Query 020198
Match_columns 329
No_of_seqs 274 out of 1382
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 07:49:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020198.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020198hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10829 ribonuclease D; Provi 100.0 1.2E-37 2.5E-42 301.4 -4.3 251 27-303 2-283 (373)
2 COG0349 Rnd Ribonuclease D [Tr 100.0 1.6E-36 3.4E-41 287.4 -6.9 247 33-303 3-279 (361)
3 TIGR01388 rnd ribonuclease D. 100.0 1E-33 2.2E-38 274.7 -5.8 229 30-283 1-233 (367)
4 cd06148 Egl_like_exo DEDDy 3'- 100.0 5E-30 1.1E-34 229.0 8.3 178 46-225 7-186 (197)
5 cd06146 mut-7_like_exo DEDDy 3 99.9 8.1E-29 1.8E-33 220.5 2.9 175 28-213 1-192 (193)
6 cd06129 RNaseD_like DEDDy 3'-5 99.9 7E-29 1.5E-33 214.7 1.4 153 41-213 5-160 (161)
7 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 6.9E-27 1.5E-31 203.3 0.6 163 33-213 3-169 (170)
8 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 1.5E-26 3.3E-31 200.3 -2.6 170 28-217 1-176 (176)
9 KOG2206 Exosome 3'-5' exoribon 99.9 8.6E-23 1.9E-27 200.8 3.4 185 9-220 179-364 (687)
10 cd06142 RNaseD_exo DEDDy 3'-5' 99.8 1.8E-20 3.8E-25 163.2 3.7 163 48-230 11-174 (178)
11 smart00474 35EXOc 3'-5' exonuc 99.7 1.9E-18 4.2E-23 148.3 2.3 168 29-217 2-172 (172)
12 cd06147 Rrp6p_like_exo DEDDy 3 99.7 9.6E-18 2.1E-22 148.8 2.8 173 25-219 2-175 (192)
13 cd00007 35EXOc 3'-5' exonuclea 99.6 3.4E-16 7.3E-21 131.9 6.7 153 51-216 2-155 (155)
14 cd09018 DEDDy_polA_RNaseD_like 99.6 3.5E-16 7.5E-21 132.1 3.6 145 52-213 2-149 (150)
15 cd06140 DNA_polA_I_Bacillus_li 99.6 5.1E-16 1.1E-20 135.5 4.6 162 50-227 4-167 (178)
16 PRK05755 DNA polymerase I; Pro 99.6 4.5E-16 9.7E-21 166.8 4.1 182 26-225 294-479 (880)
17 cd06139 DNA_polA_I_Ecoli_like_ 99.5 2.1E-14 4.6E-19 126.3 5.6 168 47-226 3-181 (193)
18 PRK14975 bifunctional 3'-5' ex 99.4 4.6E-14 1E-18 144.2 3.2 153 27-226 2-160 (553)
19 KOG2207 Predicted 3'-5' exonuc 99.4 7.9E-14 1.7E-18 138.7 0.5 181 26-218 390-587 (617)
20 KOG2405 Predicted 3'-5' exonuc 99.3 1.2E-12 2.6E-17 124.0 3.3 235 49-290 195-458 (458)
21 COG0749 PolA DNA polymerase I 99.2 2.9E-12 6.2E-17 129.5 2.2 161 50-224 23-189 (593)
22 TIGR00593 pola DNA polymerase 99.0 7E-11 1.5E-15 126.2 2.9 176 28-226 304-487 (887)
23 cd06128 DNA_polA_exo DEDDy 3'- 98.7 6.6E-09 1.4E-13 88.3 3.9 133 64-213 17-150 (151)
24 KOG2405 Predicted 3'-5' exonuc 98.0 2.9E-07 6.3E-12 87.8 -3.9 147 54-204 63-215 (458)
25 KOG4373 Predicted 3'-5' exonuc 98.0 3E-06 6.4E-11 79.8 2.0 129 64-209 146-281 (319)
26 cd06125 DnaQ_like_exo DnaQ-lik 97.1 0.0003 6.4E-09 55.5 2.3 72 52-134 1-83 (96)
27 PRK07740 hypothetical protein; 96.2 0.0053 1.1E-07 56.7 4.0 140 46-221 56-231 (244)
28 PRK06063 DNA polymerase III su 95.9 0.0064 1.4E-07 58.3 3.6 97 90-222 84-185 (313)
29 cd02396 PCBP_like_KH K homolog 95.8 0.0025 5.4E-08 46.5 -0.1 45 277-321 4-50 (65)
30 cd02394 vigilin_like_KH K homo 95.7 0.0021 4.5E-08 46.2 -0.5 42 276-317 3-44 (62)
31 TIGR00573 dnaq exonuclease, DN 95.4 0.018 3.8E-07 52.2 4.2 140 47-220 5-181 (217)
32 PRK07942 DNA polymerase III su 95.1 0.026 5.7E-07 51.7 4.2 81 104-217 95-181 (232)
33 COG1837 Predicted RNA-binding 94.8 0.0072 1.6E-07 45.6 -0.2 42 259-300 16-57 (76)
34 KOG2249 3'-5' exonuclease [Rep 94.8 0.018 3.8E-07 53.3 2.3 136 49-219 105-269 (280)
35 cd06137 DEDDh_RNase DEDDh 3'-5 94.7 0.01 2.3E-07 51.1 0.5 65 93-168 76-140 (161)
36 PRK07883 hypothetical protein; 94.6 0.015 3.2E-07 60.0 1.5 141 46-221 12-187 (557)
37 cd02393 PNPase_KH Polynucleoti 94.6 0.0065 1.4E-07 43.8 -0.9 36 275-310 4-39 (61)
38 PF13014 KH_3: KH domain 94.5 0.015 3.2E-07 38.7 0.7 27 284-310 2-28 (43)
39 cd06144 REX4_like DEDDh 3'-5' 94.4 0.0057 1.2E-07 52.2 -1.8 68 90-169 67-134 (152)
40 cd00105 KH-I K homology RNA-bi 94.4 0.014 3.1E-07 41.7 0.5 37 276-312 3-39 (64)
41 COG2176 PolC DNA polymerase II 94.2 0.04 8.7E-07 60.1 3.6 141 46-224 418-594 (1444)
42 PRK07246 bifunctional ATP-depe 94.0 0.053 1.1E-06 58.5 4.2 133 48-218 6-172 (820)
43 cd06131 DNA_pol_III_epsilon_Ec 93.9 0.033 7.1E-07 47.8 1.9 88 90-212 71-166 (167)
44 PRK00468 hypothetical protein; 93.9 0.014 3E-07 44.1 -0.4 45 259-303 16-60 (75)
45 cd06149 ISG20 DEDDh 3'-5' exon 93.8 0.014 3E-07 50.2 -0.6 69 90-168 67-136 (157)
46 PRK05711 DNA polymerase III su 93.3 0.059 1.3E-06 49.7 2.6 90 91-215 77-175 (240)
47 TIGR01406 dnaQ_proteo DNA poly 93.1 0.054 1.2E-06 49.4 2.1 92 90-216 72-172 (225)
48 TIGR01298 RNaseT ribonuclease 93.0 0.044 9.6E-07 49.0 1.3 85 104-223 107-199 (200)
49 cd06145 REX1_like DEDDh 3'-5' 92.9 0.029 6.3E-07 47.8 -0.1 65 90-168 65-129 (150)
50 TIGR01405 polC_Gram_pos DNA po 92.8 0.1 2.2E-06 58.4 4.0 137 47-221 188-360 (1213)
51 PRK06310 DNA polymerase III su 92.6 0.095 2.1E-06 48.6 2.9 133 47-217 5-175 (250)
52 smart00322 KH K homology RNA-b 92.6 0.061 1.3E-06 38.1 1.3 38 275-312 5-42 (69)
53 PRK08074 bifunctional ATP-depe 91.8 0.2 4.3E-06 54.9 4.7 108 49-168 3-145 (928)
54 PRK02821 hypothetical protein; 91.8 0.028 6.1E-07 42.6 -1.3 46 259-304 17-62 (77)
55 PRK06807 DNA polymerase III su 91.5 0.17 3.7E-06 48.5 3.5 91 90-217 78-173 (313)
56 PRK09146 DNA polymerase III su 91.5 0.28 6E-06 45.2 4.6 141 46-217 44-228 (239)
57 PRK08517 DNA polymerase III su 91.2 0.25 5.4E-06 46.0 4.1 133 47-218 66-233 (257)
58 PRK05601 DNA polymerase III su 90.7 0.26 5.7E-06 48.1 3.8 140 47-212 44-245 (377)
59 PF00013 KH_1: KH domain syndr 90.4 0.011 2.3E-07 42.1 -4.6 35 276-310 3-37 (60)
60 cd05780 DNA_polB_Kod1_like_exo 90.2 0.6 1.3E-05 41.4 5.5 105 89-211 58-194 (195)
61 PRK06309 DNA polymerase III su 90.2 0.34 7.5E-06 44.2 4.0 99 92-225 71-175 (232)
62 cd06136 TREX1_2 DEDDh 3'-5' ex 90.1 0.32 6.9E-06 42.5 3.6 53 103-169 99-158 (177)
63 cd05160 DEDDy_DNA_polB_exo DED 90.1 0.55 1.2E-05 41.4 5.1 102 89-209 65-198 (199)
64 cd06130 DNA_pol_III_epsilon_li 89.8 0.35 7.5E-06 40.6 3.5 67 90-168 67-138 (156)
65 PRK01064 hypothetical protein; 89.8 0.078 1.7E-06 40.3 -0.5 45 259-303 16-60 (78)
66 cd06143 PAN2_exo DEDDh 3'-5' e 89.6 0.044 9.6E-07 48.0 -2.3 64 92-169 93-156 (174)
67 TIGR01407 dinG_rel DnaQ family 88.9 0.38 8.2E-06 52.3 3.7 68 90-169 70-142 (850)
68 PRK09145 DNA polymerase III su 87.1 0.94 2E-05 40.3 4.5 93 90-213 101-198 (202)
69 PRK05168 ribonuclease T; Provi 86.7 0.17 3.7E-06 45.6 -0.5 87 103-224 115-209 (211)
70 PRK07247 DNA polymerase III su 85.3 1 2.2E-05 40.2 3.8 95 90-218 74-171 (195)
71 PF13482 RNase_H_2: RNase_H su 85.2 1.1 2.5E-05 37.9 3.9 146 52-212 1-163 (164)
72 cd02134 NusA_KH NusA_K homolog 82.4 0.31 6.7E-06 35.0 -0.6 34 273-306 25-58 (61)
73 PRK00448 polC DNA polymerase I 82.0 0.72 1.6E-05 52.7 1.7 95 92-222 491-590 (1437)
74 cd05785 DNA_polB_like2_exo Unc 81.5 2.5 5.4E-05 38.0 4.8 144 49-209 9-206 (207)
75 PRK06195 DNA polymerase III su 80.3 0.66 1.4E-05 44.3 0.6 95 90-221 70-169 (309)
76 cd06134 RNaseT DEDDh 3'-5' exo 78.0 0.65 1.4E-05 41.0 -0.2 77 104-215 104-188 (189)
77 PRK12704 phosphodiesterase; Pr 75.5 0.8 1.7E-05 47.0 -0.4 43 268-310 205-248 (520)
78 smart00479 EXOIII exonuclease 75.3 0.75 1.6E-05 38.8 -0.5 92 90-217 70-168 (169)
79 TIGR03319 YmdA_YtgF conserved 74.9 0.82 1.8E-05 46.9 -0.5 43 268-310 199-242 (514)
80 PRK00106 hypothetical protein; 73.1 0.97 2.1E-05 46.4 -0.4 43 268-310 220-263 (535)
81 PF13083 KH_4: KH domain; PDB: 72.4 0.3 6.4E-06 36.3 -3.3 42 262-303 18-59 (73)
82 cd02395 SF1_like-KH Splicing f 70.3 2 4.3E-05 35.4 0.8 30 282-311 15-44 (120)
83 KOG1676 K-homology type RNA bi 68.4 2.7 5.8E-05 43.2 1.5 46 277-322 322-370 (600)
84 KOG1275 PAB-dependent poly(A) 67.2 0.88 1.9E-05 48.8 -2.2 93 97-226 1009-1101(1118)
