Query 039658
Match_columns 198
No_of_seqs 136 out of 1062
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 11:53:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039658.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039658hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06146 mut-7_like_exo DEDDy 3 100.0 3.2E-41 6.9E-46 272.0 17.1 167 15-195 1-193 (193)
2 cd06141 WRN_exo DEDDy 3'-5' ex 100.0 4E-39 8.6E-44 253.8 17.9 162 18-194 1-169 (170)
3 cd06129 RNaseD_like DEDDy 3'-5 100.0 3.6E-39 7.9E-44 252.8 15.6 154 24-195 2-161 (161)
4 PRK10829 ribonuclease D; Provi 100.0 1.1E-33 2.3E-38 247.9 18.7 164 15-197 3-170 (373)
5 cd06148 Egl_like_exo DEDDy 3'- 100.0 4.6E-32 9.9E-37 219.3 12.5 152 39-198 10-178 (197)
6 COG0349 Rnd Ribonuclease D [Tr 100.0 2.4E-31 5.2E-36 229.1 14.9 161 19-197 2-166 (361)
7 PF01612 DNA_pol_A_exo1: 3'-5' 100.0 4E-31 8.7E-36 207.1 14.2 164 16-197 2-175 (176)
8 TIGR01388 rnd ribonuclease D. 100.0 4.6E-29 1E-33 218.9 18.0 162 17-197 1-166 (367)
9 KOG4373 Predicted 3'-5' exonuc 99.9 1.7E-26 3.7E-31 195.1 9.3 181 3-191 16-282 (319)
10 KOG2207 Predicted 3'-5' exonuc 99.9 8.6E-24 1.9E-28 190.1 7.7 177 8-196 385-584 (617)
11 cd06142 RNaseD_exo DEDDy 3'-5' 99.9 8.8E-21 1.9E-25 149.3 17.1 145 39-197 12-160 (178)
12 smart00474 35EXOc 3'-5' exonuc 99.9 2E-20 4.3E-25 145.3 17.6 165 16-198 2-172 (172)
13 KOG2206 Exosome 3'-5' exoribon 99.8 1.6E-19 3.4E-24 162.2 8.3 163 16-197 194-360 (687)
14 cd00007 35EXOc 3'-5' exonuclea 99.7 2.7E-17 5.8E-22 125.4 12.8 145 41-197 2-155 (155)
15 cd09018 DEDDy_polA_RNaseD_like 99.7 3.2E-17 7E-22 125.3 13.2 144 41-194 1-149 (150)
16 cd06147 Rrp6p_like_exo DEDDy 3 99.7 3.4E-16 7.3E-21 125.7 16.9 164 15-197 5-172 (192)
17 PRK05755 DNA polymerase I; Pro 99.5 1.7E-13 3.7E-18 132.4 16.3 162 15-197 296-469 (880)
18 PRK14975 bifunctional 3'-5' ex 99.5 2.7E-13 5.8E-18 125.1 10.3 140 16-197 4-144 (553)
19 cd06140 DNA_polA_I_Bacillus_li 99.2 2.2E-10 4.9E-15 90.2 12.5 145 40-197 4-156 (178)
20 cd06139 DNA_polA_I_Ecoli_like_ 99.2 9.4E-10 2E-14 87.3 13.9 147 39-197 5-170 (193)
21 TIGR00593 pola DNA polymerase 98.2 5.7E-05 1.2E-09 73.5 14.7 162 17-197 306-477 (887)
22 COG0749 PolA DNA polymerase I 98.0 8.2E-05 1.8E-09 68.9 11.2 164 18-197 6-180 (593)
23 PRK07740 hypothetical protein; 97.1 0.087 1.9E-06 44.0 17.1 150 20-197 31-226 (244)
24 cd06149 ISG20 DEDDh 3'-5' exon 97.1 0.015 3.3E-07 45.2 11.5 85 80-191 70-157 (157)
25 cd06128 DNA_polA_exo DEDDy 3'- 97.0 0.011 2.4E-07 45.0 10.5 125 55-194 20-150 (151)
26 smart00479 EXOIII exonuclease 97.0 0.0084 1.8E-07 46.1 9.8 130 41-197 2-167 (169)
27 cd06137 DEDDh_RNase DEDDh 3'-5 97.0 0.0056 1.2E-07 47.7 8.7 84 80-190 76-160 (161)
28 cd06145 REX1_like DEDDh 3'-5' 97.0 0.016 3.4E-07 44.7 11.0 81 80-190 68-149 (150)
29 KOG2249 3'-5' exonuclease [Rep 96.9 0.021 4.5E-07 48.1 11.5 83 80-194 177-263 (280)
30 cd05780 DNA_polB_Kod1_like_exo 96.9 0.012 2.6E-07 47.2 10.0 145 39-193 3-195 (195)
31 PRK06807 DNA polymerase III su 96.9 0.011 2.4E-07 51.2 10.1 128 39-197 8-172 (313)
32 cd06125 DnaQ_like_exo DnaQ-lik 96.8 0.0024 5.1E-08 45.6 4.9 72 42-123 1-83 (96)
33 cd06133 ERI-1_3'hExo_like DEDD 96.8 0.018 3.9E-07 44.7 9.8 88 80-193 81-175 (176)
34 PRK06310 DNA polymerase III su 96.6 0.088 1.9E-06 44.1 13.6 130 39-196 7-173 (250)
35 cd05160 DEDDy_DNA_polB_exo DED 96.6 0.047 1E-06 43.6 11.3 100 81-190 70-198 (199)
36 cd06143 PAN2_exo DEDDh 3'-5' e 96.6 0.0083 1.8E-07 47.7 6.6 79 81-191 95-174 (174)
37 PRK08517 DNA polymerase III su 96.6 0.055 1.2E-06 45.6 11.9 130 39-197 68-231 (257)
38 PRK07883 hypothetical protein; 96.4 0.081 1.8E-06 49.4 13.4 133 39-197 15-182 (557)
39 PRK05711 DNA polymerase III su 96.4 0.044 9.6E-07 45.7 10.4 89 80-195 79-174 (240)
40 PRK06063 DNA polymerase III su 96.3 0.15 3.2E-06 44.2 13.1 131 39-197 15-179 (313)
41 cd06144 REX4_like DEDDh 3'-5' 96.2 0.065 1.4E-06 41.2 9.9 82 80-191 70-152 (152)
42 PRK06309 DNA polymerase III su 96.2 0.35 7.5E-06 39.9 14.7 130 39-197 2-166 (232)
43 TIGR01407 dinG_rel DnaQ family 96.1 0.11 2.4E-06 50.8 12.9 129 41-197 2-165 (850)
44 PRK07246 bifunctional ATP-depe 95.8 0.36 7.7E-06 47.2 14.9 129 39-197 7-170 (820)
45 PRK07942 DNA polymerase III su 95.8 0.17 3.8E-06 41.8 11.0 83 89-196 93-179 (232)
46 PRK07247 DNA polymerase III su 95.8 0.83 1.8E-05 36.8 14.7 128 39-196 5-168 (195)
47 PRK09145 DNA polymerase III su 95.6 0.31 6.8E-06 39.2 11.8 132 39-195 29-199 (202)
48 PRK08074 bifunctional ATP-depe 95.6 0.39 8.4E-06 47.6 14.2 131 39-197 3-169 (928)
49 PRK07983 exodeoxyribonuclease 95.5 1.1 2.3E-05 36.9 14.6 86 81-196 68-153 (219)
50 TIGR01405 polC_Gram_pos DNA po 95.0 0.3 6.6E-06 49.5 11.7 131 39-197 190-355 (1213)
51 KOG1275 PAB-dependent poly(A) 95.0 0.014 3E-07 56.4 2.1 82 83-195 1008-1090(1118)
52 TIGR00573 dnaq exonuclease, DN 94.9 0.16 3.4E-06 41.5 8.0 91 80-197 80-177 (217)
53 cd06131 DNA_pol_III_epsilon_Ec 94.7 0.048 1E-06 42.2 4.2 87 80-193 74-166 (167)
54 cd05781 DNA_polB_B3_exo DEDDy 94.7 0.88 1.9E-05 36.4 11.6 149 39-193 3-188 (188)
55 cd05784 DNA_polB_II_exo DEDDy 94.2 1.7 3.6E-05 35.0 12.3 141 39-191 3-193 (193)
56 TIGR01298 RNaseT ribonuclease 94.2 0.23 5E-06 40.1 7.3 82 89-197 105-192 (200)
57 KOG2248 3'-5' exonuclease [Rep 94.2 0.25 5.5E-06 43.9 8.1 85 80-194 286-372 (380)
58 cd06134 RNaseT DEDDh 3'-5' exo 94.2 0.14 3.1E-06 40.8 6.0 81 89-196 102-188 (189)
59 KOG3657 Mitochondrial DNA poly 94.0 0.1 2.2E-06 50.3 5.5 95 89-194 241-380 (1075)
60 TIGR01406 dnaQ_proteo DNA poly 93.5 0.14 3.1E-06 42.1 4.9 89 80-195 75-170 (225)
61 PRK05168 ribonuclease T; Provi 93.3 0.2 4.4E-06 40.7 5.5 82 89-197 114-201 (211)
62 PRK09146 DNA polymerase III su 93.1 2.7 5.9E-05 34.9 12.1 134 39-197 47-227 (239)
63 cd05782 DNA_polB_like1_exo Unc 92.8 0.65 1.4E-05 37.8 7.8 131 53-191 51-207 (208)
64 cd05785 DNA_polB_like2_exo Unc 92.5 2.3 5E-05 34.5 10.6 145 39-190 9-206 (207)
65 cd06130 DNA_pol_III_epsilon_li 92.2 0.82 1.8E-05 34.5 7.3 82 80-190 70-154 (156)
66 PRK07748 sporulation inhibitor 92.1 1.1 2.3E-05 36.2 8.3 91 80-196 85-179 (207)
67 cd06127 DEDDh DEDDh 3'-5' exon 92.0 0.84 1.8E-05 33.9 7.0 81 80-190 72-158 (159)
68 PRK06195 DNA polymerase III su 91.3 1.7 3.7E-05 37.4 9.1 89 80-197 73-164 (309)
69 KOG2405 Predicted 3'-5' exonuc 89.7 0.074 1.6E-06 47.1 -0.7 148 39-195 195-359 (458)
70 PRK00448 polC DNA polymerase I 88.6 2.7 5.8E-05 43.7 9.2 84 88-197 498-584 (1437)
71 cd05779 DNA_polB_epsilon_exo D 88.3 12 0.00027 30.3 12.8 96 87-191 88-204 (204)
72 PRK05601 DNA polymerase III su 88.2 5.9 0.00013 35.3 10.0 136 39-193 46-245 (377)
73 PF13482 RNase_H_2: RNase_H su 88.0 0.22 4.8E-06 38.2 0.9 146 42-193 1-163 (164)
74 PHA02528 43 DNA polymerase; Pr 83.8 48 0.001 33.0 14.7 178 7-193 49-324 (881)
75 cd05777 DNA_polB_delta_exo DED 82.3 2.3 4.9E-05 35.0 4.4 73 117-198 153-228 (230)
76 PRK05762 DNA polymerase II; Re 81.6 49 0.0011 32.4 13.9 145 39-193 155-348 (786)
77 cd05783 DNA_polB_B1_exo DEDDy 78.6 33 0.00072 27.7 12.1 139 39-191 5-202 (204)
78 cd06136 TREX1_2 DEDDh 3'-5' ex 77.9 9.7 0.00021 29.9 6.5 82 80-192 87-176 (177)
79 PRK09182 DNA polymerase III su 77.4 46 0.00099 28.6 11.5 86 79-194 112-198 (294)
80 KOG2405 Predicted 3'-5' exonuc 71.0 0.065 1.4E-06 47.4 -8.0 128 53-185 74-215 (458)
81 PRK11779 sbcB exonuclease I; P 70.5 21 0.00045 32.9 7.6 132 39-196 6-197 (476)
82 COG4328 Predicted nuclease (RN 63.5 11 0.00025 31.2 4.0 34 40-74 2-35 (266)
83 cd06138 ExoI_N N-terminal DEDD 62.4 15 0.00032 28.9 4.4 83 81-189 76-181 (183)
84 COG0847 DnaQ DNA polymerase II 59.5 73 0.0016 25.9 8.3 132 39-195 13-180 (243)
85 cd05778 DNA_polB_zeta_exo inac 55.7 17 0.00036 29.9 3.8 65 117-190 162-230 (231)
86 COG2176 PolC DNA polymerase II 52.6 43 0.00093 34.4 6.5 90 80-197 494-586 (1444)
87 PRK06722 exonuclease; Provisio 50.1 1E+02 0.0022 26.4 7.7 89 80-195 83-179 (281)
88 PF04857 CAF1: CAF1 family rib 46.8 48 0.001 27.7 5.3 97 87-191 147-261 (262)
89 PF00169 PH: PH domain; Inter 41.4 89 0.0019 20.6 5.2 32 3-34 71-102 (104)
90 cd05776 DNA_polB_alpha_exo ina 40.5 36 0.00078 27.9 3.5 70 117-194 157-227 (234)
91 cd01247 PH_GPBP Goodpasture an 40.2 93 0.002 21.5 5.2 31 3-33 60-90 (91)
92 PF04857 CAF1: CAF1 family rib 37.0 28 0.00061 29.1 2.4 37 21-62 9-67 (262)
93 PF10108 DNA_pol_B_exo2: Predi 35.9 84 0.0018 25.7 4.9 108 79-194 42-170 (209)
94 PF13289 SIR2_2: SIR2-like dom 34.6 35 0.00076 24.9 2.4 28 77-104 76-104 (143)
95 cd07027 RNAP_RPB11_like RPB11 32.5 1E+02 0.0022 21.3 4.2 36 63-98 7-44 (83)
96 PF13269 DUF4060: Protein of u 32.3 72 0.0016 21.6 3.3 21 2-22 35-55 (73)
97 cd01246 PH_oxysterol_bp Oxyste 31.8 1.1E+02 0.0024 20.2 4.4 31 3-33 60-90 (91)
98 PRK06549 acetyl-CoA carboxylas 30.8 64 0.0014 24.3 3.2 19 1-19 2-20 (130)
99 cd00821 PH Pleckstrin homology 30.7 1.2E+02 0.0027 19.1 4.5 31 3-33 65-95 (96)
100 KOG0041 Predicted Ca2+-binding 29.5 46 0.001 27.4 2.3 43 100-146 100-144 (244)
101 PRK01146 DNA-directed RNA poly 27.2 1.4E+02 0.003 20.7 4.2 35 64-98 10-46 (85)
102 cd06927 RNAP_L L subunit of Ar 26.6 1.5E+02 0.0032 20.4 4.3 36 63-98 7-44 (83)
103 PF10507 DUF2453: Protein of u 25.9 30 0.00066 25.4 0.7 57 89-146 4-62 (111)
104 cd01265 PH_PARIS-1 PARIS-1 ple 24.9 1.8E+02 0.0038 20.1 4.5 30 3-33 63-92 (95)
105 PF00982 Glyco_transf_20: Glyc 24.6 1.6E+02 0.0034 27.1 5.2 61 5-65 230-322 (474)
106 cd07029 RNAP_I_III_AC19 AC19 s 24.3 1.3E+02 0.0029 20.7 3.7 35 64-98 8-44 (85)
107 PF09848 DUF2075: Uncharacteri 23.5 1.2E+02 0.0026 26.4 4.1 40 10-49 192-231 (352)
108 TIGR02398 gluc_glyc_Psyn gluco 23.2 2.4E+02 0.0051 26.2 6.1 61 5-65 240-331 (487)
109 KOG0304 mRNA deadenylase subun 22.8 2.2E+02 0.0048 23.7 5.1 84 86-196 139-238 (239)
110 cd01260 PH_CNK Connector enhan 22.7 1.7E+02 0.0036 20.0 4.0 29 5-33 67-95 (96)
111 smart00233 PH Pleckstrin homol 22.5 2.2E+02 0.0047 18.1 5.0 31 3-33 69-99 (102)
112 PLN03064 alpha,alpha-trehalose 21.9 2.7E+02 0.0059 28.1 6.5 61 5-65 318-409 (934)
113 PF10369 ALS_ss_C: Small subun 21.3 1.4E+02 0.0031 19.9 3.3 29 5-33 30-58 (75)
114 smart00486 POLBc DNA polymeras 21.1 1.6E+02 0.0034 26.0 4.4 70 116-193 149-220 (471)
115 PF10584 Proteasome_A_N: Prote 20.5 56 0.0012 17.1 0.8 8 173-180 14-21 (23)
116 cd01251 PH_centaurin_alpha Cen 20.5 2.3E+02 0.005 19.9 4.4 25 11-35 76-100 (103)
No 1
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=100.00 E-value=3.2e-41 Score=272.05 Aligned_cols=167 Identities=23% Similarity=0.382 Sum_probs=146.1
Q ss_pred EEEeCCHHHHHHHHHH--HHhhhccCCeEEEEeeeeccCC-----CceeEEEeeeCCeEEEEEccccC-----CchHHHH
Q 039658 15 VSVIDDADVIDKKISE--LSGMLFKMRRVVGFDVKFNSQT-----RIAEMLILSAANLCLAIQLCRLS-----RIPESVT 82 (198)
Q Consensus 15 v~v~~~~~~~~~~i~~--l~~~~~~~~~vvg~D~Ew~~~~-----~~~aliQla~~~~~~l~~l~~~~-----~~p~~L~ 82 (198)
++++++++++++++.+ +.. ..+||||+||.+.+ +++|||||||++.|+|||+..++ .+|+.|+
T Consensus 1 ~~~i~~~~el~~~~~~~~l~~-----~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~ 75 (193)
T cd06146 1 IHIVDSEEELEALLLALSLEA-----GRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLK 75 (193)
T ss_pred CeEecCHHHHHHHHHHHhhcc-----CCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHH
Confidence 4689999999999999 554 89999999998765 67999999999999999998765 4788999
Q ss_pred hhccCCCeEEEEeeecchHhhchhcCCCCC------ccCceeehHHHHHHHhCCCC-------CCCCccHHHHHHHh-CC
Q 039658 83 NFLADRTICFVGFGVDKKTASIHGKTGYPR------NCDTGIDLGHLAARVLKKPK-------LIGLTGIAELAKEV-GI 148 (198)
Q Consensus 83 ~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~------~~~~~~Dl~~la~~~~g~~~-------l~~~~sL~~l~~~~-g~ 148 (198)
++|+||+|+||||++++|+++| .+.||+ .++|++|++.+++...+... ...+.||+.||+.+ |.
T Consensus 76 ~ll~d~~i~KVg~~~~~D~~~L--~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~ 153 (193)
T cd06146 76 RLFEDPDVLKLGFGFKQDLKAL--SASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGK 153 (193)
T ss_pred HHhCCCCeeEEEechHHHHHHH--HHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCC
Confidence 9999999999999999999999 888887 47899999988875432210 01468999999999 99
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHh
Q 039658 149 DHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLS 195 (198)
Q Consensus 149 ~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~ 195 (198)
.++|+ .|+|||++||||++|+.|||.|||+++.||++|.+
T Consensus 154 -----~l~K~--~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 154 -----PLDKS--EQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred -----CcCcc--cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 99885 59999999999999999999999999999999864
No 2
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=100.00 E-value=4e-39 Score=253.78 Aligned_cols=162 Identities=28% Similarity=0.464 Sum_probs=147.3
Q ss_pred eCCHHHHHHHHHHHH-hhhccCCeEEEEeeeeccCC-----CceeEEEeeeCCeEEEEEccccCCchHHHHhhccCCCeE
Q 039658 18 IDDADVIDKKISELS-GMLFKMRRVVGFDVKFNSQT-----RIAEMLILSAANLCLAIQLCRLSRIPESVTNFLADRTIC 91 (198)
Q Consensus 18 ~~~~~~~~~~i~~l~-~~~~~~~~vvg~D~Ew~~~~-----~~~aliQla~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~ 91 (198)
++++++++++++.+. . ..+||||+||.+.+ +++|+||||+++.|+|||+.+++.+|+.|+++|++++|.
T Consensus 1 ~~~~~~~~~~~~~~~~~-----~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~~~~~~l~~ll~~~~i~ 75 (170)
T cd06141 1 TDSAQDAEEAVKELLGK-----EKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSIL 75 (170)
T ss_pred CCCHHHHHHHHHHHhcC-----CCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhhcccHHHHHHhcCCCee
Confidence 468899999999998 5 89999999999874 589999999999999999998888899999999999999
Q ss_pred EEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCC
Q 039658 92 FVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWV 170 (198)
Q Consensus 92 kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~p 170 (198)
||||++++|++.| .+.+|+.+++++|++.++. .++... ++.||+.|++.+ |. .++|+|++|+|||.+||
T Consensus 76 kv~~~~k~D~~~L--~~~~g~~~~~~~Dl~~aa~-ll~~~~--~~~~l~~l~~~~l~~-----~~~k~k~~~~s~W~~rp 145 (170)
T cd06141 76 KVGVGIKGDARKL--ARDFGIEVRGVVDLSHLAK-RVGPRR--KLVSLARLVEEVLGL-----PLSKPKKVRCSNWEARP 145 (170)
T ss_pred EEEeeeHHHHHHH--HhHcCCCCCCeeeHHHHHH-HhCCCc--CCccHHHHHHHHcCc-----ccCCCCCcccCCCCCCC
Confidence 9999999999999 8899999999999886554 555432 246999999999 99 99988889999999999
Q ss_pred CCHHHHHHHHHhHHHHHHHHHHHH
Q 039658 171 FTDKQVLHAVEEARGCYIVADKLL 194 (198)
Q Consensus 171 Lt~~Qi~YAA~Da~~~~~i~~~L~ 194 (198)
||++|++|||.|||+++.||++|.
T Consensus 146 Lt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 146 LSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999986
No 3
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=100.00 E-value=3.6e-39 Score=252.84 Aligned_cols=154 Identities=18% Similarity=0.244 Sum_probs=138.2
Q ss_pred HHHHHHHHH-hhhccCCeEEEEeeeeccCC---CceeEEEeeeC-CeEEEEEccccCCchHHHHhhccCCCeEEEEeeec
Q 039658 24 IDKKISELS-GMLFKMRRVVGFDVKFNSQT---RIAEMLILSAA-NLCLAIQLCRLSRIPESVTNFLADRTICFVGFGVD 98 (198)
Q Consensus 24 ~~~~i~~l~-~~~~~~~~vvg~D~Ew~~~~---~~~aliQla~~-~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~i~ 98 (198)
++++++++. . .++||||+||.+.+ +++|+|||||+ +.|+|||+..++..|+.|+++|+|++|+||||+++
T Consensus 2 l~~~~~~l~~~-----~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~~~~~L~~lL~d~~i~Kvg~~~k 76 (161)
T cd06129 2 LSSLCEDLSMD-----GDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIE 76 (161)
T ss_pred HHHHHHHHhcC-----CCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCccCHHHHHHHhCCCCEEEEEeccH
Confidence 566777777 5 89999999999986 78999999999 99999999987767899999999999999999999
Q ss_pred chHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q 039658 99 KKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFTDKQVL 177 (198)
Q Consensus 99 ~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~ 177 (198)
+|+++| .+.+|+.+.|++|++. ++..+|.+ .+.||+.+++++ |. .++| ..|+|||++||||++|++
T Consensus 77 ~D~~~L--~~~~gi~~~~~~D~~~-aa~ll~~~---~~~~L~~l~~~~lg~-----~l~K--~~~~s~W~~rpLt~~qi~ 143 (161)
T cd06129 77 GDLWKL--LRDFGEKLQRLFDTTI-AANLKGLP---ERWSLASLVEHFLGK-----TLDK--SISCADWSYRPLTEDQKL 143 (161)
T ss_pred HHHHHH--HHHcCCCcccHhHHHH-HHHHhCCC---CCchHHHHHHHHhCC-----CCCc--cceeccCCCCCCCHHHHH
Confidence 999999 8889999999999876 44477765 357999999999 99 8876 469999999999999999
Q ss_pred HHHHhHHHHHHHHHHHHh
Q 039658 178 HAVEEARGCYIVADKLLS 195 (198)
Q Consensus 178 YAA~Da~~~~~i~~~L~~ 195 (198)
|||.|||+++.||++|.+
T Consensus 144 YAa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 144 YAAADVYALLIIYTKLRN 161 (161)
T ss_pred HHHHHHHHHHHHHHHHhC
Confidence 999999999999999863
No 4
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=1.1e-33 Score=247.87 Aligned_cols=164 Identities=15% Similarity=0.161 Sum_probs=149.3
Q ss_pred EEEeCCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCC---CceeEEEeeeCCeEEEEEccccCCchHHHHhhccCCCeE
Q 039658 15 VSVIDDADVIDKKISELSGMLFKMRRVVGFDVKFNSQT---RIAEMLILSAANLCLAIQLCRLSRIPESVTNFLADRTIC 91 (198)
Q Consensus 15 v~v~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~---~~~aliQla~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~ 91 (198)
.++|++++++++++..+.. ..++||||||.+.. .++|||||++++.++|||+...+. ...|+++|+|++|+
T Consensus 3 ~~~I~t~~~L~~~~~~l~~-----~~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~~~d-~~~L~~ll~~~~iv 76 (373)
T PRK10829 3 YQMITTDDALASVCEAARA-----FPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITD-WSPFKALLRDPQVT 76 (373)
T ss_pred cEEeCCHHHHHHHHHHHhc-----CCeEEEecccccCccCCCceeEEEEecCCceEEEecCCccc-hHHHHHHHcCCCeE
Confidence 4689999999999999876 89999999998776 569999999999999999987654 36799999999999
Q ss_pred EEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCC
Q 039658 92 FVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWV 170 (198)
Q Consensus 92 kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~p 170 (198)
||+|++++|++.| .+.+|+.+.++||+ ++|+..+|.+ .+.||+.|++++ |+ .++|++ |+|||.+||
T Consensus 77 KV~H~~~~Dl~~l--~~~~g~~p~~~fDT-qiaa~~lg~~---~~~gl~~Lv~~~lgv-----~ldK~~--~~sDW~~RP 143 (373)
T PRK10829 77 KFLHAGSEDLEVF--LNAFGELPQPLIDT-QILAAFCGRP---LSCGFASMVEEYTGV-----TLDKSE--SRTDWLARP 143 (373)
T ss_pred EEEeChHhHHHHH--HHHcCCCcCCeeeH-HHHHHHcCCC---ccccHHHHHHHHhCC-----ccCccc--ccCCCCCCC
Confidence 9999999999999 88999999999996 5566788987 368999999999 99 999865 899999999
Q ss_pred CCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 171 FTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 171 Lt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
||++|+.|||.||++++.||++|.+.|
T Consensus 144 Ls~~ql~YAa~Dv~~L~~l~~~L~~~L 170 (373)
T PRK10829 144 LSERQCEYAAADVFYLLPIAAKLMAET 170 (373)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999998876
No 5
>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=99.98 E-value=4.6e-32 Score=219.28 Aligned_cols=152 Identities=13% Similarity=0.149 Sum_probs=129.9
Q ss_pred CeEEEEeeeeccCC--CceeEEEeeeC-CeEEEEEccccC--CchHHHHhhccCCCeEEEEeeecchHhhchhcCCCCCc
Q 039658 39 RRVVGFDVKFNSQT--RIAEMLILSAA-NLCLAIQLCRLS--RIPESVTNFLADRTICFVGFGVDKKTASIHGKTGYPRN 113 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~--~~~aliQla~~-~~~~l~~l~~~~--~~p~~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~ 113 (198)
..+||||+||...+ +++||||||++ +.++|||+..++ .+++.|+++|+|++|.||||++++|...| .+.+|+.
T Consensus 10 ~~~i~~D~E~~~~~~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L--~~~~gi~ 87 (197)
T cd06148 10 QKVIGLDCEGVNLGRKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDAL--YHQYGIK 87 (197)
T ss_pred CCEEEEEcccccCCCCCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHH--HHhcCcc
Confidence 89999999998666 78999999999 999999999875 35788999999999999999999999999 8899999
Q ss_pred cCceeehHHHHHHHhCCCC---C--CCCccHHHHHHHh-CCCCCCCCCCCC------CCCCCCCCCCCCCCHHHHHHHHH
Q 039658 114 CDTGIDLGHLAARVLKKPK---L--IGLTGIAELAKEV-GIDHNSLSNKEI------EAVTPPNWNAWVFTDKQVLHAVE 181 (198)
Q Consensus 114 ~~~~~Dl~~la~~~~g~~~---l--~~~~sL~~l~~~~-g~~~~~~~l~K~------~~~~~SdW~~~pLt~~Qi~YAA~ 181 (198)
+.|+||++ +|+..++.+. . ....||+.+++.+ |. .++|. +..++|||.+||||++|+.|||.
