Query 048832
Match_columns 211
No_of_seqs 171 out of 1256
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 13:56:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048832.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048832hhsearch_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 1.6E-33 3.6E-38 219.7 18.8 169 31-208 3-193 (193)
2 cd06141 WRN_exo DEDDy 3'-5' ex 100.0 2.6E-33 5.5E-38 214.7 19.0 167 33-207 2-169 (170)
3 cd06129 RNaseD_like DEDDy 3'-5 100.0 5.8E-33 1.3E-37 211.0 17.3 159 38-208 2-161 (161)
4 PRK10829 ribonuclease D; Provi 100.0 3.1E-28 6.8E-33 205.9 19.8 165 30-208 4-168 (373)
5 PF01612 DNA_pol_A_exo1: 3'-5' 100.0 1.4E-27 3E-32 183.1 16.2 167 30-208 2-173 (176)
6 cd06148 Egl_like_exo DEDDy 3'- 100.0 8.2E-28 1.8E-32 188.3 14.5 151 54-208 9-175 (197)
7 COG0349 Rnd Ribonuclease D [Tr 99.9 3.9E-26 8.5E-31 188.9 15.4 161 35-208 4-164 (361)
8 TIGR01388 rnd ribonuclease D. 99.9 1.4E-25 3.1E-30 190.4 19.2 163 32-208 2-164 (367)
9 smart00474 35EXOc 3'-5' exonuc 99.9 1.6E-20 3.4E-25 142.9 17.8 166 31-208 3-169 (172)
10 cd06142 RNaseD_exo DEDDy 3'-5' 99.9 2.1E-20 4.6E-25 143.7 18.3 147 55-208 12-158 (178)
11 cd06147 Rrp6p_like_exo DEDDy 3 99.8 4.1E-18 8.8E-23 132.9 18.3 164 31-208 7-170 (192)
12 cd09018 DEDDy_polA_RNaseD_like 99.8 1.2E-18 2.6E-23 130.2 13.8 147 57-207 1-149 (150)
13 KOG4373 Predicted 3'-5' exonuc 99.8 2.2E-18 4.8E-23 139.8 11.5 192 12-204 11-282 (319)
14 cd00007 35EXOc 3'-5' exonuclea 99.8 2.6E-17 5.6E-22 123.0 13.5 146 57-208 2-153 (155)
15 KOG2207 Predicted 3'-5' exonuc 99.7 6E-17 1.3E-21 140.4 8.7 171 30-208 393-583 (617)
16 PRK05755 DNA polymerase I; Pro 99.7 5.3E-15 1.2E-19 138.6 17.1 167 29-208 296-467 (880)
17 cd06140 DNA_polA_I_Bacillus_li 99.6 4.3E-15 9.4E-20 114.3 13.4 148 55-208 3-154 (178)
18 KOG2206 Exosome 3'-5' exoribon 99.6 1E-15 2.3E-20 132.2 7.3 164 30-207 194-357 (687)
19 cd06139 DNA_polA_I_Ecoli_like_ 99.5 7.3E-13 1.6E-17 102.9 15.1 150 54-208 4-168 (193)
20 COG0749 PolA DNA polymerase I 99.4 2.9E-12 6.2E-17 113.1 13.0 162 34-207 8-177 (593)
21 PRK14975 bifunctional 3'-5' ex 99.3 2E-11 4.4E-16 109.3 10.5 137 30-208 4-142 (553)
22 TIGR00593 pola DNA polymerase 99.3 2E-10 4.3E-15 107.4 16.1 160 32-208 307-475 (887)
23 cd06128 DNA_polA_exo DEDDy 3'- 99.2 6.5E-10 1.4E-14 83.2 13.4 131 72-207 17-150 (151)
24 cd06149 ISG20 DEDDh 3'-5' exon 97.9 0.00021 4.6E-09 53.9 10.1 88 98-204 68-157 (157)
25 cd06144 REX4_like DEDDh 3'-5' 97.5 0.0012 2.6E-08 49.4 9.1 84 98-204 68-152 (152)
26 cd06145 REX1_like DEDDh 3'-5' 97.4 0.003 6.4E-08 47.2 10.7 82 100-203 68-149 (150)
27 cd06143 PAN2_exo DEDDh 3'-5' e 97.3 0.00093 2E-08 51.0 7.1 81 100-204 94-174 (174)
28 PRK07740 hypothetical protein; 97.3 0.033 7.1E-07 45.1 15.8 147 36-207 33-223 (244)
29 cd06137 DEDDh_RNase DEDDh 3'-5 97.3 0.008 1.7E-07 45.4 11.5 82 100-203 76-160 (161)
30 cd06125 DnaQ_like_exo DnaQ-lik 97.2 0.0025 5.4E-08 43.9 7.7 73 58-141 1-83 (96)
31 PRK06310 DNA polymerase III su 97.2 0.018 4E-07 46.7 13.9 86 99-207 79-171 (250)
32 KOG2249 3'-5' exonuclease [Rep 97.0 0.0061 1.3E-07 49.1 9.2 86 100-207 177-263 (280)
33 cd05160 DEDDy_DNA_polB_exo DED 97.0 0.018 4E-07 44.8 11.9 102 98-203 67-198 (199)
34 PRK07883 hypothetical protein; 97.0 0.028 6.1E-07 50.9 14.3 88 99-207 87-179 (557)
35 cd05780 DNA_polB_Kod1_like_exo 97.0 0.019 4.1E-07 44.7 11.4 147 55-206 3-195 (195)
36 PRK06063 DNA polymerase III su 97.0 0.029 6.2E-07 47.1 13.0 87 98-207 85-176 (313)
37 PRK07246 bifunctional ATP-depe 96.9 0.022 4.7E-07 53.9 13.0 86 99-207 78-167 (820)
38 PRK07942 DNA polymerase III su 96.9 0.05 1.1E-06 43.7 13.4 78 109-207 93-177 (232)
39 PRK08517 DNA polymerase III su 96.9 0.06 1.3E-06 43.9 13.8 86 98-207 138-228 (257)
40 PRK06309 DNA polymerase III su 96.9 0.062 1.3E-06 43.1 13.8 128 55-207 2-163 (232)
41 PRK06807 DNA polymerase III su 96.8 0.035 7.5E-07 46.6 12.5 86 99-208 80-170 (313)
42 PRK09145 DNA polymerase III su 96.8 0.07 1.5E-06 41.8 13.4 91 99-210 103-201 (202)
43 cd06130 DNA_pol_III_epsilon_li 96.6 0.086 1.9E-06 39.0 12.0 81 99-203 69-154 (156)
44 TIGR01406 dnaQ_proteo DNA poly 96.6 0.2 4.4E-06 40.0 14.6 88 99-208 74-170 (225)
45 TIGR00573 dnaq exonuclease, DN 96.5 0.084 1.8E-06 41.8 12.3 90 99-208 79-175 (217)
46 KOG3657 Mitochondrial DNA poly 96.5 0.016 3.4E-07 53.6 8.6 99 108-206 240-379 (1075)
47 PRK09146 DNA polymerase III su 96.5 0.22 4.7E-06 40.2 14.4 87 100-207 122-224 (239)
48 PRK08074 bifunctional ATP-depe 96.3 0.12 2.5E-06 49.8 14.0 87 98-207 75-166 (928)
49 PRK06195 DNA polymerase III su 96.3 0.13 2.9E-06 43.0 12.8 86 99-208 72-162 (309)
50 PRK05711 DNA polymerase III su 96.3 0.22 4.7E-06 40.2 13.2 88 99-208 78-174 (240)
51 cd06131 DNA_pol_III_epsilon_Ec 96.2 0.25 5.4E-06 37.1 12.8 86 99-206 73-166 (167)
52 smart00479 EXOIII exonuclease 96.2 0.31 6.7E-06 36.4 13.3 88 99-209 72-166 (169)
53 cd06136 TREX1_2 DEDDh 3'-5' ex 96.1 0.18 3.9E-06 38.6 11.7 81 99-204 86-175 (177)
54 TIGR01407 dinG_rel DnaQ family 96.1 0.17 3.8E-06 48.2 13.7 65 99-168 72-141 (850)
55 PRK05601 DNA polymerase III su 96.0 0.28 6.2E-06 41.9 13.1 99 97-207 115-246 (377)
56 PRK07247 DNA polymerase III su 96.0 0.27 5.8E-06 38.4 12.1 89 98-209 75-168 (195)
57 TIGR01405 polC_Gram_pos DNA po 95.9 0.22 4.8E-06 49.0 13.8 87 98-207 261-352 (1213)
58 cd06127 DEDDh DEDDh 3'-5' exon 95.3 0.18 3.9E-06 36.8 8.6 84 98-203 70-158 (159)
59 PRK07983 exodeoxyribonuclease 95.3 1.2 2.6E-05 35.4 13.6 86 100-208 67-152 (219)
60 KOG2248 3'-5' exonuclease [Rep 94.9 0.05 1.1E-06 46.7 5.2 90 99-209 285-374 (380)
61 cd05784 DNA_polB_II_exo DEDDy 94.6 0.54 1.2E-05 36.6 9.8 103 97-204 54-193 (193)
62 cd05781 DNA_polB_B3_exo DEDDy 94.5 1.7 3.8E-05 33.6 12.9 147 55-206 3-188 (188)
63 cd05785 DNA_polB_like2_exo Unc 94.4 0.8 1.7E-05 36.1 10.6 145 55-203 9-206 (207)
64 COG2176 PolC DNA polymerase II 94.4 0.095 2.1E-06 50.6 6.1 128 54-207 420-583 (1444)
65 cd06134 RNaseT DEDDh 3'-5' exo 94.2 0.56 1.2E-05 36.3 9.2 78 109-208 102-187 (189)
66 PRK11779 sbcB exonuclease I; P 93.7 1.3 2.8E-05 39.4 11.5 90 100-208 84-196 (476)
67 PRK06722 exonuclease; Provisio 92.4 5.6 0.00012 32.9 13.3 90 98-207 81-178 (281)
68 PRK09182 DNA polymerase III su 92.3 5.8 0.00013 33.1 13.4 85 98-206 111-197 (294)
69 cd05783 DNA_polB_B1_exo DEDDy 92.3 4.6 9.9E-05 31.7 12.6 100 97-204 76-202 (204)
70 PRK05168 ribonuclease T; Provi 92.0 2.3 5.1E-05 33.5 9.8 77 109-207 114-198 (211)
71 cd05779 DNA_polB_epsilon_exo D 92.0 4.4 9.5E-05 31.8 11.2 101 98-203 77-203 (204)
72 PRK07748 sporulation inhibitor 91.5 2.9 6.3E-05 32.7 9.8 92 98-210 83-180 (207)
73 PRK00448 polC DNA polymerase I 91.5 2.3 4.9E-05 43.0 10.9 85 100-207 492-581 (1437)
74 PF09281 Taq-exonuc: Taq polym 91.4 0.92 2E-05 32.8 6.1 68 115-207 68-135 (138)
75 TIGR01298 RNaseT ribonuclease 91.2 1.9 4.2E-05 33.6 8.5 77 109-207 105-189 (200)
76 KOG1275 PAB-dependent poly(A) 89.9 0.13 2.8E-06 48.3 0.9 81 103-206 1008-1088(1118)
77 PF13482 RNase_H_2: RNase_H su 89.1 0.75 1.6E-05 34.3 4.4 141 58-206 1-163 (164)
78 KOG2405 Predicted 3'-5' exonuc 89.0 0.011 2.3E-07 50.1 -6.1 72 70-142 71-144 (458)
79 cd05782 DNA_polB_like1_exo Unc 88.9 5.1 0.00011 31.5 9.2 127 71-204 49-207 (208)
80 cd06138 ExoI_N N-terminal DEDD 87.6 3 6.6E-05 31.9 7.0 86 99-203 74-182 (183)
81 cd06133 ERI-1_3'hExo_like DEDD 84.2 13 0.00027 27.8 8.9 87 99-206 80-175 (176)
82 COG0847 DnaQ DNA polymerase II 82.0 16 0.00035 29.0 9.2 90 99-208 86-180 (243)
83 PHA02528 43 DNA polymerase; Pr 80.4 59 0.0013 31.5 15.1 53 151-206 270-324 (881)
84 PRK05762 DNA polymerase II; Re 79.0 26 0.00055 33.5 10.6 104 97-206 206-348 (786)
85 cd05778 DNA_polB_zeta_exo inac 78.0 3 6.5E-05 33.4 3.6 65 136-203 163-230 (231)
86 PTZ00315 2'-phosphotransferase 77.5 59 0.0013 29.9 14.1 97 97-211 133-256 (582)
87 cd05777 DNA_polB_delta_exo DED 72.8 6.6 0.00014 31.3 4.4 56 151-207 166-224 (230)
88 PF10108 DNA_pol_B_exo2: Predi 71.1 22 0.00048 28.1 6.9 104 97-207 40-170 (209)
89 KOG2405 Predicted 3'-5' exonuc 56.1 1.9 4.1E-05 36.9 -1.7 125 78-207 216-358 (458)
90 cd01231 PH_Lnk LNK-family Plec 52.9 46 0.001 23.1 4.9 33 14-46 73-105 (107)
91 cd05776 DNA_polB_alpha_exo ina 49.7 20 0.00043 28.6 3.3 68 136-207 158-227 (234)
92 PRK05359 oligoribonuclease; Pr 47.9 96 0.0021 23.7 6.7 14 55-68 3-16 (181)
93 TIGR00592 pol2 DNA polymerase 34.3 1.7E+02 0.0036 29.6 7.4 96 107-207 599-723 (1172)
94 cd06135 Orn DEDDh 3'-5' exonuc 32.2 1.4E+02 0.0031 22.4 5.4 27 100-126 81-111 (173)
95 PHA03334 putative DNA polymera 27.3 1.7E+02 0.0037 29.9 6.1 78 130-207 464-556 (1545)
96 PF00169 PH: PH domain; Inter 25.8 1.9E+02 0.004 18.5 6.9 36 12-47 66-101 (104)
97 cd01246 PH_oxysterol_bp Oxyste 22.7 2.1E+02 0.0047 18.1 4.4 31 16-46 59-89 (91)
98 PF04857 CAF1: CAF1 family rib 20.9 3.2E+02 0.0069 22.1 5.8 54 107-164 147-215 (262)
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=1.6e-33 Score=219.71 Aligned_cols=169 Identities=30% Similarity=0.463 Sum_probs=144.0
Q ss_pred EeCChHHHHHHHHH--HHHHhhccCCCcEEEEeeeeecCCCC-CCCCeeEEEeeeCCeeEEEeccccC-----cchHHHH
Q 048832 31 VTRSPSVVDDWISE--IERIHRRRLHCLIVGLDVEWRPSFSR-QQNPVATLQLCVGRRCLIFQIIHAR-----RIPQSLA 102 (211)
Q Consensus 31 ~~~~~~~l~~~i~~--l~~~~~~~~~~~~v~~d~e~~~~~~~-~~~~~~llql~~~~~~~i~~~~~~~-----~~~~~L~ 102 (211)
++++++++.+++.. +. ...++|||+||.+.+.. ..+++++||||+++.|++||+...+ .+++.|+
T Consensus 3 ~i~~~~el~~~~~~~~l~-------~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~ 75 (193)
T cd06146 3 IVDSEEELEALLLALSLE-------AGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLK 75 (193)
T ss_pred EecCHHHHHHHHHHHhhc-------cCCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHH
Confidence 78899999999999 54 48999999999977533 3689999999999999999997654 3677899
Q ss_pred HhhcCCCceEEEeeeHHHHHHHHHhcCC------CCCcEeecHHHHHhhccc-c-------ccccccHHHHHHHHcCccC
Q 048832 103 NFLSDEDYTFVGVGIDGDVKKLENNYGL------QVFRTVDLRPLAAEDLEI-E-------GLRFAGLKALSWEVLEKEV 168 (211)
Q Consensus 103 ~~L~~~~i~kvg~~~k~d~~~L~~~~gi------~~~~~~D~~~la~~~l~~-~-------~~~~~~L~~l~~~~L~~~l 168 (211)
++|+|++|+||||++++|+..|++.+|+ .+.|++|++.++...... + .....||++|++++||.++
T Consensus 76 ~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l 155 (193)
T cd06146 76 RLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPL 155 (193)
T ss_pred HHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCc
Confidence 9999999999999999999999888887 367899998766422211 1 1247899999999999999
Q ss_pred CCCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 169 NKPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 169 ~k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
+|.. ++|||++|||+++|+.|||.||+++++||+.|.+
T Consensus 156 ~K~~--q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 156 DKSE--QCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred Cccc--ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 8875 4899999999999999999999999999999974
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=2.6e-33 Score=214.67 Aligned_cols=167 Identities=38% Similarity=0.618 Sum_probs=147.1
Q ss_pred CChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCC-CCCCCeeEEEeeeCCeeEEEeccccCcchHHHHHhhcCCCce
Q 048832 33 RSPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFS-RQQNPVATLQLCVGRRCLIFQIIHARRIPQSLANFLSDEDYT 111 (211)
Q Consensus 33 ~~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~-~~~~~~~llql~~~~~~~i~~~~~~~~~~~~L~~~L~~~~i~ 111 (211)
++++.++++++.+.. ...++|||+||.+.+. +..+++++||||+++.|++|++.....+++.|+++|+++++.
T Consensus 2 ~~~~~~~~~~~~~~~------~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~~~~~~l~~ll~~~~i~ 75 (170)
T cd06141 2 DSAQDAEEAVKELLG------KEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSIL 75 (170)
T ss_pred CCHHHHHHHHHHHhc------CCCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhhcccHHHHHHhcCCCee
Confidence 567788889888761 3799999999998753 256899999999998999999988777889999999999999
Q ss_pred EEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHH
Q 048832 112 FVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLY 191 (211)
Q Consensus 112 kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~y 191 (211)
||||+++.|++.|.+.+|+.+.+++|++ +++ |+.++..+..||++|++++||..+.|.+..++|||..|||+++|++|
T Consensus 76 kv~~~~k~D~~~L~~~~g~~~~~~~Dl~-~aa-~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~Y 153 (170)
T cd06141 76 KVGVGIKGDARKLARDFGIEVRGVVDLS-HLA-KRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILY 153 (170)
T ss_pred EEEeeeHHHHHHHHhHcCCCCCCeeeHH-HHH-HHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHH
Confidence 9999999999999778999999999995 664 67666544579999999999999997777789999999999999999
Q ss_pred HHHhHHHHHHHHHHHh
Q 048832 192 ACLDAFIAFEIGRVLN 207 (211)
Q Consensus 192 Aa~da~~~~~L~~~L~ 207 (211)
||.||++++.||+.|.
