Query 019798
Match_columns 335
No_of_seqs 275 out of 1529
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 04:37:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019798.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019798hhsearch_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 6E-35 1.3E-39 279.9 16.9 249 27-297 2-284 (373)
2 COG0349 Rnd Ribonuclease D [Tr 100.0 4E-33 8.7E-38 261.1 13.6 246 32-298 2-281 (361)
3 TIGR01388 rnd ribonuclease D. 100.0 3.4E-32 7.4E-37 261.9 16.2 246 30-297 1-280 (367)
4 cd06148 Egl_like_exo DEDDy 3'- 100.0 2.8E-30 6.1E-35 228.8 18.0 181 46-228 7-189 (197)
5 cd06146 mut-7_like_exo DEDDy 3 100.0 8.6E-29 1.9E-33 218.6 15.6 175 28-213 1-192 (193)
6 cd06129 RNaseD_like DEDDy 3'-5 100.0 9.4E-29 2E-33 212.3 13.5 156 37-213 2-160 (161)
7 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 4.4E-27 9.5E-32 203.3 14.1 164 32-213 2-169 (170)
8 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 8.6E-27 1.9E-31 201.2 15.5 170 28-217 1-176 (176)
9 COG0749 PolA DNA polymerase I 99.9 9.9E-25 2.1E-29 216.4 7.4 229 30-274 5-242 (593)
10 PRK05755 DNA polymerase I; Pro 99.9 4.5E-24 9.7E-29 226.6 12.7 229 26-272 294-529 (880)
11 KOG2206 Exosome 3'-5' exoribon 99.9 3.6E-24 7.9E-29 207.8 7.4 249 26-296 191-477 (687)
12 cd06142 RNaseD_exo DEDDy 3'-5' 99.9 1.3E-21 2.7E-26 169.8 16.7 168 41-229 5-173 (178)
13 cd06140 DNA_polA_I_Bacillus_li 99.9 7.2E-21 1.6E-25 165.4 15.2 171 49-235 3-176 (178)
14 TIGR00593 pola DNA polymerase 99.8 8.2E-21 1.8E-25 199.9 12.0 221 28-272 304-536 (887)
15 smart00474 35EXOc 3'-5' exonuc 99.8 9.4E-20 2E-24 156.1 14.8 168 29-217 2-172 (172)
16 PRK14975 bifunctional 3'-5' ex 99.8 7E-21 1.5E-25 192.8 5.1 200 27-273 2-220 (553)
17 cd06147 Rrp6p_like_exo DEDDy 3 99.8 8.5E-19 1.8E-23 154.6 16.6 173 25-219 2-175 (192)
18 cd06139 DNA_polA_I_Ecoli_like_ 99.8 1.2E-18 2.7E-23 152.8 16.2 175 47-235 3-191 (193)
19 cd00007 35EXOc 3'-5' exonuclea 99.8 2.1E-17 4.6E-22 138.9 14.8 152 51-216 2-155 (155)
20 cd09018 DEDDy_polA_RNaseD_like 99.7 2.5E-17 5.4E-22 138.5 13.4 146 51-213 1-149 (150)
21 KOG2207 Predicted 3'-5' exonuc 99.4 2.8E-13 6.1E-18 133.2 5.9 180 26-217 390-586 (617)
22 cd06128 DNA_polA_exo DEDDy 3'- 99.3 8.7E-11 1.9E-15 99.3 14.2 132 64-213 17-150 (151)
23 KOG2405 Predicted 3'-5' exonuc 98.9 5E-10 1.1E-14 104.9 2.4 180 64-251 210-393 (458)
24 KOG2405 Predicted 3'-5' exonuc 98.3 6.4E-08 1.4E-12 91.0 -3.1 149 54-204 63-215 (458)
25 KOG4373 Predicted 3'-5' exonuc 97.9 2.8E-05 6E-10 72.4 7.3 129 64-209 146-281 (319)
26 cd06125 DnaQ_like_exo DnaQ-lik 97.9 5.8E-05 1.3E-09 59.0 7.7 72 52-134 1-83 (96)
27 PRK07740 hypothetical protein; 97.8 0.00065 1.4E-08 62.2 14.0 98 90-223 131-233 (244)
28 PRK06063 DNA polymerase III su 97.7 0.00074 1.6E-08 64.1 12.9 138 49-222 15-185 (313)
29 PRK07942 DNA polymerase III su 97.5 0.0034 7.4E-08 57.0 13.6 135 48-217 5-181 (232)
30 cd06144 REX4_like DEDDh 3'-5' 97.5 0.00053 1.2E-08 58.1 7.8 85 90-209 67-151 (152)
31 cd06149 ISG20 DEDDh 3'-5' exon 97.4 0.00083 1.8E-08 57.3 8.1 86 90-209 67-156 (157)
32 cd06137 DEDDh_RNase DEDDh 3'-5 97.3 0.0023 5.1E-08 54.6 10.2 67 92-169 75-141 (161)
33 cd06145 REX1_like DEDDh 3'-5' 97.3 0.0011 2.5E-08 55.9 7.9 65 90-168 65-129 (150)
34 PRK07246 bifunctional ATP-depe 97.2 0.0043 9.3E-08 66.3 13.5 135 48-220 6-174 (820)
35 PRK06309 DNA polymerase III su 97.2 0.011 2.4E-07 53.6 14.4 140 50-226 3-176 (232)
36 TIGR00573 dnaq exonuclease, DN 97.2 0.0038 8.3E-08 56.0 11.2 138 47-218 5-179 (217)
37 TIGR01405 polC_Gram_pos DNA po 97.2 0.0047 1E-07 68.2 13.3 139 47-221 188-360 (1213)
38 PRK06310 DNA polymerase III su 97.2 0.012 2.7E-07 54.0 14.0 133 47-217 5-175 (250)
39 COG2176 PolC DNA polymerase II 97.1 0.0027 5.8E-08 68.1 9.6 139 46-222 418-592 (1444)
40 PRK06807 DNA polymerase III su 97.0 0.011 2.3E-07 56.2 12.7 91 90-217 78-173 (313)
41 PRK09146 DNA polymerase III su 97.0 0.019 4.2E-07 52.4 13.7 143 47-218 45-229 (239)
42 PRK07883 hypothetical protein; 97.0 0.0093 2E-07 61.1 12.8 139 46-220 12-186 (557)
43 PRK06195 DNA polymerase III su 97.0 0.022 4.7E-07 54.0 14.1 100 90-226 70-174 (309)
44 cd06131 DNA_pol_III_epsilon_Ec 96.9 0.02 4.4E-07 48.8 11.8 88 90-212 71-166 (167)
45 PRK05601 DNA polymerase III su 96.8 0.027 5.9E-07 54.3 13.3 140 47-212 44-245 (377)
46 cd06130 DNA_pol_III_epsilon_li 96.8 0.027 6E-07 47.1 12.0 66 90-167 67-137 (156)
47 PRK05711 DNA polymerase III su 96.8 0.041 8.9E-07 50.3 13.8 91 90-215 76-175 (240)
48 TIGR01406 dnaQ_proteo DNA poly 96.8 0.029 6.3E-07 50.7 12.7 90 90-214 72-170 (225)
49 PRK05168 ribonuclease T; Provi 96.8 0.051 1.1E-06 48.6 14.2 87 102-223 114-208 (211)
50 PRK08517 DNA polymerase III su 96.7 0.045 9.7E-07 50.5 13.8 133 47-218 66-233 (257)
51 KOG2249 3'-5' exonuclease [Rep 96.7 0.014 3.1E-07 53.2 10.1 135 50-218 106-268 (280)
52 PRK08074 bifunctional ATP-depe 96.7 0.027 5.8E-07 61.2 14.1 133 49-218 3-171 (928)
53 cd05160 DEDDy_DNA_polB_exo DED 96.7 0.045 9.8E-07 48.1 13.1 102 89-209 65-198 (199)
54 smart00479 EXOIII exonuclease 96.6 0.045 9.7E-07 46.3 12.3 92 90-217 70-168 (169)
55 cd06136 TREX1_2 DEDDh 3'-5' ex 96.6 0.044 9.5E-07 47.5 12.2 80 92-209 86-174 (177)
56 TIGR01407 dinG_rel DnaQ family 96.5 0.028 6E-07 60.6 12.4 93 90-218 70-167 (850)
57 cd05780 DNA_polB_Kod1_like_exo 96.5 0.096 2.1E-06 46.1 13.7 145 50-212 4-195 (195)
58 cd02394 vigilin_like_KH K homo 96.4 0.0026 5.7E-08 45.1 2.6 55 273-327 7-61 (62)
59 cd06134 RNaseT DEDDh 3'-5' exo 96.4 0.07 1.5E-06 46.8 12.2 78 103-215 103-188 (189)
60 PRK09145 DNA polymerase III su 96.3 0.12 2.5E-06 45.8 13.2 133 47-213 27-198 (202)
61 cd06127 DEDDh DEDDh 3'-5' exon 96.2 0.059 1.3E-06 44.5 10.5 50 90-141 69-123 (159)
62 TIGR01298 RNaseT ribonuclease 96.2 0.02 4.4E-07 50.7 7.9 86 103-223 106-199 (200)
63 PRK00448 polC DNA polymerase I 96.1 0.032 6.8E-07 62.7 10.3 96 90-221 489-589 (1437)
64 cd06143 PAN2_exo DEDDh 3'-5' e 95.7 0.016 3.5E-07 50.1 4.7 80 93-209 94-173 (174)
65 PF13482 RNase_H_2: RNase_H su 95.5 0.23 4.9E-06 42.0 11.3 146 52-212 1-163 (164)
66 PRK07247 DNA polymerase III su 95.3 0.4 8.6E-06 42.4 12.2 133 49-217 5-170 (195)
67 PRK09182 DNA polymerase III su 94.8 0.47 1E-05 44.7 11.9 100 92-228 112-213 (294)
68 PF09281 Taq-exonuc: Taq polym 94.5 0.11 2.3E-06 42.4 5.7 69 111-216 70-138 (138)
69 cd00105 KH-I K homology RNA-bi 94.3 0.037 8E-07 39.1 2.6 55 273-327 7-63 (64)
70 PRK07748 sporulation inhibitor 94.0 1.1 2.3E-05 39.8 11.9 94 89-216 81-180 (207)
71 PRK07983 exodeoxyribonuclease 93.1 1.1 2.4E-05 40.3 10.5 80 103-216 75-154 (219)
72 cd05785 DNA_polB_like2_exo Unc 93.1 2 4.4E-05 38.2 12.1 144 49-209 9-206 (207)
73 smart00322 KH K homology RNA-b 93.1 0.1 2.2E-06 36.6 3.2 58 273-330 10-67 (69)
74 KOG3657 Mitochondrial DNA poly 92.9 0.29 6.3E-06 51.3 7.0 108 103-218 242-385 (1075)
75 PRK11779 sbcB exonuclease I; P 92.9 1.7 3.7E-05 43.7 12.4 98 91-215 82-197 (476)
76 cd02396 PCBP_like_KH K homolog 92.4 0.1 2.2E-06 37.4 2.2 55 273-327 7-64 (65)
77 PF00013 KH_1: KH domain syndr 92.1 0.055 1.2E-06 37.9 0.6 52 275-327 9-60 (60)
78 cd05784 DNA_polB_II_exo DEDDy 91.3 2.9 6.3E-05 36.8 10.8 49 151-210 139-193 (193)
79 cd06133 ERI-1_3'hExo_like DEDD 91.3 6.5 0.00014 33.2 12.8 90 90-212 78-175 (176)
80 PF10108 DNA_pol_B_exo2: Predi 90.9 8.1 0.00018 34.5 13.2 107 89-214 39-171 (209)
81 cd05781 DNA_polB_B3_exo DEDDy 90.5 11 0.00024 32.8 15.0 144 50-212 4-188 (188)
82 cd02393 PNPase_KH Polynucleoti 90.3 0.21 4.6E-06 35.4 2.2 52 272-327 8-60 (61)
83 COG0847 DnaQ DNA polymerase II 90.1 8.7 0.00019 34.6 13.2 134 49-215 13-181 (243)
84 cd05782 DNA_polB_like1_exo Unc 89.1 6.5 0.00014 34.9 11.3 129 63-210 49-207 (208)
85 PRK06722 exonuclease; Provisio 88.7 7.9 0.00017 36.2 11.8 92 89-213 79-178 (281)
86 cd06138 ExoI_N N-terminal DEDD 88.3 8.4 0.00018 33.3 11.2 29 91-119 73-102 (183)
87 KOG2248 3'-5' exonuclease [Rep 88.1 3.1 6.7E-05 40.6 9.0 88 92-213 285-372 (380)
88 cd05779 DNA_polB_epsilon_exo D 81.4 38 0.00082 30.0 12.9 104 89-210 75-204 (204)
89 KOG1275 PAB-dependent poly(A) 79.3 0.88 1.9E-05 48.3 1.2 87 97-220 1009-1095(1118)
90 PRK05359 oligoribonuclease; Pr 78.9 19 0.00041 31.3 9.3 41 90-130 82-130 (181)
91 PF13014 KH_3: KH domain 78.6 1.2 2.6E-05 28.9 1.3 27 277-303 2-28 (43)
92 cd05783 DNA_polB_B1_exo DEDDy 78.3 48 0.001 29.3 12.7 105 89-210 75-202 (204)
93 PRK05762 DNA polymerase II; Re 76.2 53 0.0011 35.4 13.5 104 89-211 205-347 (786)
94 PHA02528 43 DNA polymerase; Pr 70.7 97 0.0021 33.9 13.8 50 151-211 272-323 (881)
95 smart00341 HRDC Helicase and R 66.7 0.83 1.8E-05 33.7 -1.9 54 244-297 13-76 (81)
96 cd05776 DNA_polB_alpha_exo ina 64.3 18 0.0004 32.6 6.0 52 152-212 173-226 (234)
97 TIGR03665 arCOG04150 arCOG0415 63.9 5 0.00011 34.6 2.2 48 276-328 99-146 (172)
98 PRK13763 putative RNA-processi 57.6 7.2 0.00016 33.9 2.0 47 276-327 105-151 (180)
99 PRK00468 hypothetical protein; 51.6 10 0.00022 28.1 1.7 26 273-298 37-62 (75)
100 KOG2193 IGF-II mRNA-binding pr 51.3 9.9 0.00021 37.3 2.0 57 277-333 422-481 (584)
101 PRK02821 hypothetical protein; 49.9 10 0.00022 28.2 1.5 25 273-297 38-62 (77)
102 COG1094 Predicted RNA-binding 49.1 14 0.0003 32.5 2.4 56 266-326 98-157 (194)
103 COG1837 Predicted RNA-binding 43.7 13 0.00029 27.6 1.2 23 273-295 37-59 (76)
104 PF00570 HRDC: HRDC domain Blo 42.1 0.68 1.5E-05 33.1 -5.8 43 250-292 16-68 (68)
105 cd05777 DNA_polB_delta_exo DED 38.7 63 0.0014 29.0 5.1 55 151-214 168-225 (230)
106 cd02395 SF1_like-KH Splicing f 36.4 36 0.00078 27.5 2.8 53 275-328 15-90 (120)
107 TIGR03665 arCOG04150 arCOG0415 36.2 21 0.00045 30.8 1.5 53 272-328 4-60 (172)
108 PRK01064 hypothetical protein; 31.8 35 0.00076 25.4 1.9 25 273-297 37-61 (78)
109 cd06135 Orn DEDDh 3'-5' exonuc 30.1 64 0.0014 27.5 3.6 31 90-120 78-112 (173)
110 COG3359 Predicted exonuclease 29.4 4.6E+02 0.01 24.2 11.1 152 50-218 99-271 (278)
111 PF13083 KH_4: KH domain; PDB: 28.7 26 0.00055 25.3 0.7 25 274-298 37-61 (73)
112 PTZ00315 2'-phosphotransferase 28.5 2.5E+02 0.0054 29.2 7.9 101 89-215 132-254 (582)
113 PRK13763 putative RNA-processi 27.2 39 0.00085 29.3 1.8 54 272-328 9-66 (180)
114 cd02134 NusA_KH NusA_K homolog 24.6 43 0.00094 23.4 1.3 27 270-296 29-55 (61)
No 1
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=6e-35 Score=279.90 Aligned_cols=249 Identities=24% Similarity=0.319 Sum_probs=211.8
Q ss_pred CeEEeCCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceE
Q 019798 27 PIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITK 105 (335)
Q Consensus 27 ~~~~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~K 105 (335)
.|.+|+|+++|.+ +++. +.+.+.+|||||+.+.. +++++|+|||++++.+|+||++...+ +..|+++|+|+.+.|
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 47899999999999875 78899999999988999999987753 678999999999999
Q ss_pred EEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCC
Q 019798 106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFW 185 (335)
Q Consensus 106 V~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w 185 (335)
|+|++++|+..|++.+|+.+.++||||+|+.+++.+. .+||+.|++ +|||++++| ++.+ +||
T Consensus 78 V~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~--------~~gl~~Lv~--~~lgv~ldK-~~~~-------sDW 139 (373)
T PRK10829 78 FLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPL--------SCGFASMVE--EYTGVTLDK-SESR-------TDW 139 (373)
T ss_pred EEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCc--------cccHHHHHH--HHhCCccCc-cccc-------CCC
Confidence 9999999999998899999999999999999998642 249999999 999999985 3322 499
Q ss_pred ccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccHHHHHHhhh-hcc----cc-------cc------cCCc------
Q 019798 186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGAL-YCR----CF-------CI------NEND------ 241 (335)
Q Consensus 186 ~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~l~~~~e~-~~~----vL-------~m------e~~g------ 241 (335)
..|||+++|+.|||.||.+++.||+.|..+|.+.|.+.++.+..- .+. .. .+ ...+
T Consensus 140 ~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~ik~~~~L~~~~lavl~~ 219 (373)
T PRK10829 140 LARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQL 219 (373)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHhccccCCChHHHHHHhccccCCCHHHHHHHHH
Confidence 999999999999999999999999999999999999888765432 110 00 11 1111
Q ss_pred cCCCCCCCCCCCcccccCCCCHHHHHhhhcCCCCccc---------cccccccccHHHHHHHhhh
Q 019798 242 YVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG---------RIIGRRGSSILAIKESCNA 297 (335)
Q Consensus 242 ~~d~~~L~~~~~~l~~~~~~~e~~i~~lAg~~~~~~~---------~~~~~~~~~~~~~~~~~~~ 297 (335)
...||+..++..|.++.....++.++++|..+|.+.. ..++++|.+|+.+++.+.+
T Consensus 220 L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~~~~~~~~r~~g~~ll~~i~~a~~ 284 (373)
T PRK10829 220 LADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQA 284 (373)
T ss_pred HHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhccCChHhHHhhHHHHHHHHHHHhc
Confidence 2378888899999999999999999999999997754 4677889999999999854
No 2
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4e-33 Score=261.08 Aligned_cols=246 Identities=22% Similarity=0.273 Sum_probs=206.3
Q ss_pred CCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEEec
Q 019798 32 TNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDC 110 (335)
Q Consensus 32 ~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV~hd~ 110 (335)
++.+.++. ++... .+++.|++|||+.+.. +++++|+||++.++++++||+..... -...|..+|.|++|.||+|.+
T Consensus 2 ~~~~~l~~-~~~~~-~~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~~lIdpl~~~~-d~~~l~~Ll~d~~v~KIfHaa 78 (361)
T COG0349 2 TTGDLLAA-ACALL-RGSKAIAIDTEFMRLRTYYPRLCLIQISDGEGASLIDPLAGIL-DLPPLVALLADPNVVKIFHAA 78 (361)
T ss_pred CchhHHHH-HHHHh-cCCCceEEecccccccccCCceEEEEEecCCCceEeccccccc-ccchHHHHhcCCceeeeeccc
Confidence 45555665 77763 6788999999999885 89999999999987799999987432 257788899999999999999
Q ss_pred hhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCC
Q 019798 111 KRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPL 190 (335)
Q Consensus 111 k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL 190 (335)
++|+.+|++.+|+.+.++|||++|+.+++.+. + +||++|++ +++|++++| ++.+ +||..|||
T Consensus 79 ~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~-~-------~gl~~Lv~--~ll~v~ldK-~~q~-------SDW~~RPL 140 (361)
T COG0349 79 RFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGT-S-------HGLADLVE--ELLGVELDK-SEQR-------SDWLARPL 140 (361)
T ss_pred cccHHHHHHhcCCCCCchhHHHHHHHHhCCcc-c-------ccHHHHHH--HHhCCcccc-cccc-------cccccCCC
Confidence 99999999999999999999999999999764 3 49999999 999999985 3322 59999999
Q ss_pred CHHHHHHHHhhhhHHHHHHHHHHHHHhccccHHHHHHhhh--hccc-ccccC-Cc--------------------cCCCC
Q 019798 191 TELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGAL--YCRC-FCINE-ND--------------------YVDWP 246 (335)
Q Consensus 191 ~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~l~~~~e~--~~~v-L~me~-~g--------------------~~d~~ 246 (335)
|++|+.||+.||.|++.||..|.++|.+.|.+.++.+... +.+. ..++. .+ ...|+
T Consensus 141 s~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~~l~~r~~~~~~~~~~w~~i~~a~~~~p~~la~l~~La~wR 220 (361)
T COG0349 141 SEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFRLLPTRRTYKVLPEDAWREIKIAHSLDPRELAVLRELAAWR 220 (361)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHhhhccccccChHhHHHHhhhhhcCChHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999998887654 2221 11010 11 22899
Q ss_pred CCCCCCCcccccCCCCHHHHHhhhcCCCCccc---------cccccccccHHHHHHHhhhh
Q 019798 247 PLPPVPDYLIVEGDVPEEEILSILDVPPGKMG---------RIIGRRGSSILAIKESCNAE 298 (335)
Q Consensus 247 ~L~~~~~~l~~~~~~~e~~i~~lAg~~~~~~~---------~~~~~~~~~~~~~~~~~~~~ 298 (335)
+..++.++++......++.|+++|..+|.+.+ ...++.|..++.+++.+.+.
T Consensus 221 e~~Ar~rd~~~~~vl~de~i~~~a~~~P~~~~~l~~l~~~~~~~~~~~~~l~~~~~~a~~~ 281 (361)
T COG0349 221 EREARERDLARNFVLKDEALWELARYTPKNLKELDALGLIPKERRRHGKLLLALLANALAS 281 (361)
T ss_pred HHHHHHhccccccccchhHHHHHHHhCCCCHHHHHhccCCcccchhhhHHHHHHHHHHHhC
Confidence 99999999999999999999999999996542 46678899999999888765
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=99.98 E-value=3.4e-32 Score=261.93 Aligned_cols=246 Identities=22% Similarity=0.267 Sum_probs=205.7
Q ss_pred EeCCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEE
Q 019798 30 IVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIH 108 (335)
Q Consensus 30 ~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV~h 108 (335)
+|+|.++|.+ +++.+ ...++||||||+.+.. +++++|+||+++++.+|+||+.... .+..|+++|+|+++.||+|
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-VCEAV-RTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVII--DWSPLKELLRDESVVKVLH 76 (367)
T ss_pred CcCCHHHHHH-HHHHH-hcCCEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCcc--cHHHHHHHHCCCCceEEEe
Confidence 3788999997 99885 7789999999999875 7889999999999999999998764 3778999999999999999
Q ss_pred echhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccC
Q 019798 109 DCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYR 188 (335)
Q Consensus 109 d~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~r 188 (335)
|+|+|+++|.+.+|+.++++||||+|+|+++++. .+||+.|++ +|||+++++ ++. .++|..|
T Consensus 77 ~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~--------~~~l~~Lv~--~~Lg~~l~K-~~~-------~sdW~~r 138 (367)
T TIGR01388 77 AASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGM--------SMGYAKLVQ--EVLGVELDK-SES-------RTDWLAR 138 (367)
T ss_pred ecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCC--------CccHHHHHH--HHcCCCCCc-ccc-------cccCCCC
Confidence 9999999998666777788999999999999853 238999999 999998873 221 2589999
Q ss_pred CCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccHHHHHHhhh-hc-ccc----------------cccCCc------cCC
Q 019798 189 PLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGAL-YC-RCF----------------CINEND------YVD 244 (335)
Q Consensus 189 pL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~l~~~~e~-~~-~vL----------------~me~~g------~~d 244 (335)
||+.+|+.|||.||.+++.||+.|.++|++.|.+.++.+..- .+ +.. .+...+ ...