T Consensus 88 ~~~~fDt~-iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~-----~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~ 161 (197)
T cd06148 88 LNNVFDTQ-VADALLQEQETGGFNPDRVISLVQLLDKYLYI-----SISLKEDVKKLMREDPKFWALRPLTEDMIRYAAL 161 (197)
T ss_pred ccceeeHH-HHHHHHHHHhcCCccccccccHHHHHHHhhCC-----ChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHH
Confidence 99999975 5554443221 0 0246999999999 99 77542 24689999999999999999999
Q ss_pred hHHHHHHHHHHHHhhhC
Q 039658 182 EARGCYIVADKLLSLLN 198 (198)
Q Consensus 182 Da~~~~~i~~~L~~~l~ 198 (198)
||++++.+|+.|.+.|+
T Consensus 162 Dv~~Ll~l~~~l~~~l~ 178 (197)
T cd06148 162 DVLCLLPLYYAMLDALI 178 (197)
T ss_pred HHHhHHHHHHHHHHHhh
Confidence 99999999999998773
No 6
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.4e-31 Score=229.09 Aligned_cols=161 Identities=17% Similarity=0.161 Sum_probs=145.4
Q ss_pred CCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCC---CceeEEEeeeCCeEEEEEccccCCchHHHHhhccCCCeEEEEe
Q 039658 19 DDADVIDKKISELSGMLFKMRRVVGFDVKFNSQT---RIAEMLILSAANLCLAIQLCRLSRIPESVTNFLADRTICFVGF 95 (198)
Q Consensus 19 ~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~---~~~aliQla~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~ 95 (198)
.+.+..+.++..... .+.|++|||+.... .++||||++.++.+.+||......-.+.|..+|.|++|+||.|
T Consensus 2 ~~~~~l~~~~~~~~~-----~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~~lIdpl~~~~d~~~l~~Ll~d~~v~KIfH 76 (361)
T COG0349 2 TTGDLLAAACALLRG-----SKAIAIDTEFMRLRTYYPRLCLIQISDGEGASLIDPLAGILDLPPLVALLADPNVVKIFH 76 (361)
T ss_pred CchhHHHHHHHHhcC-----CCceEEecccccccccCCceEEEEEecCCCceEecccccccccchHHHHhcCCceeeeec
Confidence 466778888888876 78999999998776 7899999999999999999874333468999999999999999
Q ss_pred eecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCCHH
Q 039658 96 GVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFTDK 174 (198)
Q Consensus 96 ~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt~~ 174 (198)
+.++|+..| .+.||+.+.++||. ++|++.+|.+ .+.||+.||+++ |+ .++|+. |.|||.+||||++
T Consensus 77 aa~~DL~~l--~~~~g~~p~plfdT-qiAa~l~g~~---~~~gl~~Lv~~ll~v-----~ldK~~--q~SDW~~RPLs~~ 143 (361)
T COG0349 77 AARFDLEVL--LNLFGLLPTPLFDT-QIAAKLAGFG---TSHGLADLVEELLGV-----ELDKSE--QRSDWLARPLSEA 143 (361)
T ss_pred cccccHHHH--HHhcCCCCCchhHH-HHHHHHhCCc---ccccHHHHHHHHhCC-----cccccc--cccccccCCCCHH
Confidence 999999999 99999999999995 5677799988 489999999999 99 999875 9999999999999
Q ss_pred HHHHHHHhHHHHHHHHHHHHhhh
Q 039658 175 QVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 175 Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
|+.|||.|+++++.||++|.+.|
T Consensus 144 Ql~YAa~DV~yL~~l~~~L~~~L 166 (361)
T COG0349 144 QLEYAAADVEYLLPLYDKLTEEL 166 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999876
No 7
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=99.97 E-value=4e-31 Score=207.14 Aligned_cols=164 Identities=21% Similarity=0.323 Sum_probs=142.7
Q ss_pred EEeCCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCC-----CceeEEEeeeCCeEEEEEccccCC--chHHHHhhccCC
Q 039658 16 SVIDDADVIDKKISELSGMLFKMRRVVGFDVKFNSQT-----RIAEMLILSAANLCLAIQLCRLSR--IPESVTNFLADR 88 (198)
Q Consensus 16 ~v~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~-----~~~aliQla~~~~~~l~~l~~~~~--~p~~L~~~l~~~ 88 (198)
++++++++++++++.+.. .+++|||+||.+.. .++++||+|+++.|++++...... +++.|+++|+||
T Consensus 2 ~~v~~~~~l~~~~~~l~~-----~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~ 76 (176)
T PF01612_consen 2 QIVDTEEELEEAIKKLKN-----AKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDP 76 (176)
T ss_dssp EEEHSHHHHHHHHHHHTT-----TSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTT
T ss_pred EecCCHHHHHHHHHHHcC-----CCeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCC
Confidence 578999999999999997 78999999999865 569999999999999998876654 478999999999
Q ss_pred CeEEEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-C-CCCCCCCCCCCCCCCCCCC
Q 039658 89 TICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-G-IDHNSLSNKEIEAVTPPNW 166 (198)
Q Consensus 89 ~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g-~~~~~~~l~K~~~~~~SdW 166 (198)
+|.||||+++.|...| .+.+|+.+.|++|+ .+++..++.. +..||+.|++.+ | . .++| +.++++|
T Consensus 77 ~i~kv~~n~~~D~~~L--~~~~~i~~~~~~D~-~l~~~~l~~~---~~~~L~~L~~~~l~~~-----~~~~--~~~~~~~ 143 (176)
T PF01612_consen 77 NIIKVGHNAKFDLKWL--YRSFGIDLKNVFDT-MLAAYLLDPT---RSYSLKDLAEEYLGNI-----DLDK--KEQMSDW 143 (176)
T ss_dssp TSEEEESSHHHHHHHH--HHHHTS--SSEEEH-HHHHHHTTTS---TTSSHHHHHHHHHSEE-----E-GH--CCTTSST
T ss_pred CccEEEEEEechHHHH--HHHhccccCCccch-hhhhhccccc---ccccHHHHHHHHhhhc-----cCcH--HHhhccC
Confidence 9999999999999999 77799999999998 7777666655 248999999999 8 6 6654 4589999
Q ss_pred C-CCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 167 N-AWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 167 ~-~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
. ++||+++|+.|||.||+++++||++|..+|
T Consensus 144 ~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 144 RKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp TTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred CcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 9 899999999999999999999999999887
No 8
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=99.96 E-value=4.6e-29 Score=218.87 Aligned_cols=162 Identities=17% Similarity=0.142 Sum_probs=144.3
Q ss_pred EeCCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCC---CceeEEEeeeCCeEEEEEccccCCchHHHHhhccCCCeEEE
Q 039658 17 VIDDADVIDKKISELSGMLFKMRRVVGFDVKFNSQT---RIAEMLILSAANLCLAIQLCRLSRIPESVTNFLADRTICFV 93 (198)
Q Consensus 17 v~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~---~~~aliQla~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kv 93 (198)
+|+|++++++++..+.. ..+|||||||.+.. .++|||||++++.|++||+..... .+.|+++|+|++|.||
T Consensus 1 ~I~t~~~l~~~~~~l~~-----~~~ia~DtE~~~~~~y~~~l~LiQia~~~~~~liD~~~~~~-~~~L~~lL~d~~i~KV 74 (367)
T TIGR01388 1 WITTDDELATVCEAVRT-----FPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIID-WSPLKELLRDESVVKV 74 (367)
T ss_pred CcCCHHHHHHHHHHHhc-----CCEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCccc-HHHHHHHHCCCCceEE
Confidence 47899999999999987 78999999998765 569999999999999999886643 4689999999999999
Q ss_pred EeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCC
Q 039658 94 GFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFT 172 (198)
Q Consensus 94 G~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt 172 (198)
||++++|+..| .+.++..+.++||++ +|+..+|.+ .+.||+.|++.+ |. .++|. .+.|||..|||+
T Consensus 75 ~h~~k~Dl~~L--~~~~~~~~~~~fDtq-lAa~lL~~~---~~~~l~~Lv~~~Lg~-----~l~K~--~~~sdW~~rPL~ 141 (367)
T TIGR01388 75 LHAASEDLEVF--LNLFGELPQPLFDTQ-IAAAFCGFG---MSMGYAKLVQEVLGV-----ELDKS--ESRTDWLARPLT 141 (367)
T ss_pred EeecHHHHHHH--HHHhCCCCCCcccHH-HHHHHhCCC---CCccHHHHHHHHcCC-----CCCcc--cccccCCCCCCC
Confidence 99999999999 788888889999965 566688865 357999999999 99 88875 489999999999
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 173 DKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 173 ~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
++|+.|||.||++++.+|++|.+.|
T Consensus 142 ~~q~~YAa~Dv~~L~~L~~~L~~~L 166 (367)
T TIGR01388 142 DAQLEYAAADVTYLLPLYAKLMERL 166 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999998876
No 9
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=99.93 E-value=1.7e-26 Score=195.08 Aligned_cols=181 Identities=23% Similarity=0.309 Sum_probs=156.2
Q ss_pred eeEEEECCeEEEEEEeCCHHHHHHHHHHHHhhh---ccCCeEEEEeeeeccC----------------------------
Q 039658 3 IYELEIKDVKFKVSVIDDADVIDKKISELSGML---FKMRRVVGFDVKFNSQ---------------------------- 51 (198)
Q Consensus 3 ~y~v~~~~~~i~v~v~~~~~~~~~~i~~l~~~~---~~~~~vvg~D~Ew~~~---------------------------- 51 (198)
.|.|-|.|+...|+++.+...+-+|+...+... ...+.+||++++|.|.
T Consensus 16 ~~~vd~~~~~~~Vtvt~~~svi~~~i~d~~~~~~~~~s~p~vvg~~vqw~p~~~~~~~~~~~~~~~~~~~a~~~~~~~~~ 95 (319)
T KOG4373|consen 16 KYSVDFFGEELIVTVTPDSSVISRWIHDVRFLSRNFSSDPLVVGRGVQWTPPTLTPDQTIYAARDLQISVARFLHLLGSS 95 (319)
T ss_pred ceeeeecccceEEEEccCcccchhhhhhhhhcccCcccCCcccCcCcccCCCCCCccccccccchhccccccccccccCc
Confidence 478999999999999999999999999988542 1128999999999988
Q ss_pred -------------------------------------------------C-CceeEEEeeeC-CeEEEEEccccCCchHH
Q 039658 52 -------------------------------------------------T-RIAEMLILSAA-NLCLAIQLCRLSRIPES 80 (198)
Q Consensus 52 -------------------------------------------------~-~~~aliQla~~-~~~~l~~l~~~~~~p~~ 80 (198)
+ .|++.+|||++ ++|+|+|+++.+++|..
T Consensus 96 ~~~~~~kl~~~~d~~a~~~~~~~~~~~~~s~~~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~en~C~I~ql~~~~~IP~~ 175 (319)
T KOG4373|consen 96 FKHKRQKLGYGSDARASPYIDNSLEIADDSDPPFVCYRREAQPYLDMGRSDPPPDTLQLCVGENRCLIIQLIHCKRIPHE 175 (319)
T ss_pred ccccccccccccccccccccccccccccccCCcceeecccccccccccccCCCcchhhhhhcccceeeEEeeccccchHH
Confidence 1 34789999998 88999999999999999
Q ss_pred HHhhccCCCeEEEEeeecchHhhchhcC-CCCCccCceeehHHHHHHHhCCCCC--CCCccHHHHHHHh-CCCCCCCCCC
Q 039658 81 VTNFLADRTICFVGFGVDKKTASIHGKT-GYPRNCDTGIDLGHLAARVLKKPKL--IGLTGIAELAKEV-GIDHNSLSNK 156 (198)
Q Consensus 81 L~~~l~~~~i~kvG~~i~~D~~~L~~~~-~~~~~~~~~~Dl~~la~~~~g~~~l--~~~~sL~~l~~~~-g~~~~~~~l~ 156 (198)
|+.||+|+++.+||+++.+|..+| .+ .+++.+....||+.++...+|. .+ .+..++...+..+ |. .+.
T Consensus 176 LR~fl~D~~~~~vgv~~d~D~~KL--~r~~hql~I~~~~dlr~~~~d~~g~-~~~~~s~e~i~~~~~~~~~~-----~v~ 247 (319)
T KOG4373|consen 176 LRSFLEDPDHTFVGVWNDQDAGKL--ERKEHQLEIGELEDLRLLVNDSLGG-SMPNDSFEEIVSETLGYYGK-----DVR 247 (319)
T ss_pred HHHhhcCCCceEEeccccccHHHH--hhhhhcccHHhhhhHHhhcchhhcc-CccCccHHHHHHHHhhcccc-----ccc
Confidence 999999999999999999999999 66 8999999999999998888776 22 0344555555555 55 677
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 039658 157 EIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVAD 191 (198)
Q Consensus 157 K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~ 191 (198)
|+++++||||+..||+.+|+.||++|||++..+|.
T Consensus 248 l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg~ 282 (319)
T KOG4373|consen 248 LDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLGV 282 (319)
T ss_pred cChhcccccceeeeccHHHHHHHHhHHHHHHHHHH
Confidence 88899999999999999999999999999999993
No 10
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.89 E-value=8.6e-24 Score=190.05 Aligned_cols=177 Identities=16% Similarity=0.236 Sum_probs=143.7
Q ss_pred ECCeEEEEEEeCCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCC----CceeEEEeeeCCeEEEEEccccCCchH----
Q 039658 8 IKDVKFKVSVIDDADVIDKKISELSGMLFKMRRVVGFDVKFNSQT----RIAEMLILSAANLCLAIQLCRLSRIPE---- 79 (198)
Q Consensus 8 ~~~~~i~v~v~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~----~~~aliQla~~~~~~l~~l~~~~~~p~---- 79 (198)
++...-.+.++.++.+++..+ +.+..++ ..+||+|+||.|.. ++++++|++.+++++|+++......+.
T Consensus 385 ~~~~~~~i~~V~~e~El~~l~--l~~l~~e-~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~ 461 (617)
T KOG2207|consen 385 EPPWVESIGMVGNEKELRDLL--LESLSEE-LRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWH 461 (617)
T ss_pred CCCcccceeeeCCHHHHHHHH--HHHhhhc-CEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHH
Confidence 344566788999999999998 3322222 69999999999993 889999999999999999988766555
Q ss_pred -HHHhhccCCCeEEEEeeecchHhhchhcC-----CCCCc---cCceeehHHHHHHHhCCCC----C-CCCccHHHHHHH
Q 039658 80 -SVTNFLADRTICFVGFGVDKKTASIHGKT-----GYPRN---CDTGIDLGHLAARVLKKPK----L-IGLTGIAELAKE 145 (198)
Q Consensus 80 -~L~~~l~~~~i~kvG~~i~~D~~~L~~~~-----~~~~~---~~~~~Dl~~la~~~~g~~~----l-~~~~sL~~l~~~ 145 (198)
.+..+|++++|.||||++++|+..| .. .+..+ +++++++..++.+..+.+. + ...-+|+.|+..
T Consensus 462 ~~~s~if~s~~i~kvGf~~~eDL~~l--~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~ 539 (617)
T KOG2207|consen 462 LLLSQIFESKSILKVGFSMREDLEVL--EASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDC 539 (617)
T ss_pred HHHHHHccCCceeeeecchhhhHHHH--HhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHH
Confidence 4688999999999999999999999 53 22222 3567777777776554321 0 046789999999
Q ss_pred h-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhh
Q 039658 146 V-GIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSL 196 (198)
Q Consensus 146 ~-g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~ 196 (198)
+ |+ .++|++ |||||..|||+..||.|||+||.++..+|.++.+.
T Consensus 540 llg~-----~lnKte--qcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~v 584 (617)
T KOG2207|consen 540 LLGK-----KLNKTE--QCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSV 584 (617)
T ss_pred Hhhh-----hccccc--ccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhh
Confidence 9 99 999876 99999999999999999999999999999998764
No 11
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.87 E-value=8.8e-21 Score=149.31 Aligned_cols=145 Identities=21% Similarity=0.225 Sum_probs=122.1
Q ss_pred CeEEEEeeeeccCC---CceeEEEeeeCCeEEEEEccccCCchHHHHhhccCCCeEEEEeeecchHhhchhcCCCCCccC
Q 039658 39 RRVVGFDVKFNSQT---RIAEMLILSAANLCLAIQLCRLSRIPESVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCD 115 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~---~~~aliQla~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~ 115 (198)
...+|||+||.+.. .+++.+|+|+++.++++++... ..++.|+.+|+|+++.||||+++.|.+.| .+.||+..+
T Consensus 12 ~~~l~~~~e~~~~~~~~~~~~~i~l~~~~~~~~i~~~~~-~~~~~l~~ll~~~~i~kv~~d~K~~~~~L--~~~~gi~~~ 88 (178)
T cd06142 12 AGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI-GDLSPLKELLADPNIVKVFHAAREDLELL--KRDFGILPQ 88 (178)
T ss_pred CCeEEEECCccCCCcCCCceEEEEEeeCCCEEEEeCCCc-ccHHHHHHHHcCCCceEEEeccHHHHHHH--HHHcCCCCC
Confidence 56899999997653 5799999999966988876544 45677999999999999999999999999 777788877
Q ss_pred ceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 039658 116 TGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLL 194 (198)
Q Consensus 116 ~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~ 194 (198)
+++|++ +++..++.. .+.|++.+++.+ |. .+.|++ .+++|.++||+.+|+.|||.||++++.+++.|.
T Consensus 89 ~~~D~~-laayLl~p~---~~~~l~~l~~~~l~~-----~~~~~~--~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~ 157 (178)
T cd06142 89 NLFDTQ-IAARLLGLG---DSVGLAALVEELLGV-----ELDKGE--QRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLK 157 (178)
T ss_pred CcccHH-HHHHHhCCC---ccccHHHHHHHHhCC-----CCCccc--ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Confidence 789975 566566643 245999999999 98 765543 789999999999999999999999999999998
Q ss_pred hhh
Q 039658 195 SLL 197 (198)
Q Consensus 195 ~~l 197 (198)
+.|
T Consensus 158 ~~L 160 (178)
T cd06142 158 EEL 160 (178)
T ss_pred HHH
Confidence 765
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=99.87 E-value=2e-20 Score=145.33 Aligned_cols=165 Identities=21% Similarity=0.265 Sum_probs=130.8
Q ss_pred EEeCCHHHHHHHHHHHH-hhhccCCeEEEEeeeeccCC---CceeEEEeeeCC-eEEEEEccccCCchHHHHhhccCCCe
Q 039658 16 SVIDDADVIDKKISELS-GMLFKMRRVVGFDVKFNSQT---RIAEMLILSAAN-LCLAIQLCRLSRIPESVTNFLADRTI 90 (198)
Q Consensus 16 ~v~~~~~~~~~~i~~l~-~~~~~~~~vvg~D~Ew~~~~---~~~aliQla~~~-~~~l~~l~~~~~~p~~L~~~l~~~~i 90 (198)
.++++++++++|++.+. . ...+|+|+||.+.. .+++.+|+|+++ .|++++.......++.|+++|+++++
T Consensus 2 ~~i~~~~~~~~~~~~~~~~-----~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~ 76 (172)
T smart00474 2 RVVTDSETLEELLEKLRAA-----GGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETI 76 (172)
T ss_pred EEecCHHHHHHHHHHHHhc-----CCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccchhhHHHHHHHhcCCCc
Confidence 46777888899887764 3 56899999997654 579999999744 67776543333346679999999999
Q ss_pred EEEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCC
Q 039658 91 CFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAW 169 (198)
Q Consensus 91 ~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~ 169 (198)
.||||+++.|...| .+ +|+.+.+++|++ +++..+. |.- +..||+.+++.+ |. .+++ ..+.++|..+
T Consensus 77 ~kv~~d~k~~~~~L--~~-~gi~~~~~~D~~-laayll~-p~~-~~~~l~~l~~~~l~~-----~~~~--~~~~~~~~~~ 143 (172)
T smart00474 77 TKVGHNAKFDLHVL--AR-FGIELENIFDTM-LAAYLLL-GGP-SKHGLATLLKEYLGV-----ELDK--EEQKSDWGAR 143 (172)
T ss_pred eEEEechHHHHHHH--HH-CCCcccchhHHH-HHHHHHc-CCC-CcCCHHHHHHHHhCC-----CCCc--ccCccccccC
Confidence 99999999999999 65 899999999975 4543433 321 225999999999 98 6543 3456799888
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHHHhhhC
Q 039658 170 VFTDKQVLHAVEEARGCYIVADKLLSLLN 198 (198)
Q Consensus 170 pLt~~Qi~YAA~Da~~~~~i~~~L~~~l~ 198 (198)
||.++|+.||+.||++++.+++.|.+.|+
T Consensus 144 ~l~~~~~~ya~~~a~~~~~L~~~l~~~l~ 172 (172)
T smart00474 144 PLSEEQLQYAAEDADALLRLYEKLEKELE 172 (172)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 99999999999999999999999998874
No 13
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.79 E-value=1.6e-19 Score=162.17 Aligned_cols=163 Identities=17% Similarity=0.155 Sum_probs=142.8
Q ss_pred EEeCCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCC---CceeEEEeeeCCeEEEEEccccCCchHHHHhhccCCCeEE
Q 039658 16 SVIDDADVIDKKISELSGMLFKMRRVVGFDVKFNSQT---RIAEMLILSAANLCLAIQLCRLSRIPESVTNFLADRTICF 92 (198)
Q Consensus 16 ~v~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~---~~~aliQla~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~k 92 (198)
++|.+..++++....+.. ....++|.|..... +-+||+||+|++.-|+++...+...-..|+..|.||+|+|
T Consensus 194 ~~I~t~~el~~l~~~l~~-----~~Efavdlehhsyrsf~gltclmqISTr~ed~iIDt~~l~~~i~~l~e~fsdp~ivk 268 (687)
T KOG2206|consen 194 VWICTLGELEALPEILDS-----VIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKLRDHIGILNEVFSDPGIVK 268 (687)
T ss_pred eeeechHHHHHHHHHHhh-----hhhhhhhccccchhhhcCceeEEEeeccchhheehhHHHHHHHHHhhhhccCCCeEE
Confidence 578888888888888776 56789999987654 6699999999999999998765322237899999999999
Q ss_pred EEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCCC
Q 039658 93 VGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWVF 171 (198)
Q Consensus 93 vG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pL 171 (198)
|.||...|+-+| +++||+.+-|.||+.+ |.+.+|.| +.||+.|.+.+ |+ ..+| +.|..||..|||
T Consensus 269 vfhgaD~diiwl--qrdfgiyvvnLfdt~~-a~r~L~~~----r~sL~~ll~~~~~v-----~~nk--~yqladwR~rpL 334 (687)
T KOG2206|consen 269 VFHGADTDIIWL--QRDFGIYVVNLFDTIQ-ASRLLGLP----RPSLAYLLECVCGV-----LTNK--KYQLADWRIRPL 334 (687)
T ss_pred EEecCccchhhh--hccceEEEEechhhHH-HHHHhCCC----cccHHHHHHHHHhh-----hhhh--hhhhchhccccC
Confidence 999999999999 9999999999999655 66799998 78999999999 98 6654 579999999999
Q ss_pred CHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 172 TDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 172 t~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
+++++.||-.|+++++-||+.|...|
T Consensus 335 p~~Mv~yar~dthyllyiyD~lr~el 360 (687)
T KOG2206|consen 335 PEEMVRYAREDTHYLLYIYDVLRKEL 360 (687)
T ss_pred cHHHHHHHhhcchhHHHHHHHHHHHH
Confidence 99999999999999999999998765
No 14
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.75 E-value=2.7e-17 Score=125.41 Aligned_cols=145 Identities=23% Similarity=0.161 Sum_probs=110.1
Q ss_pred EEEEeeeeccCC---CceeEEEeeeCCeEEEEEccc-cCCchHHHHhhccCCCeEEEEeeecchHhhchhcCCCCCccCc
Q 039658 41 VVGFDVKFNSQT---RIAEMLILSAANLCLAIQLCR-LSRIPESVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDT 116 (198)
Q Consensus 41 vvg~D~Ew~~~~---~~~aliQla~~~~~~l~~l~~-~~~~p~~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~ 116 (198)
.+|+|+||.+.. .+++.+|+|+++.++.+.... ....++.|+++|+++.+.||||+++.|...| .+.++..+.+
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L--~~~~~~~~~~ 79 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVL--ARDGIELPGN 79 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHH--HHCCCCCCCC
Confidence 589999997653 679999999965354444332 1235667999999999999999999999999 6666666778
Q ss_pred eeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCC----CCCCCHHHHHHHHHhHHHHHHHHH
Q 039658 117 GIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWN----AWVFTDKQVLHAVEEARGCYIVAD 191 (198)
Q Consensus 117 ~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~----~~pLt~~Qi~YAA~Da~~~~~i~~ 191 (198)
++|+. +++..++... .+.||+.+++++ +. .+.+.. +.++|. .+||+.+|+.||+.||++++.+++
T Consensus 80 ~~D~~-~~ayll~~~~--~~~~l~~l~~~~l~~-----~~~~~~--~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~ 149 (155)
T cd00007 80 IFDTM-LAAYLLNPGE--GSHSLDDLAKEYLGI-----ELDKDE--QIYGKGAKTFARPLSEELLEYAAEDADALLRLYE 149 (155)
T ss_pred cccHH-HHHHHhCCCC--CcCCHHHHHHHHcCC-----CCccHH--HHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHH
Confidence 89965 5555666542 146999999999 87 543311 234442 578999999999999999999999
Q ss_pred HHHhhh
Q 039658 192 KLLSLL 197 (198)
Q Consensus 192 ~L~~~l 197 (198)
.|.+++
T Consensus 150 ~l~~~~ 155 (155)
T cd00007 150 KLLEEL 155 (155)
T ss_pred HHHhhC
Confidence 998764
No 15
>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=99.75 E-value=3.2e-17 Score=125.28 Aligned_cols=144 Identities=19% Similarity=0.154 Sum_probs=110.2
Q ss_pred EEEEeeeeccCC---CceeEEEeeeCC-eEEEEEccccCCchHHHHhhccCCCeEEEEeeecchHhhchhcCCCCCccCc
Q 039658 41 VVGFDVKFNSQT---RIAEMLILSAAN-LCLAIQLCRLSRIPESVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDT 116 (198)
Q Consensus 41 vvg~D~Ew~~~~---~~~aliQla~~~-~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~ 116 (198)
++|+|+||.+.. .+++.+|+|+++ .++++++.+....+..|+++|+|+++.|+||+++.|...| .+.+....++
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L--~~~~~~~~~~ 78 (150)
T cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGIL--LNYFIELRGI 78 (150)
T ss_pred CEEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCcccCHHHHHHHhcCCCCceeeecHHHHHHHH--HHcCCccCCc
Confidence 589999987654 679999999974 4888876542213567999999999999999999999999 6554445567
Q ss_pred eeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 039658 117 GIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLL 194 (198)
Q Consensus 117 ~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~ 194 (198)
++|+. +|+-.++... .+.+++.|++++ |. .+.+.+.+..++|..++++.+|+.||+.||++++.+++.|.
T Consensus 79 ~~D~~-laayLl~p~~--~~~~l~~l~~~~l~~-----~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 79 AFDTM-LEAYILNSVA--GRWDMDSLVERWLGH-----KLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred chhHH-HHHHHhCCCC--CCCCHHHHHHHHhCC-----CcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 79975 4555665431 145999999999 98 75442223344696678999999999999999999999874
No 16
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=99.73 E-value=3.4e-16 Score=125.67 Aligned_cols=164 Identities=16% Similarity=0.243 Sum_probs=127.3
Q ss_pred EEEeCCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCC---CceeEEEeeeCCeEEEEEccccCCchHHHHhhccCCCeE
Q 039658 15 VSVIDDADVIDKKISELSGMLFKMRRVVGFDVKFNSQT---RIAEMLILSAANLCLAIQLCRLSRIPESVTNFLADRTIC 91 (198)
Q Consensus 15 v~v~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~---~~~aliQla~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~ 91 (198)
+.++.++++++.|++.+.. ...+++|+|..+.. .+++.+|+++++.++++++.......+.|+.+|+++++.
