Query 019356
Match_columns 342
No_of_seqs 271 out of 1385
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 08:47:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019356.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019356hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10829 ribonuclease D; Provi 100.0 1.5E-38 3.2E-43 310.7 14.1 252 27-303 2-283 (373)
2 COG0349 Rnd Ribonuclease D [Tr 100.0 3.3E-36 7.3E-41 288.1 13.7 249 32-304 2-280 (361)
3 TIGR01388 rnd ribonuclease D. 100.0 2.6E-34 5.6E-39 281.5 12.7 230 30-284 1-234 (367)
4 cd06148 Egl_like_exo DEDDy 3'- 100.0 7.7E-30 1.7E-34 229.9 17.4 179 46-226 7-187 (197)
5 cd06129 RNaseD_like DEDDy 3'-5 100.0 6.8E-29 1.5E-33 216.7 14.0 153 41-213 5-160 (161)
6 cd06146 mut-7_like_exo DEDDy 3 100.0 7.8E-29 1.7E-33 222.7 14.8 175 28-213 1-192 (193)
7 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 9E-27 2E-31 204.3 13.4 164 32-213 2-169 (170)
8 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 3.8E-26 8.1E-31 199.4 13.9 170 28-217 1-176 (176)
9 cd06142 RNaseD_exo DEDDy 3'-5' 99.9 7.3E-21 1.6E-25 167.0 16.5 164 47-230 10-174 (178)
10 KOG2206 Exosome 3'-5' exoribon 99.8 8.5E-22 1.8E-26 195.8 7.4 174 25-220 190-364 (687)
11 smart00474 35EXOc 3'-5' exonuc 99.8 3.6E-18 7.8E-23 147.8 14.4 168 29-217 2-172 (172)
12 cd06147 Rrp6p_like_exo DEDDy 3 99.8 1.6E-17 3.5E-22 148.7 16.5 173 25-219 2-175 (192)
13 cd00007 35EXOc 3'-5' exonuclea 99.7 5.8E-16 1.3E-20 131.5 16.2 152 51-216 2-155 (155)
14 cd06140 DNA_polA_I_Bacillus_li 99.7 9.2E-16 2E-20 135.1 17.0 164 49-228 3-168 (178)
15 PRK05755 DNA polymerase I; Pro 99.7 4.3E-16 9.2E-21 168.5 18.0 183 26-226 294-480 (880)
16 cd09018 DEDDy_polA_RNaseD_like 99.7 7.8E-16 1.7E-20 131.0 14.5 146 51-213 1-149 (150)
17 cd06139 DNA_polA_I_Ecoli_like_ 99.6 4.9E-14 1.1E-18 125.0 17.4 168 47-228 3-183 (193)
18 PRK14975 bifunctional 3'-5' ex 99.5 3.3E-14 7.1E-19 146.7 11.6 156 27-229 2-163 (553)
19 KOG2207 Predicted 3'-5' exonuc 99.5 4.7E-14 1E-18 141.7 6.3 190 26-226 390-595 (617)
20 COG0749 PolA DNA polymerase I 99.4 5.6E-12 1.2E-16 128.7 12.7 182 31-228 6-193 (593)
21 TIGR00593 pola DNA polymerase 99.3 1.2E-10 2.6E-15 125.7 17.3 178 28-228 304-489 (887)
22 KOG2405 Predicted 3'-5' exonuc 99.2 8.7E-12 1.9E-16 119.4 4.9 220 63-290 209-458 (458)
23 cd06128 DNA_polA_exo DEDDy 3'- 99.0 1.6E-08 3.4E-13 86.7 15.4 132 64-213 17-150 (151)
24 cd02394 vigilin_like_KH K homo 98.2 1.3E-06 2.8E-11 63.8 3.7 59 277-335 4-62 (62)
25 KOG4373 Predicted 3'-5' exonuc 98.0 1.3E-05 2.8E-10 76.4 7.2 129 64-209 146-281 (319)
26 KOG2405 Predicted 3'-5' exonuc 98.0 7.7E-07 1.7E-11 85.9 -2.3 151 48-204 58-215 (458)
27 cd00105 KH-I K homology RNA-bi 97.8 3.1E-05 6.8E-10 56.3 4.2 59 276-334 3-63 (64)
28 cd02396 PCBP_like_KH K homolog 97.7 4.7E-05 1E-09 56.3 4.1 58 277-334 4-64 (65)
29 cd06125 DnaQ_like_exo DnaQ-lik 97.5 0.00038 8.1E-09 55.5 7.3 72 52-134 1-83 (96)
30 PF00013 KH_1: KH domain syndr 97.5 1.5E-05 3.2E-10 57.7 -1.4 57 277-334 4-60 (60)
31 smart00322 KH K homology RNA-b 97.4 0.00024 5.2E-09 51.4 4.9 61 277-337 7-67 (69)
32 PRK07740 hypothetical protein; 97.3 0.0092 2E-07 55.6 14.5 142 46-223 56-233 (244)
33 cd02393 PNPase_KH Polynucleoti 97.2 0.00045 9.8E-09 50.5 4.0 55 276-334 5-60 (61)
34 TIGR01298 RNaseT ribonuclease 97.0 0.022 4.7E-07 51.5 14.1 85 104-223 107-199 (200)
35 PRK06063 DNA polymerase III su 97.0 0.013 2.8E-07 56.8 13.1 97 90-222 84-185 (313)
36 TIGR00573 dnaq exonuclease, DN 96.5 0.044 9.4E-07 50.1 12.1 141 46-220 4-181 (217)
37 PRK07883 hypothetical protein; 96.4 0.058 1.3E-06 56.3 13.7 197 46-278 12-248 (557)
38 PRK07942 DNA polymerase III su 96.4 0.087 1.9E-06 48.7 13.4 82 103-217 94-181 (232)
39 PRK06310 DNA polymerase III su 96.3 0.21 4.7E-06 46.7 15.8 134 46-217 4-175 (250)
40 cd06131 DNA_pol_III_epsilon_Ec 96.3 0.043 9.4E-07 47.4 10.1 87 91-212 72-166 (167)
41 PRK05601 DNA polymerase III su 96.2 0.18 3.8E-06 49.8 15.1 141 46-212 43-245 (377)
42 PRK07246 bifunctional ATP-depe 96.2 0.096 2.1E-06 57.1 14.6 135 48-220 6-174 (820)
43 PF13014 KH_3: KH domain 96.2 0.0061 1.3E-07 41.1 3.5 39 284-322 2-43 (43)
44 cd06144 REX4_like DEDDh 3'-5' 96.2 0.014 3E-07 50.2 6.6 85 90-209 67-151 (152)
45 cd06137 DEDDh_RNase DEDDh 3'-5 96.2 0.031 6.7E-07 48.6 8.7 66 93-169 76-141 (161)
46 PRK05711 DNA polymerase III su 96.0 0.11 2.3E-06 48.5 12.1 132 49-215 4-175 (240)
47 cd06149 ISG20 DEDDh 3'-5' exon 96.0 0.03 6.6E-07 48.5 8.0 68 90-169 67-137 (157)
48 TIGR01406 dnaQ_proteo DNA poly 96.0 0.092 2E-06 48.4 11.3 90 90-214 72-170 (225)
49 PRK09146 DNA polymerase III su 96.0 0.3 6.5E-06 45.4 14.7 141 46-217 44-228 (239)
50 TIGR01405 polC_Gram_pos DNA po 95.9 0.14 3E-06 58.0 14.3 139 47-223 188-362 (1213)
51 PRK06807 DNA polymerase III su 95.9 0.19 4E-06 48.7 13.3 92 90-218 78-174 (313)
52 COG2176 PolC DNA polymerase II 95.8 0.038 8.3E-07 60.9 9.2 239 46-324 418-738 (1444)
53 cd06145 REX1_like DEDDh 3'-5' 95.8 0.063 1.4E-06 46.1 8.8 64 91-168 66-129 (150)
54 PRK08517 DNA polymerase III su 95.7 0.47 1E-05 44.7 14.8 134 46-218 65-233 (257)
55 KOG2249 3'-5' exonuclease [Rep 95.6 0.045 9.8E-07 51.2 7.5 135 50-218 106-268 (280)
56 PRK06309 DNA polymerase III su 95.5 0.64 1.4E-05 42.9 14.7 140 50-226 3-176 (232)
57 cd06130 DNA_pol_III_epsilon_li 95.3 0.43 9.3E-06 40.4 12.2 67 90-168 67-138 (156)
58 PRK08074 bifunctional ATP-depe 95.0 0.35 7.7E-06 53.5 13.5 134 49-218 3-171 (928)
59 PRK09145 DNA polymerase III su 94.9 1 2.2E-05 40.4 14.0 133 47-213 27-198 (202)
60 cd05160 DEDDy_DNA_polB_exo DED 94.6 0.97 2.1E-05 40.2 13.1 102 89-209 65-198 (199)
61 cd05780 DNA_polB_Kod1_like_exo 94.6 1.3 2.9E-05 39.5 13.9 145 50-212 4-195 (195)
62 TIGR01407 dinG_rel DnaQ family 94.4 0.69 1.5E-05 50.8 13.8 93 90-218 70-167 (850)
63 PF13482 RNase_H_2: RNase_H su 94.1 0.88 1.9E-05 39.0 11.4 146 52-212 1-163 (164)
64 PRK05168 ribonuclease T; Provi 94.1 0.19 4.2E-06 45.7 7.5 87 102-223 114-208 (211)
65 cd06143 PAN2_exo DEDDh 3'-5' e 94.0 0.085 1.8E-06 46.7 4.7 81 92-209 93-173 (174)
66 TIGR03665 arCOG04150 arCOG0415 93.7 0.07 1.5E-06 47.1 3.7 47 283-334 99-145 (172)
67 cd06136 TREX1_2 DEDDh 3'-5' ex 93.2 1.1 2.4E-05 39.5 10.5 64 92-169 86-158 (177)
68 PRK13763 putative RNA-processi 92.9 0.13 2.8E-06 45.8 4.1 47 283-334 105-151 (180)
69 PRK06195 DNA polymerase III su 92.7 0.8 1.7E-05 44.2 9.6 99 90-225 70-173 (309)
70 PRK07247 DNA polymerase III su 92.3 4.4 9.5E-05 36.5 13.3 91 90-217 74-170 (195)
71 PRK00448 polC DNA polymerase I 92.0 0.99 2.2E-05 52.0 10.6 98 91-224 490-592 (1437)
72 cd06134 RNaseT DEDDh 3'-5' exo 92.0 0.75 1.6E-05 41.0 7.9 78 103-215 103-188 (189)
73 smart00479 EXOIII exonuclease 91.9 0.75 1.6E-05 39.2 7.6 92 90-217 70-168 (169)
74 KOG1676 K-homology type RNA bi 91.4 0.17 3.7E-06 52.1 3.4 64 278-341 323-390 (600)
75 COG1837 Predicted RNA-binding 90.3 0.1 2.3E-06 39.8 0.5 43 261-303 18-60 (76)
76 COG1094 Predicted RNA-binding 90.0 0.43 9.3E-06 42.8 4.3 44 284-332 113-156 (194)
77 cd05785 DNA_polB_like2_exo Unc 89.9 8.4 0.00018 34.9 12.7 144 49-209 9-206 (207)
78 cd02395 SF1_like-KH Splicing f 89.4 0.77 1.7E-05 38.2 5.1 54 282-336 15-91 (120)
79 PRK00468 hypothetical protein; 89.0 0.13 2.8E-06 39.2 0.2 43 262-304 19-61 (75)
80 PRK07983 exodeoxyribonuclease 88.9 7 0.00015 35.8 11.5 79 104-216 76-154 (219)
81 TIGR03665 arCOG04150 arCOG0415 87.8 0.41 9E-06 42.2 2.6 57 277-336 2-61 (172)
82 PRK13763 putative RNA-processi 87.8 0.49 1.1E-05 42.1 3.1 57 276-335 6-66 (180)
83 PF09281 Taq-exonuc: Taq polym 87.2 2.2 4.7E-05 35.9 6.4 69 111-216 70-138 (138)
84 cd06127 DEDDh DEDDh 3'-5' exon 86.9 2.6 5.7E-05 34.8 7.0 50 90-141 69-123 (159)
85 PRK02821 hypothetical protein; 86.1 0.24 5.1E-06 38.0 0.1 44 262-305 20-63 (77)
86 KOG1676 K-homology type RNA bi 85.4 1.1 2.3E-05 46.5 4.4 62 274-335 231-295 (600)
87 PRK09182 DNA polymerase III su 84.2 25 0.00055 33.7 13.1 89 92-217 112-202 (294)
88 PRK04163 exosome complex RNA-b 83.6 0.65 1.4E-05 43.1 1.9 57 275-335 147-204 (235)
89 KOG2192 PolyC-binding hnRNP-K 81.4 1.5 3.3E-05 41.2 3.3 39 285-323 135-175 (390)
90 KOG3657 Mitochondrial DNA poly 81.3 4.3 9.4E-05 43.9 7.0 105 103-218 242-385 (1075)
91 cd02134 NusA_KH NusA_K homolog 81.2 1.2 2.5E-05 32.4 2.1 33 274-306 26-58 (61)
92 PRK01064 hypothetical protein; 80.7 0.68 1.5E-05 35.6 0.7 35 270-304 27-61 (78)
93 PRK07748 sporulation inhibitor 80.4 8.6 0.00019 34.6 7.9 93 90-216 82-180 (207)
94 KOG1275 PAB-dependent poly(A) 80.0 0.5 1.1E-05 51.1 -0.3 94 97-227 1009-1102(1118)
95 cd05782 DNA_polB_like1_exo Unc 78.3 52 0.0011 29.7 12.6 129 63-210 49-207 (208)
96 PF10108 DNA_pol_B_exo2: Predi 77.9 18 0.00039 33.1 9.1 106 89-213 39-170 (209)
97 PRK12704 phosphodiesterase; Pr 77.6 3.1 6.7E-05 43.2 4.6 55 268-325 205-262 (520)
98 KOG2190 PolyC-binding proteins 75.8 3 6.5E-05 42.9 3.9 65 276-340 141-208 (485)
99 cd05784 DNA_polB_II_exo DEDDy 75.2 38 0.00083 30.3 10.5 103 89-210 53-193 (193)
100 TIGR02696 pppGpp_PNP guanosine 75.1 3 6.5E-05 44.7 3.8 57 276-336 581-638 (719)
101 cd05781 DNA_polB_B3_exo DEDDy 74.5 62 0.0013 28.7 15.0 143 50-211 4-187 (188)
102 KOG2193 IGF-II mRNA-binding pr 71.3 2.3 5E-05 42.5 1.7 64 277-340 415-481 (584)
103 KOG2192 PolyC-binding hnRNP-K 69.6 6.6 0.00014 37.1 4.2 58 279-336 321-380 (390)
104 TIGR03591 polynuc_phos polyrib 66.5 4.1 8.8E-05 43.8 2.5 57 277-337 555-612 (684)
105 KOG2248 3'-5' exonuclease [Rep 65.8 34 0.00073 34.2 8.6 89 92-214 285-373 (380)
106 KOG2191 RNA-binding protein NO 65.2 12 0.00025 36.5 5.0 61 279-339 138-203 (402)
107 PRK06722 exonuclease; Provisio 64.6 30 0.00066 33.0 7.8 91 90-213 80-178 (281)
108 PF13083 KH_4: KH domain; PDB: 63.8 1.5 3.2E-05 32.8 -1.1 38 270-307 26-63 (73)
109 cd06133 ERI-1_3'hExo_like DEDD 58.9 57 0.0012 27.7 8.0 90 90-212 78-175 (176)
110 PRK00106 hypothetical protein; 58.3 7.4 0.00016 40.5 2.6 51 269-322 221-272 (535)
111 TIGR03319 YmdA_YtgF conserved 55.8 5.2 0.00011 41.5 1.0 58 269-330 200-258 (514)
112 cd02414 jag_KH jag_K homology 54.0 8.1 0.00018 29.2 1.6 32 276-307 27-58 (77)
113 PRK11779 sbcB exonuclease I; P 53.3 78 0.0017 32.6 9.0 96 91-215 82-197 (476)
114 KOG2190 PolyC-binding proteins 51.6 18 0.00039 37.3 4.1 66 273-338 338-407 (485)
115 COG1097 RRP4 RNA-binding prote 49.5 8.4 0.00018 35.8 1.2 46 276-325 149-194 (239)
116 PLN00207 polyribonucleotide nu 45.5 14 0.0003 40.8 2.2 57 276-336 688-746 (891)
117 PRK08406 transcription elongat 44.4 12 0.00026 31.9 1.3 33 276-308 102-134 (140)
118 cd05783 DNA_polB_B1_exo DEDDy 41.8 2.6E+02 0.0057 25.1 11.3 105 89-210 75-202 (204)
119 COG0847 DnaQ DNA polymerase II 39.4 1.3E+02 0.0028 27.3 7.4 92 91-215 85-181 (243)
120 PRK12705 hypothetical protein; 39.1 13 0.00029 38.4 0.9 42 269-310 194-236 (508)
121 cd06138 ExoI_N N-terminal DEDD 38.6 1.6E+02 0.0035 25.7 7.7 72 92-168 74-165 (183)
122 PRK05762 DNA polymerase II; Re 38.5 5.1E+02 0.011 28.4 13.0 104 89-211 205-347 (786)
123 cd02409 KH-II KH-II (K homolo 37.8 28 0.0006 24.5 2.2 29 278-306 30-58 (68)
124 PRK08406 transcription elongat 36.3 20 0.00044 30.5 1.4 25 279-303 38-62 (140)
125 KOG2193 IGF-II mRNA-binding pr 35.3 20 0.00043 36.1 1.4 57 269-325 487-549 (584)
126 PF07650 KH_2: KH domain syndr 34.0 14 0.0003 27.7 0.1 27 280-306 32-58 (78)
127 PRK11824 polynucleotide phosph 26.5 49 0.0011 35.7 2.6 57 276-336 557-614 (693)
128 PF02080 TrkA_C: TrkA-C domain 25.2 67 0.0014 23.0 2.5 21 314-334 50-70 (71)
129 COG5176 MSL5 Splicing factor ( 24.8 48 0.001 30.3 1.8 30 284-314 165-194 (269)
130 KOG0119 Splicing factor 1/bran 22.7 51 0.0011 33.9 1.7 53 284-336 155-226 (554)
131 COG3359 Predicted exonuclease 22.4 6.8E+02 0.015 23.8 12.4 152 50-218 99-271 (278)
132 TIGR01952 nusA_arch NusA famil 22.3 54 0.0012 28.0 1.6 26 278-303 38-63 (141)
133 cd02412 30S_S3_KH K homology R 21.8 55 0.0012 26.5 1.5 25 281-305 69-93 (109)
134 PF08235 LNS2: LNS2 (Lipin/Ned 21.1 33 0.00072 29.9 0.1 39 282-328 117-155 (157)
135 cd05777 DNA_polB_delta_exo DED 20.5 1.3E+02 0.0029 27.3 4.0 54 151-213 168-224 (230)
No 1
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=1.5e-38 Score=310.71 Aligned_cols=252 Identities=20% Similarity=0.194 Sum_probs=211.3
Q ss_pred CeEEeCCCCcccHHhhcccccCCceEEEEeeeeCCC-CCCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCceE
Q 019356 27 PIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITK 105 (342)
Q Consensus 27 ~i~~V~t~~~L~~~~l~~~l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i~K 105 (342)
.|.+|+|+++|.+ +++. +.+.+.+|||+|+.+.. +++++|+|||++++++|+||+..+.+ ++.|+++|+|+.|.|
T Consensus 2 ~~~~I~t~~~L~~-~~~~-l~~~~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~~~d--~~~L~~ll~~~~ivK 77 (373)
T PRK10829 2 NYQMITTDDALAS-VCEA-ARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITD--WSPFKALLRDPQVTK 77 (373)
T ss_pred CcEEeCCHHHHHH-HHHH-HhcCCeEEEecccccCccCCCceeEEEEecCCceEEEecCCccc--hHHHHHHHcCCCeEE
Confidence 5789999999997 9988 78899999999999875 77899999999999999999998753 688999999999999
Q ss_pred EEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCC
Q 019356 106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFW 185 (342)
Q Consensus 106 V~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW 185 (342)
|+|++++|+..|++.+|+.+.++||||+|+++++.+. .+||+.|++ ++||++++ |++.+ +||
T Consensus 78 V~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~--------~~gl~~Lv~--~~lgv~ld-K~~~~-------sDW 139 (373)
T PRK10829 78 FLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPL--------SCGFASMVE--EYTGVTLD-KSESR-------TDW 139 (373)
T ss_pred EEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCc--------cccHHHHHH--HHhCCccC-ccccc-------CCC
Confidence 9999999999998899999999999999999999642 379999999 99999998 44433 599
Q ss_pred CCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHHHHhcccccccccc-CCCCCCCCCCCCCCCCcceeccccccc
Q 019356 186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCFCI-NENDYVDWPPLPPVPGVRFIYVDYLIV 264 (342)
Q Consensus 186 ~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l~~~~~~~~r~~~~-~~~~~~~w~~~~~~~~~~~~~~~~l~~ 264 (342)
+.||||++|+.|||.||++|+.||+.|.++|++.|+++|+.+|+........ ..+....|+++.+. ..++.++|++
T Consensus 140 ~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~ik~~---~~L~~~~lav 216 (373)
T PRK10829 140 LARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNA---WQLRTRQLAC 216 (373)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHhccccCCChHHHHHHhccc---cCCCHHHHHH
Confidence 9999999999999999999999999999999999999999999854211100 11111348886544 3455678999
Q ss_pred cCCC--ChhhhhhhcCCCCCCC--------------------------ceeeccCCchHHHHHHhhc
Q 019356 265 EGDV--PEEEILSILDVPPGKM--------------------------GRIIGRRGSSILAIKESCN 303 (342)
Q Consensus 265 ~~~~--~~~~~~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~ 303 (342)
.+++ .||++|+.+|+|++++ +..++++|..++++++.+.
T Consensus 217 l~~L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~~~~~~~~r~~g~~ll~~i~~a~ 283 (373)
T PRK10829 217 LQLLADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQ 283 (373)
T ss_pred HHHHHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhccCChHhHHhhHHHHHHHHHHHh
Confidence 9996 9999999999999983 1245667777777776664
No 2
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-36 Score=288.15 Aligned_cols=249 Identities=22% Similarity=0.228 Sum_probs=205.4
Q ss_pred CCCCcccHHhhcccccCCceEEEEeeeeCCC-CCCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCceEEEeeh
Q 019356 32 TNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDC 110 (342)
Q Consensus 32 ~t~~~L~~~~l~~~l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV~hd~ 110 (342)
++.+.++. ++.. ..+++.|++|+|+.+.. +++++|+|||+.++++++||+..... -...|..+|.|++|.||+|.+
T Consensus 2 ~~~~~l~~-~~~~-~~~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~~lIdpl~~~~-d~~~l~~Ll~d~~v~KIfHaa 78 (361)
T COG0349 2 TTGDLLAA-ACAL-LRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEGASLIDPLAGIL-DLPPLVALLADPNVVKIFHAA 78 (361)
T ss_pred CchhHHHH-HHHH-hcCCCceEEecccccccccCCceEEEEEecCCCceEeccccccc-ccchHHHHhcCCceeeeeccc
Confidence 34455664 7776 67789999999999986 89999999999988899999987432 268899999999999999999
Q ss_pred hhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCC
Q 019356 111 KRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPL 190 (342)
Q Consensus 111 k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPL 190 (342)
++|+.+|++.||+.+.++|||++|+.+++.+. .+||+.|++ +++|++++ |++.+ +||..|||
T Consensus 79 ~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~--------~~gl~~Lv~--~ll~v~ld-K~~q~-------SDW~~RPL 140 (361)
T COG0349 79 RFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGT--------SHGLADLVE--ELLGVELD-KSEQR-------SDWLARPL 140 (361)
T ss_pred cccHHHHHHhcCCCCCchhHHHHHHHHhCCcc--------cccHHHHHH--HHhCCccc-ccccc-------cccccCCC
Confidence 99999999999999999999999999999863 379999999 99999999 55533 69999999
Q ss_pred cHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHHHHhcccccccc-ccCCCCCCCCCCCCCCCCcceeccccccccCCC-
Q 019356 191 TELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCF-CINENDYVDWPPLPPVPGVRFIYVDYLIVEGDV- 268 (342)
Q Consensus 191 s~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l~~~~~~~~r~~-~~~~~~~~~w~~~~~~~~~~~~~~~~l~~~~~~- 268 (342)
|++|++|||.||.||+.||+.|.++|.++|++.|+.++|...-.- ....+.-..|+.+... +..+.+++++.+++
T Consensus 141 s~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~~l~~r~~~~~~~~~~w~~i~~a---~~~~p~~la~l~~La 217 (361)
T COG0349 141 SEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFRLLPTRRTYKVLPEDAWREIKIA---HSLDPRELAVLRELA 217 (361)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHhhhccccccChHhHHHHhhhh---hcCChHHHHHHHHHH
Confidence 999999999999999999999999999999999999997531111 1111233468886652 23344578888886
Q ss_pred -ChhhhhhhcCCCCCC--------------------------CceeeccCCchHHHHHHhhcc
Q 019356 269 -PEEEILSILDVPPGK--------------------------MGRIIGRRGSSILAIKESCNA 304 (342)
Q Consensus 269 -~~~~~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~ 304 (342)
.||++++.+|+|+++ ++-.+.++|..+.++++.+.+
T Consensus 218 ~wRe~~Ar~rd~~~~~vl~de~i~~~a~~~P~~~~~l~~l~~~~~~~~~~~~~l~~~~~~a~~ 280 (361)
T COG0349 218 AWREREARERDLARNFVLKDEALWELARYTPKNLKELDALGLIPKERRRHGKLLLALLANALA 280 (361)
T ss_pred HHHHHHHHHhccccccccchhHHHHHHHhCCCCHHHHHhccCCcccchhhhHHHHHHHHHHHh
Confidence 899999999999887 334678888999988876664
No 3
>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=100.00 E-value=2.6e-34 Score=281.51 Aligned_cols=230 Identities=21% Similarity=0.221 Sum_probs=192.3
Q ss_pred EeCCCCcccHHhhcccccCCceEEEEeeeeCCC-CCCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCceEEEe
Q 019356 30 IVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIH 108 (342)
Q Consensus 30 ~V~t~~~L~~~~l~~~l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV~h 108 (342)
+|+|.+++.+ +++. +...++||||||+.+.. +++++|+|||++++++|+||+....+ ++.|+++|+|+++.||+|
T Consensus 1 ~I~t~~~l~~-~~~~-l~~~~~ia~DtE~~~~~~y~~~l~LiQia~~~~~~liD~~~~~~--~~~L~~lL~d~~i~KV~h 76 (367)
T TIGR01388 1 WITTDDELAT-VCEA-VRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIID--WSPLKELLRDESVVKVLH 76 (367)
T ss_pred CcCCHHHHHH-HHHH-HhcCCEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCccc--HHHHHHHHCCCCceEEEe
Confidence 4788899997 8888 67789999999999875 78899999999999999999987743 688999999999999999
Q ss_pred ehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCC
Q 019356 109 DCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYR 188 (342)
Q Consensus 109 d~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~R 188 (342)
|+++|+.+|.+.+|+.+.++||||+|+|+++++. .+||+.|++ +|||++++ |++. .++|..|
T Consensus 77 ~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~--------~~~l~~Lv~--~~Lg~~l~-K~~~-------~sdW~~r 138 (367)
T TIGR01388 77 AASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGM--------SMGYAKLVQ--EVLGVELD-KSES-------RTDWLAR 138 (367)
T ss_pred ecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCC--------CccHHHHHH--HHcCCCCC-cccc-------cccCCCC
Confidence 9999999998777888888999999999999853 369999999 99999988 4332 2599999
Q ss_pred CCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHHHHhcccccccc-ccCCCCCCCCCCCCCCCCcceeccccccccCC
Q 019356 189 PLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCF-CINENDYVDWPPLPPVPGVRFIYVDYLIVEGD 267 (342)
Q Consensus 189 PLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l~~~~~~~~r~~-~~~~~~~~~w~~~~~~~~~~~~~~~~l~~~~~ 267 (342)
||+++|+.|||.||.+++.||+.|.++|++.|++.|+.+|+...... ....+....|.++.+. ..+..++|++.++
T Consensus 139 PL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~i~~~---~~l~~~~l~~l~~ 215 (367)
T TIGR01388 139 PLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNA---WQLRPQQLAVLQA 215 (367)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHhccccCCCChHHHHHHhccc---ccCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999988532111 1111112348876543 3455578999998
Q ss_pred C--ChhhhhhhcCCCCCCC
Q 019356 268 V--PEEEILSILDVPPGKM 284 (342)
Q Consensus 268 ~--~~~~~~~~~~~~~~~~ 284 (342)
+ .||++|+.+|+|++++
T Consensus 216 L~~wRe~~A~~~d~p~~~i 234 (367)
T TIGR01388 216 LAAWREREARERDLPRNFV 234 (367)
T ss_pred HHHHHHHHHHHcCCCccee
Confidence 6 9999999999999883
No 4
>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=99.97 E-value=7.7e-30 Score=229.90 Aligned_cols=179 Identities=49% Similarity=0.744 Sum_probs=148.9
Q ss_pred ccCCceEEEEeeeeCCCCCCcEEEEEEEeC-CcEEEEEcCCCCh-hHHHhhHHHhcCCCceEEEeehhhhHHHHHHhcCC
Q 019356 46 SERQLVIGFDCEGVDLCRHGSLCIMQLAFP-DAIYLVDAIQGGE-TVVKACKPALESSYITKVIHDCKRDSEALYFQFGI 123 (342)
Q Consensus 46 l~~~~~Ia~D~E~~~~~~~g~l~llQLa~~-~~~~liD~~~l~~-~~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi 123 (342)
+.++..||||+|+.+.+++|++|+|||++. +++|+||+..++. .+...|+++|+++.+.||+||++.|+..|++.+|+
T Consensus 7 l~~~~~i~~D~E~~~~~~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi 86 (197)
T cd06148 7 LKKQKVIGLDCEGVNLGRKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGI 86 (197)
T ss_pred hhhCCEEEEEcccccCCCCCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHHhcCc
Confidence 567899999999998888899999999998 9999999998763 35688999999999999999999999999889999
Q ss_pred ccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhH
Q 019356 124 KLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVR 203 (342)
Q Consensus 124 ~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~ 203 (342)
.+.++|||++|+|++++..+.........||+.+++ +|+|.++++++..+...+...++|..|||+++|+.|||.||+
T Consensus 87 ~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~--~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~ 164 (197)
T cd06148 87 KLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLD--KYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVL 164 (197)
T ss_pred cccceeeHHHHHHHHHHHhcCCccccccccHHHHHH--HhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHH
Confidence 999999999999999986431111112469999999 999998874333322223345799999999999999999999
Q ss_pred HHHHHHHHHHHHHhccccHHHHH
Q 019356 204 FLPYIYHNMMKKLNQQSLWYLAV 226 (342)
Q Consensus 204 ~Ll~L~~~L~~~L~~~g~~~l~~ 226 (342)
+|+.||+.|...|.+......+.