T Consensus 139 PL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~i~~~~~l~~~~l~~l~~L~~ 218 (367)
T TIGR01388 139 PLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAA 218 (367)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHhccccCCCChHHHHHHhcccccCCHHHHHHHHHHHH
Confidence 999999999999999999999999999999998887654322 11 100 111111 238
Q ss_pred CCCCCCCCCcccccCCCCHHHHHhhhcCCCCccc---------cccccccccHHHHHHHhhh
Q 019798 245 WPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG---------RIIGRRGSSILAIKESCNA 297 (335)
Q Consensus 245 ~~~L~~~~~~l~~~~~~~e~~i~~lAg~~~~~~~---------~~~~~~~~~~~~~~~~~~~ 297 (335)
||+..++..|.++.....++.++++|..+|.++. ..++++|.+|+.+++.+.+
T Consensus 219 wRe~~A~~~d~p~~~il~d~~l~~lA~~~P~~~~~l~~~~~~~~~~r~~~~~l~~~i~~a~~ 280 (367)
T TIGR01388 219 WREREARERDLPRNFVLKEEALWELARQAPGNLTELASLGPKGSEIRKHGDTLLALVKTALA 280 (367)
T ss_pred HHHHHHHHcCCCcceeeCHHHHHHHHHhCCCCHHHHHhccCChHHHHhhHHHHHHHHHHHhh
Confidence 8999999999999999999999999999997754 4678889999999999864
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=2.8e-30 Score=228.81 Aligned_cols=181 Identities=49% Similarity=0.724 Sum_probs=150.5
Q ss_pred ccCCceEEEEEeecCCCccCcEEEEEEEeC-CceEEEEccCCCh-hhHHHHHHHHcCCCceEEEEechhcHHHHHHHcCC
Q 019798 46 SERQLVIGFDCEGVDLCRHGSLCIMQLAFP-DAIYLVDAIQGGE-TVVKACKPALESSYITKVIHDCKRDSEALYFQFGI 123 (335)
Q Consensus 46 ~~~~~~ia~D~E~~~~~~~~~l~~lqla~~-~~~~lid~~~~~~-~~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi 123 (335)
+.++.+||||+||.+.+..|++|++|+++. +++|+||+..++. .+...|+++|+++++.||+||+|+|++.|++.+|+
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 367899999999988877899999999998 9999999998763 35688999999999999999999999999878999
Q ss_pred ccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhh
Q 019798 124 KLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVR 203 (335)
Q Consensus 124 ~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~ 203 (335)
.+.++|||++|+|++++..+........+||+.+++ +|++.+++++...+...+...++|..|||+++|+.|||.||+
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 999999999999999986431111112459999999 999998874333222223345699999999999999999999
Q ss_pred HHHHHHHHHHHHHhccccHHHHHHh
Q 019798 204 FLPYIYHNMMKKLNQQSLWYLAVRG 228 (335)
Q Consensus 204 ~ll~L~~~L~~~L~~~~l~~l~~~~ 228 (335)
+++.||+.|...|.+.....+|.+.
T Consensus 165 ~Ll~l~~~l~~~l~~~~~~~~~~~~ 189 (197)
T cd06148 165 CLLPLYYAMLDALISKFLKAVFKYL 189 (197)
T ss_pred hHHHHHHHHHHHhhhhHHHHHHHHh
Confidence 9999999999999987666666544
No 5
>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=8.6e-29 Score=218.57 Aligned_cols=175 Identities=26% Similarity=0.308 Sum_probs=145.3
Q ss_pred eEEeCCccchhHHHhhhh-ccCCceEEEEEeecCCC---ccCcEEEEEEEeCCceEEEEccCCC----hhhHHHHHHHHc
Q 019798 28 IHIVTNASQLPAEFLEPS-SERQLVIGFDCEGVDLC---RHGSLCIMQLAFPDAIYLVDAIQGG----ETVVKACKPALE 99 (335)
Q Consensus 28 ~~~I~t~~~L~~~~l~~~-~~~~~~ia~D~E~~~~~---~~~~l~~lqla~~~~~~lid~~~~~----~~~~~~Lk~lLe 99 (335)
+++|+|++++.+ ++..+ +.+..+||||+||.+.. ..+++|+||||+++.+|+||+..++ +.+...|+++|+
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 88773 47889999999998763 2689999999999999999998765 235678999999
Q ss_pred CCCceEEEEechhcHHHHHHHcCCc------cceEeehhHHHHhhhhccC-CC--CCCCCcccHHhhhcCCcccCcccch
Q 019798 100 SSYITKVIHDCKRDSEALYFQFGIK------LHNVVDTQIAYSLIEEQEG-RK--RSPDDYISFVGLLADPRYCGISYQE 170 (335)
Q Consensus 100 ~~~i~KV~hd~k~D~~~L~~~~gi~------l~~vfDt~lAayLL~~~~~-~~--~l~~~~~sL~~L~~~~~~L~~~l~~ 170 (335)
|++|.||||++++|+..|++.+|+. +.+++||+.+++.+..... .. .......||+.|++ ++||.+++|
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 9999999999999999999889974 5789999998887764311 10 11123569999999 999999884
Q ss_pred hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHH
Q 019798 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (335)
Q Consensus 171 k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~ 213 (335)
... .++|..|||+++|+.|||.||++++.||+.|.
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 222 25999999999999999999999999999985
No 6
>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=9.4e-29 Score=212.27 Aligned_cols=156 Identities=31% Similarity=0.347 Sum_probs=136.0
Q ss_pred hhHHHhhhhcc-CCceEEEEEeecCCC-ccCcEEEEEEEeC-CceEEEEccCCChhhHHHHHHHHcCCCceEEEEechhc
Q 019798 37 LPAEFLEPSSE-RQLVIGFDCEGVDLC-RHGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRD 113 (335)
Q Consensus 37 L~~~~l~~~~~-~~~~ia~D~E~~~~~-~~~~l~~lqla~~-~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV~hd~k~D 113 (335)
|.+ +++.+ . +.+++|||+||.+.. +.+++|++|||++ +.+|+||+...+. .+..|+++|+|+++.||+||+|.|
T Consensus 2 l~~-~~~~l-~~~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~-~~~~L~~lL~d~~i~Kvg~~~k~D 78 (161)
T cd06129 2 LSS-LCEDL-SMDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSV-DWQGLKMLLENPSIVKALHGIEGD 78 (161)
T ss_pred HHH-HHHHH-hcCCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCcc-CHHHHHHHhCCCCEEEEEeccHHH
Confidence 454 77774 5 889999999999875 6789999999998 9999999987653 467899999999999999999999
Q ss_pred HHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHH
Q 019798 114 SEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTEL 193 (335)
Q Consensus 114 ~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~ 193 (335)
+..|++.+|+.+.++|||++++|++++.. ..||+.+++ +|+|.++++ ... .++|..|||+++
T Consensus 79 ~~~L~~~~gi~~~~~~D~~~aa~ll~~~~--------~~~L~~l~~--~~lg~~l~K-~~~-------~s~W~~rpLt~~ 140 (161)
T cd06129 79 LWKLLRDFGEKLQRLFDTTIAANLKGLPE--------RWSLASLVE--HFLGKTLDK-SIS-------CADWSYRPLTED 140 (161)
T ss_pred HHHHHHHcCCCcccHhHHHHHHHHhCCCC--------CchHHHHHH--HHhCCCCCc-cce-------eccCCCCCCCHH
Confidence 99997679999988999999999999752 238999999 999999874 332 259999999999
Q ss_pred HHHHHHhhhhHHHHHHHHHH
Q 019798 194 MVRAAADDVRFLPYIYHNMM 213 (335)
Q Consensus 194 ~~~YAa~Da~~ll~L~~~L~ 213 (335)
|+.|||.||++++.||+.|+
T Consensus 141 qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 141 QKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999986
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=99.95 E-value=4.4e-27 Score=203.34 Aligned_cols=164 Identities=23% Similarity=0.285 Sum_probs=139.5
Q ss_pred CCccchhHHHhhhhcc-CCceEEEEEeecCCC---ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEE
Q 019798 32 TNASQLPAEFLEPSSE-RQLVIGFDCEGVDLC---RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVI 107 (335)
Q Consensus 32 ~t~~~L~~~~l~~~~~-~~~~ia~D~E~~~~~---~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV~ 107 (335)
++.+++.. +++.+ . ....+|||+||.+.. ..+++++||||+++.+|+||+.... .+...|+++|+++++.||+
T Consensus 2 ~~~~~~~~-~~~~~-~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~-~~~~~l~~ll~~~~i~kv~ 78 (170)
T cd06141 2 DSAQDAEE-AVKEL-LGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMD-KLPPSLKQLLEDPSILKVG 78 (170)
T ss_pred CCHHHHHH-HHHHH-hcCCCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhh-cccHHHHHHhcCCCeeEEE
Confidence 45666776 77774 5 789999999999864 4689999999999999999998763 3567899999999999999
Q ss_pred EechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCcc
Q 019798 108 HDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTY 187 (335)
Q Consensus 108 hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~ 187 (335)
||+|+|+..|.+.+|+.+.++|||++++|++++..+. .||..|+. +|+|.++.+.+.. ..++|..
T Consensus 79 ~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~-------~~l~~l~~--~~l~~~~~k~k~~------~~s~W~~ 143 (170)
T cd06141 79 VGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKL-------VSLARLVE--EVLGLPLSKPKKV------RCSNWEA 143 (170)
T ss_pred eeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCC-------ccHHHHHH--HHcCcccCCCCCc------ccCCCCC
Confidence 9999999999878999999999999999999986322 38999999 9999988731111 1259999
Q ss_pred CCCCHHHHHHHHhhhhHHHHHHHHHH
Q 019798 188 RPLTELMVRAAADDVRFLPYIYHNMM 213 (335)
Q Consensus 188 rpL~~~~~~YAa~Da~~ll~L~~~L~ 213 (335)
|||+++|+.|||.||++++.||+.|.
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=99.95 E-value=8.6e-27 Score=201.23 Aligned_cols=170 Identities=31% Similarity=0.465 Sum_probs=144.6
Q ss_pred eEEeCCccchhHHHhhhhccCCceEEEEEeecCCC---ccCcEEEEEEEeCCceEEEEccCCChh-hHHHHHHHHcCCCc
Q 019798 28 IHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC---RHGSLCIMQLAFPDAIYLVDAIQGGET-VVKACKPALESSYI 103 (335)
Q Consensus 28 ~~~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~---~~~~l~~lqla~~~~~~lid~~~~~~~-~~~~Lk~lLe~~~i 103 (335)
|++|+|.+++.+ +++.+ .+.+.+|||+||.+.. ...+++++|+++.+.+|++++...... +...|+++|+++++
T Consensus 1 y~~v~~~~~l~~-~~~~l-~~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i 78 (176)
T PF01612_consen 1 YQIVDTEEELEE-AIKKL-KNAKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPNI 78 (176)
T ss_dssp SEEEHSHHHHHH-HHHHH-TTTSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTTS
T ss_pred CEecCCHHHHHH-HHHHH-cCCCeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCCc
Confidence 578999999997 99884 7788999999999874 367899999999988999988776543 57899999999999
Q ss_pred eEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccC-cccchhHHHHHHhcCCC
Q 019798 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCG-ISYQEKEEVRVLLRQDP 182 (335)
Q Consensus 104 ~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~-~~l~~k~~~~~~~~~~~ 182 (335)
.||+||+++|+.+|++.+|+.+.+++|||++++++++..+ .||++|+. +|+| ...+ ++ ...
T Consensus 79 ~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~--------~~L~~L~~--~~l~~~~~~-~~-------~~~ 140 (176)
T PF01612_consen 79 IKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRS--------YSLKDLAE--EYLGNIDLD-KK-------EQM 140 (176)
T ss_dssp EEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTT--------SSHHHHHH--HHHSEEE-G-HC-------CTT
T ss_pred cEEEEEEechHHHHHHHhccccCCccchhhhhhccccccc--------ccHHHHHH--HHhhhccCc-HH-------Hhh
Confidence 9999999999999987799999999999999999998643 39999999 9999 4443 22 123
Q ss_pred CCCc-cCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 019798 183 QFWT-YRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (335)
Q Consensus 183 ~~w~-~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (335)
.+|. .+|++++|+.|||.||+++++||+.|.++|+
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 5899 8999999999999999999999999999985
No 9
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.91 E-value=9.9e-25 Score=216.44 Aligned_cols=229 Identities=24% Similarity=0.223 Sum_probs=183.0
Q ss_pred EeCCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCC--ChhhHHHHHHHHcCCCceEE
Q 019798 30 IVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQG--GETVVKACKPALESSYITKV 106 (335)
Q Consensus 30 ~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~--~~~~~~~Lk~lLe~~~i~KV 106 (335)
.+.+...+.. |+... .....+++|+|+.+++ ..+.+++++++...+++|++.... .-.....|++||+++.+.|+
T Consensus 5 ~~~~~~~~~~-~~~~~-~~~~~~a~~~et~~l~~~~~~lvg~s~~~~~~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~kv 82 (593)
T COG0749 5 TITDLAVLNA-WLTKL-NAAANIAFDTETDGLDPHGADLVGLSVASEEEAAYIPLLHGPEQLNVLAALKPLLEDEGIKKV 82 (593)
T ss_pred hhhHHHHHHH-HHHHH-hhcccceeeccccccCcccCCeeEEEeeccccceeEeeccchhhhhhHHHHHHHhhCcccchh
Confidence 3444555664 66653 3334499999999987 678999999998767777765541 22357889999999999999
Q ss_pred EEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCC--C
Q 019798 107 IHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQ--F 184 (335)
Q Consensus 107 ~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~--~ 184 (335)
+||.|+|.++|. .+|+..+..||||+|+|+++|+.++| ++++|+. +|++.+....+.+ .++..+ +
T Consensus 83 ~~~~K~d~~~l~-~~Gi~~~~~~DtmlasYll~~~~~~~-------~~~~l~~--r~l~~~~~~~~~i---~~kg~~~~~ 149 (593)
T COG0749 83 GQNLKYDYKVLA-NLGIEPGVAFDTMLASYLLNPGAGAH-------NLDDLAK--RYLGLETITFEDI---AGKGKKQLT 149 (593)
T ss_pred ccccchhHHHHH-HcCCcccchHHHHHHHhccCcCcCcC-------CHHHHHH--HhcCCccchhHHh---hccccccCc
Confidence 999999999996 78966456999999999999987766 6789999 9998766533332 222222 2
Q ss_pred CccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccc-cHHHHHHhhhh-cccc-cccCCc-cCCCCCCCCCCCcccccCC
Q 019798 185 WTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS-LWYLAVRGALY-CRCF-CINEND-YVDWPPLPPVPDYLIVEGD 260 (335)
Q Consensus 185 w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~-l~~l~~~~e~~-~~vL-~me~~g-~~d~~~L~~~~~~l~~~~~ 260 (335)
+...++ +....|+++||+++++|+..|.+++.+.. +.++|.++||| ++|| .||.+| .+|.+.|..++.++..++.
T Consensus 150 ~~~~~~-~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L~~l~~~iE~Pl~~VLa~ME~~Gi~vD~~~L~~l~~el~~~l~ 228 (593)
T COG0749 150 FADVKL-EKATEYAAEDADATLRLESILEPELLKTPVLLELYEEIEMPLVRVLARMERNGIKVDVQYLKELSKELGCELA 228 (593)
T ss_pred cccchH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHhccHHHHHHHhHhcCceecHHHHHHHHHHHHHHHH
Confidence 332332 45679999999999999999998887755 69999999997 9999 999999 9999999999999999999
Q ss_pred CCHHHHHhhhcCCC
Q 019798 261 VPEEEILSILDVPP 274 (335)
Q Consensus 261 ~~e~~i~~lAg~~~ 274 (335)
.++++||++||+++
T Consensus 229 ~le~eiy~laG~~F 242 (593)
T COG0749 229 ELEEEIYELAGEEF 242 (593)
T ss_pred HHHHHHHHHhcCcC
Confidence 99999999999744
No 10
>PRK05755 DNA polymerase I; Provisional
Probab=99.91 E-value=4.5e-24 Score=226.58 Aligned_cols=229 Identities=23% Similarity=0.205 Sum_probs=193.5
Q ss_pred cCeEEeCCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCc-eEEEEccCCChhhHHHHHHHHcCCCc
Q 019798 26 VPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDA-IYLVDAIQGGETVVKACKPALESSYI 103 (335)
Q Consensus 26 ~~~~~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~-~~lid~~~~~~~~~~~Lk~lLe~~~i 103 (335)
+.|.+|++++++.. +++.+ .....++||+|++++. +.++++++|+++.++ +|+||+.......+..|+++|+++.+
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-WLAKL-KAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPAI 371 (880)
T ss_pred CceEEeCCHHHHHH-HHHHh-hccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCCC
Confidence 56788999999996 98874 6778999999999886 788999999999754 88887644332457889999999999
Q ss_pred eEEEEechhcHHHHHHHcCCcc-ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCC
Q 019798 104 TKVIHDCKRDSEALYFQFGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDP 182 (335)
Q Consensus 104 ~KV~hd~k~D~~~L~~~~gi~l-~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~ 182 (335)
.||+||+++|+.+|. .+|+.+ .++||||+|+|+++++.+ .||++|++ +|+|.++....+ ++++ .
T Consensus 372 ~kV~HNakfDl~~L~-~~gi~~~~~~~DT~iAa~Ll~~~~~--------~~L~~L~~--~ylg~~~~~~~~---~~gk-~ 436 (880)
T PRK05755 372 KKVGQNLKYDLHVLA-RYGIELRGIAFDTMLASYLLDPGRR--------HGLDSLAE--RYLGHKTISFEE---VAGK-Q 436 (880)
T ss_pred cEEEeccHhHHHHHH-hCCCCcCCCcccHHHHHHHcCCCCC--------CCHHHHHH--HHhCCCccchHH---hcCC-C
Confidence 999999999999996 689987 569999999999998642 38999999 999977532221 1222 2
Q ss_pred CCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhcc-ccHHHHHHhhhh-cccc-cccCCc-cCCCCCCCCCCCccccc
Q 019798 183 QFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ-SLWYLAVRGALY-CRCF-CINEND-YVDWPPLPPVPDYLIVE 258 (335)
Q Consensus 183 ~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~-~l~~l~~~~e~~-~~vL-~me~~g-~~d~~~L~~~~~~l~~~ 258 (335)
.+|..+|+ +.+..||+.|+.++++||..|.++|.+. +++.++.++|++ ++++ .||.+| .+|...+.++...+..+
T Consensus 437 ~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l~~l~~eiE~p~~~~l~~me~~Gi~vD~~~~~~~~~~~~~~ 515 (880)
T PRK05755 437 LTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEPGLLELYEEIELPLVPVLARMERNGIKVDREYLKELSAELAQR 515 (880)
T ss_pred CCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhhchHHHHHHHHHhcCeEeCHHHHHHHHHHHHHH
Confidence 45666676 5788999999999999999999999876 899999999997 8888 999999 99999999999999999
Q ss_pred CCCCHHHHHhhhcC
Q 019798 259 GDVPEEEILSILDV 272 (335)
Q Consensus 259 ~~~~e~~i~~lAg~ 272 (335)
+..++++|++++|.
T Consensus 516 ~~~l~~~~~~~~g~ 529 (880)
T PRK05755 516 LAELEQEIYELAGE 529 (880)
T ss_pred HHHHHHHHHHHhCC
Confidence 99999999999985
No 11
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=3.6e-24 Score=207.76 Aligned_cols=249 Identities=24% Similarity=0.350 Sum_probs=203.4
Q ss_pred cCeEEeCCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCce
Q 019798 26 VPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYIT 104 (335)
Q Consensus 26 ~~~~~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~ 104 (335)
.++.+|.+..+|.+ +.+. +.....+++|+|+.+.. +.|-.|++||+|..+.|+||.+.+.. .+..|+++|.+|++.
T Consensus 191 T~~~~I~t~~el~~-l~~~-l~~~~Efavdlehhsyrsf~gltclmqISTr~ed~iIDt~~l~~-~i~~l~e~fsdp~iv 267 (687)
T KOG2206|consen 191 TPKVWICTLGELEA-LPEI-LDSVIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKLRD-HIGILNEVFSDPGIV 267 (687)
T ss_pred cCceeeechHHHHH-HHHH-HhhhhhhhhhccccchhhhcCceeEEEeeccchhheehhHHHHH-HHHHhhhhccCCCeE
Confidence 34678888888886 8877 46778899999999885 78999999999999999999988765 456899999999999
Q ss_pred EEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCC
Q 019798 105 KVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQF 184 (335)
Q Consensus 105 KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~ 184 (335)
||+|++-.|+.||++.|||.+.|.|||..|+.+|+-++ .||+.|.+ .|+|+..+++.|. .+
T Consensus 268 kvfhgaD~diiwlqrdfgiyvvnLfdt~~a~r~L~~~r---------~sL~~ll~--~~~~v~~nk~yql--------ad 328 (687)
T KOG2206|consen 268 KVFHGADTDIIWLQRDFGIYVVNLFDTIQASRLLGLPR---------PSLAYLLE--CVCGVLTNKKYQL--------AD 328 (687)
T ss_pred EEEecCccchhhhhccceEEEEechhhHHHHHHhCCCc---------ccHHHHHH--HHHhhhhhhhhhh--------ch
Confidence 99999999999999999999999999999999999753 28999999 9999887754442 38
Q ss_pred CccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccc--cHHHHH---Hhhh--h-ccccc-------------ccCCc--
Q 019798 185 WTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS--LWYLAV---RGAL--Y-CRCFC-------------INEND-- 241 (335)
Q Consensus 185 w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~--l~~l~~---~~e~--~-~~vL~-------------me~~g-- 241 (335)
|+.|||+++|+.||.+|++|++.||+.|+..|.+.+ ..-.+. +++. . .++++ .+..+
T Consensus 329 wR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~~~~~~~~~~~d~c~~~~~k~~~~~~sy~~v~~~q~~ln~~q~~ 408 (687)
T KOG2206|consen 329 WRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAKGRAVTYSESRDMCTNGYKKKTFCTKSYLEVEDIQSRLNSSQLD 408 (687)
T ss_pred hccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhcccccccchhhhhhhcceecccCCCcchHhHHHHHhccchhHHH
Confidence 999999999999999999999999999998887643 211111 1111 0 11111 11111
Q ss_pred ----cCCCCCCCCCCCcccccCCCCHHHHHhhhcCCCCccc----------cccccccccHHHHHHHhh
Q 019798 242 ----YVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG----------RIIGRRGSSILAIKESCN 296 (335)
Q Consensus 242 ----~~d~~~L~~~~~~l~~~~~~~e~~i~~lAg~~~~~~~----------~~~~~~~~~~~~~~~~~~ 296 (335)
+..|+++-+++++.+.....+.+.+.++|.++|.+.+ ..++++..+++.++++|-
T Consensus 409 ~l~~L~~wRd~iARaeDES~~yVlpN~~ll~l~e~~P~~v~gl~~~ln~~~p~vkq~~~~~~~ii~~a~ 477 (687)
T KOG2206|consen 409 VLRALLRWRDFIARAEDESVHYVLPNDQLLKLAEERPDTVDGLLGGLNRLSPLVKQNVMDFLYIIRSAG 477 (687)
T ss_pred HHHHHHHHHHHHHhhccCCCceecccHHHHHHHHHCCccHHHHHHhccCCCHHHHHHHHHHHHHHHHHh
Confidence 3489999999999999999999999999999998765 456677788888888875
No 12
>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=99.88 E-value=1.3e-21 Score=169.75 Aligned_cols=168 Identities=29% Similarity=0.392 Sum_probs=137.2
Q ss_pred HhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEEechhcHHHHHH
Q 019798 41 FLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYF 119 (335)
Q Consensus 41 ~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~ 119 (335)
+++.+ .....+++|+|+.+.. ..++++++|+++++++|+||+... .....|+++|+|+++.||+||+|.|.+.|.+
T Consensus 5 ~~~~l-~~~~~l~~~~e~~~~~~~~~~~~~i~l~~~~~~~~i~~~~~--~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~ 81 (178)
T cd06142 5 LCERL-ASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI--GDLSPLKELLADPNIVKVFHAAREDLELLKR 81 (178)
T ss_pred HHHHH-hcCCeEEEECCccCCCcCCCceEEEEEeeCCCEEEEeCCCc--ccHHHHHHHHcCCCceEEEeccHHHHHHHHH
Confidence 44432 4456899999876654 468999999998865899986532 2466789999999999999999999999976
Q ss_pred HcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHH
Q 019798 120 QFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAA 199 (335)
Q Consensus 120 ~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa 199 (335)
.+|+..+++|||++|+|+++|..+ + |++++++ +|++.++.+ ... ..+|..+|++..++.|++
T Consensus 82 ~~gi~~~~~~D~~laayLl~p~~~-~-------~l~~l~~--~~l~~~~~~-~~~-------~~~w~~~~l~~~~~~yaa 143 (178)
T cd06142 82 DFGILPQNLFDTQIAARLLGLGDS-V-------GLAALVE--ELLGVELDK-GEQ-------RSDWSKRPLTDEQLEYAA 143 (178)
T ss_pred HcCCCCCCcccHHHHHHHhCCCcc-c-------cHHHHHH--HHhCCCCCc-ccc-------cccCCCCCCCHHHHHHHH
Confidence 569995568999999999999632 2 8899999 999987542 221 137888999999999999
Q ss_pred hhhhHHHHHHHHHHHHHhccccHHHHHHhh
Q 019798 200 DDVRFLPYIYHNMMKKLNQQSLWYLAVRGA 229 (335)
Q Consensus 200 ~Da~~ll~L~~~L~~~L~~~~l~~l~~~~e 229 (335)
.||.++++|++.|.++|++.++++++.+.+
T Consensus 144 ~~a~~l~~L~~~l~~~L~e~~l~~L~~~~~ 173 (178)
T cd06142 144 LDVRYLLPLYEKLKEELEEEGRLEWAEEEC 173 (178)
T ss_pred HhHHHHHHHHHHHHHHHHHcCcHHHHHHHH
Confidence 999999999999999999999999997654
No 13
>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=99.86 E-value=7.2e-21 Score=165.40 Aligned_cols=171 Identities=21% Similarity=0.206 Sum_probs=135.7
Q ss_pred CceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEEechhcHHHHHHHcCCccc-
Q 019798 49 QLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLH- 126 (335)
Q Consensus 49 ~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~- 126 (335)
...+++++|+.+.+ ..+++++++++.++++|+|++.. .......++++|+++++.|++||+|+|++.|. .+|+.+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~~~~~i~~~~-~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~~~~ 80 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGGGAYYIPLEL-ALLDLAALKEWLEDEKIPKVGHDAKRAYVALK-RHGIELAG 80 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCCcEEEEeccc-hHHHHHHHHHHHhCCCCceeccchhHHHHHHH-HCCCcCCC
Confidence 45678999988775 57899999999877788887432 10134568899999999999999999999995 7999885
Q ss_pred eEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHH
Q 019798 127 NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLP 206 (335)
Q Consensus 127 ~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll 206 (335)
.+||||+|+||++|+.+++ ++++++. +|++.++.+.++ +++++ .++. ++....+..|++.||.+++
T Consensus 81 ~~fDt~laaYLL~p~~~~~-------~l~~l~~--~yl~~~~~~~~~---~~~~~-~~~~-~~~~~~~~~y~~~~a~~l~ 146 (178)
T cd06140 81 VAFDTMLAAYLLDPTRSSY-------DLADLAK--RYLGRELPSDEE---VYGKG-AKFA-VPDEEVLAEHLARKAAAIA 146 (178)
T ss_pred cchhHHHHHHHcCCCCCCC-------CHHHHHH--HHcCCCCcchHH---hcCCC-CCcc-cCCHHHHHHHHHHHHHHHH
Confidence 4799999999999975434 8899999 999987653222 11221 1232 3435678899999999999
Q ss_pred HHHHHHHHHHhccccHHHHHHhhhh-cccc
Q 019798 207 YIYHNMMKKLNQQSLWYLAVRGALY-CRCF 235 (335)
Q Consensus 207 ~L~~~L~~~L~~~~l~~l~~~~e~~-~~vL 235 (335)
+|++.|.++|++++++++|.++||| ++||
T Consensus 147 ~l~~~l~~~L~~~~l~~L~~~iE~PL~~VL 176 (178)
T cd06140 147 RLAPKLEEELEENEQLELYYEVELPLAEVL 176 (178)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHhhHHHHh
Confidence 9999999999999999999999997 8887
No 14
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.84 E-value=8.2e-21 Score=199.88 Aligned_cols=221 Identities=17% Similarity=0.060 Sum_probs=173.4
Q ss_pred eEEeCCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCC--ceEEEEccC---CC-hhhHHHHHHHHcC
Q 019798 28 IHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPD--AIYLVDAIQ---GG-ETVVKACKPALES 100 (335)
Q Consensus 28 ~~~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~--~~~lid~~~---~~-~~~~~~Lk~lLe~ 100 (335)
+..|++.+++.. +++. .....+++ .+.. ..++++++++++.+ .+|+++... +. ..+...|+++|++
T Consensus 304 ~~~~~~~~~~~~-~~~~--~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 376 (887)
T TIGR00593 304 AKESEEAAPLAN-PAEK--AEVGGFVL----ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLN 376 (887)
T ss_pred ceEeCCHHHHHH-HHHh--CcCCeEEE----cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhC
Confidence 456666666775 7754 33446777 2333 46789999999853 477775431 11 2345669999999
Q ss_pred CCceEEEEechhcHHHHHHHcCCccce-EeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhc
Q 019798 101 SYITKVIHDCKRDSEALYFQFGIKLHN-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLR 179 (335)
Q Consensus 101 ~~i~KV~hd~k~D~~~L~~~~gi~l~~-vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~ 179 (335)
+.+.||+||+|+|+++|. .+|+.+.+ +||||+|+||++|+.+ + +|++++. +|++......++. .+
T Consensus 377 ~~~~~v~~n~K~d~~~l~-~~gi~~~~~~~Dt~la~yll~~~~~-~-------~l~~la~--~yl~~~~~~~~~~---~~ 442 (887)
T TIGR00593 377 EQIKKIGHDAKFLMHLLK-REGIELGGVIFDTMLAAYLLDPAQV-S-------TLDTLAR--RYLVEELILDEKI---GG 442 (887)
T ss_pred CCCcEEEeeHHHHHHHHH-hCCCCCCCcchhHHHHHHHcCCCCC-C-------CHHHHHH--HHcCcccccHHHh---cc
Confidence 999999999999999996 79999854 8999999999999642 3 8899999 9999764422221 12
Q ss_pred CCCCCCccCCCC-HHHHHHHHhhhhHHHHHHHHHHHHHhccccHHHHHHhhhh-cccc-cccCCc-cCCCCCCCCCCCcc
Q 019798 180 QDPQFWTYRPLT-ELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALY-CRCF-CINEND-YVDWPPLPPVPDYL 255 (335)
Q Consensus 180 ~~~~~w~~rpL~-~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~l~~~~e~~-~~vL-~me~~g-~~d~~~L~~~~~~l 255 (335)
++ ..|. .++ +.+..||+.||.++++||..|.++|.+.+++++|.++||| ++|| .||.+| .+|...+.++..++
T Consensus 443 ~~-~~~~--~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~l~~l~~~iE~pl~~vLa~ME~~Gi~vD~~~l~~~~~~~ 519 (887)
T TIGR00593 443 KL-AKFA--FPPLEEATEYLARRAAATKRLAEELLKELDENKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQELSQEF 519 (887)
T ss_pred CC-CCcc--cccHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHhCCEEeCHHHHHHHHHHH
Confidence 21 1232 333 5567899999999999999999999999999999999997 9999 999999 99999999999999
Q ss_pred cccCCCCHHHHHhhhcC
Q 019798 256 IVEGDVPEEEILSILDV 272 (335)
Q Consensus 256 ~~~~~~~e~~i~~lAg~ 272 (335)
..++..++++|++++|.
