Query psy12568
Match_columns 114
No_of_seqs 114 out of 1033
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 22:41:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12568.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12568hhsearch_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 1.1E-21 2.3E-26 161.8 8.6 108 5-112 105-213 (361)
2 PRK10829 ribonuclease D; Provi 99.8 2.9E-20 6.3E-25 153.7 8.9 104 6-111 110-216 (373)
3 cd06146 mut-7_like_exo DEDDy 3 99.7 9.9E-18 2.1E-22 126.4 6.6 56 9-64 138-193 (193)
4 cd06129 RNaseD_like DEDDy 3'-5 99.7 3.3E-17 7.1E-22 119.5 7.0 54 10-63 107-160 (161)
5 cd06141 WRN_exo DEDDy 3'-5' ex 99.6 9.7E-16 2.1E-20 111.3 6.8 53 11-63 115-169 (170)
6 TIGR01388 rnd ribonuclease D. 99.6 2.6E-15 5.5E-20 123.5 8.5 101 8-110 108-211 (367)
7 cd06148 Egl_like_exo DEDDy 3'- 99.5 7.2E-15 1.6E-19 110.8 5.8 60 11-70 114-181 (197)
8 PF01612 DNA_pol_A_exo1: 3'-5' 99.3 1.6E-12 3.5E-17 92.7 4.6 56 12-67 119-176 (176)
9 cd06142 RNaseD_exo DEDDy 3'-5' 99.0 2.7E-09 5.9E-14 76.8 8.6 60 11-70 105-164 (178)
10 KOG2207|consensus 98.9 6.1E-10 1.3E-14 97.1 4.1 57 11-67 530-586 (617)
11 PRK14975 bifunctional 3'-5' ex 98.7 2.4E-08 5.2E-13 86.0 6.8 58 11-69 90-147 (553)
12 KOG2206|consensus 98.7 2.1E-08 4.7E-13 87.8 5.1 63 10-72 304-366 (687)
13 smart00474 35EXOc 3'-5' exonuc 98.6 2E-07 4.3E-12 65.6 7.0 55 12-66 117-171 (172)
14 cd06147 Rrp6p_like_exo DEDDy 3 98.4 8.9E-07 1.9E-11 65.8 7.1 63 12-74 118-180 (192)
15 cd00007 35EXOc 3'-5' exonuclea 98.2 2.1E-06 4.5E-11 59.3 5.1 55 11-65 96-154 (155)
16 KOG4373|consensus 98.2 1.7E-06 3.7E-11 71.1 4.9 60 9-70 229-290 (319)
17 cd09018 DEDDy_polA_RNaseD_like 98.0 1.4E-05 3.1E-10 55.6 4.9 52 12-63 96-149 (150)
18 cd06140 DNA_polA_I_Bacillus_li 97.6 0.00022 4.7E-09 51.6 6.2 59 12-70 99-160 (178)
19 cd06139 DNA_polA_I_Ecoli_like_ 97.4 0.00069 1.5E-08 49.0 6.9 57 11-68 109-172 (193)
20 PRK05755 DNA polymerase I; Pro 96.9 0.0024 5.3E-08 58.0 6.4 54 12-69 412-472 (880)
21 TIGR00593 pola DNA polymerase 89.9 1.1 2.4E-05 41.5 6.8 59 12-70 420-481 (887)
22 COG0749 PolA DNA polymerase I 62.5 20 0.00044 32.2 5.6 60 11-70 119-184 (593)
23 KOG2249|consensus 61.1 22 0.00048 29.2 5.2 47 9-70 224-270 (280)
24 cd05160 DEDDy_DNA_polB_exo DED 49.3 43 0.00094 24.4 4.8 50 10-59 147-198 (199)
25 TIGR01298 RNaseT ribonuclease 49.0 26 0.00055 26.4 3.6 30 43-72 169-199 (200)
26 cd05780 DNA_polB_Kod1_like_exo 48.7 25 0.00054 26.1 3.5 52 10-61 140-194 (195)
27 cd06143 PAN2_exo DEDDh 3'-5' e 45.4 36 0.00078 25.9 3.9 35 10-59 139-173 (174)
28 cd05777 DNA_polB_delta_exo DED 43.6 33 0.00071 26.2 3.5 55 10-64 167-225 (230)
29 KOG2405|consensus 42.5 33 0.00071 29.8 3.5 34 33-66 328-361 (458)
30 KOG2207|consensus 42.3 23 0.00049 32.1 2.7 53 17-69 192-246 (617)
31 cd05784 DNA_polB_II_exo DEDDy 40.7 42 0.0009 25.3 3.6 49 10-60 138-193 (193)
32 PRK05168 ribonuclease T; Provi 37.1 50 0.0011 25.0 3.6 27 45-71 180-206 (211)
33 KOG3657|consensus 36.3 46 0.001 31.7 3.7 56 10-68 321-385 (1075)
34 cd06144 REX4_like DEDDh 3'-5' 36.1 51 0.0011 23.4 3.3 37 9-60 116-152 (152)
35 PRK08517 DNA polymerase III su 32.7 1E+02 0.0022 24.4 4.8 54 11-81 193-246 (257)
36 PHA02573 30.3 hypothetical pro 29.5 2.2E+02 0.0049 21.0 5.9 49 20-68 60-112 (148)
37 PF10584 Proteasome_A_N: Prote 29.3 30 0.00066 18.1 0.9 7 43-49 15-21 (23)
38 cd06137 DEDDh_RNase DEDDh 3'-5 27.0 1.2E+02 0.0026 21.7 4.0 37 10-59 124-160 (161)
39 cd05778 DNA_polB_zeta_exo inac 26.5 75 0.0016 24.4 3.0 50 10-59 176-230 (231)
40 PF13482 RNase_H_2: RNase_H su 25.1 1.1E+02 0.0025 21.3 3.5 52 10-62 101-163 (164)
41 PRK07942 DNA polymerase III su 24.8 1.4E+02 0.003 23.0 4.2 30 48-77 162-192 (232)
42 PF09355 Phage_Gp19: Phage pro 24.2 2.4E+02 0.0052 19.8 5.0 36 37-75 2-37 (116)
43 PRK07740 hypothetical protein; 24.1 1.5E+02 0.0033 23.0 4.3 46 10-72 187-232 (244)
44 KOG1275|consensus 22.4 2E+02 0.0044 27.8 5.4 61 10-86 1051-1111(1118)
45 COG1327 Predicted transcriptio 22.3 2.5E+02 0.0054 21.3 5.0 35 36-70 75-120 (156)
46 TIGR00244 transcriptional regu 22.0 2.7E+02 0.0059 20.8 5.1 35 36-70 75-120 (147)
47 PRK07983 exodeoxyribonuclease 20.8 2E+02 0.0042 22.1 4.3 33 46-81 134-166 (219)
48 TIGR01405 polC_Gram_pos DNA po 20.5 2.8E+02 0.0061 27.2 6.0 46 10-72 316-361 (1213)
No 1
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.86 E-value=1.1e-21 Score=161.84 Aligned_cols=108 Identities=25% Similarity=0.313 Sum_probs=94.1
Q ss_pred cccCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCC-hhhhhHHHHhc
Q psy12568 5 ESQQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIE-LGPLLTEVLSS 83 (114)
Q Consensus 5 ~~~~~~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~~~-~~e~~~~~~~~ 83 (114)
.|+++.++||++||++++|+++||++|.|||.+||||++|++|||.||+||+.||.+|.+++.+.|+. +.+.+..+...