T Consensus 5 ~~~i~~~~~l~~~~~~l~~-----~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~l~~~~~~~~L~~~L~~~~i~ 79 (192)
T cd06147 5 LTFVDTEEKLEELVEKLKN-----CKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNIL 79 (192)
T ss_pred cEEECCHHHHHHHHHHHhc-----CCeEEEEeEecCCccCCCceEEEEEecCCCcEEEEecccccchHHHHHHhcCCCce
Confidence 4566566788888866632 45899999875432 568889999987777766322223345699999999999
Q ss_pred EEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCC
Q 039658 92 FVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWV 170 (198)
Q Consensus 92 kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~p 170 (198)
|+||+++.|...| ...+|+.+.+.+|+. +++-.++.. +. +++.|++++ |. .+.| +.+.|||+.+|
T Consensus 80 kv~~d~K~~~~~L--~~~~gi~~~~~fD~~-laaYLL~p~---~~-~l~~l~~~yl~~-----~~~k--~~~~~~~~~~~ 145 (192)
T cd06147 80 KVFHGADSDIIWL--QRDFGLYVVNLFDTG-QAARVLNLP---RH-SLAYLLQKYCNV-----DADK--KYQLADWRIRP 145 (192)
T ss_pred EEEechHHHHHHH--HHHhCCCcCchHHHH-HHHHHhCCC---cc-cHHHHHHHHhCC-----Ccch--hhhccccccCC
Confidence 9999999999999 546788887779965 565566543 23 999999999 88 5434 34788998889
Q ss_pred CCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 171 FTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 171 Lt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
|+.+|..||+.||++++.++..|.+.|
T Consensus 146 l~~~~~~y~a~~a~~l~~L~~~L~~~L 172 (192)
T cd06147 146 LPEEMIKYAREDTHYLLYIYDRLRNEL 172 (192)
T ss_pred CCHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 999999999999999999999998876
No 17
>PRK05755 DNA polymerase I; Provisional
Probab=99.54 E-value=1.7e-13 Score=132.36 Aligned_cols=162 Identities=19% Similarity=0.198 Sum_probs=125.0
Q ss_pred EEEeCCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCC---CceeEEEeeeCCe-EEEEEccccC-CchHHHHhhccCCC
Q 039658 15 VSVIDDADVIDKKISELSGMLFKMRRVVGFDVKFNSQT---RIAEMLILSAANL-CLAIQLCRLS-RIPESVTNFLADRT 89 (198)
Q Consensus 15 v~v~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~---~~~aliQla~~~~-~~l~~l~~~~-~~p~~L~~~l~~~~ 89 (198)
..++.+++++.+|++.+.. ..+++||+|..... .+++.||+|+++. ++++++.+.. ...+.|.++|+++.
T Consensus 296 ~~~I~~~~~L~~~l~~l~~-----~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~ 370 (880)
T PRK05755 296 YETILDEEELEAWLAKLKA-----AGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPA 370 (880)
T ss_pred eEEeCCHHHHHHHHHHhhc-----cCeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCC
Confidence 4567899999999988875 78999999988753 6799999999766 7777764432 23357899999999
Q ss_pred eEEEEeeecchHhhchhcCCCCCcc-CceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCC-----CCCCC
Q 039658 90 ICFVGFGVDKKTASIHGKTGYPRNC-DTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKE-----IEAVT 162 (198)
Q Consensus 90 i~kvG~~i~~D~~~L~~~~~~~~~~-~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K-----~~~~~ 162 (198)
+.||+|+++.|+..| .+ +|+.+ .+++|. .+++..++ |+. ..||+.|++.+ |. ++.. .+..+
T Consensus 371 v~kV~HNakfDl~~L--~~-~gi~~~~~~~DT-~iAa~Ll~-~~~--~~~L~~L~~~ylg~-----~~~~~~~~~gk~~~ 438 (880)
T PRK05755 371 IKKVGQNLKYDLHVL--AR-YGIELRGIAFDT-MLASYLLD-PGR--RHGLDSLAERYLGH-----KTISFEEVAGKQLT 438 (880)
T ss_pred CcEEEeccHhHHHHH--Hh-CCCCcCCCcccH-HHHHHHcC-CCC--CCCHHHHHHHHhCC-----CccchHHhcCCCCC
Confidence 999999999999999 54 57765 578996 45664554 432 37999999999 88 5321 12233
Q ss_pred CCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 163 PPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 163 ~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
|...|+ +.|.+||+.||.++..||+.|.+.|
T Consensus 439 ---~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L 469 (880)
T PRK05755 439 ---FAQVDL-EEAAEYAAEDADVTLRLHEVLKPKL 469 (880)
T ss_pred ---ccccCH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444477 5899999999999999999998876
No 18
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.46 E-value=2.7e-13 Score=125.08 Aligned_cols=140 Identities=15% Similarity=0.043 Sum_probs=114.9
Q ss_pred EEeCCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCCCceeEEEeeeCCeEEEEEccccCCchHHHHhhccCCCeEEEEe
Q 039658 16 SVIDDADVIDKKISELSGMLFKMRRVVGFDVKFNSQTRIAEMLILSAANLCLAIQLCRLSRIPESVTNFLADRTICFVGF 95 (198)
Q Consensus 16 ~v~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~~~~aliQla~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~ 95 (198)
.+|++++++..++..+.. ..++++|+|+.+....++++|+++++.++|++.... +. .
T Consensus 4 ~~I~~~~~l~~~~~~l~~-----~~~~a~DtEf~r~~t~l~liQ~~~~~~~~liDpl~~--l~----~------------ 60 (553)
T PRK14975 4 KVILAPEELGAALERLSP-----AGVVAGDTETTGDDAAAAAAQEGEEEPRWVWASTAA--LY----P------------ 60 (553)
T ss_pred eEEeccchhHHHHHHhcc-----CCceeCCccccCCcchhheeeecCCCceEEECchHH--hH----H------------
Confidence 578899999999999987 899999999998866799999999999999985431 11 1
Q ss_pred eecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCCHH
Q 039658 96 GVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFTDK 174 (198)
Q Consensus 96 ~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt~~ 174 (198)
.| . .+|+.+.++||+ .+|+..+|.+....+.|++.+++.+ +. .++|.. +.|||. +||+++
T Consensus 61 -------~L--~-~~Gv~~~~~fDT-~LAa~lL~~~~~~~~~~l~~la~~~l~~-----~l~k~~--~~sdw~-rpls~~ 121 (553)
T PRK14975 61 -------RL--L-AAGVRVERCHDL-MLASQLLLGSEGRAGSSLSAAAARALGE-----GLDKPP--QTSALS-DPPDEE 121 (553)
T ss_pred -------HH--H-HCCCccCCCchH-HHHHHHcCCCCCcCCCCHHHHHHHHhCC-----CCCChh--hhcccc-ccchHH
Confidence 14 2 348888889996 5677788865210167999999999 99 998864 579997 899999
Q ss_pred HHHHHHHhHHHHHHHHHHHHhhh
Q 039658 175 QVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 175 Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
|+.|||.|+.++..+|..|.+.|
T Consensus 122 q~~YAa~Dv~~l~~L~~~L~~qL 144 (553)
T PRK14975 122 QLLYAAADADVLLELYAVLADQL 144 (553)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHH
Confidence 99999999999999999998876
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=99.22 E-value=2.2e-10 Score=90.25 Aligned_cols=145 Identities=21% Similarity=0.099 Sum_probs=103.6
Q ss_pred eEEEEeeeeccCC---CceeEEEeeeCCeEEEEEccccCCchHHHHhhccCCCeEEEEeeecchHhhchhcCCCCCccC-
Q 039658 40 RVVGFDVKFNSQT---RIAEMLILSAANLCLAIQLCRLSRIPESVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCD- 115 (198)
Q Consensus 40 ~vvg~D~Ew~~~~---~~~aliQla~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~- 115 (198)
..+++|+|..... .++..+++|+++.++.+.+.+.....+.|+++|+|+++.|+||+++.|...| . .+|+.+.
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~~i~l~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l--~-~~gi~~~~ 80 (178)
T cd06140 4 DEVALYVELLGENYHTADIIGLALANGGGAYYIPLELALLDLAALKEWLEDEKIPKVGHDAKRAYVAL--K-RHGIELAG 80 (178)
T ss_pred CceEEEEEEcCCCcceeeEEEEEEEeCCcEEEEeccchHHHHHHHHHHHhCCCCceeccchhHHHHHH--H-HCCCcCCC
Confidence 4566777766533 5688899999776666653321001234899999999999999999999998 4 4677765
Q ss_pred ceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCC---CCCCCHHHHHHHHHhHHHHHHHHH
Q 039658 116 TGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWN---AWVFTDKQVLHAVEEARGCYIVAD 191 (198)
Q Consensus 116 ~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~---~~pLt~~Qi~YAA~Da~~~~~i~~ 191 (198)
..+|+ .+|+-.++... +..+++.++.++ |. .+.+.. +.+.|. .++..++|..||+.||.++..+++
T Consensus 81 ~~fDt-~laaYLL~p~~--~~~~l~~l~~~yl~~-----~~~~~~--~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~ 150 (178)
T cd06140 81 VAFDT-MLAAYLLDPTR--SSYDLADLAKRYLGR-----ELPSDE--EVYGKGAKFAVPDEEVLAEHLARKAAAIARLAP 150 (178)
T ss_pred cchhH-HHHHHHcCCCC--CCCCHHHHHHHHcCC-----CCcchH--HhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHH
Confidence 45995 56765665432 235999999999 98 654311 233442 245577789999999999999999
Q ss_pred HHHhhh
Q 039658 192 KLLSLL 197 (198)
Q Consensus 192 ~L~~~l 197 (198)
.|.+.|
T Consensus 151 ~l~~~L 156 (178)
T cd06140 151 KLEEEL 156 (178)
T ss_pred HHHHHH
Confidence 998876
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=99.17 E-value=9.4e-10 Score=87.29 Aligned_cols=147 Identities=18% Similarity=0.143 Sum_probs=102.6
Q ss_pred CeEEEEeeeeccCC---CceeEEEeeeCCe-EEEEEcccc------C--CchHHHHhhccCCCeEEEEeeecchHhhchh
Q 039658 39 RRVVGFDVKFNSQT---RIAEMLILSAANL-CLAIQLCRL------S--RIPESVTNFLADRTICFVGFGVDKKTASIHG 106 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~---~~~aliQla~~~~-~~l~~l~~~------~--~~p~~L~~~l~~~~i~kvG~~i~~D~~~L~~ 106 (198)
...+++|+|..... .++..+++|.++. .+.+.+.+. . ...+.|+++|+++++.+|||+++.|...|
T Consensus 5 ~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l-- 82 (193)
T cd06139 5 AKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVL-- 82 (193)
T ss_pred CCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHHH--
Confidence 67899999865432 5688899998654 544443321 1 12234889999999999999999999999
Q ss_pred cCCCCCccC-ceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCC-----CCCCCCCCCCCCCCCHHHHHHH
Q 039658 107 KTGYPRNCD-TGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKE-----IEAVTPPNWNAWVFTDKQVLHA 179 (198)
Q Consensus 107 ~~~~~~~~~-~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K-----~~~~~~SdW~~~pLt~~Qi~YA 179 (198)
.+ +|+.+. .++|+. +++..+ .|+. ...||..+++.+ |. .+.+ .+..+..+|...|+ ..+.+||
T Consensus 83 ~~-~gi~~~~~~~Dt~-l~a~ll-~p~~-~~~~l~~l~~~~l~~-----~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya 152 (193)
T cd06139 83 AN-HGIELRGPAFDTM-LASYLL-NPGR-RRHGLDDLAERYLGH-----KTISFEDLVGKGKKQITFDQVPL-EKAAEYA 152 (193)
T ss_pred HH-CCCCCCCCcccHH-HHHHHh-CCCC-CCCCHHHHHHHHhCC-----CCccHHHHcCCCcCcCCccccCH-HHHHHHH
Confidence 43 566654 468864 455444 3431 256999999999 87 4210 11124556765556 7799999
Q ss_pred HHhHHHHHHHHHHHHhhh
Q 039658 180 VEEARGCYIVADKLLSLL 197 (198)
Q Consensus 180 A~Da~~~~~i~~~L~~~l 197 (198)
+.||.+++.+++.|.+.|
T Consensus 153 ~~d~~~~~~l~~~l~~~l 170 (193)
T cd06139 153 AEDADITLRLYELLKPKL 170 (193)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999998876
No 21
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.16 E-value=5.7e-05 Score=73.53 Aligned_cols=162 Identities=14% Similarity=0.040 Sum_probs=100.5
Q ss_pred EeCCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCCCceeEEEeeeCC-e-EEEEEccc-----cCCchHHHHhhccCCC
Q 039658 17 VIDDADVIDKKISELSGMLFKMRRVVGFDVKFNSQTRIAEMLILSAAN-L-CLAIQLCR-----LSRIPESVTNFLADRT 89 (198)
Q Consensus 17 v~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~~~~aliQla~~~-~-~~l~~l~~-----~~~~p~~L~~~l~~~~ 89 (198)
.+.+.++++.|+.. .. ...+++ ..+.+....+.-+-+|+++ . .+-+.+.. .......|+.+|+|+.
T Consensus 306 ~~~~~~~~~~~~~~-~~-----~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~ 378 (887)
T TIGR00593 306 ESEEAAPLANPAEK-AE-----VGGFVL-ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLNEQ 378 (887)
T ss_pred EeCCHHHHHHHHHh-Cc-----CCeEEE-cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhCCC
Confidence 34456777777654 21 345666 3333322345567777754 2 32222210 1111234899999999
Q ss_pred eEEEEeeecchHhhchhcCCCCCccCc-eeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCC
Q 039658 90 ICFVGFGVDKKTASIHGKTGYPRNCDT-GIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWN 167 (198)
Q Consensus 90 i~kvG~~i~~D~~~L~~~~~~~~~~~~-~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~ 167 (198)
+.|+||+++.|...| . .+|+.+.+ .+| +.+|+-.+. |+ .+.+|+.++.++ +. .+.+...+.-..+.
T Consensus 379 ~~~v~~n~K~d~~~l--~-~~gi~~~~~~~D-t~la~yll~-~~--~~~~l~~la~~yl~~-----~~~~~~~~~~~~~~ 446 (887)
T TIGR00593 379 IKKIGHDAKFLMHLL--K-REGIELGGVIFD-TMLAAYLLD-PA--QVSTLDTLARRYLVE-----ELILDEKIGGKLAK 446 (887)
T ss_pred CcEEEeeHHHHHHHH--H-hCCCCCCCcchh-HHHHHHHcC-CC--CCCCHHHHHHHHcCc-----ccccHHHhccCCCC
Confidence 999999999999999 4 46777654 588 456765654 33 245999999999 86 43321111111111
Q ss_pred CCCCC-HHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 168 AWVFT-DKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 168 ~~pLt-~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
-..++ +.+..||+.||.+.+.+|..|...|
T Consensus 447 ~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l 477 (887)
T TIGR00593 447 FAFPPLEEATEYLARRAAATKRLAEELLKEL 477 (887)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11233 3457899999999999999998876
No 22
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=97.97 E-value=8.2e-05 Score=68.95 Aligned_cols=164 Identities=19% Similarity=0.210 Sum_probs=103.4
Q ss_pred eCCHHHHHHHHHHHHhhhccCCeEEEEeeeeccCC-CceeEEEe--eeCCeEEEEEcccc-C--CchHHHHhhccCCCeE
Q 039658 18 IDDADVIDKKISELSGMLFKMRRVVGFDVKFNSQT-RIAEMLIL--SAANLCLAIQLCRL-S--RIPESVTNFLADRTIC 91 (198)
Q Consensus 18 ~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~-~~~aliQl--a~~~~~~l~~l~~~-~--~~p~~L~~~l~~~~i~ 91 (198)
+.+.+....|+..... ...+++|+|..... ....++=+ |.++..+.+-+.+- . ..-..|+.+|+++++.
T Consensus 6 ~~~~~~~~~~~~~~~~-----~~~~a~~~et~~l~~~~~~lvg~s~~~~~~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~ 80 (593)
T COG0749 6 ITDLAVLNAWLTKLNA-----AANIAFDTETDGLDPHGADLVGLSVASEEEAAYIPLLHGPEQLNVLAALKPLLEDEGIK 80 (593)
T ss_pred hhHHHHHHHHHHHHhh-----cccceeeccccccCcccCCeeEEEeeccccceeEeeccchhhhhhHHHHHHHhhCcccc
Confidence 4456667788877765 34499999987665 22333333 33333333333331 1 1235689999999999
Q ss_pred EEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCC---CCCCCC
Q 039658 92 FVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAV---TPPNWN 167 (198)
Q Consensus 92 kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~---~~SdW~ 167 (198)
|+|++.+.|...| .+ +|+.....+| ..+++-.+... . +..+++.|++.+ +. .....+.+ .-++=.
T Consensus 81 kv~~~~K~d~~~l--~~-~Gi~~~~~~D-tmlasYll~~~-~-~~~~~~~l~~r~l~~-----~~~~~~~i~~kg~~~~~ 149 (593)
T COG0749 81 KVGQNLKYDYKVL--AN-LGIEPGVAFD-TMLASYLLNPG-A-GAHNLDDLAKRYLGL-----ETITFEDIAGKGKKQLT 149 (593)
T ss_pred hhccccchhHHHH--HH-cCCcccchHH-HHHHHhccCcC-c-CcCCHHHHHHHhcCC-----ccchhHHhhccccccCc
Confidence 9999999999999 44 4555457788 45665344322 2 468899999999 76 33322111 000100
Q ss_pred CCCCC-HHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 168 AWVFT-DKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 168 ~~pLt-~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
-.... ++-..|||.||.+.+.++..|..+|
T Consensus 150 ~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l 180 (593)
T COG0749 150 FADVKLEKATEYAAEDADATLRLESILEPEL 180 (593)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 00111 3458999999999999999998654
No 23
>PRK07740 hypothetical protein; Provisional
Probab=97.09 E-value=0.087 Score=43.98 Aligned_cols=150 Identities=16% Similarity=0.109 Sum_probs=92.5
Q ss_pred CHHHHHHHHHHHHhhhccC---------CeEEEEeeeeccCC-Cc-eeEEEeee----CCeE------EEEEccc-c---
Q 039658 20 DADVIDKKISELSGMLFKM---------RRVVGFDVKFNSQT-RI-AEMLILSA----ANLC------LAIQLCR-L--- 74 (198)
Q Consensus 20 ~~~~~~~~i~~l~~~~~~~---------~~vvg~D~Ew~~~~-~~-~aliQla~----~~~~------~l~~l~~-~--- 74 (198)
+..+-+.|++.+.+..+.. ..+|.||+|++... .. -.+||++. ++.. .+++... +
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~ 110 (244)
T PRK07740 31 NALQQEAWIRSIQKEAKRDDVLDIPLTDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEH 110 (244)
T ss_pred chHHHHHHHHHHHHHhccCCccCCCccCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChh
Confidence 3357788999997664421 57999999997643 22 46788775 3322 1121110 0
Q ss_pred ----CC-----------chHH---HHhhccCCCeEEEEeeecchHhhchh--cCCCCCcc-CceeehHHHHHHHhCCCCC
Q 039658 75 ----SR-----------IPES---VTNFLADRTICFVGFGVDKKTASIHG--KTGYPRNC-DTGIDLGHLAARVLKKPKL 133 (198)
Q Consensus 75 ----~~-----------~p~~---L~~~l~~~~i~kvG~~i~~D~~~L~~--~~~~~~~~-~~~~Dl~~la~~~~g~~~l 133 (198)
.. ++.. +.+|+.+ -+.|||++..|...|.. .+.++... ...+|+..+++......
T Consensus 111 ~~~ltGIt~e~l~~ap~~~evl~~f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~-- 186 (244)
T PRK07740 111 ILELTGITAEDVAFAPPLAEVLHRFYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHER-- 186 (244)
T ss_pred heeccCCCHHHHhCCCCHHHHHHHHHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCC--
Confidence 00 1222 3444443 36899999999988732 12233332 57899888776443222
Q ss_pred CCCccHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 134 IGLTGIAELAKEVGIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 134 ~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
+..||.++++.+|+ +... .+=|..||++..+|+.++.+.+
T Consensus 187 -~~~sL~~l~~~~gi-----~~~~------------------~H~Al~Da~ata~l~~~ll~~~ 226 (244)
T PRK07740 187 -DFPTLDDALAYYGI-----PIPR------------------RHHALGDALMTAKLWAILLVEA 226 (244)
T ss_pred -CCCCHHHHHHHCCc-----CCCC------------------CCCcHHHHHHHHHHHHHHHHHH
Confidence 46799999977777 4321 1336899999999999997654
No 24
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=97.05 E-value=0.015 Score=45.17 Aligned_cols=85 Identities=18% Similarity=0.103 Sum_probs=55.0
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchhcCCCCCccCceeehHHH--HHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHL--AARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNK 156 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~l--a~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~ 156 (198)
.+.+|+. +-+.|||++..|+..| ...+ ......|+..+ +++..+.|.. ...+|..|++.+ |. .+.
T Consensus 70 ~l~~~l~--~~vlV~Hn~~~D~~~l--~~~~--~~~~~~Dt~~l~~~~~~~~~p~~-~~~~L~~L~~~~~~~-----~i~ 137 (157)
T cd06149 70 EILKILK--GKVVVGHAIHNDFKAL--KYFH--PKHMTRDTSTIPLLNRKAGFPEN-CRVSLKVLAKRLLHR-----DIQ 137 (157)
T ss_pred HHHHHcC--CCEEEEeCcHHHHHHh--cccC--CCcCEEECcccccchhhcCCccc-CChhHHHHHHHHcCh-----hhc
Confidence 4677775 3468999999999999 5432 22356786443 3334445543 468999999999 77 554
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 039658 157 EIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVAD 191 (198)
Q Consensus 157 K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~ 191 (198)
... +-+=|..||.++.++|+
T Consensus 138 ~~~---------------~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 138 VGR---------------QGHSSVEDARATMELYK 157 (157)
T ss_pred CCC---------------CCcCcHHHHHHHHHHhC
Confidence 311 11235678888877763
No 25
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=97.04 E-value=0.011 Score=45.04 Aligned_cols=125 Identities=17% Similarity=0.105 Sum_probs=75.7
Q ss_pred eeEEEeeeCCeEEEEEccccCCchHHHHhhccCCCeEEEEeeecchHhhchhcCCCCCccCc-eeehHHHHHHHhCCCCC
Q 039658 55 AEMLILSAANLCLAIQLCRLSRIPESVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDT-GIDLGHLAARVLKKPKL 133 (198)
Q Consensus 55 ~aliQla~~~~~~l~~l~~~~~~p~~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~-~~Dl~~la~~~~g~~~l 133 (198)
+.-+-+|+++.++.+.+.. ...-..|+.+|+++++.|+||+.+.+...| +.+|+...+ .+|+ .+|+-.++ |.-
T Consensus 20 ~~glal~~~~~~~yi~~~~-~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l---~~~gi~l~~~~fD~-~LAaYLL~-p~~ 93 (151)
T cd06128 20 LVGLAFAIEGVAAYIPVAH-DYALELLKPLLEDEKALKVGQNLKYDRVIL---ANYGIELRGIAFDT-MLEAYLLD-PVA 93 (151)
T ss_pred EEEEEEEcCCCeEEEeCCC-CcCHHHHHHHHcCCCCCEEeeehHHHHHHH---HHCCCCCCCcchhH-HHHHHHcC-CCC
Confidence 3335556554454443221 101245889999999999999999998888 345776655 4896 46764554 431
Q ss_pred CCCccHHHHHHHh-CCCCCCCCCCC-CCCCCCCCCCC--CCC-CHHHHHHHHHhHHHHHHHHHHHH
Q 039658 134 IGLTGIAELAKEV-GIDHNSLSNKE-IEAVTPPNWNA--WVF-TDKQVLHAVEEARGCYIVADKLL 194 (198)
Q Consensus 134 ~~~~sL~~l~~~~-g~~~~~~~l~K-~~~~~~SdW~~--~pL-t~~Qi~YAA~Da~~~~~i~~~L~ 194 (198)
+..+++.+++++ +. .+-. +. ...+.+ .++ ..+.-.|++..|.+...+++.|.
T Consensus 94 -~~~~l~~la~~yl~~-----~~~~~~~---~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 94 -GRHDMDSLAERWLKE-----KTITFEE---IAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred -CCCCHHHHHHHHcCC-----CCccHHH---HcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 214999999999 87 4211 00 000110 011 11123488888889999998875
No 26
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=97.02 E-value=0.0084 Score=46.07 Aligned_cols=130 Identities=18% Similarity=0.192 Sum_probs=79.6
Q ss_pred EEEEeeeeccCC-CceeEEEeee----CCe-EE----EEEccc-cC-------C-----------ch---HHHHhhccCC
Q 039658 41 VVGFDVKFNSQT-RIAEMLILSA----ANL-CL----AIQLCR-LS-------R-----------IP---ESVTNFLADR 88 (198)
Q Consensus 41 vvg~D~Ew~~~~-~~~aliQla~----~~~-~~----l~~l~~-~~-------~-----------~p---~~L~~~l~~~ 88 (198)
+|.||+|..... .+-.++||+. ++. .- +++... +. . +. ..+.+++.+.
T Consensus 2 ~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~~l~~~ 81 (169)
T smart00479 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLKGK 81 (169)
T ss_pred EEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHhcCC
Confidence 689999998654 3467888886 322 11 222100 00 0 11 2466777653
Q ss_pred CeEEEEeeecchHhhchh-cCCCCCc---cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCCC
Q 039658 89 TICFVGFGVDKKTASIHG-KTGYPRN---CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTPP 164 (198)
Q Consensus 89 ~i~kvG~~i~~D~~~L~~-~~~~~~~---~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~S 164 (198)
++.++.+...|...|.. ...+|.. ....+|+..+++...+.+ ..||..+++.+|. +.. .+
T Consensus 82 -~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~----~~~L~~l~~~~~~-----~~~--~~---- 145 (169)
T smart00479 82 -ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR----KYSLKKLAERLGL-----EVI--GR---- 145 (169)
T ss_pred -EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC----CCCHHHHHHHCCC-----CCC--CC----
Confidence 44444444999998831 1123332 234799988776554432 6899999998855 221 10
Q ss_pred CCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 165 NWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 165 dW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
.+.|..||.....||.++.+.+
T Consensus 146 -----------~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 146 -----------AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred -----------CcCcHHHHHHHHHHHHHHHHHh
Confidence 3779999999999999998653
No 27
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=97.01 E-value=0.0056 Score=47.72 Aligned_cols=84 Identities=14% Similarity=0.195 Sum_probs=55.6
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEI 158 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~ 158 (198)
.|.+|+.+. -+.|||++..|+..| ... ...++|...+++........+.+.+|..||+.+ |. ++...
T Consensus 76 ~~~~~i~~~-~vlVgHn~~fD~~fL--~~~----~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~-----~~~~~ 143 (161)
T cd06137 76 ALWKFIDPD-TILVGHSLQNDLDAL--RMI----HTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGL-----KIQGG 143 (161)
T ss_pred HHHHhcCCC-cEEEeccHHHHHHHH--hCc----CCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCc-----hhcCC
Confidence 456666643 457999999999999 432 346899888877543322000268999999998 88 55321
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 039658 159 EAVTPPNWNAWVFTDKQVLHAVEEARGCYIVA 190 (198)
Q Consensus 159 ~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~ 190 (198)
+ +-+=|..||.++.++|
T Consensus 144 ~---------------~~H~A~~DA~at~~l~ 160 (161)
T cd06137 144 G---------------EGHDSLEDALAAREVV 160 (161)
T ss_pred C---------------CCCCcHHHHHHHHHHh
Confidence 0 1133678888887776
No 28
>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=96.99 E-value=0.016 Score=44.68 Aligned_cols=81 Identities=19% Similarity=0.202 Sum_probs=55.4
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEI 158 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~ 158 (198)
.+.+|+. ++-+.|||++..|+..| ... ....+|...++++..+.+ .+.||..||+.+ |. .+...
