ~~~L~~~L 216 (319)
++.|.+++
T Consensus 148 ~~~l~~~~ 155 (155)
T cd00007 148 YEKLLEEL 155 (155)
T ss_pred HHHHHhhC
Confidence 99998753
No 20
>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=99.73 E-value=7.8e-17 Score=134.03 Aligned_cols=146 Identities=27% Similarity=0.327 Sum_probs=112.5
Q ss_pred eEEEEeeecCCC-CCCcEEEEEEEeC-CceEEEEccCCChhhHHHHHHHHcCCCceEEEeehhhhHHHHHHHcCCcc-cc
Q 020975 51 VIGFDCEGVDLC-RHGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKL-HN 127 (319)
Q Consensus 51 ~ia~D~E~~~~~-~~g~l~~lqls~~-~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l-~~ 127 (319)
.+++|+|+.+.. ..++++++|++++ +.+|+|++... .-....|+++|+|+++.|++||+|.|++.|. ..|+.. ++
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~-~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L~-~~~~~~~~~ 78 (150)
T cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHD-YLALELLKPLLEDEKALKVGQNLKYDRGILL-NYFIELRGI 78 (150)
T ss_pred CEEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCc-ccCHHHHHHHhcCCCCceeeecHHHHHHHHH-HcCCccCCc
Confidence 368889876543 4789999999986 44888875432 1124568899999999999999999999995 678776 46
Q ss_pred EEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHH
Q 020975 128 VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPY 207 (319)
Q Consensus 128 vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~ 207 (319)
+|||++|+|+++|.+++ .++++++. +|++.++.+.++. +++ .|..+++..++..|++.|+.++++
T Consensus 79 ~~D~~laayLl~p~~~~-------~~l~~l~~--~~l~~~~~~~~~~---~~~---~~~~~~~~~~~~~ya~~~a~~l~~ 143 (150)
T cd09018 79 AFDTMLEAYILNSVAGR-------WDMDSLVE--RWLGHKLIKFESI---AGK---LWFNQPLTEEQGRYAAEDADVTLQ 143 (150)
T ss_pred chhHHHHHHHhCCCCCC-------CCHHHHHH--HHhCCCcccHHHh---cCC---CCcccCCHHHHHHHHHHHHHHHHH
Confidence 89999999999996422 37899999 9999875432222 122 375577788999999999999999
Q ss_pred HHHHHH
Q 020975 208 IYHNMM 213 (319)
Q Consensus 208 L~~~L~ 213 (319)
|++.|.
T Consensus 144 L~~~l~ 149 (150)
T cd09018 144 IHLKLW 149 (150)
T ss_pred HHHHhc
Confidence 998874
No 21
>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=99.27 E-value=1.5e-10 Score=96.76 Aligned_cols=132 Identities=21% Similarity=0.222 Sum_probs=92.9
Q ss_pred CCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEeehhhhHHHHHHHcCCcccc-EEechhHHhhhhhhc
Q 020975 64 HGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHN-VVDTQIAYSLIEEQE 142 (319)
Q Consensus 64 ~g~l~~lqls~~~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~~-vfDt~lAayLL~~~~ 142 (319)
.+++.++.++.++++|+|++.. .. ....|+++|++..+.|++||.|.+++.| +.+|+.+.+ +||||+|+|||+|++
T Consensus 17 ~~~~~glal~~~~~~~yi~~~~-~~-~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~~LAaYLL~p~~ 93 (151)
T cd06128 17 SANLVGLAFAIEGVAAYIPVAH-DY-ALELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDTMLEAYLLDPVA 93 (151)
T ss_pred cCcEEEEEEEcCCCeEEEeCCC-Cc-CHHHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhHHHHHHHcCCCC
Confidence 5778889998865678875321 00 1455888999999999999999999999 489999854 799999999999975
Q ss_pred CCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCC-CHHHHHHHHhhhhHHHHHHHHHH
Q 020975 143 GRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPL-TELMVRAAADDVRFLPYIYHNMM 213 (319)
Q Consensus 143 ~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL-~~~~~~YAa~Da~~ll~L~~~L~ 213 (319)
++ .++++++. +|++.......+ +++++ ..+. ++ ......|++..+.++++|++.|.
T Consensus 94 ~~-------~~l~~la~--~yl~~~~~~~~~---~~gkg-~~~~--~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 94 GR-------HDMDSLAE--RWLKEKTITFEE---IAGKG-LTFN--QIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CC-------CCHHHHHH--HHcCCCCccHHH---HcCCC-CChh--hcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 32 26899999 998876221112 22221 1111 22 12234588888889999988874
No 22
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.25 E-value=4.6e-12 Score=123.28 Aligned_cols=181 Identities=22% Similarity=0.276 Sum_probs=128.6
Q ss_pred ccCeEEeCCcccchHHhh-hccccCC-CeEEEEeeecCC-C-CCCcEEEEEEEeCCceEEEEccCCCh---hhH-HHHHH
Q 020975 25 VVPIHIVTNASQLPAEFL-EPSSERQ-LVIGFDCEGVDL-C-RHGSLCIMQLAFPDAIYLVDAIQGGE---TVV-KACKP 96 (319)
Q Consensus 25 ~~~~~~I~t~~~L~~~~l-~~~l~~~-~~ia~D~E~~~~-~-~~g~l~~lqls~~~~~~~id~~~l~~---~~~-~~L~~ 96 (319)
...+.+|+++.++.. ++ +. +.++ -+||+|+||.+. . ...+++++|+++.+.+|+||+..+.. +.+ ..+..
T Consensus 389 ~~~i~~V~~e~El~~-l~l~~-l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~ 466 (617)
T KOG2207|consen 389 VESIGMVGNEKELRD-LLLES-LSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQ 466 (617)
T ss_pred ccceeeeCCHHHHHH-HHHHH-hhhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHH
Confidence 456888999999987 55 33 5545 689999999876 3 46789999999999999999987642 223 34566
Q ss_pred HHcCCCceEEEeehhhhHHHHHHHcC-Ccc-ccEEechhH-------HhhhhhhcCCCCCCCCcccHHhhhcCCcccCCc
Q 020975 97 ALESSYITKVIHDCKRDSEALYFQFG-IKL-HNVVDTQIA-------YSLIEEQEGRKRSPDDYISFVGLLADPRYCGIS 167 (319)
Q Consensus 97 lLe~~~i~KV~hd~k~d~~~L~~~~g-i~l-~~vfDt~lA-------ayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~ 167 (319)
+|+++++.|||++.+.|++++.+..+ +.. -.+-+++++ ..+.+-.-.--.+....-+|.+|.. ..+|..
T Consensus 467 if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~--~llg~~ 544 (617)
T KOG2207|consen 467 IFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTD--CLLGKK 544 (617)
T ss_pred HccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhH--HHhhhh
Confidence 99999999999999999999964222 111 112333333 3332211000001111246788887 888888
Q ss_pred cchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 020975 168 YQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (319)
Q Consensus 168 l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (319)
+++.++ . ++|..|||+..|+-|||.||.++..++..+....+
T Consensus 545 lnKteq-c-------snWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 545 LNKTEQ-C-------SNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred cccccc-c-------chhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 874332 2 48999999999999999999999999999987776
No 23
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.15 E-value=2e-07 Score=86.69 Aligned_cols=149 Identities=31% Similarity=0.499 Sum_probs=101.0
Q ss_pred EEeeecCCCCCCcEEEEEEEeCCceEEEEccCCChhhH-HHHHHHHcCCCceEEEeehhhhHHHHHHHcCCccccEEech
Q 020975 54 FDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVV-KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQ 132 (319)
Q Consensus 54 ~D~E~~~~~~~g~l~~lqls~~~~~~~id~~~l~~~~~-~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~ 132 (319)
+-.|+.+..++|++|++|.++.-..|++|++.++..++ ..+..++++.+|.|+.|+++.-++.+.+.|||.++++|||+
T Consensus 63 ~~~e~a~~~~~~~l~~~q~~~~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~q 142 (458)
T KOG2405|consen 63 VAAEGANVCRHGKLCWLQVATNCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQ 142 (458)
T ss_pred ccccCccccccCcchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhhh
Confidence 55566555678999999999877889999988876544 56788999999999999999999999999999999999999
Q ss_pred hHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccch---hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhH
Q 020975 133 IAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE---KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRF 204 (319)
Q Consensus 133 lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~---k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ 204 (319)
+|.-+-+.......+++....+..-.- +.|.+.... -++...+.-.+...|-.||.++..+.-.+..+.+
T Consensus 143 ~~d~~q~~~e~g~~~~n~~~~~q~sl~--kh~~~a~k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 143 VADVLQFSMETGGYLPNCITTLQESLI--KHLQVAPKYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred hhhhhhhcccccccCCccccchHHHHH--HHHHhcccHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 977654432221122222233333222 333322110 0010011123556799999998887776666655
No 24
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.06 E-value=2.6e-06 Score=79.38 Aligned_cols=164 Identities=34% Similarity=0.318 Sum_probs=108.1
Q ss_pred CCcEEEEEEEeCCceEEEEccCCChh-hHHHHHHHHcCCCceEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhc
Q 020975 64 HGSLCIMQLAFPDAIYLVDAIQGGET-VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQE 142 (319)
Q Consensus 64 ~g~l~~lqls~~~~~~~id~~~l~~~-~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~ 142 (319)
.+.+...+++++...|++|...-+.. .+...++.|++..+ +. |++.+...+...|++.+.+++|||+|+.++.+..
T Consensus 210 ~~e~~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~sLve~~e 286 (458)
T KOG2405|consen 210 ALEATYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIASSLVEPSE 286 (458)
T ss_pred hhhhhhhhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHHHHhhhHH
Confidence 44555578888888899988754422 23446777887654 44 9999999999999999999999999999999875
Q ss_pred -C-CCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhc
Q 020975 143 -G-RKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (319)
Q Consensus 143 -~-~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~ 220 (319)
+ ++.. ...++.-.|..+..|.+.....+++++.++..++..|..||.++.+..-++.||..++... ..+.+..
T Consensus 287 ~grr~p~-~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~----~~l~a~~ 361 (458)
T KOG2405|consen 287 YGRRHPT-SILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIF----DTLVAVC 361 (458)
T ss_pred hcccCCc-cceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHH----hhHhhhC
Confidence 3 2221 1112222222111334444333455555555666689999999999999999999998744 4455566
Q ss_pred hHHHHHhhccccccc
Q 020975 221 LWYLAVRGALYCRCF 235 (319)
Q Consensus 221 ~~~l~~~~e~~~~vl 235 (319)
+|.+...-....+|+
T Consensus 362 l~HL~~rp~~e~eci 376 (458)
T KOG2405|consen 362 LSHLTRRPYTEPECI 376 (458)
T ss_pred hHhhccCCccccchh
Confidence 666644333333444
No 25
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=97.83 E-value=4.6e-05 Score=70.15 Aligned_cols=129 Identities=18% Similarity=0.220 Sum_probs=91.2
Q ss_pred CCcEEEEEEEeC-CceEEEEccCCChhhHHHHHHHHcCCCceEEEeehhhhHHHHHH-HcCCccccEEechhHHhhhhhh
Q 020975 64 HGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYF-QFGIKLHNVVDTQIAYSLIEEQ 141 (319)
Q Consensus 64 ~g~l~~lqls~~-~~~~~id~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~-~~gi~l~~vfDt~lAayLL~~~ 141 (319)
.+....+|||++ +.|+++.....+ .+...|+.+|+|++..+||-+.+.|...|.+ .|++.+..+.|+.. +++..
T Consensus 146 ~P~~~~lqlcV~en~C~I~ql~~~~-~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~---~~~d~ 221 (319)
T KOG4373|consen 146 DPPPDTLQLCVGENRCLIIQLIHCK-RIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRL---LVNDS 221 (319)
T ss_pred CCCcchhhhhhcccceeeEEeeccc-cchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHh---hcchh
Confidence 345778999997 778888655443 3678888899999999999999999999976 78888877777654 22222
Q ss_pred cCCCCCCCCcccHHhhhcCCccc---C--CccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 020975 142 EGRKRSPDDYISFVGLLADPRYC---G--ISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (319)
Q Consensus 142 ~~~~~L~~~~~sL~~L~~~~~~l---g--~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (319)
.+. .+++ -+...++. ..+ | +.+++ .+ +.++|...||+.+|+.||+.||+....|+
T Consensus 222 ~g~-~~~~--~s~e~i~~--~~~~~~~~~v~l~~--~i------~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 222 LGG-SMPN--DSFEEIVS--ETLGYYGKDVRLDK--EI------RMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred hcc-CccC--ccHHHHHH--HHhhccccccccCh--hc------ccccceeeeccHHHHHHHHhHHHHHHHHH
Confidence 111 1111 23444554 333 3 22221 12 22699999999999999999999999999
No 26
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=97.81 E-value=0.00011 Score=56.62 Aligned_cols=72 Identities=24% Similarity=0.179 Sum_probs=54.3
Q ss_pred EEEEeeecCCC-CCCcEEEEEEEeC--CceEEEEccCCChhhHHHHHHHHcCCC-ceEEEeehhhhHHHHHHH---cCCc
Q 020975 52 IGFDCEGVDLC-RHGSLCIMQLAFP--DAIYLVDAIQGGETVVKACKPALESSY-ITKVIHDCKRDSEALYFQ---FGIK 124 (319)
Q Consensus 52 ia~D~E~~~~~-~~g~l~~lqls~~--~~~~~id~~~l~~~~~~~L~~lLe~~~-i~KV~hd~k~d~~~L~~~---~gi~ 124 (319)
+++|+|+.+.+ ....++++|++.. ++.|++| +.+++++.. ..+|+||+++|...|.+. +|+.
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~~~-----------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~ 69 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAVID-----------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLK 69 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEEeh-----------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCC
Confidence 47999999885 6788999999875 6667764 556777766 678999999999877643 3332
Q ss_pred ----cccEEechhH
Q 020975 125 ----LHNVVDTQIA 134 (319)
Q Consensus 125 ----l~~vfDt~lA 134 (319)
....+||+.+
T Consensus 70 ~p~~~~~~lDT~~l 83 (96)
T cd06125 70 YPLLAGSWIDTIKL 83 (96)
T ss_pred CCCcCCcEEEehHH
Confidence 2458999987
No 27
>PRK07740 hypothetical protein; Provisional
Probab=97.50 E-value=0.0026 Score=57.60 Aligned_cols=98 Identities=17% Similarity=0.293 Sum_probs=67.6
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHHH----cCCcc-ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCccc
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ----FGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~----~gi~l-~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~l 164 (319)
++..|..++.+. ..|+||+.+|...|.+. ++... ..++||+..+..+.+... .++|++++. ++
T Consensus 131 vl~~f~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~-------~~sL~~l~~---~~ 198 (244)
T PRK07740 131 VLHRFYAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERD-------FPTLDDALA---YY 198 (244)
T ss_pred HHHHHHHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCC-------CCCHHHHHH---HC
Confidence 345555566543 56899999999887532 33334 458999988777665422 368999996 67
Q ss_pred CCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchHH
Q 020975 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (319)
Q Consensus 165 g~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~~ 223 (319)
|++.... ++ |..||.++..|+..+..++.+.|...