T Consensus 105 l~g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~~l~~ 184 (361)
T COG0349 105 LAGFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFRLLPT 184 (361)
T ss_pred HhCCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHhhh
Confidence 46788899999999999999999999999999999999999999999999999999999999999954 44445555555
Q ss_pred ccccccccccceecccccccchhhhhhhh
Q psy12568 84 HAVTTKKSTILYFSTVSGLDTKEHRQLCL 112 (114)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 (114)
++....-|...|.++...++++.++..|+
T Consensus 185 r~~~~~~~~~~w~~i~~a~~~~p~~la~l 213 (361)
T COG0349 185 RRTYKVLPEDAWREIKIAHSLDPRELAVL 213 (361)
T ss_pred ccccccChHhHHHHhhhhhcCChHHHHHH
Confidence 65556678888988887899999998886
No 2
>PRK10829 ribonuclease D; Provisional
Probab=99.82 E-value=2.9e-20 Score=153.66 Aligned_cols=104 Identities=21% Similarity=0.315 Sum_probs=84.8
Q ss_pred ccCCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC---CChhhhhHHHHh
Q psy12568 6 SQQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG---IELGPLLTEVLS 82 (114)
Q Consensus 6 ~~~~~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~---~~~~e~~~~~~~ 82 (114)
++++.++||+.||+++||++++|++|+|||+.||||++|+.|||.||+||+.||..|.+++++.| |..+| |+.+.+
T Consensus 110 lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee-~~~l~~ 188 (373)
T PRK10829 110 CGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDE-CRLLCQ 188 (373)
T ss_pred cCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHH-HHHHHh
Confidence 45556799999999999999999999999999999999999999999999999999999999988 33444 444332
Q ss_pred cccccccccccceecccccccchhhhhhh
Q psy12568 83 SHAVTTKKSTILYFSTVSGLDTKEHRQLC 111 (114)
Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 (114)
. ......|...|.+.+..+.|+.+++..
T Consensus 189 ~-~~~~~~~~~~~~~ik~~~~L~~~~lav 216 (373)
T PRK10829 189 R-RQEVLAPEEAYRDITNAWQLRTRQLAC 216 (373)
T ss_pred c-cccCCChHHHHHHhccccCCCHHHHHH
Confidence 2 223445667788999889998666543
No 3
>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=99.72 E-value=9.9e-18 Score=126.37 Aligned_cols=56 Identities=52% Similarity=0.908 Sum_probs=53.1
Q ss_pred CCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHH
Q psy12568 9 GSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHD 64 (114)
Q Consensus 9 ~~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~ 64 (114)
..+.||++|++.+||++++|+.|+|||++||||++||.|||.||++++.||++|.+
T Consensus 138 ~~~~sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 138 SKTKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred cccCCHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 35789999999999999999999999999999999999999999999999999863
No 4
>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=99.70 E-value=3.3e-17 Score=119.48 Aligned_cols=54 Identities=41% Similarity=0.629 Sum_probs=51.8
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q psy12568 10 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLH 63 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~ 63 (114)
.+.||+.++++++|++++|+.|+|||+.||||++|+.|||.||++++.||++|+
T Consensus 107 ~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 107 ERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred CCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 467999999999999999999999999999999999999999999999999885
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=99.62 E-value=9.7e-16 Score=111.27 Aligned_cols=53 Identities=45% Similarity=0.667 Sum_probs=50.2
Q ss_pred CccHHHHHHHHhCCccC--CcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q psy12568 11 PQSLSTLVLKCFGKTLN--KQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLH 63 (114)
Q Consensus 11 ~~sL~~Lv~~~lg~~ld--K~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~ 63 (114)
+.||+.+++.++|++++ |..|+|||..||||++||.|||.||++++.||+.|.
T Consensus 115 ~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 115 LVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 46999999999999999 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=99.60 E-value=2.6e-15 Score=123.45 Aligned_cols=101 Identities=21% Similarity=0.295 Sum_probs=81.6
Q ss_pred CCCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC---CChhhhhHHHHhcc
Q psy12568 8 QGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG---IELGPLLTEVLSSH 84 (114)
Q Consensus 8 ~~~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~---~~~~e~~~~~~~~~ 84 (114)
.+..+||+.|++++||++++|+++.|||..|||+++|+.|||.||++++.||..|.+++++.| |..+| |+.+.+.