T Consensus 165 ~Ll~l~~~l~~~l~~~~~~~~~~ 187 (197)
T cd06148 165 CLLPLYYAMLDALISKFLKAVFK 187 (197)
T ss_pred hHHHHHHHHHHHhhhhHHHHHHH
Confidence 99999999999999875444444
No 5
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=99.96 E-value=6.8e-29 Score=216.70 Aligned_cols=153 Identities=31% Similarity=0.342 Sum_probs=135.5
Q ss_pred hhccccc-CCceEEEEeeeeCCC-CCCcEEEEEEEeC-CcEEEEEcCCCChhHHHhhHHHhcCCCceEEEeehhhhHHHH
Q 019356 41 FLEPSSE-RQLVIGFDCEGVDLC-RHGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEAL 117 (342)
Q Consensus 41 ~l~~~l~-~~~~Ia~D~E~~~~~-~~g~l~llQLa~~-~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~Dl~~L 117 (342)
+++. +. ..+++|||+||.+.. +.+++|+|||+++ +.+|+||+..++. .+..|+++|+|+.+.||+|+++.|+..|
T Consensus 5 ~~~~-l~~~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~-~~~~L~~lL~d~~i~Kvg~~~k~D~~~L 82 (161)
T cd06129 5 LCED-LSMDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSV-DWQGLKMLLENPSIVKALHGIEGDLWKL 82 (161)
T ss_pred HHHH-HhcCCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCcc-CHHHHHHHhCCCCEEEEEeccHHHHHHH
Confidence 6666 55 889999999999876 5789999999998 9999999987753 3678999999999999999999999999
Q ss_pred HHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHH
Q 019356 118 YFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRA 197 (342)
Q Consensus 118 ~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~Y 197 (342)
.+.+|+.+.++|||++++|++++.. ..||+.+++ +|+|.+++| .+. .+||..||||++|+.|
T Consensus 83 ~~~~gi~~~~~~D~~~aa~ll~~~~--------~~~L~~l~~--~~lg~~l~K-~~~-------~s~W~~rpLt~~qi~Y 144 (161)
T cd06129 83 LRDFGEKLQRLFDTTIAANLKGLPE--------RWSLASLVE--HFLGKTLDK-SIS-------CADWSYRPLTEDQKLY 144 (161)
T ss_pred HHHcCCCcccHhHHHHHHHHhCCCC--------CchHHHHHH--HHhCCCCCc-cce-------eccCCCCCCCHHHHHH
Confidence 7779999999999999999999752 369999999 999999974 332 2699999999999999
Q ss_pred HHHHhHHHHHHHHHHH
Q 019356 198 AADDVRFLPYIYHNMM 213 (342)
Q Consensus 198 AA~Da~~Ll~L~~~L~ 213 (342)
||.||++++.||+.|+
T Consensus 145 Aa~Da~~l~~l~~~l~ 160 (161)
T cd06129 145 AAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999999986
No 6
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.96 E-value=7.8e-29 Score=222.74 Aligned_cols=175 Identities=26% Similarity=0.327 Sum_probs=145.3
Q ss_pred eEEeCCCCcccHHhhccc-ccCCceEEEEeeeeCCC---CCCcEEEEEEEeCCcEEEEEcCCCC----hhHHHhhHHHhc
Q 019356 28 IHIVTNASQLPAEFLEPS-SERQLVIGFDCEGVDLC---RHGSLCIMQLAFPDAIYLVDAIQGG----ETVVKACKPALE 99 (342)
Q Consensus 28 i~~V~t~~~L~~~~l~~~-l~~~~~Ia~D~E~~~~~---~~g~l~llQLa~~~~~~liD~~~l~----~~~~~~L~~lLe 99 (342)
|++|+|++++.+ ++... +....+||||+||.+.. ..+++|+|||++++.+|+||+..++ +.+...|+++|+
T Consensus 1 ~~~i~~~~el~~-~~~~~~l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~ll~ 79 (193)
T cd06146 1 IHIVDSEEELEA-LLLALSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKRLFE 79 (193)
T ss_pred CeEecCHHHHHH-HHHHHhhccCCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHHHhC
Confidence 578999999997 77653 56789999999998764 2689999999999999999998775 245678999999
Q ss_pred CCCceEEEeehhhhHHHHHHhcCCc------cCceehHHHHHHhhcccc-CCC--CCCCCCCcHHHhhcCccccCCccch
Q 019356 100 SSYITKVIHDCKRDSEALYFQFGIK------LHNVVDTQIAYSLIEEQE-GRK--RSPDDYISFVGLLADPRYCGISYQE 170 (342)
Q Consensus 100 ~~~i~KV~hd~k~Dl~~L~~~~Gi~------l~~vfDtqlAa~LL~~~~-~~~--~L~~~~~sL~~Lv~~~~~Lg~~l~k 170 (342)
|++|.||||++++|+..|++.+|+. +.+++||+.+++.+.... ++. .......||++|++ ++||.+++|
T Consensus 80 d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~--~~lg~~l~K 157 (193)
T cd06146 80 DPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQ--EVLGKPLDK 157 (193)
T ss_pred CCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHH--HHhCCCcCc
Confidence 9999999999999999999899974 679999999888776421 110 11123589999999 999999984
Q ss_pred hHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHH
Q 019356 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (342)
Q Consensus 171 K~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~ 213 (342)
.+. .+||..||||++|+.|||.||++++.||++|.
T Consensus 158 -~~q-------~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 158 -SEQ-------CSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred -ccc-------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 332 26999999999999999999999999999985
No 7
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=99.94 E-value=9e-27 Score=204.28 Aligned_cols=164 Identities=23% Similarity=0.290 Sum_probs=139.5
Q ss_pred CCCCcccHHhhccccc-CCceEEEEeeeeCCC---CCCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCceEEE
Q 019356 32 TNASQLPAEFLEPSSE-RQLVIGFDCEGVDLC---RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVI 107 (342)
Q Consensus 32 ~t~~~L~~~~l~~~l~-~~~~Ia~D~E~~~~~---~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV~ 107 (342)
++.+++.+ +++. +. ....+|||+||.+.. ..+++++||||+++.+|+||+..++ .+...|+++|+++.+.||+
T Consensus 2 ~~~~~~~~-~~~~-~~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~-~~~~~l~~ll~~~~i~kv~ 78 (170)
T cd06141 2 DSAQDAEE-AVKE-LLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMD-KLPPSLKQLLEDPSILKVG 78 (170)
T ss_pred CCHHHHHH-HHHH-HhcCCCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhh-cccHHHHHHhcCCCeeEEE
Confidence 34556665 7766 55 789999999999764 4689999999999999999998763 3567899999999999999
Q ss_pred eehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCC
Q 019356 108 HDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTY 187 (342)
Q Consensus 108 hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~ 187 (342)
||++.|+..|.+.+|+.+.++|||++++|++++... ..||+.|++ +++|.++.+.+.. ..++|..
T Consensus 79 ~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~-------~~~l~~l~~--~~l~~~~~k~k~~------~~s~W~~ 143 (170)
T cd06141 79 VGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRK-------LVSLARLVE--EVLGLPLSKPKKV------RCSNWEA 143 (170)
T ss_pred eeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcC-------CccHHHHHH--HHcCcccCCCCCc------ccCCCCC
Confidence 999999999977999999999999999999998631 258999999 9999988831111 1369999
Q ss_pred CCCcHHHHHHHHHHhHHHHHHHHHHH
Q 019356 188 RPLTELMVRAAADDVRFLPYIYHNMM 213 (342)
Q Consensus 188 RPLs~~ql~YAA~Da~~Ll~L~~~L~ 213 (342)
|||+++|+.|||.||++++.||+.|.
T Consensus 144 rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 144 RPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999885
No 8
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=99.94 E-value=3.8e-26 Score=199.39 Aligned_cols=170 Identities=32% Similarity=0.470 Sum_probs=145.5
Q ss_pred eEEeCCCCcccHHhhcccccCCceEEEEeeeeCCCC---CCcEEEEEEEeCCcEEEEEcCCCChh-HHHhhHHHhcCCCc
Q 019356 28 IHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCR---HGSLCIMQLAFPDAIYLVDAIQGGET-VVKACKPALESSYI 103 (342)
Q Consensus 28 i~~V~t~~~L~~~~l~~~l~~~~~Ia~D~E~~~~~~---~g~l~llQLa~~~~~~liD~~~l~~~-~~~~L~~lLe~~~i 103 (342)
|++|+|.+++.+ +++. +...+.+|||+||.+... ...++++|+++++.+|++++...... +...|+++|+|+++
T Consensus 1 y~~v~~~~~l~~-~~~~-l~~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i 78 (176)
T PF01612_consen 1 YQIVDTEEELEE-AIKK-LKNAKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPNI 78 (176)
T ss_dssp SEEEHSHHHHHH-HHHH-HTTTSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTTS
T ss_pred CEecCCHHHHHH-HHHH-HcCCCeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCCc
Confidence 578999999997 8887 777889999999998753 56899999999999999998877643 57899999999999
Q ss_pred eEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccC-CccchhHHHHHHhcCCC
Q 019356 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCG-ISYQEKEEVRVLLRQDP 182 (342)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg-~~l~kK~~~~~l~~~~~ 182 (342)
.||+||+++|+.+|.+.+|+.+.+++||+++++++++... .||++|+. +++| ..++ ++. ..
T Consensus 79 ~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~--------~~L~~L~~--~~l~~~~~~-~~~-------~~ 140 (176)
T PF01612_consen 79 IKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRS--------YSLKDLAE--EYLGNIDLD-KKE-------QM 140 (176)
T ss_dssp EEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTT--------SSHHHHHH--HHHSEEE-G-HCC-------TT
T ss_pred cEEEEEEechHHHHHHHhccccCCccchhhhhhccccccc--------ccHHHHHH--HHhhhccCc-HHH-------hh
Confidence 9999999999999987799999999999999999998642 69999999 9999 4444 222 23
Q ss_pred CCCC-CCCCcHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 019356 183 QFWT-YRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (342)
Q Consensus 183 ~dW~-~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (342)
++|. .+||+++|+.|||.||.++++||+.|.++|+
T Consensus 141 ~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 141 SDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp SSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred ccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 6899 8999999999999999999999999999885
No 9
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.86 E-value=7.3e-21 Score=166.99 Aligned_cols=164 Identities=29% Similarity=0.399 Sum_probs=137.5
Q ss_pred cCCceEEEEeeeeCCC-CCCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCceEEEeehhhhHHHHHHhcCCcc
Q 019356 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKL 125 (342)
Q Consensus 47 ~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l 125 (342)
.....+++|+|+.+.. ..++++++|+++++++|+||+... .....|+++|+|+.+.||+||+|.|...|.+.+|+..
T Consensus 10 ~~~~~l~~~~e~~~~~~~~~~~~~i~l~~~~~~~~i~~~~~--~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~ 87 (178)
T cd06142 10 ASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI--GDLSPLKELLADPNIVKVFHAAREDLELLKRDFGILP 87 (178)
T ss_pred hcCCeEEEECCccCCCcCCCceEEEEEeeCCCEEEEeCCCc--ccHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCC
Confidence 3456899999876654 468999999998865899985533 2456789999999999999999999999976669995
Q ss_pred CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHH
Q 019356 126 HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFL 205 (342)
Q Consensus 126 ~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~L 205 (342)
+++|||++|+|++++.. ..++..+++ +|++.++.+ +.. .++|..+|++..|..||+.||.++
T Consensus 88 ~~~~D~~laayLl~p~~--------~~~l~~l~~--~~l~~~~~~-~~~-------~~~w~~~~l~~~~~~yaa~~a~~l 149 (178)
T cd06142 88 QNLFDTQIAARLLGLGD--------SVGLAALVE--ELLGVELDK-GEQ-------RSDWSKRPLTDEQLEYAALDVRYL 149 (178)
T ss_pred CCcccHHHHHHHhCCCc--------cccHHHHHH--HHhCCCCCc-ccc-------cccCCCCCCCHHHHHHHHHhHHHH
Confidence 56899999999999863 248899999 999987542 222 148999999999999999999999
Q ss_pred HHHHHHHHHHHhccccHHHHHhccc
Q 019356 206 PYIYHNMMKKLNQQSLWYLAVRGAL 230 (342)
Q Consensus 206 l~L~~~L~~~L~~~g~~~l~~~~~~ 230 (342)
++|++.|.++|++.|+++++.+|+.
T Consensus 150 ~~L~~~l~~~L~e~~l~~L~~~~~~ 174 (178)
T cd06142 150 LPLYEKLKEELEEEGRLEWAEEECE 174 (178)
T ss_pred HHHHHHHHHHHHHcCcHHHHHHHHH
Confidence 9999999999999999999998874
No 10
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=8.5e-22 Score=195.82 Aligned_cols=174 Identities=27% Similarity=0.381 Sum_probs=155.0
Q ss_pred ccCeEEeCCCCcccHHhhcccccCCceEEEEeeeeCCC-CCCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCc
Q 019356 25 VVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYI 103 (342)
Q Consensus 25 ~~~i~~V~t~~~L~~~~l~~~l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i 103 (342)
+++..+|.+..++.+ +.+. +.....+|+|+|..++. +.|-.|+|||++..+.|+||...+.+. +..|+++|.+|.+
T Consensus 190 ~T~~~~I~t~~el~~-l~~~-l~~~~Efavdlehhsyrsf~gltclmqISTr~ed~iIDt~~l~~~-i~~l~e~fsdp~i 266 (687)
T KOG2206|consen 190 ITPKVWICTLGELEA-LPEI-LDSVIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKLRDH-IGILNEVFSDPGI 266 (687)
T ss_pred ccCceeeechHHHHH-HHHH-HhhhhhhhhhccccchhhhcCceeEEEeeccchhheehhHHHHHH-HHHhhhhccCCCe
Confidence 356788999888886 7766 66678899999999986 889999999999999999999887653 5689999999999
Q ss_pred eEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCC
Q 019356 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQ 183 (342)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~ 183 (342)
.||+|++..|+.||++.|||.+.|+|||..|+++|+.+ ..||+.|.+ .|+|+..+++.|. .
T Consensus 267 vkvfhgaD~diiwlqrdfgiyvvnLfdt~~a~r~L~~~---------r~sL~~ll~--~~~~v~~nk~yql--------a 327 (687)
T KOG2206|consen 267 VKVFHGADTDIIWLQRDFGIYVVNLFDTIQASRLLGLP---------RPSLAYLLE--CVCGVLTNKKYQL--------A 327 (687)
T ss_pred EEEEecCccchhhhhccceEEEEechhhHHHHHHhCCC---------cccHHHHHH--HHHhhhhhhhhhh--------c
Confidence 99999999999999999999999999999999999986 369999999 9999988855543 4
Q ss_pred CCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccc
Q 019356 184 FWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (342)
Q Consensus 184 dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g 220 (342)
+|..|||+++|+.||..|.++|+.||+.|+..|.+.+
T Consensus 328 dwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a 364 (687)
T KOG2206|consen 328 DWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLA 364 (687)
T ss_pred hhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999999998887654
No 11
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.78 E-value=3.6e-18 Score=147.78 Aligned_cols=168 Identities=29% Similarity=0.434 Sum_probs=131.4
Q ss_pred EEeCCCCcccHHhhccccc-CCceEEEEeeeeCCC-CCCcEEEEEEEeCC-cEEEEEcCCCChhHHHhhHHHhcCCCceE
Q 019356 29 HIVTNASQLPAEFLEPSSE-RQLVIGFDCEGVDLC-RHGSLCIMQLAFPD-AIYLVDAIQGGETVVKACKPALESSYITK 105 (342)
Q Consensus 29 ~~V~t~~~L~~~~l~~~l~-~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~-~~~liD~~~l~~~~~~~L~~lLe~~~i~K 105 (342)
.+|++.+++.. +++. +. ....+++|+|+.+.. ..++++++|++.++ .+|+++.... ...+..|+++|+++.+.|
T Consensus 2 ~~i~~~~~~~~-~~~~-~~~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~-~~~~~~l~~~l~~~~~~k 78 (172)
T smart00474 2 RVVTDSETLEE-LLEK-LRAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLAL-GDDLEILKDLLEDETITK 78 (172)
T ss_pred EEecCHHHHHH-HHHH-HHhcCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccc-hhhHHHHHHHhcCCCceE
Confidence 46777777665 6654 34 456999999887654 46799999999744 5666554322 223566899999999999
Q ss_pred EEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCC
Q 019356 106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFW 185 (342)
Q Consensus 106 V~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW 185 (342)
|+||+|.|...|. .+|+.+.++|||++|+|++++..+ ..+|+.+++ +|++..+.+ .. ++ .+|
T Consensus 79 v~~d~k~~~~~L~-~~gi~~~~~~D~~laayll~p~~~-------~~~l~~l~~--~~l~~~~~~--~~----~~--~~~ 140 (172)
T smart00474 79 VGHNAKFDLHVLA-RFGIELENIFDTMLAAYLLLGGPS-------KHGLATLLK--EYLGVELDK--EE----QK--SDW 140 (172)
T ss_pred EEechHHHHHHHH-HCCCcccchhHHHHHHHHHcCCCC-------cCCHHHHHH--HHhCCCCCc--cc----Cc--ccc
Confidence 9999999999996 599999888999999999998642 148899999 899877542 11 11 378
Q ss_pred CCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 019356 186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (342)
Q Consensus 186 ~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (342)
..+|+...|..||+.||.+++.|++.|.++|.
T Consensus 141 ~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l~ 172 (172)
T smart00474 141 GARPLSEEQLQYAAEDADALLRLYEKLEKELE 172 (172)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 77888999999999999999999999998873
No 12
>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=99.76 E-value=1.6e-17 Score=148.69 Aligned_cols=173 Identities=26% Similarity=0.403 Sum_probs=135.7
Q ss_pred ccCeEEeCCCCcccHHhhcccccCCceEEEEeeeeCCC-CCCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCc
Q 019356 25 VVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYI 103 (342)
Q Consensus 25 ~~~i~~V~t~~~L~~~~l~~~l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i 103 (342)
+++|.++++.+++.. +++. +...+.+++++|+.+.. ..+.++++|++.++++|+|+.... ......|+++|+++.+
T Consensus 2 ~~~~~~i~~~~~l~~-~~~~-l~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~l~~-~~~~~~L~~~L~~~~i 78 (192)
T cd06147 2 ETPLTFVDTEEKLEE-LVEK-LKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKL-RDDMHILNEVFTDPNI 78 (192)
T ss_pred CCCcEEECCHHHHHH-HHHH-HhcCCeEEEEeEecCCccCCCceEEEEEecCCCcEEEEeccc-ccchHHHHHHhcCCCc
Confidence 467888866666664 6644 34445899999875543 367899999998766888874222 1234568999999999
Q ss_pred eEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCC
Q 019356 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQ 183 (342)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~ 183 (342)
.||+||+|.++..|.+.+|+.+.++|||++|+||+++. + .+++.|++ +|++..+. |++. .+
T Consensus 79 ~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~-~--------~~l~~l~~--~yl~~~~~-k~~~-------~~ 139 (192)
T cd06147 79 LKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-R--------HSLAYLLQ--KYCNVDAD-KKYQ-------LA 139 (192)
T ss_pred eEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCC-c--------ccHHHHHH--HHhCCCcc-hhhh-------cc
Confidence 99999999999999448899988779999999999986 3 27899999 99987653 3211 24
Q ss_pred CCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhcc
Q 019356 184 FWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ 219 (342)
Q Consensus 184 dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~ 219 (342)
+|..+||+.+|..|++.++.+++.|++.|.++|+++
T Consensus 140 ~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~ 175 (192)
T cd06147 140 DWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLER 175 (192)
T ss_pred ccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 688888899999999999999999999999999774
No 13
>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=99.70 E-value=5.8e-16 Score=131.49 Aligned_cols=152 Identities=31% Similarity=0.352 Sum_probs=113.5
Q ss_pred eEEEEeeeeCCC-CCCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCceEEEeehhhhHHHHHHhcCC-ccCce
Q 019356 51 VIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGI-KLHNV 128 (342)
Q Consensus 51 ~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi-~l~~v 128 (342)
.+++|+|+.+.. ..++++++|+++++++++++.......+.+.|+++|+++.+.||+||+|+|..+|. ..++ ...++
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~-~~~~~~~~~~ 80 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLA-RDGIELPGNI 80 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHH-HCCCCCCCCc
Confidence 578999876654 46899999999864355554322113456779999999999999999999999996 4454 44568
Q ss_pred ehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHH
Q 019356 129 VDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYI 208 (342)
Q Consensus 129 fDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L 208 (342)
|||++++|++++... ..+|+.|++ +|++....+.++.. +.. ..|..+|++..|..||+.|+.+++.|
T Consensus 81 ~D~~~~ayll~~~~~-------~~~l~~l~~--~~l~~~~~~~~~~~---~~~-~~~~~~~~~~~~~~y~~~da~~~~~l 147 (155)
T cd00007 81 FDTMLAAYLLNPGEG-------SHSLDDLAK--EYLGIELDKDEQIY---GKG-AKTFARPLSEELLEYAAEDADALLRL 147 (155)
T ss_pred ccHHHHHHHhCCCCC-------cCCHHHHHH--HHcCCCCccHHHHh---cCC-CCccccCCHHHHHHHHHHhHHHHHHH
Confidence 999999999999642 248999999 99998754222221 111 01335788999999999999999999
Q ss_pred HHHHHHHH
Q 019356 209 YHNMMKKL 216 (342)
Q Consensus 209 ~~~L~~~L 216 (342)
++.|.+++
T Consensus 148 ~~~l~~~~ 155 (155)
T cd00007 148 YEKLLEEL 155 (155)
T ss_pred HHHHHhhC
Confidence 99998753
No 14
>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=99.70 E-value=9.2e-16 Score=135.06 Aligned_cols=164 Identities=22% Similarity=0.210 Sum_probs=127.2
Q ss_pred CceEEEEeeeeCCC-CCCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCceEEEeehhhhHHHHHHhcCCccCc
Q 019356 49 QLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHN 127 (342)
Q Consensus 49 ~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~~ 127 (342)
...+++++|..+.. ..+++++++++.++++|+|+.... ......|+++|+++.+.|++||+|.|.+.| ..+|+.+.+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~~~~~i~~~~~-~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~~~~ 80 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGGGAYYIPLELA-LLDLAALKEWLEDEKIPKVGHDAKRAYVAL-KRHGIELAG 80 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCCcEEEEeccch-HHHHHHHHHHHhCCCCceeccchhHHHHHH-HHCCCcCCC
Confidence 35678888887765 467999999998767888874321 013456889999999999999999999999 478998864
Q ss_pred -eehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHH
Q 019356 128 -VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLP 206 (342)
Q Consensus 128 -vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll 206 (342)
+|||++|+||++++.++ .++.+++. +|++.++.+.++. +++. .++ .++..+.+..|++.|+.+++
T Consensus 81 ~~fDt~laaYLL~p~~~~-------~~l~~l~~--~yl~~~~~~~~~~---~~~~-~~~-~~~~~~~~~~y~~~~a~~l~ 146 (178)
T cd06140 81 VAFDTMLAAYLLDPTRSS-------YDLADLAK--RYLGRELPSDEEV---YGKG-AKF-AVPDEEVLAEHLARKAAAIA 146 (178)
T ss_pred cchhHHHHHHHcCCCCCC-------CCHHHHHH--HHcCCCCcchHHh---cCCC-CCc-ccCCHHHHHHHHHHHHHHHH
Confidence 79999999999997432 48899999 9999876532221 1111 113 24446778899999999999
Q ss_pred HHHHHHHHHHhccccHHHHHhc
Q 019356 207 YIYHNMMKKLNQQSLWYLAVRG 228 (342)
Q Consensus 207 ~L~~~L~~~L~~~g~~~l~~~~ 228 (342)
.|++.|.++|++.+++.++.+-
T Consensus 147 ~l~~~l~~~L~~~~l~~L~~~i 168 (178)
T cd06140 147 RLAPKLEEELEENEQLELYYEV 168 (178)
T ss_pred HHHHHHHHHHHHhHHHHHHHHH
Confidence 9999999999999999988753
No 15
>PRK05755 DNA polymerase I; Provisional
Probab=99.70 E-value=4.3e-16 Score=168.49 Aligned_cols=183 Identities=24% Similarity=0.231 Sum_probs=147.1
Q ss_pred cCeEEeCCCCcccHHhhcccccCCceEEEEeeeeCCC-CCCcEEEEEEEeCCc-EEEEEcCCCChhHHHhhHHHhcCCCc
Q 019356 26 VPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDA-IYLVDAIQGGETVVKACKPALESSYI 103 (342)
Q Consensus 26 ~~i~~V~t~~~L~~~~l~~~l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~-~~liD~~~l~~~~~~~L~~lLe~~~i 103 (342)
++|.+|++.+++.. +++. +.....++||+|+.+.. +.++++++|++.+++ +++||+..+.......|.++|+++.+
T Consensus 294 ~~~~~I~~~~~L~~-~l~~-l~~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~v 371 (880)
T PRK05755 294 EDYETILDEEELEA-WLAK-LKAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPAI 371 (880)
T ss_pred CceEEeCCHHHHHH-HHHH-hhccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCCC
Confidence 56788988898886 8877 56778999999999885 788999999998655 88888754332456889999999999
Q ss_pred eEEEeehhhhHHHHHHhcCCcc-CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCC
Q 019356 104 TKVIHDCKRDSEALYFQFGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDP 182 (342)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~~Gi~l-~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~ 182 (342)
.||+||+++|+.+|. .+|+.+ .++|||++|+|+++++. ..||+.|++ +|+|.++...+. ++++ .
T Consensus 372 ~kV~HNakfDl~~L~-~~gi~~~~~~~DT~iAa~Ll~~~~--------~~~L~~L~~--~ylg~~~~~~~~---~~gk-~ 436 (880)
T PRK05755 372 KKVGQNLKYDLHVLA-RYGIELRGIAFDTMLASYLLDPGR--------RHGLDSLAE--RYLGHKTISFEE---VAGK-Q 436 (880)
T ss_pred cEEEeccHhHHHHHH-hCCCCcCCCcccHHHHHHHcCCCC--------CCCHHHHHH--HHhCCCccchHH---hcCC-C
Confidence 999999999999996 679887 46999999999999863 268999999 999987532221 1222 2
Q ss_pred CCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhcc-ccHHHHH
Q 019356 183 QFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ-SLWYLAV 226 (342)
Q Consensus 183 ~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~-g~~~l~~ 226 (342)
.+|+.+|+ +.+..||+.||.+++.|+..|.++|.+. +.+.++.