T Consensus 199 gi~~~~~-----------H~-------------Al~Da~ata~l~~~ll~~~~~~~~~~ 233 (244)
T PRK07740 199 GIPIPRR-----------HH-------------ALGDALMTAKLWAILLVEAQQRGITT 233 (244)
T ss_pred CcCCCCC-----------CC-------------cHHHHHHHHHHHHHHHHHHHHcCCcC
Confidence 7654310 11 67899999999999999988766443
No 28
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.44 E-value=0.002 Score=60.47 Aligned_cols=138 Identities=18% Similarity=0.167 Sum_probs=87.4
Q ss_pred CCeEEEEeeecCCC-CCCcEEEEEEEe--C-Cc-----eEEEEccC---------CC----------hhhHHHHHHHHcC
Q 020975 49 QLVIGFDCEGVDLC-RHGSLCIMQLAF--P-DA-----IYLVDAIQ---------GG----------ETVVKACKPALES 100 (319)
Q Consensus 49 ~~~ia~D~E~~~~~-~~g~l~~lqls~--~-~~-----~~~id~~~---------l~----------~~~~~~L~~lLe~ 100 (319)
...++||+|+++++ ...+++-|+... . +. ..++.+.. +. .+++..|..++.+
T Consensus 15 ~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~l~~ 94 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRG 94 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHHHHcCC
Confidence 46789999999886 344544333321 1 21 12333211 00 1344667777765
Q ss_pred CCceEEEeehhhhHHHHHHH---cCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHH
Q 020975 101 SYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVR 175 (319)
Q Consensus 101 ~~i~KV~hd~k~d~~~L~~~---~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~ 175 (319)
. ..|+||+.+|+.+|.+. +|+.. ...+||+..+..+.+...+ ++|++|++ ++|++...
T Consensus 95 ~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~-------~kL~~l~~---~~gi~~~~----- 157 (313)
T PRK06063 95 R--TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPN-------LRLETLAA---HWGVPQQR----- 157 (313)
T ss_pred C--EEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCC-------CCHHHHHH---HcCCCCCC-----
Confidence 3 46999999999988643 45543 3589999877666543322 57899996 56765321
Q ss_pred HHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchH
Q 020975 176 VLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLW 222 (319)
Q Consensus 176 ~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~ 222 (319)
.++ |..||.++..|+..+.+++.+.+.+
T Consensus 158 ------~H~-------------Al~DA~ata~l~~~ll~~~~~~~~~ 185 (313)
T PRK06063 158 ------PHD-------------ALDDARVLAGILRPSLERARERDVW 185 (313)
T ss_pred ------CCC-------------cHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 011 6789999999999999998877653
No 29
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=97.18 E-value=0.011 Score=53.01 Aligned_cols=136 Identities=13% Similarity=0.137 Sum_probs=80.5
Q ss_pred CCCeEEEEeeecCCC-CCCcEEEEEEEe-C--C-----ceEEEEccC-CC----------h-----------hhHHHHHH
Q 020975 48 RQLVIGFDCEGVDLC-RHGSLCIMQLAF-P--D-----AIYLVDAIQ-GG----------E-----------TVVKACKP 96 (319)
Q Consensus 48 ~~~~ia~D~E~~~~~-~~g~l~~lqls~-~--~-----~~~~id~~~-l~----------~-----------~~~~~L~~ 96 (319)
+...++||+|+++++ ..++++-+++.. . + ..+++++.. +. . +++..+..
T Consensus 5 ~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~~ 84 (232)
T PRK07942 5 PGPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEIAD 84 (232)
T ss_pred cCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHHHH
Confidence 467899999999986 455554333321 1 2 234665532 10 0 11222222
Q ss_pred H----HcCCCceEEEeehhhhHHHHHH---HcCCcc---ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCC
Q 020975 97 A----LESSYITKVIHDCKRDSEALYF---QFGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGI 166 (319)
Q Consensus 97 l----Le~~~i~KV~hd~k~d~~~L~~---~~gi~l---~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~ 166 (319)
. +.+ ....|+||+.+|..+|.+ ++|... ..++||+..+..+.+... ..++|++|++ ++|+
T Consensus 85 ~l~~~~~~-~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~------~~~~L~~l~~---~~gi 154 (232)
T PRK07942 85 ALREAWAR-GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRK------GKRTLTALCE---HYGV 154 (232)
T ss_pred HHHHHhhc-CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccC------CCCCHHHHHH---HcCC
Confidence 2 223 345699999999988753 345432 358999987766554321 1257899996 5676
Q ss_pred ccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 020975 167 SYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (319)
Q Consensus 167 ~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (319)
+... ..+ |..||.++.+|+..+.++..
T Consensus 155 ~~~~-----------aH~-------------Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 155 RLDN-----------AHE-------------ATADALAAARVAWALARRFP 181 (232)
T ss_pred CCCC-----------CCC-------------hHHHHHHHHHHHHHHHHHHH
Confidence 5431 011 77899999998888877665
No 30
>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=97.12 E-value=0.0041 Score=52.00 Aligned_cols=67 Identities=22% Similarity=0.155 Sum_probs=44.8
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCcc
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l 168 (319)
++..|..++.+ .+ .|+||+.+|+.+|. .+.....++||.....+..+.. ...+||+.|++ +++|+++
T Consensus 67 ~~~~l~~~l~~-~v-lVgHn~~fD~~~L~--~~~~~~~~~dt~~l~~~~~~~~------~~~~sL~~l~~--~~lgi~~ 133 (152)
T cd06144 67 VQKKVAELLKG-RI-LVGHALKNDLKVLK--LDHPKKLIRDTSKYKPLRKTAK------GKSPSLKKLAK--QLLGLDI 133 (152)
T ss_pred HHHHHHHHhCC-CE-EEEcCcHHHHHHhc--CcCCCccEEEeEEeeccccccC------CCChhHHHHHH--HHcCccc
Confidence 45677778876 44 49999999999994 3333245789876443332211 12478999998 7888765
No 31
>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=97.03 E-value=0.0036 Score=52.68 Aligned_cols=67 Identities=24% Similarity=0.067 Sum_probs=41.5
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHHHcCCccccEEechhHHhh----hhhhcCCCCCCCCcccHHhhhcCCcccC
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSL----IEEQEGRKRSPDDYISFVGLLADPRYCG 165 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayL----L~~~~~~~~L~~~~~sL~~L~~~~~~lg 165 (319)
+...|..++.+ -..|+||+++|+.+|. .. .....+.||.....+ ..|.. ..++|..|++ +|++
T Consensus 67 v~~~l~~~l~~--~vlV~Hn~~~D~~~l~-~~-~~~~~~~Dt~~l~~~~~~~~~p~~-------~~~~L~~L~~--~~~~ 133 (157)
T cd06149 67 AQKEILKILKG--KVVVGHAIHNDFKALK-YF-HPKHMTRDTSTIPLLNRKAGFPEN-------CRVSLKVLAK--RLLH 133 (157)
T ss_pred HHHHHHHHcCC--CEEEEeCcHHHHHHhc-cc-CCCcCEEECcccccchhhcCCccc-------CChhHHHHHH--HHcC
Confidence 45667777764 3469999999999984 22 122357788543211 12211 2378999999 8876
Q ss_pred Cccc
Q 020975 166 ISYQ 169 (319)
Q Consensus 166 ~~l~ 169 (319)
..+.
T Consensus 134 ~~i~ 137 (157)
T cd06149 134 RDIQ 137 (157)
T ss_pred hhhc
Confidence 5443
No 32
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=97.01 E-value=0.024 Score=49.61 Aligned_cols=86 Identities=15% Similarity=0.170 Sum_probs=59.0
Q ss_pred ceEEEeehhhhHHHHHHH---cCCc---c--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHH
Q 020975 103 ITKVIHDCKRDSEALYFQ---FGIK---L--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEV 174 (319)
Q Consensus 103 i~KV~hd~k~d~~~L~~~---~gi~---l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~ 174 (319)
-..|+||+.+|+.+|.+. +|.. . ..++||+..+..+.+. .+|+.+++ ++|++.... +
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~~----------~~L~~l~~---~~gi~~~~~-~- 170 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYGQ----------TVLAKACQ---AAGXDFDST-Q- 170 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcCc----------ccHHHHHH---HcCCCcccc-c-
Confidence 357999999999988532 3432 1 2378998877655432 36888886 456553210 1
Q ss_pred HHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchHH
Q 020975 175 RVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (319)
Q Consensus 175 ~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~~ 223 (319)
..-|..||.++..|+..+..++.+.+.|.
T Consensus 171 --------------------~H~Al~Da~ata~lf~~l~~~~~~~~~~~ 199 (200)
T TIGR01298 171 --------------------AHSALYDTEKTAELFCEIVNRWKRLGGWP 199 (200)
T ss_pred --------------------hhhhHHhHHHHHHHHHHHHHHHHHccCCC
Confidence 11277899999999999999998887764
No 33
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.98 E-value=0.01 Score=62.73 Aligned_cols=135 Identities=19% Similarity=0.143 Sum_probs=86.5
Q ss_pred CCCeEEEEeeecCCCCCCcEEEEEEEe----CCc-----eEEEEccC-C--------C------------hhhHHHHHHH
Q 020975 48 RQLVIGFDCEGVDLCRHGSLCIMQLAF----PDA-----IYLVDAIQ-G--------G------------ETVVKACKPA 97 (319)
Q Consensus 48 ~~~~ia~D~E~~~~~~~g~l~~lqls~----~~~-----~~~id~~~-l--------~------------~~~~~~L~~l 97 (319)
....++||+|+++.+...+ +|+|+. .+. ..+|.+.. + + .+++..+..+
T Consensus 6 ~~~~vvvD~ETTGl~~~d~--IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~ 83 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNAS--IIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDL 83 (820)
T ss_pred CCCEEEEEEecCCcCCCCe--EEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHH
Confidence 3578999999998864344 445543 221 12233321 0 0 1244566677
Q ss_pred HcCCCceEEEeehhhhHHHHHHH---cCCcc-ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHH
Q 020975 98 LESSYITKVIHDCKRDSEALYFQ---FGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE 173 (319)
Q Consensus 98 Le~~~i~KV~hd~k~d~~~L~~~---~gi~l-~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~ 173 (319)
+.+ -..|+||+.+|+..|.+. .|..+ ...+||+..+..+-|... .++|.+|++ ++|++...
T Consensus 84 l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~-------~~~L~~L~~---~lgl~~~~--- 148 (820)
T PRK07246 84 IED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLE-------KYSLSHLSR---ELNIDLAD--- 148 (820)
T ss_pred hCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCC-------CCCHHHHHH---HcCCCCCC---
Confidence 765 346999999999998643 36655 457999987776665432 267899996 56765321
Q ss_pred HHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhc
Q 020975 174 VRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (319)
Q Consensus 174 ~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~ 220 (319)
.++ |..||.++..|+..|..++.+.+
T Consensus 149 --------~H~-------------Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 149 --------AHT-------------AIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred --------CCC-------------HHHHHHHHHHHHHHHHHHHhhcC
Confidence 011 77899999999999988886633
No 34
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=96.93 E-value=0.0094 Score=50.29 Aligned_cols=66 Identities=21% Similarity=0.129 Sum_probs=44.6
Q ss_pred HHHHHHHcCCCceEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCcc
Q 020975 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (319)
Q Consensus 92 ~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l 168 (319)
..|..++.+.. ..|+||+.+|+.+|. .. ...+.||...+..+.+.... ...++|..|++ +|+|.++
T Consensus 75 ~~~~~~i~~~~-vlVgHn~~fD~~fL~-~~---~~~~iDT~~l~~~~~~~~~~----~~~~~L~~L~~--~~~~~~~ 140 (161)
T cd06137 75 AALWKFIDPDT-ILVGHSLQNDLDALR-MI---HTRVVDTAILTREAVKGPLA----KRQWSLRTLCR--DFLGLKI 140 (161)
T ss_pred HHHHHhcCCCc-EEEeccHHHHHHHHh-Cc---CCCeeEehhhhhhccCCCcC----CCCccHHHHHH--HHCCchh
Confidence 34555665533 459999999999995 22 23578999877766553210 01378999998 8888665
No 35
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.92 E-value=0.021 Score=51.89 Aligned_cols=136 Identities=16% Similarity=0.170 Sum_probs=82.3
Q ss_pred ccCCCeEEEEeeecCCC-CCCcEEEEEEEe--CC-----ceEEEEccC-C----------C----------hhhHHHHHH
Q 020975 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF--PD-----AIYLVDAIQ-G----------G----------ETVVKACKP 96 (319)
Q Consensus 46 l~~~~~ia~D~E~~~~~-~~g~l~~lqls~--~~-----~~~~id~~~-l----------~----------~~~~~~L~~ 96 (319)
+++...+.||+|++++. ....++-|+... .+ ...++.+.. + . .++...+..
T Consensus 4 l~~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~~ 83 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKG 83 (250)
T ss_pred ccCCcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHHH
Confidence 34568899999999985 444443332221 12 123344321 1 0 023456666
Q ss_pred HHcCCCceEEEeehhhhHHHHHH---HcCCcc----ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccc
Q 020975 97 ALESSYITKVIHDCKRDSEALYF---QFGIKL----HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (319)
Q Consensus 97 lLe~~~i~KV~hd~k~d~~~L~~---~~gi~l----~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~ 169 (319)
++.+.. ..|+||+.+|..+|.+ .+|+.. ...+||+-.+..+... . .++|+.|++ ++|++..
T Consensus 84 fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~-~-------~~~L~~l~~---~~g~~~~ 151 (250)
T PRK06310 84 FFKEGD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDS-P-------NNSLEALAV---HFNVPYD 151 (250)
T ss_pred HhCCCC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccC-C-------CCCHHHHHH---HCCCCCC
Confidence 676544 4699999999988853 345543 3489998776654321 1 257899986 4465432
Q ss_pred hhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 020975 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (319)
Q Consensus 170 ~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (319)
. .++ |..||.++..++..+..++.
T Consensus 152 ~-----------aH~-------------Al~Da~at~~vl~~l~~~~~ 175 (250)
T PRK06310 152 G-----------NHR-------------AMKDVEINIKVFKHLCKRFR 175 (250)
T ss_pred C-----------CcC-------------hHHHHHHHHHHHHHHHHhcc
Confidence 1 011 77899999999998877664
No 36
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.89 E-value=0.041 Score=49.32 Aligned_cols=142 Identities=15% Similarity=0.060 Sum_probs=84.8
Q ss_pred CeEEEEeeecCCC-CCCcEEEEEEEe-C-Cc--eEEEEccCC-----------Ch----------hhHHHHHHHHcCCCc
Q 020975 50 LVIGFDCEGVDLC-RHGSLCIMQLAF-P-DA--IYLVDAIQG-----------GE----------TVVKACKPALESSYI 103 (319)
Q Consensus 50 ~~ia~D~E~~~~~-~~g~l~~lqls~-~-~~--~~~id~~~l-----------~~----------~~~~~L~~lLe~~~i 103 (319)
..+.||+|+++++ ...+++-|+.-. . .. ..++.+... .+ ++...+..++.+. .
T Consensus 3 ~~vv~D~ETTGl~~~~d~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~~~-~ 81 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTD-N 81 (232)
T ss_pred cEEEEEeeCCCCCCCCCEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHcCC-C
Confidence 4688999999886 445544333211 1 11 234444220 01 1234555566543 3
Q ss_pred eEEEee-hhhhHHHHHH---HcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHH
Q 020975 104 TKVIHD-CKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVL 177 (319)
Q Consensus 104 ~KV~hd-~k~d~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~ 177 (319)
..|+|| ..+|..+|.+ ++|+.. ...+||+-.+..+.+... .++|..++. . +|++...
T Consensus 82 ~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~-------~~~L~~l~~--~-~~~~~~~------- 144 (232)
T PRK06309 82 ILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLP-------KHNLQYLRQ--V-YGFEENQ------- 144 (232)
T ss_pred EEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCC-------CCCHHHHHH--H-cCCCCCC-------
Confidence 469999 5899988853 355543 358999877665554322 257888886 4 4544321
Q ss_pred hcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchHHHHH
Q 020975 178 LRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAV 226 (319)
Q Consensus 178 ~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~~l~~ 226 (319)
.++ |..||.++..++..+..++..+.+..+..
