Query 043928
Match_columns 192
No_of_seqs 130 out of 1116
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 09:36:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043928.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043928hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06146 mut-7_like_exo DEDDy 3 100.0 6.7E-41 1.5E-45 268.2 18.2 168 15-188 1-193 (193)
2 cd06141 WRN_exo DEDDy 3'-5' ex 100.0 5.7E-39 1.2E-43 251.0 19.1 164 18-188 1-170 (170)
3 cd06129 RNaseD_like DEDDy 3'-5 100.0 1.7E-38 3.8E-43 247.1 17.4 154 25-188 3-161 (161)
4 PRK10829 ribonuclease D; Provi 100.0 2.3E-32 5.1E-37 237.6 18.8 164 15-190 3-170 (373)
5 PF01612 DNA_pol_A_exo1: 3'-5' 100.0 5.4E-31 1.2E-35 204.9 14.9 166 16-191 2-176 (176)
6 cd06148 Egl_like_exo DEDDy 3'- 100.0 3.6E-31 7.7E-36 212.5 13.0 152 37-191 9-178 (197)
7 COG0349 Rnd Ribonuclease D [Tr 100.0 2.4E-29 5.3E-34 215.0 15.2 159 22-191 5-167 (361)
8 KOG4373 Predicted 3'-5' exonuc 100.0 2.9E-29 6.3E-34 210.2 10.8 180 2-184 15-282 (319)
9 TIGR01388 rnd ribonuclease D. 100.0 1.2E-27 2.7E-32 208.2 18.6 163 17-191 1-167 (367)
10 KOG2207 Predicted 3'-5' exonuc 99.9 1.6E-24 3.5E-29 193.2 9.1 171 12-188 389-583 (617)
11 smart00474 35EXOc 3'-5' exonuc 99.9 2.7E-20 5.8E-25 143.6 17.3 166 16-190 2-171 (172)
12 cd06142 RNaseD_exo DEDDy 3'-5' 99.9 3.9E-20 8.4E-25 144.6 17.8 147 37-191 11-161 (178)
13 cd00007 35EXOc 3'-5' exonuclea 99.8 3.1E-17 6.7E-22 124.2 13.7 145 40-190 2-155 (155)
14 cd09018 DEDDy_polA_RNaseD_like 99.7 5.7E-17 1.2E-21 123.0 13.6 144 40-187 1-149 (150)
15 cd06147 Rrp6p_like_exo DEDDy 3 99.7 7.9E-16 1.7E-20 122.6 17.3 164 16-191 6-173 (192)
16 KOG2206 Exosome 3'-5' exoribon 99.7 1.5E-16 3.2E-21 142.1 8.0 161 16-189 194-359 (687)
17 PRK05755 DNA polymerase I; Pro 99.5 3.9E-13 8.5E-18 128.8 16.3 165 15-190 296-469 (880)
18 PRK14975 bifunctional 3'-5' ex 99.3 5.5E-12 1.2E-16 115.5 10.4 140 16-191 4-145 (553)
19 cd06139 DNA_polA_I_Ecoli_like_ 99.3 2.8E-10 6.1E-15 89.7 14.4 151 37-190 4-170 (193)
20 cd06140 DNA_polA_I_Bacillus_li 99.3 1.1E-10 2.4E-15 91.3 11.8 147 39-191 4-157 (178)
21 TIGR00593 pola DNA polymerase 98.0 0.00021 4.5E-09 69.1 15.6 162 18-191 307-478 (887)
22 COG0749 PolA DNA polymerase I 98.0 0.00011 2.4E-09 67.6 12.0 165 19-191 7-181 (593)
23 PRK06310 DNA polymerase III su 97.4 0.011 2.4E-07 49.1 15.3 131 36-190 5-174 (250)
24 smart00479 EXOIII exonuclease 97.4 0.0066 1.4E-07 46.3 12.3 128 40-190 2-167 (169)
25 cd05780 DNA_polB_Kod1_like_exo 97.3 0.0048 1E-07 49.2 11.3 143 38-186 3-195 (195)
26 PRK07740 hypothetical protein; 97.2 0.064 1.4E-06 44.4 17.6 147 20-190 31-226 (244)
27 cd06128 DNA_polA_exo DEDDy 3'- 97.2 0.014 3E-07 44.2 12.6 126 54-187 19-150 (151)
28 PRK08517 DNA polymerase III su 97.2 0.032 6.9E-07 46.7 15.3 130 37-191 67-232 (257)
29 cd06134 RNaseT DEDDh 3'-5' exo 97.1 0.028 6.2E-07 44.6 14.2 78 89-189 102-188 (189)
30 cd06125 DnaQ_like_exo DnaQ-lik 97.1 0.0018 3.8E-08 46.0 6.4 70 41-120 1-83 (96)
31 PRK07883 hypothetical protein; 97.1 0.025 5.5E-07 52.3 15.4 133 36-190 13-182 (557)
32 cd05160 DEDDy_DNA_polB_exo DED 96.9 0.017 3.6E-07 45.9 10.9 98 80-183 69-198 (199)
33 PRK07942 DNA polymerase III su 96.9 0.051 1.1E-06 44.6 14.0 81 89-190 93-180 (232)
34 PRK05711 DNA polymerase III su 96.9 0.04 8.7E-07 45.6 13.4 129 38-189 4-175 (240)
35 cd06133 ERI-1_3'hExo_like DEDD 96.8 0.022 4.9E-07 43.8 10.9 86 80-187 81-176 (176)
36 PRK09145 DNA polymerase III su 96.8 0.11 2.4E-06 41.5 15.2 130 37-188 28-199 (202)
37 TIGR01406 dnaQ_proteo DNA poly 96.8 0.055 1.2E-06 44.3 13.3 87 80-189 75-171 (225)
38 PRK06807 DNA polymerase III su 96.8 0.035 7.5E-07 47.8 12.6 127 39-190 9-172 (313)
39 PRK06309 DNA polymerase III su 96.8 0.078 1.7E-06 43.5 14.2 129 39-190 3-166 (232)
40 cd06149 ISG20 DEDDh 3'-5' exon 96.8 0.016 3.5E-07 44.7 9.5 84 79-183 69-156 (157)
41 PRK07748 sporulation inhibitor 96.8 0.083 1.8E-06 42.5 13.9 89 80-190 85-180 (207)
42 PRK06063 DNA polymerase III su 96.7 0.041 8.9E-07 47.3 12.1 128 39-190 16-179 (313)
43 cd06131 DNA_pol_III_epsilon_Ec 96.6 0.15 3.3E-06 39.0 14.1 123 41-186 2-166 (167)
44 PRK05168 ribonuclease T; Provi 96.6 0.16 3.5E-06 41.0 14.5 79 89-190 114-201 (211)
45 TIGR00573 dnaq exonuclease, DN 96.5 0.12 2.6E-06 41.9 13.2 91 80-191 80-178 (217)
46 cd06137 DEDDh_RNase DEDDh 3'-5 96.4 0.032 6.9E-07 43.1 8.9 83 80-183 76-160 (161)
47 TIGR01407 dinG_rel DnaQ family 96.4 0.063 1.4E-06 52.1 12.8 127 40-190 2-165 (850)
48 PRK08074 bifunctional ATP-depe 96.2 0.18 3.9E-06 49.5 14.7 130 38-191 3-170 (928)
49 TIGR01405 polC_Gram_pos DNA po 96.1 0.16 3.6E-06 51.0 14.3 130 37-190 189-355 (1213)
50 cd05781 DNA_polB_B3_exo DEDDy 95.9 0.32 7E-06 38.6 12.8 142 39-186 4-188 (188)
51 TIGR01298 RNaseT ribonuclease 95.9 0.32 7E-06 38.9 12.8 79 89-190 105-192 (200)
52 cd06127 DEDDh DEDDh 3'-5' exon 95.9 0.2 4.3E-06 37.1 11.0 80 80-183 72-158 (159)
53 PRK09146 DNA polymerase III su 95.9 0.37 7.9E-06 39.9 13.4 130 38-189 47-226 (239)
54 cd06144 REX4_like DEDDh 3'-5' 95.9 0.12 2.7E-06 39.3 9.8 82 80-184 70-152 (152)
55 KOG2249 3'-5' exonuclease [Rep 95.9 0.16 3.4E-06 42.6 10.9 124 39-188 106-264 (280)
56 cd06143 PAN2_exo DEDDh 3'-5' e 95.8 0.039 8.4E-07 43.6 6.6 73 86-183 99-173 (174)
57 cd05782 DNA_polB_like1_exo Unc 95.4 0.14 3E-06 41.4 8.8 132 47-185 45-208 (208)
58 cd05777 DNA_polB_delta_exo DED 95.2 0.28 6E-06 40.1 10.1 96 86-187 85-224 (230)
59 PRK07246 bifunctional ATP-depe 95.1 0.88 1.9E-05 44.2 14.8 128 38-190 7-170 (820)
60 cd06145 REX1_like DEDDh 3'-5' 95.1 0.055 1.2E-06 41.3 5.4 81 80-183 68-149 (150)
61 cd06136 TREX1_2 DEDDh 3'-5' ex 94.8 0.74 1.6E-05 36.0 11.3 79 80-185 87-176 (177)
62 cd05784 DNA_polB_II_exo DEDDy 94.3 0.39 8.4E-06 38.4 8.8 137 39-184 4-193 (193)
63 PRK07247 DNA polymerase III su 94.3 2.2 4.8E-05 34.1 13.4 89 80-191 77-170 (195)
64 cd05785 DNA_polB_like2_exo Unc 93.9 0.84 1.8E-05 36.8 9.9 140 39-183 10-206 (207)
65 KOG3657 Mitochondrial DNA poly 93.6 0.19 4.1E-06 48.2 6.4 91 90-187 242-380 (1075)
66 cd05779 DNA_polB_epsilon_exo D 93.4 1.7 3.6E-05 35.1 10.8 92 87-184 88-204 (204)
67 PRK07983 exodeoxyribonuclease 93.1 4.1 8.8E-05 33.2 14.5 80 89-189 74-153 (219)
68 PF13482 RNase_H_2: RNase_H su 92.9 0.076 1.7E-06 40.5 2.4 139 41-186 1-163 (164)
69 KOG2248 3'-5' exonuclease [Rep 92.6 0.16 3.6E-06 44.8 4.2 85 79-187 285-372 (380)
70 PRK05601 DNA polymerase III su 92.5 2.7 5.8E-05 37.1 11.6 138 37-187 45-246 (377)
71 PRK06195 DNA polymerase III su 92.5 1 2.2E-05 38.6 8.9 87 80-191 73-165 (309)
72 cd05783 DNA_polB_B1_exo DEDDy 91.9 5.6 0.00012 31.9 12.1 136 39-184 6-202 (204)
73 PRK09182 DNA polymerase III su 91.3 7.8 0.00017 33.1 12.9 86 79-188 112-199 (294)
74 PRK00448 polC DNA polymerase I 90.9 2.1 4.6E-05 44.0 10.5 81 88-190 498-584 (1437)
75 PRK11779 sbcB exonuclease I; P 90.7 9.5 0.00021 34.8 13.6 132 38-189 6-197 (476)
76 cd06130 DNA_pol_III_epsilon_li 90.2 1.6 3.5E-05 32.7 7.1 79 80-183 70-154 (156)
77 PHA02528 43 DNA polymerase; Pr 88.7 26 0.00056 34.6 16.0 175 7-186 49-324 (881)
78 KOG2405 Predicted 3'-5' exonuc 87.1 0.27 5.9E-06 43.3 1.0 148 39-189 196-360 (458)
79 PRK06722 exonuclease; Provisio 85.9 3.8 8.2E-05 34.8 7.3 89 80-189 83-180 (281)
80 KOG1275 PAB-dependent poly(A) 78.4 1.8 3.8E-05 42.2 2.7 60 83-147 1008-1068(1118)
81 COG0847 DnaQ DNA polymerase II 76.7 24 0.00053 28.5 8.9 89 80-189 87-181 (243)
82 PRK05762 DNA polymerase II; Re 76.1 27 0.00058 33.9 10.1 142 38-186 155-348 (786)
83 cd06138 ExoI_N N-terminal DEDD 74.3 18 0.00039 28.2 7.2 83 80-182 75-181 (183)
84 PF10108 DNA_pol_B_exo2: Predi 70.0 39 0.00084 27.5 8.2 104 80-187 43-170 (209)
85 KOG2405 Predicted 3'-5' exonuc 69.1 0.11 2.4E-06 45.7 -7.0 128 51-178 72-215 (458)
86 COG4328 Predicted nuclease (RN 65.4 9.5 0.00021 31.5 3.8 34 39-74 2-35 (266)
87 cd05778 DNA_polB_zeta_exo inac 62.0 12 0.00027 30.5 4.0 65 114-183 162-230 (231)
88 PF00843 Arena_nucleocap: Aren 62.0 9.6 0.00021 34.4 3.5 131 39-178 373-526 (533)
89 PF04857 CAF1: CAF1 family rib 59.1 19 0.0004 29.9 4.7 94 87-184 147-261 (262)
90 COG2176 PolC DNA polymerase II 56.5 30 0.00065 35.3 6.1 130 37-190 420-586 (1444)
91 cd05776 DNA_polB_alpha_exo ina 50.1 19 0.00042 29.4 3.3 69 114-187 157-227 (234)
92 cd07027 RNAP_RPB11_like RPB11 46.8 42 0.00092 23.0 4.1 37 62-98 6-44 (83)
93 PF00169 PH: PH domain; Inter 45.7 83 0.0018 20.6 5.6 31 4-34 72-102 (104)
94 PRK01146 DNA-directed RNA poly 40.8 59 0.0013 22.4 4.1 35 64-98 10-46 (85)
95 cd06927 RNAP_L L subunit of Ar 38.9 67 0.0015 22.0 4.1 36 63-98 7-44 (83)
96 PRK06549 acetyl-CoA carboxylas 38.6 32 0.0007 25.8 2.7 19 1-19 2-20 (130)
97 cd07029 RNAP_I_III_AC19 AC19 s 35.7 61 0.0013 22.3 3.5 34 65-98 9-44 (85)
98 PF13289 SIR2_2: SIR2-like dom 35.1 30 0.00064 25.1 2.0 29 77-105 76-105 (143)
99 cd01246 PH_oxysterol_bp Oxyste 32.3 97 0.0021 20.3 4.1 29 4-32 61-89 (91)
100 cd06926 RNAP_II_RPB11 RPB11 su 31.6 1.4E+02 0.0029 20.9 4.8 34 65-98 17-52 (93)
101 PF02641 DUF190: Uncharacteriz 30.9 80 0.0017 22.2 3.6 39 8-46 60-99 (101)
102 PTZ00315 2'-phosphotransferase 30.5 3.2E+02 0.0069 25.9 8.2 91 80-189 136-254 (582)
103 PF00929 RNase_T: Exonuclease; 28.2 72 0.0016 23.0 3.2 81 81-183 76-164 (164)
104 cd01247 PH_GPBP Goodpasture an 27.5 1.8E+02 0.0039 19.9 4.9 29 4-32 61-89 (91)
105 smart00486 POLBc DNA polymeras 27.4 1.1E+02 0.0023 26.9 4.6 69 114-186 150-220 (471)
106 cd06404 PB1_aPKC PB1 domain is 27.4 2.1E+02 0.0046 19.7 5.6 47 3-50 2-48 (83)
107 PF00982 Glyco_transf_20: Glyc 26.6 85 0.0018 28.7 3.8 61 5-65 230-322 (474)
108 PLN02205 alpha,alpha-trehalose 26.3 1.8E+02 0.0039 28.7 6.2 64 4-67 291-387 (854)
109 KOG0304 mRNA deadenylase subun 26.1 2.5E+02 0.0054 23.2 6.0 82 85-188 138-237 (239)
110 COG5018 KapD Inhibitor of the 24.5 3.2E+02 0.0069 21.8 6.1 88 79-187 84-182 (210)
111 cd00821 PH Pleckstrin homology 24.4 1.8E+02 0.0038 18.2 4.3 29 4-32 66-94 (96)
112 KOG0083 GTPase Rab26/Rab37, sm 23.9 67 0.0015 24.6 2.2 31 61-99 7-37 (192)
113 TIGR00592 pol2 DNA polymerase 23.8 2.4E+02 0.0052 28.9 6.7 94 87-186 599-722 (1172)
114 KOG1882 Transcriptional regula 23.2 1.2E+02 0.0026 25.5 3.7 52 51-102 214-284 (293)
115 COG1993 PII-like signaling pro 22.5 2.9E+02 0.0063 20.1 5.2 27 12-38 68-94 (109)
116 PRK05641 putative acetyl-CoA c 22.2 91 0.002 24.0 2.7 19 1-19 22-40 (153)
117 smart00233 PH Pleckstrin homol 21.8 2.2E+02 0.0048 17.9 4.7 30 4-33 70-99 (102)
118 PRK05761 DNA polymerase I; Rev 21.8 5.2E+02 0.011 25.3 8.3 94 79-183 215-334 (787)
119 cd01260 PH_CNK Connector enhan 21.7 1.8E+02 0.0038 19.7 4.0 29 5-33 67-95 (96)
120 COG0417 PolB DNA polymerase el 21.6 7.7E+02 0.017 24.1 12.2 143 39-185 155-349 (792)
121 PF00181 Ribosomal_L2: Ribosom 20.6 1.6E+02 0.0035 19.7 3.4 34 39-72 34-67 (77)
122 cd03527 RuBisCO_small Ribulose 20.5 1.7E+02 0.0037 20.8 3.7 28 19-46 57-86 (99)
123 PF03633 Glyco_hydro_65C: Glyc 20.3 1.5E+02 0.0032 18.0 3.0 18 3-20 11-28 (54)
124 PF13656 RNA_pol_L_2: RNA poly 20.3 88 0.0019 21.0 2.1 22 77-98 14-36 (77)
No 1
>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=100.00 E-value=6.7e-41 Score=268.15 Aligned_cols=168 Identities=24% Similarity=0.410 Sum_probs=146.1
Q ss_pred EEEeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCC----CCCceeEEEeeeCCeEEEEeccccC-----CccHHHHHhh
Q 043928 15 VTVVDHAALIDDNVAALKALLKRQRVVGIDVKFNHR----CTKKAEMLILCAGNRCLIIQLCHLG-----QIPESLKKFL 85 (192)
Q Consensus 15 v~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~----~~~~~aliQl~~~~~~~l~~l~~~~-----~~p~~L~~~l 85 (192)
+.++++++++++++.++. ..+..+||||+||.|. ..+++||||||+++.|+|||+..++ .+|+.|+++|
T Consensus 1 ~~~i~~~~el~~~~~~~~--l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~ll 78 (193)
T cd06146 1 IHIVDSEEELEALLLALS--LEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKRLF 78 (193)
T ss_pred CeEecCHHHHHHHHHHHh--hccCCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHHHh
Confidence 368899999999999841 1257899999999987 2689999999999999999998764 4788999999
Q ss_pred cCCCeeEEEEeehhhHHHhhc-CCC------ccCcEeehHHHHHHHhCCC--------CcCcccHHHHHHHh-CcccCCC
Q 043928 86 ADETICFVGIEMNGKVDGLGR-CNL------RCKTAVELGHFAARVLKKP--------HISSFGLAKLAREV-GIHNSLA 149 (192)
Q Consensus 86 ~~~~i~kvG~~~~~D~~~L~~-~g~------~~~~~~Dl~~~a~~~~~~~--------~~~~~gL~~l~~~~-g~~l~~~ 149 (192)
+||+|+||||++++|+++|++ ||+ .++|++|++.+++...+.. .....||++||+.+ |.+++
T Consensus 79 ~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~-- 156 (193)
T cd06146 79 EDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLD-- 156 (193)
T ss_pred CCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcC--
Confidence 999999999999999999999 887 4789999999887543211 02468999999999 99999
Q ss_pred CCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 043928 150 SGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLS 188 (192)
Q Consensus 150 K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~ 188 (192)
|+.|+|||++||||++|+.|||.|||+++.||++|.+
T Consensus 157 --K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 157 --KSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred --cccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4679999999999999999999999999999999864
No 2
>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=100.00 E-value=5.7e-39 Score=251.03 Aligned_cols=164 Identities=32% Similarity=0.531 Sum_probs=147.6
Q ss_pred eCChHHHHHHHHHHHHhhcCCcEEEEeeeecCC----CCCceeEEEeeeCCeEEEEeccccCCccHHHHHhhcCCCeeEE
Q 043928 18 VDHAALIDDNVAALKALLKRQRVVGIDVKFNHR----CTKKAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICFV 93 (192)
Q Consensus 18 t~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~----~~~~~aliQl~~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kv 93 (192)
+++++.++++++.+. .+..+||||+||.|. ..+++|+||||+++.|+|||+.+++.+|+.|+++|++++|.||
T Consensus 1 ~~~~~~~~~~~~~~~---~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~~~~~~l~~ll~~~~i~kv 77 (170)
T cd06141 1 TDSAQDAEEAVKELL---GKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSILKV 77 (170)
T ss_pred CCCHHHHHHHHHHHh---cCCCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhhcccHHHHHHhcCCCeeEE
Confidence 467889999998886 256899999999997 3579999999999999999999888899999999999999999
Q ss_pred EEeehhhHHHhhc-CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHH
Q 043928 94 GIEMNGKVDGLGR-CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKF 171 (192)
Q Consensus 94 G~~~~~D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~Y 171 (192)
||++++|++.|.+ +|+.+.+++|++.++.. ++.. ....||+.|++.+ |.+++ |+|++++|||..||||++||+|
T Consensus 78 ~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~l-l~~~-~~~~~l~~l~~~~l~~~~~--k~k~~~~s~W~~rpLt~~qi~Y 153 (170)
T cd06141 78 GVGIKGDARKLARDFGIEVRGVVDLSHLAKR-VGPR-RKLVSLARLVEEVLGLPLS--KPKKVRCSNWEARPLSKEQILY 153 (170)
T ss_pred EeeeHHHHHHHHhHcCCCCCCeeeHHHHHHH-hCCC-cCCccHHHHHHHHcCcccC--CCCCcccCCCCCCCCCHHHHHH
Confidence 9999999999998 99999999999988764 4422 1346999999999 99999 9999999999999999999999
Q ss_pred HHHhHHHHHHHHHHHhc
Q 043928 172 AVHEAFAYYVIGDRVLS 188 (192)
Q Consensus 172 Aa~Da~~~~~i~~~L~~ 188 (192)
||.|||++++||++|..
T Consensus 154 Aa~Da~~~~~l~~~l~~ 170 (170)
T cd06141 154 AATDAYASLELYRKLLA 170 (170)
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 99999999999999863
No 3
>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=100.00 E-value=1.7e-38 Score=247.15 Aligned_cols=154 Identities=18% Similarity=0.265 Sum_probs=136.5
Q ss_pred HHHHHHHHHhhcCCcEEEEeeeecCC--CCCceeEEEeeeC-CeEEEEeccccCCccHHHHHhhcCCCeeEEEEeehhhH
Q 043928 25 DDNVAALKALLKRQRVVGIDVKFNHR--CTKKAEMLILCAG-NRCLIIQLCHLGQIPESLKKFLADETICFVGIEMNGKV 101 (192)
Q Consensus 25 ~~~i~~~~~~~~~~~vvG~D~Ew~~~--~~~~~aliQl~~~-~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~~~~D~ 101 (192)
+.+++++.. ..++||||+||.|. ..+++||||||++ +.|+|||+..++..|+.|+++|+|++|+||||++++|+
T Consensus 3 ~~~~~~l~~---~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~~~~~L~~lL~d~~i~Kvg~~~k~D~ 79 (161)
T cd06129 3 SSLCEDLSM---DGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDL 79 (161)
T ss_pred HHHHHHHhc---CCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCccCHHHHHHHhCCCCEEEEEeccHHHH
Confidence 344444431 57899999999997 4689999999999 89999999887767899999999999999999999999
Q ss_pred HHhhc-CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHH
Q 043928 102 DGLGR-CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAY 179 (192)
Q Consensus 102 ~~L~~-~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~ 179 (192)
++|.+ +|+.+.|++|++..+. .+|.+ .+.||++|++++ |.+++ |++|+|||+.||||++|++|||.|||++
T Consensus 80 ~~L~~~~gi~~~~~~D~~~aa~-ll~~~--~~~~L~~l~~~~lg~~l~----K~~~~s~W~~rpLt~~qi~YAa~Da~~l 152 (161)
T cd06129 80 WKLLRDFGEKLQRLFDTTIAAN-LKGLP--ERWSLASLVEHFLGKTLD----KSISCADWSYRPLTEDQKLYAAADVYAL 152 (161)
T ss_pred HHHHHHcCCCcccHhHHHHHHH-HhCCC--CCchHHHHHHHHhCCCCC----ccceeccCCCCCCCHHHHHHHHHHHHHH
Confidence 99998 9999999999988765 56644 256999999999 99998 6789999999999999999999999999
Q ss_pred HHHHHHHhc
Q 043928 180 YVIGDRVLS 188 (192)
Q Consensus 180 ~~i~~~L~~ 188 (192)
++||++|.+
T Consensus 153 ~~l~~~l~~ 161 (161)
T cd06129 153 LIIYTKLRN 161 (161)
T ss_pred HHHHHHHhC
Confidence 999999864
No 4
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=2.3e-32 Score=237.59 Aligned_cols=164 Identities=15% Similarity=0.232 Sum_probs=147.2
Q ss_pred EEEeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCC--CCCceeEEEeeeCCeEEEEeccccCCccHHHHHhhcCCCeeE
Q 043928 15 VTVVDHAALIDDNVAALKALLKRQRVVGIDVKFNHR--CTKKAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICF 92 (192)
Q Consensus 15 v~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~--~~~~~aliQl~~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~k 92 (192)
..++++++++.++++.+. ...++|+||||... ..+++|||||++++.++||++.....+ ..|.++|+|++|+|
T Consensus 3 ~~~I~t~~~L~~~~~~l~----~~~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~~~d~-~~L~~ll~~~~ivK 77 (373)
T PRK10829 3 YQMITTDDALASVCEAAR----AFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDW-SPFKALLRDPQVTK 77 (373)
T ss_pred cEEeCCHHHHHHHHHHHh----cCCeEEEecccccCccCCCceeEEEEecCCceEEEecCCccch-HHHHHHHcCCCeEE
Confidence 468999999999998864 56899999999987 567899999999999999998876543 67999999999999
Q ss_pred EEEeehhhHHHhhc-CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHH
Q 043928 93 VGIEMNGKVDGLGR-CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIK 170 (192)
Q Consensus 93 vG~~~~~D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~ 170 (192)
|+|+..+|++.|.+ +|+.+.++||++..+. .+|.+ .+.||+.|++++ |..++ |+.++|||++||||++|+.
T Consensus 78 V~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~-~lg~~--~~~gl~~Lv~~~lgv~ld----K~~~~sDW~~RPLs~~ql~ 150 (373)
T PRK10829 78 FLHAGSEDLEVFLNAFGELPQPLIDTQILAA-FCGRP--LSCGFASMVEEYTGVTLD----KSESRTDWLARPLSERQCE 150 (373)
T ss_pred EEeChHhHHHHHHHHcCCCcCCeeeHHHHHH-HcCCC--ccccHHHHHHHHhCCccC----cccccCCCCCCCCCHHHHH
Confidence 99999999999988 9999999999876665 77865 268999999999 99999 5668999999999999999
Q ss_pred HHHHhHHHHHHHHHHHhccc
Q 043928 171 FAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 171 YAa~Da~~~~~i~~~L~~~~ 190 (192)
|||.|+++++.||.+|.+.|
T Consensus 151 YAa~Dv~~L~~l~~~L~~~L 170 (373)
T PRK10829 151 YAAADVFYLLPIAAKLMAET 170 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999998765
No 5
>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=99.97 E-value=5.4e-31 Score=204.91 Aligned_cols=166 Identities=27% Similarity=0.429 Sum_probs=142.5
Q ss_pred EEeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCC----CCCceeEEEeeeCCeEEEEeccccCC--ccHHHHHhhcCCC
Q 043928 16 TVVDHAALIDDNVAALKALLKRQRVVGIDVKFNHR----CTKKAEMLILCAGNRCLIIQLCHLGQ--IPESLKKFLADET 89 (192)
Q Consensus 16 ~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~----~~~~~aliQl~~~~~~~l~~l~~~~~--~p~~L~~~l~~~~ 89 (192)
++++++++++++++.+. ..+++|||+||.+. ...++++||+|+++.|++++....+. +++.|+++|+||+
T Consensus 2 ~~v~~~~~l~~~~~~l~----~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~ 77 (176)
T PF01612_consen 2 QIVDTEEELEEAIKKLK----NAKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPN 77 (176)
T ss_dssp EEEHSHHHHHHHHHHHT----TTSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTT
T ss_pred EecCCHHHHHHHHHHHc----CCCeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCC
Confidence 57889999999999886 45799999999987 46899999999999999999876654 4789999999999
Q ss_pred eeEEEEeehhhHHHhhc-CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCC-cCCCCH
Q 043928 90 ICFVGIEMNGKVDGLGR-CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWS-ARAFSN 166 (192)
Q Consensus 90 i~kvG~~~~~D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~-~~~Ls~ 166 (192)
|.||||+++.|.+.|.+ +|+.+.|++|+ .++...++... ..||+.|+.++ | ... ++++.++++|. ++||++
T Consensus 78 i~kv~~n~~~D~~~L~~~~~i~~~~~~D~-~l~~~~l~~~~--~~~L~~L~~~~l~-~~~--~~~~~~~~~~~~~~~l~~ 151 (176)
T PF01612_consen 78 IIKVGHNAKFDLKWLYRSFGIDLKNVFDT-MLAAYLLDPTR--SYSLKDLAEEYLG-NID--LDKKEQMSDWRKARPLSE 151 (176)
T ss_dssp SEEEESSHHHHHHHHHHHHTS--SSEEEH-HHHHHHTTTST--TSSHHHHHHHHHS-EEE---GHCCTTSSTTTSSS-HH
T ss_pred ccEEEEEEechHHHHHHHhccccCCccch-hhhhhcccccc--cccHHHHHHHHhh-hcc--CcHHHhhccCCcCCCChH
Confidence 99999999999999999 99999999999 66665555331 38999999999 9 444 44778999999 899999
Q ss_pred HHHHHHHHhHHHHHHHHHHHhcccC
Q 043928 167 EQIKFAVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 167 ~Qi~YAa~Da~~~~~i~~~L~~~~~ 191 (192)
+|+.|||.||+++++||++|..+|.