T Consensus 437 ~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l~~l~~ 480 (880)
T PRK05755 437 LTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEPGLLELYE 480 (880)
T ss_pred CCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHH
Confidence 46777787 5789999999999999999999999886 5555554
No 16
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.68 E-value=7.8e-16 Score=131.01 Aligned_cols=146 Identities=26% Similarity=0.317 Sum_probs=112.8
Q ss_pred eEEEEeeeeCCC-CCCcEEEEEEEeC-CcEEEEEcCCCChhHHHhhHHHhcCCCceEEEeehhhhHHHHHHhcCCccC-c
Q 019356 51 VIGFDCEGVDLC-RHGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLH-N 127 (342)
Q Consensus 51 ~Ia~D~E~~~~~-~~g~l~llQLa~~-~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~-~ 127 (342)
++++|+|+.+.. ..++++++|++.+ +++|++++... .-....|+++|+++.+.||+||+|.|...|. ..|+... +
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~-~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L~-~~~~~~~~~ 78 (150)
T cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHD-YLALELLKPLLEDEKALKVGQNLKYDRGILL-NYFIELRGI 78 (150)
T ss_pred CEEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCc-ccCHHHHHHHhcCCCCceeeecHHHHHHHHH-HcCCccCCc
Confidence 368899876544 3679999999986 44888875431 1024668999999999999999999999994 6777665 5
Q ss_pred eehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHH
Q 019356 128 VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPY 207 (342)
Q Consensus 128 vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~ 207 (342)
+|||++|+|++++..+ ..++..|++ +|++.++.+.++. ++ +.|..++++.+|..||+.|+.++.+
T Consensus 79 ~~D~~laayLl~p~~~-------~~~l~~l~~--~~l~~~~~~~~~~---~~---~~~~~~~~~~~~~~ya~~~a~~l~~ 143 (150)
T cd09018 79 AFDTMLEAYILNSVAG-------RWDMDSLVE--RWLGHKLIKFESI---AG---KLWFNQPLTEEQGRYAAEDADVTLQ 143 (150)
T ss_pred chhHHHHHHHhCCCCC-------CCCHHHHHH--HHhCCCcccHHHh---cC---CCCcccCCHHHHHHHHHHHHHHHHH
Confidence 8999999999998641 148899999 9999875432332 11 2486678899999999999999999
Q ss_pred HHHHHH
Q 019356 208 IYHNMM 213 (342)
Q Consensus 208 L~~~L~ 213 (342)
|++.|.
T Consensus 144 L~~~l~ 149 (150)
T cd09018 144 IHLKLW 149 (150)
T ss_pred HHHHhc
Confidence 999875
No 17
>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=99.60 E-value=4.9e-14 Score=124.97 Aligned_cols=168 Identities=27% Similarity=0.294 Sum_probs=126.3
Q ss_pred cCCceEEEEeeeeCCC-CCCcEEEEEEEeCCc-EEEEEcCC------CC-hhHHHhhHHHhcCCCceEEEeehhhhHHHH
Q 019356 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDA-IYLVDAIQ------GG-ETVVKACKPALESSYITKVIHDCKRDSEAL 117 (342)
Q Consensus 47 ~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~-~~liD~~~------l~-~~~~~~L~~lLe~~~i~KV~hd~k~Dl~~L 117 (342)
.+...+++|+|+.+.. ..++++.++++..++ .++++... .. ..++..|+.+|++..+.+|+||+++|+.+|
T Consensus 3 ~~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l 82 (193)
T cd06139 3 EKAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVL 82 (193)
T ss_pred ccCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHHH
Confidence 3567899999987664 467899999997643 77776432 11 234566889999988889999999999999
Q ss_pred HHhcCCccCc-eehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcC--CCCCCCCCCCcHHH
Q 019356 118 YFQFGIKLHN-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQ--DPQFWTYRPLTELM 194 (342)
Q Consensus 118 ~~~~Gi~l~~-vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~--~~~dW~~RPLs~~q 194 (342)
..+|+.+.+ ++||++++|++++... ..+|..+++ +|++......++ ++++ +..+|...|+ ..+
T Consensus 83 -~~~gi~~~~~~~Dt~l~a~ll~p~~~-------~~~l~~l~~--~~l~~~~~~~~~---~~~k~~~~~~~~~~~~-~~~ 148 (193)
T cd06139 83 -ANHGIELRGPAFDTMLASYLLNPGRR-------RHGLDDLAE--RYLGHKTISFED---LVGKGKKQITFDQVPL-EKA 148 (193)
T ss_pred -HHCCCCCCCCcccHHHHHHHhCCCCC-------CCCHHHHHH--HHhCCCCccHHH---HcCCCcCcCCccccCH-HHH
Confidence 478988754 8999999999998641 248899999 898876321122 1111 1234554454 668
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHhc-cccHHHHHhc
Q 019356 195 VRAAADDVRFLPYIYHNMMKKLNQ-QSLWYLAVRG 228 (342)
Q Consensus 195 l~YAA~Da~~Ll~L~~~L~~~L~~-~g~~~l~~~~ 228 (342)
..||+.|+.++++|++.|.++|++ .++++++.+-
T Consensus 149 ~~ya~~d~~~~~~l~~~l~~~l~~~~~~~~l~~~i 183 (193)
T cd06139 149 AEYAAEDADITLRLYELLKPKLKEEPGLLELYEEI 183 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHH
Confidence 899999999999999999999998 8888887744
No 18
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.54 E-value=3.3e-14 Score=146.72 Aligned_cols=156 Identities=19% Similarity=0.164 Sum_probs=126.6
Q ss_pred CeEEeCCCCcccHHhhcccccCCceEEEEeeeeCCCCCCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCceEE
Q 019356 27 PIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKV 106 (342)
Q Consensus 27 ~i~~V~t~~~L~~~~l~~~l~~~~~Ia~D~E~~~~~~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV 106 (342)
.+.+|++.+++.. ++.. +...+.+++|+|+..... .+|++|++.++..|+||+... +.
T Consensus 2 ~~~~I~~~~~l~~-~~~~-l~~~~~~a~DtEf~r~~t--~l~liQ~~~~~~~~liDpl~~-------l~----------- 59 (553)
T PRK14975 2 DMKVILAPEELGA-ALER-LSPAGVVAGDTETTGDDA--AAAAAQEGEEEPRWVWASTAA-------LY----------- 59 (553)
T ss_pred CceEEeccchhHH-HHHH-hccCCceeCCccccCCcc--hhheeeecCCCceEEECchHH-------hH-----------
Confidence 4678999999996 8887 788899999999886533 899999999899999997531 11
Q ss_pred EeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCC
Q 019356 107 IHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWT 186 (342)
Q Consensus 107 ~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~ 186 (342)
..| ..+|+.+.++||||+|+|+|++..+.. ..||+.++. +++++.+++ .+.+ ++|.
T Consensus 60 --------~~L-~~~Gv~~~~~fDT~LAa~lL~~~~~~~-----~~~l~~la~--~~l~~~l~k-~~~~-------sdw~ 115 (553)
T PRK14975 60 --------PRL-LAAGVRVERCHDLMLASQLLLGSEGRA-----GSSLSAAAA--RALGEGLDK-PPQT-------SALS 115 (553)
T ss_pred --------HHH-HHCCCccCCCchHHHHHHHcCCCCCcC-----CCCHHHHHH--HHhCCCCCC-hhhh-------cccc
Confidence 114 367999988999999999999864311 368999999 999999884 3322 4896
Q ss_pred CCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhcc------ccHHHHHhcc
Q 019356 187 YRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ------SLWYLAVRGA 229 (342)
Q Consensus 187 ~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~------g~~~l~~~~~ 229 (342)
||+++.|+.||+.||.+++.||+.|.++|++. |++.++..-+
T Consensus 116 -rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~~~~~~~g~l~ll~~~E 163 (553)
T PRK14975 116 -DPPDEEQLLYAAADADVLLELYAVLADQLNRIAAAAHPGRLRLLAAAE 163 (553)
T ss_pred -ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHH
Confidence 99999999999999999999999999999886 7777666443
No 19
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.47 E-value=4.7e-14 Score=141.71 Aligned_cols=190 Identities=23% Similarity=0.254 Sum_probs=137.0
Q ss_pred cCeEEeCCCCcccHHhh-cccccCCceEEEEeeeeCC-C-CCCcEEEEEEEeCCcEEEEEcCCCC---hhHH-HhhHHHh
Q 019356 26 VPIHIVTNASQLPAEFL-EPSSERQLVIGFDCEGVDL-C-RHGSLCIMQLAFPDAIYLVDAIQGG---ETVV-KACKPAL 98 (342)
Q Consensus 26 ~~i~~V~t~~~L~~~~l-~~~l~~~~~Ia~D~E~~~~-~-~~g~l~llQLa~~~~~~liD~~~l~---~~~~-~~L~~lL 98 (342)
..+.+|+++.++.. ++ +...++.-+||+|+||... . ...+++++|+++.+.+||||...+. .+.+ ..+..+|
T Consensus 390 ~~i~~V~~e~El~~-l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~if 468 (617)
T KOG2207|consen 390 ESIGMVGNEKELRD-LLLESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQIF 468 (617)
T ss_pred cceeeeCCHHHHHH-HHHHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHHc
Confidence 67889999999997 55 3322334789999999877 3 4779999999999999999988764 2222 3557799
Q ss_pred cCCCceEEEeehhhhHHHHHH-----hcCCccC---c-eehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccc
Q 019356 99 ESSYITKVIHDCKRDSEALYF-----QFGIKLH---N-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (342)
Q Consensus 99 e~~~i~KV~hd~k~Dl~~L~~-----~~Gi~l~---~-vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~ 169 (342)
+++++.|||++.++|++++.+ .+.+.+. + .-++.++..+.+-.-.-..+....-+|+.|.. ..+|.+++
T Consensus 469 ~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~--~llg~~ln 546 (617)
T KOG2207|consen 469 ESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTD--CLLGKKLN 546 (617)
T ss_pred cCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhH--HHhhhhcc
Confidence 999999999999999999974 2333332 2 33455555554432100011112357788887 88999988
Q ss_pred hhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHHHH
Q 019356 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAV 226 (342)
Q Consensus 170 kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l~~ 226 (342)
| .+.. ++|..|||+..|+.|||.|+.++..++.++.+..+....-+-..
T Consensus 547 K-teqc-------snWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~~~~~~ek~i 595 (617)
T KOG2207|consen 547 K-TEQC-------SNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVEHDADIEKFI 595 (617)
T ss_pred c-cccc-------chhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcchhhHHHHHH
Confidence 4 3322 59999999999999999999999999999988776433333333
No 20
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.36 E-value=5.6e-12 Score=128.68 Aligned_cols=182 Identities=23% Similarity=0.222 Sum_probs=130.4
Q ss_pred eCCCCcccHHhhcccccCCceEEEEeeeeCCC-CCCcEEEEEEEeCCcEEEEEcCC--CChhHHHhhHHHhcCCCceEEE
Q 019356 31 VTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQ--GGETVVKACKPALESSYITKVI 107 (342)
Q Consensus 31 V~t~~~L~~~~l~~~l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~--l~~~~~~~L~~lLe~~~i~KV~ 107 (342)
+.+.+.+.. +... ....+.+++|+|+.+.. ..+.++++.++..+.+++++... ..-.....|++||+++...|++
T Consensus 6 ~~~~~~~~~-~~~~-~~~~~~~a~~~et~~l~~~~~~lvg~s~~~~~~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~kv~ 83 (593)
T COG0749 6 ITDLAVLNA-WLTK-LNAAANIAFDTETDGLDPHGADLVGLSVASEEEAAYIPLLHGPEQLNVLAALKPLLEDEGIKKVG 83 (593)
T ss_pred hhHHHHHHH-HHHH-HhhcccceeeccccccCcccCCeeEEEeeccccceeEeeccchhhhhhHHHHHHHhhCcccchhc
Confidence 334444453 5544 23334499999999887 46688888888865666665543 1123568999999999999999
Q ss_pred eehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCC--CC
Q 019356 108 HDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQ--FW 185 (342)
Q Consensus 108 hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~--dW 185 (342)
||.|.|.+.| +.+|+.....||||+|+|+++++.++ ++++.|++ +|++.+....+.. .++... ++
T Consensus 84 ~~~K~d~~~l-~~~Gi~~~~~~DtmlasYll~~~~~~-------~~~~~l~~--r~l~~~~~~~~~i---~~kg~~~~~~ 150 (593)
T COG0749 84 QNLKYDYKVL-ANLGIEPGVAFDTMLASYLLNPGAGA-------HNLDDLAK--RYLGLETITFEDI---AGKGKKQLTF 150 (593)
T ss_pred cccchhHHHH-HHcCCcccchHHHHHHHhccCcCcCc-------CCHHHHHH--HhcCCccchhHHh---hccccccCcc
Confidence 9999999999 57886645689999999999998654 46789999 9988766532222 122212 23
Q ss_pred CCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhcccc-HHHHHhc
Q 019356 186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSL-WYLAVRG 228 (342)
Q Consensus 186 ~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~-~~l~~~~ 228 (342)
...++ +....|+|.||..+++|+..|..+|.+... ..++..-
T Consensus 151 ~~~~~-~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L~~l~~~i 193 (593)
T COG0749 151 ADVKL-EKATEYAAEDADATLRLESILEPELLKTPVLLELYEEI 193 (593)
T ss_pred ccchH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHH
Confidence 33333 566899999999999999999998877654 5555533
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=99.27 E-value=1.2e-10 Score=125.71 Aligned_cols=178 Identities=17% Similarity=0.079 Sum_probs=125.1
Q ss_pred eEEeCCCCcccHHhhcccccCCceEEEEeeeeCCC-CCCcEEEEEEEeCC--cEEEEEcCC---CC-hhHHHhhHHHhcC
Q 019356 28 IHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPD--AIYLVDAIQ---GG-ETVVKACKPALES 100 (342)
Q Consensus 28 i~~V~t~~~L~~~~l~~~l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~--~~~liD~~~---l~-~~~~~~L~~lLe~ 100 (342)
+..+++.+++.. +++. ...+.+++ .+.. ....+.++.+++++ ..|+++... +. ......|+++|++
T Consensus 304 ~~~~~~~~~~~~-~~~~--~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 376 (887)
T TIGR00593 304 AKESEEAAPLAN-PAEK--AEVGGFVL----ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLN 376 (887)
T ss_pred ceEeCCHHHHHH-HHHh--CcCCeEEE----cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhC
Confidence 445655566664 5543 33446676 2232 35678889999853 467765321 11 2335668999999
Q ss_pred CCceEEEeehhhhHHHHHHhcCCccCc-eehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhc
Q 019356 101 SYITKVIHDCKRDSEALYFQFGIKLHN-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLR 179 (342)
Q Consensus 101 ~~i~KV~hd~k~Dl~~L~~~~Gi~l~~-vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~ 179 (342)
+.+.||+||+|+|+.+|. .+|+.+.+ +||||+|+||++++. ..+|+.++. +|++......+.. .+
T Consensus 377 ~~~~~v~~n~K~d~~~l~-~~gi~~~~~~~Dt~la~yll~~~~--------~~~l~~la~--~yl~~~~~~~~~~---~~ 442 (887)
T TIGR00593 377 EQIKKIGHDAKFLMHLLK-REGIELGGVIFDTMLAAYLLDPAQ--------VSTLDTLAR--RYLVEELILDEKI---GG 442 (887)
T ss_pred CCCcEEEeeHHHHHHHHH-hCCCCCCCcchhHHHHHHHcCCCC--------CCCHHHHHH--HHcCcccccHHHh---cc
Confidence 999999999999999994 79998865 899999999999863 248899999 9998664421221 11
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHHHHhc
Q 019356 180 QDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRG 228 (342)
Q Consensus 180 ~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l~~~~ 228 (342)
+. ..+...| .+.+..||+.||.++++|+..|.++|++.+++.++.+-
T Consensus 443 ~~-~~~~~~~-~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~l~~l~~~i 489 (887)
T TIGR00593 443 KL-AKFAFPP-LEEATEYLARRAAATKRLAEELLKELDENKLLSLYREI 489 (887)
T ss_pred CC-CCccccc-HHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHH
Confidence 11 1222222 25577899999999999999999999988888887643
No 22
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.22 E-value=8.7e-12 Score=119.44 Aligned_cols=220 Identities=28% Similarity=0.230 Sum_probs=157.6
Q ss_pred CCCcEEEEEEEeCCcEEEEEcCCCChh-HHHhhHHHhcCCCceEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccc
Q 019356 63 RHGSLCIMQLAFPDAIYLVDAIQGGET-VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQ 141 (342)
Q Consensus 63 ~~g~l~llQLa~~~~~~liD~~~l~~~-~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~ 141 (342)
..+.+..++++++++.|++|...-+.. +....++.|++.++ +. |++.+...+...|++.+.+++|||+|+.++.+.
T Consensus 209 ~~~e~~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~sLve~~ 285 (458)
T KOG2405|consen 209 LALEATYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIASSLVEPS 285 (458)
T ss_pred hhhhhhhhhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHHHHhhhH
Confidence 356677799999999999997655432 23457788888765 55 999999999999999999999999999999987
Q ss_pred c-CC-CCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhcc
Q 019356 142 E-GR-KRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ 219 (342)
Q Consensus 142 ~-~~-~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~ 219 (342)
+ ++ +.. ...+++..|..+..|.+.+...+++++.++..++.+|..||.++.+..-++.||.+|+... ..|...
T Consensus 286 e~grr~p~-~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~----~~l~a~ 360 (458)
T KOG2405|consen 286 EYGRRHPT-SILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIF----DTLVAV 360 (458)
T ss_pred HhcccCCc-cceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHH----hhHhhh
Confidence 6 33 322 1244554444323456666665677777777777889999999999999999999998844 556667
Q ss_pred ccHHHHHhcccccccccc-CCCCCCCCCCCCCCCCcce--e-----cc-c-----------------cccccCCCChhhh
Q 019356 220 SLWYLAVRGALYCRCFCI-NENDYVDWPPLPPVPGVRF--I-----YV-D-----------------YLIVEGDVPEEEI 273 (342)
Q Consensus 220 g~~~l~~~~~~~~r~~~~-~~~~~~~w~~~~~~~~~~~--~-----~~-~-----------------~l~~~~~~~~~~~ 273 (342)
..|.+..+...+.+|.+. .......|+.-|+.+-+-. + |+ + .+.+++---.+++
T Consensus 361 ~l~HL~~rp~~e~ecie~~~~~~~~~~p~gpe~QrFt~kp~~as~~r~~r~~~~lSi~~~~~~n~a~~~~aEd~~~s~e~ 440 (458)
T KOG2405|consen 361 CLSHLTRRPYTEPECIELVFGLPMEKVPGGPESQRFTAKPLTASQMRYLRKLVQLSIIMHDHLNYAHIFCAEDYRISLEF 440 (458)
T ss_pred ChHhhccCCccccchhhhcCCcchhhCCCCCCCCceeecceecchHHHHHHhhhhhhhhhhccchhhhhcccchhHHHHH
Confidence 888888899999999964 3445667887777663211 0 00 1 1111111245677
Q ss_pred hhhcCCC-CCCCceeecc
Q 019356 274 LSILDVP-PGKMGRIIGR 290 (342)
Q Consensus 274 ~~~~~~~-~~~~~~~~~~ 290 (342)
.+.++.| +++|+.++++
T Consensus 441 ~s~~s~p~~~~V~~v~~~ 458 (458)
T KOG2405|consen 441 SSSYSGPRSCDVAIVMAP 458 (458)
T ss_pred HHhhcCCCCcccccccCC
Confidence 8888998 8888877653
No 23
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=99.01 E-value=1.6e-08 Score=86.70 Aligned_cols=132 Identities=21% Similarity=0.223 Sum_probs=91.4
Q ss_pred CCcEEEEEEEeCCcEEEEEcCCCChhHHHhhHHHhcCCCceEEEeehhhhHHHHHHhcCCccCc-eehHHHHHHhhcccc
Q 019356 64 HGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHN-VVDTQIAYSLIEEQE 142 (342)
Q Consensus 64 ~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~~-vfDtqlAa~LL~~~~ 142 (342)
.+++.++.++.++++|+|+... ... ...|+++|++..+.|++||.|.+...| +.+|+.+.+ +|||++|+|||+|..
T Consensus 17 ~~~~~glal~~~~~~~yi~~~~-~~~-~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~~LAaYLL~p~~ 93 (151)
T cd06128 17 SANLVGLAFAIEGVAAYIPVAH-DYA-LELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDTMLEAYLLDPVA 93 (151)
T ss_pred cCcEEEEEEEcCCCeEEEeCCC-CcC-HHHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhHHHHHHHcCCCC
Confidence 4567778888765677775321 001 345889999999999999999999999 588998875 699999999999974
Q ss_pred CCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCC-cHHHHHHHHHHhHHHHHHHHHHH
Q 019356 143 GRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPL-TELMVRAAADDVRFLPYIYHNMM 213 (342)
Q Consensus 143 ~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPL-s~~ql~YAA~Da~~Ll~L~~~L~ 213 (342)
+. .+++++++ +|++..+..-++ ++++. .... ++ ......|++..+.++.+|++.|.
T Consensus 94 ~~-------~~l~~la~--~yl~~~~~~~~~---~~gkg-~~~~--~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 94 GR-------HDMDSLAE--RWLKEKTITFEE---IAGKG-LTFN--QIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CC-------CCHHHHHH--HHcCCCCccHHH---HcCCC-CChh--hcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 21 27799999 898876321112 22221 1001 12 12234488888888999988874
No 24
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.21 E-value=1.3e-06 Score=63.84 Aligned_cols=59 Identities=29% Similarity=0.442 Sum_probs=54.4
Q ss_pred cCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhhHHHHHHHhh
Q 019356 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAMLR 335 (342)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 335 (342)
..||+...+.+||++|++|..|.+.+++.|.|.....+.+.|.|.|+..+|.+|.++|.
T Consensus 4 i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 4 VEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred EEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHhC
Confidence 46788889999999999999999999999999988888889999999999999998863
No 25
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=98.02 E-value=1.3e-05 Score=76.35 Aligned_cols=129 Identities=17% Similarity=0.197 Sum_probs=93.7
Q ss_pred CCcEEEEEEEeC-CcEEEEEcCCCChhHHHhhHHHhcCCCceEEEeehhhhHHHHHH-hcCCccCceehHHHHHHhhccc
Q 019356 64 HGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYF-QFGIKLHNVVDTQIAYSLIEEQ 141 (342)
Q Consensus 64 ~g~l~llQLa~~-~~~~liD~~~l~~~~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~-~~Gi~l~~vfDtqlAa~LL~~~ 141 (342)
.+....+|||++ +.++++....-+ .+...|+.+|+|+..++|+-+..+|...|.+ .|++.+..+.|+... ++..
T Consensus 146 ~P~~~~lqlcV~en~C~I~ql~~~~-~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~---~~d~ 221 (319)
T KOG4373|consen 146 DPPPDTLQLCVGENRCLIIQLIHCK-RIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLL---VNDS 221 (319)
T ss_pred CCCcchhhhhhcccceeeEEeeccc-cchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhh---cchh
Confidence 446788999997 778888655433 3678888899999999999999999999987 788888777777652 2222
Q ss_pred cCCCCCCCCCCcHHHhhcCcccc---C--CccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHH
Q 019356 142 EGRKRSPDDYISFVGLLADPRYC---G--ISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (342)
Q Consensus 142 ~~~~~L~~~~~sL~~Lv~~~~~L---g--~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~ 209 (342)
.+. .++ .-++..|++ ..+ | +.+++ .. +.++|+..||+.+|+.||+.||+....|+
T Consensus 222 ~g~-~~~--~~s~e~i~~--~~~~~~~~~v~l~~--~i------~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 222 LGG-SMP--NDSFEEIVS--ETLGYYGKDVRLDK--EI------RMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred hcc-Ccc--CccHHHHHH--HHhhccccccccCh--hc------ccccceeeeccHHHHHHHHhHHHHHHHHH
Confidence 221 221 234455555 333 3 33332 12 23799999999999999999999999999
No 26
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=97.95 E-value=7.7e-07 Score=85.92 Aligned_cols=151 Identities=32% Similarity=0.533 Sum_probs=103.2
Q ss_pred CCceEEEEeeeeCCCCCCcEEEEEEEeCCcEEEEEcCCCChhH-HHhhHHHhcCCCceEEEeehhhhHHHHHHhcCCccC
Q 019356 48 RQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETV-VKACKPALESSYITKVIHDCKRDSEALYFQFGIKLH 126 (342)
Q Consensus 48 ~~~~Ia~D~E~~~~~~~g~l~llQLa~~~~~~liD~~~l~~~~-~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~ 126 (342)
.+... +-.|+++..++|++|.+|.++.-.+|++|+..++..+ ...|..++++..|.|+.|+|+.-+.++.+.|||..+
T Consensus 58 ~qn~~-~~~e~a~~~~~~~l~~~q~~~~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n 136 (458)
T KOG2405|consen 58 KQNVL-VAAEGANVCRHGKLCWLQVATNCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLN 136 (458)
T ss_pred hhcCc-ccccCccccccCcchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeec
Confidence 33443 5667777778999999999988889999998888644 467788999999999999999999999999999999
Q ss_pred ceehHHHHHHhhccccCCCCCCCCCCcHHH-hhcCccccCCccc-----hhHHHHHHhcCCCCCCCCCCCcHHHHHHHHH
Q 019356 127 NVVDTQIAYSLIEEQEGRKRSPDDYISFVG-LLADPRYCGISYQ-----EKEEVRVLLRQDPQFWTYRPLTELMVRAAAD 200 (342)
Q Consensus 127 ~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~-Lv~~~~~Lg~~l~-----kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~ 200 (342)
++|||+++.-+-....+...++..-..+.. |.+ .|.+.+. .|.+ .+.-+++..|-.||.++..+.--+.
T Consensus 137 ~v~~~q~~d~~q~~~e~g~~~~n~~~~~q~sl~k---h~~~a~k~~~~l~~r~--~~~~~n~e~~~i~~~~~s~~~~~~~ 211 (458)
T KOG2405|consen 137 NVFDTQVADVLQFSMETGGYLPNCITTLQESLIK---HLQVAPKYLSFLEKRQ--KLIQENPEVWFIRPVSPSLLKILAL 211 (458)
T ss_pred chhhhhhhhhhhhcccccccCCccccchHHHHHH---HHHhcccHHHHHHHHH--HHHhhCcceeEeecCchhHHHhhhh
Confidence 999999976554332222222222223322 222 2221110 0111 1112456779999999888777666
Q ss_pred HhHH
Q 019356 201 DVRF 204 (342)
Q Consensus 201 Da~~ 204 (342)
.+.+
T Consensus 212 e~~~ 215 (458)
T KOG2405|consen 212 EATY 215 (458)
T ss_pred hhhh
Confidence 6655
No 27
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=97.78 E-value=3.1e-05 Score=56.33 Aligned_cols=59 Identities=36% Similarity=0.501 Sum_probs=51.0
Q ss_pred hcCCCCCCCceeeccCCchHHHHHHhhcchhhcccCC--CCCCeEEEecchhhHHHHHHHh
Q 019356 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAK--GPPDKVFIIGPVKQVRKAEAML 334 (342)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 334 (342)
...||....+.+||++|++|..|.+.+++.|.|...+ ...+.|.|.|+.+++.+|..+|
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 3467888899999999999999999999999888654 4566799999999999999876
No 28
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=97.70 E-value=4.7e-05 Score=56.30 Aligned_cols=58 Identities=36% Similarity=0.559 Sum_probs=50.9
Q ss_pred cCCCCCCCceeeccCCchHHHHHHhhcchhhcccCC--CCCCe-EEEecchhhHHHHHHHh
Q 019356 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAK--GPPDK-VFIIGPVKQVRKAEAML 334 (342)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~~~~~~~ 334 (342)
.-||...++.+||+.|.+|..|.+..+|.|.|.-.. +++++ |-|.|+..++.+|..++
T Consensus 4 ~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 4 LLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 357888999999999999999999999999998766 46777 47889999999998875
No 29
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=97.52 E-value=0.00038 Score=55.50 Aligned_cols=72 Identities=24% Similarity=0.166 Sum_probs=54.5
Q ss_pred EEEEeeeeCCC-CCCcEEEEEEEeC--CcEEEEEcCCCChhHHHhhHHHhcCCC-ceEEEeehhhhHHHHHHhc---CCc
Q 019356 52 IGFDCEGVDLC-RHGSLCIMQLAFP--DAIYLVDAIQGGETVVKACKPALESSY-ITKVIHDCKRDSEALYFQF---GIK 124 (342)
Q Consensus 52 Ia~D~E~~~~~-~~g~l~llQLa~~--~~~~liD~~~l~~~~~~~L~~lLe~~~-i~KV~hd~k~Dl~~L~~~~---Gi~ 124 (342)
+++|+|+.+.. ...+++++|++.+ +..|++| +.+++++.. ..+|+||+.+|...|.+.+ |+.