T Consensus 68 ~~~~fl~-~~~vlVgHn~~fD~~fL--~~~----~~~~iDT~~l~r~~~~~~---~~~~L~~L~~~~~~~-----~i~~~ 132 (150)
T cd06145 68 KLLSLIS-PDTILVGHSLENDLKAL--KLI----HPRVIDTAILFPHPRGPP---YKPSLKNLAKKYLGR-----DIQQG 132 (150)
T ss_pred HHHHHhC-CCCEEEEcChHHHHHHh--hcc----CCCEEEcHHhccccCCCC---CChhHHHHHHHHCCc-----ceeCC
Confidence 4666775 34568999999999999 432 245899887776544433 357999999999 86 44211
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 039658 159 EAVTPPNWNAWVFTDKQVLHAVEEARGCYIVA 190 (198)
Q Consensus 159 ~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~ 190 (198)
.+.+=|..||+++..+|
T Consensus 133 ---------------~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 133 ---------------EGGHDSVEDARAALELV 149 (150)
T ss_pred ---------------CCCCCcHHHHHHHHHHh
Confidence 01133678999888876
No 29
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.90 E-value=0.021 Score=48.10 Aligned_cols=83 Identities=20% Similarity=0.296 Sum_probs=54.1
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchhcCCCCCccCceeehHH---HHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGH---LAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSN 155 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~---la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l 155 (198)
.+.+||.+ =+.|||++++|++.| .-.++-.. .=|.+. +.+ .+... .+.||+.|++++ |. ++
T Consensus 177 ev~klL~g--RIlVGHaLhnDl~~L--~l~hp~s~--iRDTs~~~pl~k-~~~~~---~tpSLK~Lt~~~Lg~-----~I 241 (280)
T KOG2249|consen 177 EVLKLLKG--RILVGHALHNDLQAL--KLEHPRSM--IRDTSKYPPLMK-LLSKK---ATPSLKKLTEALLGK-----DI 241 (280)
T ss_pred HHHHHHhC--CEEeccccccHHHHH--hhhCchhh--hcccccCchHHH-Hhhcc---CCccHHHHHHHHhch-----hh
Confidence 46778875 467999999999999 66554321 112222 111 11222 478999999999 98 55
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 039658 156 KEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLL 194 (198)
Q Consensus 156 ~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~ 194 (198)
.- .-=+ ...||.+...+|....
T Consensus 242 Q~------GeHs-----------SvEDA~AtM~LY~~vk 263 (280)
T KOG2249|consen 242 QV------GEHS-----------SVEDARATMELYKRVK 263 (280)
T ss_pred hc------cccC-----------cHHHHHHHHHHHHHHH
Confidence 32 2212 2679999999998764
No 30
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=96.89 E-value=0.012 Score=47.24 Aligned_cols=145 Identities=12% Similarity=0.226 Sum_probs=82.7
Q ss_pred CeEEEEeeeeccC-----CCceeEEEeee---CC-eEEEEEccc------cC---CchHHHHhhcc--CCCeEEEEeeec
Q 039658 39 RRVVGFDVKFNSQ-----TRIAEMLILSA---AN-LCLAIQLCR------LS---RIPESVTNFLA--DRTICFVGFGVD 98 (198)
Q Consensus 39 ~~vvg~D~Ew~~~-----~~~~aliQla~---~~-~~~l~~l~~------~~---~~p~~L~~~l~--~~~i~kvG~~i~ 98 (198)
-++++||.|-... ...=.++|||. ++ .++.++-.. .. .+-..+.+++. ||++ .+||++.
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dpdi-ivgyN~~ 81 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDV-IYTYNGD 81 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCCCE-EEecCCC
Confidence 4789999998632 11223345444 22 233222110 11 12233444454 4876 6999986
Q ss_pred -chHhhchhc-CCCCCcc------------------------CceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCC
Q 039658 99 -KKTASIHGK-TGYPRNC------------------------DTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHN 151 (198)
Q Consensus 99 -~D~~~L~~~-~~~~~~~------------------------~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~ 151 (198)
.|+..|..+ ..+|+.. .-.+|+-.++++.++.+ ..+|..+++++ |...
T Consensus 82 ~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~l~----sy~L~~v~~~~Lg~~k- 156 (195)
T cd05780 82 NFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLT----RYTLERVYEELFGIEK- 156 (195)
T ss_pred CCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCCCC----cCcHHHHHHHHhCCCC-
Confidence 599887421 1223321 13788877776554443 67999999999 8721
Q ss_pred CCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 039658 152 SLSNKEIEAVTPPN-WNAWVFTDKQVLHAVEEARGCYIVADKL 193 (198)
Q Consensus 152 ~~~l~K~~~~~~Sd-W~~~pLt~~Qi~YAA~Da~~~~~i~~~L 193 (198)
.+++- + +.+. |...+--.+=++|+..||...+.|.+.+
T Consensus 157 -~d~~~-~--~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 157 -EDVPG-E--EIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred -CcCCH-H--HHHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 11110 1 2333 4443455667999999999999998753
No 31
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.85 E-value=0.011 Score=51.19 Aligned_cols=128 Identities=18% Similarity=0.145 Sum_probs=80.8
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee----CCeE-----EEEEccc--------cCC-----------ch---HHHHhhcc
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA----ANLC-----LAIQLCR--------LSR-----------IP---ESVTNFLA 86 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~----~~~~-----~l~~l~~--------~~~-----------~p---~~L~~~l~ 86 (198)
..+|.||+|..... .+-.+|||+. .+.. .++.... +.. ++ +.+.+|+.
T Consensus 8 ~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f~~fl~ 87 (313)
T PRK06807 8 LDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLH 87 (313)
T ss_pred CCEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHHHHHHc
Confidence 57899999986432 3357777775 2221 1222110 000 11 23555665
Q ss_pred CCCeEEEEeeecchHhhchhcC---CCCC--ccCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCC
Q 039658 87 DRTICFVGFGVDKKTASIHGKT---GYPR--NCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAV 161 (198)
Q Consensus 87 ~~~i~kvG~~i~~D~~~L~~~~---~~~~--~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~ 161 (198)
+. ..|||++..|...| .+ .+|+ .....+|+..++...++.. ...+|..|++.+|+ .. +
T Consensus 88 ~~--~lVaHNa~FD~~fL--~~~~~~~gl~~~~~~~iDtl~la~~~~~~~---~~~kL~~L~~~lgi-----~~-~---- 150 (313)
T PRK06807 88 TN--VIVAHNASFDMRFL--KSNVNMLGLPEPKNKVIDTVFLAKKYMKHA---PNHKLETLKRMLGI-----RL-S---- 150 (313)
T ss_pred CC--eEEEEcHHHHHHHH--HHHHHHcCCCCCCCCEeeHHHHHHHHhCCC---CCCCHHHHHHHcCC-----CC-C----
Confidence 43 34999999999988 43 2343 3457899888877655432 35689999987777 33 1
Q ss_pred CCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 162 TPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 162 ~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
-+=|..||+++..||.++....
T Consensus 151 --------------~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 151 --------------SHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred --------------CcChHHHHHHHHHHHHHHHHhh
Confidence 2336799999999999887654
No 32
>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=96.84 E-value=0.0024 Score=45.63 Aligned_cols=72 Identities=14% Similarity=0.114 Sum_probs=51.2
Q ss_pred EEEeeeeccCC---CceeEEEeeeC--CeEEEEEccccCCchHHHHhhccCCC-eEEEEeeecchHhhchh-cCCCC---
Q 039658 42 VGFDVKFNSQT---RIAEMLILSAA--NLCLAIQLCRLSRIPESVTNFLADRT-ICFVGFGVDKKTASIHG-KTGYP--- 111 (198)
Q Consensus 42 vg~D~Ew~~~~---~~~aliQla~~--~~~~l~~l~~~~~~p~~L~~~l~~~~-i~kvG~~i~~D~~~L~~-~~~~~--- 111 (198)
++||+|..... .++.++|++.+ +..++++ +.+++.++. .++|||+...|...|.. .+.++
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~~~----------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~~ 70 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAVID----------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLKY 70 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEEeh----------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCCC
Confidence 47999987654 77999999886 5555544 778887776 78999999999877721 11122
Q ss_pred -CccCceeehHHH
Q 039658 112 -RNCDTGIDLGHL 123 (198)
Q Consensus 112 -~~~~~~~Dl~~l 123 (198)
....+.+|+..+
T Consensus 71 p~~~~~~lDT~~l 83 (96)
T cd06125 71 PLLAGSWIDTIKL 83 (96)
T ss_pred CCcCCcEEEehHH
Confidence 234678997765
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=96.76 E-value=0.018 Score=44.71 Aligned_cols=88 Identities=19% Similarity=0.288 Sum_probs=59.9
Q ss_pred HHHhhccCC-CeEEEEeeecchHhhchh-cCCC-----CCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCC
Q 039658 80 SVTNFLADR-TICFVGFGVDKKTASIHG-KTGY-----PRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNS 152 (198)
Q Consensus 80 ~L~~~l~~~-~i~kvG~~i~~D~~~L~~-~~~~-----~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~ 152 (198)
.+.+++.+. ....++++ ..|...+.. ...+ +....+.+|+..+++...+.+ ...+|..+++.+|+
T Consensus 81 ~~~~~l~~~~~~~~v~~~-~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~---~~~~L~~l~~~~gi---- 152 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWG-DWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLK---KRTGLSKALEYLGL---- 152 (176)
T ss_pred HHHHHHHhCCCeEEEeec-HhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCC---CCCCHHHHHHHCCC----
Confidence 466777765 36667776 778665521 1112 234568999999988777765 47899999988777
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 039658 153 LSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKL 193 (198)
Q Consensus 153 ~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L 193 (198)
+.. .+-+-|-.||....+++.++
T Consensus 153 -~~~-----------------~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 153 -EFE-----------------GRHHRGLDDARNIARILKRL 175 (176)
T ss_pred -CCC-----------------CCCcCcHHHHHHHHHHHHHh
Confidence 332 12234688999999998876
No 34
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.63 E-value=0.088 Score=44.09 Aligned_cols=130 Identities=15% Similarity=0.120 Sum_probs=81.0
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee----CCe-----EEEEEccc-c-------CC--------ch------HHHHhhcc
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA----ANL-----CLAIQLCR-L-------SR--------IP------ESVTNFLA 86 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~----~~~-----~~l~~l~~-~-------~~--------~p------~~L~~~l~ 86 (198)
..+|.||+|..... ..-.+||||. .+. ..+++... + .. -| +.+.+|+.
T Consensus 7 ~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~~fl~ 86 (250)
T PRK06310 7 TEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFK 86 (250)
T ss_pred CcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHHHHhC
Confidence 67999999988753 3346777765 221 12233211 0 01 11 24666775
Q ss_pred CCCeEEEEeeecchHhhchh-cCCCCCc----cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCC
Q 039658 87 DRTICFVGFGVDKKTASIHG-KTGYPRN----CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAV 161 (198)
Q Consensus 87 ~~~i~kvG~~i~~D~~~L~~-~~~~~~~----~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~ 161 (198)
+.. +.|||++..|...|.. ....|+. ....+|...+++ .++.. ...+|..|++.+|. ....
T Consensus 87 ~~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar-~~~~~---~~~~L~~l~~~~g~-----~~~~---- 152 (250)
T PRK06310 87 EGD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAK-EYGDS---PNNSLEALAVHFNV-----PYDG---- 152 (250)
T ss_pred CCC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHH-hcccC---CCCCHHHHHHHCCC-----CCCC----
Confidence 534 6899999999988831 1122332 256899887776 44432 25689999987776 4321
Q ss_pred CCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhh
Q 039658 162 TPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSL 196 (198)
Q Consensus 162 ~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~ 196 (198)
-+=|..||+++..++..+.+.
T Consensus 153 --------------aH~Al~Da~at~~vl~~l~~~ 173 (250)
T PRK06310 153 --------------NHRAMKDVEINIKVFKHLCKR 173 (250)
T ss_pred --------------CcChHHHHHHHHHHHHHHHHh
Confidence 133789999999999988654
No 35
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=96.58 E-value=0.047 Score=43.57 Aligned_cols=100 Identities=12% Similarity=0.055 Sum_probs=61.7
Q ss_pred HHhhcc--CCCeEEEEeee-cchHhhchh-cCCCCCcc------------------------CceeehHHHHHHHhCCCC
Q 039658 81 VTNFLA--DRTICFVGFGV-DKKTASIHG-KTGYPRNC------------------------DTGIDLGHLAARVLKKPK 132 (198)
Q Consensus 81 L~~~l~--~~~i~kvG~~i-~~D~~~L~~-~~~~~~~~------------------------~~~~Dl~~la~~~~g~~~ 132 (198)
+.+++. ||++ .+||++ ..|+..|.. ...+|+.. .-.+|+-.++++....
T Consensus 70 f~~~i~~~dpdi-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~l-- 146 (199)
T cd05160 70 FFDIIREYDPDI-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFKL-- 146 (199)
T ss_pred HHHHHHhcCCCE-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcCc--
Confidence 444443 4665 699999 689988832 12334333 2368887777655443
Q ss_pred CCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 039658 133 LIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVA 190 (198)
Q Consensus 133 l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~ 190 (198)
...+|..+|+.+ |... ..++- -...+|....--..-++|.-.||...+.|+
T Consensus 147 --~sy~L~~v~~~~l~~~k--~~~~~---~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 147 --KSYTLDAVAEELLGEGK--EKVDG---EIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred --ccCCHHHHHHHHhCCCC--CcCCH---HHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 467999999999 7511 12211 123333222234467999999999999886
No 36
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=96.56 E-value=0.0083 Score=47.70 Aligned_cols=79 Identities=22% Similarity=0.187 Sum_probs=54.2
Q ss_pred HHhhccCCCeEEEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCC
Q 039658 81 VTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIE 159 (198)
Q Consensus 81 L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~ 159 (198)
|.+++ +++-+.|||++.+|++.| .-.+ .-..++|...+.. .|.. ++.||+.|++.+ |. .+..
T Consensus 95 l~~li-~~~tILVGHsL~nDL~aL--~l~h--p~~~viDTa~l~~----~~~~-r~~sLk~La~~~L~~-----~IQ~-- 157 (174)
T cd06143 95 LRLLV-DLGCIFVGHGLAKDFRVI--NIQV--PKEQVIDTVELFH----LPGQ-RKLSLRFLAWYLLGE-----KIQS-- 157 (174)
T ss_pred HHHHc-CCCCEEEeccchhHHHHh--cCcC--CCcceEEcHHhcc----CCCC-CChhHHHHHHHHcCC-----cccC--
Confidence 34444 566788999999999999 4321 1257899765432 2322 478999999999 98 5532
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 039658 160 AVTPPNWNAWVFTDKQVLHAVEEARGCYIVAD 191 (198)
Q Consensus 160 ~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~ 191 (198)
. -+=...||.+++.+|+
T Consensus 158 ----~-----------~HdSvEDArAam~Ly~ 174 (174)
T cd06143 158 ----E-----------THDSIEDARTALKLYR 174 (174)
T ss_pred ----C-----------CcCcHHHHHHHHHHhC
Confidence 1 1334789999999883
No 37
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=96.55 E-value=0.055 Score=45.62 Aligned_cols=130 Identities=18% Similarity=0.178 Sum_probs=81.7
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee----CCeE-----EEEEcccc-------C-----------Cch---HHHHhhccC
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA----ANLC-----LAIQLCRL-------S-----------RIP---ESVTNFLAD 87 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~----~~~~-----~l~~l~~~-------~-----------~~p---~~L~~~l~~ 87 (198)
..++.||+|..... .+-.+|+|+. .+.. .++..... . .++ +.+.+|+.+
T Consensus 68 ~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f~~fl~~ 147 (257)
T PRK08517 68 QVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFRLFLGD 147 (257)
T ss_pred CCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHHHHHHCC
Confidence 67999999998765 3336777775 3322 12221110 0 111 245666664
Q ss_pred CCeEEEEeeecchHhhchh-cCCCCC--ccCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCCC
Q 039658 88 RTICFVGFGVDKKTASIHG-KTGYPR--NCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTPP 164 (198)
Q Consensus 88 ~~i~kvG~~i~~D~~~L~~-~~~~~~--~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~S 164 (198)
. ++|||++.-|...|.. .+.+|. -....+|.-.++++.+..+ +.||..|++.+|. +..+
T Consensus 148 ~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~----~~~L~~L~~~lgi-----~~~~------- 209 (257)
T PRK08517 148 S--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESP----RYGLSFLKELLGI-----EIEV------- 209 (257)
T ss_pred C--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCC----CCCHHHHHHHcCc-----CCCC-------
Confidence 3 5899999999988831 123333 2356788777776554433 6789999987677 4321
Q ss_pred CCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 165 NWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 165 dW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
-+=|..||.++..|+..+.+.+
T Consensus 210 -----------~HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 210 -----------HHRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred -----------CCChHHHHHHHHHHHHHHHHHh
Confidence 1336899999999999987654
No 38
>PRK07883 hypothetical protein; Validated
Probab=96.45 E-value=0.081 Score=49.39 Aligned_cols=133 Identities=17% Similarity=0.146 Sum_probs=84.9
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee----CCeE-----EEEEccc--------cCC-----------ch---HHHHhhcc
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA----ANLC-----LAIQLCR--------LSR-----------IP---ESVTNFLA 86 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~----~~~~-----~l~~l~~--------~~~-----------~p---~~L~~~l~ 86 (198)
..+|.||+|++... ..-.+|||+. ++.. .++.... +.. +. ..+.+|+.
T Consensus 15 ~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f~~fl~ 94 (557)
T PRK07883 15 VTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFAR 94 (557)
T ss_pred CCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHhc
Confidence 68999999998653 3357777775 3321 1222210 000 11 23556666
Q ss_pred CCCeEEEEeeecchHhhchh-cCCCCCcc--CceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCC
Q 039658 87 DRTICFVGFGVDKKTASIHG-KTGYPRNC--DTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTP 163 (198)
Q Consensus 87 ~~~i~kvG~~i~~D~~~L~~-~~~~~~~~--~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~ 163 (198)
+ -+.|||++..|...|.. .+.+|+.. ...+|+..+++..+..... ...+|.++++.+|+ +..
T Consensus 95 ~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~-~~~~L~~L~~~~gi-----~~~------- 159 (557)
T PRK07883 95 G--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEA-PNVRLSTLARLFGA-----TTT------- 159 (557)
T ss_pred C--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCC-CCCCHHHHHHHCCc-----ccC-------
Confidence 4 46799999999998831 12334433 4679988888765542222 56789999987677 332
Q ss_pred CCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 164 PNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 164 SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
.-+-|..||.+...|+.++.+.+
T Consensus 160 -----------~~H~Al~DA~ata~l~~~l~~~~ 182 (557)
T PRK07883 160 -----------PTHRALDDARATVDVLHGLIERL 182 (557)
T ss_pred -----------CCCCHHHHHHHHHHHHHHHHHHH
Confidence 12558999999999999987765
No 39
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.40 E-value=0.044 Score=45.71 Aligned_cols=89 Identities=13% Similarity=0.034 Sum_probs=58.0
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchh-cCCCC--Cc----cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHG-KTGYP--RN----CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNS 152 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~-~~~~~--~~----~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~ 152 (198)
.+.+|+.+. ..|||++..|+..|.. ...+| +. ...++|.-.++++.+. . .+.||..||+.+|+
T Consensus 79 ~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p--~--~~~~L~aL~~~~gi---- 148 (240)
T PRK05711 79 EFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFP--G--KRNSLDALCKRYGI---- 148 (240)
T ss_pred HHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcC--C--CCCCHHHHHHHCCC----
Confidence 456666653 3689999999988831 11222 22 2458997777765543 2 25699999998866
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHh
Q 039658 153 LSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLS 195 (198)
Q Consensus 153 ~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~ 195 (198)
+.. . .+.+=|..||+.+..||..|..
T Consensus 149 -~~~--~--------------r~~H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 149 -DNS--H--------------RTLHGALLDAEILAEVYLAMTG 174 (240)
T ss_pred -CCC--C--------------CCCCCHHHHHHHHHHHHHHHHC
Confidence 221 1 1123478999999999988864
No 40
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.25 E-value=0.15 Score=44.24 Aligned_cols=131 Identities=17% Similarity=0.098 Sum_probs=81.3
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee-----CCe-----EEEEEccc------cC--------Cch------HHHHhhccC
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA-----ANL-----CLAIQLCR------LS--------RIP------ESVTNFLAD 87 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~-----~~~-----~~l~~l~~------~~--------~~p------~~L~~~l~~ 87 (198)
..++.||+|..... ..-.+|||+. .+. ..+++... +. .-| +.|.+|+.+
T Consensus 15 ~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~l~~ 94 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRG 94 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHHHHcCC
Confidence 57999999998653 3346677764 222 12332210 00 112 246777765
Q ss_pred CCeEEEEeeecchHhhchh-cCCCCC--ccCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCCC
Q 039658 88 RTICFVGFGVDKKTASIHG-KTGYPR--NCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTPP 164 (198)
Q Consensus 88 ~~i~kvG~~i~~D~~~L~~-~~~~~~--~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~S 164 (198)
-+.|||++..|...|.. .+.+|. .....+|.-.+++.. ..+ . ...+|..+++.+|+ ....
T Consensus 95 --~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~-~~~-~-~~~kL~~l~~~~gi-----~~~~------- 157 (313)
T PRK06063 95 --RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRL-GLG-L-PNLRLETLAAHWGV-----PQQR------- 157 (313)
T ss_pred --CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHh-ccC-C-CCCCHHHHHHHcCC-----CCCC-------
Confidence 36799999999998831 112343 335689987777643 322 1 36689999988877 3321
Q ss_pred CCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 165 NWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 165 dW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
-+=|..||.++.+|+..+.+.+
T Consensus 158 -----------~H~Al~DA~ata~l~~~ll~~~ 179 (313)
T PRK06063 158 -----------PHDALDDARVLAGILRPSLERA 179 (313)
T ss_pred -----------CCCcHHHHHHHHHHHHHHHHHH
Confidence 1347899999999999887654
No 41
>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=96.24 E-value=0.065 Score=41.21 Aligned_cols=82 Identities=22% Similarity=0.248 Sum_probs=53.1
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEI 158 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~ 158 (198)
.|.+|+.+ .+ .|||++..|+..| .. +......+|...+.. ....... ...||+.||+.+ |. ++...
T Consensus 70 ~l~~~l~~-~v-lVgHn~~fD~~~L--~~--~~~~~~~~dt~~l~~-~~~~~~~-~~~sL~~l~~~~lgi-----~~~~~ 136 (152)
T cd06144 70 KVAELLKG-RI-LVGHALKNDLKVL--KL--DHPKKLIRDTSKYKP-LRKTAKG-KSPSLKKLAKQLLGL-----DIQEG 136 (152)
T ss_pred HHHHHhCC-CE-EEEcCcHHHHHHh--cC--cCCCccEEEeEEeec-cccccCC-CChhHHHHHHHHcCc-----ccCCC
Confidence 47778875 54 5999999999999 53 222245677544322 1111001 468999999998 88 55311
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 039658 159 EAVTPPNWNAWVFTDKQVLHAVEEARGCYIVAD 191 (198)
Q Consensus 159 ~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~ 191 (198)
-+=|..||.++.+||+
T Consensus 137 -----------------~H~Al~DA~at~~l~~ 152 (152)
T cd06144 137 -----------------EHSSVEDARAAMRLYR 152 (152)
T ss_pred -----------------CcCcHHHHHHHHHHhC
Confidence 1336789999988874
No 42
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.22 E-value=0.35 Score=39.95 Aligned_cols=130 Identities=13% Similarity=0.105 Sum_probs=81.1
Q ss_pred CeEEEEeeeeccCC-CceeEEEeeeC----Ce--EEEEEccc-c-------CC-----------chH---HHHhhccCCC
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSAA----NL--CLAIQLCR-L-------SR-----------IPE---SVTNFLADRT 89 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~~----~~--~~l~~l~~-~-------~~-----------~p~---~L~~~l~~~~ 89 (198)
+.++.||+|.+... .+-.+||+|.- .. ..+++.-. . .. +.. .+.+|+.+ .
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~~-~ 80 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGT-D 80 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHcC-C
Confidence 56899999998653 33478888751 11 22333211 0 00 111 34555543 3
Q ss_pred eEEEEeee-cchHhhchhcCC---CCCc--cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCC
Q 039658 90 ICFVGFGV-DKKTASIHGKTG---YPRN--CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTP 163 (198)
Q Consensus 90 i~kvG~~i-~~D~~~L~~~~~---~~~~--~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~ 163 (198)
-+.|||+. ..|...| .+. +|+. ....+|...+++... |++ .+.+|..+++.+|+ ....
T Consensus 81 ~~lVaHN~~~FD~~~L--~~e~~r~g~~~~~~~~iDt~~l~~~~~--~~~-~~~~L~~l~~~~~~-----~~~~------ 144 (232)
T PRK06309 81 NILVAHNNDAFDFPLL--RKECRRHGLEPPTLRTIDSLKWAQKYR--PDL-PKHNLQYLRQVYGF-----EENQ------ 144 (232)
T ss_pred CEEEEeCCHHHHHHHH--HHHHHHcCCCCCCCcEEeHHHHHHHHc--CCC-CCCCHHHHHHHcCC-----CCCC------
Confidence 46799995 7999888 432 3332 357899888776443 322 35689999988776 4322
Q ss_pred CCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 164 PNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 164 SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
-+=|..||+++..|+.++.+.+
T Consensus 145 ------------aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 145 ------------AHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred ------------CCCcHHHHHHHHHHHHHHHHHH
Confidence 2336899999999999987654
No 43
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=96.11 E-value=0.11 Score=50.83 Aligned_cols=129 Identities=13% Similarity=0.150 Sum_probs=81.0
Q ss_pred EEEEeeeeccCC-CceeEEEeee----CCe-----EEEEEccc-c-------CC--------ch------HHHHhhccCC
Q 039658 41 VVGFDVKFNSQT-RIAEMLILSA----ANL-----CLAIQLCR-L-------SR--------IP------ESVTNFLADR 88 (198)
Q Consensus 41 vvg~D~Ew~~~~-~~~aliQla~----~~~-----~~l~~l~~-~-------~~--------~p------~~L~~~l~~~ 88 (198)
+|.||+|.+... ..-.+||++. ++. ..+++... + .. -| +.+.+|+.+
T Consensus 2 ~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~~l~~- 80 (850)
T TIGR01407 2 YAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLED- 80 (850)
T ss_pred EEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHHHhCC-
Confidence 689999998654 4467777765 222 22333210 0 00 11 245666654
Q ss_pred CeEEEEeeecchHhhchh-cCCCCCc--cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCCCC
Q 039658 89 TICFVGFGVDKKTASIHG-KTGYPRN--CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTPPN 165 (198)
Q Consensus 89 ~i~kvG~~i~~D~~~L~~-~~~~~~~--~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~Sd 165 (198)
-++|||++..|...|.. .+..|.. ....+|.-.+++..+... ...+|..|++.+|+ .....
T Consensus 81 -~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~---~~~~L~~l~~~~gi-----~~~~~------- 144 (850)
T TIGR01407 81 -GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTE---ESYQLSELSEALGL-----THENP------- 144 (850)
T ss_pred -CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCC---CCCCHHHHHHHCCC-----CCCCC-------
Confidence 35899999999988832 1223433 467899877776544332 46799999988877 43221
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 166 WNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 166 W~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
+=|..||.+...|+.++.+.+
T Consensus 145 -----------H~Al~DA~ata~l~~~l~~~~ 165 (850)
T TIGR01407 145 -----------HRADSDAQATAELLLLLFEKM 165 (850)
T ss_pred -----------CChHHHHHHHHHHHHHHHHHH
Confidence 337889998888888886654
No 44
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.82 E-value=0.36 Score=47.19 Aligned_cols=129 Identities=17% Similarity=0.221 Sum_probs=82.3
Q ss_pred CeEEEEeeeeccCCCceeEEEeee----CCeEE-----EEEccc-c-------CC--------ch------HHHHhhccC
Q 039658 39 RRVVGFDVKFNSQTRIAEMLILSA----ANLCL-----AIQLCR-L-------SR--------IP------ESVTNFLAD 87 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~~~~aliQla~----~~~~~-----l~~l~~-~-------~~--------~p------~~L~~~l~~ 87 (198)
..+|.||+|.+.....-.+|||+. ++... ++.... + .. -| +.+.+|+.+
T Consensus 7 ~~~vvvD~ETTGl~~~d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~l~~ 86 (820)
T PRK07246 7 RKYAVVDLEATGAGPNASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIED 86 (820)
T ss_pred CCEEEEEEecCCcCCCCeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHHhCC
Confidence 679999999986642347888875 33221 122110 0 00 11 245666664
Q ss_pred CCeEEEEeeecchHhhchhcCC---CCCc-cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCC
Q 039658 88 RTICFVGFGVDKKTASIHGKTG---YPRN-CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTP 163 (198)
Q Consensus 88 ~~i~kvG~~i~~D~~~L~~~~~---~~~~-~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~ 163 (198)
-+.|||++..|...| .+. .|.. ....+|.-.+++..+.. + .+.+|..|++.+|+ +....