T Consensus 145 ----aH~-------------Al~Da~~t~~vl~~l~~~~~~~~l~~l~~ 176 (232)
T PRK06309 145 ----AHR-------------ALDDVITLHRVFSALVGDLSPQQVYDLLN 176 (232)
T ss_pred ----CCC-------------cHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 011 77899999999999888876555555544
No 37
>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=96.87 E-value=0.017 Score=51.27 Aligned_cols=142 Identities=14% Similarity=0.047 Sum_probs=82.8
Q ss_pred ccCCCeEEEEeeecCCCCCCcEEEEEEEe--CCc------eEEEEccC-CC--------------------hhhHHHHHH
Q 020975 46 SERQLVIGFDCEGVDLCRHGSLCIMQLAF--PDA------IYLVDAIQ-GG--------------------ETVVKACKP 96 (319)
Q Consensus 46 l~~~~~ia~D~E~~~~~~~g~l~~lqls~--~~~------~~~id~~~-l~--------------------~~~~~~L~~ 96 (319)
+.....+.||+|+++++....++-|+... .+. ..++.+.. .. .+++..|..
T Consensus 4 l~~~~fvv~D~ETTGl~~~~~IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~~ 83 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFAD 83 (217)
T ss_pred EEecCEEEEEecCCCCCCCCCEEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHHH
Confidence 44568899999999986322233332222 111 12333321 00 123456666
Q ss_pred HHcCCCceEEEeehhhhHHHHHHHc---CCc--c-ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccch
Q 020975 97 ALESSYITKVIHDCKRDSEALYFQF---GIK--L-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE 170 (319)
Q Consensus 97 lLe~~~i~KV~hd~k~d~~~L~~~~---gi~--l-~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~ 170 (319)
++.+ -..|+||+.+|+.+|.+.+ +.. . ..++||+..+..+.+.... ..++|..+++ ++|++...
T Consensus 84 ~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~-----~~~~L~~l~~---~~gl~~~~ 153 (217)
T TIGR00573 84 YIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPG-----KRNTLDALCK---RYEITNSH 153 (217)
T ss_pred HhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCC-----CCCCHHHHHH---HcCCCCCC
Confidence 7655 3458999999999986443 211 1 3478988766665553221 1368899986 44654220
Q ss_pred hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhh
Q 020975 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ 219 (319)
Q Consensus 171 k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~ 219 (319)
.. ..+ |..||.++..|+..+..+..+.
T Consensus 154 -~~--------~H~-------------Al~DA~~ta~l~~~l~~~~~~~ 180 (217)
T TIGR00573 154 -RA--------LHG-------------ALADAFILAKLYLVMTGKQTKY 180 (217)
T ss_pred -cc--------cCC-------------HHHHHHHHHHHHHHHHhcchhh
Confidence 00 011 7789999999999988776543
No 38
>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=96.87 E-value=0.014 Score=63.75 Aligned_cols=139 Identities=16% Similarity=0.222 Sum_probs=91.3
Q ss_pred cCCCeEEEEeeecCCC-CCCcEEEEEEEe--CCce-----EEEEccC-----------CC----------hhhHHHHHHH
Q 020975 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF--PDAI-----YLVDAIQ-----------GG----------ETVVKACKPA 97 (319)
Q Consensus 47 ~~~~~ia~D~E~~~~~-~~g~l~~lqls~--~~~~-----~~id~~~-----------l~----------~~~~~~L~~l 97 (319)
.+...+.||+|+++++ ...++.-|+... .+.. .++.+.. +. .+++..+..+
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~f 267 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFKEF 267 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHH
Confidence 4568899999999986 455544333322 1211 2222211 00 1345677777
Q ss_pred HcCCCceEEEeehhhhHHHHHH---HcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhH
Q 020975 98 LESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKE 172 (319)
Q Consensus 98 Le~~~i~KV~hd~k~d~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~ 172 (319)
+.+. ..|+||+.+|...|.+ ++|... ..++||+..+..+.+...+ ++|+.|+. + +|++...
T Consensus 268 l~~~--iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~-------~kL~~Lak--~-lgi~~~~-- 333 (1213)
T TIGR01405 268 FKDS--ILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKS-------HRLGNICK--K-LGVDLDD-- 333 (1213)
T ss_pred hCCC--eEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCC-------CCHHHHHH--H-cCCCCCC--
Confidence 7653 4599999999998863 346542 4589999988887764332 68899997 4 5765431
Q ss_pred HHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhch
Q 020975 173 EVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSL 221 (319)
Q Consensus 173 ~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~ 221 (319)
...|..||.++..++..+.+++.+.|.
T Consensus 334 ----------------------~HrAl~DA~aTa~I~~~ll~~l~~~~i 360 (1213)
T TIGR01405 334 ----------------------HHRADYDAEATAKVFKVMVEQLKEKGI 360 (1213)
T ss_pred ----------------------CcCHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 012778999999999999999987653
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=96.82 E-value=0.016 Score=48.26 Aligned_cols=65 Identities=23% Similarity=0.194 Sum_probs=42.9
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCcc
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l 168 (319)
+...+.+++.+. -..|+||+++|+.+|. ... ..++||...+....+... .++|+.|++ +|++..+
T Consensus 65 v~~~~~~fl~~~-~vlVgHn~~fD~~fL~-~~~---~~~iDT~~l~r~~~~~~~-------~~~L~~L~~--~~~~~~i 129 (150)
T cd06145 65 VQKKLLSLISPD-TILVGHSLENDLKALK-LIH---PRVIDTAILFPHPRGPPY-------KPSLKNLAK--KYLGRDI 129 (150)
T ss_pred HHHHHHHHhCCC-CEEEEcChHHHHHHhh-ccC---CCEEEcHHhccccCCCCC-------ChhHHHHHH--HHCCcce
Confidence 345666677533 3469999999999995 321 458999865443332211 368999998 8887544
No 40
>PRK07883 hypothetical protein; Validated
Probab=96.73 E-value=0.024 Score=57.33 Aligned_cols=141 Identities=16% Similarity=0.082 Sum_probs=86.6
Q ss_pred ccCCCeEEEEeeecCCCC-CCcEEEEEEEe--CCc-----eEEEEccC-----------CC----------hhhHHHHHH
Q 020975 46 SERQLVIGFDCEGVDLCR-HGSLCIMQLAF--PDA-----IYLVDAIQ-----------GG----------ETVVKACKP 96 (319)
Q Consensus 46 l~~~~~ia~D~E~~~~~~-~g~l~~lqls~--~~~-----~~~id~~~-----------l~----------~~~~~~L~~ 96 (319)
+.+...+.||+||++++. ...++-|+.-. .+. ..+|.+.. +. .+++..+..
T Consensus 12 ~~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f~~ 91 (557)
T PRK07883 12 LRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLE 91 (557)
T ss_pred CcCCCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHH
Confidence 556789999999998753 34433332221 221 22333321 01 124456667
Q ss_pred HHcCCCceEEEeehhhhHHHHHH---HcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchh
Q 020975 97 ALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK 171 (319)
Q Consensus 97 lLe~~~i~KV~hd~k~d~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k 171 (319)
++.+ ...|+||+.+|...|.+ .+|+.. ...+||+..+.-+.+.... ..++|+++++ ++|++...
T Consensus 92 fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~-----~~~~L~~L~~---~~gi~~~~- 160 (557)
T PRK07883 92 FARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEA-----PNVRLSTLAR---LFGATTTP- 160 (557)
T ss_pred HhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCC-----CCCCHHHHHH---HCCcccCC-
Confidence 7765 34589999999998853 356665 3478998765444331111 1367899985 66765431
Q ss_pred HHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhc
Q 020975 172 EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (319)
Q Consensus 172 ~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~ 220 (319)
.++ |..||.++..|+..+..++.+.|
T Consensus 161 ----------~H~-------------Al~DA~ata~l~~~l~~~~~~~~ 186 (557)
T PRK07883 161 ----------THR-------------ALDDARATVDVLHGLIERLGNLG 186 (557)
T ss_pred ----------CCC-------------HHHHHHHHHHHHHHHHHHHHhcC
Confidence 011 77899999999999988887644
No 41
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=96.69 E-value=0.059 Score=49.15 Aligned_cols=133 Identities=16% Similarity=0.055 Sum_probs=81.4
Q ss_pred ccCCCeEEEEeeecCCC-CCCcEEEEEEEe----CCc-----eEEEEccCCC--------------------hhhHHHHH
Q 020975 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-----IYLVDAIQGG--------------------ETVVKACK 95 (319)
Q Consensus 46 l~~~~~ia~D~E~~~~~-~~g~l~~lqls~----~~~-----~~~id~~~l~--------------------~~~~~~L~ 95 (319)
+.+...+.||+|+++.. ..+.+ ++|+. .++ ..++.+..+. .+++..+.
T Consensus 65 ~~~~~~vv~DiETTG~~~~~~~I--IEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f~ 142 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKKHQI--IEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFR 142 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCCCeE--EEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHHH
Confidence 34568899999999875 34443 44432 221 1233332110 13456777
Q ss_pred HHHcCCCceEEEeehhhhHHHHHH---HcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccch
Q 020975 96 PALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE 170 (319)
Q Consensus 96 ~lLe~~~i~KV~hd~k~d~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~ 170 (319)
.++.+. ..|+||+.+|..+|.+ ++|... ...+||+-.+..+-+. . .++|++|++ ++|++...
T Consensus 143 ~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~-~-------~~~L~~L~~---~lgi~~~~ 209 (257)
T PRK08517 143 LFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-P-------RYGLSFLKE---LLGIEIEV 209 (257)
T ss_pred HHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccC-C-------CCCHHHHHH---HcCcCCCC
Confidence 777753 4699999999998853 455543 3478887544332121 1 267899985 66765421
Q ss_pred hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 020975 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (319)
Q Consensus 171 k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (319)
.++ |-.||.++.+|+..+..++.
T Consensus 210 -----------~Hr-------------Al~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 210 -----------HHR-------------AYADALAAYEIFKICLLNLP 232 (257)
T ss_pred -----------CCC-------------hHHHHHHHHHHHHHHHHHhH
Confidence 011 66899999999999888775
No 42
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.62 E-value=0.042 Score=51.56 Aligned_cols=91 Identities=19% Similarity=0.150 Sum_probs=58.9
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHHH---cCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCccc
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~---~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~l 164 (319)
++..|..++.+.. -|+||+.+|...|.+. +|+.. ...+||+..+..+.+... .++|++|++ ++
T Consensus 78 vl~~f~~fl~~~~--lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~-------~~kL~~L~~---~l 145 (313)
T PRK06807 78 VLPLFLAFLHTNV--IVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAP-------NHKLETLKR---ML 145 (313)
T ss_pred HHHHHHHHHcCCe--EEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCC-------CCCHHHHHH---Hc
Confidence 4455666666543 4999999999998643 45532 358999886665554322 257899985 66
Q ss_pred CCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 020975 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (319)
Q Consensus 165 g~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (319)
|+.... ++ |-.||.++..++..+.....
T Consensus 146 gi~~~~------------H~-------------Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 146 GIRLSS------------HN-------------AFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred CCCCCC------------cC-------------hHHHHHHHHHHHHHHHHhhh
Confidence 755310 11 56778888877777776663
No 43
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.59 E-value=0.089 Score=49.29 Aligned_cols=100 Identities=14% Similarity=0.131 Sum_probs=67.0
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHH---HcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCccc
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~l 164 (319)
++..|..++.+ -..|+||+.+|..+|.+ .+|... ...+||+..+.-+.+... .++|..|++ ++
T Consensus 70 v~~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~-------~~~L~~L~~---~~ 137 (309)
T PRK06195 70 IWEKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNID-------NARLNTVNN---FL 137 (309)
T ss_pred HHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCC-------cCCHHHHHH---Hc
Confidence 44566667754 35699999999988853 355554 358999876655544322 257899986 45
Q ss_pred CCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchHHHHH
Q 020975 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAV 226 (319)
Q Consensus 165 g~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~~l~~ 226 (319)
|++.. . .-|..||.++.+|+..+.+++...+...+..
T Consensus 138 gi~~~---~----------------------H~Al~DA~ata~l~~~l~~~~~~~~~~~l~~ 174 (309)
T PRK06195 138 GYEFK---H----------------------HDALADAMACSNILLNISKELNSKDINEISK 174 (309)
T ss_pred CCCCc---c----------------------cCCHHHHHHHHHHHHHHHHHhccCCHHHHHH
Confidence 65421 0 1167899999999999988887766555443
No 44
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.56 E-value=0.078 Score=47.82 Aligned_cols=143 Identities=16% Similarity=0.163 Sum_probs=80.7
Q ss_pred ccCCCeEEEEeeecCCC-CCCcEEEEEEEe--CCc-------eEEEEccC-C--------C------------hhhHHHH
Q 020975 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF--PDA-------IYLVDAIQ-G--------G------------ETVVKAC 94 (319)
Q Consensus 46 l~~~~~ia~D~E~~~~~-~~g~l~~lqls~--~~~-------~~~id~~~-l--------~------------~~~~~~L 94 (319)
+.+...++||+|+++++ ..++++-|+.-. .+. .+++.+.. + + .+++..|
T Consensus 44 ~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~l 123 (239)
T PRK09146 44 LSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDEL 123 (239)
T ss_pred cccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHHH
Confidence 34568899999999886 445543333221 121 13333321 0 0 0233455
Q ss_pred HHHHcCCCceEEEeehhhhHHHHHHH----cCCcc-ccEEechhHHhhhhhhcCCC---CCC---CCcccHHhhhcCCcc
Q 020975 95 KPALESSYITKVIHDCKRDSEALYFQ----FGIKL-HNVVDTQIAYSLIEEQEGRK---RSP---DDYISFVGLLADPRY 163 (319)
Q Consensus 95 ~~lLe~~~i~KV~hd~k~d~~~L~~~----~gi~l-~~vfDt~lAayLL~~~~~~~---~L~---~~~~sL~~L~~~~~~ 163 (319)
..++.+ -.-|+||+.+|..+|.+. ++..+ ..++||+-.+..+.+..... .+. ...++|.+++. .
T Consensus 124 ~~~~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~---~ 198 (239)
T PRK09146 124 LEALAG--KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRL---R 198 (239)
T ss_pred HHHhCC--CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHH---H
Confidence 555544 346899999999988543 33344 35899998776554321000 000 02356788886 4
Q ss_pred cCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 020975 164 CGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (319)
Q Consensus 164 lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (319)
+|++... ..+ |..||.++..|+..+..++.
T Consensus 199 ~gl~~~~-----------~H~-------------Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 199 YGLPAYS-----------PHH-------------ALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred cCCCCCC-----------CCC-------------cHHHHHHHHHHHHHHHHHHc
Confidence 4544220 011 77899999988888777664
No 45
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=96.56 E-value=0.0086 Score=63.69 Aligned_cols=140 Identities=16% Similarity=0.224 Sum_probs=96.1
Q ss_pred ccCCCeEEEEeeecCCC-CCCcEEEEEEEe-C-Cc-------eEEEEccCC-----------C----------hhhHHHH
Q 020975 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF-P-DA-------IYLVDAIQG-----------G----------ETVVKAC 94 (319)
Q Consensus 46 l~~~~~ia~D~E~~~~~-~~g~l~~lqls~-~-~~-------~~~id~~~l-----------~----------~~~~~~L 94 (319)
+.++..+.||+|+++++ ...++ |+++. . .+ -+++++... . ++++..+
T Consensus 418 l~datyVVfDiETTGLs~~~d~i--IE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf 495 (1444)
T COG2176 418 LDDATYVVFDIETTGLSPVYDEI--IEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKF 495 (1444)
T ss_pred cccccEEEEEeecCCcCcccchh--hhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHH
Confidence 45678999999999986 55554 44443 1 12 233333321 0 1356778
Q ss_pred HHHHcCCCceEEEeehhhhHHHHHH---HcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccc
Q 020975 95 KPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (319)
Q Consensus 95 ~~lLe~~~i~KV~hd~k~d~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~ 169 (319)
+.|+.|. .-|.||+.+|+-.|.. ++|+.. +++.||.-.++.|+|...+| +|..|+. + |++.+.