85 PRK04163 exosome complex RNA-b 64.9 1.5 3.2E-05 40.3 -1.0 36 275-310 147-182 (235)
86 COG1097 RRP4 RNA-binding prote 64.2 2.8 6.1E-05 38.5 0.7 36 275-310 148-183 (239)
87 PRK12705 hypothetical protein; 61.8 2.2 4.9E-05 43.6 -0.5 43 268-310 193-236 (508)
88 PF09281 Taq-exonuc: Taq polym 60.7 2.4 5.2E-05 35.3 -0.4 68 112-216 71-138 (138)
89 cd06127 DEDDh DEDDh 3'-5' exon 59.9 2.6 5.6E-05 34.5 -0.3 49 90-140 69-122 (159)
90 KOG3657 Mitochondrial DNA poly 59.5 5.8 0.00013 42.5 2.0 108 103-218 242-385 (1075)
91 cd02414 jag_KH jag_K homology 55.4 3.5 7.6E-05 30.9 -0.3 29 276-304 27-55 (77)
92 PF10108 DNA_pol_B_exo2: Predi 55.3 9.5 0.00021 34.5 2.5 106 89-214 39-171 (209)
93 cd05781 DNA_polB_B3_exo DEDDy 55.2 29 0.00063 30.5 5.5 144 50-212 4-188 (188)
94 cd05782 DNA_polB_like1_exo Unc 48.1 29 0.00063 31.0 4.5 129 63-210 49-207 (208)
95 TIGR03591 polynuc_phos polyrib 46.7 3.3 7.2E-05 44.0 -2.2 35 276-310 554-588 (684)
96 PRK13763 putative RNA-processi 45.3 5.2 0.00011 35.2 -0.9 28 283-310 105-132 (180)
97 PRK07748 sporulation inhibitor 44.4 6.5 0.00014 35.0 -0.3 93 90-216 82-180 (207)
98 TIGR03665 arCOG04150 arCOG0415 40.6 5.8 0.00013 34.6 -1.3 28 283-310 99-126 (172)
99 TIGR02696 pppGpp_PNP guanosine 40.0 6.8 0.00015 41.7 -1.1 36 275-310 580-615 (719)
100 PRK07983 exodeoxyribonuclease 39.6 12 0.00026 34.0 0.6 79 104-216 76-154 (219)
101 PRK00228 hypothetical protein; 39.5 21 0.00045 31.7 2.1 44 281-325 39-94 (191)
102 PRK08406 transcription elongat 38.9 4.3 9.4E-05 34.3 -2.2 32 275-306 101-132 (140)
103 cd02409 KH-II KH-II (K homolo 36.4 9.2 0.0002 26.8 -0.6 30 276-305 28-57 (68)
104 KOG2190 PolyC-binding proteins 36.2 19 0.00041 36.7 1.4 40 273-312 338-377 (485)
105 PRK08406 transcription elongat 35.6 8.4 0.00018 32.5 -1.0 31 279-309 38-68 (140)
106 KOG2192 PolyC-binding hnRNP-K 29.7 35 0.00076 32.0 1.9 46 277-322 319-365 (390)
107 PF07650 KH_2: KH domain syndr 29.2 4.3 9.3E-05 30.2 -3.5 29 278-306 30-58 (78)
108 COG1094 Predicted RNA-binding 28.4 16 0.00034 32.6 -0.5 29 284-312 113-141 (194)
109 KOG2192 PolyC-binding hnRNP-K 27.1 16 0.00034 34.2 -0.8 37 285-321 135-173 (390)
110 KOG2190 PolyC-binding proteins 26.9 21 0.00045 36.4 -0.1 39 273-311 138-176 (485)
111 PRK06722 exonuclease; Provisio 25.8 26 0.00057 33.1 0.4 69 90-168 80-156 (281)
112 KOG2248 3'-5' exonuclease [Rep 25.1 27 0.00058 34.5 0.3 64 92-168 285-348 (380)
113 KOG0119 Splicing factor 1/bran 25.0 36 0.00078 34.6 1.2 27 284-310 155-181 (554)
114 KOG2193 IGF-II mRNA-binding pr 25.0 63 0.0014 32.3 2.8 43 281-323 206-251 (584)
115 KOG2193 IGF-II mRNA-binding pr 24.9 33 0.00072 34.2 0.9 44 273-316 493-536 (584)
116 KOG1676 K-homology type RNA bi 24.1 31 0.00067 35.7 0.6 36 274-309 231-266 (600)
117 cd02412 30S_S3_KH K homology R 23.7 15 0.00032 29.5 -1.5 26 280-305 68-93 (109)
118 COG5176 MSL5 Splicing factor ( 23.4 27 0.00057 31.6 -0.0 27 284-310 165-191 (269)
119 TIGR01952 nusA_arch NusA famil 22.9 23 0.00049 30.0 -0.6 32 277-308 37-68 (141)
No 1
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=1.2e-37 Score=301.43 Aligned_cols=251 Identities=20% Similarity=0.190 Sum_probs=208.5
Q ss_pred cEEEEeCCCCCCccccCCCcccceEEeeecCccccc-cCCceeEEEeecCCeeEEEecccchHHHHHhccccccccceee
Q 020198 27 PIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITK 105 (329)
Q Consensus 27 ~i~vV~t~~~L~~~~l~~~~~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLed~~i~K 105 (329)
.|.+|+|+++|.+ +++. +.+.+.+|||+|+.+.. +++++|+|||++++++|+||+..+.+ ++.|+++|+|++|.|
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 4789999999997 8887 68889999999999876 77899999999989999999998754 678999999999999
Q ss_pred eeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCc
Q 020198 106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFW 185 (329)
Q Consensus 106 V~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W 185 (329)
|+|++++|+..|++.+|+.+.++||||+|+++++.+. .+||+.|++ ++||++++| ++.+ +||
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 9999999999998889999999999999999998641 368999999 999999984 4332 599
Q ss_pred cccchHHHHHHhhcccceehHHHHHHHHHHhhhhcchheeecceeeeeee--eecCCCCCCCCCCCCCCcccccccccee
Q 020198 186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCF--CINENDYVDWPPLPPVPGVRFIYVDYLI 263 (329)
Q Consensus 186 ~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~~~~~~~~~~r~~--~~~~~~~~~w~~~~~~~~~~~~~~~~l~ 263 (329)
+.||||++|+.|||.||++|+.||+.|.++|.+.|.+.|+.+++...... ...++ ...|+++.+.. .+++++|+
T Consensus 140 ~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~-~~~~~~ik~~~---~L~~~~la 215 (373)
T PRK10829 140 LARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAP-EEAYRDITNAW---QLRTRQLA 215 (373)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHhccccCCCh-HHHHHHhcccc---CCCHHHHH
Confidence 99999999999999999999999999999999999999999887532111 11111 13488865443 34678999
Q ss_pred eccC--CCcccceecccCCCCCc--------------------------ceeecccCceeeeeecccc
Q 020198 264 VEGD--VPEEEILSILDVPPGKM--------------------------GRIIGRRGSSILAIKESCN 303 (329)
Q Consensus 264 ~~~~--~~~~~~~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~ 303 (329)
+.++ .-||++|+..|+||+++ +..++++|..|+++++.+.
T Consensus 216 vl~~L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~~~~~~~~r~~g~~ll~~i~~a~ 283 (373)
T PRK10829 216 CLQLLADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQ 283 (373)
T ss_pred HHHHHHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhccCChHhHHhhHHHHHHHHHHHh
Confidence 9998 88999999999999872 1345567777766666554
No 2
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-36 Score=287.43 Aligned_cols=247 Identities=21% Similarity=0.214 Sum_probs=200.2
Q ss_pred CCCCCCccccCCCcccceEEeeecCccccc-cCCceeEEEeecCCeeEEEecccchHHHHHhccccccccceeeeecccc
Q 020198 33 NASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCK 111 (329)
Q Consensus 33 t~~~L~~~~l~~~~~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLed~~i~KV~hd~k 111 (329)
+.+.++. ++.. ..+.+.|++|+|+.+.. +++++|+|||+.++++++||+.....+ ...|..+|.|++|.||+|.++
T Consensus 3 ~~~~l~~-~~~~-~~~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~~lIdpl~~~~d-~~~l~~Ll~d~~v~KIfHaa~ 79 (361)
T COG0349 3 TGDLLAA-ACAL-LRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEGASLIDPLAGILD-LPPLVALLADPNVVKIFHAAR 79 (361)
T ss_pred chhHHHH-HHHH-hcCCCceEEecccccccccCCceEEEEEecCCCceEecccccccc-cchHHHHhcCCceeeeecccc
Confidence 3444554 6655 46788999999999886 899999999999888999999874222 578888999999999999999
Q ss_pred CccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchH
Q 020198 112 RDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLT 191 (329)
Q Consensus 112 ~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs 191 (329)
+|+.+|++.||+.+.++|||++|+.+++.+. .+||++|++ +++|++++| .+. .+||+.||||
T Consensus 80 ~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~--------~~gl~~Lv~--~ll~v~ldK-~~q-------~SDW~~RPLs 141 (361)
T COG0349 80 FDLEVLLNLFGLLPTPLFDTQIAAKLAGFGT--------SHGLADLVE--ELLGVELDK-SEQ-------RSDWLARPLS 141 (361)
T ss_pred ccHHHHHHhcCCCCCchhHHHHHHHHhCCcc--------cccHHHHHH--HHhCCcccc-ccc-------ccccccCCCC
Confidence 9999999999999999999999999999763 378999999 999999984 443 3599999999
Q ss_pred HHHHHhhcccceehHHHHHHHHHHhhhhcchheeecceeeeeee-eecCCCCCCCCCCCCCCccccccccceeeccC--C
Q 020198 192 ELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCF-CINENDYVDWPPLPPVPGVRFIYVDYLIVEGD--V 268 (329)
Q Consensus 192 ~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~~~~~~~~~~r~~-~~~~~~~~~w~~~~~~~~~~~~~~~~l~~~~~--~ 268 (329)
++|++|||.||.||+.||..|.++|.++|++.|+.++|.+.-.- +.....-..|+.+.. -+..++++|++.++ .
