Query psy12569
Match_columns 94
No_of_seqs 126 out of 1025
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 22:42:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12569.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12569hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0349 Rnd Ribonuclease D [Tr 99.9 6.8E-23 1.5E-27 160.1 8.0 81 1-81 99-182 (361)
2 PRK10829 ribonuclease D; Provi 99.9 2.2E-22 4.8E-27 157.7 8.5 81 2-82 104-187 (373)
3 cd06129 RNaseD_like DEDDy 3'-5 99.8 2.9E-20 6.3E-25 129.2 6.9 64 2-65 97-160 (161)
4 cd06146 mut-7_like_exo DEDDy 3 99.8 5.2E-19 1.1E-23 126.9 6.5 54 12-65 139-192 (193)
5 cd06141 WRN_exo DEDDy 3'-5' ex 99.7 5.8E-18 1.3E-22 117.4 7.0 64 2-65 103-169 (170)
6 TIGR01388 rnd ribonuclease D. 99.7 7.9E-17 1.7E-21 125.7 8.4 81 2-82 100-183 (367)
7 cd06148 Egl_like_exo DEDDy 3'- 99.7 3.3E-17 7.1E-22 117.6 4.5 71 2-72 95-181 (197)
8 PF01612 DNA_pol_A_exo1: 3'-5' 99.5 3.1E-14 6.7E-19 97.1 5.9 67 2-68 107-175 (176)
9 cd06142 RNaseD_exo DEDDy 3'-5' 99.3 1.1E-11 2.3E-16 85.4 8.1 72 2-73 94-165 (178)
10 KOG2207|consensus 99.3 4.3E-12 9.4E-17 104.4 5.2 77 13-93 530-606 (617)
11 PRK14975 bifunctional 3'-5' ex 99.2 3.9E-11 8.4E-16 97.9 7.0 69 2-71 76-147 (553)
12 KOG2206|consensus 99.1 1.6E-10 3.5E-15 95.5 5.4 70 3-73 296-365 (687)
13 smart00474 35EXOc 3'-5' exonuc 98.9 6.7E-09 1.5E-13 70.0 7.0 67 2-68 104-171 (172)
14 cd06147 Rrp6p_like_exo DEDDy 3 98.8 1.3E-08 2.9E-13 72.0 7.1 72 2-74 107-178 (192)
15 cd00007 35EXOc 3'-5' exonuclea 98.7 2.4E-08 5.3E-13 66.0 5.7 66 2-67 84-154 (155)
16 cd09018 DEDDy_polA_RNaseD_like 98.6 1.3E-07 2.8E-12 63.0 5.2 64 2-65 83-149 (150)
17 KOG4373|consensus 98.4 4.4E-07 9.5E-12 70.6 5.5 61 14-76 232-294 (319)
18 cd06140 DNA_polA_I_Bacillus_li 98.2 4.4E-06 9.5E-11 57.8 6.7 71 2-72 86-160 (178)
19 cd06139 DNA_polA_I_Ecoli_like_ 98.1 2.2E-05 4.7E-10 54.3 7.6 68 2-70 97-172 (193)
20 PRK05755 DNA polymerase I; Pro 97.9 3E-05 6.4E-10 66.6 7.2 66 2-71 400-472 (880)
21 TIGR00593 pola DNA polymerase 95.5 0.051 1.1E-06 47.5 6.8 71 2-72 408-481 (887)
22 COG0749 PolA DNA polymerase I 82.8 4.3 9.4E-05 34.5 6.2 70 3-72 108-184 (593)
23 cd05780 DNA_polB_Kod1_like_exo 81.1 2.2 4.9E-05 30.2 3.4 59 4-63 133-194 (195)
24 KOG2207|consensus 79.1 1.7 3.7E-05 36.9 2.6 56 16-71 189-246 (617)
25 PRK07740 hypothetical protein; 73.1 14 0.0003 27.4 5.8 46 12-74 187-232 (244)
26 KOG3657|consensus 70.3 11 0.00023 33.8 5.2 60 8-70 317-385 (1075)
27 PRK08517 DNA polymerase III su 69.5 26 0.00056 26.3 6.7 52 13-81 193-244 (257)
28 PRK06309 DNA polymerase III su 67.4 27 0.00058 25.5 6.2 32 50-86 148-179 (232)
29 KOG2405|consensus 66.4 9.2 0.0002 31.4 3.8 47 35-81 328-378 (458)
30 KOG1275|consensus 66.1 13 0.00028 33.6 4.9 69 7-91 1046-1114(1118)
31 cd05160 DEDDy_DNA_polB_exo DED 62.3 20 0.00044 24.9 4.6 50 12-61 147-198 (199)
32 cd05784 DNA_polB_II_exo DEDDy 59.8 15 0.00031 26.4 3.6 48 13-62 139-193 (193)
33 cd05777 DNA_polB_delta_exo DED 59.2 14 0.0003 26.9 3.4 55 13-67 168-226 (230)
34 cd06128 DNA_polA_exo DEDDy 3'- 56.5 54 0.0012 21.6 5.8 63 2-65 83-150 (151)
35 KOG2249|consensus 53.5 39 0.00085 26.3 5.1 48 8-70 221-268 (280)
36 cd06143 PAN2_exo DEDDh 3'-5' e 51.3 24 0.00051 25.5 3.5 34 13-61 140-173 (174)
37 smart00479 EXOIII exonuclease 51.2 29 0.00062 22.9 3.8 40 13-68 128-167 (169)
38 PRK06063 DNA polymerase III su 48.5 66 0.0014 24.8 5.8 27 48-74 159-185 (313)
39 PRK07883 hypothetical protein; 47.4 67 0.0015 26.8 6.0 51 13-80 144-195 (557)
40 cd06137 DEDDh_RNase DEDDh 3'-5 47.1 45 0.00097 22.8 4.3 37 12-61 124-160 (161)
41 TIGR01405 polC_Gram_pos DNA po 45.1 51 0.0011 30.4 5.3 45 13-74 317-361 (1213)
42 cd05778 DNA_polB_zeta_exo inac 44.3 26 0.00057 25.6 2.9 49 13-61 177-230 (231)
43 PRK07983 exodeoxyribonuclease 43.8 45 0.00098 24.4 4.1 39 48-89 134-172 (219)
44 TIGR01298 RNaseT ribonuclease 42.5 41 0.00089 24.0 3.6 28 45-72 169-196 (200)
45 cd06144 REX4_like DEDDh 3'-5' 41.8 36 0.00079 22.9 3.1 36 12-62 117-152 (152)
46 PRK07246 bifunctional ATP-depe 37.9 95 0.0021 27.2 5.7 51 6-73 125-175 (820)
47 PRK05168 ribonuclease T; Provi 37.0 57 0.0012 23.4 3.7 27 47-73 180-206 (211)
48 PRK00448 polC DNA polymerase I 36.9 77 0.0017 29.8 5.2 46 12-74 545-590 (1437)
49 TIGR01407 dinG_rel DnaQ family 36.3 1.8E+02 0.0038 25.4 7.1 49 7-72 121-169 (850)
50 PRK06310 DNA polymerase III su 35.4 1.5E+02 0.0033 21.9 5.9 19 50-68 156-174 (250)
51 cd06133 ERI-1_3'hExo_like DEDD 35.2 1E+02 0.0022 20.5 4.5 44 5-64 132-175 (176)
52 PF10584 Proteasome_A_N: Prote 34.1 23 0.0005 17.5 0.9 7 45-51 15-21 (23)
53 cd08318 Death_NMPP84 Death dom 33.7 1.2E+02 0.0026 18.8 4.8 38 39-82 2-39 (86)
54 cd06145 REX1_like DEDDh 3'-5' 33.4 95 0.0021 20.9 4.2 37 12-61 113-149 (150)
55 PF13482 RNase_H_2: RNase_H su 31.3 82 0.0018 20.9 3.5 51 13-64 102-163 (164)
56 cd06127 DEDDh DEDDh 3'-5' exon 31.0 1.1E+02 0.0023 19.4 3.9 16 46-61 143-158 (159)
57 PF09355 Phage_Gp19: Phage pro 30.8 1.6E+02 0.0034 19.6 4.8 38 39-79 2-39 (116)
58 PRK06807 DNA polymerase III su 30.7 1.4E+02 0.0031 23.0 5.2 46 7-70 129-174 (313)
59 PF05121 GvpK: Gas vesicle pro 30.6 1.6E+02 0.0034 19.2 5.1 63 13-78 11-75 (88)
60 cd06149 ISG20 DEDDh 3'-5' exon 30.3 97 0.0021 21.1 3.8 37 12-61 120-156 (157)
61 cd05781 DNA_polB_B3_exo DEDDy 29.5 95 0.0021 21.9 3.8 50 13-63 131-187 (188)
62 PF06621 SIM_C: Single-minded 29.4 28 0.00061 27.2 1.0 23 22-44 31-55 (292)
63 PRK08074 bifunctional ATP-depe 26.4 2.1E+02 0.0046 25.4 6.0 44 12-72 130-173 (928)
64 PF04664 OGFr_N: Opioid growth 25.8 1.9E+02 0.004 21.5 4.8 43 35-77 60-102 (213)
65 PF13811 DUF4186: Domain of un 25.1 49 0.0011 22.4 1.5 17 35-51 82-102 (111)
66 cd03725 SOCS_ASB6 SOCS (suppre 23.9 1.2E+02 0.0026 16.9 2.7 38 13-50 3-40 (44)
67 PF06648 DUF1160: Protein of u 22.8 2.2E+02 0.0048 19.4 4.4 63 16-78 39-104 (122)
68 PF00872 Transposase_mut: Tran 22.1 12 0.00026 29.5 -2.2 45 13-57 117-172 (381)
69 cd05783 DNA_polB_B1_exo DEDDy 21.9 2.3E+02 0.0049 20.3 4.6 47 12-62 155-202 (204)
70 PHA02528 43 DNA polymerase; Pr 21.6 1.1E+02 0.0024 27.3 3.3 50 13-63 272-323 (881)
71 PF11567 PfUIS3: Plasmodium fa 21.3 1.5E+02 0.0033 19.5 3.2 27 41-67 41-67 (101)
72 cd05779 DNA_polB_epsilon_exo D 21.0 1.5E+02 0.0032 21.4 3.5 48 13-62 154-204 (204)
73 PRK12607 phosphoribosylaminoim 20.6 3.6E+02 0.0077 21.3 5.7 46 34-79 145-200 (313)
74 PF12720 DUF3807: Protein of u 20.0 65 0.0014 23.2 1.4 15 35-49 43-57 (172)
No 1
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=6.8e-23 Score=160.10 Aligned_cols=81 Identities=33% Similarity=0.481 Sum_probs=75.0
Q ss_pred ChhchhhcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCC---chh
Q psy12569 1 MRIATGASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIE---LGP 77 (94)
Q Consensus 1 ~qiAa~~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~---~~e 77 (94)
.|||+.+||++.++||+.||++++|+++||++|.|||.+||||++|++|||.||.||+.||+.|.++|.+.|+. +++
T Consensus 99 TqiAa~l~g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~e 178 (361)
T COG0349 99 TQIAAKLAGFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDE 178 (361)
T ss_pred HHHHHHHhCCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHH
Confidence 38999999999899999999999999999999999999999999999999999999999999999999999954 555
Q ss_pred hHHH
Q psy12569 78 LLTE 81 (94)
Q Consensus 78 ~~~~ 81 (94)
|..+
T Consensus 179 f~~l 182 (361)
T COG0349 179 FRLL 182 (361)
T ss_pred HHHh
Confidence 5444
No 2
>PRK10829 ribonuclease D; Provisional
Probab=99.87 E-value=2.2e-22 Score=157.72 Aligned_cols=81 Identities=26% Similarity=0.361 Sum_probs=74.9
Q ss_pred hhchhhcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC---CCchhh
Q psy12569 2 RIATGASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG---IELGPL 78 (94)
Q Consensus 2 qiAa~~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~---~~~~e~ 78 (94)
|+|+.+||++.++||+.||+++||+.++|++|+|||++||||++|++|||.||+||++||+.|.++|.+.| |..+|+
T Consensus 104 qiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~ 183 (373)
T PRK10829 104 QILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDEC 183 (373)
T ss_pred HHHHHHcCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHH
Confidence 79999999998899999999999999999999999999999999999999999999999999999999977 456666
Q ss_pred HHHh
Q psy12569 79 LTEV 82 (94)
Q Consensus 79 ~~~~ 82 (94)
..+.