T Consensus 154 Aa~Da~~~~~l~~~l~ 169 (170)
T cd06141 154 AATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999999986
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=5.8e-33 Score=210.98 Aligned_cols=159 Identities=28% Similarity=0.400 Sum_probs=136.9
Q ss_pred HHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeC-CeeEEEeccccCcchHHHHHhhcCCCceEEEee
Q 048832 38 VDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVG-RRCLIFQIIHARRIPQSLANFLSDEDYTFVGVG 116 (211)
Q Consensus 38 l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~-~~~~i~~~~~~~~~~~~L~~~L~~~~i~kvg~~ 116 (211)
++++++.+.. ..+++|||+||.+.+ ...++++++|||++ +.|++||+...+..++.|+++|+++++.||||+
T Consensus 2 l~~~~~~l~~------~~~~ig~D~E~~~~~-~~~~~~~liQl~~~~~~~~l~d~~~~~~~~~~L~~lL~d~~i~Kvg~~ 74 (161)
T cd06129 2 LSSLCEDLSM------DGDVIAFDMEWPPGR-RYYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHG 74 (161)
T ss_pred HHHHHHHHhc------CCCEEEEECCccCCC-CCCCceEEEEEEECCCCEEEEecccCccCHHHHHHHhCCCCEEEEEec
Confidence 4556666652 379999999999875 34688999999999 789999998776678899999999999999999
Q ss_pred eHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHHHHHhH
Q 048832 117 IDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLYACLDA 196 (211)
Q Consensus 117 ~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~da 196 (211)
++.|++.|.+.+|+.+.+++|++ +++ |+.++. .+.||+++++++||..++|.. +.|||+.|||+++|+.|||.||
T Consensus 75 ~k~D~~~L~~~~gi~~~~~~D~~-~aa-~ll~~~-~~~~L~~l~~~~lg~~l~K~~--~~s~W~~rpLt~~qi~YAa~Da 149 (161)
T cd06129 75 IEGDLWKLLRDFGEKLQRLFDTT-IAA-NLKGLP-ERWSLASLVEHFLGKTLDKSI--SCADWSYRPLTEDQKLYAAADV 149 (161)
T ss_pred cHHHHHHHHHHcCCCcccHhHHH-HHH-HHhCCC-CCchHHHHHHHHhCCCCCccc--eeccCCCCCCCHHHHHHHHHHH
Confidence 99999999767999999999995 665 565554 357999999999999997754 5899999999999999999999
Q ss_pred HHHHHHHHHHhc
Q 048832 197 FIAFEIGRVLNA 208 (211)
Q Consensus 197 ~~~~~L~~~L~~ 208 (211)
++++.||+.|++
T Consensus 150 ~~l~~l~~~l~~ 161 (161)
T cd06129 150 YALLIIYTKLRN 161 (161)
T ss_pred HHHHHHHHHHhC
Confidence 999999999974
No 4
>PRK10829 ribonuclease D; Provisional
Probab=99.96 E-value=3.1e-28 Score=205.89 Aligned_cols=165 Identities=18% Similarity=0.167 Sum_probs=145.2
Q ss_pred EEeCChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEeccccCcchHHHHHhhcCCC
Q 048832 30 QVTRSPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIHARRIPQSLANFLSDED 109 (211)
Q Consensus 30 ~~~~~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~~~~~~~~L~~~L~~~~ 109 (211)
.++++++++.++++.+. ..+.+|+|+|+.... ...+++++|||++++.+++||+..... .+.|.++|+|++
T Consensus 4 ~~I~t~~~L~~~~~~l~-------~~~~lalDtEf~~~~-ty~~~l~LiQl~~~~~~~LiD~l~~~d-~~~L~~ll~~~~ 74 (373)
T PRK10829 4 QMITTDDALASVCEAAR-------AFPAIALDTEFVRTR-TYYPQLGLIQLYDGEQLSLIDPLGITD-WSPFKALLRDPQ 74 (373)
T ss_pred EEeCCHHHHHHHHHHHh-------cCCeEEEecccccCc-cCCCceeEEEEecCCceEEEecCCccc-hHHHHHHHcCCC
Confidence 57899999999999876 489999999987653 556789999999988899999876543 568999999999
Q ss_pred ceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHH
Q 048832 110 YTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQV 189 (211)
Q Consensus 110 i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~ 189 (211)
++||+|++++|+..|.+.+|+.+.++|||+ +|+..++.+. +.||+.|++++||..++|.++ .+||+.|||+++|+
T Consensus 75 ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTq-iaa~~lg~~~--~~gl~~Lv~~~lgv~ldK~~~--~sDW~~RPLs~~ql 149 (373)
T PRK10829 75 VTKFLHAGSEDLEVFLNAFGELPQPLIDTQ-ILAAFCGRPL--SCGFASMVEEYTGVTLDKSES--RTDWLARPLSERQC 149 (373)
T ss_pred eEEEEeChHhHHHHHHHHcCCCcCCeeeHH-HHHHHcCCCc--cccHHHHHHHHhCCccCcccc--cCCCCCCCCCHHHH
Confidence 999999999999999788999999999995 6766776542 689999999999999999875 78999999999999
Q ss_pred HHHHHhHHHHHHHHHHHhc
Q 048832 190 LYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 190 ~yAa~da~~~~~L~~~L~~ 208 (211)
+|||.||.+++.||+.|.+
T Consensus 150 ~YAa~Dv~~L~~l~~~L~~ 168 (373)
T PRK10829 150 EYAAADVFYLLPIAAKLMA 168 (373)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999764
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=99.96 E-value=1.4e-27 Score=183.05 Aligned_cols=167 Identities=26% Similarity=0.344 Sum_probs=139.7
Q ss_pred EEeCChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCC-CCCCCeeEEEeeeCCeeEEEeccccCc--chHHHHHhhc
Q 048832 30 QVTRSPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFS-RQQNPVATLQLCVGRRCLIFQIIHARR--IPQSLANFLS 106 (211)
Q Consensus 30 ~~~~~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~-~~~~~~~llql~~~~~~~i~~~~~~~~--~~~~L~~~L~ 106 (211)
++++++++++++++.+. ..+.+|||+||.+... ....+++++|+|+++.+++++...... ++..|+++|+
T Consensus 2 ~~v~~~~~l~~~~~~l~-------~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~ 74 (176)
T PF01612_consen 2 QIVDTEEELEEAIKKLK-------NAKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLE 74 (176)
T ss_dssp EEEHSHHHHHHHHHHHT-------TTSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHT
T ss_pred EecCCHHHHHHHHHHHc-------CCCeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHh
Confidence 46788899999999987 3679999999998753 247888999999999889887766544 4789999999
Q ss_pred CCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcC-ccCCCCCCccccCCC-CCCC
Q 048832 107 DEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLE-KEVNKPRNITLSAWD-TRVL 184 (211)
Q Consensus 107 ~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~-~~l~k~~~~~~s~W~-~~~L 184 (211)
++++.|||||++.|.+.|.+.+|+.+.+.+|+ ++++ ++.++.. ++||++|+.+++| ...++. ...++|. .+||
T Consensus 75 ~~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~-~l~~-~~l~~~~-~~~L~~L~~~~l~~~~~~~~--~~~~~~~~~~~l 149 (176)
T PF01612_consen 75 DPNIIKVGHNAKFDLKWLYRSFGIDLKNVFDT-MLAA-YLLDPTR-SYSLKDLAEEYLGNIDLDKK--EQMSDWRKARPL 149 (176)
T ss_dssp TTTSEEEESSHHHHHHHHHHHHTS--SSEEEH-HHHH-HHTTTST-TSSHHHHHHHHHSEEE-GHC--CTTSSTTTSSS-
T ss_pred CCCccEEEEEEechHHHHHHHhccccCCccch-hhhh-hcccccc-cccHHHHHHHHhhhccCcHH--HhhccCCcCCCC
Confidence 99999999999999999987799999999999 7885 7777753 3999999999999 444443 3588999 8999
Q ss_pred CHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 185 TPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 185 ~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
+++|+.|||.||+++++|++.|.+
T Consensus 150 ~~~~~~YAa~D~~~~~~l~~~l~~ 173 (176)
T PF01612_consen 150 SEEQIEYAAQDAVVTFRLYEKLKP 173 (176)
T ss_dssp HHHHHHHHHHHHHTHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999874
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=99.95 E-value=8.2e-28 Score=188.27 Aligned_cols=151 Identities=19% Similarity=0.211 Sum_probs=128.3
Q ss_pred CCcEEEEeeeeecCCCCCCCCeeEEEeeeC-CeeEEEeccccC--cchHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCC
Q 048832 54 HCLIVGLDVEWRPSFSRQQNPVATLQLCVG-RRCLIFQIIHAR--RIPQSLANFLSDEDYTFVGVGIDGDVKKLENNYGL 130 (211)
Q Consensus 54 ~~~~v~~d~e~~~~~~~~~~~~~llql~~~-~~~~i~~~~~~~--~~~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi 130 (211)
...++|||+||.+.. ..++++++|+|+. +.+|+||+...+ .+.+.|+++|+++++.||||+++.|.+.|.+.+|+
T Consensus 9 ~~~~i~~D~E~~~~~--~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi 86 (197)
T cd06148 9 KQKVIGLDCEGVNLG--RKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGI 86 (197)
T ss_pred hCCEEEEEcccccCC--CCCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHHhcCc
Confidence 478999999997654 2678999999999 889999998764 35678999999999999999999999999778999
Q ss_pred CCCcEeecHHHHHhhccccccc-------cccHHHHHHHHcCccCCCCC------CccccCCCCCCCCHHHHHHHHHhHH
Q 048832 131 QVFRTVDLRPLAAEDLEIEGLR-------FAGLKALSWEVLEKEVNKPR------NITLSAWDTRVLTPAQVLYACLDAF 197 (211)
Q Consensus 131 ~~~~~~D~~~la~~~l~~~~~~-------~~~L~~l~~~~L~~~l~k~~------~~~~s~W~~~~L~~~q~~yAa~da~ 197 (211)
.+.|+||+ ++|+ |++++... ..|++++++++|+.++.|.. ..+.++|..|||+++|+.|||.||+
T Consensus 87 ~~~~~fDt-~iA~-~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~ 164 (197)
T cd06148 87 KLNNVFDT-QVAD-ALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVL 164 (197)
T ss_pred cccceeeH-HHHH-HHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHH
Confidence 99999999 5775 66665322 36999999999998876421 2347899999999999999999999
Q ss_pred HHHHHHHHHhc
Q 048832 198 IAFEIGRVLNA 208 (211)
Q Consensus 198 ~~~~L~~~L~~ 208 (211)
+++.|+..|.+
T Consensus 165 ~Ll~l~~~l~~ 175 (197)
T cd06148 165 CLLPLYYAMLD 175 (197)
T ss_pred hHHHHHHHHHH
Confidence 99999998865
No 7
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=3.9e-26 Score=188.95 Aligned_cols=161 Identities=20% Similarity=0.185 Sum_probs=140.5
Q ss_pred hHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEeccccCcchHHHHHhhcCCCceEEE
Q 048832 35 PSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIHARRIPQSLANFLSDEDYTFVG 114 (211)
Q Consensus 35 ~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~~~~~~~~L~~~L~~~~i~kvg 114 (211)
.+.++++..... ..+.|++|+|+.... ...+++++||++.++++.+||+.....-.+.|..+|.|++|+||.
T Consensus 4 ~~~l~~~~~~~~-------~~~~iAiDTEf~r~~-t~~p~LcLIQi~~~e~~~lIdpl~~~~d~~~l~~Ll~d~~v~KIf 75 (361)
T COG0349 4 GDLLAAACALLR-------GSKAIAIDTEFMRLR-TYYPRLCLIQISDGEGASLIDPLAGILDLPPLVALLADPNVVKIF 75 (361)
T ss_pred hhHHHHHHHHhc-------CCCceEEeccccccc-ccCCceEEEEEecCCCceEecccccccccchHHHHhcCCceeeee
Confidence 344666666655 368999999987664 678999999999998899999976444566889999999999999
Q ss_pred eeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHHHHH
Q 048832 115 VGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLYACL 194 (211)
Q Consensus 115 ~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~ 194 (211)
|...+|+..|.+.||+.+.++|||+ +|+.+.|-+. ++||++|+++++|..++|+++ .|||.+||||++|++|||.
T Consensus 76 Haa~~DL~~l~~~~g~~p~plfdTq-iAa~l~g~~~--~~gl~~Lv~~ll~v~ldK~~q--~SDW~~RPLs~~Ql~YAa~ 150 (361)
T COG0349 76 HAARFDLEVLLNLFGLLPTPLFDTQ-IAAKLAGFGT--SHGLADLVEELLGVELDKSEQ--RSDWLARPLSEAQLEYAAA 150 (361)
T ss_pred ccccccHHHHHHhcCCCCCchhHHH-HHHHHhCCcc--cccHHHHHHHHhCCccccccc--ccccccCCCCHHHHHHHHH
Confidence 9999999999988899999999995 7766777654 999999999999999999886 8999999999999999999
Q ss_pred hHHHHHHHHHHHhc
Q 048832 195 DAFIAFEIGRVLNA 208 (211)
Q Consensus 195 da~~~~~L~~~L~~ 208 (211)
|+.+++.||.+|.+
T Consensus 151 DV~yL~~l~~~L~~ 164 (361)
T COG0349 151 DVEYLLPLYDKLTE 164 (361)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999875
No 8
>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=99.94 E-value=1.4e-25 Score=190.40 Aligned_cols=163 Identities=21% Similarity=0.193 Sum_probs=139.3
Q ss_pred eCChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEeccccCcchHHHHHhhcCCCce
Q 048832 32 TRSPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIHARRIPQSLANFLSDEDYT 111 (211)
Q Consensus 32 ~~~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~~~~~~~~L~~~L~~~~i~ 111 (211)
+++++++.++++.+. ..+++|+|+||.... ...+++++|||++++.+++||+.... ..+.|.++|+|+++.
T Consensus 2 I~t~~~l~~~~~~l~-------~~~~ia~DtE~~~~~-~y~~~l~LiQia~~~~~~liD~~~~~-~~~~L~~lL~d~~i~ 72 (367)
T TIGR01388 2 ITTDDELATVCEAVR-------TFPFVALDTEFVRER-TFWPQLGLIQVADGEQLALIDPLVII-DWSPLKELLRDESVV 72 (367)
T ss_pred cCCHHHHHHHHHHHh-------cCCEEEEeccccCCC-CCCCcceEEEEeeCCeEEEEeCCCcc-cHHHHHHHHCCCCce
Confidence 677888999999987 378999999997653 45678999999999999999987553 467899999999999
Q ss_pred EEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHH
Q 048832 112 FVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLY 191 (211)
Q Consensus 112 kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~y 191 (211)
||+|++|.|++.|.+.+|....++||+ ++|+ |+++++. +.|++.|++++||..++|++ +.++|..+||+.+|+.|
T Consensus 73 KV~h~~k~Dl~~L~~~~~~~~~~~fDt-qlAa-~lL~~~~-~~~l~~Lv~~~Lg~~l~K~~--~~sdW~~rPL~~~q~~Y 147 (367)
T TIGR01388 73 KVLHAASEDLEVFLNLFGELPQPLFDT-QIAA-AFCGFGM-SMGYAKLVQEVLGVELDKSE--SRTDWLARPLTDAQLEY 147 (367)
T ss_pred EEEeecHHHHHHHHHHhCCCCCCcccH-HHHH-HHhCCCC-CccHHHHHHHHcCCCCCccc--ccccCCCCCCCHHHHHH
Confidence 999999999999976666666678999 5785 6766653 57999999999999998764 37899999999999999
Q ss_pred HHHhHHHHHHHHHHHhc
Q 048832 192 ACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 192 Aa~da~~~~~L~~~L~~ 208 (211)
||.||++++.|++.|.+
T Consensus 148 Aa~Dv~~L~~L~~~L~~ 164 (367)
T TIGR01388 148 AAADVTYLLPLYAKLME 164 (367)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999998853
No 9
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.87 E-value=1.6e-20 Score=142.95 Aligned_cols=166 Identities=25% Similarity=0.275 Sum_probs=128.8
Q ss_pred EeCChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCC-eeEEEeccccCcchHHHHHhhcCCC
Q 048832 31 VTRSPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGR-RCLIFQIIHARRIPQSLANFLSDED 109 (211)
Q Consensus 31 ~~~~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~-~~~i~~~~~~~~~~~~L~~~L~~~~ 109 (211)
++++++++.+|++.+.. ....+++|+|+.+.. ....+++++|+|.++ .+|+++.......+..|+++|+++.
T Consensus 3 ~i~~~~~~~~~~~~~~~------~~~~l~~~~e~~~~~-~~~~~~~~l~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~ 75 (172)
T smart00474 3 VVTDSETLEELLEKLRA------AGGEVALDTETTGLN-SYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDET 75 (172)
T ss_pred EecCHHHHHHHHHHHHh------cCCeEEEeccccCCc-cCCCCEEEEEEeEcCCceEEEEeccchhhHHHHHHHhcCCC
Confidence 55666778888765531 146899999986543 335788999999754 5666544323334566899999999
Q ss_pred ceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHH
Q 048832 110 YTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQV 189 (211)
Q Consensus 110 i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~ 189 (211)
+.|+|||+|.|.+.|. .+|+.+.+.+|+ ++++ |+++|+.+.++|+++++.+++..+.+ ....++|..+++..+|+
T Consensus 76 ~~kv~~d~k~~~~~L~-~~gi~~~~~~D~-~laa-yll~p~~~~~~l~~l~~~~l~~~~~~--~~~~~~~~~~~l~~~~~ 150 (172)
T smart00474 76 ITKVGHNAKFDLHVLA-RFGIELENIFDT-MLAA-YLLLGGPSKHGLATLLKEYLGVELDK--EEQKSDWGARPLSEEQL 150 (172)
T ss_pred ceEEEechHHHHHHHH-HCCCcccchhHH-HHHH-HHHcCCCCcCCHHHHHHHHhCCCCCc--ccCccccccCCCCHHHH
Confidence 9999999999999996 599999988999 6885 88888755479999999999877643 12245887788899999
Q ss_pred HHHHHhHHHHHHHHHHHhc
Q 048832 190 LYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 190 ~yAa~da~~~~~L~~~L~~ 208 (211)
.||+.||+++++|++.|.+
T Consensus 151 ~ya~~~a~~~~~L~~~l~~ 169 (172)
T smart00474 151 QYAAEDADALLRLYEKLEK 169 (172)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 9999999999999998865
No 10
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.87 E-value=2.1e-20 Score=143.65 Aligned_cols=147 Identities=24% Similarity=0.275 Sum_probs=120.2
Q ss_pred CcEEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEeccccCcchHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCc
Q 048832 55 CLIVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIHARRIPQSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFR 134 (211)
Q Consensus 55 ~~~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~~~~~~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~ 134 (211)
...+++|+|+.+.. ...+++.++|+|+++.+++|++... ..++.|+++|+++++.|+|||+|.|.+.|.+.+|+...+
T Consensus 12 ~~~l~~~~e~~~~~-~~~~~~~~i~l~~~~~~~~i~~~~~-~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~ 89 (178)
T cd06142 12 AGVIAVDTEFMRLN-TYYPRLCLIQISTGGEVYLIDPLAI-GDLSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQN 89 (178)
T ss_pred CCeEEEECCccCCC-cCCCceEEEEEeeCCCEEEEeCCCc-ccHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCC
Confidence 56899999876543 2357889999999855888886543 456679999999999999999999999997666998445
Q ss_pred EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 135 TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 135 ~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
.+|+ ++++ |+++|+. +++++++++++++..+.+.+ ..++|..++++.+|+.||+.||+++++|++.|.+
T Consensus 90 ~~D~-~laa-yLl~p~~-~~~l~~l~~~~l~~~~~~~~--~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~ 158 (178)
T cd06142 90 LFDT-QIAA-RLLGLGD-SVGLAALVEELLGVELDKGE--QRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKE 158 (178)
T ss_pred cccH-HHHH-HHhCCCc-cccHHHHHHHHhCCCCCccc--ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHH
Confidence 6999 6885 8889874 36999999999998765543 4679999999999999999999999999988753
No 11
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=99.81 E-value=4.1e-18 Score=132.94 Aligned_cols=164 Identities=20% Similarity=0.244 Sum_probs=125.6
Q ss_pred EeCChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEeccccCcchHHHHHhhcCCCc
Q 048832 31 VTRSPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIHARRIPQSLANFLSDEDY 110 (211)
Q Consensus 31 ~~~~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~~~~~~~~L~~~L~~~~i 110 (211)
++.+++.+..|++.+. ....+++++|..+.. +...++.++|++.++++++|++.........|+++|+++++
T Consensus 7 ~i~~~~~l~~~~~~l~-------~~~~l~~~~e~~~~~-~~~~~~~~l~l~~~~~~~~i~~l~~~~~~~~L~~~L~~~~i 78 (192)
T cd06147 7 FVDTEEKLEELVEKLK-------NCKEIAVDLEHHSYR-SYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNI 78 (192)
T ss_pred EECCHHHHHHHHHHHh-------cCCeEEEEeEecCCc-cCCCceEEEEEecCCCcEEEEecccccchHHHHHHhcCCCc
Confidence 4444466788776553 245899999764332 23567888999987667777632222344568899999999
Q ss_pred eEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHH
Q 048832 111 TFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVL 190 (211)
Q Consensus 111 ~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~ 190 (211)
.|+||++|.+.+.|.+.+|+.+.+.||+ ++++ |+++|+ + +++++++++||+..+.| +.+.++|+.+||..+|..
T Consensus 79 ~kv~~d~K~~~~~L~~~~gi~~~~~fD~-~laa-YLL~p~-~-~~l~~l~~~yl~~~~~k--~~~~~~~~~~~l~~~~~~ 152 (192)
T cd06147 79 LKVFHGADSDIIWLQRDFGLYVVNLFDT-GQAA-RVLNLP-R-HSLAYLLQKYCNVDADK--KYQLADWRIRPLPEEMIK 152 (192)
T ss_pred eEEEechHHHHHHHHHHhCCCcCchHHH-HHHH-HHhCCC-c-ccHHHHHHHHhCCCcch--hhhccccccCCCCHHHHH
Confidence 9999999999999954789998888999 6885 999998 5 59999999999876433 223567877788889999
Q ss_pred HHHHhHHHHHHHHHHHhc
Q 048832 191 YACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 191 yAa~da~~~~~L~~~L~~ 208 (211)
|++.+|.++++|++.|.+
T Consensus 153 y~a~~a~~l~~L~~~L~~ 170 (192)
T cd06147 153 YAREDTHYLLYIYDRLRN 170 (192)
T ss_pred HHHhhHHHHHHHHHHHHH
Confidence 999999999999988754
No 12
>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=99.80 E-value=1.2e-18 Score=130.16 Aligned_cols=147 Identities=22% Similarity=0.159 Sum_probs=113.7
Q ss_pred EEEEeeeeecCCCCCCCCeeEEEeeeCCe-eEEEeccccCcchHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCc-
Q 048832 57 IVGLDVEWRPSFSRQQNPVATLQLCVGRR-CLIFQIIHARRIPQSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFR- 134 (211)
Q Consensus 57 ~v~~d~e~~~~~~~~~~~~~llql~~~~~-~~i~~~~~~~~~~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~- 134 (211)
++++|+|+.+.. +...+++++|+|.+++ ++++++.+..-..+.|+++|+++++.|+|||+|.|.+.|. ..|+.+.+
T Consensus 1 ~~~~~~e~~~~~-~~~~~~~~l~l~~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L~-~~~~~~~~~ 78 (150)
T cd09018 1 VFAFDTETDSLD-NISANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILL-NYFIELRGI 78 (150)
T ss_pred CEEEEeecCCCC-CCCceEEEEEEEcCCCcEEEEEcCCcccCHHHHHHHhcCCCCceeeecHHHHHHHHH-HcCCccCCc
Confidence 378899876543 3357889999998754 8888765421135678999999999999999999999994 67877776
Q ss_pred EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 135 TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 135 ~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
.+|+ ++|+ |+++|...+.+++++++++|+..+.+.+++..++|..+++..+|+.||+.+|+++++|++.|.
T Consensus 79 ~~D~-~laa-yLl~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 79 AFDT-MLEA-YILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred chhH-HHHH-HHhCCCCCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4899 6885 898997513599999999998875442222233585577888899999999999999999885
No 13
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=99.78 E-value=2.2e-18 Score=139.85 Aligned_cols=192 Identities=36% Similarity=0.639 Sum_probs=156.4
Q ss_pred CCCCceeEEEeCCeEEEEEEeCChHHHHHHHHHHHHHhhc-cCCCcEEEEeeeeecCC----------------------
Q 048832 12 YNTHDEYTVHFYDDVVFTQVTRSPSVVDDWISEIERIHRR-RLHCLIVGLDVEWRPSF---------------------- 68 (211)
Q Consensus 12 ~~~~~~~~v~~~~~~i~~~~~~~~~~l~~~i~~l~~~~~~-~~~~~~v~~d~e~~~~~---------------------- 68 (211)
|.++-.|.|.|.++...|+++.+...+.+|+..+.....+ ..++.++|++++|++..
T Consensus 11 ~~t~~~~~vd~~~~~~~Vtvt~~~svi~~~i~d~~~~~~~~~s~p~vvg~~vqw~p~~~~~~~~~~~~~~~~~~~a~~~~ 90 (319)
T KOG4373|consen 11 YATVQKYSVDFFGEELIVTVTPDSSVISRWIHDVRFLSRNFSSDPLVVGRGVQWTPPTLTPDQTIYAARDLQISVARFLH 90 (319)
T ss_pred cccccceeeeecccceEEEEccCcccchhhhhhhhhcccCcccCCcccCcCcccCCCCCCccccccccchhccccccccc
Confidence 6677789999999999999999999999999887643211 23578999999998761
Q ss_pred -----------------------------------C-C----------------CCCCeeEEEeeeCC-eeEEEeccccC
Q 048832 69 -----------------------------------S-R----------------QQNPVATLQLCVGR-RCLIFQIIHAR 95 (211)
Q Consensus 69 -----------------------------------~-~----------------~~~~~~llql~~~~-~~~i~~~~~~~ 95 (211)
. + ..++++.+|||+++ .|+|+++.+..
T Consensus 91 ~~~~~~~~~~~kl~~~~d~~a~~~~~~~~~~~~~s~~~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~en~C~I~ql~~~~ 170 (319)
T KOG4373|consen 91 LLGSSFKHKRQKLGYGSDARASPYIDNSLEIADDSDPPFVCYRREAQPYLDMGRSDPPPDTLQLCVGENRCLIIQLIHCK 170 (319)
T ss_pred cccCcccccccccccccccccccccccccccccccCCcceeecccccccccccccCCCcchhhhhhcccceeeEEeeccc
Confidence 0 0 23456789999995 69999999988
Q ss_pred cchHHHHHhhcCCCceEEEeeeHHHHHHHHH-hcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcC---ccCCCC
Q 048832 96 RIPQSLANFLSDEDYTFVGVGIDGDVKKLEN-NYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLE---KEVNKP 171 (211)
Q Consensus 96 ~~~~~L~~~L~~~~i~kvg~~~k~d~~~L~~-~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~---~~l~k~ 171 (211)
.+|..|+.||+|++.++||.+...|..+|.+ .|+++|....|+..++..-++. +..+.+...+++..++ ..+.++
T Consensus 171 ~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g~-~~~~~s~e~i~~~~~~~~~~~v~l~ 249 (319)
T KOG4373|consen 171 RIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLGG-SMPNDSFEEIVSETLGYYGKDVRLD 249 (319)
T ss_pred cchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhhcc-CccCccHHHHHHHHhhccccccccC
Confidence 9999999999999999999999999999987 8999998888987666544433 3335667777777665 346677
Q ss_pred CCccccCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 048832 172 RNITLSAWDTRVLTPAQVLYACLDAFIAFEIGR 204 (211)
Q Consensus 172 ~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~ 204 (211)
+.+++|+|+..+|+.+|+.||+.|||+...++.