T Consensus 142 ~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~~l~~r~~~~~~~~~~w~~i~~---a~~~~p~~la~l~~La~ 218 (361)
T COG0349 142 EAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFRLLPTRRTYKVLPEDAWREIKI---AHSLDPRELAVLRELAA 218 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHhhhccccccChHhHHHHhhh---hhcCChHHHHHHHHHHH
Confidence 99999999999999999999999999999999999887531111 111122345988665 22346678888887 7
Q ss_pred CcccceecccCCCCC--------------------------cceeecccCceeeeeecccc
Q 020198 269 PEEEILSILDVPPGK--------------------------MGRIIGRRGSSILAIKESCN 303 (329)
Q Consensus 269 ~~~~~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~ 303 (329)
-||++|+.+|+|+++ ++.++.++|..++++.+.+.
T Consensus 219 wRe~~Ar~rd~~~~~vl~de~i~~~a~~~P~~~~~l~~l~~~~~~~~~~~~~l~~~~~~a~ 279 (361)
T COG0349 219 WREREARERDLARNFVLKDEALWELARYTPKNLKELDALGLIPKERRRHGKLLLALLANAL 279 (361)
T ss_pred HHHHHHHHhccccccccchhHHHHHHHhCCCCHHHHHhccCCcccchhhhHHHHHHHHHHH
Confidence 788899999999876 34466778888887775554
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=99.97 E-value=1e-33 Score=274.67 Aligned_cols=229 Identities=21% Similarity=0.214 Sum_probs=189.1
Q ss_pred EEeCCCCCCccccCCCcccceEEeeecCccccc-cCCceeEEEeecCCeeEEEecccchHHHHHhccccccccceeeeec
Q 020198 30 IVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIH 108 (329)
Q Consensus 30 vV~t~~~L~~~~l~~~~~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLed~~i~KV~h 108 (329)
+|+|.++|.+ +++. +...++||||+|+.+.. +++++|+|||++++++|+||+....+ ++.|+++|+|+++.||+|
T Consensus 1 ~I~t~~~l~~-~~~~-l~~~~~ia~DtE~~~~~~y~~~l~LiQia~~~~~~liD~~~~~~--~~~L~~lL~d~~i~KV~h 76 (367)
T TIGR01388 1 WITTDDELAT-VCEA-VRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIID--WSPLKELLRDESVVKVLH 76 (367)
T ss_pred CcCCHHHHHH-HHHH-HhcCCEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCccc--HHHHHHHHCCCCceEEEe
Confidence 3678888886 8877 57789999999999875 78899999999999999999987643 678999999999999999
Q ss_pred cccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCcccc
Q 020198 109 DCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYR 188 (329)
Q Consensus 109 d~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~R 188 (329)
|+|+|+.+|.+.+|+.+.++||||+|+|+++++. ..||+.|++ +|||++++| .+. .++|..|
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 9999999997766777788999999999999752 257999999 999999873 322 3599999
Q ss_pred chHHHHHHhhcccceehHHHHHHHHHHhhhhcchheeecceeeeeee-eecCCCCCCCCCCCCCCccccccccceeeccC
Q 020198 189 PLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCF-CINENDYVDWPPLPPVPGVRFIYVDYLIVEGD 267 (329)
Q Consensus 189 PLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~~~~~~~~~~r~~-~~~~~~~~~w~~~~~~~~~~~~~~~~l~~~~~ 267 (329)
||+++|+.|||.||.+++.||+.|.++|++.|.+.|+.+++...... ....+....|.++.+. +.+++++|++.++
T Consensus 139 PL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~i~~~---~~l~~~~l~~l~~ 215 (367)
T TIGR01388 139 PLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNA---WQLRPQQLAVLQA 215 (367)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHhccccCCCChHHHHHHhccc---ccCCHHHHHHHHH
Confidence 99999999999999999999999999999999999988876532111 1111112338875543 3356789999998
Q ss_pred --CCcccceecccCCCCC
Q 020198 268 --VPEEEILSILDVPPGK 283 (329)
Q Consensus 268 --~~~~~~~~~~~~~~~~ 283 (329)
.=||++|+.+|+|+++
T Consensus 216 L~~wRe~~A~~~d~p~~~ 233 (367)
T TIGR01388 216 LAAWREREARERDLPRNF 233 (367)
T ss_pred HHHHHHHHHHHcCCCcce
Confidence 7899999999999987
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=99.96 E-value=5e-30 Score=229.00 Aligned_cols=178 Identities=49% Similarity=0.751 Sum_probs=147.4
Q ss_pred cccceEEeeecCccccccCCceeEEEeecC-CeeEEEecccchH-HHHHhccccccccceeeeeccccCccchhheecce
Q 020198 46 SERQLVIGFDCEGVDLCRHGSLCIMQLAFP-DAIYLVDAIQGGE-TVVKACKPALESSYITKVIHDCKRDSEALYFQFGI 123 (329)
Q Consensus 46 ~~~~~~Ia~D~E~~~~~~~g~l~llQLa~~-~~~~liD~~~l~~-~~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi 123 (329)
+.++..||||+|+.+.+++|++|+|||++. +++|+||+..++. .+...|+++|+++++.||+||+|+|+..|++.+|+
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 466899999999998877899999999998 9999999998763 35688999999999999999999999999778999
Q ss_pred eecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccce
Q 020198 124 KLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVR 203 (329)
Q Consensus 124 ~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~ 203 (329)
.+.++|||++|+|++++..+.........||+.+++ +|||++++++......++...++|..|||+++|+.|||.||+
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 999999999999999987531111112468999999 999999864333222223345799999999999999999999
Q ss_pred ehHHHHHHHHHHhhhhcchhee
Q 020198 204 FLPYIYHNMMKKLNQQSLWYLA 225 (329)
Q Consensus 204 ~Ll~L~~~L~~~L~~~g~~~~~ 225 (329)
+|+.||+.|...|.+......+
T Consensus 165 ~Ll~l~~~l~~~l~~~~~~~~~ 186 (197)
T cd06148 165 CLLPLYYAMLDALISKFLKAVF 186 (197)
T ss_pred hHHHHHHHHHHHhhhhHHHHHH
Confidence 9999999999999986444333
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=99.95 E-value=8.1e-29 Score=220.55 Aligned_cols=175 Identities=26% Similarity=0.308 Sum_probs=144.3
Q ss_pred EEEEeCCCCCCccccCCC-cccceEEeeecCccccc---cCCceeEEEeecCCeeEEEecccch----HHHHHhcccccc
Q 020198 28 IHIVTNASQLPAEFLEPS-SERQLVIGFDCEGVDLC---RHGSLCIMQLAFPDAIYLVDAIQGG----ETVVKACKPALE 99 (329)
Q Consensus 28 i~vV~t~~~L~~~~l~~~-~~~~~~Ia~D~E~~~~~---~~g~l~llQLa~~~~~~liD~~~l~----~~~~~~L~~lLe 99 (329)
|++|+|++++.+ ++..+ +....+||||+||.+.. ..+++|+|||++++.+|+||+..++ +.+...|+++|+
T Consensus 1 ~~~i~~~~el~~-~~~~~~l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~ll~ 79 (193)
T cd06146 1 IHIVDSEEELEA-LLLALSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKRLFE 79 (193)
T ss_pred CeEecCHHHHHH-HHHHHhhccCCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHHHhC
Confidence 578999999997 77653 46789999999998664 2689999999999999999998775 245678999999
Q ss_pred ccceeeeeccccCccchhheeccee------ecccchhHHHHHHHHhHhc-CC--CCCCCeeeeeecccCCcccCCccch
Q 020198 100 SSYITKVIHDCKRDSEALYFQFGIK------LHNVVDTQIAYSLIEEQEG-RK--RSPDDYISFVGLLADPRYCGISYQE 170 (329)
Q Consensus 100 d~~i~KV~hd~k~Dl~~L~~~~Gi~------l~~vfDt~lA~~LL~~~~~-~~--~l~~~~~sL~~L~~~~~~Lg~~l~~ 170 (329)
|++|.||||++++|+..|++.+|+. +.+++||+.+++.+..... +. .......||++|++ ++||.+++|
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 9999999999999999999889874 5789999998887764311 00 00113579999999 999999974
Q ss_pred hHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHH
Q 020198 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (329)
Q Consensus 171 k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~ 213 (329)
... -+||..||||++|+.|||.||++++.||+.|.
T Consensus 158 -~~q-------~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 158 -SEQ-------CSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred -ccc-------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 332 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=99.94 E-value=7e-29 Score=214.66 Aligned_cols=153 Identities=31% Similarity=0.342 Sum_probs=133.1
Q ss_pred ccCCCcc-cceEEeeecCccccc-cCCceeEEEeecC-CeeEEEecccchHHHHHhccccccccceeeeeccccCccchh
Q 020198 41 FLEPSSE-RQLVIGFDCEGVDLC-RHGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEAL 117 (329)
Q Consensus 41 ~l~~~~~-~~~~Ia~D~E~~~~~-~~g~l~llQLa~~-~~~~liD~~~l~~~~~~~L~~lLed~~i~KV~hd~k~Dl~~L 117 (329)
+++. +. ..++||||+||.+.. +.+++|+|||+++ +.+|+||+..++. .+..|+++|+|+++.||+|+++.|+..|
T Consensus 5 ~~~~-l~~~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~-~~~~L~~lL~d~~i~Kvg~~~k~D~~~L 82 (161)
T cd06129 5 LCED-LSMDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSV-DWQGLKMLLENPSIVKALHGIEGDLWKL 82 (161)
T ss_pred HHHH-HhcCCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCcc-CHHHHHHHhCCCCEEEEEeccHHHHHHH
Confidence 4544 34 789999999999876 5789999999998 9999999987753 3677899999999999999999999999
Q ss_pred heecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchHHHHHHh
Q 020198 118 YFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRA 197 (329)
Q Consensus 118 ~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~Y 197 (329)
.+.+|+.+.++|||++++|++++.. ..||+.+++ +|||..++| ... .++|..|||+++|+.|
T Consensus 83 ~~~~gi~~~~~~D~~~aa~ll~~~~--------~~~L~~l~~--~~lg~~l~K-~~~-------~s~W~~rpLt~~qi~Y 144 (161)
T cd06129 83 LRDFGEKLQRLFDTTIAANLKGLPE--------RWSLASLVE--HFLGKTLDK-SIS-------CADWSYRPLTEDQKLY 144 (161)
T ss_pred HHHcCCCcccHhHHHHHHHHhCCCC--------CchHHHHHH--HHhCCCCCc-cce-------eccCCCCCCCHHHHHH
Confidence 7679999999999999999998742 258999999 999999974 332 3599999999999999
Q ss_pred hcccceehHHHHHHHH
Q 020198 198 AADDVRFLPYIYHNMM 213 (329)
Q Consensus 198 AA~Da~~Ll~L~~~L~ 213 (329)
||.||++++.||+.|+
T Consensus 145 Aa~Da~~l~~l~~~l~ 160 (161)
T cd06129 145 AAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999999985
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=99.92 E-value=6.9e-27 Score=203.26 Aligned_cols=163 Identities=23% Similarity=0.292 Sum_probs=136.1
Q ss_pred CCCCCCccccCCCcc-cceEEeeecCccccc---cCCceeEEEeecCCeeEEEecccchHHHHHhccccccccceeeeec
Q 020198 33 NASQLPAEFLEPSSE-RQLVIGFDCEGVDLC---RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIH 108 (329)
Q Consensus 33 t~~~L~~~~l~~~~~-~~~~Ia~D~E~~~~~---~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLed~~i~KV~h 108 (329)
+.+++.. +++. +. +...||||+||.+.. +.+++++|||++++.+|+||+..+. .+...|+++|+++++.||+|
T Consensus 3 ~~~~~~~-~~~~-~~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~-~~~~~l~~ll~~~~i~kv~~ 79 (170)
T cd06141 3 SAQDAEE-AVKE-LLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMD-KLPPSLKQLLEDPSILKVGV 79 (170)
T ss_pred CHHHHHH-HHHH-HhcCCCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhh-cccHHHHHHhcCCCeeEEEe
Confidence 3344554 5555 34 789999999998764 4689999999999999999998763 34677899999999999999
Q ss_pred cccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCcccc
Q 020198 109 DCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYR 188 (329)
Q Consensus 109 d~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~R 188 (329)
|+++|+..|.+.+|+.+.++|||++++|++++... ..||++|++ +++|.++++.+.. ..++|..|
T Consensus 80 ~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~-------~~~l~~l~~--~~l~~~~~k~k~~------~~s~W~~r 144 (170)
T cd06141 80 GIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRK-------LVSLARLVE--EVLGLPLSKPKKV------RCSNWEAR 144 (170)
T ss_pred eeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcC-------CccHHHHHH--HHcCcccCCCCCc------ccCCCCCC
Confidence 99999999977899999999999999999997531 247999999 9999988731111 13699999
Q ss_pred chHHHHHHhhcccceehHHHHHHHH
Q 020198 189 PLTELMVRAAADDVRFLPYIYHNMM 213 (329)
Q Consensus 189 PLs~~ql~YAA~Da~~Ll~L~~~L~ 213 (329)
||+++|+.|||.||++++.||+.|.