T Consensus 496 ~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh-------~Lg~l~k--k-~~v~le 563 (1444)
T COG2176 496 REFIGDS--ILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSH-------RLGTLCK--K-LGVELE 563 (1444)
T ss_pred HHHhcCc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhc-------chHHHHH--H-hCccHH
Confidence 8888874 3599999999988753 356655 46999999999999987664 6788886 3 455442
Q ss_pred hhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchHH
Q 020975 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (319)
Q Consensus 170 ~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~~ 223 (319)
. ..-|--|+.++-++...+.+++++.|...
T Consensus 564 ---~---------------------hHRA~yDaeat~~vf~~f~~~~ke~Gi~~ 593 (1444)
T COG2176 564 ---R---------------------HHRADYDAEATAKVFFVFLKDLKEKGITN 593 (1444)
T ss_pred ---H---------------------hhhhhhhHHHHHHHHHHHHHHHHHhchhh
Confidence 1 11255689999999999999999876543
No 46
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.51 E-value=0.084 Score=47.65 Aligned_cols=90 Identities=21% Similarity=0.238 Sum_probs=57.2
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHH---HcCCcc------ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcC
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL------HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLAD 160 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~---~~gi~l------~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~ 160 (319)
++..+..++.+. ..|+||+.+|+.+|.+ .+|..+ ..++||+..+..+.|+. ..+|+.|++
T Consensus 76 v~~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~--------~~~L~aL~~- 144 (240)
T PRK05711 76 VADEFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGK--------RNSLDALCK- 144 (240)
T ss_pred HHHHHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCC--------CCCHHHHHH-
Confidence 344566666553 3589999999988853 344222 34889988776665542 257999997
Q ss_pred CcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHH
Q 020975 161 PRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMK 214 (319)
Q Consensus 161 ~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~ 214 (319)
+ +|++... |. ..-|-.||.++..+|..+..
T Consensus 145 -~-~gi~~~~-----------------r~-----~H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 145 -R-YGIDNSH-----------------RT-----LHGALLDAEILAEVYLAMTG 174 (240)
T ss_pred -H-CCCCCCC-----------------CC-----CCCHHHHHHHHHHHHHHHHC
Confidence 4 4653221 00 01177899999888877753
No 47
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=96.47 E-value=0.06 Score=45.25 Aligned_cols=88 Identities=19% Similarity=0.178 Sum_probs=55.0
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHHH---cCCcc-----ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCC
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKL-----HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADP 161 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~---~gi~l-----~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~ 161 (319)
+...|..++.+. ..|+||+.+|+.+|.+. +|... ...+||+..+..+.+. . ..+|+++++
T Consensus 71 v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~-~-------~~~L~~l~~-- 138 (167)
T cd06131 71 IADEFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPG-K-------PNSLDALCK-- 138 (167)
T ss_pred HHHHHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCC-C-------CCCHHHHHH--
Confidence 345677777653 35899999999888532 33321 3479998766554432 1 257899996
Q ss_pred cccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHH
Q 020975 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (319)
Q Consensus 162 ~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L 212 (319)
++|++.... ... -|..||.++..|+..|
T Consensus 139 -~~~i~~~~~---------~~H-------------~Al~Da~~~a~l~~~l 166 (167)
T cd06131 139 -RFGIDNSHR---------TLH-------------GALLDAELLAEVYLEL 166 (167)
T ss_pred -HCCCCCCCC---------CCC-------------ChHHHHHHHHHHHHHh
Confidence 456543210 001 1778899888887654
No 48
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=96.43 E-value=0.074 Score=50.71 Aligned_cols=143 Identities=12% Similarity=0.147 Sum_probs=82.7
Q ss_pred ccCCCeEEEEeeecCCC-CCCcEEEEE-EEeC--C---c--eEEEEccC------C-C------------hhhHHHHHHH
Q 020975 46 SERQLVIGFDCEGVDLC-RHGSLCIMQ-LAFP--D---A--IYLVDAIQ------G-G------------ETVVKACKPA 97 (319)
Q Consensus 46 l~~~~~ia~D~E~~~~~-~~g~l~~lq-ls~~--~---~--~~~id~~~------l-~------------~~~~~~L~~l 97 (319)
+.+..+++||+|+++++ ...++.-|. +... + . ..+|.+.. + + .+++..|.++
T Consensus 43 ~~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~~f 122 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLDRL 122 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHHHH
Confidence 44578999999999986 445433221 1111 1 1 12332211 0 1 1355677778
Q ss_pred HcCCCceEEEeehhhhHHHHHHHc-------------------------------CCcc-ccEEechhHHhhhhhhcCCC
Q 020975 98 LESSYITKVIHDCKRDSEALYFQF-------------------------------GIKL-HNVVDTQIAYSLIEEQEGRK 145 (319)
Q Consensus 98 Le~~~i~KV~hd~k~d~~~L~~~~-------------------------------gi~l-~~vfDt~lAayLL~~~~~~~ 145 (319)
+.+. ..|+||+.+|+.+|.+.+ ++.. ..++||+-.+..+.+...+
T Consensus 123 L~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~- 199 (377)
T PRK05601 123 IDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALDD- 199 (377)
T ss_pred hCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCCC-
Confidence 8754 469999999999885432 1222 2489998888888775433
Q ss_pred CCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHH
Q 020975 146 RSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (319)
Q Consensus 146 ~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L 212 (319)
+.|..|+. ++|++.+.... +. .-..+| ..+ .+-.|+..+..|+..+
T Consensus 200 ------~rL~~La~---~lGi~~p~~~A--~~------~Ra~~p--~~~--l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 200 ------IRIRGVAH---TLGLDAPAAEA--SV------ERAQVP--HRQ--LCREETLLVARLYFAL 245 (377)
T ss_pred ------CCHHHHHH---HhCCCCCchhh--hh------hhhcCC--hhh--hhhHHHHHHHHHHHHh
Confidence 57899996 67877653111 00 001111 121 1336888888888775
No 49
>PRK05168 ribonuclease T; Provisional
Probab=96.42 E-value=0.17 Score=44.64 Aligned_cols=86 Identities=20% Similarity=0.257 Sum_probs=58.0
Q ss_pred CceEEEeehhhhHHHHHH---HcCCc---c--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHH
Q 020975 102 YITKVIHDCKRDSEALYF---QFGIK---L--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE 173 (319)
Q Consensus 102 ~i~KV~hd~k~d~~~L~~---~~gi~---l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~ 173 (319)
+...|+||+.+|+..|.+ ++|+. . ..++||...+..+.+. .+|..+++ ++|+++... .
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~----------~~L~~l~~---~~gl~~~~~-~ 179 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQ----------TVLAKACQ---AAGIEFDNK-E 179 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCC----------CCHHHHHH---HCCCCCCCC-C
Confidence 456799999999988853 34542 1 1479997766554331 36888886 456554210 0
Q ss_pred HHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchH
Q 020975 174 VRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLW 222 (319)
Q Consensus 174 ~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~ 222 (319)
.+. |..||.++..|+..+..++.+.|.|
T Consensus 180 --------~H~-------------Al~DA~ata~l~~~l~~~~~~~~~~ 207 (211)
T PRK05168 180 --------AHS-------------ALYDTEKTAELFCEIVNRWKRLGGW 207 (211)
T ss_pred --------CCC-------------hHHHHHHHHHHHHHHHHHHHHccCC
Confidence 011 7789999999999999999877655
No 50
>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=96.41 E-value=0.073 Score=47.54 Aligned_cols=90 Identities=21% Similarity=0.211 Sum_probs=58.5
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHH---HcC--Cc-c---ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcC
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFG--IK-L---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLAD 160 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~---~~g--i~-l---~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~ 160 (319)
++..|..++.+. ..|+||+.+|+.+|.+ .+| +. + ..++||+..+..+.|.. .++|++|++
T Consensus 72 v~~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~--------~~~L~~L~~- 140 (225)
T TIGR01406 72 IADEFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQ--------RNSLDALCK- 140 (225)
T ss_pred HHHHHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCC--------CCCHHHHHH-
Confidence 345666677653 3589999999988853 345 22 1 35899988776655531 268999997
Q ss_pred CcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHH
Q 020975 161 PRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMK 214 (319)
Q Consensus 161 ~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~ 214 (319)
+ +|++.... . ..+ |..||..+..+|..|..
T Consensus 141 -~-~gi~~~~r-~--------~H~-------------Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 141 -R-FKVDNSHR-T--------LHG-------------ALLDAHLLAEVYLALTG 170 (225)
T ss_pred -h-cCCCCCCC-C--------CcC-------------HHHHHHHHHHHHHHHHc
Confidence 4 46543210 0 011 77899999999887754
No 51
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.37 E-value=0.031 Score=50.38 Aligned_cols=136 Identities=18% Similarity=0.151 Sum_probs=82.7
Q ss_pred CeEEEEeeecCCCCCCcEEEEE---EEeCCceEEEEccCCC---------------h----------hhHHHHHHHHcCC
Q 020975 50 LVIGFDCEGVDLCRHGSLCIMQ---LAFPDAIYLVDAIQGG---------------E----------TVVKACKPALESS 101 (319)
Q Consensus 50 ~~ia~D~E~~~~~~~g~l~~lq---ls~~~~~~~id~~~l~---------------~----------~~~~~L~~lLe~~ 101 (319)
.+||+|||-.+.+..|+.+.++ |-......++|-.-.. . .+-..+.++|.+
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL~g- 184 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLLKG- 184 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHHHhC-
Confidence 5899999998887666555443 3333223344432110 0 011345557776
Q ss_pred CceEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCC
Q 020975 102 YITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQD 181 (319)
Q Consensus 102 ~i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~ 181 (319)
-..|||++++|+.+|.-.|.- .-+-||.-.--|..--... ...||..|.+ .+||.++- . ++
T Consensus 185 -RIlVGHaLhnDl~~L~l~hp~--s~iRDTs~~~pl~k~~~~~-----~tpSLK~Lt~--~~Lg~~IQ-~-------Ge- 245 (280)
T KOG2249|consen 185 -RILVGHALHNDLQALKLEHPR--SMIRDTSKYPPLMKLLSKK-----ATPSLKKLTE--ALLGKDIQ-V-------GE- 245 (280)
T ss_pred -CEEeccccccHHHHHhhhCch--hhhcccccCchHHHHhhcc-----CCccHHHHHH--HHhchhhh-c-------cc-
Confidence 345999999999999633322 2355886643333310011 2369999999 99997663 1 11
Q ss_pred CCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhh
Q 020975 182 PQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ 219 (319)
Q Consensus 182 ~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~ 219 (319)
.+ ..+||.++.+||...+.+-++.
T Consensus 246 -Hs-------------SvEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 246 -HS-------------SVEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred -cC-------------cHHHHHHHHHHHHHHHHHHHHH
Confidence 11 3589999999999988777653
No 52
>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=96.22 E-value=0.11 Score=42.97 Aligned_cols=66 Identities=18% Similarity=0.077 Sum_probs=45.1
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHH---HcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCccc
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~l 164 (319)
++..|..++++ ...|+||+.+|..+|.+ .+|+.. ...+||+..+..+.+... .++|..+++ ++
T Consensus 67 v~~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~-------~~~L~~l~~---~~ 134 (156)
T cd06130 67 VWPEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLP-------NHKLNTVAE---HL 134 (156)
T ss_pred HHHHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCC-------CCCHHHHHH---Hc
Confidence 45677778876 35699999999998853 346554 358999876655544322 257899986 56
Q ss_pred CCc
Q 020975 165 GIS 167 (319)
Q Consensus 165 g~~ 167 (319)
|+.
T Consensus 135 g~~ 137 (156)
T cd06130 135 GIE 137 (156)
T ss_pred CCC
Confidence 654
No 53
>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=96.20 E-value=0.12 Score=44.94 Aligned_cols=102 Identities=18% Similarity=0.119 Sum_probs=62.6
Q ss_pred hhHHHHHHHHcC--CCceEEEeeh-hhhHHHHHH---HcCCcc-----------------------c-cEEechhHHhhh
Q 020975 89 TVVKACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKL-----------------------H-NVVDTQIAYSLI 138 (319)
Q Consensus 89 ~~~~~L~~lLe~--~~i~KV~hd~-k~d~~~L~~---~~gi~l-----------------------~-~vfDt~lAayLL 138 (319)
+++..+..++.+ |.+ .+|||. .+|+..|.+ .+|+.. + .++|+.....-.
T Consensus 65 ~lL~~f~~~i~~~dpdi-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~ 143 (199)
T cd05160 65 ELLKRFFDIIREYDPDI-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRD 143 (199)
T ss_pred HHHHHHHHHHHhcCCCE-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHh
Confidence 345566666654 554 599999 799988753 355544 1 267887655332
Q ss_pred hhhcCCCCCCCCcccHHhhhcCCcccCCccchh--HHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 020975 139 EEQEGRKRSPDDYISFVGLLADPRYCGISYQEK--EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (319)
Q Consensus 139 ~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k--~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (319)
.+ . ..++|+.+++ .+++..-.+. +.... ..|... ....++|+-.||..+++|+
T Consensus 144 ~~-l-------~sy~L~~v~~--~~l~~~k~~~~~~~~~~------~~~~~~--~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 144 FK-L-------KSYTLDAVAE--ELLGEGKEKVDGEIIED------AEWEED--PERLIEYNLKDAELTLQIL 198 (199)
T ss_pred cC-c-------ccCCHHHHHH--HHhCCCCCcCCHHHHhh------ccCcch--HHHHHHHHHHHHHHHHHhh
Confidence 22 1 2478999999 8887532211 11110 012221 2678999999999999885
No 54
>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=96.14 E-value=0.15 Score=44.31 Aligned_cols=144 Identities=15% Similarity=0.161 Sum_probs=82.6
Q ss_pred CeEEEEeeecCC---C--CCCcEEEEEEEeCCceEEEEc----------cCCChhhHHHHHHHHcC--CCceEEEeeh-h
Q 020975 50 LVIGFDCEGVDL---C--RHGSLCIMQLAFPDAIYLVDA----------IQGGETVVKACKPALES--SYITKVIHDC-K 111 (319)
Q Consensus 50 ~~ia~D~E~~~~---~--~~g~l~~lqls~~~~~~~id~----------~~l~~~~~~~L~~lLe~--~~i~KV~hd~-k 111 (319)
..++||.|+.+. + ....+..|++...+...++.. ..-..+++..+..++.. |++ .++||. .