T Consensus 520 ~~~l~~le~~i~~~~g~ 536 (887)
T TIGR00593 520 GEEIADLEEEIYELAGE 536 (887)
T ss_pred HHHHHHHHHHHHHHhCC
Confidence 99999999999999986
No 15
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.83 E-value=9.4e-20 Score=156.13 Aligned_cols=168 Identities=29% Similarity=0.447 Sum_probs=131.7
Q ss_pred EEeCCccchhHHHhhhhcc-CCceEEEEEeecCCC-ccCcEEEEEEEeCC-ceEEEEccCCChhhHHHHHHHHcCCCceE
Q 019798 29 HIVTNASQLPAEFLEPSSE-RQLVIGFDCEGVDLC-RHGSLCIMQLAFPD-AIYLVDAIQGGETVVKACKPALESSYITK 105 (335)
Q Consensus 29 ~~I~t~~~L~~~~l~~~~~-~~~~ia~D~E~~~~~-~~~~l~~lqla~~~-~~~lid~~~~~~~~~~~Lk~lLe~~~i~K 105 (335)
.+|++.+++.+ +++.+ . ....+++|+|+.+.. ..++++++|+++.+ .+|+++... ....+..|+++|+++.+.|
T Consensus 2 ~~i~~~~~~~~-~~~~~-~~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~-~~~~~~~l~~~l~~~~~~k 78 (172)
T smart00474 2 RVVTDSETLEE-LLEKL-RAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLA-LGDDLEILKDLLEDETITK 78 (172)
T ss_pred EEecCHHHHHH-HHHHH-HhcCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEecc-chhhHHHHHHHhcCCCceE
Confidence 56788877775 77653 4 456899999987664 47899999999754 455544322 2223566899999999999
Q ss_pred EEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCC
Q 019798 106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFW 185 (335)
Q Consensus 106 V~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w 185 (335)
|+||+|+|+++|. ++|+.+.++||||+|+|+++|..+.+ +|+.++. +|++..+++ . .++ .+|
T Consensus 79 v~~d~k~~~~~L~-~~gi~~~~~~D~~laayll~p~~~~~-------~l~~l~~--~~l~~~~~~--~----~~~--~~~ 140 (172)
T smart00474 79 VGHNAKFDLHVLA-RFGIELENIFDTMLAAYLLLGGPSKH-------GLATLLK--EYLGVELDK--E----EQK--SDW 140 (172)
T ss_pred EEechHHHHHHHH-HCCCcccchhHHHHHHHHHcCCCCcC-------CHHHHHH--HHhCCCCCc--c----cCc--ccc
Confidence 9999999999996 59999988899999999999864323 8899999 999876542 1 111 278
Q ss_pred ccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 019798 186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (335)
Q Consensus 186 ~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (335)
..+|+...+..||+.||+++++|++.|.++|.
T Consensus 141 ~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l~ 172 (172)
T smart00474 141 GARPLSEEQLQYAAEDADALLRLYEKLEKELE 172 (172)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 77888999999999999999999999998873
No 16
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.82 E-value=7e-21 Score=192.79 Aligned_cols=200 Identities=19% Similarity=0.136 Sum_probs=166.9
Q ss_pred CeEEeCCccchhHHHhhhhccCCceEEEEEeecCCCccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEE
Q 019798 27 PIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKV 106 (335)
Q Consensus 27 ~~~~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV 106 (335)
.+.+|++.+++.. ++..+ ...+.+++|+|+..... .+|++|++.++..|+||+... +. ++
T Consensus 2 ~~~~I~~~~~l~~-~~~~l-~~~~~~a~DtEf~r~~t--~l~liQ~~~~~~~~liDpl~~----l~---~~--------- 61 (553)
T PRK14975 2 DMKVILAPEELGA-ALERL-SPAGVVAGDTETTGDDA--AAAAAQEGEEEPRWVWASTAA----LY---PR--------- 61 (553)
T ss_pred CceEEeccchhHH-HHHHh-ccCCceeCCccccCCcc--hhheeeecCCCceEEECchHH----hH---HH---------
Confidence 4678999999996 99884 78899999999876533 899999998889999987531 11 11
Q ss_pred EEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCc
Q 019798 107 IHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWT 186 (335)
Q Consensus 107 ~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~ 186 (335)
| ..+|+.+.++||||+|+|+|++..+.. ..||+.++. +|+++.+++.++ + ++|.
T Consensus 62 ----------L-~~~Gv~~~~~fDT~LAa~lL~~~~~~~-----~~~l~~la~--~~l~~~l~k~~~-~-------sdw~ 115 (553)
T PRK14975 62 ----------L-LAAGVRVERCHDLMLASQLLLGSEGRA-----GSSLSAAAA--RALGEGLDKPPQ-T-------SALS 115 (553)
T ss_pred ----------H-HHCCCccCCCchHHHHHHHcCCCCCcC-----CCCHHHHHH--HHhCCCCCChhh-h-------cccc
Confidence 4 367999888999999999999865311 238999999 999998874332 2 3796
Q ss_pred cCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhcc------ccHHHHHHhhhh-cccc-cccCCc-cCCCCCCCCCCCccc-
Q 019798 187 YRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ------SLWYLAVRGALY-CRCF-CINEND-YVDWPPLPPVPDYLI- 256 (335)
Q Consensus 187 ~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~------~l~~l~~~~e~~-~~vL-~me~~g-~~d~~~L~~~~~~l~- 256 (335)
||+++.|..||+.|+.+++.||..|.++|++. ++..++.++|++ ++++ .||.+| .+|.+.+.++..++.
T Consensus 116 -rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~~~~~~~g~l~ll~~~E~~~~~~l~~me~~Gi~~D~~~~~~~~~~~~~ 194 (553)
T PRK14975 116 -DPPDEEQLLYAAADADVLLELYAVLADQLNRIAAAAHPGRLRLLAAAESAGALAAAEMELAGLPWDTDVHEALLAELLG 194 (553)
T ss_pred -ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHhhHHHHHHHHHHhCeEeCHHHHHHHHHHHhc
Confidence 99999999999999999999999999999987 899999999997 8899 999999 999999888877777
Q ss_pred ---------ccCCCCHHHHHhhhcCC
Q 019798 257 ---------VEGDVPEEEILSILDVP 273 (335)
Q Consensus 257 ---------~~~~~~e~~i~~lAg~~ 273 (335)
.++..++++|++++|.+
T Consensus 195 ~~~~~~~~~~~~~~l~~~i~~~~g~~ 220 (553)
T PRK14975 195 PRPAAGGRPARLAELAAEIREALGRP 220 (553)
T ss_pred ccccccchHHHHHHHHHHHHHHhCCC
Confidence 56779999999999864
No 17
>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=99.81 E-value=8.5e-19 Score=154.61 Aligned_cols=173 Identities=26% Similarity=0.413 Sum_probs=136.4
Q ss_pred ccCeEEeCCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCc
Q 019798 25 VVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYI 103 (335)
Q Consensus 25 ~~~~~~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i 103 (335)
+.+|.+|++.+++.. +++.+ ...+.+++++|+.+.. ..+++++++++.++.+|+|++... ......|+++|+++.+
T Consensus 2 ~~~~~~i~~~~~l~~-~~~~l-~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~l~~-~~~~~~L~~~L~~~~i 78 (192)
T cd06147 2 ETPLTFVDTEEKLEE-LVEKL-KNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKL-RDDMHILNEVFTDPNI 78 (192)
T ss_pred CCCcEEECCHHHHHH-HHHHH-hcCCeEEEEeEecCCccCCCceEEEEEecCCCcEEEEeccc-ccchHHHHHHhcCCCc
Confidence 467888966677775 77553 4456899999876543 468899999998766888874222 2234568899999999
Q ss_pred eEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCC
Q 019798 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQ 183 (335)
Q Consensus 104 ~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~ 183 (335)
.||+||+|.+++.|.+.+|+.+.++||||+|+||++|+ + + +++.|++ +||+..+. |.+ ...
T Consensus 79 ~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~-~-~-------~l~~l~~--~yl~~~~~-k~~-------~~~ 139 (192)
T cd06147 79 LKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-R-H-------SLAYLLQ--KYCNVDAD-KKY-------QLA 139 (192)
T ss_pred eEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCC-c-c-------cHHHHHH--HHhCCCcc-hhh-------hcc
Confidence 99999999999999547899987779999999999996 3 3 7899999 99987643 211 112
Q ss_pred CCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhcc
Q 019798 184 FWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ 219 (335)
Q Consensus 184 ~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~ 219 (335)
+|..+|+..++..|++.+|.++++|++.|.++|+++
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 587788888899999999999999999999999875
No 18
>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=99.80 E-value=1.2e-18 Score=152.75 Aligned_cols=175 Identities=27% Similarity=0.304 Sum_probs=135.2
Q ss_pred cCCceEEEEEeecCCC-ccCcEEEEEEEeCC-ceEEEEccCC------C-hhhHHHHHHHHcCCCceEEEEechhcHHHH
Q 019798 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAFPD-AIYLVDAIQG------G-ETVVKACKPALESSYITKVIHDCKRDSEAL 117 (335)
Q Consensus 47 ~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~-~~~lid~~~~------~-~~~~~~Lk~lLe~~~i~KV~hd~k~D~~~L 117 (335)
.+...+++|+|+++.. ..+++++++++..+ ..+++++... . ..++..|+++|++..+.+|+||+|+|+.+|
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 3567899999988775 57889999999864 4777764321 1 234566899999988899999999999999
Q ss_pred HHHcCCccc-eEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcC--CCCCCccCCCCHHH
Q 019798 118 YFQFGIKLH-NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQ--DPQFWTYRPLTELM 194 (335)
Q Consensus 118 ~~~~gi~l~-~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~--~~~~w~~rpL~~~~ 194 (335)
. .+|+.+. .++||++++|+++|+..++ |++.+++ +|++......++ ++++ +..+|...|+ ..+
T Consensus 83 ~-~~gi~~~~~~~Dt~l~a~ll~p~~~~~-------~l~~l~~--~~l~~~~~~~~~---~~~k~~~~~~~~~~~~-~~~ 148 (193)
T cd06139 83 A-NHGIELRGPAFDTMLASYLLNPGRRRH-------GLDDLAE--RYLGHKTISFED---LVGKGKKQITFDQVPL-EKA 148 (193)
T ss_pred H-HCCCCCCCCcccHHHHHHHhCCCCCCC-------CHHHHHH--HHhCCCCccHHH---HcCCCcCcCCccccCH-HHH
Confidence 5 7899875 4899999999999964223 8899999 999865321122 1121 2234544444 667
Q ss_pred HHHHHhhhhHHHHHHHHHHHHHhc-cccHHHHHHhhhh-cccc
Q 019798 195 VRAAADDVRFLPYIYHNMMKKLNQ-QSLWYLAVRGALY-CRCF 235 (335)
Q Consensus 195 ~~YAa~Da~~ll~L~~~L~~~L~~-~~l~~l~~~~e~~-~~vL 235 (335)
..||+.|+.++++|++.|.++|.+ .+++++|.++||| ++||
T Consensus 149 ~~ya~~d~~~~~~l~~~l~~~l~~~~~~~~l~~~iE~Pl~~vL 191 (193)
T cd06139 149 AEYAAEDADITLRLYELLKPKLKEEPGLLELYEEIEMPLIPVL 191 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhccHHHHh
Confidence 889999999999999999999998 8999999999997 7876
No 19
>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=99.76 E-value=2.1e-17 Score=138.95 Aligned_cols=152 Identities=32% Similarity=0.384 Sum_probs=114.4
Q ss_pred eEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEEechhcHHHHHHHcCCcc-ceE
Q 019798 51 VIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKL-HNV 128 (335)
Q Consensus 51 ~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l-~~v 128 (335)
.+++|+|+.+.. ..++++++|+++++++++++.......+...|+++|+++.+.||+||+|+|.++|. ..++.. +++
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 578999987664 47899999999864466664332113456779999999999999999999999996 555544 568
Q ss_pred eehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHH
Q 019798 129 VDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYI 208 (335)
Q Consensus 129 fDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L 208 (335)
|||++++|+++|...++ ||+.+++ +|++..+.+.++.. +.+. .|..++++..+..||+.|+.++++|
T Consensus 81 ~D~~~~ayll~~~~~~~-------~l~~l~~--~~l~~~~~~~~~~~---~~~~-~~~~~~~~~~~~~y~~~da~~~~~l 147 (155)
T cd00007 81 FDTMLAAYLLNPGEGSH-------SLDDLAK--EYLGIELDKDEQIY---GKGA-KTFARPLSEELLEYAAEDADALLRL 147 (155)
T ss_pred ccHHHHHHHhCCCCCcC-------CHHHHHH--HHcCCCCccHHHHh---cCCC-CccccCCHHHHHHHHHHhHHHHHHH
Confidence 99999999999964222 8899999 99997754212221 1111 1435778899999999999999999
Q ss_pred HHHHHHHH
Q 019798 209 YHNMMKKL 216 (335)
Q Consensus 209 ~~~L~~~L 216 (335)
++.|.+++
T Consensus 148 ~~~l~~~~ 155 (155)
T cd00007 148 YEKLLEEL 155 (155)
T ss_pred HHHHHhhC
Confidence 99998763
No 20
>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=99.74 E-value=2.5e-17 Score=138.54 Aligned_cols=146 Identities=27% Similarity=0.328 Sum_probs=113.2
Q ss_pred eEEEEEeecCCC-ccCcEEEEEEEeC-CceEEEEccCCChhhHHHHHHHHcCCCceEEEEechhcHHHHHHHcCCccc-e
Q 019798 51 VIGFDCEGVDLC-RHGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLH-N 127 (335)
Q Consensus 51 ~ia~D~E~~~~~-~~~~l~~lqla~~-~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~-~ 127 (335)
++++|+|+.+.. ..++++++|++++ +.+|++++... ......|+++|+++++.||+||+|.|++.|. .+|+... +
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 378899876554 4689999999986 44888875432 1124568899999999999999999999995 6787764 5
Q ss_pred EeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHH
Q 019798 128 VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPY 207 (335)
Q Consensus 128 vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~ 207 (335)
+|||++|+|+++|..+++ +++.|++ +||+.++.+.++. .++ .|..+++..+|+.||+.|+.++++
T Consensus 79 ~~D~~laayLl~p~~~~~-------~l~~l~~--~~l~~~~~~~~~~---~~~---~~~~~~~~~~~~~ya~~~a~~l~~ 143 (150)
T cd09018 79 AFDTMLEAYILNSVAGRW-------DMDSLVE--RWLGHKLIKFESI---AGK---LWFNQPLTEEQGRYAAEDADVTLQ 143 (150)
T ss_pred chhHHHHHHHhCCCCCCC-------CHHHHHH--HHhCCCcccHHHh---cCC---CCcccCCHHHHHHHHHHHHHHHHH
Confidence 899999999999964222 7899999 9999875432321 121 385577789999999999999999
Q ss_pred HHHHHH
Q 019798 208 IYHNMM 213 (335)
Q Consensus 208 L~~~L~ 213 (335)
|++.|.
T Consensus 144 L~~~l~ 149 (150)
T cd09018 144 IHLKLW 149 (150)
T ss_pred HHHHhc
Confidence 999875
No 21
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.40 E-value=2.8e-13 Score=133.22 Aligned_cols=180 Identities=22% Similarity=0.265 Sum_probs=130.4
Q ss_pred cCeEEeCCccchhHHHh-hhhccCC-ceEEEEEeecCC-C-ccCcEEEEEEEeCCceEEEEccCCCh---hhH-HHHHHH
Q 019798 26 VPIHIVTNASQLPAEFL-EPSSERQ-LVIGFDCEGVDL-C-RHGSLCIMQLAFPDAIYLVDAIQGGE---TVV-KACKPA 97 (335)
Q Consensus 26 ~~~~~I~t~~~L~~~~l-~~~~~~~-~~ia~D~E~~~~-~-~~~~l~~lqla~~~~~~lid~~~~~~---~~~-~~Lk~l 97 (335)
..+.+|+++.++.. ++ +.+ ... -+||+|+||.+. . ...+++++|+++.+++|+||+.++.. +.+ ..+..+
T Consensus 390 ~~i~~V~~e~El~~-l~l~~l-~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~i 467 (617)
T KOG2207|consen 390 ESIGMVGNEKELRD-LLLESL-SEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQI 467 (617)
T ss_pred cceeeeCCHHHHHH-HHHHHh-hhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHH
Confidence 56888999999997 55 443 344 689999999876 3 57799999999999999999987642 233 345669
Q ss_pred HcCCCceEEEEechhcHHHHHHHc-----CCcc---ce-EeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCccc
Q 019798 98 LESSYITKVIHDCKRDSEALYFQF-----GIKL---HN-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (335)
Q Consensus 98 Le~~~i~KV~hd~k~D~~~L~~~~-----gi~l---~~-vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l 168 (335)
|+++++.|||++...|++++.+.. ...+ .+ +-++.++..+.+-.-.-.++.+..-+|..|.. ..+|..+
T Consensus 468 f~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~--~llg~~l 545 (617)
T KOG2207|consen 468 FESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTD--CLLGKKL 545 (617)
T ss_pred ccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhH--HHhhhhc
Confidence 999999999999999999997422 2222 12 22333443333321111111112236778888 8889888
Q ss_pred chhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 019798 169 QEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (335)
Q Consensus 169 ~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (335)
++.++ . ++|..|||+..|+.|||.||.++..++..+.+...
T Consensus 546 nKteq-c-------snWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 546 NKTEQ-C-------SNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred ccccc-c-------chhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 74333 2 48999999999999999999999999999987776
No 22
>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=99.29 E-value=8.7e-11 Score=99.27 Aligned_cols=132 Identities=21% Similarity=0.229 Sum_probs=93.1
Q ss_pred cCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceEEEEechhcHHHHHHHcCCccce-EeehhHHHHhhhhcc
Q 019798 64 HGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHN-VVDTQIAYSLIEEQE 142 (335)
Q Consensus 64 ~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~~-vfDt~lAayLL~~~~ 142 (335)
.+++.++.+++.+++|+|++.. .. ....|+++|++..+.|++||.|.+++.|. .+|+.+.+ +||||+|+|||+|++
T Consensus 17 ~~~~~glal~~~~~~~yi~~~~-~~-~~~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~l~~~~fD~~LAaYLL~p~~ 93 (151)
T cd06128 17 SANLVGLAFAIEGVAAYIPVAH-DY-ALELLKPLLEDEKALKVGQNLKYDRVILA-NYGIELRGIAFDTMLEAYLLDPVA 93 (151)
T ss_pred cCcEEEEEEEcCCCeEEEeCCC-Cc-CHHHHHHHHcCCCCCEEeeehHHHHHHHH-HCCCCCCCcchhHHHHHHHcCCCC
Confidence 5678889999876688875321 00 14458899999999999999999999994 89999865 799999999999975
Q ss_pred CCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCC-CHHHHHHHHhhhhHHHHHHHHHH
Q 019798 143 GRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPL-TELMVRAAADDVRFLPYIYHNMM 213 (335)
Q Consensus 143 ~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL-~~~~~~YAa~Da~~ll~L~~~L~ 213 (335)
+.+ ++++++. +|++..+...++ +++++ ..+. ++ ......|++..+.++++|++.|.
T Consensus 94 ~~~-------~l~~la~--~yl~~~~~~~~~---~~gkg-~~~~--~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 94 GRH-------DMDSLAE--RWLKEKTITFEE---IAGKG-LTFN--QIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CCC-------CHHHHHH--HHcCCCCccHHH---HcCCC-CChh--hcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 322 6789999 999876221112 22321 1111 12 12234478888889999988874
No 23
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.91 E-value=5e-10 Score=104.90 Aligned_cols=180 Identities=31% Similarity=0.277 Sum_probs=131.9
Q ss_pred cCcEEEEEEEeCCceEEEEccCCChhhH-HHHHHHHcCCCceEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhcc
Q 019798 64 HGSLCIMQLAFPDAIYLVDAIQGGETVV-KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQE 142 (335)
Q Consensus 64 ~~~l~~lqla~~~~~~lid~~~~~~~~~-~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~ 142 (335)
.+++..+++|++...|++|...-+..++ ..+++.|++..+ +. |++.+...+...|++.+.+++|||+|+.++.+.+
T Consensus 210 ~~e~~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~sLve~~e 286 (458)
T KOG2405|consen 210 ALEATYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIASSLVEPSE 286 (458)
T ss_pred hhhhhhhhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHHHHhhhHH
Confidence 4556668999999999999876543233 447888988765 55 9999999999999999999999999999999876
Q ss_pred --CCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccc
Q 019798 143 --GRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (335)
Q Consensus 143 --~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~ 220 (335)
++++. ...+|+..|..+++|.+.+...+++++.++..++.+|..||.++....-++.||.+++... ..+....