T Consensus 184 ~~l~ 187 (373)
T PRK10829 184 RLLC 187 (373)
T ss_pred HHHH
Confidence 5443
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=99.82 E-value=2.9e-20 Score=129.24 Aligned_cols=64 Identities=38% Similarity=0.541 Sum_probs=60.8
Q ss_pred hhchhhcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q psy12569 2 RIATGASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLH 65 (94)
Q Consensus 2 qiAa~~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~ 65 (94)
++|+.++|.+.+.||+.++++++|+.++|..|+|||++||||++|+.|||.||++++.||++|.
T Consensus 97 ~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 97 TIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHhCCCCCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 6788999987678999999999999999999999999999999999999999999999999986
No 4
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.77 E-value=5.2e-19 Score=126.93 Aligned_cols=54 Identities=54% Similarity=0.922 Sum_probs=52.2
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q psy12569 12 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLH 65 (94)
Q Consensus 12 ~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~ 65 (94)
.+.||+.||+++||+.++|+.|+|||++||||++|+.|||.||++++.||++|.
T Consensus 139 ~~~sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 139 KTKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred ccCCHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 478999999999999999999999999999999999999999999999999986
No 5
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=99.74 E-value=5.8e-18 Score=117.35 Aligned_cols=64 Identities=38% Similarity=0.512 Sum_probs=58.5
Q ss_pred hhchhhcCCC-CCccHHHHHHHHhCCccC--CcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q psy12569 2 RIATGASTQG-SPQSLSTLVLKCFGKTLN--KQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLH 65 (94)
Q Consensus 2 qiAa~~lg~~-~~~sL~~lv~~~lg~~ld--K~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~ 65 (94)
++|+.+++.. .+.||+.+++.++|..++ |..|+|||..||||++||+|||.||++++.||..|.
T Consensus 103 ~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 103 SHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 6788888876 347999999999999999 777999999999999999999999999999999885
No 6
>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=99.69 E-value=7.9e-17 Score=125.70 Aligned_cols=81 Identities=27% Similarity=0.394 Sum_probs=74.0
Q ss_pred hhchhhcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC---CCchhh
Q psy12569 2 RIATGASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG---IELGPL 78 (94)
Q Consensus 2 qiAa~~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~---~~~~e~ 78 (94)
|+|+.+||.+.+.||+.|++++||+.++|++++|||..||||++|+.|||.||++++.||..|.+.|.+.| |..+|+
T Consensus 100 qlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee~ 179 (367)
T TIGR01388 100 QIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEEC 179 (367)
T ss_pred HHHHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHH
Confidence 78999999987789999999999999999999999999999999999999999999999999999999887 446666
Q ss_pred HHHh
Q psy12569 79 LTEV 82 (94)
Q Consensus 79 ~~~~ 82 (94)
....
T Consensus 180 ~~l~ 183 (367)
T TIGR01388 180 TLLT 183 (367)
T ss_pred HHHh
Confidence 6544
No 7
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.68 E-value=3.3e-17 Score=117.65 Aligned_cols=71 Identities=28% Similarity=0.416 Sum_probs=62.0
Q ss_pred hhchhhcCCCC--------CccHHHHHHHHhCCccCC--------cccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q psy12569 2 RIATGASTQGS--------PQSLSTLVLKCFGKTLNK--------QDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLH 65 (94)
Q Consensus 2 qiAa~~lg~~~--------~~sL~~lv~~~lg~~ldK--------~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~ 65 (94)
|+|+.+++.+. +.||+.++++++|++++| ..++|||..||||++|+.|||.||++|+.||..|.
T Consensus 95 ~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~ 174 (197)
T cd06148 95 QVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAML 174 (197)
T ss_pred HHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHH
Confidence 56777775432 379999999999999976 45889999999999999999999999999999999
Q ss_pred HHHHHcC
Q psy12569 66 DQCARQG 72 (94)
Q Consensus 66 ~~l~~~~ 72 (94)
..|.+..
T Consensus 175 ~~l~~~~ 181 (197)
T cd06148 175 DALISKF 181 (197)
T ss_pred HHhhhhH
Confidence 9998864
No 8
>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=99.51 E-value=3.1e-14 Score=97.14 Aligned_cols=67 Identities=34% Similarity=0.514 Sum_probs=60.2
Q ss_pred hhchhhcCCCCCccHHHHHHHHhC-CccCCcccccCCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q psy12569 2 RIATGASTQGSPQSLSTLVLKCFG-KTLNKQDQFSNWE-NRPLRPSQISYAALDAFCLLQVYQVLHDQC 68 (94)
Q Consensus 2 qiAa~~lg~~~~~sL~~lv~~~lg-~~ldK~~q~SdW~-~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l 68 (94)
++|+.+++...+.||+.|+.+++| ..++|+.+++||. .+||+++|+.|||.||.+++.||..|.++|
T Consensus 107 ~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 107 MLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp HHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred hhhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 467788887766999999999999 8888999999999 999999999999999999999999999886
No 9
>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=99.31 E-value=1.1e-11 Score=85.35 Aligned_cols=72 Identities=36% Similarity=0.580 Sum_probs=65.8
Q ss_pred hhchhhcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCC
Q psy12569 2 RIATGASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGI 73 (94)
Q Consensus 2 qiAa~~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~ 73 (94)
++|+-+++.+.+.||..++++++|..+.|+.++++|..+||+.+|+.||+.||.++..++..+.+++++.|+
T Consensus 94 ~laayLl~p~~~~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~l 165 (178)
T cd06142 94 QIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGR 165 (178)
T ss_pred HHHHHHhCCCccccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCc
Confidence 678888987655799999999999998877799999999999999999999999999999999999998863
No 10
>KOG2207|consensus
Probab=99.28 E-value=4.3e-12 Score=104.44 Aligned_cols=77 Identities=36% Similarity=0.518 Sum_probs=68.1
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCCchhhHHHhhhhhhccccc
Q psy12569 13 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGPLLTEVLSSHAVTTKK 92 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~~~e~~~~~~~~~~~~~~~ 92 (94)
.-+|+.|...++|..++|++|||||..|||...||-|||.|+.+++.+|.++++.-.. ..+.-..+-+||.+++||
T Consensus 530 ~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~~----~~~~ek~i~es~~~~~~~ 605 (617)
T KOG2207|consen 530 TKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVEH----DADIEKFICESHLGRPKK 605 (617)
T ss_pred hhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcch----hhHHHHHHHHHhcCCccc
Confidence 4579999999999999999999999999999999999999999999999999998662 444556788899999775
Q ss_pred C
Q psy12569 93 S 93 (94)
Q Consensus 93 ~ 93 (94)
.
T Consensus 606 ~ 606 (617)
T KOG2207|consen 606 K 606 (617)
T ss_pred c
Confidence 3
No 11
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.20 E-value=3.9e-11 Score=97.90 Aligned_cols=69 Identities=35% Similarity=0.400 Sum_probs=65.6
Q ss_pred hhchhhcCCCC---CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHc
Q psy12569 2 RIATGASTQGS---PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQ 71 (94)
Q Consensus 2 qiAa~~lg~~~---~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~ 71 (94)
|+|+.+||.+. +.||+.++++++|+.++|..+.|||. |||+++|+.||+.||.++..||..+.+++.+.