T Consensus 250 ~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg~ 282 (319)
T KOG4373|consen 250 KEIRMSDWSVYPLSDDQLLQASIDVYVCHKLGV 282 (319)
T ss_pred hhcccccceeeeccHHHHHHHHhHHHHHHHHHH
Confidence 789999999999999999999999999999874
No 14
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.76 E-value=2.6e-17 Score=123.02 Aligned_cols=146 Identities=23% Similarity=0.163 Sum_probs=109.2
Q ss_pred EEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEeccc-cCcchHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCC-c
Q 048832 57 IVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIH-ARRIPQSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVF-R 134 (211)
Q Consensus 57 ~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~-~~~~~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~-~ 134 (211)
.+++|+|+.+.. ....++.++|+|+++++++++... .....+.|+++|+++.+.|||||+|.|.+.|. ..++... +
T Consensus 2 ~l~~d~e~~~~~-~~~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~-~~~~~~~~~ 79 (155)
T cd00007 2 EVAFDTETTGLN-YHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLA-RDGIELPGN 79 (155)
T ss_pred ceEEEEecCCCC-cCCCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHH-HCCCCCCCC
Confidence 578999876543 335788999999864355555432 12355668999999999999999999999995 4555444 4
Q ss_pred EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCC----CCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 135 TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAW----DTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 135 ~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W----~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
.+|+ ++++ |+.+|...+++|+++++++++..+.+.++ ..+| ..++++.+|..||+.||.++++|++.|.+
T Consensus 80 ~~D~-~~~a-yll~~~~~~~~l~~l~~~~l~~~~~~~~~--~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~ 153 (155)
T cd00007 80 IFDT-MLAA-YLLNPGEGSHSLDDLAKEYLGIELDKDEQ--IYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLE 153 (155)
T ss_pred cccH-HHHH-HHhCCCCCcCCHHHHHHHHcCCCCccHHH--HhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHh
Confidence 6899 6775 88888753579999999999877543222 2233 24678888999999999999999999875
No 15
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.69 E-value=6e-17 Score=140.38 Aligned_cols=171 Identities=22% Similarity=0.355 Sum_probs=132.2
Q ss_pred EEeCChHHHHHHH-HHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEeccccCcc-----hHHHHH
Q 048832 30 QVTRSPSVVDDWI-SEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIHARRI-----PQSLAN 103 (211)
Q Consensus 30 ~~~~~~~~l~~~i-~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~~~~~-----~~~L~~ 103 (211)
..+.++.++..++ +.+.. +...||+|+||.+.-....++++++|++..+.+|++|+...... ...+..
T Consensus 393 ~~V~~e~El~~l~l~~l~~------e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~ 466 (617)
T KOG2207|consen 393 GMVGNEKELRDLLLESLSE------ELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQ 466 (617)
T ss_pred eeeCCHHHHHHHHHHHhhh------cCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHH
Confidence 3777788888776 23332 24789999999987334578999999999999999999764322 235678
Q ss_pred hhcCCCceEEEeeeHHHHHHHHH-----hcCCCCCc---EeecHHHHHhhccc------cccccccHHHHHHHHcCccCC
Q 048832 104 FLSDEDYTFVGVGIDGDVKKLEN-----NYGLQVFR---TVDLRPLAAEDLEI------EGLRFAGLKALSWEVLEKEVN 169 (211)
Q Consensus 104 ~L~~~~i~kvg~~~k~d~~~L~~-----~~gi~~~~---~~D~~~la~~~l~~------~~~~~~~L~~l~~~~L~~~l~ 169 (211)
+|+++++.|||+++..|++.+.+ ++.+++.+ .++...++..+..- -.....+|++|....+|..++
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 99999999999999999999964 33344432 34444555444222 123478899999999999999
Q ss_pred CCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 170 KPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 170 k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
|.++ +|||..|||+..|+.|||.||.++..++..+.+
T Consensus 547 Kteq--csnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~ 583 (617)
T KOG2207|consen 547 KTEQ--CSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCS 583 (617)
T ss_pred cccc--cchhhcCCchhhHHHHHHhcchhhHHHHHHHHh
Confidence 9886 999999999999999999999999999988764
No 16
>PRK05755 DNA polymerase I; Provisional
Probab=99.65 E-value=5.3e-15 Score=138.59 Aligned_cols=167 Identities=19% Similarity=0.232 Sum_probs=129.5
Q ss_pred EEEeCChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCCe-eEEEeccccC-cchHHHHHhhc
Q 048832 29 TQVTRSPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGRR-CLIFQIIHAR-RIPQSLANFLS 106 (211)
Q Consensus 29 ~~~~~~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~~-~~i~~~~~~~-~~~~~L~~~L~ 106 (211)
..++++++.+.+|++.+. ....+++|+|..+.. ....++.++|++..++ ++++++.+.+ ...+.|.++|+
T Consensus 296 ~~~I~~~~~L~~~l~~l~-------~~~~~a~DtEt~~l~-~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~ 367 (880)
T PRK05755 296 YETILDEEELEAWLAKLK-------AAGLFAFDTETTSLD-PMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLE 367 (880)
T ss_pred eEEeCCHHHHHHHHHHhh-------ccCeEEEEeccCCCC-cccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHh
Confidence 346778888999998876 378899999987764 4567888999999875 8888885532 35567899999
Q ss_pred CCCceEEEeeeHHHHHHHHHhcCCCCCc-EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCc--cccCCCCCC
Q 048832 107 DEDYTFVGVGIDGDVKKLENNYGLQVFR-TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNI--TLSAWDTRV 183 (211)
Q Consensus 107 ~~~i~kvg~~~k~d~~~L~~~~gi~~~~-~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~--~~s~W~~~~ 183 (211)
++.+.||+||++.|++.|. .+|+.+.+ ++|+ ++++ |+++|+. .++|++++++++|.++...+++ ...+|+..|
T Consensus 368 d~~v~kV~HNakfDl~~L~-~~gi~~~~~~~DT-~iAa-~Ll~~~~-~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~p 443 (880)
T PRK05755 368 DPAIKKVGQNLKYDLHVLA-RYGIELRGIAFDT-MLAS-YLLDPGR-RHGLDSLAERYLGHKTISFEEVAGKQLTFAQVD 443 (880)
T ss_pred CCCCcEEEeccHhHHHHHH-hCCCCcCCCcccH-HHHH-HHcCCCC-CCCHHHHHHHHhCCCccchHHhcCCCCCccccC
Confidence 9999999999999999995 67998765 6899 6775 8888875 4999999999998764211100 022344445
Q ss_pred CCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 184 LTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 184 L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
+ +.+..||+.|+.++++|+..|.+
T Consensus 444 l-e~~~~YAa~Dv~~~~~L~~~L~~ 467 (880)
T PRK05755 444 L-EEAAEYAAEDADVTLRLHEVLKP 467 (880)
T ss_pred H-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 5 46899999999999999998865
No 17
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=99.65 E-value=4.3e-15 Score=114.27 Aligned_cols=148 Identities=18% Similarity=0.064 Sum_probs=110.3
Q ss_pred CcEEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEeccccCcchHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCc
Q 048832 55 CLIVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIHARRIPQSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFR 134 (211)
Q Consensus 55 ~~~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~~~~~~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~ 134 (211)
...+++++|..... ....++.+++++.+++++++++.+.....+.|+++|+++++.|++||+|.+.+.|. .+|+.+.+
T Consensus 3 ~~~~~~~~~~~~~~-~~~~~l~~i~l~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~~~~ 80 (178)
T cd06140 3 ADEVALYVELLGEN-YHTADIIGLALANGGGAYYIPLELALLDLAALKEWLEDEKIPKVGHDAKRAYVALK-RHGIELAG 80 (178)
T ss_pred CCceEEEEEEcCCC-cceeeEEEEEEEeCCcEEEEeccchHHHHHHHHHHHhCCCCceeccchhHHHHHHH-HCCCcCCC
Confidence 45677888876543 34577888999987667777754210123458899999999999999999999994 78999887
Q ss_pred E-eecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCC---CCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 135 T-VDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWD---TRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 135 ~-~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~---~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
. ||+ ++|+ |+++|+.+++++++++.++++.++.+.++ ...|. .++....+..|++.+|.++++|++.|.+
T Consensus 81 ~~fDt-~laa-YLL~p~~~~~~l~~l~~~yl~~~~~~~~~--~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~ 154 (178)
T cd06140 81 VAFDT-MLAA-YLLDPTRSSYDLADLAKRYLGRELPSDEE--VYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEE 154 (178)
T ss_pred cchhH-HHHH-HHcCCCCCCCCHHHHHHHHcCCCCcchHH--hcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5 899 7885 99999865579999999999987644221 22231 2333555888999999999999988754
No 18
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.61 E-value=1e-15 Score=132.22 Aligned_cols=164 Identities=21% Similarity=0.195 Sum_probs=136.3
Q ss_pred EEeCChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEeccccCcchHHHHHhhcCCC
Q 048832 30 QVTRSPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIHARRIPQSLANFLSDED 109 (211)
Q Consensus 30 ~~~~~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~~~~~~~~L~~~L~~~~ 109 (211)
+.+.+..++.+..+.+.. ...+++|.|... ++...+-.+++||++.+.-|+||...+......|++.|.+|+
T Consensus 194 ~~I~t~~el~~l~~~l~~-------~~Efavdlehhs-yrsf~gltclmqISTr~ed~iIDt~~l~~~i~~l~e~fsdp~ 265 (687)
T KOG2206|consen 194 VWICTLGELEALPEILDS-------VIEFAVDLEHHS-YRSFLGLTCLMQISTRTEDFIIDTFKLRDHIGILNEVFSDPG 265 (687)
T ss_pred eeeechHHHHHHHHHHhh-------hhhhhhhccccc-hhhhcCceeEEEeeccchhheehhHHHHHHHHHhhhhccCCC
Confidence 355566667777776653 577899999754 345678889999999988899888765555568999999999
Q ss_pred ceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHH
Q 048832 110 YTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQV 189 (211)
Q Consensus 110 i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~ 189 (211)
++||.|+.-.|+.+|.+.|||-+.|.||+. -|...|+.| .++|+.|.+.+.|...+|. .+..+|..|||+.+++
T Consensus 266 ivkvfhgaD~diiwlqrdfgiyvvnLfdt~-~a~r~L~~~---r~sL~~ll~~~~~v~~nk~--yqladwR~rpLp~~Mv 339 (687)
T KOG2206|consen 266 IVKVFHGADTDIIWLQRDFGIYVVNLFDTI-QASRLLGLP---RPSLAYLLECVCGVLTNKK--YQLADWRIRPLPEEMV 339 (687)
T ss_pred eEEEEecCccchhhhhccceEEEEechhhH-HHHHHhCCC---cccHHHHHHHHHhhhhhhh--hhhchhccccCcHHHH
Confidence 999999999999999999999999999995 565567655 7899999999998766554 3478999999999999
Q ss_pred HHHHHhHHHHHHHHHHHh
Q 048832 190 LYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 190 ~yAa~da~~~~~L~~~L~ 207 (211)
.||-.|..+++.||+.|+
T Consensus 340 ~yar~dthyllyiyD~lr 357 (687)
T KOG2206|consen 340 RYAREDTHYLLYIYDVLR 357 (687)
T ss_pred HHHhhcchhHHHHHHHHH
Confidence 999999999999999886
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=99.52 E-value=7.3e-13 Score=102.86 Aligned_cols=150 Identities=21% Similarity=0.226 Sum_probs=107.8
Q ss_pred CCcEEEEeeeeecCCCCCCCCeeEEEeeeCCe-eEEEecccc--------CcchHHHHHhhcCCCceEEEeeeHHHHHHH
Q 048832 54 HCLIVGLDVEWRPSFSRQQNPVATLQLCVGRR-CLIFQIIHA--------RRIPQSLANFLSDEDYTFVGVGIDGDVKKL 124 (211)
Q Consensus 54 ~~~~v~~d~e~~~~~~~~~~~~~llql~~~~~-~~i~~~~~~--------~~~~~~L~~~L~~~~i~kvg~~~k~d~~~L 124 (211)
....+++|+|..+.. ....++..+++|..++ .+++++.+. ......|+++|++..+.+|+||++.|++.|
T Consensus 4 ~~~~~a~d~e~~~~~-~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l 82 (193)
T cd06139 4 KAKVFAFDTETTSLD-PMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVL 82 (193)
T ss_pred cCCeEEEEeecCCCC-cCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHHH
Confidence 367899999875543 3356777899997654 666665431 123344888999988899999999999999
Q ss_pred HHhcCCCCCcE-eecHHHHHhhccccccccccHHHHHHHHcCccCCC-----CCCccccCCCCCCCCHHHHHHHHHhHHH
Q 048832 125 ENNYGLQVFRT-VDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNK-----PRNITLSAWDTRVLTPAQVLYACLDAFI 198 (211)
Q Consensus 125 ~~~~gi~~~~~-~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k-----~~~~~~s~W~~~~L~~~q~~yAa~da~~ 198 (211)
. .+|+.+.+. +|+ ++++ |+++|+..+++|+++++++++....+ ++.....+|...++ ..+..||+.|+.+
T Consensus 83 ~-~~gi~~~~~~~Dt-~l~a-~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~~d~~~ 158 (193)
T cd06139 83 A-NHGIELRGPAFDT-MLAS-YLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADI 158 (193)
T ss_pred H-HCCCCCCCCcccH-HHHH-HHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHHHHHHH
Confidence 4 789888764 788 6775 88899753579999999998765211 11111334543333 5588899999999
Q ss_pred HHHHHHHHhc
Q 048832 199 AFEIGRVLNA 208 (211)
Q Consensus 199 ~~~L~~~L~~ 208 (211)
+++|++.|.+
T Consensus 159 ~~~l~~~l~~ 168 (193)
T cd06139 159 TLRLYELLKP 168 (193)
T ss_pred HHHHHHHHHH
Confidence 9999988864
No 20
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.42 E-value=2.9e-12 Score=113.07 Aligned_cols=162 Identities=20% Similarity=0.228 Sum_probs=118.9
Q ss_pred ChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEecccc---CcchHHHHHhhcCCCc
Q 048832 34 SPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIHA---RRIPQSLANFLSDEDY 110 (211)
Q Consensus 34 ~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~~---~~~~~~L~~~L~~~~i 110 (211)
+.+.+..|+..... ...+++|+|..+.+. ....+.++.++.++.++++++.+. -.....|++||+++.+
T Consensus 8 ~~~~~~~~~~~~~~-------~~~~a~~~et~~l~~-~~~~lvg~s~~~~~~~~yi~~~~~~~~~~~~~~l~~~l~~~~~ 79 (593)
T COG0749 8 DLAVLNAWLTKLNA-------AANIAFDTETDGLDP-HGADLVGLSVASEEEAAYIPLLHGPEQLNVLAALKPLLEDEGI 79 (593)
T ss_pred HHHHHHHHHHHHhh-------cccceeeccccccCc-ccCCeeEEEeeccccceeEeeccchhhhhhHHHHHHHhhCccc
Confidence 34457778777653 344999999988763 566666677887776666677652 1356789999999999
Q ss_pred eEEEeeeHHHHHHHHHhcCCCCCc-EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCC---CCCCC-
Q 048832 111 TFVGVGIDGDVKKLENNYGLQVFR-TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWD---TRVLT- 185 (211)
Q Consensus 111 ~kvg~~~k~d~~~L~~~~gi~~~~-~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~---~~~L~- 185 (211)
.|+|||.|.|.+.|. .+|+. .+ .+|+ |+++ |+++|+...++++++++++++.+....+.+....-. .....
T Consensus 80 ~kv~~~~K~d~~~l~-~~Gi~-~~~~~Dt-mlas-Yll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~ 155 (593)
T COG0749 80 KKVGQNLKYDYKVLA-NLGIE-PGVAFDT-MLAS-YLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKL 155 (593)
T ss_pred chhccccchhHHHHH-HcCCc-ccchHHH-HHHH-hccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchH
Confidence 999999999999995 78966 45 4798 7995 999999888999999999998765433221111100 00112
Q ss_pred HHHHHHHHHhHHHHHHHHHHHh
Q 048832 186 PAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 186 ~~q~~yAa~da~~~~~L~~~L~ 207 (211)
+....|++.||.++++|+..|.
T Consensus 156 ~~~~~y~a~~a~~~~~L~~~l~ 177 (593)
T COG0749 156 EKATEYAAEDADATLRLESILE 177 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3368999999999999999886
No 21
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.29 E-value=2e-11 Score=109.30 Aligned_cols=137 Identities=24% Similarity=0.196 Sum_probs=108.4
Q ss_pred EEeCChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCCeeEEEeccccCcchHHHHHhhcCCC
Q 048832 30 QVTRSPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGRRCLIFQIIHARRIPQSLANFLSDED 109 (211)
Q Consensus 30 ~~~~~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~~~~i~~~~~~~~~~~~L~~~L~~~~ 109 (211)
.++.+++.+.+++..+. ..+.+++|+|..... ..++++|++.++.++++|... .+.++
T Consensus 4 ~~I~~~~~l~~~~~~l~-------~~~~~a~DtEf~r~~----t~l~liQ~~~~~~~~liDpl~------~l~~~----- 61 (553)
T PRK14975 4 KVILAPEELGAALERLS-------PAGVVAGDTETTGDD----AAAAAAQEGEEEPRWVWASTA------ALYPR----- 61 (553)
T ss_pred eEEeccchhHHHHHHhc-------cCCceeCCccccCCc----chhheeeecCCCceEEECchH------HhHHH-----
Confidence 35667778888888877 479999999987543 278899999888888886531 12211
Q ss_pred ceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccc--cccHHHHHHHHcCccCCCCCCccccCCCCCCCCHH
Q 048832 110 YTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLR--FAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPA 187 (211)
Q Consensus 110 i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~--~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~ 187 (211)
| ..+|+.+.++||+ ++|+ |+++++.. +.+++.+++++|+..++|.++ .++|. +|++.+
T Consensus 62 --------------L-~~~Gv~~~~~fDT-~LAa-~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~--~sdw~-rpls~~ 121 (553)
T PRK14975 62 --------------L-LAAGVRVERCHDL-MLAS-QLLLGSEGRAGSSLSAAAARALGEGLDKPPQ--TSALS-DPPDEE 121 (553)
T ss_pred --------------H-HHCCCccCCCchH-HHHH-HHcCCCCCcCCCCHHHHHHHHhCCCCCChhh--hcccc-ccchHH
Confidence 4 3569988889999 6886 77776532 689999999999999988665 68896 899999
Q ss_pred HHHHHHHhHHHHHHHHHHHhc
Q 048832 188 QVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 188 q~~yAa~da~~~~~L~~~L~~ 208 (211)
|+.||+.|+.++.+|+..|.+
T Consensus 122 q~~YAa~Dv~~l~~L~~~L~~ 142 (553)
T PRK14975 122 QLLYAAADADVLLELYAVLAD 142 (553)
T ss_pred HHHHHHHHhHHHHHHHHHHHH
Confidence 999999999999999988864
No 22
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.26 E-value=2e-10 Score=107.36 Aligned_cols=160 Identities=14% Similarity=0.027 Sum_probs=108.3
Q ss_pred eCChHHHHHHHHHHHHHhhccCCCcEEEEeeeeecCCCCCCCCeeEEEeeeCC-e-eEEEeccc-----cCcchHHHHHh
Q 048832 32 TRSPSVVDDWISEIERIHRRRLHCLIVGLDVEWRPSFSRQQNPVATLQLCVGR-R-CLIFQIIH-----ARRIPQSLANF 104 (211)
Q Consensus 32 ~~~~~~l~~~i~~l~~~~~~~~~~~~v~~d~e~~~~~~~~~~~~~llql~~~~-~-~~i~~~~~-----~~~~~~~L~~~ 104 (211)
+.+.+.+.+|++. . ....+++ .... +....+..+.+|+++ + ++++++.. .....+.|+++
T Consensus 307 ~~~~~~~~~~~~~-~-------~~~~~~~----~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 373 (887)
T TIGR00593 307 SEEAAPLANPAEK-A-------EVGGFVL----ERLL-DQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARW 373 (887)
T ss_pred eCCHHHHHHHHHh-C-------cCCeEEE----cCcc-cccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHH
Confidence 3344567777644 1 2446666 1211 234567778899865 3 56665431 11233458999
Q ss_pred hcCCCceEEEeeeHHHHHHHHHhcCCCCCcE-eecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCC
Q 048832 105 LSDEDYTFVGVGIDGDVKKLENNYGLQVFRT-VDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRV 183 (211)
Q Consensus 105 L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~-~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~ 183 (211)
|+++.+.|+|||+|+|++.|. .+|+.+.+. +|+ ++++ |+++|+. .++|++++.+||+..+.+.+++....+.-..
T Consensus 374 l~~~~~~~v~~n~K~d~~~l~-~~gi~~~~~~~Dt-~la~-yll~~~~-~~~l~~la~~yl~~~~~~~~~~~~~~~~~~~ 449 (887)
T TIGR00593 374 LLNEQIKKIGHDAKFLMHLLK-REGIELGGVIFDT-MLAA-YLLDPAQ-VSTLDTLARRYLVEELILDEKIGGKLAKFAF 449 (887)
T ss_pred HhCCCCcEEEeeHHHHHHHHH-hCCCCCCCcchhH-HHHH-HHcCCCC-CCCHHHHHHHHcCcccccHHHhccCCCCccc
Confidence 999999999999999999995 799998875 799 7885 9999975 4699999999998664432211111111112
Q ss_pred CCHH-HHHHHHHhHHHHHHHHHHHhc
Q 048832 184 LTPA-QVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 184 L~~~-q~~yAa~da~~~~~L~~~L~~ 208 (211)
++.+ ...||+.||.++++|+..|.+
T Consensus 450 ~~~~~~~~ya~~d~~~~~~L~~~l~~ 475 (887)
T TIGR00593 450 PPLEEATEYLARRAAATKRLAEELLK 475 (887)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333 578999999999999988754
No 23
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=99.20 E-value=6.5e-10 Score=83.20 Aligned_cols=131 Identities=18% Similarity=0.129 Sum_probs=90.1
Q ss_pred CCCeeEEEeeeCCeeEEEeccccCcchHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcE-eecHHHHHhhccccc
Q 048832 72 QNPVATLQLCVGRRCLIFQIIHARRIPQSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRT-VDLRPLAAEDLEIEG 150 (211)
Q Consensus 72 ~~~~~llql~~~~~~~i~~~~~~~~~~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~-~D~~~la~~~l~~~~ 150 (211)
..++..+.++.+++++++++.. ....+.|+++|+++.+.|++||+|.+.+.| +.+|+.+.+. ||+ +||+ ||++|+
T Consensus 17 ~~~~~glal~~~~~~~yi~~~~-~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~-~LAa-YLL~p~ 92 (151)
T cd06128 17 SANLVGLAFAIEGVAAYIPVAH-DYALELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDT-MLEA-YLLDPV 92 (151)
T ss_pred cCcEEEEEEEcCCCeEEEeCCC-CcCHHHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhH-HHHH-HHcCCC
Confidence 3556667888765566665321 102446889999999999999999999999 5789998886 899 7995 999997
Q ss_pred cccccHHHHHHHHcCccCCCCCCccccC-CCCCCC-CHHHHHHHHHhHHHHHHHHHHHh
Q 048832 151 LRFAGLKALSWEVLEKEVNKPRNITLSA-WDTRVL-TPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 151 ~~~~~L~~l~~~~L~~~l~k~~~~~~s~-W~~~~L-~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
.+..+++++++++|+..+....++.... ... .+ ..+...|++..|.++++|++.|.