T Consensus 287 ~grr~p~-~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~----~~l~a~~ 361 (458)
T KOG2405|consen 287 YGRRHPT-SILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIF----DTLVAVC 361 (458)
T ss_pred hcccCCc-cceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHH----hhHhhhC
Confidence 33433 2355665555534577766665677777788888899999999999999999999998854 4455667
Q ss_pred cHHHHHHhhhhcccc-cccCCccCCCCCCCCC
Q 019798 221 LWYLAVRGALYCRCF-CINENDYVDWPPLPPV 251 (335)
Q Consensus 221 l~~l~~~~e~~~~vL-~me~~g~~d~~~L~~~ 251 (335)
+|.+...--.+.+|+ +|...-+.+|+--.+.
T Consensus 362 l~HL~~rp~~e~ecie~~~~~~~~~~p~gpe~ 393 (458)
T KOG2405|consen 362 LSHLTRRPYTEPECIELVFGLPMEKVPGGPES 393 (458)
T ss_pred hHhhccCCccccchhhhcCCcchhhCCCCCCC
Confidence 777766555556666 4433325566544443
No 24
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.25 E-value=6.4e-08 Score=91.01 Aligned_cols=149 Identities=31% Similarity=0.499 Sum_probs=100.3
Q ss_pred EEEeecCCCccCcEEEEEEEeCCceEEEEccCCChhhH-HHHHHHHcCCCceEEEEechhcHHHHHHHcCCccceEeehh
Q 019798 54 FDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVV-KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQ 132 (335)
Q Consensus 54 ~D~E~~~~~~~~~l~~lqla~~~~~~lid~~~~~~~~~-~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~ 132 (335)
.-.|+....++|++|++|.++.-..|++|++.++..++ ..|..++++.+|.|+.|+|+.-+..+.++|||.++++|||+
T Consensus 63 ~~~e~a~~~~~~~l~~~q~~~~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~q 142 (458)
T KOG2405|consen 63 VAAEGANVCRHGKLCWLQVATNCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQ 142 (458)
T ss_pred ccccCccccccCcchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhhh
Confidence 45566666688999999999888889999988876444 67888999999999999999999999999999999999999
Q ss_pred HHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccch---hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhH
Q 019798 133 IAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE---KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRF 204 (335)
Q Consensus 133 lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~---k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ 204 (335)
+|.-+-+.......+++....+.+-+- +.|.+.... -+....+.-.++..|-.||.++....-.+..+.+
T Consensus 143 ~~d~~q~~~e~g~~~~n~~~~~q~sl~--kh~~~a~k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 143 VADVLQFSMETGGYLPNCITTLQESLI--KHLQVAPKYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred hhhhhhhcccccccCCccccchHHHHH--HHHHhcccHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 976554332211222222222332222 233322110 0111112224566799999998877665555554
No 25
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=97.92 E-value=2.8e-05 Score=72.43 Aligned_cols=129 Identities=18% Similarity=0.201 Sum_probs=93.1
Q ss_pred cCcEEEEEEEeC-CceEEEEccCCChhhHHHHHHHHcCCCceEEEEechhcHHHHHH-HcCCccceEeehhHHHHhhhhc
Q 019798 64 HGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYF-QFGIKLHNVVDTQIAYSLIEEQ 141 (335)
Q Consensus 64 ~~~l~~lqla~~-~~~~lid~~~~~~~~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~-~~gi~l~~vfDt~lAayLL~~~ 141 (335)
.+....+|||++ +.++++....-+ .+...|+.+|+|++.++||-+..+|...|.+ .|++.+....|+-. ++++.
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-RIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRL---LVNDS 221 (319)
T ss_pred CCCcchhhhhhcccceeeEEeeccc-cchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHh---hcchh
Confidence 355778999997 778887555433 4678888999999999999999999999876 78888877777654 23332
Q ss_pred cCCCCCCCCcccHHhhhcCCcccCc-----ccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 019798 142 EGRKRSPDDYISFVGLLADPRYCGI-----SYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (335)
Q Consensus 142 ~~~~~l~~~~~sL~~L~~~~~~L~~-----~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (335)
.+. .++ .-|...|+. ..++. .+++ .+ +.++|...||+.+|+.||+.||++.+.|+
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 222 222 225556665 44442 2221 12 23599999999999999999999999999
No 26
>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=97.89 E-value=5.8e-05 Score=58.96 Aligned_cols=72 Identities=24% Similarity=0.179 Sum_probs=54.5
Q ss_pred EEEEEeecCCC-ccCcEEEEEEEeC--CceEEEEccCCChhhHHHHHHHHcCCC-ceEEEEechhcHHHHHHH---cCCc
Q 019798 52 IGFDCEGVDLC-RHGSLCIMQLAFP--DAIYLVDAIQGGETVVKACKPALESSY-ITKVIHDCKRDSEALYFQ---FGIK 124 (335)
Q Consensus 52 ia~D~E~~~~~-~~~~l~~lqla~~--~~~~lid~~~~~~~~~~~Lk~lLe~~~-i~KV~hd~k~D~~~L~~~---~gi~ 124 (335)
+++|+|+++.. ...+++++|++.. ++.|++| +.+++++.. ..+|+||+.+|+..|.+. +|+.
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 47999999886 6788999999875 6677765 556777765 678999999999877643 3332
Q ss_pred ----cceEeehhHH
Q 019798 125 ----LHNVVDTQIA 134 (335)
Q Consensus 125 ----l~~vfDt~lA 134 (335)
....+||+.+
T Consensus 70 ~p~~~~~~lDT~~l 83 (96)
T cd06125 70 YPLLAGSWIDTIKL 83 (96)
T ss_pred CCCcCCcEEEehHH
Confidence 2458999987
No 27
>PRK07740 hypothetical protein; Provisional
Probab=97.79 E-value=0.00065 Score=62.21 Aligned_cols=98 Identities=17% Similarity=0.289 Sum_probs=68.2
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHHH----cCCcc-ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCccc
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ----FGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~----~gi~l-~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (335)
++..+..++.+. ..|+||+.+|...|.+. ++... ..++||+..+..+.+... ..||++++. ++
T Consensus 131 vl~~f~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~-------~~sL~~l~~---~~ 198 (244)
T PRK07740 131 VLHRFYAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERD-------FPTLDDALA---YY 198 (244)
T ss_pred HHHHHHHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCC-------CCCHHHHHH---HC
Confidence 345555555543 56899999999887532 34344 358999988877766432 248899986 67
Q ss_pred CcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccHH
Q 019798 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (335)
Q Consensus 165 ~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~ 223 (335)
|++.... .-|..||..+..|+..+..++.+.|...
T Consensus 199 gi~~~~~------------------------H~Al~Da~ata~l~~~ll~~~~~~~~~~ 233 (244)
T PRK07740 199 GIPIPRR------------------------HHALGDALMTAKLWAILLVEAQQRGITT 233 (244)
T ss_pred CcCCCCC------------------------CCcHHHHHHHHHHHHHHHHHHHHcCCcC
Confidence 7755310 1177899999999999999998766543
No 28
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.67 E-value=0.00074 Score=64.12 Aligned_cols=138 Identities=17% Similarity=0.141 Sum_probs=88.2
Q ss_pred CceEEEEEeecCCC-ccCcEEEEEEEe--C-Cc-----eEEEEccC---------CC----------hhhHHHHHHHHcC
Q 019798 49 QLVIGFDCEGVDLC-RHGSLCIMQLAF--P-DA-----IYLVDAIQ---------GG----------ETVVKACKPALES 100 (335)
Q Consensus 49 ~~~ia~D~E~~~~~-~~~~l~~lqla~--~-~~-----~~lid~~~---------~~----------~~~~~~Lk~lLe~ 100 (335)
...++||+|+++++ ...+++-|.... . +. ..++.+.. +. .+++..|..++.+
T Consensus 15 ~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~l~~ 94 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRG 94 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHHHHcCC
Confidence 46889999999886 334443333221 1 21 12343321 00 1345667777765
Q ss_pred CCceEEEEechhcHHHHHHH---cCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHH
Q 019798 101 SYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVR 175 (335)
Q Consensus 101 ~~i~KV~hd~k~D~~~L~~~---~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~ 175 (335)
. ..|+||+.+|+.+|.+. +|+.. ..++||+..+..+.+...++ +|.+|++ ++|++...
T Consensus 95 ~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~-------kL~~l~~---~~gi~~~~----- 157 (313)
T PRK06063 95 R--TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNL-------RLETLAA---HWGVPQQR----- 157 (313)
T ss_pred C--EEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCC-------CHHHHHH---HcCCCCCC-----
Confidence 3 46999999999988643 55543 35899998777666543333 7788886 66765321
Q ss_pred HHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccH
Q 019798 176 VLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLW 222 (335)
Q Consensus 176 ~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~ 222 (335)
.+-|..||.++..|+..+.+++.+.+.+
T Consensus 158 -------------------~H~Al~DA~ata~l~~~ll~~~~~~~~~ 185 (313)
T PRK06063 158 -------------------PHDALDDARVLAGILRPSLERARERDVW 185 (313)
T ss_pred -------------------CCCcHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 0127789999999999999998877653
No 29
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=97.45 E-value=0.0034 Score=57.03 Aligned_cols=135 Identities=14% Similarity=0.187 Sum_probs=81.2
Q ss_pred CCceEEEEEeecCCC-ccCcEEEEEEEe-C--C-----ceEEEEccC-CC----------h-----------hhHHHHHH
Q 019798 48 RQLVIGFDCEGVDLC-RHGSLCIMQLAF-P--D-----AIYLVDAIQ-GG----------E-----------TVVKACKP 96 (335)
Q Consensus 48 ~~~~ia~D~E~~~~~-~~~~l~~lqla~-~--~-----~~~lid~~~-~~----------~-----------~~~~~Lk~ 96 (335)
+...++||+||++++ ..++++-+.+.. . + ..+++++.. +. . +++..+..
T Consensus 5 ~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~~ 84 (232)
T PRK07942 5 PGPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEIAD 84 (232)
T ss_pred cCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHHHH
Confidence 457899999999986 445543322211 1 2 234666532 10 0 12222222
Q ss_pred H----HcCCCceEEEEechhcHHHHHH---HcCCcc---ceEeehhHHHHhhhhcc-CCCCCCCCcccHHhhhcCCcccC
Q 019798 97 A----LESSYITKVIHDCKRDSEALYF---QFGIKL---HNVVDTQIAYSLIEEQE-GRKRSPDDYISFVGLLADPRYCG 165 (335)
Q Consensus 97 l----Le~~~i~KV~hd~k~D~~~L~~---~~gi~l---~~vfDt~lAayLL~~~~-~~~~l~~~~~sL~~L~~~~~~L~ 165 (335)
. +.+. ...|+||+.+|..+|.+ ++|... ..++||+..+..+.+.. ++ .+|.+|++ ++|
T Consensus 85 ~l~~~~~~~-~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~-------~~L~~l~~---~~g 153 (232)
T PRK07942 85 ALREAWARG-VPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGK-------RTLTALCE---HYG 153 (232)
T ss_pred HHHHHhhcC-CEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCC-------CCHHHHHH---HcC
Confidence 2 2233 35599999999988753 355432 35899998776665432 22 37889986 567
Q ss_pred cccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 019798 166 ISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (335)
Q Consensus 166 ~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (335)
++... ..-|..||.++.+|+..+..+..
T Consensus 154 i~~~~------------------------aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 154 VRLDN------------------------AHEATADALAAARVAWALARRFP 181 (232)
T ss_pred CCCCC------------------------CCChHHHHHHHHHHHHHHHHHHH
Confidence 65431 01177899999999999877665
No 30
>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=97.45 E-value=0.00053 Score=58.05 Aligned_cols=85 Identities=25% Similarity=0.228 Sum_probs=55.5
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccc
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~ 169 (335)
++..|..++.+ .+ .|+||+.+|+.+|. .+.....++||........+.. ....||+.|++ +|+|+++.
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 45677788876 44 49999999999994 3333345889876443333211 02358999998 78887653
Q ss_pred hhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 019798 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (335)
Q Consensus 170 ~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (335)
... .-|..||.++..||
T Consensus 135 ~~~-----------------------H~Al~DA~at~~l~ 151 (152)
T cd06144 135 EGE-----------------------HSSVEDARAAMRLY 151 (152)
T ss_pred CCC-----------------------cCcHHHHHHHHHHh
Confidence 100 11678899888876
No 31
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=97.37 E-value=0.00083 Score=57.25 Aligned_cols=86 Identities=21% Similarity=0.052 Sum_probs=51.8
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHHHcCCccceEeehhHHHHh----hhhccCCCCCCCCcccHHhhhcCCcccC
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSL----IEEQEGRKRSPDDYISFVGLLADPRYCG 165 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayL----L~~~~~~~~l~~~~~sL~~L~~~~~~L~ 165 (335)
+...+..++.+ -..|+||+++|+.+|.. ......+.||.....+ ..|.. ...+|..|++ +|++
T Consensus 67 v~~~l~~~l~~--~vlV~Hn~~~D~~~l~~--~~~~~~~~Dt~~l~~~~~~~~~p~~-------~~~~L~~L~~--~~~~ 133 (157)
T cd06149 67 AQKEILKILKG--KVVVGHAIHNDFKALKY--FHPKHMTRDTSTIPLLNRKAGFPEN-------CRVSLKVLAK--RLLH 133 (157)
T ss_pred HHHHHHHHcCC--CEEEEeCcHHHHHHhcc--cCCCcCEEECcccccchhhcCCccc-------CChhHHHHHH--HHcC
Confidence 45667777764 35699999999999852 2222357788543211 12221 2348999999 8876
Q ss_pred cccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 019798 166 ISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (335)
Q Consensus 166 ~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (335)
..+.. ... ..-|..||.++.+||
T Consensus 134 ~~i~~-------------~~~--------~H~Al~DA~at~~l~ 156 (157)
T cd06149 134 RDIQV-------------GRQ--------GHSSVEDARATMELY 156 (157)
T ss_pred hhhcC-------------CCC--------CcCcHHHHHHHHHHh
Confidence 54431 000 011668888888876
No 32
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=97.31 E-value=0.0023 Score=54.64 Aligned_cols=67 Identities=22% Similarity=0.153 Sum_probs=45.1
Q ss_pred HHHHHHHcCCCceEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccc
Q 019798 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (335)
Q Consensus 92 ~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~ 169 (335)
..+..++.+.. ..|+||+.+|+.+|.. . ...+.||...+..+.+.... ....+|..|++ +|+|.++.
T Consensus 75 ~~~~~~i~~~~-vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~~~~~~~~~~----~~~~~L~~L~~--~~~~~~~~ 141 (161)
T cd06137 75 AALWKFIDPDT-ILVGHSLQNDLDALRM-I---HTRVVDTAILTREAVKGPLA----KRQWSLRTLCR--DFLGLKIQ 141 (161)
T ss_pred HHHHHhcCCCc-EEEeccHHHHHHHHhC-c---CCCeeEehhhhhhccCCCcC----CCCccHHHHHH--HHCCchhc
Confidence 34566665533 4699999999999952 2 23588999887766653210 01348999998 88887653
No 33
>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=97.28 E-value=0.0011 Score=55.94 Aligned_cols=65 Identities=23% Similarity=0.184 Sum_probs=43.2
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCccc
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l 168 (335)
+...+.+++.+.. ..|+||+++|+.+|. .. ...++||...+....+... ..+|..|++ +|++..+
T Consensus 65 v~~~~~~fl~~~~-vlVgHn~~fD~~fL~-~~---~~~~iDT~~l~r~~~~~~~-------~~~L~~L~~--~~~~~~i 129 (150)
T cd06145 65 VQKKLLSLISPDT-ILVGHSLENDLKALK-LI---HPRVIDTAILFPHPRGPPY-------KPSLKNLAK--KYLGRDI 129 (150)
T ss_pred HHHHHHHHhCCCC-EEEEcChHHHHHHhh-cc---CCCEEEcHHhccccCCCCC-------ChhHHHHHH--HHCCcce
Confidence 3456666775333 569999999999995 22 1458999876544333221 248899999 8888544
No 34
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.24 E-value=0.0043 Score=66.33 Aligned_cols=135 Identities=19% Similarity=0.141 Sum_probs=88.3
Q ss_pred CCceEEEEEeecCCCccCcEEEEEEEe----CCc-----eEEEEccC-C----------C----------hhhHHHHHHH
Q 019798 48 RQLVIGFDCEGVDLCRHGSLCIMQLAF----PDA-----IYLVDAIQ-G----------G----------ETVVKACKPA 97 (335)
Q Consensus 48 ~~~~ia~D~E~~~~~~~~~l~~lqla~----~~~-----~~lid~~~-~----------~----------~~~~~~Lk~l 97 (335)
....++||+|+++++...+ +++|+. .++ ..+|.+.. + . .+++..+..+
T Consensus 6 ~~~~vvvD~ETTGl~~~d~--IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~ 83 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNAS--IIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDL 83 (820)
T ss_pred CCCEEEEEEecCCcCCCCe--EEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHH
Confidence 3578999999999863344 455553 222 12333321 0 0 1344566677
Q ss_pred HcCCCceEEEEechhcHHHHHHH---cCCcc-ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHH
Q 019798 98 LESSYITKVIHDCKRDSEALYFQ---FGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE 173 (335)
Q Consensus 98 Le~~~i~KV~hd~k~D~~~L~~~---~gi~l-~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~ 173 (335)
+.+. ..|+||+.+|+..|.+. .|..+ ...+||+..+..+-|...++ +|.+|++ ++|++...
T Consensus 84 l~~~--~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~-------~L~~L~~---~lgl~~~~--- 148 (820)
T PRK07246 84 IEDC--IFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKY-------SLSHLSR---ELNIDLAD--- 148 (820)
T ss_pred hCCC--EEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCC-------CHHHHHH---HcCCCCCC---
Confidence 7653 46999999999998643 46655 35899998877776654334 7889997 56765421
Q ss_pred HHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccc
Q 019798 174 VRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (335)
Q Consensus 174 ~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~ 220 (335)
.+-|..||.++..|+..|..++...+
T Consensus 149 ---------------------~H~Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 149 ---------------------AHTAIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred ---------------------CCCHHHHHHHHHHHHHHHHHHHhhcC
Confidence 01277899999999999998887644
No 35
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.24 E-value=0.011 Score=53.65 Aligned_cols=140 Identities=16% Similarity=0.123 Sum_probs=85.2
Q ss_pred ceEEEEEeecCCC-ccCcEEEEEEEe-C---Cc--eEEEEccCC-----------Ch----------hhHHHHHHHHcCC
Q 019798 50 LVIGFDCEGVDLC-RHGSLCIMQLAF-P---DA--IYLVDAIQG-----------GE----------TVVKACKPALESS 101 (335)
Q Consensus 50 ~~ia~D~E~~~~~-~~~~l~~lqla~-~---~~--~~lid~~~~-----------~~----------~~~~~Lk~lLe~~ 101 (335)
..+.||+||++++ ...++ ++++. . .. ..++.+... .+ ++...+..++.+.
T Consensus 3 ~~vv~D~ETTGl~~~~d~I--Ieig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~~~ 80 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRI--IEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTD 80 (232)
T ss_pred cEEEEEeeCCCCCCCCCEE--EEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHcCC
Confidence 4689999999986 44444 44442 1 12 234444321 01 2334555566543
Q ss_pred CceEEEEe-chhcHHHHHH---HcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHH
Q 019798 102 YITKVIHD-CKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVR 175 (335)
Q Consensus 102 ~i~KV~hd-~k~D~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~ 175 (335)
...|+|| ..+|..+|.+ ++|+.. ...+||+-.+..+.+...++ +|..|++ ++|++...
T Consensus 81 -~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~-------~L~~l~~---~~~~~~~~----- 144 (232)
T PRK06309 81 -NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKH-------NLQYLRQ---VYGFEENQ----- 144 (232)
T ss_pred -CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCC-------CHHHHHH---HcCCCCCC-----
Confidence 3569999 4899988853 355553 35899987776665532233 7788886 44654321
Q ss_pred HHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccHHHHH
Q 019798 176 VLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAV 226 (335)
Q Consensus 176 ~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~l~~ 226 (335)
..-|..||.++..|+..+..++..+.+..+..
T Consensus 145 -------------------aH~Al~Da~~t~~vl~~l~~~~~~~~l~~l~~ 176 (232)
T PRK06309 145 -------------------AHRALDDVITLHRVFSALVGDLSPQQVYDLLN 176 (232)
T ss_pred -------------------CCCcHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 01177999999999999988886544444443
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=97.24 E-value=0.0038 Score=56.05 Aligned_cols=138 Identities=16% Similarity=0.124 Sum_probs=82.4
Q ss_pred cCCceEEEEEeecCCCccCcEEEEEEEe----CCc------eEEEEccC-CC--------------------hhhHHHHH
Q 019798 47 ERQLVIGFDCEGVDLCRHGSLCIMQLAF----PDA------IYLVDAIQ-GG--------------------ETVVKACK 95 (335)
Q Consensus 47 ~~~~~ia~D~E~~~~~~~~~l~~lqla~----~~~------~~lid~~~-~~--------------------~~~~~~Lk 95 (335)
.....+.||+||++++.... +++|+. .+. .+++.+.. .. .+++..+.
T Consensus 5 ~~~~fvv~D~ETTGl~~~~~--IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~ 82 (217)
T TIGR00573 5 VLDTETTGDNETTGLYAGHD--IIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFA 82 (217)
T ss_pred EecCEEEEEecCCCCCCCCC--EEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHH
Confidence 45688999999999863222 344432 111 12333321 00 12445666
Q ss_pred HHHcCCCceEEEEechhcHHHHHHHc---CCc--c-ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccc
Q 019798 96 PALESSYITKVIHDCKRDSEALYFQF---GIK--L-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (335)
Q Consensus 96 ~lLe~~~i~KV~hd~k~D~~~L~~~~---gi~--l-~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~ 169 (335)
.++.+. ..|+||+.+|+.+|.+.+ +.. . ..++||+..+..+.+....+ ..+|..+++ ++|++..
T Consensus 83 ~~~~~~--~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~-----~~~L~~l~~---~~gl~~~ 152 (217)
T TIGR00573 83 DYIRGA--ELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGK-----RNTLDALCK---RYEITNS 152 (217)
T ss_pred HHhCCC--EEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCC-----CCCHHHHHH---HcCCCCC
Confidence 666552 468999999999986443 221 2 34789987666665542222 247889887 4565422
Q ss_pred hhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhc
Q 019798 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (335)
Q Consensus 170 ~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (335)
. .. ..-|..||.++..|+..+..+..+
T Consensus 153 ~-~~---------------------~H~Al~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 153 H-RA---------------------LHGALADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred C-cc---------------------cCCHHHHHHHHHHHHHHHHhcchh
Confidence 0 00 112778999999999999877654
No 37
>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=97.19 E-value=0.0047 Score=68.16 Aligned_cols=139 Identities=16% Similarity=0.229 Sum_probs=91.8
Q ss_pred cCCceEEEEEeecCCC-ccCcEEEEEEEe--CCce-----EEEEccC-C----------C----------hhhHHHHHHH
Q 019798 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF--PDAI-----YLVDAIQ-G----------G----------ETVVKACKPA 97 (335)
Q Consensus 47 ~~~~~ia~D~E~~~~~-~~~~l~~lqla~--~~~~-----~lid~~~-~----------~----------~~~~~~Lk~l 97 (335)
.+...+.||+||++++ ...++.-+.... .+.. .+|.+.. + . .+++..+..+
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~f 267 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFKEF 267 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHH
Confidence 4567899999999986 444443332221 2211 2232211 0 0 1355677777
Q ss_pred HcCCCceEEEEechhcHHHHHH---HcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhH
Q 019798 98 LESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKE 172 (335)
Q Consensus 98 Le~~~i~KV~hd~k~D~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~ 172 (335)
+.+. ..|+||+.+|...|.+ ++|+.. ..++||+..++.+.|...++ +|+.|++ + +|++...
T Consensus 268 l~~~--iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~-------kL~~Lak--~-lgi~~~~-- 333 (1213)
T TIGR01405 268 FKDS--ILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSH-------RLGNICK--K-LGVDLDD-- 333 (1213)
T ss_pred hCCC--eEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCC-------CHHHHHH--H-cCCCCCC--
Confidence 7653 4599999999998863 356643 35899999888887754444 8899997 4 5765431
Q ss_pred HHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhcccc
Q 019798 173 EVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSL 221 (335)
Q Consensus 173 ~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l 221 (335)
.+.|..||.++..|+..+.+++.+.+.
T Consensus 334 ----------------------~HrAl~DA~aTa~I~~~ll~~l~~~~i 360 (1213)
T TIGR01405 334 ----------------------HHRADYDAEATAKVFKVMVEQLKEKGI 360 (1213)
T ss_pred ----------------------CcCHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 123789999999999999999987653
No 38
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.16 E-value=0.012 Score=54.00 Aligned_cols=133 Identities=17% Similarity=0.219 Sum_probs=82.3
Q ss_pred cCCceEEEEEeecCCC-ccCcEEEEEEEe----CC-----ceEEEEccC-CC--------------------hhhHHHHH
Q 019798 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PD-----AIYLVDAIQ-GG--------------------ETVVKACK 95 (335)
Q Consensus 47 ~~~~~ia~D~E~~~~~-~~~~l~~lqla~----~~-----~~~lid~~~-~~--------------------~~~~~~Lk 95 (335)
++...+.||+||++++ ...++ ++|+. .+ ...+|.+.. .. .++...+.