T Consensus 145 pLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 145 PLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999885
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=99.91 E-value=1.5e-26 Score=200.28 Aligned_cols=170 Identities=32% Similarity=0.470 Sum_probs=143.5
Q ss_pred EEEEeCCCCCCccccCCCcccceEEeeecCcccccc---CCceeEEEeecCCeeEEEecccchHH-HHHhccccccccce
Q 020198 28 IHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCR---HGSLCIMQLAFPDAIYLVDAIQGGET-VVKACKPALESSYI 103 (329)
Q Consensus 28 i~vV~t~~~L~~~~l~~~~~~~~~Ia~D~E~~~~~~---~g~l~llQLa~~~~~~liD~~~l~~~-~~~~L~~lLed~~i 103 (329)
|++|+|.+++.+ +++. +...+.+|||+|+.+... ..+++++|+++++.+|++++...+.. +...|+++|+|+++
T Consensus 1 y~~v~~~~~l~~-~~~~-l~~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i 78 (176)
T PF01612_consen 1 YQIVDTEEELEE-AIKK-LKNAKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPNI 78 (176)
T ss_dssp SEEEHSHHHHHH-HHHH-HTTTSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTTS
T ss_pred CEecCCHHHHHH-HHHH-HcCCCeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCCc
Confidence 578999999997 8876 567789999999988753 56899999999999999998876643 57889999999999
Q ss_pred eeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccC-CccchhHHHHHHHhcCC
Q 020198 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCG-ISYQEKEEVRVLLRQDP 182 (329)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg-~~l~~k~~~~~l~~~~~ 182 (329)
.||+||+++|+.+|++.+|+.+.+++||+++++++++... .||++|+. +|+| ..++ ++. ..
T Consensus 79 ~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~--------~~L~~L~~--~~l~~~~~~-~~~-------~~ 140 (176)
T PF01612_consen 79 IKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRS--------YSLKDLAE--EYLGNIDLD-KKE-------QM 140 (176)
T ss_dssp EEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTT--------SSHHHHHH--HHHSEEE-G-HCC-------TT
T ss_pred cEEEEEEechHHHHHHHhccccCCccchhhhhhccccccc--------ccHHHHHH--HHhhhccCc-HHH-------hh
Confidence 9999999999999987799999999999999999998642 57999999 9999 4443 222 23
Q ss_pred CCcc-ccchHHHHHHhhcccceehHHHHHHHHHHhh
Q 020198 183 QFWT-YRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (329)
Q Consensus 183 ~~W~-~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (329)
++|. .+||+++|+.|||.||.++++||+.|.++|+
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 8999999999999999999999999999885
No 9
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.86 E-value=8.6e-23 Score=200.80 Aligned_cols=185 Identities=27% Similarity=0.361 Sum_probs=162.6
Q ss_pred ccccCCCCCCCCCCCCcccEEEEeCCCCCCccccCCCcccceEEeeecCccccc-cCCceeEEEeecCCeeEEEecccch
Q 020198 9 THIPLSSDPDGKPIDSVVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGG 87 (329)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~i~vV~t~~~L~~~~l~~~~~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~ 87 (329)
...|.++.|++++ ++.+|.+..+|.+ +.+. +.....+|+|+|..+.. +.|-.|+|||++....|+||.+.+.
T Consensus 179 ~~~~~~~~~le~T-----~~~~I~t~~el~~-l~~~-l~~~~Efavdlehhsyrsf~gltclmqISTr~ed~iIDt~~l~ 251 (687)
T KOG2206|consen 179 EGEPRKSSPLEIT-----PKVWICTLGELEA-LPEI-LDSVIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKLR 251 (687)
T ss_pred cccccCCCccccc-----CceeeechHHHHH-HHHH-HhhhhhhhhhccccchhhhcCceeEEEeeccchhheehhHHHH
Confidence 3456777888887 6888999998886 7665 56678899999999886 7899999999999889999999887
Q ss_pred HHHHHhccccccccceeeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCc
Q 020198 88 ETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGIS 167 (329)
Q Consensus 88 ~~~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~ 167 (329)
+. +..|+++|.+|.+.||+|++..|+.||++.|||.+.|+|||..|+++|+.+ +.||+.|.+ .|+|+.
T Consensus 252 ~~-i~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvnLfdt~~a~r~L~~~---------r~sL~~ll~--~~~~v~ 319 (687)
T KOG2206|consen 252 DH-IGILNEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVNLFDTIQASRLLGLP---------RPSLAYLLE--CVCGVL 319 (687)
T ss_pred HH-HHHhhhhccCCCeEEEEecCccchhhhhccceEEEEechhhHHHHHHhCCC---------cccHHHHHH--HHHhhh
Confidence 54 569999999999999999999999999999999999999999999999976 367999999 999998
Q ss_pred cchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhc
Q 020198 168 YQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (329)
Q Consensus 168 l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g 220 (329)
.+++.+. .+|..|||+++|+.||-.|+++++.||+.|+..|.+.+
T Consensus 320 ~nk~yql--------adwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a 364 (687)
T KOG2206|consen 320 TNKKYQL--------ADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLA 364 (687)
T ss_pred hhhhhhh--------chhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHh
Confidence 8754443 39999999999999999999999999999998887755
No 10
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.80 E-value=1.8e-20 Score=163.19 Aligned_cols=163 Identities=29% Similarity=0.406 Sum_probs=134.1
Q ss_pred cceEEeeecCccccc-cCCceeEEEeecCCeeEEEecccchHHHHHhccccccccceeeeeccccCccchhheecceeec
Q 020198 48 RQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLH 126 (329)
Q Consensus 48 ~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~ 126 (329)
....+++|+|+.+.. ..++++++|+++++++|+||+... .....|+++|+|+.+.||+||+|.|...|.+.+|+..+
T Consensus 11 ~~~~l~~~~e~~~~~~~~~~~~~i~l~~~~~~~~i~~~~~--~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~ 88 (178)
T cd06142 11 SAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI--GDLSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQ 88 (178)
T ss_pred cCCeEEEECCccCCCcCCCceEEEEEeeCCCEEEEeCCCc--ccHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCC
Confidence 345899999876554 368899999998855899875432 24566889999999999999999999999765699855
Q ss_pred ccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehH
Q 020198 127 NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLP 206 (329)
Q Consensus 127 ~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll 206 (329)
++|||++|+|++++..+ .+|+++++ +|++..+.+ .+. .++|..+|++..|..||+.||.+++
T Consensus 89 ~~~D~~laayLl~p~~~--------~~l~~l~~--~~l~~~~~~-~~~-------~~~w~~~~l~~~~~~yaa~~a~~l~ 150 (178)
T cd06142 89 NLFDTQIAARLLGLGDS--------VGLAALVE--ELLGVELDK-GEQ-------RSDWSKRPLTDEQLEYAALDVRYLL 150 (178)
T ss_pred CcccHHHHHHHhCCCcc--------ccHHHHHH--HHhCCCCCc-ccc-------cccCCCCCCCHHHHHHHHHhHHHHH
Confidence 68999999999998531 37999999 999987542 222 1379889999999999999999999
Q ss_pred HHHHHHHHHhhhhcchheeeccee
Q 020198 207 YIYHNMMKKLNQQSLWYLAVRGAL 230 (329)
Q Consensus 207 ~L~~~L~~~L~~~g~~~~~~~~~~ 230 (329)
+|++.|.++|++.|+++++.+++.
T Consensus 151 ~L~~~l~~~L~e~~l~~L~~~~~~ 174 (178)
T cd06142 151 PLYEKLKEELEEEGRLEWAEEECE 174 (178)
T ss_pred HHHHHHHHHHHHcCcHHHHHHHHH
Confidence 999999999999999999887653
No 11
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.71 E-value=1.9e-18 Score=148.31 Aligned_cols=168 Identities=29% Similarity=0.436 Sum_probs=128.3
Q ss_pred EEEeCCCCCCccccCCCcc-cceEEeeecCccccc-cCCceeEEEeecCC-eeEEEecccchHHHHHhccccccccceee
Q 020198 29 HIVTNASQLPAEFLEPSSE-RQLVIGFDCEGVDLC-RHGSLCIMQLAFPD-AIYLVDAIQGGETVVKACKPALESSYITK 105 (329)
Q Consensus 29 ~vV~t~~~L~~~~l~~~~~-~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~-~~~liD~~~l~~~~~~~L~~lLed~~i~K 105 (329)
.+|++.+++.. +++. +. ....+++|+|+.+.. ..++++++|++.++ .+|+++.... ...+..|+++|+++.+.|
T Consensus 2 ~~i~~~~~~~~-~~~~-~~~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~-~~~~~~l~~~l~~~~~~k 78 (172)
T smart00474 2 RVVTDSETLEE-LLEK-LRAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLAL-GDDLEILKDLLEDETITK 78 (172)
T ss_pred EEecCHHHHHH-HHHH-HHhcCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccc-hhhHHHHHHHhcCCCceE
Confidence 45666666664 5543 23 346899999886654 36789999999643 5666544322 223566889999999999
Q ss_pred eeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCc
Q 020198 106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFW 185 (329)
Q Consensus 106 V~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W 185 (329)
|+||+|.|...|.+ +|+.+.++|||++|+|++++..+. .+|+.+++ +|++..+++. . + ..+|
T Consensus 79 v~~d~k~~~~~L~~-~gi~~~~~~D~~laayll~p~~~~-------~~l~~l~~--~~l~~~~~~~-~-----~--~~~~ 140 (172)
T smart00474 79 VGHNAKFDLHVLAR-FGIELENIFDTMLAAYLLLGGPSK-------HGLATLLK--EYLGVELDKE-E-----Q--KSDW 140 (172)
T ss_pred EEechHHHHHHHHH-CCCcccchhHHHHHHHHHcCCCCc-------CCHHHHHH--HHhCCCCCcc-c-----C--cccc
Confidence 99999999999964 999998899999999999986421 37899998 8998776421 1 1 1378
Q ss_pred cccchHHHHHHhhcccceehHHHHHHHHHHhh
Q 020198 186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (329)
Q Consensus 186 ~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (329)
..+|+...|..||+.||.++++|++.|.++|.