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dpdi-ivgyN~~~ 82 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDV-IYTYNGDN 82 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCCCE-EEecCCCC
Confidence 568999999742 1 234555555544322222211 11112455666666665 765 599997 4
Q ss_pred hhHHHHHHH---cCCccc------------------------cEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCccc
Q 020975 112 RDSEALYFQ---FGIKLH------------------------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (319)
Q Consensus 112 ~d~~~L~~~---~gi~l~------------------------~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~l 164 (319)
+|+..|..+ +|+... ..+|++....- . ..+ ..++|+.+++ .+|
T Consensus 83 FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~---~---~~l--~sy~L~~v~~--~~L 152 (195)
T cd05780 83 FDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARR---T---LNL--TRYTLERVYE--ELF 152 (195)
T ss_pred CcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHh---h---CCC--CcCcHHHHHH--HHh
Confidence 799877533 455421 15676654321 1 111 2478999999 899
Q ss_pred CCccch--hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHH
Q 020975 165 GISYQE--KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHN 211 (319)
Q Consensus 165 g~~l~~--k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~ 211 (319)
|.+-.+ .+++.. -|...+--...++|+..||..+++|.+.
T Consensus 153 g~~k~d~~~~~i~~-------~~~~~~~~~~l~~Y~~~D~~lt~~L~~~ 194 (195)
T cd05780 153 GIEKEDVPGEEIAE-------AWDSGENLERLFRYSMEDAKYTYEIGKE 194 (195)
T ss_pred CCCCCcCCHHHHHH-------HHhCCCchHHHHHHhHHHHHHHHHHHhh
Confidence 965332 122222 2332222367899999999999999865
No 55
>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=96.05 E-value=0.072 Score=56.78 Aligned_cols=93 Identities=18% Similarity=0.173 Sum_probs=62.4
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHH---HcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCccc
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~l 164 (319)
+...|..++.+. ..|+||+.+|..+|.+ .+|+.. ...+||+-.+..+.+... .++|.+|++ ++
T Consensus 70 v~~~l~~~l~~~--~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~-------~~~L~~l~~---~~ 137 (850)
T TIGR01407 70 VAQEIYDLLEDG--IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEE-------SYQLSELSE---AL 137 (850)
T ss_pred HHHHHHHHhCCC--EEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCC-------CCCHHHHHH---HC
Confidence 445666777653 4699999999988853 356653 458999977776665432 267899986 56
Q ss_pred CCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhh
Q 020975 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (319)
Q Consensus 165 g~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (319)
|++... .++ |..||.++..|+..+..++.+
T Consensus 138 gi~~~~-----------~H~-------------Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 138 GLTHEN-----------PHR-------------ADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred CCCCCC-----------CCC-------------hHHHHHHHHHHHHHHHHHHHh
Confidence 765431 011 667888888877777776654
No 56
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.01 E-value=0.17 Score=42.14 Aligned_cols=92 Identities=21% Similarity=0.219 Sum_probs=61.3
Q ss_pred hHHHHHHHHcCCCceEEEeeh-hhhHHHHHH---HcCCcc---ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCc
Q 020975 90 VVKACKPALESSYITKVIHDC-KRDSEALYF---QFGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPR 162 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~-k~d~~~L~~---~~gi~l---~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~ 162 (319)
+...+..++.+. ..++||. ++|..+|.+ .+|+.. ...+||+..++...+.. ..+|+.+++
T Consensus 70 ~~~~~~~~l~~~--~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~--------~~~L~~l~~--- 136 (169)
T smart00479 70 VLEELLEFLKGK--ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR--------KYSLKKLAE--- 136 (169)
T ss_pred HHHHHHHHhcCC--EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC--------CCCHHHHHH---
Confidence 456777788764 3478888 999998863 244432 23799987776655421 268999996
Q ss_pred ccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 020975 163 YCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (319)
Q Consensus 163 ~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (319)
++|++... . ...|..||..+..|+..+.+++.
T Consensus 137 ~~~~~~~~-------------~----------~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 137 RLGLEVIG-------------R----------AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred HCCCCCCC-------------C----------CcCcHHHHHHHHHHHHHHHHHhh
Confidence 45544321 0 12277899999999998877653
No 57
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.98 E-value=0.077 Score=57.05 Aligned_cols=93 Identities=18% Similarity=0.172 Sum_probs=63.8
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHH---HcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCccc
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~l 164 (319)
+...|..++.+ ...|+||+.+|+..|.+ .+|+.. ...+||+-.+..+-|... .++|.+|++ ++
T Consensus 74 v~~~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~-------~~~L~~l~~---~l 141 (928)
T PRK08074 74 VAPEIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAE-------SYKLRDLSE---EL 141 (928)
T ss_pred HHHHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCC-------CCCHHHHHH---hC
Confidence 44567777765 34699999999999863 346553 358999877777666432 267899996 56
Q ss_pred CCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhh
Q 020975 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (319)
Q Consensus 165 g~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (319)
|+.... .++ |-.||.++..|+..|.+++.+
T Consensus 142 ~i~~~~-----------~H~-------------Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 142 GLEHDQ-----------PHR-------------ADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred CCCCCC-----------CCC-------------hHHHHHHHHHHHHHHHHHHHh
Confidence 754321 011 667888888888888777765
No 58
>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=95.91 E-value=0.17 Score=43.38 Aligned_cols=63 Identities=27% Similarity=0.251 Sum_probs=41.7
Q ss_pred HHHHHHHcC--CCceEEEeeh-hhhHHHHHH---HcCCcc---ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCc
Q 020975 92 KACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPR 162 (319)
Q Consensus 92 ~~L~~lLe~--~~i~KV~hd~-k~d~~~L~~---~~gi~l---~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~ 162 (319)
+.|..++.. ....-|+||+ .+|+..|.+ ++|... ..++||+-.+..+.+ +|++|+. +
T Consensus 86 ~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~------------~L~~l~~--~ 151 (177)
T cd06136 86 NLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ------------SLGSLYK--R 151 (177)
T ss_pred HHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh------------hHHHHHH--H
Confidence 445555543 2356799998 899998853 356554 235799876665543 4899987 7
Q ss_pred ccCCcc
Q 020975 163 YCGISY 168 (319)
Q Consensus 163 ~lg~~l 168 (319)
++|++.
T Consensus 152 ~~~~~~ 157 (177)
T cd06136 152 LFGQEP 157 (177)
T ss_pred HhCCCc
Confidence 777654
No 59
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=95.84 E-value=0.32 Score=42.51 Aligned_cols=136 Identities=16% Similarity=0.135 Sum_probs=76.1
Q ss_pred cCCCeEEEEeeecCCC-CCCcEEEEEEEe-C-Cc-------eEEEEccC-C--------C------------hhhHHHHH
Q 020975 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF-P-DA-------IYLVDAIQ-G--------G------------ETVVKACK 95 (319)
Q Consensus 47 ~~~~~ia~D~E~~~~~-~~g~l~~lqls~-~-~~-------~~~id~~~-l--------~------------~~~~~~L~ 95 (319)
.....+.+|+|++++. ..+.++-|+.-. . +. ..+|.+.. + + .+++..+.
T Consensus 27 ~~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~~~ 106 (202)
T PRK09145 27 PPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLL 106 (202)
T ss_pred CCCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHHHH
Confidence 4467899999999886 345543333221 2 21 12333321 0 0 13455677
Q ss_pred HHHcCCCceEEEeehhhhHHHHHHH----cCCcc-ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccch
Q 020975 96 PALESSYITKVIHDCKRDSEALYFQ----FGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE 170 (319)
Q Consensus 96 ~lLe~~~i~KV~hd~k~d~~~L~~~----~gi~l-~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~ 170 (319)
.++.+. ..|+||+.+|...|.+. +|..+ ...+|++-..+-.....-... ...++|+++++ ++|++...
T Consensus 107 ~~i~~~--~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~--~~~~~L~~l~~---~~gi~~~~ 179 (202)
T PRK09145 107 AFIGNR--PLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDA--YIDLRFDAILK---HLDLPVLG 179 (202)
T ss_pred HHHcCC--eEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCc--ccCCCHHHHHH---HcCCCCCC
Confidence 777653 46999999999988533 34444 347898643321111000000 01368999996 55764421
Q ss_pred hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHH
Q 020975 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (319)
Q Consensus 171 k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~ 213 (319)
. .+ |..||.++..|+..|.
T Consensus 180 --~---------H~-------------Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 180 --R---------HD-------------ALNDAIMAALIFLRLR 198 (202)
T ss_pred --C---------CC-------------cHHHHHHHHHHHHHHH
Confidence 0 11 6689999988888774
No 60
>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=95.20 E-value=0.26 Score=40.12 Aligned_cols=50 Identities=18% Similarity=0.044 Sum_probs=34.5
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHHHc---C--CccccEEechhHHhhhhhh
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYFQF---G--IKLHNVVDTQIAYSLIEEQ 141 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~---g--i~l~~vfDt~lAayLL~~~ 141 (319)
+...+..++++ ...|+||..+|..+|.+.+ | ......+||+..+..+.+.
T Consensus 69 ~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~ 123 (159)
T cd06127 69 VLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPG 123 (159)
T ss_pred HHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCC
Confidence 45667778876 4579999999999886433 2 1224589999866555543
No 61
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=95.07 E-value=0.13 Score=57.45 Aligned_cols=96 Identities=16% Similarity=0.196 Sum_probs=66.5
Q ss_pred HHHHHHHHcCCCceEEEeehhhhHHHHH---HHcCCc-c-ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccC
Q 020975 91 VKACKPALESSYITKVIHDCKRDSEALY---FQFGIK-L-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCG 165 (319)
Q Consensus 91 ~~~L~~lLe~~~i~KV~hd~k~d~~~L~---~~~gi~-l-~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg 165 (319)
+..+..++.+ ...|+||+.+|...|. +++|+. + ...+||+-.++.+.+... .++|+.|++ .+|
T Consensus 490 L~~f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k-------~~kL~~LAk---~lG 557 (1437)
T PRK00448 490 LPKFKEFCGD--SILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELK-------SHRLNTLAK---KFG 557 (1437)
T ss_pred HHHHHHHhCC--CEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccc-------cccHHHHHH---HcC
Confidence 3444555543 5679999999997763 346664 3 458999988887766432 367899996 456
Q ss_pred CccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchH
Q 020975 166 ISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLW 222 (319)
Q Consensus 166 ~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~ 222 (319)
+..... .-|..||.++..|+..+..++.+.|..
T Consensus 558 L~~~~~------------------------HrAl~DA~aTa~lf~~ll~~l~~~gi~ 590 (1437)
T PRK00448 558 VELEHH------------------------HRADYDAEATAYLLIKFLKDLKEKGIT 590 (1437)
T ss_pred CCCCCC------------------------cChHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 654310 117789999999999999999876543
No 62
>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=94.98 E-value=0.49 Score=39.50 Aligned_cols=146 Identities=17% Similarity=0.142 Sum_probs=68.4
Q ss_pred EEEEeeecCCC-CCCcEEEEEEEe--CCceE-EEEccCCCh----hhHHHHHHHHcCCCceEEEee-hhhhHHHHHHHc-
Q 020975 52 IGFDCEGVDLC-RHGSLCIMQLAF--PDAIY-LVDAIQGGE----TVVKACKPALESSYITKVIHD-CKRDSEALYFQF- 121 (319)
Q Consensus 52 ia~D~E~~~~~-~~g~l~~lqls~--~~~~~-~id~~~l~~----~~~~~L~~lLe~~~i~KV~hd-~k~d~~~L~~~~- 121 (319)
+.||+|++++. ..+.+.+++++. .++.. +.+...... .+.+.+ ..+.+... .|+|| ..+|.-.|.+.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~-~~l~~~~~-iv~yng~~FD~p~L~~~~~ 78 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFF-ELLDEADN-IVTYNGKNFDIPFLKRRAK 78 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH---HHHHTT---EEESSTTTTHHHHHHHHH-
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHH-HHHhcCCe-EEEEeCcccCHHHHHHHHH
Confidence 46899999885 466777788876 33332 433222221 122223 45555544 36666 577998886543
Q ss_pred --CCc-cccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccch----hHHHHHHhcCCCCCCccCCCCHHH
Q 020975 122 --GIK-LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE----KEEVRVLLRQDPQFWTYRPLTELM 194 (319)
Q Consensus 122 --gi~-l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~----k~~~~~~~~~~~~~w~~rpL~~~~ 194 (319)
++. ..+.+|++-..+-... ..+||+.+.. ++|.+-.. ..+....+....... ....-+..
T Consensus 79 ~~~~~~~~~~iDl~~~~~~~~~---------~~~~Lk~ve~---~lg~~~~~~~~~G~~~~~~~~~~~~~~-~~~~~~~i 145 (164)
T PF13482_consen 79 RYGLPPPFNHIDLLKIIKKHFL---------ESYSLKNVEK---FLGIERRDDDISGSESVKLYKEYLETG-DPEALEEI 145 (164)
T ss_dssp HHHH--GGGEEEHHHHHT-TTS---------CCTT--SHHH--------------HHHHHHHHHH---TTG-GTS--HHH
T ss_pred HcCCCcccchhhHHHHHHhccC---------CCCCHHHHhh---hcccccccCCCCHHHHHHHHHHHHhcC-CHHHHHHH
Confidence 333 3468898775432111 1367888875 57765431 011111111100000 11234888
Q ss_pred HHHHHhhhhHHHHHHHHH
Q 020975 195 VRAAADDVRFLPYIYHNM 212 (319)
Q Consensus 195 ~~YAa~Da~~ll~L~~~L 212 (319)
+.|.-.|+..+.+|++.|
T Consensus 146 ~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 146 LEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 999999999999999876
No 63
>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=94.95 E-value=0.07 Score=45.61 Aligned_cols=81 Identities=17% Similarity=0.096 Sum_probs=53.1
Q ss_pred HHHHHHHcCCCceEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchh
Q 020975 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK 171 (319)
Q Consensus 92 ~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k 171 (319)
..|..++. +....|||++.+|+.+|. .-..-..+.||.+... .+. + +..||..|+. .|||..+..
T Consensus 93 ~~l~~li~-~~tILVGHsL~nDL~aL~--l~hp~~~viDTa~l~~--~~~-~------r~~sLk~La~--~~L~~~IQ~- 157 (174)
T cd06143 93 LKLRLLVD-LGCIFVGHGLAKDFRVIN--IQVPKEQVIDTVELFH--LPG-Q------RKLSLRFLAW--YLLGEKIQS- 157 (174)
T ss_pred HHHHHHcC-CCCEEEeccchhHHHHhc--CcCCCcceEEcHHhcc--CCC-C------CChhHHHHHH--HHcCCcccC-
Confidence 44555554 444569999999999984 2111246899975321 121 1 2379999999 999987742
Q ss_pred HHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 020975 172 EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (319)
Q Consensus 172 ~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (319)
+ ..+ ..+||.+++.||
T Consensus 158 ~---------~Hd-------------SvEDArAam~Ly 173 (174)
T cd06143 158 E---------THD-------------SIEDARTALKLY 173 (174)
T ss_pred C---------CcC-------------cHHHHHHHHHHh
Confidence 0 122 458999999987
No 64
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=94.29 E-value=1.2 Score=38.74 Aligned_cols=94 Identities=15% Similarity=0.157 Sum_probs=56.3
Q ss_pred hHHHHHHHHcCCCceEEEeehh-hhHHHHHHHcCCcccc--EEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCC
Q 020975 90 VVKACKPALESSYITKVIHDCK-RDSEALYFQFGIKLHN--VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGI 166 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k-~d~~~L~~~~gi~l~~--vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~ 166 (319)
++..+..++.+. ..|+||+. +|+.+|. .+|..+.+ .+||.-..+..... ..+.+ ..++|.+|++ ++|+
T Consensus 74 vl~~f~~f~~~~--~lVaHNa~~fD~~fL~-~~g~~~~~~~~idt~~~~~~~~~~-~~~~~--~~~~L~~La~---~~gi 144 (195)
T PRK07247 74 VLAAFKEFVGEL--PLIGYNAQKSDLPILA-ENGLDLSDQYQVDLYDEAFERRSS-DLNGI--ANLKLQTVAD---FLGI 144 (195)
T ss_pred HHHHHHHHHCCC--eEEEEeCcHhHHHHHH-HcCCCcCCCceeehHHHHHHhhcc-ccCCC--CCCCHHHHHH---hcCC
Confidence 456777777654 36999995 8999995 67876643 45654222111100 00011 2367899986 6676
Q ss_pred ccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 020975 167 SYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (319)
Q Consensus 167 ~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (319)
+.. . ++ |..||.++..++..|...-+
T Consensus 145 ~~~---~---------Hr-------------Al~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 145 KGR---G---------HN-------------SLEDARMTARVYESFLESDQ 170 (195)
T ss_pred CCC---C---------cC-------------CHHHHHHHHHHHHHHHhhcc
Confidence 421 0 11 66899999988888765544
No 65
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=94.11 E-value=1.4 Score=41.06 Aligned_cols=103 Identities=14% Similarity=0.030 Sum_probs=57.5
Q ss_pred HHHHHHHcCCCceEEEeehhhhHHHHHHHcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccc
Q 020975 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (319)
Q Consensus 92 ~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~ 169 (319)
..+..+++... ..|+||+.+|..+|. .+.... ....+++.......+.. ..++|.+|+. . +|....