T Consensus 5 ~~~~~v~~D~ETTGl~~~~d~I--IEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~ 82 (250)
T PRK06310 5 KDTEFVCLDCETTGLDVKKDRI--IEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIK 82 (250)
T ss_pred cCCcEEEEEEeCCCCCCCCCeE--EEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHH
Confidence 4568899999999985 34443 33332 12 123444321 10 12345666
Q ss_pred HHHcCCCceEEEEechhcHHHHHH---HcCCcc----ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCccc
Q 019798 96 PALESSYITKVIHDCKRDSEALYF---QFGIKL----HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (335)
Q Consensus 96 ~lLe~~~i~KV~hd~k~D~~~L~~---~~gi~l----~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l 168 (335)
.++.+.. ..|+||+.+|..+|.+ .+|+.. ..++||+-.+..+... .+ .+|..|++ ++|++.
T Consensus 83 ~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~-~~-------~~L~~l~~---~~g~~~ 150 (250)
T PRK06310 83 GFFKEGD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDS-PN-------NSLEALAV---HFNVPY 150 (250)
T ss_pred HHhCCCC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccC-CC-------CCHHHHHH---HCCCCC
Confidence 6676544 4699999999988853 345543 3489998877654321 12 37888886 446543
Q ss_pred chhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 019798 169 QEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (335)
Q Consensus 169 ~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (335)
.. ..-|..||.++..++..+..++.
T Consensus 151 ~~------------------------aH~Al~Da~at~~vl~~l~~~~~ 175 (250)
T PRK06310 151 DG------------------------NHRAMKDVEINIKVFKHLCKRFR 175 (250)
T ss_pred CC------------------------CcChHHHHHHHHHHHHHHHHhcc
Confidence 21 11277999999999999887663
No 39
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=97.07 E-value=0.0027 Score=68.13 Aligned_cols=139 Identities=16% Similarity=0.222 Sum_probs=97.4
Q ss_pred ccCCceEEEEEeecCCC-ccCcEEEEEEEe----CCc-----eEEEEccCC-----------C----------hhhHHHH
Q 019798 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-----IYLVDAIQG-----------G----------ETVVKAC 94 (335)
Q Consensus 46 ~~~~~~ia~D~E~~~~~-~~~~l~~lqla~----~~~-----~~lid~~~~-----------~----------~~~~~~L 94 (335)
+.++..+.||+||++++ .+.++ |+++. .++ -+++++... . .+++..+
T Consensus 418 l~datyVVfDiETTGLs~~~d~i--IE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf 495 (1444)
T COG2176 418 LDDATYVVFDIETTGLSPVYDEI--IEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKF 495 (1444)
T ss_pred cccccEEEEEeecCCcCcccchh--hhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHH
Confidence 35678999999999996 55553 55553 121 233433321 0 2466778
Q ss_pred HHHHcCCCceEEEEechhcHHHHHH---HcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccc
Q 019798 95 KPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (335)
Q Consensus 95 k~lLe~~~i~KV~hd~k~D~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~ 169 (335)
+.++.|. .-|.||+.+|+-.|.. .+|+.. +++.||.-.++.|+|...+| +|..|+. + |++.+.
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--K-LGVELE 563 (1444)
T ss_pred HHHhcCc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhc-------chHHHHH--H-hCccHH
Confidence 8888874 4599999999988753 356655 45999999999999988777 6678887 3 354432
Q ss_pred hhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccH
Q 019798 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLW 222 (335)
Q Consensus 170 ~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~ 222 (335)
+..-|--|+.++-+++-.+.+.+++.|..
T Consensus 564 ------------------------~hHRA~yDaeat~~vf~~f~~~~ke~Gi~ 592 (1444)
T COG2176 564 ------------------------RHHRADYDAEATAKVFFVFLKDLKEKGIT 592 (1444)
T ss_pred ------------------------HhhhhhhhHHHHHHHHHHHHHHHHHhchh
Confidence 12336679999999999999999987644
No 40
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=97.05 E-value=0.011 Score=56.20 Aligned_cols=91 Identities=19% Similarity=0.159 Sum_probs=61.7
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHHH---cCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCccc
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~---~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (335)
++..+..++.+.. .|+||+.+|+..|.+. +|+.. ..++||+..+..+.+...+ .+|..|++ ++
T Consensus 78 vl~~f~~fl~~~~--lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~-------~kL~~L~~---~l 145 (313)
T PRK06807 78 VLPLFLAFLHTNV--IVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPN-------HKLETLKR---ML 145 (313)
T ss_pred HHHHHHHHHcCCe--EEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCC-------CCHHHHHH---Hc
Confidence 4455666665543 4999999999998643 45532 3489998876655553322 37888886 66
Q ss_pred CcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 019798 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (335)
Q Consensus 165 ~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (335)
|++.. .+-|-.||.++..|+..+.....
T Consensus 146 gi~~~-------------------------~H~Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 146 GIRLS-------------------------SHNAFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred CCCCC-------------------------CcChHHHHHHHHHHHHHHHHhhh
Confidence 75431 11267899999999998888774
No 41
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=97.02 E-value=0.019 Score=52.39 Aligned_cols=143 Identities=15% Similarity=0.126 Sum_probs=81.5
Q ss_pred cCCceEEEEEeecCCC-ccCcEEEEEEEe--CCc-------eEEEEccC-C----------C----------hhhHHHHH
Q 019798 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF--PDA-------IYLVDAIQ-G----------G----------ETVVKACK 95 (335)
Q Consensus 47 ~~~~~ia~D~E~~~~~-~~~~l~~lqla~--~~~-------~~lid~~~-~----------~----------~~~~~~Lk 95 (335)
.+...++||+||++++ ...+++-|.... .+. .++|.+.. . . .+++..+.
T Consensus 45 ~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~l~ 124 (239)
T PRK09146 45 SEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELL 124 (239)
T ss_pred ccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHHHH
Confidence 4567899999999986 444433222221 121 13443321 0 0 12334555
Q ss_pred HHHcCCCceEEEEechhcHHHHHHH----cCCcc-ceEeehhHHHHhhhhccCCC---CCC---CCcccHHhhhcCCccc
Q 019798 96 PALESSYITKVIHDCKRDSEALYFQ----FGIKL-HNVVDTQIAYSLIEEQEGRK---RSP---DDYISFVGLLADPRYC 164 (335)
Q Consensus 96 ~lLe~~~i~KV~hd~k~D~~~L~~~----~gi~l-~~vfDt~lAayLL~~~~~~~---~l~---~~~~sL~~L~~~~~~L 164 (335)
.++.+ . ..|+||+.+|..+|.+. +|..+ ..++||+-.+.-+.+..... .+. ....+|.+++. ++
T Consensus 125 ~~~~~-~-~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~---~~ 199 (239)
T PRK09146 125 EALAG-K-VVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRL---RY 199 (239)
T ss_pred HHhCC-C-EEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHH---Hc
Confidence 55544 2 46899999999988643 34444 35899998776654421000 000 02346777776 44
Q ss_pred CcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhc
Q 019798 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (335)
Q Consensus 165 ~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (335)
|++... ..-|..||.++..|+..+..++..
T Consensus 200 gl~~~~------------------------~H~Al~DA~ata~l~~~~~~~~~~ 229 (239)
T PRK09146 200 GLPAYS------------------------PHHALTDAIATAELLQAQIAHHFS 229 (239)
T ss_pred CCCCCC------------------------CCCcHHHHHHHHHHHHHHHHHHcC
Confidence 654221 112778999999999998877743
No 42
>PRK07883 hypothetical protein; Validated
Probab=97.02 E-value=0.0093 Score=61.05 Aligned_cols=139 Identities=16% Similarity=0.108 Sum_probs=86.9
Q ss_pred ccCCceEEEEEeecCCC-ccCcEEEEEEEe----CCc-----eEEEEccC-----------CC----------hhhHHHH
Q 019798 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-----IYLVDAIQ-----------GG----------ETVVKAC 94 (335)
Q Consensus 46 ~~~~~~ia~D~E~~~~~-~~~~l~~lqla~----~~~-----~~lid~~~-----------~~----------~~~~~~L 94 (335)
+.+...+.||+||++++ ....+ ++|+. .+. ..+|.+.. +. .+++..+
T Consensus 12 ~~~~~~Vv~D~ETTGl~p~~~~I--IEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f 89 (557)
T PRK07883 12 LRDVTFVVVDLETTGGSPAGDAI--TEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAF 89 (557)
T ss_pred CcCCCEEEEEEecCCCCCCCCeE--EEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHH
Confidence 35678999999999885 33343 34432 221 23443321 01 1244566
Q ss_pred HHHHcCCCceEEEEechhcHHHHHH---HcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccc
Q 019798 95 KPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (335)
Q Consensus 95 k~lLe~~~i~KV~hd~k~D~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~ 169 (335)
..++.+ ...|+||+.+|...|.+ .+|+.. ...+||+..+.-+.+.... ...+|.+|++ ++|++..
T Consensus 90 ~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~-----~~~~L~~L~~---~~gi~~~ 159 (557)
T PRK07883 90 LEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEA-----PNVRLSTLAR---LFGATTT 159 (557)
T ss_pred HHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCC-----CCCCHHHHHH---HCCcccC
Confidence 677765 34589999999998853 456665 2488998766544431111 1347889886 6776543
Q ss_pred hhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccc
Q 019798 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (335)
Q Consensus 170 ~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~ 220 (335)
. .+-|..||.++..|+..+..++.+.+
T Consensus 160 ~------------------------~H~Al~DA~ata~l~~~l~~~~~~~~ 186 (557)
T PRK07883 160 P------------------------THRALDDARATVDVLHGLIERLGNLG 186 (557)
T ss_pred C------------------------CCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 1 02278999999999999999987644
No 43
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.97 E-value=0.022 Score=54.03 Aligned_cols=100 Identities=14% Similarity=0.130 Sum_probs=67.7
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHH---HcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCccc
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (335)
++..+..++.+ -..|+||+.+|+.+|.+ .+|+.. ..++||+..+.-+.+...++ +|..|++ ++
T Consensus 70 v~~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~-------~L~~L~~---~~ 137 (309)
T PRK06195 70 IWEKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNA-------RLNTVNN---FL 137 (309)
T ss_pred HHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcC-------CHHHHHH---Hc
Confidence 44566667754 35699999999988853 356554 34899987665555443233 7788886 55
Q ss_pred CcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccHHHHH
Q 019798 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAV 226 (335)
Q Consensus 165 ~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~l~~ 226 (335)
|++.. .+-|..||.++.+|+..+.+++...++..+..
T Consensus 138 gi~~~-------------------------~H~Al~DA~ata~l~~~l~~~~~~~~~~~l~~ 174 (309)
T PRK06195 138 GYEFK-------------------------HHDALADAMACSNILLNISKELNSKDINEISK 174 (309)
T ss_pred CCCCc-------------------------ccCCHHHHHHHHHHHHHHHHHhccCCHHHHHH
Confidence 65421 02277899999999999998887766555444
No 44
>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=96.86 E-value=0.02 Score=48.75 Aligned_cols=88 Identities=19% Similarity=0.213 Sum_probs=56.0
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHHH---cCCc-----cceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCC
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIK-----LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADP 161 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~---~gi~-----l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~ 161 (335)
++..|..++.+. ..|+||+.+|..+|.+. +|.. ...++||+..+..+.+. .. .+|+++++
T Consensus 71 v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~-~~-------~~L~~l~~-- 138 (167)
T cd06131 71 IADEFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPG-KP-------NSLDALCK-- 138 (167)
T ss_pred HHHHHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCC-CC-------CCHHHHHH--
Confidence 445677777653 35899999999888532 3432 13489998766554442 12 37899997
Q ss_pred cccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHH
Q 019798 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (335)
Q Consensus 162 ~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L 212 (335)
++|++.... ...-|..||..+..|+..|
T Consensus 139 -~~~i~~~~~----------------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 139 -RFGIDNSHR----------------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred -HCCCCCCCC----------------------CCCChHHHHHHHHHHHHHh
Confidence 557543210 0122778999998888665
No 45
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=96.83 E-value=0.027 Score=54.26 Aligned_cols=140 Identities=11% Similarity=0.126 Sum_probs=83.5
Q ss_pred cCCceEEEEEeecCCC-ccCcEEEEEEE---e--CC---c--eEEEEccC---------CC----------hhhHHHHHH
Q 019798 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLA---F--PD---A--IYLVDAIQ---------GG----------ETVVKACKP 96 (335)
Q Consensus 47 ~~~~~ia~D~E~~~~~-~~~~l~~lqla---~--~~---~--~~lid~~~---------~~----------~~~~~~Lk~ 96 (335)
.+...++||+|+++++ ...++ |+|+ . .+ . ..+|.+.. +. .+++..|.+
T Consensus 44 ~~~~fVvlDiETTGLdp~~drI--IeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~~ 121 (377)
T PRK05601 44 EAAPFVAVSIQTSGIHPSTSRL--ITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLDR 121 (377)
T ss_pred CCCCEEEEEEECCCCCCCCCeE--EEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHHH
Confidence 4568999999999986 44443 3332 1 11 1 12333321 00 135667777
Q ss_pred HHcCCCceEEEEechhcHHHHHHHc-------------------------------CCcc-ceEeehhHHHHhhhhccCC
Q 019798 97 ALESSYITKVIHDCKRDSEALYFQF-------------------------------GIKL-HNVVDTQIAYSLIEEQEGR 144 (335)
Q Consensus 97 lLe~~~i~KV~hd~k~D~~~L~~~~-------------------------------gi~l-~~vfDt~lAayLL~~~~~~ 144 (335)
++.+. ..|+||+.+|+.+|.+.+ ++.. ..++||+-.+..+.+...+
T Consensus 122 fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~ 199 (377)
T PRK05601 122 LIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALDD 199 (377)
T ss_pred HhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCCC
Confidence 88754 469999999999886432 1222 2489999888888875444
Q ss_pred CCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHH
Q 019798 145 KRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (335)
Q Consensus 145 ~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L 212 (335)
| +|..|++ ++|++.+.... +. .-..+| ..+ .+-+|+..+..||..+
T Consensus 200 ~-------rL~~La~---~lGi~~p~~~A--~~------~Ra~~p--~~~--l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 200 I-------RIRGVAH---TLGLDAPAAEA--SV------ERAQVP--HRQ--LCREETLLVARLYFAL 245 (377)
T ss_pred C-------CHHHHHH---HhCCCCCchhh--hh------hhhcCC--hhh--hhhHHHHHHHHHHHHh
Confidence 4 7789996 67877642110 00 001111 111 1336899999998776
No 46
>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=96.80 E-value=0.027 Score=47.15 Aligned_cols=66 Identities=18% Similarity=0.077 Sum_probs=45.1
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHH---HcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCccc
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (335)
++..|..++.+ ...|+||+.+|..+|.+ .+|+.. ...+||+..+..+.+... ..+|..|++ ++
T Consensus 67 v~~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~-------~~~L~~l~~---~~ 134 (156)
T cd06130 67 VWPEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLP-------NHKLNTVAE---HL 134 (156)
T ss_pred HHHHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCC-------CCCHHHHHH---Hc
Confidence 45677778876 35699999999998853 356554 348999877665544322 237888886 56
Q ss_pred Ccc
Q 019798 165 GIS 167 (335)
Q Consensus 165 ~~~ 167 (335)
|++
T Consensus 135 g~~ 137 (156)
T cd06130 135 GIE 137 (156)
T ss_pred CCC
Confidence 654
No 47
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.78 E-value=0.041 Score=50.26 Aligned_cols=91 Identities=22% Similarity=0.255 Sum_probs=58.5
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHH---HcCCcc------ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcC
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL------HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLAD 160 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~---~~gi~l------~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~ 160 (335)
++..+..++.+. ..|+||+.+|+.+|.+ .+|..+ ..++||...+..+.|.. + .+|+.|++
T Consensus 76 v~~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~-~-------~~L~aL~~- 144 (240)
T PRK05711 76 VADEFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGK-R-------NSLDALCK- 144 (240)
T ss_pred HHHHHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCC-C-------CCHHHHHH-
Confidence 345566666553 3589999999988753 344222 34899988777666642 2 28899997
Q ss_pred CcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHH
Q 019798 161 PRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (335)
Q Consensus 161 ~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~ 215 (335)
+ +|++... |. ..-|-.||..+..+|..|...
T Consensus 145 -~-~gi~~~~-----------------r~-----~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 145 -R-YGIDNSH-----------------RT-----LHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred -H-CCCCCCC-----------------CC-----CCCHHHHHHHHHHHHHHHHCc
Confidence 4 4653221 00 122778999999999887643
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=96.78 E-value=0.029 Score=50.72 Aligned_cols=90 Identities=22% Similarity=0.253 Sum_probs=59.2
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHH---HcC--Cc-c---ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcC
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFG--IK-L---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLAD 160 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~---~~g--i~-l---~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~ 160 (335)
++..+..++.+. ..|+||+.+|+.+|.+ .+| +. + ..++||+..+..+.|.. ..+|+.|++
T Consensus 72 v~~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~--------~~~L~~L~~- 140 (225)
T TIGR01406 72 IADEFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQ--------RNSLDALCK- 140 (225)
T ss_pred HHHHHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCC--------CCCHHHHHH-
Confidence 445666677653 3599999999988853 355 22 1 35899998777665532 238899997
Q ss_pred CcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHH
Q 019798 161 PRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMK 214 (335)
Q Consensus 161 ~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~ 214 (335)
+ +|++... |. ..-|..||..+..+|..|..
T Consensus 141 -~-~gi~~~~-----------------r~-----~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 141 -R-FKVDNSH-----------------RT-----LHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred -h-cCCCCCC-----------------CC-----CcCHHHHHHHHHHHHHHHHc
Confidence 4 4654321 00 11277999999999988754
No 49
>PRK05168 ribonuclease T; Provisional
Probab=96.78 E-value=0.051 Score=48.57 Aligned_cols=87 Identities=18% Similarity=0.226 Sum_probs=59.1
Q ss_pred CceEEEEechhcHHHHHH---HcCCc---c--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHH
Q 019798 102 YITKVIHDCKRDSEALYF---QFGIK---L--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE 173 (335)
Q Consensus 102 ~i~KV~hd~k~D~~~L~~---~~gi~---l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~ 173 (335)
....|+||+.+|+..|.+ ++|+. . ..++||...+..+.+. .+|..+++ ++|+++...
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~----------~~L~~l~~---~~gl~~~~~-- 178 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQ----------TVLAKACQ---AAGIEFDNK-- 178 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCC----------CCHHHHHH---HCCCCCCCC--
Confidence 356799999999988753 35542 1 1479998766655332 26788886 456654210
Q ss_pred HHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccHH
Q 019798 174 VRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (335)
Q Consensus 174 ~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~ 223 (335)
. ..-|..||..+..|+..+..++.+.|.|.
T Consensus 179 ----------~----------~H~Al~DA~ata~l~~~l~~~~~~~~~~~ 208 (211)
T PRK05168 179 ----------E----------AHSALYDTEKTAELFCEIVNRWKRLGGWP 208 (211)
T ss_pred ----------C----------CCChHHHHHHHHHHHHHHHHHHHHccCCC
Confidence 0 11277999999999999999998777653
No 50
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=96.74 E-value=0.045 Score=50.52 Aligned_cols=133 Identities=17% Similarity=0.082 Sum_probs=82.2
Q ss_pred cCCceEEEEEeecCCC-ccCcEEEEEEEe----CCc-----eEEEEccCCC--------------------hhhHHHHHH
Q 019798 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-----IYLVDAIQGG--------------------ETVVKACKP 96 (335)
Q Consensus 47 ~~~~~ia~D~E~~~~~-~~~~l~~lqla~----~~~-----~~lid~~~~~--------------------~~~~~~Lk~ 96 (335)
.+...+.||+||++.. ..++ +++|+. .++ ..++.+.... .+++..+..
T Consensus 66 ~~~~~vv~DiETTG~~~~~~~--IIEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f~~ 143 (257)
T PRK08517 66 KDQVFCFVDIETNGSKPKKHQ--IIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFRL 143 (257)
T ss_pred CCCCEEEEEEeCCCCCCCCCe--EEEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHHHH
Confidence 4567899999999875 3334 344442 221 1233332110 135567777
Q ss_pred HHcCCCceEEEEechhcHHHHHH---HcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchh
Q 019798 97 ALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK 171 (335)
Q Consensus 97 lLe~~~i~KV~hd~k~D~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k 171 (335)
++.+. ..|+||+.+|..+|.+ ++|... +..+||+-.+..+-+. .+ .+|++|++ ++|++...
T Consensus 144 fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~-~~-------~~L~~L~~---~lgi~~~~- 209 (257)
T PRK08517 144 FLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-PR-------YGLSFLKE---LLGIEIEV- 209 (257)
T ss_pred HHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccC-CC-------CCHHHHHH---HcCcCCCC-
Confidence 77654 4699999999988853 455543 3478887554332221 12 37888886 66765421
Q ss_pred HHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhc
Q 019798 172 EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (335)
Q Consensus 172 ~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (335)
..-|-.||.++.+|+..+..++..
T Consensus 210 -----------------------~HrAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 210 -----------------------HHRAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred -----------------------CCChHHHHHHHHHHHHHHHHHhHH
Confidence 011778999999999999888753
No 51
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.73 E-value=0.014 Score=53.16 Aligned_cols=135 Identities=18% Similarity=0.156 Sum_probs=81.9
Q ss_pred ceEEEEEeecCCCccCcEEE---EEEEeCCceEEEEccCCC---------------h----------hhHHHHHHHHcCC
Q 019798 50 LVIGFDCEGVDLCRHGSLCI---MQLAFPDAIYLVDAIQGG---------------E----------TVVKACKPALESS 101 (335)
Q Consensus 50 ~~ia~D~E~~~~~~~~~l~~---lqla~~~~~~lid~~~~~---------------~----------~~~~~Lk~lLe~~ 101 (335)
.+||+|||-++.+..|+.++ ++|-......++|-.-.. . .+-..+..+|.+
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 58999999998865555444 444333222344432110 0 111345557765
Q ss_pred CceEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCC
Q 019798 102 YITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQD 181 (335)
Q Consensus 102 ~i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~ 181 (335)
. +.|||+++.|+.+|.-.|.- .-+-||.-.--|...-... ...||..|++ .+||.++.. ++
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--SMIRDTSKYPPLMKLLSKK-----ATPSLKKLTE--ALLGKDIQV--------GE- 245 (280)
T ss_pred C-EEeccccccHHHHHhhhCch--hhhcccccCchHHHHhhcc-----CCccHHHHHH--HHhchhhhc--------cc-
Confidence 3 45999999999999633322 2255876543333310001 2359999999 999977641 11
Q ss_pred CCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhc
Q 019798 182 PQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (335)
Q Consensus 182 ~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (335)
.+ ..+||.++.+||...+.+-++
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 458999999999998877765
No 52
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.72 E-value=0.027 Score=61.21 Aligned_cols=133 Identities=19% Similarity=0.171 Sum_probs=85.6
Q ss_pred CceEEEEEeecCCC-ccCcEEEEEEEe----CCce-----EEEEccC-C----------C----------hhhHHHHHHH
Q 019798 49 QLVIGFDCEGVDLC-RHGSLCIMQLAF----PDAI-----YLVDAIQ-G----------G----------ETVVKACKPA 97 (335)
Q Consensus 49 ~~~ia~D~E~~~~~-~~~~l~~lqla~----~~~~-----~lid~~~-~----------~----------~~~~~~Lk~l 97 (335)
...+.||+||++.+ ..+ -.+|||+. .++. .+|.+.. + . .++...+..+
T Consensus 3 ~~~vvvD~ETTG~~p~~~-d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~~ 81 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKG-DKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVEL 81 (928)
T ss_pred CCEEEEEEeCCCCCCCCC-CcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHHHH
Confidence 46789999999875 222 23455554 2221 2343321 0 0 1344567777
Q ss_pred HcCCCceEEEEechhcHHHHHH---HcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhH
Q 019798 98 LESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKE 172 (335)
Q Consensus 98 Le~~~i~KV~hd~k~D~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~ 172 (335)
+.+. ..|+||+.+|..+|.+ ..|+.. ...+||+-.+..+-|...++ +|.+|++ ++|++...
T Consensus 82 l~~~--~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~-------~L~~l~~---~l~i~~~~-- 147 (928)
T PRK08074 82 LEGA--YFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESY-------KLRDLSE---ELGLEHDQ-- 147 (928)
T ss_pred hCCC--eEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCC-------CHHHHHH---hCCCCCCC--
Confidence 7653 4699999999998863 356553 35899988777776654333 7788886 56764321
Q ss_pred HHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhc
Q 019798 173 EVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (335)
Q Consensus 173 ~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (335)
.+-|-.||.++..|+..|.+++..