T Consensus 141 ~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l~ 172 (172)
T smart00474 141 GARPLSEEQLQYAAEDADALLRLYEKLEKELE 172 (172)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 77888999999999999999999999998873
No 12
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=99.68 E-value=9.6e-18 Score=148.84 Aligned_cols=173 Identities=26% Similarity=0.400 Sum_probs=131.8
Q ss_pred cccEEEEeCCCCCCccccCCCcccceEEeeecCccccc-cCCceeEEEeecCCeeEEEecccchHHHHHhccccccccce
Q 020198 25 VVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYI 103 (329)
Q Consensus 25 ~~~i~vV~t~~~L~~~~l~~~~~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLed~~i 103 (329)
+.+|.++++.+++.. +++. +...+.+++++|+.+.. ..++++++|++.++++|+|++.... .....|+++|+++.+
T Consensus 2 ~~~~~~i~~~~~l~~-~~~~-l~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~l~~~-~~~~~L~~~L~~~~i 78 (192)
T cd06147 2 ETPLTFVDTEEKLEE-LVEK-LKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLR-DDMHILNEVFTDPNI 78 (192)
T ss_pred CCCcEEECCHHHHHH-HHHH-HhcCCeEEEEeEecCCccCCCceEEEEEecCCCcEEEEecccc-cchHHHHHHhcCCCc
Confidence 357888855565664 5543 23345889999764433 3678999999987668888642221 224568889999999
Q ss_pred eeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCC
Q 020198 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQ 183 (329)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~ 183 (329)
.||+||+|.++..|.+.+|+.+.++|||++|+||+++. + .+|+.+++ +||+..++ |.+. .+
T Consensus 79 ~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~-~--------~~l~~l~~--~yl~~~~~-k~~~-------~~ 139 (192)
T cd06147 79 LKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-R--------HSLAYLLQ--KYCNVDAD-KKYQ-------LA 139 (192)
T ss_pred eEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCC-c--------ccHHHHHH--HHhCCCcc-hhhh-------cc
Confidence 99999999999999536899988779999999999986 3 25899999 99987653 3111 23
Q ss_pred CccccchHHHHHHhhcccceehHHHHHHHHHHhhhh
Q 020198 184 FWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ 219 (329)
Q Consensus 184 ~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~ 219 (329)
+|..+||..+|..|++.++.++++|++.|.++|+++
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 588788888899999999999999999999999874
No 13
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.63 E-value=3.4e-16 Score=131.90 Aligned_cols=153 Identities=29% Similarity=0.306 Sum_probs=112.1
Q ss_pred EEeeecCccccc-cCCceeEEEeecCCeeEEEecccchHHHHHhccccccccceeeeeccccCccchhheecceeecccc
Q 020198 51 VIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVV 129 (329)
Q Consensus 51 ~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vf 129 (329)
.+++|+|+.+.. ..++++++|++++++++++........+.+.|+++|+++.+.||+||+|+|...|.+.++....++|
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~ 81 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIF 81 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcc
Confidence 478899876554 4678999999986435555322212345677889999999999999999999999654333345689
Q ss_pred hhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHH
Q 020198 130 DTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (329)
Q Consensus 130 Dt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~ 209 (329)
||++++|++++...+ .+|+++++ +|++..+.+.++.. +... .|..+|++..+..||+.|+.++++|+
T Consensus 82 D~~~~ayll~~~~~~-------~~l~~l~~--~~l~~~~~~~~~~~---~~~~-~~~~~~~~~~~~~y~~~da~~~~~l~ 148 (155)
T cd00007 82 DTMLAAYLLNPGEGS-------HSLDDLAK--EYLGIELDKDEQIY---GKGA-KTFARPLSEELLEYAAEDADALLRLY 148 (155)
T ss_pred cHHHHHHHhCCCCCc-------CCHHHHHH--HHcCCCCccHHHHh---cCCC-CccccCCHHHHHHHHHHhHHHHHHHH
Confidence 999999999986421 37999999 99998754222221 1111 13357889999999999999999999
Q ss_pred HHHHHHh
Q 020198 210 HNMMKKL 216 (329)
Q Consensus 210 ~~L~~~L 216 (329)
+.|.+++
T Consensus 149 ~~l~~~~ 155 (155)
T cd00007 149 EKLLEEL 155 (155)
T ss_pred HHHHhhC
Confidence 9998764
No 14
>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=99.60 E-value=3.5e-16 Score=132.08 Aligned_cols=145 Identities=26% Similarity=0.327 Sum_probs=110.1
Q ss_pred EeeecCccccc-cCCceeEEEeecC-CeeEEEecccchHHHHHhccccccccceeeeeccccCccchhheecceeec-cc
Q 020198 52 IGFDCEGVDLC-RHGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLH-NV 128 (329)
Q Consensus 52 Ia~D~E~~~~~-~~g~l~llQLa~~-~~~~liD~~~l~~~~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~-~v 128 (329)
+++|+|+.+.. ..++++++|++.+ +++|++++... .-....|+++|+|+++.||+||+|.|+..|. ..|+... ++
T Consensus 2 ~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~-~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L~-~~~~~~~~~~ 79 (150)
T cd09018 2 FAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHD-YLALELLKPLLEDEKALKVGQNLKYDRGILL-NYFIELRGIA 79 (150)
T ss_pred EEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCc-ccCHHHHHHHhcCCCCceeeecHHHHHHHHH-HcCCccCCcc
Confidence 67888765543 3678999999986 44888874421 1014568889999999999999999999995 4676665 57
Q ss_pred chhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHH
Q 020198 129 VDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYI 208 (329)
Q Consensus 129 fDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L 208 (329)
|||++|+||+++.+++ .+|+.|++ +||+..+.+.++.. + ++|..++++.+|..||+.|+.++.+|
T Consensus 80 ~D~~laayLl~p~~~~-------~~l~~l~~--~~l~~~~~~~~~~~---~---~~~~~~~~~~~~~~ya~~~a~~l~~L 144 (150)
T cd09018 80 FDTMLEAYILNSVAGR-------WDMDSLVE--RWLGHKLIKFESIA---G---KLWFNQPLTEEQGRYAAEDADVTLQI 144 (150)
T ss_pred hhHHHHHHHhCCCCCC-------CCHHHHHH--HHhCCCcccHHHhc---C---CCCcccCCHHHHHHHHHHHHHHHHHH
Confidence 9999999999986311 36899999 99998754323321 1 14856788999999999999999999
Q ss_pred HHHHH
Q 020198 209 YHNMM 213 (329)
Q Consensus 209 ~~~L~ 213 (329)
++.|.
T Consensus 145 ~~~l~ 149 (150)
T cd09018 145 HLKLW 149 (150)
T ss_pred HHHhc
Confidence 98874
No 15
>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=99.60 E-value=5.1e-16 Score=135.54 Aligned_cols=162 Identities=22% Similarity=0.222 Sum_probs=122.7
Q ss_pred eEEeeecCccccc-cCCceeEEEeecCCeeEEEecccchHHHHHhccccccccceeeeeccccCccchhheecceeecc-
Q 020198 50 LVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHN- 127 (329)
Q Consensus 50 ~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~- 127 (329)
..+++++|..+.. ..+++++++++.++++|+|++... ......++++|+++++.|++||+|.|++.|. .+|+.+.+
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~~i~l~~~~~~~~i~~~~~-~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~~~~~ 81 (178)
T cd06140 4 DEVALYVELLGENYHTADIIGLALANGGGAYYIPLELA-LLDLAALKEWLEDEKIPKVGHDAKRAYVALK-RHGIELAGV 81 (178)
T ss_pred CceEEEEEEcCCCcceeeEEEEEEEeCCcEEEEeccch-HHHHHHHHHHHhCCCCceeccchhHHHHHHH-HCCCcCCCc
Confidence 4567777776654 467899999998767888864321 0134568889999999999999999999995 58998865
Q ss_pred cchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHH
Q 020198 128 VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPY 207 (329)
Q Consensus 128 vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~ 207 (329)
+|||++|+||+++..++ .++++++. +|++.++.+.++. +++. .++ .++....+..|++.|+.++++
T Consensus 82 ~fDt~laaYLL~p~~~~-------~~l~~l~~--~yl~~~~~~~~~~---~~~~-~~~-~~~~~~~~~~y~~~~a~~l~~ 147 (178)
T cd06140 82 AFDTMLAAYLLDPTRSS-------YDLADLAK--RYLGRELPSDEEV---YGKG-AKF-AVPDEEVLAEHLARKAAAIAR 147 (178)
T ss_pred chhHHHHHHHcCCCCCC-------CCHHHHHH--HHcCCCCcchHHh---cCCC-CCc-ccCCHHHHHHHHHHHHHHHHH
Confidence 79999999999997432 36899999 9999876432322 1221 113 244467788999999999999
Q ss_pred HHHHHHHHhhhhcchheeec
Q 020198 208 IYHNMMKKLNQQSLWYLAVR 227 (329)
Q Consensus 208 L~~~L~~~L~~~g~~~~~~~ 227 (329)
|++.|.++|++++++.++.+
T Consensus 148 l~~~l~~~L~~~~l~~L~~~ 167 (178)
T cd06140 148 LAPKLEEELEENEQLELYYE 167 (178)
T ss_pred HHHHHHHHHHHhHHHHHHHH
Confidence 99999999999888887653
No 16
>PRK05755 DNA polymerase I; Provisional
Probab=99.59 E-value=4.5e-16 Score=166.76 Aligned_cols=182 Identities=25% Similarity=0.239 Sum_probs=143.8
Q ss_pred ccEEEEeCCCCCCccccCCCcccceEEeeecCccccc-cCCceeEEEeecCCe-eEEEecccchHHHHHhccccccccce
Q 020198 26 VPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDA-IYLVDAIQGGETVVKACKPALESSYI 103 (329)
Q Consensus 26 ~~i~vV~t~~~L~~~~l~~~~~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~-~~liD~~~l~~~~~~~L~~lLed~~i 103 (329)
+.|.+|++++++.. +++. +.....++||+|+.++. +.++++++|++..++ +++|++..+....+..|.++|+++.+
T Consensus 294 ~~~~~I~~~~~L~~-~l~~-l~~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~v 371 (880)
T PRK05755 294 EDYETILDEEELEA-WLAK-LKAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPAI 371 (880)
T ss_pred CceEEeCCHHHHHH-HHHH-hhccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCCC
Confidence 46778888888886 8876 45678899999999876 688999999998655 88887644332356788999999999
Q ss_pred eeeeccccCccchhheecceee-cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCC
Q 020198 104 TKVIHDCKRDSEALYFQFGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDP 182 (329)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~~Gi~l-~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~ 182 (329)
.||+||+++|+..|. .+|+.+ .++|||++|+|+++++. ..||+.+++ +|+|.++...+.. +++ .