T Consensus 93 ~~~~~l~~la~~yl~~~~~~~~~~~gkg~~~~-~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 93 AGRHDMDSLAERWLKEKTITFEEIAGKGLTFN-QIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CCCCCHHHHHHHHcCCCCccHHHHcCCCCChh-hcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 6524999999999886621100010000 000 12 11134478888999999999875
No 24
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=97.87 E-value=0.00021 Score=53.85 Aligned_cols=88 Identities=19% Similarity=0.195 Sum_probs=56.4
Q ss_pred hHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHH--HHhhccccccccccHHHHHHHHcCccCCCCCCcc
Q 048832 98 PQSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPL--AAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNIT 175 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~l--a~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~ 175 (211)
.+.+.+++.+ -+.|||+++.|+..|... .......|+..+ +..+.+.|...+++|+.|++++++..+....+
T Consensus 68 ~~~l~~~l~~--~vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~-- 141 (157)
T cd06149 68 QKEILKILKG--KVVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQ-- 141 (157)
T ss_pred HHHHHHHcCC--CEEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCC--
Confidence 3456667763 568999999999988422 111235687433 22233456556799999999998766643221
Q ss_pred ccCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 048832 176 LSAWDTRVLTPAQVLYACLDAFIAFEIGR 204 (211)
Q Consensus 176 ~s~W~~~~L~~~q~~yAa~da~~~~~L~~ 204 (211)
..+ |..||.++.+|++
T Consensus 142 ~H~-------------Al~DA~at~~l~~ 157 (157)
T cd06149 142 GHS-------------SVEDARATMELYK 157 (157)
T ss_pred CcC-------------cHHHHHHHHHHhC
Confidence 122 6678888887763
No 25
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=97.48 E-value=0.0012 Score=49.44 Aligned_cols=84 Identities=19% Similarity=0.173 Sum_probs=55.0
Q ss_pred hHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccc-cccccHHHHHHHHcCccCCCCCCccc
Q 048832 98 PQSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEG-LRFAGLKALSWEVLEKEVNKPRNITL 176 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~-~~~~~L~~l~~~~L~~~l~k~~~~~~ 176 (211)
.+.|.+++.+ -+.|||++..|+..|. .+..-...+|+..+.. +. .+. ..+++|+.++++++|.++... .
T Consensus 68 ~~~l~~~l~~--~vlVgHn~~fD~~~L~--~~~~~~~~~dt~~l~~-~~-~~~~~~~~sL~~l~~~~lgi~~~~~----~ 137 (152)
T cd06144 68 QKKVAELLKG--RILVGHALKNDLKVLK--LDHPKKLIRDTSKYKP-LR-KTAKGKSPSLKKLAKQLLGLDIQEG----E 137 (152)
T ss_pred HHHHHHHhCC--CEEEEcCcHHHHHHhc--CcCCCccEEEeEEeec-cc-cccCCCChhHHHHHHHHcCcccCCC----C
Confidence 3456778875 3569999999999994 2332234577744331 22 221 358999999999998765321 1
Q ss_pred cCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 048832 177 SAWDTRVLTPAQVLYACLDAFIAFEIGR 204 (211)
Q Consensus 177 s~W~~~~L~~~q~~yAa~da~~~~~L~~ 204 (211)
.+ |..||.++.+|++
T Consensus 138 H~-------------Al~DA~at~~l~~ 152 (152)
T cd06144 138 HS-------------SVEDARAAMRLYR 152 (152)
T ss_pred cC-------------cHHHHHHHHHHhC
Confidence 22 7789999888763
No 26
>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=97.43 E-value=0.003 Score=47.22 Aligned_cols=82 Identities=23% Similarity=0.239 Sum_probs=53.9
Q ss_pred HHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCC
Q 048832 100 SLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAW 179 (211)
Q Consensus 100 ~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W 179 (211)
.+.+|+.. ..+.|||+++.|+..|. ... ...+|+..++.... +...+++|+.|++++++..+....+ ..+
T Consensus 68 ~~~~fl~~-~~vlVgHn~~fD~~fL~-~~~---~~~iDT~~l~r~~~--~~~~~~~L~~L~~~~~~~~i~~~~~--~H~- 137 (150)
T cd06145 68 KLLSLISP-DTILVGHSLENDLKALK-LIH---PRVIDTAILFPHPR--GPPYKPSLKNLAKKYLGRDIQQGEG--GHD- 137 (150)
T ss_pred HHHHHhCC-CCEEEEcChHHHHHHhh-ccC---CCEEEcHHhccccC--CCCCChhHHHHHHHHCCcceeCCCC--CCC-
Confidence 45666652 35789999999999994 321 34689976664222 2224789999999998755432111 112
Q ss_pred CCCCCCHHHHHHHHHhHHHHHHHH
Q 048832 180 DTRVLTPAQVLYACLDAFIAFEIG 203 (211)
Q Consensus 180 ~~~~L~~~q~~yAa~da~~~~~L~ 203 (211)
|..||.++.+|+
T Consensus 138 ------------Al~DA~~t~~l~ 149 (150)
T cd06145 138 ------------SVEDARAALELV 149 (150)
T ss_pred ------------cHHHHHHHHHHh
Confidence 678898888876
No 27
>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=97.34 E-value=0.00093 Score=50.99 Aligned_cols=81 Identities=23% Similarity=0.360 Sum_probs=55.7
Q ss_pred HHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCC
Q 048832 100 SLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAW 179 (211)
Q Consensus 100 ~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W 179 (211)
.|..++ ++..+.|||++..|++.|. .-.+-..++|+..+. ..|..+..+|+.|++++||..+..+ ..+
T Consensus 94 ~l~~li-~~~tILVGHsL~nDL~aL~--l~hp~~~viDTa~l~----~~~~~r~~sLk~La~~~L~~~IQ~~----~Hd- 161 (174)
T cd06143 94 KLRLLV-DLGCIFVGHGLAKDFRVIN--IQVPKEQVIDTVELF----HLPGQRKLSLRFLAWYLLGEKIQSE----THD- 161 (174)
T ss_pred HHHHHc-CCCCEEEeccchhHHHHhc--CcCCCcceEEcHHhc----cCCCCCChhHHHHHHHHcCCcccCC----CcC-
Confidence 344444 4556789999999999883 211223578996432 2344458999999999999887532 222
Q ss_pred CCCCCCHHHHHHHHHhHHHHHHHHH
Q 048832 180 DTRVLTPAQVLYACLDAFIAFEIGR 204 (211)
Q Consensus 180 ~~~~L~~~q~~yAa~da~~~~~L~~ 204 (211)
+.+||.++++||+
T Consensus 162 ------------SvEDArAam~Ly~ 174 (174)
T cd06143 162 ------------SIEDARTALKLYR 174 (174)
T ss_pred ------------cHHHHHHHHHHhC
Confidence 4689999998873
No 28
>PRK07740 hypothetical protein; Provisional
Probab=97.27 E-value=0.033 Score=45.09 Aligned_cols=147 Identities=16% Similarity=0.119 Sum_probs=85.1
Q ss_pred HHHHHHHHHHHHHhhcc-------CCCcEEEEeeeeecCCCCCCCCeeEEEeeeC---Ce-e----E--EEeccc-c---
Q 048832 36 SVVDDWISEIERIHRRR-------LHCLIVGLDVEWRPSFSRQQNPVATLQLCVG---RR-C----L--IFQIIH-A--- 94 (211)
Q Consensus 36 ~~l~~~i~~l~~~~~~~-------~~~~~v~~d~e~~~~~~~~~~~~~llql~~~---~~-~----~--i~~~~~-~--- 94 (211)
..-..|++.+.+..+.. .....+.+|+|+++...... -.+|+++.- ++ . + ++.... .
T Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vv~D~ETTGl~p~~~--deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~ 110 (244)
T PRK07740 33 LQQEAWIRSIQKEAKRDDVLDIPLTDLPFVVFDLETTGFSPQQG--DEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEH 110 (244)
T ss_pred HHHHHHHHHHHHHhccCCccCCCccCCCEEEEEEeCCCCCCCCC--CeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChh
Confidence 45677888876543321 33478999999987542111 234666541 11 1 1 122211 0
Q ss_pred ---------------Ccc---hHHHHHhhcCCCceEEEeeeHHHHHHHHH----hcCCCCCc-EeecHHHHHhhcccccc
Q 048832 95 ---------------RRI---PQSLANFLSDEDYTFVGVGIDGDVKKLEN----NYGLQVFR-TVDLRPLAAEDLEIEGL 151 (211)
Q Consensus 95 ---------------~~~---~~~L~~~L~~~~i~kvg~~~k~d~~~L~~----~~gi~~~~-~~D~~~la~~~l~~~~~ 151 (211)
..+ ...|.+++.+ -+.|||++..|...|.+ .++..... .+|+..++. .+ .|..
T Consensus 111 ~~~ltGIt~e~l~~ap~~~evl~~f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r-~l-~~~~ 186 (244)
T PRK07740 111 ILELTGITAEDVAFAPPLAEVLHRFYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTK-LL-AHER 186 (244)
T ss_pred heeccCCCHHHHhCCCCHHHHHHHHHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHH-HH-cCCC
Confidence 012 2334445553 46889999999988753 23444443 689977664 33 3444
Q ss_pred ccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 152 RFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 152 ~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
..++|+++++. +|.+.... ++ |..||.++.+|+..+.
T Consensus 187 ~~~sL~~l~~~-~gi~~~~~-----H~-------------Al~Da~ata~l~~~ll 223 (244)
T PRK07740 187 DFPTLDDALAY-YGIPIPRR-----HH-------------ALGDALMTAKLWAILL 223 (244)
T ss_pred CCCCHHHHHHH-CCcCCCCC-----CC-------------cHHHHHHHHHHHHHHH
Confidence 58899999965 56654321 11 6678888888877663
No 29
>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=97.26 E-value=0.008 Score=45.40 Aligned_cols=82 Identities=23% Similarity=0.288 Sum_probs=55.0
Q ss_pred HHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhcccccc---ccccHHHHHHHHcCccCCCCCCccc
Q 048832 100 SLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGL---RFAGLKALSWEVLEKEVNKPRNITL 176 (211)
Q Consensus 100 ~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~---~~~~L~~l~~~~L~~~l~k~~~~~~ 176 (211)
.|.+++.+. -+.|||++..|+..|. .. -...+|+..++. .+ .|.. .+++|+.|+++++|.++..... .
T Consensus 76 ~~~~~i~~~-~vlVgHn~~fD~~fL~-~~---~~~~iDT~~l~~-~~-~~~~~~~~~~~L~~L~~~~~~~~~~~~~~--~ 146 (161)
T cd06137 76 ALWKFIDPD-TILVGHSLQNDLDALR-MI---HTRVVDTAILTR-EA-VKGPLAKRQWSLRTLCRDFLGLKIQGGGE--G 146 (161)
T ss_pred HHHHhcCCC-cEEEeccHHHHHHHHh-Cc---CCCeeEehhhhh-hc-cCCCcCCCCccHHHHHHHHCCchhcCCCC--C
Confidence 455566542 4679999999999994 22 123689987775 33 2332 4799999999999876643111 1
Q ss_pred cCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 048832 177 SAWDTRVLTPAQVLYACLDAFIAFEIG 203 (211)
Q Consensus 177 s~W~~~~L~~~q~~yAa~da~~~~~L~ 203 (211)
.+ |..||.++.+|+
T Consensus 147 H~-------------A~~DA~at~~l~ 160 (161)
T cd06137 147 HD-------------SLEDALAAREVV 160 (161)
T ss_pred CC-------------cHHHHHHHHHHh
Confidence 22 678888887775
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=97.24 E-value=0.0025 Score=43.91 Aligned_cols=73 Identities=21% Similarity=0.196 Sum_probs=51.4
Q ss_pred EEEeeeeecCCCCCCCCeeEEEeeeC--CeeEEEeccccCcchHHHHHhhcCCC-ceEEEeeeHHHHHHHHHh---cCCC
Q 048832 58 VGLDVEWRPSFSRQQNPVATLQLCVG--RRCLIFQIIHARRIPQSLANFLSDED-YTFVGVGIDGDVKKLENN---YGLQ 131 (211)
Q Consensus 58 v~~d~e~~~~~~~~~~~~~llql~~~--~~~~i~~~~~~~~~~~~L~~~L~~~~-i~kvg~~~k~d~~~L~~~---~gi~ 131 (211)
+++|+|..+.. +...++.++|++.. ++.++++ +.+++++.. ..+||||...|...|.+. +|..
T Consensus 1 ~~~DiEt~~~~-~~~~~i~~i~~~~~~~~~~~~~~----------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~ 69 (96)
T cd06125 1 IAIDTEATGLD-GAVHEIIEIALADVNPEDTAVID----------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLK 69 (96)
T ss_pred CEEEEECCCCC-CCCCcEEEEEEEEccCCCEEEeh----------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCC
Confidence 47899987754 56788899999887 3555544 667887766 788999999998777643 3433
Q ss_pred C----CcEeecHHH
Q 048832 132 V----FRTVDLRPL 141 (211)
Q Consensus 132 ~----~~~~D~~~l 141 (211)
. ...+|+..+
T Consensus 70 ~p~~~~~~lDT~~l 83 (96)
T cd06125 70 YPLLAGSWIDTIKL 83 (96)
T ss_pred CCCcCCcEEEehHH
Confidence 2 235788544
No 31
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.22 E-value=0.018 Score=46.70 Aligned_cols=86 Identities=19% Similarity=0.191 Sum_probs=57.4
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCC----CcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQV----FRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKP 171 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~----~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~ 171 (211)
+.+.+++.+. -..||||+..|...|.+ +.|+.. ...+|+..++. .++ ...+++|+.+++.+ |.+...
T Consensus 79 ~~~~~fl~~~-~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar-~~~--~~~~~~L~~l~~~~-g~~~~~- 152 (250)
T PRK06310 79 PQIKGFFKEG-DYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAK-EYG--DSPNNSLEALAVHF-NVPYDG- 152 (250)
T ss_pred HHHHHHhCCC-CEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHH-hcc--cCCCCCHHHHHHHC-CCCCCC-
Confidence 3566666553 46899999999988864 345543 23689987775 332 22368999999776 544321
Q ss_pred CCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 172 RNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 172 ~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
. .-|..||.++..|+..+.
T Consensus 153 ----a-------------H~Al~Da~at~~vl~~l~ 171 (250)
T PRK06310 153 ----N-------------HRAMKDVEINIKVFKHLC 171 (250)
T ss_pred ----C-------------cChHHHHHHHHHHHHHHH
Confidence 1 227788988888887765
No 32
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=97.04 E-value=0.0061 Score=49.12 Aligned_cols=86 Identities=16% Similarity=0.181 Sum_probs=56.2
Q ss_pred HHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhcc-ccccccccHHHHHHHHcCccCCCCCCccccC
Q 048832 100 SLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLE-IEGLRFAGLKALSWEVLEKEVNKPRNITLSA 178 (211)
Q Consensus 100 ~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~-~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~ 178 (211)
.+.++|.. -+.|||+++.|+..|.-.+.- .-+-||+..-. +.. .+.....||..|++.+||.++.-++. .
T Consensus 177 ev~klL~g--RIlVGHaLhnDl~~L~l~hp~--s~iRDTs~~~p-l~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeH--s-- 247 (280)
T KOG2249|consen 177 EVLKLLKG--RILVGHALHNDLQALKLEHPR--SMIRDTSKYPP-LMKLLSKKATPSLKKLTEALLGKDIQVGEH--S-- 247 (280)
T ss_pred HHHHHHhC--CEEeccccccHHHHHhhhCch--hhhcccccCch-HHHHhhccCCccHHHHHHHHhchhhhcccc--C--
Confidence 45567764 467999999999999533321 12347753211 111 12335889999999999988854441 1
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 179 WDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 179 W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
..+||-++.+||....
T Consensus 248 -------------SvEDA~AtM~LY~~vk 263 (280)
T KOG2249|consen 248 -------------SVEDARATMELYKRVK 263 (280)
T ss_pred -------------cHHHHHHHHHHHHHHH
Confidence 3578889999988764
No 33
>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=97.03 E-value=0.018 Score=44.76 Aligned_cols=102 Identities=20% Similarity=0.216 Sum_probs=61.3
Q ss_pred hHHHHHhhcC--CCceEEEeee-HHHHHHHHH---hcCCCCC----------------------c--EeecHHHHHhhcc
Q 048832 98 PQSLANFLSD--EDYTFVGVGI-DGDVKKLEN---NYGLQVF----------------------R--TVDLRPLAAEDLE 147 (211)
Q Consensus 98 ~~~L~~~L~~--~~i~kvg~~~-k~d~~~L~~---~~gi~~~----------------------~--~~D~~~la~~~l~ 147 (211)
...+..++.+ |. +.+|||. ..|+..|.+ .+|+... | .+|+-.++....
T Consensus 67 L~~f~~~i~~~dpd-iivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~- 144 (199)
T cd05160 67 LKRFFDIIREYDPD-ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDF- 144 (199)
T ss_pred HHHHHHHHHhcCCC-EEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhc-
Confidence 4444555554 33 4789999 678877763 4566551 2 368855554322
Q ss_pred ccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 048832 148 IEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIG 203 (211)
Q Consensus 148 ~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~ 203 (211)
+ ..+++|+.+++.+|+..-..-..-....|....-...-++|+-.||..+++|+
T Consensus 145 -~-l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 145 -K-LKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred -C-cccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 2 45899999999999853211111011222111122346999999999999886
No 34
>PRK07883 hypothetical protein; Validated
Probab=97.01 E-value=0.028 Score=50.88 Aligned_cols=88 Identities=16% Similarity=0.037 Sum_probs=58.2
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCCC--cEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQVF--RTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRN 173 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~~--~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~ 173 (211)
..+..|+.+ .+.|+||+..|...|.+ .+|+... ..+|+..++...+...+..+++|+++++. +|.+...
T Consensus 87 ~~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~-~gi~~~~--- 160 (557)
T PRK07883 87 PAFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLARL-FGATTTP--- 160 (557)
T ss_pred HHHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHHH-CCcccCC---
Confidence 355667764 56789999999988863 4576654 25899777753332124458999999974 5665421
Q ss_pred ccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 174 ITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 174 ~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
.++ |..||.++..|+..+.
T Consensus 161 --~H~-------------Al~DA~ata~l~~~l~ 179 (557)
T PRK07883 161 --THR-------------ALDDARATVDVLHGLI 179 (557)
T ss_pred --CCC-------------HHHHHHHHHHHHHHHH
Confidence 122 7788888877776654
No 35
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=96.97 E-value=0.019 Score=44.73 Aligned_cols=147 Identities=20% Similarity=0.306 Sum_probs=82.4
Q ss_pred CcEEEEeeeeecCC---CCCCCCeeEEEeeeCC-e-eEEEe--------c-cccCcchHHHHHhhcC--CCceEEEeeeH
Q 048832 55 CLIVGLDVEWRPSF---SRQQNPVATLQLCVGR-R-CLIFQ--------I-IHARRIPQSLANFLSD--EDYTFVGVGID 118 (211)
Q Consensus 55 ~~~v~~d~e~~~~~---~~~~~~~~llql~~~~-~-~~i~~--------~-~~~~~~~~~L~~~L~~--~~i~kvg~~~k 118 (211)
-.+++||+|..... .+...++-.|+++..+ + ++.+. . ....++...+..++.. |. ..+|||..
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dpd-iivgyN~~ 81 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPD-VIYTYNGD 81 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCCC-EEEecCCC
Confidence 46899999986322 1223444334433322 2 22111 0 0001234445555554 65 46899985
Q ss_pred -HHHHHHHH---hcCCCC----------------------Cc--EeecHHHHHhhccccccccccHHHHHHHHcCccCCC
Q 048832 119 -GDVKKLEN---NYGLQV----------------------FR--TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNK 170 (211)
Q Consensus 119 -~d~~~L~~---~~gi~~----------------------~~--~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k 170 (211)
.|+..|.+ .+|+.. .| .+|+-.++...+ ...+++|+.+++++||.+-..
T Consensus 82 ~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~---~l~sy~L~~v~~~~Lg~~k~d 158 (195)
T cd05780 82 NFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTL---NLTRYTLERVYEELFGIEKED 158 (195)
T ss_pred CCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhC---CCCcCcHHHHHHHHhCCCCCc
Confidence 58877753 345542 12 367755554322 235899999999999964221
Q ss_pred C--CCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 048832 171 P--RNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVL 206 (211)
Q Consensus 171 ~--~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L 206 (211)
- +++. .-|....--.+-++|+..||..+++|.+.|
T Consensus 159 ~~~~~i~-~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 159 VPGEEIA-EAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred CCHHHHH-HHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 1 1111 124433333457999999999999998764
No 36
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.96 E-value=0.029 Score=47.13 Aligned_cols=87 Identities=22% Similarity=0.084 Sum_probs=57.1
Q ss_pred hHHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCCC--cEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCC
Q 048832 98 PQSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQVF--RTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPR 172 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~~--~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~ 172 (211)
.+.|.+++.+ -+.|+||+..|+..|.+ ++|.... ..+|+..++. .+ .+...+++|+++++++ |.+...
T Consensus 85 ~~~l~~~l~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar-~~-~~~~~~~kL~~l~~~~-gi~~~~-- 157 (313)
T PRK06063 85 AGEVAELLRG--RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELAR-RL-GLGLPNLRLETLAAHW-GVPQQR-- 157 (313)
T ss_pred HHHHHHHcCC--CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHH-Hh-ccCCCCCCHHHHHHHc-CCCCCC--
Confidence 3456677764 46899999999998864 3455433 4689976764 33 2334588999999864 654321
Q ss_pred CccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 173 NITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 173 ~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
.++ |..||.++.+|+..+.
T Consensus 158 ---~H~-------------Al~DA~ata~l~~~ll 176 (313)
T PRK06063 158 ---PHD-------------ALDDARVLAGILRPSL 176 (313)
T ss_pred ---CCC-------------cHHHHHHHHHHHHHHH
Confidence 122 6678888777766553
No 37
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.89 E-value=0.022 Score=53.94 Aligned_cols=86 Identities=24% Similarity=0.213 Sum_probs=58.3
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHHh---cCCCCCc-EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCc
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLENN---YGLQVFR-TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNI 174 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~~---~gi~~~~-~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~ 174 (211)
+.+.+++.+ -+.||||+..|+..|.+. .|..+.+ .+|+..++... .|...+++|.++++. +|.+....
T Consensus 78 ~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~--~p~~~~~~L~~L~~~-lgl~~~~~--- 149 (820)
T PRK07246 78 RHIYDLIED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVF--FPTLEKYSLSHLSRE-LNIDLADA--- 149 (820)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHH--hCCCCCCCHHHHHHH-cCCCCCCC---
Confidence 456667764 568999999999988643 3666555 48997777533 355558999999986 56554321
Q ss_pred cccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 175 TLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 175 ~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
++ |..||.++..|+..|.