T Consensus 148 ----------------------~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 148 ----------------------PHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred ----------------------CCChHHHHHHHHHHHHHHHHHHHh
Confidence 011678999999999999888865
No 53
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=96.70 E-value=0.045 Score=48.07 Aligned_cols=102 Identities=18% Similarity=0.104 Sum_probs=62.5
Q ss_pred hhHHHHHHHHcC--CCceEEEEec-hhcHHHHHH---HcCCcc-----------------------c-eEeehhHHHHhh
Q 019798 89 TVVKACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKL-----------------------H-NVVDTQIAYSLI 138 (335)
Q Consensus 89 ~~~~~Lk~lLe~--~~i~KV~hd~-k~D~~~L~~---~~gi~l-----------------------~-~vfDt~lAayLL 138 (335)
+++..+..++.+ |.+ .||||. .+|+..|.. .+|+.. + .++|+...+.-.
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 345556666654 454 599999 799988763 355554 1 267887765433
Q ss_pred hhccCCCCCCCCcccHHhhhcCCcccCcccch--hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 019798 139 EEQEGRKRSPDDYISFVGLLADPRYCGISYQE--KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (335)
Q Consensus 139 ~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~--k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (335)
.+ .. ..+|+.+++ .+|+..-.+ ...... ..|.. -....++|+-.||..+++|+
T Consensus 144 ~~-l~-------sy~L~~v~~--~~l~~~k~~~~~~~~~~------~~~~~--~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 144 FK-LK-------SYTLDAVAE--ELLGEGKEKVDGEIIED------AEWEE--DPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred cC-cc-------cCCHHHHHH--HHhCCCCCcCCHHHHhh------ccCcc--hHHHHHHHHHHHHHHHHHhh
Confidence 22 22 248899999 888753221 111110 01221 12678999999999999886
No 54
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.65 E-value=0.045 Score=46.28 Aligned_cols=92 Identities=21% Similarity=0.219 Sum_probs=62.4
Q ss_pred hHHHHHHHHcCCCceEEEEec-hhcHHHHHH---HcCCcc---ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCc
Q 019798 90 VVKACKPALESSYITKVIHDC-KRDSEALYF---QFGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPR 162 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~-k~D~~~L~~---~~gi~l---~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~ 162 (335)
++..+..++.+. ..|+||. ++|..+|.+ .+|+.. ...+||+..++...+.. ..+|.++++
T Consensus 70 ~~~~~~~~l~~~--~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~--------~~~L~~l~~--- 136 (169)
T smart00479 70 VLEELLEFLKGK--ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR--------KYSLKKLAE--- 136 (169)
T ss_pred HHHHHHHHhcCC--EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC--------CCCHHHHHH---
Confidence 456777788764 3578888 999998863 245432 23799988776665432 248899997
Q ss_pred ccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 019798 163 YCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (335)
Q Consensus 163 ~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (335)
++|++... . ...|..||..+.+|+..+.+++.
T Consensus 137 ~~~~~~~~-------------~----------~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 137 RLGLEVIG-------------R----------AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred HCCCCCCC-------------C----------CcCcHHHHHHHHHHHHHHHHHhh
Confidence 45544321 0 13378999999999999987653
No 55
>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=96.60 E-value=0.044 Score=47.53 Aligned_cols=80 Identities=26% Similarity=0.219 Sum_probs=52.2
Q ss_pred HHHHHHHcC--CCceEEEEec-hhcHHHHHH---HcCCcc---ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCc
Q 019798 92 KACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPR 162 (335)
Q Consensus 92 ~~Lk~lLe~--~~i~KV~hd~-k~D~~~L~~---~~gi~l---~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~ 162 (335)
+.+..++.. .....|+||+ .+|+..|.+ ++|+.. ...+||+-.+..+.+ +|.+|++ +
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 445555543 2346799998 899998853 356553 235799876665443 6788887 7
Q ss_pred ccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 019798 163 YCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (335)
Q Consensus 163 ~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (335)
++|++... ..-|..||.++.+++
T Consensus 152 ~~~~~~~~------------------------~H~A~~Da~at~~v~ 174 (177)
T cd06136 152 LFGQEPKN------------------------SHTAEGDVLALLKCA 174 (177)
T ss_pred HhCCCccc------------------------ccchHHHHHHHHHHH
Confidence 77765431 122778888887765
No 56
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=96.51 E-value=0.028 Score=60.58 Aligned_cols=93 Identities=17% Similarity=0.148 Sum_probs=64.9
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHH---HcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCccc
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (335)
+...+..++.+. ..|+||+.+|..+|.+ .+|+.. ...+||+-.+..+.|...++ +|.+|++ ++
T Consensus 70 v~~~l~~~l~~~--~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~-------~L~~l~~---~~ 137 (850)
T TIGR01407 70 VAQEIYDLLEDG--IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESY-------QLSELSE---AL 137 (850)
T ss_pred HHHHHHHHhCCC--EEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCC-------CHHHHHH---HC
Confidence 445666777653 4699999999988853 356653 45899998777776643333 7889986 56
Q ss_pred CcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhc
Q 019798 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (335)
Q Consensus 165 ~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (335)
|++... .+-|..||.++..|+..+..++.+
T Consensus 138 gi~~~~------------------------~H~Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 138 GLTHEN------------------------PHRADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred CCCCCC------------------------CCChHHHHHHHHHHHHHHHHHHHh
Confidence 765431 012778999999998888887764
No 57
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=96.48 E-value=0.096 Score=46.12 Aligned_cols=145 Identities=14% Similarity=0.163 Sum_probs=83.0
Q ss_pred ceEEEEEeecCCC-----ccCcEEEEEEEeCCceEEEEc----------cCCChhhHHHHHHHHcC--CCceEEEEech-
Q 019798 50 LVIGFDCEGVDLC-----RHGSLCIMQLAFPDAIYLVDA----------IQGGETVVKACKPALES--SYITKVIHDCK- 111 (335)
Q Consensus 50 ~~ia~D~E~~~~~-----~~~~l~~lqla~~~~~~lid~----------~~~~~~~~~~Lk~lLe~--~~i~KV~hd~k- 111 (335)
..++||.|+.+.. ....+..|+++..+...++.. ..-..+++..+..++.. |.+ .+|||..
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 5789999997431 234555555544322222211 11112455666666665 764 5999975
Q ss_pred hcHHHHHHH---cCCccc------------------------eEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCccc
Q 019798 112 RDSEALYFQ---FGIKLH------------------------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (335)
Q Consensus 112 ~D~~~L~~~---~gi~l~------------------------~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (335)
+|+..|..+ +|+... ..+|++....- ..++ ...+|+.+++ ++|
T Consensus 83 FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~------~~~l--~sy~L~~v~~--~~L 152 (195)
T cd05780 83 FDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARR------TLNL--TRYTLERVYE--ELF 152 (195)
T ss_pred CcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHh------hCCC--CcCcHHHHHH--HHh
Confidence 799887633 455421 26777664431 1112 2358899999 899
Q ss_pred Ccccch--hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHH
Q 019798 165 GISYQE--KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (335)
Q Consensus 165 ~~~l~~--k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L 212 (335)
|.+-.+ .+++.. -|...+--...+.|+..||..+++|...+
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 964322 122221 23333223678999999999999998653
No 58
>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=96.40 E-value=0.0026 Score=45.15 Aligned_cols=55 Identities=31% Similarity=0.441 Sum_probs=49.5
Q ss_pred CCCccccccccccccHHHHHHHhhhhhhhcCCCCCCCcceeccchhhHHHHHHHH
Q 019798 273 PPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAML 327 (335)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 327 (335)
++...+.++|++|.+|..+.+.+++.|.+.....+++.+.+.||...|.+|.++|
T Consensus 7 p~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 7 PKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred CHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHh
Confidence 4455678999999999999999999999999888889999999999999999876
No 59
>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=96.39 E-value=0.07 Score=46.79 Aligned_cols=78 Identities=21% Similarity=0.221 Sum_probs=52.4
Q ss_pred ceEEEEechhcHHHHHH---HcCCc---c--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHH
Q 019798 103 ITKVIHDCKRDSEALYF---QFGIK---L--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEV 174 (335)
Q Consensus 103 i~KV~hd~k~D~~~L~~---~~gi~---l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~ 174 (335)
...|+||+.+|+..|.+ .+|+. . ..++||+..+..+.+. + +|..+++ ++|++.... .
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~~---~-------~L~~l~~---~~gi~~~~~-~- 167 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQ---T-------VLAKACQ---AAGIEFDNK-E- 167 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhCC---C-------cHHHHHH---HCCCCCCCC-C-
Confidence 45799999999988753 45652 1 2479998887766542 2 6788886 457654210 0
Q ss_pred HHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHH
Q 019798 175 RVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (335)
Q Consensus 175 ~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~ 215 (335)
..-|..||..+..|+..|.++
T Consensus 168 --------------------~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 168 --------------------AHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred --------------------CcChHHHHHHHHHHHHHHHHh
Confidence 112778999999999888654
No 60
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.29 E-value=0.12 Score=45.82 Aligned_cols=133 Identities=17% Similarity=0.153 Sum_probs=76.6
Q ss_pred cCCceEEEEEeecCCC-ccCcEEEEEEEe---C-Cc-------eEEEEccC-C----------C----------hhhHHH
Q 019798 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF---P-DA-------IYLVDAIQ-G----------G----------ETVVKA 93 (335)
Q Consensus 47 ~~~~~ia~D~E~~~~~-~~~~l~~lqla~---~-~~-------~~lid~~~-~----------~----------~~~~~~ 93 (335)
.....+.+|+|+++++ ..+++ ++|+. . +. .++|.+.. . . .+++..
T Consensus 27 ~~~~~vviD~ETTGl~~~~d~I--ieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~ 104 (202)
T PRK09145 27 PPDEWVALDCETTGLDPRRAEI--VSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQ 104 (202)
T ss_pred CCCCEEEEEeECCCCCCCCCce--EEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHH
Confidence 4567899999999986 34443 44442 2 21 12343321 0 0 134556
Q ss_pred HHHHHcCCCceEEEEechhcHHHHHHH----cCCccc-eEeehhHHHHh-hhhccCCCCCCCCcccHHhhhcCCcccCcc
Q 019798 94 CKPALESSYITKVIHDCKRDSEALYFQ----FGIKLH-NVVDTQIAYSL-IEEQEGRKRSPDDYISFVGLLADPRYCGIS 167 (335)
Q Consensus 94 Lk~lLe~~~i~KV~hd~k~D~~~L~~~----~gi~l~-~vfDt~lAayL-L~~~~~~~~l~~~~~sL~~L~~~~~~L~~~ 167 (335)
+..++.+. ..|+||+.+|...|.+. +|..+. ..+|++-..+- ....... . ....+|+++++ ++|++
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 77777653 46999999999988533 355543 47898643321 1110000 0 01358899986 55764
Q ss_pred cchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHH
Q 019798 168 YQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (335)
Q Consensus 168 l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~ 213 (335)
... ..-|..||.++..||..|.
T Consensus 177 ~~~------------------------~H~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 177 VLG------------------------RHDALNDAIMAALIFLRLR 198 (202)
T ss_pred CCC------------------------CCCcHHHHHHHHHHHHHHH
Confidence 421 0116789999999998775
No 61
>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=96.24 E-value=0.059 Score=44.51 Aligned_cols=50 Identities=16% Similarity=-0.006 Sum_probs=34.9
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHHHcC-----CccceEeehhHHHHhhhhc
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFG-----IKLHNVVDTQIAYSLIEEQ 141 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~g-----i~l~~vfDt~lAayLL~~~ 141 (335)
+...+..++++ ...|+||+.+|..+|.+.+. ......+||+..+..+.+.
T Consensus 69 ~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~ 123 (159)
T cd06127 69 VLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPG 123 (159)
T ss_pred HHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCC
Confidence 45667778876 45799999999998864432 2224589999876655543
No 62
>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=96.21 E-value=0.02 Score=50.71 Aligned_cols=86 Identities=15% Similarity=0.154 Sum_probs=59.9
Q ss_pred ceEEEEechhcHHHHHHH---cCCc---c--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHH
Q 019798 103 ITKVIHDCKRDSEALYFQ---FGIK---L--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEV 174 (335)
Q Consensus 103 i~KV~hd~k~D~~~L~~~---~gi~---l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~ 174 (335)
-..|+||+.+|+.+|.+. +|.. . ..++||+..+..+.+. .+|..+++ ++|++...
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~~----------~~L~~l~~---~~gi~~~~---- 168 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYGQ----------TVLAKACQ---AAGXDFDS---- 168 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcCc----------ccHHHHHH---HcCCCccc----
Confidence 357999999999988632 3432 1 2379998877655432 26788886 45654321
Q ss_pred HHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccHH
Q 019798 175 RVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (335)
Q Consensus 175 ~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~ 223 (335)
.+..-|..||.++..|+..+..++.+.+.|.
T Consensus 169 ------------------~~~H~Al~Da~ata~lf~~l~~~~~~~~~~~ 199 (200)
T TIGR01298 169 ------------------TQAHSALYDTEKTAELFCEIVNRWKRLGGWP 199 (200)
T ss_pred ------------------cchhhhHHhHHHHHHHHHHHHHHHHHccCCC
Confidence 0123377899999999999999998888774
No 63
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=96.11 E-value=0.032 Score=62.74 Aligned_cols=96 Identities=17% Similarity=0.216 Sum_probs=67.2
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHH---HHcCCc-c-ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCccc
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALY---FQFGIK-L-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~---~~~gi~-l-~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (335)
++..+..++.+ ...|+||+.+|...|. +++|+. + ...+||+-.++.+.+...+ .+|..|++ .+
T Consensus 489 aL~~f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~-------~kL~~LAk---~l 556 (1437)
T PRK00448 489 VLPKFKEFCGD--SILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKS-------HRLNTLAK---KF 556 (1437)
T ss_pred HHHHHHHHhCC--CEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCcccc-------ccHHHHHH---Hc
Confidence 34444555543 5679999999997763 356664 3 3589999888877764433 37889887 45
Q ss_pred CcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhcccc
Q 019798 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSL 221 (335)
Q Consensus 165 ~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l 221 (335)
|+.... .+-|..||.++..|+..+.+++.+.|.
T Consensus 557 GL~~~~------------------------~HrAl~DA~aTa~lf~~ll~~l~~~gi 589 (1437)
T PRK00448 557 GVELEH------------------------HHRADYDAEATAYLLIKFLKDLKEKGI 589 (1437)
T ss_pred CCCCCC------------------------CcChHHHHHHHHHHHHHHHHHHHHcCC
Confidence 765431 023789999999999999999987654
No 64
>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=95.71 E-value=0.016 Score=50.12 Aligned_cols=80 Identities=18% Similarity=0.117 Sum_probs=53.0
Q ss_pred HHHHHHcCCCceEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhH
Q 019798 93 ACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKE 172 (335)
Q Consensus 93 ~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~ 172 (335)
.|..++. +....|||++..|+.+|. .-..-..+.||.+... .+.. +..||..|++ +|||..+..
T Consensus 94 ~l~~li~-~~tILVGHsL~nDL~aL~--l~hp~~~viDTa~l~~--~~~~-------r~~sLk~La~--~~L~~~IQ~-- 157 (174)
T cd06143 94 KLRLLVD-LGCIFVGHGLAKDFRVIN--IQVPKEQVIDTVELFH--LPGQ-------RKLSLRFLAW--YLLGEKIQS-- 157 (174)
T ss_pred HHHHHcC-CCCEEEeccchhHHHHhc--CcCCCcceEEcHHhcc--CCCC-------CChhHHHHHH--HHcCCcccC--
Confidence 4555554 444669999999999984 2111246899976322 1211 2459999999 999987752
Q ss_pred HHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 019798 173 EVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (335)
Q Consensus 173 ~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (335)
. ..+ ..+||.+++.||
T Consensus 158 ~--------~Hd-------------SvEDArAam~Ly 173 (174)
T cd06143 158 E--------THD-------------SIEDARTALKLY 173 (174)
T ss_pred C--------CcC-------------cHHHHHHHHHHh
Confidence 0 112 468999999998
No 65
>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=95.55 E-value=0.23 Score=42.02 Aligned_cols=146 Identities=17% Similarity=0.139 Sum_probs=68.7
Q ss_pred EEEEEeecCCC-ccCcEEEEEEEe--CCce-EEEEccCCCh----hhHHHHHHHHcCCCceEEEEe-chhcHHHHHHHc-
Q 019798 52 IGFDCEGVDLC-RHGSLCIMQLAF--PDAI-YLVDAIQGGE----TVVKACKPALESSYITKVIHD-CKRDSEALYFQF- 121 (335)
Q Consensus 52 ia~D~E~~~~~-~~~~l~~lqla~--~~~~-~lid~~~~~~----~~~~~Lk~lLe~~~i~KV~hd-~k~D~~~L~~~~- 121 (335)
+.||+||+++. ..+.+.++.++. .++. ++.+...... .+.+.+ ..+.+... .|+|| ..+|...|.+.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~-~~l~~~~~-iv~yng~~FD~p~L~~~~~ 78 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFF-ELLDEADN-IVTYNGKNFDIPFLKRRAK 78 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH---HHHHTT---EEESSTTTTHHHHHHHHH-
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHH-HHHhcCCe-EEEEeCcccCHHHHHHHHH
Confidence 46999999885 456777788775 3333 2443322221 122223 45555543 46777 467998886543
Q ss_pred --CCc-cceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccch----hHHHHHHhcCCCCCCccCCCCHHH
Q 019798 122 --GIK-LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE----KEEVRVLLRQDPQFWTYRPLTELM 194 (335)
Q Consensus 122 --gi~-l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~----k~~~~~~~~~~~~~w~~rpL~~~~ 194 (335)
++. ..+.+|++-..+-... ...||+.+.. ++|..-.. ..+....+....... .....+..
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 343 3468899875431111 1347778775 57765431 111111111100010 12234788
Q ss_pred HHHHHhhhhHHHHHHHHH
Q 019798 195 VRAAADDVRFLPYIYHNM 212 (335)
Q Consensus 195 ~~YAa~Da~~ll~L~~~L 212 (335)
+.|.-.|+..+.+|++.|
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 999999999999999987
No 66
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=95.27 E-value=0.4 Score=42.38 Aligned_cols=133 Identities=17% Similarity=0.138 Sum_probs=75.7
Q ss_pred CceEEEEEeecCCCccCcEEEEEEEe----CCce-----EEEEccC-----------CC----------hhhHHHHHHHH
Q 019798 49 QLVIGFDCEGVDLCRHGSLCIMQLAF----PDAI-----YLVDAIQ-----------GG----------ETVVKACKPAL 98 (335)
Q Consensus 49 ~~~ia~D~E~~~~~~~~~l~~lqla~----~~~~-----~lid~~~-----------~~----------~~~~~~Lk~lL 98 (335)
...+++|+|+++++...+ +++|+. .+.. .++.+.. +. .+++..+..++
T Consensus 5 ~~~vvlD~EtTGl~~~~e--IIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~~f~ 82 (195)
T PRK07247 5 ETYIAFDLEFNTVNGVSH--IIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFV 82 (195)
T ss_pred CeEEEEEeeCCCCCCCCe--EEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHHHHH
Confidence 467899999988764344 456653 2211 1222211 00 13556777777
Q ss_pred cCCCceEEEEech-hcHHHHHHHcCCccce--EeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHH
Q 019798 99 ESSYITKVIHDCK-RDSEALYFQFGIKLHN--VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVR 175 (335)
Q Consensus 99 e~~~i~KV~hd~k-~D~~~L~~~~gi~l~~--vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~ 175 (335)
.+. ..|+||+. +|+.+|. .+|..+.+ .+||.-..+...... .+.+ ...+|..|++ ++|++.. .
T Consensus 83 ~~~--~lVaHNa~~fD~~fL~-~~g~~~~~~~~idt~~~~~~~~~~~-~~~~--~~~~L~~La~---~~gi~~~--~--- 148 (195)
T PRK07247 83 GEL--PLIGYNAQKSDLPILA-ENGLDLSDQYQVDLYDEAFERRSSD-LNGI--ANLKLQTVAD---FLGIKGR--G--- 148 (195)
T ss_pred CCC--eEEEEeCcHhHHHHHH-HcCCCcCCCceeehHHHHHHhhccc-cCCC--CCCCHHHHHH---hcCCCCC--C---
Confidence 654 36999995 8999995 67877643 456642221111000 0011 1247888886 6676421 0
Q ss_pred HHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHh
Q 019798 176 VLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (335)
Q Consensus 176 ~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~ 217 (335)
.-|..||.++..++..|...-+
T Consensus 149 --------------------HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 149 --------------------HNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred --------------------cCCHHHHHHHHHHHHHHHhhcc
Confidence 1167899999999988865544
No 67
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=94.81 E-value=0.47 Score=44.68 Aligned_cols=100 Identities=14% Similarity=0.037 Sum_probs=57.0
Q ss_pred HHHHHHHcCCCceEEEEechhcHHHHHHHcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccc
Q 019798 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (335)
Q Consensus 92 ~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~ 169 (335)
..+..+++... ..|+||+.+|..+|. .+.... ....+++.......+... ..+|.+|+. + +|....
T Consensus 112 ~~l~~fl~~~~-vlVAHNA~FD~~fL~-~~~~~~~~~~~~ct~~~i~~~~~~~~-------~~kL~~La~--~-~g~~~~ 179 (294)
T PRK09182 112 AAVDALIAPAD-LIIAHNAGFDRPFLE-RFSPVFATKPWACSVSEIDWSARGFE-------GTKLGYLAG--Q-AGFFHE 179 (294)
T ss_pred HHHHHHhcCCC-EEEEeCHHHHHHHHH-HHHHhccCCcccccHHHHhhccccCC-------CCCHHHHHH--H-cCCCCC
Confidence 45666777643 569999999999996 443332 235566643211112112 237788887 4 342110
Q ss_pred hhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccHHHHHHh
Q 019798 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRG 228 (335)
Q Consensus 170 ~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~l~~~~ 228 (335)
..-|..||.++..|+...........+..++...
T Consensus 180 -------------------------aHrAl~Da~Ata~ll~~~l~~~~~~~l~~Ll~~~ 213 (294)
T PRK09182 180 -------------------------GHRAVDDCQALLELLARPLPETGQPPLAELLEAS 213 (294)
T ss_pred -------------------------CcChHHHHHHHHHHHHHHHhhcCCcCHHHHHHHh
Confidence 1227889999988887655544433444444433
No 68
>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=94.47 E-value=0.11 Score=42.42 Aligned_cols=69 Identities=17% Similarity=0.207 Sum_probs=42.4
Q ss_pred hhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCC
Q 019798 111 KRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPL 190 (335)
Q Consensus 111 k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL 190 (335)
..|+.++...-|+.+..--|-|+.+||++|.++ ....+++ +|++- +|...
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 456666556789999888899999999999753 4577888 88773 45322
Q ss_pred CHHHHHHHHhhhhHHHHHHHHHHHHH
Q 019798 191 TELMVRAAADDVRFLPYIYHNMMKKL 216 (335)
Q Consensus 191 ~~~~~~YAa~Da~~ll~L~~~L~~~L 216 (335)
|+..|.++.+|+..|.++|
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 6788888999999988775
No 69
>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=94.32 E-value=0.037 Score=39.05 Aligned_cols=55 Identities=36% Similarity=0.545 Sum_probs=44.6
Q ss_pred CCCccccccccccccHHHHHHHhhhhhhhcCCC--CCCCcceeccchhhHHHHHHHH
Q 019798 273 PPGKMGRIIGRRGSSILAIKESCNAEILIGGAK--GPPDKVFIIGPVKQVRKAEAML 327 (335)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 327 (335)
|....+.++|++|..|..+.+.+.+.|.+.... ..+..+.+.|+.+.+.+|..+|
T Consensus 7 p~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 7 PSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred chhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 345567999999999999999988887777643 3456688899999999998876
No 70
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=93.97 E-value=1.1 Score=39.83 Aligned_cols=94 Identities=13% Similarity=0.059 Sum_probs=59.0
Q ss_pred hhHHHHHHHHcCCCceEEEEechhcHHHHHH---HcCCcc---ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCc
Q 019798 89 TVVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPR 162 (335)
Q Consensus 89 ~~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~---~~gi~l---~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~ 162 (335)
+++..|..++.+... .++|+..+|+..|.+ .+|+.. ....|++.....+.+... ..+|.++++
T Consensus 81 evl~~f~~~~~~~~~-~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~-------~~~L~~~~~--- 149 (207)
T PRK07748 81 ELVEKLAEYDKRCKP-TIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERN-------QTGLWKAIE--- 149 (207)
T ss_pred HHHHHHHHHhCcCCe-EEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCC-------CCCHHHHHH---
Confidence 355677778876333 355778999988853 356543 347788765543333221 248888886
Q ss_pred ccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHH
Q 019798 163 YCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKL 216 (335)
Q Consensus 163 ~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L 216 (335)
++|++... . ..-|..||..+..|+..|....
T Consensus 150 ~~gi~~~~-------------~----------~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 150 EYGKEGTG-------------K----------HHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred HcCCCCCC-------------C----------CcChHHHHHHHHHHHHHHHhCc
Confidence 56764321 0 0127789999999999887663
No 71
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=93.12 E-value=1.1 Score=40.35 Aligned_cols=80 Identities=14% Similarity=-0.019 Sum_probs=52.5
Q ss_pred ceEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCC
Q 019798 103 ITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDP 182 (335)
Q Consensus 103 i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~ 182 (335)
-..|+||+.+|..+|. ..+ ...+||+-.+..+-|+. .+ ++..|+. ++++..... .