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~~~-----------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~ 69 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAVID-----------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLK 69 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEEeh-----------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCC
Confidence 47999998875 6789999999875 6677775 556777765 6789999999998876543 332
Q ss_pred ----cCceehHHHH
Q 019356 125 ----LHNVVDTQIA 134 (342)
Q Consensus 125 ----l~~vfDtqlA 134 (342)
....+||+.+
T Consensus 70 ~p~~~~~~lDT~~l 83 (96)
T cd06125 70 YPLLAGSWIDTIKL 83 (96)
T ss_pred CCCcCCcEEEehHH
Confidence 2458899987
No 30
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=97.46 E-value=1.5e-05 Score=57.74 Aligned_cols=57 Identities=40% Similarity=0.618 Sum_probs=48.5
Q ss_pred cCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhhHHHHHHHh
Q 019356 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAML 334 (342)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 (342)
..||+...+++||++|++|..|.+.+++.|.|-.. +..+.|.|.|+.++|.+|.+++
T Consensus 4 i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 4 IEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-TEEEEEEEEESHHHHHHHHHHH
T ss_pred EEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-CCcEEEEEEeCHHHHHHHHhhC
Confidence 45677778999999999999999999999999553 2234688999999999999875
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=97.45 E-value=0.00024 Score=51.37 Aligned_cols=61 Identities=33% Similarity=0.443 Sum_probs=52.8
Q ss_pred cCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhhHHHHHHHhhhc
Q 019356 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAMLRGR 337 (342)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 337 (342)
..||+..++.+||++|++|..|.+.+++.|.+...+.....+.|.|+..++.+|...+...
T Consensus 7 i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~ 67 (69)
T smart00322 7 VLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEI 67 (69)
T ss_pred EEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHH
Confidence 4578888999999999999999999999999976554456799999999999999888653
No 32
>PRK07740 hypothetical protein; Provisional
Probab=97.26 E-value=0.0092 Score=55.65 Aligned_cols=142 Identities=17% Similarity=0.237 Sum_probs=89.5
Q ss_pred ccCCceEEEEeeeeCCCCCCcEEEEEEEe----CCcE------EEEEcCC-----------CC----------hhHHHhh
Q 019356 46 SERQLVIGFDCEGVDLCRHGSLCIMQLAF----PDAI------YLVDAIQ-----------GG----------ETVVKAC 94 (342)
Q Consensus 46 l~~~~~Ia~D~E~~~~~~~g~l~llQLa~----~~~~------~liD~~~-----------l~----------~~~~~~L 94 (342)
+.+...+.||+|+.+.+....-.+++|+. ++.. .++.+.. +. .+++..+
T Consensus 56 ~~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl~~f 135 (244)
T PRK07740 56 LTDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRF 135 (244)
T ss_pred ccCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHHHHH
Confidence 45568999999998875221112455553 2222 1222211 01 1233455
Q ss_pred HHHhcCCCceEEEeehhhhHHHHHHh----cCCcc-CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccc
Q 019356 95 KPALESSYITKVIHDCKRDSEALYFQ----FGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (342)
Q Consensus 95 ~~lLe~~~i~KV~hd~k~Dl~~L~~~----~Gi~l-~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~ 169 (342)
..++.+. .-|+||+.+|...|.+. ++... ..++||+..+..+.+.. ...+|.++++ ++|++..
T Consensus 136 ~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~-------~~~sL~~l~~---~~gi~~~ 203 (244)
T PRK07740 136 YAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHER-------DFPTLDDALA---YYGIPIP 203 (244)
T ss_pred HHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCC-------CCCCHHHHHH---HCCcCCC
Confidence 5556553 45899999999888532 33333 35899999888776542 1468999996 6787654
Q ss_pred hhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHH
Q 019356 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (342)
Q Consensus 170 kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~ 223 (342)
.. + + |..||..+..|+..+..++.+.|...
T Consensus 204 ~~-H----------~-------------Al~Da~ata~l~~~ll~~~~~~~~~~ 233 (244)
T PRK07740 204 RR-H----------H-------------ALGDALMTAKLWAILLVEAQQRGITT 233 (244)
T ss_pred CC-C----------C-------------cHHHHHHHHHHHHHHHHHHHHcCCcC
Confidence 21 1 1 77899999999999999998766443
No 33
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.21 E-value=0.00045 Score=50.50 Aligned_cols=55 Identities=29% Similarity=0.509 Sum_probs=48.5
Q ss_pred hcCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecc-hhhHHHHHHHh
Q 019356 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGP-VKQVRKAEAML 334 (342)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 334 (342)
...||+.+.+++||+.|++|..|.+..++.|.|.- . ..|-|.|+ ...+.+|.+++
T Consensus 5 ~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-~---g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 5 TMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-D---GTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred EEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-C---CEEEEEeCCHHHHHHHHHHh
Confidence 45789999999999999999999999999999976 2 47999999 77888888775
No 34
>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=97.03 E-value=0.022 Score=51.47 Aligned_cols=85 Identities=15% Similarity=0.158 Sum_probs=60.3
Q ss_pred eEEEeehhhhHHHHHHh---cCCc-----cCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHH
Q 019356 104 TKVIHDCKRDSEALYFQ---FGIK-----LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVR 175 (342)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~---~Gi~-----l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~ 175 (342)
.-|+||+.+|+.+|.+. +|.. ...++||...+..+.+. .+|..+++ ++|++... .+
T Consensus 107 ~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~~----------~~L~~l~~---~~gi~~~~-~~-- 170 (200)
T TIGR01298 107 ILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYGQ----------TVLAKACQ---AAGXDFDS-TQ-- 170 (200)
T ss_pred EEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcCc----------ccHHHHHH---HcCCCccc-cc--
Confidence 46999999999998643 3432 12379999887755432 46888886 55765421 01
Q ss_pred HHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHH
Q 019356 176 VLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (342)
Q Consensus 176 ~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~ 223 (342)
..-|..||..+..|+..|..++.+.|.|.
T Consensus 171 -------------------~H~Al~Da~ata~lf~~l~~~~~~~~~~~ 199 (200)
T TIGR01298 171 -------------------AHSALYDTEKTAELFCEIVNRWKRLGGWP 199 (200)
T ss_pred -------------------hhhhHHhHHHHHHHHHHHHHHHHHccCCC
Confidence 12277899999999999999998888774
No 35
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.01 E-value=0.013 Score=56.77 Aligned_cols=97 Identities=22% Similarity=0.224 Sum_probs=69.6
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHHh---cCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCcccc
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~---~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~L 164 (342)
++..|..++.+. .-|+||+.+|+.+|.+. +|+.. ...+||+..+..+.+... .++|.+|++ ++
T Consensus 84 v~~~l~~~l~~~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~-------~~kL~~l~~---~~ 151 (313)
T PRK06063 84 IAGEVAELLRGR--TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLP-------NLRLETLAA---HW 151 (313)
T ss_pred HHHHHHHHcCCC--EEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCC-------CCCHHHHHH---Hc
Confidence 445667777654 45999999999998643 45543 358999988877665432 357889996 66
Q ss_pred CCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccH
Q 019356 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLW 222 (342)
Q Consensus 165 g~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~ 222 (342)
|++... .| + |..||.++..|+..+.+++.+.+.|
T Consensus 152 gi~~~~-~H----------~-------------Al~DA~ata~l~~~ll~~~~~~~~~ 185 (313)
T PRK06063 152 GVPQQR-PH----------D-------------ALDDARVLAGILRPSLERARERDVW 185 (313)
T ss_pred CCCCCC-CC----------C-------------cHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 765431 11 1 7789999999999999999887764
No 36
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.51 E-value=0.044 Score=50.06 Aligned_cols=141 Identities=15% Similarity=0.093 Sum_probs=84.2
Q ss_pred ccCCceEEEEeeeeCCCCCCcEEEEEEEe----CCc------EEEEEcCC-C----------C----------hhHHHhh
Q 019356 46 SERQLVIGFDCEGVDLCRHGSLCIMQLAF----PDA------IYLVDAIQ-G----------G----------ETVVKAC 94 (342)
Q Consensus 46 l~~~~~Ia~D~E~~~~~~~g~l~llQLa~----~~~------~~liD~~~-l----------~----------~~~~~~L 94 (342)
+.....+.||+|+.++..... +++|+. .+. ..++.+.. + . .+++..+
T Consensus 4 l~~~~fvv~D~ETTGl~~~~~--IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~ 81 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAGHD--IIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDF 81 (217)
T ss_pred EEecCEEEEEecCCCCCCCCC--EEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHH
Confidence 345688999999998763222 455542 111 22333321 0 0 1234556
Q ss_pred HHHhcCCCceEEEeehhhhHHHHHHhcC---Cc--c-CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCcc
Q 019356 95 KPALESSYITKVIHDCKRDSEALYFQFG---IK--L-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (342)
Q Consensus 95 ~~lLe~~~i~KV~hd~k~Dl~~L~~~~G---i~--l-~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l 168 (342)
..++.+. .-|+||+.+|..+|.+.+. .. . ..++||.-.++.+.+.... ...+|..+++ ++|++.
T Consensus 82 ~~~~~~~--~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~-----~~~~L~~l~~---~~gl~~ 151 (217)
T TIGR00573 82 ADYIRGA--ELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPG-----KRNTLDALCK---RYEITN 151 (217)
T ss_pred HHHhCCC--EEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCC-----CCCCHHHHHH---HcCCCC
Confidence 6666653 3589999999999975532 21 1 3478988766655443211 2468899986 457543
Q ss_pred chhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccc
Q 019356 169 QEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (342)
Q Consensus 169 ~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g 220 (342)
.. .. ..+ |..||.++..|+..+.++..+.+
T Consensus 152 ~~-~~--------~H~-------------Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 152 SH-RA--------LHG-------------ALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred CC-cc--------cCC-------------HHHHHHHHHHHHHHHHhcchhhc
Confidence 20 00 011 77899999999999988766533
No 37
>PRK07883 hypothetical protein; Validated
Probab=96.41 E-value=0.058 Score=56.26 Aligned_cols=197 Identities=16% Similarity=0.100 Sum_probs=111.8
Q ss_pred ccCCceEEEEeeeeCCCC-CCcEEEEEEEe----CCc-----EEEEEcCC-----------CC----------hhHHHhh
Q 019356 46 SERQLVIGFDCEGVDLCR-HGSLCIMQLAF----PDA-----IYLVDAIQ-----------GG----------ETVVKAC 94 (342)
Q Consensus 46 l~~~~~Ia~D~E~~~~~~-~g~l~llQLa~----~~~-----~~liD~~~-----------l~----------~~~~~~L 94 (342)
+.+...+.||+|+.+++. .+. +++|+. .+. ..+|++.. +. .+++..+
T Consensus 12 ~~~~~~Vv~D~ETTGl~p~~~~--IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f 89 (557)
T PRK07883 12 LRDVTFVVVDLETTGGSPAGDA--ITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAF 89 (557)
T ss_pred CcCCCEEEEEEecCCCCCCCCe--EEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHH
Confidence 556789999999998753 233 444442 221 23444321 11 1234566
Q ss_pred HHHhcCCCceEEEeehhhhHHHHHH---hcCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccc
Q 019356 95 KPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (342)
Q Consensus 95 ~~lLe~~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~ 169 (342)
..++.+. ..|+||+.+|...|.+ .+|+.. ...+||+..+.-+-+.... ...+|.+|++ ++|++..
T Consensus 90 ~~fl~~~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~-----~~~~L~~L~~---~~gi~~~ 159 (557)
T PRK07883 90 LEFARGA--VLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEA-----PNVRLSTLAR---LFGATTT 159 (557)
T ss_pred HHHhcCC--EEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCC-----CCCCHHHHHH---HCCcccC
Confidence 6677653 4589999999999864 356654 2478998866544331111 2468899985 6787643
Q ss_pred hhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHHHHhccccccccccCCCCCCCCCCCC
Q 019356 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCFCINENDYVDWPPLP 249 (342)
Q Consensus 170 kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l~~~~~~~~r~~~~~~~~~~~w~~~~ 249 (342)
. .| -|..||.++..|+..+.+++.+.|...+..--...................+|
T Consensus 160 ~-~H-----------------------~Al~DA~ata~l~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~lP 215 (557)
T PRK07883 160 P-TH-----------------------RALDDARATVDVLHGLIERLGNLGVHTLEELLTYLPRVTPAQRRKRHLADGLP 215 (557)
T ss_pred C-CC-----------------------CHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHhhhhcChhhhcchHHHhhCC
Confidence 1 11 27899999999999999999875543322211110110000001223346688
Q ss_pred CCCCcceeccc--cccccCCC--ChhhhhhhcC
Q 019356 250 PVPGVRFIYVD--YLIVEGDV--PEEEILSILD 278 (342)
Q Consensus 250 ~~~~~~~~~~~--~l~~~~~~--~~~~~~~~~~ 278 (342)
..||+=..++. .+..++.. .+..+.+-.+
T Consensus 216 ~~PGVY~~~d~~g~viYVGKAknLr~Rv~sYF~ 248 (557)
T PRK07883 216 HAPGVYLFRGPSGEVLYVGTAVNLRRRVRSYFT 248 (557)
T ss_pred CCceEEEEECCCCcEEEeehhhhHHHHHHHHcC
Confidence 88888555552 34444443 3555554443
No 38
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.39 E-value=0.087 Score=48.70 Aligned_cols=82 Identities=12% Similarity=0.174 Sum_probs=56.1
Q ss_pred ceEEEeehhhhHHHHHHh---cCCc---cCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHH
Q 019356 103 ITKVIHDCKRDSEALYFQ---FGIK---LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRV 176 (342)
Q Consensus 103 i~KV~hd~k~Dl~~L~~~---~Gi~---l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~ 176 (342)
...|+||+.+|...|.+. +|+. ...++||...+..+.+... ...+|.+|++ ++|++... .+
T Consensus 94 ~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~------~~~~L~~l~~---~~gi~~~~-aH--- 160 (232)
T PRK07942 94 VPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRK------GKRTLTALCE---HYGVRLDN-AH--- 160 (232)
T ss_pred CEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccC------CCCCHHHHHH---HcCCCCCC-CC---
Confidence 345999999999888543 4543 2358999988776654321 1357899996 56776541 11
Q ss_pred HhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 019356 177 LLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (342)
Q Consensus 177 l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (342)
+ |..||.++..|+..|.++..
T Consensus 161 -------~-------------Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 161 -------E-------------ATADALAAARVAWALARRFP 181 (232)
T ss_pred -------C-------------hHHHHHHHHHHHHHHHHHHH
Confidence 1 77899999999988877665
No 39
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.32 E-value=0.21 Score=46.66 Aligned_cols=134 Identities=18% Similarity=0.221 Sum_probs=83.4
Q ss_pred ccCCceEEEEeeeeCCC-CCCcEEEEEEEe----CC-----cEEEEEcCC-C----------Ch----------hHHHhh
Q 019356 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PD-----AIYLVDAIQ-G----------GE----------TVVKAC 94 (342)
Q Consensus 46 l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~----~~-----~~~liD~~~-l----------~~----------~~~~~L 94 (342)
+.+...+.||+|+.+.. ...+ +++|+. .+ -..+|.+.. + .+ ++...+
T Consensus 4 l~~~~~v~~D~ETTGl~~~~d~--IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~ 81 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDVKKDR--IIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQI 81 (250)
T ss_pred ccCCcEEEEEEeCCCCCCCCCe--EEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHH
Confidence 34567899999999875 3333 344432 22 223454321 1 10 233456
Q ss_pred HHHhcCCCceEEEeehhhhHHHHHHh---cCCcc----CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCc
Q 019356 95 KPALESSYITKVIHDCKRDSEALYFQ---FGIKL----HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGIS 167 (342)
Q Consensus 95 ~~lLe~~~i~KV~hd~k~Dl~~L~~~---~Gi~l----~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~ 167 (342)
.+++.+.. .-|+||+.+|...|.+. .|+.. ..++||+-.++.+... ...+|++|++ ++|++
T Consensus 82 ~~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~--------~~~~L~~l~~---~~g~~ 149 (250)
T PRK06310 82 KGFFKEGD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDS--------PNNSLEALAV---HFNVP 149 (250)
T ss_pred HHHhCCCC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccC--------CCCCHHHHHH---HCCCC
Confidence 66666533 45999999999998543 35543 3489999877765421 1368889986 45765
Q ss_pred cchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 019356 168 YQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (342)
Q Consensus 168 l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (342)
... .+ + |..||.++..++..+..++.
T Consensus 150 ~~~-aH----------~-------------Al~Da~at~~vl~~l~~~~~ 175 (250)
T PRK06310 150 YDG-NH----------R-------------AMKDVEINIKVFKHLCKRFR 175 (250)
T ss_pred CCC-Cc----------C-------------hHHHHHHHHHHHHHHHHhcc
Confidence 431 11 1 77899999999999887663
No 40
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=96.26 E-value=0.043 Score=47.42 Aligned_cols=87 Identities=20% Similarity=0.196 Sum_probs=56.4
Q ss_pred HHhhHHHhcCCCceEEEeehhhhHHHHHHh---cCCc-----cCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCcc
Q 019356 91 VKACKPALESSYITKVIHDCKRDSEALYFQ---FGIK-----LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPR 162 (342)
Q Consensus 91 ~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~---~Gi~-----l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~ 162 (342)
...|.+++++.. .|+||+.+|..+|.+. +|+. ....+||+..+..+.+.. ..+|+++++
T Consensus 72 ~~~l~~~l~~~~--lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~--------~~~L~~l~~--- 138 (167)
T cd06131 72 ADEFLDFIRGAE--LVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGK--------PNSLDALCK--- 138 (167)
T ss_pred HHHHHHHHCCCe--EEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCC--------CCCHHHHHH---
Confidence 456666776643 4899999999888543 3332 134799987766554321 358899996
Q ss_pred ccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHH
Q 019356 163 YCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (342)
Q Consensus 163 ~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L 212 (342)
++|++...+. ..-|..||..+..|+..|
T Consensus 139 ~~~i~~~~~~----------------------~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 139 RFGIDNSHRT----------------------LHGALLDAELLAEVYLEL 166 (167)
T ss_pred HCCCCCCCCC----------------------CCChHHHHHHHHHHHHHh
Confidence 5576543100 112778999998888665
No 41
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=96.24 E-value=0.18 Score=49.82 Aligned_cols=141 Identities=11% Similarity=0.129 Sum_probs=84.3
Q ss_pred ccCCceEEEEeeeeCCC-CCCcEEEEEEEe-----CC-----cEEEEEcCC------C-C------------hhHHHhhH
Q 019356 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF-----PD-----AIYLVDAIQ------G-G------------ETVVKACK 95 (342)
Q Consensus 46 l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~-----~~-----~~~liD~~~------l-~------------~~~~~~L~ 95 (342)
+.+...++||+|+.+++ ..++ +|+|+. .+ -..+|++.. + + .+++..|.
T Consensus 43 ~~~~~fVvlDiETTGLdp~~dr--IIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~ 120 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTSR--LITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLD 120 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCCe--EEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHH
Confidence 45578999999999986 3443 344431 11 123443321 0 1 13456777
Q ss_pred HHhcCCCceEEEeehhhhHHHHHHhc-------------------------------CCcc-CceehHHHHHHhhccccC
Q 019356 96 PALESSYITKVIHDCKRDSEALYFQF-------------------------------GIKL-HNVVDTQIAYSLIEEQEG 143 (342)
Q Consensus 96 ~lLe~~~i~KV~hd~k~Dl~~L~~~~-------------------------------Gi~l-~~vfDtqlAa~LL~~~~~ 143 (342)
+++.+. ..|+||+.+|+.+|.+.+ ++.. ..++||.-.++.+.+...
T Consensus 121 ~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~ 198 (377)
T PRK05601 121 RLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALD 198 (377)
T ss_pred HHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCC
Confidence 788764 359999999999886532 1222 248999998888877533
Q ss_pred CCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHH
Q 019356 144 RKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (342)
Q Consensus 144 ~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L 212 (342)
.++|..|++ ++|++.+. ...++.+ ..+| ..+ .+-.|+.++..|+..+
T Consensus 199 -------~~rL~~La~---~lGi~~p~--~~A~~~R------a~~p--~~~--l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 199 -------DIRIRGVAH---TLGLDAPA--AEASVER------AQVP--HRQ--LCREETLLVARLYFAL 245 (377)
T ss_pred -------CCCHHHHHH---HhCCCCCc--hhhhhhh------hcCC--hhh--hhhHHHHHHHHHHHHh
Confidence 367899996 67887653 1111000 0111 121 1336899999998876
No 42
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.23 E-value=0.096 Score=57.14 Aligned_cols=135 Identities=18% Similarity=0.122 Sum_probs=87.7
Q ss_pred CCceEEEEeeeeCCCCCCcEEEEEEEe----CCc-----EEEEEcCC-C----------C----------hhHHHhhHHH
Q 019356 48 RQLVIGFDCEGVDLCRHGSLCIMQLAF----PDA-----IYLVDAIQ-G----------G----------ETVVKACKPA 97 (342)
Q Consensus 48 ~~~~Ia~D~E~~~~~~~g~l~llQLa~----~~~-----~~liD~~~-l----------~----------~~~~~~L~~l 97 (342)
....++||+|+.+.+..+ .++||+. ++. ..+|.|.. + . .++...+.++
T Consensus 6 ~~~~vvvD~ETTGl~~~d--~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~ 83 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNA--SIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDL 83 (820)
T ss_pred CCCEEEEEEecCCcCCCC--eEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHH
Confidence 357899999999875333 4566653 221 22333321 1 0 1234566667
Q ss_pred hcCCCceEEEeehhhhHHHHHHh---cCCccC-ceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHH
Q 019356 98 LESSYITKVIHDCKRDSEALYFQ---FGIKLH-NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE 173 (342)
Q Consensus 98 Le~~~i~KV~hd~k~Dl~~L~~~---~Gi~l~-~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~ 173 (342)
+.+. ..|+||+.+|+..|.+. .|..+. ..+||...+..+-+... ..+|.+|++ ++|++... .|
T Consensus 84 l~~~--~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~-------~~~L~~L~~---~lgl~~~~-~H 150 (820)
T PRK07246 84 IEDC--IFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLE-------KYSLSHLSR---ELNIDLAD-AH 150 (820)
T ss_pred hCCC--EEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCC-------CCCHHHHHH---HcCCCCCC-CC
Confidence 7763 35999999999999643 355543 47899988777655422 368899996 56765431 11
Q ss_pred HHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccc
Q 019356 174 VRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (342)
Q Consensus 174 ~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g 220 (342)
+ |..||.++..|+..|..++.+.+
T Consensus 151 ----------~-------------Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 151 ----------T-------------AIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred ----------C-------------HHHHHHHHHHHHHHHHHHHhhcC
Confidence 1 77899999999999998887643
No 43
>PF13014 KH_3: KH domain
Probab=96.21 E-value=0.0061 Score=41.10 Aligned_cols=39 Identities=41% Similarity=0.565 Sum_probs=32.4
Q ss_pred CceeeccCCchHHHHHHhhcchhhccc---CCCCCCeEEEec
Q 019356 284 MGRIIGRRGSSILAIKESCNAEILIGG---AKGPPDKVFIIG 322 (342)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~ 322 (342)
.+.+||++|++|..|.+.++|.|.|-- +...++.|.|.|
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 578999999999999999999999987 444555577766
No 44
>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=96.20 E-value=0.014 Score=50.21 Aligned_cols=85 Identities=25% Similarity=0.212 Sum_probs=54.9
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccc
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~ 169 (342)
++..|..++.+ .+ -|+||+.+|+.+|. .+.....++||.....+..... ....||+.|++ +++|+++.
T Consensus 67 ~~~~l~~~l~~-~v-lVgHn~~fD~~~L~--~~~~~~~~~dt~~l~~~~~~~~------~~~~sL~~l~~--~~lgi~~~ 134 (152)
T cd06144 67 VQKKVAELLKG-RI-LVGHALKNDLKVLK--LDHPKKLIRDTSKYKPLRKTAK------GKSPSLKKLAK--QLLGLDIQ 134 (152)
T ss_pred HHHHHHHHhCC-CE-EEEcCcHHHHHHhc--CcCCCccEEEeEEeeccccccC------CCChhHHHHHH--HHcCcccC
Confidence 45667778876 43 49999999999994 3333345788876433332210 12579999998 78897653
Q ss_pred hhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHH
Q 019356 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (342)
Q Consensus 170 kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~ 209 (342)
...+ + |..||.++..|+
T Consensus 135 ~~~H----------~-------------Al~DA~at~~l~ 151 (152)
T cd06144 135 EGEH----------S-------------SVEDARAAMRLY 151 (152)
T ss_pred CCCc----------C-------------cHHHHHHHHHHh
Confidence 1111 1 678888887776
No 45
>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=96.17 E-value=0.031 Score=48.58 Aligned_cols=66 Identities=23% Similarity=0.158 Sum_probs=45.0
Q ss_pred hhHHHhcCCCceEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccc
Q 019356 93 ACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (342)
Q Consensus 93 ~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~ 169 (342)
.|.+++.+.. .-|+||+.+|+.+|.. . ...++||...+..+.+.... +..++|..|++ +++|.++.
T Consensus 76 ~~~~~i~~~~-vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~~~~~~~~~~----~~~~~L~~L~~--~~~~~~~~ 141 (161)
T cd06137 76 ALWKFIDPDT-ILVGHSLQNDLDALRM-I---HTRVVDTAILTREAVKGPLA----KRQWSLRTLCR--DFLGLKIQ 141 (161)
T ss_pred HHHHhcCCCc-EEEeccHHHHHHHHhC-c---CCCeeEehhhhhhccCCCcC----CCCccHHHHHH--HHCCchhc
Confidence 4555665533 3599999999999942 2 24588999988776553210 02479999998 88887653
No 46
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.04 E-value=0.11 Score=48.49 Aligned_cols=132 Identities=18% Similarity=0.181 Sum_probs=79.4
Q ss_pred CceEEEEeeeeCCCCCCcEEEEEEEe----C----Cc--EEEEEcCC-CC--------------------hhHHHhhHHH
Q 019356 49 QLVIGFDCEGVDLCRHGSLCIMQLAF----P----DA--IYLVDAIQ-GG--------------------ETVVKACKPA 97 (342)
Q Consensus 49 ~~~Ia~D~E~~~~~~~g~l~llQLa~----~----~~--~~liD~~~-l~--------------------~~~~~~L~~l 97 (342)
...+.||+|+.++.....-.+|+|+. . +. -.+|++.. +. .++...+.++
T Consensus 4 ~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~f 83 (240)
T PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83 (240)
T ss_pred CeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHHHHH
Confidence 35789999999886321123444442 1 11 24555421 11 1233456666
Q ss_pred hcCCCceEEEeehhhhHHHHHHh---cCCcc------CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCcc
Q 019356 98 LESSYITKVIHDCKRDSEALYFQ---FGIKL------HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (342)
Q Consensus 98 Le~~~i~KV~hd~k~Dl~~L~~~---~Gi~l------~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l 168 (342)
+.+.. .|+||+.+|+..|.+. +|... ..++||...++.+.+.. ..+|.+|++ + +|++.
T Consensus 84 i~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~--------~~~L~aL~~--~-~gi~~ 150 (240)
T PRK05711 84 IRGAE--LIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGK--------RNSLDALCK--R-YGIDN 150 (240)
T ss_pred hCCCE--EEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCC--------CCCHHHHHH--H-CCCCC
Confidence 66543 4899999999988643 34221 34899998877665542 358899997 4 46543
Q ss_pred chhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHH
Q 019356 169 QEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (342)
Q Consensus 169 ~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~ 215 (342)
.. |. ..-|..||..+..+|..|...
T Consensus 151 ~~-----------------r~-----~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 151 SH-----------------RT-----LHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred CC-----------------CC-----CCCHHHHHHHHHHHHHHHHCc
Confidence 21 00 112778999999999888644
No 47
>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=96.04 E-value=0.03 Score=48.52 Aligned_cols=68 Identities=22% Similarity=0.074 Sum_probs=41.1
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHHhcCCccCceehHHHHH---HhhccccCCCCCCCCCCcHHHhhcCccccCC
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAY---SLIEEQEGRKRSPDDYISFVGLLADPRYCGI 166 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa---~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~ 166 (342)
+...+..++.+. .-|+|++++|+.+|... .....+.||.... +....+. ...++|..|++ ++++.