T Consensus 76 ~LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~~sdw~-rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 76 MLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALS-DPPDEEQLLYAAADADVLLELYAVLADQLNRI 147 (553)
T ss_pred HHHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChhhhcccc-ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence 78999999876 79999999999999999999999997 99999999999999999999999999999876
No 12
>KOG2206|consensus
Probab=99.07 E-value=1.6e-10 Score=95.48 Aligned_cols=70 Identities=30% Similarity=0.388 Sum_probs=66.6
Q ss_pred hchhhcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCC
Q psy12569 3 IATGASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGI 73 (94)
Q Consensus 3 iAa~~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~ 73 (94)
.|.++||.+ +.||..|.+.++|+..+|.+|..||..|||+++++.||..|.+|++.||+.|+..+.+.+-
T Consensus 296 ~a~r~L~~~-r~sL~~ll~~~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~ 365 (687)
T KOG2206|consen 296 QASRLLGLP-RPSLAYLLECVCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAK 365 (687)
T ss_pred HHHHHhCCC-cccHHHHHHHHHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhc
Confidence 478999999 7999999999999999999999999999999999999999999999999999998888773
No 13
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=98.90 E-value=6.7e-09 Score=69.97 Aligned_cols=67 Identities=36% Similarity=0.551 Sum_probs=56.7
Q ss_pred hhchhhcCCCC-CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q psy12569 2 RIATGASTQGS-PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQC 68 (94)
Q Consensus 2 qiAa~~lg~~~-~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l 68 (94)
++|+-++.... ..||+.++.+++|..+++..+.++|..+||..+|+.||+.||++++.|+..+.+.+
T Consensus 104 ~laayll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 104 MLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred HHHHHHHcCCCCcCCHHHHHHHHhCCCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46666554432 26999999999999987766778998899999999999999999999999998875
No 14
>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=98.83 E-value=1.3e-08 Score=72.02 Aligned_cols=72 Identities=26% Similarity=0.366 Sum_probs=63.0
Q ss_pred hhchhhcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCC
Q psy12569 2 RIATGASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIE 74 (94)
Q Consensus 2 qiAa~~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~ 74 (94)
++|+-+++.+ ..+|..+++++||..++|..+.+||+.+||+.+|..||+.|+.++..|+..|...|.+..-.
T Consensus 107 ~laaYLL~p~-~~~l~~l~~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~~~~ 178 (192)
T cd06147 107 GQAARVLNLP-RHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERANA 178 (192)
T ss_pred HHHHHHhCCC-cccHHHHHHHHhCCCcchhhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHhccc
Confidence 6788899887 56999999999998765656788999889999999999999999999999999999776543
No 15
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=98.75 E-value=2.4e-08 Score=66.04 Aligned_cols=66 Identities=32% Similarity=0.444 Sum_probs=54.9
Q ss_pred hhchhhcCCCC-CccHHHHHHHHhCCccCCcccccCCC----CCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q psy12569 2 RIATGASTQGS-PQSLSTLVLKCFGKTLNKQDQFSNWE----NRPLRPSQISYAALDAFCLLQVYQVLHDQ 67 (94)
Q Consensus 2 qiAa~~lg~~~-~~sL~~lv~~~lg~~ldK~~q~SdW~----~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~ 67 (94)
++|+.+++.+. +.||+.++++++|..+.+..+.++|. .+||+.+|+.||+.|+.+++.|+..+.++
T Consensus 84 ~~~ayll~~~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 84 MLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred HHHHHHhCCCCCcCCHHHHHHHHcCCCCccHHHHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 57788888765 67999999999999876544455653 58999999999999999999999998865
No 16
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=98.57 E-value=1.3e-07 Score=63.05 Aligned_cols=64 Identities=28% Similarity=0.273 Sum_probs=52.7
Q ss_pred hhchhhcCCCC-CccHHHHHHHHhCCccCC-cc-cccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q psy12569 2 RIATGASTQGS-PQSLSTLVLKCFGKTLNK-QD-QFSNWENRPLRPSQISYAALDAFCLLQVYQVLH 65 (94)
Q Consensus 2 qiAa~~lg~~~-~~sL~~lv~~~lg~~ldK-~~-q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~ 65 (94)
++|+-+++.+. +.+|..+++++||..+.| +. ..++|..+|++.+|+.||+.|+.++..|++.|.
T Consensus 83 ~laayLl~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 83 MLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 67888888754 579999999999998665 32 334596689999999999999999999998774
No 17
>KOG4373|consensus
Probab=98.42 E-value=4.4e-07 Score=70.56 Aligned_cols=61 Identities=20% Similarity=0.362 Sum_probs=44.7
Q ss_pred ccHHHHHHHHhC--CccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCCch
Q psy12569 14 QSLSTLVLKCFG--KTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELG 76 (94)
Q Consensus 14 ~sL~~lv~~~lg--~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~~~ 76 (94)
.++......+-| +.++|.-++|||+..||+.+|+.||++||+....++ ..+.+.+.++.++
T Consensus 232 e~i~~~~~~~~~~~v~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg--~~~~~w~~~~~~~ 294 (319)
T KOG4373|consen 232 EEIVSETLGYYGKDVRLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLG--VLERLWEVKLLLS 294 (319)
T ss_pred HHHHHHHhhccccccccChhcccccceeeeccHHHHHHHHhHHHHHHHHH--HHHHHHHHhcccc
Confidence 344444444445 556666799999999999999999999999999999 4444445444433
No 18
>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=98.24 E-value=4.4e-06 Score=57.76 Aligned_cols=71 Identities=13% Similarity=0.106 Sum_probs=58.7
Q ss_pred hhchhhcCCCC-CccHHHHHHHHhCCccCCcccccCCC---CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12569 2 RIATGASTQGS-PQSLSTLVLKCFGKTLNKQDQFSNWE---NRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 72 (94)
Q Consensus 2 qiAa~~lg~~~-~~sL~~lv~~~lg~~ldK~~q~SdW~---~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~ 72 (94)
+||+-+++.+. +.++..++.+++|..+.+..+.+.|. .++..+.|.+||+.|+.++..++..+.++|++.+
T Consensus 86 ~laaYLL~p~~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~ 160 (178)
T cd06140 86 MLAAYLLDPTRSSYDLADLAKRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEENE 160 (178)
T ss_pred HHHHHHcCCCCCCCCHHHHHHHHcCCCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 67888898765 37999999999999987644455552 3566788999999999999999999999998875
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=98.08 E-value=2.2e-05 Score=54.35 Aligned_cols=68 Identities=24% Similarity=0.343 Sum_probs=53.6
Q ss_pred hhchhhcCCCC-CccHHHHHHHHhCCcc-------CCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q psy12569 2 RIATGASTQGS-PQSLSTLVLKCFGKTL-------NKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCAR 70 (94)
Q Consensus 2 qiAa~~lg~~~-~~sL~~lv~~~lg~~l-------dK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~ 70 (94)
.+++.++.... +.||..++++++|..+ .|..+..+|...|+ ..+.+||+.|+.++..|+..+.+++.+
T Consensus 97 ~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 97 MLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45667776544 5799999999998763 23335666766566 779999999999999999999999977
No 20
>PRK05755 DNA polymerase I; Provisional
Probab=97.94 E-value=3e-05 Score=66.58 Aligned_cols=66 Identities=26% Similarity=0.286 Sum_probs=54.3
Q ss_pred hhchhhcCCCCCccHHHHHHHHhCCccC-------CcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHc
Q psy12569 2 RIATGASTQGSPQSLSTLVLKCFGKTLN-------KQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQ 71 (94)
Q Consensus 2 qiAa~~lg~~~~~sL~~lv~~~lg~~ld-------K~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~ 71 (94)
++|+.+++.+.+.||+.++++++|+.+. |..+.++ +|+ +.|..||+.||.++..||..+.+.|.+.
T Consensus 400 ~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~---~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~ 472 (880)
T PRK05755 400 MLASYLLDPGRRHGLDSLAERYLGHKTISFEEVAGKQLTFAQ---VDL-EEAAEYAAEDADVTLRLHEVLKPKLLEE 472 (880)
T ss_pred HHHHHHcCCCCCCCHHHHHHHHhCCCccchHHhcCCCCCccc---cCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5788888876558999999999998852 3334444 477 5899999999999999999999998875
No 21
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.48 E-value=0.051 Score=47.48 Aligned_cols=71 Identities=13% Similarity=0.031 Sum_probs=51.0
Q ss_pred hhchhhcCCCCCccHHHHHHHHhCCccCCcccccCCCC--CCCC-HHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12569 2 RIATGASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWEN--RPLR-PSQISYAALDAFCLLQVYQVLHDQCARQG 72 (94)
Q Consensus 2 qiAa~~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~--rpLt-~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~ 72 (94)
.||+-++....+.+|..++.++||..+.+......|.. ..++ +.+..||+.||.+.+.||..+...+.+.+
T Consensus 408 ~la~yll~~~~~~~l~~la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~ 481 (887)
T TIGR00593 408 MLAAYLLDPAQVSTLDTLARRYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELDENK 481 (887)
T ss_pred HHHHHHcCCCCCCCHHHHHHHHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 46777887655579999999999977554222222211 1333 34578999999999999999999998654
No 22
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=82.85 E-value=4.3 Score=34.46 Aligned_cols=70 Identities=19% Similarity=0.237 Sum_probs=46.7
Q ss_pred hchhhcCCCC-CccHHHHHHHHhCCccCCcccccCCCCCCCC------HHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12569 3 IATGASTQGS-PQSLSTLVLKCFGKTLNKQDQFSNWENRPLR------PSQISYAALDAFCLLQVYQVLHDQCARQG 72 (94)
Q Consensus 3 iAa~~lg~~~-~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt------~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~ 72 (94)
+|+-++..+. .+++..|++++++...-......+-....++ +.-..||+.|+...+.++..+...+.+..
