Query 045621
Match_columns 205
No_of_seqs 151 out of 1110
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 03:50:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045621.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045621hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06146 mut-7_like_exo DEDDy 3 99.9 1.7E-24 3.8E-29 179.9 14.9 131 47-184 3-193 (193)
2 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 1.1E-23 2.4E-28 170.0 15.5 127 49-183 2-169 (170)
3 cd06129 RNaseD_like DEDDy 3'-5 99.9 3.5E-23 7.5E-28 166.9 13.4 104 76-184 28-161 (161)
4 PRK10829 ribonuclease D; Provi 99.9 2E-21 4.4E-26 176.4 15.4 145 46-200 4-184 (373)
5 KOG4373 Predicted 3'-5' exonuc 99.9 2.7E-21 5.8E-26 170.4 11.7 161 25-186 8-288 (319)
6 COG0349 Rnd Ribonuclease D [Tr 99.8 4.9E-20 1.1E-24 165.5 12.8 121 75-200 31-180 (361)
7 TIGR01388 rnd ribonuclease D. 99.7 2E-17 4.3E-22 150.1 14.3 143 48-200 2-180 (367)
8 PF01612 DNA_pol_A_exo1: 3'-5' 99.7 2.9E-17 6.4E-22 131.0 12.8 128 48-185 4-174 (176)
9 cd06148 Egl_like_exo DEDDy 3'- 99.7 1.8E-17 3.9E-22 138.0 10.3 111 75-186 23-177 (197)
10 cd06142 RNaseD_exo DEDDy 3'-5' 99.3 1.1E-11 2.4E-16 99.6 11.2 122 77-203 28-177 (178)
11 KOG2207 Predicted 3'-5' exonuc 99.3 1.4E-12 3E-17 123.0 6.4 133 46-185 393-584 (617)
12 smart00474 35EXOc 3'-5' exonuc 99.2 1.4E-09 3E-14 85.8 14.6 129 49-185 5-170 (172)
13 cd09018 DEDDy_polA_RNaseD_like 99.1 1.6E-09 3.5E-14 84.4 10.0 105 77-183 15-149 (150)
14 cd00007 35EXOc 3'-5' exonuclea 98.9 8.9E-09 1.9E-13 79.6 10.5 105 77-185 16-154 (155)
15 cd06147 Rrp6p_like_exo DEDDy 3 98.8 3.2E-07 7E-12 75.5 14.2 103 77-185 40-171 (192)
16 PRK14975 bifunctional 3'-5' ex 98.7 5.4E-08 1.2E-12 92.8 9.0 129 48-189 6-147 (553)
17 KOG2206 Exosome 3'-5' exoribon 98.6 7.1E-08 1.5E-12 91.4 7.8 103 76-185 227-359 (687)
18 PRK05755 DNA polymerase I; Pro 98.3 1.1E-05 2.3E-10 81.0 13.9 131 47-188 298-471 (880)
19 cd06140 DNA_polA_I_Bacillus_li 97.8 0.0001 2.2E-09 59.3 8.2 86 97-186 48-156 (178)
20 cd06139 DNA_polA_I_Ecoli_like_ 97.7 0.00039 8.5E-09 56.1 9.7 85 97-186 59-170 (193)
21 TIGR00593 pola DNA polymerase 95.3 0.075 1.6E-06 53.9 8.7 90 95-186 368-477 (887)
22 COG0749 PolA DNA polymerase I 89.1 1.3 2.8E-05 43.2 7.0 98 94-191 67-185 (593)
23 cd06137 DEDDh_RNase DEDDh 3'-5 87.2 2 4.4E-05 34.3 6.1 67 95-179 75-160 (161)
24 cd06128 DNA_polA_exo DEDDy 3'- 87.0 5.8 0.00013 30.7 8.5 67 112-183 80-150 (151)
25 cd06145 REX1_like DEDDh 3'-5' 86.5 2.4 5.2E-05 33.5 6.1 67 95-179 67-149 (150)
26 cd06143 PAN2_exo DEDDh 3'-5' e 82.4 2.6 5.6E-05 34.9 4.8 63 96-180 94-174 (174)
27 PRK08517 DNA polymerase III su 81.0 13 0.00028 32.4 8.8 72 95-187 139-232 (257)
28 cd06144 REX4_like DEDDh 3'-5' 80.2 2.3 5.1E-05 33.5 3.7 66 95-180 69-152 (152)
29 PRK07740 hypothetical protein; 79.7 14 0.00031 31.6 8.7 25 166-190 206-230 (244)
30 PRK06807 DNA polymerase III su 79.2 12 0.00027 33.5 8.4 24 166-189 152-175 (313)
31 TIGR01407 dinG_rel DnaQ family 78.9 14 0.00031 37.3 9.6 47 128-193 126-172 (850)
32 PRK07246 bifunctional ATP-depe 78.3 13 0.00028 37.6 9.1 77 95-192 78-176 (820)
33 cd06133 ERI-1_3'hExo_like DEDD 76.9 17 0.00036 28.5 7.8 51 112-182 125-175 (176)
34 PRK08074 bifunctional ATP-depe 76.5 17 0.00038 37.2 9.5 78 95-193 76-176 (928)
35 KOG1275 PAB-dependent poly(A) 74.5 3.5 7.7E-05 42.1 3.8 66 99-185 1008-1091(1118)
36 PRK07883 hypothetical protein; 74.2 19 0.00042 34.8 8.7 23 166-188 162-184 (557)
37 PRK07942 DNA polymerase III su 74.0 28 0.0006 29.6 8.8 26 166-191 160-185 (232)
38 cd06130 DNA_pol_III_epsilon_li 73.8 19 0.0004 27.7 7.2 33 128-180 123-155 (156)
39 cd06149 ISG20 DEDDh 3'-5' exon 73.2 6.3 0.00014 31.4 4.4 38 128-180 120-157 (157)
40 PRK07748 sporulation inhibitor 72.9 29 0.00062 28.7 8.5 22 165-186 159-180 (207)
41 cd05777 DNA_polB_delta_exo DED 72.4 8 0.00017 32.7 5.1 72 109-185 149-226 (230)
42 PRK06309 DNA polymerase III su 70.9 31 0.00068 29.2 8.4 20 167-186 147-166 (232)
43 cd05780 DNA_polB_Kod1_like_exo 69.7 8.4 0.00018 31.7 4.5 66 112-182 127-195 (195)
44 PRK06063 DNA polymerase III su 69.0 32 0.0007 30.7 8.4 23 164-186 157-179 (313)
45 cd05778 DNA_polB_zeta_exo inac 67.3 13 0.00029 31.6 5.4 72 105-179 154-230 (231)
46 PRK06310 DNA polymerase III su 67.2 40 0.00086 29.0 8.4 20 166-185 154-173 (250)
47 cd06127 DEDDh DEDDh 3'-5' exon 66.9 40 0.00086 25.1 7.5 17 163-179 142-158 (159)
48 KOG3657 Mitochondrial DNA poly 66.5 9.8 0.00021 38.7 4.9 63 129-196 322-394 (1075)
49 PRK09145 DNA polymerase III su 66.1 37 0.00081 27.9 7.7 22 164-185 179-200 (202)
50 cd05160 DEDDy_DNA_polB_exo DED 63.9 21 0.00045 29.0 5.8 68 109-179 129-198 (199)
51 smart00479 EXOIII exonuclease 58.8 37 0.0008 26.1 6.1 53 112-185 114-166 (169)
52 PRK06195 DNA polymerase III su 56.6 70 0.0015 28.3 8.2 21 166-186 144-164 (309)
53 TIGR00573 dnaq exonuclease, DN 56.2 59 0.0013 27.1 7.3 26 164-189 155-180 (217)
54 cd06136 TREX1_2 DEDDh 3'-5' ex 51.5 60 0.0013 26.1 6.5 68 95-181 86-176 (177)
55 cd05776 DNA_polB_alpha_exo ina 51.4 19 0.00041 30.6 3.6 73 106-183 150-227 (234)
56 TIGR01405 polC_Gram_pos DNA po 50.9 84 0.0018 33.6 8.8 71 95-186 262-355 (1213)
57 cd06131 DNA_pol_III_epsilon_Ec 50.8 85 0.0019 24.4 7.1 19 164-182 148-166 (167)
58 cd05784 DNA_polB_II_exo DEDDy 49.2 59 0.0013 26.9 6.1 69 107-180 117-193 (193)
59 cd06125 DnaQ_like_exo DnaQ-lik 47.5 68 0.0015 23.2 5.6 39 76-119 13-61 (96)
60 cd01231 PH_Lnk LNK-family Plec 42.4 71 0.0015 24.4 5.0 35 28-62 71-105 (107)
61 PRK05168 ribonuclease T; Provi 39.7 1.5E+02 0.0032 24.6 7.2 29 164-192 179-207 (211)
62 PRK11779 sbcB exonuclease I; P 35.5 1.4E+02 0.0031 28.5 7.1 26 164-189 176-201 (476)
63 PRK09146 DNA polymerase III su 34.6 2.7E+02 0.0059 23.7 8.2 24 163-186 204-227 (239)
64 TIGR01406 dnaQ_proteo DNA poly 33.7 1.3E+02 0.0028 25.4 5.9 24 166-189 152-175 (225)
65 cd06134 RNaseT DEDDh 3'-5' exo 32.8 1.6E+02 0.0035 23.9 6.3 23 163-185 166-188 (189)
66 cd01246 PH_oxysterol_bp Oxyste 32.3 88 0.0019 21.3 4.1 31 32-62 59-89 (91)
67 KOG2248 3'-5' exonuclease [Rep 32.1 42 0.0009 31.2 2.9 74 94-186 284-375 (380)
68 PF00169 PH: PH domain; Inter 31.9 1.6E+02 0.0035 19.8 6.1 36 28-63 66-101 (104)
69 PRK05711 DNA polymerase III su 30.6 1.5E+02 0.0033 25.4 6.0 25 165-189 155-179 (240)
70 KOG0685 Flavin-containing amin 28.4 42 0.00091 32.2 2.2 35 129-163 391-426 (498)
71 smart00486 POLBc DNA polymeras 27.8 1.1E+02 0.0024 27.6 4.9 68 112-182 151-220 (471)
72 COG0847 DnaQ DNA polymerase II 27.1 3.6E+02 0.0078 22.3 8.2 47 128-191 141-188 (243)
73 PRK07247 DNA polymerase III su 25.7 1.1E+02 0.0023 25.4 4.0 22 166-187 149-170 (195)
74 PHA02528 43 DNA polymerase; Pr 25.3 1.1E+02 0.0024 31.5 4.7 70 109-182 251-324 (881)
75 PTZ00166 DNA polymerase delta 24.7 1.6E+02 0.0035 31.0 5.8 75 106-183 405-483 (1054)
76 cd01265 PH_PARIS-1 PARIS-1 ple 24.4 2.7E+02 0.0058 19.9 5.6 32 31-63 61-92 (95)
77 PF12317 IFT46_B_C: Intraflage 24.0 82 0.0018 27.0 3.0 49 48-104 112-164 (214)
78 KOG2249 3'-5' exonuclease [Rep 23.9 1.5E+02 0.0033 26.3 4.7 72 95-185 176-265 (280)
79 PF15406 PH_6: Pleckstrin homo 23.4 1.8E+02 0.0039 22.4 4.5 51 9-62 60-110 (112)
80 TIGR01298 RNaseT ribonuclease 23.4 3E+02 0.0066 22.5 6.4 27 163-189 169-195 (200)
81 cd05783 DNA_polB_B1_exo DEDDy 23.3 1.4E+02 0.003 24.9 4.3 48 127-180 154-202 (204)
82 cd06138 ExoI_N N-terminal DEDD 23.0 3E+02 0.0064 22.1 6.1 17 163-179 166-182 (183)
83 PRK00448 polC DNA polymerase I 22.6 4.1E+02 0.0089 29.2 8.4 40 128-186 545-584 (1437)
84 PRK07983 exodeoxyribonuclease 21.7 4.9E+02 0.011 21.9 7.9 21 165-185 133-153 (219)
85 COG4573 GatZ Predicted tagatos 21.6 1.9E+02 0.0042 26.8 5.0 84 34-140 226-323 (426)
86 cd01257 PH_IRS Insulin recepto 20.8 2.2E+02 0.0047 21.1 4.5 29 33-62 71-99 (101)
87 PRK06722 exonuclease; Provisio 20.2 1.9E+02 0.0042 25.6 4.7 19 166-184 161-179 (281)
No 1
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.92 E-value=1.7e-24 Score=179.93 Aligned_cols=131 Identities=24% Similarity=0.391 Sum_probs=103.0
Q ss_pred EcCCHHHHHHHHHHH-HHhhhccccceee-----------ccCCceeeEEEE------EEeeC--------CCCHHHHHh
Q 045621 47 VTSRASDVDRWIART-INVHRRRLHRLIT-----------NKLQKVAIIQLC------LFHKD--------RMPQSLVDF 100 (205)
Q Consensus 47 vT~~~~~v~~wi~~~-~~~~~~~~~~lvv-----------~~~~~vaLiQLc------L~~~~--------~~p~~L~~f 100 (205)
+..+++.+.+++.++ +.. .+.|. +..+++|||||| ||++. .+|+.|+++
T Consensus 3 ~i~~~~el~~~~~~~~l~~-----~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~l 77 (193)
T cd06146 3 IVDSEEELEALLLALSLEA-----GRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKRL 77 (193)
T ss_pred EecCHHHHHHHHHHHhhcc-----CCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHHH
Confidence 346789999999995 221 22222 236899999999 77753 256789999
Q ss_pred hcCCCeeEEEe--------------------------eeHHHHHHHhcCCc--------chhcccHHHHHHHHcCccccc
Q 045621 101 LDNDKFTFVGT--------------------------MDVADMAAAKYDDE--------ELKTFGLKRLVLKFLHVEMEK 146 (205)
Q Consensus 101 L~d~~i~kvGv--------------------------~Dl~~la~~~lg~~--------~~~~~gL~~Lv~~~lg~~l~K 146 (205)
|+||+|+|||+ +|++.+|+...+.. ...+.||++|++++||+.++|
T Consensus 78 l~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K 157 (193)
T cd06146 78 FEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDK 157 (193)
T ss_pred hCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCc
Confidence 99999999999 55566665332210 024689999999999999999
Q ss_pred CCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHH
Q 045621 147 SKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKK 184 (205)
Q Consensus 147 ~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~ 184 (205)
..+ +|||++||||++|++|||.|||+++.||++|.+
T Consensus 158 ~~q--~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 158 SEQ--CSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred ccc--cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 876 999999999999999999999999999999863
No 2
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=99.91 E-value=1.1e-23 Score=169.97 Aligned_cols=127 Identities=33% Similarity=0.548 Sum_probs=105.3
Q ss_pred CCHHHHHHHHHHHH-Hhhhccccceee-----------ccCCceeeEEEE------EEee---CCCCHHHHHhhcCCCee
Q 045621 49 SRASDVDRWIARTI-NVHRRRLHRLIT-----------NKLQKVAIIQLC------LFHK---DRMPQSLVDFLDNDKFT 107 (205)
Q Consensus 49 ~~~~~v~~wi~~~~-~~~~~~~~~lvv-----------~~~~~vaLiQLc------L~~~---~~~p~~L~~fL~d~~i~ 107 (205)
++++.+++|++.+. . .+.+. +..+++|+|||| ||++ +.+|+.|++||++++|+
T Consensus 2 ~~~~~~~~~~~~~~~~------~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~~~~~~l~~ll~~~~i~ 75 (170)
T cd06141 2 DSAQDAEEAVKELLGK------EKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSIL 75 (170)
T ss_pred CCHHHHHHHHHHHhcC------CCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhhcccHHHHHHhcCCCee
Confidence 57888999999887 3 22222 145799999999 6764 46799999999999999
Q ss_pred EEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHH
Q 045621 108 FVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRY 167 (205)
Q Consensus 108 kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~Y 167 (205)
|||+ +|++.++. .++.. ..+.||+.|++.++|..++|++.+++|||..||||++|++|
T Consensus 76 kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~-ll~~~-~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~Y 153 (170)
T cd06141 76 KVGVGIKGDARKLARDFGIEVRGVVDLSHLAK-RVGPR-RKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILY 153 (170)
T ss_pred EEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHH-HhCCC-cCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHH
Confidence 9999 67777665 34422 13469999999999999998888889999999999999999
Q ss_pred HHhhHHHHHHHHHHHH
Q 045621 168 AAIDAFVSFKLAIELK 183 (205)
Q Consensus 168 AA~DA~~~~~I~~~L~ 183 (205)
||.|||++++||++|.