T Consensus 152 ~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 152 EQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 9999999999999999999998763
No 6
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.97 E-value=3.6e-31 Score=212.47 Aligned_cols=152 Identities=17% Similarity=0.235 Sum_probs=129.9
Q ss_pred CCcEEEEeeeecCC-CCCceeEEEeeeC-CeEEEEeccccC--CccHHHHHhhcCCCeeEEEEeehhhHHHhhc-CCCcc
Q 043928 37 RQRVVGIDVKFNHR-CTKKAEMLILCAG-NRCLIIQLCHLG--QIPESLKKFLADETICFVGIEMNGKVDGLGR-CNLRC 111 (192)
Q Consensus 37 ~~~vvG~D~Ew~~~-~~~~~aliQl~~~-~~~~l~~l~~~~--~~p~~L~~~l~~~~i~kvG~~~~~D~~~L~~-~g~~~ 111 (192)
+.++||||+||... ..+++||||+|++ +.++|||+..++ .++..|+++|++++|.||||++++|.+.|.+ +|+.+
T Consensus 9 ~~~~i~~D~E~~~~~~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~ 88 (197)
T cd06148 9 KQKVIGLDCEGVNLGRKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGIKL 88 (197)
T ss_pred hCCEEEEEcccccCCCCCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHHhcCccc
Confidence 57899999999866 5679999999999 999999998775 3578999999999999999999999999987 99999
Q ss_pred CcEeehHHHHHHHhCCC------CcCcccHHHHHHHh-CcccCCCCC------CCcccCCCCcCCCCHHHHHHHHHhHHH
Q 043928 112 KTAVELGHFAARVLKKP------HISSFGLAKLAREV-GIHNSLASG------FNGYAPSWSARAFSNEQIKFAVHEAFA 178 (192)
Q Consensus 112 ~~~~Dl~~~a~~~~~~~------~~~~~gL~~l~~~~-g~~l~~~K~------k~~~~S~W~~~~Ls~~Qi~YAa~Da~~ 178 (192)
.|++|++..+. .++.. .....||+.+++++ |.+++ |. ++.++|||.+||||++|+.|||.||++
T Consensus 89 ~~~fDt~iA~~-lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~--k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~ 165 (197)
T cd06148 89 NNVFDTQVADA-LLQEQETGGFNPDRVISLVQLLDKYLYISIS--LKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLC 165 (197)
T ss_pred cceeeHHHHHH-HHHHHhcCCccccccccHHHHHHHhhCCChH--HHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHh
Confidence 99999875443 33211 01246999999999 99986 32 356889999999999999999999999
Q ss_pred HHHHHHHHhcccC
Q 043928 179 YYVIGDRVLSSLD 191 (192)
Q Consensus 179 ~~~i~~~L~~~~~ 191 (192)
++++|..|.+.|-
T Consensus 166 Ll~l~~~l~~~l~ 178 (197)
T cd06148 166 LLPLYYAMLDALI 178 (197)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999998763
No 7
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2.4e-29 Score=215.04 Aligned_cols=159 Identities=19% Similarity=0.198 Sum_probs=139.3
Q ss_pred HHHHHHHHHHHHhhcCCcEEEEeeeecCC--CCCceeEEEeeeCCeEEEEeccccCCccHHHHHhhcCCCeeEEEEeehh
Q 043928 22 ALIDDNVAALKALLKRQRVVGIDVKFNHR--CTKKAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICFVGIEMNG 99 (192)
Q Consensus 22 ~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~--~~~~~aliQl~~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~~~~ 99 (192)
..++.+..... ....|++|||+... ..+++||||+|.++.+.+|++.....-.+.|..+|.|++|+||.|..++
T Consensus 5 ~~l~~~~~~~~----~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~~lIdpl~~~~d~~~l~~Ll~d~~v~KIfHaa~~ 80 (361)
T COG0349 5 DLLAAACALLR----GSKAIAIDTEFMRLRTYYPRLCLIQISDGEGASLIDPLAGILDLPPLVALLADPNVVKIFHAARF 80 (361)
T ss_pred hHHHHHHHHhc----CCCceEEecccccccccCCceEEEEEecCCCceEecccccccccchHHHHhcCCceeeeeccccc
Confidence 34444454443 45799999999987 7899999999999999999998743334689999999999999999999
Q ss_pred hHHHhhc-CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHH
Q 043928 100 KVDGLGR-CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAF 177 (192)
Q Consensus 100 D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~ 177 (192)
|+..|.+ ||+.+.++||.+..++ ..|.+. +.||+.||+++ |+.++ |+.|.|||.+||||++|+.|||.|++
T Consensus 81 DL~~l~~~~g~~p~plfdTqiAa~-l~g~~~--~~gl~~Lv~~ll~v~ld----K~~q~SDW~~RPLs~~Ql~YAa~DV~ 153 (361)
T COG0349 81 DLEVLLNLFGLLPTPLFDTQIAAK-LAGFGT--SHGLADLVEELLGVELD----KSEQRSDWLARPLSEAQLEYAAADVE 153 (361)
T ss_pred cHHHHHHhcCCCCCchhHHHHHHH-HhCCcc--cccHHHHHHHHhCCccc----ccccccccccCCCCHHHHHHHHHHHH
Confidence 9999999 9999999999776555 778763 89999999999 99999 67799999999999999999999999
Q ss_pred HHHHHHHHHhcccC
Q 043928 178 AYYVIGDRVLSSLD 191 (192)
Q Consensus 178 ~~~~i~~~L~~~~~ 191 (192)
++++||.+|.+.|.
T Consensus 154 yL~~l~~~L~~~L~ 167 (361)
T COG0349 154 YLLPLYDKLTEELA 167 (361)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999988764
No 8
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=99.96 E-value=2.9e-29 Score=210.24 Aligned_cols=180 Identities=27% Similarity=0.410 Sum_probs=159.5
Q ss_pred cceEEEEcCcEEEEEEeCChHHHHHHHHHHHHhh----cCCcEEEEeeeecCC---------------------------
Q 043928 2 GKYELDIQGNNMKVTVVDHAALIDDNVAALKALL----KRQRVVGIDVKFNHR--------------------------- 50 (192)
Q Consensus 2 ~~y~v~~~g~~i~v~vt~~~~~~~~~i~~~~~~~----~~~~vvG~D~Ew~~~--------------------------- 50 (192)
.+|.|.|+|+...|+++.++..+.+|+...+... .++.+||++++|+|.
T Consensus 15 ~~~~vd~~~~~~~Vtvt~~~svi~~~i~d~~~~~~~~~s~p~vvg~~vqw~p~~~~~~~~~~~~~~~~~~~a~~~~~~~~ 94 (319)
T KOG4373|consen 15 QKYSVDFFGEELIVTVTPDSSVISRWIHDVRFLSRNFSSDPLVVGRGVQWTPPTLTPDQTIYAARDLQISVARFLHLLGS 94 (319)
T ss_pred cceeeeecccceEEEEccCcccchhhhhhhhhcccCcccCCcccCcCcccCCCCCCccccccccchhccccccccccccC
Confidence 4789999999999999999999999999998552 346899999999986
Q ss_pred --------------------------------------------------CCCceeEEEeeeC-CeEEEEeccccCCccH
Q 043928 51 --------------------------------------------------CTKKAEMLILCAG-NRCLIIQLCHLGQIPE 79 (192)
Q Consensus 51 --------------------------------------------------~~~~~aliQl~~~-~~~~l~~l~~~~~~p~ 79 (192)
..++++.+|||++ +.|+|+|+.+.+.+|.
T Consensus 95 ~~~~~~~kl~~~~d~~a~~~~~~~~~~~~~s~~~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~en~C~I~ql~~~~~IP~ 174 (319)
T KOG4373|consen 95 SFKHKRQKLGYGSDARASPYIDNSLEIADDSDPPFVCYRREAQPYLDMGRSDPPPDTLQLCVGENRCLIIQLIHCKRIPH 174 (319)
T ss_pred cccccccccccccccccccccccccccccccCCcceeecccccccccccccCCCcchhhhhhcccceeeEEeeccccchH
Confidence 2457889999999 6999999999999999
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhc--CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh----CcccCCCCCCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGR--CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV----GIHNSLASGFN 153 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~--~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~----g~~l~~~K~k~ 153 (192)
.|+.||+|++++|||+++.+|..||++ |++.+....||+.++...+|. .+.+.|.-.+++.. |..+. ++++
T Consensus 175 ~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g~-~~~~~s~e~i~~~~~~~~~~~v~--l~~~ 251 (319)
T KOG4373|consen 175 ELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLGG-SMPNDSFEEIVSETLGYYGKDVR--LDKE 251 (319)
T ss_pred HHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhhcc-CccCccHHHHHHHHhhccccccc--cChh
Confidence 999999999999999999999999998 999999999999999988886 34455655665555 44466 8899
Q ss_pred cccCCCCcCCCCHHHHHHHHHhHHHHHHHHH
Q 043928 154 GYAPSWSARAFSNEQIKFAVHEAFAYYVIGD 184 (192)
Q Consensus 154 ~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~ 184 (192)
+++|||+-.+|+.+|+.||++|+|++.++|.
T Consensus 252 i~msdw~~~~Ls~~Ql~~asidvy~c~~lg~ 282 (319)
T KOG4373|consen 252 IRMSDWSVYPLSDDQLLQASIDVYVCHKLGV 282 (319)
T ss_pred cccccceeeeccHHHHHHHHhHHHHHHHHHH
Confidence 9999999999999999999999999999994
No 9
>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=99.96 E-value=1.2e-27 Score=208.23 Aligned_cols=163 Identities=17% Similarity=0.222 Sum_probs=142.2
Q ss_pred EeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCC--CCCceeEEEeeeCCeEEEEeccccCCccHHHHHhhcCCCeeEEE
Q 043928 17 VVDHAALIDDNVAALKALLKRQRVVGIDVKFNHR--CTKKAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICFVG 94 (192)
Q Consensus 17 vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~--~~~~~aliQl~~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG 94 (192)
++++++++..+++.+. ...+|||||||... ..+++|||||++++.|+||++..... .+.|.++|+|++|+|||
T Consensus 1 ~I~t~~~l~~~~~~l~----~~~~ia~DtE~~~~~~y~~~l~LiQia~~~~~~liD~~~~~~-~~~L~~lL~d~~i~KV~ 75 (367)
T TIGR01388 1 WITTDDELATVCEAVR----TFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIID-WSPLKELLRDESVVKVL 75 (367)
T ss_pred CcCCHHHHHHHHHHHh----cCCEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCccc-HHHHHHHHCCCCceEEE
Confidence 3678899999998886 45899999999986 56889999999999999999876644 46899999999999999
Q ss_pred EeehhhHHHhhc-CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHHH
Q 043928 95 IEMNGKVDGLGR-CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKFA 172 (192)
Q Consensus 95 ~~~~~D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YA 172 (192)
|++++|+..|.+ +|..+.+++|++..+. .+|.. .+.||+.|++++ |..++ | ..++|||..+||+++|+.||
T Consensus 76 h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~-lL~~~--~~~~l~~Lv~~~Lg~~l~--K--~~~~sdW~~rPL~~~q~~YA 148 (367)
T TIGR01388 76 HAASEDLEVFLNLFGELPQPLFDTQIAAA-FCGFG--MSMGYAKLVQEVLGVELD--K--SESRTDWLARPLTDAQLEYA 148 (367)
T ss_pred eecHHHHHHHHHHhCCCCCCcccHHHHHH-HhCCC--CCccHHHHHHHHcCCCCC--c--ccccccCCCCCCCHHHHHHH
Confidence 999999999998 8888899999876554 66643 246999999999 99999 5 35789999999999999999
Q ss_pred HHhHHHHHHHHHHHhcccC
Q 043928 173 VHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 173 a~Da~~~~~i~~~L~~~~~ 191 (192)
|.||++++.+|.+|.++|.
T Consensus 149 a~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 149 AADVTYLLPLYAKLMERLE 167 (367)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 9999999999999988763
No 10
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.91 E-value=1.6e-24 Score=193.20 Aligned_cols=171 Identities=21% Similarity=0.311 Sum_probs=141.4
Q ss_pred EEEEEEeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCC---CCCceeEEEeeeCCeEEEEeccccCCccH-----HHHH
Q 043928 12 NMKVTVVDHAALIDDNVAALKALLKRQRVVGIDVKFNHR---CTKKAEMLILCAGNRCLIIQLCHLGQIPE-----SLKK 83 (192)
Q Consensus 12 ~i~v~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~---~~~~~aliQl~~~~~~~l~~l~~~~~~p~-----~L~~ 83 (192)
.-.+.++.++.+++..+ +.+..++..+||+|+||.|+ .++++|++|++.++.++|+++......+. .+..
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 VESIGMVGNEKELRDLL--LESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQ 466 (617)
T ss_pred ccceeeeCCHHHHHHHH--HHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHH
Confidence 44578899999999887 22222334899999999998 58999999999999999999987766665 4689
Q ss_pred hhcCCCeeEEEEeehhhHHHhhc------CCCc---cCcEeehHHHHHHHhCCC------CcCcccHHHHHHHh-CcccC
Q 043928 84 FLADETICFVGIEMNGKVDGLGR------CNLR---CKTAVELGHFAARVLKKP------HISSFGLAKLAREV-GIHNS 147 (192)
Q Consensus 84 ~l~~~~i~kvG~~~~~D~~~L~~------~g~~---~~~~~Dl~~~a~~~~~~~------~~~~~gL~~l~~~~-g~~l~ 147 (192)
+|+++++.||||++.+|+..|+. +.+. +++++++..++....+.+ .....||+.|+..+ |..++
T Consensus 467 if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~ln 546 (617)
T KOG2207|consen 467 IFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLN 546 (617)
T ss_pred HccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhcc
Confidence 99999999999999999999993 3333 346677777776654432 12367899999999 99999
Q ss_pred CCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 043928 148 LASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLS 188 (192)
Q Consensus 148 ~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~ 188 (192)
|+.|||||.+|||+..||.|||+||.++.+||.++.+
T Consensus 547 ----KteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~ 583 (617)
T KOG2207|consen 547 ----KTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCS 583 (617)
T ss_pred ----cccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHh
Confidence 6779999999999999999999999999999999875
No 11
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.86 E-value=2.7e-20 Score=143.56 Aligned_cols=166 Identities=25% Similarity=0.311 Sum_probs=131.5
Q ss_pred EEeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCCC--CCceeEEEeeeCC-eEEEEeccccCCccHHHHHhhcCCCeeE
Q 043928 16 TVVDHAALIDDNVAALKALLKRQRVVGIDVKFNHRC--TKKAEMLILCAGN-RCLIIQLCHLGQIPESLKKFLADETICF 92 (192)
Q Consensus 16 ~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~~--~~~~aliQl~~~~-~~~l~~l~~~~~~p~~L~~~l~~~~i~k 92 (192)
.++++++.++.|++.+.. ....+|+|+||.+.. ..+++.+|+|+++ .|++++....+..++.|+++|+++++.|
T Consensus 2 ~~i~~~~~~~~~~~~~~~---~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~k 78 (172)
T smart00474 2 RVVTDSETLEELLEKLRA---AGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITK 78 (172)
T ss_pred EEecCHHHHHHHHHHHHh---cCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccchhhHHHHHHHhcCCCceE
Confidence 356666888888765520 346999999998763 6789999999744 6777654333344667999999999999
Q ss_pred EEEeehhhHHHhhcCCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHH
Q 043928 93 VGIEMNGKVDGLGRCNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKF 171 (192)
Q Consensus 93 vG~~~~~D~~~L~~~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~Y 171 (192)
+||+++.|...|.++|+.+.+++|++..+.. +. |.....||+.+++.+ |..++ + ..+.++|..+||.++|+.|
T Consensus 79 v~~d~k~~~~~L~~~gi~~~~~~D~~laayl-l~-p~~~~~~l~~l~~~~l~~~~~--~--~~~~~~~~~~~l~~~~~~y 152 (172)
T smart00474 79 VGHNAKFDLHVLARFGIELENIFDTMLAAYL-LL-GGPSKHGLATLLKEYLGVELD--K--EEQKSDWGARPLSEEQLQY 152 (172)
T ss_pred EEechHHHHHHHHHCCCcccchhHHHHHHHH-Hc-CCCCcCCHHHHHHHHhCCCCC--c--ccCccccccCCCCHHHHHH
Confidence 9999999999997799999998998766542 22 322335999999999 98876 3 4456799888999999999
Q ss_pred HHHhHHHHHHHHHHHhccc
Q 043928 172 AVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 172 Aa~Da~~~~~i~~~L~~~~ 190 (192)
||.||+++++++..|.++|
T Consensus 153 a~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 153 AAEDADALLRLYEKLEKEL 171 (172)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 9999999999999998875
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=99.86 E-value=3.9e-20 Score=144.56 Aligned_cols=147 Identities=21% Similarity=0.295 Sum_probs=122.9
Q ss_pred CCcEEEEeeeecCCC--CCceeEEEeeeCCeEEEEeccccCCccHHHHHhhcCCCeeEEEEeehhhHHHhhc-CCCccCc
Q 043928 37 RQRVVGIDVKFNHRC--TKKAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICFVGIEMNGKVDGLGR-CNLRCKT 113 (192)
Q Consensus 37 ~~~vvG~D~Ew~~~~--~~~~aliQl~~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~~~~D~~~L~~-~g~~~~~ 113 (192)
....+|+|+||.+.. ..+++.+|+|+++.|++|++... ..++.|+.+|+|+++.|+||+++.|.+.|.+ +|+..++
T Consensus 11 ~~~~l~~~~e~~~~~~~~~~~~~i~l~~~~~~~~i~~~~~-~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~ 89 (178)
T cd06142 11 SAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI-GDLSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQN 89 (178)
T ss_pred cCCeEEEECCccCCCcCCCceEEEEEeeCCCEEEEeCCCc-ccHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCC
Confidence 346999999998763 67899999999966999986544 3667799999999999999999999999988 7999777
Q ss_pred EeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcccC
Q 043928 114 AVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 114 ~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~~ 191 (192)
++|+... ...++ |.. +.||+.+++++ |..+. + +..+++|.++||+.+|+.|||.||++++.++..|.++|.
T Consensus 90 ~~D~~la-ayLl~-p~~-~~~l~~l~~~~l~~~~~--~--~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~ 161 (178)
T cd06142 90 LFDTQIA-ARLLG-LGD-SVGLAALVEELLGVELD--K--GEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELE 161 (178)
T ss_pred cccHHHH-HHHhC-CCc-cccHHHHHHHHhCCCCC--c--ccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 8998654 43555 422 35999999999 99877 4 237799999999999999999999999999999988763
No 13
>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=99.75 E-value=3.1e-17 Score=124.17 Aligned_cols=145 Identities=24% Similarity=0.187 Sum_probs=111.3
Q ss_pred EEEEeeeecCCC--CCceeEEEeeeCCeEEEEeccc-cCCccHHHHHhhcCCCeeEEEEeehhhHHHhhc-CCCccCcEe
Q 043928 40 VVGIDVKFNHRC--TKKAEMLILCAGNRCLIIQLCH-LGQIPESLKKFLADETICFVGIEMNGKVDGLGR-CNLRCKTAV 115 (192)
Q Consensus 40 vvG~D~Ew~~~~--~~~~aliQl~~~~~~~l~~l~~-~~~~p~~L~~~l~~~~i~kvG~~~~~D~~~L~~-~g~~~~~~~ 115 (192)
.+|+|+||.+.. ..+++.+|+|+++.++.+.... ....++.|+++|+++++.||||+++.|...|.+ ++..+.+++
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~ 81 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIF 81 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcc
Confidence 689999998763 6789999999975455554432 123566799999999999999999999999988 555567889
Q ss_pred ehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCC----cCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 116 ELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWS----ARAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 116 Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~----~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
|+...+. .++ |...+.||+.|++++ |..+. +.. +.++|. .++|+.+|+.||+.||+++++++..|.+++
T Consensus 82 D~~~~ay-ll~-~~~~~~~l~~l~~~~l~~~~~--~~~--~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~~ 155 (155)
T cd00007 82 DTMLAAY-LLN-PGEGSHSLDDLAKEYLGIELD--KDE--QIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEEL 155 (155)
T ss_pred cHHHHHH-HhC-CCCCcCCHHHHHHHHcCCCCc--cHH--HHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhhC
Confidence 9866654 444 322135999999999 98865 311 234442 578999999999999999999999998753
No 14
>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=99.74 E-value=5.7e-17 Score=122.99 Aligned_cols=144 Identities=17% Similarity=0.112 Sum_probs=111.6
Q ss_pred EEEEeeeecCCC--CCceeEEEeeeCCe-EEEEeccccCCccHHHHHhhcCCCeeEEEEeehhhHHHhhcCCCc-cCcEe
Q 043928 40 VVGIDVKFNHRC--TKKAEMLILCAGNR-CLIIQLCHLGQIPESLKKFLADETICFVGIEMNGKVDGLGRCNLR-CKTAV 115 (192)
Q Consensus 40 vvG~D~Ew~~~~--~~~~aliQl~~~~~-~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~~~~D~~~L~~~g~~-~~~~~ 115 (192)
++|+|+||.+.. ..+++.+|+|+++. ++++++...+..+..|+++|+|+++.|+||+++.|...|.+.|+. ..+++
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~~~~~ 80 (150)
T cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAF 80 (150)
T ss_pred CEEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCcccCHHHHHHHhcCCCCceeeecHHHHHHHHHHcCCccCCcch
Confidence 589999998763 68899999999854 888886542213567999999999999999999999999875554 44679
Q ss_pred ehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 043928 116 ELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVL 187 (192)
Q Consensus 116 Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~ 187 (192)
|+...+- .++ |...+.+|+.|++++ |..+. +.++...++|..++++.+|+.||+.||++++.++..|.
T Consensus 81 D~~laay-Ll~-p~~~~~~l~~l~~~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 81 DTMLEAY-ILN-SVAGRWDMDSLVERWLGHKLI--KFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred hHHHHHH-HhC-CCCCCCCHHHHHHHHhCCCcc--cHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9876654 444 422135999999999 99865 31223334596678999999999999999999999875
No 15
>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=99.71 E-value=7.9e-16 Score=122.62 Aligned_cols=164 Identities=20% Similarity=0.231 Sum_probs=128.4
Q ss_pred EEeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCCC--CCceeEEEeeeCCeEEEEeccccCCccHHHHHhhcCCCeeEE
Q 043928 16 TVVDHAALIDDNVAALKALLKRQRVVGIDVKFNHRC--TKKAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICFV 93 (192)
Q Consensus 16 ~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~~--~~~~aliQl~~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kv 93 (192)
.++.+++.++.|++.+. ...++++|+|..+.. ..+++.+|+++++.+++|++.......+.|+++|+++++.|+
T Consensus 6 ~~i~~~~~l~~~~~~l~----~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~l~~~~~~~~L~~~L~~~~i~kv 81 (192)
T cd06147 6 TFVDTEEKLEELVEKLK----NCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILKV 81 (192)
T ss_pred EEECCHHHHHHHHHHHh----cCCeEEEEeEecCCccCCCceEEEEEecCCCcEEEEecccccchHHHHHHhcCCCceEE
Confidence 34445577888875542 235999999876543 568899999998877777632222234569999999999999
Q ss_pred EEeehhhHHHhhc-CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHH
Q 043928 94 GIEMNGKVDGLGR-CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKF 171 (192)
Q Consensus 94 G~~~~~D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~Y 171 (192)
||+++.|...|.+ +|+.+.+.+|+...+- .++ |. +. +|+.|++++ |..+. | +.+.+||+.+||+.+|..|
T Consensus 82 ~~d~K~~~~~L~~~~gi~~~~~fD~~laaY-LL~-p~-~~-~l~~l~~~yl~~~~~--k--~~~~~~~~~~~l~~~~~~y 153 (192)
T cd06147 82 FHGADSDIIWLQRDFGLYVVNLFDTGQAAR-VLN-LP-RH-SLAYLLQKYCNVDAD--K--KYQLADWRIRPLPEEMIKY 153 (192)
T ss_pred EechHHHHHHHHHHhCCCcCchHHHHHHHH-HhC-CC-cc-cHHHHHHHHhCCCcc--h--hhhccccccCCCCHHHHHH
Confidence 9999999999984 8998888899866553 455 43 34 999999999 98875 5 3567889888999999999
Q ss_pred HHHhHHHHHHHHHHHhcccC
Q 043928 172 AVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 172 Aa~Da~~~~~i~~~L~~~~~ 191 (192)
|+.||.+++.++..|.++|.
T Consensus 154 ~a~~a~~l~~L~~~L~~~L~ 173 (192)
T cd06147 154 AREDTHYLLYIYDRLRNELL 173 (192)
T ss_pred HHhhHHHHHHHHHHHHHHHH
Confidence 99999999999999988764
No 16
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.66 E-value=1.5e-16 Score=142.14 Aligned_cols=161 Identities=16% Similarity=0.165 Sum_probs=135.5
Q ss_pred EEeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCC--CCCceeEEEeeeCCeEEEEeccccC-CccHHHHHhhcCCCeeE
Q 043928 16 TVVDHAALIDDNVAALKALLKRQRVVGIDVKFNHR--CTKKAEMLILCAGNRCLIIQLCHLG-QIPESLKKFLADETICF 92 (192)
Q Consensus 16 ~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~--~~~~~aliQl~~~~~~~l~~l~~~~-~~p~~L~~~l~~~~i~k 92 (192)
+.+++..+++...+.+. ....+++|.|.... .-+-.||+|++|...=+||+....- .+ ..|+..|+||+|+|
T Consensus 194 ~~I~t~~el~~l~~~l~----~~~Efavdlehhsyrsf~gltclmqISTr~ed~iIDt~~l~~~i-~~l~e~fsdp~ivk 268 (687)
T KOG2206|consen 194 VWICTLGELEALPEILD----SVIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKLRDHI-GILNEVFSDPGIVK 268 (687)
T ss_pred eeeechHHHHHHHHHHh----hhhhhhhhccccchhhhcCceeEEEeeccchhheehhHHHHHHH-HHhhhhccCCCeEE
Confidence 34555555555544443 23577889997765 5678899999999999999976542 33 37899999999999
Q ss_pred EEEeehhhHHHhhc-CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHH
Q 043928 93 VGIEMNGKVDGLGR-CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIK 170 (192)
Q Consensus 93 vG~~~~~D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~ 170 (192)
|.||.-.|+-.|.+ ||+.+-|.+|..... +.+|.| +.||+.|.+.+ |+-.+ |+.|..||..|||+++++.
T Consensus 269 vfhgaD~diiwlqrdfgiyvvnLfdt~~a~-r~L~~~---r~sL~~ll~~~~~v~~n----k~yqladwR~rpLp~~Mv~ 340 (687)
T KOG2206|consen 269 VFHGADTDIIWLQRDFGIYVVNLFDTIQAS-RLLGLP---RPSLAYLLECVCGVLTN----KKYQLADWRIRPLPEEMVR 340 (687)
T ss_pred EEecCccchhhhhccceEEEEechhhHHHH-HHhCCC---cccHHHHHHHHHhhhhh----hhhhhchhccccCcHHHHH
Confidence 99999999999999 999999999976654 478887 89999999999 99988 7889999999999999999
Q ss_pred HHHHhHHHHHHHHHHHhcc
Q 043928 171 FAVHEAFAYYVIGDRVLSS 189 (192)
Q Consensus 171 YAa~Da~~~~~i~~~L~~~ 189 (192)
||=.|+.+++.||+.|...
T Consensus 341 yar~dthyllyiyD~lr~e 359 (687)
T KOG2206|consen 341 YAREDTHYLLYIYDVLRKE 359 (687)
T ss_pred HHhhcchhHHHHHHHHHHH
Confidence 9999999999999998743
No 17
>PRK05755 DNA polymerase I; Provisional
Probab=99.52 E-value=3.9e-13 Score=128.82 Aligned_cols=165 Identities=18% Similarity=0.191 Sum_probs=127.8
Q ss_pred EEEeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCC--CCCceeEEEeeeCCe-EEEEeccccC-CccHHHHHhhcCCCe
Q 043928 15 VTVVDHAALIDDNVAALKALLKRQRVVGIDVKFNHR--CTKKAEMLILCAGNR-CLIIQLCHLG-QIPESLKKFLADETI 90 (192)
Q Consensus 15 v~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~--~~~~~aliQl~~~~~-~~l~~l~~~~-~~p~~L~~~l~~~~i 90 (192)
..++.+++.+..|++.+. ...+++||+|.++. ...+++.||+|+++. ++++.+.+.. ...+.|.++|+++.+
T Consensus 296 ~~~I~~~~~L~~~l~~l~----~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~v 371 (880)
T PRK05755 296 YETILDEEELEAWLAKLK----AAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPAI 371 (880)
T ss_pred eEEeCCHHHHHHHHHHhh----ccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCCC
Confidence 456778899999987775 35799999999876 578899999999986 7888764422 233578999999999
Q ss_pred eEEEEeehhhHHHhhcCCCcc-CcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCC---CCCcccCCCCcCCCC
Q 043928 91 CFVGIEMNGKVDGLGRCNLRC-KTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLAS---GFNGYAPSWSARAFS 165 (192)
Q Consensus 91 ~kvG~~~~~D~~~L~~~g~~~-~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K---~k~~~~S~W~~~~Ls 165 (192)
.||+|+++.|+..|.++|+.+ .+++|....+. .++ |.. ..||+.|++++ |..+...+ .+.. +|+..|+
T Consensus 372 ~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~-Ll~-~~~-~~~L~~L~~~ylg~~~~~~~~~~gk~~---~~~~~pl- 444 (880)
T PRK05755 372 KKVGQNLKYDLHVLARYGIELRGIAFDTMLASY-LLD-PGR-RHGLDSLAERYLGHKTISFEEVAGKQL---TFAQVDL- 444 (880)
T ss_pred cEEEeccHhHHHHHHhCCCCcCCCcccHHHHHH-HcC-CCC-CCCHHHHHHHHhCCCccchHHhcCCCC---CccccCH-
Confidence 999999999999998888775 57899766543 444 433 38999999999 98853101 1233 3444477
Q ss_pred HHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 166 NEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 166 ~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
+.|.+||+.|+.++..||.+|.+.|
T Consensus 445 e~~~~YAa~Dv~~~~~L~~~L~~~L 469 (880)
T PRK05755 445 EEAAEYAAEDADVTLRLHEVLKPKL 469 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999999999999998876
No 18
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.34 E-value=5.5e-12 Score=115.47 Aligned_cols=140 Identities=14% Similarity=0.041 Sum_probs=110.6
Q ss_pred EEeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCCCCCceeEEEeeeCCeEEEEeccccCCccHHHHHhhcCCCeeEEEE
Q 043928 16 TVVDHAALIDDNVAALKALLKRQRVVGIDVKFNHRCTKKAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICFVGI 95 (192)
Q Consensus 16 ~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~~~~~~aliQl~~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~ 95 (192)
.++.+++.+..++..+. ...++++|+|+.+... .++++|++.++.++|++.... + ..+
T Consensus 4 ~~I~~~~~l~~~~~~l~----~~~~~a~DtEf~r~~t-~l~liQ~~~~~~~~liDpl~~--l----~~~----------- 61 (553)
T PRK14975 4 KVILAPEELGAALERLS----PAGVVAGDTETTGDDA-AAAAAQEGEEEPRWVWASTAA--L----YPR----------- 61 (553)
T ss_pred eEEeccchhHHHHHHhc----cCCceeCCccccCCcc-hhheeeecCCCceEEECchHH--h----HHH-----------
Confidence 46777788888887775 4689999999998633 899999999999999995431 2 111
Q ss_pred eehhhHHHhhcCCCccCcEeehHHHHHHHhCCCC-cCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHHHH
Q 043928 96 EMNGKVDGLGRCNLRCKTAVELGHFAARVLKKPH-ISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKFAV 173 (192)
Q Consensus 96 ~~~~D~~~L~~~g~~~~~~~Dl~~~a~~~~~~~~-~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa 173 (192)
|.++|+.+.+++|++-.+. .++... ..+.|++.+++.+ |..++ | ..+.|||. +||+++|+.|||
T Consensus 62 --------L~~~Gv~~~~~fDT~LAa~-lL~~~~~~~~~~l~~la~~~l~~~l~--k--~~~~sdw~-rpls~~q~~YAa 127 (553)
T PRK14975 62 --------LLAAGVRVERCHDLMLASQ-LLLGSEGRAGSSLSAAAARALGEGLD--K--PPQTSALS-DPPDEEQLLYAA 127 (553)
T ss_pred --------HHHCCCccCCCchHHHHHH-HcCCCCCcCCCCHHHHHHHHhCCCCC--C--hhhhcccc-ccchHHHHHHHH
Confidence 4447888889999765544 666431 0157999999999 99999 5 34579997 899999999999
Q ss_pred HhHHHHHHHHHHHhcccC
Q 043928 174 HEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 174 ~Da~~~~~i~~~L~~~~~ 191 (192)
.|+.++..+|..|.++|.