T Consensus 67 v~~~l~~~l~~~--vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~p~------~~~~~L~~L~~--~~~~~ 134 (157)
T cd06149 67 AQKEILKILKGK--VVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKAGFPE------NCRVSLKVLAK--RLLHR 134 (157)
T ss_pred HHHHHHHHcCCC--EEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhcCCcc------cCChhHHHHHH--HHcCh
Confidence 446666777653 45999999999999422 2223477875432 1111111 12478999998 88765
Q ss_pred ccc
Q 019356 167 SYQ 169 (342)
Q Consensus 167 ~l~ 169 (342)
.+.
T Consensus 135 ~i~ 137 (157)
T cd06149 135 DIQ 137 (157)
T ss_pred hhc
Confidence 443
No 48
>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=95.97 E-value=0.092 Score=48.35 Aligned_cols=90 Identities=21% Similarity=0.220 Sum_probs=60.2
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHH---hcC--Cc-c---CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcC
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFG--IK-L---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLAD 160 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~---~~G--i~-l---~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~ 160 (342)
++..|.+++.+.. -|+||+.+|..+|.+ .+| +. + ..++||+..++.+.+.. ..+|.+|++
T Consensus 72 v~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~--------~~~L~~L~~- 140 (225)
T TIGR01406 72 IADEFLDFIGGSE--LVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQ--------RNSLDALCK- 140 (225)
T ss_pred HHHHHHHHhCCCE--EEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCC--------CCCHHHHHH-
Confidence 3455666776643 489999999999864 345 22 1 35899999877665431 368999997
Q ss_pred ccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHH
Q 019356 161 PRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMK 214 (342)
Q Consensus 161 ~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~ 214 (342)
.+|++... |. ..-|..||..+..+|..|..
T Consensus 141 --~~gi~~~~-----------------r~-----~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 141 --RFKVDNSH-----------------RT-----LHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred --hcCCCCCC-----------------CC-----CcCHHHHHHHHHHHHHHHHc
Confidence 45654321 00 01178999999999988864
No 49
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=95.96 E-value=0.3 Score=45.44 Aligned_cols=141 Identities=15% Similarity=0.150 Sum_probs=82.2
Q ss_pred ccCCceEEEEeeeeCCC-CCCcEEEEEEEe----CCc-------EEEEEcCC-C----------C----------hhHHH
Q 019356 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-------IYLVDAIQ-G----------G----------ETVVK 92 (342)
Q Consensus 46 l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~----~~~-------~~liD~~~-l----------~----------~~~~~ 92 (342)
+.+...++||+|+.+++ ..++ +++|+. ++. .+++.+.. + . .+++.
T Consensus 44 ~~~~~~vviD~ETTGl~p~~d~--IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~ 121 (239)
T PRK09146 44 LSEVPFVALDFETTGLDAEQDA--IVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILD 121 (239)
T ss_pred cccCCEEEEEeECCCCCCCCCc--EEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHH
Confidence 44568899999999876 3444 344432 221 23444321 0 1 02234
Q ss_pred hhHHHhcCCCceEEEeehhhhHHHHHHh----cCCcc-CceehHHHHHHhhccccCCC---CCC---CCCCcHHHhhcCc
Q 019356 93 ACKPALESSYITKVIHDCKRDSEALYFQ----FGIKL-HNVVDTQIAYSLIEEQEGRK---RSP---DDYISFVGLLADP 161 (342)
Q Consensus 93 ~L~~lLe~~~i~KV~hd~k~Dl~~L~~~----~Gi~l-~~vfDtqlAa~LL~~~~~~~---~L~---~~~~sL~~Lv~~~ 161 (342)
.|...+.+. .-|+||+.+|..+|.+. .+..+ ..++||+..++-+.+..... .+. ...++|.++++
T Consensus 122 ~l~~~~~~~--~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~-- 197 (239)
T PRK09146 122 ELLEALAGK--VVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRL-- 197 (239)
T ss_pred HHHHHhCCC--EEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHH--
Confidence 455555442 35899999999998653 33333 35899999877654321000 000 02467888886
Q ss_pred cccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 019356 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (342)
Q Consensus 162 ~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (342)
.+|++... . .-|..||.++..|+..+..++.
T Consensus 198 -~~gl~~~~-~-----------------------H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 198 -RYGLPAYS-P-----------------------HHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred -HcCCCCCC-C-----------------------CCcHHHHHHHHHHHHHHHHHHc
Confidence 45654321 0 1177899999999998887774
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=95.92 E-value=0.14 Score=57.96 Aligned_cols=139 Identities=16% Similarity=0.218 Sum_probs=92.6
Q ss_pred cCCceEEEEeeeeCCC-CCCcEEEEEEEe----CCc-----EEEEEcCC-C----------C----------hhHHHhhH
Q 019356 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-----IYLVDAIQ-G----------G----------ETVVKACK 95 (342)
Q Consensus 47 ~~~~~Ia~D~E~~~~~-~~g~l~llQLa~----~~~-----~~liD~~~-l----------~----------~~~~~~L~ 95 (342)
.+...+.||+|+.+++ ..++ +++|+. .+. ..+|.|.. + . .+++..+.
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~--IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~ 265 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDE--IIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFK 265 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCe--EEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHH
Confidence 4568999999999875 3444 344442 221 12333221 0 0 13456677
Q ss_pred HHhcCCCceEEEeehhhhHHHHHH---hcCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccch
Q 019356 96 PALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE 170 (342)
Q Consensus 96 ~lLe~~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~k 170 (342)
.++.+. ..|+||+.+|...|.+ .+|+.+ ..++||+..++.+.+... .++|..|++ .+|+++..
T Consensus 266 ~fl~~~--iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k-------~~kL~~Lak---~lgi~~~~ 333 (1213)
T TIGR01405 266 EFFKDS--ILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYK-------SHRLGNICK---KLGVDLDD 333 (1213)
T ss_pred HHhCCC--eEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCC-------CCCHHHHHH---HcCCCCCC
Confidence 777663 4599999999999864 356543 358999998888776432 468899996 46776541
Q ss_pred hHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHH
Q 019356 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (342)
Q Consensus 171 K~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~ 223 (342)
. ..|..||.++..|+..|.+++++.|...
T Consensus 334 -~-----------------------HrAl~DA~aTa~I~~~ll~~l~~~~i~~ 362 (1213)
T TIGR01405 334 -H-----------------------HRADYDAEATAKVFKVMVEQLKEKGITN 362 (1213)
T ss_pred -C-----------------------cCHHHHHHHHHHHHHHHHHHHHHcCCcc
Confidence 1 2278999999999999999998766433
No 51
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=95.86 E-value=0.19 Score=48.72 Aligned_cols=92 Identities=18% Similarity=0.153 Sum_probs=63.0
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHHh---cCCc-c-CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCcccc
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIK-L-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~---~Gi~-l-~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~L 164 (342)
++..+..++.+.. -|+||+.+|...|.+. +|+. + ...+||+..+..+.+... ..+|..|++ ++
T Consensus 78 vl~~f~~fl~~~~--lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~-------~~kL~~L~~---~l 145 (313)
T PRK06807 78 VLPLFLAFLHTNV--IVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAP-------NHKLETLKR---ML 145 (313)
T ss_pred HHHHHHHHHcCCe--EEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCC-------CCCHHHHHH---Hc
Confidence 3455556666543 3999999999998653 4553 2 348899987765554321 357889985 67
Q ss_pred CCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhc
Q 019356 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (342)
Q Consensus 165 g~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (342)
|+... .| + |-.||.++..++..+......
T Consensus 146 gi~~~--~H----------~-------------Al~DA~~ta~l~~~l~~~~~~ 174 (313)
T PRK06807 146 GIRLS--SH----------N-------------AFDDCITCAAVYQKCASIEEE 174 (313)
T ss_pred CCCCC--Cc----------C-------------hHHHHHHHHHHHHHHHHhhhh
Confidence 76541 11 1 678999999999999888854
No 52
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=95.84 E-value=0.038 Score=60.89 Aligned_cols=239 Identities=21% Similarity=0.272 Sum_probs=147.9
Q ss_pred ccCCceEEEEeeeeCCC-CCCcEEEEEEEe---C-C-----cEEEEEcCC-C----------C----------hhHHHhh
Q 019356 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF---P-D-----AIYLVDAIQ-G----------G----------ETVVKAC 94 (342)
Q Consensus 46 l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~---~-~-----~~~liD~~~-l----------~----------~~~~~~L 94 (342)
+.++..+.||.|+.+++ .+.. ++|++. . + --+++++.. + . ++++..+
T Consensus 418 l~datyVVfDiETTGLs~~~d~--iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf 495 (1444)
T COG2176 418 LDDATYVVFDIETTGLSPVYDE--IIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKF 495 (1444)
T ss_pred cccccEEEEEeecCCcCcccch--hhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHH
Confidence 45678999999999986 5554 455553 1 1 123333321 1 0 1356777
Q ss_pred HHHhcCCCceEEEeehhhhHHHHHH---hcCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccc
Q 019356 95 KPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (342)
Q Consensus 95 ~~lLe~~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~ 169 (342)
++++.+. .-|.||+.+|+-.|.. .+|+.+ +.++||.-.++.|.|...+| +|..|+. -||+.+.
T Consensus 496 ~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh-------~Lg~l~k---k~~v~le 563 (1444)
T COG2176 496 REFIGDS--ILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSH-------RLGTLCK---KLGVELE 563 (1444)
T ss_pred HHHhcCc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhc-------chHHHHH---HhCccHH
Confidence 8888775 3499999999998854 356655 45999999999999987654 6688886 4566553
Q ss_pred hhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHHHHhc------cccccccccCC----
Q 019356 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRG------ALYCRCFCINE---- 239 (342)
Q Consensus 170 kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l~~~~------~~~~r~~~~~~---- 239 (342)
..+ -|-.|+.++-.++-.+.+.+++.|...+..-. ..+.|.+....
T Consensus 564 -~hH-----------------------RA~yDaeat~~vf~~f~~~~ke~Gi~~l~eln~~l~~~~~ykr~r~~h~~i~v 619 (1444)
T COG2176 564 -RHH-----------------------RADYDAEATAKVFFVFLKDLKEKGITNLSELNDKLSSEDLYKRLRPKHATIYV 619 (1444)
T ss_pred -Hhh-----------------------hhhhhHHHHHHHHHHHHHHHHHhchhhHHHHhHhhhhhHHHhhccccceEEEE
Confidence 222 25679999999999999999998755443322 23555551110
Q ss_pred -C-------------CCC-CCCCCCCCCCcceecc-cccccc-----CCC----------ChhhhhhhcCC----CCCCC
Q 019356 240 -N-------------DYV-DWPPLPPVPGVRFIYV-DYLIVE-----GDV----------PEEEILSILDV----PPGKM 284 (342)
Q Consensus 240 -~-------------~~~-~w~~~~~~~~~~~~~~-~~l~~~-----~~~----------~~~~~~~~~~~----~~~~~ 284 (342)
+ .+. -+...|.+|.-..-+. .+|.+- +++ .=++++..||. ||+--
T Consensus 620 knq~GlKnLykLvS~s~~kyf~~~PrI~~S~L~~~regLligsac~~Gelf~a~l~k~~ee~e~iak~YDfIei~pp~~y 699 (1444)
T COG2176 620 KNQVGLKNLYKLVSISHTKYFYGRPRIPRSVLKKNREGLLIGSACSEGELFDAALQKPDEEVEEIAKFYDFIEIQPPANY 699 (1444)
T ss_pred echHhHHHHHHHHHHHHHHhhccCCCCcHHHHHHhhcCeeeccCccchHHHHHHHhCCHHHHHHHHHhcCeEEecCchhh
Confidence 0 011 1334555551111111 122211 110 23567788885 77776
Q ss_pred ceeeccCCch-HHHHHHhhcchhhcccCCCCCCeEEEecch
Q 019356 285 GRIIGRRGSS-ILAIKESCNAEILIGGAKGPPDKVFIIGPV 324 (342)
Q Consensus 285 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 324 (342)
...|.+.|.+ .-+|++.-+-.|-+|-..+-| |...|-+
T Consensus 700 ~~li~~e~~~~~e~l~~~~k~li~~g~~l~K~--Vvatgn~ 738 (1444)
T COG2176 700 AHLIEREGLKDKEALKEIIKKLIKLGKKLNKP--VVATGNV 738 (1444)
T ss_pred hhHHHhcccCcHHHHHHHHHHHHHHHHHhCCc--EEEeCCc
Confidence 6677777776 788888888888888766654 5555554
No 53
>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=95.79 E-value=0.063 Score=46.12 Aligned_cols=64 Identities=22% Similarity=0.176 Sum_probs=42.7
Q ss_pred HHhhHHHhcCCCceEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCcc
Q 019356 91 VKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (342)
Q Consensus 91 ~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l 168 (342)
...+.+++.+.. .-|+||+.+|+.+|. .. ...++||...+....+.. ...+|..|++ +|++..+
T Consensus 66 ~~~~~~fl~~~~-vlVgHn~~fD~~fL~-~~---~~~~iDT~~l~r~~~~~~-------~~~~L~~L~~--~~~~~~i 129 (150)
T cd06145 66 QKKLLSLISPDT-ILVGHSLENDLKALK-LI---HPRVIDTAILFPHPRGPP-------YKPSLKNLAK--KYLGRDI 129 (150)
T ss_pred HHHHHHHhCCCC-EEEEcChHHHHHHhh-cc---CCCEEEcHHhccccCCCC-------CChhHHHHHH--HHCCcce
Confidence 445666775323 459999999999994 22 234899987655433321 1368999998 8887544
No 54
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=95.66 E-value=0.47 Score=44.68 Aligned_cols=134 Identities=16% Similarity=0.063 Sum_probs=83.1
Q ss_pred ccCCceEEEEeeeeCCC-CCCcEEEEEEEe----CCc-----EEEEEcCCCC--------------------hhHHHhhH
Q 019356 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-----IYLVDAIQGG--------------------ETVVKACK 95 (342)
Q Consensus 46 l~~~~~Ia~D~E~~~~~-~~g~l~llQLa~----~~~-----~~liD~~~l~--------------------~~~~~~L~ 95 (342)
+.+...+.+|+|+.+.. ..++ +++|+. .++ ..++.+..+. .+++..+.
T Consensus 65 ~~~~~~vv~DiETTG~~~~~~~--IIEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f~ 142 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKKHQ--IIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFR 142 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCCCe--EEEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHHH
Confidence 34567899999999875 3333 455542 221 1233332111 12455667
Q ss_pred HHhcCCCceEEEeehhhhHHHHHH---hcCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccch
Q 019356 96 PALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE 170 (342)
Q Consensus 96 ~lLe~~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~k 170 (342)
.++.+. ..|+||+.+|..+|.+ .+|... ...+||+-.+..+-+. ...+|++|++ ++|++..
T Consensus 143 ~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~--------~~~~L~~L~~---~lgi~~~- 208 (257)
T PRK08517 143 LFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES--------PRYGLSFLKE---LLGIEIE- 208 (257)
T ss_pred HHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccC--------CCCCHHHHHH---HcCcCCC-
Confidence 777764 3599999999998853 455543 3477887655432221 1368899985 6787643
Q ss_pred hHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhc
Q 019356 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (342)
Q Consensus 171 K~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (342)
..+ + |..||.++.+|+..+..++..
T Consensus 209 ~~H----------r-------------Al~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 209 VHH----------R-------------AYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred CCC----------C-------------hHHHHHHHHHHHHHHHHHhHH
Confidence 111 1 778999999999999888753
No 55
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=95.61 E-value=0.045 Score=51.21 Aligned_cols=135 Identities=19% Similarity=0.167 Sum_probs=82.1
Q ss_pred ceEEEEeeeeCCCCCCcEEE---EEEEeCCcEEEEEcCCC---------------Ch----------hHHHhhHHHhcCC
Q 019356 50 LVIGFDCEGVDLCRHGSLCI---MQLAFPDAIYLVDAIQG---------------GE----------TVVKACKPALESS 101 (342)
Q Consensus 50 ~~Ia~D~E~~~~~~~g~l~l---lQLa~~~~~~liD~~~l---------------~~----------~~~~~L~~lLe~~ 101 (342)
.+||+|||-++.+..|+.++ +.|-...+..++|-.-. .. .+-..+.++|.+
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL~g- 184 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLLKG- 184 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHHHhC-
Confidence 59999999998876655544 34433334455562211 10 011345567776
Q ss_pred CceEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCC
Q 019356 102 YITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQD 181 (342)
Q Consensus 102 ~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~ 181 (342)
. +.|||+.+.|+.+|+-.+.- .-+-||.-.--|...-. + +...||..|.+ .+||.++-. ++
T Consensus 185 R-IlVGHaLhnDl~~L~l~hp~--s~iRDTs~~~pl~k~~~-~----~~tpSLK~Lt~--~~Lg~~IQ~-Ge-------- 245 (280)
T KOG2249|consen 185 R-ILVGHALHNDLQALKLEHPR--SMIRDTSKYPPLMKLLS-K----KATPSLKKLTE--ALLGKDIQV-GE-------- 245 (280)
T ss_pred C-EEeccccccHHHHHhhhCch--hhhcccccCchHHHHhh-c----cCCccHHHHHH--HHhchhhhc-cc--------
Confidence 3 34999999999999633321 23567765333322100 0 12579999999 999976541 11
Q ss_pred CCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhc
Q 019356 182 PQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (342)
Q Consensus 182 ~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (342)
.+ ..+||.+..+||.....+-++
T Consensus 246 -Hs-------------SvEDA~AtM~LY~~vk~qwe~ 268 (280)
T KOG2249|consen 246 -HS-------------SVEDARATMELYKRVKVQWEK 268 (280)
T ss_pred -cC-------------cHHHHHHHHHHHHHHHHHHHH
Confidence 01 458999999999998755543
No 56
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=95.45 E-value=0.64 Score=42.88 Aligned_cols=140 Identities=16% Similarity=0.089 Sum_probs=84.9
Q ss_pred ceEEEEeeeeCCC-CCCcEEEEEEEe-C---C--cEEEEEcCC-C----------Ch----------hHHHhhHHHhcCC
Q 019356 50 LVIGFDCEGVDLC-RHGSLCIMQLAF-P---D--AIYLVDAIQ-G----------GE----------TVVKACKPALESS 101 (342)
Q Consensus 50 ~~Ia~D~E~~~~~-~~g~l~llQLa~-~---~--~~~liD~~~-l----------~~----------~~~~~L~~lLe~~ 101 (342)
..+.||+|+.+++ ..++ +++|+. . . -..++++.. + .+ ++...+.+++.+.
T Consensus 3 ~~vv~D~ETTGl~~~~d~--IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~~~ 80 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDR--IIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTD 80 (232)
T ss_pred cEEEEEeeCCCCCCCCCE--EEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHcCC
Confidence 4688999999875 3444 455543 1 1 233455421 1 11 1223455556543
Q ss_pred CceEEEee-hhhhHHHHHH---hcCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHH
Q 019356 102 YITKVIHD-CKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVR 175 (342)
Q Consensus 102 ~i~KV~hd-~k~Dl~~L~~---~~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~ 175 (342)
-.-|+|| ..+|...|.+ .+|+.. ...+||+-.+..+.+... ..+|..+++ ++|++... .+
T Consensus 81 -~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~-------~~~L~~l~~---~~~~~~~~-aH-- 146 (232)
T PRK06309 81 -NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLP-------KHNLQYLRQ---VYGFEENQ-AH-- 146 (232)
T ss_pred -CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCC-------CCCHHHHHH---HcCCCCCC-CC--
Confidence 3459999 5899998864 345543 358999887776654321 357888886 44654331 11
Q ss_pred HHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHHHH
Q 019356 176 VLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAV 226 (342)
Q Consensus 176 ~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l~~ 226 (342)
+ |..||.++..++..+..++....+..+..
T Consensus 147 --------~-------------Al~Da~~t~~vl~~l~~~~~~~~l~~l~~ 176 (232)
T PRK06309 147 --------R-------------ALDDVITLHRVFSALVGDLSPQQVYDLLN 176 (232)
T ss_pred --------C-------------cHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 1 77899999999999988886544444443
No 57
>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=95.30 E-value=0.43 Score=40.41 Aligned_cols=67 Identities=19% Similarity=0.095 Sum_probs=45.6
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHH---hcCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCcccc
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~L 164 (342)
++..|..++++. ..|+||+.+|...|.+ .+|+.. ...+||+..+..+.+... ..+|..+++ ++
T Consensus 67 v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~-------~~~L~~l~~---~~ 134 (156)
T cd06130 67 VWPEIKPFLGGS--LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLP-------NHKLNTVAE---HL 134 (156)
T ss_pred HHHHHHHHhCCC--EEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCC-------CCCHHHHHH---Hc
Confidence 445677778763 4599999999999854 345543 348999887766544321 368899986 56
Q ss_pred CCcc
Q 019356 165 GISY 168 (342)
Q Consensus 165 g~~l 168 (342)
|+..
T Consensus 135 g~~~ 138 (156)
T cd06130 135 GIEL 138 (156)
T ss_pred CCCc
Confidence 7644
No 58
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.02 E-value=0.35 Score=53.52 Aligned_cols=134 Identities=17% Similarity=0.124 Sum_probs=85.0
Q ss_pred CceEEEEeeeeCCCCCCcEEEEEEEe----CCc-----EEEEEcCC-C----------C----------hhHHHhhHHHh
Q 019356 49 QLVIGFDCEGVDLCRHGSLCIMQLAF----PDA-----IYLVDAIQ-G----------G----------ETVVKACKPAL 98 (342)
Q Consensus 49 ~~~Ia~D~E~~~~~~~g~l~llQLa~----~~~-----~~liD~~~-l----------~----------~~~~~~L~~lL 98 (342)
...+.||+|+.+......-.+|||+. .++ ..+|.+.. + . .++...|..++
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 46789999998764221124566664 222 12444321 0 1 12345667777
Q ss_pred cCCCceEEEeehhhhHHHHHHh---cCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHH
Q 019356 99 ESSYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE 173 (342)
Q Consensus 99 e~~~i~KV~hd~k~Dl~~L~~~---~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~ 173 (342)
.+. ..|+||+.+|...|.+. .|+.. ...+||.-.+..+-+... .++|.+|++ ++|+.... .|
T Consensus 83 ~~~--~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~-------~~~L~~l~~---~l~i~~~~-~H 149 (928)
T PRK08074 83 EGA--YFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAE-------SYKLRDLSE---ELGLEHDQ-PH 149 (928)
T ss_pred CCC--eEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCC-------CCCHHHHHH---hCCCCCCC-CC
Confidence 754 45999999999998643 45543 358999887777665422 367899996 66765431 11
Q ss_pred HHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhc
Q 019356 174 VRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (342)
Q Consensus 174 ~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (342)
+ |-.||.++..|+..|.+++.+
T Consensus 150 ----------~-------------Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 150 ----------R-------------ADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred ----------C-------------hHHHHHHHHHHHHHHHHHHHh
Confidence 1 668888888888888887765
No 59
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=94.86 E-value=1 Score=40.41 Aligned_cols=133 Identities=18% Similarity=0.149 Sum_probs=77.1
Q ss_pred cCCceEEEEeeeeCCC-CCCcEEEEEEEe----CCc-------EEEEEcCC-C----------C----------hhHHHh
Q 019356 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-------IYLVDAIQ-G----------G----------ETVVKA 93 (342)
Q Consensus 47 ~~~~~Ia~D~E~~~~~-~~g~l~llQLa~----~~~-------~~liD~~~-l----------~----------~~~~~~ 93 (342)
.....+.+|+|+.+.. ..++ +++|+. ++. ..+|.+.. + . .+++..
T Consensus 27 ~~~~~vviD~ETTGl~~~~d~--IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~ 104 (202)
T PRK09145 27 PPDEWVALDCETTGLDPRRAE--IVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQ 104 (202)
T ss_pred CCCCEEEEEeECCCCCCCCCc--eEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHH
Confidence 4568899999999875 3344 344442 221 12444321 0 0 123456
Q ss_pred hHHHhcCCCceEEEeehhhhHHHHHHh----cCCccC-ceehHHHHHHh-hccccCCCCCCCCCCcHHHhhcCccccCCc
Q 019356 94 CKPALESSYITKVIHDCKRDSEALYFQ----FGIKLH-NVVDTQIAYSL-IEEQEGRKRSPDDYISFVGLLADPRYCGIS 167 (342)
Q Consensus 94 L~~lLe~~~i~KV~hd~k~Dl~~L~~~----~Gi~l~-~vfDtqlAa~L-L~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~ 167 (342)
+..++.+. ..|+|++.+|...|.+. +|..+. ..+|+.-..+- ....... . ....+|+++++ ++|++
T Consensus 105 ~~~~i~~~--~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~-~--~~~~~L~~l~~---~~gi~ 176 (202)
T PRK09145 105 LLAFIGNR--PLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPD-A--YIDLRFDAILK---HLDLP 176 (202)
T ss_pred HHHHHcCC--eEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCC-c--ccCCCHHHHHH---HcCCC
Confidence 66677654 35999999999998643 344443 47888643321 1111000 0 01468999996 56765
Q ss_pred cchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHH
Q 019356 168 YQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (342)
Q Consensus 168 l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~ 213 (342)
... .+ + |..||.++..|+..|.
T Consensus 177 ~~~-~H----------~-------------Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 177 VLG-RH----------D-------------ALNDAIMAALIFLRLR 198 (202)
T ss_pred CCC-CC----------C-------------cHHHHHHHHHHHHHHH
Confidence 431 11 1 7789999999988775
No 60
>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=94.61 E-value=0.97 Score=40.18 Aligned_cols=102 Identities=18% Similarity=0.109 Sum_probs=63.4
Q ss_pred hHHHhhHHHhcC--CCceEEEeeh-hhhHHHHHH---hcCCcc-----------------------C-ceehHHHHHHhh
Q 019356 89 TVVKACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKL-----------------------H-NVVDTQIAYSLI 138 (342)
Q Consensus 89 ~~~~~L~~lLe~--~~i~KV~hd~-k~Dl~~L~~---~~Gi~l-----------------------~-~vfDtqlAa~LL 138 (342)
+++..+..++++ |.+ -|+||. .+|+..|.. .+|+.. + .++|+.....-.
T Consensus 65 ~lL~~f~~~i~~~dpdi-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~ 143 (199)
T cd05160 65 ELLKRFFDIIREYDPDI-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRD 143 (199)
T ss_pred HHHHHHHHHHHhcCCCE-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHh
Confidence 345566666654 444 499999 789998864 355544 1 267888765543
Q ss_pred ccccCCCCCCCCCCcHHHhhcCccccCCccch--hHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHH
Q 019356 139 EEQEGRKRSPDDYISFVGLLADPRYCGISYQE--KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (342)
Q Consensus 139 ~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~k--K~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~ 209 (342)
.. . ...+|..+++ .+++..-.+ .+.... ..|.. -....++|+-.||..++.|+
T Consensus 144 ~~-l-------~sy~L~~v~~--~~l~~~k~~~~~~~~~~------~~~~~--~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 144 FK-L-------KSYTLDAVAE--ELLGEGKEKVDGEIIED------AEWEE--DPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred cC-c-------ccCCHHHHHH--HHhCCCCCcCCHHHHhh------ccCcc--hHHHHHHHHHHHHHHHHHhh
Confidence 32 1 2478999998 888753221 111110 01322 23678999999999998875
No 61
>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=94.57 E-value=1.3 Score=39.51 Aligned_cols=145 Identities=14% Similarity=0.160 Sum_probs=82.9
Q ss_pred ceEEEEeeeeCCC-----CCCcEEEEEEEeC-Cc-EEEEEcC--------CCChhHHHhhHHHhcC--CCceEEEeehh-
Q 019356 50 LVIGFDCEGVDLC-----RHGSLCIMQLAFP-DA-IYLVDAI--------QGGETVVKACKPALES--SYITKVIHDCK- 111 (342)
Q Consensus 50 ~~Ia~D~E~~~~~-----~~g~l~llQLa~~-~~-~~liD~~--------~l~~~~~~~L~~lLe~--~~i~KV~hd~k- 111 (342)
..++||.|+.+.. ....+..|++... .+ ++..... .-..+++..+..++.. |.+ -++||..