T Consensus 112 ~~l~~fl~~~~-vlVAHNA~FD~~fL~-~~~~~~~~~~~~ct~~~i~~~~~~~-------~~~kL~~La~--~-~g~~~~ 179 (294)
T PRK09182 112 AAVDALIAPAD-LIIAHNAGFDRPFLE-RFSPVFATKPWACSVSEIDWSARGF-------EGTKLGYLAG--Q-AGFFHE 179 (294)
T ss_pred HHHHHHhcCCC-EEEEeCHHHHHHHHH-HHHHhccCCcccccHHHHhhccccC-------CCCCHHHHHH--H-cCCCCC
Confidence 45666777643 569999999999995 443332 23455554221111111 1367899886 4 342110
Q ss_pred hhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhchHHHHHhhccc
Q 020975 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALY 231 (319)
Q Consensus 170 ~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~~~l~~~~e~~ 231 (319)
. .-|..||.++..|............+..++.....+
T Consensus 180 -----------------a--------HrAl~Da~Ata~ll~~~l~~~~~~~l~~Ll~~~~~~ 216 (294)
T PRK09182 180 -----------------G--------HRAVDDCQALLELLARPLPETGQPPLAELLEASRRS 216 (294)
T ss_pred -----------------C--------cChHHHHHHHHHHHHHHHhhcCCcCHHHHHHHhccC
Confidence 0 117789999988777555444434455555544433
No 66
>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=93.99 E-value=0.16 Score=40.81 Aligned_cols=71 Identities=18% Similarity=0.185 Sum_probs=41.9
Q ss_pred eehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCcc
Q 020975 108 HDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTY 187 (319)
Q Consensus 108 hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~ 187 (319)
-++| |+.++...-|+.+...-|-|+.+|||+|.++ +...+++ +|++- .|..
T Consensus 68 ~~AK-~LAv~a~~~G~~v~PGDDPlLlAYLlDPsNt---------~p~~var--RY~~~-----------------~W~~ 118 (138)
T PF09281_consen 68 ALAK-DLAVHALREGVVVEPGDDPLLLAYLLDPSNT---------NPEGVAR--RYLGG-----------------EWPE 118 (138)
T ss_dssp TTHH-HHHHHHHHTT----B---HHHHHHHH-TT-----------SHHHHHH--HH-TS--------------------S
T ss_pred HHHH-HHHHHHHhcCcccCCCCCcchhhhhcCccCC---------ChHHHHH--HhcCC-----------------CCCc
Confidence 3444 4444435789999888899999999999753 3677888 88763 4532
Q ss_pred CCCCHHHHHHHHhhhhHHHHHHHHHHHHH
Q 020975 188 RPLTELMVRAAADDVRFLPYIYHNMMKKL 216 (319)
Q Consensus 188 rpL~~~~~~YAa~Da~~ll~L~~~L~~~L 216 (319)
. |+.+|.++.+|+..|..+|
T Consensus 119 d---------A~~RA~~t~~L~~~L~prL 138 (138)
T PF09281_consen 119 D---------AATRALATARLLRALPPRL 138 (138)
T ss_dssp S---------HHHHHHHHHHHHHHHHHHT
T ss_pred c---------HHHHHHHHHHHHHHhhhcC
Confidence 2 6788888999999888765
No 67
>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=93.36 E-value=2.1 Score=37.60 Aligned_cols=145 Identities=16% Similarity=0.186 Sum_probs=77.9
Q ss_pred CCeEEEEeeecCCC--C-----CCcEEEEEEEeC--Cc-eEEEEccCCC-hhhHHHHHHHHcC--CCceEEEeeh-hhhH
Q 020975 49 QLVIGFDCEGVDLC--R-----HGSLCIMQLAFP--DA-IYLVDAIQGG-ETVVKACKPALES--SYITKVIHDC-KRDS 114 (319)
Q Consensus 49 ~~~ia~D~E~~~~~--~-----~g~l~~lqls~~--~~-~~~id~~~l~-~~~~~~L~~lLe~--~~i~KV~hd~-k~d~ 114 (319)
-..++||+|..+.+ . .+.-.+++|+.. +. ..++...... .+++..+..++.+ |++ .+|||. .+|+
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdi-i~g~N~~~FD~ 87 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPDV-IEGHNIFRFDL 87 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccCCCCHHHHHHHHHHHHHHhCCCE-EeccCCcccCH
Confidence 46789999986532 1 122346666652 21 1222111111 2455555555554 564 479998 7898
Q ss_pred HHHHH---HcCCccc--------------------------------cEEechhHHhhhhhhcCCCCCCCCcccHHhhhc
Q 020975 115 EALYF---QFGIKLH--------------------------------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLA 159 (319)
Q Consensus 115 ~~L~~---~~gi~l~--------------------------------~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~ 159 (319)
..|.+ .+|+... .++|++.+..-.+.. .+.+ ..++|+.+++
T Consensus 88 pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~--~~~l--~sysL~~Va~ 163 (207)
T cd05785 88 PYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVS--SRDL--PSYGLKAVAK 163 (207)
T ss_pred HHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhccc--ccCC--CCCCHHHHHH
Confidence 77652 3554431 136776643322111 1122 2478999997
Q ss_pred CCcc--cCCc-cc-hhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 020975 160 DPRY--CGIS-YQ-EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (319)
Q Consensus 160 ~~~~--lg~~-l~-~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (319)
.+ ++.. .+ ..+++.. -|...+ +..++|+..||..++.|+
T Consensus 164 --~~g~~~~~k~d~~~~~I~~-------l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 164 --HFGLASPDRTYIDGRQIAE-------VWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred --HhcccCCCcCCCCHHHHHH-------HHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 54 2211 11 1123322 344332 788999999999999875
No 68
>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=92.26 E-value=1.3 Score=38.31 Aligned_cols=78 Identities=21% Similarity=0.204 Sum_probs=51.4
Q ss_pred ceEEEeehhhhHHHHHH---HcCCc---c--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHH
Q 020975 103 ITKVIHDCKRDSEALYF---QFGIK---L--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEV 174 (319)
Q Consensus 103 i~KV~hd~k~d~~~L~~---~~gi~---l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~ 174 (319)
...|+||+.+|+..|.+ ++|+. . ..++||+..+..+.+. .+|+.+++ ++|++.... .
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~~----------~~L~~l~~---~~gi~~~~~-~- 167 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQ----------TVLAKACQ---AAGIEFDNK-E- 167 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhCC----------CcHHHHHH---HCCCCCCCC-C-
Confidence 45799999999988853 35651 1 2479998877666442 36888886 456653210 0
Q ss_pred HHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHH
Q 020975 175 RVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (319)
Q Consensus 175 ~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~ 215 (319)
..+ |..||.++..|+..+.++
T Consensus 168 -------~H~-------------Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 168 -------AHS-------------ALYDTQKTAELFCKIVNR 188 (189)
T ss_pred -------CcC-------------hHHHHHHHHHHHHHHHHh
Confidence 011 678999998888777643
No 69
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=91.95 E-value=7.6 Score=33.53 Aligned_cols=144 Identities=16% Similarity=0.163 Sum_probs=79.9
Q ss_pred CeEEEEeeecCC---C--CCCcEEEEEEEeC-CceEEEEccCCC-hhhHHHHHHHHcC--CCceEEEeeh-hhhHHHHHH
Q 020975 50 LVIGFDCEGVDL---C--RHGSLCIMQLAFP-DAIYLVDAIQGG-ETVVKACKPALES--SYITKVIHDC-KRDSEALYF 119 (319)
Q Consensus 50 ~~ia~D~E~~~~---~--~~g~l~~lqls~~-~~~~~id~~~l~-~~~~~~L~~lLe~--~~i~KV~hd~-k~d~~~L~~ 119 (319)
..++||.|+.+. + ....+..|+++.. +...++-..... .+++..+..++.. |.+ .++||. .+|+-.|..
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~-i~gyN~~~FDlpyl~~ 82 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDI-IVGYNSNAFDWPYLVE 82 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCE-EEecCCCcCcHHHHHH
Confidence 568999999732 1 2356666666653 434443211122 2455666665554 454 479995 588876642
Q ss_pred ---HcCCccc----------------------cEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCc--cch--
Q 020975 120 ---QFGIKLH----------------------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGIS--YQE-- 170 (319)
Q Consensus 120 ---~~gi~l~----------------------~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~--l~~-- 170 (319)
.+|+.+. ..+|++-... .. ..+ ..++|+.+++ +||.. ..+
T Consensus 83 Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~---~~---~~l--~~y~L~~Va~---~Lg~~k~~~k~~ 151 (188)
T cd05781 83 RARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAE---EI---PEV--KVKTLENVAE---YLGVMKKSERVL 151 (188)
T ss_pred HHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHH---hh---CCC--CCCCHHHHHH---HHCCCccccccC
Confidence 4565431 1456554322 11 111 2478999886 57752 111
Q ss_pred --hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHH
Q 020975 171 --KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (319)
Q Consensus 171 --k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L 212 (319)
..++.. -|....-....+.|+..|+..++.|+..+
T Consensus 152 ~~~~~i~~-------~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 152 IEWYRIYE-------YWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred CCHHHHHH-------HHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 112211 24331123788999999999999998753
No 70
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=90.75 E-value=0.75 Score=47.81 Aligned_cols=105 Identities=16% Similarity=0.177 Sum_probs=61.6
Q ss_pred ceEEEeehhhhHHHHHHHcCCccc--cEEechhHHhhhh----hhc----------------CCC-CC-----C----CC
Q 020975 103 ITKVIHDCKRDSEALYFQFGIKLH--NVVDTQIAYSLIE----EQE----------------GRK-RS-----P----DD 150 (319)
Q Consensus 103 i~KV~hd~k~d~~~L~~~~gi~l~--~vfDt~lAayLL~----~~~----------------~~~-~L-----~----~~ 150 (319)
-..||||+.+|..-+...|.|.-. ...|||-.+-... ..+ ..+ .. + ..
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 456999999999988888987753 3679998764321 110 000 00 0 00
Q ss_pred cccHHhhhcCCcccCCc-cchhHHHHHHhcCCCCCCccCCCC------HHHHHHHHhhhhHHHHHHHHHHHHHhh
Q 020975 151 YISFVGLLADPRYCGIS-YQEKEEVRVLLRQDPQFWTYRPLT------ELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (319)
Q Consensus 151 ~~sL~~L~~~~~~lg~~-l~~k~~~~~~~~~~~~~w~~rpL~------~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (319)
.-||.++.. -++|.. ++| +. +. .|...+.+ .+.+.|||.|++++.+++..+-+...+
T Consensus 322 ~NSL~dVhk--~~c~~~~LdK-t~-Rd-------~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fle 385 (1075)
T KOG3657|consen 322 LNSLVDVHK--FHCGIDALDK-TP-RD-------SFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLE 385 (1075)
T ss_pred hHHHHHHHH--hhCCCCcccc-ch-HH-------hhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHH
Confidence 123444554 555654 432 11 11 11111110 345899999999999999988887766
No 71
>PRK11779 sbcB exonuclease I; Provisional
Probab=89.98 E-value=4.5 Score=40.23 Aligned_cols=98 Identities=12% Similarity=0.025 Sum_probs=54.1
Q ss_pred HHHHHHHHcCCCceEEEee-hhhhHHHHHHHcCCcc-----------c---cEEechhHHhhhhhhcCCCC---CCCCcc
Q 020975 91 VKACKPALESSYITKVIHD-CKRDSEALYFQFGIKL-----------H---NVVDTQIAYSLIEEQEGRKR---SPDDYI 152 (319)
Q Consensus 91 ~~~L~~lLe~~~i~KV~hd-~k~d~~~L~~~~gi~l-----------~---~vfDt~lAayLL~~~~~~~~---L~~~~~ 152 (319)
+..+..++..+....|||| +.+|..++.+.+.... + .++|++-+.|.+.+..-... -....+
T Consensus 82 ~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~ 161 (476)
T PRK11779 82 AARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSF 161 (476)
T ss_pred HHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCC
Confidence 3456666754455679997 7899988754321110 1 12354455555443210000 001246
Q ss_pred cHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHH
Q 020975 153 SFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (319)
Q Consensus 153 sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~ 215 (319)
+|++|+. .+|++... .++ |-.||.++..|+..+..+
T Consensus 162 rLe~L~~---~~gI~~~~-----------AHd-------------ALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 162 KLEHLTK---ANGIEHEN-----------AHD-------------AMSDVYATIAMAKLIKQK 197 (476)
T ss_pred cHHHHHH---HcCCCCCC-----------CCC-------------cHHHHHHHHHHHHHHHHh
Confidence 7888886 44654320 011 668999999988888866
No 72
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=89.86 E-value=3 Score=37.01 Aligned_cols=80 Identities=14% Similarity=-0.029 Sum_probs=51.6
Q ss_pred ceEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCC
Q 020975 103 ITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDP 182 (319)
Q Consensus 103 i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~ 182 (319)
-..|+||+.+|..+|. ..+ ...+||+-.+..+-|+. .+++..|+. ++++..... .
T Consensus 75 ~~lVaHNa~FD~~~L~-~~~---~~~idTl~lar~l~p~~--------~~~l~~L~~---~~~l~~~~~-~--------- 129 (219)
T PRK07983 75 EWYVAHNASFDRRVLP-EMP---GEWICTMKLARRLWPGI--------KYSNMALYK---SRKLNVQTP-P--------- 129 (219)
T ss_pred CEEEEeCcHhhHHHHh-CcC---CCcEeHHHHHHHHccCC--------CCCHHHHHH---HcCCCCCCC-C---------
Confidence 3569999999999995 322 45799998887666642 146788885 455432100 0
Q ss_pred CCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHH
Q 020975 183 QFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKL 216 (319)
Q Consensus 183 ~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L 216 (319)
... ..-|..||.++..|+..+.+..