T Consensus 128 ~Dv~~l~~L~~~L~~qL~ 145 (553)
T PRK14975 128 ADADVLLELYAVLADQLN 145 (553)
T ss_pred HHhHHHHHHHHHHHHHHH
Confidence 999999999999988763
No 19
>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=99.25 E-value=2.8e-10 Score=89.67 Aligned_cols=151 Identities=17% Similarity=0.188 Sum_probs=107.8
Q ss_pred CCcEEEEeeeecCC--CCCceeEEEeeeCCe-EEEEecccc------C--CccHHHHHhhcCCCeeEEEEeehhhHHHhh
Q 043928 37 RQRVVGIDVKFNHR--CTKKAEMLILCAGNR-CLIIQLCHL------G--QIPESLKKFLADETICFVGIEMNGKVDGLG 105 (192)
Q Consensus 37 ~~~vvG~D~Ew~~~--~~~~~aliQl~~~~~-~~l~~l~~~------~--~~p~~L~~~l~~~~i~kvG~~~~~D~~~L~ 105 (192)
+...+++|+|.... ...++..+++|.++. .+.+.+.+. . ...+.|+++|++..+.+|||+++.|...|.
T Consensus 4 ~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l~ 83 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVLA 83 (193)
T ss_pred cCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHHHH
Confidence 45789999987654 257888899998764 555544321 1 122348899999999999999999999998
Q ss_pred cCCCccC-cEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCC-CC--CCCcccCCCCcCCCCHHHHHHHHHhHHHHH
Q 043928 106 RCNLRCK-TAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSL-AS--GFNGYAPSWSARAFSNEQIKFAVHEAFAYY 180 (192)
Q Consensus 106 ~~g~~~~-~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~-~K--~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~ 180 (192)
++|+.+. .++|+..++. .+ .|.....||.++++++ |..... .+ .+..+..+|...|+ .++.+||+.||.+++
T Consensus 84 ~~gi~~~~~~~Dt~l~a~-ll-~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~ 160 (193)
T cd06139 84 NHGIELRGPAFDTMLASY-LL-NPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADITL 160 (193)
T ss_pred HCCCCCCCCcccHHHHHH-Hh-CCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHHHHHHHHH
Confidence 8887765 4588766654 33 3433246999999999 876320 00 11124456765555 779999999999999
Q ss_pred HHHHHHhccc
Q 043928 181 VIGDRVLSSL 190 (192)
Q Consensus 181 ~i~~~L~~~~ 190 (192)
.++..|.+.+
T Consensus 161 ~l~~~l~~~l 170 (193)
T cd06139 161 RLYELLKPKL 170 (193)
T ss_pred HHHHHHHHHH
Confidence 9999998776
No 20
>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=99.25 E-value=1.1e-10 Score=91.35 Aligned_cols=147 Identities=23% Similarity=0.163 Sum_probs=106.9
Q ss_pred cEEEEeeeecCC--CCCceeEEEeeeCCeEEEEeccccCCccHHHHHhhcCCCeeEEEEeehhhHHHhhcCCCccCc-Ee
Q 043928 39 RVVGIDVKFNHR--CTKKAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICFVGIEMNGKVDGLGRCNLRCKT-AV 115 (192)
Q Consensus 39 ~vvG~D~Ew~~~--~~~~~aliQl~~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~~~~D~~~L~~~g~~~~~-~~ 115 (192)
..+.+|+|.... ...++..+++|++++++.+.+.......+.|+++|+|+++.|+||+++.|...|.++|+.+.+ .+
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~~i~l~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~~~~~~f 83 (178)
T cd06140 4 DEVALYVELLGENYHTADIIGLALANGGGAYYIPLELALLDLAALKEWLEDEKIPKVGHDAKRAYVALKRHGIELAGVAF 83 (178)
T ss_pred CceEEEEEEcCCCcceeeEEEEEEEeCCcEEEEeccchHHHHHHHHHHHhCCCCceeccchhHHHHHHHHCCCcCCCcch
Confidence 356777777654 356788899999887777764321001234889999999999999999999999778887764 58
Q ss_pred ehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCC---cCCCCHHHHHHHHHhHHHHHHHHHHHhcccC
Q 043928 116 ELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWS---ARAFSNEQIKFAVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 116 Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~---~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~~ 191 (192)
|+.-. ...++ |.....++..++.++ |..+. + ..+.+.|. .++..++|..||+.||.++..++..|.++|.
T Consensus 84 Dt~la-aYLL~-p~~~~~~l~~l~~~yl~~~~~--~--~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~ 157 (178)
T cd06140 84 DTMLA-AYLLD-PTRSSYDLADLAKRYLGRELP--S--DEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELE 157 (178)
T ss_pred hHHHH-HHHcC-CCCCCCCHHHHHHHHcCCCCc--c--hHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 86544 43454 432235999999999 98866 3 11233442 2455777899999999999999999988763
No 21
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.02 E-value=0.00021 Score=69.14 Aligned_cols=162 Identities=17% Similarity=0.072 Sum_probs=100.6
Q ss_pred eCChHHHHHHHHHHHHhhcCCcEEEEeeeecCCCCCceeEEEeeeCC-e-EEEEeccc-----cCCccHHHHHhhcCCCe
Q 043928 18 VDHAALIDDNVAALKALLKRQRVVGIDVKFNHRCTKKAEMLILCAGN-R-CLIIQLCH-----LGQIPESLKKFLADETI 90 (192)
Q Consensus 18 t~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~~~~~~aliQl~~~~-~-~~l~~l~~-----~~~~p~~L~~~l~~~~i 90 (192)
+.+.+.++.|++. .....+++ ..+.| ....+.-+-+|+++ . .+.+.+.. .......|+.+|+|+.+
T Consensus 307 ~~~~~~~~~~~~~-----~~~~~~~~-~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~ 379 (887)
T TIGR00593 307 SEEAAPLANPAEK-----AEVGGFVL-ERLLD-QLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLNEQI 379 (887)
T ss_pred eCCHHHHHHHHHh-----CcCCeEEE-cCccc-ccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhCCCC
Confidence 3455666776643 12335666 33333 13445567778765 3 33332220 01112348899999999
Q ss_pred eEEEEeehhhHHHhhcCCCccCc-EeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCC-HH
Q 043928 91 CFVGIEMNGKVDGLGRCNLRCKT-AVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFS-NE 167 (192)
Q Consensus 91 ~kvG~~~~~D~~~L~~~g~~~~~-~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls-~~ 167 (192)
.|+||+++.|+..|.++|+.+.+ ++|.. +|...++ |.. +.+|+.++.++ +..+. +.....-.++....++ ++
T Consensus 380 ~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~-la~yll~-~~~-~~~l~~la~~yl~~~~~--~~~~~~~~~~~~~~~~~~~ 454 (887)
T TIGR00593 380 KKIGHDAKFLMHLLKREGIELGGVIFDTM-LAAYLLD-PAQ-VSTLDTLARRYLVEELI--LDEKIGGKLAKFAFPPLEE 454 (887)
T ss_pred cEEEeeHHHHHHHHHhCCCCCCCcchhHH-HHHHHcC-CCC-CCCHHHHHHHHcCcccc--cHHHhccCCCCcccccHHH
Confidence 99999999999999888888765 57754 4444444 422 35999999999 87754 2111110111111333 34
Q ss_pred HHHHHHHhHHHHHHHHHHHhcccC
Q 043928 168 QIKFAVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 168 Qi~YAa~Da~~~~~i~~~L~~~~~ 191 (192)
...||+.||.+.+.+|..|...|.
T Consensus 455 ~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 455 ATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 578999999999999999988764
No 22
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=97.97 E-value=0.00011 Score=67.61 Aligned_cols=165 Identities=18% Similarity=0.201 Sum_probs=105.5
Q ss_pred CChHHHHHHHHHHHHhhcCCcEEEEeeeecCCCCCceeEEEee--eCCeEEEEeccc-cC--CccHHHHHhhcCCCeeEE
Q 043928 19 DHAALIDDNVAALKALLKRQRVVGIDVKFNHRCTKKAEMLILC--AGNRCLIIQLCH-LG--QIPESLKKFLADETICFV 93 (192)
Q Consensus 19 ~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~~~~~~aliQl~--~~~~~~l~~l~~-~~--~~p~~L~~~l~~~~i~kv 93 (192)
.+......|+..... .+. +++|+|.........+++=++ .++..+.+-+.+ .. ..-..|+.+|+++.+.|+
T Consensus 7 ~~~~~~~~~~~~~~~---~~~-~a~~~et~~l~~~~~~lvg~s~~~~~~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~kv 82 (593)
T COG0749 7 TDLAVLNAWLTKLNA---AAN-IAFDTETDGLDPHGADLVGLSVASEEEAAYIPLLHGPEQLNVLAALKPLLEDEGIKKV 82 (593)
T ss_pred hHHHHHHHHHHHHhh---ccc-ceeeccccccCcccCCeeEEEeeccccceeEeeccchhhhhhHHHHHHHhhCcccchh
Confidence 345566667665542 334 999999987633333444333 333333343333 11 123578999999999999
Q ss_pred EEeehhhHHHhhcCCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcc---cCCCCcCCCC-HHH
Q 043928 94 GIEMNGKVDGLGRCNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGY---APSWSARAFS-NEQ 168 (192)
Q Consensus 94 G~~~~~D~~~L~~~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~---~S~W~~~~Ls-~~Q 168 (192)
|++.+.|...|.++|+.....+|. .++.-.+ .|.....++..|++++ |.... ..+.+- .++=.-.... ++-
T Consensus 83 ~~~~K~d~~~l~~~Gi~~~~~~Dt-mlasYll-~~~~~~~~~~~l~~r~l~~~~~--~~~~i~~kg~~~~~~~~~~~~~~ 158 (593)
T COG0749 83 GQNLKYDYKVLANLGIEPGVAFDT-MLASYLL-NPGAGAHNLDDLAKRYLGLETI--TFEDIAGKGKKQLTFADVKLEKA 158 (593)
T ss_pred ccccchhHHHHHHcCCcccchHHH-HHHHhcc-CcCcCcCCHHHHHHHhcCCccc--hhHHhhccccccCccccchHHHH
Confidence 999999999999988664456774 5554333 3444468999999999 88755 222111 0110000111 344
Q ss_pred HHHHHHhHHHHHHHHHHHhcccC
Q 043928 169 IKFAVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 169 i~YAa~Da~~~~~i~~~L~~~~~ 191 (192)
..|||.||.+.++++..|...+.
T Consensus 159 ~~y~a~~a~~~~~L~~~l~~~l~ 181 (593)
T COG0749 159 TEYAAEDADATLRLESILEPELL 181 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Confidence 89999999999999999987654
No 23
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.44 E-value=0.011 Score=49.11 Aligned_cols=131 Identities=15% Similarity=0.127 Sum_probs=85.8
Q ss_pred cCCcEEEEeeeecCCCCCceeEEEeeeC----C-----eEEEEecccc--------CCc--------c------HHHHHh
Q 043928 36 KRQRVVGIDVKFNHRCTKKAEMLILCAG----N-----RCLIIQLCHL--------GQI--------P------ESLKKF 84 (192)
Q Consensus 36 ~~~~vvG~D~Ew~~~~~~~~aliQl~~~----~-----~~~l~~l~~~--------~~~--------p------~~L~~~ 84 (192)
++..+|.||+|.+.....+-.+||+|.- + ...+++.... ..+ | +.+.+|
T Consensus 5 ~~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~~f 84 (250)
T PRK06310 5 KDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGF 84 (250)
T ss_pred cCCcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHHHH
Confidence 3468999999999764444567777652 1 1223333210 001 1 256667
Q ss_pred hcCCCeeEEEEeehhhHHHhhc----CCCcc----CcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCccc
Q 043928 85 LADETICFVGIEMNGKVDGLGR----CNLRC----KTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYA 156 (192)
Q Consensus 85 l~~~~i~kvG~~~~~D~~~L~~----~g~~~----~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~ 156 (192)
+.+. -+.|||++..|...|.+ .|+.. ...+|...+++. ++. ....+|.+|++.+|.+.. .
T Consensus 85 l~~~-~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~-~~~--~~~~~L~~l~~~~g~~~~--~------ 152 (250)
T PRK06310 85 FKEG-DYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKE-YGD--SPNNSLEALAVHFNVPYD--G------ 152 (250)
T ss_pred hCCC-CEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHh-ccc--CCCCCHHHHHHHCCCCCC--C------
Confidence 7543 46899999999998875 45533 468999888874 442 125789999987766544 1
Q ss_pred CCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 157 PSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 157 S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
-+=|..||+++.+++..+.++.
T Consensus 153 ------------aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 153 ------------NHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred ------------CcChHHHHHHHHHHHHHHHHhc
Confidence 1337899999999999987654
No 24
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=97.36 E-value=0.0066 Score=46.31 Aligned_cols=128 Identities=20% Similarity=0.203 Sum_probs=82.7
Q ss_pred EEEEeeeecCCCCCceeEEEeeeCC----e-E----EEEeccc-c----------------CC--cc---HHHHHhhcCC
Q 043928 40 VVGIDVKFNHRCTKKAEMLILCAGN----R-C----LIIQLCH-L----------------GQ--IP---ESLKKFLADE 88 (192)
Q Consensus 40 vvG~D~Ew~~~~~~~~aliQl~~~~----~-~----~l~~l~~-~----------------~~--~p---~~L~~~l~~~ 88 (192)
+|.||+|.+.....+-.++|++.-. . . .++++.. + +. +. ..+.+++.+.
T Consensus 2 ~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~~l~~~ 81 (169)
T smart00479 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLKGK 81 (169)
T ss_pred EEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHhcCC
Confidence 6899999987644456777777522 1 1 1222210 0 00 11 2566677653
Q ss_pred CeeEEEEeehhhHHHhhc----CCCcc---CcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCCCc
Q 043928 89 TICFVGIEMNGKVDGLGR----CNLRC---KTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSWSA 161 (192)
Q Consensus 89 ~i~kvG~~~~~D~~~L~~----~g~~~---~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~ 161 (192)
++.++.+...|...|.+ +|+.. ...+|+..+++...+.+ ..+|..+++.+|.+.. .+
T Consensus 82 -~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~---~~~L~~l~~~~~~~~~----~~-------- 145 (169)
T smart00479 82 -ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR---KYSLKKLAERLGLEVI----GR-------- 145 (169)
T ss_pred -EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC---CCCHHHHHHHCCCCCC----CC--------
Confidence 43344444999999987 45432 34799988887655433 7899999998866544 11
Q ss_pred CCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 162 RAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 162 ~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
.+.|..||....+||.++.+++
T Consensus 146 -------~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 146 -------AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred -------CcCcHHHHHHHHHHHHHHHHHh
Confidence 3778999999999999998754
No 25
>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=97.31 E-value=0.0048 Score=49.23 Aligned_cols=143 Identities=12% Similarity=0.215 Sum_probs=85.3
Q ss_pred CcEEEEeeeecCC------CCCceeEEEeeeCC--eEEEEecc------ccC---CccHHHHHhhcC--CCeeEEEEeeh
Q 043928 38 QRVVGIDVKFNHR------CTKKAEMLILCAGN--RCLIIQLC------HLG---QIPESLKKFLAD--ETICFVGIEMN 98 (192)
Q Consensus 38 ~~vvG~D~Ew~~~------~~~~~aliQl~~~~--~~~l~~l~------~~~---~~p~~L~~~l~~--~~i~kvG~~~~ 98 (192)
-+++.||+|.... ...++-.|-++... .++.++-. ... .+-..+.+++.. |++ .+||++.
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dpdi-ivgyN~~ 81 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDV-IYTYNGD 81 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCCCE-EEecCCC
Confidence 3699999998632 23444333333322 23322211 011 111334444544 764 7999885
Q ss_pred -hhHHHhhc----CCCccC------------------------cEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCC
Q 043928 99 -GKVDGLGR----CNLRCK------------------------TAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSL 148 (192)
Q Consensus 99 -~D~~~L~~----~g~~~~------------------------~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~ 148 (192)
.|+..|.+ +|+... -.+|+-.+++..++. .+.+|..+++++ |.+-.
T Consensus 82 ~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~l---~sy~L~~v~~~~Lg~~k~- 157 (195)
T cd05780 82 NFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNL---TRYTLERVYEELFGIEKE- 157 (195)
T ss_pred CCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCCC---CcCcHHHHHHHHhCCCCC-
Confidence 59998865 666422 268887777654443 478999999999 87532
Q ss_pred CCCCCcccCC-CCcCCCCHHHHHHHHHhHHHHHHHHHHH
Q 043928 149 ASGFNGYAPS-WSARAFSNEQIKFAVHEAFAYYVIGDRV 186 (192)
Q Consensus 149 ~K~k~~~~S~-W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L 186 (192)
.-..-+.+. |...+--.+=++|+..||...++|.+++
T Consensus 158 -d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 158 -DVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred -cCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 111112333 4444455667999999999999998764
No 26
>PRK07740 hypothetical protein; Provisional
Probab=97.23 E-value=0.064 Score=44.41 Aligned_cols=147 Identities=12% Similarity=0.068 Sum_probs=92.0
Q ss_pred ChHHHHHHHHHHHHhhc----------CCcEEEEeeeecCCCCCc-eeEEEeeeC----CeE------EEEecccc----
Q 043928 20 HAALIDDNVAALKALLK----------RQRVVGIDVKFNHRCTKK-AEMLILCAG----NRC------LIIQLCHL---- 74 (192)
Q Consensus 20 ~~~~~~~~i~~~~~~~~----------~~~vvG~D~Ew~~~~~~~-~aliQl~~~----~~~------~l~~l~~~---- 74 (192)
+..+-..|++++....+ +.++|.||+|++...+.+ -.+||++.- +.. .+++....
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~ 110 (244)
T PRK07740 31 NALQQEAWIRSIQKEAKRDDVLDIPLTDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEH 110 (244)
T ss_pred chHHHHHHHHHHHHHhccCCccCCCccCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChh
Confidence 33577788888854431 237999999998653222 356666642 111 12222110
Q ss_pred -----C----------CccH---HHHHhhcCCCeeEEEEeehhhHHHhhc-----CCCcc-CcEeehHHHHHHHhCCCCc
Q 043928 75 -----G----------QIPE---SLKKFLADETICFVGIEMNGKVDGLGR-----CNLRC-KTAVELGHFAARVLKKPHI 130 (192)
Q Consensus 75 -----~----------~~p~---~L~~~l~~~~i~kvG~~~~~D~~~L~~-----~g~~~-~~~~Dl~~~a~~~~~~~~~ 130 (192)
+ .++. .+.+|+.+ -+.|||++..|...|.+ ++... ...+|+..+++.... ..
T Consensus 111 ~~~ltGIt~e~l~~ap~~~evl~~f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~--~~ 186 (244)
T PRK07740 111 ILELTGITAEDVAFAPPLAEVLHRFYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAH--ER 186 (244)
T ss_pred heeccCCCHHHHhCCCCHHHHHHHHHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcC--CC
Confidence 0 1122 33444443 36889999999998865 23332 478999888875433 23
Q ss_pred CcccHHHHHHHhCcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 131 SSFGLAKLAREVGIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 131 ~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
...||.++++.+|.+.. . . +=|.-||.+..+|+.++.+++
T Consensus 187 ~~~sL~~l~~~~gi~~~--~--~----------------H~Al~Da~ata~l~~~ll~~~ 226 (244)
T PRK07740 187 DFPTLDDALAYYGIPIP--R--R----------------HHALGDALMTAKLWAILLVEA 226 (244)
T ss_pred CCCCHHHHHHHCCcCCC--C--C----------------CCcHHHHHHHHHHHHHHHHHH
Confidence 47899999976677666 1 1 336799999999999997664
No 27
>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=97.23 E-value=0.014 Score=44.18 Aligned_cols=126 Identities=16% Similarity=0.104 Sum_probs=79.2
Q ss_pred ceeEEEeeeCCeEEEEeccccCCccHHHHHhhcCCCeeEEEEeehhhHHHhhcCCCccCcE-eehHHHHHHHhCCCCcCc
Q 043928 54 KAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICFVGIEMNGKVDGLGRCNLRCKTA-VELGHFAARVLKKPHISS 132 (192)
Q Consensus 54 ~~aliQl~~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~~~~D~~~L~~~g~~~~~~-~Dl~~~a~~~~~~~~~~~ 132 (192)
++.-+-+|+++.++.+.+.. +..-..|+.+|+++++.|+|++.+.+...|.++|+...+. +|+. +|.-.++ |..+.
T Consensus 19 ~~~glal~~~~~~~yi~~~~-~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~~~fD~~-LAaYLL~-p~~~~ 95 (151)
T cd06128 19 NLVGLAFAIEGVAAYIPVAH-DYALELLKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTM-LEAYLLD-PVAGR 95 (151)
T ss_pred cEEEEEEEcCCCeEEEeCCC-CcCHHHHHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCCcchhHH-HHHHHcC-CCCCC
Confidence 34446666665555554221 1012458899999999999999999999987788887764 7865 5554454 53331
Q ss_pred ccHHHHHHHh-CcccCCCC-CCCcccCCCCc--CCC-CHHHHHHHHHhHHHHHHHHHHHh
Q 043928 133 FGLAKLAREV-GIHNSLAS-GFNGYAPSWSA--RAF-SNEQIKFAVHEAFAYYVIGDRVL 187 (192)
Q Consensus 133 ~gL~~l~~~~-g~~l~~~K-~k~~~~S~W~~--~~L-s~~Qi~YAa~Da~~~~~i~~~L~ 187 (192)
.++.++++++ +..+- . +. + ..+.+ .++ ..+.-.|++..|.+.+.++..|.
T Consensus 96 ~~l~~la~~yl~~~~~--~~~~-~--~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 96 HDMDSLAERWLKEKTI--TFEE-I--AGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CCHHHHHHHHcCCCCc--cHHH-H--cCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3999999999 87732 1 00 0 00100 011 11123488888889999988875
No 28
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=97.17 E-value=0.032 Score=46.67 Aligned_cols=130 Identities=23% Similarity=0.273 Sum_probs=83.1
Q ss_pred CCcEEEEeeeecCCCCCceeEEEeee----CCe-----EEEEecccc----------------C--Ccc---HHHHHhhc
Q 043928 37 RQRVVGIDVKFNHRCTKKAEMLILCA----GNR-----CLIIQLCHL----------------G--QIP---ESLKKFLA 86 (192)
Q Consensus 37 ~~~vvG~D~Ew~~~~~~~~aliQl~~----~~~-----~~l~~l~~~----------------~--~~p---~~L~~~l~ 86 (192)
+..++.+|+|++.....+-.+|+++. ++. ..++..... + .++ ..+.+|+.
T Consensus 67 ~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f~~fl~ 146 (257)
T PRK08517 67 DQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFRLFLG 146 (257)
T ss_pred CCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHHHHHHC
Confidence 35799999999976333335666553 221 122222110 0 111 24566666
Q ss_pred CCCeeEEEEeehhhHHHhhc----CCCc--cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCCC
Q 043928 87 DETICFVGIEMNGKVDGLGR----CNLR--CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSWS 160 (192)
Q Consensus 87 ~~~i~kvG~~~~~D~~~L~~----~g~~--~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~ 160 (192)
+ -++|||++..|...|.+ +|.. ....+|.-++++..+..+ +.||..|++.+|.+.. +
T Consensus 147 ~--~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~---~~~L~~L~~~lgi~~~--~---------- 209 (257)
T PRK08517 147 D--SVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESP---RYGLSFLKELLGIEIE--V---------- 209 (257)
T ss_pred C--CeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCC---CCCHHHHHHHcCcCCC--C----------
Confidence 4 35899999999988864 4543 345788777877554433 6789999986676654 2
Q ss_pred cCCCCHHHHHHHHHhHHHHHHHHHHHhcccC
Q 043928 161 ARAFSNEQIKFAVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 161 ~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~~ 191 (192)
-+=|..||.++.+|+.++..+++
T Consensus 210 --------~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 210 --------HHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred --------CCChHHHHHHHHHHHHHHHHHhH
Confidence 13367999999999999987653
No 29
>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=97.15 E-value=0.028 Score=44.59 Aligned_cols=78 Identities=14% Similarity=0.152 Sum_probs=57.6
Q ss_pred CeeEEEEeehhhHHHhhc----CCCc-----cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCC
Q 043928 89 TICFVGIEMNGKVDGLGR----CNLR-----CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSW 159 (192)
Q Consensus 89 ~i~kvG~~~~~D~~~L~~----~g~~-----~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W 159 (192)
+-+.|||++..|...|.+ +|+. ...++|.-.+++...+ ..+|..+|+.+|.+.+ .
T Consensus 102 ~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~-----~~~L~~l~~~~gi~~~--~--------- 165 (189)
T cd06134 102 RAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG-----QTVLAKACQAAGIEFD--N--------- 165 (189)
T ss_pred CCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC-----CCcHHHHHHHCCCCCC--C---------
Confidence 457999999999988875 5652 2357999898876543 3469999987777653 1
Q ss_pred CcCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 043928 160 SARAFSNEQIKFAVHEAFAYYVIGDRVLSS 189 (192)
Q Consensus 160 ~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~ 189 (192)
++-+=|..||.+..+++.+|.++
T Consensus 166 -------~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 166 -------KEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred -------CCCcChHHHHHHHHHHHHHHHHh
Confidence 11234789999999999999865
No 30
>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=97.15 E-value=0.0018 Score=45.97 Aligned_cols=70 Identities=17% Similarity=0.171 Sum_probs=53.2
Q ss_pred EEEeeeecCC--CCCceeEEEeeeC--CeEEEEeccccCCccHHHHHhhcCCC-eeEEEEeehhhHHHhhc----CCC--
Q 043928 41 VGIDVKFNHR--CTKKAEMLILCAG--NRCLIIQLCHLGQIPESLKKFLADET-ICFVGIEMNGKVDGLGR----CNL-- 109 (192)
Q Consensus 41 vG~D~Ew~~~--~~~~~aliQl~~~--~~~~l~~l~~~~~~p~~L~~~l~~~~-i~kvG~~~~~D~~~L~~----~g~-- 109 (192)
+.+|+|.... ..+++.+||++.+ ++.++++ +.+++.+.. .++|||+...|...|.+ +|.
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~~~----------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~~ 70 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAVID----------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLKY 70 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEEeh----------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCCC
Confidence 4799999875 6788999999888 4555544 777888777 78999999999988876 343
Q ss_pred --ccCcEeehHHH
Q 043928 110 --RCKTAVELGHF 120 (192)
Q Consensus 110 --~~~~~~Dl~~~ 120 (192)
.....+|+..+
T Consensus 71 p~~~~~~lDT~~l 83 (96)
T cd06125 71 PLLAGSWIDTIKL 83 (96)
T ss_pred CCcCCcEEEehHH
Confidence 23568887765
No 31
>PRK07883 hypothetical protein; Validated
Probab=97.12 E-value=0.025 Score=52.31 Aligned_cols=133 Identities=17% Similarity=0.188 Sum_probs=87.9
Q ss_pred cCCcEEEEeeeecCCCCCceeEEEeee----CCe-----EEEEecccc---------C-------C---cc---HHHHHh
Q 043928 36 KRQRVVGIDVKFNHRCTKKAEMLILCA----GNR-----CLIIQLCHL---------G-------Q---IP---ESLKKF 84 (192)
Q Consensus 36 ~~~~vvG~D~Ew~~~~~~~~aliQl~~----~~~-----~~l~~l~~~---------~-------~---~p---~~L~~~ 84 (192)
.+..+|.||+|++......-.+||++. ++. ..+++.... + . +. ..+.+|
T Consensus 13 ~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f~~f 92 (557)
T PRK07883 13 RDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEF 92 (557)
T ss_pred cCCCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHH
Confidence 346899999999976444456677665 221 122222110 0 0 11 245566
Q ss_pred hcCCCeeEEEEeehhhHHHhhc----CCCcc--CcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCC
Q 043928 85 LADETICFVGIEMNGKVDGLGR----CNLRC--KTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPS 158 (192)
Q Consensus 85 l~~~~i~kvG~~~~~D~~~L~~----~g~~~--~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~ 158 (192)
+.+ -+.|||++..|...|.+ +|+.. ...+|...+++..+........+|.++++.+|.+.. .
T Consensus 93 l~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~----~------ 160 (557)
T PRK07883 93 ARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTT----P------ 160 (557)
T ss_pred hcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccC----C------
Confidence 664 56789999999999875 56654 367899888876554223457889999986677654 1
Q ss_pred CCcCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 159 WSARAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 159 W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
-+-|..||.+..+|+.++.+++
T Consensus 161 ----------~H~Al~DA~ata~l~~~l~~~~ 182 (557)
T PRK07883 161 ----------THRALDDARATVDVLHGLIERL 182 (557)
T ss_pred ----------CCCHHHHHHHHHHHHHHHHHHH
Confidence 2447899999999999987764
No 32
>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=96.92 E-value=0.017 Score=45.87 Aligned_cols=98 Identities=13% Similarity=0.120 Sum_probs=64.4
Q ss_pred HHHHhhcC--CCeeEEEEee-hhhHHHhhc----CCCcc------------------------CcEeehHHHHHHHhCCC
Q 043928 80 SLKKFLAD--ETICFVGIEM-NGKVDGLGR----CNLRC------------------------KTAVELGHFAARVLKKP 128 (192)
Q Consensus 80 ~L~~~l~~--~~i~kvG~~~-~~D~~~L~~----~g~~~------------------------~~~~Dl~~~a~~~~~~~ 128 (192)
.+.+++.+ |+ +.+||++ ..|+..|.+ +|+.. .-.+|+-.+++....