T Consensus 108 lasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~~ 184 (593)
T COG0749 108 LASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLKTP 184 (593)
T ss_pred HHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 4555555443 5899999999998765443322111111122 23389999999999999999998765544
No 23
>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=81.08 E-value=2.2 Score=30.22 Aligned_cols=59 Identities=14% Similarity=0.190 Sum_probs=40.1
Q ss_pred chhhcCCCCCccHHHHHHHHhCCccCC-c-ccccC-CCCCCCCHHHHHHHHHhHHHHHHHHHH
Q psy12569 4 ATGASTQGSPQSLSTLVLKCFGKTLNK-Q-DQFSN-WENRPLRPSQISYAALDAFCLLQVYQV 63 (94)
Q Consensus 4 Aa~~lg~~~~~sL~~lv~~~lg~~ldK-~-~q~Sd-W~~rpLt~~Qi~YAA~Dv~~l~~l~~~ 63 (94)
+......+ +.+|..+++++||.+... + .+.+. |...+--..=++|...||...+.|..+
T Consensus 133 ~~~~~~l~-sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~ 194 (195)
T cd05780 133 ARRTLNLT-RYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKE 194 (195)
T ss_pred HHhhCCCC-cCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhh
Confidence 33444444 689999999999986322 1 13343 444444455699999999999998765
No 24
>KOG2207|consensus
Probab=79.13 E-value=1.7 Score=36.94 Aligned_cols=56 Identities=14% Similarity=0.045 Sum_probs=48.3
Q ss_pred HHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHH--HHHHHHHHHHHc
Q psy12569 16 LSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQ--VYQVLHDQCARQ 71 (94)
Q Consensus 16 L~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~--l~~~l~~~l~~~ 71 (94)
--.+.+..+..-+.|+.|+++|..+++|+.|.-|+..+...+.. +++.+++.+.+.
T Consensus 189 ~~~~e~~~ldlIls~k~q~a~~ll~~~~~~q~p~v~fld~~v~~~~~v~e~~~~~~e~ 246 (617)
T KOG2207|consen 189 DNAFEQLMLDLILSKKLQIADELLRHLTELQKPYVEFLDQMVLDNFIVDERCAHLLER 246 (617)
T ss_pred hhhHHHHhccHhhccchhHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 33456666778888999999999999999999999999999999 888888887776
No 25
>PRK07740 hypothetical protein; Provisional
Probab=73.05 E-value=14 Score=27.38 Aligned_cols=46 Identities=17% Similarity=0.308 Sum_probs=34.8
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCC
Q psy12569 12 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIE 74 (94)
Q Consensus 12 ~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~ 74 (94)
.+.||.+++. ++|++.+.. .=|..||.....||.++...+.+.|..
T Consensus 187 ~~~sL~~l~~-~~gi~~~~~----------------H~Al~Da~ata~l~~~ll~~~~~~~~~ 232 (244)
T PRK07740 187 DFPTLDDALA-YYGIPIPRR----------------HHALGDALMTAKLWAILLVEAQQRGIT 232 (244)
T ss_pred CCCCHHHHHH-HCCcCCCCC----------------CCcHHHHHHHHHHHHHHHHHHHHcCCc
Confidence 3577888875 467755431 226899999999999999999988754
No 26
>KOG3657|consensus
Probab=70.27 E-value=11 Score=33.84 Aligned_cols=60 Identities=23% Similarity=0.131 Sum_probs=46.2
Q ss_pred cCCCCCccHHHHHHHHhCCc-cCCcccccCCCCCCCCHHH--------HHHHHHhHHHHHHHHHHHHHHHHH
Q psy12569 8 STQGSPQSLSTLVLKCFGKT-LNKQDQFSNWENRPLRPSQ--------ISYAALDAFCLLQVYQVLHDQCAR 70 (94)
Q Consensus 8 lg~~~~~sL~~lv~~~lg~~-ldK~~q~SdW~~rpLt~~Q--------i~YAA~Dv~~l~~l~~~l~~~l~~ 70 (94)
+|...-.||.++.+.+||+. +||+.+-+.= .++.+| +.|-|.||+....||.++....-+
T Consensus 317 L~~SS~NSL~dVhk~~c~~~~LdKt~Rd~Fv---s~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fle 385 (1075)
T KOG3657|consen 317 LGRSSLNSLVDVHKFHCGIDALDKTPRDSFV---SGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLE 385 (1075)
T ss_pred hhhhhhHHHHHHHHhhCCCCccccchHHhhh---cCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHH
Confidence 56666789999999999998 9998754322 344454 579999999999999998776433
No 27
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=69.52 E-value=26 Score=26.32 Aligned_cols=52 Identities=15% Similarity=0.085 Sum_probs=34.9
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCCchhhHHH
Q psy12569 13 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGPLLTE 81 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~~~e~~~~ 81 (94)
+.||..+++ ++|++.+.. .=|..||.....|+..+..++...-...++..+.
T Consensus 193 ~~~L~~L~~-~lgi~~~~~----------------HrAl~DA~ata~ll~~ll~~~~~~~~t~~~L~~~ 244 (257)
T PRK08517 193 RYGLSFLKE-LLGIEIEVH----------------HRAYADALAAYEIFKICLLNLPSYIKTTEDLIDF 244 (257)
T ss_pred CCCHHHHHH-HcCcCCCCC----------------CChHHHHHHHHHHHHHHHHHhHHhhcCHHHHHHH
Confidence 567877776 467654422 2378999999999999998876543334444433
No 28
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=67.43 E-value=27 Score=25.49 Aligned_cols=32 Identities=19% Similarity=0.151 Sum_probs=23.5
Q ss_pred HHHhHHHHHHHHHHHHHHHHHcCCCchhhHHHhhhhh
Q psy12569 50 AALDAFCLLQVYQVLHDQCARQGIELGPLLTEVLSSH 86 (94)
Q Consensus 50 AA~Dv~~l~~l~~~l~~~l~~~~~~~~e~~~~~~~~~ 86 (94)
|..||+++..|+..+...+.. +++..+.+.+.
T Consensus 148 Al~Da~~t~~vl~~l~~~~~~-----~~l~~l~~~~~ 179 (232)
T PRK06309 148 ALDDVITLHRVFSALVGDLSP-----QQVYDLLNESC 179 (232)
T ss_pred cHHHHHHHHHHHHHHHHHHHH-----hhHHHHHHhhc
Confidence 789999999999999887642 44555554444
No 29
>KOG2405|consensus
Probab=66.45 E-value=9.2 Score=31.35 Aligned_cols=47 Identities=17% Similarity=0.201 Sum_probs=35.8
Q ss_pred cCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH----HHHcCCCchhhHHH
Q psy12569 35 SNWENRPLRPSQISYAALDAFCLLQVYQVLHDQ----CARQGIELGPLLTE 81 (94)
Q Consensus 35 SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~----l~~~~~~~~e~~~~ 81 (94)
-+|..||.|+...+-++.||..|..++..+.+. |...+..+.|....
T Consensus 328 ~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a~~l~HL~~rp~~e~ecie~ 378 (458)
T KOG2405|consen 328 PRWVIRPSTEIADHLLHRDVISLLGIFDTLVAVCLSHLTRRPYTEPECIEL 378 (458)
T ss_pred CcceecccHHHHHHHHHHHHHHHHHHHhhHhhhChHhhccCCccccchhhh
Confidence 479999999999999999999999998776654 33344555554433
No 30
>KOG1275|consensus
Probab=66.14 E-value=13 Score=33.57 Aligned_cols=69 Identities=19% Similarity=0.131 Sum_probs=54.2
Q ss_pred hcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCCchhhHHHhhhhh
Q psy12569 7 ASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGPLLTEVLSSH 86 (94)
Q Consensus 7 ~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~~~e~~~~~~~~~ 86 (94)
++|.+.-.||+-|+.++||.++.-+.- .. .-||++.+.||++..+ |+++|..++++..+.+.++
T Consensus 1046 ~~~s~R~LSLrfLa~~lLg~~IQ~~~H----DS-----------IeDA~taLkLYk~Yl~-lkeq~~~~~~l~niye~gr 1109 (1118)
T KOG1275|consen 1046 RLGSQRMLSLRFLAWELLGETIQMEAH----DS-----------IEDARTALKLYKKYLK-LKEQGKLESELRNIYECGR 1109 (1118)
T ss_pred ecccccEEEHHHHHHHHhcchhhcccc----cc-----------HHHHHHHHHHHHHHHH-HHHhhHHHHHHHHHhhcCc
Confidence 345555799999999999987744332 21 6899999999998764 7888998999999999998
Q ss_pred hcccc
Q psy12569 87 AVTTK 91 (94)
Q Consensus 87 ~~~~~ 91 (94)
..-.|
T Consensus 1110 ~~q~k 1114 (1118)
T KOG1275|consen 1110 PNQFK 1114 (1118)
T ss_pred cccCC
Confidence 87655
No 31
>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=62.27 E-value=20 Score=24.92 Aligned_cols=50 Identities=20% Similarity=0.171 Sum_probs=34.4
Q ss_pred CCccHHHHHHHHhCCccCCc--ccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q psy12569 12 SPQSLSTLVLKCFGKTLNKQ--DQFSNWENRPLRPSQISYAALDAFCLLQVY 61 (94)
Q Consensus 12 ~~~sL~~lv~~~lg~~ldK~--~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~ 61 (94)
.+.+|..+++.++|..-+.- ....+|....--..-++|...||...+.|+
T Consensus 147 ~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 147 KSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred ccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 36899999999998743221 144553222334456999999999998876
No 32
>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=59.82 E-value=15 Score=26.43 Aligned_cols=48 Identities=10% Similarity=0.150 Sum_probs=33.3
Q ss_pred CccHHHHHHHHhCCccCC-cc-----ccc-CCCCCCCCHHHHHHHHHhHHHHHHHHH
Q psy12569 13 PQSLSTLVLKCFGKTLNK-QD-----QFS-NWENRPLRPSQISYAALDAFCLLQVYQ 62 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK-~~-----q~S-dW~~rpLt~~Qi~YAA~Dv~~l~~l~~ 62 (94)
+.+|..+++++||..-+. .. ..+ -|...+ ..-++|...||...+.||+
T Consensus 139 sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 139 SFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred cCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 689999999999964221 11 112 233333 4669999999999998873
No 33
>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=59.16 E-value=14 Score=26.90 Aligned_cols=55 Identities=18% Similarity=0.251 Sum_probs=38.6
Q ss_pred CccHHHHHHHHhCCccC-Cc-ccccCCCC-CCCC-HHHHHHHHHhHHHHHHHHHHHHHH
Q psy12569 13 PQSLSTLVLKCFGKTLN-KQ-DQFSNWEN-RPLR-PSQISYAALDAFCLLQVYQVLHDQ 67 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ld-K~-~q~SdW~~-rpLt-~~Qi~YAA~Dv~~l~~l~~~l~~~ 67 (94)
+.+|..+++++||..-. =+ ...++|.. .|=. ..=++|...||...+.|+.++.-.