T Consensus 130 -~~~--------aHrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 130 -GLH--------HHRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred -CCC--------CCcHHHHHHHHHHHHHHHHHHc
Confidence 000 1117789999999888876544
No 73
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=89.81 E-value=4.2 Score=35.35 Aligned_cols=49 Identities=12% Similarity=0.119 Sum_probs=32.3
Q ss_pred cccHHhhhcCCcccCCccch------hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHH
Q 020975 151 YISFVGLLADPRYCGISYQE------KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYH 210 (319)
Q Consensus 151 ~~sL~~L~~~~~~lg~~l~~------k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~ 210 (319)
+++|+++++ .+||..-.+ ..++.. -|...+ ...++|+..||..+++|++
T Consensus 139 sy~L~~Va~--~~Lg~~K~~~~~~~~~~eI~~-------~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 139 SFSLENVAQ--ELLGEGKLIHDVDDRGAEIER-------LFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred cCCHHHHHH--HHhCCCccccCcccCHHHHHH-------HHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 578999999 899853111 012221 233323 5789999999999999863
No 74
>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=87.74 E-value=6.2 Score=34.81 Aligned_cols=107 Identities=16% Similarity=0.083 Sum_probs=65.5
Q ss_pred hhHHHHHHHHcCCCceEEEeehh-hhHHHHHH---HcCCccccE-------------------EechhHHhhhhhhcCCC
Q 020975 89 TVVKACKPALESSYITKVIHDCK-RDSEALYF---QFGIKLHNV-------------------VDTQIAYSLIEEQEGRK 145 (319)
Q Consensus 89 ~~~~~L~~lLe~~~i~KV~hd~k-~d~~~L~~---~~gi~l~~v-------------------fDt~lAayLL~~~~~~~ 145 (319)
+++..+...++......|+||.| +|+-.|.. .+|+.+... +|||-. +.+.+ ++
T Consensus 39 ~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~--l~~~g-~~- 114 (209)
T PF10108_consen 39 ELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDL--LSFYG-AK- 114 (209)
T ss_pred HHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHH--HhccC-cc-
Confidence 45677777887666667999975 88877643 367775322 454432 22222 11
Q ss_pred CCCCCcccHHhhhcCCcccCCccch---hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHH
Q 020975 146 RSPDDYISFVGLLADPRYCGISYQE---KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMK 214 (319)
Q Consensus 146 ~L~~~~~sL~~L~~~~~~lg~~l~~---k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~ 214 (319)
...||+.|+. .+|++-.. -.++.. -|.+..+ ++...||-.||..+..||-.+..
T Consensus 115 ----~~~sLd~la~---~lgiPgK~~idGs~V~~-------~y~~g~i-~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 115 ----ARTSLDELAA---LLGIPGKDDIDGSQVAE-------LYQEGDI-DEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred ----ccCCHHHHHH---HcCCCCCCCCCHHHHHH-------HHHcCCH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 1368999984 88865310 112222 2333333 56789999999999999877643
No 75
>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=86.02 E-value=15 Score=32.18 Aligned_cols=129 Identities=12% Similarity=0.071 Sum_probs=73.0
Q ss_pred CCCcEEEEEEEe---CCceEEE-EccCCCh-hhHHHHHHHHcCCCceEEEeeh-hhhHHHHHH---HcCCccc-------
Q 020975 63 RHGSLCIMQLAF---PDAIYLV-DAIQGGE-TVVKACKPALESSYITKVIHDC-KRDSEALYF---QFGIKLH------- 126 (319)
Q Consensus 63 ~~g~l~~lqls~---~~~~~~i-d~~~l~~-~~~~~L~~lLe~~~i~KV~hd~-k~d~~~L~~---~~gi~l~------- 126 (319)
..++++.|+++. .+..+.+ ......+ +++..+..++++.....|+||. .+|+-.|.. .+|+.+.
T Consensus 49 ~~~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~ 128 (208)
T cd05782 49 PFHKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGN 128 (208)
T ss_pred ccCceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCccc
Confidence 467888888876 3333322 1111112 4566666666653335699998 689987753 3566421
Q ss_pred -----------cEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccc-h--hHHHHHHhcCCCCCCccCCCCH
Q 020975 127 -----------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ-E--KEEVRVLLRQDPQFWTYRPLTE 192 (319)
Q Consensus 127 -----------~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~-~--k~~~~~~~~~~~~~w~~rpL~~ 192 (319)
..+|++-...-.+. ...++|+.+++ +||.+-. + -.++.. .|...+ -.
T Consensus 129 ~~~~y~~r~~~~h~DL~~~~~~~~~--------~~~~~L~~va~---~lG~~~K~d~~G~~v~~-------~y~~g~-~~ 189 (208)
T cd05782 129 KDWNYRNRYSERHLDLMDLLAFYGA--------RARASLDLLAK---LLGIPGKMDVDGSQVWE-------LYAEGK-LD 189 (208)
T ss_pred chhhccCcCCCCcccHHHHHhccCc--------cCCCCHHHHHH---HhCCCCCcCCCHHHHHH-------HHHcCC-hH
Confidence 15676654321111 02368998875 6775211 0 112221 344333 36
Q ss_pred HHHHHHHhhhhHHHHHHH
Q 020975 193 LMVRAAADDVRFLPYIYH 210 (319)
Q Consensus 193 ~~~~YAa~Da~~ll~L~~ 210 (319)
...+|+..||..+..||-
T Consensus 190 ~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 190 EIAEYCETDVLNTYLLYL 207 (208)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 789999999999998874
No 76
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=84.90 E-value=23 Score=30.95 Aligned_cols=105 Identities=12% Similarity=0.064 Sum_probs=59.6
Q ss_pred hhHHHHHHHHcCCCceEEEeeh-hhhHHHHHH---HcCCcc----------------ccEEechhHHh--hhh-hhcCCC
Q 020975 89 TVVKACKPALESSYITKVIHDC-KRDSEALYF---QFGIKL----------------HNVVDTQIAYS--LIE-EQEGRK 145 (319)
Q Consensus 89 ~~~~~L~~lLe~~~i~KV~hd~-k~d~~~L~~---~~gi~l----------------~~vfDt~lAay--LL~-~~~~~~ 145 (319)
+++..+..++.+.. ..|+||. .+|+-.|.. .+|+.. ...+|++-... .+. ...+ .
T Consensus 75 ~lL~~F~~~i~~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~-~ 152 (204)
T cd05783 75 ELIREAFKIISEYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFG-N 152 (204)
T ss_pred HHHHHHHHHHhcCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhc-c
Confidence 45666666777664 4678996 588877643 467661 12566644211 110 0000 0
Q ss_pred CCCCCcccHHhhhcCCcccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHH
Q 020975 146 RSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYH 210 (319)
Q Consensus 146 ~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~ 210 (319)
.+ ..++|+++++ .+||..-.+... .-+... .+..+.|+..||..++.|..
T Consensus 153 ~~--~~~~L~~Va~--~~lg~~K~~~~~---------~i~~~~--~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 153 KY--REYTLDAVAK--ALLGEGKVELEK---------NISELN--LYELAEYNYRDAELTLELTT 202 (204)
T ss_pred cc--ccCcHHHHHH--HhcCCCcccCCc---------hhhhhc--HHHHHHhhHHHHHHHHHHhc
Confidence 11 2478999998 888853111100 112111 27789999999999998864
No 77
>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=84.87 E-value=21 Score=29.62 Aligned_cols=90 Identities=16% Similarity=0.187 Sum_probs=53.1
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHH---HcCCc-----cccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCC
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIK-----LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADP 161 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~---~~gi~-----l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~ 161 (319)
++..+..++.+..-..+.|+.++|...+.+ .++.. ....+|++..+..+.+... .++|++++.
T Consensus 78 vl~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~-------~~~L~~l~~-- 148 (176)
T cd06133 78 VLKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKK-------RTGLSKALE-- 148 (176)
T ss_pred HHHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCC-------CCCHHHHHH--
Confidence 456777788774112356667898765432 23332 1458899876665544211 368999985
Q ss_pred cccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHH
Q 020975 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (319)
Q Consensus 162 ~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L 212 (319)
++|++... . .++ |-.||.++..++..+
T Consensus 149 -~~gi~~~~--~--------~H~-------------Al~DA~~~a~l~~~~ 175 (176)
T cd06133 149 -YLGLEFEG--R--------HHR-------------GLDDARNIARILKRL 175 (176)
T ss_pred -HCCCCCCC--C--------CcC-------------cHHHHHHHHHHHHHh
Confidence 66765431 0 011 557888887776654
No 78
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=83.91 E-value=7.3 Score=37.56 Aligned_cols=89 Identities=22% Similarity=0.186 Sum_probs=55.9
Q ss_pred HHHHHHHcCCCceEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchh
Q 020975 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK 171 (319)
Q Consensus 92 ~~L~~lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k 171 (319)
..|+.++....| -|||..-.|+.+|.-.| ..+.||.+ ++....+... ...+|..|++ .|||..+..
T Consensus 285 ~~l~~~~~~~TI-LVGHSLenDL~aLKl~H----~~ViDTa~---lf~~~~g~~~---~k~sLk~L~~--~~L~~~Iq~- 350 (380)
T KOG2248|consen 285 KELLELISKNTI-LVGHSLENDLKALKLDH----PSVIDTAV---LFKHPTGPYP---FKSSLKNLAK--SYLGKLIQE- 350 (380)
T ss_pred HHHHhhcCcCcE-EEeechhhHHHHHhhhC----CceeeeeE---EEecCCCCcc---chHHHHHHHH--HHHHHHHhc-
Confidence 467776665555 59999999999995322 45789985 3333322111 1257999999 898854420
Q ss_pred HHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHH
Q 020975 172 EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMK 214 (319)
Q Consensus 172 ~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~ 214 (319)
+..+.+ +.+||.+++.|......
T Consensus 351 -------~~~~Hd-------------S~eDA~acm~Lv~~k~~ 373 (380)
T KOG2248|consen 351 -------GVGGHD-------------SVEDALACMKLVKLKIK 373 (380)
T ss_pred -------cCCCCc-------------cHHHHHHHHHHHHHHHh
Confidence 011112 56889988888766543
No 79
>PRK06722 exonuclease; Provisional
Probab=83.65 E-value=37 Score=31.41 Aligned_cols=91 Identities=12% Similarity=0.031 Sum_probs=50.0
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHHH---cCCccc-----cEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCC
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKLH-----NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADP 161 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~~---~gi~l~-----~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~ 161 (319)
++..+..++.+.. -++|++++|...|.+. +|+... ..+|++-.++-+-+.... ...+|..+++
T Consensus 80 Vl~ef~~fig~~~--lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~-----~~~sL~~l~~-- 150 (281)
T PRK06722 80 IIEKFIQFIGEDS--IFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFE-----HTPSLQSAVE-- 150 (281)
T ss_pred HHHHHHHHHCCCc--EEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhcc-----CCCCHHHHHH--
Confidence 4566777776543 3678889999888643 555431 124554322211111101 1257999996
Q ss_pred cccCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHH
Q 020975 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (319)
Q Consensus 162 ~~lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~ 213 (319)
++|++... . .+. |-.||..+..|+..+.
T Consensus 151 -~lgL~~~g--~--------~Hr-------------AL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 151 -QLGLIWEG--K--------QHR-------------ALADAENTANILLKAY 178 (281)
T ss_pred -HCCCCCCC--C--------CcC-------------cHHHHHHHHHHHHHHh
Confidence 66765421 0 011 5567777777776655
No 80
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=82.16 E-value=36 Score=30.18 Aligned_cols=134 Identities=16% Similarity=0.058 Sum_probs=79.3
Q ss_pred CCeEEEEeeecCCC-CCCcEEEEEEEe---C---Cc--eEEEEccC-CC--------------------hhhHHHHHHHH
Q 020975 49 QLVIGFDCEGVDLC-RHGSLCIMQLAF---P---DA--IYLVDAIQ-GG--------------------ETVVKACKPAL 98 (319)
Q Consensus 49 ~~~ia~D~E~~~~~-~~g~l~~lqls~---~---~~--~~~id~~~-l~--------------------~~~~~~L~~lL 98 (319)
...+.||+|+++.. ...+++-|..-. . +. -.++.+.. +. .+++..+..++
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~i 92 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDFI 92 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 36799999999876 344443333222 1 11 13344421 00 12334555666
Q ss_pred cCCCceEEEeehhhhHHHHHH---HcCCcc--ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHH
Q 020975 99 ESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE 173 (319)
Q Consensus 99 e~~~i~KV~hd~k~d~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~ 173 (319)
.+. -.-|+||+.+|+..|.. .++..+ ..+.||.-.+.-..++.. ..+|+.|+. .+|+.... ..
T Consensus 93 ~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~-------~~~L~~l~~---~~gi~~~~-~~ 160 (243)
T COG0847 93 GGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFD-------RSSLDALAE---RLGIDRNP-FH 160 (243)
T ss_pred CCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCc-------cchHHHHHH---HcCCCcCC-cC
Confidence 654 45699999999998853 344443 347788887766666422 257899985 55654220 00
Q ss_pred HHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHH
Q 020975 174 VRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (319)
Q Consensus 174 ~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~ 215 (319)
. .-|..|+.++..++..+...
T Consensus 161 ----------~-----------H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 161 ----------P-----------HRALFDALALAELFLLLQTG 181 (243)
T ss_pred ----------C-----------cchHHHHHHHHHHHHHHHhc
Confidence 0 11678899998888888764
No 81
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=75.82 E-value=0.49 Score=34.57 Aligned_cols=54 Identities=15% Similarity=0.246 Sum_probs=42.9
Q ss_pred CCCCCCCCCCCcccccCccChHHHHHhhccCCCCcc----------hhhccccchHHHHHHhcc
Q 020975 243 VDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG----------RIIGRRGSSILAIKESCN 296 (319)
Q Consensus 243 ~d~~~l~a~~~~l~~~~~~~~~~i~~~ag~~~~~~~----------~~~~~~~~~~~~~~~~~~ 296 (319)
..|+...+...+.++..+..++.|.++|..+|.+.. ..+++.|..++.+++.+.
T Consensus 12 ~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~~~~~~~~g~~~~~~i~~~~ 75 (81)
T smart00341 12 RQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEAS 75 (81)
T ss_pred HHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 356666677788899999999999999999996433 466778888888888764
No 82
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=74.40 E-value=28 Score=30.33 Aligned_cols=92 Identities=14% Similarity=0.096 Sum_probs=56.4
Q ss_pred hHHHHHHHHcCCCceEEEeehhhhHHHHHH---HcCCcc---ccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcc
Q 020975 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRY 163 (319)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~d~~~L~~---~~gi~l---~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~ 163 (319)
++..|..++.+.... ++|+..+|+..|.+ .+|+.. ....|++.....+.+... .++|.++++ +
T Consensus 82 vl~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~-------~~~L~~~~~---~ 150 (207)
T PRK07748 82 LVEKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERN-------QTGLWKAIE---E 150 (207)
T ss_pred HHHHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCC-------CCCHHHHHH---H
Confidence 556777788763333 55668999988854 346543 346677764433332211 268899886 5
Q ss_pred cCCccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHH
Q 020975 164 CGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (319)
Q Consensus 164 lg~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~ 215 (319)
+|++... . . .-|..||.++..|+..+...
T Consensus 151 ~gi~~~~--~--------~-------------H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 151 YGKEGTG--K--------H-------------HCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred cCCCCCC--C--------C-------------cChHHHHHHHHHHHHHHHhC
Confidence 6654321 0 0 11678999999888887765
No 83
>PHA02528 43 DNA polymerase; Provisional
Probab=71.67 E-value=75 Score=34.34 Aligned_cols=50 Identities=8% Similarity=0.011 Sum_probs=34.9
Q ss_pred cccHHhhhcCCcccCCccch--hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHH
Q 020975 151 YISFVGLLADPRYCGISYQE--KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHN 211 (319)
Q Consensus 151 ~~sL~~L~~~~~~lg~~l~~--k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~ 211 (319)
.++|+.+++ .+||..-.. .+.+.. -|... ....+.|+..||..+++|...