T Consensus 87 --~~lVaHN~~FD~~fL--~~~~~~~g~~~~~~~iDT~~la~~~~p~--~-~~~~L~~L~~~lgl-----~~~~~----- 149 (820)
T PRK07246 87 --CIFVAHNVKFDANLL--AEALFLEGYELRTPRVDTVELAQVFFPT--L-EKYSLSHLSRELNI-----DLADA----- 149 (820)
T ss_pred --CEEEEECcHHHHHHH--HHHHHHcCCCCCCCceeHHHHHHHHhCC--C-CCCCHHHHHHHcCC-----CCCCC-----
Confidence 458999999999888 332 2322 24679977777655432 2 46799999988777 33211
Q ss_pred CCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 164 PNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 164 SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
+=|..||.++..++.+|.+.+
T Consensus 150 -------------H~Al~DA~ata~L~~~l~~~l 170 (820)
T PRK07246 150 -------------HTAIADARATAELFLKLLQKI 170 (820)
T ss_pred -------------CCHHHHHHHHHHHHHHHHHHH
Confidence 337899999999999988765
No 45
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=95.78 E-value=0.17 Score=41.78 Aligned_cols=83 Identities=17% Similarity=0.051 Sum_probs=54.2
Q ss_pred CeEEEEeeecchHhhchh-cCCCCCc---cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCCC
Q 039658 89 TICFVGFGVDKKTASIHG-KTGYPRN---CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTPP 164 (198)
Q Consensus 89 ~i~kvG~~i~~D~~~L~~-~~~~~~~---~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~S 164 (198)
+.+.|||+...|...|.. .+.+|.. ...++|.-.+++....... ++.+|..|++.+|+ .....
T Consensus 93 ~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~--~~~~L~~l~~~~gi-----~~~~a------ 159 (232)
T PRK07942 93 GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRK--GKRTLTALCEHYGV-----RLDNA------ 159 (232)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccC--CCCCHHHHHHHcCC-----CCCCC------
Confidence 446699999999988831 1223432 3468896655543322211 35689999988877 44321
Q ss_pred CCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhh
Q 039658 165 NWNAWVFTDKQVLHAVEEARGCYIVADKLLSL 196 (198)
Q Consensus 165 dW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~ 196 (198)
+=|..||.++..|+.++.+.
T Consensus 160 ------------H~Al~Da~ata~l~~~l~~~ 179 (232)
T PRK07942 160 ------------HEATADALAAARVAWALARR 179 (232)
T ss_pred ------------CChHHHHHHHHHHHHHHHHH
Confidence 23688999999999988654
No 46
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=95.75 E-value=0.83 Score=36.85 Aligned_cols=128 Identities=16% Similarity=0.241 Sum_probs=74.9
Q ss_pred CeEEEEeeeeccCCCceeEEEeee----CCe-EEEEEc-ccc-----------C-----------Cch---HHHHhhccC
Q 039658 39 RRVVGFDVKFNSQTRIAEMLILSA----ANL-CLAIQL-CRL-----------S-----------RIP---ESVTNFLAD 87 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~~~~aliQla~----~~~-~~l~~l-~~~-----------~-----------~~p---~~L~~~l~~ 87 (198)
..+|.||+|+.....+-.+|||+. ++. .-.++. ... . .++ +.+.+|+.+
T Consensus 5 ~~~vvlD~EtTGl~~~~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~~f~~~ 84 (195)
T PRK07247 5 ETYIAFDLEFNTVNGVSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFVGE 84 (195)
T ss_pred CeEEEEEeeCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHHHHHCC
Confidence 578999999875432345888875 332 112211 100 0 011 245666654
Q ss_pred CCeEEEEeeec-chHhhchhcCCCCCccC--ceeehHHHHH-HHh-CCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCC
Q 039658 88 RTICFVGFGVD-KKTASIHGKTGYPRNCD--TGIDLGHLAA-RVL-KKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVT 162 (198)
Q Consensus 88 ~~i~kvG~~i~-~D~~~L~~~~~~~~~~~--~~~Dl~~la~-~~~-g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~ 162 (198)
. ..|||++. .|+..| .+ .|..+. ..+|+-..+. +.. -.|.+ ...+|..|++.+|+ ... .
T Consensus 85 ~--~lVaHNa~~fD~~fL--~~-~g~~~~~~~~idt~~~~~~~~~~~~~~~-~~~~L~~La~~~gi-----~~~-~---- 148 (195)
T PRK07247 85 L--PLIGYNAQKSDLPIL--AE-NGLDLSDQYQVDLYDEAFERRSSDLNGI-ANLKLQTVADFLGI-----KGR-G---- 148 (195)
T ss_pred C--eEEEEeCcHhHHHHH--HH-cCCCcCCCceeehHHHHHHhhccccCCC-CCCCHHHHHHhcCC-----CCC-C----
Confidence 4 47999997 799998 43 344433 3355433321 111 12333 45789999988777 321 1
Q ss_pred CCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhh
Q 039658 163 PPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSL 196 (198)
Q Consensus 163 ~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~ 196 (198)
+=|..||+++..||.+|.++
T Consensus 149 --------------HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 149 --------------HNSLEDARMTARVYESFLES 168 (195)
T ss_pred --------------cCCHHHHHHHHHHHHHHHhh
Confidence 22678999999999998764
No 47
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=95.63 E-value=0.31 Score=39.16 Aligned_cols=132 Identities=16% Similarity=0.123 Sum_probs=78.8
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee----CCeE-------EEEEccc-cC------------------Cch---HHHHhh
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA----ANLC-------LAIQLCR-LS------------------RIP---ESVTNF 84 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~----~~~~-------~l~~l~~-~~------------------~~p---~~L~~~ 84 (198)
..+|.||+|.+... ..-.+|||+. ++.. .+++... ++ .++ +.+.++
T Consensus 29 ~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~~~~~ 108 (202)
T PRK09145 29 DEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAF 108 (202)
T ss_pred CCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHHHHHH
Confidence 58999999998643 2346777775 2322 2222211 00 011 245566
Q ss_pred ccCCCeEEEEeeecchHhhchhc--CCCCCc-cCceeehHHHHHHHhC--CCCCCCCccHHHHHHHhCCCCCCCCCCCCC
Q 039658 85 LADRTICFVGFGVDKKTASIHGK--TGYPRN-CDTGIDLGHLAARVLK--KPKLIGLTGIAELAKEVGIDHNSLSNKEIE 159 (198)
Q Consensus 85 l~~~~i~kvG~~i~~D~~~L~~~--~~~~~~-~~~~~Dl~~la~~~~g--~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~ 159 (198)
+.+ -..|||++..|...|... +.++.. +...+|+..++..... .+.-....+|..+++.+|+ +....
T Consensus 109 i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi-----~~~~~- 180 (202)
T PRK09145 109 IGN--RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHLDL-----PVLGR- 180 (202)
T ss_pred HcC--CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCC-----CCCCC-
Confidence 654 347999999999888321 123333 3468898776543221 2210035799999988877 43221
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHh
Q 039658 160 AVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLS 195 (198)
Q Consensus 160 ~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~ 195 (198)
+=|..||++...||.+|..
T Consensus 181 -----------------H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 181 -----------------HDALNDAIMAALIFLRLRK 199 (202)
T ss_pred -----------------CCcHHHHHHHHHHHHHHHh
Confidence 2268999999999998864
No 48
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.55 E-value=0.39 Score=47.55 Aligned_cols=131 Identities=18% Similarity=0.185 Sum_probs=83.3
Q ss_pred CeEEEEeeeeccCC-C-ceeEEEeee----CCeE-----EEEEccc--------cCC--------ch------HHHHhhc
Q 039658 39 RRVVGFDVKFNSQT-R-IAEMLILSA----ANLC-----LAIQLCR--------LSR--------IP------ESVTNFL 85 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~-~~aliQla~----~~~~-----~l~~l~~--------~~~--------~p------~~L~~~l 85 (198)
..+|.||+|.+... . .-.+|||+. ++.. .+++... +.. -| +.|.+|+
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~~l 82 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELL 82 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHHHHh
Confidence 57899999988653 2 246888887 3332 1222210 000 11 2356677
Q ss_pred cCCCeEEEEeeecchHhhchh-cCCCCCc--cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCC
Q 039658 86 ADRTICFVGFGVDKKTASIHG-KTGYPRN--CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVT 162 (198)
Q Consensus 86 ~~~~i~kvG~~i~~D~~~L~~-~~~~~~~--~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~ 162 (198)
.+ -++|||++..|...|.. ....|.. ....+|...+++..+.. . ...+|..|++.+|+ .....
T Consensus 83 ~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~--~-~~~~L~~l~~~l~i-----~~~~~---- 148 (928)
T PRK08074 83 EG--AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPT--A-ESYKLRDLSEELGL-----EHDQP---- 148 (928)
T ss_pred CC--CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCC--C-CCCCHHHHHHhCCC-----CCCCC----
Confidence 53 46899999999999832 1123332 35789988887655432 2 46789999988876 33222
Q ss_pred CCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 163 PPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 163 ~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
+=|..||.+...++.+|.+.+
T Consensus 149 --------------H~Al~DA~ata~l~~~l~~~~ 169 (928)
T PRK08074 149 --------------HRADSDAEVTAELFLQLLNKL 169 (928)
T ss_pred --------------CChHHHHHHHHHHHHHHHHHH
Confidence 236889999999999987754
No 49
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=95.50 E-value=1.1 Score=36.93 Aligned_cols=86 Identities=9% Similarity=0.016 Sum_probs=58.3
Q ss_pred HHhhccCCCeEEEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCC
Q 039658 81 VTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEA 160 (198)
Q Consensus 81 L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~ 160 (198)
+.+|.. .-+.|||++..|...| .. + ....+|.-.+|++.+. ++ ..++..|++.+|+ ..+.+.
T Consensus 68 ~~~~~~--~~~lVaHNa~FD~~~L--~~-~---~~~~idTl~lar~l~p--~~--~~~l~~L~~~~~l-----~~~~~~- 129 (219)
T PRK07983 68 IPHYYG--SEWYVAHNASFDRRVL--PE-M---PGEWICTMKLARRLWP--GI--KYSNMALYKSRKL-----NVQTPP- 129 (219)
T ss_pred HHHHcC--CCEEEEeCcHhhHHHH--hC-c---CCCcEeHHHHHHHHcc--CC--CCCHHHHHHHcCC-----CCCCCC-
Confidence 344433 4478999999999999 43 2 2478998787876553 33 4688899977765 321110
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhh
Q 039658 161 VTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSL 196 (198)
Q Consensus 161 ~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~ 196 (198)
. .+-+=|..||+++..++.++.+.
T Consensus 130 --~----------~~aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 130 --G----------LHHHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred --C----------CCCCcHHHHHHHHHHHHHHHHHH
Confidence 0 12355899999999999998753
No 50
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=95.01 E-value=0.3 Score=49.53 Aligned_cols=131 Identities=17% Similarity=0.196 Sum_probs=84.8
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee----CCeEE-----EEEccc-----------cC--------Cch---HHHHhhcc
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA----ANLCL-----AIQLCR-----------LS--------RIP---ESVTNFLA 86 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~----~~~~~-----l~~l~~-----------~~--------~~p---~~L~~~l~ 86 (198)
..+|.||+|.+... ..-.+|||+. .+... ++.... +. .+. +.+.+|+.
T Consensus 190 ~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~fl~ 269 (1213)
T TIGR01405 190 ATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFKEFFK 269 (1213)
T ss_pred CcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHhC
Confidence 68999999998654 3457777775 22221 111110 00 011 24566665
Q ss_pred CCCeEEEEeeecchHhhchh-cCCCCCc--cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCC
Q 039658 87 DRTICFVGFGVDKKTASIHG-KTGYPRN--CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTP 163 (198)
Q Consensus 87 ~~~i~kvG~~i~~D~~~L~~-~~~~~~~--~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~ 163 (198)
+ -+.|||++..|...|.. ...+|.. ....+|+-.+++... |.+ +..+|..|++.+|+ .+..
T Consensus 270 ~--~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~--p~~-k~~kL~~Lak~lgi-----~~~~------ 333 (1213)
T TIGR01405 270 D--SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALN--PEY-KSHRLGNICKKLGV-----DLDD------ 333 (1213)
T ss_pred C--CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHh--ccC-CCCCHHHHHHHcCC-----CCCC------
Confidence 4 36799999999998832 1234443 357899888776543 333 57899999998877 3321
Q ss_pred CCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 164 PNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 164 SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
-+-|..||.++..|+.++.+.+
T Consensus 334 ------------~HrAl~DA~aTa~I~~~ll~~l 355 (1213)
T TIGR01405 334 ------------HHRADYDAEATAKVFKVMVEQL 355 (1213)
T ss_pred ------------CcCHHHHHHHHHHHHHHHHHHH
Confidence 2679999999999999998765
No 51
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=94.98 E-value=0.014 Score=56.43 Aligned_cols=82 Identities=24% Similarity=0.302 Sum_probs=57.7
Q ss_pred hhccCCCeEEEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCC
Q 039658 83 NFLADRTICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAV 161 (198)
Q Consensus 83 ~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~ 161 (198)
.+|-+.+++|||||..+|.+.+ . ..+..+-.+|.-.+. .+|.. +..||+-||..+ |- . +
T Consensus 1008 ~~Li~~GviFVGHGL~nDFrvI--N--i~Vp~~QiiDTv~lf--~~~s~---R~LSLrfLa~~lLg~-----~------I 1067 (1118)
T KOG1275|consen 1008 RLLIQRGVIFVGHGLQNDFRVI--N--IHVPEEQIIDTVTLF--RLGSQ---RMLSLRFLAWELLGE-----T------I 1067 (1118)
T ss_pred HHHHHcCcEEEcccccccceEE--E--EecChhhheeeeEEE--ecccc---cEEEHHHHHHHHhcc-----h------h
Confidence 6788999999999999999988 2 122233467743332 34543 578999999999 87 3 4
Q ss_pred CCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHh
Q 039658 162 TPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLS 195 (198)
Q Consensus 162 ~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~ 195 (198)
|+.+=.. ..||...+++|++-..
T Consensus 1068 Q~~~HDS-----------IeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1068 QMEAHDS-----------IEDARTALKLYKKYLK 1090 (1118)
T ss_pred hcccccc-----------HHHHHHHHHHHHHHHH
Confidence 5544444 6788888888877543
No 52
>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=94.94 E-value=0.16 Score=41.50 Aligned_cols=91 Identities=11% Similarity=0.048 Sum_probs=59.2
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchhcCCC----CC--ccCceeehHHHHHHHhC-CCCCCCCccHHHHHHHhCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHGKTGY----PR--NCDTGIDLGHLAARVLK-KPKLIGLTGIAELAKEVGIDHNS 152 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~----~~--~~~~~~Dl~~la~~~~g-~~~l~~~~sL~~l~~~~g~~~~~ 152 (198)
.+.+|+.+ -+.|||++..|...| .+.+ +. .....+|+..+++...+ .+. .+.+|..+++.+|+
T Consensus 80 ~~~~~~~~--~~lVaHNa~FD~~fL--~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~--~~~~L~~l~~~~gl---- 149 (217)
T TIGR00573 80 DFADYIRG--AELVIHNASFDVGFL--NYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPG--KRNTLDALCKRYEI---- 149 (217)
T ss_pred HHHHHhCC--CEEEEeccHHHHHHH--HHHHHHhcCCCCCccceecHHHHHHHHHHhCCC--CCCCHHHHHHHcCC----
Confidence 45666654 357899999999999 4432 11 23467887666654332 221 35689999988866
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 153 LSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 153 ~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
.... .+-+=|..||.++..|+.++.+..
T Consensus 150 -~~~~----------------~~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 150 -TNSH----------------RALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred -CCCC----------------cccCCHHHHHHHHHHHHHHHHhcc
Confidence 3210 012336899999999999987653
No 53
>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=94.70 E-value=0.048 Score=42.16 Aligned_cols=87 Identities=17% Similarity=0.104 Sum_probs=56.9
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchh-cCCCCC-----ccCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHG-KTGYPR-----NCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSL 153 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~-~~~~~~-----~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~ 153 (198)
.|.+|+.+. ..|||++..|...|.. ...+|. .....+|...+++..... ...+|..+++.+|+
T Consensus 74 ~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~----~~~~L~~l~~~~~i----- 142 (167)
T cd06131 74 EFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPG----KPNSLDALCKRFGI----- 142 (167)
T ss_pred HHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCC----CCCCHHHHHHHCCC-----
Confidence 455666653 3599999999988831 112222 235689977777644322 25689999998866
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 039658 154 SNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKL 193 (198)
Q Consensus 154 ~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L 193 (198)
+... .+-+-|..||.....|+..|
T Consensus 143 ~~~~----------------~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 143 DNSH----------------RTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCC----------------CCCCChHHHHHHHHHHHHHh
Confidence 3321 12355899999999999776
No 54
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=94.66 E-value=0.88 Score=36.36 Aligned_cols=149 Identities=17% Similarity=0.165 Sum_probs=79.8
Q ss_pred CeEEEEeeeecc-----CC--CceeEEEeee-CCeEEEEEccccC--CchHHHHhhc--cCCCeEEEEeee-cchHhhch
Q 039658 39 RRVVGFDVKFNS-----QT--RIAEMLILSA-ANLCLAIQLCRLS--RIPESVTNFL--ADRTICFVGFGV-DKKTASIH 105 (198)
Q Consensus 39 ~~vvg~D~Ew~~-----~~--~~~aliQla~-~~~~~l~~l~~~~--~~p~~L~~~l--~~~~i~kvG~~i-~~D~~~L~ 105 (198)
-+++.||.|-.. +. .++-+|-++. .+...++--...+ .+-..+.+++ .||+++ +|+++ ..|+..|.
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~i-~gyN~~~FDlpyl~ 81 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDII-VGYNSNAFDWPYLV 81 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCEE-EecCCCcCcHHHHH
Confidence 468999999862 22 4455555554 2333332111111 1222334444 357764 79997 47887773
Q ss_pred h-cCCCCCccC----------------------ceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCC
Q 039658 106 G-KTGYPRNCD----------------------TGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVT 162 (198)
Q Consensus 106 ~-~~~~~~~~~----------------------~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~ 162 (198)
. .+.+|+.+. -.+|+-.++++.... .+.+|..+|+.+|....+-..+-+. .+
T Consensus 82 ~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l----~~y~L~~Va~~Lg~~k~~~k~~~~~-~~ 156 (188)
T cd05781 82 ERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEV----KVKTLENVAEYLGVMKKSERVLIEW-YR 156 (188)
T ss_pred HHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCCC----CCCCHHHHHHHHCCCccccccCCCH-HH
Confidence 2 112332211 178877766654333 4789999997556510000011010 01
Q ss_pred CC-CCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 039658 163 PP-NWNAWVFTDKQVLHAVEEARGCYIVADKL 193 (198)
Q Consensus 163 ~S-dW~~~pLt~~Qi~YAA~Da~~~~~i~~~L 193 (198)
.. -|....-..+=..|...|+...+.||+++
T Consensus 157 i~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 157 IYEYWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred HHHHHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 12 34432144778999999999999999864
No 55
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=94.24 E-value=1.7 Score=35.02 Aligned_cols=141 Identities=9% Similarity=0.012 Sum_probs=74.3
Q ss_pred CeEEEEeeeeccCCCceeEEEeeeC--CeEEEEEcccc---------C---CchHHHHhhc--cCCCeEEEEeeecc-hH
Q 039658 39 RRVVGFDVKFNSQTRIAEMLILSAA--NLCLAIQLCRL---------S---RIPESVTNFL--ADRTICFVGFGVDK-KT 101 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~~~~aliQla~~--~~~~l~~l~~~---------~---~~p~~L~~~l--~~~~i~kvG~~i~~-D~ 101 (198)
-++++||+|-... +++-.+.+... +.++++-.+.. . .+-..+.+++ .||+| .+||++.+ |+
T Consensus 3 l~~~~fDIE~~~~-~~i~~i~~~~~~~~~i~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i~~~dPDv-i~g~N~~~FD~ 80 (193)
T cd05784 3 LKVVSLDIETSMD-GELYSIGLYGEGQERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQYDPDI-IIGWNVINFDL 80 (193)
T ss_pred ccEEEEEeecCCC-CCEEEEEeecCCCCEEEEECCCCCCCCCEEEEECCHHHHHHHHHHHHHhhCCCE-EEECCCcCcCH
Confidence 4689999998543 23333333222 22333322111 1 1112333344 35675 59999964 88
Q ss_pred hhchh-cCCCCCcc--------------------------CceeehHHHHHH-HhCCCCCCCCccHHHHHHHh-CCCCCC
Q 039658 102 ASIHG-KTGYPRNC--------------------------DTGIDLGHLAAR-VLKKPKLIGLTGIAELAKEV-GIDHNS 152 (198)
Q Consensus 102 ~~L~~-~~~~~~~~--------------------------~~~~Dl~~la~~-~~g~~~l~~~~sL~~l~~~~-g~~~~~ 152 (198)
..|.. ...+|+.+ .-.+|+-.++++ .++ + ...+|..+|+++ |..
T Consensus 81 ~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~k---l-~sy~L~~Va~~~Lg~~--- 153 (193)
T cd05784 81 RLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYH---F-ESFSLENVAQELLGEG--- 153 (193)
T ss_pred HHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccCC---C-CcCCHHHHHHHHhCCC---
Confidence 77731 11222221 015776555543 222 2 477999999999 751
Q ss_pred CCCCCCCCC---CCC-CCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 039658 153 LSNKEIEAV---TPP-NWNAWVFTDKQVLHAVEEARGCYIVAD 191 (198)
Q Consensus 153 ~~l~K~~~~---~~S-dW~~~pLt~~Qi~YAA~Da~~~~~i~~ 191 (198)
..+....+ ..+ -|...+ +.-++|+..||+..+++++
T Consensus 154 -K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 154 -KLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred -ccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 11110000 111 233333 4679999999999998874
No 56
>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=94.22 E-value=0.23 Score=40.09 Aligned_cols=82 Identities=12% Similarity=0.058 Sum_probs=56.3
Q ss_pred CeEEEEeeecchHhhchh-cCCCCCc-----cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCC
Q 039658 89 TICFVGFGVDKKTASIHG-KTGYPRN-----CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVT 162 (198)
Q Consensus 89 ~i~kvG~~i~~D~~~L~~-~~~~~~~-----~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~ 162 (198)
+-+.|||++.-|...|.. .+.+|.. ....+|.-.+++... | ..+|..+++.+|+ ...
T Consensus 105 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~--~----~~~L~~l~~~~gi-----~~~------ 167 (200)
T TIGR01298 105 RAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAY--G----QTVLAKACQAAGX-----DFD------ 167 (200)
T ss_pred CCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHc--C----cccHHHHHHHcCC-----Ccc------
Confidence 446899999999998831 1123332 235899888776443 3 3479999987776 321
Q ss_pred CCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 163 PPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 163 ~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
..+-+=|..||.+..+++.++.+.+
T Consensus 168 ----------~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 168 ----------STQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred ----------ccchhhhHHhHHHHHHHHHHHHHHH
Confidence 1245568899999999999987654
No 57
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=94.20 E-value=0.25 Score=43.94 Aligned_cols=85 Identities=19% Similarity=0.219 Sum_probs=56.4
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhC-CCCCCCCccHHHHHHHh-CCCCCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLK-KPKLIGLTGIAELAKEV-GIDHNSLSNKE 157 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g-~~~l~~~~sL~~l~~~~-g~~~~~~~l~K 157 (198)
.|+. |-+++-+-|||+..+|++.| ... -..++|.+.+..-..| .| .+.||+.|++.+ |. .+.
T Consensus 286 ~l~~-~~~~~TILVGHSLenDL~aL--Kl~----H~~ViDTa~lf~~~~g~~~---~k~sLk~L~~~~L~~-----~Iq- 349 (380)
T KOG2248|consen 286 ELLE-LISKNTILVGHSLENDLKAL--KLD----HPSVIDTAVLFKHPTGPYP---FKSSLKNLAKSYLGK-----LIQ- 349 (380)
T ss_pred HHHh-hcCcCcEEEeechhhHHHHH--hhh----CCceeeeeEEEecCCCCcc---chHHHHHHHHHHHHH-----HHh-
Confidence 4666 44566678999999999999 543 3567886654433334 24 578899999999 98 554
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 039658 158 IEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLL 194 (198)
Q Consensus 158 ~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~ 194 (198)
....++ =++.||+++.++.....
T Consensus 350 ~~~~~H--------------dS~eDA~acm~Lv~~k~ 372 (380)
T KOG2248|consen 350 EGVGGH--------------DSVEDALACMKLVKLKI 372 (380)
T ss_pred ccCCCC--------------ccHHHHHHHHHHHHHHH
Confidence 111111 13778888888765543
No 58
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=94.17 E-value=0.14 Score=40.85 Aligned_cols=81 Identities=15% Similarity=0.105 Sum_probs=56.3
Q ss_pred CeEEEEeeecchHhhchh-cCCCCC-----ccCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCC
Q 039658 89 TICFVGFGVDKKTASIHG-KTGYPR-----NCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVT 162 (198)
Q Consensus 89 ~i~kvG~~i~~D~~~L~~-~~~~~~-----~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~ 162 (198)
+-+.|||++.-|...|.. .+.+|+ .+...+|.-.+++...+ ..+|..+|+.+|+ +++.
T Consensus 102 ~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~------~~~L~~l~~~~gi-----~~~~----- 165 (189)
T cd06134 102 RAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG------QTVLAKACQAAGI-----EFDN----- 165 (189)
T ss_pred CCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC------CCcHHHHHHHCCC-----CCCC-----
Confidence 347899999999988832 123454 23458998888775533 3469999988777 4321
Q ss_pred CCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhh
Q 039658 163 PPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSL 196 (198)
Q Consensus 163 ~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~ 196 (198)
.+-+=|..||.+...++.++.+.
T Consensus 166 -----------~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 166 -----------KEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred -----------CCCcChHHHHHHHHHHHHHHHHh
Confidence 12344789999999999998764
No 59
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=94.04 E-value=0.1 Score=50.32 Aligned_cols=95 Identities=21% Similarity=0.161 Sum_probs=62.9
Q ss_pred CeEEEEeeecchHhhchhcCCCCCccC--ceeehHHHHHHHhCC------------------------CC--------C-
Q 039658 89 TICFVGFGVDKKTASIHGKTGYPRNCD--TGIDLGHLAARVLKK------------------------PK--------L- 133 (198)
Q Consensus 89 ~i~kvG~~i~~D~~~L~~~~~~~~~~~--~~~Dl~~la~~~~g~------------------------~~--------l- 133 (198)
.=++|||++..|-.++ .+.|.++-. .++|...+.....|. |. +
T Consensus 241 e~liVGHNVsfDRaRi--rEeY~i~~Sk~rFlDTMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~~pWL~ 318 (1075)
T KOG3657|consen 241 EQLIVGHNVSFDRARI--REEYNINGSKIRFLDTMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDYDNPWLG 318 (1075)
T ss_pred CceEEeccccchHHHH--HHHHhccccceeeeechhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhhhhhhhh
Confidence 4578999999999999 788877643 456755442211110 00 0
Q ss_pred -CCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHH--------HHHHHhHHHHHHHHHHHH
Q 039658 134 -IGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFTDKQV--------LHAVEEARGCYIVADKLL 194 (198)
Q Consensus 134 -~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi--------~YAA~Da~~~~~i~~~L~ 194 (198)
.+..||.+.++.+ |.+ .++|+++-.. -.++.+|| .|.|.|+|+.-+||.++.
T Consensus 319 ~SS~NSL~dVhk~~c~~~----~LdKt~Rd~F-----vs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lf 380 (1075)
T KOG3657|consen 319 RSSLNSLVDVHKFHCGID----ALDKTPRDSF-----VSGTKEQIRENFQPLMNYCARDVIATHQVFFRLF 380 (1075)
T ss_pred hhhhHHHHHHHHhhCCCC----ccccchHHhh-----hcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHh
Confidence 1345777777777 772 3888764322 13555554 799999999999999875
No 60
>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=93.46 E-value=0.14 Score=42.11 Aligned_cols=89 Identities=15% Similarity=0.065 Sum_probs=59.0
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchh-cCCCC--Cc----cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHG-KTGYP--RN----CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNS 152 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~-~~~~~--~~----~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~ 152 (198)
.|.+|+.+. ..|||++..|...|.. ...+| .. ...++|.-.++++.+ |. .+.+|..||+.+|+
T Consensus 75 ~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~--p~--~~~~L~~L~~~~gi---- 144 (225)
T TIGR01406 75 EFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERF--PG--QRNSLDALCKRFKV---- 144 (225)
T ss_pred HHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHc--CC--CCCCHHHHHHhcCC----
Confidence 355666653 3589999999988831 11233 11 257899777776554 32 25799999999876
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHh
Q 039658 153 LSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLS 195 (198)
Q Consensus 153 ~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~ 195 (198)
+... .+.+=|..||..+..||..|..