T Consensus 372 ~kV~HNakfDl~~L~-~~gi~~~~~~~DT~iAa~Ll~~~~--------~~~L~~L~~--~ylg~~~~~~~~~---~gk-~ 436 (880)
T PRK05755 372 KKVGQNLKYDLHVLA-RYGIELRGIAFDTMLASYLLDPGR--------RHGLDSLAE--RYLGHKTISFEEV---AGK-Q 436 (880)
T ss_pred cEEEeccHhHHHHHH-hCCCCcCCCcccHHHHHHHcCCCC--------CCCHHHHHH--HHhCCCccchHHh---cCC-C
Confidence 999999999999996 479887 45999999999999863 157999999 9999875322221 222 3
Q ss_pred CCccccchHHHHHHhhcccceehHHHHHHHHHHhhhh-cchhee
Q 020198 183 QFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ-SLWYLA 225 (329)
Q Consensus 183 ~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~-g~~~~~ 225 (329)
.+|+.+|+ +.+..||+.||.++++||..|.++|.+. +.+.++
T Consensus 437 ~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l~~l~ 479 (880)
T PRK05755 437 LTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEPGLLELY 479 (880)
T ss_pred CCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHH
Confidence 46777787 4789999999999999999999999876 555444
No 17
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=99.50 E-value=2.1e-14 Score=126.31 Aligned_cols=168 Identities=27% Similarity=0.299 Sum_probs=123.1
Q ss_pred ccceEEeeecCccccc-cCCceeEEEeecCCe-eEEEeccc-------chHHHHHhccccccccceeeeeccccCccchh
Q 020198 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDA-IYLVDAIQ-------GGETVVKACKPALESSYITKVIHDCKRDSEAL 117 (329)
Q Consensus 47 ~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~~-~~liD~~~-------l~~~~~~~L~~lLed~~i~KV~hd~k~Dl~~L 117 (329)
.+...+++|+|..+.. +.++++.++++..++ .++++... ....++..|+.+|++..+.+|+||+|+|+..|
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 3567899999887665 467899999997643 66664322 11234566888999888889999999999999
Q ss_pred heecceeecc-cchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchHHHHHH
Q 020198 118 YFQFGIKLHN-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVR 196 (329)
Q Consensus 118 ~~~~Gi~l~~-vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~ 196 (329)
. .+|+.+.+ ++||++++|++++...+ .+|+.+++ +|++......++.... +....+|...|+ ..+..
T Consensus 83 ~-~~gi~~~~~~~Dt~l~a~ll~p~~~~-------~~l~~l~~--~~l~~~~~~~~~~~~k-~~~~~~~~~~~~-~~~~~ 150 (193)
T cd06139 83 A-NHGIELRGPAFDTMLASYLLNPGRRR-------HGLDDLAE--RYLGHKTISFEDLVGK-GKKQITFDQVPL-EKAAE 150 (193)
T ss_pred H-HCCCCCCCCcccHHHHHHHhCCCCCC-------CCHHHHHH--HHhCCCCccHHHHcCC-CcCcCCccccCH-HHHHH
Confidence 5 58888754 89999999999986412 47899999 8988663211221110 111234555555 66889
Q ss_pred hhcccceehHHHHHHHHHHhhh-hcchheee
Q 020198 197 AAADDVRFLPYIYHNMMKKLNQ-QSLWYLAV 226 (329)
Q Consensus 197 YAA~Da~~Ll~L~~~L~~~L~~-~g~~~~~~ 226 (329)
||+.|+.++++|++.|.++|++ .++++++.
T Consensus 151 ya~~d~~~~~~l~~~l~~~l~~~~~~~~l~~ 181 (193)
T cd06139 151 YAAEDADITLRLYELLKPKLKEEPGLLELYE 181 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhHHHHHH
Confidence 9999999999999999999998 77777765
No 18
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.43 E-value=4.6e-14 Score=144.23 Aligned_cols=153 Identities=20% Similarity=0.179 Sum_probs=122.5
Q ss_pred cEEEEeCCCCCCccccCCCcccceEEeeecCccccccCCceeEEEeecCCeeEEEecccchHHHHHhccccccccceeee
Q 020198 27 PIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKV 106 (329)
Q Consensus 27 ~i~vV~t~~~L~~~~l~~~~~~~~~Ia~D~E~~~~~~~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLed~~i~KV 106 (329)
.+.+|++.+++.. ++.. +...+.+++|+|+..... .+|++|++.++..|+||+... +.+
T Consensus 2 ~~~~I~~~~~l~~-~~~~-l~~~~~~a~DtEf~r~~t--~l~liQ~~~~~~~~liDpl~~----l~~------------- 60 (553)
T PRK14975 2 DMKVILAPEELGA-ALER-LSPAGVVAGDTETTGDDA--AAAAAQEGEEEPRWVWASTAA----LYP------------- 60 (553)
T ss_pred CceEEeccchhHH-HHHH-hccCCceeCCccccCCcc--hhheeeecCCCceEEECchHH----hHH-------------
Confidence 4678999999996 8877 578899999999886433 899999999899999998631 121
Q ss_pred eccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCcc
Q 020198 107 IHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWT 186 (329)
Q Consensus 107 ~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~ 186 (329)
.|. .+|+.+.++||||+|+|+|++..+.. ..|++.+++ +|+++.+++.++ + ++|.
T Consensus 61 ---------~L~-~~Gv~~~~~fDT~LAa~lL~~~~~~~-----~~~l~~la~--~~l~~~l~k~~~-~-------sdw~ 115 (553)
T PRK14975 61 ---------RLL-AAGVRVERCHDLMLASQLLLGSEGRA-----GSSLSAAAA--RALGEGLDKPPQ-T-------SALS 115 (553)
T ss_pred ---------HHH-HCCCccCCCchHHHHHHHcCCCCCcC-----CCCHHHHHH--HHhCCCCCChhh-h-------cccc
Confidence 143 46888888999999999999864211 257999999 999999874332 2 4896
Q ss_pred ccchHHHHHHhhcccceehHHHHHHHHHHhhhh------cchheee
Q 020198 187 YRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ------SLWYLAV 226 (329)
Q Consensus 187 ~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~------g~~~~~~ 226 (329)
||+++.|+.||+.||.+++.||+.|.++|++. |++.++.
T Consensus 116 -rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~~~~~~~g~l~ll~ 160 (553)
T PRK14975 116 -DPPDEEQLLYAAADADVLLELYAVLADQLNRIAAAAHPGRLRLLA 160 (553)
T ss_pred -ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhhhcccchhHHHHHH
Confidence 99999999999999999999999999999876 6666544
No 19
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.37 E-value=7.9e-14 Score=138.70 Aligned_cols=181 Identities=22% Similarity=0.257 Sum_probs=131.0
Q ss_pred ccEEEEeCCCCCCcccc-CCCcccc-eEEeeecCcccc-c-cCCceeEEEeecCCeeEEEecccchH---HHH-Hhcccc
Q 020198 26 VPIHIVTNASQLPAEFL-EPSSERQ-LVIGFDCEGVDL-C-RHGSLCIMQLAFPDAIYLVDAIQGGE---TVV-KACKPA 97 (329)
Q Consensus 26 ~~i~vV~t~~~L~~~~l-~~~~~~~-~~Ia~D~E~~~~-~-~~g~l~llQLa~~~~~~liD~~~l~~---~~~-~~L~~l 97 (329)
..+.+|+++.++.. ++ +. +... -+||+|+||... . ...+++++|+++.+.+||||..++.. +.+ ..+..+
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-LLLES-LSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQI 467 (617)
T ss_pred cceeeeCCHHHHHH-HHHHH-hhhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHH
Confidence 46888999998886 55 23 3334 799999999876 3 46799999999999999999988642 323 345679
Q ss_pred ccccceeeeeccccCccchhheecc-----eeec---c-cchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCcc
Q 020198 98 LESSYITKVIHDCKRDSEALYFQFG-----IKLH---N-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (329)
Q Consensus 98 Led~~i~KV~hd~k~Dl~~L~~~~G-----i~l~---~-vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l 168 (329)
|+++++.|||++..+|++.|.+..+ +.+. + .-++.++..+.+..-.-..+....-+|+.|.. ..+|..+
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 9999999999999999999974222 2221 1 23344444433321000011112346788887 8889888
Q ss_pred chhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhh
Q 020198 169 QEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (329)
Q Consensus 169 ~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (329)
++ .+.. ++|..|||+..|+.|||.||..+..++..+.+..+.