T Consensus 168 sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~~~ 226 (230)
T cd05777 168 SYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCL 226 (230)
T ss_pred cCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHhhH
Confidence 68999999999996432 11 13444432 2322 345999999999999999988643
No 34
>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=56.53 E-value=54 Score=21.56 Aligned_cols=63 Identities=13% Similarity=0.063 Sum_probs=37.0
Q ss_pred hhchhhcCCCCC-ccHHHHHHHHhCCccCC-cccccCCCCC--CC-CHHHHHHHHHhHHHHHHHHHHHH
Q psy12569 2 RIATGASTQGSP-QSLSTLVLKCFGKTLNK-QDQFSNWENR--PL-RPSQISYAALDAFCLLQVYQVLH 65 (94)
Q Consensus 2 qiAa~~lg~~~~-~sL~~lv~~~lg~~ldK-~~q~SdW~~r--pL-t~~Qi~YAA~Dv~~l~~l~~~l~ 65 (94)
.||+=+++-... .++..+++++|+..+-. .. ...+... ++ ..+.-+|++..+.++..|+..|.
T Consensus 83 ~LAaYLL~p~~~~~~l~~la~~yl~~~~~~~~~-~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 83 MLEAYLLDPVAGRHDMDSLAERWLKEKTITFEE-IAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred HHHHHHcCCCCCCCCHHHHHHHHcCCCCccHHH-HcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 467777776543 59999999999877321 11 1111100 12 11124488888888888887764
No 35
>KOG2249|consensus
Probab=53.47 E-value=39 Score=26.29 Aligned_cols=48 Identities=21% Similarity=0.281 Sum_probs=38.1
Q ss_pred cCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q psy12569 8 STQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCAR 70 (94)
Q Consensus 8 lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~ 70 (94)
+......||+.|.+.+||..+.-++..| --|+.+.+.||......-.+
T Consensus 221 ~~~~~tpSLK~Lt~~~Lg~~IQ~GeHsS---------------vEDA~AtM~LY~~vk~qwe~ 268 (280)
T KOG2249|consen 221 LSKKATPSLKKLTEALLGKDIQVGEHSS---------------VEDARATMELYKRVKVQWEK 268 (280)
T ss_pred hhccCCccHHHHHHHHhchhhhccccCc---------------HHHHHHHHHHHHHHHHHHHH
Confidence 3444578999999999999988777544 57999999999998876444
No 36
>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=51.26 E-value=24 Score=25.46 Aligned_cols=34 Identities=24% Similarity=0.277 Sum_probs=25.7
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q psy12569 13 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVY 61 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~ 61 (94)
+.||+.|++++||..+....-. ..-||.+.+.||
T Consensus 140 ~~sLk~La~~~L~~~IQ~~~Hd---------------SvEDArAam~Ly 173 (174)
T cd06143 140 KLSLRFLAWYLLGEKIQSETHD---------------SIEDARTALKLY 173 (174)
T ss_pred ChhHHHHHHHHcCCcccCCCcC---------------cHHHHHHHHHHh
Confidence 6899999999999998653211 256777777776
No 37
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=51.16 E-value=29 Score=22.89 Aligned_cols=40 Identities=20% Similarity=0.194 Sum_probs=28.6
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q psy12569 13 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQC 68 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l 68 (94)
..||..+++. +|++..-. ...|..||.....||..+.+..
T Consensus 128 ~~~L~~l~~~-~~~~~~~~---------------~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 128 KYSLKKLAER-LGLEVIGR---------------AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred CCCHHHHHHH-CCCCCCCC---------------CcCcHHHHHHHHHHHHHHHHHh
Confidence 5677777765 44433211 3779999999999999998764
No 38
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=48.55 E-value=66 Score=24.77 Aligned_cols=27 Identities=15% Similarity=0.047 Sum_probs=23.3
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHcCCC
Q psy12569 48 SYAALDAFCLLQVYQVLHDQCARQGIE 74 (94)
Q Consensus 48 ~YAA~Dv~~l~~l~~~l~~~l~~~~~~ 74 (94)
.=|..||..+..|+..+.+++.+.+..
T Consensus 159 H~Al~DA~ata~l~~~ll~~~~~~~~~ 185 (313)
T PRK06063 159 HDALDDARVLAGILRPSLERARERDVW 185 (313)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 347899999999999999999888753
No 39
>PRK07883 hypothetical protein; Validated
Probab=47.36 E-value=67 Score=26.83 Aligned_cols=51 Identities=33% Similarity=0.322 Sum_probs=37.1
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCC-CchhhHH
Q psy12569 13 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGI-ELGPLLT 80 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~-~~~e~~~ 80 (94)
+.+|..+++ ++|++... -.=|..||.....|+..+..++...|. ..+++..
T Consensus 144 ~~~L~~L~~-~~gi~~~~----------------~H~Al~DA~ata~l~~~l~~~~~~~~~~~~~~l~~ 195 (557)
T PRK07883 144 NVRLSTLAR-LFGATTTP----------------THRALDDARATVDVLHGLIERLGNLGVHTLEELLT 195 (557)
T ss_pred CCCHHHHHH-HCCcccCC----------------CCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence 567888766 56765432 245899999999999999999988775 3444433
No 40
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=47.08 E-value=45 Score=22.76 Aligned_cols=37 Identities=22% Similarity=0.144 Sum_probs=24.6
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q psy12569 12 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVY 61 (94)
Q Consensus 12 ~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~ 61 (94)
.+.+|..|++.++|.++...... .=|..||.....||
T Consensus 124 ~~~~L~~L~~~~~~~~~~~~~~~-------------H~A~~DA~at~~l~ 160 (161)
T cd06137 124 RQWSLRTLCRDFLGLKIQGGGEG-------------HDSLEDALAAREVV 160 (161)
T ss_pred CCccHHHHHHHHCCchhcCCCCC-------------CCcHHHHHHHHHHh
Confidence 46999999999999877542111 11456777666665
No 41
>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=45.14 E-value=51 Score=30.39 Aligned_cols=45 Identities=27% Similarity=0.405 Sum_probs=37.0
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCC
Q psy12569 13 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIE 74 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~ 74 (94)
..+|..+++. +|++++. -.-|..||..+..||..+.+++.+.|..
T Consensus 317 ~~kL~~Lak~-lgi~~~~----------------~HrAl~DA~aTa~I~~~ll~~l~~~~i~ 361 (1213)
T TIGR01405 317 SHRLGNICKK-LGVDLDD----------------HHRADYDAEATAKVFKVMVEQLKEKGIT 361 (1213)
T ss_pred CCCHHHHHHH-cCCCCCC----------------CcCHHHHHHHHHHHHHHHHHHHHHcCCc
Confidence 6788888876 5776543 2678999999999999999999998864
No 42
>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=44.25 E-value=26 Score=25.62 Aligned_cols=49 Identities=12% Similarity=0.191 Sum_probs=35.6
Q ss_pred CccHHHHHHHHhCCccCCcc--cccCCCC---CCCCHHHHHHHHHhHHHHHHHH
Q psy12569 13 PQSLSTLVLKCFGKTLNKQD--QFSNWEN---RPLRPSQISYAALDAFCLLQVY 61 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK~~--q~SdW~~---rpLt~~Qi~YAA~Dv~~l~~l~ 61 (94)
+.+|..++.++||.+.+.=. +.++|-. ..--..=++|-..|+...+.|.