T Consensus 69 ~f~~~i~~~dpd-iivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~-- 145 (199)
T cd05160 69 RFFDIIREYDPD-ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK-- 145 (199)
T ss_pred HHHHHHHhcCCC-EEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcC--
Confidence 34455543 44 4899999 779998875 67655 136888888775443
Q ss_pred CcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHH
Q 043928 129 HISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIG 183 (192)
Q Consensus 129 ~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~ 183 (192)
..+.+|..+|+.+ |.+-. .-..-...+|....--.+=++|.-.||...++|+
T Consensus 146 -l~sy~L~~v~~~~l~~~k~--~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 146 -LKSYTLDAVAEELLGEGKE--KVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred -cccCCHHHHHHHHhCCCCC--cCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 3478999999999 76422 1111123333222334566999999999999986
No 33
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.92 E-value=0.051 Score=44.64 Aligned_cols=81 Identities=14% Similarity=0.044 Sum_probs=56.3
Q ss_pred CeeEEEEeehhhHHHhhc----CCCc---cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCCCc
Q 043928 89 TICFVGIEMNGKVDGLGR----CNLR---CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSWSA 161 (192)
Q Consensus 89 ~i~kvG~~~~~D~~~L~~----~g~~---~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~ 161 (192)
+.+.|||+...|...|.+ +|+. ...++|.-.+++...... ..+.+|.++++.+|.+.. . .
T Consensus 93 ~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~-~~~~~L~~l~~~~gi~~~--~--a-------- 159 (232)
T PRK07942 93 GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYR-KGKRTLTALCEHYGVRLD--N--A-------- 159 (232)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhccc-CCCCCHHHHHHHcCCCCC--C--C--------
Confidence 456699999999988865 5643 246788766665332211 125689999988777665 2 1
Q ss_pred CCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 162 RAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 162 ~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
+=|..||.++.+|+.+|.++.
T Consensus 160 --------H~Al~Da~ata~l~~~l~~~~ 180 (232)
T PRK07942 160 --------HEATADALAAARVAWALARRF 180 (232)
T ss_pred --------CChHHHHHHHHHHHHHHHHHH
Confidence 226789999999999987653
No 34
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.91 E-value=0.04 Score=45.64 Aligned_cols=129 Identities=13% Similarity=0.105 Sum_probs=81.3
Q ss_pred CcEEEEeeeecCCCCC-ceeEEEeee---------CC-eEEEEeccc-cC---------------Ccc------HHHHHh
Q 043928 38 QRVVGIDVKFNHRCTK-KAEMLILCA---------GN-RCLIIQLCH-LG---------------QIP------ESLKKF 84 (192)
Q Consensus 38 ~~vvG~D~Ew~~~~~~-~~aliQl~~---------~~-~~~l~~l~~-~~---------------~~p------~~L~~~ 84 (192)
.++|.||+|.+..... .-.+|+|+. ++ ...+++... ++ .-| +.+.+|
T Consensus 4 ~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~f 83 (240)
T PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83 (240)
T ss_pred CeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHHHHH
Confidence 4689999999976332 456777753 11 122333321 00 001 245666
Q ss_pred hcCCCeeEEEEeehhhHHHhhc----CCC--c----cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCc
Q 043928 85 LADETICFVGIEMNGKVDGLGR----CNL--R----CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNG 154 (192)
Q Consensus 85 l~~~~i~kvG~~~~~D~~~L~~----~g~--~----~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~ 154 (192)
+.+. ..|||++..|+..|.. +|. . ...++|.-.+++..+.. .+.+|.+||+.+|.+.. .+
T Consensus 84 i~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~---~~~~L~aL~~~~gi~~~----~r- 153 (240)
T PRK05711 84 IRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPG---KRNSLDALCKRYGIDNS----HR- 153 (240)
T ss_pred hCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCC---CCCCHHHHHHHCCCCCC----CC-
Confidence 6653 3589999999998875 442 2 23588987888765532 25699999998775433 11
Q ss_pred ccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 043928 155 YAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSS 189 (192)
Q Consensus 155 ~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~ 189 (192)
+.+=|..||..+.+||.+|...
T Consensus 154 -------------~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 154 -------------TLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred -------------CCCCHHHHHHHHHHHHHHHHCc
Confidence 1234789999999999988753
No 35
>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=96.85 E-value=0.022 Score=43.81 Aligned_cols=86 Identities=16% Similarity=0.180 Sum_probs=59.9
Q ss_pred HHHHhhcCC-CeeEEEEeehhhHHHhhc----CCC-----ccCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCC
Q 043928 80 SLKKFLADE-TICFVGIEMNGKVDGLGR----CNL-----RCKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLA 149 (192)
Q Consensus 80 ~L~~~l~~~-~i~kvG~~~~~D~~~L~~----~g~-----~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~ 149 (192)
.+.+++.+. ....++++ ..|...+.+ ++. ...+.+|+..++...++.+ ...+|.++++.+|.+..
T Consensus 81 ~~~~~l~~~~~~~~v~~~-~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~--~~~~L~~l~~~~gi~~~-- 155 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWG-DWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLK--KRTGLSKALEYLGLEFE-- 155 (176)
T ss_pred HHHHHHHhCCCeEEEeec-HhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCC--CCCCHHHHHHHCCCCCC--
Confidence 567778765 36667775 788765543 333 3458999999998777654 47899999987766554
Q ss_pred CCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 043928 150 SGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVL 187 (192)
Q Consensus 150 K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~ 187 (192)
. +-+-|--||..+.+|+.+|.
T Consensus 156 ~-----------------~~H~Al~DA~~~a~l~~~~~ 176 (176)
T cd06133 156 G-----------------RHHRGLDDARNIARILKRLL 176 (176)
T ss_pred C-----------------CCcCcHHHHHHHHHHHHHhC
Confidence 1 12336789999999998763
No 36
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.85 E-value=0.11 Score=41.52 Aligned_cols=130 Identities=18% Similarity=0.207 Sum_probs=79.9
Q ss_pred CCcEEEEeeeecCCCCCceeEEEeee----CCe-------EEEEeccc-c--------C----------Ccc---HHHHH
Q 043928 37 RQRVVGIDVKFNHRCTKKAEMLILCA----GNR-------CLIIQLCH-L--------G----------QIP---ESLKK 83 (192)
Q Consensus 37 ~~~vvG~D~Ew~~~~~~~~aliQl~~----~~~-------~~l~~l~~-~--------~----------~~p---~~L~~ 83 (192)
+..+|.+|+|.+...+.+-.+||++. ++. ..+++... + + .++ +.+.+
T Consensus 28 ~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~~~~ 107 (202)
T PRK09145 28 PDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLA 107 (202)
T ss_pred CCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHHHHH
Confidence 35899999999975333345666664 222 12333321 0 0 011 24556
Q ss_pred hhcCCCeeEEEEeehhhHHHhhc-----CCCcc-CcEeehHHHHHHHhC--CC-CcCcccHHHHHHHhCcccCCCCCCCc
Q 043928 84 FLADETICFVGIEMNGKVDGLGR-----CNLRC-KTAVELGHFAARVLK--KP-HISSFGLAKLAREVGIHNSLASGFNG 154 (192)
Q Consensus 84 ~l~~~~i~kvG~~~~~D~~~L~~-----~g~~~-~~~~Dl~~~a~~~~~--~~-~~~~~gL~~l~~~~g~~l~~~K~k~~ 154 (192)
++.+ -..|||++..|...|.+ +|... ...+|+..++..... .+ ...+.+|.++++.+|.+.. ..
T Consensus 108 ~i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~--~~--- 180 (202)
T PRK09145 108 FIGN--RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVL--GR--- 180 (202)
T ss_pred HHcC--CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCC--CC---
Confidence 6664 35799999999998865 34433 468898776542211 12 1235789999987776654 21
Q ss_pred ccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 043928 155 YAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLS 188 (192)
Q Consensus 155 ~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~ 188 (192)
+=|..||+++.+||.+|.+
T Consensus 181 ---------------H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 181 ---------------HDALNDAIMAALIFLRLRK 199 (202)
T ss_pred ---------------CCcHHHHHHHHHHHHHHHh
Confidence 2267899999999998854
No 37
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=96.80 E-value=0.055 Score=44.26 Aligned_cols=87 Identities=13% Similarity=0.070 Sum_probs=61.7
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhc----CC--Cc-c---CcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGR----CN--LR-C---KTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLA 149 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~----~g--~~-~---~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~ 149 (192)
.+.+|+.+. ..|||++..|...|.. +| +. + ..++|.-.+++..+.. .+.+|.++|+.+|.+..
T Consensus 75 ~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~---~~~~L~~L~~~~gi~~~-- 147 (225)
T TIGR01406 75 EFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPG---QRNSLDALCKRFKVDNS-- 147 (225)
T ss_pred HHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCC---CCCCHHHHHHhcCCCCC--
Confidence 455666653 4589999999998875 55 22 1 4789988888765532 25799999998876544
Q ss_pred CCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 043928 150 SGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSS 189 (192)
Q Consensus 150 K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~ 189 (192)
. + +.+=|..||..+.+||..|...
T Consensus 148 ~--r--------------~~H~Al~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 148 H--R--------------TLHGALLDAHLLAEVYLALTGG 171 (225)
T ss_pred C--C--------------CCcCHHHHHHHHHHHHHHHHcC
Confidence 1 1 1233789999999999988653
No 38
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.79 E-value=0.035 Score=47.79 Aligned_cols=127 Identities=17% Similarity=0.136 Sum_probs=81.5
Q ss_pred cEEEEeeeecCCCCCceeEEEeee-----CCe----EEEEecccc---------C----------Ccc---HHHHHhhcC
Q 043928 39 RVVGIDVKFNHRCTKKAEMLILCA-----GNR----CLIIQLCHL---------G----------QIP---ESLKKFLAD 87 (192)
Q Consensus 39 ~vvG~D~Ew~~~~~~~~aliQl~~-----~~~----~~l~~l~~~---------~----------~~p---~~L~~~l~~ 87 (192)
.+|.||+|.+...+.+-.+||++. +.. ..++++... + .++ +.+.+|+.+
T Consensus 9 ~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f~~fl~~ 88 (313)
T PRK06807 9 DYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88 (313)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHHHHHHcC
Confidence 699999999765444456777764 211 122222110 0 011 245556654
Q ss_pred CCeeEEEEeehhhHHHhhc----CCCc--cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCCCc
Q 043928 88 ETICFVGIEMNGKVDGLGR----CNLR--CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSWSA 161 (192)
Q Consensus 88 ~~i~kvG~~~~~D~~~L~~----~g~~--~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~ 161 (192)
. ..|||++..|.+.|.+ +|+. ....+|...+++..++. ....+|..|++.+|.+.+
T Consensus 89 ~--~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~--~~~~kL~~L~~~lgi~~~-------------- 150 (313)
T PRK06807 89 N--VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKH--APNHKLETLKRMLGIRLS-------------- 150 (313)
T ss_pred C--eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCC--CCCCCHHHHHHHcCCCCC--------------
Confidence 4 3499999999999986 5653 34689988888765542 236789999976664432
Q ss_pred CCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 162 RAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 162 ~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
-+=|..||+++.+||.++.+..
T Consensus 151 -------~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 151 -------SHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred -------CcChHHHHHHHHHHHHHHHHhh
Confidence 2336789999999999887654
No 39
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.79 E-value=0.078 Score=43.49 Aligned_cols=129 Identities=13% Similarity=0.138 Sum_probs=83.8
Q ss_pred cEEEEeeeecCCCCCceeEEEeeeCC------eEEEEecccc---------C----------CccH---HHHHhhcCCCe
Q 043928 39 RVVGIDVKFNHRCTKKAEMLILCAGN------RCLIIQLCHL---------G----------QIPE---SLKKFLADETI 90 (192)
Q Consensus 39 ~vvG~D~Ew~~~~~~~~aliQl~~~~------~~~l~~l~~~---------~----------~~p~---~L~~~l~~~~i 90 (192)
+++-||+|.+.....+-.+||+|.-+ ...+++.... + .+.. .+.+|+. ..-
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 ALIFYDTETTGTQIDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCG-TDN 81 (232)
T ss_pred cEEEEEeeCCCCCCCCCEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHc-CCC
Confidence 58999999997644445788887532 2223333211 0 0111 3455554 345
Q ss_pred eEEEEee-hhhHHHhhc----CCCc--cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCCCcCC
Q 043928 91 CFVGIEM-NGKVDGLGR----CNLR--CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSWSARA 163 (192)
Q Consensus 91 ~kvG~~~-~~D~~~L~~----~g~~--~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~~~ 163 (192)
+.|||++ ..|...|.+ +|+. ....+|...+++..++ .....+|..+++.+|.+.. .
T Consensus 82 ~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~--~~~~~~L~~l~~~~~~~~~--~------------- 144 (232)
T PRK06309 82 ILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRP--DLPKHNLQYLRQVYGFEEN--Q------------- 144 (232)
T ss_pred EEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcC--CCCCCCHHHHHHHcCCCCC--C-------------
Confidence 7899995 799999875 4543 2478999888875433 2235789999887765544 1
Q ss_pred CCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 164 FSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 164 Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
-+=|..||+++.+|+.++.+++
T Consensus 145 -----aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 145 -----AHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred -----CCCcHHHHHHHHHHHHHHHHHH
Confidence 1336799999999999988654
No 40
>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=96.78 E-value=0.016 Score=44.70 Aligned_cols=84 Identities=18% Similarity=0.116 Sum_probs=55.5
Q ss_pred HHHHHhhcCCCeeEEEEeehhhHHHhhc-CCCccCcEeehHHH--HHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCc
Q 043928 79 ESLKKFLADETICFVGIEMNGKVDGLGR-CNLRCKTAVELGHF--AARVLKKPHISSFGLAKLAREV-GIHNSLASGFNG 154 (192)
Q Consensus 79 ~~L~~~l~~~~i~kvG~~~~~D~~~L~~-~g~~~~~~~Dl~~~--a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~ 154 (192)
+.+.+|+. +-+.|||++..|++.|.. +. ....+|+..+ +++..+.|.....+|..|++.+ |..+. ...
T Consensus 69 ~~l~~~l~--~~vlV~Hn~~~D~~~l~~~~~--~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~--~~~-- 140 (157)
T cd06149 69 KEILKILK--GKVVVGHAIHNDFKALKYFHP--KHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQ--VGR-- 140 (157)
T ss_pred HHHHHHcC--CCEEEEeCcHHHHHHhcccCC--CcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhc--CCC--
Confidence 35677776 457899999999998876 22 2246676543 3333344544568999999999 88776 211
Q ss_pred ccCCCCcCCCCHHHHHHHHHhHHHHHHHH
Q 043928 155 YAPSWSARAFSNEQIKFAVHEAFAYYVIG 183 (192)
Q Consensus 155 ~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~ 183 (192)
+-+=|.-||.++.++|
T Consensus 141 -------------~~H~Al~DA~at~~l~ 156 (157)
T cd06149 141 -------------QGHSSVEDARATMELY 156 (157)
T ss_pred -------------CCcCcHHHHHHHHHHh
Confidence 1122457888887776
No 41
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=96.76 E-value=0.083 Score=42.47 Aligned_cols=89 Identities=17% Similarity=0.110 Sum_probs=62.5
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhc----CCCcc---CcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGR----CNLRC---KTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGF 152 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~----~g~~~---~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k 152 (192)
.|.+|+.+...+.+++ ...|+..|.+ +|+.. ...+|+..+.+..++.. ...+|..+++.+|.+.. .
T Consensus 85 ~f~~~~~~~~~~iv~~-~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~--~~~~L~~~~~~~gi~~~--~-- 157 (207)
T PRK07748 85 KLAEYDKRCKPTIVTW-GNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGER--NQTGLWKAIEEYGKEGT--G-- 157 (207)
T ss_pred HHHHHhCcCCeEEEEE-CHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcC--CCCCHHHHHHHcCCCCC--C--
Confidence 5677787645566665 5889999975 56643 46788887766555432 35799999988776643 1
Q ss_pred CcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 153 NGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 153 ~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
+ -+-|..||..+.+|+.+|..+.
T Consensus 158 ~---------------~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 158 K---------------HHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred C---------------CcChHHHHHHHHHHHHHHHhCc
Confidence 0 1337899999999999998763
No 42
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.67 E-value=0.041 Score=47.30 Aligned_cols=128 Identities=15% Similarity=0.093 Sum_probs=83.4
Q ss_pred cEEEEeeeecCCCCCceeEEEeee----CC------eEEEEecccc-------C-------Ccc------HHHHHhhcCC
Q 043928 39 RVVGIDVKFNHRCTKKAEMLILCA----GN------RCLIIQLCHL-------G-------QIP------ESLKKFLADE 88 (192)
Q Consensus 39 ~vvG~D~Ew~~~~~~~~aliQl~~----~~------~~~l~~l~~~-------~-------~~p------~~L~~~l~~~ 88 (192)
.++.||+|.+......-.+||++. .+ ...+++.... + .-| +.|.+|+.+
T Consensus 16 ~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~l~~- 94 (313)
T PRK06063 16 GWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRG- 94 (313)
T ss_pred CEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHHHHcCC-
Confidence 699999999976444345666654 11 1223332210 0 012 356777765
Q ss_pred CeeEEEEeehhhHHHhhc----CCCc--cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCCCcC
Q 043928 89 TICFVGIEMNGKVDGLGR----CNLR--CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSWSAR 162 (192)
Q Consensus 89 ~i~kvG~~~~~D~~~L~~----~g~~--~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~~ 162 (192)
-+.|||++..|...|.+ +|.. ....+|.-.+++... +...+.+|..+++.+|.+.. ..
T Consensus 95 -~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~--~~~~~~kL~~l~~~~gi~~~--~~----------- 158 (313)
T PRK06063 95 -RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLG--LGLPNLRLETLAAHWGVPQQ--RP----------- 158 (313)
T ss_pred -CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhc--cCCCCCCHHHHHHHcCCCCC--CC-----------
Confidence 36899999999999976 4543 346899888887532 22346789999987776544 11
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 163 AFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 163 ~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
+=|.-||.++.+|+..+++++
T Consensus 159 -------H~Al~DA~ata~l~~~ll~~~ 179 (313)
T PRK06063 159 -------HDALDDARVLAGILRPSLERA 179 (313)
T ss_pred -------CCcHHHHHHHHHHHHHHHHHH
Confidence 336789999999999887654
No 43
>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=96.63 E-value=0.15 Score=39.05 Aligned_cols=123 Identities=14% Similarity=0.076 Sum_probs=78.5
Q ss_pred EEEeeeecCCCC-CceeEEEeeeC---------C-eEEEEecccc-C------------------Ccc---HHHHHhhcC
Q 043928 41 VGIDVKFNHRCT-KKAEMLILCAG---------N-RCLIIQLCHL-G------------------QIP---ESLKKFLAD 87 (192)
Q Consensus 41 vG~D~Ew~~~~~-~~~aliQl~~~---------~-~~~l~~l~~~-~------------------~~p---~~L~~~l~~ 87 (192)
|.||+|.+.... .+-.+||++.- + ...+++.... + .+. +.|.+|+.+
T Consensus 2 v~~D~ETTGl~~~~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~l~~ 81 (167)
T cd06131 2 IVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRG 81 (167)
T ss_pred EEEEeeCCCCCCCCCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHHHHCC
Confidence 679999987633 44578887631 1 1334443211 0 011 245566665
Q ss_pred CCeeEEEEeehhhHHHhhc----CCCc-----cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCC
Q 043928 88 ETICFVGIEMNGKVDGLGR----CNLR-----CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPS 158 (192)
Q Consensus 88 ~~i~kvG~~~~~D~~~L~~----~g~~-----~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~ 158 (192)
. ..|||++..|...|.+ +|.. ....+|...+++..+.. ...+|.++++.+|.+.+ .
T Consensus 82 ~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~---~~~~L~~l~~~~~i~~~--~-------- 146 (167)
T cd06131 82 A--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPG---KPNSLDALCKRFGIDNS--H-------- 146 (167)
T ss_pred C--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCC---CCCCHHHHHHHCCCCCC--C--------
Confidence 3 3589999999998865 3432 34689988787754422 25689999998775543 1
Q ss_pred CCcCCCCHHHHHHHHHhHHHHHHHHHHH
Q 043928 159 WSARAFSNEQIKFAVHEAFAYYVIGDRV 186 (192)
Q Consensus 159 W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L 186 (192)
.+-+-|..||....+||.+|
T Consensus 147 --------~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 147 --------RTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred --------CCCCChHHHHHHHHHHHHHh
Confidence 12355889999999999876
No 44
>PRK05168 ribonuclease T; Provisional
Probab=96.59 E-value=0.16 Score=41.02 Aligned_cols=79 Identities=13% Similarity=0.051 Sum_probs=58.0
Q ss_pred CeeEEEEeehhhHHHhhc----CCCc-----cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCC
Q 043928 89 TICFVGIEMNGKVDGLGR----CNLR-----CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSW 159 (192)
Q Consensus 89 ~i~kvG~~~~~D~~~L~~----~g~~-----~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W 159 (192)
+-+.|||++..|+..|.+ +|+. ...++|.-.+++..++ ..+|..+++.+|.++. ..
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~-----~~~L~~l~~~~gl~~~--~~-------- 178 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG-----QTVLAKACQAAGIEFD--NK-------- 178 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC-----CCCHHHHHHHCCCCCC--CC--------
Confidence 578999999999988875 5542 1258999888875443 3479999987776654 11
Q ss_pred CcCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 160 SARAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 160 ~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
+-+=|..||.+..+|+.++.+++
T Consensus 179 --------~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 179 --------EAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred --------CCCChHHHHHHHHHHHHHHHHHH
Confidence 12337899999999999988764
No 45
>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=96.49 E-value=0.12 Score=41.88 Aligned_cols=91 Identities=13% Similarity=0.068 Sum_probs=61.0
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhc-C----CC--ccCcEeehHHHHHHHhC-CCCcCcccHHHHHHHhCcccCCCCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGR-C----NL--RCKTAVELGHFAARVLK-KPHISSFGLAKLAREVGIHNSLASG 151 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~-~----g~--~~~~~~Dl~~~a~~~~~-~~~~~~~gL~~l~~~~g~~l~~~K~ 151 (192)
.+.+|+.+ -+.|||++..|...|.+ + +. ....++|+..+++..++ .+ ..+.+|..+++.+|.+..
T Consensus 80 ~~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~-~~~~~L~~l~~~~gl~~~---- 152 (217)
T TIGR00573 80 DFADYIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFP-GKRNTLDALCKRYEITNS---- 152 (217)
T ss_pred HHHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCC-CCCCCHHHHHHHcCCCCC----
Confidence 45666654 46789999999999987 3 22 22467887777654332 12 135689999987765432
Q ss_pred CCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcccC
Q 043928 152 FNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 152 k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~~ 191 (192)
.+ +-+=|..||.++.+|+.++.++..
T Consensus 153 ~~--------------~~H~Al~DA~~ta~l~~~l~~~~~ 178 (217)
T TIGR00573 153 HR--------------ALHGALADAFILAKLYLVMTGKQT 178 (217)
T ss_pred Cc--------------ccCCHHHHHHHHHHHHHHHHhcch
Confidence 10 123368999999999999987653
No 46
>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=96.40 E-value=0.032 Score=43.11 Aligned_cols=83 Identities=20% Similarity=0.310 Sum_probs=57.4
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhcCCCccCcEeehHHHHHHHhCCCC-cCcccHHHHHHHh-CcccCCCCCCCcccC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGRCNLRCKTAVELGHFAARVLKKPH-ISSFGLAKLAREV-GIHNSLASGFNGYAP 157 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~~g~~~~~~~Dl~~~a~~~~~~~~-~~~~gL~~l~~~~-g~~l~~~K~k~~~~S 157 (192)
.|.+|+.+. -+.|||++..|++.|... ...++|...+++.....+. ..+.+|+.||+.+ |.++. ...
T Consensus 76 ~~~~~i~~~-~vlVgHn~~fD~~fL~~~---~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~--~~~----- 144 (161)
T cd06137 76 ALWKFIDPD-TILVGHSLQNDLDALRMI---HTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQ--GGG----- 144 (161)
T ss_pred HHHHhcCCC-cEEEeccHHHHHHHHhCc---CCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhc--CCC-----
Confidence 456666642 468999999999999862 2368999888875443221 0368999999998 98876 210
Q ss_pred CCCcCCCCHHHHHHHHHhHHHHHHHH
Q 043928 158 SWSARAFSNEQIKFAVHEAFAYYVIG 183 (192)
Q Consensus 158 ~W~~~~Ls~~Qi~YAa~Da~~~~~i~ 183 (192)
+-+=|..||.++.++|
T Consensus 145 ----------~~H~A~~DA~at~~l~ 160 (161)
T cd06137 145 ----------EGHDSLEDALAAREVV 160 (161)
T ss_pred ----------CCCCcHHHHHHHHHHh
Confidence 1133567888888776
No 47
>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=96.39 E-value=0.063 Score=52.08 Aligned_cols=127 Identities=15% Similarity=0.188 Sum_probs=83.0
Q ss_pred EEEEeeeecCCCCCceeEEEeeeC----Ce-----EEEEeccc-c--------C-------Ccc------HHHHHhhcCC
Q 043928 40 VVGIDVKFNHRCTKKAEMLILCAG----NR-----CLIIQLCH-L--------G-------QIP------ESLKKFLADE 88 (192)
Q Consensus 40 vvG~D~Ew~~~~~~~~aliQl~~~----~~-----~~l~~l~~-~--------~-------~~p------~~L~~~l~~~ 88 (192)
+|.+|+|.+......-.+||++.- +. ..++++.. + + .-| +.+.+|+.+
T Consensus 2 ~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~~l~~- 80 (850)
T TIGR01407 2 YAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLED- 80 (850)
T ss_pred EEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHHHhCC-
Confidence 789999999764445667776541 11 22333221 0 0 011 345667654
Q ss_pred CeeEEEEeehhhHHHhhc----CCCc--cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCCCcC
Q 043928 89 TICFVGIEMNGKVDGLGR----CNLR--CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSWSAR 162 (192)
Q Consensus 89 ~i~kvG~~~~~D~~~L~~----~g~~--~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~~ 162 (192)
-++|||++..|...|.+ +|+. ....+|.-.+++..++ ...+.+|.+|++.+|.+.. ..
T Consensus 81 -~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p--~~~~~~L~~l~~~~gi~~~--~~----------- 144 (850)
T TIGR01407 81 -GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFP--TEESYQLSELSEALGLTHE--NP----------- 144 (850)
T ss_pred -CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcC--CCCCCCHHHHHHHCCCCCC--CC-----------
Confidence 35899999999999875 5654 4578998888775443 3347899999998876655 21
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 163 AFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 163 ~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
+=|..||.+..+|+.++.+++
T Consensus 145 -------H~Al~DA~ata~l~~~l~~~~ 165 (850)
T TIGR01407 145 -------HRADSDAQATAELLLLLFEKM 165 (850)
T ss_pred -------CChHHHHHHHHHHHHHHHHHH
Confidence 336789999888888886653
No 48
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.19 E-value=0.18 Score=49.50 Aligned_cols=130 Identities=18% Similarity=0.251 Sum_probs=85.5
Q ss_pred CcEEEEeeeecCCCCC-ceeEEEeee----CCeE-----EEEecccc---------C-------Ccc------HHHHHhh
Q 043928 38 QRVVGIDVKFNHRCTK-KAEMLILCA----GNRC-----LIIQLCHL---------G-------QIP------ESLKKFL 85 (192)
Q Consensus 38 ~~vvG~D~Ew~~~~~~-~~aliQl~~----~~~~-----~l~~l~~~---------~-------~~p------~~L~~~l 85 (192)
..+|.+|+|.+..... .-.+||++. +++. .+++.... + .-| +.|.+|+
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~~l 82 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELL 82 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHHHHh
Confidence 3689999999865222 246788876 2221 23333210 0 011 2466777
Q ss_pred cCCCeeEEEEeehhhHHHhhc----CCCc--cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCC
Q 043928 86 ADETICFVGIEMNGKVDGLGR----CNLR--CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSW 159 (192)
Q Consensus 86 ~~~~i~kvG~~~~~D~~~L~~----~g~~--~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W 159 (192)
. +-++|||++..|...|.+ .|+. ....+|.-.+++..+ |...+.+|..|++.+|.+.. ..
T Consensus 83 ~--~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~--p~~~~~~L~~l~~~l~i~~~--~~-------- 148 (928)
T PRK08074 83 E--GAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILL--PTAESYKLRDLSEELGLEHD--QP-------- 148 (928)
T ss_pred C--CCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhc--CCCCCCCHHHHHHhCCCCCC--CC--------
Confidence 6 456899999999999975 4554 246899888887554 33346789999997765544 22
Q ss_pred CcCCCCHHHHHHHHHhHHHHHHHHHHHhcccC
Q 043928 160 SARAFSNEQIKFAVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 160 ~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~~ 191 (192)
+=|--||.+..+++.+|.+++.
T Consensus 149 ----------H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 149 ----------HRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred ----------CChHHHHHHHHHHHHHHHHHHH
Confidence 2367899999999999987653
No 49
>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=96.12 E-value=0.16 Score=51.01 Aligned_cols=130 Identities=18% Similarity=0.193 Sum_probs=88.5
Q ss_pred CCcEEEEeeeecCCCCCceeEEEeeeCC---eEE------EEeccc-c----------------C--Ccc---HHHHHhh
Q 043928 37 RQRVVGIDVKFNHRCTKKAEMLILCAGN---RCL------IIQLCH-L----------------G--QIP---ESLKKFL 85 (192)
Q Consensus 37 ~~~vvG~D~Ew~~~~~~~~aliQl~~~~---~~~------l~~l~~-~----------------~--~~p---~~L~~~l 85 (192)
+..+|.||+|.+......-.+||++.-. ... ++++.. + + .+. +.+.+|+
T Consensus 189 ~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~fl 268 (1213)
T TIGR01405 189 DATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFKEFF 268 (1213)
T ss_pred CCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHh
Confidence 4589999999997644455677776421 111 222110 0 0 011 2456677
Q ss_pred cCCCeeEEEEeehhhHHHhhc----CCCc--cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCC
Q 043928 86 ADETICFVGIEMNGKVDGLGR----CNLR--CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSW 159 (192)
Q Consensus 86 ~~~~i~kvG~~~~~D~~~L~~----~g~~--~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W 159 (192)
.+ -+.|||++..|...|.+ +|+. ....+|+-.+++..+ |.....+|..|++.+|.++. .