T Consensus 108 ~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee-~~~l~~~- 185 (367)
T TIGR01388 108 FGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEE-CTLLTDR- 185 (367)
T ss_pred CCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHH-HHHHhcc-
Confidence 344679999999999999999999999999999999999999999999999999999999988 33444 4443322
Q ss_pred cccccccccceecccccccchhhhhh
Q psy12568 85 AVTTKKSTILYFSTVSGLDTKEHRQL 110 (114)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 (114)
......|...|.+.+..+.|+..++.
T Consensus 186 ~~~~~~~~~~~~~i~~~~~l~~~~l~ 211 (367)
T TIGR01388 186 RTYVVNPEDAWRDIKNAWQLRPQQLA 211 (367)
T ss_pred ccCCCChHHHHHHhcccccCCHHHHH
Confidence 22334567778888888888766554
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=99.55 E-value=7.2e-15 Score=110.83 Aligned_cols=60 Identities=32% Similarity=0.464 Sum_probs=55.6
Q ss_pred CccHHHHHHHHhCCccCC--------cccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12568 11 PQSLSTLVLKCFGKTLNK--------QDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 70 (114)
Q Consensus 11 ~~sL~~Lv~~~lg~~ldK--------~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~ 70 (114)
.+||+++++.++|++++| ..++|||..||||++|+.|||.||++|+.||+.|...+.+..
T Consensus 114 ~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~~ 181 (197)
T cd06148 114 VISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISKF 181 (197)
T ss_pred cccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhhH
Confidence 479999999999999976 457899999999999999999999999999999999998765
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=99.32 E-value=1.6e-12 Score=92.67 Aligned_cols=56 Identities=39% Similarity=0.640 Sum_probs=51.6
Q ss_pred ccHHHHHHHHhC-CccCCcccccCCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy12568 12 QSLSTLVLKCFG-KTLNKQDQFSNWE-NRPLRPSQISYAALDAFCLLQVYQVLHDQCA 67 (114)
Q Consensus 12 ~sL~~Lv~~~lg-~~ldK~~q~SdW~-~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~ 67 (114)
.||++|+.+++| ..++|+.+++||. .+||+++|+.|||.||++++.||+.|.++|+
T Consensus 119 ~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 119 YSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp SSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred ccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 899999999999 8888999999999 9999999999999999999999999999873
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=99.00 E-value=2.7e-09 Score=76.77 Aligned_cols=60 Identities=38% Similarity=0.661 Sum_probs=56.5
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12568 11 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 70 (114)
Q Consensus 11 ~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~ 70 (114)
+.||..++++++|.++.|+.++++|..+||+.+|+.||+.||.+++.++..+.+++++.|
T Consensus 105 ~~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~ 164 (178)
T cd06142 105 SVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEG 164 (178)
T ss_pred cccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Confidence 359999999999999888779999999999999999999999999999999999999987
No 10
>KOG2207|consensus
Probab=98.94 E-value=6.1e-10 Score=97.07 Aligned_cols=57 Identities=42% Similarity=0.673 Sum_probs=54.5
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy12568 11 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCA 67 (114)
Q Consensus 11 ~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~ 67 (114)
.-+|+.|...++|..++|++|+|||..|||+..||.|||.|+.+++.+|.++.+...
T Consensus 530 ~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 530 TKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred hhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 457999999999999999999999999999999999999999999999999998876
No 11
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=98.73 E-value=2.4e-08 Score=86.00 Aligned_cols=58 Identities=40% Similarity=0.481 Sum_probs=55.3
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHc
Q psy12568 11 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQ 69 (114)
Q Consensus 11 ~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~ 69 (114)
..||+.++..++|+.++|..+.|||. |||+++|+.||+.||.++..||..+.+++++.
T Consensus 90 ~~~l~~la~~~l~~~l~k~~~~sdw~-rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 90 GSSLSAAAARALGEGLDKPPQTSALS-DPPDEEQLLYAAADADVLLELYAVLADQLNRI 147 (553)
T ss_pred CCCHHHHHHHHhCCCCCChhhhcccc-ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence 68999999999999999999999997 99999999999999999999999999999765
No 12
>KOG2206|consensus
Probab=98.68 E-value=2.1e-08 Score=87.77 Aligned_cols=63 Identities=32% Similarity=0.464 Sum_probs=59.4
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCC
Q psy12568 10 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIE 72 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~~~ 72 (114)
...||+-|.+.++|+-.+|++|..||..|||+++++.||..|.+|++.||+.|+..+.+.+..