T Consensus 154 Aa~Da~~~~~l~~~l~ 169 (170)
T cd06141 154 AATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999999986
No 3
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=99.90 E-value=3.5e-23 Score=166.88 Aligned_cols=104 Identities=28% Similarity=0.342 Sum_probs=89.2
Q ss_pred cCCceeeEEEE-------EEeeC---CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCc
Q 045621 76 KLQKVAIIQLC-------LFHKD---RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDE 125 (205)
Q Consensus 76 ~~~~vaLiQLc-------L~~~~---~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~ 125 (205)
..+++|||||| ||++. ..|+.|+++|+|++|+|||+ +|++..+. .+|.+
T Consensus 28 ~~~~~~liQl~~~~~~~~l~d~~~~~~~~~~L~~lL~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~-ll~~~ 106 (161)
T cd06129 28 YYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAAN-LKGLP 106 (161)
T ss_pred CCCceEEEEEEECCCCEEEEecccCccCHHHHHHHhCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHH-HhCCC
Confidence 46899999999 77753 36899999999999999999 67766554 45543
Q ss_pred chhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHH
Q 045621 126 ELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKK 184 (205)
Q Consensus 126 ~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~ 184 (205)
.+.||++|+++++|..++|..+ +|||++||||++|++|||.|||++++||++|.+
T Consensus 107 --~~~~L~~l~~~~lg~~l~K~~~--~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 107 --ERWSLASLVEHFLGKTLDKSIS--CADWSYRPLTEDQKLYAAADVYALLIIYTKLRN 161 (161)
T ss_pred --CCchHHHHHHHHhCCCCCccce--eccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3679999999999999988665 999999999999999999999999999999863
No 4
>PRK10829 ribonuclease D; Provisional
Probab=99.87 E-value=2e-21 Score=176.44 Aligned_cols=145 Identities=19% Similarity=0.211 Sum_probs=118.2
Q ss_pred EEcCCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE------EEeeCCC--CHHHHHhhcCCCeeEE
Q 045621 46 TVTSRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC------LFHKDRM--PQSLVDFLDNDKFTFV 109 (205)
Q Consensus 46 tvT~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc------L~~~~~~--p~~L~~fL~d~~i~kv 109 (205)
.+..+++.+.+++...... ..+.+ ++.+++|||||+ ||++-.+ ...|+++|+|++|+||
T Consensus 4 ~~I~t~~~L~~~~~~l~~~-----~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~~~d~~~L~~ll~~~~ivKV 78 (373)
T PRK10829 4 QMITTDDALASVCEAARAF-----PAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKF 78 (373)
T ss_pred EEeCCHHHHHHHHHHHhcC-----CeEEEecccccCccCCCceeEEEEecCCceEEEecCCccchHHHHHHHcCCCeEEE
Confidence 3557888899999986542 23333 367889999998 6664332 4789999999999999
Q ss_pred Ee--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHH
Q 045621 110 GT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAA 169 (205)
Q Consensus 110 Gv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA 169 (205)
+| ||++..|+ .+|.+ .+.||+.|++++||+.++|.++ +|||.+||||++|++|||
T Consensus 79 ~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~-~lg~~--~~~gl~~Lv~~~lgv~ldK~~~--~sDW~~RPLs~~ql~YAa 153 (373)
T PRK10829 79 LHAGSEDLEVFLNAFGELPQPLIDTQILAA-FCGRP--LSCGFASMVEEYTGVTLDKSES--RTDWLARPLSERQCEYAA 153 (373)
T ss_pred EeChHhHHHHHHHHcCCCcCCeeeHHHHHH-HcCCC--ccccHHHHHHHHhCCccCcccc--cCCCCCCCCCHHHHHHHH
Confidence 98 78866664 67764 4789999999999999999998 999999999999999999
Q ss_pred hhHHHHHHHHHHHHHhHHcCCCCCccccccc
Q 045621 170 IDAFVSFKLAIELKKEIIALPKPTTFDAFCC 200 (205)
Q Consensus 170 ~DA~~~~~I~~~L~~~~~~~p~~~~~~~~~~ 200 (205)
.|+++++.||.+|.+......+-+|...-|+
T Consensus 154 ~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~ 184 (373)
T PRK10829 154 ADVFYLLPIAAKLMAETEAAGWLPAALDECR 184 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence 9999999999999988666666666655554
No 5
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=99.86 E-value=2.7e-21 Score=170.38 Aligned_cols=161 Identities=25% Similarity=0.385 Sum_probs=134.3
Q ss_pred CCCCCCCceeEEEeCCcEEEEEEcCCHHHHHHHHHHHHHhhhc-cccceee--------c--------------------
Q 045621 25 SIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRR-RLHRLIT--------N-------------------- 75 (205)
Q Consensus 25 ~~~~~~~~~y~V~f~g~~I~vtvT~~~~~v~~wi~~~~~~~~~-~~~~lvv--------~-------------------- 75 (205)
...+-++..|.|.|+|+...+++|.+.+.+.+||.++....+. ..+|++| .
T Consensus 8 ~~~~~t~~~~~vd~~~~~~~Vtvt~~~svi~~~i~d~~~~~~~~~s~p~vvg~~vqw~p~~~~~~~~~~~~~~~~~~~a~ 87 (319)
T KOG4373|consen 8 IGSYATVQKYSVDFFGEELIVTVTPDSSVISRWIHDVRFLSRNFSSDPLVVGRGVQWTPPTLTPDQTIYAARDLQISVAR 87 (319)
T ss_pred ccccccccceeeeecccceEEEEccCcccchhhhhhhhhcccCcccCCcccCcCcccCCCCCCccccccccchhcccccc
Confidence 4567899999999999999999999999999999998865321 1244444 0
Q ss_pred ---------------------------------------------------------cCCceeeEEEE----------EE
Q 045621 76 ---------------------------------------------------------KLQKVAIIQLC----------LF 88 (205)
Q Consensus 76 ---------------------------------------------------------~~~~vaLiQLc----------L~ 88 (205)
..++++++||| |+
T Consensus 88 ~~~~~~~~~~~~~~kl~~~~d~~a~~~~~~~~~~~~~s~~~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~en~C~I~ql~ 167 (319)
T KOG4373|consen 88 FLHLLGSSFKHKRQKLGYGSDARASPYIDNSLEIADDSDPPFVCYRREAQPYLDMGRSDPPPDTLQLCVGENRCLIIQLI 167 (319)
T ss_pred ccccccCcccccccccccccccccccccccccccccccCCcceeecccccccccccccCCCcchhhhhhcccceeeEEee
Confidence 25678999999 56
Q ss_pred eeCCCCHHHHHhhcCCCeeEEEe---------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcC---ccc
Q 045621 89 HKDRMPQSLVDFLDNDKFTFVGT---------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLH---VEM 144 (205)
Q Consensus 89 ~~~~~p~~L~~fL~d~~i~kvGv---------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg---~~l 144 (205)
|++.+|..|+.||+||+++|||+ .||+.++...+|. .+.+.|...++.+.+| ..+
T Consensus 168 ~~~~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g~-~~~~~s~e~i~~~~~~~~~~~v 246 (319)
T KOG4373|consen 168 HCKRIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLGG-SMPNDSFEEIVSETLGYYGKDV 246 (319)
T ss_pred ccccchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhhcc-CccCccHHHHHHHHhhcccccc
Confidence 77889999999999999999999 6777777777775 5677888888888887 448
Q ss_pred ccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621 145 EKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 145 ~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~ 186 (205)
.|++.|+||||...+|+++|+.||++|||+|..+|..-..+.
T Consensus 247 ~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg~~~~~w~ 288 (319)
T KOG4373|consen 247 RLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLGVLERLWE 288 (319)
T ss_pred ccChhcccccceeeeccHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 899999999999999999999999999999999996665553
No 6
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=4.9e-20 Score=165.45 Aligned_cols=121 Identities=24% Similarity=0.234 Sum_probs=100.0
Q ss_pred ccCCceeeEEEE------EEeeC---CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCc
Q 045621 75 NKLQKVAIIQLC------LFHKD---RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDE 125 (205)
Q Consensus 75 ~~~~~vaLiQLc------L~~~~---~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~ 125 (205)
++++++||||+| |++.- .-.+.|..+|.|++|+||.| ||++..+ ..+|.+
T Consensus 31 t~~p~LcLIQi~~~e~~~lIdpl~~~~d~~~l~~Ll~d~~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa-~l~g~~ 109 (361)
T COG0349 31 TYYPRLCLIQISDGEGASLIDPLAGILDLPPLVALLADPNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAA-KLAGFG 109 (361)
T ss_pred ccCCceEEEEEecCCCceEecccccccccchHHHHhcCCceeeeeccccccHHHHHHhcCCCCCchhHHHHHH-HHhCCc
Confidence 488999999999 77742 34689999999999999977 4444444 356654
Q ss_pred chhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcCCCCCccccccc
Q 045621 126 ELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCC 200 (205)
Q Consensus 126 ~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~p~~~~~~~~~~ 200 (205)
.+.||++||++++|+.|+|+++ .|||.+||||++|+.|||.|++|++.||.+|.++...-.+-++...-|+
T Consensus 110 --~~~gl~~Lv~~ll~v~ldK~~q--~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~ 180 (361)
T COG0349 110 --TSHGLADLVEELLGVELDKSEQ--RSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFR 180 (361)
T ss_pred --ccccHHHHHHHHhCCccccccc--ccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHH
Confidence 3999999999999999999999 9999999999999999999999999999999998555445555544444
No 7
>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=99.75 E-value=2e-17 Score=150.06 Aligned_cols=143 Identities=19% Similarity=0.213 Sum_probs=113.7
Q ss_pred cCCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE------EEeeC--CCCHHHHHhhcCCCeeEEEe
Q 045621 48 TSRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC------LFHKD--RMPQSLVDFLDNDKFTFVGT 111 (205)
Q Consensus 48 T~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc------L~~~~--~~p~~L~~fL~d~~i~kvGv 111 (205)
..+++.+..++.++... ..+.+ ++.+++|||||+ ||++- .....|.++|+|++|+|||+
T Consensus 2 I~t~~~l~~~~~~l~~~-----~~ia~DtE~~~~~~y~~~l~LiQia~~~~~~liD~~~~~~~~~L~~lL~d~~i~KV~h 76 (367)
T TIGR01388 2 ITTDDELATVCEAVRTF-----PFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLH 76 (367)
T ss_pred cCCHHHHHHHHHHHhcC-----CEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCcccHHHHHHHHCCCCceEEEe
Confidence 35788899999988753 22222 357889999999 66643 23578999999999999988
Q ss_pred --------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhh
Q 045621 112 --------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAID 171 (205)
Q Consensus 112 --------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~D 171 (205)
||++..| ..+|.. .+.||+.|++++||..++|.++ +|||..|||+++|+.|||.|
T Consensus 77 ~~k~Dl~~L~~~~~~~~~~~fDtqlAa-~lL~~~--~~~~l~~Lv~~~Lg~~l~K~~~--~sdW~~rPL~~~q~~YAa~D 151 (367)
T TIGR01388 77 AASEDLEVFLNLFGELPQPLFDTQIAA-AFCGFG--MSMGYAKLVQEVLGVELDKSES--RTDWLARPLTDAQLEYAAAD 151 (367)
T ss_pred ecHHHHHHHHHHhCCCCCCcccHHHHH-HHhCCC--CCccHHHHHHHHcCCCCCcccc--cccCCCCCCCHHHHHHHHHH
Confidence 7876655 467653 3569999999999999999866 99999999999999999999
Q ss_pred HHHHHHHHHHHHHhHHcCCCCCccccccc
Q 045621 172 AFVSFKLAIELKKEIIALPKPTTFDAFCC 200 (205)
Q Consensus 172 A~~~~~I~~~L~~~~~~~p~~~~~~~~~~ 200 (205)
|++++.+|.+|.+......+-+|...-|.
T Consensus 152 v~~L~~L~~~L~~~L~~~g~~~w~~ee~~ 180 (367)
T TIGR01388 152 VTYLLPLYAKLMERLEESGRLAWLEEECT 180 (367)
T ss_pred HHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence 99999999999888665556655554444
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=99.74 E-value=2.9e-17 Score=131.00 Aligned_cols=128 Identities=29% Similarity=0.481 Sum_probs=98.1
Q ss_pred cCCHHHHHHHHHHHHHhhhccccceee----------ccCCceeeEEEE------EEeeC---C--CCHHHHHhhcCCCe
Q 045621 48 TSRASDVDRWIARTINVHRRRLHRLIT----------NKLQKVAIIQLC------LFHKD---R--MPQSLVDFLDNDKF 106 (205)
Q Consensus 48 T~~~~~v~~wi~~~~~~~~~~~~~lvv----------~~~~~vaLiQLc------L~~~~---~--~p~~L~~fL~d~~i 106 (205)
..+.+.+++|++.+... ..+.+ ....++++||+| +++.. . ++..|+++|+||+|
T Consensus 4 v~~~~~l~~~~~~l~~~-----~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i 78 (176)
T PF01612_consen 4 VDTEEELEEAIKKLKNA-----KVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPNI 78 (176)
T ss_dssp EHSHHHHHHHHHHHTTT-----SEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTTS
T ss_pred cCCHHHHHHHHHHHcCC-----CeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCCc
Confidence 45788899999988764 23332 246789999999 33321 1 35799999999999
Q ss_pred eEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcC-cccccCCcccccCCC-CCCCCHHH
Q 045621 107 TFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLH-VEMEKSKRITLSKWD-VNNLSKQQ 164 (205)
Q Consensus 107 ~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg-~~l~K~~~v~~SnW~-~rpLs~~Q 164 (205)
+|||+ +|+ .++...++.. .+.||+.|+.+++| ..++|... +++|. ++||+++|
T Consensus 79 ~kv~~n~~~D~~~L~~~~~i~~~~~~D~-~l~~~~l~~~--~~~~L~~L~~~~l~~~~~~~~~~--~~~~~~~~~l~~~~ 153 (176)
T PF01612_consen 79 IKVGHNAKFDLKWLYRSFGIDLKNVFDT-MLAAYLLDPT--RSYSLKDLAEEYLGNIDLDKKEQ--MSDWRKARPLSEEQ 153 (176)
T ss_dssp EEEESSHHHHHHHHHHHHTS--SSEEEH-HHHHHHTTTS--TTSSHHHHHHHHHSEEE-GHCCT--TSSTTTSSS-HHHH
T ss_pred cEEEEEEechHHHHHHHhccccCCccch-hhhhhccccc--ccccHHHHHHHHhhhccCcHHHh--hccCCcCCCChHHH
Confidence 99999 555 4444444433 23899999999999 55555554 99999 89999999
Q ss_pred HHHHHhhHHHHHHHHHHHHHh
Q 045621 165 IRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 165 i~YAA~DA~~~~~I~~~L~~~ 185 (205)
++|||.||+++++||++|..+
T Consensus 154 ~~YAa~D~~~~~~l~~~l~~~ 174 (176)
T PF01612_consen 154 IEYAAQDAVVTFRLYEKLKPQ 174 (176)
T ss_dssp HHHHHHHHHTHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999875
No 9
>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=99.73 E-value=1.8e-17 Score=138.00 Aligned_cols=111 Identities=23% Similarity=0.366 Sum_probs=87.2
Q ss_pred ccCCceeeEEEE-------EEeeCC-----CCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhc
Q 045621 75 NKLQKVAIIQLC-------LFHKDR-----MPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKY 122 (205)
Q Consensus 75 ~~~~~vaLiQLc-------L~~~~~-----~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~l 122 (205)
+..+++||||+| ||++-. ++..|+++|+|++|.|||+ +|++..+. .+
T Consensus 23 ~~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~-lL 101 (197)
T cd06148 23 GRKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADA-LL 101 (197)
T ss_pred CCCCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHH-HH
Confidence 356789999999 676532 3578999999999999998 66654432 33
Q ss_pred CCc------chhcccHHHHHHHHcCcccccCC------cccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621 123 DDE------ELKTFGLKRLVLKFLHVEMEKSK------RITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 123 g~~------~~~~~gL~~Lv~~~lg~~l~K~~------~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~ 186 (205)
+.. .....||++++++++|..++|.. +-++|||.+||||++|+.|||.||++++.+|+.|....