T Consensus 75 ~~lVaHNa~FD~~~L~-~~~---~~~idTl~lar~l~p~~-~~-------~l~~L~~---~~~l~~~~~-~--------- 129 (219)
T PRK07983 75 EWYVAHNASFDRRVLP-EMP---GEWICTMKLARRLWPGI-KY-------SNMALYK---SRKLNVQTP-P--------- 129 (219)
T ss_pred CEEEEeCcHhhHHHHh-CcC---CCcEeHHHHHHHHccCC-CC-------CHHHHHH---HcCCCCCCC-C---------
Confidence 3569999999999995 322 45899999887766653 23 6677776 556432100 0
Q ss_pred CCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHH
Q 019798 183 QFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKL 216 (335)
Q Consensus 183 ~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L 216 (335)
.. ...-|..||.++..|+..+.+..
T Consensus 130 -~~--------~aHrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 130 -GL--------HHHRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred -CC--------CCCcHHHHHHHHHHHHHHHHHHc
Confidence 00 01237899999999998887544
No 72
>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=93.10 E-value=2 Score=38.21 Aligned_cols=144 Identities=16% Similarity=0.182 Sum_probs=78.0
Q ss_pred CceEEEEEeecCCC--c-----cCcEEEEEEEeC--Cc-eEEEEccCCC-hhhHHHHHHHHcC--CCceEEEEec-hhcH
Q 019798 49 QLVIGFDCEGVDLC--R-----HGSLCIMQLAFP--DA-IYLVDAIQGG-ETVVKACKPALES--SYITKVIHDC-KRDS 114 (335)
Q Consensus 49 ~~~ia~D~E~~~~~--~-----~~~l~~lqla~~--~~-~~lid~~~~~-~~~~~~Lk~lLe~--~~i~KV~hd~-k~D~ 114 (335)
-..++||+|+.+.+ . .+.-.+++|+.. +. ..++...... .+++..+..++.+ |.+ .+|||. .+|+
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 46789999986542 1 223346777762 21 1122111111 2455555555554 564 479998 7899
Q ss_pred HHHHH---HcCCccc-------------------------------e-EeehhHHHHhhhhccCCCCCCCCcccHHhhhc
Q 019798 115 EALYF---QFGIKLH-------------------------------N-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLA 159 (335)
Q Consensus 115 ~~L~~---~~gi~l~-------------------------------~-vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~ 159 (335)
..|.+ .+|+... . ++|++.+..-.+.. .+.+ ...||+.+++
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 87652 3554431 1 36777643322111 1122 1348899987
Q ss_pred CCcc--cCc---ccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 019798 160 DPRY--CGI---SYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (335)
Q Consensus 160 ~~~~--L~~---~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (335)
.+ ++. .++ .+++.. .|...+ +..++|+..||..++.|+
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 54 221 111 123222 344332 688999999999999885
No 73
>smart00322 KH K homology RNA-binding domain.
Probab=93.10 E-value=0.1 Score=36.56 Aligned_cols=58 Identities=34% Similarity=0.460 Sum_probs=47.2
Q ss_pred CCCccccccccccccHHHHHHHhhhhhhhcCCCCCCCcceeccchhhHHHHHHHHhhh
Q 019798 273 PPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAMLRGR 330 (335)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (335)
++...+.++|++|..|-.+.+..++.+.+.+.......+.+.|+..++..|..+|+..
T Consensus 10 ~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~ 67 (69)
T smart00322 10 PADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEI 67 (69)
T ss_pred cchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHH
Confidence 3456788999999999999999999888866444445677888999999999988754
No 74
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=92.88 E-value=0.29 Score=51.26 Aligned_cols=108 Identities=15% Similarity=0.142 Sum_probs=63.6
Q ss_pred ceEEEEechhcHHHHHHHcCCccc--eEeehhHHHHhhh----hcc----------------CCC---------CCC-CC
Q 019798 103 ITKVIHDCKRDSEALYFQFGIKLH--NVVDTQIAYSLIE----EQE----------------GRK---------RSP-DD 150 (335)
Q Consensus 103 i~KV~hd~k~D~~~L~~~~gi~l~--~vfDt~lAayLL~----~~~----------------~~~---------~l~-~~ 150 (335)
-+.||||..+|-.-+...|.|.-. ...|||-++-... .++ .++ .|. ..
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 466999999999988888998763 3779997654321 111 000 000 00
Q ss_pred cccHHhhhcCCcccCcc-cchhHHHHHHhcCCCCCCccCCCC---HHHHHHHHhhhhHHHHHHHHHHHHHhc
Q 019798 151 YISFVGLLADPRYCGIS-YQEKEEVRVLLRQDPQFWTYRPLT---ELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (335)
Q Consensus 151 ~~sL~~L~~~~~~L~~~-l~~k~~~~~~~~~~~~~w~~rpL~---~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (335)
.-||.++.+ .|+|.. +++ +. +..|-+. . ..++. .+.+.|||.|++.+.++|..+-+...+
T Consensus 322 ~NSL~dVhk--~~c~~~~LdK-t~-Rd~Fvs~--~--~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fle 385 (1075)
T KOG3657|consen 322 LNSLVDVHK--FHCGIDALDK-TP-RDSFVSG--T--KEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLE 385 (1075)
T ss_pred hHHHHHHHH--hhCCCCcccc-ch-HHhhhcC--c--HHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHH
Confidence 124566666 777766 542 21 1111100 0 00111 345789999999999999988887765
No 75
>PRK11779 sbcB exonuclease I; Provisional
Probab=92.85 E-value=1.7 Score=43.69 Aligned_cols=98 Identities=12% Similarity=0.038 Sum_probs=54.2
Q ss_pred HHHHHHHHcCCCceEEEEe-chhcHHHHHHHcCCcc-----------c---eEeehhHHHHhhhhccCCCC-C--CCCcc
Q 019798 91 VKACKPALESSYITKVIHD-CKRDSEALYFQFGIKL-----------H---NVVDTQIAYSLIEEQEGRKR-S--PDDYI 152 (335)
Q Consensus 91 ~~~Lk~lLe~~~i~KV~hd-~k~D~~~L~~~~gi~l-----------~---~vfDt~lAayLL~~~~~~~~-l--~~~~~ 152 (335)
+..+..++..+....|||| +.+|..++.+.+.... + .++|++-+.|.+.+..-... . .....
T Consensus 82 ~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~ 161 (476)
T PRK11779 82 AARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSF 161 (476)
T ss_pred HHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCC
Confidence 4456667754445579997 7899988754331110 1 12355555554443210000 0 00134
Q ss_pred cHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHH
Q 019798 153 SFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (335)
Q Consensus 153 sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~ 215 (335)
+|+.|+. .+|++... ..-|-.||.++..|+..+..+
T Consensus 162 rLe~L~~---~~gI~~~~------------------------AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 162 KLEHLTK---ANGIEHEN------------------------AHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred cHHHHHH---HcCCCCCC------------------------CCCcHHHHHHHHHHHHHHHHh
Confidence 7788886 44654321 112778999999999988866
No 76
>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=92.38 E-value=0.1 Score=37.43 Aligned_cols=55 Identities=35% Similarity=0.569 Sum_probs=44.5
Q ss_pred CCCccccccccccccHHHHHHHhhhhhhhcCCC--CCCCcc-eeccchhhHHHHHHHH
Q 019798 273 PPGKMGRIIGRRGSSILAIKESCNAEILIGGAK--GPPDKV-FIIGPVKQVRKAEAML 327 (335)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~-~~~~~~~~~~~~~~~~ 327 (335)
|....+.+||++|..|..+.+...|.+.+.-.. +++++. -+.|+..++.+|..++
T Consensus 7 p~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 7 PSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 345678999999999999999999999988765 466665 5668888899998765
No 77
>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=92.11 E-value=0.055 Score=37.93 Aligned_cols=52 Identities=40% Similarity=0.569 Sum_probs=42.2
Q ss_pred CccccccccccccHHHHHHHhhhhhhhcCCCCCCCcceeccchhhHHHHHHHH
Q 019798 275 GKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAML 327 (335)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 327 (335)
...+.++|++|..+..+.+.+++.|.+-.. +..+.+.+.|+...|.+|.+++
T Consensus 9 ~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 9 SLVGRIIGKKGSNIKEIEEETGVKIQIPDD-DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHTGGGHHHHHHHHHHTSEEEEEST-TEEEEEEEEESHHHHHHHHHHH
T ss_pred HHcCEEECCCCCcHHHhhhhcCeEEEEcCC-CCcEEEEEEeCHHHHHHHHhhC
Confidence 345689999999999999999999999655 2233566679999999999875
No 78
>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=91.34 E-value=2.9 Score=36.81 Aligned_cols=49 Identities=12% Similarity=0.119 Sum_probs=31.7
Q ss_pred cccHHhhhcCCcccCcccch------hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHH
Q 019798 151 YISFVGLLADPRYCGISYQE------KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYH 210 (335)
Q Consensus 151 ~~sL~~L~~~~~~L~~~l~~------k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~ 210 (335)
..+|+++++ ++||..-.+ ..+... .|...+ ...++|+..||..+++|++
T Consensus 139 sy~L~~Va~--~~Lg~~K~~~~~~~~~~eI~~-------~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 139 SFSLENVAQ--ELLGEGKLIHDVDDRGAEIER-------LFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred cCCHHHHHH--HHhCCCccccCcccCHHHHHH-------HHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 348899999 899852111 012211 233333 5789999999999999873
No 79
>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=91.25 E-value=6.5 Score=33.21 Aligned_cols=90 Identities=16% Similarity=0.192 Sum_probs=54.8
Q ss_pred hHHHHHHHHcCCCceEEEEechhcHHHHHH---HcCCc-----cceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCC
Q 019798 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIK-----LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADP 161 (335)
Q Consensus 90 ~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~---~~gi~-----l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~ 161 (335)
++..+..++.+..-..+.|+.++|...+.+ .++.. ....+|++-.+..+.+... ..+|.+++.
T Consensus 78 vl~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~-------~~~L~~l~~-- 148 (176)
T cd06133 78 VLKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKK-------RTGLSKALE-- 148 (176)
T ss_pred HHHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCC-------CCCHHHHHH--
Confidence 456777788774113466667899765432 23332 2458899877665544321 248889886
Q ss_pred cccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHH
Q 019798 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (335)
Q Consensus 162 ~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L 212 (335)
++|++... . ..-|-.||..+..++..|
T Consensus 149 -~~gi~~~~--~---------------------~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 149 -YLGLEFEG--R---------------------HHRGLDDARNIARILKRL 175 (176)
T ss_pred -HCCCCCCC--C---------------------CcCcHHHHHHHHHHHHHh
Confidence 66765431 0 112667888888887765
No 80
>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=90.94 E-value=8.1 Score=34.50 Aligned_cols=107 Identities=17% Similarity=0.086 Sum_probs=66.8
Q ss_pred hhHHHHHHHHcCCCceEEEEech-hcHHHHHH---HcCCccce-------------------EeehhHHHHhhhhccCCC
Q 019798 89 TVVKACKPALESSYITKVIHDCK-RDSEALYF---QFGIKLHN-------------------VVDTQIAYSLIEEQEGRK 145 (335)
Q Consensus 89 ~~~~~Lk~lLe~~~i~KV~hd~k-~D~~~L~~---~~gi~l~~-------------------vfDt~lAayLL~~~~~~~ 145 (335)
++++.+...++......|+||.+ +|+-+|.. .+|+.+.. -+|||-. +-+.+ +++
T Consensus 39 ~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~--l~~~g-~~~ 115 (209)
T PF10108_consen 39 ELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDL--LSFYG-AKA 115 (209)
T ss_pred HHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHH--HhccC-ccc
Confidence 46777777888666667999965 88877642 37777522 2566543 22222 122
Q ss_pred CCCCCcccHHhhhcCCcccCcccch---hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHH
Q 019798 146 RSPDDYISFVGLLADPRYCGISYQE---KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMK 214 (335)
Q Consensus 146 ~l~~~~~sL~~L~~~~~~L~~~l~~---k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~ 214 (335)
..||+.|+. .||++-.. -+++..+ |....+ ++...|+-.||..+..||-.+..
T Consensus 116 -----~~sLd~la~---~lgiPgK~~idGs~V~~~-------y~~g~i-~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 116 -----RTSLDELAA---LLGIPGKDDIDGSQVAEL-------YQEGDI-DEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred -----cCCHHHHHH---HcCCCCCCCCCHHHHHHH-------HHcCCH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 358988885 88865310 1233322 332232 56789999999999999887754
No 81
>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=90.48 E-value=11 Score=32.83 Aligned_cols=144 Identities=16% Similarity=0.170 Sum_probs=79.5
Q ss_pred ceEEEEEeecCCC-----ccCcEEEEEEEeC-CceEEEEccCCC-hhhHHHHHHHHcC--CCceEEEEec-hhcHHHHH-
Q 019798 50 LVIGFDCEGVDLC-----RHGSLCIMQLAFP-DAIYLVDAIQGG-ETVVKACKPALES--SYITKVIHDC-KRDSEALY- 118 (335)
Q Consensus 50 ~~ia~D~E~~~~~-----~~~~l~~lqla~~-~~~~lid~~~~~-~~~~~~Lk~lLe~--~~i~KV~hd~-k~D~~~L~- 118 (335)
..++||.|+.+.. ....+..|+++.. +...++-..... .+++..+-.++.. |.+ .+|||. .+|+-.|.
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 5789999997421 2346666666653 433343211122 2455666665554 453 479994 58887764
Q ss_pred --HHcCCccc----------------------eEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcc--cch--
Q 019798 119 --FQFGIKLH----------------------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGIS--YQE-- 170 (335)
Q Consensus 119 --~~~gi~l~----------------------~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~--l~~-- 170 (335)
..+|+.+. ..+|+.-... .. ..+ ...+|+.+++ +||.. ..+
T Consensus 83 Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~---~~---~~l--~~y~L~~Va~---~Lg~~k~~~k~~ 151 (188)
T cd05781 83 RARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAE---EI---PEV--KVKTLENVAE---YLGVMKKSERVL 151 (188)
T ss_pred HHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHH---hh---CCC--CCCCHHHHHH---HHCCCccccccC
Confidence 24665431 1556554322 11 112 2358888875 57752 110
Q ss_pred --hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHH
Q 019798 171 --KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (335)
Q Consensus 171 --k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L 212 (335)
..+... -|....-......|+..|+..++.|+..+
T Consensus 152 ~~~~~i~~-------~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 152 IEWYRIYE-------YWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred CCHHHHHH-------HHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 112211 24432123688999999999999998753
No 82
>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=90.33 E-value=0.21 Score=35.35 Aligned_cols=52 Identities=31% Similarity=0.513 Sum_probs=42.7
Q ss_pred CCCCccccccccccccHHHHHHHhhhhhhhcCCCCCCCcceeccc-hhhHHHHHHHH
Q 019798 272 VPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGP-VKQVRKAEAML 327 (335)
Q Consensus 272 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 327 (335)
.+|...+++||+.|.+|..+.+..++.|.|.- ...+-+.|+ ...+.+|.+++
T Consensus 8 Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~----~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 8 IPPDKIRDVIGPGGKTIKKIIEETGVKIDIED----DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eChhheeeeECCCchHHHHHHHHHCCEEEeCC----CCEEEEEeCCHHHHHHHHHHh
Confidence 46677789999999999999999999988875 245777787 56688888775
No 83
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=90.10 E-value=8.7 Score=34.60 Aligned_cols=134 Identities=19% Similarity=0.119 Sum_probs=80.7
Q ss_pred CceEEEEEeecCCC-ccCcEEEE---EEEeC---Cc--eEEEEccCC-C--------------------hhhHHHHHHHH
Q 019798 49 QLVIGFDCEGVDLC-RHGSLCIM---QLAFP---DA--IYLVDAIQG-G--------------------ETVVKACKPAL 98 (335)
Q Consensus 49 ~~~ia~D~E~~~~~-~~~~l~~l---qla~~---~~--~~lid~~~~-~--------------------~~~~~~Lk~lL 98 (335)
...+.||+|+++.. ...+++-| .+... +. -.++.+... . .++...+..++
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~i 92 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDFI 92 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 36799999999886 34443332 22222 12 134444210 0 12345555666
Q ss_pred cCCCceEEEEechhcHHHHHH---HcCCcc--ceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHH
Q 019798 99 ESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE 173 (335)
Q Consensus 99 e~~~i~KV~hd~k~D~~~L~~---~~gi~l--~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~ 173 (335)
.+. -.-|+||+.+|+..|.. .++..+ ..+.||.-.+.-..++... .+|+.|+. ++|+.... ..
T Consensus 93 ~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~-------~~L~~l~~---~~gi~~~~-~~ 160 (243)
T COG0847 93 GGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDR-------SSLDALAE---RLGIDRNP-FH 160 (243)
T ss_pred CCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCcc-------chHHHHHH---HcCCCcCC-cC
Confidence 664 35699999999998853 344443 3578998877766665222 37888886 56654210 00
Q ss_pred HHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHH
Q 019798 174 VRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (335)
Q Consensus 174 ~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~ 215 (335)
+ .-|..||.++..+|..+...
T Consensus 161 ---------------~------H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 161 ---------------P------HRALFDALALAELFLLLQTG 181 (243)
T ss_pred ---------------C------cchHHHHHHHHHHHHHHHhc
Confidence 0 22778999999999888774
No 84
>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=89.12 E-value=6.5 Score=34.95 Aligned_cols=129 Identities=12% Similarity=0.076 Sum_probs=73.7
Q ss_pred ccCcEEEEEEEe---CCceEEE-EccCCC-hhhHHHHHHHHcCCCceEEEEec-hhcHHHHHH---HcCCccc-------
Q 019798 63 RHGSLCIMQLAF---PDAIYLV-DAIQGG-ETVVKACKPALESSYITKVIHDC-KRDSEALYF---QFGIKLH------- 126 (335)
Q Consensus 63 ~~~~l~~lqla~---~~~~~li-d~~~~~-~~~~~~Lk~lLe~~~i~KV~hd~-k~D~~~L~~---~~gi~l~------- 126 (335)
..++++.|+++. .+..+.+ ...... .+++..+..++++.....|+||. .+|+-.|.. .+|+.+.
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 457888888876 3433333 111112 24666666666653335699997 689987753 3666421
Q ss_pred -----------eEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCccc--c-hhHHHHHHhcCCCCCCccCCCCH
Q 019798 127 -----------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY--Q-EKEEVRVLLRQDPQFWTYRPLTE 192 (335)
Q Consensus 127 -----------~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l--~-~k~~~~~~~~~~~~~w~~rpL~~ 192 (335)
..+|++-...-.+. . ...+|+.+++ +||.+- + .-+++.. .|...+ -.
T Consensus 129 ~~~~y~~r~~~~h~DL~~~~~~~~~---~-----~~~~L~~va~---~lG~~~K~d~~G~~v~~-------~y~~g~-~~ 189 (208)
T cd05782 129 KDWNYRNRYSERHLDLMDLLAFYGA---R-----ARASLDLLAK---LLGIPGKMDVDGSQVWE-------LYAEGK-LD 189 (208)
T ss_pred chhhccCcCCCCcccHHHHHhccCc---c-----CCCCHHHHHH---HhCCCCCcCCCHHHHHH-------HHHcCC-hH
Confidence 15677764321111 0 1348888875 677521 1 0122222 344433 36
Q ss_pred HHHHHHHhhhhHHHHHHH
Q 019798 193 LMVRAAADDVRFLPYIYH 210 (335)
Q Consensus 193 ~~~~YAa~Da~~ll~L~~ 210 (335)
....|+..||..+..||.
T Consensus 190 ~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 190 EIAEYCETDVLNTYLLYL 207 (208)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 788999999999999874
No 85
>PRK06722 exonuclease; Provisional
Probab=88.71 E-value=7.9 Score=36.23 Aligned_cols=92 Identities=13% Similarity=0.031 Sum_probs=53.1
Q ss_pred hhHHHHHHHHcCCCceEEEEechhcHHHHHH---HcCCccc-----eEeehhHHHHhhhhccCCCCCCCCcccHHhhhcC
Q 019798 89 TVVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKLH-----NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLAD 160 (335)
Q Consensus 89 ~~~~~Lk~lLe~~~i~KV~hd~k~D~~~L~~---~~gi~l~-----~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~ 160 (335)
+++..+..++.+.. -|+|++++|...|.+ .+|+... ..+|++-.++-+-+.... ...||..+++
T Consensus 79 eVl~ef~~fig~~~--lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~-----~~~sL~~l~~- 150 (281)
T PRK06722 79 QIIEKFIQFIGEDS--IFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFE-----HTPSLQSAVE- 150 (281)
T ss_pred HHHHHHHHHHCCCc--EEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhcc-----CCCCHHHHHH-
Confidence 35566777776543 377888999988864 3555431 135665433222111101 1247899986
Q ss_pred CcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHH
Q 019798 161 PRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (335)
Q Consensus 161 ~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~ 213 (335)
++|++.... ..-|-.||..+..|+..|.
T Consensus 151 --~lgL~~~g~-----------------------~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 151 --QLGLIWEGK-----------------------QHRALADAENTANILLKAY 178 (281)
T ss_pred --HCCCCCCCC-----------------------CcCcHHHHHHHHHHHHHHh
Confidence 667654210 0116678888888887776
No 86
>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=88.30 E-value=8.4 Score=33.32 Aligned_cols=29 Identities=17% Similarity=0.120 Sum_probs=19.6
Q ss_pred HHHHHHHHcCCCceEEEEe-chhcHHHHHH
Q 019798 91 VKACKPALESSYITKVIHD-CKRDSEALYF 119 (335)
Q Consensus 91 ~~~Lk~lLe~~~i~KV~hd-~k~D~~~L~~ 119 (335)
+..+..++..+....|+|| +.+|..+|.+
T Consensus 73 l~~~~~~~~~~~~~lVahn~~~FD~~fL~~ 102 (183)
T cd06138 73 IAKIHRLFNTPGTCIVGYNNIRFDDEFLRF 102 (183)
T ss_pred HHHHHHHHccCCCcEEeeCchhhHHHHHHH
Confidence 3456666654443458997 7999998864
No 87
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=88.09 E-value=3.1 Score=40.58 Aligned_cols=88 Identities=20% Similarity=0.159 Sum_probs=55.5
Q ss_pred HHHHHHHcCCCceEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchh
Q 019798 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK 171 (335)
Q Consensus 92 ~~Lk~lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k 171 (335)
..|+.++.... .-|||..-.|+.+|+-.| ..+.||.+ ++....+.+. ...||..|++ .|||..+..
T Consensus 285 ~~l~~~~~~~T-ILVGHSLenDL~aLKl~H----~~ViDTa~---lf~~~~g~~~---~k~sLk~L~~--~~L~~~Iq~- 350 (380)
T KOG2248|consen 285 KELLELISKNT-ILVGHSLENDLKALKLDH----PSVIDTAV---LFKHPTGPYP---FKSSLKNLAK--SYLGKLIQE- 350 (380)
T ss_pred HHHHhhcCcCc-EEEeechhhHHHHHhhhC----CceeeeeE---EEecCCCCcc---chHHHHHHHH--HHHHHHHhc-
Confidence 46777665555 459999999999996322 35789984 2333332211 2358999999 899865431
Q ss_pred HHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHH
Q 019798 172 EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (335)
Q Consensus 172 ~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~ 213 (335)
. ..+.+ +.+||..++.|.....
T Consensus 351 -~------~~~Hd-------------S~eDA~acm~Lv~~k~ 372 (380)
T KOG2248|consen 351 -G------VGGHD-------------SVEDALACMKLVKLKI 372 (380)
T ss_pred -c------CCCCc-------------cHHHHHHHHHHHHHHH
Confidence 0 01111 5688998888876543
No 88
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=81.44 E-value=38 Score=30.02 Aligned_cols=104 Identities=13% Similarity=0.072 Sum_probs=57.5
Q ss_pred hhHHHHHHHHcC--CCceEEEEec-hhcHHHHHH---HcCCccc------------------eEeehhHHHHhhhhccCC
Q 019798 89 TVVKACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKLH------------------NVVDTQIAYSLIEEQEGR 144 (335)
Q Consensus 89 ~~~~~Lk~lLe~--~~i~KV~hd~-k~D~~~L~~---~~gi~l~------------------~vfDt~lAayLL~~~~~~ 144 (335)
+++..+..++.+ |.+ .+|+|. .+|+-.|.. .+|+.+. ..+|++-... ..
T Consensus 75 ~lL~~f~~~i~~~~Pd~-i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~---~~--- 147 (204)
T cd05779 75 ALLQRFFEHIREVKPHI-IVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVK---RD--- 147 (204)
T ss_pred HHHHHHHHHHHHhCCCE-EEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHH---Hh---
Confidence 345555555554 444 488884 588877642 3555432 0345543211 10
Q ss_pred CCCCCCcccHHhhhcCCcccCcccch--hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHH
Q 019798 145 KRSPDDYISFVGLLADPRYCGISYQE--KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYH 210 (335)
Q Consensus 145 ~~l~~~~~sL~~L~~~~~~L~~~l~~--k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~ 210 (335)
..+.....+|+.+++ .+||..-.. ..+... -|...+ +..++|+..||..++.||.
T Consensus 148 ~~l~~~sysLd~Va~--~~Lg~~K~~~~~~~I~~-------~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 148 SYLPQGSQGLKAVTK--AKLGYDPVELDPEDMVP-------LAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred hcCCCCCccHHHHHH--HHhCCCcCcCCHHHHHH-------HHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 000011347889998 889853111 112111 344433 6789999999999999983
No 89
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=79.29 E-value=0.88 Score=48.28 Aligned_cols=87 Identities=20% Similarity=0.205 Sum_probs=59.1
Q ss_pred HHcCCCceEEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHH
Q 019798 97 ALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRV 176 (335)
Q Consensus 97 lLe~~~i~KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~ 176 (335)
+|-+-.+..|||+++.|.+++ +..+....++||.+.- ..+. + +.+||..|+. .+||.++.. +.