T Consensus 304 ~r~sL~~ll~~~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~~ 366 (687)
T KOG2206|consen 304 PRPSLAYLLECVCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAKG 366 (687)
T ss_pred CcccHHHHHHHHHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhcc
Confidence 468999999999999999999999999999999999999999999999999999999887733
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=98.59 E-value=2e-07 Score=65.61 Aligned_cols=55 Identities=40% Similarity=0.665 Sum_probs=50.7
Q ss_pred ccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q psy12568 12 QSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQC 66 (114)
Q Consensus 12 ~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l 66 (114)
.||+.++.+++|..++|..+.++|..+||.++|+.||+.||++++.|+..+.+++
T Consensus 117 ~~l~~l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 117 HGLATLLKEYLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred CCHHHHHHHHhCCCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5999999999999987766778998899999999999999999999999999876
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=98.42 E-value=8.9e-07 Score=65.78 Aligned_cols=63 Identities=30% Similarity=0.476 Sum_probs=56.4
Q ss_pred ccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCChh
Q psy12568 12 QSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELG 74 (114)
Q Consensus 12 ~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~~~~~ 74 (114)
.+|..++++++|..++|+.+.|||..+||+.+|..||+.|+.++..|+..|..+++++...++
T Consensus 118 ~~l~~l~~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~~~~~~ 180 (192)
T cd06147 118 HSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERANALA 180 (192)
T ss_pred ccHHHHHHHHhCCCcchhhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHhccccc
Confidence 499999999999876565678899988999999999999999999999999999988886655
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=98.25 E-value=2.1e-06 Score=59.31 Aligned_cols=55 Identities=35% Similarity=0.508 Sum_probs=46.3
Q ss_pred CccHHHHHHHHhCCccCCcccccCCC----CCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Q psy12568 11 PQSLSTLVLKCFGKTLNKQDQFSNWE----NRPLRPSQISYAALDAFCLLQVYQVLHDQ 65 (114)
Q Consensus 11 ~~sL~~Lv~~~lg~~ldK~~q~SdW~----~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~ 65 (114)
..||+.++++++|..+.+..+.++|. .+|++.+|+.||+.|+.+++.|+..+.++
T Consensus 96 ~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 96 SHSLDDLAKEYLGIELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred cCCHHHHHHHHcCCCCccHHHHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 35999999999999876544455653 58899999999999999999999998875
No 16
>KOG4373|consensus
Probab=98.22 E-value=1.7e-06 Score=71.06 Aligned_cols=60 Identities=20% Similarity=0.335 Sum_probs=45.2
Q ss_pred CCCccHHHHHHHHhC--CccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12568 9 GSPQSLSTLVLKCFG--KTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 70 (114)
Q Consensus 9 ~~~~sL~~Lv~~~lg--~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~ 70 (114)
....++......+-| +.++|.-++|||+..||+.+||.||+.||+....++ ..+++.+..
T Consensus 229 ~s~e~i~~~~~~~~~~~v~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg--~~~~~w~~~ 290 (319)
T KOG4373|consen 229 DSFEEIVSETLGYYGKDVRLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLG--VLERLWEVK 290 (319)
T ss_pred ccHHHHHHHHhhccccccccChhcccccceeeeccHHHHHHHHhHHHHHHHHH--HHHHHHHHh
Confidence 334555555556666 455666699999999999999999999999999999 344444444
No 17
>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=97.96 E-value=1.4e-05 Score=55.58 Aligned_cols=52 Identities=35% Similarity=0.385 Sum_probs=43.7
Q ss_pred ccHHHHHHHHhCCccCC-cc-cccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q psy12568 12 QSLSTLVLKCFGKTLNK-QD-QFSNWENRPLRPSQISYAALDAFCLLQVYQVLH 63 (114)
Q Consensus 12 ~sL~~Lv~~~lg~~ldK-~~-q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~ 63 (114)
.+|..++++++|+.+.| +. ..++|..+|++.+|+.||+.||.++..|+..|.
T Consensus 96 ~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 96 WDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred CCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 59999999999999765 32 234596689999999999999999999998874
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=97.59 E-value=0.00022 Score=51.62 Aligned_cols=59 Identities=14% Similarity=0.151 Sum_probs=49.4
Q ss_pred ccHHHHHHHHhCCccCCcccccCCC---CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12568 12 QSLSTLVLKCFGKTLNKQDQFSNWE---NRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 70 (114)
Q Consensus 12 ~sL~~Lv~~~lg~~ldK~~q~SdW~---~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~ 70 (114)
.++.+++.+++|+++.+..+.+.|. .++..+.|..||+.||.++..++..+.+++++.+
T Consensus 99 ~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~ 160 (178)
T cd06140 99 YDLADLAKRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEENE 160 (178)
T ss_pred CCHHHHHHHHcCCCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 5999999999999987644455552 3566777899999999999999999999998875
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=97.41 E-value=0.00069 Score=49.03 Aligned_cols=57 Identities=25% Similarity=0.383 Sum_probs=46.5
Q ss_pred CccHHHHHHHHhCCcc-------CCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q psy12568 11 PQSLSTLVLKCFGKTL-------NKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCAR 68 (114)
Q Consensus 11 ~~sL~~Lv~~~lg~~l-------dK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~ 68 (114)
..||..++++++|..+ .|+.+..+|...|+ ..+..||+.|+.++..|+..+.+++.+
T Consensus 109 ~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 109 RHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred CCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4699999999998763 23345566765566 779999999999999999999999977
No 20
>PRK05755 DNA polymerase I; Provisional
Probab=96.88 E-value=0.0024 Score=57.96 Aligned_cols=54 Identities=28% Similarity=0.327 Sum_probs=45.2
Q ss_pred ccHHHHHHHHhCCccC-------CcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHc
Q psy12568 12 QSLSTLVLKCFGKTLN-------KQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQ 69 (114)
Q Consensus 12 ~sL~~Lv~~~lg~~ld-------K~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~ 69 (114)
.||+.+++.++|+++. |..+.++| |+ +.|..||+.||.+++.||..+.+++.+.