T Consensus 102 ~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l 177 (197)
T cd06148 102 QEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDAL 177 (197)
T ss_pred HHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 211 01246999999999999987521 23489999999999999999999999999999998873
No 10
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.34 E-value=1.1e-11 Score=99.57 Aligned_cols=122 Identities=24% Similarity=0.306 Sum_probs=93.6
Q ss_pred CCceeeEEEE------EEeeC--CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchh
Q 045621 77 LQKVAIIQLC------LFHKD--RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEELK 128 (205)
Q Consensus 77 ~~~vaLiQLc------L~~~~--~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~ 128 (205)
..+++.+|+| +|++. ..++.|+.+|+|+++.|||+ +|+...+ ..++.. .
T Consensus 28 ~~~~~~i~l~~~~~~~~i~~~~~~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laa-yLl~p~--~ 104 (178)
T cd06142 28 YPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAA-RLLGLG--D 104 (178)
T ss_pred CCceEEEEEeeCCCEEEEeCCCcccHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCCcccHHHHH-HHhCCC--c
Confidence 4678899998 33222 24566999999999999998 4554333 344432 2
Q ss_pred cccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcCCCCCcccccccccc
Q 045621 129 TFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCCFQI 203 (205)
Q Consensus 129 ~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~p~~~~~~~~~~~~~ 203 (205)
+.||+.+++.++|..+.|.+ .+++|++++|+.+|+.|||.||++++.++..|.+.......-+.+..-|+++|
T Consensus 105 ~~~l~~l~~~~l~~~~~~~~--~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~l~~L~~~~~~~~~ 177 (178)
T cd06142 105 SVGLAALVEELLGVELDKGE--QRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGRLEWAEEECELLL 177 (178)
T ss_pred cccHHHHHHHHhCCCCCccc--ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHhh
Confidence 45999999999999877755 48999999999999999999999999999999988655555666666676664
No 11
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.34 E-value=1.4e-12 Score=122.96 Aligned_cols=133 Identities=20% Similarity=0.276 Sum_probs=98.7
Q ss_pred EEcCCHHHHHHHHHHHHHhhhccccceee-----------ccCCceeeEEEE------EEee---CCCC-----HHHHHh
Q 045621 46 TVTSRASDVDRWIARTINVHRRRLHRLIT-----------NKLQKVAIIQLC------LFHK---DRMP-----QSLVDF 100 (205)
Q Consensus 46 tvT~~~~~v~~wi~~~~~~~~~~~~~lvv-----------~~~~~vaLiQLc------L~~~---~~~p-----~~L~~f 100 (205)
.+..++..++..+-+-++. ++.+| ..+++++++|+. |+++ ...+ ..+..+
T Consensus 393 ~~V~~e~El~~l~l~~l~~-----e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~i 467 (617)
T KOG2207|consen 393 GMVGNEKELRDLLLESLSE-----ELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQI 467 (617)
T ss_pred eeeCCHHHHHHHHHHHhhh-----cCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHH
Confidence 3446788787777322221 22233 247899999999 5664 2333 468899
Q ss_pred hcCCCeeEEEe---eeHHHHH-------------------------HHhcCCc------chhcccHHHHHHHHcCccccc
Q 045621 101 LDNDKFTFVGT---MDVADMA-------------------------AAKYDDE------ELKTFGLKRLVLKFLHVEMEK 146 (205)
Q Consensus 101 L~d~~i~kvGv---~Dl~~la-------------------------~~~lg~~------~~~~~gL~~Lv~~~lg~~l~K 146 (205)
|+++.|.|||| -|+..+. .++.+.. .-...||+.|+..++|+.++|
T Consensus 468 f~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnK 547 (617)
T KOG2207|consen 468 FESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNK 547 (617)
T ss_pred ccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhccc
Confidence 99999999999 4443333 2222110 014788999999999999999
Q ss_pred CCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621 147 SKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 147 ~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~ 185 (205)
.++ +|||..|||+..||.|||+||.+++.||.++.+.
T Consensus 548 teq--csnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~v 584 (617)
T KOG2207|consen 548 TEQ--CSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSV 584 (617)
T ss_pred ccc--cchhhcCCchhhHHHHHHhcchhhHHHHHHHHhh
Confidence 999 9999999999999999999999999999999876
No 12
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.17 E-value=1.4e-09 Score=85.76 Aligned_cols=129 Identities=25% Similarity=0.317 Sum_probs=90.0
Q ss_pred CCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE----EEe---e---CCCCHHHHHhhcCCCeeEEE
Q 045621 49 SRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC----LFH---K---DRMPQSLVDFLDNDKFTFVG 110 (205)
Q Consensus 49 ~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc----L~~---~---~~~p~~L~~fL~d~~i~kvG 110 (205)
.+++.+.+|+.++... . ..+.+ ....+++.+|+| .+. . ...++.|+++|+++++.|||
T Consensus 5 ~~~~~~~~~~~~~~~~---~-~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~kv~ 80 (172)
T smart00474 5 TDSETLEELLEKLRAA---G-GEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVG 80 (172)
T ss_pred cCHHHHHHHHHHHHhc---C-CeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccchhhHHHHHHHhcCCCceEEE
Confidence 3447788988655211 0 12222 125678999999 111 1 12345699999999999999
Q ss_pred e-------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhh
Q 045621 111 T-------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAID 171 (205)
Q Consensus 111 v-------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~D 171 (205)
+ +|+...+. .+. +.....||+.+++.++|..++| ....++|..++|.++|+.|||.|
T Consensus 81 ~d~k~~~~~L~~~gi~~~~~~D~~laay-ll~-p~~~~~~l~~l~~~~l~~~~~~--~~~~~~~~~~~l~~~~~~ya~~~ 156 (172)
T smart00474 81 HNAKFDLHVLARFGIELENIFDTMLAAY-LLL-GGPSKHGLATLLKEYLGVELDK--EEQKSDWGARPLSEEQLQYAAED 156 (172)
T ss_pred echHHHHHHHHHCCCcccchhHHHHHHH-HHc-CCCCcCCHHHHHHHHhCCCCCc--ccCccccccCCCCHHHHHHHHHH
Confidence 9 45544443 222 2113359999999999988755 33467998899999999999999
Q ss_pred HHHHHHHHHHHHHh
Q 045621 172 AFVSFKLAIELKKE 185 (205)
Q Consensus 172 A~~~~~I~~~L~~~ 185 (205)
|++++.+++.|.+.
T Consensus 157 a~~~~~L~~~l~~~ 170 (172)
T smart00474 157 ADALLRLYEKLEKE 170 (172)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999998765
No 13
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.05 E-value=1.6e-09 Score=84.36 Aligned_cols=105 Identities=26% Similarity=0.307 Sum_probs=78.1
Q ss_pred CCceeeEEEE-------EEeeCC---CCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcc
Q 045621 77 LQKVAIIQLC-------LFHKDR---MPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEE 126 (205)
Q Consensus 77 ~~~vaLiQLc-------L~~~~~---~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~ 126 (205)
..+++.+|+| ++++.. .+..|+++|+|+++.|+|+ +|+...+. .++..
T Consensus 15 ~~~~~~l~l~~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~~~~~D~~laay-Ll~p~- 92 (150)
T cd09018 15 SANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFDTMLEAY-ILNSV- 92 (150)
T ss_pred CceEEEEEEEcCCCcEEEEEcCCcccCHHHHHHHhcCCCCceeeecHHHHHHHHHHcCCccCCcchhHHHHHH-HhCCC-
Confidence 4567888888 333221 3567999999999999988 67655553 45432
Q ss_pred hhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHH
Q 045621 127 LKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELK 183 (205)
Q Consensus 127 ~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~ 183 (205)
-.+.+|+.|+++++|..+.|.+++..++|..++|+.+|+.||+.||++++.++..|.
T Consensus 93 ~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 93 AGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred CCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 113599999999999886552334445696688999999999999999999998874
No 14
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=98.95 E-value=8.9e-09 Score=79.64 Aligned_cols=105 Identities=25% Similarity=0.305 Sum_probs=76.4
Q ss_pred CCceeeEEEE----EEee--C----CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcc
Q 045621 77 LQKVAIIQLC----LFHK--D----RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEE 126 (205)
Q Consensus 77 ~~~vaLiQLc----L~~~--~----~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~ 126 (205)
..+++++|+| .+.+ . .+++.|+++|+++++.|||+ +|+..++. .++...
T Consensus 16 ~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ay-ll~~~~ 94 (155)
T cd00007 16 RGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLAAY-LLNPGE 94 (155)
T ss_pred CCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcccHHHHHH-HhCCCC
Confidence 4578889988 2221 1 23445999999999999999 56654443 444321
Q ss_pred hhcccHHHHHHHHcCcccccCCcccccCCC----CCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621 127 LKTFGLKRLVLKFLHVEMEKSKRITLSKWD----VNNLSKQQIRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 127 ~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~----~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~ 185 (205)
.+.||+.|+++++|..+.+..+ .++|. .++|+.+|+.||+.||+++++++..|.+.
T Consensus 95 -~~~~l~~l~~~~l~~~~~~~~~--~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 95 -GSHSLDDLAKEYLGIELDKDEQ--IYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred -CcCCHHHHHHHHcCCCCccHHH--HhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 1469999999999988655333 44542 57899999999999999999999998764
No 15
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=98.76 E-value=3.2e-07 Score=75.52 Aligned_cols=103 Identities=19% Similarity=0.295 Sum_probs=77.1
Q ss_pred CCceeeEEEE----EEee-----CCCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcch
Q 045621 77 LQKVAIIQLC----LFHK-----DRMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEEL 127 (205)
Q Consensus 77 ~~~vaLiQLc----L~~~-----~~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~ 127 (205)
..++..+|+| .+.+ ......|+++|+++++.|+|+ +|+...| ..++ ++
T Consensus 40 ~~~~~~l~l~~~~~~~~i~~l~~~~~~~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laa-YLL~-p~- 116 (192)
T cd06147 40 LGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAA-RVLN-LP- 116 (192)
T ss_pred CCceEEEEEecCCCcEEEEecccccchHHHHHHhcCCCceEEEechHHHHHHHHHHhCCCcCchHHHHHHH-HHhC-CC-
Confidence 3567888988 2222 223445999999999999988 3444433 2444 33
Q ss_pred hcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621 128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~ 185 (205)
. .+|+.|++++||..++|. -+++||+.+||+.+|..||+.||++++.++..|...
T Consensus 117 ~-~~l~~l~~~yl~~~~~k~--~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~ 171 (192)
T cd06147 117 R-HSLAYLLQKYCNVDADKK--YQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNE 171 (192)
T ss_pred c-ccHHHHHHHHhCCCcchh--hhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 3 499999999999775452 347889888999999999999999999999988665
No 16
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=98.70 E-value=5.4e-08 Score=92.83 Aligned_cols=129 Identities=16% Similarity=0.095 Sum_probs=95.1
Q ss_pred cCCHHHHHHHHHHHHHhhhccccceee------ccCCceeeEEEE------EEeeCCCCHHHHHhhcCCCeeEEEeeeHH
Q 045621 48 TSRASDVDRWIARTINVHRRRLHRLIT------NKLQKVAIIQLC------LFHKDRMPQSLVDFLDNDKFTFVGTMDVA 115 (205)
Q Consensus 48 T~~~~~v~~wi~~~~~~~~~~~~~lvv------~~~~~vaLiQLc------L~~~~~~p~~L~~fL~d~~i~kvGv~Dl~ 115 (205)
..+++.+..++.++... +.+. +....++++|++ |++.-. .+..+|...++..-++||++
T Consensus 6 I~~~~~l~~~~~~l~~~------~~~a~DtEf~r~~t~l~liQ~~~~~~~~liDpl~---~l~~~L~~~Gv~~~~~fDT~ 76 (553)
T PRK14975 6 ILAPEELGAALERLSPA------GVVAGDTETTGDDAAAAAAQEGEEEPRWVWASTA---ALYPRLLAAGVRVERCHDLM 76 (553)
T ss_pred EeccchhHHHHHHhccC------CceeCCccccCCcchhheeeecCCCceEEECchH---HhHHHHHHCCCccCCCchHH
Confidence 34566677888877653 2222 223379999998 554211 25555655566655679997
Q ss_pred HHHHHhcCCcc-hhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcC
Q 045621 116 DMAAAKYDDEE-LKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIAL 189 (205)
Q Consensus 116 ~la~~~lg~~~-~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~ 189 (205)
..+. .++... ..+.||+.+++.++|..++|..+ .|||. +||+++|..|||.|+.++..+|..|.+.....
T Consensus 77 LAa~-lL~~~~~~~~~~l~~la~~~l~~~l~k~~~--~sdw~-rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 77 LASQ-LLLGSEGRAGSSLSAAAARALGEGLDKPPQ--TSALS-DPPDEEQLLYAAADADVLLELYAVLADQLNRI 147 (553)
T ss_pred HHHH-HcCCCCCcCCCCHHHHHHHHhCCCCCChhh--hcccc-ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence 7764 677531 11679999999999999999887 89997 89999999999999999999999998885544
No 17
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=98.65 E-value=7.1e-08 Score=91.38 Aligned_cols=103 Identities=19% Similarity=0.240 Sum_probs=85.8
Q ss_pred cCCceeeEEEE------EEee----CCCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCc
Q 045621 76 KLQKVAIIQLC------LFHK----DRMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDE 125 (205)
Q Consensus 76 ~~~~vaLiQLc------L~~~----~~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~ 125 (205)
+.+=.||+|++ +++- +.+ ..|++.++||+|.||.+ ||+...+ .++|.
T Consensus 227 f~gltclmqISTr~ed~iIDt~~l~~~i-~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvnLfdt~~a~-r~L~~- 303 (687)
T KOG2206|consen 227 FLGLTCLMQISTRTEDFIIDTFKLRDHI-GILNEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVNLFDTIQAS-RLLGL- 303 (687)
T ss_pred hcCceeEEEeeccchhheehhHHHHHHH-HHhhhhccCCCeEEEEecCccchhhhhccceEEEEechhhHHHH-HHhCC-
Confidence 56678999999 3331 123 38999999999999955 5544433 46765
Q ss_pred chhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621 126 ELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 126 ~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~ 185 (205)
.+.||+-|.+.+.|+..+|..| ..||..|||+++.+.||-.|.+|++-||+.|+..