T Consensus 177 sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 177 NYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred cCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 68999999999998654332 6788832 1233445899999999888764
No 43
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=43.82 E-value=45 Score=24.37 Aligned_cols=39 Identities=10% Similarity=0.055 Sum_probs=28.6
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHcCCCchhhHHHhhhhhhcc
Q psy12569 48 SYAALDAFCLLQVYQVLHDQCARQGIELGPLLTEVLSSHAVT 89 (94)
Q Consensus 48 ~YAA~Dv~~l~~l~~~l~~~l~~~~~~~~e~~~~~~~~~~~~ 89 (94)
.=|..||+.+..|+..+.+ ..+|..+++.+..+....++
T Consensus 134 HrAl~Da~ata~ll~~l~~---~~~~~~~~l~~~~~~~~~~~ 172 (219)
T PRK07983 134 HRALYDCYITAALLIDIMN---TSGWTAEEMADITGRPSLLT 172 (219)
T ss_pred CcHHHHHHHHHHHHHHHHH---HcCCCHHHHHHHhcCCccCC
Confidence 3488999999999988864 46777777777766555544
No 44
>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=42.52 E-value=41 Score=23.97 Aligned_cols=28 Identities=18% Similarity=0.189 Sum_probs=24.0
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12569 45 SQISYAALDAFCLLQVYQVLHDQCARQG 72 (94)
Q Consensus 45 ~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~ 72 (94)
.+-.=|..||.....||..+..++.+.+
T Consensus 169 ~~~H~Al~Da~ata~lf~~l~~~~~~~~ 196 (200)
T TIGR01298 169 TQAHSALYDTEKTAELFCEIVNRWKRLG 196 (200)
T ss_pred cchhhhHHhHHHHHHHHHHHHHHHHHcc
Confidence 3556688999999999999999998766
No 45
>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=41.79 E-value=36 Score=22.94 Aligned_cols=36 Identities=19% Similarity=0.339 Sum_probs=25.9
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q psy12569 12 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQ 62 (94)
Q Consensus 12 ~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~ 62 (94)
.+.||+.+++.++|+.+.... .=|..||.....||+
T Consensus 117 ~~~sL~~l~~~~lgi~~~~~~---------------H~Al~DA~at~~l~~ 152 (152)
T cd06144 117 KSPSLKKLAKQLLGLDIQEGE---------------HSSVEDARAAMRLYR 152 (152)
T ss_pred CChhHHHHHHHHcCcccCCCC---------------cCcHHHHHHHHHHhC
Confidence 468999999999998765311 115778888887763
No 46
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=37.90 E-value=95 Score=27.22 Aligned_cols=51 Identities=18% Similarity=0.022 Sum_probs=35.3
Q ss_pred hhcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCC
Q psy12569 6 GASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGI 73 (94)
Q Consensus 6 ~~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~ 73 (94)
.+.....+.+|..+++. +|++.... .=|..||.....||..+.+++...+.
T Consensus 125 ~~~p~~~~~~L~~L~~~-lgl~~~~~----------------H~Al~DA~ata~L~~~l~~~l~~l~~ 175 (820)
T PRK07246 125 VFFPTLEKYSLSHLSRE-LNIDLADA----------------HTAIADARATAELFLKLLQKIESLPK 175 (820)
T ss_pred HHhCCCCCCCHHHHHHH-cCCCCCCC----------------CCHHHHHHHHHHHHHHHHHHHhhcCc
Confidence 33333335778887764 67654322 23789999999999999998877664
No 47
>PRK05168 ribonuclease T; Provisional
Probab=36.97 E-value=57 Score=23.43 Aligned_cols=27 Identities=15% Similarity=0.089 Sum_probs=23.2
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHcCC
Q psy12569 47 ISYAALDAFCLLQVYQVLHDQCARQGI 73 (94)
Q Consensus 47 i~YAA~Dv~~l~~l~~~l~~~l~~~~~ 73 (94)
-.=|..||.....||..+..++.+.+.
T Consensus 180 ~H~Al~DA~ata~l~~~l~~~~~~~~~ 206 (211)
T PRK05168 180 AHSALYDTEKTAELFCEIVNRWKRLGG 206 (211)
T ss_pred CCChHHHHHHHHHHHHHHHHHHHHccC
Confidence 344889999999999999999988774
No 48
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=36.90 E-value=77 Score=29.83 Aligned_cols=46 Identities=26% Similarity=0.309 Sum_probs=35.7
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCC
Q psy12569 12 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIE 74 (94)
Q Consensus 12 ~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~ 74 (94)
.+.+|..+++. +|+.++.. .-|..||..+..||..+.+++.+.|+.
T Consensus 545 k~~kL~~LAk~-lGL~~~~~----------------HrAl~DA~aTa~lf~~ll~~l~~~gi~ 590 (1437)
T PRK00448 545 KSHRLNTLAKK-FGVELEHH----------------HRADYDAEATAYLLIKFLKDLKEKGIT 590 (1437)
T ss_pred ccccHHHHHHH-cCCCCCCC----------------cChHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 35677777764 56655422 668999999999999999999988865
No 49
>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=36.27 E-value=1.8e+02 Score=25.43 Aligned_cols=49 Identities=18% Similarity=0.129 Sum_probs=34.8
Q ss_pred hcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12569 7 ASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 72 (94)
Q Consensus 7 ~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~ 72 (94)
+.....+.+|..+++. +|+..+.. .=|..||.....|+..+.+++....
T Consensus 121 ~~p~~~~~~L~~l~~~-~gi~~~~~----------------H~Al~DA~ata~l~~~l~~~~~~l~ 169 (850)
T TIGR01407 121 FFPTEESYQLSELSEA-LGLTHENP----------------HRADSDAQATAELLLLLFEKMEKLP 169 (850)
T ss_pred hcCCCCCCCHHHHHHH-CCCCCCCC----------------CChHHHHHHHHHHHHHHHHHHHhcC
Confidence 3333346788888776 67765433 3378999999999999998887644
No 50
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=35.44 E-value=1.5e+02 Score=21.86 Aligned_cols=19 Identities=21% Similarity=0.223 Sum_probs=16.8
Q ss_pred HHHhHHHHHHHHHHHHHHH
Q psy12569 50 AALDAFCLLQVYQVLHDQC 68 (94)
Q Consensus 50 AA~Dv~~l~~l~~~l~~~l 68 (94)
|..||.....|+..+.+.+
T Consensus 156 Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 156 AMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred hHHHHHHHHHHHHHHHHhc
Confidence 7899999999999998754
No 51
>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=35.24 E-value=1e+02 Score=20.51 Aligned_cols=44 Identities=14% Similarity=0.057 Sum_probs=27.4
Q ss_pred hhhcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q psy12569 5 TGASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVL 64 (94)
Q Consensus 5 a~~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l 64 (94)
....|.....+|..++.. +|+..+ .+-.-|..||.....|+..|
T Consensus 132 ~~~~~~~~~~~L~~l~~~-~gi~~~---------------~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 132 AKFYGLKKRTGLSKALEY-LGLEFE---------------GRHHRGLDDARNIARILKRL 175 (176)
T ss_pred HHHhCCCCCCCHHHHHHH-CCCCCC---------------CCCcCcHHHHHHHHHHHHHh
Confidence 334444445667766643 455443 22345789999999998775
No 52
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=34.09 E-value=23 Score=17.46 Aligned_cols=7 Identities=43% Similarity=0.605 Sum_probs=5.4
Q ss_pred HHHHHHH
Q psy12569 45 SQISYAA 51 (94)
Q Consensus 45 ~Qi~YAA 51 (94)
-||+||.
T Consensus 15 ~QVEYA~ 21 (23)
T PF10584_consen 15 FQVEYAM 21 (23)
T ss_dssp HHHHHHH
T ss_pred EeeEeee
Confidence 4899985
No 53
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=33.74 E-value=1.2e+02 Score=18.84 Aligned_cols=38 Identities=11% Similarity=0.052 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCCchhhHHHh
Q psy12569 39 NRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGPLLTEV 82 (94)
Q Consensus 39 ~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~~~e~~~~~ 82 (94)
.+|||++|+..-| -.|...-.....+.|+...++-.+-
T Consensus 2 ~~~~t~~~l~~ia------~~iG~~Wk~Lar~LGls~~dI~~i~ 39 (86)
T cd08318 2 SKPVTGEQITVFA------NKLGEDWKTLAPHLEMKDKEIRAIE 39 (86)
T ss_pred CCCCCHHHHHHHH------HHHhhhHHHHHHHcCCCHHHHHHHH
Confidence 4799999998765 3455666666677888877765553
No 54
>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=33.44 E-value=95 Score=20.93 Aligned_cols=37 Identities=22% Similarity=0.251 Sum_probs=24.2
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q psy12569 12 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVY 61 (94)
Q Consensus 12 ~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~ 61 (94)
.+.||..|++.++|..+.... + ..=|..||.....||
T Consensus 113 ~~~~L~~L~~~~~~~~i~~~~---~----------~H~Al~DA~~t~~l~ 149 (150)
T cd06145 113 YKPSLKNLAKKYLGRDIQQGE---G----------GHDSVEDARAALELV 149 (150)
T ss_pred CChhHHHHHHHHCCcceeCCC---C----------CCCcHHHHHHHHHHh
Confidence 357999999999886554311 1 112467888777776
No 55
>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=31.27 E-value=82 Score=20.91 Aligned_cols=51 Identities=16% Similarity=0.217 Sum_probs=26.3
Q ss_pred CccHHHHHHHHhCCccCCcc----c----ccCCCC---CCCCHHHHHHHHHhHHHHHHHHHHH
Q psy12569 13 PQSLSTLVLKCFGKTLNKQD----Q----FSNWEN---RPLRPSQISYAALDAFCLLQVYQVL 64 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK~~----q----~SdW~~---rpLt~~Qi~YAA~Dv~~l~~l~~~l 64 (94)
+.||+.+... +|+.-++.. . ...|.. +...+..++|...||..+..|+..|
T Consensus 102 ~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 102 SYSLKNVEKF-LGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp CTT--SHHH------------HHHHHHHHHH---TTGGTS--HHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHhhh-cccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5688887765 777655221 1 122311 3577888999999999999999876
No 56
>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=31.02 E-value=1.1e+02 Score=19.39 Aligned_cols=16 Identities=19% Similarity=0.144 Sum_probs=12.3
Q ss_pred HHHHHHHhHHHHHHHH
Q psy12569 46 QISYAALDAFCLLQVY 61 (94)
Q Consensus 46 Qi~YAA~Dv~~l~~l~ 61 (94)
+-.=|..||..+..||
T Consensus 143 ~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 143 GAHRALADALATAELL 158 (159)
T ss_pred CCCCcHHHHHHHHHHh
Confidence 4455889999888876
No 57
>PF09355 Phage_Gp19: Phage protein Gp19/Gp15/Gp42; InterPro: IPR018963 This entry is represented by Mycobacteriophage D29, Gp19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=30.80 E-value=1.6e+02 Score=19.64 Aligned_cols=38 Identities=26% Similarity=0.399 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCCchhhH
Q psy12569 39 NRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGPLL 79 (94)
Q Consensus 39 ~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~~~e~~ 79 (94)
.||||+++...|. ..|-..-+.++.+..+.|..+++.+
T Consensus 2 ~R~Lt~~E~~~a~---~LL~~As~~Ir~~~~~~g~dld~~~ 39 (116)
T PF09355_consen 2 WRPLTPEEQARAE---ALLEDASDLIRDRIPRVGKDLDAKI 39 (116)
T ss_pred CCCCCHHHHHHHH---HHHHHHHHHHHHhhhhcCCCHHHHH
Confidence 3799999988876 5556666777777777777766544
No 58
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=30.74 E-value=1.4e+02 Score=22.99 Aligned_cols=46 Identities=22% Similarity=0.124 Sum_probs=30.7
Q ss_pred hcCCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q psy12569 7 ASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCAR 70 (94)
Q Consensus 7 ~lg~~~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~ 70 (94)
+.+.....+|..+++ .+|+.. +-.=|..||.+...||..+....+.