T Consensus 412 ~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~---pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~ 472 (880)
T PRK05755 412 HGLDSLAERYLGHKTISFEEVAGKQLTFAQV---DL-EEAAEYAAEDADVTLRLHEVLKPKLLEE 472 (880)
T ss_pred CCHHHHHHHHhCCCccchHHhcCCCCCcccc---CH-HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 8999999999998852 33344444 77 5899999999999999999999998775
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=89.87 E-value=1.1 Score=41.54 Aligned_cols=59 Identities=14% Similarity=0.047 Sum_probs=42.7
Q ss_pred ccHHHHHHHHhCCccCCcccccCCC--CCCCC-HHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12568 12 QSLSTLVLKCFGKTLNKQDQFSNWE--NRPLR-PSQISYAALDAFCLLQVYQVLHDQCARQG 70 (114)
Q Consensus 12 ~sL~~Lv~~~lg~~ldK~~q~SdW~--~RPLs-~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~ 70 (114)
.||..++.+++|.++.+......|. ...++ +.+..||+.||.+.+.||..+.+++.+.+
T Consensus 420 ~~l~~la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~ 481 (887)
T TIGR00593 420 STLDTLARRYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELDENK 481 (887)
T ss_pred CCHHHHHHHHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4999999999998765422222221 11333 34578999999999999999999997654
No 22
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=62.46 E-value=20 Score=32.21 Aligned_cols=60 Identities=17% Similarity=0.212 Sum_probs=40.8
Q ss_pred CccHHHHHHHHhCCccCCcccc-----cCCCCCCCC-HHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12568 11 PQSLSTLVLKCFGKTLNKQDQF-----SNWENRPLR-PSQISYAALDAFCLLQVYQVLHDQCARQG 70 (114)
Q Consensus 11 ~~sL~~Lv~~~lg~~ldK~~q~-----SdW~~RPLs-~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~ 70 (114)
..++.+|++++++.+.-..+.. ++=+..-.. +.-..|||.||...+.++..+..++.+..
T Consensus 119 ~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~~ 184 (593)
T COG0749 119 AHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLKTP 184 (593)
T ss_pred cCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 4789999999999765433211 111111122 34499999999999999999998765543
No 23
>KOG2249|consensus
Probab=61.07 E-value=22 Score=29.17 Aligned_cols=47 Identities=21% Similarity=0.262 Sum_probs=39.5
Q ss_pred CCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcC
Q psy12568 9 GSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 70 (114)
Q Consensus 9 ~~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~ 70 (114)
+...||..|.+.+||.++--.+..| .-||.+.+.||..+..++.+..
T Consensus 224 ~~tpSLK~Lt~~~Lg~~IQ~GeHsS---------------vEDA~AtM~LY~~vk~qwe~~~ 270 (280)
T KOG2249|consen 224 KATPSLKKLTEALLGKDIQVGEHSS---------------VEDARATMELYKRVKVQWEKIE 270 (280)
T ss_pred cCCccHHHHHHHHhchhhhccccCc---------------HHHHHHHHHHHHHHHHHHHHHh
Confidence 4568999999999999998777544 6899999999999998876654
No 24
>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=49.32 E-value=43 Score=24.42 Aligned_cols=50 Identities=20% Similarity=0.174 Sum_probs=34.6
Q ss_pred CCccHHHHHHHHhCCccCC--cccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q psy12568 10 SPQSLSTLVLKCFGKTLNK--QDQFSNWENRPLRPSQISYAALDAFCLLQVY 59 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK--~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~ 59 (114)
...+|..+++.++|.+-.. .....+|....--..-++|...||...+.|+
T Consensus 147 ~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 147 KSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred ccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 4578999999999974222 1145554222334556999999999998886
No 25
>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=49.01 E-value=26 Score=26.37 Aligned_cols=30 Identities=17% Similarity=0.151 Sum_probs=25.5
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHcC-CC
Q psy12568 43 SQISYAALDAFCLLQVYQVLHDQCARQG-IE 72 (114)
Q Consensus 43 ~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~-~~ 72 (114)
.+-.=|..||.....|+..+.+++.+.| |+
T Consensus 169 ~~~H~Al~Da~ata~lf~~l~~~~~~~~~~~ 199 (200)
T TIGR01298 169 TQAHSALYDTEKTAELFCEIVNRWKRLGGWP 199 (200)
T ss_pred cchhhhHHhHHHHHHHHHHHHHHHHHccCCC
Confidence 4566688999999999999999998877 54
No 26
>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=48.74 E-value=25 Score=26.11 Aligned_cols=52 Identities=13% Similarity=0.241 Sum_probs=37.3
Q ss_pred CCccHHHHHHHHhCCccCC-c-ccccC-CCCCCCCHHHHHHHHHhHHHHHHHHHH
Q psy12568 10 SPQSLSTLVLKCFGKTLNK-Q-DQFSN-WENRPLRPSQISYAALDAFCLLQVYQV 61 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK-~-~q~Sd-W~~RPLs~~Qi~YAA~Dv~~ll~l~~~ 61 (114)
...+|..+++.+||.+-.. + .+.+. |...+--..-++|+..||...+.|...
T Consensus 140 ~sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~ 194 (195)
T cd05780 140 TRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKE 194 (195)
T ss_pred CcCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhh
Confidence 4678999999999986321 1 13333 444445566799999999999998765
No 27
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=45.41 E-value=36 Score=25.89 Aligned_cols=35 Identities=23% Similarity=0.267 Sum_probs=26.8
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q psy12568 10 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVY 59 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~ 59 (114)
.++||+.|++++||.++....-. ..-||.+.+.||
T Consensus 139 r~~sLk~La~~~L~~~IQ~~~Hd---------------SvEDArAam~Ly 173 (174)
T cd06143 139 RKLSLRFLAWYLLGEKIQSETHD---------------SIEDARTALKLY 173 (174)
T ss_pred CChhHHHHHHHHcCCcccCCCcC---------------cHHHHHHHHHHh
Confidence 36899999999999998753211 267888888887
No 28
>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=43.60 E-value=33 Score=26.21 Aligned_cols=55 Identities=16% Similarity=0.239 Sum_probs=38.6
Q ss_pred CCccHHHHHHHHhCCccC-Cc-ccccCCC-CCCCC-HHHHHHHHHhHHHHHHHHHHHHH
Q psy12568 10 SPQSLSTLVLKCFGKTLN-KQ-DQFSNWE-NRPLR-PSQISYAALDAFCLLQVYQVLHD 64 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ld-K~-~q~SdW~-~RPLs-~~Qi~YAA~Dv~~ll~l~~~l~~ 64 (114)
...+|..+++.+||.+-. =+ ...++|. ..|=. ..-++|...||...+.|+.++.-
T Consensus 167 ~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~~ 225 (230)
T cd05777 167 RSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMC 225 (230)
T ss_pred ccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHhh
Confidence 467899999999996532 12 2344443 23322 34599999999999999988764
No 29
>KOG2405|consensus
Probab=42.54 E-value=33 Score=29.83 Aligned_cols=34 Identities=24% Similarity=0.425 Sum_probs=29.9
Q ss_pred cCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Q psy12568 33 SNWENRPLRPSQISYAALDAFCLLQVYQVLHDQC 66 (114)
Q Consensus 33 SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l 66 (114)
-+|..||.++....-++.||.+|+.++..+....