T Consensus 304 --~r~sL~~ll~~~~~v~~nk~yq--ladwR~rpLp~~Mv~yar~dthyllyiyD~lr~e 359 (687)
T KOG2206|consen 304 --PRPSLAYLLECVCGVLTNKKYQ--LADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKE 359 (687)
T ss_pred --CcccHHHHHHHHHhhhhhhhhh--hchhccccCcHHHHHHHhhcchhHHHHHHHHHHH
Confidence 4899999999999999999888 9999999999999999999999999999999866
No 18
>PRK05755 DNA polymerase I; Provisional
Probab=98.31 E-value=1.1e-05 Score=81.03 Aligned_cols=131 Identities=20% Similarity=0.314 Sum_probs=89.1
Q ss_pred EcCCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE-------EEeeCCCC----HHHHHhhcCCCee
Q 045621 47 VTSRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC-------LFHKDRMP----QSLVDFLDNDKFT 107 (205)
Q Consensus 47 vT~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc-------L~~~~~~p----~~L~~fL~d~~i~ 107 (205)
+..+++.+.+|+..+... ..+.+ ....+++.+|+| ++.+..++ +.|+++|+|+.+.
T Consensus 298 ~I~~~~~L~~~l~~l~~~-----~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~v~ 372 (880)
T PRK05755 298 TILDEEELEAWLAKLKAA-----GLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPAIK 372 (880)
T ss_pred EeCCHHHHHHHHHHhhcc-----CeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCCCc
Confidence 345788899999877532 12222 246778999998 33333333 5799999999999
Q ss_pred EEEe---eeHHHHH----------------HHhcCCcchhcccHHHHHHHHcCccccc-----CCcccccCCCCCCCCHH
Q 045621 108 FVGT---MDVADMA----------------AAKYDDEELKTFGLKRLVLKFLHVEMEK-----SKRITLSKWDVNNLSKQ 163 (205)
Q Consensus 108 kvGv---~Dl~~la----------------~~~lg~~~~~~~gL~~Lv~~~lg~~l~K-----~~~v~~SnW~~rpLs~~ 163 (205)
|||+ +|+..+. ...++ ++. ..||+.|+++++|..+.. ++..++++| |+ +.
T Consensus 373 kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~-~~~-~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~---pl-e~ 446 (880)
T PRK05755 373 KVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLD-PGR-RHGLDSLAERYLGHKTISFEEVAGKQLTFAQV---DL-EE 446 (880)
T ss_pred EEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcC-CCC-CCCHHHHHHHHhCCCccchHHhcCCCCCcccc---CH-HH
Confidence 9999 4444332 22333 222 389999999999977421 122234444 66 58
Q ss_pred HHHHHHhhHHHHHHHHHHHHHhHHc
Q 045621 164 QIRYAAIDAFVSFKLAIELKKEIIA 188 (205)
Q Consensus 164 Qi~YAA~DA~~~~~I~~~L~~~~~~ 188 (205)
|.+||+.||.+++.||.+|.+.-..
T Consensus 447 ~~~YAa~Dv~~~~~L~~~L~~~L~~ 471 (880)
T PRK05755 447 AAEYAAEDADVTLRLHEVLKPKLLE 471 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999987433
No 19
>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=97.81 E-value=0.0001 Score=59.28 Aligned_cols=86 Identities=21% Similarity=0.235 Sum_probs=62.6
Q ss_pred HHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCC
Q 045621 97 LVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWD 156 (205)
Q Consensus 97 L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~ 156 (205)
|+++|+|+++.|+|+ +|+...+ ..++.. -.+.++++++.+++|..+.+..+ .+.|+
T Consensus 48 l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~~~~~~fDt~laa-YLL~p~-~~~~~l~~l~~~yl~~~~~~~~~--~~~~~ 123 (178)
T cd06140 48 LKEWLEDEKIPKVGHDAKRAYVALKRHGIELAGVAFDTMLAA-YLLDPT-RSSYDLADLAKRYLGRELPSDEE--VYGKG 123 (178)
T ss_pred HHHHHhCCCCceeccchhHHHHHHHHCCCcCCCcchhHHHHH-HHcCCC-CCCCCHHHHHHHHcCCCCcchHH--hcCCC
Confidence 888899998888877 5554444 345432 12369999999999988765333 44442
Q ss_pred ---CCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621 157 ---VNNLSKQQIRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 157 ---~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~ 186 (205)
.++..++|..|||.||.+++.++..|.+.-
T Consensus 124 ~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L 156 (178)
T cd06140 124 AKFAVPDEEVLAEHLARKAAAIARLAPKLEEEL 156 (178)
T ss_pred CCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 245577789999999999999999998763
No 20
>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=97.68 E-value=0.00039 Score=56.14 Aligned_cols=85 Identities=25% Similarity=0.319 Sum_probs=58.4
Q ss_pred HHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCccc-------ccCCc
Q 045621 97 LVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEM-------EKSKR 149 (205)
Q Consensus 97 L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l-------~K~~~ 149 (205)
|+++|++.++++||+ +|+..+|. .+. +...+.||+.+++.++|..+ .|.+
T Consensus 59 l~~~l~~~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~-ll~-p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~- 135 (193)
T cd06139 59 LKPLLEDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASY-LLN-PGRRRHGLDDLAERYLGHKTISFEDLVGKGK- 135 (193)
T ss_pred HHHHHhCCCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHH-HhC-CCCCCCCHHHHHHHHhCCCCccHHHHcCCCc-
Confidence 666676666666666 55555553 232 22225699999999998652 1222
Q ss_pred ccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621 150 ITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 150 v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~ 186 (205)
...+|...++ .++.+||+.||.+++.++..|.+..
T Consensus 136 -~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l 170 (193)
T cd06139 136 -KQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKL 170 (193)
T ss_pred -CcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2556765555 7799999999999999999998773
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=95.34 E-value=0.075 Score=53.91 Aligned_cols=90 Identities=21% Similarity=0.194 Sum_probs=58.6
Q ss_pred HHHHHhhcCCCeeEEEe---eeHHHHH----------------HHhcCCcchhcccHHHHHHHHcCcccccCCcccccCC
Q 045621 95 QSLVDFLDNDKFTFVGT---MDVADMA----------------AAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKW 155 (205)
Q Consensus 95 ~~L~~fL~d~~i~kvGv---~Dl~~la----------------~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW 155 (205)
..|+.+|+|+.+.|+|+ +|+..+. ...+... .+.+|+.++.++++..+.+...+....+
T Consensus 368 ~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~la~yll~~~--~~~~l~~la~~yl~~~~~~~~~~~~~~~ 445 (887)
T TIGR00593 368 DKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLAAYLLDPA--QVSTLDTLARRYLVEELILDEKIGGKLA 445 (887)
T ss_pred HHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHHHHHHcCCC--CCCCHHHHHHHHcCcccccHHHhccCCC
Confidence 34899999999999999 4443332 2233321 2359999999999976544222111111
Q ss_pred CCCCCCH-HHHHHHHhhHHHHHHHHHHHHHhH
Q 045621 156 DVNNLSK-QQIRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 156 ~~rpLs~-~Qi~YAA~DA~~~~~I~~~L~~~~ 186 (205)
.-..+.. ....||+.||.+.+.++..|....
T Consensus 446 ~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l 477 (887)
T TIGR00593 446 KFAFPPLEEATEYLARRAAATKRLAEELLKEL 477 (887)
T ss_pred CcccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1113433 357899999999999999998763
No 22
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=89.13 E-value=1.3 Score=43.20 Aligned_cols=98 Identities=20% Similarity=0.249 Sum_probs=63.3
Q ss_pred CHHHHHhhcCCCeeEEEe---eeHHHHHHHh--------------cCCcchhcccHHHHHHHHcCcccccCCcccccCCC
Q 045621 94 PQSLVDFLDNDKFTFVGT---MDVADMAAAK--------------YDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWD 156 (205)
Q Consensus 94 p~~L~~fL~d~~i~kvGv---~Dl~~la~~~--------------lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~ 156 (205)
-..|+.+|+|+++.|+|. +|...+++.- +-.++-...+++.|++.++|......+.+.-..=.
T Consensus 67 ~~~l~~~l~~~~~~kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~ 146 (593)
T COG0749 67 LAALKPLLEDEGIKKVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKK 146 (593)
T ss_pred HHHHHHHhhCcccchhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccc
Confidence 468999999999999999 6665555421 00112235789999999988665433331111111
Q ss_pred C---CCCC-HHHHHHHHhhHHHHHHHHHHHHHhHHcCCC
Q 045621 157 V---NNLS-KQQIRYAAIDAFVSFKLAIELKKEIIALPK 191 (205)
Q Consensus 157 ~---rpLs-~~Qi~YAA~DA~~~~~I~~~L~~~~~~~p~ 191 (205)
. .... +.-..|||.||.+.+.++..|.......|.
T Consensus 147 ~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~ 185 (593)
T COG0749 147 QLTFADVKLEKATEYAAEDADATLRLESILEPELLKTPV 185 (593)
T ss_pred cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 1 0111 234899999999999999999876554443
No 23
>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=87.24 E-value=2 Score=34.27 Aligned_cols=67 Identities=21% Similarity=0.318 Sum_probs=41.3
Q ss_pred HHHHHhhcCCCeeEEEe---e-------------eHHHHHHHhcCCcch---hcccHHHHHHHHcCcccccCCcccccCC
Q 045621 95 QSLVDFLDNDKFTFVGT---M-------------DVADMAAAKYDDEEL---KTFGLKRLVLKFLHVEMEKSKRITLSKW 155 (205)
Q Consensus 95 ~~L~~fL~d~~i~kvGv---~-------------Dl~~la~~~lg~~~~---~~~gL~~Lv~~~lg~~l~K~~~v~~SnW 155 (205)
+.|.+|+.+.. +.||+ + |...+++.... .. .+.+|+.|++.++|.++.....
T Consensus 75 ~~~~~~i~~~~-vlVgHn~~fD~~fL~~~~~~~iDT~~l~~~~~~--~~~~~~~~~L~~L~~~~~~~~~~~~~~------ 145 (161)
T cd06137 75 AALWKFIDPDT-ILVGHSLQNDLDALRMIHTRVVDTAILTREAVK--GPLAKRQWSLRTLCRDFLGLKIQGGGE------ 145 (161)
T ss_pred HHHHHhcCCCc-EEEeccHHHHHHHHhCcCCCeeEehhhhhhccC--CCcCCCCccHHHHHHHHCCchhcCCCC------
Confidence 45666776533 45777 4 44455543222 12 4789999999999987754111
Q ss_pred CCCCCCHHHHHHHHhhHHHHHHHH
Q 045621 156 DVNNLSKQQIRYAAIDAFVSFKLA 179 (205)
Q Consensus 156 ~~rpLs~~Qi~YAA~DA~~~~~I~ 179 (205)
-+=|..||.++.++|
T Consensus 146 ---------~H~A~~DA~at~~l~ 160 (161)
T cd06137 146 ---------GHDSLEDALAAREVV 160 (161)
T ss_pred ---------CCCcHHHHHHHHHHh
Confidence 122678888888776
No 24
>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=86.95 E-value=5.8 Score=30.67 Aligned_cols=67 Identities=21% Similarity=0.230 Sum_probs=37.1
Q ss_pred eeHHHHHHHhcCCcchhcccHHHHHHHHcCccccc-CCcccccCCCC--CCC-CHHHHHHHHhhHHHHHHHHHHHH
Q 045621 112 MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEK-SKRITLSKWDV--NNL-SKQQIRYAAIDAFVSFKLAIELK 183 (205)
Q Consensus 112 ~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K-~~~v~~SnW~~--rpL-s~~Qi~YAA~DA~~~~~I~~~L~ 183 (205)
+|+...+ ..++.. -...+++++++++|+..+-. .. + ..+++ ..+ -.+.-.|++..|.+.+.++..|.
T Consensus 80 fD~~LAa-YLL~p~-~~~~~l~~la~~yl~~~~~~~~~-~--~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 80 FDTMLEA-YLLDPV-AGRHDMDSLAERWLKEKTITFEE-I--AGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred hhHHHHH-HHcCCC-CCCCCHHHHHHHHcCCCCccHHH-H--cCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 6775444 455532 12139999999998876211 10 1 01110 011 11123488888888888888774
No 25
>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=86.48 E-value=2.4 Score=33.53 Aligned_cols=67 Identities=18% Similarity=0.214 Sum_probs=39.7
Q ss_pred HHHHHhhcCCCeeEEEe---eeHH-------------HHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCC
Q 045621 95 QSLVDFLDNDKFTFVGT---MDVA-------------DMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVN 158 (205)
Q Consensus 95 ~~L~~fL~d~~i~kvGv---~Dl~-------------~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~r 158 (205)
+.+.+|+.+ +-+.||+ +|++ .+++...+. ..+.+|+.|+++++|..+....
T Consensus 67 ~~~~~fl~~-~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~r~~~~~--~~~~~L~~L~~~~~~~~i~~~~---------- 133 (150)
T cd06145 67 KKLLSLISP-DTILVGHSLENDLKALKLIHPRVIDTAILFPHPRGP--PYKPSLKNLAKKYLGRDIQQGE---------- 133 (150)
T ss_pred HHHHHHhCC-CCEEEEcChHHHHHHhhccCCCEEEcHHhccccCCC--CCChhHHHHHHHHCCcceeCCC----------
Confidence 466677752 2345787 5544 444322221 2357999999999886654210
Q ss_pred CCCHHHHHHHHhhHHHHHHHH
Q 045621 159 NLSKQQIRYAAIDAFVSFKLA 179 (205)
Q Consensus 159 pLs~~Qi~YAA~DA~~~~~I~ 179 (205)
+.+=|.-||.++.+||
T Consensus 134 -----~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 134 -----GGHDSVEDARAALELV 149 (150)
T ss_pred -----CCCCcHHHHHHHHHHh
Confidence 0122678999988876
No 26
>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=82.43 E-value=2.6 Score=34.88 Aligned_cols=63 Identities=19% Similarity=0.217 Sum_probs=41.4
Q ss_pred HHHHhhcCCCeeEEEe------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCC
Q 045621 96 SLVDFLDNDKFTFVGT------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDV 157 (205)
Q Consensus 96 ~L~~fL~d~~i~kvGv------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~ 157 (205)
.|.+++ +++.+.||+ +|...+.. .+...+.||+.|++++||..|.....
T Consensus 94 ~l~~li-~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~----~~~~r~~sLk~La~~~L~~~IQ~~~H-------- 160 (174)
T cd06143 94 KLRLLV-DLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFH----LPGQRKLSLRFLAWYLLGEKIQSETH-------- 160 (174)
T ss_pred HHHHHc-CCCCEEEeccchhHHHHhcCcCCCcceEEcHHhcc----CCCCCChhHHHHHHHHcCCcccCCCc--------
Confidence 455555 455677999 44433322 12224789999999999999865321
Q ss_pred CCCCHHHHHHHHhhHHHHHHHHH
Q 045621 158 NNLSKQQIRYAAIDAFVSFKLAI 180 (205)
Q Consensus 158 rpLs~~Qi~YAA~DA~~~~~I~~ 180 (205)
=..-||.+++++|+
T Consensus 161 ---------dSvEDArAam~Ly~ 174 (174)
T cd06143 161 ---------DSIEDARTALKLYR 174 (174)
T ss_pred ---------CcHHHHHHHHHHhC
Confidence 12679999998873
No 27
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=80.98 E-value=13 Score=32.38 Aligned_cols=72 Identities=19% Similarity=0.211 Sum_probs=43.9
Q ss_pred HHHHHhhcCCCeeEEEe---eeHHHHHHHh--cCCcc-----------------hhcccHHHHHHHHcCcccccCCcccc
Q 045621 95 QSLVDFLDNDKFTFVGT---MDVADMAAAK--YDDEE-----------------LKTFGLKRLVLKFLHVEMEKSKRITL 152 (205)
Q Consensus 95 ~~L~~fL~d~~i~kvGv---~Dl~~la~~~--lg~~~-----------------~~~~gL~~Lv~~~lg~~l~K~~~v~~ 152 (205)
..+.+|+.+. ++||+ ||...+.+.. .|.+. ..+.||+.|++. +|.+.++.