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dpdi-ivgyN~~~ 82 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDV-IYTYNGDN 82 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCCCE-EEecCCCC
Confidence 5688999997431 2345544444442 22 2211111 1112455666666665 664 4899975
Q ss_pred hhHHHHHH---hcCCccC------------------------ceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCcccc
Q 019356 112 RDSEALYF---QFGIKLH------------------------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (342)
Q Consensus 112 ~Dl~~L~~---~~Gi~l~------------------------~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~L 164 (342)
+|+..|.. .+|+... ..+|+.....-. ..+ ...+|..+++ ++|
T Consensus 83 FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~------~~l--~sy~L~~v~~--~~L 152 (195)
T cd05780 83 FDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRT------LNL--TRYTLERVYE--ELF 152 (195)
T ss_pred CcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhh------CCC--CcCcHHHHHH--HHh
Confidence 79988864 3455421 167777654321 112 2578999998 899
Q ss_pred CCccch--hHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHH
Q 019356 165 GISYQE--KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (342)
Q Consensus 165 g~~l~k--K~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L 212 (342)
|.+-.+ .++... -|...+--...++|+..||..+++|.+.+
T Consensus 153 g~~k~d~~~~~i~~-------~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 153 GIEKEDVPGEEIAE-------AWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred CCCCCcCCHHHHHH-------HHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 975321 122211 23333334678999999999999988653
No 62
>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=94.40 E-value=0.69 Score=50.76 Aligned_cols=93 Identities=17% Similarity=0.141 Sum_probs=63.9
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHH---hcCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCcccc
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~L 164 (342)
+...+.+++.+. ..|+||+.+|..+|.+ .+|+.+ ...+||+-.+..+.+... ..+|.+|++ ++
T Consensus 70 v~~~l~~~l~~~--~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~-------~~~L~~l~~---~~ 137 (850)
T TIGR01407 70 VAQEIYDLLEDG--IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEE-------SYQLSELSE---AL 137 (850)
T ss_pred HHHHHHHHhCCC--EEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCC-------CCCHHHHHH---HC
Confidence 345666677653 3599999999999864 356553 458999987777665432 368899986 56
Q ss_pred CCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhc
Q 019356 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (342)
Q Consensus 165 g~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (342)
|++... .| + |..||.++..|+..+.+++.+
T Consensus 138 gi~~~~-~H----------~-------------Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 138 GLTHEN-PH----------R-------------ADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred CCCCCC-CC----------C-------------hHHHHHHHHHHHHHHHHHHHh
Confidence 765431 11 1 677888888888888777654
No 63
>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=94.13 E-value=0.88 Score=38.96 Aligned_cols=146 Identities=17% Similarity=0.142 Sum_probs=68.7
Q ss_pred EEEEeeeeCCC-CCCcEEEEEEEe--CCc-EEEEEcCCCCh----hHHHhhHHHhcCCCceEEEee-hhhhHHHHHHhc-
Q 019356 52 IGFDCEGVDLC-RHGSLCIMQLAF--PDA-IYLVDAIQGGE----TVVKACKPALESSYITKVIHD-CKRDSEALYFQF- 121 (342)
Q Consensus 52 Ia~D~E~~~~~-~~g~l~llQLa~--~~~-~~liD~~~l~~----~~~~~L~~lLe~~~i~KV~hd-~k~Dl~~L~~~~- 121 (342)
+.||+|+.++. ..+.+.++.++. .++ .++.+...-+. .+.+.+ ..+.+.... |+|| ..+|..+|.+.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~-~~l~~~~~i-v~yng~~FD~p~L~~~~~ 78 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFF-ELLDEADNI-VTYNGKNFDIPFLKRRAK 78 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH---HHHHTT--E-EESSTTTTHHHHHHHHH-
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHH-HHHhcCCeE-EEEeCcccCHHHHHHHHH
Confidence 46899999875 456788888885 333 32333222221 122223 345554433 6666 567999996544
Q ss_pred --CCc-cCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccch----hHHHHHHhcCCCCCCCCCCCcHHH
Q 019356 122 --GIK-LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE----KEEVRVLLRQDPQFWTYRPLTELM 194 (342)
Q Consensus 122 --Gi~-l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~k----K~~~~~l~~~~~~dW~~RPLs~~q 194 (342)
++. ..+.+|++-..+-... ...||..+.. ++|..-.. ..+...++....... .....+.+
T Consensus 79 ~~~~~~~~~~iDl~~~~~~~~~---------~~~~Lk~ve~---~lg~~~~~~~~~G~~~~~~~~~~~~~~-~~~~~~~i 145 (164)
T PF13482_consen 79 RYGLPPPFNHIDLLKIIKKHFL---------ESYSLKNVEK---FLGIERRDDDISGSESVKLYKEYLETG-DPEALEEI 145 (164)
T ss_dssp HHHH--GGGEEEHHHHHT-TTS---------CCTT--SHHH--------------HHHHHHHHHH---TTG-GTS--HHH
T ss_pred HcCCCcccchhhHHHHHHhccC---------CCCCHHHHhh---hcccccccCCCCHHHHHHHHHHHHhcC-CHHHHHHH
Confidence 333 3468898875532111 1467777775 57765431 111111121100010 12345889
Q ss_pred HHHHHHHhHHHHHHHHHH
Q 019356 195 VRAAADDVRFLPYIYHNM 212 (342)
Q Consensus 195 l~YAA~Da~~Ll~L~~~L 212 (342)
+.|.-.|+..+..|++.|
T Consensus 146 ~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 146 LEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 999999999999999876
No 64
>PRK05168 ribonuclease T; Provisional
Probab=94.13 E-value=0.19 Score=45.67 Aligned_cols=87 Identities=18% Similarity=0.247 Sum_probs=60.1
Q ss_pred CceEEEeehhhhHHHHHH---hcCCc---c--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHH
Q 019356 102 YITKVIHDCKRDSEALYF---QFGIK---L--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE 173 (342)
Q Consensus 102 ~i~KV~hd~k~Dl~~L~~---~~Gi~---l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~ 173 (342)
....|+||+.+|+..|.+ .+|+. . ..++||...+..+.+. .+|..+++ ++|+++.. ..
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~----------~~L~~l~~---~~gl~~~~-~~ 179 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQ----------TVLAKACQ---AAGIEFDN-KE 179 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCC----------CCHHHHHH---HCCCCCCC-CC
Confidence 345699999999988854 34542 1 2479998877655432 36788886 45765431 00
Q ss_pred HHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHH
Q 019356 174 VRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (342)
Q Consensus 174 ~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~ 223 (342)
..-|..||..+..|+..|..++.+.|.|.
T Consensus 180 ---------------------~H~Al~DA~ata~l~~~l~~~~~~~~~~~ 208 (211)
T PRK05168 180 ---------------------AHSALYDTEKTAELFCEIVNRWKRLGGWP 208 (211)
T ss_pred ---------------------CCChHHHHHHHHHHHHHHHHHHHHccCCC
Confidence 01178899999999999999998877664
No 65
>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=94.01 E-value=0.085 Score=46.75 Aligned_cols=81 Identities=16% Similarity=0.087 Sum_probs=53.3
Q ss_pred HhhHHHhcCCCceEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchh
Q 019356 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK 171 (342)
Q Consensus 92 ~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK 171 (342)
..|..++.. ...-|||+...|+.+|. +-..-..+.||.+... ...+ +..||..|++ ++||..+-..
T Consensus 93 ~~l~~li~~-~tILVGHsL~nDL~aL~--l~hp~~~viDTa~l~~---~~~~------r~~sLk~La~--~~L~~~IQ~~ 158 (174)
T cd06143 93 LKLRLLVDL-GCIFVGHGLAKDFRVIN--IQVPKEQVIDTVELFH---LPGQ------RKLSLRFLAW--YLLGEKIQSE 158 (174)
T ss_pred HHHHHHcCC-CCEEEeccchhHHHHhc--CcCCCcceEEcHHhcc---CCCC------CChhHHHHHH--HHcCCcccCC
Confidence 345555643 34569999999999993 2111246899976432 1111 2579999999 9999876521
Q ss_pred HHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHH
Q 019356 172 EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (342)
Q Consensus 172 ~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~ 209 (342)
+ .+ ..+||.+.+.||
T Consensus 159 ~----------Hd-------------SvEDArAam~Ly 173 (174)
T cd06143 159 T----------HD-------------SIEDARTALKLY 173 (174)
T ss_pred C----------cC-------------cHHHHHHHHHHh
Confidence 1 12 458999998887
No 66
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=93.71 E-value=0.07 Score=47.14 Aligned_cols=47 Identities=36% Similarity=0.438 Sum_probs=42.4
Q ss_pred CCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhhHHHHHHHh
Q 019356 283 KMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAML 334 (342)
Q Consensus 283 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 (342)
..+++||+.|.++.+|-...++.|.|.| ..|.|+|...++..|..++
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~-----~~v~i~G~~~~~~~A~~~i 145 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG-----KTVGIIGDPEQVQIAREAI 145 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC-----CEEEEECCHHHHHHHHHHH
Confidence 4689999999999999999999999975 7899999999999887655
No 67
>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=93.22 E-value=1.1 Score=39.49 Aligned_cols=64 Identities=27% Similarity=0.261 Sum_probs=41.3
Q ss_pred HhhHHHhcC--CCceEEEeeh-hhhHHHHHH---hcCCccC---ceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCcc
Q 019356 92 KACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKLH---NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPR 162 (342)
Q Consensus 92 ~~L~~lLe~--~~i~KV~hd~-k~Dl~~L~~---~~Gi~l~---~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~ 162 (342)
+.+..++.. ....-|+||+ .+|...|.+ ++|+.+. ..+||+-.+..+.+ +|.+|++ +
T Consensus 86 ~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~------------~L~~l~~--~ 151 (177)
T cd06136 86 NLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ------------SLGSLYK--R 151 (177)
T ss_pred HHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh------------hHHHHHH--H
Confidence 345555543 2345699998 899998854 3455432 25798877664432 6788887 7
Q ss_pred ccCCccc
Q 019356 163 YCGISYQ 169 (342)
Q Consensus 163 ~Lg~~l~ 169 (342)
++|++..
T Consensus 152 ~~~~~~~ 158 (177)
T cd06136 152 LFGQEPK 158 (177)
T ss_pred HhCCCcc
Confidence 7787654
No 68
>PRK13763 putative RNA-processing protein; Provisional
Probab=92.85 E-value=0.13 Score=45.80 Aligned_cols=47 Identities=36% Similarity=0.468 Sum_probs=41.6
Q ss_pred CCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhhHHHHHHHh
Q 019356 283 KMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAML 334 (342)
Q Consensus 283 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 (342)
..+++||+.|.++.+|-..+++.|.|-+ +.|.|+|+..++..|...+
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~-----~~v~i~G~~~~~~~A~~~I 151 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYG-----KTVAIIGDPEQVEIAREAI 151 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcC-----CEEEEEeCHHHHHHHHHHH
Confidence 4699999999999999999999999975 5599999999998886544
No 69
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=92.69 E-value=0.8 Score=44.17 Aligned_cols=99 Identities=14% Similarity=0.150 Sum_probs=66.4
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHH---hcCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCcccc
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~L 164 (342)
++..|.+++.+. .-|+||+.+|...|.+ .+|+.. ...+||+..+.-+-+... ..+|..|++ .+
T Consensus 70 v~~~~~~fl~~~--~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~-------~~~L~~L~~---~~ 137 (309)
T PRK06195 70 IWEKIKHYFNNN--LVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNID-------NARLNTVNN---FL 137 (309)
T ss_pred HHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCC-------cCCHHHHHH---Hc
Confidence 345666667553 4599999999988854 345543 248999876665544321 357888886 56
Q ss_pred CCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHHH
Q 019356 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLA 225 (342)
Q Consensus 165 g~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l~ 225 (342)
|+... . .-|..||..+..|+..|.+++...+...+.
T Consensus 138 gi~~~--~-----------------------H~Al~DA~ata~l~~~l~~~~~~~~~~~l~ 173 (309)
T PRK06195 138 GYEFK--H-----------------------HDALADAMACSNILLNISKELNSKDINEIS 173 (309)
T ss_pred CCCCc--c-----------------------cCCHHHHHHHHHHHHHHHHHhccCCHHHHH
Confidence 75432 1 127789999999999999888766554433
No 70
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=92.30 E-value=4.4 Score=36.48 Aligned_cols=91 Identities=15% Similarity=0.167 Sum_probs=56.4
Q ss_pred HHHhhHHHhcCCCceEEEeehh-hhHHHHHHhcCCccCc--eehHHH---HHHhhccccCCCCCCCCCCcHHHhhcCccc
Q 019356 90 VVKACKPALESSYITKVIHDCK-RDSEALYFQFGIKLHN--VVDTQI---AYSLIEEQEGRKRSPDDYISFVGLLADPRY 163 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k-~Dl~~L~~~~Gi~l~~--vfDtql---Aa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~ 163 (342)
++..+..++.+.. .|+||+. +|+..|. ..|..+.+ .+||.- .......+ .+ ..++|.+|++ +
T Consensus 74 vl~~f~~f~~~~~--lVaHNa~~fD~~fL~-~~g~~~~~~~~idt~~~~~~~~~~~~~----~~--~~~~L~~La~---~ 141 (195)
T PRK07247 74 VLAAFKEFVGELP--LIGYNAQKSDLPILA-ENGLDLSDQYQVDLYDEAFERRSSDLN----GI--ANLKLQTVAD---F 141 (195)
T ss_pred HHHHHHHHHCCCe--EEEEeCcHhHHHHHH-HcCCCcCCCceeehHHHHHHhhccccC----CC--CCCCHHHHHH---h
Confidence 4456677776553 5999985 8999994 67776543 355532 11111111 11 2468899986 6
Q ss_pred cCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 019356 164 CGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (342)
Q Consensus 164 Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (342)
+|++.. .+ + |..||..+..++..|...-+
T Consensus 142 ~gi~~~--~H----------r-------------Al~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 142 LGIKGR--GH----------N-------------SLEDARMTARVYESFLESDQ 170 (195)
T ss_pred cCCCCC--Cc----------C-------------CHHHHHHHHHHHHHHHhhcc
Confidence 776532 11 1 67899999999988865543
No 71
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=92.01 E-value=0.99 Score=52.05 Aligned_cols=98 Identities=16% Similarity=0.200 Sum_probs=68.3
Q ss_pred HHhhHHHhcCCCceEEEeehhhhHHHHH---HhcCCc-c-CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccC
Q 019356 91 VKACKPALESSYITKVIHDCKRDSEALY---FQFGIK-L-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCG 165 (342)
Q Consensus 91 ~~~L~~lLe~~~i~KV~hd~k~Dl~~L~---~~~Gi~-l-~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg 165 (342)
+..+..++.+ ...|.|++.+|...|. +.+|+. + ...+||+-.++.+.+... ..+|..|++ .+|
T Consensus 490 L~~f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k-------~~kL~~LAk---~lG 557 (1437)
T PRK00448 490 LPKFKEFCGD--SILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELK-------SHRLNTLAK---KFG 557 (1437)
T ss_pred HHHHHHHhCC--CEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccc-------cccHHHHHH---HcC
Confidence 3444444544 4569999999998763 356664 2 358999988887765432 468899996 467
Q ss_pred CccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHH
Q 019356 166 ISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYL 224 (342)
Q Consensus 166 ~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l 224 (342)
+.... . .-|-.||.++..|+..|.+++.+.|...+
T Consensus 558 L~~~~-~-----------------------HrAl~DA~aTa~lf~~ll~~l~~~gi~~~ 592 (1437)
T PRK00448 558 VELEH-H-----------------------HRADYDAEATAYLLIKFLKDLKEKGITNL 592 (1437)
T ss_pred CCCCC-C-----------------------cChHHHHHHHHHHHHHHHHHHHHcCCCCH
Confidence 65542 1 22788999999999999999987665443
No 72
>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=91.97 E-value=0.75 Score=41.02 Aligned_cols=78 Identities=19% Similarity=0.191 Sum_probs=52.8
Q ss_pred ceEEEeehhhhHHHHHH---hcCCc-----cCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHH
Q 019356 103 ITKVIHDCKRDSEALYF---QFGIK-----LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEV 174 (342)
Q Consensus 103 i~KV~hd~k~Dl~~L~~---~~Gi~-----l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~ 174 (342)
..-|+||+.+|...|.+ .+|+. ...++||...+..+.+. .+|..+++ ++|++... ..
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~~----------~~L~~l~~---~~gi~~~~-~~- 167 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQ----------TVLAKACQ---AAGIEFDN-KE- 167 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhCC----------CcHHHHHH---HCCCCCCC-CC-
Confidence 35699999999988863 35552 12479999988766442 36788886 45765421 00
Q ss_pred HHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHH
Q 019356 175 RVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (342)
Q Consensus 175 ~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~ 215 (342)
..-|..||..+..|+..|.++
T Consensus 168 --------------------~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 168 --------------------AHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred --------------------CcChHHHHHHHHHHHHHHHHh
Confidence 011778999999999888653
No 73
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=91.85 E-value=0.75 Score=39.18 Aligned_cols=92 Identities=21% Similarity=0.240 Sum_probs=62.5
Q ss_pred HHHhhHHHhcCCCceEEEeeh-hhhHHHHHHh---cCCcc---CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCcc
Q 019356 90 VVKACKPALESSYITKVIHDC-KRDSEALYFQ---FGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPR 162 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~-k~Dl~~L~~~---~Gi~l---~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~ 162 (342)
+...+..++.+.. .|+|++ ++|..+|.+. +|+.. ...+||+..++...+.. ..+|..+++
T Consensus 70 ~~~~~~~~l~~~~--~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~--------~~~L~~l~~--- 136 (169)
T smart00479 70 VLEELLEFLKGKI--LVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR--------KYSLKKLAE--- 136 (169)
T ss_pred HHHHHHHHhcCCE--EEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC--------CCCHHHHHH---
Confidence 4566777886643 477888 9999998642 44432 23799988777665431 368899996
Q ss_pred ccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 019356 163 YCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (342)
Q Consensus 163 ~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (342)
++|++.... ...|..||..+..|+..+.+++.
T Consensus 137 ~~~~~~~~~-----------------------~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 137 RLGLEVIGR-----------------------AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred HCCCCCCCC-----------------------CcCcHHHHHHHHHHHHHHHHHhh
Confidence 556543310 13388999999999999987653
No 74
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=91.39 E-value=0.17 Score=52.14 Aligned_cols=64 Identities=30% Similarity=0.585 Sum_probs=52.9
Q ss_pred CCCCCCCceeeccCCchHHHHHHhhcchhhccc---CCCCCCeEEEe-cchhhHHHHHHHhhhccccc
Q 019356 278 DVPPGKMGRIIGRRGSSILAIKESCNAEILIGG---AKGPPDKVFII-GPVKQVRKAEAMLRGRMLEM 341 (342)
Q Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 341 (342)
-||++|.+++|||.|-||-.|-+...|-+=+== ...|+.|+|+| |-..+|--|..++|.||=++
T Consensus 323 ~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~ 390 (600)
T KOG1676|consen 323 KVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDI 390 (600)
T ss_pred eccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHHHhccc
Confidence 479999999999999999999998887654432 24567789987 88889999999999998653
No 75
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=90.28 E-value=0.1 Score=39.84 Aligned_cols=43 Identities=30% Similarity=0.512 Sum_probs=34.3
Q ss_pred cccccCCCChhhhhhhcCCCCCCCceeeccCCchHHHHHHhhc
Q 019356 261 YLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCN 303 (342)
Q Consensus 261 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 (342)
.+.+..+..+..+.-.+.+.|+-||.+||++|.+|.||.-.-.
T Consensus 18 ~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~ 60 (76)
T COG1837 18 DVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLS 60 (76)
T ss_pred ceEEEEEecCCeEEEEEEECcccccceecCCChhHHHHHHHHH
Confidence 3445555566777888999999999999999999999986543
No 76
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=90.02 E-value=0.43 Score=42.84 Aligned_cols=44 Identities=43% Similarity=0.534 Sum_probs=40.0
Q ss_pred CceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhhHHHHHH
Q 019356 284 MGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEA 332 (342)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 332 (342)
.||+||+.|.|-.+|-...++.|.++| +.|-|||+.++|+-|..
T Consensus 113 kgRIIG~~GkTr~~IE~lt~~~I~V~g-----~tVaiiG~~~~v~iAr~ 156 (194)
T COG1094 113 KGRIIGREGKTRRAIEELTGVYISVYG-----KTVAIIGGFEQVEIARE 156 (194)
T ss_pred hceeeCCCchHHHHHHHHhCCeEEEeC-----cEEEEecChhhhHHHHH
Confidence 489999999999999999999999999 68999999988877654
No 77
>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=89.86 E-value=8.4 Score=34.91 Aligned_cols=144 Identities=16% Similarity=0.182 Sum_probs=79.0
Q ss_pred CceEEEEeeeeCCC--C-----CCcEEEEEEEeC--Cc-EEEEEcCCCC-hhHHHhhHHHhcC--CCceEEEeeh-hhhH
Q 019356 49 QLVIGFDCEGVDLC--R-----HGSLCIMQLAFP--DA-IYLVDAIQGG-ETVVKACKPALES--SYITKVIHDC-KRDS 114 (342)
Q Consensus 49 ~~~Ia~D~E~~~~~--~-----~g~l~llQLa~~--~~-~~liD~~~l~-~~~~~~L~~lLe~--~~i~KV~hd~-k~Dl 114 (342)
-..++||+|..+.. . ...-.++||+.. ++ ..++...... .+++..+..++.. |.+ .++||. .+|+
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdi-i~g~N~~~FD~ 87 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPDV-IEGHNIFRFDL 87 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccCCCCHHHHHHHHHHHHHHhCCCE-EeccCCcccCH
Confidence 46789999986532 1 223457777752 22 2222111111 2455566555554 554 379998 7899
Q ss_pred HHHHH---hcCCccC-------------------------------c-eehHHHHHHhhccccCCCCCCCCCCcHHHhhc
Q 019356 115 EALYF---QFGIKLH-------------------------------N-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLA 159 (342)
Q Consensus 115 ~~L~~---~~Gi~l~-------------------------------~-vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~ 159 (342)
..|.. .+|+... . ++|++.+..-.+.. .+.+ ...+|..+++
T Consensus 88 pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~--~~~l--~sysL~~Va~ 163 (207)
T cd05785 88 PYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVS--SRDL--PSYGLKAVAK 163 (207)
T ss_pred HHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhccc--ccCC--CCCCHHHHHH
Confidence 88753 3554431 1 36776654422211 1122 2468899987
Q ss_pred Cccc--cCC---ccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHH
Q 019356 160 DPRY--CGI---SYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (342)
Q Consensus 160 ~~~~--Lg~---~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~ 209 (342)
.+ ++. .++ .++... .|...+ +...+|+..||..++.|+
T Consensus 164 --~~g~~~~~k~d~~-~~~I~~-------l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 164 --HFGLASPDRTYID-GRQIAE-------VWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred --HhcccCCCcCCCC-HHHHHH-------HHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 54 221 112 122222 354442 788999999999998875
No 78
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=89.40 E-value=0.77 Score=38.21 Aligned_cols=54 Identities=28% Similarity=0.473 Sum_probs=44.4
Q ss_pred CCCceeeccCCchHHHHHHhhcchhhcccCCC--------------------CCCeEEEecch---hhHHHHHHHhhh
Q 019356 282 GKMGRIIGRRGSSILAIKESCNAEILIGGAKG--------------------PPDKVFIIGPV---KQVRKAEAMLRG 336 (342)
Q Consensus 282 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~---~~~~~~~~~~~~ 336 (342)
..+|++||-+|.||..|.+..++.|.|-|- | -|=.|+|.++- ..+.+|..++..
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~-gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ 91 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGK-GSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEE 91 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecC-cccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHH
Confidence 457999999999999999999999999984 2 13569999987 677888777653
No 79
>PRK00468 hypothetical protein; Provisional
Probab=89.01 E-value=0.13 Score=39.25 Aligned_cols=43 Identities=30% Similarity=0.486 Sum_probs=32.1
Q ss_pred ccccCCCChhhhhhhcCCCCCCCceeeccCCchHHHHHHhhcc
Q 019356 262 LIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCNA 304 (342)
Q Consensus 262 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 304 (342)
+.+.....++.+.-...++|.-+|++|||+|.+|.||....+|
T Consensus 19 v~V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~a 61 (75)
T PRK00468 19 VQVNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKA 61 (75)
T ss_pred EEEEEEeCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHHH
Confidence 3333333445566778889999999999999999999876554
No 80
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=88.85 E-value=7 Score=35.84 Aligned_cols=79 Identities=14% Similarity=-0.018 Sum_probs=52.2
Q ss_pred eEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCC
Q 019356 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQ 183 (342)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~ 183 (342)
.-|+||+.+|...|. ..+ ...+||+-.++.+-++. ..++..|++ ++|+..... +
T Consensus 76 ~lVaHNa~FD~~~L~-~~~---~~~idTl~lar~l~p~~--------~~~l~~L~~---~~~l~~~~~-~---------- 129 (219)
T PRK07983 76 WYVAHNASFDRRVLP-EMP---GEWICTMKLARRLWPGI--------KYSNMALYK---SRKLNVQTP-P---------- 129 (219)
T ss_pred EEEEeCcHhhHHHHh-CcC---CCcEeHHHHHHHHccCC--------CCCHHHHHH---HcCCCCCCC-C----------
Confidence 459999999999994 322 45899999887766542 256778885 556543100 0
Q ss_pred CCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHH
Q 019356 184 FWTYRPLTELMVRAAADDVRFLPYIYHNMMKKL 216 (342)
Q Consensus 184 dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L 216 (342)
... ..-|..||.++..|+..+.+..
T Consensus 130 ~~~--------aHrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 130 GLH--------HHRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred CCC--------CCcHHHHHHHHHHHHHHHHHHc
Confidence 000 1227899999999998887544
No 81
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=87.81 E-value=0.41 Score=42.24 Aligned_cols=57 Identities=23% Similarity=0.381 Sum_probs=46.0
Q ss_pred cCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEE---ecchhhHHHHHHHhhh
Q 019356 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFI---IGPVKQVRKAEAMLRG 336 (342)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~ 336 (342)
..||+.+++.+||..|.+|..|.+.+++.|-|--.. ..|.| -+....+-||..++..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~---g~V~I~~~t~d~~~i~kA~~~I~~ 61 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSET---GEVKIEEEDEDPLAVMKAREVVKA 61 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCC---ceEEEecCCCCHHHHHHHHHHHHH
Confidence 358999999999999999999999999999987422 24666 3667788888877643
No 82
>PRK13763 putative RNA-processing protein; Provisional
Probab=87.77 E-value=0.49 Score=42.11 Aligned_cols=57 Identities=23% Similarity=0.435 Sum_probs=48.0
Q ss_pred hcCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEe----cchhhHHHHHHHhh
Q 019356 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFII----GPVKQVRKAEAMLR 335 (342)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~ 335 (342)
...||+.|++.+||..|.+|..|.+.+++.|-|=-.. .+|+|. +....+-||..++.
T Consensus 6 ~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~---g~V~I~~~~~~d~~~i~kA~~~I~ 66 (180)
T PRK13763 6 YVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSET---GEVIIEPTDGEDPLAVLKARDIVK 66 (180)
T ss_pred EEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCC---CeEEEEeCCCCCHHHHHHHHHHHH
Confidence 4578999999999999999999999999999887532 468886 67788888887765
No 83
>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase []. ; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 4DF4_A 3T3F_A 1QSY_A 3OJS_A 3PO5_A 3OJU_A 1QTM_A 1QSS_A 3PY8_A 4DFJ_A ....
Probab=87.23 E-value=2.2 Score=35.92 Aligned_cols=69 Identities=17% Similarity=0.207 Sum_probs=40.5
Q ss_pred hhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCC
Q 019356 111 KRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPL 190 (342)
Q Consensus 111 k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPL 190 (342)
..|+.++...-|+.+..--|-++.+||+++.++ +...+++ +|+|- +|...