T Consensus 328 ~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a~~ 361 (458)
T KOG2405|consen 328 PRWVIRPSTEIADHLLHRDVISLLGIFDTLVAVC 361 (458)
T ss_pred CcceecccHHHHHHHHHHHHHHHHHHHhhHhhhC
Confidence 3799999999999999999999999887666653
No 30
>KOG2207|consensus
Probab=42.31 E-value=23 Score=32.06 Aligned_cols=53 Identities=15% Similarity=0.063 Sum_probs=44.8
Q ss_pred HHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHH--HHHHHHHHHHHc
Q psy12568 17 LVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQ--VYQVLHDQCARQ 69 (114)
Q Consensus 17 Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~--l~~~l~~~l~~~ 69 (114)
+....+..-+.|+.|+++|..+++++.|.-|+..+...+.. ++..+.+.+.+.
T Consensus 192 ~e~~~ldlIls~k~q~a~~ll~~~~~~q~p~v~fld~~v~~~~~v~e~~~~~~e~ 246 (617)
T KOG2207|consen 192 FEQLMLDLILSKKLQIADELLRHLTELQKPYVEFLDQMVLDNFIVDERCAHLLER 246 (617)
T ss_pred HHHHhccHhhccchhHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34556666677888999999999999999999999999999 777777777666
No 31
>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=40.67 E-value=42 Score=25.35 Aligned_cols=49 Identities=10% Similarity=0.148 Sum_probs=33.7
Q ss_pred CCccHHHHHHHHhCCccCC-cc-----ccc-CCCCCCCCHHHHHHHHHhHHHHHHHHH
Q psy12568 10 SPQSLSTLVLKCFGKTLNK-QD-----QFS-NWENRPLRPSQISYAALDAFCLLQVYQ 60 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK-~~-----q~S-dW~~RPLs~~Qi~YAA~Dv~~ll~l~~ 60 (114)
.+.+|..+++.+||..-+. .. ..+ -|...+ ..-++|...||...++|++
T Consensus 138 ~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 138 ESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred CcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 4678999999999974221 11 111 244333 4669999999999998873
No 32
>PRK05168 ribonuclease T; Provisional
Probab=37.11 E-value=50 Score=25.00 Aligned_cols=27 Identities=15% Similarity=0.089 Sum_probs=23.3
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHcCC
Q psy12568 45 ISYAALDAFCLLQVYQVLHDQCARQGI 71 (114)
Q Consensus 45 i~YAA~Dv~~ll~l~~~l~~~l~~~~~ 71 (114)
-.=|..||.....||..+.+++.+.|.
T Consensus 180 ~H~Al~DA~ata~l~~~l~~~~~~~~~ 206 (211)
T PRK05168 180 AHSALYDTEKTAELFCEIVNRWKRLGG 206 (211)
T ss_pred CCChHHHHHHHHHHHHHHHHHHHHccC
Confidence 344789999999999999999988874
No 33
>KOG3657|consensus
Probab=36.26 E-value=46 Score=31.68 Aligned_cols=56 Identities=25% Similarity=0.148 Sum_probs=43.0
Q ss_pred CCccHHHHHHHHhCCc-cCCcccccCCCCCCCCHHH--------HHHHHHhHHHHHHHHHHHHHHHHH
Q psy12568 10 SPQSLSTLVLKCFGKT-LNKQDQFSNWENRPLRPSQ--------ISYAALDAFCLLQVYQVLHDQCAR 68 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~-ldK~~q~SdW~~RPLs~~Q--------i~YAA~Dv~~ll~l~~~l~~~l~~ 68 (114)
.-.||.++.+-+||+. ++|+.+-+.= .++.+| +.|-|.||+...+||..+.-...+
T Consensus 321 S~NSL~dVhk~~c~~~~LdKt~Rd~Fv---s~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fle 385 (1075)
T KOG3657|consen 321 SLNSLVDVHKFHCGIDALDKTPRDSFV---SGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLE 385 (1075)
T ss_pred hhHHHHHHHHhhCCCCccccchHHhhh---cCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHH
Confidence 3467899999999999 9998754322 234444 579999999999999998877655
No 34
>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=36.12 E-value=51 Score=23.36 Aligned_cols=37 Identities=22% Similarity=0.389 Sum_probs=26.7
Q ss_pred CCCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q psy12568 9 GSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQ 60 (114)
Q Consensus 9 ~~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~ 60 (114)
..+.||+.|++.++|+++.... .=|..||.....||+
T Consensus 116 ~~~~sL~~l~~~~lgi~~~~~~---------------H~Al~DA~at~~l~~ 152 (152)
T cd06144 116 GKSPSLKKLAKQLLGLDIQEGE---------------HSSVEDARAAMRLYR 152 (152)
T ss_pred CCChhHHHHHHHHcCcccCCCC---------------cCcHHHHHHHHHHhC
Confidence 3578999999999998775321 115778888887763
No 35
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=32.66 E-value=1e+02 Score=24.39 Aligned_cols=54 Identities=15% Similarity=0.063 Sum_probs=34.5
Q ss_pred CccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCChhhhhHHHH
Q psy12568 11 PQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGPLLTEVL 81 (114)
Q Consensus 11 ~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~~~~~e~~~~~~ 81 (114)
+.||..+++ .+|++.+.. .=|..||.....|+..+..++...-...+++.+...