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvI--Ni~Vp~~QiiDTv~lf--~~~s---~----R~LSLrfLa~--~lLg~~IQ~--~~-- 1071 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVI--NIHVPEEQIIDTVTLF--RLGS---Q----RMLSLRFLAW--ELLGETIQM--EA-- 1071 (1118)
T ss_pred HHHHcCcEEEcccccccceEE--EEecChhhheeeeEEE--eccc---c----cEEEHHHHHH--HHhcchhhc--cc--
Confidence 566778899999999999876 2333334599997732 2221 2 2469999999 899976531 10
Q ss_pred HhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccc
Q 019798 177 LLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (335)
Q Consensus 177 ~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~ 220 (335)
.| ..+||+.++.||.+.. +|+++|
T Consensus 1072 ------HD-------------SIeDA~taLkLYk~Yl-~lkeq~ 1095 (1118)
T KOG1275|consen 1072 ------HD-------------SIEDARTALKLYKKYL-KLKEQG 1095 (1118)
T ss_pred ------cc-------------cHHHHHHHHHHHHHHH-HHHHhh
Confidence 11 4589999999999985 455544
No 90
>PRK05359 oligoribonuclease; Provisional
Probab=78.94 E-value=19 Score=31.25 Aligned_cols=41 Identities=12% Similarity=-0.009 Sum_probs=23.6
Q ss_pred hHHHHHHHHcC----CCceEEEEechhcHHHHHHHc---CCccc-eEee
Q 019798 90 VVKACKPALES----SYITKVIHDCKRDSEALYFQF---GIKLH-NVVD 130 (335)
Q Consensus 90 ~~~~Lk~lLe~----~~i~KV~hd~k~D~~~L~~~~---gi~l~-~vfD 130 (335)
++..+..++.+ ....-++||+.+|..+|.+.+ |..+. ...|
T Consensus 82 ~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~D 130 (181)
T PRK05359 82 AEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLD 130 (181)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccc
Confidence 33445555542 123348999999999886433 44443 2456
No 91
>PF13014 KH_3: KH domain
Probab=78.58 E-value=1.2 Score=28.87 Aligned_cols=27 Identities=48% Similarity=0.724 Sum_probs=24.5
Q ss_pred cccccccccccHHHHHHHhhhhhhhcC
Q 019798 277 MGRIIGRRGSSILAIKESCNAEILIGG 303 (335)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 (335)
.+.+||++|.+|..+.+.+.+.|.+--
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEECC
Confidence 367899999999999999999998877
No 92
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=78.32 E-value=48 Score=29.32 Aligned_cols=105 Identities=12% Similarity=0.073 Sum_probs=58.7
Q ss_pred hhHHHHHHHHcCCCceEEEEec-hhcHHHHHH---HcCCcc----------------ceEeehhHHHH--hhh-hccCCC
Q 019798 89 TVVKACKPALESSYITKVIHDC-KRDSEALYF---QFGIKL----------------HNVVDTQIAYS--LIE-EQEGRK 145 (335)
Q Consensus 89 ~~~~~Lk~lLe~~~i~KV~hd~-k~D~~~L~~---~~gi~l----------------~~vfDt~lAay--LL~-~~~~~~ 145 (335)
+++..+..++.+.. ..|++|. .+|+-.|.. .+|+.. ...+|+.-... .+. ...+ .
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 45666666777654 5678995 488877642 467661 12566644311 110 0000 0
Q ss_pred CCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHH
Q 019798 146 RSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYH 210 (335)
Q Consensus 146 ~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~ 210 (335)
.+ ...+|+.+++ .+||.. |..... .-|... .+..+.|+..||..+++|..
T Consensus 153 ~~--~~~~L~~Va~--~~lg~~---K~~~~~------~i~~~~--~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 153 KY--REYTLDAVAK--ALLGEG---KVELEK------NISELN--LYELAEYNYRDAELTLELTT 202 (204)
T ss_pred cc--ccCcHHHHHH--HhcCCC---cccCCc------hhhhhc--HHHHHHhhHHHHHHHHHHhc
Confidence 11 2348899998 888852 111100 012111 26788999999999998864
No 93
>PRK05762 DNA polymerase II; Reviewed
Probab=76.23 E-value=53 Score=35.36 Aligned_cols=104 Identities=15% Similarity=0.153 Sum_probs=58.4
Q ss_pred hhHHHHHHHHcC--CCceEEEEec-hhcHHHHHH---HcCCccc---------------------------eEeehhHHH
Q 019798 89 TVVKACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKLH---------------------------NVVDTQIAY 135 (335)
Q Consensus 89 ~~~~~Lk~lLe~--~~i~KV~hd~-k~D~~~L~~---~~gi~l~---------------------------~vfDt~lAa 135 (335)
+++..+..++.. |+| .+|||. .+|+..|.+ .+|+.+. -++|+.-..
T Consensus 205 ~LL~~F~~~i~~~DPDI-IvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~ 283 (786)
T PRK05762 205 ALLEKFNAWFAEHDPDV-IIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDAL 283 (786)
T ss_pred HHHHHHHHHHHhcCCCE-EEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHH
Confidence 445555555444 665 489995 479987753 3555421 145555432
Q ss_pred HhhhhccCCCCCCCCcccHHhhhcCCcccCcccc--hh----HHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHH
Q 019798 136 SLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ--EK----EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (335)
Q Consensus 136 yLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~--~k----~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~ 209 (335)
.-... .+ ...+|+.+++ ++||..-. .. .+... .|... ....+.|+..||..+++|+
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 1347889998 88874321 00 11111 23321 2567899999999999999
Q ss_pred HH
Q 019798 210 HN 211 (335)
Q Consensus 210 ~~ 211 (335)
.+
T Consensus 346 ~k 347 (786)
T PRK05762 346 EK 347 (786)
T ss_pred HH
Confidence 84
No 94
>PHA02528 43 DNA polymerase; Provisional
Probab=70.70 E-value=97 Score=33.89 Aligned_cols=50 Identities=8% Similarity=0.005 Sum_probs=33.9
Q ss_pred cccHHhhhcCCcccCcccch--hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHH
Q 019798 151 YISFVGLLADPRYCGISYQE--KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHN 211 (335)
Q Consensus 151 ~~sL~~L~~~~~~L~~~l~~--k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~ 211 (335)
..+|+.+++ ++||..-.. .++... -|...+ ...++|+..||..+++|...
T Consensus 272 SYsLe~VA~--~~LG~~K~d~~~~eI~~-------l~~~d~--~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 272 SYRLDYIAE--VELGKKKLDYSDGPFKK-------FRETDH--QKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred cCCHHHHHH--HHhCCCCccCCHHHHHH-------HHhcCH--HHHHHHHHHHHHHHHHHHHH
Confidence 347899998 899853321 122222 233222 67799999999999999988
No 95
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=66.71 E-value=0.83 Score=33.74 Aligned_cols=54 Identities=15% Similarity=0.256 Sum_probs=41.9
Q ss_pred CCCCCCCCCCcccccCCCCHHHHHhhhcCCCCccc----------cccccccccHHHHHHHhhh
Q 019798 244 DWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG----------RIIGRRGSSILAIKESCNA 297 (335)
Q Consensus 244 d~~~L~~~~~~l~~~~~~~e~~i~~lAg~~~~~~~----------~~~~~~~~~~~~~~~~~~~ 297 (335)
.|+.-.+...+.+......++.|.++|..+|.+.. ..+.++|..++.+++.+.+
T Consensus 13 ~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~~~~~~~~g~~~~~~i~~~~~ 76 (81)
T smart00341 13 QWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASD 76 (81)
T ss_pred HHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45555566778888999999999999999997753 4567778888888887643
No 96
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=64.28 E-value=18 Score=32.61 Aligned_cols=52 Identities=13% Similarity=0.200 Sum_probs=32.7
Q ss_pred ccHHhhhcCCcccCcccch--hHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHH
Q 019798 152 ISFVGLLADPRYCGISYQE--KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (335)
Q Consensus 152 ~sL~~L~~~~~~L~~~l~~--k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L 212 (335)
.+|.++++ .+||..-.+ ..+... -|....--...++|+..||..+++|...|
T Consensus 173 Y~L~~va~--~~Lg~~k~di~~~~i~~-------~~~~~~~l~~l~~y~~~Da~l~~~L~~kl 226 (234)
T cd05776 173 YDLTELSQ--QVLGIERQDIDPEEILN-------MYNDSESLLKLLEHTEKDAYLILQLMFKL 226 (234)
T ss_pred CChHHHHH--HHhCcCcccCCHHHHHH-------HHhCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48889998 899853211 112211 24321111456899999999999998876
No 97
>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=63.87 E-value=5 Score=34.61 Aligned_cols=48 Identities=35% Similarity=0.432 Sum_probs=42.1
Q ss_pred ccccccccccccHHHHHHHhhhhhhhcCCCCCCCcceeccchhhHHHHHHHHh
Q 019798 276 KMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAMLR 328 (335)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 (335)
..|++||+.|.++..+...+.+.+.+.| ..+.++|....+..|+..+.
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~-----~~v~i~G~~~~~~~A~~~i~ 146 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG-----KTVGIIGDPEQVQIAREAIE 146 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC-----CEEEEECCHHHHHHHHHHHH
Confidence 4689999999999999999999998875 67889999999999887664
No 98
>PRK13763 putative RNA-processing protein; Provisional
Probab=57.56 E-value=7.2 Score=33.91 Aligned_cols=47 Identities=36% Similarity=0.468 Sum_probs=40.6
Q ss_pred ccccccccccccHHHHHHHhhhhhhhcCCCCCCCcceeccchhhHHHHHHHH
Q 019798 276 KMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAML 327 (335)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 327 (335)
..|++||+.|.++..+...+.+.|.+.+ +.+.++|+...+..|+..+
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 4689999999999999999999998876 3488999999988887655
No 99
>PRK00468 hypothetical protein; Provisional
Probab=51.63 E-value=10 Score=28.13 Aligned_cols=26 Identities=35% Similarity=0.667 Sum_probs=21.5
Q ss_pred CCCccccccccccccHHHHHHHhhhh
Q 019798 273 PPGKMGRIIGRRGSSILAIKESCNAE 298 (335)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 298 (335)
.|..+|++|||.|.++.++..-.+|-
T Consensus 37 ~~~D~GrVIGk~Gr~i~AIRtvv~aa 62 (75)
T PRK00468 37 APEDMGKVIGKQGRIAKAIRTVVKAA 62 (75)
T ss_pred ChhhCcceecCCChhHHHHHHHHHHH
Confidence 47889999999999999888776543
No 100
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=51.34 E-value=9.9 Score=37.25 Aligned_cols=57 Identities=32% Similarity=0.476 Sum_probs=49.4
Q ss_pred cccccccccccHHHHHHHhhhhhhhcCCCCCCCc---ceeccchhhHHHHHHHHhhhhcc
Q 019798 277 MGRIIGRRGSSILAIKESCNAEILIGGAKGPPDK---VFIIGPVKQVRKAEAMLRGRMLE 333 (335)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~ 333 (335)
.|-+||++|..|--+..-+-|+|+|..+++|+.+ +.+.||.-..=||.--+-||+-+
T Consensus 422 vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikE 481 (584)
T KOG2193|consen 422 VGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKE 481 (584)
T ss_pred HHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhh
Confidence 3678999999999999999999999999999865 67789998888998888888643
No 101
>PRK02821 hypothetical protein; Provisional
Probab=49.92 E-value=10 Score=28.24 Aligned_cols=25 Identities=32% Similarity=0.684 Sum_probs=21.7
Q ss_pred CCCccccccccccccHHHHHHHhhh
Q 019798 273 PPGKMGRIIGRRGSSILAIKESCNA 297 (335)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~ 297 (335)
.|..+|++|||+|..+-++..-..|
T Consensus 38 ~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 38 HPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred ChhhCcceeCCCCchHHHHHHHHHH
Confidence 4788999999999999999887754
No 102
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=49.08 E-value=14 Score=32.50 Aligned_cols=56 Identities=34% Similarity=0.439 Sum_probs=43.6
Q ss_pred HHhhhcCCCC----ccccccccccccHHHHHHHhhhhhhhcCCCCCCCcceeccchhhHHHHHHH
Q 019798 266 ILSILDVPPG----KMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAM 326 (335)
Q Consensus 266 i~~lAg~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 326 (335)
|-++++..+. --||+||+.|.+-..+-...++.|.+.|. .+=+||+.++|+-|+..
T Consensus 98 i~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-----tVaiiG~~~~v~iAr~A 157 (194)
T COG1094 98 LKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK-----TVAIIGGFEQVEIAREA 157 (194)
T ss_pred HHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc-----EEEEecChhhhHHHHHH
Confidence 3445554333 34799999999999999999999999994 46689999998877643
No 103
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=43.67 E-value=13 Score=27.58 Aligned_cols=23 Identities=39% Similarity=0.794 Sum_probs=19.5
Q ss_pred CCCccccccccccccHHHHHHHh
Q 019798 273 PPGKMGRIIGRRGSSILAIKESC 295 (335)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~ 295 (335)
-|..||++|||.|.++-++..--
T Consensus 37 ~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 37 APEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CcccccceecCCChhHHHHHHHH
Confidence 47899999999999998887654
No 104
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=42.11 E-value=0.68 Score=33.09 Aligned_cols=43 Identities=21% Similarity=0.259 Sum_probs=28.1
Q ss_pred CCCCcccccCCCCHHHHHhhhcCCCCccc----------cccccccccHHHHH
Q 019798 250 PVPDYLIVEGDVPEEEILSILDVPPGKMG----------RIIGRRGSSILAIK 292 (335)
Q Consensus 250 ~~~~~l~~~~~~~e~~i~~lAg~~~~~~~----------~~~~~~~~~~~~~~ 292 (335)
+...+.++.....++.+.++|...|.+.. ..+.++|..|++++
T Consensus 16 A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i~g~~~~~~~~~g~~il~~I 68 (68)
T PF00570_consen 16 AREEDVPPYRILSDEALLEIAKRLPTSIEELLQIPGMGKRKVRKYGDEILEII 68 (68)
T ss_dssp HHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTSTTCGHHHHHHCHHHHHHHH
T ss_pred HHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHccCCCHHHHHHHHHHHHhhC
Confidence 33445566677888899999999997653 56677888887764
No 105
>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=38.66 E-value=63 Score=28.96 Aligned_cols=55 Identities=13% Similarity=0.092 Sum_probs=36.0
Q ss_pred cccHHhhhcCCcccCcccch--hHHHHHHhcCCCCCCccCCCC-HHHHHHHHhhhhHHHHHHHHHHH
Q 019798 151 YISFVGLLADPRYCGISYQE--KEEVRVLLRQDPQFWTYRPLT-ELMVRAAADDVRFLPYIYHNMMK 214 (335)
Q Consensus 151 ~~sL~~L~~~~~~L~~~l~~--k~~~~~~~~~~~~~w~~rpL~-~~~~~YAa~Da~~ll~L~~~L~~ 214 (335)
..+|+++++ ++||..-.. .++... -|...|-. ...++|+..||..+++|+.+|.-
T Consensus 168 sy~L~~Va~--~~Lg~~k~d~~~~~i~~-------~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~~ 225 (230)
T cd05777 168 SYSLNSVSA--HFLGEQKEDVHYSIITD-------LQNGNPETRRRLAVYCLKDAYLPLRLLDKLMC 225 (230)
T ss_pred cCcHHHHHH--HHhCCCCCCCCHHHHHH-------HHccCHhHhHHHHHhhHHHHHHHHHHHHHHhh
Confidence 458899998 899854321 122221 23322311 46789999999999999998853
No 106
>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=36.37 E-value=36 Score=27.55 Aligned_cols=53 Identities=30% Similarity=0.538 Sum_probs=40.0
Q ss_pred CccccccccccccHHHHHHHhhhhhhhcCCCC-------------C-------CCcceeccch---hhHHHHHHHHh
Q 019798 275 GKMGRIIGRRGSSILAIKESCNAEILIGGAKG-------------P-------PDKVFIIGPV---KQVRKAEAMLR 328 (335)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~-------~~~~~~~~~~---~~~~~~~~~~~ 328 (335)
...|++||-+|.++-.+.+...+.|.|.|. | | |..++|.++- ..+.+|..++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~-gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~ 90 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGK-GSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIE 90 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecC-cccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHH
Confidence 567899999999999999999999999984 2 1 2346555554 34777776654
No 107
>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=36.20 E-value=21 Score=30.77 Aligned_cols=53 Identities=23% Similarity=0.376 Sum_probs=39.9
Q ss_pred CCCCccccccccccccHHHHHHHhhhhhhhcCCCCCCCcceec----cchhhHHHHHHHHh
Q 019798 272 VPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFII----GPVKQVRKAEAMLR 328 (335)
Q Consensus 272 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~ 328 (335)
.|+.+.+.+||+.|.+|..+.+.+++.|.|---+ ..+.| +....+.+|..++.
T Consensus 4 Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~----g~V~I~~~t~d~~~i~kA~~~I~ 60 (172)
T TIGR03665 4 IPKDRIGVLIGKGGETKKEIEERTGVKLDIDSET----GEVKIEEEDEDPLAVMKAREVVK 60 (172)
T ss_pred CCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCC----ceEEEecCCCCHHHHHHHHHHHH
Confidence 4678889999999999999999999998887432 23344 33445788877764
No 108
>PRK01064 hypothetical protein; Provisional
Probab=31.84 E-value=35 Score=25.44 Aligned_cols=25 Identities=32% Similarity=0.563 Sum_probs=21.1
Q ss_pred CCCccccccccccccHHHHHHHhhh
Q 019798 273 PPGKMGRIIGRRGSSILAIKESCNA 297 (335)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~ 297 (335)
.+..+|++|||+|.++-++..-..+
T Consensus 37 ~~~D~g~vIGk~G~~i~air~l~~~ 61 (78)
T PRK01064 37 AKPDIGKIIGKEGRTIKAIRTLLVS 61 (78)
T ss_pred CcccceEEECCCCccHHHHHHHHHH
Confidence 4678899999999999999887643
No 109
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. 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. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=30.09 E-value=64 Score=27.50 Aligned_cols=31 Identities=6% Similarity=-0.124 Sum_probs=21.1
Q ss_pred hHHHHHHHHcC----CCceEEEEechhcHHHHHHH
Q 019798 90 VVKACKPALES----SYITKVIHDCKRDSEALYFQ 120 (335)
Q Consensus 90 ~~~~Lk~lLe~----~~i~KV~hd~k~D~~~L~~~ 120 (335)
++..+..++.+ .....++||+.+|..+|.+.
T Consensus 78 vl~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~ 112 (173)
T cd06135 78 AEAELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKY 112 (173)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHH
Confidence 34455566653 24567899999999988643
No 110
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=29.39 E-value=4.6e+02 Score=24.24 Aligned_cols=152 Identities=22% Similarity=0.157 Sum_probs=82.8
Q ss_pred ceEEEEEeecCCCccC-cEEEEEEEeC-CceEEEEccCCC--hhhHHHHHHHHcCCCc-eEEEEech-hcHHHHH----H
Q 019798 50 LVIGFDCEGVDLCRHG-SLCIMQLAFP-DAIYLVDAIQGG--ETVVKACKPALESSYI-TKVIHDCK-RDSEALY----F 119 (335)
Q Consensus 50 ~~ia~D~E~~~~~~~~-~l~~lqla~~-~~~~lid~~~~~--~~~~~~Lk~lLe~~~i-~KV~hd~k-~D~~~L~----~ 119 (335)
....||+||++++..+ .+.++..+.. +....|--.-+. ..-...+..++.++.. ..|.+|.| +|+-.++ .
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 4788999999998544 4555555553 333433211111 1112334446665532 34777754 7887765 1
Q ss_pred HcCCccc-eEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccch-------hHHHHHHhcCCCCCCccCC--
Q 019798 120 QFGIKLH-NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE-------KEEVRVLLRQDPQFWTYRP-- 189 (335)
Q Consensus 120 ~~gi~l~-~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~-------k~~~~~~~~~~~~~w~~rp-- 189 (335)
+....+. .-||++-.+.-+.. |.|+ ..+|+. ++ ++||+.-.+ .+-.+ .|.+-+
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 2333343 47999887765552 2333 235544 44 688864321 01111 122111
Q ss_pred -CCHHHHHHHHhhhhHHHHHHHHHHHHHhc
Q 019798 190 -LTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (335)
Q Consensus 190 -L~~~~~~YAa~Da~~ll~L~~~L~~~L~~ 218 (335)
+-...+.|=-+|+.-+..|+..+.+++.+
T Consensus 242 ~ll~~l~~hN~eDvlnL~~i~~h~~~~i~~ 271 (278)
T COG3359 242 GLLDGLVLHNREDVLNLPTIIKHVSKKILE 271 (278)
T ss_pred HHHHHHHHccHHHHHhHHHHHHHHHHHHHH
Confidence 11344566678898899999888887764
No 111
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=28.69 E-value=26 Score=25.35 Aligned_cols=25 Identities=32% Similarity=0.554 Sum_probs=21.1
Q ss_pred CCccccccccccccHHHHHHHhhhh
Q 019798 274 PGKMGRIIGRRGSSILAIKESCNAE 298 (335)
Q Consensus 274 ~~~~~~~~~~~~~~~~~~~~~~~~~ 298 (335)
+...|+.|||+|.++.|+..-+++-
T Consensus 37 ~ed~g~lIGk~G~tl~ALq~l~~~~ 61 (73)
T PF13083_consen 37 GEDAGRLIGKHGKTLNALQYLVNAA 61 (73)
T ss_dssp SCCCHHHCTTHHHHHHHHHHHHHHH
T ss_pred CCccceEECCCCeeHHHHHHHHHHH
Confidence 3567899999999999999888754
No 112
>PTZ00315 2'-phosphotransferase; Provisional
Probab=28.47 E-value=2.5e+02 Score=29.20 Aligned_cols=101 Identities=17% Similarity=0.151 Sum_probs=55.8
Q ss_pred hhHHHHHHHHcCCC--------ceEEEEechhcHH-HHHH------HcCCcc--ceEeehh-HHHHhhhhcc----CCCC
Q 019798 89 TVVKACKPALESSY--------ITKVIHDCKRDSE-ALYF------QFGIKL--HNVVDTQ-IAYSLIEEQE----GRKR 146 (335)
Q Consensus 89 ~~~~~Lk~lLe~~~--------i~KV~hd~k~D~~-~L~~------~~gi~l--~~vfDt~-lAayLL~~~~----~~~~ 146 (335)
+++..+..+|.+.. -..++|+..+|+. .|.+ .+|+.. ...+|++ ..+..+.+.. +...
T Consensus 132 eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~ 211 (582)
T PTZ00315 132 VVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGAT 211 (582)
T ss_pred HHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCccccccccccc
Confidence 35667777887643 1358999999985 5532 235554 2356654 2233333310 0000
Q ss_pred CCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCCccCCCCHHHHHHHHhhhhHHHHHHHHHHHH
Q 019798 147 SPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (335)
Q Consensus 147 l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~ 215 (335)
-.....+|.++++ ++|++...+. .-|-.||..+.+|+..|..+
T Consensus 212 ~~~~~~~L~~al~---~lgL~~eGr~-----------------------HrAlDDA~ntA~L~~~Ll~~ 254 (582)
T PTZ00315 212 PPLGPSDMPDMLQ---MLGLPLQGRH-----------------------HSGIDDCRNIAAVLCELLRR 254 (582)
T ss_pred cccCCcCHHHHHH---HCCCCCCCCC-----------------------cCcHHHHHHHHHHHHHHHHc
Confidence 0012358889886 6776543100 11557888888888777543
No 113
>PRK13763 putative RNA-processing protein; Provisional
Probab=27.24 E-value=39 Score=29.28 Aligned_cols=54 Identities=24% Similarity=0.449 Sum_probs=39.9
Q ss_pred CCCCccccccccccccHHHHHHHhhhhhhhcCCCCCCCcceec----cchhhHHHHHHHHh
Q 019798 272 VPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFII----GPVKQVRKAEAMLR 328 (335)
Q Consensus 272 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~ 328 (335)
.||.+.+.+||..|..|..+.+.+++.|.|--.+ ..+++. +....+.+|..++.
T Consensus 9 IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~---g~V~I~~~~~~d~~~i~kA~~~I~ 66 (180)
T PRK13763 9 IPKDRIGVLIGKKGETKKEIEERTGVKLEIDSET---GEVIIEPTDGEDPLAVLKARDIVK 66 (180)
T ss_pred cCHHHhhhHhccchhHHHHHHHHHCcEEEEECCC---CeEEEEeCCCCCHHHHHHHHHHHH
Confidence 4778899999999999999999999888887532 234332 23344778876665
No 114
>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=24.60 E-value=43 Score=23.39 Aligned_cols=27 Identities=22% Similarity=0.423 Sum_probs=22.5
Q ss_pred hcCCCCccccccccccccHHHHHHHhh
Q 019798 270 LDVPPGKMGRIIGRRGSSILAIKESCN 296 (335)
Q Consensus 270 Ag~~~~~~~~~~~~~~~~~~~~~~~~~ 296 (335)
.-.+++.++..||++|.+|..+.+.++
T Consensus 29 v~V~~~~~~~aIGk~G~nI~~~~~l~~ 55 (61)
T cd02134 29 VVVPDDQLGLAIGKGGQNVRLASKLLG 55 (61)
T ss_pred EEECcccceeeECCCCHHHHHHHHHHC
Confidence 344678999999999999999988774
Done!