T Consensus 145 -~~~~----------------r~~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 145 -DNSH----------------RTLHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred -CCCC----------------CCCcCHHHHHHHHHHHHHHHHc
Confidence 3211 0123378999999999998864
No 61
>PRK05168 ribonuclease T; Provisional
Probab=93.31 E-value=0.2 Score=40.73 Aligned_cols=82 Identities=12% Similarity=0.058 Sum_probs=56.8
Q ss_pred CeEEEEeeecchHhhchh-cCCCCCc-----cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCC
Q 039658 89 TICFVGFGVDKKTASIHG-KTGYPRN-----CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVT 162 (198)
Q Consensus 89 ~i~kvG~~i~~D~~~L~~-~~~~~~~-----~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~ 162 (198)
+-+.|||++.-|+..|.. .+.+|+. +..++|.-.+++...+ ..+|..+++.+|+ .+..
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~------~~~L~~l~~~~gl-----~~~~----- 177 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG------QTVLAKACQAAGI-----EFDN----- 177 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC------CCCHHHHHHHCCC-----CCCC-----
Confidence 567999999999988831 1233432 2358998888765432 3479999988777 4321
Q ss_pred CCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 163 PPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 163 ~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
.+-+=|..||++..+|+.++.+.+
T Consensus 178 -----------~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 178 -----------KEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred -----------CCCCChHHHHHHHHHHHHHHHHHH
Confidence 112337999999999999998765
No 62
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=93.14 E-value=2.7 Score=34.92 Aligned_cols=134 Identities=13% Similarity=0.082 Sum_probs=78.9
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee----CCeE-------EEEEccc-c-------C-----------CchH---HHHhh
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA----ANLC-------LAIQLCR-L-------S-----------RIPE---SVTNF 84 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~----~~~~-------~l~~l~~-~-------~-----------~~p~---~L~~~ 84 (198)
..++.||+|..... ..-.+|||+. ++.. .+++.-. + . .++. .+.++
T Consensus 47 ~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~l~~~ 126 (239)
T PRK09146 47 VPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEA 126 (239)
T ss_pred CCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHHHHHH
Confidence 68999999998543 2346666664 2221 2222210 0 0 1122 34444
Q ss_pred ccCCCeEEEEeeecchHhhchhc--CCCCCc-cCceeehHHHHHHHhCC------CCC----CCCccHHHHHHHhCCCCC
Q 039658 85 LADRTICFVGFGVDKKTASIHGK--TGYPRN-CDTGIDLGHLAARVLKK------PKL----IGLTGIAELAKEVGIDHN 151 (198)
Q Consensus 85 l~~~~i~kvG~~i~~D~~~L~~~--~~~~~~-~~~~~Dl~~la~~~~g~------~~l----~~~~sL~~l~~~~g~~~~ 151 (198)
+.+ -+.|||+..-|...|... +.++.. ....+|.-.+++..... +.+ ....+|..+++.+|+
T Consensus 127 ~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl--- 201 (239)
T PRK09146 127 LAG--KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGL--- 201 (239)
T ss_pred hCC--CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHcCC---
Confidence 443 468999999999988321 112222 34689988887754321 000 024578888988776
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 152 SLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 152 ~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
+... -+=|..||.++..|+..+.+..
T Consensus 202 --~~~~------------------~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 202 --PAYS------------------PHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred --CCCC------------------CCCcHHHHHHHHHHHHHHHHHH
Confidence 3221 1347899999999999987654
No 63
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=92.83 E-value=0.65 Score=37.78 Aligned_cols=131 Identities=13% Similarity=0.042 Sum_probs=71.9
Q ss_pred CceeEEEeee---CCeEEEEEccccC---CchHHHHhhccCCCeEEEEeee-cchHhhchhc-CCCCCccC---------
Q 039658 53 RIAEMLILSA---ANLCLAIQLCRLS---RIPESVTNFLADRTICFVGFGV-DKKTASIHGK-TGYPRNCD--------- 115 (198)
Q Consensus 53 ~~~aliQla~---~~~~~l~~l~~~~---~~p~~L~~~l~~~~i~kvG~~i-~~D~~~L~~~-~~~~~~~~--------- 115 (198)
+++.+|-++. .+..+.+.-.... .+-..+.+++.+..-+.|||+. .-|+-.|..+ ..+|+.+.
T Consensus 51 ~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~ 130 (208)
T cd05782 51 HKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKD 130 (208)
T ss_pred CceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccch
Confidence 6677777665 3333322211111 1223445555542225689998 5899777321 12343211
Q ss_pred ---------ceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHH
Q 039658 116 ---------TGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGC 186 (198)
Q Consensus 116 ---------~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~ 186 (198)
..+|+-++.+. .+.. ...+|..+|+.+|.+ ....++-+ .+ ..-|.... -++=.+|...||...
T Consensus 131 ~~y~~r~~~~h~DL~~~~~~-~~~~---~~~~L~~va~~lG~~-~K~d~~G~-~v-~~~y~~g~-~~~I~~Yc~~Dv~~t 202 (208)
T cd05782 131 WNYRNRYSERHLDLMDLLAF-YGAR---ARASLDLLAKLLGIP-GKMDVDGS-QV-WELYAEGK-LDEIAEYCETDVLNT 202 (208)
T ss_pred hhccCcCCCCcccHHHHHhc-cCcc---CCCCHHHHHHHhCCC-CCcCCCHH-HH-HHHHHcCC-hHHHHHHHHHHHHHH
Confidence 27888776642 2322 478999999766662 11122111 01 22454434 556789999999999
Q ss_pred HHHHH
Q 039658 187 YIVAD 191 (198)
Q Consensus 187 ~~i~~ 191 (198)
+.||.
T Consensus 203 ~~l~l 207 (208)
T cd05782 203 YLLYL 207 (208)
T ss_pred HHHHh
Confidence 99985
No 64
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=92.48 E-value=2.3 Score=34.50 Aligned_cols=145 Identities=13% Similarity=0.117 Sum_probs=76.6
Q ss_pred CeEEEEeeeeccCC---------CceeEEEeeeC--C-eEEEEEccccCCchHHHHh---hc--cCCCeEEEEeee-cch
Q 039658 39 RRVVGFDVKFNSQT---------RIAEMLILSAA--N-LCLAIQLCRLSRIPESVTN---FL--ADRTICFVGFGV-DKK 100 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~---------~~~aliQla~~--~-~~~l~~l~~~~~~p~~L~~---~l--~~~~i~kvG~~i-~~D 100 (198)
-++++||.|-.... ..-.++|||.. + .-.++... ...-..-|.. ++ .||+| .+||++ ..|
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~-~~~E~~lL~~f~~~i~~~dPdi-i~g~N~~~FD 86 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAE-DAAEKELLEELVAIIRERDPDV-IEGHNIFRFD 86 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccC-CCCHHHHHHHHHHHHHHhCCCE-EeccCCcccC
Confidence 57999999985432 22458888872 2 12222111 1111223444 44 35785 589999 679
Q ss_pred Hhhchh-cCCCCCcc--------------------------------CceeehHHHHHHH-hCCCCCCCCccHHHHHHHh
Q 039658 101 TASIHG-KTGYPRNC--------------------------------DTGIDLGHLAARV-LKKPKLIGLTGIAELAKEV 146 (198)
Q Consensus 101 ~~~L~~-~~~~~~~~--------------------------------~~~~Dl~~la~~~-~g~~~l~~~~sL~~l~~~~ 146 (198)
+..|.. .+.+|+.. .-++|+-.++++. ....++ ...||..+|+.+
T Consensus 87 ~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l-~sysL~~Va~~~ 165 (207)
T cd05785 87 LPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDL-PSYGLKAVAKHF 165 (207)
T ss_pred HHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCC-CCCCHHHHHHHh
Confidence 877731 01122211 1236876655431 111223 456999999987
Q ss_pred CCC-CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 039658 147 GID-HNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVA 190 (198)
Q Consensus 147 g~~-~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~ 190 (198)
|.. +....++- +.+ ..-|...+ +.=++|+..||...+.|+
T Consensus 166 g~~~~~k~d~~~-~~I-~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 166 GLASPDRTYIDG-RQI-AEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred cccCCCcCCCCH-HHH-HHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 540 00011110 111 12344432 677999999999998876
No 65
>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=92.17 E-value=0.82 Score=34.53 Aligned_cols=82 Identities=21% Similarity=0.220 Sum_probs=55.4
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchh-cCCCCC--ccCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHG-KTGYPR--NCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNK 156 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~-~~~~~~--~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~ 156 (198)
.|.+++.+ -+.|||++..|...|.. .+.+|+ .....+|+..+++..++. + ...+|..+++.+|. ...
T Consensus 70 ~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~--~-~~~~L~~l~~~~g~-----~~~ 139 (156)
T cd06130 70 EIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPL--L-PNHKLNTVAEHLGI-----ELN 139 (156)
T ss_pred HHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhcc--C-CCCCHHHHHHHcCC-----Ccc
Confidence 46677765 46899999999998831 112333 345789988777655443 2 46799999988776 432
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 039658 157 EIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVA 190 (198)
Q Consensus 157 K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~ 190 (198)
. +=|..||.....|+
T Consensus 140 -~------------------H~Al~Da~~ta~l~ 154 (156)
T cd06130 140 -H------------------HDALEDARACAEIL 154 (156)
T ss_pred -C------------------cCchHHHHHHHHHH
Confidence 2 23577888887776
No 66
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=92.11 E-value=1.1 Score=36.22 Aligned_cols=91 Identities=11% Similarity=0.045 Sum_probs=59.8
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchh-cCCCCCcc---CceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHG-KTGYPRNC---DTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSN 155 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~-~~~~~~~~---~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l 155 (198)
.|.+|+.+...+.+++ ...|+..|.. .+.+|+.. ...+|+..+.+...+.. ...||..+++.+|+ +.
T Consensus 85 ~f~~~~~~~~~~iv~~-~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~---~~~~L~~~~~~~gi-----~~ 155 (207)
T PRK07748 85 KLAEYDKRCKPTIVTW-GNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGER---NQTGLWKAIEEYGK-----EG 155 (207)
T ss_pred HHHHHhCcCCeEEEEE-CHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcC---CCCCHHHHHHHcCC-----CC
Confidence 4677777645556665 5789988832 12334432 46788876665555543 36799999988876 32
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhh
Q 039658 156 KEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSL 196 (198)
Q Consensus 156 ~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~ 196 (198)
.. + -+-|..||+++..|+.+|...
T Consensus 156 ~~-------~----------~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 156 TG-------K----------HHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred CC-------C----------CcChHHHHHHHHHHHHHHHhC
Confidence 11 0 133789999999999998754
No 67
>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=91.98 E-value=0.84 Score=33.86 Aligned_cols=81 Identities=20% Similarity=0.161 Sum_probs=54.9
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchhcCCC-----CCccCceeehHHHHHHHhCCCCCCCCccHHHH-HHHhCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHGKTGY-----PRNCDTGIDLGHLAARVLKKPKLIGLTGIAEL-AKEVGIDHNSL 153 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~-----~~~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l-~~~~g~~~~~~ 153 (198)
.+.+++.+ -+.|||++..|...| .+.+ .......+|+..+++..++.+ ...++..+ ++.+|.
T Consensus 72 ~~~~~l~~--~~~v~~n~~fD~~~l--~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~---~~~~l~~~~~~~~~~----- 139 (159)
T cd06127 72 EFLEFLGG--RVLVAHNASFDLRFL--NRELRRLGGPPLPNPWIDTLRLARRLLPGL---RSHRLGLLLAERYGI----- 139 (159)
T ss_pred HHHHHHCC--CEEEEeCcHhhHHHH--HHHHHHhCCCCCCCCeeEHHHHHHHHcCCC---CcCchHHHHHHHcCC-----
Confidence 45667765 568999999999888 4432 245578999988887666654 35677777 443354
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 039658 154 SNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVA 190 (198)
Q Consensus 154 ~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~ 190 (198)
... +.+-|..||.++.++|
T Consensus 140 ~~~------------------~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 140 PLE------------------GAHRALADALATAELL 158 (159)
T ss_pred CCC------------------CCCCcHHHHHHHHHHh
Confidence 221 2344788999888876
No 68
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=91.34 E-value=1.7 Score=37.42 Aligned_cols=89 Identities=11% Similarity=0.098 Sum_probs=61.2
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchh-cCCCCCc--cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHG-KTGYPRN--CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNK 156 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~-~~~~~~~--~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~ 156 (198)
.|.+|+.+ -+.|||++..|...|.. .+.++.. ....+|.-.++++.+.. + ...+|..|++.+|+ ...
T Consensus 73 ~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~--~-~~~~L~~L~~~~gi-----~~~ 142 (309)
T PRK06195 73 KIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSN--I-DNARLNTVNNFLGY-----EFK 142 (309)
T ss_pred HHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCC--C-CcCCHHHHHHHcCC-----CCc
Confidence 45666653 46899999999988832 1123332 34688987777765532 2 35789999988876 321
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 157 EIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 157 K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
-+=|..||+++..|+..|.+.+
T Consensus 143 -------------------~H~Al~DA~ata~l~~~l~~~~ 164 (309)
T PRK06195 143 -------------------HHDALADAMACSNILLNISKEL 164 (309)
T ss_pred -------------------ccCCHHHHHHHHHHHHHHHHHh
Confidence 1457899999999999987654
No 69
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=89.75 E-value=0.074 Score=47.06 Aligned_cols=148 Identities=15% Similarity=0.042 Sum_probs=87.7
Q ss_pred CeEEEEeeeeccCC--CceeEEEeeeCCeEEEEEccccC-CchHH-HHhhccCCCeEEEEeeecchHhhchhcCCCCCcc
Q 039658 39 RRVVGFDVKFNSQT--RIAEMLILSAANLCLAIQLCRLS-RIPES-VTNFLADRTICFVGFGVDKKTASIHGKTGYPRNC 114 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~--~~~aliQla~~~~~~l~~l~~~~-~~p~~-L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~ 114 (198)
-.+||.|.--.-.. ....++|+|+++..+++|....+ .++.. .+.-|++-.+ +- +...+...| ...|+...
T Consensus 195 ~~~i~~~~~s~~~~~~~e~~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l--~~~y~~~L 269 (458)
T KOG2405|consen 195 VWFIRPVSPSLLKILALEATYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQL--DTTYHSAL 269 (458)
T ss_pred eeEeecCchhHHHhhhhhhhhhhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHH--HhHHHHHH
Confidence 56666665432211 23445799999999999987554 23333 5666665544 22 778888888 88899999
Q ss_pred CceeehHHHHHH-----HhCCCC----CCCCccHHH---HHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q 039658 115 DTGIDLGHLAAR-----VLKKPK----LIGLTGIAE---LAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVE 181 (198)
Q Consensus 115 ~~~~Dl~~la~~-----~~g~~~----l~~~~sL~~---l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~ 181 (198)
.|++|.+ ++.+ .+|+.. +....+|.. .+..- +. +-.+.+--+....+|.-||-|+...+-++-
T Consensus 270 ~nVkDtQ-ia~sLve~~e~grr~p~~~lIsft~Lq~~~~y~~~s~~~---~eev~~~l~~dp~~w~irp~te~~~~~~h~ 345 (458)
T KOG2405|consen 270 KNVKDTQ-IASSLVEPSEYGRRHPTSILISFTCLQTYIFYIKASGLI---FEEVAKILEADPPRWVIRPSTEIADHLLHR 345 (458)
T ss_pred HhhHHHH-HHHHHhhhHHhcccCCccceeeeEeccccceeehhhhhh---HHHHHHHHhcCCCcceecccHHHHHHHHHH
Confidence 9999955 4443 334320 001111111 00000 00 000111111122379999999999999999
Q ss_pred hHHHHHHHHHHHHh
Q 039658 182 EARGCYIVADKLLS 195 (198)
Q Consensus 182 Da~~~~~i~~~L~~ 195 (198)
|+.++..++..+.+
T Consensus 346 dv~~Ll~~~~~l~a 359 (458)
T KOG2405|consen 346 DVISLLGIFDTLVA 359 (458)
T ss_pred HHHHHHHHHhhHhh
Confidence 99999998866643
No 70
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=88.61 E-value=2.7 Score=43.66 Aligned_cols=84 Identities=18% Similarity=0.076 Sum_probs=58.6
Q ss_pred CCeEEEEeeecchHhhchh-cCCCCC--ccCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCCCC
Q 039658 88 RTICFVGFGVDKKTASIHG-KTGYPR--NCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVTPP 164 (198)
Q Consensus 88 ~~i~kvG~~i~~D~~~L~~-~~~~~~--~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~~S 164 (198)
.+.+.|+|+...|...|.. .+..|+ -....+|.-.+++.... .. .+.+|..||+.+|+ .....
T Consensus 498 gg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p--~~-k~~kL~~LAk~lGL-----~~~~~------ 563 (1437)
T PRK00448 498 GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYP--EL-KSHRLNTLAKKFGV-----ELEHH------ 563 (1437)
T ss_pred CCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcC--cc-ccccHHHHHHHcCC-----CCCCC------
Confidence 4567899999999876621 123344 23567897776664432 22 57899999998876 43211
Q ss_pred CCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 165 NWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 165 dW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
+-|..||+++..|+.++.+.+
T Consensus 564 ------------HrAl~DA~aTa~lf~~ll~~l 584 (1437)
T PRK00448 564 ------------HRADYDAEATAYLLIKFLKDL 584 (1437)
T ss_pred ------------cChHHHHHHHHHHHHHHHHHH
Confidence 668999999999999998765
No 71
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=88.27 E-value=12 Score=30.26 Aligned_cols=96 Identities=17% Similarity=0.094 Sum_probs=55.4
Q ss_pred CCCeEEEEeee-cchHhhchh-cCCCCCcc--------C----------ceeehHHHHHHHhCCCCCCCCccHHHHHHHh
Q 039658 87 DRTICFVGFGV-DKKTASIHG-KTGYPRNC--------D----------TGIDLGHLAARVLKKPKLIGLTGIAELAKEV 146 (198)
Q Consensus 87 ~~~i~kvG~~i-~~D~~~L~~-~~~~~~~~--------~----------~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~ 146 (198)
+|++ .+|+++ .-|+..|.. ...+|+.. . -.+|+=++.++....+. +..+|...|+.+
T Consensus 88 ~Pd~-i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~--~sysLd~Va~~~ 164 (204)
T cd05779 88 KPHI-IVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQ--GSQGLKAVTKAK 164 (204)
T ss_pred CCCE-EEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCC--CCccHHHHHHHH
Confidence 5676 588887 578877731 11223221 1 15787666654221110 356899999998
Q ss_pred -CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 039658 147 -GIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVAD 191 (198)
Q Consensus 147 -g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~ 191 (198)
|... ..++ .+.+.. -|...+ +.=++|+..||...+.+|.
T Consensus 165 Lg~~K--~~~~-~~~I~~-~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 165 LGYDP--VELD-PEDMVP-LAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred hCCCc--CcCC-HHHHHH-HHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 8611 1111 011111 455544 5679999999999999983
No 72
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=88.22 E-value=5.9 Score=35.30 Aligned_cols=136 Identities=13% Similarity=0.056 Sum_probs=76.7
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee-----CCe-----EEEEEccc------cCC-----------c---hHHHHhhccC
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA-----ANL-----CLAIQLCR------LSR-----------I---PESVTNFLAD 87 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~-----~~~-----~~l~~l~~------~~~-----------~---p~~L~~~l~~ 87 (198)
..+|.||+|..... ..-.+|+|+. ++. ..++.... +.. + -+.|.+|+.+
T Consensus 46 ~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~~fL~g 125 (377)
T PRK05601 46 APFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLDRLIDG 125 (377)
T ss_pred CCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHHHHhCC
Confidence 67999999988764 3346676642 121 11222111 000 1 1346777774
Q ss_pred CCeEEEEeeecchHhhchhc--C--------------------------CC-CC-ccCceeehHHHHHHHhCCCCCCCCc
Q 039658 88 RTICFVGFGVDKKTASIHGK--T--------------------------GY-PR-NCDTGIDLGHLAARVLKKPKLIGLT 137 (198)
Q Consensus 88 ~~i~kvG~~i~~D~~~L~~~--~--------------------------~~-~~-~~~~~~Dl~~la~~~~g~~~l~~~~ 137 (198)
. +.|+|+...|...|... + .+ ++ .+..++|.-.++++.+ |.+ ...
T Consensus 126 ~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~--p~l-~~~ 200 (377)
T PRK05601 126 R--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQG--VAL-DDI 200 (377)
T ss_pred C--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHc--CCC-CCC
Confidence 3 57999999999877310 0 01 11 2246899777777554 222 467
Q ss_pred cHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH---HhHHHHHHHHHHH
Q 039658 138 GIAELAKEVGIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAV---EEARGCYIVADKL 193 (198)
Q Consensus 138 sL~~l~~~~g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA---~Da~~~~~i~~~L 193 (198)
.|..||+.+|+ ..+-. .-.....|.--.+ -||.++..||.++
T Consensus 201 rL~~La~~lGi-----~~p~~---------~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 201 RIRGVAHTLGL-----DAPAA---------EASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred CHHHHHHHhCC-----CCCch---------hhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 89999999877 33210 0011112221222 3888998888875
No 73
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=88.04 E-value=0.22 Score=38.24 Aligned_cols=146 Identities=12% Similarity=0.081 Sum_probs=69.2
Q ss_pred EEEeeeec---cCCCceeEEEeee--CCe-EEEEEccccC-CchHHHH---hhccCCCeEEEEeee-cchHhhchhc-CC
Q 039658 42 VGFDVKFN---SQTRIAEMLILSA--ANL-CLAIQLCRLS-RIPESVT---NFLADRTICFVGFGV-DKKTASIHGK-TG 109 (198)
Q Consensus 42 vg~D~Ew~---~~~~~~aliQla~--~~~-~~l~~l~~~~-~~p~~L~---~~l~~~~i~kvG~~i-~~D~~~L~~~-~~ 109 (198)
+-||+|.. |..+.+-++-++. ++. ....+....+ .....+. +++..... .|+|+. ..|...|... ..
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~l~~~~~-iv~yng~~FD~p~L~~~~~~ 79 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFFELLDEADN-IVTYNGKNFDIPFLKRRAKR 79 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH--HHHHTT---EEESSTTTTHHHHHHHHH-H
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHHHHHhcCCe-EEEEeCcccCHHHHHHHHHH
Confidence 35899988 3225566776664 333 3244433222 1222333 34555554 455665 5699888322 23
Q ss_pred CCCc-cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCC-CCCCCCC---CCCCHHHHHHHHHhHH
Q 039658 110 YPRN-CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAV-TPPNWNA---WVFTDKQVLHAVEEAR 184 (198)
Q Consensus 110 ~~~~-~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~-~~SdW~~---~pLt~~Qi~YAA~Da~ 184 (198)
+++. ..+.+||...+.+... + ..||+.+++.+|.....-.++..+.+ .-..|.. +...++-+.|.-.|+.
T Consensus 80 ~~~~~~~~~iDl~~~~~~~~~-~----~~~Lk~ve~~lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~Dv~ 154 (164)
T PF13482_consen 80 YGLPPPFNHIDLLKIIKKHFL-E----SYSLKNVEKFLGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNEDDVR 154 (164)
T ss_dssp HHH--GGGEEEHHHHHT-TTS-C----CTT--SHHH-----------HHHHHHHHHH---TTGGTS--HHHHHHHHHHHH
T ss_pred cCCCcccchhhHHHHHHhccC-C----CCCHHHHhhhcccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Confidence 4444 7789999887753322 3 56899998887551100011100000 0011211 2467788999999999
Q ss_pred HHHHHHHHH
Q 039658 185 GCYIVADKL 193 (198)
Q Consensus 185 ~~~~i~~~L 193 (198)
.+..|++.|
T Consensus 155 ~~~~L~~~l 163 (164)
T PF13482_consen 155 ATRRLYEWL 163 (164)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHh
Confidence 999999876
No 74
>PHA02528 43 DNA polymerase; Provisional
Probab=83.80 E-value=48 Score=33.00 Aligned_cols=178 Identities=11% Similarity=0.071 Sum_probs=100.7
Q ss_pred EECCeEEEEEEeCCHHHHHHHHHHHHhhh------------------------c-cCCeEEEEeeeeccCC-----C--c
Q 039658 7 EIKDVKFKVSVIDDADVIDKKISELSGML------------------------F-KMRRVVGFDVKFNSQT-----R--I 54 (198)
Q Consensus 7 ~~~~~~i~v~v~~~~~~~~~~i~~l~~~~------------------------~-~~~~vvg~D~Ew~~~~-----~--~ 54 (198)
.|.|.-+.-....+..++.+|.+.+...- . ..-++++||+|-.... . +
T Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~merfi~~~~~~~~~~~~~~~~p~lrv~s~DIE~~~~~gfP~p~~~~ 128 (881)
T PHA02528 49 DIYGKNCRPKKFDSMRDARKWMKRMKDVGFEALGMDDFKLQYISDTYPGEIKYDRSKIRIANLDIEVTAEDGFPDPEEAK 128 (881)
T ss_pred ccCCCEEeEEECCCHHHHHHHHHHHHhcCCceeehhHHhhhhhhhhcCCCCCCCCCCccEEEEEEEECCCCCCCCcccCC
Confidence 35677788888889999999998877651 0 1268999999986421 1 1
Q ss_pred eeEEEeee----CCeEEEEEcc--------------c---------cCC---chHHHHhhc--cCCCeEEEEeeec-chH
Q 039658 55 AEMLILSA----ANLCLAIQLC--------------R---------LSR---IPESVTNFL--ADRTICFVGFGVD-KKT 101 (198)
Q Consensus 55 ~aliQla~----~~~~~l~~l~--------------~---------~~~---~p~~L~~~l--~~~~i~kvG~~i~-~D~ 101 (198)
=-+++|+. .+++.++.+. . .+. +-..+.+++ .||+|+ +||++. .|+
T Consensus 129 d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~eLL~~F~~~i~~~DPDII-~GyNi~~FDl 207 (881)
T PHA02528 129 YEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTEREMLLEYINFWEENTPVIF-TGWNVELFDV 207 (881)
T ss_pred CcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCeeEEEcCCHHHHHHHHHHHHHHhCCcEE-EecCCccCCH
Confidence 13555554 3344444330 0 011 112233333 478874 899985 588
Q ss_pred hhchhc--CCCCCc----------------------------cC--ceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CC
Q 039658 102 ASIHGK--TGYPRN----------------------------CD--TGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GI 148 (198)
Q Consensus 102 ~~L~~~--~~~~~~----------------------------~~--~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~ 148 (198)
..|..+ +.+|.. +. -.+|+-++++.. ....+ ...+|..+|+++ |.