T Consensus 150 --H~-------------Al~DA~ata~L~~~l~ 167 (820)
T PRK07246 150 --HT-------------AIADARATAELFLKLL 167 (820)
T ss_pred --CC-------------HHHHHHHHHHHHHHHH
Confidence 11 6677777777776654
No 38
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.89 E-value=0.05 Score=43.66 Aligned_cols=78 Identities=18% Similarity=0.099 Sum_probs=49.2
Q ss_pred CceEEEeeeHHHHHHHHH---hcCCCC--C-cEeecHHHHHhhccccc-cccccHHHHHHHHcCccCCCCCCccccCCCC
Q 048832 109 DYTFVGVGIDGDVKKLEN---NYGLQV--F-RTVDLRPLAAEDLEIEG-LRFAGLKALSWEVLEKEVNKPRNITLSAWDT 181 (211)
Q Consensus 109 ~i~kvg~~~k~d~~~L~~---~~gi~~--~-~~~D~~~la~~~l~~~~-~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~ 181 (211)
..+.|+||...|...|.+ ++|... . .++|+..++. .+ .+. ..+++|+++++.+ |.+.... ++
T Consensus 93 ~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~-~~-~~~~~~~~~L~~l~~~~-gi~~~~a-----H~--- 161 (232)
T PRK07942 93 GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDK-AV-DRYRKGKRTLTALCEHY-GVRLDNA-----HE--- 161 (232)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHh-hh-hcccCCCCCHHHHHHHc-CCCCCCC-----CC---
Confidence 456799999999988853 345431 2 3579865553 22 121 1368999999874 6554321 12
Q ss_pred CCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 182 RVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 182 ~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
|..||.++.+|+..|.
T Consensus 162 ----------Al~Da~ata~l~~~l~ 177 (232)
T PRK07942 162 ----------ATADALAAARVAWALA 177 (232)
T ss_pred ----------hHHHHHHHHHHHHHHH
Confidence 6778888777776664
No 39
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=96.87 E-value=0.06 Score=43.93 Aligned_cols=86 Identities=26% Similarity=0.254 Sum_probs=56.3
Q ss_pred hHHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCC-Cc-EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCC
Q 048832 98 PQSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQV-FR-TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPR 172 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~-~~-~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~ 172 (211)
...+..++.+ -+.||||+..|...|.+ ++|... .+ .+|+..++..++.. .+++|+.+++. +|.+..+
T Consensus 138 l~~f~~fl~~--~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~---~~~~L~~L~~~-lgi~~~~-- 209 (257)
T PRK08517 138 LEEFRLFLGD--SVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES---PRYGLSFLKEL-LGIEIEV-- 209 (257)
T ss_pred HHHHHHHHCC--CeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccC---CCCCHHHHHHH-cCcCCCC--
Confidence 3456677765 36899999999988853 445432 23 47887777544422 37899999875 5654321
Q ss_pred CccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 173 NITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 173 ~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
.++ |..||.++.+|+..+.
T Consensus 210 ---~Hr-------------Al~DA~ata~ll~~ll 228 (257)
T PRK08517 210 ---HHR-------------AYADALAAYEIFKICL 228 (257)
T ss_pred ---CCC-------------hHHHHHHHHHHHHHHH
Confidence 112 6778888888877664
No 40
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.87 E-value=0.062 Score=43.09 Aligned_cols=128 Identities=17% Similarity=0.063 Sum_probs=76.6
Q ss_pred CcEEEEeeeeecCCCCCCCCeeEEEeeeCC----e--eEEEecccc-------------------C---cchHHHHHhhc
Q 048832 55 CLIVGLDVEWRPSFSRQQNPVATLQLCVGR----R--CLIFQIIHA-------------------R---RIPQSLANFLS 106 (211)
Q Consensus 55 ~~~v~~d~e~~~~~~~~~~~~~llql~~~~----~--~~i~~~~~~-------------------~---~~~~~L~~~L~ 106 (211)
...+.||+|.++.. .... .+++++.-+ . ..++..... + ++.+.+.+++.
T Consensus 2 ~~~vv~D~ETTGl~-~~~d--~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~ 78 (232)
T PRK06309 2 PALIFYDTETTGTQ-IDKD--RIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCG 78 (232)
T ss_pred CcEEEEEeeCCCCC-CCCC--EEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHc
Confidence 35789999998764 2222 456776421 1 223333220 0 12224555554
Q ss_pred CCCceEEEeee-HHHHHHHHH---hcCCCCC--cEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCC
Q 048832 107 DEDYTFVGVGI-DGDVKKLEN---NYGLQVF--RTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWD 180 (211)
Q Consensus 107 ~~~i~kvg~~~-k~d~~~L~~---~~gi~~~--~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~ 180 (211)
+ .-..||||. ..|...|.+ ++|+... ..+|+..++..+ .|+..+++|..+++.+ |.+... .++
T Consensus 79 ~-~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~--~~~~~~~~L~~l~~~~-~~~~~~-----aH~-- 147 (232)
T PRK06309 79 T-DNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKY--RPDLPKHNLQYLRQVY-GFEENQ-----AHR-- 147 (232)
T ss_pred C-CCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHH--cCCCCCCCHHHHHHHc-CCCCCC-----CCC--
Confidence 3 356799995 899988864 3455432 368998777533 3444478999999776 543321 122
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 181 TRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 181 ~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
|..||+++.+|+..+.
T Consensus 148 -----------Al~Da~~t~~vl~~l~ 163 (232)
T PRK06309 148 -----------ALDDVITLHRVFSALV 163 (232)
T ss_pred -----------cHHHHHHHHHHHHHHH
Confidence 7788999998887765
No 41
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.83 E-value=0.035 Score=46.63 Aligned_cols=86 Identities=17% Similarity=0.119 Sum_probs=55.5
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCC-Cc-EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQV-FR-TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRN 173 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~-~~-~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~ 173 (211)
+.+.+|+.+. ..|||++..|...|.+ .+|+.. .+ .+|+..++..+. |...+++|+++++. +|.+. +
T Consensus 80 ~~f~~fl~~~--~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~--~~~~~~kL~~L~~~-lgi~~-~--- 150 (313)
T PRK06807 80 PLFLAFLHTN--VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYM--KHAPNHKLETLKRM-LGIRL-S--- 150 (313)
T ss_pred HHHHHHHcCC--eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHh--CCCCCCCHHHHHHH-cCCCC-C---
Confidence 4555666543 4589999999998864 346532 33 589977775433 33357899999865 46544 1
Q ss_pred ccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 174 ITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 174 ~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
.++ |..||.++..|+..+.+
T Consensus 151 --~H~-------------Al~DA~~ta~l~~~l~~ 170 (313)
T PRK06807 151 --SHN-------------AFDDCITCAAVYQKCAS 170 (313)
T ss_pred --CcC-------------hHHHHHHHHHHHHHHHH
Confidence 112 66788888777766543
No 42
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.80 E-value=0.07 Score=41.75 Aligned_cols=91 Identities=21% Similarity=0.201 Sum_probs=59.1
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHHh----cCCCCCc-EeecHHHHHhhcc--cc-ccccccHHHHHHHHcCccCCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLENN----YGLQVFR-TVDLRPLAAEDLE--IE-GLRFAGLKALSWEVLEKEVNK 170 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~~----~gi~~~~-~~D~~~la~~~l~--~~-~~~~~~L~~l~~~~L~~~l~k 170 (211)
+.+.+++.+ ...|||+...|...|.+. +|..+.. .+|+..++..+.. .| +..+++|+++++++ |.+..+
T Consensus 103 ~~~~~~i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~-gi~~~~ 179 (202)
T PRK09145 103 RQLLAFIGN--RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHL-DLPVLG 179 (202)
T ss_pred HHHHHHHcC--CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHc-CCCCCC
Confidence 455666664 457999999999888632 3555554 5788655422211 12 22368999999775 654421
Q ss_pred CCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcCC
Q 048832 171 PRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNAND 210 (211)
Q Consensus 171 ~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~~~ 210 (211)
.++ |..||.++..|+..|.+-+
T Consensus 180 -----~H~-------------Al~DA~ata~l~~~l~~~~ 201 (202)
T PRK09145 180 -----RHD-------------ALNDAIMAALIFLRLRKGD 201 (202)
T ss_pred -----CCC-------------cHHHHHHHHHHHHHHHhcC
Confidence 122 7789999999999987654
No 43
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=96.57 E-value=0.086 Score=39.03 Aligned_cols=81 Identities=25% Similarity=0.139 Sum_probs=54.4
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCCC--cEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQVF--RTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRN 173 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~~--~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~ 173 (211)
+.|.+++.+ ...||||+..|...|.+ .+|+... ..+|+..++.. + .+...+++|+.+++. +|.+.. .
T Consensus 69 ~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~-~-~~~~~~~~L~~l~~~-~g~~~~-~-- 140 (156)
T cd06130 69 PEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARR-V-WPLLPNHKLNTVAEH-LGIELN-H-- 140 (156)
T ss_pred HHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHH-H-hccCCCCCHHHHHHH-cCCCcc-C--
Confidence 456777775 46899999999998863 3465533 35899666643 2 233457999999987 465443 1
Q ss_pred ccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 048832 174 ITLSAWDTRVLTPAQVLYACLDAFIAFEIG 203 (211)
Q Consensus 174 ~~~s~W~~~~L~~~q~~yAa~da~~~~~L~ 203 (211)
++ |..||.++.+|+
T Consensus 141 ---H~-------------Al~Da~~ta~l~ 154 (156)
T cd06130 141 ---HD-------------ALEDARACAEIL 154 (156)
T ss_pred ---cC-------------chHHHHHHHHHH
Confidence 12 667888887775
No 44
>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=96.56 E-value=0.2 Score=39.96 Aligned_cols=88 Identities=24% Similarity=0.281 Sum_probs=57.4
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCC--C-C---CcEeecHHHHHhhccccccccccHHHHHHHHcCccCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGL--Q-V---FRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVN 169 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi--~-~---~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~ 169 (211)
..|..|+.+ ...|+||+..|...|.+ ++|. . + ..++|+..++... .|+ .+++|+.+++++ |.+..
T Consensus 74 ~~f~~fi~~--~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~--~p~-~~~~L~~L~~~~-gi~~~ 147 (225)
T TIGR01406 74 DEFLDFIGG--SELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARER--FPG-QRNSLDALCKRF-KVDNS 147 (225)
T ss_pred HHHHHHhCC--CEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHH--cCC-CCCCHHHHHHhc-CCCCC
Confidence 455666764 35689999999988863 3452 2 1 3468986666432 354 368999999986 54321
Q ss_pred CCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 170 KPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 170 k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
.. . .++ |..||.++.+|+..|..
T Consensus 148 ~r-~--~H~-------------Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 148 HR-T--LHG-------------ALLDAHLLAEVYLALTG 170 (225)
T ss_pred CC-C--CcC-------------HHHHHHHHHHHHHHHHc
Confidence 11 0 122 78899999998888754
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=96.54 E-value=0.084 Score=41.85 Aligned_cols=90 Identities=20% Similarity=0.147 Sum_probs=55.3
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHHhc---CC--CCC-cEeecHHHHHhhccc-cccccccHHHHHHHHcCccCCCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLENNY---GL--QVF-RTVDLRPLAAEDLEI-EGLRFAGLKALSWEVLEKEVNKP 171 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~---gi--~~~-~~~D~~~la~~~l~~-~~~~~~~L~~l~~~~L~~~l~k~ 171 (211)
+.+..|+.+ -..||||+..|...|.+.+ +. ... ..+|+..++...... ++ .+++|..+++++ |.+....
T Consensus 79 ~~~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~-~~~~L~~l~~~~-gl~~~~~ 154 (217)
T TIGR00573 79 EDFADYIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPG-KRNTLDALCKRY-EITNSHR 154 (217)
T ss_pred HHHHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCC-CCCCHHHHHHHc-CCCCCCc
Confidence 455666654 4678999999999997543 22 122 357876555322211 22 367899999876 5432100
Q ss_pred CCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 172 RNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 172 ~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
. ..+ |..||.++.+|+..+.+
T Consensus 155 ~---~H~-------------Al~DA~~ta~l~~~l~~ 175 (217)
T TIGR00573 155 A---LHG-------------ALADAFILAKLYLVMTG 175 (217)
T ss_pred c---cCC-------------HHHHHHHHHHHHHHHHh
Confidence 0 122 77899999998887754
No 46
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=96.50 E-value=0.016 Score=53.59 Aligned_cols=99 Identities=11% Similarity=0.092 Sum_probs=61.6
Q ss_pred CCceEEEeeeHHHHHHHHHhcCCCCCc--EeecHHHHHhh--------------------------------ccccc---
Q 048832 108 EDYTFVGVGIDGDVKKLENNYGLQVFR--TVDLRPLAAED--------------------------------LEIEG--- 150 (211)
Q Consensus 108 ~~i~kvg~~~k~d~~~L~~~~gi~~~~--~~D~~~la~~~--------------------------------l~~~~--- 150 (211)
..-.+||||..+|...+++.|+++-.+ ++|++-|--.. +.+|.
T Consensus 240 ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~~pWL~~ 319 (1075)
T KOG3657|consen 240 KEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDYDNPWLGR 319 (1075)
T ss_pred CCceEEeccccchHHHHHHHHhccccceeeeechhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhhhhhhhhh
Confidence 346789999999999998899987654 35885331000 11121
Q ss_pred cccccHHHHHHHHcCcc-CCCCCCccccCCCCCCCCHH---HHHHHHHhHHHHHHHHHHH
Q 048832 151 LRFAGLKALSWEVLEKE-VNKPRNITLSAWDTRVLTPA---QVLYACLDAFIAFEIGRVL 206 (211)
Q Consensus 151 ~~~~~L~~l~~~~L~~~-l~k~~~~~~s~W~~~~L~~~---q~~yAa~da~~~~~L~~~L 206 (211)
.+..||.++++.+.+.. ++|.....+..-...++.++ -+.|+|.|++++.+++.++
T Consensus 320 SS~NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~l 379 (1075)
T KOG3657|consen 320 SSLNSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRL 379 (1075)
T ss_pred hhhHHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 12456888888888876 66654211111011111121 2889999999999998775
No 47
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.47 E-value=0.22 Score=40.22 Aligned_cols=87 Identities=15% Similarity=-0.030 Sum_probs=54.2
Q ss_pred HHHHhhcCCCceEEEeeeHHHHHHHHHh----cCCCCCc-EeecHHHHHhhccc------c---c--cccccHHHHHHHH
Q 048832 100 SLANFLSDEDYTFVGVGIDGDVKKLENN----YGLQVFR-TVDLRPLAAEDLEI------E---G--LRFAGLKALSWEV 163 (211)
Q Consensus 100 ~L~~~L~~~~i~kvg~~~k~d~~~L~~~----~gi~~~~-~~D~~~la~~~l~~------~---~--~~~~~L~~l~~~~ 163 (211)
.|..++.+ -+.|||++..|...|.+. .|..+.. .+|+..++..++.. + + ..+++|.++++++
T Consensus 122 ~l~~~~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~ 199 (239)
T PRK09146 122 ELLEALAG--KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRY 199 (239)
T ss_pred HHHHHhCC--CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHc
Confidence 44444443 468999999999888643 3444444 58998777533211 0 0 1367899999874
Q ss_pred cCccCCCCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 164 LEKEVNKPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 164 L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
|.+... . .-|..||.++..|+..+.
T Consensus 200 -gl~~~~-----~-------------H~Al~DA~ata~l~~~~~ 224 (239)
T PRK09146 200 -GLPAYS-----P-------------HHALTDAIATAELLQAQI 224 (239)
T ss_pred -CCCCCC-----C-------------CCcHHHHHHHHHHHHHHH
Confidence 543321 1 227788998888877654
No 48
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.34 E-value=0.12 Score=49.79 Aligned_cols=87 Identities=23% Similarity=0.181 Sum_probs=57.1
Q ss_pred hHHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCCC--cEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCC
Q 048832 98 PQSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQVF--RTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPR 172 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~~--~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~ 172 (211)
.+.|..++.+ .+.||||+..|...|.+ ..|+... ..+|+..++..+ .|...+++|++|++.+ |.+.....
T Consensus 75 ~~~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~--~p~~~~~~L~~l~~~l-~i~~~~~H 149 (928)
T PRK08074 75 APEIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARIL--LPTAESYKLRDLSEEL-GLEHDQPH 149 (928)
T ss_pred HHHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHh--cCCCCCCCHHHHHHhC-CCCCCCCC
Confidence 3456677764 56899999999998864 3455432 358998777533 3555689999999874 55432221
Q ss_pred CccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 173 NITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 173 ~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
+ |-.||.++.+|+..|.
T Consensus 150 -----~-------------Al~DA~ata~l~~~l~ 166 (928)
T PRK08074 150 -----R-------------ADSDAEVTAELFLQLL 166 (928)
T ss_pred -----C-------------hHHHHHHHHHHHHHHH
Confidence 1 5567777776666553
No 49
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.31 E-value=0.13 Score=43.01 Aligned_cols=86 Identities=14% Similarity=0.108 Sum_probs=57.0
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCCC--cEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQVF--RTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRN 173 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~~--~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~ 173 (211)
+.|.+++.+ -+.|+||+..|+..|.+ .+|.... ..+|+..++..++ |+..+++|..|++.+ |.+..
T Consensus 72 ~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~--~~~~~~~L~~L~~~~-gi~~~---- 142 (309)
T PRK06195 72 EKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFY--SNIDNARLNTVNNFL-GYEFK---- 142 (309)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHc--CCCCcCCHHHHHHHc-CCCCc----
Confidence 456666653 57899999999988853 3565543 3579976775333 444578999999885 54321
Q ss_pred ccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 174 ITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 174 ~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
. .-|..||.++.+|+..|.+
T Consensus 143 --~-------------H~Al~DA~ata~l~~~l~~ 162 (309)
T PRK06195 143 --H-------------HDALADAMACSNILLNISK 162 (309)
T ss_pred --c-------------cCCHHHHHHHHHHHHHHHH
Confidence 1 2267788888877766643
No 50
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.25 E-value=0.22 Score=40.25 Aligned_cols=88 Identities=18% Similarity=0.217 Sum_probs=56.0
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCC------CcEeecHHHHHhhccccccccccHHHHHHHHcCccCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQV------FRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVN 169 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~------~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~ 169 (211)
..+.+|+.+ ...|+||+..|+..|.+ ++|..+ ..++|+-.++. .+ .|+ .+++|+.|++++ |.+..
T Consensus 78 ~~f~~fi~~--~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar-~~-~p~-~~~~L~aL~~~~-gi~~~ 151 (240)
T PRK05711 78 DEFLDFIRG--AELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMAR-RM-FPG-KRNSLDALCKRY-GIDNS 151 (240)
T ss_pred HHHHHHhCC--CEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHH-HH-cCC-CCCCHHHHHHHC-CCCCC
Confidence 345566654 34689999999988863 344322 24689866664 33 354 367999999876 54321
Q ss_pred CCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 170 KPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 170 k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
.. . .++ |..||.++.+++..|..
T Consensus 152 ~r-~--~H~-------------AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 152 HR-T--LHG-------------ALLDAEILAEVYLAMTG 174 (240)
T ss_pred CC-C--CCC-------------HHHHHHHHHHHHHHHHC
Confidence 11 0 122 77899999998887753
No 51
>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=96.21 E-value=0.25 Score=37.10 Aligned_cols=86 Identities=24% Similarity=0.220 Sum_probs=55.4
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHHh---cCCC----C-CcEeecHHHHHhhccccccccccHHHHHHHHcCccCCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLENN---YGLQ----V-FRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNK 170 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~~---~gi~----~-~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k 170 (211)
+.|..++.+ -..||||+..|...|.+. +|.. . ...+|+..++.... |. ..++|+++++++ |.+...
T Consensus 73 ~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~--~~-~~~~L~~l~~~~-~i~~~~ 146 (167)
T cd06131 73 DEFLDFIRG--AELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKF--PG-KPNSLDALCKRF-GIDNSH 146 (167)
T ss_pred HHHHHHHCC--CeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHc--CC-CCCCHHHHHHHC-CCCCCC
Confidence 456667765 346899999999888632 3332 1 23589966664322 33 367999999886 543321
Q ss_pred CCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 048832 171 PRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVL 206 (211)
Q Consensus 171 ~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L 206 (211)
. +...|..||.++.+|+..|
T Consensus 147 ~----------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 147 R----------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred C----------------CCCChHHHHHHHHHHHHHh
Confidence 1 1122788999999998776
No 52
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.20 E-value=0.31 Score=36.36 Aligned_cols=88 Identities=24% Similarity=0.148 Sum_probs=57.8
Q ss_pred HHHHHhhcCCCceEEEeee-HHHHHHHHH---hcCCCCC---cEeecHHHHHhhccccccccccHHHHHHHHcCccCCCC
Q 048832 99 QSLANFLSDEDYTFVGVGI-DGDVKKLEN---NYGLQVF---RTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKP 171 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~-k~d~~~L~~---~~gi~~~---~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~ 171 (211)
..+..++.+. ..++|+. +.|...|.+ .+|+... ..+|+..++.... ++ .+.+|+++++.+. .+....
T Consensus 72 ~~~~~~l~~~--~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~--~~-~~~~L~~l~~~~~-~~~~~~ 145 (169)
T smart00479 72 EELLEFLKGK--ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALN--PG-RKYSLKKLAERLG-LEVIGR 145 (169)
T ss_pred HHHHHHhcCC--EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHC--CC-CCCCHHHHHHHCC-CCCCCC
Confidence 4566777653 4567777 999998864 3454332 2589977764333 33 2899999998764 322110
Q ss_pred CCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcC
Q 048832 172 RNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNAN 209 (211)
Q Consensus 172 ~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~~ 209 (211)
...|..||.++.+|+..+.+.
T Consensus 146 -----------------~H~A~~Da~~t~~l~~~~~~~ 166 (169)
T smart00479 146 -----------------AHRALDDARATAKLFKKLVER 166 (169)
T ss_pred -----------------CcCcHHHHHHHHHHHHHHHHH
Confidence 133889999999999888653
No 53
>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=96.12 E-value=0.18 Score=38.58 Aligned_cols=81 Identities=19% Similarity=0.133 Sum_probs=52.8
Q ss_pred HHHHHhhcC--CCceEEEeee-HHHHHHHHH---hcCCCCC--c-EeecHHHHHhhccccccccccHHHHHHHHcCccCC
Q 048832 99 QSLANFLSD--EDYTFVGVGI-DGDVKKLEN---NYGLQVF--R-TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVN 169 (211)
Q Consensus 99 ~~L~~~L~~--~~i~kvg~~~-k~d~~~L~~---~~gi~~~--~-~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~ 169 (211)
+.|..|+.. ...+.||||+ ..|+..|.+ ++|+... . .+|+..++. .+ .+ +|++|+++++|.+..
T Consensus 86 ~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r-~~-~~-----~L~~l~~~~~~~~~~ 158 (177)
T cd06136 86 NLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFR-EL-DQ-----SLGSLYKRLFGQEPK 158 (177)
T ss_pred HHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHh-hh-Hh-----hHHHHHHHHhCCCcc
Confidence 456666653 3467899998 799988853 3565542 2 368865553 22 12 899999988776543
Q ss_pred CCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 048832 170 KPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGR 204 (211)
Q Consensus 170 k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~ 204 (211)
.. .-|..||.++.+++.
T Consensus 159 ~~------------------H~A~~Da~at~~v~~ 175 (177)
T cd06136 159 NS------------------HTAEGDVLALLKCAL 175 (177)
T ss_pred cc------------------cchHHHHHHHHHHHh
Confidence 21 227888988887753
No 54
>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=96.09 E-value=0.17 Score=48.20 Aligned_cols=65 Identities=23% Similarity=0.224 Sum_probs=45.0
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCC-CCc-EeecHHHHHhhccccccccccHHHHHHHHcCccC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQ-VFR-TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEV 168 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~-~~~-~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l 168 (211)
+.|.+++.+ -+.||||+..|...|.+ .+|+. ..+ .+|+..++. .+ .|...+++|.++++. +|.+.