T Consensus 129 ~~~~~~~~kL~~L~~-~lgi~~-----------------~~H~Al~DA~~ta~l~~~l~~~~~~ 174 (313)
T PRK06807 129 YMKHAPNHKLETLKR-MLGIRL-----------------SSHNAFDDCITCAAVYQKCASIEEE 174 (313)
T ss_pred HhCCCCCCCHHHHHH-HcCCCC-----------------CCcChHHHHHHHHHHHHHHHHhhhh
Confidence 333333467777764 456554 1233789999999999999998843
No 59
>PF05121 GvpK: Gas vesicle protein K ; InterPro: IPR007805 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. Proteins containing this domain are involved in the formation of gas vesicles [].; GO: 0031412 gas vesicle organization
Probab=30.57 E-value=1.6e+02 Score=19.16 Aligned_cols=63 Identities=22% Similarity=0.335 Sum_probs=42.5
Q ss_pred CccHHHHHHHHhCC--ccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCCchhh
Q psy12569 13 PQSLSTLVLKCFGK--TLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGPL 78 (94)
Q Consensus 13 ~~sL~~lv~~~lg~--~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~~~e~ 78 (94)
..||..||-.++-. .+-+.+-.---+.-.||++|++=+. ..+..+-..+.+.....|+..+++
T Consensus 11 ~~gL~~LVLtvVELLRqlmErQAiRRme~G~Lse~qiErlG---~tLm~Le~~~~~l~~~~gl~~~dL 75 (88)
T PF05121_consen 11 ERGLARLVLTVVELLRQLMERQAIRRMEAGSLSEEQIERLG---ETLMKLEEAMEELCERFGLTPEDL 75 (88)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHH---HHHHHHHHHHHHHHHHcCCCHHHh
Confidence 35666666666542 2222221222235689999999998 478888899999888999887753
No 60
>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=30.28 E-value=97 Score=21.10 Aligned_cols=37 Identities=19% Similarity=0.228 Sum_probs=25.0
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q psy12569 12 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVY 61 (94)
Q Consensus 12 ~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~ 61 (94)
.+.+|..|+++++|..+....+. .| |..||.+..+||
T Consensus 120 ~~~~L~~L~~~~~~~~i~~~~~~----H~---------Al~DA~at~~l~ 156 (157)
T cd06149 120 CRVSLKVLAKRLLHRDIQVGRQG----HS---------SVEDARATMELY 156 (157)
T ss_pred CChhHHHHHHHHcChhhcCCCCC----cC---------cHHHHHHHHHHh
Confidence 35899999999998777653221 11 356777777766
No 61
>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=29.54 E-value=95 Score=21.93 Aligned_cols=50 Identities=14% Similarity=0.219 Sum_probs=34.1
Q ss_pred CccHHHHHHHHhCCc--cCCcc----cc-cCCCCCCCCHHHHHHHHHhHHHHHHHHHH
Q psy12569 13 PQSLSTLVLKCFGKT--LNKQD----QF-SNWENRPLRPSQISYAALDAFCLLQVYQV 63 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~--ldK~~----q~-SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~ 63 (94)
+.+|..+++ +||.. .+|.. +. .-|...---..=.+|...|+.....|+..
T Consensus 131 ~y~L~~Va~-~Lg~~k~~~k~~~~~~~i~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~ 187 (188)
T cd05781 131 VKTLENVAE-YLGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGLAEK 187 (188)
T ss_pred CCCHHHHHH-HHCCCccccccCCCHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHhh
Confidence 689999987 58863 23322 22 23443214467799999999999999875
No 62
>PF06621 SIM_C: Single-minded protein C-terminus; InterPro: IPR010578 In Drosophila, single-minded (sim) is a transcription factor that acts as the master regulator of neurogenesis. Two mammalian homologs of Sim which have been identified, Sim1 and Sim2, are novel heterodimerisation partners for ARNT in vitro, and may function both as positive and negative transcriptional regulators in vivo, during embryogenesis and in the adult organism []. SIM2 is thought to contribute to some specific Down syndrome phenotypes []. There is a high level of homology among mammalian and Drosophila sim proteins in their amino-terminal half where the conserved bHLH (see PDOC00038 from PROSITEDOC, IPR001092 from INTERPRO), PAS (see PDOC50112 from PROSITEDOC, IPR000014 from INTERPRO) and PAC motifs are present (IPR001610 from INTERPRO). The PAC region occurs C-terminal to the PAS domains and are proposed to contribute to the PAS domain fold [, , ]. In contrast, the carboxy-terminal parts are only conserved in vertebrates []. The Sim1 C terminus contains a Ser-rich region, whereas the Sim2 C terminus both contain Ser/Thr-rich regions, Pro/Ser-rich regions, Pro/Ala-rich regions, and positively charged regions. Sim2s, a splice variant of Sim2, still contains the Ser/Thr- and Pro/Ser-rich regions shown to harbor repressive activities, but is missing the Pro/Ala-rich repressor region [, , ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=29.35 E-value=28 Score=27.21 Aligned_cols=23 Identities=13% Similarity=0.278 Sum_probs=19.2
Q ss_pred HHhCCccCCcc--cccCCCCCCCCH
Q psy12569 22 KCFGKTLNKQD--QFSNWENRPLRP 44 (94)
Q Consensus 22 ~~lg~~ldK~~--q~SdW~~rpLt~ 44 (94)
.|-++.+||.+ |.++|...|+|+
T Consensus 31 QyssF~~dr~ec~Q~g~W~~Sp~t~ 55 (292)
T PF06621_consen 31 QYSSFQTDRSECDQDGQWGGSPPTD 55 (292)
T ss_pred CCCccccccccccCCCccccCCCCC
Confidence 35567889988 999999999994
No 63
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=26.36 E-value=2.1e+02 Score=25.38 Aligned_cols=44 Identities=18% Similarity=0.170 Sum_probs=30.9
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12569 12 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 72 (94)
Q Consensus 12 ~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~ 72 (94)
.+.+|..|++. +|+..+.. .=|..||.....||..|.+++....
T Consensus 130 ~~~~L~~l~~~-l~i~~~~~----------------H~Al~DA~ata~l~~~l~~~~~~l~ 173 (928)
T PRK08074 130 ESYKLRDLSEE-LGLEHDQP----------------HRADSDAEVTAELFLQLLNKLERLP 173 (928)
T ss_pred CCCCHHHHHHh-CCCCCCCC----------------CChHHHHHHHHHHHHHHHHHHHhcC
Confidence 35667777664 56544322 3378999999999999999887644
No 64
>PF04664 OGFr_N: Opioid growth factor receptor (OGFr) conserved region; InterPro: IPR006757 Opioid peptides act as growth factors in neural and non-neural cells and tissues, in addition to serving in neurotransmission/neuromodulation in the nervous system. The opioid growth factor receptor is an integral membrane protein associated with the nucleus. This conserved domain is situated at the N terminus of the member proteins with a series of imperfect repeats lying immediately to its C-terminal [].; GO: 0004872 receptor activity, 0016020 membrane
Probab=25.76 E-value=1.9e+02 Score=21.46 Aligned_cols=43 Identities=23% Similarity=0.127 Sum_probs=36.8
Q ss_pred cCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCCchh
Q psy12569 35 SNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGP 77 (94)
Q Consensus 35 SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~~~e 77 (94)
-||.+++||.+.++.-..|-..--.+-..+.-+|.=.|+...+
T Consensus 60 ~N~~Ap~Lt~~ei~~f~~d~~i~~r~l~s~~lML~FyGi~l~~ 102 (213)
T PF04664_consen 60 FNPHAPPLTPEEIEAFRSDPEIQKRLLRSYDLMLDFYGIELVD 102 (213)
T ss_pred CCCCCCCCCHHHHHHHhcCHHHHHHHHHHHHHHHHhcceeeec
Confidence 9999999999999999999888888888888888777766543
No 65
>PF13811 DUF4186: Domain of unknown function (DUF4186)
Probab=25.09 E-value=49 Score=22.39 Aligned_cols=17 Identities=24% Similarity=0.622 Sum_probs=13.4
Q ss_pred cCCCC----CCCCHHHHHHHH
Q psy12569 35 SNWEN----RPLRPSQISYAA 51 (94)
Q Consensus 35 SdW~~----rpLt~~Qi~YAA 51 (94)
..|.. ++||++|++|-.