T Consensus 193 ~~~L~~L~~-~lgi~~~~~----------------HrAl~DA~ata~ll~~ll~~~~~~~~t~~~L~~~~k 246 (257)
T PRK08517 193 RYGLSFLKE-LLGIEIEVH----------------HRAYADALAAYEIFKICLLNLPSYIKTTEDLIDFSK 246 (257)
T ss_pred CCCHHHHHH-HcCcCCCCC----------------CChHHHHHHHHHHHHHHHHHhHHhhcCHHHHHHHhh
Confidence 456666665 456654422 337899999999999999888654333444444433
No 36
>PHA02573 30.3 hypothetical protein; Provisional
Probab=29.54 E-value=2.2e+02 Score=21.01 Aligned_cols=49 Identities=14% Similarity=0.203 Sum_probs=28.8
Q ss_pred HHhCCccCCc-ccccCCCCCCCCHHHHHH-HHHhHHHHHHH--HHHHHHHHHH
Q psy12568 20 KCFGKTLNKQ-DQFSNWENRPLRPSQISY-AALDAFCLLQV--YQVLHDQCAR 68 (114)
Q Consensus 20 ~~lg~~ldK~-~q~SdW~~RPLs~~Qi~Y-AA~Dv~~ll~l--~~~l~~~l~~ 68 (114)
+-+|.+...- .++.+|...|+....+.| ..++..+..+. +..+++.|..
T Consensus 60 K~LGR~v~~f~~~~~~W~~~~~~r~~~~~~~im~~a~~aKF~Qn~~Lr~~LL~ 112 (148)
T PHA02573 60 KFKGRKKKWAQDQTLYWKGVPIHRYSEAYQELIENAYFEMAIQNKGFRKALLA 112 (148)
T ss_pred HHHhCcccCCcccccchhccchhhhHHHHHHHHHHHHHHHHhcCHHHHHHHHh
Confidence 3455544432 256689999999999988 22222233222 5566666655
No 37
>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=29.34 E-value=30 Score=18.09 Aligned_cols=7 Identities=43% Similarity=0.605 Sum_probs=5.5
Q ss_pred HHHHHHH
Q psy12568 43 SQISYAA 49 (114)
Q Consensus 43 ~Qi~YAA 49 (114)
-||+||-
T Consensus 15 ~QVEYA~ 21 (23)
T PF10584_consen 15 FQVEYAM 21 (23)
T ss_dssp HHHHHHH
T ss_pred EeeEeee
Confidence 4899985
No 38
>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=27.03 E-value=1.2e+02 Score=21.73 Aligned_cols=37 Identities=22% Similarity=0.144 Sum_probs=25.0
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q psy12568 10 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVY 59 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~ 59 (114)
.+.+|..|++.++|+++...... .=|..||.....||
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 46899999999999887542111 11456777776665
No 39
>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=26.47 E-value=75 Score=24.44 Aligned_cols=50 Identities=12% Similarity=0.198 Sum_probs=36.5
Q ss_pred CCccHHHHHHHHhCCccCCc--ccccCCC---CCCCCHHHHHHHHHhHHHHHHHH
Q psy12568 10 SPQSLSTLVLKCFGKTLNKQ--DQFSNWE---NRPLRPSQISYAALDAFCLLQVY 59 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK~--~q~SdW~---~RPLs~~Qi~YAA~Dv~~ll~l~ 59 (114)
...||..++..+||.+.+.= .+.++|- ...-...-++|-..||...++|.
T Consensus 176 ~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 176 TNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred ccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 35789999999999975542 2678883 22344556899999999888774
No 40
>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=25.06 E-value=1.1e+02 Score=21.26 Aligned_cols=52 Identities=15% Similarity=0.214 Sum_probs=26.5
Q ss_pred CCccHHHHHHHHhCCccCCcc----c----ccCCCC---CCCCHHHHHHHHHhHHHHHHHHHHH
Q psy12568 10 SPQSLSTLVLKCFGKTLNKQD----Q----FSNWEN---RPLRPSQISYAALDAFCLLQVYQVL 62 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK~~----q----~SdW~~---RPLs~~Qi~YAA~Dv~~ll~l~~~l 62 (114)
...||+.+... +|++-++.. + -..|.. +...+..++|...||..+..|++.|
T Consensus 101 ~~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 101 ESYSLKNVEKF-LGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp CCTT--SHHH------------HHHHHHHHHH---TTGGTS--HHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHhhh-cccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45678777665 777655221 1 122321 3578888999999999999999876
No 41
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=24.82 E-value=1.4e+02 Score=22.95 Aligned_cols=30 Identities=20% Similarity=0.170 Sum_probs=23.4
Q ss_pred HHHhHHHHHHHHHHHHHHHHHcC-CChhhhh
Q psy12568 48 AALDAFCLLQVYQVLHDQCARQG-IELGPLL 77 (114)
Q Consensus 48 AA~Dv~~ll~l~~~l~~~l~~~~-~~~~e~~ 77 (114)
|..||.....|+..+.++..+.+ ...+++.
T Consensus 162 Al~Da~ata~l~~~l~~~~~~l~~~~~~~l~ 192 (232)
T PRK07942 162 ATADALAAARVAWALARRFPELAALSPAELH 192 (232)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhcCCHHHHH
Confidence 78999999999999999887664 4444443
No 42
>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=24.21 E-value=2.4e+02 Score=19.84 Aligned_cols=36 Identities=28% Similarity=0.414 Sum_probs=25.9
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCChhh
Q psy12568 37 NRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGP 75 (114)
Q Consensus 37 ~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~~~~~e 75 (114)
.|||++++..-|. ..|-...+.|+.+....|..+++
T Consensus 2 ~R~Lt~~E~~~a~---~LL~~As~~Ir~~~~~~g~dld~ 37 (116)
T PF09355_consen 2 WRPLTPEEQARAE---ALLEDASDLIRDRIPRVGKDLDA 37 (116)
T ss_pred CCCCCHHHHHHHH---HHHHHHHHHHHHhhhhcCCCHHH
Confidence 4899999988876 55556667777777766666543
No 43
>PRK07740 hypothetical protein; Provisional
Probab=24.11 E-value=1.5e+02 Score=23.01 Aligned_cols=46 Identities=17% Similarity=0.308 Sum_probs=34.2
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCC
Q psy12568 10 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIE 72 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~~~ 72 (114)
...||.+++. ++|++.+.. .=|..||.....|+.++..++.+.|..