T Consensus 546 nK-teqc-------snWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~~ 587 (617)
T KOG2207|consen 546 NK-TEQC-------SNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVEH 587 (617)
T ss_pred cc-cccc-------chhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcch
Confidence 74 3322 499999999999999999999999999999887774
No 20
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.29 E-value=1.2e-12 Score=123.96 Aligned_cols=235 Identities=27% Similarity=0.214 Sum_probs=166.7
Q ss_pred ceEEeeecCccccccCCceeEEEeecCCeeEEEecccchHH-HHHhccccccccceeeeeccccCccchhheecceeecc
Q 020198 49 QLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGET-VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHN 127 (329)
Q Consensus 49 ~~~Ia~D~E~~~~~~~g~l~llQLa~~~~~~liD~~~l~~~-~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~ 127 (329)
...|+.|.-..-..-.+.+..+++++++..|++|...-+.. +....++.|++.++ +. |++.+...|..+|++.+.+
T Consensus 195 ~~~i~~~~~s~~~~~~~e~~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~n 271 (458)
T KOG2405|consen 195 VWFIRPVSPSLLKILALEATYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKN 271 (458)
T ss_pred eeEeecCchhHHHhhhhhhhhhhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHh
Confidence 34455554332112345666799999999999998754321 23457778888765 55 9999999999999999999
Q ss_pred cchhHHHHHHHHhHh-cCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehH
Q 020198 128 VVDTQIAYSLIEEQE-GRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLP 206 (329)
Q Consensus 128 vfDt~lA~~LL~~~~-~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll 206 (329)
++|||+|+.|+.+.+ +++.-....+++-.|..+..|.+.+..++++++.++.+++..|..||.++.+..-++.||.+|+
T Consensus 272 VkDtQia~sLve~~e~grr~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll 351 (458)
T KOG2405|consen 272 VKDTQIASSLVEPSEYGRRHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLL 351 (458)
T ss_pred hHHHHHHHHHhhhHHhcccCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHH
Confidence 999999999999876 3332122356666665534567766666777777777777789999999999999999999998
Q ss_pred HHHHHHHHHhhhhcchheeecceeeeeeeee-cCCCCCCCCCCCCCCccccc--------ccc-----------------
Q 020198 207 YIYHNMMKKLNQQSLWYLAVRGALYCRCFCI-NENDYVDWPPLPPVPGVRFI--------YVD----------------- 260 (329)
Q Consensus 207 ~L~~~L~~~L~~~g~~~~~~~~~~~~r~~~~-~~~~~~~w~~~~~~~~~~~~--------~~~----------------- 260 (329)
... ..+.....|.+.++..++.+|.|. .......|+.-|+.+.+... +-|
T Consensus 352 ~~~----~~l~a~~l~HL~~rp~~e~ecie~~~~~~~~~~p~gpe~QrFt~kp~~as~~r~~r~~~~lSi~~~~~~n~a~ 427 (458)
T KOG2405|consen 352 GIF----DTLVAVCLSHLTRRPYTEPECIELVFGLPMEKVPGGPESQRFTAKPLTASQMRYLRKLVQLSIIMHDHLNYAH 427 (458)
T ss_pred HHH----hhHhhhChHhhccCCccccchhhhcCCcchhhCCCCCCCCceeecceecchHHHHHHhhhhhhhhhhccchhh
Confidence 744 566667889999999999999954 44456779988888864310 001
Q ss_pred ceeeccCCCcccceecccCC-CCCcceeecc
Q 020198 261 YLIVEGDVPEEEILSILDVP-PGKMGRIIGR 290 (329)
Q Consensus 261 ~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 290 (329)
.+.+++---.+|+.+.++.| +++|+.++++
T Consensus 428 ~~~aEd~~~s~e~~s~~s~p~~~~V~~v~~~ 458 (458)
T KOG2405|consen 428 IFCAEDYRISLEFSSSYSGPRSCDVAIVMAP 458 (458)
T ss_pred hhcccchhHHHHHHHhhcCCCCcccccccCC
Confidence 11111113346778888998 8888888764
No 21
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.23 E-value=2.9e-12 Score=129.46 Aligned_cols=161 Identities=24% Similarity=0.220 Sum_probs=119.5
Q ss_pred eEEeeecCccccc-cCCceeEEEeecCCeeEEEeccc--chHHHHHhccccccccceeeeeccccCccchhheecceeec
Q 020198 50 LVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQ--GGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLH 126 (329)
Q Consensus 50 ~~Ia~D~E~~~~~-~~g~l~llQLa~~~~~~liD~~~--l~~~~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~ 126 (329)
..+++|+|+.+.. ..+.+.++.++..+.++++.... ..-.....|+++|+++...|++||.|.|.+.|.+ +|+...
T Consensus 23 ~~~a~~~et~~l~~~~~~lvg~s~~~~~~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~kv~~~~K~d~~~l~~-~Gi~~~ 101 (593)
T COG0749 23 ANIAFDTETDGLDPHGADLVGLSVASEEEAAYIPLLHGPEQLNVLAALKPLLEDEGIKKVGQNLKYDYKVLAN-LGIEPG 101 (593)
T ss_pred ccceeeccccccCcccCCeeEEEeeccccceeEeeccchhhhhhHHHHHHHhhCcccchhccccchhHHHHHH-cCCccc
Confidence 3399999999887 46688888888765555553332 1123568899999999999999999999999964 886645
Q ss_pred ccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCC--CCccccchHHHHHHhhccccee
Q 020198 127 NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDP--QFWTYRPLTELMVRAAADDVRF 204 (329)
Q Consensus 127 ~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~--~~W~~RPLs~~ql~YAA~Da~~ 204 (329)
..||||+|+|+++++.++ +++++|++ +|++.+....+.+. ++.. -++...++ +....|+|.||.+
T Consensus 102 ~~~DtmlasYll~~~~~~-------~~~~~l~~--r~l~~~~~~~~~i~---~kg~~~~~~~~~~~-~~~~~y~a~~a~~ 168 (593)
T COG0749 102 VAFDTMLASYLLNPGAGA-------HNLDDLAK--RYLGLETITFEDIA---GKGKKQLTFADVKL-EKATEYAAEDADA 168 (593)
T ss_pred chHHHHHHHhccCcCcCc-------CCHHHHHH--HhcCCccchhHHhh---ccccccCccccchH-HHHHHHHHHHHHH
Confidence 689999999999998655 45899999 99887664333322 2211 13433444 4468999999999
Q ss_pred hHHHHHHHHHHhhhhcc-hhe
Q 020198 205 LPYIYHNMMKKLNQQSL-WYL 224 (329)
Q Consensus 205 Ll~L~~~L~~~L~~~g~-~~~ 224 (329)
+++|+..|..++.+... ..+
T Consensus 169 ~~~L~~~l~~~l~~~~~L~~l 189 (593)
T COG0749 169 TLRLESILEPELLKTPVLLEL 189 (593)
T ss_pred HHHHHHHHHHHhhhhhhHHHH
Confidence 99999999988877543 444
No 22
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.05 E-value=7e-11 Score=126.23 Aligned_cols=176 Identities=18% Similarity=0.093 Sum_probs=120.3
Q ss_pred EEEEeCCCCCCccccCCCcccceEEeeecCccccc-cCCceeEEEeecCC--eeEEEeccc---ch-HHHHHhccccccc
Q 020198 28 IHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPD--AIYLVDAIQ---GG-ETVVKACKPALES 100 (329)
Q Consensus 28 i~vV~t~~~L~~~~l~~~~~~~~~Ia~D~E~~~~~-~~g~l~llQLa~~~--~~~liD~~~---l~-~~~~~~L~~lLed 100 (329)
+..+.+.+++.. +++. ...+.+++ .+.. ....+.++.+++++ ..|+++... +. ......|+++|++
T Consensus 304 ~~~~~~~~~~~~-~~~~--~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 376 (887)
T TIGR00593 304 AKESEEAAPLAN-PAEK--AEVGGFVL----ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLN 376 (887)
T ss_pred ceEeCCHHHHHH-HHHh--CcCCeEEE----cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhC
Confidence 444545555554 5532 23345666 2222 35678888888753 366664221 11 2334668999999
Q ss_pred cceeeeeccccCccchhheecceeecc-cchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHh
Q 020198 101 SYITKVIHDCKRDSEALYFQFGIKLHN-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLR 179 (329)
Q Consensus 101 ~~i~KV~hd~k~Dl~~L~~~~Gi~l~~-vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~ 179 (329)
+.+.||+||+|+|+..|. .+|+.+.+ +||||+|+||+++..+ .+|++++. +|++..+...+.. .+
T Consensus 377 ~~~~~v~~n~K~d~~~l~-~~gi~~~~~~~Dt~la~yll~~~~~--------~~l~~la~--~yl~~~~~~~~~~---~~ 442 (887)
T TIGR00593 377 EQIKKIGHDAKFLMHLLK-REGIELGGVIFDTMLAAYLLDPAQV--------STLDTLAR--RYLVEELILDEKI---GG 442 (887)
T ss_pred CCCcEEEeeHHHHHHHHH-hCCCCCCCcchhHHHHHHHcCCCCC--------CCHHHHHH--HHcCcccccHHHh---cc
Confidence 999999999999999996 58998865 7999999999998532 37999999 9998664322221 12
Q ss_pred cCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcchheee
Q 020198 180 QDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAV 226 (329)
Q Consensus 180 ~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~~~~ 226 (329)
+. ..+...|+ +.+..||+.||.++++||..|.++|.+.+++.++.
T Consensus 443 ~~-~~~~~~~~-~~~~~ya~~d~~~~~~L~~~l~~~l~~~~l~~l~~ 487 (887)
T TIGR00593 443 KL-AKFAFPPL-EEATEYLARRAAATKRLAEELLKELDENKLLSLYR 487 (887)
T ss_pred CC-CCcccccH-HHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHH
Confidence 11 12333332 45678999999999999999999998877776654
No 23
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=98.75 E-value=6.6e-09 Score=88.26 Aligned_cols=133 Identities=22% Similarity=0.219 Sum_probs=88.6
Q ss_pred CCceeEEEeecCCeeEEEecccchHHHHHhccccccccceeeeeccccCccchhheecceeecc-cchhHHHHHHHHhHh
Q 020198 64 HGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHN-VVDTQIAYSLIEEQE 142 (329)
Q Consensus 64 ~g~l~llQLa~~~~~~liD~~~l~~~~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~-vfDt~lA~~LL~~~~ 142 (329)
.+++.++.++.++++|+|++.. ... ...|+++|++..+.|++||.|.+...|. .+|+.+.+ .|||+||+|||+|.+
T Consensus 17 ~~~~~glal~~~~~~~yi~~~~-~~~-~~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~l~~~~fD~~LAaYLL~p~~ 93 (151)
T cd06128 17 SANLVGLAFAIEGVAAYIPVAH-DYA-LELLKPLLEDEKALKVGQNLKYDRVILA-NYGIELRGIAFDTMLEAYLLDPVA 93 (151)
T ss_pred cCcEEEEEEEcCCCeEEEeCCC-CcC-HHHHHHHHcCCCCCEEeeehHHHHHHHH-HCCCCCCCcchhHHHHHHHcCCCC
Confidence 3567778888765577774211 001 3457889999999999999999999994 68998876 699999999999964
Q ss_pred cCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHH
Q 020198 143 GRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (329)
Q Consensus 143 ~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~ 213 (329)
+. . +++++++ +||+..+..-++ ++++. ......++ .....|++..+.++.+|++.|.
T Consensus 94 ~~------~-~l~~la~--~yl~~~~~~~~~---~~gkg-~~~~~~~~-~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 94 GR------H-DMDSLAE--RWLKEKTITFEE---IAGKG-LTFNQIAL-EEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CC------C-CHHHHHH--HHcCCCCccHHH---HcCCC-CChhhcCH-HHHHHHHHHHHHHHHHHHHHhh
Confidence 31 2 5889998 898876221122 22221 10011112 2234478777888888888774
No 24
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.02 E-value=2.9e-07 Score=87.84 Aligned_cols=147 Identities=31% Similarity=0.492 Sum_probs=98.2
Q ss_pred eecCccccccCCceeEEEeecCCeeEEEecccchHHHH-HhccccccccceeeeeccccCccchhheecceeecccchhH
Q 020198 54 FDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVV-KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQ 132 (329)
Q Consensus 54 ~D~E~~~~~~~g~l~llQLa~~~~~~liD~~~l~~~~~-~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~ 132 (329)
+-.|+++..++|++|.+|.++.-.+|++|+..++..++ +.|..++++..|.|+.|+|+.-+.++.++|||.++++|||+
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 55677777789999999999988899999998876544 67888999999999999999999999999999999999999
Q ss_pred HHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHH----HHHH-HhcCCCCccccchHHHHHHhhccccee
Q 020198 133 IAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE----VRVL-LRQDPQFWTYRPLTELMVRAAADDVRF 204 (329)
Q Consensus 133 lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~----~~~l-~~~~~~~W~~RPLs~~ql~YAA~Da~~ 204 (329)
++.-+-........+++.-..+.+-+- +.|.+.. |.. .+.+ .-.++..|-.||.++..+.-.+..+.+
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--KHLQVAP--KYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred hhhhhhhcccccccCCccccchHHHHH--HHHHhcc--cHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 965443221111112221112221111 1222111 100 0111 113566799999988876665555544
No 25
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=97.97 E-value=3e-06 Score=79.81 Aligned_cols=129 Identities=18% Similarity=0.220 Sum_probs=92.5
Q ss_pred CCceeEEEeecC-CeeEEEecccchHHHHHhccccccccceeeeeccccCccchhhe-ecceeecccchhHHHHHHHHhH
Q 020198 64 HGSLCIMQLAFP-DAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYF-QFGIKLHNVVDTQIAYSLIEEQ 141 (329)
Q Consensus 64 ~g~l~llQLa~~-~~~~liD~~~l~~~~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~-~~Gi~l~~vfDt~lA~~LL~~~ 141 (329)
.+....+||+.+ +.++++...... .+...|+.+|+|++.++|+-...+|...|.+ .|++.+..+.|+.. +++..