T Consensus 139 ~~f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~~~-lgi~~~~~----- 210 (257)
T PRK08517 139 EEFRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKEL-LGIEIEVH----- 210 (257)
T ss_pred HHHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHHHH-cCcCCCCC-----
Confidence 4666777653 47888 7766554321 11110 124556666553 45544433
Q ss_pred cCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHH
Q 045621 153 SKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEII 187 (205)
Q Consensus 153 SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~ 187 (205)
+=|..||.++.+|+..+..+.+
T Consensus 211 -------------HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 211 -------------HRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred -------------CChHHHHHHHHHHHHHHHHHhH
Confidence 3478999999999999987754
No 28
>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=80.23 E-value=2.3 Score=33.53 Aligned_cols=66 Identities=18% Similarity=0.312 Sum_probs=42.9
Q ss_pred HHHHHhhcCCCeeEEEe---eeHHHHHHHh-------------cCCcc-hhcccHHHHHHHHcCcccc-cCCcccccCCC
Q 045621 95 QSLVDFLDNDKFTFVGT---MDVADMAAAK-------------YDDEE-LKTFGLKRLVLKFLHVEME-KSKRITLSKWD 156 (205)
Q Consensus 95 ~~L~~fL~d~~i~kvGv---~Dl~~la~~~-------------lg~~~-~~~~gL~~Lv~~~lg~~l~-K~~~v~~SnW~ 156 (205)
+.|.+|+.+ .+ .||+ +|++.+.... ..... ..+.||+.+++.++|..+. ..++
T Consensus 69 ~~l~~~l~~-~v-lVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~------- 139 (152)
T cd06144 69 KKVAELLKG-RI-LVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHS------- 139 (152)
T ss_pred HHHHHHhCC-CE-EEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcC-------
Confidence 567788876 44 4888 7776553210 00000 2468999999999998764 3343
Q ss_pred CCCCCHHHHHHHHhhHHHHHHHHH
Q 045621 157 VNNLSKQQIRYAAIDAFVSFKLAI 180 (205)
Q Consensus 157 ~rpLs~~Qi~YAA~DA~~~~~I~~ 180 (205)
|..||.++.+||+
T Consensus 140 -----------Al~DA~at~~l~~ 152 (152)
T cd06144 140 -----------SVEDARAAMRLYR 152 (152)
T ss_pred -----------cHHHHHHHHHHhC
Confidence 6789999998873
No 29
>PRK07740 hypothetical protein; Provisional
Probab=79.70 E-value=14 Score=31.64 Aligned_cols=25 Identities=28% Similarity=0.032 Sum_probs=20.4
Q ss_pred HHHHhhHHHHHHHHHHHHHhHHcCC
Q 045621 166 RYAAIDAFVSFKLAIELKKEIIALP 190 (205)
Q Consensus 166 ~YAA~DA~~~~~I~~~L~~~~~~~p 190 (205)
+=|..||....+|+.++........
T Consensus 206 H~Al~Da~ata~l~~~ll~~~~~~~ 230 (244)
T PRK07740 206 HHALGDALMTAKLWAILLVEAQQRG 230 (244)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHcC
Confidence 3478999999999999988865543
No 30
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=79.20 E-value=12 Score=33.45 Aligned_cols=24 Identities=8% Similarity=-0.179 Sum_probs=19.2
Q ss_pred HHHHhhHHHHHHHHHHHHHhHHcC
Q 045621 166 RYAAIDAFVSFKLAIELKKEIIAL 189 (205)
Q Consensus 166 ~YAA~DA~~~~~I~~~L~~~~~~~ 189 (205)
+=|..||+++.+||.++....+..
T Consensus 152 H~Al~DA~~ta~l~~~l~~~~~~~ 175 (313)
T PRK06807 152 HNAFDDCITCAAVYQKCASIEEEA 175 (313)
T ss_pred cChHHHHHHHHHHHHHHHHhhhhc
Confidence 447899999999999998885333
No 31
>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=78.89 E-value=14 Score=37.30 Aligned_cols=47 Identities=28% Similarity=0.328 Sum_probs=34.7
Q ss_pred hcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcCCCCC
Q 045621 128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPT 193 (205)
Q Consensus 128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~p~~~ 193 (205)
.+.+|.+|++. +|...+..++ |..||.+..+|+.++..+.+.+|...
T Consensus 126 ~~~~L~~l~~~-~gi~~~~~H~------------------Al~DA~ata~l~~~l~~~~~~l~~~~ 172 (850)
T TIGR01407 126 ESYQLSELSEA-LGLTHENPHR------------------ADSDAQATAELLLLLFEKMEKLPLDT 172 (850)
T ss_pred CCCCHHHHHHH-CCCCCCCCCC------------------hHHHHHHHHHHHHHHHHHHHhcCCcc
Confidence 35667777666 5665554444 88999999999999998877777653
No 32
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=78.25 E-value=13 Score=37.63 Aligned_cols=77 Identities=25% Similarity=0.407 Sum_probs=50.0
Q ss_pred HHHHHhhcCCCeeEEEe---eeHHHHHHHh--cCC-----------------cchhcccHHHHHHHHcCcccccCCcccc
Q 045621 95 QSLVDFLDNDKFTFVGT---MDVADMAAAK--YDD-----------------EELKTFGLKRLVLKFLHVEMEKSKRITL 152 (205)
Q Consensus 95 ~~L~~fL~d~~i~kvGv---~Dl~~la~~~--lg~-----------------~~~~~~gL~~Lv~~~lg~~l~K~~~v~~ 152 (205)
+.+.+|+.+ -+.||+ ||+..+.+.. .|. +...+.+|.++++. +|.+....++
T Consensus 78 ~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~-lgl~~~~~H~--- 151 (820)
T PRK07246 78 RHIYDLIED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRE-LNIDLADAHT--- 151 (820)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHH-cCCCCCCCCC---
Confidence 456677765 346888 7776664421 111 11235667777665 5655444444
Q ss_pred cCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcCCCC
Q 045621 153 SKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKP 192 (205)
Q Consensus 153 SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~p~~ 192 (205)
|..||.++.+++.+|..+...+|..
T Consensus 152 ---------------Al~DA~ata~L~~~l~~~l~~l~~~ 176 (820)
T PRK07246 152 ---------------AIADARATAELFLKLLQKIESLPKE 176 (820)
T ss_pred ---------------HHHHHHHHHHHHHHHHHHHhhcCch
Confidence 8999999999999999887777654
No 33
>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=76.94 E-value=17 Score=28.50 Aligned_cols=51 Identities=24% Similarity=0.188 Sum_probs=36.2
Q ss_pred eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHH
Q 045621 112 MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIEL 182 (205)
Q Consensus 112 ~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L 182 (205)
+|++.+++...|.. ...+|.++++. +|..... +-+-|-.||..+.+|+.++
T Consensus 125 ~D~~~~~~~~~~~~--~~~~L~~l~~~-~gi~~~~-----------------~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 125 IDLKKEFAKFYGLK--KRTGLSKALEY-LGLEFEG-----------------RHHRGLDDARNIARILKRL 175 (176)
T ss_pred EEHHHHHHHHhCCC--CCCCHHHHHHH-CCCCCCC-----------------CCcCcHHHHHHHHHHHHHh
Confidence 78888877655543 57888888766 5766551 1234789999999998876
No 34
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=76.47 E-value=17 Score=37.19 Aligned_cols=78 Identities=24% Similarity=0.342 Sum_probs=49.5
Q ss_pred HHHHHhhcCCCeeEEEe---eeHHHHHHHh--cCC------------------cchhcccHHHHHHHHcCcccccCCccc
Q 045621 95 QSLVDFLDNDKFTFVGT---MDVADMAAAK--YDD------------------EELKTFGLKRLVLKFLHVEMEKSKRIT 151 (205)
Q Consensus 95 ~~L~~fL~d~~i~kvGv---~Dl~~la~~~--lg~------------------~~~~~~gL~~Lv~~~lg~~l~K~~~v~ 151 (205)
+.|.+|+.+ .++||+ ||++.+.... .|. +...+.+|..|++. +|...+..++
T Consensus 76 ~~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~-l~i~~~~~H~-- 150 (928)
T PRK08074 76 PEIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEE-LGLEHDQPHR-- 150 (928)
T ss_pred HHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHh-CCCCCCCCCC--
Confidence 466777764 356787 6666554321 111 11234566666665 4555444444
Q ss_pred ccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcCCCCC
Q 045621 152 LSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPT 193 (205)
Q Consensus 152 ~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~p~~~ 193 (205)
|-.||.+..+++.+|.++...+|...
T Consensus 151 ----------------Al~DA~ata~l~~~l~~~~~~l~~~~ 176 (928)
T PRK08074 151 ----------------ADSDAEVTAELFLQLLNKLERLPLVT 176 (928)
T ss_pred ----------------hHHHHHHHHHHHHHHHHHHHhcCCcC
Confidence 88999999999999999988876544
No 35
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=74.50 E-value=3.5 Score=42.08 Aligned_cols=66 Identities=21% Similarity=0.293 Sum_probs=46.4
Q ss_pred HhhcCCCeeEEEe------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCC
Q 045621 99 DFLDNDKFTFVGT------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNL 160 (205)
Q Consensus 99 ~fL~d~~i~kvGv------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpL 160 (205)
.+|-+-+++|||+ +|.-.+. .+|. .+..||+-||.++||..|. +.+-+.
T Consensus 1008 ~~Li~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf--~~~s--~R~LSLrfLa~~lLg~~IQ------~~~HDS--- 1074 (1118)
T KOG1275|consen 1008 RLLIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLF--RLGS--QRMLSLRFLAWELLGETIQ------MEAHDS--- 1074 (1118)
T ss_pred HHHHHcCcEEEcccccccceEEEEecChhhheeeeEEE--eccc--ccEEEHHHHHHHHhcchhh------cccccc---
Confidence 6889999999999 3332222 1332 2689999999999998764 334343
Q ss_pred CHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621 161 SKQQIRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 161 s~~Qi~YAA~DA~~~~~I~~~L~~~ 185 (205)
--||...+++|++..+.
T Consensus 1075 --------IeDA~taLkLYk~Yl~l 1091 (1118)
T KOG1275|consen 1075 --------IEDARTALKLYKKYLKL 1091 (1118)
T ss_pred --------HHHHHHHHHHHHHHHHH
Confidence 56888888888876554
No 36
>PRK07883 hypothetical protein; Validated
Probab=74.23 E-value=19 Score=34.81 Aligned_cols=23 Identities=17% Similarity=0.023 Sum_probs=19.3
Q ss_pred HHHHhhHHHHHHHHHHHHHhHHc
Q 045621 166 RYAAIDAFVSFKLAIELKKEIIA 188 (205)
Q Consensus 166 ~YAA~DA~~~~~I~~~L~~~~~~ 188 (205)
+=|..||.+..+|+.++......
T Consensus 162 H~Al~DA~ata~l~~~l~~~~~~ 184 (557)
T PRK07883 162 HRALDDARATVDVLHGLIERLGN 184 (557)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHh
Confidence 55899999999999999887543
No 37
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=74.00 E-value=28 Score=29.58 Aligned_cols=26 Identities=23% Similarity=0.286 Sum_probs=20.9
Q ss_pred HHHHhhHHHHHHHHHHHHHhHHcCCC
Q 045621 166 RYAAIDAFVSFKLAIELKKEIIALPK 191 (205)
Q Consensus 166 ~YAA~DA~~~~~I~~~L~~~~~~~p~ 191 (205)
+=|..||.++.+|+.++.+..+.+..
T Consensus 160 H~Al~Da~ata~l~~~l~~~~~~l~~ 185 (232)
T PRK07942 160 HEATADALAAARVAWALARRFPELAA 185 (232)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34889999999999999888765533
No 38
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=73.78 E-value=19 Score=27.69 Aligned_cols=33 Identities=18% Similarity=0.199 Sum_probs=21.2
Q ss_pred hcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHH
Q 045621 128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAI 180 (205)
Q Consensus 128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~ 180 (205)
.+.+|+.+++. +|.... .+ =|..||....+|+.
T Consensus 123 ~~~~L~~l~~~-~g~~~~-~H------------------~Al~Da~~ta~l~~ 155 (156)
T cd06130 123 PNHKLNTVAEH-LGIELN-HH------------------DALEDARACAEILL 155 (156)
T ss_pred CCCCHHHHHHH-cCCCcc-Cc------------------CchHHHHHHHHHHh
Confidence 45566666665 455444 33 37889988888763
No 39
>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=73.23 E-value=6.3 Score=31.38 Aligned_cols=38 Identities=21% Similarity=0.246 Sum_probs=26.7
Q ss_pred hcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHH
Q 045621 128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAI 180 (205)
Q Consensus 128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~ 180 (205)
.+.+|+.|++.++|..+....+ -+=|..||-++.++|+
T Consensus 120 ~~~~L~~L~~~~~~~~i~~~~~---------------~H~Al~DA~at~~l~~ 157 (157)
T cd06149 120 CRVSLKVLAKRLLHRDIQVGRQ---------------GHSSVEDARATMELYK 157 (157)
T ss_pred CChhHHHHHHHHcChhhcCCCC---------------CcCcHHHHHHHHHHhC
Confidence 5689999999998877754211 1225678888888763
No 40
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=72.94 E-value=29 Score=28.74 Aligned_cols=22 Identities=18% Similarity=0.211 Sum_probs=19.1
Q ss_pred HHHHHhhHHHHHHHHHHHHHhH
Q 045621 165 IRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 165 i~YAA~DA~~~~~I~~~L~~~~ 186 (205)
-+-|..||+.+.+|+.++....
T Consensus 159 ~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 159 HHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred CcChHHHHHHHHHHHHHHHhCc
Confidence 3569999999999999998874
No 41
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=72.43 E-value=8 Score=32.69 Aligned_cols=72 Identities=19% Similarity=0.335 Sum_probs=49.8
Q ss_pred EEe--eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccc-cC-CcccccCCC-CCCCC-HHHHHHHHhhHHHHHHHHHHH
Q 045621 109 VGT--MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEME-KS-KRITLSKWD-VNNLS-KQQIRYAAIDAFVSFKLAIEL 182 (205)
Q Consensus 109 vGv--~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~-K~-~~v~~SnW~-~rpLs-~~Qi~YAA~DA~~~~~I~~~L 182 (205)
.|. +|+=.+++... .+.+.+|+.+++++||..-. -+ +. +++|. ..+=. ..=++|...||...++|+.+|
T Consensus 149 ~GR~~iD~~~~~~~~~---kl~sy~L~~Va~~~Lg~~k~d~~~~~--i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl 223 (230)
T cd05777 149 EGRIQFDLLQVIQRDY---KLRSYSLNSVSAHFLGEQKEDVHYSI--ITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKL 223 (230)
T ss_pred cCEEeeeHHHHHHHhc---CcccCcHHHHHHHHhCCCCCCCCHHH--HHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHH
Confidence 455 99887776532 35799999999999995422 11 23 34443 22221 345899999999999999998
Q ss_pred HHh
Q 045621 183 KKE 185 (205)
Q Consensus 183 ~~~ 185 (205)
.-.
T Consensus 224 ~~~ 226 (230)
T cd05777 224 MCL 226 (230)
T ss_pred hhH
Confidence 754
No 42
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=70.87 E-value=31 Score=29.16 Aligned_cols=20 Identities=15% Similarity=0.107 Sum_probs=17.2
Q ss_pred HHHhhHHHHHHHHHHHHHhH
Q 045621 167 YAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 167 YAA~DA~~~~~I~~~L~~~~ 186 (205)
=|..||+++..|+.++....