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 3567777775 467655431 226899999999999999999988854
No 44
>KOG1275|consensus
Probab=22.35 E-value=2e+02 Score=27.81 Aligned_cols=61 Identities=20% Similarity=0.167 Sum_probs=43.1
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCChhhhhHHHHhcccc
Q psy12568 10 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIELGPLLTEVLSSHAV 86 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~~~~~e~~~~~~~~~~~ 86 (114)
..+||+-|+..+||.++.-..- .. .-||+..+.||++..+ |+++|.-+.++....+..|..
T Consensus 1051 R~LSLrfLa~~lLg~~IQ~~~H----DS-----------IeDA~taLkLYk~Yl~-lkeq~~~~~~l~niye~gr~~ 1111 (1118)
T KOG1275|consen 1051 RMLSLRFLAWELLGETIQMEAH----DS-----------IEDARTALKLYKKYLK-LKEQGKLESELRNIYECGRPN 1111 (1118)
T ss_pred cEEEHHHHHHHHhcchhhcccc----cc-----------HHHHHHHHHHHHHHHH-HHHhhHHHHHHHHHhhcCccc
Confidence 5789999999999987754332 21 6799999999998765 567776656655444444443
No 45
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=22.35 E-value=2.5e+02 Score=21.25 Aligned_cols=35 Identities=20% Similarity=0.267 Sum_probs=26.5
Q ss_pred CCCCCCHHHHHHHHHhHHHHH-----------HHHHHHHHHHHHcC
Q psy12568 36 ENRPLRPSQISYAALDAFCLL-----------QVYQVLHDQCARQG 70 (114)
Q Consensus 36 ~~RPLs~~Qi~YAA~Dv~~ll-----------~l~~~l~~~l~~~~ 70 (114)
.+||.+.+||+=|+.++..-+ .|.+..++.|++.+
T Consensus 75 ~KRpVs~e~ie~~v~~ie~~Lr~~g~~EV~S~~IG~~VM~~Lk~lD 120 (156)
T COG1327 75 EKRPVSSEQIEEAVSHIERQLRSSGEREVPSKEIGELVMEELKKLD 120 (156)
T ss_pred hcCCCCHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcc
Confidence 359999999999999886543 46677777776654
No 46
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=22.01 E-value=2.7e+02 Score=20.75 Aligned_cols=35 Identities=17% Similarity=0.142 Sum_probs=26.0
Q ss_pred CCCCCCHHHHHHHHHhHHHHH-----------HHHHHHHHHHHHcC
Q psy12568 36 ENRPLRPSQISYAALDAFCLL-----------QVYQVLHDQCARQG 70 (114)
Q Consensus 36 ~~RPLs~~Qi~YAA~Dv~~ll-----------~l~~~l~~~l~~~~ 70 (114)
.+||.|.+||+=.+.++..-+ .|.+..++.|++.+
T Consensus 75 ~KRpVs~e~ie~~v~~Ie~~l~~~~~~EI~S~~IGe~Vm~~L~~lD 120 (147)
T TIGR00244 75 EKRPVSFDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLD 120 (147)
T ss_pred cCCCCCHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHhhcC
Confidence 369999999999888876544 56666777766654
No 47
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=20.81 E-value=2e+02 Score=22.14 Aligned_cols=33 Identities=9% Similarity=0.034 Sum_probs=23.6
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHcCCChhhhhHHHH
Q psy12568 46 SYAALDAFCLLQVYQVLHDQCARQGIELGPLLTEVL 81 (114)
Q Consensus 46 ~YAA~Dv~~ll~l~~~l~~~l~~~~~~~~e~~~~~~ 81 (114)
.=|..||+....|+..+.+ ..||..+++.+..+
T Consensus 134 HrAl~Da~ata~ll~~l~~---~~~~~~~~l~~~~~ 166 (219)
T PRK07983 134 HRALYDCYITAALLIDIMN---TSGWTAEEMADITG 166 (219)
T ss_pred CcHHHHHHHHHHHHHHHHH---HcCCCHHHHHHHhc
Confidence 3478999999999987764 56676666555544
No 48
>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=20.53 E-value=2.8e+02 Score=27.18 Aligned_cols=46 Identities=26% Similarity=0.397 Sum_probs=36.3
Q ss_pred CCccHHHHHHHHhCCccCCcccccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCCC
Q psy12568 10 SPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQGIE 72 (114)
Q Consensus 10 ~~~sL~~Lv~~~lg~~ldK~~q~SdW~~RPLs~~Qi~YAA~Dv~~ll~l~~~l~~~l~~~~~~ 72 (114)
...+|..|++. +|++++- -.-|..||..+..||..+.+++++.|..
T Consensus 316 k~~kL~~Lak~-lgi~~~~----------------~HrAl~DA~aTa~I~~~ll~~l~~~~i~ 361 (1213)
T TIGR01405 316 KSHRLGNICKK-LGVDLDD----------------HHRADYDAEATAKVFKVMVEQLKEKGIT 361 (1213)
T ss_pred CCCCHHHHHHH-cCCCCCC----------------CcCHHHHHHHHHHHHHHHHHHHHHcCCc
Confidence 35677887775 4776542 2679999999999999999999998855
Done!