T Consensus 72 ~~l~~~l~~--~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~-~~-~p~~~~~~L~~l~~~-~gi~~ 141 (850)
T TIGR01407 72 QEIYDLLED--GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQ-IF-FPTEESYQLSELSEA-LGLTH 141 (850)
T ss_pred HHHHHHhCC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHH-Hh-cCCCCCCCHHHHHHH-CCCCC
Confidence 456667764 45899999999988863 35655 233 589977764 33 354568999999988 46554
No 55
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=96.00 E-value=0.28 Score=41.93 Aligned_cols=99 Identities=9% Similarity=0.030 Sum_probs=58.5
Q ss_pred chHHHHHhhcCCCceEEEeeeHHHHHHHHHhc-------------------------------CCCCCc-EeecHHHHHh
Q 048832 97 IPQSLANFLSDEDYTFVGVGIDGDVKKLENNY-------------------------------GLQVFR-TVDLRPLAAE 144 (211)
Q Consensus 97 ~~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~-------------------------------gi~~~~-~~D~~~la~~ 144 (211)
+.+.|.+++.+ -+.|+||+..|+..|.+.+ ++...+ ++|+-.++.
T Consensus 115 Vl~el~~fL~g--~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LAR- 191 (377)
T PRK05601 115 ILKPLDRLIDG--RTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATAR- 191 (377)
T ss_pred HHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHH-
Confidence 34567777874 4689999999999876432 123333 589977774
Q ss_pred hccccccccccHHHHHHHHcCccCCCCC-CccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 145 DLEIEGLRFAGLKALSWEVLEKEVNKPR-NITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 145 ~l~~~~~~~~~L~~l~~~~L~~~l~k~~-~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
.+ .|...++.|..+++++ |++.+... ++.... -+..+ .+-.||-++..|+..++
T Consensus 192 rl-~p~l~~~rL~~La~~l-Gi~~p~~~A~~~Ra~-----~p~~~--l~~~Da~ll~~l~~~~~ 246 (377)
T PRK05601 192 RQ-GVALDDIRIRGVAHTL-GLDAPAAEASVERAQ-----VPHRQ--LCREETLLVARLYFALR 246 (377)
T ss_pred HH-cCCCCCCCHHHHHHHh-CCCCCchhhhhhhhc-----CChhh--hhhHHHHHHHHHHHHhh
Confidence 33 3555689999999985 65543211 000000 11111 12247888888887753
No 56
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=95.96 E-value=0.27 Score=38.40 Aligned_cols=89 Identities=16% Similarity=0.176 Sum_probs=56.9
Q ss_pred hHHHHHhhcCCCceEEEeeeH-HHHHHHHHhcCCCCCcE--eecHHHHH-hhc-cccccccccHHHHHHHHcCccCCCCC
Q 048832 98 PQSLANFLSDEDYTFVGVGID-GDVKKLENNYGLQVFRT--VDLRPLAA-EDL-EIEGLRFAGLKALSWEVLEKEVNKPR 172 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k-~d~~~L~~~~gi~~~~~--~D~~~la~-~~l-~~~~~~~~~L~~l~~~~L~~~l~k~~ 172 (211)
.+.+..|+.+. ..||||+. .|+..|. ..|..+.+. +|+...+- ... ..|+..+++|.+|++++ |.+..
T Consensus 75 l~~f~~f~~~~--~lVaHNa~~fD~~fL~-~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~-gi~~~--- 147 (195)
T PRK07247 75 LAAFKEFVGEL--PLIGYNAQKSDLPILA-ENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADFL-GIKGR--- 147 (195)
T ss_pred HHHHHHHHCCC--eEEEEeCcHhHHHHHH-HcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHhc-CCCCC---
Confidence 34566677643 57999995 7999995 678776542 56532221 111 12444679999999864 65321
Q ss_pred CccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcC
Q 048832 173 NITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNAN 209 (211)
Q Consensus 173 ~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~~ 209 (211)
.++ |..||.++..|+..|.+-
T Consensus 148 ---~Hr-------------Al~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 148 ---GHN-------------SLEDARMTARVYESFLES 168 (195)
T ss_pred ---CcC-------------CHHHHHHHHHHHHHHHhh
Confidence 122 678899999888887654
No 57
>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=95.94 E-value=0.22 Score=49.04 Aligned_cols=87 Identities=18% Similarity=0.168 Sum_probs=60.1
Q ss_pred hHHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCC-C-cEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCC
Q 048832 98 PQSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQV-F-RTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPR 172 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~-~-~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~ 172 (211)
.+.+.+|+.+ -+.|+||+..|...|.+ ++|... . ..+|+..++. .+ .|+..+++|+.+++++ |.+...
T Consensus 261 l~~f~~fl~~--~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar-~l-~p~~k~~kL~~Lak~l-gi~~~~-- 333 (1213)
T TIGR01405 261 LEKFKEFFKD--SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELAR-AL-NPEYKSHRLGNICKKL-GVDLDD-- 333 (1213)
T ss_pred HHHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHH-HH-hccCCCCCHHHHHHHc-CCCCCC--
Confidence 4456667764 46799999999998864 346542 2 3589977764 33 4566789999999884 655432
Q ss_pred CccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 173 NITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 173 ~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
...|..||.++.+|+..|.
T Consensus 334 ----------------~HrAl~DA~aTa~I~~~ll 352 (1213)
T TIGR01405 334 ----------------HHRADYDAEATAKVFKVMV 352 (1213)
T ss_pred ----------------CcCHHHHHHHHHHHHHHHH
Confidence 1337788888888877765
No 58
>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=95.28 E-value=0.18 Score=36.83 Aligned_cols=84 Identities=24% Similarity=0.158 Sum_probs=52.8
Q ss_pred hHHHHHhhcCCCceEEEeeeHHHHHHHHHhc---C--CCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCC
Q 048832 98 PQSLANFLSDEDYTFVGVGIDGDVKKLENNY---G--LQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPR 172 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~---g--i~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~ 172 (211)
...+.+++.. ...|||+...|...|.+.+ | ......+|+..++.... +....+++..+....++....+
T Consensus 70 ~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~~-- 143 (159)
T cd06127 70 LPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLL--PGLRSHRLGLLLAERYGIPLEG-- 143 (159)
T ss_pred HHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHc--CCCCcCchHHHHHHHcCCCCCC--
Confidence 3456677776 6789999999999886543 2 22234689976664333 3334678888744444532211
Q ss_pred CccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 048832 173 NITLSAWDTRVLTPAQVLYACLDAFIAFEIG 203 (211)
Q Consensus 173 ~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~ 203 (211)
.++ |..||.++.+|+
T Consensus 144 ---~H~-------------Al~Da~~t~~l~ 158 (159)
T cd06127 144 ---AHR-------------ALADALATAELL 158 (159)
T ss_pred ---CCC-------------cHHHHHHHHHHh
Confidence 222 778888888775
No 59
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=95.26 E-value=1.2 Score=35.45 Aligned_cols=86 Identities=15% Similarity=0.064 Sum_probs=54.6
Q ss_pred HHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCC
Q 048832 100 SLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAW 179 (211)
Q Consensus 100 ~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W 179 (211)
.+.++.. .-+.||||+..|...|. ..+ ...+|+..++..++ |+. .+++..|++.+ +.....++..
T Consensus 67 v~~~~~~--~~~lVaHNa~FD~~~L~-~~~---~~~idTl~lar~l~--p~~-~~~l~~L~~~~-~l~~~~~~~~----- 131 (219)
T PRK07983 67 VIPHYYG--SEWYVAHNASFDRRVLP-EMP---GEWICTMKLARRLW--PGI-KYSNMALYKSR-KLNVQTPPGL----- 131 (219)
T ss_pred HHHHHcC--CCEEEEeCcHhhHHHHh-CcC---CCcEeHHHHHHHHc--cCC-CCCHHHHHHHc-CCCCCCCCCC-----
Confidence 3445443 45789999999999984 332 24689977775444 443 48898888754 5432111100
Q ss_pred CCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 180 DTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 180 ~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
+..-|..||+++..|+..+.+
T Consensus 132 --------~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 132 --------HHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred --------CCCcHHHHHHHHHHHHHHHHH
Confidence 123388899999998888763
No 60
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=94.92 E-value=0.05 Score=46.68 Aligned_cols=90 Identities=18% Similarity=0.179 Sum_probs=59.5
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSA 178 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~ 178 (211)
..|+.|+ +++-+-|||++..|+..|+-.| ..++|++.+.. +-..|.....+|+.|++.+||..+. .....++
T Consensus 285 ~~l~~~~-~~~TILVGHSLenDL~aLKl~H----~~ViDTa~lf~-~~~g~~~~k~sLk~L~~~~L~~~Iq--~~~~~Hd 356 (380)
T KOG2248|consen 285 KELLELI-SKNTILVGHSLENDLKALKLDH----PSVIDTAVLFK-HPTGPYPFKSSLKNLAKSYLGKLIQ--EGVGGHD 356 (380)
T ss_pred HHHHhhc-CcCcEEEeechhhHHHHHhhhC----CceeeeeEEEe-cCCCCccchHHHHHHHHHHHHHHHh--ccCCCCc
Confidence 4566655 4556679999999999995433 23679975442 1111113578899999999997765 1111223
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHhcC
Q 048832 179 WDTRVLTPAQVLYACLDAFIAFEIGRVLNAN 209 (211)
Q Consensus 179 W~~~~L~~~q~~yAa~da~~~~~L~~~L~~~ 209 (211)
++.||.++.+|......+
T Consensus 357 -------------S~eDA~acm~Lv~~k~~~ 374 (380)
T KOG2248|consen 357 -------------SVEDALACMKLVKLKIKN 374 (380)
T ss_pred -------------cHHHHHHHHHHHHHHHhc
Confidence 578999999887766544
No 61
>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=94.59 E-value=0.54 Score=36.64 Aligned_cols=103 Identities=16% Similarity=0.125 Sum_probs=57.9
Q ss_pred chHHHHHhhcCCC-ceEEEeeeH-HHHHHHHH---hcCCCC------------------------Cc--EeecHHHHHhh
Q 048832 97 IPQSLANFLSDED-YTFVGVGID-GDVKKLEN---NYGLQV------------------------FR--TVDLRPLAAED 145 (211)
Q Consensus 97 ~~~~L~~~L~~~~-i~kvg~~~k-~d~~~L~~---~~gi~~------------------------~~--~~D~~~la~~~ 145 (211)
+...+..++..-+ -+.+|||.. .|+..|.+ .+|+.. .| .+|+-.+....
T Consensus 54 lL~~f~~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~ 133 (193)
T cd05784 54 LLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTA 133 (193)
T ss_pred HHHHHHHHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHc
Confidence 3444444554432 246799885 47766652 345442 12 35663333211
Q ss_pred ccccccccccHHHHHHHHcCccCC-CCC-----CccccCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 048832 146 LEIEGLRFAGLKALSWEVLEKEVN-KPR-----NITLSAWDTRVLTPAQVLYACLDAFIAFEIGR 204 (211)
Q Consensus 146 l~~~~~~~~~L~~l~~~~L~~~l~-k~~-----~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~ 204 (211)
. ....+++|+.+++++||..-. ... ++. .-|...+ ..-++|+..||..+++|++
T Consensus 134 ~--~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~-~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 134 T--YHFESFSLENVAQELLGEGKLIHDVDDRGAEIE-RLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred c--CCCCcCCHHHHHHHHhCCCccccCcccCHHHHH-HHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 1 134689999999999985211 111 111 1243322 3569999999999999863
No 62
>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=94.48 E-value=1.7 Score=33.57 Aligned_cols=147 Identities=18% Similarity=0.253 Sum_probs=79.2
Q ss_pred CcEEEEeeeeecCC---CCCCCCeeEEEeeeCC-eeEEEec--cccCcchHHHHHhhcCCCc-eEEEeee-HHHHHHHH-
Q 048832 55 CLIVGLDVEWRPSF---SRQQNPVATLQLCVGR-RCLIFQI--IHARRIPQSLANFLSDEDY-TFVGVGI-DGDVKKLE- 125 (211)
Q Consensus 55 ~~~v~~d~e~~~~~---~~~~~~~~llql~~~~-~~~i~~~--~~~~~~~~~L~~~L~~~~i-~kvg~~~-k~d~~~L~- 125 (211)
-.+++||+|..... .+...++-.|+++..+ ...++-- ....++...+..++..-+. +.+|+|. ..|+..|.
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~i~gyN~~~FDlpyl~~ 82 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVE 82 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCEEEecCCCcCcHHHHHH
Confidence 46899999986322 1233555555555433 2223211 1111344455555554322 3568886 46776654
Q ss_pred --HhcCCCCC--------------------c--EeecHHHHHhhccccccccccHHHHHHHHcCcc--CCCCC----Ccc
Q 048832 126 --NNYGLQVF--------------------R--TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKE--VNKPR----NIT 175 (211)
Q Consensus 126 --~~~gi~~~--------------------~--~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~--l~k~~----~~~ 175 (211)
+.+|+.+. | .+|+-.+.... ....+++|+.+|+ +||.. ..|.. ++
T Consensus 83 Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~---~~l~~y~L~~Va~-~Lg~~k~~~k~~~~~~~i- 157 (188)
T cd05781 83 RARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEI---PEVKVKTLENVAE-YLGVMKKSERVLIEWYRI- 157 (188)
T ss_pred HHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhh---CCCCCCCHHHHHH-HHCCCccccccCCCHHHH-
Confidence 34565432 1 46764444322 1245899999997 57752 11111 11
Q ss_pred ccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 048832 176 LSAWDTRVLTPAQVLYACLDAFIAFEIGRVL 206 (211)
Q Consensus 176 ~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L 206 (211)
..-|....-..+-.+|+..|+..++.|++.+
T Consensus 158 ~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 158 YEYWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred HHHHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 1134332133557999999999999998764
No 63
>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=94.44 E-value=0.8 Score=36.07 Aligned_cols=145 Identities=16% Similarity=0.124 Sum_probs=76.4
Q ss_pred CcEEEEeeeeecCCC-----CCCCCeeEEEeeeCC--e-eEEEecccc--CcchHHHHHhhcC--CCceEEEeee-HHHH
Q 048832 55 CLIVGLDVEWRPSFS-----RQQNPVATLQLCVGR--R-CLIFQIIHA--RRIPQSLANFLSD--EDYTFVGVGI-DGDV 121 (211)
Q Consensus 55 ~~~v~~d~e~~~~~~-----~~~~~~~llql~~~~--~-~~i~~~~~~--~~~~~~L~~~L~~--~~i~kvg~~~-k~d~ 121 (211)
-.+++||+|...... +....-.++||+... + -.++..... .++...+..++.. |. +.+|||. ..|+
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPd-ii~g~N~~~FD~ 87 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPD-VIEGHNIFRFDL 87 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccCCCCHHHHHHHHHHHHHHhCCC-EEeccCCcccCH
Confidence 468999999864321 112223467777642 2 122211111 1234444444444 55 4579988 5687
Q ss_pred HHHHH---hcCCCC------------------------------Cc-E-eecHHHHHhhc-cccccccccHHHHHHHHcC
Q 048832 122 KKLEN---NYGLQV------------------------------FR-T-VDLRPLAAEDL-EIEGLRFAGLKALSWEVLE 165 (211)
Q Consensus 122 ~~L~~---~~gi~~------------------------------~~-~-~D~~~la~~~l-~~~~~~~~~L~~l~~~~L~ 165 (211)
..|.+ .+|+.. .| . +|+-.+...+- ......+++|+.+|+.+ |
T Consensus 88 pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~-g 166 (207)
T cd05785 88 PYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHF-G 166 (207)
T ss_pred HHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHh-c
Confidence 76652 355543 12 2 57744332211 11233578999999986 3
Q ss_pred ccCCCCCCcc----ccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 048832 166 KEVNKPRNIT----LSAWDTRVLTPAQVLYACLDAFIAFEIG 203 (211)
Q Consensus 166 ~~l~k~~~~~----~s~W~~~~L~~~q~~yAa~da~~~~~L~ 203 (211)
..-.+..++. ..-|... ..+-++|+..||..+++|+
T Consensus 167 ~~~~~k~d~~~~~I~~l~~~~--~~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 167 LASPDRTYIDGRQIAEVWRSD--PARLLAYALDDVRETEGLA 206 (207)
T ss_pred ccCCCcCCCCHHHHHHHHhcC--HHHHHHHHHHHHHHHHHhh
Confidence 2111001111 1234433 2457999999999999886
No 64
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=94.44 E-value=0.095 Score=50.56 Aligned_cols=128 Identities=16% Similarity=0.146 Sum_probs=79.6
Q ss_pred CCcEEEEeeeeecCCCCCCCCeeEEEeeeCC--e-------eEEEecccc----------------------CcchHHHH
Q 048832 54 HCLIVGLDVEWRPSFSRQQNPVATLQLCVGR--R-------CLIFQIIHA----------------------RRIPQSLA 102 (211)
Q Consensus 54 ~~~~v~~d~e~~~~~~~~~~~~~llql~~~~--~-------~~i~~~~~~----------------------~~~~~~L~ 102 (211)
.+..|.||+|.++.+.. .+. +||++... + -+.+.+.+. .++...++
T Consensus 420 datyVVfDiETTGLs~~-~d~--iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf~ 496 (1444)
T COG2176 420 DATYVVFDIETTGLSPV-YDE--IIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKFR 496 (1444)
T ss_pred cccEEEEEeecCCcCcc-cch--hhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHHH
Confidence 46789999999887632 222 36666421 1 112222220 12456678
Q ss_pred HhhcCCCceEEEeeeHHHHHHHHH---hcCCC-CCc-EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCcccc
Q 048832 103 NFLSDEDYTFVGVGIDGDVKKLEN---NYGLQ-VFR-TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLS 177 (211)
Q Consensus 103 ~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~-~~~-~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s 177 (211)
.|+.| -+.|.||+..|+..|.. .+|+. ..+ ++|+-+|| ..++|..++|+|..+|+++ +..+
T Consensus 497 ~~~~d--~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~la--r~L~P~~ksh~Lg~l~kk~-~v~l--------- 562 (1444)
T COG2176 497 EFIGD--SILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELA--RALNPEFKSHRLGTLCKKL-GVEL--------- 562 (1444)
T ss_pred HHhcC--cEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHH--HHhChhhhhcchHHHHHHh-CccH---------
Confidence 88876 46799999999988863 34554 345 48996666 3457888899999999986 4433
Q ss_pred CCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 178 AWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 178 ~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
++...|--||.++-++...+.
T Consensus 563 ---------e~hHRA~yDaeat~~vf~~f~ 583 (1444)
T COG2176 563 ---------ERHHRADYDAEATAKVFFVFL 583 (1444)
T ss_pred ---------HHhhhhhhhHHHHHHHHHHHH
Confidence 233445556666666554443
No 65
>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=94.24 E-value=0.56 Score=36.30 Aligned_cols=78 Identities=18% Similarity=0.063 Sum_probs=51.7
Q ss_pred CceEEEeeeHHHHHHHHH---hcCCC---C--CcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCC
Q 048832 109 DYTFVGVGIDGDVKKLEN---NYGLQ---V--FRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWD 180 (211)
Q Consensus 109 ~i~kvg~~~k~d~~~L~~---~~gi~---~--~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~ 180 (211)
..+.||||+..|...|.+ ++|+. . ...+|+..++. .+ .+ ..+|+.+++++ |.+....+ .
T Consensus 102 ~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~-~~-~~---~~~L~~l~~~~-gi~~~~~~---~---- 168 (189)
T cd06134 102 RAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAG-LA-YG---QTVLAKACQAA-GIEFDNKE---A---- 168 (189)
T ss_pred CCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHH-HH-hC---CCcHHHHHHHC-CCCCCCCC---C----
Confidence 357899999999988863 45652 1 13689977775 33 23 45799999874 55432111 1
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 181 TRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 181 ~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
.-|..||.++.+|+..|.+
T Consensus 169 ---------H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 169 ---------HSALYDTQKTAELFCKIVN 187 (189)
T ss_pred ---------cChHHHHHHHHHHHHHHHH
Confidence 2277899999999888764
No 66
>PRK11779 sbcB exonuclease I; Provisional
Probab=93.72 E-value=1.3 Score=39.40 Aligned_cols=90 Identities=14% Similarity=0.053 Sum_probs=51.4
Q ss_pred HHHHhhcCCCceEEEee-eHHHHHHHHHhcCCC----------CCc-EeecHHHHHh-hccc------c----ccccccH
Q 048832 100 SLANFLSDEDYTFVGVG-IDGDVKKLENNYGLQ----------VFR-TVDLRPLAAE-DLEI------E----GLRFAGL 156 (211)
Q Consensus 100 ~L~~~L~~~~i~kvg~~-~k~d~~~L~~~~gi~----------~~~-~~D~~~la~~-~l~~------~----~~~~~~L 156 (211)
.+..++..+..+.|||| +..|...++..+... -.+ .+|+-.++.. +... | +..++.|
T Consensus 84 ~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rL 163 (476)
T PRK11779 84 RIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKL 163 (476)
T ss_pred HHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcH
Confidence 55667765556789997 689998775432111 011 2343333221 2111 2 2346899
Q ss_pred HHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 157 KALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 157 ~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
+.|++.+ |.+... . .-|..||.++..|+..|.+
T Consensus 164 e~L~~~~-gI~~~~-----A-------------HdALsDa~aT~~la~~l~~ 196 (476)
T PRK11779 164 EHLTKAN-GIEHEN-----A-------------HDAMSDVYATIAMAKLIKQ 196 (476)
T ss_pred HHHHHHc-CCCCCC-----C-------------CCcHHHHHHHHHHHHHHHH
Confidence 9999875 543321 1 2277888888888877764
No 67
>PRK06722 exonuclease; Provisional
Probab=92.38 E-value=5.6 Score=32.94 Aligned_cols=90 Identities=12% Similarity=-0.026 Sum_probs=52.1
Q ss_pred hHHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCCCc-----EeecHHHHHhhccccccccccHHHHHHHHcCccCC
Q 048832 98 PQSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQVFR-----TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVN 169 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~~~-----~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~ 169 (211)
...+.+|+.+. . .++|+...|...|.+ .+|+.... .+|++.++......-....++|..+++.+ |++..
T Consensus 81 l~ef~~fig~~-~-lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~l-gL~~~ 157 (281)
T PRK06722 81 IEKFIQFIGED-S-IFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQL-GLIWE 157 (281)
T ss_pred HHHHHHHHCCC-c-EEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHC-CCCCC
Confidence 34566677653 2 356667999988864 35655422 36776555322211011356899999875 54432
Q ss_pred CCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 170 KPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 170 k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
+. . .-|-.||.++.+|+..|.