T Consensus 147 ~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 147 RALDDVITLHRVFSALVGDL 166 (232)
T ss_pred CcHHHHHHHHHHHHHHHHHH
Confidence 38899999999999988663
No 43
>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=69.73 E-value=8.4 Score=31.67 Aligned_cols=66 Identities=21% Similarity=0.438 Sum_probs=46.4
Q ss_pred eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccc-cC-CcccccC-CCCCCCCHHHHHHHHhhHHHHHHHHHHH
Q 045621 112 MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEME-KS-KRITLSK-WDVNNLSKQQIRYAAIDAFVSFKLAIEL 182 (205)
Q Consensus 112 ~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~-K~-~~v~~Sn-W~~rpLs~~Qi~YAA~DA~~~~~I~~~L 182 (205)
+|+-.+++... .+.+.+|+.+++++||.+-. -+ +. .+. |....--..=++|+-.||...++|..++
T Consensus 127 lDl~~~~~~~~---~l~sy~L~~v~~~~Lg~~k~d~~~~~--i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 127 VDLYPVARRTL---NLTRYTLERVYEELFGIEKEDVPGEE--IAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred EeHHHHHHhhC---CCCcCcHHHHHHHHhCCCCCcCCHHH--HHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 99988887543 34799999999999996522 11 22 333 4444444456899999999999998753
No 44
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=68.97 E-value=32 Score=30.69 Aligned_cols=23 Identities=17% Similarity=-0.125 Sum_probs=18.8
Q ss_pred HHHHHHhhHHHHHHHHHHHHHhH
Q 045621 164 QIRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 164 Qi~YAA~DA~~~~~I~~~L~~~~ 186 (205)
+-+=|..||.++.+|+..+.++.
T Consensus 157 ~~H~Al~DA~ata~l~~~ll~~~ 179 (313)
T PRK06063 157 RPHDALDDARVLAGILRPSLERA 179 (313)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHH
Confidence 34558899999999999998773
No 45
>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=67.30 E-value=13 Score=31.56 Aligned_cols=72 Identities=17% Similarity=0.311 Sum_probs=50.7
Q ss_pred CeeEEEe--eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCC---CCCCHHHHHHHHhhHHHHHHHH
Q 045621 105 KFTFVGT--MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDV---NNLSKQQIRYAAIDAFVSFKLA 179 (205)
Q Consensus 105 ~i~kvGv--~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~---rpLs~~Qi~YAA~DA~~~~~I~ 179 (205)
.+...|. +|+-.+++..+ .+.+.+|..++.++||...+.-..-..++|-+ ..-...=++|...||...++|.
T Consensus 154 ~~~i~GRi~lD~~~~~r~~~---kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 154 GIKIVGRHILNVWRLMRSEL---ALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred ceEEeeEEEeEhHHHHHHHc---CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 3455577 99987776543 35799999999999998655433334678732 2234445899999999988774
No 46
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=67.17 E-value=40 Score=29.03 Aligned_cols=20 Identities=25% Similarity=0.170 Sum_probs=16.7
Q ss_pred HHHHhhHHHHHHHHHHHHHh
Q 045621 166 RYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 166 ~YAA~DA~~~~~I~~~L~~~ 185 (205)
+=|..||+++..++..+...
T Consensus 154 H~Al~Da~at~~vl~~l~~~ 173 (250)
T PRK06310 154 HRAMKDVEINIKVFKHLCKR 173 (250)
T ss_pred cChHHHHHHHHHHHHHHHHh
Confidence 34889999999999998754
No 47
>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=66.87 E-value=40 Score=25.15 Aligned_cols=17 Identities=24% Similarity=0.227 Sum_probs=13.6
Q ss_pred HHHHHHHhhHHHHHHHH
Q 045621 163 QQIRYAAIDAFVSFKLA 179 (205)
Q Consensus 163 ~Qi~YAA~DA~~~~~I~ 179 (205)
.+-+-|..||.++.+|+
T Consensus 142 ~~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 142 EGAHRALADALATAELL 158 (159)
T ss_pred CCCCCcHHHHHHHHHHh
Confidence 45567899999998886
No 48
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=66.46 E-value=9.8 Score=38.75 Aligned_cols=63 Identities=21% Similarity=0.290 Sum_probs=48.3
Q ss_pred cccHHHHHHHHcCcc-cccCCcccccCCCCCCCCHHHH--------HHHHhhHHHHHHHHHHHHHh-HHcCCCCCccc
Q 045621 129 TFGLKRLVLKFLHVE-MEKSKRITLSKWDVNNLSKQQI--------RYAAIDAFVSFKLAIELKKE-IIALPKPTTFD 196 (205)
Q Consensus 129 ~~gL~~Lv~~~lg~~-l~K~~~v~~SnW~~rpLs~~Qi--------~YAA~DA~~~~~I~~~L~~~-~~~~p~~~~~~ 196 (205)
--||.+.++..+|.. ++|..+ -..- .++.+|| .|.|.|+|+..+||.++.-. .+.-|-|.|+-
T Consensus 322 ~NSL~dVhk~~c~~~~LdKt~R---d~Fv--s~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~FlercPHPaTla 394 (1075)
T KOG3657|consen 322 LNSLVDVHKFHCGIDALDKTPR---DSFV--SGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLERCPHPATLA 394 (1075)
T ss_pred hHHHHHHHHhhCCCCccccchH---Hhhh--cCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHhCCChHhHH
Confidence 456888888888866 888765 2222 3555654 69999999999999999988 88888887753
No 49
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=66.14 E-value=37 Score=27.85 Aligned_cols=22 Identities=23% Similarity=0.184 Sum_probs=18.1
Q ss_pred HHHHHHhhHHHHHHHHHHHHHh
Q 045621 164 QIRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 164 Qi~YAA~DA~~~~~I~~~L~~~ 185 (205)
+-+=|..||+++.+||.+|+..
T Consensus 179 ~~H~Al~DA~ata~l~~~l~~~ 200 (202)
T PRK09145 179 GRHDALNDAIMAALIFLRLRKG 200 (202)
T ss_pred CCCCcHHHHHHHHHHHHHHHhc
Confidence 3455899999999999998754
No 50
>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=63.91 E-value=21 Score=28.95 Aligned_cols=68 Identities=18% Similarity=0.259 Sum_probs=44.1
Q ss_pred EEe--eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHH
Q 045621 109 VGT--MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLA 179 (205)
Q Consensus 109 vGv--~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~ 179 (205)
.|. +|+-.+++.... +.+.+|+.++++++|..-..-..-.+.+|....--..=++|.-.||...++|+
T Consensus 129 ~gr~~~D~~~~~r~~~~---l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 129 KGRVVFDLLAAYKRDFK---LKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred eccEeeehHHHHHHhcC---cccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 355 999888876443 47899999999999853221111113343122223445899999999999886
No 51
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=58.78 E-value=37 Score=26.14 Aligned_cols=53 Identities=26% Similarity=0.276 Sum_probs=33.5
Q ss_pred eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621 112 MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 112 ~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~ 185 (205)
+|+..+++...+. ...+|+++++. +|.+..-. .+.|..||....+|+.++.+.
T Consensus 114 iD~~~~~~~~~~~---~~~~L~~l~~~-~~~~~~~~-----------------~H~A~~Da~~t~~l~~~~~~~ 166 (169)
T smart00479 114 IDTLKLARALNPG---RKYSLKKLAER-LGLEVIGR-----------------AHRALDDARATAKLFKKLVER 166 (169)
T ss_pred eEHHHHHHHHCCC---CCCCHHHHHHH-CCCCCCCC-----------------CcCcHHHHHHHHHHHHHHHHH
Confidence 5555555433321 26677777766 34332211 367999999999999999875
No 52
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=56.56 E-value=70 Score=28.32 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=18.1
Q ss_pred HHHHhhHHHHHHHHHHHHHhH
Q 045621 166 RYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 166 ~YAA~DA~~~~~I~~~L~~~~ 186 (205)
+=|.-||+++.+|+..+.++.
T Consensus 144 H~Al~DA~ata~l~~~l~~~~ 164 (309)
T PRK06195 144 HDALADAMACSNILLNISKEL 164 (309)
T ss_pred cCCHHHHHHHHHHHHHHHHHh
Confidence 668999999999999997763
No 53
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.15 E-value=59 Score=27.10 Aligned_cols=26 Identities=23% Similarity=0.238 Sum_probs=20.7
Q ss_pred HHHHHHhhHHHHHHHHHHHHHhHHcC
Q 045621 164 QIRYAAIDAFVSFKLAIELKKEIIAL 189 (205)
Q Consensus 164 Qi~YAA~DA~~~~~I~~~L~~~~~~~ 189 (205)
+-+=|..||.++.+|+.++....+..
T Consensus 155 ~~H~Al~DA~~ta~l~~~l~~~~~~~ 180 (217)
T TIGR00573 155 ALHGALADAFILAKLYLVMTGKQTKY 180 (217)
T ss_pred ccCCHHHHHHHHHHHHHHHHhcchhh
Confidence 34558899999999999998885444
No 54
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=51.48 E-value=60 Score=26.12 Aligned_cols=68 Identities=21% Similarity=0.255 Sum_probs=40.3
Q ss_pred HHHHHhhcC--CCeeEEEe----eeHHHHHHHh--cCCc---------------chhcccHHHHHHHHcCcccccCCccc
Q 045621 95 QSLVDFLDN--DKFTFVGT----MDVADMAAAK--YDDE---------------ELKTFGLKRLVLKFLHVEMEKSKRIT 151 (205)
Q Consensus 95 ~~L~~fL~d--~~i~kvGv----~Dl~~la~~~--lg~~---------------~~~~~gL~~Lv~~~lg~~l~K~~~v~ 151 (205)
+.|.+|+.. ...+.||+ ||++.+.... .|.. .+.+ +|++|++.++|.+....++
T Consensus 86 ~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~-~L~~l~~~~~~~~~~~~H~-- 162 (177)
T cd06136 86 NLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ-SLGSLYKRLFGQEPKNSHT-- 162 (177)
T ss_pred HHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh-hHHHHHHHHhCCCcccccc--
Confidence 456677654 23566777 7887664432 1110 0112 5666666666665554444
Q ss_pred ccCCCCCCCCHHHHHHHHhhHHHHHHHHHH
Q 045621 152 LSKWDVNNLSKQQIRYAAIDAFVSFKLAIE 181 (205)
Q Consensus 152 ~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~ 181 (205)
|..||.++.+++.+
T Consensus 163 ----------------A~~Da~at~~v~~~ 176 (177)
T cd06136 163 ----------------AEGDVLALLKCALH 176 (177)
T ss_pred ----------------hHHHHHHHHHHHhh
Confidence 88999999888753
No 55
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=51.42 E-value=19 Score=30.60 Aligned_cols=73 Identities=15% Similarity=0.191 Sum_probs=48.8
Q ss_pred eeEEEe--eeHHHHHHHhcCCcchhcccHHHHHHHHcCc-ccccC-Cccccc-CCCCCCCCHHHHHHHHhhHHHHHHHHH
Q 045621 106 FTFVGT--MDVADMAAAKYDDEELKTFGLKRLVLKFLHV-EMEKS-KRITLS-KWDVNNLSKQQIRYAAIDAFVSFKLAI 180 (205)
Q Consensus 106 i~kvGv--~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~-~l~K~-~~v~~S-nW~~rpLs~~Qi~YAA~DA~~~~~I~~ 180 (205)
....|. +|+-..++.... ..+++|..+++++||. ..+=+ +. .. -|....--..=++|...||+..++|..
T Consensus 150 ~~~~GRl~~D~~~~~k~~~~---~~sY~L~~va~~~Lg~~k~di~~~~--i~~~~~~~~~l~~l~~y~~~Da~l~~~L~~ 224 (234)
T cd05776 150 ELTAGRLLCDTYLSAKELIR---CKSYDLTELSQQVLGIERQDIDPEE--ILNMYNDSESLLKLLEHTEKDAYLILQLMF 224 (234)
T ss_pred ccccCchhhccHHHHHHHhC---CCCCChHHHHHHHhCcCcccCCHHH--HHHHHhCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444576 999888876543 4799999999999995 22211 12 22 243311112237899999999999999
Q ss_pred HHH
Q 045621 181 ELK 183 (205)
Q Consensus 181 ~L~ 183 (205)
+|.
T Consensus 225 kl~ 227 (234)
T cd05776 225 KLN 227 (234)
T ss_pred HHC
Confidence 875
No 56
>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=50.92 E-value=84 Score=33.56 Aligned_cols=71 Identities=18% Similarity=0.251 Sum_probs=45.2
Q ss_pred HHHHHhhcCCCeeEEEe---eeHHHHHHHh--cCC------------------cchhcccHHHHHHHHcCcccccCCccc
Q 045621 95 QSLVDFLDNDKFTFVGT---MDVADMAAAK--YDD------------------EELKTFGLKRLVLKFLHVEMEKSKRIT 151 (205)
Q Consensus 95 ~~L~~fL~d~~i~kvGv---~Dl~~la~~~--lg~------------------~~~~~~gL~~Lv~~~lg~~l~K~~~v~ 151 (205)
+.+.+|+.+ -+.||+ ||+..+.... .|. ++....+|..|++. +|..++.
T Consensus 262 ~~f~~fl~~--~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~-lgi~~~~----- 333 (1213)
T TIGR01405 262 EKFKEFFKD--SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKK-LGVDLDD----- 333 (1213)
T ss_pred HHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHH-cCCCCCC-----
Confidence 456677765 355888 6665554321 111 12345677777766 4655433
Q ss_pred ccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621 152 LSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 152 ~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~ 186 (205)
-+-|..||.++.+|+.++.++.
T Consensus 334 -------------~HrAl~DA~aTa~I~~~ll~~l 355 (1213)
T TIGR01405 334 -------------HHRADYDAEATAKVFKVMVEQL 355 (1213)
T ss_pred -------------CcCHHHHHHHHHHHHHHHHHHH
Confidence 2569999999999999998764
No 57
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=50.85 E-value=85 Score=24.41 Aligned_cols=19 Identities=26% Similarity=0.268 Sum_probs=16.0
Q ss_pred HHHHHHhhHHHHHHHHHHH
Q 045621 164 QIRYAAIDAFVSFKLAIEL 182 (205)
Q Consensus 164 Qi~YAA~DA~~~~~I~~~L 182 (205)
+-+-|..||.+..+|+.+|
T Consensus 148 ~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 148 TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCChHHHHHHHHHHHHHh
Confidence 4567999999999999776
No 58
>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=49.21 E-value=59 Score=26.91 Aligned_cols=69 Identities=14% Similarity=0.267 Sum_probs=43.6
Q ss_pred eEEEe--eeHHHHHHH-hcCCcchhcccHHHHHHHHcCcc-cccCCcc---ccc-CCCCCCCCHHHHHHHHhhHHHHHHH
Q 045621 107 TFVGT--MDVADMAAA-KYDDEELKTFGLKRLVLKFLHVE-MEKSKRI---TLS-KWDVNNLSKQQIRYAAIDAFVSFKL 178 (205)
Q Consensus 107 ~kvGv--~Dl~~la~~-~lg~~~~~~~gL~~Lv~~~lg~~-l~K~~~v---~~S-nW~~rpLs~~Qi~YAA~DA~~~~~I 178 (205)
...|. +|+-.+.+. .+ .+.+.+|+.+++++||.. .+.+..+ .++ -|...+ ..=++|+..||+..+++
T Consensus 117 ~i~GR~~~D~~~~~k~~~~---kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L 191 (193)
T cd05784 117 SLPGRVVLDGIDALKTATY---HFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRI 191 (193)
T ss_pred EEeeEEEEEhHHHHHHccC---CCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHH
Confidence 33466 998666653 12 257999999999999953 2111100 122 234333 35599999999999988
Q ss_pred HH
Q 045621 179 AI 180 (205)
Q Consensus 179 ~~ 180 (205)
++
T Consensus 192 ~~ 193 (193)
T cd05784 192 FE 193 (193)
T ss_pred hC
Confidence 63
No 59
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=47.46 E-value=68 Score=23.16 Aligned_cols=39 Identities=23% Similarity=0.298 Sum_probs=27.9
Q ss_pred cCCceeeEEEEE------EeeCCCCHHHHHhhcCCC-eeEEEe---eeHHHHHH
Q 045621 76 KLQKVAIIQLCL------FHKDRMPQSLVDFLDNDK-FTFVGT---MDVADMAA 119 (205)
Q Consensus 76 ~~~~vaLiQLcL------~~~~~~p~~L~~fL~d~~-i~kvGv---~Dl~~la~ 119 (205)
..+++.++|++. +..+ +.+++.+.. ..+||+ +|+..+.+
T Consensus 13 ~~~~i~~i~~~~~~~~~~~~~~-----f~~~l~~~~~~v~V~hn~~fD~~fL~~ 61 (96)
T cd06125 13 AVHEIIEIALADVNPEDTAVID-----LKDILRDKPLAILVGHNGSFDLPFLNN 61 (96)
T ss_pred CCCcEEEEEEEEccCCCEEEeh-----HHHHHhhCCCCEEEEeCcHHhHHHHHH
Confidence 556788888872 2222 889999877 777888 88866654
No 60
>cd01231 PH_Lnk LNK-family Pleckstrin homology (PH) domain. LNK-family Pleckstrin homology (PH) domain. The Lnk family of proteins consists of Lnk, APS and SH2B. They are adaptor proteins consisting of a PH domain and an SH2 domain, which mediates signaling through growth factor receptors. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. The lnk family PH domain is likely involved in targeting of the adaptor proteins to the plasma membrane.