T Consensus 70 AK~LAv~a~~~G~~v~PGDDPlLlAYLlDPsNt---------~p~~var--RY~~~-----------------~W~~d-- 119 (138)
T PF09281_consen 70 AKDLAVHALREGVVVEPGDDPLLLAYLLDPSNT---------NPEGVAR--RYLGG-----------------EWPED-- 119 (138)
T ss_dssp HHHHHHHHHHTT----B---HHHHHHHH-TT-----------SHHHHHH--HH-TS--------------------SS--
T ss_pred HHHHHHHHHhcCcccCCCCCcchhhhhcCccCC---------ChHHHHH--HhcCC-----------------CCCcc--
Confidence 456666556789888877899999999999753 4467777 88763 45332
Q ss_pred cHHHHHHHHHHhHHHHHHHHHHHHHH
Q 019356 191 TELMVRAAADDVRFLPYIYHNMMKKL 216 (342)
Q Consensus 191 s~~ql~YAA~Da~~Ll~L~~~L~~~L 216 (342)
|+..+...-+|+..|..+|
T Consensus 120 -------A~~RA~~t~~L~~~L~prL 138 (138)
T PF09281_consen 120 -------AATRALATARLLRALPPRL 138 (138)
T ss_dssp -------HHHHHHHHHHHHHHHHHHT
T ss_pred -------HHHHHHHHHHHHHHhhhcC
Confidence 6677777888888887664
No 84
>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=86.92 E-value=2.6 Score=34.85 Aligned_cols=50 Identities=16% Similarity=-0.006 Sum_probs=35.0
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHHhcC-----CccCceehHHHHHHhhccc
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFG-----IKLHNVVDTQIAYSLIEEQ 141 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~G-----i~l~~vfDtqlAa~LL~~~ 141 (342)
+...+..++++ -..|+||+.+|..+|.+.+. ......+||+..+..+.+.
T Consensus 69 ~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~ 123 (159)
T cd06127 69 VLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPG 123 (159)
T ss_pred HHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCC
Confidence 45667777876 35699999999999865433 2234589999877665543
No 85
>PRK02821 hypothetical protein; Provisional
Probab=86.11 E-value=0.24 Score=38.03 Aligned_cols=44 Identities=23% Similarity=0.383 Sum_probs=32.2
Q ss_pred ccccCCCChhhhhhhcCCCCCCCceeeccCCchHHHHHHhhcch
Q 019356 262 LIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCNAE 305 (342)
Q Consensus 262 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 305 (342)
+.+..+..++...-...++|.-+|++||++|.+|.||....+|-
T Consensus 20 V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~ 63 (77)
T PRK02821 20 VRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI 63 (77)
T ss_pred EEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh
Confidence 33333333444556677789999999999999999998877763
No 86
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=85.41 E-value=1.1 Score=46.48 Aligned_cols=62 Identities=29% Similarity=0.486 Sum_probs=50.5
Q ss_pred hhhcCCCCCCCceeeccCCchHHHHHHhhcchhhcc---cCCCCCCeEEEecchhhHHHHHHHhh
Q 019356 274 LSILDVPPGKMGRIIGRRGSSILAIKESCNAEILIG---GAKGPPDKVFIIGPVKQVRKAEAMLR 335 (342)
Q Consensus 274 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~ 335 (342)
-.+.+||..++|.+||+.|-+|..|-....+.|-|= +++.|---+-|||++.++-.|+.++.
T Consensus 231 ~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~ 295 (600)
T KOG1676|consen 231 TREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELIN 295 (600)
T ss_pred eeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHH
Confidence 346789999999999999999999999888988773 33333333889999999999998764
No 87
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=84.18 E-value=25 Score=33.69 Aligned_cols=89 Identities=12% Similarity=0.030 Sum_probs=51.4
Q ss_pred HhhHHHhcCCCceEEEeehhhhHHHHHHhcCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccc
Q 019356 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (342)
Q Consensus 92 ~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~ 169 (342)
..+..+++... .-|+||+.+|..+|.+ +.... ....+++.......... ...+|.+|+. .+|....
T Consensus 112 ~~l~~fl~~~~-vlVAHNA~FD~~fL~~-~~~~~~~~~~~ct~~~i~~~~~~~-------~~~kL~~La~---~~g~~~~ 179 (294)
T PRK09182 112 AAVDALIAPAD-LIIAHNAGFDRPFLER-FSPVFATKPWACSVSEIDWSARGF-------EGTKLGYLAG---QAGFFHE 179 (294)
T ss_pred HHHHHHhcCCC-EEEEeCHHHHHHHHHH-HHHhccCCcccccHHHHhhccccC-------CCCCHHHHHH---HcCCCCC
Confidence 45666776643 4589999999999954 33222 23455554322111111 1367888886 3452111
Q ss_pred hhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 019356 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (342)
Q Consensus 170 kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (342)
. .=|..||.++..|...+.....
T Consensus 180 --a-----------------------HrAl~Da~Ata~ll~~~l~~~~ 202 (294)
T PRK09182 180 --G-----------------------HRAVDDCQALLELLARPLPETG 202 (294)
T ss_pred --C-----------------------cChHHHHHHHHHHHHHHHhhcC
Confidence 1 1178899999888876654443
No 88
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=83.59 E-value=0.65 Score=43.08 Aligned_cols=57 Identities=30% Similarity=0.613 Sum_probs=47.9
Q ss_pred hhcCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchh-hHHHHHHHhh
Q 019356 275 SILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVK-QVRKAEAMLR 335 (342)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 335 (342)
-...|||.+.+++||.+|..|..|.+.++++|.||- --+|+|-|+-. .+-+|..++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~----NG~VwI~~~~~~~~~~a~~~I~ 204 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ----NGRIWIKGPDEEDEEIAIEAIK 204 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC----CcEEEEeeCCHHHHHHHHHHHH
Confidence 346789999999999999999999999999999986 26899999987 5666666654
No 89
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=81.36 E-value=1.5 Score=41.22 Aligned_cols=39 Identities=41% Similarity=0.731 Sum_probs=34.9
Q ss_pred ceeeccCCchHHHHHHhhcc--hhhcccCCCCCCeEEEecc
Q 019356 285 GRIIGRRGSSILAIKESCNA--EILIGGAKGPPDKVFIIGP 323 (342)
Q Consensus 285 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ 323 (342)
+-+|||.|+.|-.+.+.|.| .||.|-..+--|||.|||-
T Consensus 135 g~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g 175 (390)
T KOG2192|consen 135 GGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGG 175 (390)
T ss_pred cceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecC
Confidence 56799999999999999985 6888999999999999974
No 90
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=81.27 E-value=4.3 Score=43.87 Aligned_cols=105 Identities=16% Similarity=0.161 Sum_probs=61.9
Q ss_pred ceEEEeehhhhHHHHHHhcCCccCc--eehHHHHHHhhc----ccc----------------CCC-CCC-------C--C
Q 019356 103 ITKVIHDCKRDSEALYFQFGIKLHN--VVDTQIAYSLIE----EQE----------------GRK-RSP-------D--D 150 (342)
Q Consensus 103 i~KV~hd~k~Dl~~L~~~~Gi~l~~--vfDtqlAa~LL~----~~~----------------~~~-~L~-------~--~ 150 (342)
-..||||..+|..-+..+|.|.-.. .+|||-++-... .++ .++ ... + .
T Consensus 242 ~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~~pWL~~SS 321 (1075)
T KOG3657|consen 242 QLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDYDNPWLGRSS 321 (1075)
T ss_pred ceEEeccccchHHHHHHHHhccccceeeeechhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhhhhhhhhhhh
Confidence 4569999999999998889987643 789997654321 111 000 000 0 0
Q ss_pred CCcHHHhhcCccccCCc-cchhHHHHHHhcCCCCCCCCCCCc------HHHHHHHHHHhHHHHHHHHHHHHHHhc
Q 019356 151 YISFVGLLADPRYCGIS-YQEKEEVRVLLRQDPQFWTYRPLT------ELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (342)
Q Consensus 151 ~~sL~~Lv~~~~~Lg~~-l~kK~~~~~l~~~~~~dW~~RPLs------~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (342)
.-||.++.. -++|.. ++ |+. |. +|-.-++. .+.+.|+|.|++...+++..+-....+
T Consensus 322 ~NSL~dVhk--~~c~~~~Ld-Kt~-Rd-------~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fle 385 (1075)
T KOG3657|consen 322 LNSLVDVHK--FHCGIDALD-KTP-RD-------SFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLE 385 (1075)
T ss_pred hHHHHHHHH--hhCCCCccc-cch-HH-------hhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHH
Confidence 124444444 566665 44 221 11 12111111 345899999999999999988777654
No 91
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=81.21 E-value=1.2 Score=32.37 Aligned_cols=33 Identities=21% Similarity=0.364 Sum_probs=27.5
Q ss_pred hhhcCCCCCCCceeeccCCchHHHHHHhhcchh
Q 019356 274 LSILDVPPGKMGRIIGRRGSSILAIKESCNAEI 306 (342)
Q Consensus 274 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 306 (342)
....-|+++.++.+||+.|.+|..+.+.++-.|
T Consensus 26 ~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I 58 (61)
T cd02134 26 RARVVVPDDQLGLAIGKGGQNVRLASKLLGEKI 58 (61)
T ss_pred EEEEEECcccceeeECCCCHHHHHHHHHHCCCe
Confidence 445667899999999999999999998877444
No 92
>PRK01064 hypothetical protein; Provisional
Probab=80.72 E-value=0.68 Score=35.59 Aligned_cols=35 Identities=31% Similarity=0.496 Sum_probs=29.5
Q ss_pred hhhhhhhcCCCCCCCceeeccCCchHHHHHHhhcc
Q 019356 270 EEEILSILDVPPGKMGRIIGRRGSSILAIKESCNA 304 (342)
Q Consensus 270 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 304 (342)
...+.-...+.+..+|++||++|.+|.||....++
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~ 61 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVS 61 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHHHH
Confidence 44566778889999999999999999999887664
No 93
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=80.35 E-value=8.6 Score=34.61 Aligned_cols=93 Identities=15% Similarity=0.104 Sum_probs=58.5
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHHh---cCCcc---CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccc
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRY 163 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~---~Gi~l---~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~ 163 (342)
++..|.+++.+.... ++|++.+|+..|.+. +|+.. ....|++.....+.+.. ...+|..+++ +
T Consensus 82 vl~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~-------~~~~L~~~~~---~ 150 (207)
T PRK07748 82 LVEKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGER-------NQTGLWKAIE---E 150 (207)
T ss_pred HHHHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcC-------CCCCHHHHHH---H
Confidence 456677778763222 557788999888643 46543 34778887654443221 1368899886 5
Q ss_pred cCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHH
Q 019356 164 CGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKL 216 (342)
Q Consensus 164 Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L 216 (342)
+|++..... .-|..||..+..|+..|....
T Consensus 151 ~gi~~~~~~-----------------------H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 151 YGKEGTGKH-----------------------HCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred cCCCCCCCC-----------------------cChHHHHHHHHHHHHHHHhCc
Confidence 676532111 117789999999999887653
No 94
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=80.02 E-value=0.5 Score=51.09 Aligned_cols=94 Identities=19% Similarity=0.209 Sum_probs=66.8
Q ss_pred HhcCCCceEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchhHHHHH
Q 019356 97 ALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRV 176 (342)
Q Consensus 97 lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~ 176 (342)
+|-+-.++.|||+...|...+ ..-+....++||..... ++.+ +.+||..|+- .+||.++-...
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvI--Ni~Vp~~QiiDTv~lf~-~~s~--------R~LSLrfLa~--~lLg~~IQ~~~---- 1071 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVI--NIHVPEEQIIDTVTLFR-LGSQ--------RMLSLRFLAW--ELLGETIQMEA---- 1071 (1118)
T ss_pred HHHHcCcEEEcccccccceEE--EEecChhhheeeeEEEe-cccc--------cEEEHHHHHH--HHhcchhhccc----
Confidence 566778999999999999877 23333345999877422 2222 2589999998 89997653111
Q ss_pred HhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHHHhccccHHHHHh
Q 019356 177 LLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVR 227 (342)
Q Consensus 177 l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~l~~~ 227 (342)
.| ..+||+..+.||+++. +|+++|+.+-...
T Consensus 1072 ------HD-------------SIeDA~taLkLYk~Yl-~lkeq~~~~~~l~ 1102 (1118)
T KOG1275|consen 1072 ------HD-------------SIEDARTALKLYKKYL-KLKEQGKLESELR 1102 (1118)
T ss_pred ------cc-------------cHHHHHHHHHHHHHHH-HHHHhhHHHHHHH
Confidence 12 4589999999999996 7888887776664
No 95
>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=78.27 E-value=52 Score=29.72 Aligned_cols=129 Identities=12% Similarity=0.073 Sum_probs=74.3
Q ss_pred CCCcEEEEEEEe---CCcEEEE-EcCCCC-hhHHHhhHHHhcCCCceEEEeeh-hhhHHHHHH---hcCCccC-------
Q 019356 63 RHGSLCIMQLAF---PDAIYLV-DAIQGG-ETVVKACKPALESSYITKVIHDC-KRDSEALYF---QFGIKLH------- 126 (342)
Q Consensus 63 ~~g~l~llQLa~---~~~~~li-D~~~l~-~~~~~~L~~lLe~~~i~KV~hd~-k~Dl~~L~~---~~Gi~l~------- 126 (342)
..++++.|.++. .++.+.+ ...... .+++..+...+++-...-|+||. .+|+..|.. .+|+.+.
T Consensus 49 ~~~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~ 128 (208)
T cd05782 49 PFHKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGN 128 (208)
T ss_pred ccCceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCccc
Confidence 357788888775 3333333 111122 24566666666652224589997 689998864 3666321
Q ss_pred -----------ceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCc--cc-hhHHHHHHhcCCCCCCCCCCCcH
Q 019356 127 -----------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGIS--YQ-EKEEVRVLLRQDPQFWTYRPLTE 192 (342)
Q Consensus 127 -----------~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~--l~-kK~~~~~l~~~~~~dW~~RPLs~ 192 (342)
..+|++-...-.+. ....+|..+++ +||.+ .+ +-+++-. .|.... -+
T Consensus 129 ~~~~y~~r~~~~h~DL~~~~~~~~~--------~~~~~L~~va~---~lG~~~K~d~~G~~v~~-------~y~~g~-~~ 189 (208)
T cd05782 129 KDWNYRNRYSERHLDLMDLLAFYGA--------RARASLDLLAK---LLGIPGKMDVDGSQVWE-------LYAEGK-LD 189 (208)
T ss_pred chhhccCcCCCCcccHHHHHhccCc--------cCCCCHHHHHH---HhCCCCCcCCCHHHHHH-------HHHcCC-hH
Confidence 15677765432221 02478888875 67762 11 0122221 344434 46
Q ss_pred HHHHHHHHHhHHHHHHHH
Q 019356 193 LMVRAAADDVRFLPYIYH 210 (342)
Q Consensus 193 ~ql~YAA~Da~~Ll~L~~ 210 (342)
...+|+..||..+..||.
T Consensus 190 ~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 190 EIAEYCETDVLNTYLLYL 207 (208)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 789999999999988874
No 96
>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=77.92 E-value=18 Score=33.06 Aligned_cols=106 Identities=17% Similarity=0.094 Sum_probs=67.2
Q ss_pred hHHHhhHHHhcCCCceEEEeehh-hhHHHHHH---hcCCccCc-------------------eehHHHHHHhhccccCCC
Q 019356 89 TVVKACKPALESSYITKVIHDCK-RDSEALYF---QFGIKLHN-------------------VVDTQIAYSLIEEQEGRK 145 (342)
Q Consensus 89 ~~~~~L~~lLe~~~i~KV~hd~k-~Dl~~L~~---~~Gi~l~~-------------------vfDtqlAa~LL~~~~~~~ 145 (342)
+++..+...++.....-|.||.+ +|+..|.. .+|+.+.. -+|||-. +-+.+ ++
T Consensus 39 ~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~--l~~~g-~~- 114 (209)
T PF10108_consen 39 ELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDL--LSFYG-AK- 114 (209)
T ss_pred HHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHH--HhccC-cc-
Confidence 45677777787655566999965 89988853 37776532 2566644 22222 11
Q ss_pred CCCCCCCcHHHhhcCccccCCccc---hhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHH
Q 019356 146 RSPDDYISFVGLLADPRYCGISYQ---EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (342)
Q Consensus 146 ~L~~~~~sL~~Lv~~~~~Lg~~l~---kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~ 213 (342)
...||..|+. .||++-. +-+++..+ |..-.+ ++...|+-.||..+..||-.+.
T Consensus 115 ----~~~sLd~la~---~lgiPgK~~idGs~V~~~-------y~~g~i-~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 115 ----ARTSLDELAA---LLGIPGKDDIDGSQVAEL-------YQEGDI-DEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred ----ccCCHHHHHH---HcCCCCCCCCCHHHHHHH-------HHcCCH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 2478998884 8887521 02233322 333333 5678999999999999998775
No 97
>PRK12704 phosphodiesterase; Provisional
Probab=77.63 E-value=3.1 Score=43.16 Aligned_cols=55 Identities=33% Similarity=0.706 Sum_probs=45.1
Q ss_pred CChhhhhhhcCCCCCCC-ceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEec--chh
Q 019356 268 VPEEEILSILDVPPGKM-GRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIG--PVK 325 (342)
Q Consensus 268 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~ 325 (342)
..-|..-++..+|..-| |++|||-|.+|.++.+.+..+|.|-- -|+-|++-| |+.
T Consensus 205 ~~~e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd---tp~~v~ls~~~~~r 262 (520)
T PRK12704 205 HVAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---TPEAVILSGFDPIR 262 (520)
T ss_pred hhhhhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC---CCCeEEEecCChhh
Confidence 34556677888887666 99999999999999999999999954 588888876 555
No 98
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=75.79 E-value=3 Score=42.86 Aligned_cols=65 Identities=35% Similarity=0.501 Sum_probs=55.2
Q ss_pred hcCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCe---EEEecchhhHHHHHHHhhhcccc
Q 019356 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDK---VFIIGPVKQVRKAEAMLRGRMLE 340 (342)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~ 340 (342)
++=||...+|.+||++|..|-.|.+.+.|-|.|-+.--|.-- |-|-|-+..|.||-..+-+.|++
T Consensus 141 RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 141 RLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLE 208 (485)
T ss_pred EEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHh
Confidence 334677788999999999999999999999999886444322 88999999999999999998887
No 99
>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=75.18 E-value=38 Score=30.31 Aligned_cols=103 Identities=15% Similarity=0.101 Sum_probs=58.3
Q ss_pred hHHHhhHHHhcC--CCceEEEeehh-hhHHHHHH---hcCCccC------------------------c--eehHHHHHH
Q 019356 89 TVVKACKPALES--SYITKVIHDCK-RDSEALYF---QFGIKLH------------------------N--VVDTQIAYS 136 (342)
Q Consensus 89 ~~~~~L~~lLe~--~~i~KV~hd~k-~Dl~~L~~---~~Gi~l~------------------------~--vfDtqlAa~ 136 (342)
+++..+..++.. |.+ -++||.. +|+..|.+ .+|+.+. + ++|+.-...
T Consensus 53 ~lL~~f~~~i~~~dPDv-i~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k 131 (193)
T cd05784 53 SLLLALIAWFAQYDPDI-IIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALK 131 (193)
T ss_pred HHHHHHHHHHHhhCCCE-EEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHH
Confidence 345555555544 454 4899965 58888753 3444321 1 566543322
Q ss_pred hhccccCCCCCCCCCCcHHHhhcCccccCCccchh------HHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHH
Q 019356 137 LIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK------EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYH 210 (342)
Q Consensus 137 LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK------~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~ 210 (342)
- . ...+ ...+|.++++ ++||..-.+. .+... .|...+ ....+|+..||..+++|++
T Consensus 132 ~---~--~~kl--~sy~L~~Va~--~~Lg~~K~~~~~~~~~~eI~~-------~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 132 T---A--TYHF--ESFSLENVAQ--ELLGEGKLIHDVDDRGAEIER-------LFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred H---c--cCCC--CcCCHHHHHH--HHhCCCccccCcccCHHHHHH-------HHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 1 0 0111 2578999998 8998531110 11111 244333 5789999999999998863
No 100
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=75.11 E-value=3 Score=44.75 Aligned_cols=57 Identities=30% Similarity=0.479 Sum_probs=47.3
Q ss_pred hcCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhh-HHHHHHHhhh
Q 019356 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQ-VRKAEAMLRG 336 (342)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 336 (342)
...|||.|++.+||-.|.+|.+|.+..++.|-|-- --+|+|.|+-++ +.||..++.+
T Consensus 581 ~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d----~G~V~I~a~d~~~~~~A~~~I~~ 638 (719)
T TIGR02696 581 TVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED----DGTVYIGAADGPSAEAARAMINA 638 (719)
T ss_pred EEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec----CcEEEEEeCCHHHHHHHHHHHHH
Confidence 45678999999999999999999999999999876 357999998654 5677777654
No 101
>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=74.48 E-value=62 Score=28.69 Aligned_cols=143 Identities=17% Similarity=0.170 Sum_probs=79.3
Q ss_pred ceEEEEeeeeCCC-----CCCcEEEEEEEeC-CcEEEEEcCCCC-hhHHHhhHHHhcC--CCceEEEeeh-hhhHHHHHH
Q 019356 50 LVIGFDCEGVDLC-----RHGSLCIMQLAFP-DAIYLVDAIQGG-ETVVKACKPALES--SYITKVIHDC-KRDSEALYF 119 (342)
Q Consensus 50 ~~Ia~D~E~~~~~-----~~g~l~llQLa~~-~~~~liD~~~l~-~~~~~~L~~lLe~--~~i~KV~hd~-k~Dl~~L~~ 119 (342)
..++||.|+.+.. ..+.+..|+++.. +...++-..... .+++..+..++.. |.+ -++||. .+|+..|..
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~-i~gyN~~~FDlpyl~~ 82 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDI-IVGYNSNAFDWPYLVE 82 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCE-EEecCCCcCcHHHHHH
Confidence 5689999997421 2345666665553 334444221122 2455666665554 443 378884 588888753
Q ss_pred ---hcCCccC----------------------ceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCc--cc---
Q 019356 120 ---QFGIKLH----------------------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGIS--YQ--- 169 (342)
Q Consensus 120 ---~~Gi~l~----------------------~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~--l~--- 169 (342)
.+|+.+. -.+|+.-...-.. .+ ...+|.++++ +||.. ..
T Consensus 83 Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~------~l--~~y~L~~Va~---~Lg~~k~~~k~~ 151 (188)
T cd05781 83 RARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP------EV--KVKTLENVAE---YLGVMKKSERVL 151 (188)
T ss_pred HHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC------CC--CCCCHHHHHH---HHCCCccccccC
Confidence 4665431 0456555332111 12 2478888885 57752 11
Q ss_pred -hhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHH
Q 019356 170 -EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHN 211 (342)
Q Consensus 170 -kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~ 211 (342)
.-.+.-. -|....-.....+|+..|+..+..|+..
T Consensus 152 ~~~~~i~~-------~~~~~~~~~~l~~Y~~~D~~~t~~l~~~ 187 (188)
T cd05781 152 IEWYRIYE-------YWDDEKKRDILLKYNRDDARSTYGLAEK 187 (188)
T ss_pred CCHHHHHH-------HHcCcccHHHHHHHHHHHHHHHHHHHhh
Confidence 0112211 3543212378899999999999999875
No 102
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=71.28 E-value=2.3 Score=42.48 Aligned_cols=64 Identities=30% Similarity=0.466 Sum_probs=55.8
Q ss_pred cCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCe---EEEecchhhHHHHHHHhhhcccc
Q 019356 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDK---VFIIGPVKQVRKAEAMLRGRMLE 340 (342)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~ 340 (342)
.=||...+|-+||.+|..|--|.+-+.|-|-|--+..|.-+ |.|-||....=||.--+-||+-|
T Consensus 415 ~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikE 481 (584)
T KOG2193|consen 415 MFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKE 481 (584)
T ss_pred eeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhh
Confidence 34677778999999999999999999999999988877654 88889999999999988888754
No 103
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=69.59 E-value=6.6 Score=37.07 Aligned_cols=58 Identities=31% Similarity=0.558 Sum_probs=48.3
Q ss_pred CCCCCCceeeccCCchHHHHHHhhcchhhccc-CCCCCCeEEEe-cchhhHHHHHHHhhh
Q 019356 279 VPPGKMGRIIGRRGSSILAIKESCNAEILIGG-AKGPPDKVFII-GPVKQVRKAEAMLRG 336 (342)
Q Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~ 336 (342)
||.---+.+||+.|..|.-|.....|.|-|-. ..|-||+|.+| |...|+..|+-+|..
T Consensus 321 ip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn 380 (390)
T KOG2192|consen 321 IPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQN 380 (390)
T ss_pred cccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHH
Confidence 33333478999999999999999999999998 57899997655 999999999887753
No 104
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=66.47 E-value=4.1 Score=43.76 Aligned_cols=57 Identities=28% Similarity=0.376 Sum_probs=46.6
Q ss_pred cCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhh-HHHHHHHhhhc
Q 019356 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQ-VRKAEAMLRGR 337 (342)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 337 (342)
..|||.|++.+||.+|.+|.+|.+..++.|-|-- --+|+|.++-++ +.||.+++...
T Consensus 555 ~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d----dG~V~i~~~~~~~~~~a~~~I~~~ 612 (684)
T TIGR03591 555 IKINPDKIRDVIGPGGKVIREITEETGAKIDIED----DGTVKIAASDGEAAEAAIKMIEGI 612 (684)
T ss_pred EecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec----CeEEEEEECcHHHHHHHHHHHHhh
Confidence 6778999999999999999999999999999965 257888887654 66777776543
No 105
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=65.83 E-value=34 Score=34.16 Aligned_cols=89 Identities=22% Similarity=0.186 Sum_probs=55.0
Q ss_pred HhhHHHhcCCCceEEEeehhhhHHHHHHhcCCccCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccchh
Q 019356 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK 171 (342)
Q Consensus 92 ~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~kK 171 (342)
..|..++....| -|||..-.|+.+|.-.| ..+.||.+ ++....+... ...||..|++ .|||..+..
T Consensus 285 ~~l~~~~~~~TI-LVGHSLenDL~aLKl~H----~~ViDTa~---lf~~~~g~~~---~k~sLk~L~~--~~L~~~Iq~- 350 (380)
T KOG2248|consen 285 KELLELISKNTI-LVGHSLENDLKALKLDH----PSVIDTAV---LFKHPTGPYP---FKSSLKNLAK--SYLGKLIQE- 350 (380)
T ss_pred HHHHhhcCcCcE-EEeechhhHHHHHhhhC----CceeeeeE---EEecCCCCcc---chHHHHHHHH--HHHHHHHhc-
Confidence 456666655554 59999999999995322 35789984 2333322111 1467899998 888854420
Q ss_pred HHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHH
Q 019356 172 EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMK 214 (342)
Q Consensus 172 ~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~ 214 (342)
. ....+ +.+||..++.|......
T Consensus 351 -~------~~~Hd-------------S~eDA~acm~Lv~~k~~ 373 (380)
T KOG2248|consen 351 -G------VGGHD-------------SVEDALACMKLVKLKIK 373 (380)
T ss_pred -c------CCCCc-------------cHHHHHHHHHHHHHHHh
Confidence 0 00012 66888888888766543
No 106
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=65.17 E-value=12 Score=36.49 Aligned_cols=61 Identities=33% Similarity=0.442 Sum_probs=47.9
Q ss_pred CCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCC----Ce-EEEecchhhHHHHHHHhhhccc
Q 019356 279 VPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPP----DK-VFIIGPVKQVRKAEAMLRGRML 339 (342)
Q Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~-~~~~~~~~~~~~~~~~~~~~~~ 339 (342)
+|...-+.+||+.|++|.+|.++..+-|-|-=+|+-- || |-++|...+.+||-.++--|+.
T Consensus 138 vPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~ 203 (402)
T KOG2191|consen 138 VPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQ 203 (402)
T ss_pred ccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhh
Confidence 4667779999999999999999999998886433221 22 7789999999999877766654
No 107
>PRK06722 exonuclease; Provisional
Probab=64.58 E-value=30 Score=33.01 Aligned_cols=91 Identities=14% Similarity=0.073 Sum_probs=52.6
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHHh---cCCccC-----ceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCc
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKLH-----NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADP 161 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~~---~Gi~l~-----~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~ 161 (342)
++..+..++.+..+ |+|++.+|...|.+. +|+... ..+|++-.++-+-+... ....||..+++
T Consensus 80 Vl~ef~~fig~~~l--vahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~-----~~~~sL~~l~~-- 150 (281)
T PRK06722 80 IIEKFIQFIGEDSI--FVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELF-----EHTPSLQSAVE-- 150 (281)
T ss_pred HHHHHHHHHCCCcE--EEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhc-----cCCCCHHHHHH--
Confidence 45566777765433 778889999988653 555431 13677643322111100 11358999996
Q ss_pred cccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHH
Q 019356 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (342)
Q Consensus 162 ~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~ 213 (342)
++|++.....+ + |-.||..+..|+..|.