T Consensus 158 -g~---~-------------HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 158 -GK---Q-------------HRALADAENTANILLKAY 178 (281)
T ss_pred -CC---C-------------cCcHHHHHHHHHHHHHHh
Confidence 11 1 226678888888877765
No 68
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=92.34 E-value=5.8 Score=33.05 Aligned_cols=85 Identities=13% Similarity=-0.002 Sum_probs=51.2
Q ss_pred hHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCc--EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCcc
Q 048832 98 PQSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFR--TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNIT 175 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~--~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~ 175 (211)
.+.+..++... -+.|+||+..|...|.+ +.....+ ..++.... -+..++..+++|..|+..+ |. .. +
T Consensus 111 ~~~l~~fl~~~-~vlVAHNA~FD~~fL~~-~~~~~~~~~~~ct~~~i--~~~~~~~~~~kL~~La~~~-g~-~~---~-- 179 (294)
T PRK09182 111 PAAVDALIAPA-DLIIAHNAGFDRPFLER-FSPVFATKPWACSVSEI--DWSARGFEGTKLGYLAGQA-GF-FH---E-- 179 (294)
T ss_pred HHHHHHHhcCC-CEEEEeCHHHHHHHHHH-HHHhccCCcccccHHHH--hhccccCCCCCHHHHHHHc-CC-CC---C--
Confidence 34677777763 46799999999999954 3332222 23332111 1223344589999999875 41 11 0
Q ss_pred ccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 048832 176 LSAWDTRVLTPAQVLYACLDAFIAFEIGRVL 206 (211)
Q Consensus 176 ~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L 206 (211)
. .-|..||.++..|....
T Consensus 180 a-------------HrAl~Da~Ata~ll~~~ 197 (294)
T PRK09182 180 G-------------HRAVDDCQALLELLARP 197 (294)
T ss_pred C-------------cChHHHHHHHHHHHHHH
Confidence 1 22788898888877643
No 69
>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=92.26 E-value=4.6 Score=31.69 Aligned_cols=100 Identities=19% Similarity=0.147 Sum_probs=58.0
Q ss_pred chHHHHHhhcCCCceEEEeeeH-HHHHHHH---HhcCCC--------------CCc--EeecHHHHHh-----hcccccc
Q 048832 97 IPQSLANFLSDEDYTFVGVGID-GDVKKLE---NNYGLQ--------------VFR--TVDLRPLAAE-----DLEIEGL 151 (211)
Q Consensus 97 ~~~~L~~~L~~~~i~kvg~~~k-~d~~~L~---~~~gi~--------------~~~--~~D~~~la~~-----~l~~~~~ 151 (211)
+...+.+++.+. -..+|+|.. .|+..|. +.+|+. +.+ .+|+-..... |.-....
T Consensus 76 lL~~F~~~i~~~-~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~ 154 (204)
T cd05783 76 LIREAFKIISEY-PIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKY 154 (204)
T ss_pred HHHHHHHHHhcC-CEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcccc
Confidence 444555666665 356788874 5776664 346766 112 2677433211 1000123
Q ss_pred ccccHHHHHHHHcCcc-CCCCCCccccCCCCCCCC-HHHHHHHHHhHHHHHHHHH
Q 048832 152 RFAGLKALSWEVLEKE-VNKPRNITLSAWDTRVLT-PAQVLYACLDAFIAFEIGR 204 (211)
Q Consensus 152 ~~~~L~~l~~~~L~~~-l~k~~~~~~s~W~~~~L~-~~q~~yAa~da~~~~~L~~ 204 (211)
.+++|+.+|+.+||.. +.-+.++ |. +. .+-++|+..||..+++|..
T Consensus 155 ~~~~L~~Va~~~lg~~K~~~~~~i----~~---~~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 155 REYTLDAVAKALLGEGKVELEKNI----SE---LNLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccCcHHHHHHHhcCCCcccCCchh----hh---hcHHHHHHhhHHHHHHHHHHhc
Confidence 5899999999999852 2111111 11 12 3359999999999999864
No 70
>PRK05168 ribonuclease T; Provisional
Probab=92.00 E-value=2.3 Score=33.46 Aligned_cols=77 Identities=18% Similarity=0.056 Sum_probs=49.3
Q ss_pred CceEEEeeeHHHHHHHHH---hcCCC---CC--cEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCC
Q 048832 109 DYTFVGVGIDGDVKKLEN---NYGLQ---VF--RTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWD 180 (211)
Q Consensus 109 ~i~kvg~~~k~d~~~L~~---~~gi~---~~--~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~ 180 (211)
+.+.||||+..|+..|.+ ++|+. .. .++|+..++.... + ..+|..+++++ |.++.... .+
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~--~---~~~L~~l~~~~-gl~~~~~~---~H--- 181 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLAL--G---QTVLAKACQAA-GIEFDNKE---AH--- 181 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHc--C---CCCHHHHHHHC-CCCCCCCC---CC---
Confidence 467899999999988863 34542 11 3689977775322 2 35799999874 55432111 11
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 181 TRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 181 ~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
-|..||.++.+|+..|.
T Consensus 182 ----------~Al~DA~ata~l~~~l~ 198 (211)
T PRK05168 182 ----------SALYDTEKTAELFCEIV 198 (211)
T ss_pred ----------ChHHHHHHHHHHHHHHH
Confidence 26778888887777664
No 71
>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=92.00 E-value=4.4 Score=31.85 Aligned_cols=101 Identities=17% Similarity=0.079 Sum_probs=57.0
Q ss_pred hHHHHHhhcC--CCceEEEeee-HHHHHHHH---HhcCCCCC----------------c--EeecHHHHHhhcccccccc
Q 048832 98 PQSLANFLSD--EDYTFVGVGI-DGDVKKLE---NNYGLQVF----------------R--TVDLRPLAAEDLEIEGLRF 153 (211)
Q Consensus 98 ~~~L~~~L~~--~~i~kvg~~~-k~d~~~L~---~~~gi~~~----------------~--~~D~~~la~~~l~~~~~~~ 153 (211)
...+.+++.+ |.+ .+|+|. ..|+..|. +.+|+.+. + .+|+-.+..... .....+
T Consensus 77 L~~f~~~i~~~~Pd~-i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~-~l~~~s 154 (204)
T cd05779 77 LQRFFEHIREVKPHI-IVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDS-YLPQGS 154 (204)
T ss_pred HHHHHHHHHHhCCCE-EEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhh-cCCCCC
Confidence 3344445544 443 578877 45776654 24555422 1 256644432210 111237
Q ss_pred ccHHHHHHHHcCccCCC--CCCccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 048832 154 AGLKALSWEVLEKEVNK--PRNITLSAWDTRVLTPAQVLYACLDAFIAFEIG 203 (211)
Q Consensus 154 ~~L~~l~~~~L~~~l~k--~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~ 203 (211)
++|+.+|+.+||..-.. ..++. .-|...+ .+-++|+..||..++.||
T Consensus 155 ysLd~Va~~~Lg~~K~~~~~~~I~-~~~~~~~--~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 155 QGLKAVTKAKLGYDPVELDPEDMV-PLAREDP--QTLASYSVSDAVATYYLY 203 (204)
T ss_pred ccHHHHHHHHhCCCcCcCCHHHHH-HHHhCCc--HHHHhccHHHHHHHHHHh
Confidence 89999999999852111 11111 1455433 457999999999999987
No 72
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=91.48 E-value=2.9 Score=32.73 Aligned_cols=92 Identities=21% Similarity=0.098 Sum_probs=56.7
Q ss_pred hHHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCCC--c-EeecHHHHHhhccccccccccHHHHHHHHcCccCCCC
Q 048832 98 PQSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQVF--R-TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKP 171 (211)
Q Consensus 98 ~~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~~--~-~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~ 171 (211)
.+.|.+++.+.....+ |+...|+..|.+ .+|+... + .+|+..+...+. +....++|.++++++ |.+....
T Consensus 83 l~~f~~~~~~~~~~iv-~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~--~~~~~~~L~~~~~~~-gi~~~~~ 158 (207)
T PRK07748 83 VEKLAEYDKRCKPTIV-TWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFF--GERNQTGLWKAIEEY-GKEGTGK 158 (207)
T ss_pred HHHHHHHhCcCCeEEE-EECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHh--CcCCCCCHHHHHHHc-CCCCCCC
Confidence 4457777876444444 456889988863 3565432 2 467755443333 223468999988874 5432110
Q ss_pred CCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcCC
Q 048832 172 RNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNAND 210 (211)
Q Consensus 172 ~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~~~ 210 (211)
. ..|..||.++.+|+..|.+++
T Consensus 159 ----~-------------H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 159 ----H-------------HCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred ----C-------------cChHHHHHHHHHHHHHHHhCc
Confidence 1 227789999999999887663
No 73
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=91.46 E-value=2.3 Score=42.95 Aligned_cols=85 Identities=19% Similarity=0.147 Sum_probs=56.1
Q ss_pred HHHHhhcCCCceEEEeeeHHHHHHHH---HhcCCC-CCc-EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCc
Q 048832 100 SLANFLSDEDYTFVGVGIDGDVKKLE---NNYGLQ-VFR-TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNI 174 (211)
Q Consensus 100 ~L~~~L~~~~i~kvg~~~k~d~~~L~---~~~gi~-~~~-~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~ 174 (211)
.+..|+. ....|+|+...|...|. +++|+. +.+ .+|+..++. ...|....++|+++++++ |......
T Consensus 492 ~f~~fig--g~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar--~l~p~~k~~kL~~LAk~l-GL~~~~~--- 563 (1437)
T PRK00448 492 KFKEFCG--DSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSR--FLYPELKSHRLNTLAKKF-GVELEHH--- 563 (1437)
T ss_pred HHHHHhC--CCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHH--HHcCccccccHHHHHHHc-CCCCCCC---
Confidence 3344443 46789999999987664 345663 333 479866653 334555689999999874 6544321
Q ss_pred cccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 175 TLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 175 ~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
..|..||.++.+|+..|.
T Consensus 564 ---------------HrAl~DA~aTa~lf~~ll 581 (1437)
T PRK00448 564 ---------------HRADYDAEATAYLLIKFL 581 (1437)
T ss_pred ---------------cChHHHHHHHHHHHHHHH
Confidence 227788888888877764
No 74
>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase []. ; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 4DF4_A 3T3F_A 1QSY_A 3OJS_A 3PO5_A 3OJU_A 1QTM_A 1QSS_A 3PY8_A 4DFJ_A ....
Probab=91.42 E-value=0.92 Score=32.77 Aligned_cols=68 Identities=19% Similarity=0.085 Sum_probs=37.9
Q ss_pred eeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHHHHH
Q 048832 115 VGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLYACL 194 (211)
Q Consensus 115 ~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~ 194 (211)
.+.| |+..+...-|+.+..--|- +|.+ ||++|. +.+...++++|++- +|... |+.
T Consensus 68 ~~AK-~LAv~a~~~G~~v~PGDDP-lLlA-YLlDPs--Nt~p~~varRY~~~-----------~W~~d---------A~~ 122 (138)
T PF09281_consen 68 ALAK-DLAVHALREGVVVEPGDDP-LLLA-YLLDPS--NTNPEGVARRYLGG-----------EWPED---------AAT 122 (138)
T ss_dssp TTHH-HHHHHHHHTT----B---H-HHHH-HHH-TT----SHHHHHHHH-TS--------------SS---------HHH
T ss_pred HHHH-HHHHHHHhcCcccCCCCCc-chhh-hhcCcc--CCChHHHHHHhcCC-----------CCCcc---------HHH
Confidence 3344 4444445668877655565 6775 999985 88999999999852 45443 777
Q ss_pred hHHHHHHHHHHHh
Q 048832 195 DAFIAFEIGRVLN 207 (211)
Q Consensus 195 da~~~~~L~~~L~ 207 (211)
+|.+..+|++.|.
T Consensus 123 RA~~t~~L~~~L~ 135 (138)
T PF09281_consen 123 RALATARLLRALP 135 (138)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhh
Confidence 8888888887774
No 75
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=91.25 E-value=1.9 Score=33.64 Aligned_cols=77 Identities=19% Similarity=0.101 Sum_probs=49.2
Q ss_pred CceEEEeeeHHHHHHHHH---hcCCC---C--CcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCC
Q 048832 109 DYTFVGVGIDGDVKKLEN---NYGLQ---V--FRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWD 180 (211)
Q Consensus 109 ~i~kvg~~~k~d~~~L~~---~~gi~---~--~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~ 180 (211)
+-+.||||+..|...|.+ ++|.. . ...+|+..++... .| ..+|+.+++++ |.+...
T Consensus 105 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~--~~---~~~L~~l~~~~-gi~~~~---------- 168 (200)
T TIGR01298 105 RAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLA--YG---QTVLAKACQAA-GXDFDS---------- 168 (200)
T ss_pred CCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHH--cC---cccHHHHHHHc-CCCccc----------
Confidence 456899999999988863 33442 1 1268997777432 23 45799999864 543210
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 181 TRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 181 ~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
.+..-|..||.++.+|+..|.
T Consensus 169 ------~~~H~Al~Da~ata~lf~~l~ 189 (200)
T TIGR01298 169 ------TQAHSALYDTEKTAELFCEIV 189 (200)
T ss_pred ------cchhhhHHhHHHHHHHHHHHH
Confidence 123347778888887776664
No 76
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=89.90 E-value=0.13 Score=48.31 Aligned_cols=81 Identities=23% Similarity=0.371 Sum_probs=53.9
Q ss_pred HhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCCCCC
Q 048832 103 NFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAWDTR 182 (211)
Q Consensus 103 ~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~ 182 (211)
.+|-+-.+++|||+++.|.+.+ ...+.-..++|+..+. .+ +..+..+|.-||..+||..+.-. .+|
T Consensus 1008 ~~Li~~GviFVGHGL~nDFrvI--Ni~Vp~~QiiDTv~lf--~~--~s~R~LSLrfLa~~lLg~~IQ~~----~HD---- 1073 (1118)
T KOG1275|consen 1008 RLLIQRGVIFVGHGLQNDFRVI--NIHVPEEQIIDTVTLF--RL--GSQRMLSLRFLAWELLGETIQME----AHD---- 1073 (1118)
T ss_pred HHHHHcCcEEEcccccccceEE--EEecChhhheeeeEEE--ec--ccccEEEHHHHHHHHhcchhhcc----ccc----
Confidence 3677888999999999998766 1233323478884322 22 44568999999999998665311 222
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHH
Q 048832 183 VLTPAQVLYACLDAFIAFEIGRVL 206 (211)
Q Consensus 183 ~L~~~q~~yAa~da~~~~~L~~~L 206 (211)
..+||..++.||+.-
T Consensus 1074 ---------SIeDA~taLkLYk~Y 1088 (1118)
T KOG1275|consen 1074 ---------SIEDARTALKLYKKY 1088 (1118)
T ss_pred ---------cHHHHHHHHHHHHHH
Confidence 346777777776653
No 77
>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=89.08 E-value=0.75 Score=34.33 Aligned_cols=141 Identities=16% Similarity=0.132 Sum_probs=65.6
Q ss_pred EEEeeeeecCCCCCCCCeeEEEeeeC--Ce-eEEEeccccC-cchHHHH---HhhcCCCceEEEeee-HHHHHHHHHh--
Q 048832 58 VGLDVEWRPSFSRQQNPVATLQLCVG--RR-CLIFQIIHAR-RIPQSLA---NFLSDEDYTFVGVGI-DGDVKKLENN-- 127 (211)
Q Consensus 58 v~~d~e~~~~~~~~~~~~~llql~~~--~~-~~i~~~~~~~-~~~~~L~---~~L~~~~i~kvg~~~-k~d~~~L~~~-- 127 (211)
+-||+|+++.. +..+.+-++.++.. ++ ..+.+....+ .....+. .++.... ..++|+. ..|...|.+.
T Consensus 1 l~~DIET~Gl~-~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~l~~~~-~iv~yng~~FD~p~L~~~~~ 78 (164)
T PF13482_consen 1 LFFDIETTGLS-PDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFFELLDEAD-NIVTYNGKNFDIPFLKRRAK 78 (164)
T ss_dssp --EEEEESS-G-G-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH--HHHHTT---EEESSTTTTHHHHHHHHH-
T ss_pred CcEEecCCCCC-CCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHHHHHhcCC-eEEEEeCcccCHHHHHHHHH
Confidence 35899998664 33456677777752 22 2232322211 1122222 3455443 3567775 5688887643
Q ss_pred -cCCC-CCcEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCcc-------ccCCCC---CCCCHHHHHHHHHh
Q 048832 128 -YGLQ-VFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNIT-------LSAWDT---RVLTPAQVLYACLD 195 (211)
Q Consensus 128 -~gi~-~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~-------~s~W~~---~~L~~~q~~yAa~d 195 (211)
+++. ..+.+|+...+.... ..+.+|+.++.. ||..-.+.. +. ...|.. +....+.+.|.-.|
T Consensus 79 ~~~~~~~~~~iDl~~~~~~~~----~~~~~Lk~ve~~-lg~~~~~~~-~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~D 152 (164)
T PF13482_consen 79 RYGLPPPFNHIDLLKIIKKHF----LESYSLKNVEKF-LGIERRDDD-ISGSESVKLYKEYLETGDPEALEEILEYNEDD 152 (164)
T ss_dssp HHHH--GGGEEEHHHHHT-TT----SCCTT--SHHH-------------HHHHHHHHHH---TTGGTS--HHHHHHHHHH
T ss_pred HcCCCcccchhhHHHHHHhcc----CCCCCHHHHhhh-cccccccCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 3444 334689966553222 247789998877 564433111 11 112211 12445579999999
Q ss_pred HHHHHHHHHHH
Q 048832 196 AFIAFEIGRVL 206 (211)
Q Consensus 196 a~~~~~L~~~L 206 (211)
+.++.+|++.|
T Consensus 153 v~~~~~L~~~l 163 (164)
T PF13482_consen 153 VRATRRLYEWL 163 (164)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHh
Confidence 99999999876
No 78
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=89.01 E-value=0.011 Score=50.11 Aligned_cols=72 Identities=19% Similarity=0.209 Sum_probs=58.2
Q ss_pred CCCCCeeEEEeeeCCeeEEEeccccCc--chHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHH
Q 048832 70 RQQNPVATLQLCVGRRCLIFQIIHARR--IPQSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLA 142 (211)
Q Consensus 70 ~~~~~~~llql~~~~~~~i~~~~~~~~--~~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la 142 (211)
...++++.+|.++.-..|++++...+. +...+..++++++|.|+.|++.--.+.++..|||...+++|++ .+
T Consensus 71 ~~~~~l~~~q~~~~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~q-~~ 144 (458)
T KOG2405|consen 71 CRHGKLCWLQVATNCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQ-VA 144 (458)
T ss_pred cccCcchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhhh-hh
Confidence 345688889888776778888765432 4456788999999999999999888888888999999999995 45
No 79
>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=88.93 E-value=5.1 Score=31.53 Aligned_cols=127 Identities=14% Similarity=0.089 Sum_probs=71.6
Q ss_pred CCCCeeEEEeeeC---CeeEEEe-cccc--CcchHHHHHhhcCCCceEEEeeeH-HHHHHHHH---hcCCCCCc------
Q 048832 71 QQNPVATLQLCVG---RRCLIFQ-IIHA--RRIPQSLANFLSDEDYTFVGVGID-GDVKKLEN---NYGLQVFR------ 134 (211)
Q Consensus 71 ~~~~~~llql~~~---~~~~i~~-~~~~--~~~~~~L~~~L~~~~i~kvg~~~k-~d~~~L~~---~~gi~~~~------ 134 (211)
..+++..|.++.. ++.+.+. .... .++...+..++++.....||||.+ .|+-.|.. .+|+.+..
T Consensus 49 ~~~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~ 128 (208)
T cd05782 49 PFHKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGN 128 (208)
T ss_pred ccCceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCccc
Confidence 4577777777662 3322221 1111 134445555566533467999984 68877753 35664321
Q ss_pred ------------EeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCcc----ccCCCCCCCCHHHHHHHHHhHHH
Q 048832 135 ------------TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNIT----LSAWDTRVLTPAQVLYACLDAFI 198 (211)
Q Consensus 135 ------------~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~----~s~W~~~~L~~~q~~yAa~da~~ 198 (211)
.+|+..+.+. .+. ..+.+|+.+++ .||.+ .|. .+. ..-|.... -.+-.+|+..||..
T Consensus 129 ~~~~y~~r~~~~h~DL~~~~~~-~~~--~~~~~L~~va~-~lG~~-~K~-d~~G~~v~~~y~~g~-~~~I~~Yc~~Dv~~ 201 (208)
T cd05782 129 KDWNYRNRYSERHLDLMDLLAF-YGA--RARASLDLLAK-LLGIP-GKM-DVDGSQVWELYAEGK-LDEIAEYCETDVLN 201 (208)
T ss_pred chhhccCcCCCCcccHHHHHhc-cCc--cCCCCHHHHHH-HhCCC-CCc-CCCHHHHHHHHHcCC-hHHHHHHHHHHHHH
Confidence 3566444431 111 35899999986 56652 221 111 12344433 34579999999999
Q ss_pred HHHHHH
Q 048832 199 AFEIGR 204 (211)
Q Consensus 199 ~~~L~~ 204 (211)
++.|+.
T Consensus 202 t~~l~l 207 (208)
T cd05782 202 TYLLYL 207 (208)
T ss_pred HHHHHh
Confidence 999875
No 80
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=87.58 E-value=3 Score=31.91 Aligned_cols=86 Identities=15% Similarity=0.003 Sum_probs=50.3
Q ss_pred HHHHHhhcCCCceEEEee-eHHHHHHHHHh---cCCCC-------Cc-EeecHHHHHhhc-ccc----------cccccc
Q 048832 99 QSLANFLSDEDYTFVGVG-IDGDVKKLENN---YGLQV-------FR-TVDLRPLAAEDL-EIE----------GLRFAG 155 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~-~k~d~~~L~~~---~gi~~-------~~-~~D~~~la~~~l-~~~----------~~~~~~ 155 (211)
+.+..++..+....|||+ +..|...|.+. .|... .+ .+|+-.++..+. ..| +..+++
T Consensus 74 ~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~ 153 (183)
T cd06138 74 AKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFK 153 (183)
T ss_pred HHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchh
Confidence 345566665455578986 78999988643 33321 11 357755554221 112 234688
Q ss_pred HHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 048832 156 LKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIG 203 (211)
Q Consensus 156 L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~ 203 (211)
|+++++++ |.+.. +..-|..||.++.+|.
T Consensus 154 L~~l~~~~-gi~~~------------------~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 154 LEDLAQAN-GIEHS------------------NAHDALSDVEATIALA 182 (183)
T ss_pred HHHHHHHC-CCCcc------------------ccccHHHHHHHHHHHh
Confidence 99999874 54431 1233778888887664
No 81
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=84.16 E-value=13 Score=27.78 Aligned_cols=87 Identities=23% Similarity=0.204 Sum_probs=52.6
Q ss_pred HHHHHhhcCC-CceEEEeeeHHHHHHHHH---hcCCC-----CCcEeecHHHHHhhccccccccccHHHHHHHHcCccCC
Q 048832 99 QSLANFLSDE-DYTFVGVGIDGDVKKLEN---NYGLQ-----VFRTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVN 169 (211)
Q Consensus 99 ~~L~~~L~~~-~i~kvg~~~k~d~~~L~~---~~gi~-----~~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~ 169 (211)
+.+.+++.+. ....+++ .+.|...+.+ .++.. ....+|+..++....+.+ ...+|.++++.+ |.+..