T Consensus 208 pYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD~~dl~k~~-~~~~l-~SYsLe~VA~~~LG~ 285 (881)
T PHA02528 208 PYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILDYLDLYKKF-TFTNQ-PSYRLDYIAEVELGK 285 (881)
T ss_pred HHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEeHHHHHHHh-hhccc-ccCCHHHHHHHHhCC
Confidence 666311 011211 11 135544444432 22223 467899999998 86
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 039658 149 DHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKL 193 (198)
Q Consensus 149 ~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L 193 (198)
... .++ .+ ..+.|..... ..=++|...||...+.|+.++
T Consensus 286 ~K~--d~~-~~--eI~~l~~~d~-~~l~~Ynl~Da~Lv~~L~~kl 324 (881)
T PHA02528 286 KKL--DYS-DG--PFKKFRETDH-QKYIEYNIIDVELVDRLDDKR 324 (881)
T ss_pred CCc--cCC-HH--HHHHHHhcCH-HHHHHHHHHHHHHHHHHHHHH
Confidence 110 111 11 2233433222 456999999999999999984
No 75
>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=82.33 E-value=2.3 Score=34.97 Aligned_cols=73 Identities=16% Similarity=0.126 Sum_probs=46.3
Q ss_pred eeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCC-CCC-CHHHHHHHHHhHHHHHHHHHHH
Q 039658 117 GIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNA-WVF-TDKQVLHAVEEARGCYIVADKL 193 (198)
Q Consensus 117 ~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~-~pL-t~~Qi~YAA~Da~~~~~i~~~L 193 (198)
.+|+-.++++... + ...+|..+|+++ |... ..++- + ..++|.. .|= -..-++|...||...++|+.+|
T Consensus 153 ~iD~~~~~~~~~k---l-~sy~L~~Va~~~Lg~~k--~d~~~-~--~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl 223 (230)
T cd05777 153 QFDLLQVIQRDYK---L-RSYSLNSVSAHFLGEQK--EDVHY-S--IITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKL 223 (230)
T ss_pred eeeHHHHHHHhcC---c-ccCcHHHHHHHHhCCCC--CCCCH-H--HHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHH
Confidence 3566555554332 3 578999999999 8611 11211 1 2334432 332 2456999999999999999999
Q ss_pred HhhhC
Q 039658 194 LSLLN 198 (198)
Q Consensus 194 ~~~l~ 198 (198)
.-+.|
T Consensus 224 ~~~~~ 228 (230)
T cd05777 224 MCLVN 228 (230)
T ss_pred hhHcc
Confidence 87654
No 76
>PRK05762 DNA polymerase II; Reviewed
Probab=81.62 E-value=49 Score=32.38 Aligned_cols=145 Identities=8% Similarity=0.060 Sum_probs=77.2
Q ss_pred CeEEEEeeeeccCCCceeEEEeee--CCeEEEEEcccc---------C---CchHHHHhhc--cCCCeEEEEeeec-chH
Q 039658 39 RRVVGFDVKFNSQTRIAEMLILSA--ANLCLAIQLCRL---------S---RIPESVTNFL--ADRTICFVGFGVD-KKT 101 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~~~~aliQla~--~~~~~l~~l~~~---------~---~~p~~L~~~l--~~~~i~kvG~~i~-~D~ 101 (198)
-++++||.|-... .++..|.++. ++.++++-.+.. . .+-..+.+++ .||+| .+||++. .|+
T Consensus 155 lrvlsfDIE~~~~-~~i~sI~~~~~~~~~vi~ig~~~~~~~~~v~~~~sE~~LL~~F~~~i~~~DPDI-IvGyNi~~FDl 232 (786)
T PRK05762 155 LKVVSLDIETSNK-GELYSIGLEGCGQRPVIMLGPPNGEALDFLEYVADEKALLEKFNAWFAEHDPDV-IIGWNVVQFDL 232 (786)
T ss_pred CeEEEEEEEEcCC-CceEEeeecCCCCCeEEEEECCCCCCcceEEEcCCHHHHHHHHHHHHHhcCCCE-EEEeCCCCCcH
Confidence 6899999998654 2333333321 123333332211 1 1212233333 36886 4899985 698
Q ss_pred hhchhc-CCCCCcc---------------------------CceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCC
Q 039658 102 ASIHGK-TGYPRNC---------------------------DTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNS 152 (198)
Q Consensus 102 ~~L~~~-~~~~~~~---------------------------~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~ 152 (198)
..|..+ +.+|+.. .-.+|+-.++++... .+ ...+|..+|+++ |...
T Consensus 233 pyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~--~l-~sysL~~Va~~~Lg~~K-- 307 (786)
T PRK05762 233 RLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATW--VF-DSFSLEYVSQRLLGEGK-- 307 (786)
T ss_pred HHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhc--cC-CCCCHHHHHHHHhCCCe--
Confidence 777311 1122211 125777666654431 12 467899999999 7510
Q ss_pred CCCCCC-CCC-CC-CCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 039658 153 LSNKEI-EAV-TP-PNWNAWVFTDKQVLHAVEEARGCYIVADKL 193 (198)
Q Consensus 153 ~~l~K~-~~~-~~-SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L 193 (198)
..... .+. ++ .-|... .+.-.+|...||...+.|++++
T Consensus 308 -~~~d~~~~~~eI~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 308 -AIDDPYDRMDEIDRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred -eccCccccHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 00000 000 01 123221 2456899999999999999865
No 77
>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=78.57 E-value=33 Score=27.66 Aligned_cols=139 Identities=9% Similarity=0.086 Sum_probs=77.6
Q ss_pred CeEEEEeeeeccC----C-Cc----eeEEEeeeCC-----eEEEEEccc----------------cC---CchHHHHhhc
Q 039658 39 RRVVGFDVKFNSQ----T-RI----AEMLILSAAN-----LCLAIQLCR----------------LS---RIPESVTNFL 85 (198)
Q Consensus 39 ~~vvg~D~Ew~~~----~-~~----~aliQla~~~-----~~~l~~l~~----------------~~---~~p~~L~~~l 85 (198)
-++++||.|-... + ++ -.++||+..+ +.+++.... .. .+-..+.+++
T Consensus 5 lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i 84 (204)
T cd05783 5 LKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKELIREAFKII 84 (204)
T ss_pred ceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEEEEEecCCcccccccCCCCCeEEecCCHHHHHHHHHHHH
Confidence 5789999998632 1 11 3578888632 244443110 01 1223455566
Q ss_pred cCCCeEEEEeee-cchHhhchh-cCCCCCc----------------cCceeehHHHHHH-H-----hCCCCCCCCccHHH
Q 039658 86 ADRTICFVGFGV-DKKTASIHG-KTGYPRN----------------CDTGIDLGHLAAR-V-----LKKPKLIGLTGIAE 141 (198)
Q Consensus 86 ~~~~i~kvG~~i-~~D~~~L~~-~~~~~~~----------------~~~~~Dl~~la~~-~-----~g~~~l~~~~sL~~ 141 (198)
.+.. +.+|+++ ..|+..|.. .+.+|+. ..-.+|+-+.+.. . ++. ++ ...+|..
T Consensus 85 ~~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~-~~-~~~~L~~ 161 (204)
T cd05783 85 SEYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGN-KY-REYTLDA 161 (204)
T ss_pred hcCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcc-cc-ccCcHHH
Confidence 6554 5678887 488877742 1233443 1235787654432 1 121 12 4679999
Q ss_pred HHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCC-HHHHHHHHHhHHHHHHHHH
Q 039658 142 LAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFT-DKQVLHAVEEARGCYIVAD 191 (198)
Q Consensus 142 l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt-~~Qi~YAA~Da~~~~~i~~ 191 (198)
+|+.+ |.. ...+. ..+.. +. ++=+.|+..||...+.|+.
T Consensus 162 Va~~~lg~~--K~~~~--~~i~~-------~~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 162 VAKALLGEG--KVELE--KNISE-------LNLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred HHHHhcCCC--cccCC--chhhh-------hcHHHHHHhhHHHHHHHHHHhc
Confidence 99999 761 11221 11211 12 3458999999999998864
No 78
>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=77.88 E-value=9.7 Score=29.86 Aligned_cols=82 Identities=15% Similarity=0.094 Sum_probs=52.0
Q ss_pred HHHhhccC--CCeEEEEeee-cchHhhchh-cCCCCCcc---CceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCC
Q 039658 80 SVTNFLAD--RTICFVGFGV-DKKTASIHG-KTGYPRNC---DTGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHN 151 (198)
Q Consensus 80 ~L~~~l~~--~~i~kvG~~i-~~D~~~L~~-~~~~~~~~---~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~ 151 (198)
.+.+|+.. ...+.|||++ .-|...|.. ...+|... ..++|.-.+++.. .+ +|..|++.+ |.
T Consensus 87 ~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~-------~~-~L~~l~~~~~~~--- 155 (177)
T cd06136 87 LIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFREL-------DQ-SLGSLYKRLFGQ--- 155 (177)
T ss_pred HHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhh-------Hh-hHHHHHHHHhCC---
Confidence 46666653 3468999998 899998831 11234332 3457865555422 12 799999986 87
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHH
Q 039658 152 SLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADK 192 (198)
Q Consensus 152 ~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~ 192 (198)
+... -+=|..||.++.+++.+
T Consensus 156 --~~~~------------------~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 156 --EPKN------------------SHTAEGDVLALLKCALH 176 (177)
T ss_pred --Cccc------------------ccchHHHHHHHHHHHhh
Confidence 4432 13478899998887753
No 79
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=77.44 E-value=46 Score=28.60 Aligned_cols=86 Identities=12% Similarity=0.041 Sum_probs=49.7
Q ss_pred HHHHhhccCCCeEEEEeeecchHhhchhcCCCCC-ccCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCC
Q 039658 79 ESVTNFLADRTICFVGFGVDKKTASIHGKTGYPR-NCDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKE 157 (198)
Q Consensus 79 ~~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~-~~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K 157 (198)
+.+..|+.... +.|||++..|...| .+.+.- ......+.-... .+..+.. ...+|..|++.+|. .-+
T Consensus 112 ~~l~~fl~~~~-vlVAHNA~FD~~fL--~~~~~~~~~~~~~ct~~~i--~~~~~~~-~~~kL~~La~~~g~-----~~~- 179 (294)
T PRK09182 112 AAVDALIAPAD-LIIAHNAGFDRPFL--ERFSPVFATKPWACSVSEI--DWSARGF-EGTKLGYLAGQAGF-----FHE- 179 (294)
T ss_pred HHHHHHhcCCC-EEEEeCHHHHHHHH--HHHHHhccCCcccccHHHH--hhccccC-CCCCHHHHHHHcCC-----CCC-
Confidence 35677777643 67999999999888 432211 111122211111 1111222 46789999987753 110
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 039658 158 IEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLL 194 (198)
Q Consensus 158 ~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~ 194 (198)
-+=|..||+++..|+....
T Consensus 180 ------------------aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 180 ------------------GHRAVDDCQALLELLARPL 198 (294)
T ss_pred ------------------CcChHHHHHHHHHHHHHHH
Confidence 1337899999999988654
No 80
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=71.03 E-value=0.065 Score=47.39 Aligned_cols=128 Identities=13% Similarity=0.006 Sum_probs=83.0
Q ss_pred CceeEEEeeeCCeEEEEEccccC--CchHHHHhhccCCCeEEEEeeecchHhhchhcCCCCCccCceeehHHHHH-HHhC
Q 039658 53 RIAEMLILSAANLCLAIQLCRLS--RIPESVTNFLADRTICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAA-RVLK 129 (198)
Q Consensus 53 ~~~aliQla~~~~~~l~~l~~~~--~~p~~L~~~l~~~~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~-~~~g 129 (198)
.|+|=+|.++.-++|+++++-.+ .+...+..|+++++|.|+-|.++.=.+.+ ...||+..+|++|++. +. ..+|
T Consensus 74 ~~l~~~q~~~~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~--~~~~~i~~n~v~~~q~-~d~~q~~ 150 (458)
T KOG2405|consen 74 GKLCWLQVATNCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCL--SHQYGILLNNVFDTQV-ADVLQFS 150 (458)
T ss_pred CcchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHh--cccceeeecchhhhhh-hhhhhhc
Confidence 68999999999999999987654 24567899999999999999988777777 7889999999999765 32 1222
Q ss_pred C---CCCCCCcc---HHHHHHHh-CCCCCCC-CCCCCC---CCCCCCCCCCCCCHHHHHHHHHhHHH
Q 039658 130 K---PKLIGLTG---IAELAKEV-GIDHNSL-SNKEIE---AVTPPNWNAWVFTDKQVLHAVEEARG 185 (198)
Q Consensus 130 ~---~~l~~~~s---L~~l~~~~-g~~~~~~-~l~K~~---~~~~SdW~~~pLt~~Qi~YAA~Da~~ 185 (198)
. +.+ ...+ =.+|.+++ -.+ .|. .|.|.. ...+--|--||-++.-..--|..|.+
T Consensus 151 ~e~g~~~-~n~~~~~q~sl~kh~~~a~-k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 151 METGGYL-PNCITTLQESLIKHLQVAP-KYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred ccccccC-CccccchHHHHHHHHHhcc-cHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 1 011 1111 23445555 221 111 111110 01355677788888777766666665
No 81
>PRK11779 sbcB exonuclease I; Provisional
Probab=70.52 E-value=21 Score=32.93 Aligned_cols=132 Identities=14% Similarity=0.200 Sum_probs=73.6
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee----CC-------eEEEEEccc--c--------CC----------c--h---HHH
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA----AN-------LCLAIQLCR--L--------SR----------I--P---ESV 81 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~----~~-------~~~l~~l~~--~--------~~----------~--p---~~L 81 (198)
..++.||+|..... ..=.+||+|. .+ ....++... . .+ . + +.+
T Consensus 6 ~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~~i 85 (476)
T PRK11779 6 PTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAARI 85 (476)
T ss_pred CcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHH
Confidence 67999999988764 2346777774 21 122233321 0 00 1 1 135
Q ss_pred HhhccCCCeEEEEee-ecchHhhchhcCCCCC-----------ccCceeehHHHHHHH--h-----CCC----CCCCCcc
Q 039658 82 TNFLADRTICFVGFG-VDKKTASIHGKTGYPR-----------NCDTGIDLGHLAARV--L-----KKP----KLIGLTG 138 (198)
Q Consensus 82 ~~~l~~~~i~kvG~~-i~~D~~~L~~~~~~~~-----------~~~~~~Dl~~la~~~--~-----g~~----~l~~~~s 138 (198)
.+++..++-+.|||+ +..|...| ...+.. ..+..+|+=++++.. + ..| +. ....
T Consensus 86 ~~~l~~~~~~lVGhNni~FD~efl--r~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~-~s~r 162 (476)
T PRK11779 86 HAEFSQPGTCILGYNNIRFDDEVT--RYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGL-PSFK 162 (476)
T ss_pred HHHHhcCCCEEEEeCchhhcHHHH--HHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCC-CCCc
Confidence 666765666789996 78999877 332211 111223433333311 1 111 11 2467
Q ss_pred HHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhh
Q 039658 139 IAELAKEVGIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSL 196 (198)
Q Consensus 139 L~~l~~~~g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~ 196 (198)
|..|++.+|+ .... -+=|..||++...|+..|.+.
T Consensus 163 Le~L~~~~gI-----~~~~------------------AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 163 LEHLTKANGI-----EHEN------------------AHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHHHHHcCC-----CCCC------------------CCCcHHHHHHHHHHHHHHHHh
Confidence 8888888776 2211 133788999999999888754
No 82
>COG4328 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=63.45 E-value=11 Score=31.24 Aligned_cols=34 Identities=26% Similarity=0.243 Sum_probs=27.3
Q ss_pred eEEEEeeeeccCCCceeEEEeeeCCeEEEEEcccc
Q 039658 40 RVVGFDVKFNSQTRIAEMLILSAANLCLAIQLCRL 74 (198)
Q Consensus 40 ~vvg~D~Ew~~~~~~~aliQla~~~~~~l~~l~~~ 74 (198)
++||||.-|.......+-+|+..+ .|.|.++.+.
T Consensus 2 ~fvGiDlaW~~~ppg~~cl~~~dg-~~~i~~~~rr 35 (266)
T COG4328 2 KFVGIDLAWASRPPGLCCLQLADG-GLLIGDLARR 35 (266)
T ss_pred ceEEeeeecccCCCceEEEEEcCC-CceEeechhh
Confidence 689999999988666888888887 7777777553
No 83
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=62.42 E-value=15 Score=28.93 Aligned_cols=83 Identities=13% Similarity=0.226 Sum_probs=47.8
Q ss_pred HHhhccCCCeEEEEee-ecchHhhchhcCC---CCCc--------cCceeehHHHHHHHh-------CCC----CCCCCc
Q 039658 81 VTNFLADRTICFVGFG-VDKKTASIHGKTG---YPRN--------CDTGIDLGHLAARVL-------KKP----KLIGLT 137 (198)
Q Consensus 81 L~~~l~~~~i~kvG~~-i~~D~~~L~~~~~---~~~~--------~~~~~Dl~~la~~~~-------g~~----~l~~~~ 137 (198)
+..|+..+.-+.|||+ +..|...| ... .+.. ....+|.-.+++... ..| .+ ...
T Consensus 76 ~~~~~~~~~~~lVahn~~~FD~~fL--~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~-~~~ 152 (183)
T cd06138 76 IHRLFNTPGTCIVGYNNIRFDDEFL--RFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGK-PSF 152 (183)
T ss_pred HHHHHccCCCcEEeeCchhhHHHHH--HHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCC-cch
Confidence 4566654555568986 78999888 332 2221 123466655554321 111 11 246
Q ss_pred cHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHH
Q 039658 138 GIAELAKEVGIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIV 189 (198)
Q Consensus 138 sL~~l~~~~g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i 189 (198)
+|..+++.+|+ ... +-+-|..||....+|
T Consensus 153 ~L~~l~~~~gi-----~~~------------------~~H~Al~Da~~ta~l 181 (183)
T cd06138 153 KLEDLAQANGI-----EHS------------------NAHDALSDVEATIAL 181 (183)
T ss_pred hHHHHHHHCCC-----Ccc------------------ccccHHHHHHHHHHH
Confidence 79999988776 321 225578888877655
No 84
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=59.50 E-value=73 Score=25.85 Aligned_cols=132 Identities=14% Similarity=0.146 Sum_probs=80.4
Q ss_pred CeEEEEeeeeccCC-CceeEEEeee-----CCeE-----EEEEccc-cC-------C--------------chHHHHhhc
Q 039658 39 RRVVGFDVKFNSQT-RIAEMLILSA-----ANLC-----LAIQLCR-LS-------R--------------IPESVTNFL 85 (198)
Q Consensus 39 ~~vvg~D~Ew~~~~-~~~aliQla~-----~~~~-----~l~~l~~-~~-------~--------------~p~~L~~~l 85 (198)
...+.||+|..... .+-.+|+|+. +... .+++.-. ++ . ..+.+.+|+
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~i 92 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDFI 92 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 36799999998765 3556666654 3111 2233211 00 0 112355666
Q ss_pred cCCCeEEEEeeecchHhhchh-cCCCCCc--cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCCCCCCCC
Q 039658 86 ADRTICFVGFGVDKKTASIHG-KTGYPRN--CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNKEIEAVT 162 (198)
Q Consensus 86 ~~~~i~kvG~~i~~D~~~L~~-~~~~~~~--~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~K~~~~~ 162 (198)
.+. -..|+|+...|...|.. ...++.. ....+|.-.+++..+.. . ...+|..|++.+|+ ......
T Consensus 93 ~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~--~-~~~~L~~l~~~~gi-----~~~~~~--- 160 (243)
T COG0847 93 GGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPG--F-DRSSLDALAERLGI-----DRNPFH--- 160 (243)
T ss_pred CCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCC--C-ccchHHHHHHHcCC-----CcCCcC---
Confidence 654 46799999999988831 1233333 45667766666655443 1 47899999997677 321111
Q ss_pred CCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHh
Q 039658 163 PPNWNAWVFTDKQVLHAVEEARGCYIVADKLLS 195 (198)
Q Consensus 163 ~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~ 195 (198)
+ +=|..||.++..+|..+..
T Consensus 161 -------~------H~Al~Da~~~a~~~~~~~~ 180 (243)
T COG0847 161 -------P------HRALFDALALAELFLLLQT 180 (243)
T ss_pred -------C------cchHHHHHHHHHHHHHHHh
Confidence 1 3389999999999998876
No 85
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=55.67 E-value=17 Score=29.93 Aligned_cols=65 Identities=9% Similarity=-0.071 Sum_probs=43.6
Q ss_pred eeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCC---CCCCHHHHHHHHHhHHHHHHHH
Q 039658 117 GIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNA---WVFTDKQVLHAVEEARGCYIVA 190 (198)
Q Consensus 117 ~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~---~pLt~~Qi~YAA~Da~~~~~i~ 190 (198)
++|+-.++++.+.. ...+|..++.++ |. ..+.-..-+.++|-+ ..-...=+.|...||...++|.
T Consensus 162 ~lD~~~~~r~~~kl----~sYsL~~V~~~~L~~-----~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 162 ILNVWRLMRSELAL----TNYTLENVVYHVLHQ-----RIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred EeEhHHHHHHHcCc----ccCCHHHHHHHHhCC-----CCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 46776666654433 467999999999 87 433222235677732 2344566999999999998874
No 86
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=52.60 E-value=43 Score=34.45 Aligned_cols=90 Identities=18% Similarity=0.174 Sum_probs=62.6
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchh-cCCCCCcc--CceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCCCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHG-KTGYPRNC--DTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHNSLSNK 156 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~-~~~~~~~~--~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~~~~l~ 156 (198)
.+++|+. +-+.|.|++..|+..|.. ...+++.+ ++++|.=.+|+.. .|.+ ++.+|..||+.+|+ .+
T Consensus 494 kf~~~~~--d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L--~P~~-ksh~Lg~l~kk~~v-----~l- 562 (1444)
T COG2176 494 KFREFIG--DSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARAL--NPEF-KSHRLGTLCKKLGV-----EL- 562 (1444)
T ss_pred HHHHHhc--CcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHh--Chhh-hhcchHHHHHHhCc-----cH-
Confidence 3566665 346799999999998821 12345544 6889977776533 3444 68899999999976 33
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhhh
Q 039658 157 EIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSLL 197 (198)
Q Consensus 157 K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~l 197 (198)
++.+=|-.||-++-.++..+.+.|
T Consensus 563 -----------------e~hHRA~yDaeat~~vf~~f~~~~ 586 (1444)
T COG2176 563 -----------------ERHHRADYDAEATAKVFFVFLKDL 586 (1444)
T ss_pred -----------------HHhhhhhhhHHHHHHHHHHHHHHH
Confidence 445567788888888887776654
No 87
>PRK06722 exonuclease; Provisional
Probab=50.10 E-value=1e+02 Score=26.43 Aligned_cols=89 Identities=15% Similarity=0.200 Sum_probs=54.6
Q ss_pred HHHhhccCCCeEEEEeeecchHhhchh-cCCCCCcc-----CceeehHHHHHHHhCC--CCCCCCccHHHHHHHhCCCCC
Q 039658 80 SVTNFLADRTICFVGFGVDKKTASIHG-KTGYPRNC-----DTGIDLGHLAARVLKK--PKLIGLTGIAELAKEVGIDHN 151 (198)
Q Consensus 80 ~L~~~l~~~~i~kvG~~i~~D~~~L~~-~~~~~~~~-----~~~~Dl~~la~~~~g~--~~l~~~~sL~~l~~~~g~~~~ 151 (198)
.+.+|+.+. .+.+.+ ...|.+.|.. ...+|+.. ...+|++.++...+.. + ...||..+++.+|+
T Consensus 83 ef~~fig~~-~lvahn-a~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~---~~~sL~~l~~~lgL--- 154 (281)
T PRK06722 83 KFIQFIGED-SIFVTW-GKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFE---HTPSLQSAVEQLGL--- 154 (281)
T ss_pred HHHHHHCCC-cEEEEE-eHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhcc---CCCCHHHHHHHCCC---
Confidence 456666653 344555 5889988832 12345443 2347887766543321 2 24689999988877
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHh
Q 039658 152 SLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLS 195 (198)
Q Consensus 152 ~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~ 195 (198)
+... +-+=|-.||..+..|+.++.+
T Consensus 155 --~~~g-----------------~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 155 --IWEG-----------------KQHRALADAENTANILLKAYS 179 (281)
T ss_pred --CCCC-----------------CCcCcHHHHHHHHHHHHHHhc
Confidence 3321 112367899999999998874
No 88
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=46.85 E-value=48 Score=27.70 Aligned_cols=97 Identities=19% Similarity=0.008 Sum_probs=50.5
Q ss_pred CCCeEEEEeeecchHhhchhcCCC-C-Cc-------------cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCCCC
Q 039658 87 DRTICFVGFGVDKKTASIHGKTGY-P-RN-------------CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGIDHN 151 (198)
Q Consensus 87 ~~~i~kvG~~i~~D~~~L~~~~~~-~-~~-------------~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~~~ 151 (198)
+.++..|||+.-.|+-.| .+.| | ++ ...++|+..++. ... . ...||..+++.++...+
T Consensus 147 ~~~~p~Vghn~~~Dl~~l--~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~-~~~-~---~~~~L~~l~~~l~~~~~ 219 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYL--YKKFIGPLPETLEEFKELLRELFPRIYDTKYLAE-ECP-G---KSTSLQELAEELGIRRN 219 (262)
T ss_dssp CC-SEEEESSTHHHHHHH--HHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHT-STT-T---S-SSHHHHHHHTTSTT-
T ss_pred ccCCcEEEeChHhHHHHH--HHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHH-hcc-c---cccCHHHHHHHhCCCcc
Confidence 345889999999999887 4322 1 11 246899877664 222 1 36799999998833110
Q ss_pred CCCCCC--CC-CCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 039658 152 SLSNKE--IE-AVTPPNWNAWVFTDKQVLHAVEEARGCYIVAD 191 (198)
Q Consensus 152 ~~~l~K--~~-~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~ 191 (198)
+....+ .. .....+|. .+-..++.+=|+.|||..-.++-
T Consensus 220 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~HeAGyDA~mTg~~F~ 261 (262)
T PF04857_consen 220 PSSISSPEGFPSYDEEKNN-FPMFGEKAHEAGYDAYMTGCVFI 261 (262)
T ss_dssp ---EEE-TTS--------------SS-TTSHHHHHHHHHHHHH
T ss_pred ccccccccccccccccccc-cccCCCCCCCcchHHHHHHHHHc
Confidence 000000 00 11111221 13345557789999999877763
No 89
>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=41.36 E-value=89 Score=20.60 Aligned_cols=32 Identities=9% Similarity=0.109 Sum_probs=26.0
Q ss_pred eeEEEECCeEEEEEEeCCHHHHHHHHHHHHhh
Q 039658 3 IYELEIKDVKFKVSVIDDADVIDKKISELSGM 34 (198)
Q Consensus 3 ~y~v~~~~~~i~v~v~~~~~~~~~~i~~l~~~ 34 (198)
.+.|.+.+...-+..++++++.++|+..+...
T Consensus 71 ~f~i~~~~~~~~~~~~~s~~~~~~W~~~i~~~ 102 (104)
T PF00169_consen 71 CFEITTPNGKSYLFSAESEEERKRWIQAIQKA 102 (104)
T ss_dssp EEEEEETTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred EEEEEeCCCcEEEEEcCCHHHHHHHHHHHHHH
Confidence 46788877766667799999999999999763
No 90
>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=40.46 E-value=36 Score=27.95 Aligned_cols=70 Identities=20% Similarity=0.095 Sum_probs=42.2
Q ss_pred eeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 039658 117 GIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLL 194 (198)
Q Consensus 117 ~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~ 194 (198)
++|+-..+++.... ...+|..+|+.+ |.... +++ .+.+ ..-|....--..=++|...||+..+.|..+|.
T Consensus 157 ~~D~~~~~k~~~~~----~sY~L~~va~~~Lg~~k~--di~-~~~i-~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl~ 227 (234)
T cd05776 157 LCDTYLSAKELIRC----KSYDLTELSQQVLGIERQ--DID-PEEI-LNMYNDSESLLKLLEHTEKDAYLILQLMFKLN 227 (234)
T ss_pred hhccHHHHHHHhCC----CCCChHHHHHHHhCcCcc--cCC-HHHH-HHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 46666656544432 478999999999 86111 221 1111 11233311223448999999999999999874
No 91
>cd01247 PH_GPBP Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. The GPBP protein is a kinase that phosphorylates an N-terminal region of the alpha 3 chain of type IV collagen , which is commonly known as the goodpasture antigen. It has has an N-terminal PH domain and a C-terminal START domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cyt
Probab=40.19 E-value=93 Score=21.53 Aligned_cols=31 Identities=0% Similarity=-0.012 Sum_probs=23.7
Q ss_pred eeEEEECCeEEEEEEeCCHHHHHHHHHHHHh
Q 039658 3 IYELEIKDVKFKVSVIDDADVIDKKISELSG 33 (198)
Q Consensus 3 ~y~v~~~~~~i~v~v~~~~~~~~~~i~~l~~ 33 (198)
.|.|...+...-...++++++.++|++.|..
T Consensus 60 ~F~i~~~~~r~~~L~A~s~~e~~~Wi~al~~ 90 (91)
T cd01247 60 RFDISVNENVVWYLRAENSQSRLLWMDSVVR 90 (91)
T ss_pred EEEEEeCCCeEEEEEeCCHHHHHHHHHHHhh
Confidence 4556666656666678999999999999874
No 92
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=36.96 E-value=28 Score=29.08 Aligned_cols=37 Identities=11% Similarity=0.263 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHhhhccCCeEEEEeeeeccCC----------------------CceeEEEeee
Q 039658 21 ADVIDKKISELSGMLFKMRRVVGFDVKFNSQT----------------------RIAEMLILSA 62 (198)
Q Consensus 21 ~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~~~~----------------------~~~aliQla~ 62 (198)
++++..+.+.+.. ..+|+||+|+..-. ....+||+.-
T Consensus 9 ~~~l~~i~~~i~~-----~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Gl 67 (262)
T PF04857_consen 9 EEELPEILQAISK-----ADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGL 67 (262)
T ss_dssp HHHHHHHHHHHHH-----SSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEE
T ss_pred HHHHHHHHHHHhh-----CCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeE
Confidence 4455566666655 88999999995332 4588999874
No 93
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=35.93 E-value=84 Score=25.73 Aligned_cols=108 Identities=13% Similarity=0.078 Sum_probs=61.1
Q ss_pred HHHHhhccCCCeEEEEeeec-chHhhchhc-CCCCCccC-------------------ceeehHHHHHHHhCCCCCCCCc
Q 039658 79 ESVTNFLADRTICFVGFGVD-KKTASIHGK-TGYPRNCD-------------------TGIDLGHLAARVLKKPKLIGLT 137 (198)
Q Consensus 79 ~~L~~~l~~~~i~kvG~~i~-~D~~~L~~~-~~~~~~~~-------------------~~~Dl~~la~~~~g~~~l~~~~ 137 (198)
..+.++++...-..|+|+.+ .|+-.|..+ --+|+.+. ..+||-++.+ ..|.. .+.