T Consensus 151 -~lgL~~~g~~H----------r-------------AL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 151 -QLGLIWEGKQH----------R-------------ALADAENTANILLKAY 178 (281)
T ss_pred -HCCCCCCCCCc----------C-------------cHHHHHHHHHHHHHHh
Confidence 67765431111 1 5677887777777765
No 108
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=63.78 E-value=1.5 Score=32.82 Aligned_cols=38 Identities=24% Similarity=0.403 Sum_probs=30.2
Q ss_pred hhhhhhhcCCCCCCCceeeccCCchHHHHHHhhcchhh
Q 019356 270 EEEILSILDVPPGKMGRIIGRRGSSILAIKESCNAEIL 307 (342)
Q Consensus 270 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 307 (342)
.+...-..++.+...|++||++|.++.||--.+++-..
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~~ 63 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAAN 63 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHHH
Confidence 44555667777888999999999999999888875443
No 109
>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=58.92 E-value=57 Score=27.73 Aligned_cols=90 Identities=16% Similarity=0.215 Sum_probs=54.8
Q ss_pred HHHhhHHHhcCCCceEEEeehhhhHHHHHH---hcCCc-----cCceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCc
Q 019356 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIK-----LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADP 161 (342)
Q Consensus 90 ~~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~---~~Gi~-----l~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~ 161 (342)
++..+.+++.+..-..+.|+..+|...+.+ .++.. ....+|++-.+..+.+.. ...+|.++++
T Consensus 78 vl~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~-------~~~~L~~l~~-- 148 (176)
T cd06133 78 VLKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLK-------KRTGLSKALE-- 148 (176)
T ss_pred HHHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCC-------CCCCHHHHHH--
Confidence 456777788774112356667888765532 23332 245889997766554321 1478899985
Q ss_pred cccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHH
Q 019356 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (342)
Q Consensus 162 ~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L 212 (342)
++|++..... .-|-.||..+..++..|
T Consensus 149 -~~gi~~~~~~-----------------------H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 149 -YLGLEFEGRH-----------------------HRGLDDARNIARILKRL 175 (176)
T ss_pred -HCCCCCCCCC-----------------------cCcHHHHHHHHHHHHHh
Confidence 6676554111 11667888888887765
No 110
>PRK00106 hypothetical protein; Provisional
Probab=58.31 E-value=7.4 Score=40.50 Aligned_cols=51 Identities=29% Similarity=0.635 Sum_probs=41.3
Q ss_pred ChhhhhhhcCCCCCCC-ceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEec
Q 019356 269 PEEEILSILDVPPGKM-GRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIG 322 (342)
Q Consensus 269 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 322 (342)
.-|.--++..+|..-| |++|||-|.+|+++...+..++.|- .-|+-|.+-|
T Consensus 221 ~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---dtp~~v~lS~ 272 (535)
T PRK00106 221 VTEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID---DTPEVVVLSG 272 (535)
T ss_pred hhhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc---CCCCeEEEeC
Confidence 4455567788887666 9999999999999999999999994 4677776655
No 111
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=55.80 E-value=5.2 Score=41.47 Aligned_cols=58 Identities=33% Similarity=0.669 Sum_probs=43.4
Q ss_pred ChhhhhhhcCCCCCCC-ceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhhHHHH
Q 019356 269 PEEEILSILDVPPGKM-GRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKA 330 (342)
Q Consensus 269 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (342)
.-|...++..+|..-| |++|||-|.+|.++.+.+..++.|-- -|.-|.|-| -.-||..
T Consensus 200 ~~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd---tp~~v~ls~-fdp~rre 258 (514)
T TIGR03319 200 VAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---TPEAVILSG-FDPVRRE 258 (514)
T ss_pred hhhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC---CCCeEEecC-CchHHHH
Confidence 4455567778877666 99999999999999999999999954 466666544 3344443
No 112
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=54.05 E-value=8.1 Score=29.17 Aligned_cols=32 Identities=22% Similarity=0.432 Sum_probs=25.8
Q ss_pred hcCCCCCCCceeeccCCchHHHHHHhhcchhh
Q 019356 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEIL 307 (342)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 307 (342)
..++.+..+++.||++|.++.||--..|+-+.
T Consensus 27 ~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 27 EVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 35666778899999999999999888775444
No 113
>PRK11779 sbcB exonuclease I; Provisional
Probab=53.30 E-value=78 Score=32.61 Aligned_cols=96 Identities=13% Similarity=0.065 Sum_probs=54.9
Q ss_pred HHhhHHHhcCCCceEEEee-hhhhHHHHHHhcCCcc-----------C---ceehHHHHHHhhcccc-----CCCCCCCC
Q 019356 91 VKACKPALESSYITKVIHD-CKRDSEALYFQFGIKL-----------H---NVVDTQIAYSLIEEQE-----GRKRSPDD 150 (342)
Q Consensus 91 ~~~L~~lLe~~~i~KV~hd-~k~Dl~~L~~~~Gi~l-----------~---~vfDtqlAa~LL~~~~-----~~~~L~~~ 150 (342)
+..+...+..+...-|+|| +.+|..++.+.+.... + .++|+.-+.+.+.+.. ...+. .
T Consensus 82 ~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~--~ 159 (476)
T PRK11779 82 AARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGL--P 159 (476)
T ss_pred HHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCC--C
Confidence 3455666654444569997 6899988754331110 1 2345555555543321 00011 2
Q ss_pred CCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHH
Q 019356 151 YISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (342)
Q Consensus 151 ~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~ 215 (342)
.++|..|++ .+|++... . .+ |-.||.++..|+..+.++
T Consensus 160 s~rLe~L~~---~~gI~~~~-A----------Hd-------------ALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 160 SFKLEHLTK---ANGIEHEN-A----------HD-------------AMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCcHHHHHH---HcCCCCCC-C----------CC-------------cHHHHHHHHHHHHHHHHh
Confidence 478888886 45654321 1 11 778999999999988866
No 114
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=51.58 E-value=18 Score=37.26 Aligned_cols=66 Identities=29% Similarity=0.450 Sum_probs=50.5
Q ss_pred hhhhcCCCCCCCceeeccCCchHHHHHHhhcchhhcccCC---CCCCeEEEe-cchhhHHHHHHHhhhcc
Q 019356 273 ILSILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAK---GPPDKVFII-GPVKQVRKAEAMLRGRM 338 (342)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~-~~~~~~~~~~~~~~~~~ 338 (342)
+-..+=||....+.+||+.|+.|.+|.+.-.|.|.|.+.. +.-|+.+.| |-+.+.-.|+-.++.++
T Consensus 338 v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~ 407 (485)
T KOG2190|consen 338 VTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARL 407 (485)
T ss_pred eeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhccccc
Confidence 4566778888899999999999999999999999999866 444555544 66666666666555443
No 115
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=49.50 E-value=8.4 Score=35.81 Aligned_cols=46 Identities=35% Similarity=0.789 Sum_probs=39.2
Q ss_pred hcCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchh
Q 019356 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVK 325 (342)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 325 (342)
..+|+|.|.+++||++|+-+.-+++.-+.+|++|= .| +|.|=|+..
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-NG---~IWV~~~~~ 194 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-NG---RIWVDGENE 194 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-CC---EEEecCCCc
Confidence 46789999999999999999999999999999985 32 677777765
No 116
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=45.51 E-value=14 Score=40.82 Aligned_cols=57 Identities=28% Similarity=0.377 Sum_probs=46.6
Q ss_pred hcCCCCCCCceeeccCCchHHHHHHhhcch-hhcccCCCCCCeEEEecchhh-HHHHHHHhhh
Q 019356 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAE-ILIGGAKGPPDKVFIIGPVKQ-VRKAEAMLRG 336 (342)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 336 (342)
...|+|.|++.+||-.|.+|.+|.+..++. |-|.- .-+|+|.|+-++ +.+|..++.+
T Consensus 688 ~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d----dg~V~I~a~d~~~i~~A~~~I~~ 746 (891)
T PLN00207 688 IMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD----DGTVKITAKDLSSLEKSKAIISS 746 (891)
T ss_pred EEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC----CeeEEEEeCCHHHHHHHHHHHHH
Confidence 456789999999999999999999999999 88876 357999997654 6667666654
No 117
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=44.45 E-value=12 Score=31.90 Aligned_cols=33 Identities=27% Similarity=0.442 Sum_probs=27.8
Q ss_pred hcCCCCCCCceeeccCCchHHHHHHhhcchhhc
Q 019356 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILI 308 (342)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 308 (342)
...|+++.++++||++|.+|..+.+.++-.+-|
T Consensus 102 ~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 102 YVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 356889999999999999999999988766543
No 118
>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=41.76 E-value=2.6e+02 Score=25.09 Aligned_cols=105 Identities=12% Similarity=0.076 Sum_probs=58.6
Q ss_pred hHHHhhHHHhcCCCceEEEeeh-hhhHHHHHH---hcCCcc----------------CceehHHHHHH--hhc-cccCCC
Q 019356 89 TVVKACKPALESSYITKVIHDC-KRDSEALYF---QFGIKL----------------HNVVDTQIAYS--LIE-EQEGRK 145 (342)
Q Consensus 89 ~~~~~L~~lLe~~~i~KV~hd~-k~Dl~~L~~---~~Gi~l----------------~~vfDtqlAa~--LL~-~~~~~~ 145 (342)
+++..+..++.+.. .-|++|. .+|+..|.. .+|+.. .-.+|+.-... .+. ...+ .
T Consensus 75 ~lL~~F~~~i~~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~-~ 152 (204)
T cd05783 75 ELIREAFKIISEYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFG-N 152 (204)
T ss_pred HHHHHHHHHHhcCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhc-c
Confidence 45666666776654 4578885 488888753 467651 11456544211 110 0000 0
Q ss_pred CCCCCCCcHHHhhcCccccCCccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHH
Q 019356 146 RSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYH 210 (342)
Q Consensus 146 ~L~~~~~sL~~Lv~~~~~Lg~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~ 210 (342)
.+ +..+|.++++ .+||.. |.... ..-|... .+...+|+..||..+..|..
T Consensus 153 ~~--~~~~L~~Va~--~~lg~~---K~~~~------~~i~~~~--~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 153 KY--REYTLDAVAK--ALLGEG---KVELE------KNISELN--LYELAEYNYRDAELTLELTT 202 (204)
T ss_pred cc--ccCcHHHHHH--HhcCCC---cccCC------chhhhhc--HHHHHHhhHHHHHHHHHHhc
Confidence 11 2578999998 788853 11110 0112111 36789999999999988764
No 119
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=39.39 E-value=1.3e+02 Score=27.34 Aligned_cols=92 Identities=17% Similarity=0.057 Sum_probs=60.7
Q ss_pred HHhhHHHhcCCCceEEEeehhhhHHHHHH---hcCCcc--CceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccC
Q 019356 91 VKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCG 165 (342)
Q Consensus 91 ~~~L~~lLe~~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg 165 (342)
...+..++.+. -.-|.||+.+|...|.. .++..+ ..+.||.-...-..++.. ..+|..|+. .+|
T Consensus 85 ~~~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~-------~~~L~~l~~---~~g 153 (243)
T COG0847 85 LPEFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFD-------RSSLDALAE---RLG 153 (243)
T ss_pred HHHHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCc-------cchHHHHHH---HcC
Confidence 34455566553 34599999999999853 344443 347899988777766522 468888885 667
Q ss_pred CccchhHHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHHHHHHHH
Q 019356 166 ISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (342)
Q Consensus 166 ~~l~kK~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~ 215 (342)
+.... .. ..-|..|+.++..++..+...
T Consensus 154 i~~~~-~~---------------------~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 154 IDRNP-FH---------------------PHRALFDALALAELFLLLQTG 181 (243)
T ss_pred CCcCC-cC---------------------CcchHHHHHHHHHHHHHHHhc
Confidence 65220 00 012778999999999888874
No 120
>PRK12705 hypothetical protein; Provisional
Probab=39.05 E-value=13 Score=38.38 Aligned_cols=42 Identities=31% Similarity=0.605 Sum_probs=34.4
Q ss_pred ChhhhhhhcCCCCCCC-ceeeccCCchHHHHHHhhcchhhccc
Q 019356 269 PEEEILSILDVPPGKM-GRIIGRRGSSILAIKESCNAEILIGG 310 (342)
Q Consensus 269 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (342)
.-|.-.++.++|..-| |++|||-|.+|+++...+..++.|--
T Consensus 194 ~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 194 ASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred hhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 3445567777876666 99999999999999999999998843
No 121
>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=38.57 E-value=1.6e+02 Score=25.69 Aligned_cols=72 Identities=13% Similarity=-0.011 Sum_probs=38.1
Q ss_pred HhhHHHhcCCCceEEEee-hhhhHHHHHHh---cCCcc--------CceehHHHHHHhh---ccc-----cCCCCCCCCC
Q 019356 92 KACKPALESSYITKVIHD-CKRDSEALYFQ---FGIKL--------HNVVDTQIAYSLI---EEQ-----EGRKRSPDDY 151 (342)
Q Consensus 92 ~~L~~lLe~~~i~KV~hd-~k~Dl~~L~~~---~Gi~l--------~~vfDtqlAa~LL---~~~-----~~~~~L~~~~ 151 (342)
..+..++..+...-|+|| +.+|...|.+. .|..+ ...+||.-.++++ .+. ...+.+ ..
T Consensus 74 ~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~--~~ 151 (183)
T cd06138 74 AKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGK--PS 151 (183)
T ss_pred HHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCC--cc
Confidence 445556654333358886 78999998643 33321 1235776544432 221 000011 14
Q ss_pred CcHHHhhcCccccCCcc
Q 019356 152 ISFVGLLADPRYCGISY 168 (342)
Q Consensus 152 ~sL~~Lv~~~~~Lg~~l 168 (342)
.+|.+|++ ++|++.
T Consensus 152 ~~L~~l~~---~~gi~~ 165 (183)
T cd06138 152 FKLEDLAQ---ANGIEH 165 (183)
T ss_pred hhHHHHHH---HCCCCc
Confidence 67899996 467654
No 122
>PRK05762 DNA polymerase II; Reviewed
Probab=38.53 E-value=5.1e+02 Score=28.39 Aligned_cols=104 Identities=15% Similarity=0.157 Sum_probs=59.1
Q ss_pred hHHHhhHHHhcC--CCceEEEeeh-hhhHHHHHH---hcCCccC---------------------------ceehHHHHH
Q 019356 89 TVVKACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKLH---------------------------NVVDTQIAY 135 (342)
Q Consensus 89 ~~~~~L~~lLe~--~~i~KV~hd~-k~Dl~~L~~---~~Gi~l~---------------------------~vfDtqlAa 135 (342)
+++..+..++.. |.+. ++||. .+|+..|.+ .+|+.+. -++|+....
T Consensus 205 ~LL~~F~~~i~~~DPDII-vGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~ 283 (786)
T PRK05762 205 ALLEKFNAWFAEHDPDVI-IGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDAL 283 (786)
T ss_pred HHHHHHHHHHHhcCCCEE-EEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHH
Confidence 345555555544 6654 89995 479988753 3555321 044555443
Q ss_pred HhhccccCCCCCCCCCCcHHHhhcCccccCCccc--hh----HHHHHHhcCCCCCCCCCCCcHHHHHHHHHHhHHHHHHH
Q 019356 136 SLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ--EK----EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (342)
Q Consensus 136 ~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~--kK----~~~~~l~~~~~~dW~~RPLs~~ql~YAA~Da~~Ll~L~ 209 (342)
.-... .+ ...+|..+++ .+||..-. .. .+... .|... .....+|+..||..++.|+
T Consensus 284 k~~~~-----~l--~sysL~~Va~--~~Lg~~K~~~d~~~~~~eI~~-------~~~~~--~~~l~~Y~l~Da~lt~~L~ 345 (786)
T PRK05762 284 KSATW-----VF--DSFSLEYVSQ--RLLGEGKAIDDPYDRMDEIDR-------RFAED--KPALARYNLKDCELVTRIF 345 (786)
T ss_pred HHhhc-----cC--CCCCHHHHHH--HHhCCCeeccCccccHHHHHH-------HHhhh--HHHHHHHHHHHHHHHHHHH
Confidence 21110 11 2468888888 88874321 00 11111 23322 2577899999999999999
Q ss_pred HH
Q 019356 210 HN 211 (342)
Q Consensus 210 ~~ 211 (342)
.+
T Consensus 346 ~k 347 (786)
T PRK05762 346 EK 347 (786)
T ss_pred HH
Confidence 83
No 123
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=37.75 E-value=28 Score=24.50 Aligned_cols=29 Identities=28% Similarity=0.497 Sum_probs=22.1
Q ss_pred CCCCCCCceeeccCCchHHHHHHhhcchh
Q 019356 278 DVPPGKMGRIIGRRGSSILAIKESCNAEI 306 (342)
Q Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 306 (342)
.+..+..+.+||++|.++.++....+.-+
T Consensus 30 ~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 30 VVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 33444678999999999999988766443
No 124
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=36.35 E-value=20 Score=30.52 Aligned_cols=25 Identities=32% Similarity=0.591 Sum_probs=21.7
Q ss_pred CCCCCCceeeccCCchHHHHHHhhc
Q 019356 279 VPPGKMGRIIGRRGSSILAIKESCN 303 (342)
Q Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~ 303 (342)
|++|.+|..||.+|+.|.+|.+..+
T Consensus 38 V~~~~vG~~IG~~G~rI~~i~e~lg 62 (140)
T PRK08406 38 VKEGDMGLAIGKGGENVKRLEEKLG 62 (140)
T ss_pred EeCCCccccCCcCchHHHHHHHHhC
Confidence 3578899999999999999987765
No 125
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=35.30 E-value=20 Score=36.07 Aligned_cols=57 Identities=30% Similarity=0.595 Sum_probs=42.7
Q ss_pred Chhhhh--hhcCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCe----EEEecchh
Q 019356 269 PEEEIL--SILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDK----VFIIGPVK 325 (342)
Q Consensus 269 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~ 325 (342)
|.|++. ....||..-.||+||+.|.+++++-..-.||+.|---.-|.+. |=|||-.-
T Consensus 487 PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfy 549 (584)
T KOG2193|consen 487 PKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFY 549 (584)
T ss_pred chhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhh
Confidence 555543 4556777778999999999999999999999998765533332 66788643
No 126
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=33.99 E-value=14 Score=27.68 Aligned_cols=27 Identities=33% Similarity=0.605 Sum_probs=23.8
Q ss_pred CCCCCceeeccCCchHHHHHHhhcchh
Q 019356 280 PPGKMGRIIGRRGSSILAIKESCNAEI 306 (342)
Q Consensus 280 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 306 (342)
-.++.+.+||++|++|..|.+...-++
T Consensus 32 ~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 32 KASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp EESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred eCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 356778999999999999999998777
No 127
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=26.50 E-value=49 Score=35.70 Aligned_cols=57 Identities=28% Similarity=0.439 Sum_probs=44.3
Q ss_pred hcCCCCCCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhhH-HHHHHHhhh
Q 019356 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQV-RKAEAMLRG 336 (342)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 336 (342)
...|+|.|++.+||..|.+|..|.+...+.|=|-- --+|+|.++-++. .+|..++..
T Consensus 557 ~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d----~G~v~i~~~~~~~~~~a~~~I~~ 614 (693)
T PRK11824 557 TIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED----DGTVKIAATDGEAAEAAKERIEG 614 (693)
T ss_pred eecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC----CceEEEEcccHHHHHHHHHHHHH
Confidence 45678888999999999999999999999877632 3468999876554 466666654
No 128
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=25.20 E-value=67 Score=22.96 Aligned_cols=21 Identities=10% Similarity=0.407 Sum_probs=18.0
Q ss_pred CCCeEEEecchhhHHHHHHHh
Q 019356 314 PPDKVFIIGPVKQVRKAEAML 334 (342)
Q Consensus 314 ~~~~~~~~~~~~~~~~~~~~~ 334 (342)
+-|.++++|+.+.+.++.+++
T Consensus 50 ~gD~l~v~g~~~~i~~~~~~~ 70 (71)
T PF02080_consen 50 AGDILIVVGDPEDIERFRELF 70 (71)
T ss_dssp TTEEEEEEEEHHHHHHHHHHT
T ss_pred CCCEEEEEECHHHHHHHHHhh
Confidence 457899999999999988765
No 129
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=24.80 E-value=48 Score=30.33 Aligned_cols=30 Identities=37% Similarity=0.668 Sum_probs=27.3
Q ss_pred CceeeccCCchHHHHHHhhcchhhcccCCCC
Q 019356 284 MGRIIGRRGSSILAIKESCNAEILIGGAKGP 314 (342)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 314 (342)
+|+.||-+|.|...+.+-.+|.|+|-| +|-
T Consensus 165 VGLliGPRG~Tlk~le~~s~akIaIRG-~gs 194 (269)
T COG5176 165 VGLLIGPRGSTLKQLERISRAKIAIRG-SGS 194 (269)
T ss_pred eEEEecCCcchHHHHHHHhCCeEEEec-ccc
Confidence 689999999999999999999999998 443
No 130
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=22.66 E-value=51 Score=33.90 Aligned_cols=53 Identities=32% Similarity=0.553 Sum_probs=39.8
Q ss_pred CceeeccCCchHHHHHHhhcchhhccc------CCCCCCe------------EEEecchhh-HHHHHHHhhh
Q 019356 284 MGRIIGRRGSSILAIKESCNAEILIGG------AKGPPDK------------VFIIGPVKQ-VRKAEAMLRG 336 (342)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~------------~~~~~~~~~-~~~~~~~~~~ 336 (342)
+|++||-+|.|.-.|.+.++|.|.|=| -|+-+|. +.|.+--.| |.||-|++.-
T Consensus 155 vGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vien 226 (554)
T KOG0119|consen 155 VGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIEN 226 (554)
T ss_pred eEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHH
Confidence 689999999999999999999999987 2223331 677775544 6677776654
No 131
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=22.36 E-value=6.8e+02 Score=23.76 Aligned_cols=152 Identities=22% Similarity=0.152 Sum_probs=87.2
Q ss_pred ceEEEEeeeeCCCCCC-cEEEEEEEeC-CcEEEEEcCCCC--hhHHHhhHHHhcCCCc-eEEEeeh-hhhHHHHHH----
Q 019356 50 LVIGFDCEGVDLCRHG-SLCIMQLAFP-DAIYLVDAIQGG--ETVVKACKPALESSYI-TKVIHDC-KRDSEALYF---- 119 (342)
Q Consensus 50 ~~Ia~D~E~~~~~~~g-~l~llQLa~~-~~~~liD~~~l~--~~~~~~L~~lLe~~~i-~KV~hd~-k~Dl~~L~~---- 119 (342)
....||+|+.++++.| .+.++..+.. +....|--.-+. +.-...|..++.++.. ..|.+|. ++|...+.+
T Consensus 99 ~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~~Vrq~~lp~p~~E~avle~fl~~~~~~~lvsfNGkaFD~PfikR~v~~ 178 (278)
T COG3359 99 DVAFFDIETTGLDRAGNTITLVGGARGVDDTMHVRQHFLPAPEEEVAVLENFLHDPDFNMLVSFNGKAFDIPFIKRMVRD 178 (278)
T ss_pred ceEEEeeeccccCCCCCeEEEEEEEEccCceEEEEeecCCCcchhhHHHHHHhcCCCcceEEEecCcccCcHHHHHHHhc
Confidence 4888999999998644 5666666663 444555322222 1112345556666522 2366664 589988862
Q ss_pred hcCCccC-ceehHHHHHHhhccccCCCCCCCCCCcHHHhhcCccccCCccch-------hHHHHHHhcCCCCCCCCCC--
Q 019356 120 QFGIKLH-NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE-------KEEVRVLLRQDPQFWTYRP-- 189 (342)
Q Consensus 120 ~~Gi~l~-~vfDtqlAa~LL~~~~~~~~L~~~~~sL~~Lv~~~~~Lg~~l~k-------K~~~~~l~~~~~~dW~~RP-- 189 (342)
.+...+. .-||++..++=+.. |.|+ .-+|.. ++ ++||++=.+ .+..+ .|.+-+
T Consensus 179 ~~el~l~~~H~DL~h~~RRlwk----~~l~--~c~Lk~-VE--r~LGi~R~edtdG~~~p~lyr--------~~~~~~dp 241 (278)
T COG3359 179 RLELSLEFGHFDLYHPSRRLWK----HLLP--RCGLKT-VE--RILGIRREEDTDGYDGPELYR--------LYRRYGDP 241 (278)
T ss_pred ccccCccccchhhhhhhhhhhh----ccCC--CCChhh-HH--HHhCccccccCCCcchHHHHH--------HHHHcCCH
Confidence 2334443 47899988776663 2333 245543 44 688864221 11111 122111
Q ss_pred -CcHHHHHHHHHHhHHHHHHHHHHHHHHhc
Q 019356 190 -LTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (342)
Q Consensus 190 -Ls~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (342)
+-...+.|=-.|+.-|..|+..+.+++.+
T Consensus 242 ~ll~~l~~hN~eDvlnL~~i~~h~~~~i~~ 271 (278)
T COG3359 242 GLLDGLVLHNREDVLNLPTIIKHVSKKILE 271 (278)
T ss_pred HHHHHHHHccHHHHHhHHHHHHHHHHHHHH
Confidence 22445667788999999999998887764
No 132
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=22.30 E-value=54 Score=28.02 Aligned_cols=26 Identities=31% Similarity=0.538 Sum_probs=21.9
Q ss_pred CCCCCCCceeeccCCchHHHHHHhhc
Q 019356 278 DVPPGKMGRIIGRRGSSILAIKESCN 303 (342)
Q Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 (342)
=|.+|.+|..||.+|+.|.+|.+..+
T Consensus 38 vV~~g~vG~~IG~~G~rIk~i~el~g 63 (141)
T TIGR01952 38 VVKEGEMGAAIGKGGENVKRLEELIG 63 (141)
T ss_pred EEcCCCccccCCCCchHHHHHHHhcC
Confidence 35688899999999999999977665
No 133
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=21.80 E-value=55 Score=26.45 Aligned_cols=25 Identities=24% Similarity=0.493 Sum_probs=20.6
Q ss_pred CCCCceeeccCCchHHHHHHhhcch
Q 019356 281 PGKMGRIIGRRGSSILAIKESCNAE 305 (342)
Q Consensus 281 ~~~~~~~~~~~~~~~~~~~~~~~~~ 305 (342)
-++-+.+||++|++|.+|.+.....
T Consensus 69 t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 69 TARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred eCCCCcccCCchHHHHHHHHHHHHH
Confidence 4455899999999999999887655
No 134
>PF08235 LNS2: LNS2 (Lipin/Ned1/Smp2); InterPro: IPR013209 This domain is found in Saccharomyces cerevisiae (Baker's yeast) protein SMP2, proteins with an N-terminal lipin domain (IPR007651 from INTERPRO) and phosphatidylinositol transfer proteins []. SMP2 is involved in plasmid maintenance and respiration []. Lipin proteins are involved in adipose tissue development and insulin resistance [].
Probab=21.13 E-value=33 Score=29.89 Aligned_cols=39 Identities=21% Similarity=0.276 Sum_probs=25.4
Q ss_pred CCCceeeccCCchHHHHHHhhcchhhcccCCCCCCeEEEecchhhHH
Q 019356 282 GKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVR 328 (342)
Q Consensus 282 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 (342)
...+. ..-.|.+...+..-.++-| |++|||+|||.-+++
T Consensus 117 ~~~pf-~agfGN~~tDv~aY~~vGi-------p~~rIF~I~~~g~~~ 155 (157)
T PF08235_consen 117 DGNPF-YAGFGNRSTDVIAYKAVGI-------PKSRIFIINPKGEVK 155 (157)
T ss_pred CCCeE-EEecCCcHHHHHHHHHcCC-------ChhhEEEECCCCeEe
Confidence 34444 4555666666665554433 789999999987654
No 135
>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=20.50 E-value=1.3e+02 Score=27.31 Aligned_cols=54 Identities=13% Similarity=0.111 Sum_probs=36.0
Q ss_pred CCcHHHhhcCccccCCccch--hHHHHHHhcCCCCCCCCCCCc-HHHHHHHHHHhHHHHHHHHHHH
Q 019356 151 YISFVGLLADPRYCGISYQE--KEEVRVLLRQDPQFWTYRPLT-ELMVRAAADDVRFLPYIYHNMM 213 (342)
Q Consensus 151 ~~sL~~Lv~~~~~Lg~~l~k--K~~~~~l~~~~~~dW~~RPLs-~~ql~YAA~Da~~Ll~L~~~L~ 213 (342)
..+|.++++ ++||..-.. .+.... -|...|-. ...++|+..||.+.++|..+|.
T Consensus 168 sy~L~~Va~--~~Lg~~k~d~~~~~i~~-------~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 168 SYSLNSVSA--HFLGEQKEDVHYSIITD-------LQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred cCcHHHHHH--HHhCCCCCCCCHHHHHH-------HHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 578899998 888854221 112211 24333321 4679999999999999999885
Done!