T Consensus 82 ~KWH~Ip~gr~Lt~~eq~yiv 102 (111)
T PF13811_consen 82 EKWHGIPKGRELTEEEQAYIV 102 (111)
T ss_pred HHHhCCCCCCCCCHHHHHHHH
Confidence 45654 899999999965
No 66
>cd03725 SOCS_ASB6 SOCS (suppressors of cytokine signaling) box of ASB6-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. ASB6 interacts with the adaptor protein APS and recruits elongin B/C to the insulin receptor signaling complex. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=23.90 E-value=1.2e+02 Score=16.93 Aligned_cols=38 Identities=18% Similarity=0.072 Sum_probs=26.7
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHH
Q psy12569 13 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYA 50 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt~~Qi~YA 50 (94)
+.||+.|+...+...+.+.........-||...-++|=
T Consensus 3 P~sLqhLCR~~Ir~~lg~~~~~~~i~~LpLP~~Lk~yL 40 (44)
T cd03725 3 PPPLKHLCRVFIRLCLRPWPVDVKVKALPLPDRLKWYL 40 (44)
T ss_pred CcCHHHHHHHHHHHhcCccccccccccCCCCHHHHHHh
Confidence 57899999998877776543222345558888888874
No 67
>PF06648 DUF1160: Protein of unknown function (DUF1160); InterPro: IPR010594 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf75; it is a family of uncharacterised viral proteins.
Probab=22.83 E-value=2.2e+02 Score=19.43 Aligned_cols=63 Identities=16% Similarity=0.217 Sum_probs=37.6
Q ss_pred HHHHHHHHhCCccCCcc--c-ccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCCchhh
Q psy12569 16 LSTLVLKCFGKTLNKQD--Q-FSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGPL 78 (94)
Q Consensus 16 L~~lv~~~lg~~ldK~~--q-~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~l~~~l~~~~~~~~e~ 78 (94)
|-.+..-++.-+++-.. . .+.=..-.||..|+.|=..-++.=..|-..+..-.....+..+++
T Consensus 39 l~~Il~mFl~~eid~e~~y~l~~~~d~~~LT~~Qi~Yl~~~~~~n~~I~~Il~~~vd~~~l~dddi 104 (122)
T PF06648_consen 39 LIKILKMFLNDEIDVEDMYNLFGAVDGLKLTRSQIDYLYNRVYNNRYIINILQKFVDGQHLTDDDI 104 (122)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHhcccHhhcCHHHHHHHHHHHHccHHHHHHHHHHhcCccCCcccH
Confidence 33444444444444333 1 122222389999999999888877777666666665555555543
No 68
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=22.06 E-value=12 Score=29.49 Aligned_cols=45 Identities=20% Similarity=0.493 Sum_probs=35.1
Q ss_pred CccHHHHHHHHhC-CccCCcc----------cccCCCCCCCCHHHHHHHHHhHHHH
Q psy12569 13 PQSLSTLVLKCFG-KTLNKQD----------QFSNWENRPLRPSQISYAALDAFCL 57 (94)
Q Consensus 13 ~~sL~~lv~~~lg-~~ldK~~----------q~SdW~~rpLt~~Qi~YAA~Dv~~l 57 (94)
.......++.++| ..+.|+. ....|..|||+....-|--.|+.+.
T Consensus 117 tr~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R~L~~~~y~~l~iD~~~~ 172 (381)
T PF00872_consen 117 TRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNRPLESEPYPYLWIDGTYF 172 (381)
T ss_pred cccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhhccccccccceeeeeeec
Confidence 3456777888888 7777765 3589999999999888888887654
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=21.87 E-value=2.3e+02 Score=20.34 Aligned_cols=47 Identities=19% Similarity=0.152 Sum_probs=30.3
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCC-HHHHHHHHHhHHHHHHHHH
Q psy12569 12 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLR-PSQISYAALDAFCLLQVYQ 62 (94)
Q Consensus 12 ~~~sL~~lv~~~lg~~ldK~~q~SdW~~rpLt-~~Qi~YAA~Dv~~l~~l~~ 62 (94)
.+.+|..+++.+||.. |..-.+.... +. ++=++|...||.....|..
T Consensus 155 ~~~~L~~Va~~~lg~~--K~~~~~~i~~--~~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 155 REYTLDAVAKALLGEG--KVELEKNISE--LNLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccCcHHHHHHHhcCCC--cccCCchhhh--hcHHHHHHhhHHHHHHHHHHhc
Confidence 3689999999999962 2221111111 12 3338999999998887753
No 70
>PHA02528 43 DNA polymerase; Provisional
Probab=21.57 E-value=1.1e+02 Score=27.32 Aligned_cols=50 Identities=14% Similarity=0.158 Sum_probs=36.6
Q ss_pred CccHHHHHHHHhCCccCC--cccccCCCCCCCCHHHHHHHHHhHHHHHHHHHH
Q psy12569 13 PQSLSTLVLKCFGKTLNK--QDQFSNWENRPLRPSQISYAALDAFCLLQVYQV 63 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK--~~q~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~~ 63 (94)
+.+|..+++++||..-.. ....++|...+. ..=++|...||.....|+.+
T Consensus 272 SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~-~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 272 SYRLDYIAEVELGKKKLDYSDGPFKKFRETDH-QKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred cCCHHHHHHHHhCCCCccCCHHHHHHHHhcCH-HHHHHHHHHHHHHHHHHHHH
Confidence 688999999999974433 124444443332 44599999999999999988
No 71
>PF11567 PfUIS3: Plasmodium falciparum UIS3 membrane protein; InterPro: IPR021626 UIS3 is a membrane protein essential for sporozoite development in infected hepatocytes. This family is 130-229 of the Plasmodium falciparum UIS3 protein which is compact and has an all alpha-helical structure.PfUIS3(130-229) interacts with lipids, phospholipid lysosomes, the human liver fatty acid-binding protein and with the lipid phosphatidylethanolamine. The interaction with liver fatty acid-binding protein provides the parasite with a method to import essential fatty acids/lipids during rapid growth phases of sporozoites []. ; PDB: 2VWA_C.
Probab=21.30 E-value=1.5e+02 Score=19.47 Aligned_cols=27 Identities=22% Similarity=0.224 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHHHHH
Q psy12569 41 PLRPSQISYAALDAFCLLQVYQVLHDQ 67 (94)
Q Consensus 41 pLt~~Qi~YAA~Dv~~l~~l~~~l~~~ 67 (94)
.||.+|-.|-.+|--|+..+-+.|.+.
T Consensus 41 ~LSn~Qq~y~ind~dY~rkiVQ~L~E~ 67 (101)
T PF11567_consen 41 NLSNEQQKYLINDYDYIRKIVQTLDEN 67 (101)
T ss_dssp HS-HHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred hcCcHHHHHHhchHHHHHHHHHHHHhc
Confidence 489999999999999998888777663
No 72
>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=20.96 E-value=1.5e+02 Score=21.43 Aligned_cols=48 Identities=19% Similarity=0.212 Sum_probs=33.7
Q ss_pred CccHHHHHHHHhCCccCCc-c-c-ccCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q psy12569 13 PQSLSTLVLKCFGKTLNKQ-D-Q-FSNWENRPLRPSQISYAALDAFCLLQVYQ 62 (94)
Q Consensus 13 ~~sL~~lv~~~lg~~ldK~-~-q-~SdW~~rpLt~~Qi~YAA~Dv~~l~~l~~ 62 (94)
+.+|..+++.+||..-..- . . ..=|...| +.=++|...||.....||.
T Consensus 154 sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 154 SQGLKAVTKAKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred CccHHHHHHHHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 6889999999999732111 1 1 11455544 5669999999999998873
No 73
>PRK12607 phosphoribosylaminoimidazole-succinocarboxamide synthase; Provisional
Probab=20.56 E-value=3.6e+02 Score=21.25 Aligned_cols=46 Identities=15% Similarity=0.128 Sum_probs=32.9
Q ss_pred ccCC--CCCCCCHHHHHH--------HHHhHHHHHHHHHHHHHHHHHcCCCchhhH
Q psy12569 34 FSNW--ENRPLRPSQISY--------AALDAFCLLQVYQVLHDQCARQGIELGPLL 79 (94)
Q Consensus 34 ~SdW--~~rpLt~~Qi~Y--------AA~Dv~~l~~l~~~l~~~l~~~~~~~~e~~ 79 (94)
..+. ..+++|.+++.- +..=.-..+.||..+.+...+.|+.+-++.
T Consensus 145 K~d~g~hD~~Is~~~~~~~~~~~~~~~~~i~~~al~i~~~~~~~~~~~GiiLvD~K 200 (313)
T PRK12607 145 KAEEGGHDEPISPEEILAQGLLTPEDWDELSKYALALFARGQEMAAERGLILVDTK 200 (313)
T ss_pred cCcccCCCCCCCHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEe
Confidence 4677 778999999732 222234678899999999999998765543
No 74
>PF12720 DUF3807: Protein of unknown function (DUF3807); InterPro: IPR024526 This is a family of conserved fungal proteins of unknown function.
Probab=20.01 E-value=65 Score=23.17 Aligned_cols=15 Identities=27% Similarity=0.264 Sum_probs=12.0
Q ss_pred cCCCCCCCCHHHHHH
Q psy12569 35 SNWENRPLRPSQISY 49 (94)
Q Consensus 35 SdW~~rpLt~~Qi~Y 49 (94)
.|=..|-||++||+.
T Consensus 43 pDGVKRTLTDEQI~I 57 (172)
T PF12720_consen 43 PDGVKRTLTDEQIEI 57 (172)
T ss_pred CCCCcccccHHHHHH
Confidence 455679999999974
Done!