Probab=42.41 E-value=71 Score=24.41 Aligned_cols=35 Identities=9% Similarity=0.213 Sum_probs=28.3
Q ss_pred CCCCceeEEEeCCcEEEEEEcCCHHHHHHHHHHHH
Q 045621 28 PLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTI 62 (205)
Q Consensus 28 ~~~~~~y~V~f~g~~I~vtvT~~~~~v~~wi~~~~ 62 (205)
|...+++.+...+..=++.-|.|++.+..|+.++.
T Consensus 71 PD~~nTFvLK~~~~~eyI~Ea~d~~q~~SWla~Ir 105 (107)
T cd01231 71 PDNLYTFVLKVDDNTDIIFEVGDEQQLNSWLAELR 105 (107)
T ss_pred cCcccEEEEEecCCceEEEEcCCHHHHHHHHHHHh
Confidence 45667788888777766777899999999999885
No 61
>PRK05168 ribonuclease T; Provisional
Probab=39.70 E-value=1.5e+02 Score=24.63 Aligned_cols=29 Identities=17% Similarity=-0.015 Sum_probs=23.2
Q ss_pred HHHHHHhhHHHHHHHHHHHHHhHHcCCCC
Q 045621 164 QIRYAAIDAFVSFKLAIELKKEIIALPKP 192 (205)
Q Consensus 164 Qi~YAA~DA~~~~~I~~~L~~~~~~~p~~ 192 (205)
+-+=|..||.+..+|+.++..+...++..
T Consensus 179 ~~H~Al~DA~ata~l~~~l~~~~~~~~~~ 207 (211)
T PRK05168 179 EAHSALYDTEKTAELFCEIVNRWKRLGGW 207 (211)
T ss_pred CCCChHHHHHHHHHHHHHHHHHHHHccCC
Confidence 45568999999999999999886666443
No 62
>PRK11779 sbcB exonuclease I; Provisional
Probab=35.53 E-value=1.4e+02 Score=28.47 Aligned_cols=26 Identities=19% Similarity=0.230 Sum_probs=20.3
Q ss_pred HHHHHHhhHHHHHHHHHHHHHhHHcC
Q 045621 164 QIRYAAIDAFVSFKLAIELKKEIIAL 189 (205)
Q Consensus 164 Qi~YAA~DA~~~~~I~~~L~~~~~~~ 189 (205)
+-+=|..||++...|+..+.+..|.+
T Consensus 176 ~AHdALsDa~aT~~la~~l~~~qP~l 201 (476)
T PRK11779 176 NAHDAMSDVYATIAMAKLIKQKQPKL 201 (476)
T ss_pred CCCCcHHHHHHHHHHHHHHHHhChHH
Confidence 34558899999999999998775544
No 63
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=34.59 E-value=2.7e+02 Score=23.72 Aligned_cols=24 Identities=17% Similarity=-0.018 Sum_probs=20.0
Q ss_pred HHHHHHHhhHHHHHHHHHHHHHhH
Q 045621 163 QQIRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 163 ~Qi~YAA~DA~~~~~I~~~L~~~~ 186 (205)
.+-+=|..||.++.+|+..+....
T Consensus 204 ~~~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 204 YSPHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHH
Confidence 344668999999999999998774
No 64
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=33.74 E-value=1.3e+02 Score=25.42 Aligned_cols=24 Identities=21% Similarity=0.159 Sum_probs=19.2
Q ss_pred HHHHhhHHHHHHHHHHHHHhHHcC
Q 045621 166 RYAAIDAFVSFKLAIELKKEIIAL 189 (205)
Q Consensus 166 ~YAA~DA~~~~~I~~~L~~~~~~~ 189 (205)
+=|..||..+.+||..|......+
T Consensus 152 H~Al~DA~~~a~v~~~l~~~~~~~ 175 (225)
T TIGR01406 152 HGALLDAHLLAEVYLALTGGQESL 175 (225)
T ss_pred cCHHHHHHHHHHHHHHHHcCCcch
Confidence 448999999999999997764443
No 65
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=32.83 E-value=1.6e+02 Score=23.91 Aligned_cols=23 Identities=13% Similarity=0.105 Sum_probs=18.8
Q ss_pred HHHHHHHhhHHHHHHHHHHHHHh
Q 045621 163 QQIRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 163 ~Qi~YAA~DA~~~~~I~~~L~~~ 185 (205)
.+-+=|..||....+++.++.++
T Consensus 166 ~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 166 KEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCcChHHHHHHHHHHHHHHHHh
Confidence 34566899999999999998753
No 66
>cd01246 PH_oxysterol_bp Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=32.28 E-value=88 Score=21.32 Aligned_cols=31 Identities=16% Similarity=0.333 Sum_probs=23.4
Q ss_pred ceeEEEeCCcEEEEEEcCCHHHHHHHHHHHH
Q 045621 32 NIWGINFGEDYFVTTVTSRASDVDRWIARTI 62 (205)
Q Consensus 32 ~~y~V~f~g~~I~vtvT~~~~~v~~wi~~~~ 62 (205)
..+.|...++......+.+.++..+|+..+.
T Consensus 59 ~~F~i~~~~~~~~~~~a~s~~e~~~Wi~al~ 89 (91)
T cd01246 59 KCFTIDTGGDKTLHLRANSEEERQRWVDALE 89 (91)
T ss_pred cEEEEEcCCCCEEEEECCCHHHHHHHHHHHH
Confidence 4566666665666667889999999998875
No 67
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=32.11 E-value=42 Score=31.15 Aligned_cols=74 Identities=20% Similarity=0.218 Sum_probs=46.6
Q ss_pred CHHHHHhhcCCCeeEEEe----------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccc--cCCcccccCC
Q 045621 94 PQSLVDFLDNDKFTFVGT----------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEME--KSKRITLSKW 155 (205)
Q Consensus 94 p~~L~~fL~d~~i~kvGv----------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~--K~~~v~~SnW 155 (205)
-..|+.|+ +++-+-||+ +|.+.+.....|. .....+|+.|++.+||..+. .+..
T Consensus 284 q~~l~~~~-~~~TILVGHSLenDL~aLKl~H~~ViDTa~lf~~~~g~-~~~k~sLk~L~~~~L~~~Iq~~~~~H------ 355 (380)
T KOG2248|consen 284 QKELLELI-SKNTILVGHSLENDLKALKLDHPSVIDTAVLFKHPTGP-YPFKSSLKNLAKSYLGKLIQEGVGGH------ 355 (380)
T ss_pred HHHHHhhc-CcCcEEEeechhhHHHHHhhhCCceeeeeEEEecCCCC-ccchHHHHHHHHHHHHHHHhccCCCC------
Confidence 36777854 455566999 4444333222221 02467799999999998887 2221
Q ss_pred CCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621 156 DVNNLSKQQIRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 156 ~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~ 186 (205)
. ..-||.+++++........
T Consensus 356 d-----------S~eDA~acm~Lv~~k~~~~ 375 (380)
T KOG2248|consen 356 D-----------SVEDALACMKLVKLKIKNS 375 (380)
T ss_pred c-----------cHHHHHHHHHHHHHHHhcc
Confidence 1 2689999999887665553
No 68
>PF00169 PH: PH domain; InterPro: IPR001849 The pleckstrin homology (PH) domain is a domain of about 100 residues that occurs in a wide range of proteins involved in intracellular signalling or as constituents of the cytoskeleton [, , , , , , ]. The pleckstrin homology domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. The 3D structure of several PH domains has been determined []. All known cases have a common structure consisting of two perpendicular anti-parallel beta sheets, followed by a C-terminal amphipathic helix. The loops connecting the beta-strands differ greatly in length, making the PH domain relatively difficult to detect. There are no totally invariant residues within the PH domain. Proteins reported to contain one more PH domains belong to the following families: Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. Pleckstrin is one of the rare proteins to contains two PH domains. Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family. Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily. Insulin Receptor Substrate 1 (IRS-1). Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr. Cytoskeletal proteins such as dynamin (see IPR001401 from INTERPRO), Caenorhabditis elegans kinesin-like protein unc-104 (see IPR001752 from INTERPRO), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1. Mammalian phosphatidylinositol-specific phospholipase C (PI-PLC) (see IPR000909 from INTERPRO) isoforms gamma and delta. Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues. Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w. Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac. Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1). C. elegans protein MIG-10. C. elegans hypothetical proteins C04D8.1, K06H7.4 and ZK632.12. S. cerevisiae hypothetical proteins YBR129c and YHR155w. ; GO: 0005515 protein binding; PDB: 1DYN_B 2DYN_B 3SNH_A 3ZYS_C 1X05_A 2I5F_A 1ZM0_B 1XX0_A 2I5C_C 3A8P_D ....
Probab=31.93 E-value=1.6e+02 Score=19.80 Aligned_cols=36 Identities=14% Similarity=0.150 Sum_probs=29.2
Q ss_pred CCCCceeEEEeCCcEEEEEEcCCHHHHHHHHHHHHH
Q 045621 28 PLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTIN 63 (205)
Q Consensus 28 ~~~~~~y~V~f~g~~I~vtvT~~~~~v~~wi~~~~~ 63 (205)
......+.|.+.+.......+++.+...+|+..+..
T Consensus 66 ~~~~~~f~i~~~~~~~~~~~~~s~~~~~~W~~~i~~ 101 (104)
T PF00169_consen 66 KKRKNCFEITTPNGKSYLFSAESEEERKRWIQAIQK 101 (104)
T ss_dssp SSSSSEEEEEETTSEEEEEEESSHHHHHHHHHHHHH
T ss_pred cCCCcEEEEEeCCCcEEEEEcCCHHHHHHHHHHHHH
Confidence 466778888888886666678899999999998864
No 69
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=30.59 E-value=1.5e+02 Score=25.39 Aligned_cols=25 Identities=16% Similarity=0.169 Sum_probs=20.2
Q ss_pred HHHHHhhHHHHHHHHHHHHHhHHcC
Q 045621 165 IRYAAIDAFVSFKLAIELKKEIIAL 189 (205)
Q Consensus 165 i~YAA~DA~~~~~I~~~L~~~~~~~ 189 (205)
.+=|..||..+.+||.++.....++
T Consensus 155 ~H~AL~DA~~~A~v~~~l~~~~~~l 179 (240)
T PRK05711 155 LHGALLDAEILAEVYLAMTGGQTSL 179 (240)
T ss_pred CCCHHHHHHHHHHHHHHHHCccccc
Confidence 4558999999999999998765544
No 70
>KOG0685 consensus Flavin-containing amine oxidase [Coenzyme transport and metabolism]
Probab=28.36 E-value=42 Score=32.19 Aligned_cols=35 Identities=37% Similarity=0.546 Sum_probs=29.9
Q ss_pred cccHHHHHHHHcC-cccccCCcccccCCCCCCCCHH
Q 045621 129 TFGLKRLVLKFLH-VEMEKSKRITLSKWDVNNLSKQ 163 (205)
Q Consensus 129 ~~gL~~Lv~~~lg-~~l~K~~~v~~SnW~~rpLs~~ 163 (205)
.-++..|-+.+++ ..+.|++++-+|+|...|+.-.
T Consensus 391 ~e~~~~~lr~fl~n~~iP~p~kilRs~W~snp~frG 426 (498)
T KOG0685|consen 391 LEGLTKLLRKFLKNPEIPKPKKILRSQWISNPFFRG 426 (498)
T ss_pred HHHHHHHHHHhcCCCCCCCchhhhhhcccCCCccCc
Confidence 4567788889999 9999999999999999888644
No 71
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=27.76 E-value=1.1e+02 Score=27.60 Aligned_cols=68 Identities=21% Similarity=0.328 Sum_probs=47.3
Q ss_pred eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccc-cCCcccccCCCCC-CCCHHHHHHHHhhHHHHHHHHHHH
Q 045621 112 MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEME-KSKRITLSKWDVN-NLSKQQIRYAAIDAFVSFKLAIEL 182 (205)
Q Consensus 112 ~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~-K~~~v~~SnW~~r-pLs~~Qi~YAA~DA~~~~~I~~~L 182 (205)
+|+-.+++.... +.+.+|+.+++++||..-. =+..--...|... ..-..-++|...||..+.+++.++
T Consensus 151 ~Dl~~~~~~~~k---l~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 151 IDLYNLYKNKLK---LPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEhHHHHHHHhC---cccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999888876543 4689999999999993221 1111113344433 234567999999999999999997
No 72
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=27.14 E-value=3.6e+02 Score=22.30 Aligned_cols=47 Identities=19% Similarity=0.176 Sum_probs=31.9
Q ss_pred hcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHh-HHcCCC
Q 045621 128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKE-IIALPK 191 (205)
Q Consensus 128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~-~~~~p~ 191 (205)
...+|+.|+. .+|+.-.. .. -+=|..||+++..+|..+... ....+.