T Consensus 80 ~~~~~~l~~~~~~~~v~~-~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~--~~~~L~~l~~~~-gi~~~ 155 (176)
T cd06133 80 KEFLEWLGKNGKYAFVTW-GDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLK--KRTGLSKALEYL-GLEFE 155 (176)
T ss_pred HHHHHHHHhCCCeEEEee-cHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCC--CCCCHHHHHHHC-CCCCC
Confidence 4667778764 2344444 5788665532 23332 124689987775444332 589999999765 65543
Q ss_pred CCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 048832 170 KPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVL 206 (211)
Q Consensus 170 k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L 206 (211)
++ .++ |-.||.++.+++..|
T Consensus 156 -~~---~H~-------------Al~DA~~~a~l~~~~ 175 (176)
T cd06133 156 -GR---HHR-------------GLDDARNIARILKRL 175 (176)
T ss_pred -CC---CcC-------------cHHHHHHHHHHHHHh
Confidence 11 222 678899988888765
No 82
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=82.00 E-value=16 Score=29.02 Aligned_cols=90 Identities=22% Similarity=0.200 Sum_probs=57.1
Q ss_pred HHHHHhhcCCCceEEEeeeHHHHHHHHH---hcCCCCC--cEeecHHHHHhhccccccccccHHHHHHHHcCccCCCCCC
Q 048832 99 QSLANFLSDEDYTFVGVGIDGDVKKLEN---NYGLQVF--RTVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRN 173 (211)
Q Consensus 99 ~~L~~~L~~~~i~kvg~~~k~d~~~L~~---~~gi~~~--~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~ 173 (211)
+.+.+++.+. -..|+||...|...|.. .++..+. ..+|+-.++... .|+....+|+.+++ .+|..-....
T Consensus 86 ~~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~--~~~~~~~~L~~l~~-~~gi~~~~~~- 160 (243)
T COG0847 86 PEFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRH--FPGFDRSSLDALAE-RLGIDRNPFH- 160 (243)
T ss_pred HHHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHH--cCCCccchHHHHHH-HcCCCcCCcC-
Confidence 3455666654 57799999999998863 3444432 246775565422 35545899999999 4465422111
Q ss_pred ccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 048832 174 ITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNA 208 (211)
Q Consensus 174 ~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~ 208 (211)
. .-|..||.++..++..+..
T Consensus 161 --~-------------H~Al~Da~~~a~~~~~~~~ 180 (243)
T COG0847 161 --P-------------HRALFDALALAELFLLLQT 180 (243)
T ss_pred --C-------------cchHHHHHHHHHHHHHHHh
Confidence 1 2277888888888777654
No 83
>PHA02528 43 DNA polymerase; Provisional
Probab=80.38 E-value=59 Score=31.55 Aligned_cols=53 Identities=11% Similarity=-0.036 Sum_probs=35.9
Q ss_pred cccccHHHHHHHHcCccCCCC--CCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 048832 151 LRFAGLKALSWEVLEKEVNKP--RNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVL 206 (211)
Q Consensus 151 ~~~~~L~~l~~~~L~~~l~k~--~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L 206 (211)
..+++|+.+++++||..-..- +.+. .-|...+ ..-++|+..||..+++|..++
T Consensus 270 l~SYsLe~VA~~~LG~~K~d~~~~eI~-~l~~~d~--~~l~~Ynl~Da~Lv~~L~~kl 324 (881)
T PHA02528 270 QPSYRLDYIAEVELGKKKLDYSDGPFK-KFRETDH--QKYIEYNIIDVELVDRLDDKR 324 (881)
T ss_pred cccCCHHHHHHHHhCCCCccCCHHHHH-HHHhcCH--HHHHHHHHHHHHHHHHHHHHH
Confidence 458999999999998532211 1111 1233221 446999999999999998874
No 84
>PRK05762 DNA polymerase II; Reviewed
Probab=78.98 E-value=26 Score=33.47 Aligned_cols=104 Identities=16% Similarity=0.201 Sum_probs=59.0
Q ss_pred chHHHHHhhcC--CCceEEEeeeH-HHHHHHHH---hcCCCC-------------------------Cc--EeecHHHHH
Q 048832 97 IPQSLANFLSD--EDYTFVGVGID-GDVKKLEN---NYGLQV-------------------------FR--TVDLRPLAA 143 (211)
Q Consensus 97 ~~~~L~~~L~~--~~i~kvg~~~k-~d~~~L~~---~~gi~~-------------------------~~--~~D~~~la~ 143 (211)
+...+..++.. |.+ .+|||+. .|+..|.+ .+|+.+ .| .+|+-.++.
T Consensus 206 LL~~F~~~i~~~DPDI-IvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k 284 (786)
T PRK05762 206 LLEKFNAWFAEHDPDV-IIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALK 284 (786)
T ss_pred HHHHHHHHHHhcCCCE-EEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHH
Confidence 44444445544 554 5799874 58776652 345532 12 245543333
Q ss_pred hhccccccccccHHHHHHHHcCccCC--CC----CCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 048832 144 EDLEIEGLRFAGLKALSWEVLEKEVN--KP----RNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVL 206 (211)
Q Consensus 144 ~~l~~~~~~~~~L~~l~~~~L~~~l~--k~----~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L 206 (211)
... . ...+++|+.+++++|+..-. .. +++ ..-|... ...-++|...||..+++|+.++
T Consensus 285 ~~~-~-~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI-~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 285 SAT-W-VFDSFSLEYVSQRLLGEGKAIDDPYDRMDEI-DRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred Hhh-c-cCCCCCHHHHHHHHhCCCeeccCccccHHHH-HHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 221 1 23589999999999984321 11 111 1123211 2346899999999999998854
No 85
>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=77.97 E-value=3 Score=33.39 Aligned_cols=65 Identities=20% Similarity=0.241 Sum_probs=41.1
Q ss_pred eecHHHHHhhccccccccccHHHHHHHHcCccCCCCCCccccCC-CCC--CCCHHHHHHHHHhHHHHHHHH
Q 048832 136 VDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNKPRNITLSAW-DTR--VLTPAQVLYACLDAFIAFEIG 203 (211)
Q Consensus 136 ~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W-~~~--~L~~~q~~yAa~da~~~~~L~ 203 (211)
+|+-.++...+ ...+++|+.++.++||...+.-..-..+.| ... .-...-++|...||...++|.
T Consensus 163 lD~~~~~r~~~---kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 163 LNVWRLMRSEL---ALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred eEhHHHHHHHc---CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 57654443222 345899999999999976543221123345 221 123346999999999998874
No 86
>PTZ00315 2'-phosphotransferase; Provisional
Probab=77.47 E-value=59 Score=29.89 Aligned_cols=97 Identities=14% Similarity=0.014 Sum_probs=57.1
Q ss_pred chHHHHHhhcCCC--------ceEEEeeeHHHHH-HHHH------hcCCCCCc--EeecHH-HHHhhccc---------c
Q 048832 97 IPQSLANFLSDED--------YTFVGVGIDGDVK-KLEN------NYGLQVFR--TVDLRP-LAAEDLEI---------E 149 (211)
Q Consensus 97 ~~~~L~~~L~~~~--------i~kvg~~~k~d~~-~L~~------~~gi~~~~--~~D~~~-la~~~l~~---------~ 149 (211)
+.+.+..||.+.. -..++|+...|++ .|.+ ..|+.... .+|++. ++..++.+ +
T Consensus 133 Vl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~ 212 (582)
T PTZ00315 133 VYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATP 212 (582)
T ss_pred HHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCcccccccccccc
Confidence 3455667776542 1467899999986 4532 23555432 457642 33212211 1
Q ss_pred ccccccHHHHHHHHcCccCCCCCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcCCC
Q 048832 150 GLRFAGLKALSWEVLEKEVNKPRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLNANDV 211 (211)
Q Consensus 150 ~~~~~~L~~l~~~~L~~~l~k~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~~~~~ 211 (211)
....++|.+|++. +|++... + . .-|-.||..+.+|...|.+.++
T Consensus 213 ~~~~~~L~~al~~-lgL~~eG-r---~-------------HrAlDDA~ntA~L~~~Ll~~g~ 256 (582)
T PTZ00315 213 PLGPSDMPDMLQM-LGLPLQG-R---H-------------HSGIDDCRNIAAVLCELLRRGL 256 (582)
T ss_pred ccCCcCHHHHHHH-CCCCCCC-C---C-------------cCcHHHHHHHHHHHHHHHHcCC
Confidence 2356899999986 4655321 1 1 1156788888889888887653
No 87
>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=72.81 E-value=6.6 Score=31.29 Aligned_cols=56 Identities=21% Similarity=0.202 Sum_probs=37.5
Q ss_pred cccccHHHHHHHHcCccCCCC--CCccccCCCCCCCC-HHHHHHHHHhHHHHHHHHHHHh
Q 048832 151 LRFAGLKALSWEVLEKEVNKP--RNITLSAWDTRVLT-PAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 151 ~~~~~L~~l~~~~L~~~l~k~--~~~~~s~W~~~~L~-~~q~~yAa~da~~~~~L~~~L~ 207 (211)
..+++|+.+|+++||..-..- +.+. .-|+..+-. ..-++|+..||..+++|..+|.
T Consensus 166 l~sy~L~~Va~~~Lg~~k~d~~~~~i~-~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 166 LRSYSLNSVSAHFLGEQKEDVHYSIIT-DLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred cccCcHHHHHHHHhCCCCCCCCHHHHH-HHHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 458999999999998532211 1211 123323222 3469999999999999998875
No 88
>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=71.12 E-value=22 Score=28.06 Aligned_cols=104 Identities=16% Similarity=0.071 Sum_probs=62.2
Q ss_pred chHHHHHhhcCCCceEEEeeeH-HHHHHHHH---hcCCCCCcE-------------------eecHHHHHhhcccccccc
Q 048832 97 IPQSLANFLSDEDYTFVGVGID-GDVKKLEN---NYGLQVFRT-------------------VDLRPLAAEDLEIEGLRF 153 (211)
Q Consensus 97 ~~~~L~~~L~~~~i~kvg~~~k-~d~~~L~~---~~gi~~~~~-------------------~D~~~la~~~l~~~~~~~ 153 (211)
+...+..+++......|+||.+ .|+-.|.. .+|+.+... +|+..+.+ ..+ ..+.
T Consensus 40 lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~-~~g--~~~~ 116 (209)
T PF10108_consen 40 LLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLS-FYG--AKAR 116 (209)
T ss_pred HHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHh-ccC--cccc
Confidence 4455555666656678999986 58877653 367766432 45533322 111 2358
Q ss_pred ccHHHHHHHHcCccCCCCCCcccc----CCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 154 AGLKALSWEVLEKEVNKPRNITLS----AWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 154 ~~L~~l~~~~L~~~l~k~~~~~~s----~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
.+|+.||.- ||++- |.. +..| -|....+ .+-..|+-.||..++.||-++.
T Consensus 117 ~sLd~la~~-lgiPg-K~~-idGs~V~~~y~~g~i-~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 117 TSLDELAAL-LGIPG-KDD-IDGSQVAELYQEGDI-DEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred CCHHHHHHH-cCCCC-CCC-CCHHHHHHHHHcCCH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 899998864 57643 321 1111 2322222 2358999999999999998764
No 89
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=56.07 E-value=1.9 Score=36.95 Aligned_cols=125 Identities=14% Similarity=0.047 Sum_probs=74.7
Q ss_pred EEeeeCCeeEEEeccccCc-c-hHHHHHhhcCCCceEEEeeeHHHHHHHHHhcCCCCCcEeecHHHHHhhcccccc--cc
Q 048832 78 LQLCVGRRCLIFQIIHARR-I-PQSLANFLSDEDYTFVGVGIDGDVKKLENNYGLQVFRTVDLRPLAAEDLEIEGL--RF 153 (211)
Q Consensus 78 lql~~~~~~~i~~~~~~~~-~-~~~L~~~L~~~~i~kvg~~~k~d~~~L~~~~gi~~~~~~D~~~la~~~l~~~~~--~~ 153 (211)
.+++.+...+++|....+. . ..-.++.|+...+ +. |.+.+...+.-.|++.+.|++|+| ++. .+..+.. +.
T Consensus 216 m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQ-ia~-sLve~~e~grr 290 (458)
T KOG2405|consen 216 MNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQ-IAS-SLVEPSEYGRR 290 (458)
T ss_pred hhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHH-HHH-HHhhhHHhccc
Confidence 5677776677777754321 1 2224556665444 33 889999988888999999999995 664 3433322 23
Q ss_pred ccHHHHHHHH-cCcc-------CCCCCC----cc--ccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 154 AGLKALSWEV-LEKE-------VNKPRN----IT--LSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 154 ~~L~~l~~~~-L~~~-------l~k~~~----~~--~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
+....+.... |+.. ..+.+. +. -.+|.-||.++....-++.|+..+......|.
T Consensus 291 ~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~ 358 (458)
T KOG2405|consen 291 HPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLV 358 (458)
T ss_pred CCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHh
Confidence 3333322221 1110 001110 01 23699999999988889999999887665543
No 90
>cd01231 PH_Lnk LNK-family Pleckstrin homology (PH) domain. LNK-family Pleckstrin homology (PH) domain. The Lnk family of proteins consists of Lnk, APS and SH2B. They are adaptor proteins consisting of a PH domain and an SH2 domain, which mediates signaling through growth factor receptors. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. The lnk family PH domain is likely involved in targeting of the adaptor proteins to the plasma membrane.
Probab=52.92 E-value=46 Score=23.13 Aligned_cols=33 Identities=9% Similarity=0.279 Sum_probs=27.5
Q ss_pred CCceeEEEeCCeEEEEEEeCChHHHHHHHHHHH
Q 048832 14 THDEYTVHFYDDVVFTQVTRSPSVVDDWISEIE 46 (211)
Q Consensus 14 ~~~~~~v~~~~~~i~~~~~~~~~~l~~~i~~l~ 46 (211)
+-++|.+...+..=++.-+.+++++.+|+..++
T Consensus 73 ~~nTFvLK~~~~~eyI~Ea~d~~q~~SWla~Ir 105 (107)
T cd01231 73 NLYTFVLKVDDNTDIIFEVGDEQQLNSWLAELR 105 (107)
T ss_pred cccEEEEEecCCceEEEEcCCHHHHHHHHHHHh
Confidence 557888899887767678889999999999875
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=49.70 E-value=20 Score=28.64 Aligned_cols=68 Identities=24% Similarity=0.195 Sum_probs=41.9
Q ss_pred eecHHHHHhhccccccccccHHHHHHHHcCccCCC--CCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 136 VDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVNK--PRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 136 ~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~k--~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
+|+...+...+ ...+++|.++++.+||.+-.. .+++ ..-|....--..-++|...||+.+++|...|.
T Consensus 158 ~D~~~~~k~~~---~~~sY~L~~va~~~Lg~~k~di~~~~i-~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl~ 227 (234)
T cd05776 158 CDTYLSAKELI---RCKSYDLTELSQQVLGIERQDIDPEEI-LNMYNDSESLLKLLEHTEKDAYLILQLMFKLN 227 (234)
T ss_pred hccHHHHHHHh---CCCCCChHHHHHHHhCcCcccCCHHHH-HHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 57755553332 246899999999999852111 1111 11243311112248999999999999998875
No 92
>PRK05359 oligoribonuclease; Provisional
Probab=47.94 E-value=96 Score=23.66 Aligned_cols=14 Identities=14% Similarity=-0.017 Sum_probs=12.0
Q ss_pred CcEEEEeeeeecCC
Q 048832 55 CLIVGLDVEWRPSF 68 (211)
Q Consensus 55 ~~~v~~d~e~~~~~ 68 (211)
...+.+|+|.++.+
T Consensus 3 ~~~vvlD~ETTGLd 16 (181)
T PRK05359 3 DNLIWIDLEMTGLD 16 (181)
T ss_pred CcEEEEEeecCCCC
Confidence 57899999998876
No 93
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.28 E-value=1.7e+02 Score=29.58 Aligned_cols=96 Identities=22% Similarity=0.194 Sum_probs=56.0
Q ss_pred CCCceEEEeeeH-HHHHHHHH---hcCCC---------------------CCc--EeecHHHHHhhccccccccccHHHH
Q 048832 107 DEDYTFVGVGID-GDVKKLEN---NYGLQ---------------------VFR--TVDLRPLAAEDLEIEGLRFAGLKAL 159 (211)
Q Consensus 107 ~~~i~kvg~~~k-~d~~~L~~---~~gi~---------------------~~~--~~D~~~la~~~l~~~~~~~~~L~~l 159 (211)
||.+ .+|||+. .|+..|.+ .+++. +.| ++|+...+..++ . ..+++|..+
T Consensus 599 DPDi-i~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~-~--~~sy~L~~v 674 (1172)
T TIGR00592 599 DPDE-IVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELI-R--CKSYDLSEL 674 (1172)
T ss_pred CCCE-EEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHHh-C--cCCCCHHHH
Confidence 7764 5699885 46666543 22322 334 368865554333 2 358999999
Q ss_pred HHHHcCccCCC--CCCccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 048832 160 SWEVLEKEVNK--PRNITLSAWDTRVLTPAQVLYACLDAFIAFEIGRVLN 207 (211)
Q Consensus 160 ~~~~L~~~l~k--~~~~~~s~W~~~~L~~~q~~yAa~da~~~~~L~~~L~ 207 (211)
+..+||.+-.. ...+. .-|....--..-++|...||..+++|...|.
T Consensus 675 ~~~~L~~~k~~~~~~~i~-~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l~ 723 (1172)
T TIGR00592 675 VQQILKTERKVIPIDNIN-NMYSESSSLTYLLEHTWKDAMFILQIMCELN 723 (1172)
T ss_pred HHHHhCCCCcccCHHHHH-HHHhCcHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999842110 00110 1233221122358899999999999887653
No 94
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=32.22 E-value=1.4e+02 Score=22.40 Aligned_cols=27 Identities=19% Similarity=0.386 Sum_probs=18.9
Q ss_pred HHHHhhcC----CCceEEEeeeHHHHHHHHH
Q 048832 100 SLANFLSD----EDYTFVGVGIDGDVKKLEN 126 (211)
Q Consensus 100 ~L~~~L~~----~~i~kvg~~~k~d~~~L~~ 126 (211)
.+.+|+.+ .....+||++..|...|.+
T Consensus 81 ~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~ 111 (173)
T cd06135 81 ELLEFIKKYVPKGKSPLAGNSVHQDRRFLDK 111 (173)
T ss_pred HHHHHHHHhcCCCCCceeecchhhCHHHHHH
Confidence 45556653 3467789999999988864
No 95
>PHA03334 putative DNA polymerase catalytic subunit; Provisional
Probab=27.35 E-value=1.7e+02 Score=29.94 Aligned_cols=78 Identities=14% Similarity=0.181 Sum_probs=46.6
Q ss_pred CCCCc--EeecHHHHHhhccccccccccHHHHHHHHcCccCC--------CCCCcccc----CCCCCCCCHH-HHHHHHH
Q 048832 130 LQVFR--TVDLRPLAAEDLEIEGLRFAGLKALSWEVLEKEVN--------KPRNITLS----AWDTRVLTPA-QVLYACL 194 (211)
Q Consensus 130 i~~~~--~~D~~~la~~~l~~~~~~~~~L~~l~~~~L~~~l~--------k~~~~~~s----~W~~~~L~~~-q~~yAa~ 194 (211)
+.+.| ++|+-.+.....-+-..++++|..+++++||..-+ |-+++..+ -|...+-+.. -..|+..
T Consensus 464 v~~~GrviiDMy~Vc~~K~~~~kL~sYkLNTVA~~~LgeqKp~k~~~k~~K~eDV~YkeI~~lf~~g~e~RaRla~YCLk 543 (1545)
T PHA03334 464 SHGFGAHIIDLMRVCNTKSIKAKCSSRKLDTVARLIISKSKPHKNPPKIGKMDDVKYTEMDGMFTAGGAALARYLIYNLV 543 (1545)
T ss_pred eeeccEEEEehHHHHhhcccccCccCCcHHHHHHHHHhcccccccccccCcccCCCHHHHHHHHhcChhhHHHHHHHHHH
Confidence 44556 37885544321111234589999999999986431 22222222 2222222222 4789999
Q ss_pred hHHHHHHHHHHHh
Q 048832 195 DAFIAFEIGRVLN 207 (211)
Q Consensus 195 da~~~~~L~~~L~ 207 (211)
||...++|.+.|.
T Consensus 544 DA~LvlrLlkkl~ 556 (1545)
T PHA03334 544 DSELLIRIAKNLD 556 (1545)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988774
No 96
>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=25.84 E-value=1.9e+02 Score=18.50 Aligned_cols=36 Identities=11% Similarity=0.248 Sum_probs=29.9
Q ss_pred CCCCceeEEEeCCeEEEEEEeCChHHHHHHHHHHHH
Q 048832 12 YNTHDEYTVHFYDDVVFTQVTRSPSVVDDWISEIER 47 (211)
Q Consensus 12 ~~~~~~~~v~~~~~~i~~~~~~~~~~l~~~i~~l~~ 47 (211)
......+.|.+++.......++++++..+|++.+..
T Consensus 66 ~~~~~~f~i~~~~~~~~~~~~~s~~~~~~W~~~i~~ 101 (104)
T PF00169_consen 66 KKRKNCFEITTPNGKSYLFSAESEEERKRWIQAIQK 101 (104)
T ss_dssp SSSSSEEEEEETTSEEEEEEESSHHHHHHHHHHHHH
T ss_pred cCCCcEEEEEeCCCcEEEEEcCCHHHHHHHHHHHHH
Confidence 456778899999986666788999999999998864
No 97
>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=22.67 E-value=2.1e+02 Score=18.12 Aligned_cols=31 Identities=16% Similarity=0.295 Sum_probs=23.2
Q ss_pred ceeEEEeCCeEEEEEEeCChHHHHHHHHHHH
Q 048832 16 DEYTVHFYDDVVFTQVTRSPSVVDDWISEIE 46 (211)
Q Consensus 16 ~~~~v~~~~~~i~~~~~~~~~~l~~~i~~l~ 46 (211)
..+.|..+++....-.+++.++..+|+..+.
T Consensus 59 ~~F~i~~~~~~~~~~~a~s~~e~~~Wi~al~ 89 (91)
T cd01246 59 KCFTIDTGGDKTLHLRANSEEERQRWVDALE 89 (91)
T ss_pred cEEEEEcCCCCEEEEECCCHHHHHHHHHHHH
Confidence 4666666665555567889999999998875
No 98
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=20.89 E-value=3.2e+02 Score=22.09 Aligned_cols=54 Identities=22% Similarity=0.104 Sum_probs=33.9
Q ss_pred CCCceEEEeeeHHHHHHHHHhcCCCC---------------CcEeecHHHHHhhccccccccccHHHHHHHHc
Q 048832 107 DEDYTFVGVGIDGDVKKLENNYGLQV---------------FRTVDLRPLAAEDLEIEGLRFAGLKALSWEVL 164 (211)
Q Consensus 107 ~~~i~kvg~~~k~d~~~L~~~~gi~~---------------~~~~D~~~la~~~l~~~~~~~~~L~~l~~~~L 164 (211)
+.+.++||||.-.|+-.|.+.+--++ +.++|+..++ .... ....+|+.+++.+-
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la-~~~~---~~~~~L~~l~~~l~ 215 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLA-EECP---GKSTSLQELAEELG 215 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHH-TSTT---TS-SSHHHHHHHTT
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHH-Hhcc---ccccCHHHHHHHhC
Confidence 34588999999999977765431122 3578985444 2321 24788999998753
Done!