T Consensus 272 SYsLe~VA~--~~LG~~K~d~~~~eI~~-------l~~~d--~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 272 SYRLDYIAE--VELGKKKLDYSDGPFKK-------FRETD--HQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred cCCHHHHHH--HHhCCCCccCCHHHHHH-------HHhcC--HHHHHHHHHHHHHHHHHHHHH
Confidence 478999999 899864332 122322 23222 267899999999999999987
No 84
>PRK05762 DNA polymerase II; Reviewed
Probab=70.73 E-value=68 Score=34.15 Aligned_cols=104 Identities=15% Similarity=0.160 Sum_probs=58.9
Q ss_pred hhHHHHHHHHcC--CCceEEEeeh-hhhHHHHHH---HcCCccc---------------------------cEEechhHH
Q 020975 89 TVVKACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKLH---------------------------NVVDTQIAY 135 (319)
Q Consensus 89 ~~~~~L~~lLe~--~~i~KV~hd~-k~d~~~L~~---~~gi~l~---------------------------~vfDt~lAa 135 (319)
+.+..+..++.. |+|. +|||. .+|+..|.+ .+|+.+. .++|++-..
T Consensus 205 ~LL~~F~~~i~~~DPDII-vGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~ 283 (786)
T PRK05762 205 ALLEKFNAWFAEHDPDVI-IGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDAL 283 (786)
T ss_pred HHHHHHHHHHHhcCCCEE-EEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHH
Confidence 345555555444 6654 89996 578877653 3455421 134554432
Q ss_pred hhhhhhcCCCCCCCCcccHHhhhcCCcccCCccc--hh----HHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 020975 136 SLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ--EK----EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (319)
Q Consensus 136 yLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~--~k----~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (319)
.-.. +.+ ..++|+.+++ .+||..-. .. .++.. .|... ....+.|+..||..++.|+
T Consensus 284 k~~~-----~~l--~sysL~~Va~--~~Lg~~K~~~d~~~~~~eI~~-------~~~~~--~~~l~~Y~l~Da~lt~~L~ 345 (786)
T PRK05762 284 KSAT-----WVF--DSFSLEYVSQ--RLLGEGKAIDDPYDRMDEIDR-------RFAED--KPALARYNLKDCELVTRIF 345 (786)
T ss_pred HHhh-----ccC--CCCCHHHHHH--HHhCCCeeccCccccHHHHHH-------HHhhh--HHHHHHHHHHHHHHHHHHH
Confidence 2110 011 2478999998 88874321 01 11211 23321 2677899999999999998
Q ss_pred HH
Q 020975 210 HN 211 (319)
Q Consensus 210 ~~ 211 (319)
..
T Consensus 346 ~k 347 (786)
T PRK05762 346 EK 347 (786)
T ss_pred HH
Confidence 83
No 85
>PRK05359 oligoribonuclease; Provisional
Probab=70.36 E-value=43 Score=28.60 Aligned_cols=40 Identities=13% Similarity=-0.010 Sum_probs=23.1
Q ss_pred HHHHHHHHcC----CCceEEEeehhhhHHHHHHHc---CCccc-cEEe
Q 020975 91 VKACKPALES----SYITKVIHDCKRDSEALYFQF---GIKLH-NVVD 130 (319)
Q Consensus 91 ~~~L~~lLe~----~~i~KV~hd~k~d~~~L~~~~---gi~l~-~vfD 130 (319)
+..|..++.. ....-++|++.+|..+|.+.+ |..+. .+.|
T Consensus 83 ~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~D 130 (181)
T PRK05359 83 EAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLD 130 (181)
T ss_pred HHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccc
Confidence 3445555542 223348999999999886433 44442 3456
No 86
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=68.19 E-value=2.6 Score=44.44 Aligned_cols=88 Identities=19% Similarity=0.224 Sum_probs=59.9
Q ss_pred HHcCCCceEEEeehhhhHHHHHHHcCCccccEEechhHHhhhhhhcCCCCCCCCcccHHhhhcCCcccCCccchhHHHHH
Q 020975 97 ALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRV 176 (319)
Q Consensus 97 lLe~~~i~KV~hd~k~d~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~L~~~~~sL~~L~~~~~~lg~~l~~k~~~~~ 176 (319)
+|-+-.+..|||++++|..++ +.-+.-..++||...-. +.. + +.+||..|+- .+||.++.. +.
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvI--Ni~Vp~~QiiDTv~lf~-~~s----~----R~LSLrfLa~--~lLg~~IQ~-~~--- 1071 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVI--NIHVPEEQIIDTVTLFR-LGS----Q----RMLSLRFLAW--ELLGETIQM-EA--- 1071 (1118)
T ss_pred HHHHcCcEEEcccccccceEE--EEecChhhheeeeEEEe-ccc----c----cEEEHHHHHH--HHhcchhhc-cc---
Confidence 567788999999999999766 23233245899977322 222 1 2479999998 899866531 10
Q ss_pred HhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhhhch
Q 020975 177 LLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSL 221 (319)
Q Consensus 177 ~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~~ 221 (319)
++ ..+||...+.||+... +|+++|.
T Consensus 1072 ------HD-------------SIeDA~taLkLYk~Yl-~lkeq~~ 1096 (1118)
T KOG1275|consen 1072 ------HD-------------SIEDARTALKLYKKYL-KLKEQGK 1096 (1118)
T ss_pred ------cc-------------cHHHHHHHHHHHHHHH-HHHHhhH
Confidence 11 3589999999999986 5566554
No 87
>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=64.37 E-value=0.3 Score=34.55 Aligned_cols=48 Identities=21% Similarity=0.286 Sum_probs=30.8
Q ss_pred CCCCCCCCCcccccCccChHHHHHhhccCCCCcc----------hhhccccchHHHHH
Q 020975 245 WPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG----------RIIGRRGSSILAIK 292 (319)
Q Consensus 245 ~~~l~a~~~~l~~~~~~~~~~i~~~ag~~~~~~~----------~~~~~~~~~~~~~~ 292 (319)
||.-.+...+.++..+..++.+.++|...|.+.+ ..++++|..|++++
T Consensus 11 ~R~~~A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i~g~~~~~~~~~g~~il~~I 68 (68)
T PF00570_consen 11 WREELAREEDVPPYRILSDEALLEIAKRLPTSIEELLQIPGMGKRKVRKYGDEILEII 68 (68)
T ss_dssp HHHHHHHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTSTTCGHHHHHHCHHHHHHHH
T ss_pred HHHHHHHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHccCCCHHHHHHHHHHHHhhC
Confidence 3334444556677778889999999999885443 56678888887764
No 88
>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=57.03 E-value=34 Score=29.10 Aligned_cols=29 Identities=17% Similarity=0.120 Sum_probs=19.6
Q ss_pred HHHHHHHHcCCCceEEEee-hhhhHHHHHH
Q 020975 91 VKACKPALESSYITKVIHD-CKRDSEALYF 119 (319)
Q Consensus 91 ~~~L~~lLe~~~i~KV~hd-~k~d~~~L~~ 119 (319)
+..+..++..+....|+|| +.+|...|.+
T Consensus 73 l~~~~~~~~~~~~~lVahn~~~FD~~fL~~ 102 (183)
T cd06138 73 IAKIHRLFNTPGTCIVGYNNIRFDDEFLRF 102 (183)
T ss_pred HHHHHHHHccCCCcEEeeCchhhHHHHHHH
Confidence 3455566654444458987 7999999864
No 89
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=55.82 E-value=4.7 Score=27.72 Aligned_cols=41 Identities=27% Similarity=0.407 Sum_probs=33.0
Q ss_pred CCCCcchhhccccchHHHHHHhcchhhhccCCCCCCChhhh
Q 020975 273 PPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVSL 313 (319)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 313 (319)
++...+.++++.|.+|..|.+.++..+.|.....++..|++
T Consensus 7 p~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I 47 (62)
T cd02394 7 PKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITI 47 (62)
T ss_pred CHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEE
Confidence 44556789999999999999999999999887655655543
No 90
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=41.70 E-value=33 Score=30.42 Aligned_cols=54 Identities=13% Similarity=0.111 Sum_probs=36.4
Q ss_pred cccHHhhhcCCcccCCccch--hHHHHHHhcCCCCCCccCCCC-HHHHHHHHhhhhHHHHHHHHHH
Q 020975 151 YISFVGLLADPRYCGISYQE--KEEVRVLLRQDPQFWTYRPLT-ELMVRAAADDVRFLPYIYHNMM 213 (319)
Q Consensus 151 ~~sL~~L~~~~~~lg~~l~~--k~~~~~~~~~~~~~w~~rpL~-~~~~~YAa~Da~~ll~L~~~L~ 213 (319)
.++|+++++ .+||..-.+ .+++.. -|...|-. ...++|+..||..+++|...|.
T Consensus 168 sy~L~~Va~--~~Lg~~k~d~~~~~i~~-------~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 168 SYSLNSVSA--HFLGEQKEDVHYSIITD-------LQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred cCcHHHHHH--HHhCCCCCCCCHHHHHH-------HHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 578999999 899854322 122221 23222211 4679999999999999999875
No 91
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=30.24 E-value=23 Score=24.66 Aligned_cols=37 Identities=35% Similarity=0.628 Sum_probs=30.4
Q ss_pred CCcchhhccccchHHHHHHhcchhhhccCCC--CCCChh
Q 020975 275 GKMGRIIGRRGSSILAIKESCNAEILIGGAK--GPPDKV 311 (319)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~ 311 (319)
...++++++.|..|..|.+...+.+.|.-.. ++++|+
T Consensus 9 ~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~ 47 (65)
T cd02396 9 SQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERV 47 (65)
T ss_pred HHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceE
Confidence 4567899999999999999999998887655 466665
No 92
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=28.88 E-value=3.8e+02 Score=30.94 Aligned_cols=153 Identities=14% Similarity=0.104 Sum_probs=82.3
Q ss_pred CCCeEEEEeeecCCC--C----CCcEEEEEEEeCCceEEEEccCC-C-----------h------------hhHHHHHHH
Q 020975 48 RQLVIGFDCEGVDLC--R----HGSLCIMQLAFPDAIYLVDAIQG-G-----------E------------TVVKACKPA 97 (319)
Q Consensus 48 ~~~~ia~D~E~~~~~--~----~g~l~~lqls~~~~~~~id~~~l-~-----------~------------~~~~~L~~l 97 (319)
+..++|||.|++.++ . ...+-.|+--+.+++|+|--..+ . + +-..-|+.+
T Consensus 245 dp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F~v~Ne~dEv~Ll~Rf 324 (2173)
T KOG1798|consen 245 DPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPFCVFNEPDEVGLLQRF 324 (2173)
T ss_pred CceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCccccccceEEecCCcHHHHHHHH
Confidence 456899999998764 1 34565565556788888721111 0 0 012345666
Q ss_pred HcC-----CCceEEEeehh-hhHHHHH---HHcCCcccc----EEec---hhHHhhhhhh-----cCCCCCCCCcccHHh
Q 020975 98 LES-----SYITKVIHDCK-RDSEALY---FQFGIKLHN----VVDT---QIAYSLIEEQ-----EGRKRSPDDYISFVG 156 (319)
Q Consensus 98 Le~-----~~i~KV~hd~k-~d~~~L~---~~~gi~l~~----vfDt---~lAayLL~~~-----~~~~~L~~~~~sL~~ 156 (319)
|+. |.|. |.+|.. +|+-.+. ..||+.+.. .-|. .-+.|.+.-+ .+..-||..+.||++
T Consensus 325 FeHiq~~kP~ii-vTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLPqGSqgLKA 403 (2173)
T KOG1798|consen 325 FEHIQEVKPTII-VTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLPQGSQGLKA 403 (2173)
T ss_pred HHHHHhcCCcEE-EEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccCCCcccchhH
Confidence 665 5554 666653 5654442 247877631 2231 2222222211 122234444567887
Q ss_pred hhcCCcccCC---ccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHH
Q 020975 157 LLADPRYCGI---SYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (319)
Q Consensus 157 L~~~~~~lg~---~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~ 213 (319)
... .-||. +++ .+.... + ...=+..+..|.+.||.++..||=..-
T Consensus 404 VTk--aKLGYdPvEvd-PEdM~~--------~-A~EkPQ~lasYSVSDAVATYyLYMkYV 451 (2173)
T KOG1798|consen 404 VTK--AKLGYDPVEVD-PEDMVR--------M-AMEKPQTLASYSVSDAVATYYLYMKYV 451 (2173)
T ss_pred HHH--HhhCCCcccCC-HHHhhh--------h-hhhCchhhhhcchHHHHHHHHHHHHHh
Confidence 776 66664 333 122111 0 111246778999999999999986554
No 93
>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=27.15 E-value=67 Score=28.11 Aligned_cols=103 Identities=13% Similarity=0.106 Sum_probs=58.0
Q ss_pred hhHHHHHHHHcC--CCceEEEeeh-hhhHHHHHH---HcCCccc--------c----------EEechhHHhhhhhhcCC
Q 020975 89 TVVKACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKLH--------N----------VVDTQIAYSLIEEQEGR 144 (319)
Q Consensus 89 ~~~~~L~~lLe~--~~i~KV~hd~-k~d~~~L~~---~~gi~l~--------~----------vfDt~lAayLL~~~~~~ 144 (319)
+++..+..++.+ |.+ .++||. .+|+-.|.. .+|+.+. . .+|++-. +...
T Consensus 75 ~lL~~f~~~i~~~~Pd~-i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~---~~~~--- 147 (204)
T cd05779 75 ALLQRFFEHIREVKPHI-IVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRW---VKRD--- 147 (204)
T ss_pred HHHHHHHHHHHHhCCCE-EEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHH---HHHh---
Confidence 345555555554 444 488886 588876642 3565432 0 3444421 1110
Q ss_pred CCCCCCcccHHhhhcCCcccCCccch--hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 020975 145 KRSPDDYISFVGLLADPRYCGISYQE--KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (319)
Q Consensus 145 ~~L~~~~~sL~~L~~~~~~lg~~l~~--k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (319)
..+..+.++|+.+++ .+||..-.. ..++.. -|...+ +..+.|+..||..++.||
T Consensus 148 ~~l~~~sysLd~Va~--~~Lg~~K~~~~~~~I~~-------~~~~~~--~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 148 SYLPQGSQGLKAVTK--AKLGYDPVELDPEDMVP-------LAREDP--QTLASYSVSDAVATYYLY 203 (204)
T ss_pred hcCCCCCccHHHHHH--HHhCCCcCcCCHHHHHH-------HHhCCc--HHHHhccHHHHHHHHHHh
Confidence 011112478999998 889863211 112211 344433 678999999999999987
No 94
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=25.04 E-value=84 Score=26.45 Aligned_cols=30 Identities=7% Similarity=-0.109 Sum_probs=20.9
Q ss_pred hHHHHHHHHcC----CCceEEEeehhhhHHHHHH
Q 020975 90 VVKACKPALES----SYITKVIHDCKRDSEALYF 119 (319)
Q Consensus 90 ~~~~L~~lLe~----~~i~KV~hd~k~d~~~L~~ 119 (319)
++..|..++.+ ....-++||+.+|..+|.+
T Consensus 78 vl~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~ 111 (173)
T cd06135 78 AEAELLEFIKKYVPKGKSPLAGNSVHQDRRFLDK 111 (173)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCHHHHHH
Confidence 34456666654 2456789999999998864
No 95
>PF13014 KH_3: KH domain
Probab=24.91 E-value=33 Score=21.61 Aligned_cols=27 Identities=48% Similarity=0.724 Sum_probs=23.9
Q ss_pred cchhhccccchHHHHHHhcchhhhccC
Q 020975 277 MGRIIGRRGSSILAIKESCNAEILIGG 303 (319)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 (319)
.+.+|++.|.+|..|.+.+.+.+.|--
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEECC
Confidence 356899999999999999999988876
Done!