T Consensus 269 ~~--~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~--p~~k~~kL~~Lak~lgi~~~--~--------- 333 (1213)
T TIGR01405 269 KD--SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALN--PEYKSHRLGNICKKLGVDLD--D--------- 333 (1213)
T ss_pred CC--CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHh--ccCCCCCHHHHHHHcCCCCC--C---------
Confidence 64 46799999999998875 5654 347899988887543 33457899999998777766 1
Q ss_pred CcCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 160 SARAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 160 ~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
-+-|..||.++.+|+.++.+.+
T Consensus 334 ---------~HrAl~DA~aTa~I~~~ll~~l 355 (1213)
T TIGR01405 334 ---------HHRADYDAEATAKVFKVMVEQL 355 (1213)
T ss_pred ---------CcCHHHHHHHHHHHHHHHHHHH
Confidence 1778999999999999988654
No 50
>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=95.94 E-value=0.32 Score=38.59 Aligned_cols=142 Identities=16% Similarity=0.232 Sum_probs=83.1
Q ss_pred cEEEEeeeecC-----C-CCCceeEEEeeeCC-eEEEEeccccC--CccHHHHHhh--cCCCeeEEEEee-hhhHHHhhc
Q 043928 39 RVVGIDVKFNH-----R-CTKKAEMLILCAGN-RCLIIQLCHLG--QIPESLKKFL--ADETICFVGIEM-NGKVDGLGR 106 (192)
Q Consensus 39 ~vvG~D~Ew~~-----~-~~~~~aliQl~~~~-~~~l~~l~~~~--~~p~~L~~~l--~~~~i~kvG~~~-~~D~~~L~~ 106 (192)
+++.||+|... + ...++-+|-++..+ ..-++--...+ .+-..+.+++ .||++ .+|+++ ..|+..|..
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 68999999873 2 34566666666533 22222111111 1222334444 34554 569987 569988864
Q ss_pred ----CCCccC----------------------cEeehHHHHHHHhCCCCcCcccHHHHHHHhCc--ccCCCCCC-C-ccc
Q 043928 107 ----CNLRCK----------------------TAVELGHFAARVLKKPHISSFGLAKLAREVGI--HNSLASGF-N-GYA 156 (192)
Q Consensus 107 ----~g~~~~----------------------~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~--~l~~~K~k-~-~~~ 156 (192)
+|+.+. -.+|+=.+++.... ..+.+|..+|+.+|. +-. |.. . .+.
T Consensus 83 Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~---l~~y~L~~Va~~Lg~~k~~~--k~~~~~~~i 157 (188)
T cd05781 83 RARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE---VKVKTLENVAEYLGVMKKSE--RVLIEWYRI 157 (188)
T ss_pred HHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC---CCCCCHHHHHHHHCCCcccc--ccCCCHHHH
Confidence 775432 16887777664332 347899999986564 222 111 0 011
Q ss_pred -CCCCcCCCCHHHHHHHHHhHHHHHHHHHHH
Q 043928 157 -PSWSARAFSNEQIKFAVHEAFAYYVIGDRV 186 (192)
Q Consensus 157 -S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L 186 (192)
.-|....--.+=.+|+..||...+.||+++
T Consensus 158 ~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 158 YEYWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred HHHHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 235442245777999999999999999864
No 51
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=95.92 E-value=0.32 Score=38.94 Aligned_cols=79 Identities=15% Similarity=0.073 Sum_probs=57.9
Q ss_pred CeeEEEEeehhhHHHhhc----CCCc-----cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCC
Q 043928 89 TICFVGIEMNGKVDGLGR----CNLR-----CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSW 159 (192)
Q Consensus 89 ~i~kvG~~~~~D~~~L~~----~g~~-----~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W 159 (192)
+-+.|||++..|+..|.+ +|.. ....+|.-.+++..+ | ..+|..+++.+|.+..
T Consensus 105 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~--~---~~~L~~l~~~~gi~~~------------ 167 (200)
T TIGR01298 105 RAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAY--G---QTVLAKACQAAGXDFD------------ 167 (200)
T ss_pred CCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHc--C---cccHHHHHHHcCCCcc------------
Confidence 456999999999999975 4542 234899988887543 2 3579999986666543
Q ss_pred CcCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 160 SARAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 160 ~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
..+-+=|.-||.+..+|+.++.+++
T Consensus 168 ------~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 168 ------STQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred ------ccchhhhHHhHHHHHHHHHHHHHHH
Confidence 1234568899999999999988754
No 52
>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=95.91 E-value=0.2 Score=37.06 Aligned_cols=80 Identities=21% Similarity=0.128 Sum_probs=54.3
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhc-C---C--CccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGR-C---N--LRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGF 152 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~-~---g--~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k 152 (192)
.+.+++.. -+.|||++..|...|.+ + | ......+|+..+++...+.+ ...++..+.... |....
T Consensus 72 ~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~--~~~~l~~~~~~~~~~~~~----- 142 (159)
T cd06127 72 EFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGL--RSHRLGLLLAERYGIPLE----- 142 (159)
T ss_pred HHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCC--CcCchHHHHHHHcCCCCC-----
Confidence 45667775 57899999999998877 3 3 44568999998887655543 356677663223 43222
Q ss_pred CcccCCCCcCCCCHHHHHHHHHhHHHHHHHH
Q 043928 153 NGYAPSWSARAFSNEQIKFAVHEAFAYYVIG 183 (192)
Q Consensus 153 ~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~ 183 (192)
+-+-|..||..+.++|
T Consensus 143 ---------------~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 143 ---------------GAHRALADALATAELL 158 (159)
T ss_pred ---------------CCCCcHHHHHHHHHHh
Confidence 2345778898888876
No 53
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=95.90 E-value=0.37 Score=39.85 Aligned_cols=130 Identities=17% Similarity=0.119 Sum_probs=79.0
Q ss_pred CcEEEEeeeecCCCCCceeEEEeeeC----Ce-------EEEEeccc-c--------C----------CccH---HHHHh
Q 043928 38 QRVVGIDVKFNHRCTKKAEMLILCAG----NR-------CLIIQLCH-L--------G----------QIPE---SLKKF 84 (192)
Q Consensus 38 ~~vvG~D~Ew~~~~~~~~aliQl~~~----~~-------~~l~~l~~-~--------~----------~~p~---~L~~~ 84 (192)
..++.||+|.+.....+-.+||++.- +. ..+++... + + .++. .+.++
T Consensus 47 ~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~l~~~ 126 (239)
T PRK09146 47 VPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEA 126 (239)
T ss_pred CCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHHHHHH
Confidence 47999999999753333455555531 11 22333311 0 0 1122 34444
Q ss_pred hcCCCeeEEEEeehhhHHHhhc-----CCCc-cCcEeehHHHHHHHhCCC------C-----cCcccHHHHHHHhCcccC
Q 043928 85 LADETICFVGIEMNGKVDGLGR-----CNLR-CKTAVELGHFAARVLKKP------H-----ISSFGLAKLAREVGIHNS 147 (192)
Q Consensus 85 l~~~~i~kvG~~~~~D~~~L~~-----~g~~-~~~~~Dl~~~a~~~~~~~------~-----~~~~gL~~l~~~~g~~l~ 147 (192)
+.+ -+.|||+..-|...|.+ .+.. ...++|.-.+++...... . ....+|..+++.+|.+..
T Consensus 127 ~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl~~~ 204 (239)
T PRK09146 127 LAG--KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGLPAY 204 (239)
T ss_pred hCC--CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHcCCCCC
Confidence 443 46899999999998865 2333 246899888887543210 0 124568888887666544
Q ss_pred CCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 043928 148 LASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSS 189 (192)
Q Consensus 148 ~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~ 189 (192)
. -+=|..||.++.+|+..+.+.
T Consensus 205 --~------------------~H~Al~DA~ata~l~~~~~~~ 226 (239)
T PRK09146 205 --S------------------PHHALTDAIATAELLQAQIAH 226 (239)
T ss_pred --C------------------CCCcHHHHHHHHHHHHHHHHH
Confidence 1 134789999999999988754
No 54
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=95.87 E-value=0.12 Score=39.33 Aligned_cols=82 Identities=18% Similarity=0.165 Sum_probs=53.3
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhcCCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGRCNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPS 158 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~ 158 (192)
.|.+|+.+ .+ .|||++..|+..|.. +......+|...+.......+ ..+.||+++|+.+ |.++. . ..
T Consensus 70 ~l~~~l~~-~v-lVgHn~~fD~~~L~~-~~~~~~~~dt~~l~~~~~~~~-~~~~sL~~l~~~~lgi~~~--~-~~----- 137 (152)
T cd06144 70 KVAELLKG-RI-LVGHALKNDLKVLKL-DHPKKLIRDTSKYKPLRKTAK-GKSPSLKKLAKQLLGLDIQ--E-GE----- 137 (152)
T ss_pred HHHHHhCC-CE-EEEcCcHHHHHHhcC-cCCCccEEEeEEeeccccccC-CCChhHHHHHHHHcCcccC--C-CC-----
Confidence 57788875 44 599999999999975 111134666554432111111 2478999999998 98765 2 11
Q ss_pred CCcCCCCHHHHHHHHHhHHHHHHHHH
Q 043928 159 WSARAFSNEQIKFAVHEAFAYYVIGD 184 (192)
Q Consensus 159 W~~~~Ls~~Qi~YAa~Da~~~~~i~~ 184 (192)
+=|.-||.++.+||+
T Consensus 138 -----------H~Al~DA~at~~l~~ 152 (152)
T cd06144 138 -----------HSSVEDARAAMRLYR 152 (152)
T ss_pred -----------cCcHHHHHHHHHHhC
Confidence 336789999988874
No 55
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=95.86 E-value=0.16 Score=42.59 Aligned_cols=124 Identities=17% Similarity=0.224 Sum_probs=74.3
Q ss_pred cEEEEeeeecCC-CCCceeE---EEeeeCCeEEEEecc-cc------------C--------Ccc-----HHHHHhhcCC
Q 043928 39 RVVGIDVKFNHR-CTKKAEM---LILCAGNRCLIIQLC-HL------------G--------QIP-----ESLKKFLADE 88 (192)
Q Consensus 39 ~vvG~D~Ew~~~-~~~~~al---iQl~~~~~~~l~~l~-~~------------~--------~~p-----~~L~~~l~~~ 88 (192)
++|++|||.+.. .....++ +-|-....-+|||-. .+ + ..| ....+||..
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 599999999986 3333333 333344444455432 11 1 112 245678885
Q ss_pred CeeEEEEeehhhHHHhhc-CCCccCcEeehHH---HHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCC
Q 043928 89 TICFVGIEMNGKVDGLGR-CNLRCKTAVELGH---FAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARA 163 (192)
Q Consensus 89 ~i~kvG~~~~~D~~~L~~-~g~~~~~~~Dl~~---~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~ 163 (192)
=+-|||++.+|++.|.- +.-.. .=|.+. +.+ .+ .+....||+.|++++ |.++..+. . |
T Consensus 185 -RIlVGHaLhnDl~~L~l~hp~s~--iRDTs~~~pl~k-~~--~~~~tpSLK~Lt~~~Lg~~IQ~Ge----H-s------ 247 (280)
T KOG2249|consen 185 -RILVGHALHNDLQALKLEHPRSM--IRDTSKYPPLMK-LL--SKKATPSLKKLTEALLGKDIQVGE----H-S------ 247 (280)
T ss_pred -CEEeccccccHHHHHhhhCchhh--hcccccCchHHH-Hh--hccCCccHHHHHHHHhchhhhccc----c-C------
Confidence 45799999999999975 32110 112221 111 11 222478999999999 99988222 1 1
Q ss_pred CCHHHHHHHHHhHHHHHHHHHHHhc
Q 043928 164 FSNEQIKFAVHEAFAYYVIGDRVLS 188 (192)
Q Consensus 164 Ls~~Qi~YAa~Da~~~~~i~~~L~~ 188 (192)
..-||-+..++|.++..
T Consensus 248 --------SvEDA~AtM~LY~~vk~ 264 (280)
T KOG2249|consen 248 --------SVEDARATMELYKRVKV 264 (280)
T ss_pred --------cHHHHHHHHHHHHHHHH
Confidence 14689999999987653
No 56
>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=95.75 E-value=0.039 Score=43.56 Aligned_cols=73 Identities=15% Similarity=0.090 Sum_probs=53.2
Q ss_pred cCCCeeEEEEeehhhHHHhhc-CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCC
Q 043928 86 ADETICFVGIEMNGKVDGLGR-CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARA 163 (192)
Q Consensus 86 ~~~~i~kvG~~~~~D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~ 163 (192)
-+++-+.|||++.+|++.|.- +. -..++|.+.+.. .|...+.||+.|++++ |..+. ..
T Consensus 99 i~~~tILVGHsL~nDL~aL~l~hp--~~~viDTa~l~~----~~~~r~~sLk~La~~~L~~~IQ--~~------------ 158 (174)
T cd06143 99 VDLGCIFVGHGLAKDFRVINIQVP--KEQVIDTVELFH----LPGQRKLSLRFLAWYLLGEKIQ--SE------------ 158 (174)
T ss_pred cCCCCEEEeccchhHHHHhcCcCC--CcceEEcHHhcc----CCCCCChhHHHHHHHHcCCccc--CC------------
Confidence 456778999999999999974 11 237899876643 2322378999999999 99988 21
Q ss_pred CCHHHHHHHHHhHHHHHHHH
Q 043928 164 FSNEQIKFAVHEAFAYYVIG 183 (192)
Q Consensus 164 Ls~~Qi~YAa~Da~~~~~i~ 183 (192)
-+-..-||.+++++|
T Consensus 159 -----~HdSvEDArAam~Ly 173 (174)
T cd06143 159 -----THDSIEDARTALKLY 173 (174)
T ss_pred -----CcCcHHHHHHHHHHh
Confidence 022357899998887
No 57
>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=95.38 E-value=0.14 Score=41.44 Aligned_cols=132 Identities=12% Similarity=0.061 Sum_probs=76.9
Q ss_pred ecCCCCCceeEEEeee---CCeEEEEeccccC---CccHHHHHhhcCCCeeEEEEee-hhhHHHhhc----CCCccC---
Q 043928 47 FNHRCTKKAEMLILCA---GNRCLIIQLCHLG---QIPESLKKFLADETICFVGIEM-NGKVDGLGR----CNLRCK--- 112 (192)
Q Consensus 47 w~~~~~~~~aliQl~~---~~~~~l~~l~~~~---~~p~~L~~~l~~~~i~kvG~~~-~~D~~~L~~----~g~~~~--- 112 (192)
+.|...+++.+|-++. .+.-+.+.-.... .+-..+.+++.+.+-+.||+++ ..|+-.|.. +|+...
T Consensus 45 ~l~~~~~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~ 124 (208)
T cd05782 45 FLPLPFHKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYF 124 (208)
T ss_pred CCccccCceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCcccc
Confidence 3333567777777776 3333323211111 1223444555542235699988 569998865 777422
Q ss_pred ---------------cEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCC---CcccCCCCcCCCCHHHHHHHHH
Q 043928 113 ---------------TAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGF---NGYAPSWSARAFSNEQIKFAVH 174 (192)
Q Consensus 113 ---------------~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k---~~~~S~W~~~~Ls~~Qi~YAa~ 174 (192)
..+||-.+.+. .+. ..+.+|..+|+.+|.+ . |.. +.-..-|.... -++=.+|+..
T Consensus 125 ~~~~~~~~y~~r~~~~h~DL~~~~~~-~~~--~~~~~L~~va~~lG~~-~--K~d~~G~~v~~~y~~g~-~~~I~~Yc~~ 197 (208)
T cd05782 125 DLGNKDWNYRNRYSERHLDLMDLLAF-YGA--RARASLDLLAKLLGIP-G--KMDVDGSQVWELYAEGK-LDEIAEYCET 197 (208)
T ss_pred CcccchhhccCcCCCCcccHHHHHhc-cCc--cCCCCHHHHHHHhCCC-C--CcCCCHHHHHHHHHcCC-hHHHHHHHHH
Confidence 16787776653 222 3478999999866652 2 211 11123455434 5667899999
Q ss_pred hHHHHHHHHHH
Q 043928 175 EAFAYYVIGDR 185 (192)
Q Consensus 175 Da~~~~~i~~~ 185 (192)
|+...+.||.+
T Consensus 198 Dv~~t~~l~lr 208 (208)
T cd05782 198 DVLNTYLLYLR 208 (208)
T ss_pred HHHHHHHHHhC
Confidence 99999999853
No 58
>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=95.17 E-value=0.28 Score=40.10 Aligned_cols=96 Identities=13% Similarity=0.181 Sum_probs=60.0
Q ss_pred cCCCeeEEEEeehh-hHHHhhc----CCCcc------------------------------------CcEeehHHHHHHH
Q 043928 86 ADETICFVGIEMNG-KVDGLGR----CNLRC------------------------------------KTAVELGHFAARV 124 (192)
Q Consensus 86 ~~~~i~kvG~~~~~-D~~~L~~----~g~~~------------------------------------~~~~Dl~~~a~~~ 124 (192)
.||+| .+||++.+ |+..|.+ +|+.. +-.+|+-.+++..
T Consensus 85 ~DPDi-i~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~iD~~~~~~~~ 163 (230)
T cd05777 85 VDPDI-ITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVIQRD 163 (230)
T ss_pred cCCCE-EEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEEeeeHHHHHHHh
Confidence 46776 78998854 9988764 55431 0124554444432
Q ss_pred hCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCC-cCCC-CHHHHHHHHHhHHHHHHHHHHHh
Q 043928 125 LKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWS-ARAF-SNEQIKFAVHEAFAYYVIGDRVL 187 (192)
Q Consensus 125 ~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~-~~~L-s~~Qi~YAa~Da~~~~~i~~~L~ 187 (192)
. ...+.+|..+|+++ |.+-.-...+ ..++|. ..|= -..=++|...||...++|+.+|.
T Consensus 164 ~---kl~sy~L~~Va~~~Lg~~k~d~~~~--~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 164 Y---KLRSYSLNSVSAHFLGEQKEDVHYS--IITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred c---CcccCcHHHHHHHHhCCCCCCCCHH--HHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 2 23478999999999 8653211112 234443 2222 24569999999999999999885
No 59
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.12 E-value=0.88 Score=44.17 Aligned_cols=128 Identities=16% Similarity=0.219 Sum_probs=83.9
Q ss_pred CcEEEEeeeecCCCCCceeEEEeeeC----Ce-----EEEEeccc-c--------C-------Ccc------HHHHHhhc
Q 043928 38 QRVVGIDVKFNHRCTKKAEMLILCAG----NR-----CLIIQLCH-L--------G-------QIP------ESLKKFLA 86 (192)
Q Consensus 38 ~~vvG~D~Ew~~~~~~~~aliQl~~~----~~-----~~l~~l~~-~--------~-------~~p------~~L~~~l~ 86 (192)
..++.+|+|.+.... .-.+||++.- +. ..++++.. + + .-| +.+.+|+.
T Consensus 7 ~~~vvvD~ETTGl~~-~d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~l~ 85 (820)
T PRK07246 7 RKYAVVDLEATGAGP-NASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIE 85 (820)
T ss_pred CCEEEEEEecCCcCC-CCeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHHhC
Confidence 479999999987532 3467787642 22 11222211 0 0 011 24566776
Q ss_pred CCCeeEEEEeehhhHHHhhc----CCCcc-CcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCCCc
Q 043928 87 DETICFVGIEMNGKVDGLGR----CNLRC-KTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSWSA 161 (192)
Q Consensus 87 ~~~i~kvG~~~~~D~~~L~~----~g~~~-~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~ 161 (192)
+ -+.|||++..|...|.+ .|... ...+|.-.+++..++ ...+.+|..+|+.+|.+.. ..
T Consensus 86 ~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p--~~~~~~L~~L~~~lgl~~~--~~---------- 149 (820)
T PRK07246 86 D--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFP--TLEKYSLSHLSRELNIDLA--DA---------- 149 (820)
T ss_pred C--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhC--CCCCCCHHHHHHHcCCCCC--CC----------
Confidence 4 55899999999998875 24433 356888888876553 3347899999987776655 21
Q ss_pred CCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 162 RAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 162 ~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
+=|..||.++.+++.+|.+++
T Consensus 150 --------H~Al~DA~ata~L~~~l~~~l 170 (820)
T PRK07246 150 --------HTAIADARATAELFLKLLQKI 170 (820)
T ss_pred --------CCHHHHHHHHHHHHHHHHHHH
Confidence 237799999999999988764
No 60
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=95.08 E-value=0.055 Score=41.32 Aligned_cols=81 Identities=17% Similarity=0.185 Sum_probs=57.1
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhcCCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGRCNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPS 158 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~ 158 (192)
.+.+|+. ++-+.|||++..|++.|.... ..++|...+++..++.+ .+.+|..||+.+ |..+. ..
T Consensus 68 ~~~~fl~-~~~vlVgHn~~fD~~fL~~~~---~~~iDT~~l~r~~~~~~--~~~~L~~L~~~~~~~~i~--~~------- 132 (150)
T cd06145 68 KLLSLIS-PDTILVGHSLENDLKALKLIH---PRVIDTAILFPHPRGPP--YKPSLKNLAKKYLGRDIQ--QG------- 132 (150)
T ss_pred HHHHHhC-CCCEEEEcChHHHHHHhhccC---CCEEEcHHhccccCCCC--CChhHHHHHHHHCCccee--CC-------
Confidence 5566674 345789999999999998721 35899888877544432 367999999999 87665 10
Q ss_pred CCcCCCCHHHHHHHHHhHHHHHHHH
Q 043928 159 WSARAFSNEQIKFAVHEAFAYYVIG 183 (192)
Q Consensus 159 W~~~~Ls~~Qi~YAa~Da~~~~~i~ 183 (192)
.+-+=|.-||.++.+||
T Consensus 133 --------~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 133 --------EGGHDSVEDARAALELV 149 (150)
T ss_pred --------CCCCCcHHHHHHHHHHh
Confidence 01133667888888876
No 61
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=94.80 E-value=0.74 Score=36.01 Aligned_cols=79 Identities=16% Similarity=0.107 Sum_probs=54.8
Q ss_pred HHHHhhcC--CCeeEEEEee-hhhHHHhhc----CCCcc---CcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCC
Q 043928 80 SLKKFLAD--ETICFVGIEM-NGKVDGLGR----CNLRC---KTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSL 148 (192)
Q Consensus 80 ~L~~~l~~--~~i~kvG~~~-~~D~~~L~~----~g~~~---~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~ 148 (192)
.|.+|+.. ...+.|||++ ..|...|.+ +|... ..++|.-.+++... + +|.+|++.+ |.+..
T Consensus 87 ~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~------~-~L~~l~~~~~~~~~~- 158 (177)
T cd06136 87 LIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD------Q-SLGSLYKRLFGQEPK- 158 (177)
T ss_pred HHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH------h-hHHHHHHHHhCCCcc-
Confidence 46666653 3478999998 899999975 56543 23478666665321 2 899999987 88776
Q ss_pred CCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHH
Q 043928 149 ASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDR 185 (192)
Q Consensus 149 ~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~ 185 (192)
. -+=|..||.++.+++.+
T Consensus 159 -~------------------~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 159 -N------------------SHTAEGDVLALLKCALH 176 (177)
T ss_pred -c------------------ccchHHHHHHHHHHHhh
Confidence 2 13477899999888753
No 62
>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=94.33 E-value=0.39 Score=38.41 Aligned_cols=137 Identities=15% Similarity=0.185 Sum_probs=76.3
Q ss_pred cEEEEeeeecCCCCCceeEEEeeeCC--eEEEEecccc---------C---CccHHHHHhhc--CCCeeEEEEeehh-hH
Q 043928 39 RVVGIDVKFNHRCTKKAEMLILCAGN--RCLIIQLCHL---------G---QIPESLKKFLA--DETICFVGIEMNG-KV 101 (192)
Q Consensus 39 ~vvG~D~Ew~~~~~~~~aliQl~~~~--~~~l~~l~~~---------~---~~p~~L~~~l~--~~~i~kvG~~~~~-D~ 101 (192)
++++||+|-.. .+++-++.+.... .++++-.+.. . .+-..+.+++. ||+ +.+||++.+ |+
T Consensus 4 ~~~~fDIE~~~--~~~i~~i~~~~~~~~~i~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i~~~dPD-vi~g~N~~~FD~ 80 (193)
T cd05784 4 KVVSLDIETSM--DGELYSIGLYGEGQERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQYDPD-IIIGWNVINFDL 80 (193)
T ss_pred cEEEEEeecCC--CCCEEEEEeecCCCCEEEEECCCCCCCCCEEEEECCHHHHHHHHHHHHHhhCCC-EEEECCCcCcCH
Confidence 68999999753 2233333332322 2333322111 1 11123444444 444 478998865 99
Q ss_pred HHhhc----CCCccC-------------c-------------EeehHHHHHH-HhCCCCcCcccHHHHHHHh-CcccCCC
Q 043928 102 DGLGR----CNLRCK-------------T-------------AVELGHFAAR-VLKKPHISSFGLAKLAREV-GIHNSLA 149 (192)
Q Consensus 102 ~~L~~----~g~~~~-------------~-------------~~Dl~~~a~~-~~~~~~~~~~gL~~l~~~~-g~~l~~~ 149 (192)
..|.+ +|+.+. + .+|+-.+.+. .+. ..+.+|.++|+++ |..-.-
T Consensus 81 ~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~k---l~sy~L~~Va~~~Lg~~K~~- 156 (193)
T cd05784 81 RLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYH---FESFSLENVAQELLGEGKLI- 156 (193)
T ss_pred HHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccCC---CCcCCHHHHHHHHhCCCccc-
Confidence 88864 565431 1 5776555543 122 3478999999999 863220
Q ss_pred CCCC---cccC-CCCcCCCCHHHHHHHHHhHHHHHHHHH
Q 043928 150 SGFN---GYAP-SWSARAFSNEQIKFAVHEAFAYYVIGD 184 (192)
Q Consensus 150 K~k~---~~~S-~W~~~~Ls~~Qi~YAa~Da~~~~~i~~ 184 (192)
.+.. ...+ -|.+.+ ..-++|+..||+.+++|++
T Consensus 157 ~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 157 HDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred cCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 1110 0112 244333 4679999999999999873
No 63
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=94.31 E-value=2.2 Score=34.10 Aligned_cols=89 Identities=18% Similarity=0.185 Sum_probs=57.6
Q ss_pred HHHHhhcCCCeeEEEEeeh-hhHHHhhcCCCccCc--EeehHHHHHHHh--CCCCcCcccHHHHHHHhCcccCCCCCCCc
Q 043928 80 SLKKFLADETICFVGIEMN-GKVDGLGRCNLRCKT--AVELGHFAARVL--KKPHISSFGLAKLAREVGIHNSLASGFNG 154 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~-~D~~~L~~~g~~~~~--~~Dl~~~a~~~~--~~~~~~~~gL~~l~~~~g~~l~~~K~k~~ 154 (192)
.+.+|+.+. ..|||++. .|+..|.++|..+.+ .+|+-..+.... -.|.....+|..||+.+|.+.. .
T Consensus 77 ~f~~f~~~~--~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~~--~---- 148 (195)
T PRK07247 77 AFKEFVGEL--PLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADFLGIKGR--G---- 148 (195)
T ss_pred HHHHHHCCC--eEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHhcCCCCC--C----
Confidence 556667644 47999996 799999876655443 356443331111 1233346789999987765422 1
Q ss_pred ccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcccC
Q 043928 155 YAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 155 ~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~~ 191 (192)
+=|.-||.++.+||.+|+....
T Consensus 149 ---------------HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 149 ---------------HNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred ---------------cCCHHHHHHHHHHHHHHHhhcc
Confidence 2257899999999999987643
No 64
>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=93.87 E-value=0.84 Score=36.83 Aligned_cols=140 Identities=12% Similarity=0.206 Sum_probs=79.0
Q ss_pred cEEEEeeeecCC--------CCCceeEEEeeeCC--e-EEEEeccccC--CccHHHHHhh--cCCCeeEEEEee-hhhHH
Q 043928 39 RVVGIDVKFNHR--------CTKKAEMLILCAGN--R-CLIIQLCHLG--QIPESLKKFL--ADETICFVGIEM-NGKVD 102 (192)
Q Consensus 39 ~vvG~D~Ew~~~--------~~~~~aliQl~~~~--~-~~l~~l~~~~--~~p~~L~~~l--~~~~i~kvG~~~-~~D~~ 102 (192)
++++||+|-... ....-.++|+|... . -.++.....+ .+-..+.+++ .||+ +.+||++ ..|+.
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPd-ii~g~N~~~FD~p 88 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPD-VIEGHNIFRFDLP 88 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccCCCCHHHHHHHHHHHHHHhCCC-EEeccCCcccCHH
Confidence 799999998543 12234678887743 1 1222211111 1112334444 3566 5679988 67999
Q ss_pred Hhhc----CCCccC--------------------------------cEeehHHHHHHH-hCCCCcCcccHHHHHHHhCcc
Q 043928 103 GLGR----CNLRCK--------------------------------TAVELGHFAARV-LKKPHISSFGLAKLAREVGIH 145 (192)
Q Consensus 103 ~L~~----~g~~~~--------------------------------~~~Dl~~~a~~~-~~~~~~~~~gL~~l~~~~g~~ 145 (192)
.|.+ +|+... -.+|+-.+++.. .......+-+|..+|+.+|..
T Consensus 89 yl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~ 168 (207)
T cd05785 89 YLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLA 168 (207)
T ss_pred HHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHhccc
Confidence 8864 665431 126776665531 011123467999999987542
Q ss_pred cCCCCC----CCcccCCCCcCCCCHHHHHHHHHhHHHHHHHH
Q 043928 146 NSLASG----FNGYAPSWSARAFSNEQIKFAVHEAFAYYVIG 183 (192)
Q Consensus 146 l~~~K~----k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~ 183 (192)
-. .|. +.+ ..-|...+ ++=++|+..||...++|+
T Consensus 169 ~~-~k~d~~~~~I-~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 169 SP-DRTYIDGRQI-AEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred CC-CcCCCCHHHH-HHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 21 011 111 23455442 677999999999999885
No 65
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=93.61 E-value=0.19 Score=48.16 Aligned_cols=91 Identities=14% Similarity=0.154 Sum_probs=59.9
Q ss_pred eeEEEEeehhhHHHhhc-CCCccC--cEeehHHHHHHHh--------------------------------CCCCcCc--
Q 043928 90 ICFVGIEMNGKVDGLGR-CNLRCK--TAVELGHFAARVL--------------------------------KKPHISS-- 132 (192)
Q Consensus 90 i~kvG~~~~~D~~~L~~-~g~~~~--~~~Dl~~~a~~~~--------------------------------~~~~~~~-- 132 (192)
=++|||+++.|-.++++ |+++-. .++|...+.-... +.|+...
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 57899999999999999 887532 4566544321111 1233333
Q ss_pred -ccHHHHHHHh-Ccc-cCCCCCCCcccCCCCcCCCCHHHH--------HHHHHhHHHHHHHHHHHh
Q 043928 133 -FGLAKLAREV-GIH-NSLASGFNGYAPSWSARAFSNEQI--------KFAVHEAFAYYVIGDRVL 187 (192)
Q Consensus 133 -~gL~~l~~~~-g~~-l~~~K~k~~~~S~W~~~~Ls~~Qi--------~YAa~Da~~~~~i~~~L~ 187 (192)
-||.+.++-+ |.. ++ |.++- ... .++.||| .|.|.|+++..+||.++.