T Consensus 141 ~~~~L~~l~~-~~gi~~~~-~~---------------~H~Al~Da~~~a~~~~~~~~~~~~~~~~ 188 (243)
T COG0847 141 DRSSLDALAE-RLGIDRNP-FH---------------PHRALFDALALAELFLLLQTGLLLKAPL 188 (243)
T ss_pred ccchHHHHHH-HcCCCcCC-cC---------------CcchHHHHHHHHHHHHHHHhcccccCch
Confidence 5777888888 56765331 11 033899999999999999984 444433
No 73
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=25.75 E-value=1.1e+02 Score=25.42 Aligned_cols=22 Identities=9% Similarity=-0.050 Sum_probs=18.5
Q ss_pred HHHHhhHHHHHHHHHHHHHhHH
Q 045621 166 RYAAIDAFVSFKLAIELKKEII 187 (205)
Q Consensus 166 ~YAA~DA~~~~~I~~~L~~~~~ 187 (205)
+=|.-||+++..|+.+|+..++
T Consensus 149 HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 149 HNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred cCCHHHHHHHHHHHHHHHhhcc
Confidence 4478999999999999988743
No 74
>PHA02528 43 DNA polymerase; Provisional
Probab=25.31 E-value=1.1e+02 Score=31.55 Aligned_cols=70 Identities=16% Similarity=0.175 Sum_probs=47.3
Q ss_pred EEe--eeHHHHHHHhcCCcchhcccHHHHHHHHcCccccc--CCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHH
Q 045621 109 VGT--MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEK--SKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIEL 182 (205)
Q Consensus 109 vGv--~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K--~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L 182 (205)
.|. +|+=++.+. .....+.+.+|+.+++++||..-.. .+. .+.|-.... ..=++|...||.....|+.++
T Consensus 251 ~GRv~lD~~dl~k~-~~~~~l~SYsLe~VA~~~LG~~K~d~~~~e--I~~l~~~d~-~~l~~Ynl~Da~Lv~~L~~kl 324 (881)
T PHA02528 251 SGISILDYLDLYKK-FTFTNQPSYRLDYIAEVELGKKKLDYSDGP--FKKFRETDH-QKYIEYNIIDVELVDRLDDKR 324 (881)
T ss_pred cceEEEeHHHHHHH-hhhcccccCCHHHHHHHHhCCCCccCCHHH--HHHHHhcCH-HHHHHHHHHHHHHHHHHHHHH
Confidence 355 888777764 2223357899999999999953322 122 344433221 445899999999999999984
No 75
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=24.72 E-value=1.6e+02 Score=30.96 Aligned_cols=75 Identities=23% Similarity=0.374 Sum_probs=49.2
Q ss_pred eeEEEe--eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCC-CCC-CHHHHHHHHhhHHHHHHHHHH
Q 045621 106 FTFVGT--MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDV-NNL-SKQQIRYAAIDAFVSFKLAIE 181 (205)
Q Consensus 106 i~kvGv--~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~-rpL-s~~Qi~YAA~DA~~~~~I~~~ 181 (205)
+...|. +|+=.+++... .+.+.+|.+++.++||..-..-..-.+++|.. .+= ...=+.|...||+..++|..+
T Consensus 405 ~~i~GR~~iDl~~~~~~~~---kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~k 481 (1054)
T PTZ00166 405 INIEGRIQFDVMDLIRRDY---KLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDK 481 (1054)
T ss_pred eEeeeEEEEEHHHHHHHhc---CcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHH
Confidence 344466 99877776532 35799999999999995432111112445532 121 122488999999999999999
Q ss_pred HH
Q 045621 182 LK 183 (205)
Q Consensus 182 L~ 183 (205)
|.
T Consensus 482 l~ 483 (1054)
T PTZ00166 482 LL 483 (1054)
T ss_pred Hh
Confidence 85
No 76
>cd01265 PH_PARIS-1 PARIS-1 pleckstrin homology (PH) domain. PARIS-1 pleckstrin homology (PH) domain. PARIS-1 contains a PH domain and a TBC-type GTPase catalytic domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=24.43 E-value=2.7e+02 Score=19.95 Aligned_cols=32 Identities=9% Similarity=0.249 Sum_probs=24.1
Q ss_pred CceeEEEeCCcEEEEEEcCCHHHHHHHHHHHHH
Q 045621 31 HNIWGINFGEDYFVTTVTSRASDVDRWIARTIN 63 (205)
Q Consensus 31 ~~~y~V~f~g~~I~vtvT~~~~~v~~wi~~~~~ 63 (205)
...+.|..+ +.+....++++++.++||+.+..
T Consensus 61 ~~~F~i~t~-~r~y~l~A~s~~e~~~Wi~al~~ 92 (95)
T cd01265 61 KGRFEIHSN-NEVIALKASSDKQMNYWLQALQS 92 (95)
T ss_pred CCEEEEEcC-CcEEEEECCCHHHHHHHHHHHHh
Confidence 346666554 46677789999999999988754
No 77
>PF12317 IFT46_B_C: Intraflagellar transport complex B protein 46 C terminal; InterPro: IPR022088 This entry represents proteins is found in eukaryotes. Proteins are typically between 298 and 416 amino acids in length. It is thought to be a flagellar protein of complex B and like all IFT proteins, it is required for transport of IFT particles into the flagella [].
Probab=24.01 E-value=82 Score=27.02 Aligned_cols=49 Identities=16% Similarity=0.367 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHHHHhhhccccceee----ccCCceeeEEEEEEeeCCCCHHHHHhhcCC
Q 045621 48 TSRASDVDRWIARTINVHRRRLHRLIT----NKLQKVAIIQLCLFHKDRMPQSLVDFLDND 104 (205)
Q Consensus 48 T~~~~~v~~wi~~~~~~~~~~~~~lvv----~~~~~vaLiQLcL~~~~~~p~~L~~fL~d~ 104 (205)
.+++.++++||.++...|+.+.-+ .| ..+.-=.|+| ..|+.+.++|.+-
T Consensus 112 e~n~k~Id~WI~~i~elHr~kp~~-tV~Y~~~mPdId~LMq-------eWP~e~Ee~L~~~ 164 (214)
T PF12317_consen 112 EKNPKEIDKWIESIEELHRSKPPP-TVHYSKPMPDIDTLMQ-------EWPPEFEELLKKV 164 (214)
T ss_pred hhCHHHHHHHHHHHHHHHhcCCCC-ceecCCCCCCHHHHHH-------HCcHHHHHHHhhc
Confidence 467899999999999988775211 22 1222234444 6899999999873
No 78
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=23.88 E-value=1.5e+02 Score=26.34 Aligned_cols=72 Identities=19% Similarity=0.264 Sum_probs=47.9
Q ss_pred HHHHHhhcCCCeeEEEe---eeHHHHHHH--------hcCCc-------chhcccHHHHHHHHcCcccccCCcccccCCC
Q 045621 95 QSLVDFLDNDKFTFVGT---MDVADMAAA--------KYDDE-------ELKTFGLKRLVLKFLHVEMEKSKRITLSKWD 156 (205)
Q Consensus 95 ~~L~~fL~d~~i~kvGv---~Dl~~la~~--------~lg~~-------~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~ 156 (205)
....+||.+ + +.||+ =|++.|--. .-.++ ...+.||+.|++++||..|.-.+. .|
T Consensus 176 ~ev~klL~g-R-IlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeH--sS--- 248 (280)
T KOG2249|consen 176 KEVLKLLKG-R-ILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEH--SS--- 248 (280)
T ss_pred HHHHHHHhC-C-EEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhcccc--Cc---
Confidence 466778877 3 44898 455443211 00011 114789999999999998876543 11
Q ss_pred CCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621 157 VNNLSKQQIRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 157 ~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~ 185 (205)
--||-+.+.+|.+....
T Consensus 249 ------------vEDA~AtM~LY~~vk~q 265 (280)
T KOG2249|consen 249 ------------VEDARATMELYKRVKVQ 265 (280)
T ss_pred ------------HHHHHHHHHHHHHHHHH
Confidence 57999999999998776
No 79
>PF15406 PH_6: Pleckstrin homology domain
Probab=23.36 E-value=1.8e+02 Score=22.42 Aligned_cols=51 Identities=25% Similarity=0.324 Sum_probs=37.8
Q ss_pred CCCccccccccCCCCCCCCCCCCceeEEEeCCcEEEEEEcCCHHHHHHHHHHHH
Q 045621 9 SPKPAEIKPLAYNSSSSIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTI 62 (205)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~y~V~f~g~~I~vtvT~~~~~v~~wi~~~~ 62 (205)
+-.|++|-||+ .-++.+....+.+.+.+.|. -++-=..+++.-+.|+..+.
T Consensus 60 ka~P~GiinLa--dase~~~~g~~kF~f~~~G~-khtF~A~s~aERD~Wv~~lk 110 (112)
T PF15406_consen 60 KASPSGIINLA--DASEPEKDGSNKFHFKIKGH-KHTFEAASAAERDNWVAQLK 110 (112)
T ss_pred ccCCcceEehh--hccccccCCCceEEEEeCCc-eeeeecCCHHHhccHHHHhh
Confidence 35799999993 34445677788888888665 45555678899999998764
No 80
>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=23.36 E-value=3e+02 Score=22.54 Aligned_cols=27 Identities=22% Similarity=0.091 Sum_probs=22.2
Q ss_pred HHHHHHHhhHHHHHHHHHHHHHhHHcC
Q 045621 163 QQIRYAAIDAFVSFKLAIELKKEIIAL 189 (205)
Q Consensus 163 ~Qi~YAA~DA~~~~~I~~~L~~~~~~~ 189 (205)
.|-+=|..||..+.+|+.++..+...+
T Consensus 169 ~~~H~Al~Da~ata~lf~~l~~~~~~~ 195 (200)
T TIGR01298 169 TQAHSALYDTEKTAELFCEIVNRWKRL 195 (200)
T ss_pred cchhhhHHhHHHHHHHHHHHHHHHHHc
Confidence 467779999999999999998884433
No 81
>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=23.27 E-value=1.4e+02 Score=24.86 Aligned_cols=48 Identities=19% Similarity=0.239 Sum_probs=32.1
Q ss_pred hhcccHHHHHHHHcCc-ccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHH
Q 045621 127 LKTFGLKRLVLKFLHV-EMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAI 180 (205)
Q Consensus 127 ~~~~gL~~Lv~~~lg~-~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~ 180 (205)
+.+.+|+++++++||. +++-+.+|..-+ ..+=++|+..||...+.|+.
T Consensus 154 ~~~~~L~~Va~~~lg~~K~~~~~~i~~~~------~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 154 YREYTLDAVAKALLGEGKVELEKNISELN------LYELAEYNYRDAELTLELTT 202 (204)
T ss_pred cccCcHHHHHHHhcCCCcccCCchhhhhc------HHHHHHhhHHHHHHHHHHhc
Confidence 4688999999999994 233322322111 13348999999999888764
No 82
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=22.97 E-value=3e+02 Score=22.08 Aligned_cols=17 Identities=24% Similarity=0.135 Sum_probs=12.4
Q ss_pred HHHHHHHhhHHHHHHHH
Q 045621 163 QQIRYAAIDAFVSFKLA 179 (205)
Q Consensus 163 ~Qi~YAA~DA~~~~~I~ 179 (205)
.+-+-|..||....+|.
T Consensus 166 ~~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 166 SNAHDALSDVEATIALA 182 (183)
T ss_pred cccccHHHHHHHHHHHh
Confidence 45567889998887653
No 83
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=22.56 E-value=4.1e+02 Score=29.15 Aligned_cols=40 Identities=33% Similarity=0.376 Sum_probs=28.5
Q ss_pred hcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621 128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI 186 (205)
Q Consensus 128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~ 186 (205)
.+.+|+.|++. +|..+... +-|--||.++.+|+.++.++.
T Consensus 545 k~~kL~~LAk~-lGL~~~~~------------------HrAl~DA~aTa~lf~~ll~~l 584 (1437)
T PRK00448 545 KSHRLNTLAKK-FGVELEHH------------------HRADYDAEATAYLLIKFLKDL 584 (1437)
T ss_pred ccccHHHHHHH-cCCCCCCC------------------cChHHHHHHHHHHHHHHHHHH
Confidence 35566666665 45544332 558999999999999998774
No 84
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=21.68 E-value=4.9e+02 Score=21.87 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=17.6
Q ss_pred HHHHHhhHHHHHHHHHHHHHh
Q 045621 165 IRYAAIDAFVSFKLAIELKKE 185 (205)
Q Consensus 165 i~YAA~DA~~~~~I~~~L~~~ 185 (205)
-+=|.-||+++.+++.++.+.
T Consensus 133 aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 133 HHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred CCcHHHHHHHHHHHHHHHHHH
Confidence 345899999999999999854
No 85
>COG4573 GatZ Predicted tagatose 6-phosphate kinase [Carbohydrate transport and metabolism]
Probab=21.60 E-value=1.9e+02 Score=26.82 Aligned_cols=84 Identities=19% Similarity=0.340 Sum_probs=54.6
Q ss_pred eEEEeCCcEEEEEEcCCHHHHHHHHHHHHHhhhccccceee---ccCCceeeEEEEEEeeCCCCHHHHHhhcCC-CeeEE
Q 045621 34 WGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLIT---NKLQKVAIIQLCLFHKDRMPQSLVDFLDND-KFTFV 109 (205)
Q Consensus 34 y~V~f~g~~I~vtvT~~~~~v~~wi~~~~~~~~~~~~~lvv---~~~~~vaLiQLcL~~~~~~p~~L~~fL~d~-~i~kv 109 (205)
..|.|++.+|...-....+.+..||++.- .+|+ +.. -.-+..|+.+..|. .|.||
T Consensus 226 PGVEFd~~~Vi~Y~p~~A~aLs~~i~~~~--------~~VfEAHSTD-------------YQT~~Al~aLV~DhfaILKV 284 (426)
T COG4573 226 PGVEFDHTNVIDYQPQKAQALSAWIENTP--------GLVFEAHSTD-------------YQTPQALRALVRDHFAILKV 284 (426)
T ss_pred CCcccCCCceeecCHHHHHHHHHHHhhCC--------CeEEeecccC-------------cCCHHHHHHHHhcCceeEee
Confidence 56788888877765556666777776552 3444 110 03578999998884 68999
Q ss_pred Ee----------eeHHHHHHHhcCCcchhcccHHHHHHHHc
Q 045621 110 GT----------MDVADMAAAKYDDEELKTFGLKRLVLKFL 140 (205)
Q Consensus 110 Gv----------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~l 140 (205)
|- |-|..++....+.. ...+|.+..++++
T Consensus 285 GPaLTFAlREAlfaL~~Ie~eL~~~~--~~s~l~~v~e~vM 323 (426)
T COG4573 285 GPALTFALREALFALAQIEEELIPPE--QRSGLRAVMEEVM 323 (426)
T ss_pred cchHHHHHHHHHHHHHHHHHHhcChh--hcccHHHHHHHHH
Confidence 88 55566665555422 4567888777764
No 86
>cd01257 PH_IRS Insulin receptor substrate (IRS) pleckstrin homology (PH) domain. Insulin receptor substrate (IRS) pleckstrin homology (PH) domain. PH domains are only found in eukaryotes, and are often involved in targeting proteins to the plasma membrane via lipid binding. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes. The IRS PH domain targets IRS molecules to the plasma membrane, usually in response to insulin stimulation.
Probab=20.78 E-value=2.2e+02 Score=21.10 Aligned_cols=29 Identities=10% Similarity=0.359 Sum_probs=21.5
Q ss_pred eeEEEeCCcEEEEEEcCCHHHHHHHHHHHH
Q 045621 33 IWGINFGEDYFVTTVTSRASDVDRWIARTI 62 (205)
Q Consensus 33 ~y~V~f~g~~I~vtvT~~~~~v~~wi~~~~ 62 (205)
...+.. .+.....+++++++.++|++.+.
T Consensus 71 ~f~i~t-~dr~f~l~aese~E~~~Wi~~i~ 99 (101)
T cd01257 71 LIALYT-RDEYFAVAAENEAEQDSWYQALL 99 (101)
T ss_pred EEEEEe-CCceEEEEeCCHHHHHHHHHHHh
Confidence 344434 44577778999999999999875
No 87
>PRK06722 exonuclease; Provisional
Probab=20.24 E-value=1.9e+02 Score=25.56 Aligned_cols=19 Identities=16% Similarity=0.048 Sum_probs=16.0
Q ss_pred HHHHhhHHHHHHHHHHHHH
Q 045621 166 RYAAIDAFVSFKLAIELKK 184 (205)
Q Consensus 166 ~YAA~DA~~~~~I~~~L~~ 184 (205)
+=|-.||..+.+|+.++..
T Consensus 161 HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 161 HRALADAENTANILLKAYS 179 (281)
T ss_pred cCcHHHHHHHHHHHHHHhc
Confidence 4478999999999999874
Done!