T Consensus 42 ~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~-~~g~~---~~~ 117 (209)
T PF10108_consen 42 QDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLS-FYGAK---ART 117 (209)
T ss_pred HHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHh-ccCcc---ccC
Confidence 34555555545567999975 798766311 12344432 2466554432 12222 578
Q ss_pred cHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHH
Q 039658 138 GIAELAKEVGIDHNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLL 194 (198)
Q Consensus 138 sL~~l~~~~g~~~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~ 194 (198)
||..||..+|+|- ...++-++ +. .-|....+ ++=..|.-.||...+.||.++.
T Consensus 118 sLd~la~~lgiPg-K~~idGs~-V~-~~y~~g~i-~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 118 SLDELAALLGIPG-KDDIDGSQ-VA-ELYQEGDI-DEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred CHHHHHHHcCCCC-CCCCCHHH-HH-HHHHcCCH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 9999998888832 22332221 11 11322222 2236899999999999998875
No 94
>PF13289 SIR2_2: SIR2-like domain
Probab=34.56 E-value=35 Score=24.88 Aligned_cols=28 Identities=18% Similarity=0.583 Sum_probs=21.1
Q ss_pred chHHHHhhccCCCeEEEEeeecc-hHhhc
Q 039658 77 IPESVTNFLADRTICFVGFGVDK-KTASI 104 (198)
Q Consensus 77 ~p~~L~~~l~~~~i~kvG~~i~~-D~~~L 104 (198)
++..|+.++.+..++++|++... |++.+
T Consensus 76 ~~~~l~~~l~~~~~lfiGys~~D~~i~~~ 104 (143)
T PF13289_consen 76 FPNFLRSLLRSKTLLFIGYSFNDPDIRQL 104 (143)
T ss_pred HHHHHHHHHcCCCEEEEEECCCCHHHHHH
Confidence 44567888899999999999863 34444
No 95
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=32.46 E-value=1e+02 Score=21.29 Aligned_cols=36 Identities=8% Similarity=0.241 Sum_probs=25.0
Q ss_pred CCeEEEEEccccC-CchHHHH-hhccCCCeEEEEeeec
Q 039658 63 ANLCLAIQLCRLS-RIPESVT-NFLADRTICFVGFGVD 98 (198)
Q Consensus 63 ~~~~~l~~l~~~~-~~p~~L~-~~l~~~~i~kvG~~i~ 98 (198)
.+.+..|.+..-+ .+...|+ .++.||+|.++|+.+.
T Consensus 7 ~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fAgY~vp 44 (83)
T cd07027 7 EKNSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIK 44 (83)
T ss_pred CCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecC
Confidence 4456666665443 3555665 6779999999999874
No 96
>PF13269 DUF4060: Protein of unknown function (DUF4060)
Probab=32.34 E-value=72 Score=21.65 Aligned_cols=21 Identities=19% Similarity=0.431 Sum_probs=17.5
Q ss_pred ceeEEEECCeEEEEEEeCCHH
Q 039658 2 CIYELEIKDVKFKVSVIDDAD 22 (198)
Q Consensus 2 ~~y~v~~~~~~i~v~v~~~~~ 22 (198)
++|+|.++++.+.|.|++-.+
T Consensus 35 ~tY~i~v~~~k~~VEVvnR~~ 55 (73)
T PF13269_consen 35 ETYTIKVRGKKVAVEVVNRRK 55 (73)
T ss_pred EEEEEEECCEEEEEEEEecch
Confidence 589999999999998775443
No 97
>cd01246 PH_oxysterol_bp Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=31.79 E-value=1.1e+02 Score=20.18 Aligned_cols=31 Identities=6% Similarity=0.019 Sum_probs=22.2
Q ss_pred eeEEEECCeEEEEEEeCCHHHHHHHHHHHHh
Q 039658 3 IYELEIKDVKFKVSVIDDADVIDKKISELSG 33 (198)
Q Consensus 3 ~y~v~~~~~~i~v~v~~~~~~~~~~i~~l~~ 33 (198)
.+.|...++..-.-.++++++.++|+..+..
T Consensus 60 ~F~i~~~~~~~~~~~a~s~~e~~~Wi~al~~ 90 (91)
T cd01246 60 CFTIDTGGDKTLHLRANSEEERQRWVDALEL 90 (91)
T ss_pred EEEEEcCCCCEEEEECCCHHHHHHHHHHHHh
Confidence 3455555545555668899999999998864
No 98
>PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=30.84 E-value=64 Score=24.34 Aligned_cols=19 Identities=11% Similarity=0.349 Sum_probs=16.5
Q ss_pred CceeEEEECCeEEEEEEeC
Q 039658 1 MCIYELEIKDVKFKVSVID 19 (198)
Q Consensus 1 ~~~y~v~~~~~~i~v~v~~ 19 (198)
|+.|+|.+||+...|++=.
T Consensus 2 mk~~~itvng~~y~V~vee 20 (130)
T PRK06549 2 LRKFKITIDGKEYLVEMEE 20 (130)
T ss_pred CceEEEEECCEEEEEEEEE
Confidence 6789999999999988755
No 99
>cd00821 PH Pleckstrin homology (PH) domain. Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=30.72 E-value=1.2e+02 Score=19.14 Aligned_cols=31 Identities=13% Similarity=0.185 Sum_probs=22.2
Q ss_pred eeEEEECCeEEEEEEeCCHHHHHHHHHHHHh
Q 039658 3 IYELEIKDVKFKVSVIDDADVIDKKISELSG 33 (198)
Q Consensus 3 ~y~v~~~~~~i~v~v~~~~~~~~~~i~~l~~ 33 (198)
.+.|...++....-.+.++++.++|++.+..
T Consensus 65 ~f~i~~~~~~~~~~~~~s~~~~~~W~~~l~~ 95 (96)
T cd00821 65 CFEIRTPDGRSYLLQAESEEEREEWIEALQS 95 (96)
T ss_pred EEEEecCCCcEEEEEeCCHHHHHHHHHHHhc
Confidence 4566665544445567889999999999864
No 100
>KOG0041 consensus Predicted Ca2+-binding protein, EF-Hand protein superfamily [General function prediction only]
Probab=29.46 E-value=46 Score=27.36 Aligned_cols=43 Identities=30% Similarity=0.372 Sum_probs=33.3
Q ss_pred hHhhchhcCCCCCccCceeehHHH--HHHHhCCCCCCCCccHHHHHHHh
Q 039658 100 KTASIHGKTGYPRNCDTGIDLGHL--AARVLKKPKLIGLTGIAELAKEV 146 (198)
Q Consensus 100 D~~~L~~~~~~~~~~~~~~Dl~~l--a~~~~g~~~l~~~~sL~~l~~~~ 146 (198)
|+..+ ...|.-.-.+.+||..+ ..+.+|.|. ...||+.|..++
T Consensus 100 ~~~~~--Fk~yDe~rDgfIdl~ELK~mmEKLgapQ--THL~lK~mikeV 144 (244)
T KOG0041|consen 100 DAESM--FKQYDEDRDGFIDLMELKRMMEKLGAPQ--THLGLKNMIKEV 144 (244)
T ss_pred HHHHH--HHHhcccccccccHHHHHHHHHHhCCch--hhHHHHHHHHHh
Confidence 55555 56677777899999987 456889885 368999999998
No 101
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=27.16 E-value=1.4e+02 Score=20.65 Aligned_cols=35 Identities=11% Similarity=0.221 Sum_probs=24.2
Q ss_pred CeEEEEEccccC-CchHHHH-hhccCCCeEEEEeeec
Q 039658 64 NLCLAIQLCRLS-RIPESVT-NFLADRTICFVGFGVD 98 (198)
Q Consensus 64 ~~~~l~~l~~~~-~~p~~L~-~~l~~~~i~kvG~~i~ 98 (198)
+.+..|.+..-+ .+...|+ .++.||+|.|+|+.+.
T Consensus 10 ~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vp 46 (85)
T PRK01146 10 DNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDID 46 (85)
T ss_pred CCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecC
Confidence 446666665443 3555665 6779999999999875
No 102
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=26.60 E-value=1.5e+02 Score=20.40 Aligned_cols=36 Identities=8% Similarity=0.216 Sum_probs=24.0
Q ss_pred CCeEEEEEccccC-CchHHHH-hhccCCCeEEEEeeec
Q 039658 63 ANLCLAIQLCRLS-RIPESVT-NFLADRTICFVGFGVD 98 (198)
Q Consensus 63 ~~~~~l~~l~~~~-~~p~~L~-~~l~~~~i~kvG~~i~ 98 (198)
.+.+..|.+..-+ .+...|+ .++.||+|.|.|+.+.
T Consensus 7 ~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vp 44 (83)
T cd06927 7 EDNELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIE 44 (83)
T ss_pred CCCEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecC
Confidence 3445556555433 3555665 6678999999999865
No 103
>PF10507 DUF2453: Protein of unknown function (DUF2453); InterPro: IPR019537 The function of these transmembrane protein is not known.
Probab=25.86 E-value=30 Score=25.45 Aligned_cols=57 Identities=18% Similarity=0.259 Sum_probs=31.8
Q ss_pred CeEEEEeeecchHhhchhcCCCCCccCceeehHHHHHHHhCCC--CCCCCccHHHHHHHh
Q 039658 89 TICFVGFGVDKKTASIHGKTGYPRNCDTGIDLGHLAARVLKKP--KLIGLTGIAELAKEV 146 (198)
Q Consensus 89 ~i~kvG~~i~~D~~~L~~~~~~~~~~~~~~Dl~~la~~~~g~~--~l~~~~sL~~l~~~~ 146 (198)
.|.+||||+-...-.+.+-........-.+-++.+|+..+|.- +. ...++...+|.+
T Consensus 4 avPfvgFGflDN~iMI~AGd~Id~~lg~~~giStmAAAalGN~vSDv-~Gi~~~~~vE~~ 62 (111)
T PF10507_consen 4 AVPFVGFGFLDNAIMIIAGDYIDNTLGVTFGISTMAAAALGNLVSDV-AGIGLGGYVERL 62 (111)
T ss_pred cCccceehhhhhhHHHHcchHHHHHHHHHHhHHHHHHHHHhhhhhhh-hhhHHHHHHHHH
Confidence 5678999998777776322222222334455667776666642 22 234555555555
No 104
>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=24.92 E-value=1.8e+02 Score=20.14 Aligned_cols=30 Identities=7% Similarity=0.100 Sum_probs=22.6
Q ss_pred eeEEEECCeEEEEEEeCCHHHHHHHHHHHHh
Q 039658 3 IYELEIKDVKFKVSVIDDADVIDKKISELSG 33 (198)
Q Consensus 3 ~y~v~~~~~~i~v~v~~~~~~~~~~i~~l~~ 33 (198)
.|.|.. ++++....++|+++.++|++.+..
T Consensus 63 ~F~i~t-~~r~y~l~A~s~~e~~~Wi~al~~ 92 (95)
T cd01265 63 RFEIHS-NNEVIALKASSDKQMNYWLQALQS 92 (95)
T ss_pred EEEEEc-CCcEEEEECCCHHHHHHHHHHHHh
Confidence 345543 445567789999999999999875
No 105
>PF00982 Glyco_transf_20: Glycosyltransferase family 20; InterPro: IPR001830 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 20 GT20 from CAZY comprises enzymes with only one known activity; alpha, alpha-trehalose-phosphate synthase [UDP-forming] (2.4.1.15 from EC). Synthesis of trehalose in the yeast Saccharomyces cerevisiae is catalysed by the trehalose-6-phosphate (Tre6P) synthase/phosphatase complex, which is composed of at least three different subunits encoded by the genes TPS1, TPS2, and TSL1. Tps1 and Tps2 carry the catalytic activities of trehalose synthesis, namely Tre6P synthase (Tps1) and Tre6P phosphatase (Tps2), while TsI1 has regulatory functions. There is some evidence that TsI1 and Tps3 may share a common function with respect to regulation and/or structural stabilisation of the Tre6P synthase/phosphatase complex in exponentially growing, heat-shocked cells []. OtsA (trehalose-6-phosphate synthase) from Escherichia coli has homology to the full-length TPS1, the N-terminal part of TPS2 and an internal region of TPS3 (TSL1) of yeast [].; GO: 0003824 catalytic activity, 0005992 trehalose biosynthetic process; PDB: 1UQU_A 2WTX_A 1UQT_B 1GZ5_B.
Probab=24.61 E-value=1.6e+02 Score=27.14 Aligned_cols=61 Identities=16% Similarity=0.324 Sum_probs=32.7
Q ss_pred EEEECCeEEEEEEeC---CHHH---------HHHHHHHHHhhhcc-CCeEEEEee-eec-----------------cCC-
Q 039658 5 ELEIKDVKFKVSVID---DADV---------IDKKISELSGMLFK-MRRVVGFDV-KFN-----------------SQT- 52 (198)
Q Consensus 5 ~v~~~~~~i~v~v~~---~~~~---------~~~~i~~l~~~~~~-~~~vvg~D~-Ew~-----------------~~~- 52 (198)
+|.++|+.+.|.+.- +++. +.++++.++...++ +..++|+|- ++. |..
T Consensus 230 ~v~~~Gr~v~v~~~pigId~~~~~~~~~~~~v~~~~~~l~~~~~~~~~ii~gvDrld~~kGi~~kl~Afe~fL~~~P~~~ 309 (474)
T PF00982_consen 230 TVEYNGRRVRVGVFPIGIDPDAFAQLARSPEVQERAEELREKFKGKRKIIVGVDRLDYTKGIPEKLRAFERFLERYPEYR 309 (474)
T ss_dssp -EEETTEEEEEEE------HHHHHHHHH-S---HHHHHHHHHTTT-SEEEEEE--B-GGG-HHHHHHHHHHHHHH-GGGT
T ss_pred eEEECCEEEEEEEeeccCChHHHHhhccChHHHHHHHHHHHhcCCCcEEEEEeccchhhcCHHHHHHHHHHHHHhCcCcc
Confidence 588889988887432 2322 34455666665554 367999994 222 221
Q ss_pred CceeEEEeeeCCe
Q 039658 53 RIAEMLILSAANL 65 (198)
Q Consensus 53 ~~~aliQla~~~~ 65 (198)
+++.++|++..++
T Consensus 310 ~kv~liQi~~psr 322 (474)
T PF00982_consen 310 GKVVLIQIAVPSR 322 (474)
T ss_dssp TTEEEEEE--B-S
T ss_pred CcEEEEEEeeccC
Confidence 6799999998654
No 106
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=24.30 E-value=1.3e+02 Score=20.74 Aligned_cols=35 Identities=11% Similarity=0.355 Sum_probs=23.5
Q ss_pred CeEEEEEccccC-CchHHHH-hhccCCCeEEEEeeec
Q 039658 64 NLCLAIQLCRLS-RIPESVT-NFLADRTICFVGFGVD 98 (198)
Q Consensus 64 ~~~~l~~l~~~~-~~p~~L~-~~l~~~~i~kvG~~i~ 98 (198)
..+..|.+..-+ .+-..|+ .++.||+|.++|+.+-
T Consensus 8 ~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vp 44 (85)
T cd07029 8 ESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIP 44 (85)
T ss_pred CCeEEEEEeCCCcchHHHHHHHHhhCCCceEEeeccc
Confidence 345556554433 3555665 5668999999999974
No 107
>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function. It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].
Probab=23.53 E-value=1.2e+02 Score=26.37 Aligned_cols=40 Identities=20% Similarity=0.248 Sum_probs=33.8
Q ss_pred CeEEEEEEeCCHHHHHHHHHHHHhhhccCCeEEEEeeeec
Q 039658 10 DVKFKVSVIDDADVIDKKISELSGMLFKMRRVVGFDVKFN 49 (198)
Q Consensus 10 ~~~i~v~v~~~~~~~~~~i~~l~~~~~~~~~vvg~D~Ew~ 49 (198)
...+++.+++++++++++|+.-.........+.|++.+|.
T Consensus 192 ~~~yd~~~f~~~~~~~~~i~~k~~~~~~~rlvA~~~w~~~ 231 (352)
T PF09848_consen 192 DENYDFRVFDSPEEMKEAIKEKNKEGGLSRLVAGYCWPWK 231 (352)
T ss_pred CCceeEEEECCHHHHHHHHHHHhcccCCceEEEecccccc
Confidence 5678899999999999999988765443368899999999
No 108
>TIGR02398 gluc_glyc_Psyn glucosylglycerol-phosphate synthase. Glucosylglycerol-phosphate synthase catalyzes the key step in the biosynthesis of the osmolyte glucosylglycerol. It is known in several cyanobacteria and in Pseudomonas anguilliseptica. The enzyme is closely related to the alpha,alpha-trehalose-phosphate synthase, likewise involved in osmolyte biosynthesis, of E. coli and many other bacteria. A close homolog from Xanthomonas campestris is excluded from this model and scores between trusted and noise.
Probab=23.20 E-value=2.4e+02 Score=26.15 Aligned_cols=61 Identities=7% Similarity=0.139 Sum_probs=37.9
Q ss_pred EEEECCeEEEEEEeCCH---H---------HHHHHHHHHHhhhccCCeEEEEee-eec-----------------cCC-C
Q 039658 5 ELEIKDVKFKVSVIDDA---D---------VIDKKISELSGMLFKMRRVVGFDV-KFN-----------------SQT-R 53 (198)
Q Consensus 5 ~v~~~~~~i~v~v~~~~---~---------~~~~~i~~l~~~~~~~~~vvg~D~-Ew~-----------------~~~-~ 53 (198)
.|..+|..+.|.+.-.. + ++.+..+.++..++++..++|+|= .+. |.. +
T Consensus 240 ~v~~~gr~v~v~~~PiGID~~~f~~~~~~~~~~~~~~~lr~~~~~~kiIl~VDRLDy~KGI~~kl~Afe~~L~~~Pe~~g 319 (487)
T TIGR02398 240 ALDTGNRVVKLGAHPVGTDPERIRSALAAASIREMMERIRSELAGVKLILSAERVDYTKGILEKLNAYERLLERRPELLG 319 (487)
T ss_pred ceeECCEEEEEEEEECEecHHHHHHHhcCchHHHHHHHHHHHcCCceEEEEecccccccCHHHHHHHHHHHHHhCccccC
Confidence 36778888887654332 2 233445556655555578899881 221 222 5
Q ss_pred ceeEEEeeeCCe
Q 039658 54 IAEMLILSAANL 65 (198)
Q Consensus 54 ~~aliQla~~~~ 65 (198)
++.++|++++++
T Consensus 320 kv~Lvqi~~psr 331 (487)
T TIGR02398 320 KVTLVTACVPAA 331 (487)
T ss_pred ceEEEEEeCCCc
Confidence 699999998764
No 109
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=22.76 E-value=2.2e+02 Score=23.71 Aligned_cols=84 Identities=18% Similarity=0.070 Sum_probs=56.7
Q ss_pred cCCCeEEEEeeecchHhhchhcC-----CCCCc-----------cCceeehHHHHHHHhCCCCCCCCccHHHHHHHhCCC
Q 039658 86 ADRTICFVGFGVDKKTASIHGKT-----GYPRN-----------CDTGIDLGHLAARVLKKPKLIGLTGIAELAKEVGID 149 (198)
Q Consensus 86 ~~~~i~kvG~~i~~D~~~L~~~~-----~~~~~-----------~~~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~g~~ 149 (198)
.+++|.+|.+....|...| .+ ..|.. ...++|+..++...-|.. .+.||..+|+.+|+.
T Consensus 139 ~~~~V~WvTFhs~YDfgYL--lK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~---l~~GL~~lA~~L~~~ 213 (239)
T KOG0304|consen 139 LDENVTWVTFHSGYDFGYL--LKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLS---LKGGLQRLADLLGLK 213 (239)
T ss_pred ccCceEEEEeeccchHHHH--HHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhh---hhcCHHHHHHHhCCC
Confidence 4689999999999999877 32 11111 257788887776332322 377999999988541
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhHHHHHHHHHHHHhh
Q 039658 150 HNSLSNKEIEAVTPPNWNAWVFTDKQVLHAVEEARGCYIVADKLLSL 196 (198)
Q Consensus 150 ~~~~~l~K~~~~~~SdW~~~pLt~~Qi~YAA~Da~~~~~i~~~L~~~ 196 (198)
+..+- +-|..|+.....++.+|+++
T Consensus 214 ----RvG~~------------------HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 214 ----RVGIA------------------HQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred ----eeecc------------------cccCcHHHHHHHHHHHHHhc
Confidence 33221 23678888888888888764
No 110
>cd01260 PH_CNK Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. CNK is believed to regulate the activity and the subcellular localization of RAS activated RAF. CNK is composed of N-terminal SAM and PDZ domains along with a central or C-terminal PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskelet
Probab=22.72 E-value=1.7e+02 Score=19.96 Aligned_cols=29 Identities=10% Similarity=-0.046 Sum_probs=20.2
Q ss_pred EEEECCeEEEEEEeCCHHHHHHHHHHHHh
Q 039658 5 ELEIKDVKFKVSVIDDADVIDKKISELSG 33 (198)
Q Consensus 5 ~v~~~~~~i~v~v~~~~~~~~~~i~~l~~ 33 (198)
.|...+...-.-.++|++++++|+..+..
T Consensus 67 ~I~~~~~~~~~f~a~s~~e~~~Wi~ai~~ 95 (96)
T cd01260 67 KVCHPVYKSFYFAAETLDDLSQWVNHLIT 95 (96)
T ss_pred EECCCCCcEEEEEeCCHHHHHHHHHHHHh
Confidence 34333434445568999999999999864
No 111
>smart00233 PH Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
Probab=22.46 E-value=2.2e+02 Score=18.10 Aligned_cols=31 Identities=10% Similarity=0.183 Sum_probs=22.8
Q ss_pred eeEEEECCeEEEEEEeCCHHHHHHHHHHHHh
Q 039658 3 IYELEIKDVKFKVSVIDDADVIDKKISELSG 33 (198)
Q Consensus 3 ~y~v~~~~~~i~v~v~~~~~~~~~~i~~l~~ 33 (198)
.+.|...+...-+-.+.++++...|++.+..
T Consensus 69 ~f~l~~~~~~~~~f~~~s~~~~~~W~~~i~~ 99 (102)
T smart00233 69 CFEIKTADRRSYLLQAESEEEREEWVDALRK 99 (102)
T ss_pred EEEEEecCCceEEEEcCCHHHHHHHHHHHHH
Confidence 3456665554555578899999999999975
No 112
>PLN03064 alpha,alpha-trehalose-phosphate synthase (UDP-forming); Provisional
Probab=21.85 E-value=2.7e+02 Score=28.08 Aligned_cols=61 Identities=16% Similarity=0.223 Sum_probs=37.8
Q ss_pred EEEECCeEEEEEEeC---C---------HHHHHHHHHHHHhhhccCCeEEEEee-ee-----------------ccCC-C
Q 039658 5 ELEIKDVKFKVSVID---D---------ADVIDKKISELSGMLFKMRRVVGFDV-KF-----------------NSQT-R 53 (198)
Q Consensus 5 ~v~~~~~~i~v~v~~---~---------~~~~~~~i~~l~~~~~~~~~vvg~D~-Ew-----------------~~~~-~ 53 (198)
.|.++|..+.|.+.- + ..++.++++.++..++++..++|+|- ++ .|.. .
T Consensus 318 ~v~~~Gr~v~V~~~PiGID~~~f~~~~~~~~v~~~~~~lr~~~~g~kiIlgVDRLD~~KGI~~kL~AfE~fL~~~Pe~r~ 397 (934)
T PLN03064 318 GVEDQGRLTRVAAFPIGIDSDRFIRALETPQVQQHIKELKERFAGRKVMLGVDRLDMIKGIPQKILAFEKFLEENPEWRD 397 (934)
T ss_pred eEEECCEEEEEEEEeCEEcHHHHHHHhcChhHHHHHHHHHHHhCCceEEEEeeccccccCHHHHHHHHHHHHHhCccccC
Confidence 466777766654221 1 23455667777766665578999882 11 2332 6
Q ss_pred ceeEEEeeeCCe
Q 039658 54 IAEMLILSAANL 65 (198)
Q Consensus 54 ~~aliQla~~~~ 65 (198)
++.++|+++.++
T Consensus 398 kVVLvQIa~psr 409 (934)
T PLN03064 398 KVVLLQIAVPTR 409 (934)
T ss_pred CEEEEEEcCCCC
Confidence 799999998554
No 113
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=21.35 E-value=1.4e+02 Score=19.89 Aligned_cols=29 Identities=14% Similarity=0.176 Sum_probs=23.8
Q ss_pred EEEECCeEEEEEEeCCHHHHHHHHHHHHh
Q 039658 5 ELEIKDVKFKVSVIDDADVIDKKISELSG 33 (198)
Q Consensus 5 ~v~~~~~~i~v~v~~~~~~~~~~i~~l~~ 33 (198)
-|.++.+.+.+.++.+++.++.+++.+..
T Consensus 30 ivd~~~~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 30 IVDVSPDSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp EEEEETTEEEEEEEE-HHHHHHHHHHSTG
T ss_pred EEEECCCEEEEEEcCCHHHHHHHHHHhhh
Confidence 45667788888999999999999999976
No 114
>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=21.12 E-value=1.6e+02 Score=26.01 Aligned_cols=70 Identities=20% Similarity=0.106 Sum_probs=45.3
Q ss_pred ceeehHHHHHHHhCCCCCCCCccHHHHHHHh-CCCCCCCCCCCCCCCCCCCCCCC-CCCHHHHHHHHHhHHHHHHHHHHH
Q 039658 116 TGIDLGHLAARVLKKPKLIGLTGIAELAKEV-GIDHNSLSNKEIEAVTPPNWNAW-VFTDKQVLHAVEEARGCYIVADKL 193 (198)
Q Consensus 116 ~~~Dl~~la~~~~g~~~l~~~~sL~~l~~~~-g~~~~~~~l~K~~~~~~SdW~~~-pLt~~Qi~YAA~Da~~~~~i~~~L 193 (198)
-.+|+-.++++..+. ...+|..+++.+ |... .+++.. .-...|... ..-..-+.|...||..++.++.++
T Consensus 149 ~~~Dl~~~~~~~~kl----~~~~L~~va~~~l~~~k--~d~~~~--~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 149 LVIDLYNLYKNKLKL----PSYKLDTVAEYLLGKEK--DDLPYK--DIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEEEhHHHHHHHhCc----ccCCHHHHHHHHhCCCC--CCCCHH--HHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457776666655543 467899999999 7511 122211 112334432 244578999999999999999986
No 115
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=20.54 E-value=56 Score=17.12 Aligned_cols=8 Identities=38% Similarity=-0.089 Sum_probs=5.8
Q ss_pred HHHHHHHH
Q 039658 173 DKQVLHAV 180 (198)
Q Consensus 173 ~~Qi~YAA 180 (198)
--|++||.
T Consensus 14 l~QVEYA~ 21 (23)
T PF10584_consen 14 LFQVEYAM 21 (23)
T ss_dssp BHHHHHHH
T ss_pred EEeeEeee
Confidence 46888884
No 116
>cd01251 PH_centaurin_alpha Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following growth factor stimulation by specific binding of its PH domain to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 2 is constitutively bound to the plasma membrane since it binds phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate with equal affinity. 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 specifici
Probab=20.45 E-value=2.3e+02 Score=19.90 Aligned_cols=25 Identities=8% Similarity=0.019 Sum_probs=20.1
Q ss_pred eEEEEEEeCCHHHHHHHHHHHHhhh
Q 039658 11 VKFKVSVIDDADVIDKKISELSGML 35 (198)
Q Consensus 11 ~~i~v~v~~~~~~~~~~i~~l~~~~ 35 (198)
++.....++|+++.++|++.|....
T Consensus 76 ~Rty~l~a~s~~e~~~Wi~ai~~v~ 100 (103)
T cd01251 76 ERKFLFACETEQDRREWIAAFQNVL 100 (103)
T ss_pred CeEEEEECCCHHHHHHHHHHHHHHh
Confidence 4555668899999999999998743
Done!