T Consensus 322 ~NSL~dVhk~~c~~~~Ld--Kt~Rd---~Fv--s~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lf 380 (1075)
T KOG3657|consen 322 LNSLVDVHKFHCGIDALD--KTPRD---SFV--SGTKEQIRENFQPLMNYCARDVIATHQVFFRLF 380 (1075)
T ss_pred hHHHHHHHHhhCCCCccc--cchHH---hhh--cCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHh
Confidence 3566666666 666 88 65542 222 4566665 699999999999999875
No 66
>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=93.37 E-value=1.7 Score=35.12 Aligned_cols=92 Identities=15% Similarity=0.070 Sum_probs=58.1
Q ss_pred CCCeeEEEEee-hhhHHHhhc----CCCccC--------c----------EeehHHHHHHHhCCCCcCcccHHHHHHHh-
Q 043928 87 DETICFVGIEM-NGKVDGLGR----CNLRCK--------T----------AVELGHFAARVLKKPHISSFGLAKLAREV- 142 (192)
Q Consensus 87 ~~~i~kvG~~~-~~D~~~L~~----~g~~~~--------~----------~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~- 142 (192)
+|++ .+|+++ ..|+..|.+ +|+... + .+|+=.+++...-.+ ...-+|...|+.+
T Consensus 88 ~Pd~-i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~-~~sysLd~Va~~~L 165 (204)
T cd05779 88 KPHI-IVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLP-QGSQGLKAVTKAKL 165 (204)
T ss_pred CCCE-EEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCC-CCCccHHHHHHHHh
Confidence 4555 688876 569988864 676532 1 577766665321111 1367899999988
Q ss_pred Ccc-cCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHH
Q 043928 143 GIH-NSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGD 184 (192)
Q Consensus 143 g~~-l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~ 184 (192)
|.. .+. ..+.+.. -|...+ ++=++|+-.||...+.+|.
T Consensus 166 g~~K~~~-~~~~I~~-~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 166 GYDPVEL-DPEDMVP-LAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred CCCcCcC-CHHHHHH-HHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 863 221 1112221 565544 5679999999999999983
No 67
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=93.11 E-value=4.1 Score=33.19 Aligned_cols=80 Identities=9% Similarity=0.014 Sum_probs=57.8
Q ss_pred CeeEEEEeehhhHHHhhcCCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCCCcCCCCHHH
Q 043928 89 TICFVGIEMNGKVDGLGRCNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSWSARAFSNEQ 168 (192)
Q Consensus 89 ~i~kvG~~~~~D~~~L~~~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~~~Ls~~Q 168 (192)
.-+.|||++..|...|...+ ...+|.-.+|+..++. . ..++..|++.+|...+ .+. . .+
T Consensus 74 ~~~lVaHNa~FD~~~L~~~~---~~~idTl~lar~l~p~--~-~~~l~~L~~~~~l~~~--~~~---~----------~~ 132 (219)
T PRK07983 74 SEWYVAHNASFDRRVLPEMP---GEWICTMKLARRLWPG--I-KYSNMALYKSRKLNVQ--TPP---G----------LH 132 (219)
T ss_pred CCEEEEeCcHhhHHHHhCcC---CCcEeHHHHHHHHccC--C-CCCHHHHHHHcCCCCC--CCC---C----------CC
Confidence 45789999999999997632 3789988888876643 2 4788899876665443 100 0 12
Q ss_pred HHHHHHhHHHHHHHHHHHhcc
Q 043928 169 IKFAVHEAFAYYVIGDRVLSS 189 (192)
Q Consensus 169 i~YAa~Da~~~~~i~~~L~~~ 189 (192)
-+=|..||+++.+++.++.+.
T Consensus 133 aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 133 HHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred CCcHHHHHHHHHHHHHHHHHH
Confidence 355899999999999998854
No 68
>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=92.93 E-value=0.076 Score=40.55 Aligned_cols=139 Identities=12% Similarity=0.104 Sum_probs=71.0
Q ss_pred EEEeeeecCC--CCCceeEEEeee--CCeEE-EEeccccC-CccHHHHH---hhcCCCeeEEEEee-hhhHHHhhc----
Q 043928 41 VGIDVKFNHR--CTKKAEMLILCA--GNRCL-IIQLCHLG-QIPESLKK---FLADETICFVGIEM-NGKVDGLGR---- 106 (192)
Q Consensus 41 vG~D~Ew~~~--~~~~~aliQl~~--~~~~~-l~~l~~~~-~~p~~L~~---~l~~~~i~kvG~~~-~~D~~~L~~---- 106 (192)
+-||+|..+. ..+.+-++-++. ++... ..+....+ .-...+.+ ++..... .++|+. ..|...|.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~l~~~~~-iv~yng~~FD~p~L~~~~~~ 79 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFFELLDEADN-IVTYNGKNFDIPFLKRRAKR 79 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH--HHHHTT---EEESSTTTTHHHHHHHHH-H
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHHHHHhcCCe-EEEEeCcccCHHHHHHHHHH
Confidence 3589999855 346677777774 33333 44433221 11223333 4555544 455654 669988876
Q ss_pred CCCc-cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCC---CCc---ccCCCC---cCCCCHHHHHHHHHhH
Q 043928 107 CNLR-CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASG---FNG---YAPSWS---ARAFSNEQIKFAVHEA 176 (192)
Q Consensus 107 ~g~~-~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~---k~~---~~S~W~---~~~Ls~~Qi~YAa~Da 176 (192)
+++. ..+.+||...+++... .+.||+.+++.+|..-. ++ ... ....|. .+...++-+.|.-.|+
T Consensus 80 ~~~~~~~~~iDl~~~~~~~~~----~~~~Lk~ve~~lg~~~~--~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~Dv 153 (164)
T PF13482_consen 80 YGLPPPFNHIDLLKIIKKHFL----ESYSLKNVEKFLGIERR--DDDISGSESVKLYKEYLETGDPEALEEILEYNEDDV 153 (164)
T ss_dssp HHH--GGGEEEHHHHHT-TTS----CCTT--SHHH-------------HHHHHHHHHH---TTGGTS--HHHHHHHHHHH
T ss_pred cCCCcccchhhHHHHHHhccC----CCCCHHHHhhhcccccc--cCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence 4554 6789999988764222 36789999988733222 10 010 011221 1357788899999999
Q ss_pred HHHHHHHHHH
Q 043928 177 FAYYVIGDRV 186 (192)
Q Consensus 177 ~~~~~i~~~L 186 (192)
..+..|++.|
T Consensus 154 ~~~~~L~~~l 163 (164)
T PF13482_consen 154 RATRRLYEWL 163 (164)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHh
Confidence 9999999876
No 69
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=92.59 E-value=0.16 Score=44.79 Aligned_cols=85 Identities=16% Similarity=0.177 Sum_probs=60.0
Q ss_pred HHHHHhhcCCCeeEEEEeehhhHHHhhc-CCCccCcEeehHHHHHHHhCC-CCcCcccHHHHHHHh-CcccCCCCCCCcc
Q 043928 79 ESLKKFLADETICFVGIEMNGKVDGLGR-CNLRCKTAVELGHFAARVLKK-PHISSFGLAKLAREV-GIHNSLASGFNGY 155 (192)
Q Consensus 79 ~~L~~~l~~~~i~kvG~~~~~D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~-~~~~~~gL~~l~~~~-g~~l~~~K~k~~~ 155 (192)
..|+. |-+++-+-|||+..+|++.|+- |+ .++|.+.+.....|. | ...+|+.|++.+ |..+....+..
T Consensus 285 ~~l~~-~~~~~TILVGHSLenDL~aLKl~H~----~ViDTa~lf~~~~g~~~--~k~sLk~L~~~~L~~~Iq~~~~~H-- 355 (380)
T KOG2248|consen 285 KELLE-LISKNTILVGHSLENDLKALKLDHP----SVIDTAVLFKHPTGPYP--FKSSLKNLAKSYLGKLIQEGVGGH-- 355 (380)
T ss_pred HHHHh-hcCcCcEEEeechhhHHHHHhhhCC----ceeeeeEEEecCCCCcc--chHHHHHHHHHHHHHHHhccCCCC--
Confidence 34566 5677888999999999999997 65 788887665433442 3 367899999999 98776111111
Q ss_pred cCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 043928 156 APSWSARAFSNEQIKFAVHEAFAYYVIGDRVL 187 (192)
Q Consensus 156 ~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~ 187 (192)
=.+.||.+++++.....
T Consensus 356 ---------------dS~eDA~acm~Lv~~k~ 372 (380)
T KOG2248|consen 356 ---------------DSVEDALACMKLVKLKI 372 (380)
T ss_pred ---------------ccHHHHHHHHHHHHHHH
Confidence 12579999988876443
No 70
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=92.52 E-value=2.7 Score=37.14 Aligned_cols=138 Identities=9% Similarity=0.053 Sum_probs=81.2
Q ss_pred CCcEEEEeeeecCCCCCceeEEEeee---C-C------eEEEEecccc-------C-------------CccHHHHHhhc
Q 043928 37 RQRVVGIDVKFNHRCTKKAEMLILCA---G-N------RCLIIQLCHL-------G-------------QIPESLKKFLA 86 (192)
Q Consensus 37 ~~~vvG~D~Ew~~~~~~~~aliQl~~---~-~------~~~l~~l~~~-------~-------------~~p~~L~~~l~ 86 (192)
+..++.||+|.+......-.+|+|+. . + ...+++.... + .+-+.|.+|+.
T Consensus 45 ~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~~fL~ 124 (377)
T PRK05601 45 AAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLDRLID 124 (377)
T ss_pred CCCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHHHHhC
Confidence 34799999999987444456676631 1 1 1223322110 0 01135778887
Q ss_pred CCCeeEEEEeehhhHHHhhc-C-------------------------------CCc-cCcEeehHHHHHHHhCCCCcCcc
Q 043928 87 DETICFVGIEMNGKVDGLGR-C-------------------------------NLR-CKTAVELGHFAARVLKKPHISSF 133 (192)
Q Consensus 87 ~~~i~kvG~~~~~D~~~L~~-~-------------------------------g~~-~~~~~Dl~~~a~~~~~~~~~~~~ 133 (192)
+ -+.|+|+...|...|.+ + ++. +..++|.-.+++..+ |...+.
T Consensus 125 g--~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~--p~l~~~ 200 (377)
T PRK05601 125 G--RTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQG--VALDDI 200 (377)
T ss_pred C--CEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHc--CCCCCC
Confidence 4 35799999999998765 2 111 235799888887544 334578
Q ss_pred cHHHHHHHhCcccCCCCC-CCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 043928 134 GLAKLAREVGIHNSLASG-FNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVL 187 (192)
Q Consensus 134 gL~~l~~~~g~~l~~~K~-k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~ 187 (192)
.|..+|+.+|...+ -. -++++..-.-+.|+ --||-++..||.++.
T Consensus 201 rL~~La~~lGi~~p--~~~A~~~Ra~~p~~~l~-------~~Da~ll~~l~~~~~ 246 (377)
T PRK05601 201 RIRGVAHTLGLDAP--AAEASVERAQVPHRQLC-------REETLLVARLYFALR 246 (377)
T ss_pred CHHHHHHHhCCCCC--chhhhhhhhcCChhhhh-------hHHHHHHHHHHHHhh
Confidence 99999998887764 10 01111111111111 138899999998763
No 71
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=92.47 E-value=1 Score=38.57 Aligned_cols=87 Identities=14% Similarity=0.114 Sum_probs=63.5
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhc----CCCcc--CcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGR----CNLRC--KTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFN 153 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~----~g~~~--~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~ 153 (192)
.|.+|+.+ -+.|||++..|...|.+ +|... ..++|.-.+++..++. ....+|..|++.+|.+..
T Consensus 73 ~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~--~~~~~L~~L~~~~gi~~~------ 142 (309)
T PRK06195 73 KIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSN--IDNARLNTVNNFLGYEFK------ 142 (309)
T ss_pred HHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCC--CCcCCHHHHHHHcCCCCc------
Confidence 45666653 56899999999998865 55543 3688988888765532 236789999987764322
Q ss_pred cccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcccC
Q 043928 154 GYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSSLD 191 (192)
Q Consensus 154 ~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~~ 191 (192)
-+=|.-||+++.+|+.+|.+++.
T Consensus 143 ---------------~H~Al~DA~ata~l~~~l~~~~~ 165 (309)
T PRK06195 143 ---------------HHDALADAMACSNILLNISKELN 165 (309)
T ss_pred ---------------ccCCHHHHHHHHHHHHHHHHHhc
Confidence 15578999999999999987653
No 72
>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=91.89 E-value=5.6 Score=31.95 Aligned_cols=136 Identities=12% Similarity=0.114 Sum_probs=78.6
Q ss_pred cEEEEeeeecCC--------CCCceeEEEeeeCC-----eEEEEeccc----------------cC---CccHHHHHhhc
Q 043928 39 RVVGIDVKFNHR--------CTKKAEMLILCAGN-----RCLIIQLCH----------------LG---QIPESLKKFLA 86 (192)
Q Consensus 39 ~vvG~D~Ew~~~--------~~~~~aliQl~~~~-----~~~l~~l~~----------------~~---~~p~~L~~~l~ 86 (192)
++++||+|-... ....-.+||++..+ +.+++.... .. .+-..+.+++.
T Consensus 6 rilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~ 85 (204)
T cd05783 6 KRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKELIREAFKIIS 85 (204)
T ss_pred eEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEEEEEecCCcccccccCCCCCeEEecCCHHHHHHHHHHHHh
Confidence 699999998632 11113567777633 344443110 01 11134455566
Q ss_pred CCCeeEEEEee-hhhHHHhhc----CCCc----------------cCcEeehHHHHHH------HhCCCCcCcccHHHHH
Q 043928 87 DETICFVGIEM-NGKVDGLGR----CNLR----------------CKTAVELGHFAAR------VLKKPHISSFGLAKLA 139 (192)
Q Consensus 87 ~~~i~kvG~~~-~~D~~~L~~----~g~~----------------~~~~~Dl~~~a~~------~~~~~~~~~~gL~~l~ 139 (192)
+.. +.+|+++ ..|+..|.+ +|+. -.-.+|+-..+.. .++. ...+.+|.++|
T Consensus 86 ~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~-~~~~~~L~~Va 163 (204)
T cd05783 86 EYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGN-KYREYTLDAVA 163 (204)
T ss_pred cCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcc-ccccCcHHHHH
Confidence 554 5678977 569998865 7776 1235777554331 0111 12478999999
Q ss_pred HHh-Ccc-cCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHH
Q 043928 140 REV-GIH-NSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGD 184 (192)
Q Consensus 140 ~~~-g~~-l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~ 184 (192)
+.+ |.. ++ -+..+. .. =.++=+.|+..||...++|+.
T Consensus 164 ~~~lg~~K~~--~~~~i~----~~--~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 164 KALLGEGKVE--LEKNIS----EL--NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred HHhcCCCccc--CCchhh----hh--cHHHHHHhhHHHHHHHHHHhc
Confidence 999 863 34 212222 11 113448999999999998864
No 73
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=91.30 E-value=7.8 Score=33.05 Aligned_cols=86 Identities=15% Similarity=-0.013 Sum_probs=51.8
Q ss_pred HHHHHhhcCCCeeEEEEeehhhHHHhhc-CC-CccCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCccc
Q 043928 79 ESLKKFLADETICFVGIEMNGKVDGLGR-CN-LRCKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYA 156 (192)
Q Consensus 79 ~~L~~~l~~~~i~kvG~~~~~D~~~L~~-~g-~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~ 156 (192)
..+..|+... -+.|||++..|...|.+ +. +......+.-... .+..+...+.+|..|+..+| . . . .
T Consensus 112 ~~l~~fl~~~-~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i--~~~~~~~~~~kL~~La~~~g-~-~--~-~---- 179 (294)
T PRK09182 112 AAVDALIAPA-DLIIAHNAGFDRPFLERFSPVFATKPWACSVSEI--DWSARGFEGTKLGYLAGQAG-F-F--H-E---- 179 (294)
T ss_pred HHHHHHhcCC-CEEEEeCHHHHHHHHHHHHHhccCCcccccHHHH--hhccccCCCCCHHHHHHHcC-C-C--C-C----
Confidence 3566777653 46799999999999977 21 1111222211111 12222234678999998766 1 1 1 0
Q ss_pred CCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 043928 157 PSWSARAFSNEQIKFAVHEAFAYYVIGDRVLS 188 (192)
Q Consensus 157 S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~ 188 (192)
-+=|..||.++.+|+.+.+.
T Consensus 180 ------------aHrAl~Da~Ata~ll~~~l~ 199 (294)
T PRK09182 180 ------------GHRAVDDCQALLELLARPLP 199 (294)
T ss_pred ------------CcChHHHHHHHHHHHHHHHh
Confidence 13378999999999986653
No 74
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=90.95 E-value=2.1 Score=44.00 Aligned_cols=81 Identities=17% Similarity=0.144 Sum_probs=60.4
Q ss_pred CCeeEEEEeehhhHHHhhc----CCCc--cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCCCc
Q 043928 88 ETICFVGIEMNGKVDGLGR----CNLR--CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSWSA 161 (192)
Q Consensus 88 ~~i~kvG~~~~~D~~~L~~----~g~~--~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~ 161 (192)
.+.+.|+|+...|...|.+ .|+. ....+|.-.+++..+ |.....+|..||+.+|..+. . .
T Consensus 498 gg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~--p~~k~~kL~~LAk~lGL~~~--~--~-------- 563 (1437)
T PRK00448 498 GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLY--PELKSHRLNTLAKKFGVELE--H--H-------- 563 (1437)
T ss_pred CCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHc--CccccccHHHHHHHcCCCCC--C--C--------
Confidence 4578899999999987753 5553 346788777776543 33457899999997777666 1 1
Q ss_pred CCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 162 RAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 162 ~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
+-|..||.++.+|+.++.+++
T Consensus 564 --------HrAl~DA~aTa~lf~~ll~~l 584 (1437)
T PRK00448 564 --------HRADYDAEATAYLLIKFLKDL 584 (1437)
T ss_pred --------cChHHHHHHHHHHHHHHHHHH
Confidence 668899999999999998764
No 75
>PRK11779 sbcB exonuclease I; Provisional
Probab=90.74 E-value=9.5 Score=34.83 Aligned_cols=132 Identities=11% Similarity=0.108 Sum_probs=75.5
Q ss_pred CcEEEEeeeecCCCCCceeEEEeeeC----C-------eEEEEeccc-----c------CC---------c--c---HHH
Q 043928 38 QRVVGIDVKFNHRCTKKAEMLILCAG----N-------RCLIIQLCH-----L------GQ---------I--P---ESL 81 (192)
Q Consensus 38 ~~vvG~D~Ew~~~~~~~~aliQl~~~----~-------~~~l~~l~~-----~------~~---------~--p---~~L 81 (192)
..++-+|+|.+......-.+||++.= + ....+++.. . +- . + +.+
T Consensus 6 ~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~~i 85 (476)
T PRK11779 6 PTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAARI 85 (476)
T ss_pred CcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHH
Confidence 47999999999874444567777641 1 123333321 0 00 0 0 145
Q ss_pred HHhhcCCCeeEEEEe-ehhhHHHhhc-CC---Cc--------cCcEeehHHHHHHHhC-------CC----CcCcccHHH
Q 043928 82 KKFLADETICFVGIE-MNGKVDGLGR-CN---LR--------CKTAVELGHFAARVLK-------KP----HISSFGLAK 137 (192)
Q Consensus 82 ~~~l~~~~i~kvG~~-~~~D~~~L~~-~g---~~--------~~~~~Dl~~~a~~~~~-------~~----~~~~~gL~~ 137 (192)
.+++..++.+.|||+ +..|...|+. +. +. ....+|+=++++..+. -| ......|..
T Consensus 86 ~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~ 165 (476)
T PRK11779 86 HAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEH 165 (476)
T ss_pred HHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHHH
Confidence 667765666789996 7899988876 31 11 1112344343332110 01 112467888
Q ss_pred HHHHhCcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 043928 138 LAREVGIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSS 189 (192)
Q Consensus 138 l~~~~g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~ 189 (192)
|++.+|.+.. +-+=|..||++..+|+..+.++
T Consensus 166 L~~~~gI~~~--------------------~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 166 LTKANGIEHE--------------------NAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHHcCCCCC--------------------CCCCcHHHHHHHHHHHHHHHHh
Confidence 8876665544 1134778999999999988765
No 76
>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=90.21 E-value=1.6 Score=32.66 Aligned_cols=79 Identities=22% Similarity=0.124 Sum_probs=56.4
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhc----CCCc--cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGR----CNLR--CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFN 153 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~----~g~~--~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~ 153 (192)
.|.+++.+ -+.|||++..|...|.+ +|+. ....+|+..+++..++. ..+.+|..+++.+|.+..
T Consensus 70 ~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~--~~~~~L~~l~~~~g~~~~------ 139 (156)
T cd06130 70 EIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPL--LPNHKLNTVAEHLGIELN------ 139 (156)
T ss_pred HHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhcc--CCCCCHHHHHHHcCCCcc------
Confidence 56777775 46899999999999975 4554 34789998888765543 347899999987664332
Q ss_pred cccCCCCcCCCCHHHHHHHHHhHHHHHHHH
Q 043928 154 GYAPSWSARAFSNEQIKFAVHEAFAYYVIG 183 (192)
Q Consensus 154 ~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~ 183 (192)
-+=|..||....+|+
T Consensus 140 ---------------~H~Al~Da~~ta~l~ 154 (156)
T cd06130 140 ---------------HHDALEDARACAEIL 154 (156)
T ss_pred ---------------CcCchHHHHHHHHHH
Confidence 133567888887776
No 77
>PHA02528 43 DNA polymerase; Provisional
Probab=88.74 E-value=26 Score=34.56 Aligned_cols=175 Identities=14% Similarity=0.176 Sum_probs=102.8
Q ss_pred EEcCcEEEEEEeCChHHHHHHHHHHHHh------------------h--------cCCcEEEEeeeecCC---CCC---c
Q 043928 7 DIQGNNMKVTVVDHAALIDDNVAALKAL------------------L--------KRQRVVGIDVKFNHR---CTK---K 54 (192)
Q Consensus 7 ~~~g~~i~v~vt~~~~~~~~~i~~~~~~------------------~--------~~~~vvG~D~Ew~~~---~~~---~ 54 (192)
.|.|+.+.-....+..+..+|++.+... + ++-++++||+|-.+. +.+ +
T Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~merfi~~~~~~~~~~~~~~~~p~lrv~s~DIE~~~~~gfP~p~~~~ 128 (881)
T PHA02528 49 DIYGKNCRPKKFDSMRDARKWMKRMKDVGFEALGMDDFKLQYISDTYPGEIKYDRSKIRIANLDIEVTAEDGFPDPEEAK 128 (881)
T ss_pred ccCCCEEeEEECCCHHHHHHHHHHHHhcCCceeehhHHhhhhhhhhcCCCCCCCCCCccEEEEEEEECCCCCCCCcccCC
Confidence 4778899999999999999999988654 0 122799999998652 111 1
Q ss_pred eeEEEeeeC----CeEEEEecc---------c--------------cCCccH---HHHHhh--cCCCeeEEEEeeh-hhH
Q 043928 55 AEMLILCAG----NRCLIIQLC---------H--------------LGQIPE---SLKKFL--ADETICFVGIEMN-GKV 101 (192)
Q Consensus 55 ~aliQl~~~----~~~~l~~l~---------~--------------~~~~p~---~L~~~l--~~~~i~kvG~~~~-~D~ 101 (192)
--+++++.. ++..++.+. . .+.-.. .+.+++ .||+| .+|+++. .|+
T Consensus 129 d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~eLL~~F~~~i~~~DPDI-I~GyNi~~FDl 207 (881)
T PHA02528 129 YEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTEREMLLEYINFWEENTPVI-FTGWNVELFDV 207 (881)
T ss_pred CcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCeeEEEcCCHHHHHHHHHHHHHHhCCcE-EEecCCccCCH
Confidence 135555542 244455430 0 010012 233343 56665 6889874 588
Q ss_pred HHhhc-----CCCcc----------------------------C--cEeehHHHHHHHhCCCCcCcccHHHHHHHh-Ccc
Q 043928 102 DGLGR-----CNLRC----------------------------K--TAVELGHFAARVLKKPHISSFGLAKLAREV-GIH 145 (192)
Q Consensus 102 ~~L~~-----~g~~~----------------------------~--~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~ 145 (192)
..|.+ +|... . -.+|+-++++.. ......+.+|..+|+++ |..
T Consensus 208 pYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD~~dl~k~~-~~~~l~SYsLe~VA~~~LG~~ 286 (881)
T PHA02528 208 PYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILDYLDLYKKF-TFTNQPSYRLDYIAEVELGKK 286 (881)
T ss_pred HHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEeHHHHHHHh-hhcccccCCHHHHHHHHhCCC
Confidence 87754 34321 0 024444444431 11223477899999998 874
Q ss_pred cCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHH
Q 043928 146 NSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRV 186 (192)
Q Consensus 146 l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L 186 (192)
-. .-..-..+.|..... +.=++|...||...++|+.++
T Consensus 287 K~--d~~~~eI~~l~~~d~-~~l~~Ynl~Da~Lv~~L~~kl 324 (881)
T PHA02528 287 KL--DYSDGPFKKFRETDH-QKYIEYNIIDVELVDRLDDKR 324 (881)
T ss_pred Cc--cCCHHHHHHHHhcCH-HHHHHHHHHHHHHHHHHHHHH
Confidence 33 110112234433222 556999999999999999983
No 78
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=87.08 E-value=0.27 Score=43.27 Aligned_cols=148 Identities=13% Similarity=0.078 Sum_probs=91.5
Q ss_pred cEEEEeeeecCC-CCCceeEEEeeeCCeEEEEeccccC-CccHH-HHHhhcCCCeeEEEEeehhhHHHhhc-CCCccCcE
Q 043928 39 RVVGIDVKFNHR-CTKKAEMLILCAGNRCLIIQLCHLG-QIPES-LKKFLADETICFVGIEMNGKVDGLGR-CNLRCKTA 114 (192)
Q Consensus 39 ~vvG~D~Ew~~~-~~~~~aliQl~~~~~~~l~~l~~~~-~~p~~-L~~~l~~~~i~kvG~~~~~D~~~L~~-~g~~~~~~ 114 (192)
.+||.|.-.... -...+-+.|+|+++..++++....+ .++.. .+..|++..+ +- +...+...|.. |+....|+
T Consensus 196 ~~i~~~~~s~~~~~~~e~~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nV 272 (458)
T KOG2405|consen 196 WFIRPVSPSLLKILALEATYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNV 272 (458)
T ss_pred eEeecCchhHHHhhhhhhhhhhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhh
Confidence 677777543322 2233445799999999999986544 23333 5667776555 32 77778888887 99999999
Q ss_pred eehHHHH----HHHhCCCC--c---CcccHHH---HHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHH
Q 043928 115 VELGHFA----ARVLKKPH--I---SSFGLAK---LAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYV 181 (192)
Q Consensus 115 ~Dl~~~a----~~~~~~~~--~---~~~gL~~---l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~ 181 (192)
+|.+... .+.+|+.+ . ....|+. .+... +......+--+....+|.-||-|+.-.+-++-|+.++..
T Consensus 273 kDtQia~sLve~~e~grr~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~ 352 (458)
T KOG2405|consen 273 KDTQIASSLVEPSEYGRRHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLG 352 (458)
T ss_pred HHHHHHHHHhhhHHhcccCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHH
Confidence 9976542 22344321 1 1222322 12222 221110011112224799999999999999999999999
Q ss_pred HHHHHhcc
Q 043928 182 IGDRVLSS 189 (192)
Q Consensus 182 i~~~L~~~ 189 (192)
++..+.+.
T Consensus 353 ~~~~l~a~ 360 (458)
T KOG2405|consen 353 IFDTLVAV 360 (458)
T ss_pred HHhhHhhh
Confidence 88777653
No 79
>PRK06722 exonuclease; Provisional
Probab=85.93 E-value=3.8 Score=34.80 Aligned_cols=89 Identities=15% Similarity=0.167 Sum_probs=57.6
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhc----CCCccC-----cEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGR----CNLRCK-----TAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLAS 150 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~----~g~~~~-----~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K 150 (192)
.+.+|+.+. .+.+ +....|.+.|.+ +|+... ..+|++.++...+..-.....||..+++.+|.+.. .
T Consensus 83 ef~~fig~~-~lva-hna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~lgL~~~--g 158 (281)
T PRK06722 83 KFIQFIGED-SIFV-TWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIWE--G 158 (281)
T ss_pred HHHHHHCCC-cEEE-EEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHCCCCCC--C
Confidence 456667653 3444 456899998876 666432 35888887754332111124689999998877654 1
Q ss_pred CCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 043928 151 GFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSS 189 (192)
Q Consensus 151 ~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~ 189 (192)
+ -+=|-.||..+.+|+.+|.+.
T Consensus 159 --~---------------~HrAL~DA~~TA~L~l~l~~~ 180 (281)
T PRK06722 159 --K---------------QHRALADAENTANILLKAYSE 180 (281)
T ss_pred --C---------------CcCcHHHHHHHHHHHHHHhcc
Confidence 1 123678999999999998854
No 80
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=78.37 E-value=1.8 Score=42.24 Aligned_cols=60 Identities=17% Similarity=0.216 Sum_probs=42.4
Q ss_pred HhhcCCCeeEEEEeehhhHHHhhcCCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccC
Q 043928 83 KFLADETICFVGIEMNGKVDGLGRCNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNS 147 (192)
Q Consensus 83 ~~l~~~~i~kvG~~~~~D~~~L~~~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~ 147 (192)
++|-+..++|||||..+|.+.+.- .+..+..+|.-.+.. +|. -...||+-||.++ |..+.
T Consensus 1008 ~~Li~~GviFVGHGL~nDFrvINi-~Vp~~QiiDTv~lf~--~~s--~R~LSLrfLa~~lLg~~IQ 1068 (1118)
T KOG1275|consen 1008 RLLIQRGVIFVGHGLQNDFRVINI-HVPEEQIIDTVTLFR--LGS--QRMLSLRFLAWELLGETIQ 1068 (1118)
T ss_pred HHHHHcCcEEEcccccccceEEEE-ecChhhheeeeEEEe--ccc--ccEEEHHHHHHHHhcchhh
Confidence 678899999999999999987753 111223566544432 332 2368999999999 98776
No 81
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=76.74 E-value=24 Score=28.47 Aligned_cols=89 Identities=16% Similarity=0.100 Sum_probs=62.9
Q ss_pred HHHHhhcCCCeeEEEEeehhhHHHhhc----CCCc--cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCC
Q 043928 80 SLKKFLADETICFVGIEMNGKVDGLGR----CNLR--CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFN 153 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~~D~~~L~~----~g~~--~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~ 153 (192)
.+.+|+.+. -..|+|+...|...|.. ++.. ....+|.-.+++..+.. ....+|..|+.++|.... ....
T Consensus 87 ~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~--~~~~~L~~l~~~~gi~~~--~~~~ 161 (243)
T COG0847 87 EFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPG--FDRSSLDALAERLGIDRN--PFHP 161 (243)
T ss_pred HHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCC--CccchHHHHHHHcCCCcC--CcCC
Confidence 455666654 66899999999999875 5555 34667766777654433 347899999996677643 1111
Q ss_pred cccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 043928 154 GYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSS 189 (192)
Q Consensus 154 ~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~ 189 (192)
+=|..||.++..+|..+...
T Consensus 162 ----------------H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 162 ----------------HRALFDALALAELFLLLQTG 181 (243)
T ss_pred ----------------cchHHHHHHHHHHHHHHHhc
Confidence 34889999999999988763
No 82
>PRK05762 DNA polymerase II; Reviewed
Probab=76.14 E-value=27 Score=33.93 Aligned_cols=142 Identities=10% Similarity=0.139 Sum_probs=78.3
Q ss_pred CcEEEEeeeecCCCCCceeEEEeee-CC-eEEEEecccc---------C---CccHHHHHhh--cCCCeeEEEEeeh-hh
Q 043928 38 QRVVGIDVKFNHRCTKKAEMLILCA-GN-RCLIIQLCHL---------G---QIPESLKKFL--ADETICFVGIEMN-GK 100 (192)
Q Consensus 38 ~~vvG~D~Ew~~~~~~~~aliQl~~-~~-~~~l~~l~~~---------~---~~p~~L~~~l--~~~~i~kvG~~~~-~D 100 (192)
-++++||+|-... .++..|.++. ++ .++++-.+.. . .+-..+.+++ .||+| .+|+++. .|
T Consensus 155 lrvlsfDIE~~~~--~~i~sI~~~~~~~~~vi~ig~~~~~~~~~v~~~~sE~~LL~~F~~~i~~~DPDI-IvGyNi~~FD 231 (786)
T PRK05762 155 LKVVSLDIETSNK--GELYSIGLEGCGQRPVIMLGPPNGEALDFLEYVADEKALLEKFNAWFAEHDPDV-IIGWNVVQFD 231 (786)
T ss_pred CeEEEEEEEEcCC--CceEEeeecCCCCCeEEEEECCCCCCcceEEEcCCHHHHHHHHHHHHHhcCCCE-EEEeCCCCCc
Confidence 4799999998642 2333333311 11 3333332211 1 1112334444 35664 6899875 59
Q ss_pred HHHhhc----CCCccC---------------------------cEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCC
Q 043928 101 VDGLGR----CNLRCK---------------------------TAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSL 148 (192)
Q Consensus 101 ~~~L~~----~g~~~~---------------------------~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~ 148 (192)
+..|.+ +|+... -.+|+-.+++.... ...+.+|..+|+++ |..-.-
T Consensus 232 lpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~--~l~sysL~~Va~~~Lg~~K~~ 309 (786)
T PRK05762 232 LRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATW--VFDSFSLEYVSQRLLGEGKAI 309 (786)
T ss_pred HHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhc--cCCCCCHHHHHHHHhCCCeec
Confidence 988864 666421 15676666654321 13478899999999 764220
Q ss_pred CCC-CC-ccc-CCCCcCCCCHHHHHHHHHhHHHHHHHHHHH
Q 043928 149 ASG-FN-GYA-PSWSARAFSNEQIKFAVHEAFAYYVIGDRV 186 (192)
Q Consensus 149 ~K~-k~-~~~-S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L 186 (192)
..+ .+ .+. .-|... .+.-++|...||...+.|+.++
T Consensus 310 ~d~~~~~~eI~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 310 DDPYDRMDEIDRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred cCccccHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 011 00 011 123321 2456899999999999999854
No 83
>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=74.25 E-value=18 Score=28.17 Aligned_cols=83 Identities=19% Similarity=0.195 Sum_probs=49.2
Q ss_pred HHHHhhcCCCeeEEEEe-ehhhHHHhhc----CCCcc--------CcEeehHHHHHHHh-------CCC----CcCcccH
Q 043928 80 SLKKFLADETICFVGIE-MNGKVDGLGR----CNLRC--------KTAVELGHFAARVL-------KKP----HISSFGL 135 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~-~~~D~~~L~~----~g~~~--------~~~~Dl~~~a~~~~-------~~~----~~~~~gL 135 (192)
.+.+|+..+.-+.|||+ +..|...|.+ .|..+ ...+|.-.+++... ..| .....+|
T Consensus 75 ~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L 154 (183)
T cd06138 75 KIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKL 154 (183)
T ss_pred HHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhH
Confidence 34566655555678986 7899999875 34321 22456655555321 011 1124678
Q ss_pred HHHHHHhCcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHH
Q 043928 136 AKLAREVGIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVI 182 (192)
Q Consensus 136 ~~l~~~~g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i 182 (192)
.++++.+|.+.. +-+-|..||....+|
T Consensus 155 ~~l~~~~gi~~~--------------------~~H~Al~Da~~ta~l 181 (183)
T cd06138 155 EDLAQANGIEHS--------------------NAHDALSDVEATIAL 181 (183)
T ss_pred HHHHHHCCCCcc--------------------ccccHHHHHHHHHHH
Confidence 899886665543 124577888887665
No 84
>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=70.00 E-value=39 Score=27.49 Aligned_cols=104 Identities=13% Similarity=0.104 Sum_probs=61.9
Q ss_pred HHHHhhcCCCeeEEEEeeh-hhHHHhhc----CCCccCc-------------------EeehHHHHHHHhCCCCcCcccH
Q 043928 80 SLKKFLADETICFVGIEMN-GKVDGLGR----CNLRCKT-------------------AVELGHFAARVLKKPHISSFGL 135 (192)
Q Consensus 80 ~L~~~l~~~~i~kvG~~~~-~D~~~L~~----~g~~~~~-------------------~~Dl~~~a~~~~~~~~~~~~gL 135 (192)
.+.++++...-..|+|+.+ .|+-.|.. +|+.+.. -+||-++.. ..|. ....||
T Consensus 43 ~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~-~~g~--~~~~sL 119 (209)
T PF10108_consen 43 DFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLS-FYGA--KARTSL 119 (209)
T ss_pred HHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHh-ccCc--cccCCH
Confidence 4455555545567999875 59988864 8887543 355555443 2232 247899
Q ss_pred HHHHHHhCcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 043928 136 AKLAREVGIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVL 187 (192)
Q Consensus 136 ~~l~~~~g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~ 187 (192)
..||..+|++-...=+.+.=..-|....+ ++=..|.-.|+...+.||.++.
T Consensus 120 d~la~~lgiPgK~~idGs~V~~~y~~g~i-~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 120 DELAALLGIPGKDDIDGSQVAELYQEGDI-DEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred HHHHHHcCCCCCCCCCHHHHHHHHHcCCH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 99999887652100001100012332221 2235799999999999998764
No 85
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=69.08 E-value=0.11 Score=45.69 Aligned_cols=128 Identities=16% Similarity=0.112 Sum_probs=82.0
Q ss_pred CCCceeEEEeeeCCeEEEEeccccCC--ccHHHHHhhcCCCeeEEEEeehhhHHHhhc-CCCccCcEeehHHHHHHHhCC
Q 043928 51 CTKKAEMLILCAGNRCLIIQLCHLGQ--IPESLKKFLADETICFVGIEMNGKVDGLGR-CNLRCKTAVELGHFAARVLKK 127 (192)
Q Consensus 51 ~~~~~aliQl~~~~~~~l~~l~~~~~--~p~~L~~~l~~~~i~kvG~~~~~D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~ 127 (192)
...|+|=+|.++.-+.+++++...+. ....+..|+++++|.|+-++++.=.+.+.. ||+..+|++|.+.--...+|.
T Consensus 72 ~~~~l~~~q~~~~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~q~~d~~q~~~ 151 (458)
T KOG2405|consen 72 RHGKLCWLQVATNCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVADVLQFSM 151 (458)
T ss_pred ccCcchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhhhhhhhhhhcc
Confidence 35689999999999999999875542 345788999999999998888877777777 999999999987621111221
Q ss_pred ---CCcCccc--H-HHHHHHh--Ccc----cC-CCCCCCcccCCCCcCCCCHHHHHHHHHhHHH
Q 043928 128 ---PHISSFG--L-AKLAREV--GIH----NS-LASGFNGYAPSWSARAFSNEQIKFAVHEAFA 178 (192)
Q Consensus 128 ---~~~~~~g--L-~~l~~~~--g~~----l~-~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~ 178 (192)
....+.+ + .+|.+++ ..+ |. +-|--...+--|--||-++.-..--|..|.+
T Consensus 152 e~g~~~~n~~~~~q~sl~kh~~~a~k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 152 ETGGYLPNCITTLQESLIKHLQVAPKYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred cccccCCccccchHHHHHHHHHhcccHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 0111222 1 2333333 111 11 0000012345688888888877777777766
No 86
>COG4328 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=65.38 E-value=9.5 Score=31.48 Aligned_cols=34 Identities=32% Similarity=0.410 Sum_probs=27.2
Q ss_pred cEEEEeeeecCCCCCceeEEEeeeCCeEEEEecccc
Q 043928 39 RVVGIDVKFNHRCTKKAEMLILCAGNRCLIIQLCHL 74 (192)
Q Consensus 39 ~vvG~D~Ew~~~~~~~~aliQl~~~~~~~l~~l~~~ 74 (192)
++||||.-|... ++..+-+|+..+ .|.|.++.+.
T Consensus 2 ~fvGiDlaW~~~-ppg~~cl~~~dg-~~~i~~~~rr 35 (266)
T COG4328 2 KFVGIDLAWASR-PPGLCCLQLADG-GLLIGDLARR 35 (266)
T ss_pred ceEEeeeecccC-CCceEEEEEcCC-CceEeechhh
Confidence 589999999985 466777888888 8888887654
No 87
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=62.02 E-value=12 Score=30.49 Aligned_cols=65 Identities=9% Similarity=0.062 Sum_probs=44.1
Q ss_pred EeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCc---CCCCHHHHHHHHHhHHHHHHHH
Q 043928 114 AVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSA---RAFSNEQIKFAVHEAFAYYVIG 183 (192)
Q Consensus 114 ~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~---~~Ls~~Qi~YAa~Da~~~~~i~ 183 (192)
++|+-.+++.... ..+-+|..+|.++ |.+.+ .-.--..++|.+ ..-...=+.|...||...++|.
T Consensus 162 ~lD~~~~~r~~~k---l~sYsL~~V~~~~L~~~k~--~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 162 ILNVWRLMRSELA---LTNYTLENVVYHVLHQRIP--LYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred EeEhHHHHHHHcC---cccCCHHHHHHHHhCCCCC--CCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 3566555554332 3478999999999 98766 222334578842 2344556899999999999875
No 88
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=61.99 E-value=9.6 Score=34.41 Aligned_cols=131 Identities=11% Similarity=-0.006 Sum_probs=68.2
Q ss_pred cEEEEeeeecCCCCCceeEEEeeeCCeEEEEecccc--------------------CCccHHHHHhh-cCCCeeEEEEee
Q 043928 39 RVVGIDVKFNHRCTKKAEMLILCAGNRCLIIQLCHL--------------------GQIPESLKKFL-ADETICFVGIEM 97 (192)
Q Consensus 39 ~vvG~D~Ew~~~~~~~~aliQl~~~~~~~l~~l~~~--------------------~~~p~~L~~~l-~~~~i~kvG~~~ 97 (192)
.-.=+|+|-.|..+-.+|+.|=+++...-.|+-++. +.-|.-+..++ .-|.-..+....
T Consensus 373 ~ttWiDIEG~p~DPVElAiyQP~sg~YiHcyR~P~D~K~FK~~SKysHGillkDl~~aqPGL~S~vi~~LP~~MVlT~QG 452 (533)
T PF00843_consen 373 ATTWIDIEGPPNDPVELAIYQPSSGNYIHCYREPHDEKQFKNQSKYSHGILLKDLENAQPGLTSAVIELLPKNMVLTCQG 452 (533)
T ss_dssp S-EEEEEESETTSESEEEEEETTTTEEEEEE---S-HHHHHHHHHHTT-B-GGGCTTB-TTHHHHHHHHS-TT-EEEESS
T ss_pred CCeeEecCCCCCCCeEEEEeccCCCcEEEEecCCcchhhhcccccccccccHHHHhhhccchHHHHHHhCCcCcEEEeeC
Confidence 577799999987777789999999887666775532 11233333333 335556677788
Q ss_pred hhhHHHhhc-CCCccCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcCCCCHHHHHHHHHh
Q 043928 98 NGKVDGLGR-CNLRCKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSARAFSNEQIKFAVHE 175 (192)
Q Consensus 98 ~~D~~~L~~-~g~~~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~D 175 (192)
..|+++|.. +|-+--.++|+.--..+.......-=--+..||... |+-+. |.|+-. ..+-| .=+.|-+|
T Consensus 453 sDDIrkLld~hGRrDiKlvDV~lt~eqaR~FEd~VWd~f~~LC~~H~GvVv~--KKKkg~-----~~~~t--~PHCALlD 523 (533)
T PF00843_consen 453 SDDIRKLLDMHGRRDIKLVDVKLTSEQARKFEDQVWDRFGHLCKKHTGVVVK--KKKKGK-----KPEST--NPHCALLD 523 (533)
T ss_dssp HHHHHHHHHCTT-TTSEEEE----HHHHTTTHHHHHHHHGGG---B-S-EEE----SSSS------EEE-------HHHH
T ss_pred hHHHHHHHHhcCCCcceEEEeecCHHHHHHHHHHHHHHHHHHHHhcCceEEe--cccCCC-----CCCCC--CchHHHHH
Confidence 999999999 887766889986544332221100012367889999 99888 434311 11111 34677777
Q ss_pred HHH
Q 043928 176 AFA 178 (192)
Q Consensus 176 a~~ 178 (192)
+..
T Consensus 524 CiM 526 (533)
T PF00843_consen 524 CIM 526 (533)
T ss_dssp HHH
T ss_pred HHH
Confidence 753
No 89
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=59.09 E-value=19 Score=29.95 Aligned_cols=94 Identities=17% Similarity=0.016 Sum_probs=53.5
Q ss_pred CCCeeEEEEeehhhHHHhhc--CCCc--------------cCcEeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccC--
Q 043928 87 DETICFVGIEMNGKVDGLGR--CNLR--------------CKTAVELGHFAARVLKKPHISSFGLAKLAREV-GIHNS-- 147 (192)
Q Consensus 87 ~~~i~kvG~~~~~D~~~L~~--~g~~--------------~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~-- 147 (192)
+.+...|||+.-.|+-.|.+ +|-- ...++|+..++.. .. ....||+.+++.+ -.+-.
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~-~~---~~~~~L~~l~~~l~~~~~~~~ 222 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEE-CP---GKSTSLQELAEELGIRRNPSS 222 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTS-TT---TS-SSHHHHHHHTTSTT----
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHh-cc---ccccCHHHHHHHhCCCccccc
Confidence 44588999999999999887 6622 2358888888753 11 2368999999998 33311
Q ss_pred --CCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHH
Q 043928 148 --LASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGD 184 (192)
Q Consensus 148 --~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~ 184 (192)
.........+.....+-..++.+=|+.|||..-.++-
T Consensus 223 ~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~~F~ 261 (262)
T PF04857_consen 223 ISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGCVFI 261 (262)
T ss_dssp EEE-TTS-------------SS-TTSHHHHHHHHHHHHH
T ss_pred cccccccccccccccccccCCCCCCCcchHHHHHHHHHc
Confidence 0000000111111123345558889999999888774
No 90
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=56.50 E-value=30 Score=35.27 Aligned_cols=130 Identities=16% Similarity=0.138 Sum_probs=84.4
Q ss_pred CCcEEEEeeeecCCCCCceeEEEeeeCC--eE-------EEEecccc-----------------CCcc-----HHHHHhh
Q 043928 37 RQRVVGIDVKFNHRCTKKAEMLILCAGN--RC-------LIIQLCHL-----------------GQIP-----ESLKKFL 85 (192)
Q Consensus 37 ~~~vvG~D~Ew~~~~~~~~aliQl~~~~--~~-------~l~~l~~~-----------------~~~p-----~~L~~~l 85 (192)
+..+|-||+|.+.....-=-+||++.-. .- +.+.+.+. +..| +.+++|+
T Consensus 420 datyVVfDiETTGLs~~~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf~~~~ 499 (1444)
T COG2176 420 DATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKFREFI 499 (1444)
T ss_pred cccEEEEEeecCCcCcccchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHHHHHh
Confidence 4579999999987744444566776532 11 11111110 0011 2456677
Q ss_pred cCCCeeEEEEeehhhHHHhhc----CCCcc--CcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCCCcccCCC
Q 043928 86 ADETICFVGIEMNGKVDGLGR----CNLRC--KTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGFNGYAPSW 159 (192)
Q Consensus 86 ~~~~i~kvG~~~~~D~~~L~~----~g~~~--~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k~~~~S~W 159 (192)
. +-+.|.|++..|+..|.. +|+.+ +.++|.=.+|+... |...+.+|..+|+.+|+.+.
T Consensus 500 ~--d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~--P~~ksh~Lg~l~kk~~v~le------------ 563 (1444)
T COG2176 500 G--DSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALN--PEFKSHRLGTLCKKLGVELE------------ 563 (1444)
T ss_pred c--CcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhC--hhhhhcchHHHHHHhCccHH------------
Confidence 6 456899999999999976 66654 47899888887432 55678999999987766554
Q ss_pred CcCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 043928 160 SARAFSNEQIKFAVHEAFAYYVIGDRVLSSL 190 (192)
Q Consensus 160 ~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~~ 190 (192)
+-+=|-.||-+.-+++..+.+.+
T Consensus 564 --------~hHRA~yDaeat~~vf~~f~~~~ 586 (1444)
T COG2176 564 --------RHHRADYDAEATAKVFFVFLKDL 586 (1444)
T ss_pred --------HhhhhhhhHHHHHHHHHHHHHHH
Confidence 33446678888888877776543
No 91
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=50.07 E-value=19 Score=29.36 Aligned_cols=69 Identities=12% Similarity=0.155 Sum_probs=42.8
Q ss_pred EeehHHHHHHHhCCCCcCcccHHHHHHHh-Ccc-cCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 043928 114 AVELGHFAARVLKKPHISSFGLAKLAREV-GIH-NSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVL 187 (192)
Q Consensus 114 ~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~-l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~ 187 (192)
++|+-..++.... ..+.+|.++|+.+ |.+ .+. ..+.+. .-|....--..=++|...||+..++|+.+|.
T Consensus 157 ~~D~~~~~k~~~~---~~sY~L~~va~~~Lg~~k~di-~~~~i~-~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl~ 227 (234)
T cd05776 157 LCDTYLSAKELIR---CKSYDLTELSQQVLGIERQDI-DPEEIL-NMYNDSESLLKLLEHTEKDAYLILQLMFKLN 227 (234)
T ss_pred hhccHHHHHHHhC---CCCCChHHHHHHHhCcCcccC-CHHHHH-HHHhCHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 4566666654433 3478999999999 873 221 111221 2344312223348899999999999998874
No 92
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=46.84 E-value=42 Score=23.01 Aligned_cols=37 Identities=11% Similarity=0.282 Sum_probs=26.2
Q ss_pred eCCeEEEEeccccC-CccHHHH-HhhcCCCeeEEEEeeh
Q 043928 62 AGNRCLIIQLCHLG-QIPESLK-KFLADETICFVGIEMN 98 (192)
Q Consensus 62 ~~~~~~l~~l~~~~-~~p~~L~-~~l~~~~i~kvG~~~~ 98 (192)
-.+.+..|.+..-+ ++...|+ .++.||+|.|+||.+.
T Consensus 6 ~~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fAgY~vp 44 (83)
T cd07027 6 KEKNSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIK 44 (83)
T ss_pred cCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecC
Confidence 34467777776544 4555665 6779999999999874
No 93
>PF00169 PH: PH domain; InterPro: IPR001849 The pleckstrin homology (PH) domain is a domain of about 100 residues that occurs in a wide range of proteins involved in intracellular signalling or as constituents of the cytoskeleton [, , , , , , ]. The pleckstrin homology domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. The 3D structure of several PH domains has been determined []. All known cases have a common structure consisting of two perpendicular anti-parallel beta sheets, followed by a C-terminal amphipathic helix. The loops connecting the beta-strands differ greatly in length, making the PH domain relatively difficult to detect. There are no totally invariant residues within the PH domain. Proteins reported to contain one more PH domains belong to the following families: Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. Pleckstrin is one of the rare proteins to contains two PH domains. Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family. Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily. Insulin Receptor Substrate 1 (IRS-1). Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr. Cytoskeletal proteins such as dynamin (see IPR001401 from INTERPRO), Caenorhabditis elegans kinesin-like protein unc-104 (see IPR001752 from INTERPRO), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1. Mammalian phosphatidylinositol-specific phospholipase C (PI-PLC) (see IPR000909 from INTERPRO) isoforms gamma and delta. Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues. Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w. Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac. Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1). C. elegans protein MIG-10. C. elegans hypothetical proteins C04D8.1, K06H7.4 and ZK632.12. S. cerevisiae hypothetical proteins YBR129c and YHR155w. ; GO: 0005515 protein binding; PDB: 1DYN_B 2DYN_B 3SNH_A 3ZYS_C 1X05_A 2I5F_A 1ZM0_B 1XX0_A 2I5C_C 3A8P_D ....
Probab=45.68 E-value=83 Score=20.61 Aligned_cols=31 Identities=6% Similarity=0.103 Sum_probs=25.5
Q ss_pred eEEEEcCcEEEEEEeCChHHHHHHHHHHHHh
Q 043928 4 YELDIQGNNMKVTVVDHAALIDDNVAALKAL 34 (192)
Q Consensus 4 y~v~~~g~~i~v~vt~~~~~~~~~i~~~~~~ 34 (192)
+.|.+.+....+..++++++...|++.+...
T Consensus 72 f~i~~~~~~~~~~~~~s~~~~~~W~~~i~~~ 102 (104)
T PF00169_consen 72 FEITTPNGKSYLFSAESEEERKRWIQAIQKA 102 (104)
T ss_dssp EEEEETTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred EEEEeCCCcEEEEEcCCHHHHHHHHHHHHHH
Confidence 5677778767778899999999999998753
No 94
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=40.83 E-value=59 Score=22.40 Aligned_cols=35 Identities=14% Similarity=0.218 Sum_probs=24.9
Q ss_pred CeEEEEeccccC-CccHHHH-HhhcCCCeeEEEEeeh
Q 043928 64 NRCLIIQLCHLG-QIPESLK-KFLADETICFVGIEMN 98 (192)
Q Consensus 64 ~~~~l~~l~~~~-~~p~~L~-~~l~~~~i~kvG~~~~ 98 (192)
+.+..|.+..-+ ++...|+ .++.+|+|.|+||.+.
T Consensus 10 ~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vp 46 (85)
T PRK01146 10 DNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDID 46 (85)
T ss_pred CCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecC
Confidence 356667665444 3555665 6779999999999775
No 95
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=38.91 E-value=67 Score=21.99 Aligned_cols=36 Identities=14% Similarity=0.212 Sum_probs=24.7
Q ss_pred CCeEEEEeccccC-CccHHHH-HhhcCCCeeEEEEeeh
Q 043928 63 GNRCLIIQLCHLG-QIPESLK-KFLADETICFVGIEMN 98 (192)
Q Consensus 63 ~~~~~l~~l~~~~-~~p~~L~-~~l~~~~i~kvG~~~~ 98 (192)
.+.+..|.+..-+ ++...|+ .++.||+|.|.||.+.
T Consensus 7 ~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vp 44 (83)
T cd06927 7 EDNELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIE 44 (83)
T ss_pred CCCEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecC
Confidence 3456666665443 3555665 6779999999999775
No 96
>PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=38.59 E-value=32 Score=25.75 Aligned_cols=19 Identities=21% Similarity=0.539 Sum_probs=16.2
Q ss_pred CcceEEEEcCcEEEEEEeC
Q 043928 1 MGKYELDIQGNNMKVTVVD 19 (192)
Q Consensus 1 ~~~y~v~~~g~~i~v~vt~ 19 (192)
|.+|+|.++|+...|+|=.
T Consensus 2 mk~~~itvng~~y~V~vee 20 (130)
T PRK06549 2 LRKFKITIDGKEYLVEMEE 20 (130)
T ss_pred CceEEEEECCEEEEEEEEE
Confidence 7789999999988887754
No 97
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=35.74 E-value=61 Score=22.30 Aligned_cols=34 Identities=15% Similarity=0.349 Sum_probs=23.8
Q ss_pred eEEEEeccccC-CccHHHH-HhhcCCCeeEEEEeeh
Q 043928 65 RCLIIQLCHLG-QIPESLK-KFLADETICFVGIEMN 98 (192)
Q Consensus 65 ~~~l~~l~~~~-~~p~~L~-~~l~~~~i~kvG~~~~ 98 (192)
.+..|.+..-+ ++-..|+ .++.||+|.|+||.+-
T Consensus 9 n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vp 44 (85)
T cd07029 9 SCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIP 44 (85)
T ss_pred CeEEEEEeCCCcchHHHHHHHHhhCCCceEEeeccc
Confidence 56666665433 3555666 5679999999999873
No 98
>PF13289 SIR2_2: SIR2-like domain
Probab=35.09 E-value=30 Score=25.08 Aligned_cols=29 Identities=28% Similarity=0.552 Sum_probs=21.9
Q ss_pred ccHHHHHhhcCCCeeEEEEeehh-hHHHhh
Q 043928 77 IPESLKKFLADETICFVGIEMNG-KVDGLG 105 (192)
Q Consensus 77 ~p~~L~~~l~~~~i~kvG~~~~~-D~~~L~ 105 (192)
++..|+.+|.+..++++|++... |++.+.
T Consensus 76 ~~~~l~~~l~~~~~lfiGys~~D~~i~~~l 105 (143)
T PF13289_consen 76 FPNFLRSLLRSKTLLFIGYSFNDPDIRQLL 105 (143)
T ss_pred HHHHHHHHHcCCCEEEEEECCCCHHHHHHH
Confidence 44677888999999999999864 455444
No 99
>cd01246 PH_oxysterol_bp Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=32.32 E-value=97 Score=20.28 Aligned_cols=29 Identities=17% Similarity=0.199 Sum_probs=21.4
Q ss_pred eEEEEcCcEEEEEEeCChHHHHHHHHHHH
Q 043928 4 YELDIQGNNMKVTVVDHAALIDDNVAALK 32 (192)
Q Consensus 4 y~v~~~g~~i~v~vt~~~~~~~~~i~~~~ 32 (192)
+.|...+.......++++++..+|+..+.
T Consensus 61 F~i~~~~~~~~~~~a~s~~e~~~Wi~al~ 89 (91)
T cd01246 61 FTIDTGGDKTLHLRANSEEERQRWVDALE 89 (91)
T ss_pred EEEEcCCCCEEEEECCCHHHHHHHHHHHH
Confidence 45554454555667899999999998875
No 100
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=31.59 E-value=1.4e+02 Score=20.92 Aligned_cols=34 Identities=15% Similarity=0.334 Sum_probs=24.4
Q ss_pred eEEEEeccccC-CccHHHH-HhhcCCCeeEEEEeeh
Q 043928 65 RCLIIQLCHLG-QIPESLK-KFLADETICFVGIEMN 98 (192)
Q Consensus 65 ~~~l~~l~~~~-~~p~~L~-~~l~~~~i~kvG~~~~ 98 (192)
.|..|.+..-+ ++-..|+ .++.+|+|.|+||.+.
T Consensus 17 n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fagY~vp 52 (93)
T cd06926 17 NAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVP 52 (93)
T ss_pred cEEEEEEeCCCchHHHHHHHHHhcCCCeeEEeeccC
Confidence 67777776444 3445565 6779999999999774
No 101
>PF02641 DUF190: Uncharacterized ACR, COG1993; InterPro: IPR003793 This is an uncharacterised domain found in proteins of unknown function.; PDB: 2DCL_C 1O51_A.
Probab=30.93 E-value=80 Score=22.24 Aligned_cols=39 Identities=21% Similarity=0.311 Sum_probs=29.0
Q ss_pred EcCc-EEEEEEeCChHHHHHHHHHHHHhhcCCcEEEEeee
Q 043928 8 IQGN-NMKVTVVDHAALIDDNVAALKALLKRQRVVGIDVK 46 (192)
Q Consensus 8 ~~g~-~i~v~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~E 46 (192)
...+ ++.|.++++++.++..+..+....+++.++-=|+|
T Consensus 60 l~~~lPvvIe~id~~eki~~~l~~l~~~~~~glit~~~v~ 99 (101)
T PF02641_consen 60 LSDDLPVVIEFIDTEEKIEAFLPELKELVKDGLITLEDVE 99 (101)
T ss_dssp -TTS-EEEEEEEEEHHHHHHHHHHHCTT-SSSEEEEEEEE
T ss_pred hcCCCCEEEEEEcCHHHHHHHHHHHHHHcCCCEEEEEEEE
Confidence 3344 88899999999999999998766666666655554
No 102
>PTZ00315 2'-phosphotransferase; Provisional
Probab=30.47 E-value=3.2e+02 Score=25.86 Aligned_cols=91 Identities=10% Similarity=0.057 Sum_probs=56.9
Q ss_pred HHHHhhcCCCe--------eEEEEeehhhHH-Hhhc-------CCCc--cCcEeehHH-HHHHHhC---------CCCcC
Q 043928 80 SLKKFLADETI--------CFVGIEMNGKVD-GLGR-------CNLR--CKTAVELGH-FAARVLK---------KPHIS 131 (192)
Q Consensus 80 ~L~~~l~~~~i--------~kvG~~~~~D~~-~L~~-------~g~~--~~~~~Dl~~-~a~~~~~---------~~~~~ 131 (192)
.+.+||.+... ..+++....|++ .|.+ .|+. ....+|++. +++..++ .+...
T Consensus 136 ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~~~~ 215 (582)
T PTZ00315 136 EALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATPPLG 215 (582)
T ss_pred HHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCccccccccccccccC
Confidence 45667765431 467788899986 4532 2443 346888863 4432222 11234
Q ss_pred cccHHHHHHHhCcccCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 043928 132 SFGLAKLAREVGIHNSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLSS 189 (192)
Q Consensus 132 ~~gL~~l~~~~g~~l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~~ 189 (192)
..+|.+|++.+|.+.. .+ -+=|--||....+|+.+|.++
T Consensus 216 ~~~L~~al~~lgL~~e----Gr---------------~HrAlDDA~ntA~L~~~Ll~~ 254 (582)
T PTZ00315 216 PSDMPDMLQMLGLPLQ----GR---------------HHSGIDDCRNIAAVLCELLRR 254 (582)
T ss_pred CcCHHHHHHHCCCCCC----CC---------------CcCcHHHHHHHHHHHHHHHHc
Confidence 5799999997777755 11 012458999999999998865
No 103
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=28.24 E-value=72 Score=22.96 Aligned_cols=81 Identities=19% Similarity=0.150 Sum_probs=42.8
Q ss_pred HHHhhcCCCeeEEEEeehhhHHHhhc----C-CCc---cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccCCCCCC
Q 043928 81 LKKFLADETICFVGIEMNGKVDGLGR----C-NLR---CKTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNSLASGF 152 (192)
Q Consensus 81 L~~~l~~~~i~kvG~~~~~D~~~L~~----~-g~~---~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~~~K~k 152 (192)
+.+++. +..+.||++...|+..+.+ + +.. ....+|...++...++. ....+|..+++.+|.+.. +
T Consensus 76 ~~~~~~-~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~l~~l~~~~~~~~~--~-- 148 (164)
T PF00929_consen 76 FEEFLK-KNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPN--RKKYSLDDLAEYFGIPFD--G-- 148 (164)
T ss_dssp HHHHHH-HHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHH--HHHHSHHHHHHHTTSSST--S--
T ss_pred hhhhhh-cccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhc--cccCCHHHHHHHcCCCCC--C--
Confidence 455564 2356778776666544433 1 111 12233333332222211 124789999998865555 2
Q ss_pred CcccCCCCcCCCCHHHHHHHHHhHHHHHHHH
Q 043928 153 NGYAPSWSARAFSNEQIKFAVHEAFAYYVIG 183 (192)
Q Consensus 153 ~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~ 183 (192)
+ . +=|..||+...+||
T Consensus 149 ~-----~----------H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 149 T-----A----------HDALDDARATAELF 164 (164)
T ss_dssp T-----T----------TSHHHHHHHHHHHH
T ss_pred C-----C----------cChHHHHHHHhCcC
Confidence 1 1 22678888888876
No 104
>cd01247 PH_GPBP Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. The GPBP protein is a kinase that phosphorylates an N-terminal region of the alpha 3 chain of type IV collagen , which is commonly known as the goodpasture antigen. It has has an N-terminal PH domain and a C-terminal START domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cyt
Probab=27.54 E-value=1.8e+02 Score=19.87 Aligned_cols=29 Identities=3% Similarity=0.011 Sum_probs=22.1
Q ss_pred eEEEEcCcEEEEEEeCChHHHHHHHHHHH
Q 043928 4 YELDIQGNNMKVTVVDHAALIDDNVAALK 32 (192)
Q Consensus 4 y~v~~~g~~i~v~vt~~~~~~~~~i~~~~ 32 (192)
+.|...+........+++++.+.|++.+.
T Consensus 61 F~i~~~~~r~~~L~A~s~~e~~~Wi~al~ 89 (91)
T cd01247 61 FDISVNENVVWYLRAENSQSRLLWMDSVV 89 (91)
T ss_pred EEEEeCCCeEEEEEeCCHHHHHHHHHHHh
Confidence 44555555666677899999999999885
No 105
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=27.44 E-value=1.1e+02 Score=26.86 Aligned_cols=69 Identities=13% Similarity=0.287 Sum_probs=44.9
Q ss_pred EeehHHHHHHHhCCCCcCcccHHHHHHHh-CcccCCCCCCCcccCCCCcC-CCCHHHHHHHHHhHHHHHHHHHHH
Q 043928 114 AVELGHFAARVLKKPHISSFGLAKLAREV-GIHNSLASGFNGYAPSWSAR-AFSNEQIKFAVHEAFAYYVIGDRV 186 (192)
Q Consensus 114 ~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~-g~~l~~~K~k~~~~S~W~~~-~Ls~~Qi~YAa~Da~~~~~i~~~L 186 (192)
.+|+-.+++...+ ....+|..+++.+ |..... =+...-...|... ..-.+-++|...||..+++++.++
T Consensus 150 ~~Dl~~~~~~~~k---l~~~~L~~va~~~l~~~k~d-~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 150 VIDLYNLYKNKLK---LPSYKLDTVAEYLLGKEKDD-LPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEEhHHHHHHHhC---cccCCHHHHHHHHhCCCCCC-CCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677666665443 3478899999999 843220 1011122344432 344678999999999999999986
No 106
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=27.41 E-value=2.1e+02 Score=19.74 Aligned_cols=47 Identities=9% Similarity=0.241 Sum_probs=30.7
Q ss_pred ceEEEEcCcEEEEEEeCChHHHHHHHHHHHHhhcCCcEEEEeeeecCC
Q 043928 3 KYELDIQGNNMKVTVVDHAALIDDNVAALKALLKRQRVVGIDVKFNHR 50 (192)
Q Consensus 3 ~y~v~~~g~~i~v~vt~~~~~~~~~i~~~~~~~~~~~vvG~D~Ew~~~ 50 (192)
++++.|+|. |.++.++-+...+...+++...++-..--.|=+-|.-.
T Consensus 2 ~~K~~y~gd-i~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~DE 48 (83)
T cd06404 2 RVKAAYNGD-IMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDE 48 (83)
T ss_pred eEEEEecCc-EEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEECC
Confidence 456777776 44667777777888888888776433334455566643
No 107
>PF00982 Glyco_transf_20: Glycosyltransferase family 20; InterPro: IPR001830 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 20 GT20 from CAZY comprises enzymes with only one known activity; alpha, alpha-trehalose-phosphate synthase [UDP-forming] (2.4.1.15 from EC). Synthesis of trehalose in the yeast Saccharomyces cerevisiae is catalysed by the trehalose-6-phosphate (Tre6P) synthase/phosphatase complex, which is composed of at least three different subunits encoded by the genes TPS1, TPS2, and TSL1. Tps1 and Tps2 carry the catalytic activities of trehalose synthesis, namely Tre6P synthase (Tps1) and Tre6P phosphatase (Tps2), while TsI1 has regulatory functions. There is some evidence that TsI1 and Tps3 may share a common function with respect to regulation and/or structural stabilisation of the Tre6P synthase/phosphatase complex in exponentially growing, heat-shocked cells []. OtsA (trehalose-6-phosphate synthase) from Escherichia coli has homology to the full-length TPS1, the N-terminal part of TPS2 and an internal region of TPS3 (TSL1) of yeast [].; GO: 0003824 catalytic activity, 0005992 trehalose biosynthetic process; PDB: 1UQU_A 2WTX_A 1UQT_B 1GZ5_B.
Probab=26.58 E-value=85 Score=28.65 Aligned_cols=61 Identities=16% Similarity=0.364 Sum_probs=31.6
Q ss_pred EEEEcCcEEEEEEeCC---hH---------HHHHHHHHHHHhhcC--CcEEEEee-eecCC-----------------CC
Q 043928 5 ELDIQGNNMKVTVVDH---AA---------LIDDNVAALKALLKR--QRVVGIDV-KFNHR-----------------CT 52 (192)
Q Consensus 5 ~v~~~g~~i~v~vt~~---~~---------~~~~~i~~~~~~~~~--~~vvG~D~-Ew~~~-----------------~~ 52 (192)
.|..+|+.+.|.+..- ++ .+.++++.+....+. ..++|+|- ++.-. ..
T Consensus 230 ~v~~~Gr~v~v~~~pigId~~~~~~~~~~~~v~~~~~~l~~~~~~~~~ii~gvDrld~~kGi~~kl~Afe~fL~~~P~~~ 309 (474)
T PF00982_consen 230 TVEYNGRRVRVGVFPIGIDPDAFAQLARSPEVQERAEELREKFKGKRKIIVGVDRLDYTKGIPEKLRAFERFLERYPEYR 309 (474)
T ss_dssp -EEETTEEEEEEE------HHHHHHHHH-S---HHHHHHHHHTTT-SEEEEEE--B-GGG-HHHHHHHHHHHHHH-GGGT
T ss_pred eEEECCEEEEEEEeeccCChHHHHhhccChHHHHHHHHHHHhcCCCcEEEEEeccchhhcCHHHHHHHHHHHHHhCcCcc
Confidence 5778888888766332 22 223445555554433 35999994 33322 46
Q ss_pred CceeEEEeeeCCe
Q 043928 53 KKAEMLILCAGNR 65 (192)
Q Consensus 53 ~~~aliQl~~~~~ 65 (192)
+++.+||+|++++
T Consensus 310 ~kv~liQi~~psr 322 (474)
T PF00982_consen 310 GKVVLIQIAVPSR 322 (474)
T ss_dssp TTEEEEEE--B-S
T ss_pred CcEEEEEEeeccC
Confidence 8999999999875
No 108
>PLN02205 alpha,alpha-trehalose-phosphate synthase [UDP-forming]
Probab=26.31 E-value=1.8e+02 Score=28.75 Aligned_cols=64 Identities=16% Similarity=0.256 Sum_probs=38.5
Q ss_pred eEEEEcCcEEEEEEeC---Ch---------HHHHHHHHHHHHhhc---CCcEEEEe-eeec-----------------CC
Q 043928 4 YELDIQGNNMKVTVVD---HA---------ALIDDNVAALKALLK---RQRVVGID-VKFN-----------------HR 50 (192)
Q Consensus 4 y~v~~~g~~i~v~vt~---~~---------~~~~~~i~~~~~~~~---~~~vvG~D-~Ew~-----------------~~ 50 (192)
..++.+|..+.|.+.. ++ ..+...++++...++ +..++|+| +.+. |.
T Consensus 291 ~~~~~~Gr~v~v~~~PigId~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ilgVDrlD~~KGi~~kl~A~e~~L~~~P~ 370 (854)
T PLN02205 291 IGLEYYGRTVSIKILPVGIHMGQLQSVLSLPETEAKVKELIKQFCDQDRIMLLGVDDMDIFKGISLKLLAMEQLLMQHPE 370 (854)
T ss_pred eeEEECCcEEEEEEEeCeEcHHHHHHHhcChhHHHHHHHHHHHhccCCCEEEEEccCcccccCHHHHHHHHHHHHHhCcc
Confidence 4566777777665421 12 223445666665553 23699999 2322 22
Q ss_pred CCCceeEEEeeeCCeEE
Q 043928 51 CTKKAEMLILCAGNRCL 67 (192)
Q Consensus 51 ~~~~~aliQl~~~~~~~ 67 (192)
..+++.|||+|++++.-
T Consensus 371 ~~gkvvlvQia~psr~~ 387 (854)
T PLN02205 371 WQGKVVLVQIANPARGK 387 (854)
T ss_pred ccCCEEEEEEecCCCcc
Confidence 56899999999987643
No 109
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=26.14 E-value=2.5e+02 Score=23.23 Aligned_cols=82 Identities=13% Similarity=0.029 Sum_probs=55.7
Q ss_pred hcCCCeeEEEEeehhhHHHhhc--CC--Cc-------------cCcEeehHHHHHHHhCCCCcCcccHHHHHHHhC-ccc
Q 043928 85 LADETICFVGIEMNGKVDGLGR--CN--LR-------------CKTAVELGHFAARVLKKPHISSFGLAKLAREVG-IHN 146 (192)
Q Consensus 85 l~~~~i~kvG~~~~~D~~~L~~--~g--~~-------------~~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g-~~l 146 (192)
..+++|..|.+....|.-+|-+ -+ +. ...+.|+..+++..-| .....||+.+|..+| .+.
T Consensus 138 v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~--~~l~~GL~~lA~~L~~~Rv 215 (239)
T KOG0304|consen 138 VLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEG--LSLKGGLQRLADLLGLKRV 215 (239)
T ss_pred hccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhh--hhhhcCHHHHHHHhCCCee
Confidence 3678999999999999988876 22 11 2367888887763212 123789999999884 445
Q ss_pred CCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 043928 147 SLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVLS 188 (192)
Q Consensus 147 ~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~~ 188 (192)
. + . +-|.-|+......|.+|.+
T Consensus 216 G--~--~----------------HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 216 G--I--A----------------HQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred e--c--c----------------cccCcHHHHHHHHHHHHHh
Confidence 5 2 1 2255677777777777764
No 110
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=24.52 E-value=3.2e+02 Score=21.82 Aligned_cols=88 Identities=19% Similarity=0.081 Sum_probs=55.2
Q ss_pred HHHHHhhcCCCeeEEE---EeehhhHHHhhc----CCCcc----CcEeehHHHHHHHhCCCCcCcccHHHHHHHhCcccC
Q 043928 79 ESLKKFLADETICFVG---IEMNGKVDGLGR----CNLRC----KTAVELGHFAARVLKKPHISSFGLAKLAREVGIHNS 147 (192)
Q Consensus 79 ~~L~~~l~~~~i~kvG---~~~~~D~~~L~~----~g~~~----~~~~Dl~~~a~~~~~~~~~~~~gL~~l~~~~g~~l~ 147 (192)
..+.++|+--+--+-| ....-|++.|.+ +++.+ ...+||+.-.+..++.|. ..||..+.+++|....
T Consensus 84 E~f~r~L~~h~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr--~tgln~ale~~G~sf~ 161 (210)
T COG5018 84 EDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPR--LTGLNKALEEYGDSFT 161 (210)
T ss_pred HHHHHHHHhcCcccCCccccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCc--cccHHHHHHHhccccC
Confidence 3455555433333333 334568888875 55543 368999998888888873 5899999998876655
Q ss_pred CCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 043928 148 LASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRVL 187 (192)
Q Consensus 148 ~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L~ 187 (192)
- + -+=|--||.-+++|+..+.
T Consensus 162 --G--~---------------~HraldDArn~~rl~klv~ 182 (210)
T COG5018 162 --G--T---------------HHRALDDARNAYRLFKLVE 182 (210)
T ss_pred --C--c---------------hhhhHHHHHHHHHHHHHHc
Confidence 1 1 1224567777777766554
No 111
>cd00821 PH Pleckstrin homology (PH) domain. Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=24.42 E-value=1.8e+02 Score=18.24 Aligned_cols=29 Identities=10% Similarity=0.196 Sum_probs=20.8
Q ss_pred eEEEEcCcEEEEEEeCChHHHHHHHHHHH
Q 043928 4 YELDIQGNNMKVTVVDHAALIDDNVAALK 32 (192)
Q Consensus 4 y~v~~~g~~i~v~vt~~~~~~~~~i~~~~ 32 (192)
+.|...+.......+.++++...|+..+.
T Consensus 66 f~i~~~~~~~~~~~~~s~~~~~~W~~~l~ 94 (96)
T cd00821 66 FEIRTPDGRSYLLQAESEEEREEWIEALQ 94 (96)
T ss_pred EEEecCCCcEEEEEeCCHHHHHHHHHHHh
Confidence 44555553444566889999999999885
No 112
>KOG0083 consensus GTPase Rab26/Rab37, small G protein superfamily [General function prediction only]
Probab=23.88 E-value=67 Score=24.60 Aligned_cols=31 Identities=42% Similarity=0.883 Sum_probs=21.5
Q ss_pred eeCCeEEEEeccccCCccHHHHHhhcCCCeeEEEEeehh
Q 043928 61 CAGNRCLIIQLCHLGQIPESLKKFLADETICFVGIEMNG 99 (192)
Q Consensus 61 ~~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~~~~ 99 (192)
|+++.|++++... +. ||++.-|.-||.+.++
T Consensus 7 ~~gktcllir~kd-ga-------fl~~~fistvgid~rn 37 (192)
T KOG0083|consen 7 CTGKTCLLIRFKD-GA-------FLAGNFISTVGIDFRN 37 (192)
T ss_pred ccCceEEEEEecc-Cc-------eecCceeeeeeecccc
Confidence 7889999999753 21 5666666667766654
No 113
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.76 E-value=2.4e+02 Score=28.93 Aligned_cols=94 Identities=13% Similarity=0.120 Sum_probs=58.0
Q ss_pred CCCeeEEEEeehh-hHHHhhc----CCCcc---------------------C--cEeehHHHHHHHhCCCCcCcccHHHH
Q 043928 87 DETICFVGIEMNG-KVDGLGR----CNLRC---------------------K--TAVELGHFAARVLKKPHISSFGLAKL 138 (192)
Q Consensus 87 ~~~i~kvG~~~~~-D~~~L~~----~g~~~---------------------~--~~~Dl~~~a~~~~~~~~~~~~gL~~l 138 (192)
||++ .+|+++.+ |++.|.+ .++.. . -++|+-..++..+.. .+.+|..+
T Consensus 599 DPDi-i~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~~~---~sy~L~~v 674 (1172)
T TIGR00592 599 DPDE-IVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELIRC---KSYDLSEL 674 (1172)
T ss_pred CCCE-EEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHHhCc---CCCCHHHH
Confidence 8875 56888854 8877654 33321 1 257777777655433 37899999
Q ss_pred HHHh-Ccc-cCCCCCCCcccCCCCcCCCCHHHHHHHHHhHHHHHHHHHHH
Q 043928 139 AREV-GIH-NSLASGFNGYAPSWSARAFSNEQIKFAVHEAFAYYVIGDRV 186 (192)
Q Consensus 139 ~~~~-g~~-l~~~K~k~~~~S~W~~~~Ls~~Qi~YAa~Da~~~~~i~~~L 186 (192)
++++ |.+ .+. ....+. .-|....--..=+.|...||...++|+.+|
T Consensus 675 ~~~~L~~~k~~~-~~~~i~-~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l 722 (1172)
T TIGR00592 675 VQQILKTERKVI-PIDNIN-NMYSESSSLTYLLEHTWKDAMFILQIMCEL 722 (1172)
T ss_pred HHHHhCCCCccc-CHHHHH-HHHhCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999 853 110 001111 224432223455899999999999998765
No 114
>KOG1882 consensus Transcriptional regulator SNIP1, contains FHA domain [Signal transduction mechanisms]
Probab=23.21 E-value=1.2e+02 Score=25.49 Aligned_cols=52 Identities=17% Similarity=0.132 Sum_probs=34.5
Q ss_pred CCCceeEEEeeeCC------------eEEEEeccccC-------CccHHHHHhhcCCCeeEEEEeehhhHH
Q 043928 51 CTKKAEMLILCAGN------------RCLIIQLCHLG-------QIPESLKKFLADETICFVGIEMNGKVD 102 (192)
Q Consensus 51 ~~~~~aliQl~~~~------------~~~l~~l~~~~-------~~p~~L~~~l~~~~i~kvG~~~~~D~~ 102 (192)
...+-|+||.-.-. +|+|++|...+ .|++.=.-=|...+++|+||+..+++-
T Consensus 214 cSKQHaviQyR~v~~~r~dGt~grrvkpYiiDLgS~NgTfLNnk~IepqRYyEL~ekDvlkfgfs~rEyvl 284 (293)
T KOG1882|consen 214 CSKQHAVIQYRLVEFTRADGTVGRRVKPYIIDLGSGNGTFLNNKVIEPQRYYELREKDVLKFGFSSREYVL 284 (293)
T ss_pred ccccceeeeeeecccccCCCccceeeeeEEEecCCCCcceecCcccCchheeeeecCceeeeccchHHHHH
Confidence 34677899985411 69999997542 233322223456789999999988764
No 115
>COG1993 PII-like signaling protein [Signal transduction mechanisms]
Probab=22.49 E-value=2.9e+02 Score=20.09 Aligned_cols=27 Identities=26% Similarity=0.373 Sum_probs=22.9
Q ss_pred EEEEEEeCChHHHHHHHHHHHHhhcCC
Q 043928 12 NMKVTVVDHAALIDDNVAALKALLKRQ 38 (192)
Q Consensus 12 ~i~v~vt~~~~~~~~~i~~~~~~~~~~ 38 (192)
++.|.++++++.+++.+..+......+
T Consensus 68 PVviEvVD~eekI~~~l~~l~e~~~~~ 94 (109)
T COG1993 68 PVVVEVVDEEEKIERFLPELDEIIKNG 94 (109)
T ss_pred CEEEEEeCCHHHHHHHHHHHHHHhhcc
Confidence 678999999999999999998765444
No 116
>PRK05641 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=22.20 E-value=91 Score=23.97 Aligned_cols=19 Identities=21% Similarity=0.503 Sum_probs=15.6
Q ss_pred CcceEEEEcCcEEEEEEeC
Q 043928 1 MGKYELDIQGNNMKVTVVD 19 (192)
Q Consensus 1 ~~~y~v~~~g~~i~v~vt~ 19 (192)
|++|+|.++|+...|++=+
T Consensus 22 ~~~~~itvnG~~y~V~vee 40 (153)
T PRK05641 22 PGKFRVSFEGKTYEVEAKG 40 (153)
T ss_pred CccEEEEECCEEEEEEEEE
Confidence 7889999999988776633
No 117
>smart00233 PH Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
Probab=21.84 E-value=2.2e+02 Score=17.93 Aligned_cols=30 Identities=13% Similarity=0.206 Sum_probs=22.2
Q ss_pred eEEEEcCcEEEEEEeCChHHHHHHHHHHHH
Q 043928 4 YELDIQGNNMKVTVVDHAALIDDNVAALKA 33 (192)
Q Consensus 4 y~v~~~g~~i~v~vt~~~~~~~~~i~~~~~ 33 (192)
+.|...+....+-.++++++...|+..+..
T Consensus 70 f~l~~~~~~~~~f~~~s~~~~~~W~~~i~~ 99 (102)
T smart00233 70 FEIKTADRRSYLLQAESEEEREEWVDALRK 99 (102)
T ss_pred EEEEecCCceEEEEcCCHHHHHHHHHHHHH
Confidence 445555554556778999999999998864
No 118
>PRK05761 DNA polymerase I; Reviewed
Probab=21.80 E-value=5.2e+02 Score=25.28 Aligned_cols=94 Identities=13% Similarity=0.063 Sum_probs=54.8
Q ss_pred HHHHHhhcCCCeeEEEEee-hhhHHHhhc----CCCccC---------c-EeehHHHHHHHhCCC--------CcCcccH
Q 043928 79 ESLKKFLADETICFVGIEM-NGKVDGLGR----CNLRCK---------T-AVELGHFAARVLKKP--------HISSFGL 135 (192)
Q Consensus 79 ~~L~~~l~~~~i~kvG~~~-~~D~~~L~~----~g~~~~---------~-~~Dl~~~a~~~~~~~--------~~~~~gL 135 (192)
..+.+++.+-+...+ +++ ..|+..|.+ +|+... . .+|+-..+.. .+.+ .....+|
T Consensus 215 ~~f~~~i~~~dPdi~-yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~-~~~~~y~~~~~~~~~~ysL 292 (787)
T PRK05761 215 AELFDIILEYPPVVT-FNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQN-KAVRSYAFYGKYRHREARL 292 (787)
T ss_pred HHHHHHHHhcCCEEE-EcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheee-cceeeeeccceeecccCCh
Confidence 345555654444333 554 569988865 776532 0 1666444321 1111 1115689
Q ss_pred HHHHHHh-Ccc-cCCCCCCCcccCCCCcCCCCHHH-HHHHHHhHHHHHHHH
Q 043928 136 AKLAREV-GIH-NSLASGFNGYAPSWSARAFSNEQ-IKFAVHEAFAYYVIG 183 (192)
Q Consensus 136 ~~l~~~~-g~~-l~~~K~k~~~~S~W~~~~Ls~~Q-i~YAa~Da~~~~~i~ 183 (192)
...++.+ |.. ++ -+..+. .++.+. ++|+..||...+.|.
T Consensus 293 ~~Va~~~Lg~~K~~--~~~~i~-------~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 293 DAVGRALLGISKVE--LETNIS-------ELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred HHHHHHHhCCCccc--cccccc-------ccCHHHHHHHHHHHHHHHHHHH
Confidence 9999989 864 44 222222 245444 899999999999984
No 119
>cd01260 PH_CNK Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. CNK is believed to regulate the activity and the subcellular localization of RAS activated RAF. CNK is composed of N-terminal SAM and PDZ domains along with a central or C-terminal PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskelet
Probab=21.69 E-value=1.8e+02 Score=19.66 Aligned_cols=29 Identities=7% Similarity=-0.135 Sum_probs=20.1
Q ss_pred EEEEcCcEEEEEEeCChHHHHHHHHHHHH
Q 043928 5 ELDIQGNNMKVTVVDHAALIDDNVAALKA 33 (192)
Q Consensus 5 ~v~~~g~~i~v~vt~~~~~~~~~i~~~~~ 33 (192)
.|...+.....-.++++++..+|+..+..
T Consensus 67 ~I~~~~~~~~~f~a~s~~e~~~Wi~ai~~ 95 (96)
T cd01260 67 KVCHPVYKSFYFAAETLDDLSQWVNHLIT 95 (96)
T ss_pred EECCCCCcEEEEEeCCHHHHHHHHHHHHh
Confidence 33333434555668999999999998863
No 120
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=21.61 E-value=7.7e+02 Score=24.11 Aligned_cols=143 Identities=14% Similarity=0.167 Sum_probs=78.6
Q ss_pred cEEEEeeeecCC-------CCCceeEEEeeeCCeEEE-------------EeccccC-CccHHHHHhh--cCCCeeEEEE
Q 043928 39 RVVGIDVKFNHR-------CTKKAEMLILCAGNRCLI-------------IQLCHLG-QIPESLKKFL--ADETICFVGI 95 (192)
Q Consensus 39 ~vvG~D~Ew~~~-------~~~~~aliQl~~~~~~~l-------------~~l~~~~-~~p~~L~~~l--~~~~i~kvG~ 95 (192)
++++||+|-... ..+++..+..+....-.. +..+..+ .+-..+..++ .||+| .+|+
T Consensus 155 ~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~~~~~~~~~~~~~v~~~~~e~e~l~~~~~~i~~~dPdV-Ivgy 233 (792)
T COG0417 155 RVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLIEVFIYTSGEGFSVEVVISEAELLERFVELIREYDPDV-IVGY 233 (792)
T ss_pred eEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCccccccccCCCCceeEEecCHHHHHHHHHHHHHhcCCCE-EEec
Confidence 689999997654 345666777666543211 1111111 1112333333 56666 4677
Q ss_pred eeh-hhHHHhhc----CCCccC---------------------cEeehHHHHH-HHhCCCCcCcccHHHHHHHh-CcccC
Q 043928 96 EMN-GKVDGLGR----CNLRCK---------------------TAVELGHFAA-RVLKKPHISSFGLAKLAREV-GIHNS 147 (192)
Q Consensus 96 ~~~-~D~~~L~~----~g~~~~---------------------~~~Dl~~~a~-~~~~~~~~~~~gL~~l~~~~-g~~l~ 147 (192)
+.. .|...|.+ +|+... ..+|+-..+. +.+ +....+|...++.+ +..-.
T Consensus 234 n~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~---~~~~ysl~~v~~~~l~~~k~ 310 (792)
T COG0417 234 NGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPL---NLKSYSLEAVSEALLGEGKR 310 (792)
T ss_pred cCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhhc---ccccccHHHHHHHhcccccc
Confidence 765 79988864 676554 4677777665 222 23478899999988 66431
Q ss_pred CCCCCCcccCCCCcCCCC-HHHHHHHHHhHHHHHHHHHH
Q 043928 148 LASGFNGYAPSWSARAFS-NEQIKFAVHEAFAYYVIGDR 185 (192)
Q Consensus 148 ~~K~k~~~~S~W~~~~Ls-~~Qi~YAa~Da~~~~~i~~~ 185 (192)
...+...-+.-|...+-+ ..++.|.-.|+.....+..+
T Consensus 311 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~~ 349 (792)
T COG0417 311 EDIPYDSMEEIWPDWADSKLRLLLYNLSDADLVLRILLK 349 (792)
T ss_pred cccCccchhhccccCccchhHHHHHHHHHHHHHHHHHHH
Confidence 001111111233333322 44567777777777766654
No 121
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=20.56 E-value=1.6e+02 Score=19.67 Aligned_cols=34 Identities=15% Similarity=0.256 Sum_probs=27.1
Q ss_pred cEEEEeeeecCCCCCceeEEEeeeCCeEEEEecc
Q 043928 39 RVVGIDVKFNHRCTKKAEMLILCAGNRCLIIQLC 72 (192)
Q Consensus 39 ~vvG~D~Ew~~~~~~~~aliQl~~~~~~~l~~l~ 72 (192)
.-+-.++|+.|....++|+|..-.+...+++-..
T Consensus 34 ~g~V~~i~~DP~Rsa~iAlV~~~~g~~~yiiA~e 67 (77)
T PF00181_consen 34 KGIVIDIEYDPNRSAPIALVKYEDGEKRYIIAPE 67 (77)
T ss_dssp EEEEEEEEEETTTSSEEEEEEETTSEEEEEEEBT
T ss_pred cEEEEEEEecCCcCccEEEEEecCCcEEEEEeEC
Confidence 3566789999988899999999887777776543
No 122
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=20.52 E-value=1.7e+02 Score=20.83 Aligned_cols=28 Identities=25% Similarity=0.312 Sum_probs=20.0
Q ss_pred CChHHHHHHHHHHHHhhcCC--cEEEEeee
Q 043928 19 DHAALIDDNVAALKALLKRQ--RVVGIDVK 46 (192)
Q Consensus 19 ~~~~~~~~~i~~~~~~~~~~--~vvG~D~E 46 (192)
.+++++-.-|++.+..+.+. +++|||--
T Consensus 57 ~d~~~Vl~ei~~C~~~~p~~YVRliG~D~~ 86 (99)
T cd03527 57 TDPAQVLREIEACRKAYPDHYVRVVGFDNY 86 (99)
T ss_pred CCHHHHHHHHHHHHHHCCCCeEEEEEEeCC
Confidence 56777777777777666443 89999965
No 123
>PF03633 Glyco_hydro_65C: Glycosyl hydrolase family 65, C-terminal domain ; InterPro: IPR005194 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This family of glycosyl hydrolases (GH65 from CAZY) contains this domain and includes vacuolar acid trehalase and maltose phosphorylases. Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown [].; PDB: 1H54_A.
Probab=20.33 E-value=1.5e+02 Score=18.05 Aligned_cols=18 Identities=17% Similarity=0.473 Sum_probs=12.7
Q ss_pred ceEEEEcCcEEEEEEeCC
Q 043928 3 KYELDIQGNNMKVTVVDH 20 (192)
Q Consensus 3 ~y~v~~~g~~i~v~vt~~ 20 (192)
+|.+.+.|..+.|+++.+
T Consensus 11 ~F~~~~rg~~l~v~i~~~ 28 (54)
T PF03633_consen 11 SFRLRYRGHWLEVEITHE 28 (54)
T ss_dssp EEEEEETTEEEEEEEETT
T ss_pred EEEEEECCEEEEEEEECC
Confidence 466777788777777665
No 124
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=20.26 E-value=88 Score=21.00 Aligned_cols=22 Identities=23% Similarity=0.484 Sum_probs=16.7
Q ss_pred ccHHHH-HhhcCCCeeEEEEeeh
Q 043928 77 IPESLK-KFLADETICFVGIEMN 98 (192)
Q Consensus 77 ~p~~L~-~~l~~~~i~kvG~~~~ 98 (192)
+.-.|+ .++.||+|.++||.+.
T Consensus 14 lgNlLr~~L~~~p~V~fagY~vp 36 (77)
T PF13656_consen 14 LGNLLRYELLKDPDVEFAGYRVP 36 (77)
T ss_dssp HHHHHHHCCTTSTTEEEEEEEES
T ss_pred HHHHHHHHHhhCCCeEEEEeccC
Confidence 334555 5679999999999874
Done!