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 345778999997 788888655443 3567888889999999999999999999987 78888877777665 33332
Q ss_pred hcCCCCCCCeeeeeecccCCcccC-----CccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHH
Q 020198 142 EGRKRSPDDYISFVGLLADPRYCG-----ISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (329)
Q Consensus 142 ~~~~~l~~~~~sL~~L~~~~~~Lg-----~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~ 209 (329)
.+. ++++ -++..+++ ..+| +.+++ .+ +.++|+..||+.+|+.||+.||+....|+
T Consensus 222 ~g~-~~~~--~s~e~i~~--~~~~~~~~~v~l~~--~i------~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 222 LGG-SMPN--DSFEEIVS--ETLGYYGKDVRLDK--EI------RMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred hcc-CccC--ccHHHHHH--HHhhccccccccCh--hc------ccccceeeeccHHHHHHHHhHHHHHHHHH
Confidence 222 2221 23444554 3333 22221 22 24699999999999999999999999999
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=97.10 E-value=0.0003 Score=55.53 Aligned_cols=72 Identities=24% Similarity=0.166 Sum_probs=51.7
Q ss_pred EeeecCccccc-cCCceeEEEeecC--CeeEEEecccchHHHHHhccccccccc-eeeeeccccCccchhheec---cee
Q 020198 52 IGFDCEGVDLC-RHGSLCIMQLAFP--DAIYLVDAIQGGETVVKACKPALESSY-ITKVIHDCKRDSEALYFQF---GIK 124 (329)
Q Consensus 52 Ia~D~E~~~~~-~~g~l~llQLa~~--~~~~liD~~~l~~~~~~~L~~lLed~~-i~KV~hd~k~Dl~~L~~~~---Gi~ 124 (329)
+++|+|+.+.. +..+++++|+..+ +..|++| +.+++++.. ..+|+||+.+|...|.+.+ |+.
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 47999998876 6778999999875 6677775 444565554 5679999999988776433 222
Q ss_pred ----ecccchhHHH
Q 020198 125 ----LHNVVDTQIA 134 (329)
Q Consensus 125 ----l~~vfDt~lA 134 (329)
....+||+.+
T Consensus 70 ~p~~~~~~lDT~~l 83 (96)
T cd06125 70 YPLLAGSWIDTIKL 83 (96)
T ss_pred CCCcCCcEEEehHH
Confidence 2357898876
No 27
>PRK07740 hypothetical protein; Provisional
Probab=96.16 E-value=0.0053 Score=56.71 Aligned_cols=140 Identities=16% Similarity=0.257 Sum_probs=84.9
Q ss_pred cccceEEeeecCccccccCCceeEEEeec----CCee----E--EEeccc-----------chH----------HHHHhc
Q 020198 46 SERQLVIGFDCEGVDLCRHGSLCIMQLAF----PDAI----Y--LVDAIQ-----------GGE----------TVVKAC 94 (329)
Q Consensus 46 ~~~~~~Ia~D~E~~~~~~~g~l~llQLa~----~~~~----~--liD~~~-----------l~~----------~~~~~L 94 (329)
+.+...+.||+|+++.+....-.+|+|+. ++.. | ++.|.. +.+ +++..+
T Consensus 56 ~~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl~~f 135 (244)
T PRK07740 56 LTDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRF 135 (244)
T ss_pred ccCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHHHHH
Confidence 45668999999998875321112355553 2222 1 232221 000 233445
Q ss_pred cccccccceeeeeccccCccchhhee----cceee-cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccc
Q 020198 95 KPALESSYITKVIHDCKRDSEALYFQ----FGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (329)
Q Consensus 95 ~~lLed~~i~KV~hd~k~Dl~~L~~~----~Gi~l-~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~ 169 (329)
..++.+. ..|+||+.+|...|.+. ++... ..++||+..++.+.+... ..+|+++++ ++|++..
T Consensus 136 ~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~-------~~sL~~l~~---~~gi~~~ 203 (244)
T PRK07740 136 YAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERD-------FPTLDDALA---YYGIPIP 203 (244)
T ss_pred HHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCC-------CCCHHHHHH---HCCcCCC
Confidence 4555543 35899999999877432 23333 358999988776655321 357899885 6787654
Q ss_pred hhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcc
Q 020198 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSL 221 (329)
Q Consensus 170 ~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~ 221 (329)
.. + -|..||..+..|+..+..++.+.|.
T Consensus 204 ~~-H-----------------------~Al~Da~ata~l~~~ll~~~~~~~~ 231 (244)
T PRK07740 204 RR-H-----------------------HALGDALMTAKLWAILLVEAQQRGI 231 (244)
T ss_pred CC-C-----------------------CcHHHHHHHHHHHHHHHHHHHHcCC
Confidence 21 1 1567899999999999988877553
No 28
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=95.95 E-value=0.0064 Score=58.26 Aligned_cols=97 Identities=22% Similarity=0.253 Sum_probs=66.1
Q ss_pred HHHhccccccccceeeeeccccCccchhhee---cceee--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCccc
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~---~Gi~l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (329)
++..|..++.+. ..|+||+.+|+..|.+. +|+.. ...+||+..++.+.+...+ ++|.+|++ ++
T Consensus 84 v~~~l~~~l~~~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~-------~kL~~l~~---~~ 151 (313)
T PRK06063 84 IAGEVAELLRGR--TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPN-------LRLETLAA---HW 151 (313)
T ss_pred HHHHHHHHcCCC--EEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCC-------CCHHHHHH---Hc
Confidence 445666777654 34999999999988643 34433 3478999877766543222 45888885 56
Q ss_pred CCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcch
Q 020198 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLW 222 (329)
Q Consensus 165 g~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~ 222 (329)
|++.. .. .-|-.||.++..|+..+.+++.+.+.|
T Consensus 152 gi~~~-~~-----------------------H~Al~DA~ata~l~~~ll~~~~~~~~~ 185 (313)
T PRK06063 152 GVPQQ-RP-----------------------HDALDDARVLAGILRPSLERARERDVW 185 (313)
T ss_pred CCCCC-CC-----------------------CCcHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 76542 11 116678899999999999998887765
No 29
>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=95.76 E-value=0.0025 Score=46.49 Aligned_cols=45 Identities=33% Similarity=0.572 Sum_probs=38.4
Q ss_pred ccCCCCCcceeecccCceeeeeecccceeEEeccCC--CCCCcccee
Q 020198 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAK--GPPDKDESL 321 (329)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 321 (329)
.-||...+|.+||++|++|..|.+..+|.|.|.-.. ++++|++.|
T Consensus 4 ~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I 50 (65)
T cd02396 4 LLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTI 50 (65)
T ss_pred EEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEE
Confidence 457888899999999999999999999999998766 467776544
No 30
>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=95.74 E-value=0.0021 Score=46.18 Aligned_cols=42 Identities=26% Similarity=0.377 Sum_probs=35.6
Q ss_pred cccCCCCCcceeecccCceeeeeecccceeEEeccCCCCCCc
Q 020198 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDK 317 (329)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 317 (329)
...||+...+.+||++|++|..|.+.+++.|.|.....+.+.
T Consensus 3 ~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~ 44 (62)
T cd02394 3 EVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDT 44 (62)
T ss_pred EEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCE
Confidence 356888889999999999999999999999999986633333
No 31
>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=95.43 E-value=0.018 Score=52.16 Aligned_cols=140 Identities=15% Similarity=0.121 Sum_probs=81.4
Q ss_pred ccceEEeeecCccccccCCceeEEEeec----CC----e--eEEEeccc-----------ch----------HHHHHhcc
Q 020198 47 ERQLVIGFDCEGVDLCRHGSLCIMQLAF----PD----A--IYLVDAIQ-----------GG----------ETVVKACK 95 (329)
Q Consensus 47 ~~~~~Ia~D~E~~~~~~~g~l~llQLa~----~~----~--~~liD~~~-----------l~----------~~~~~~L~ 95 (329)
.....+.||+|++++..... +++|+. .+ . ..++.|.. +. .+++..+.
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 45678999999998763222 445542 11 1 12333321 00 12344555
Q ss_pred ccccccceeeeeccccCccchhheecc---ee--e-cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccc
Q 020198 96 PALESSYITKVIHDCKRDSEALYFQFG---IK--L-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (329)
Q Consensus 96 ~lLed~~i~KV~hd~k~Dl~~L~~~~G---i~--l-~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~ 169 (329)
.++.+. ..|+||+.+|+..|.+.+. .. . ..++||.-.++.+.+.... ...+|..+++ ++|++..
T Consensus 83 ~~~~~~--~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~-----~~~~L~~l~~---~~gl~~~ 152 (217)
T TIGR00573 83 DYIRGA--ELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPG-----KRNTLDALCK---RYEITNS 152 (217)
T ss_pred HHhCCC--EEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCC-----CCCCHHHHHH---HcCCCCC
Confidence 666553 3489999999999865432 11 1 2478988766666554211 1357888886 4565432
Q ss_pred hhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhc
Q 020198 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQS 220 (329)
Q Consensus 170 ~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g 220 (329)
. .. ..-|..||.++..|+..+..+..+.+
T Consensus 153 ~-~~---------------------~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 153 H-RA---------------------LHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred C-cc---------------------cCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 0 00 01166789999999999988776543
No 32
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=95.07 E-value=0.026 Score=51.66 Aligned_cols=81 Identities=12% Similarity=0.175 Sum_probs=51.4
Q ss_pred eeeeccccCccchhhee---ccee---ecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHH
Q 020198 104 TKVIHDCKRDSEALYFQ---FGIK---LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVL 177 (329)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~---~Gi~---l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l 177 (329)
..|+||+.+|...|.+. +|+. ...++||....+.+.+.... ..+|.+|++ ++|++... .+
T Consensus 95 ~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~------~~~L~~l~~---~~gi~~~~-aH---- 160 (232)
T PRK07942 95 PVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKG------KRTLTALCE---HYGVRLDN-AH---- 160 (232)
T ss_pred EEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCC------CCCHHHHHH---HcCCCCCC-CC----
Confidence 45999999999887533 3433 13478999877665543111 246888886 56776531 11
Q ss_pred HhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhh
Q 020198 178 LRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (329)
Q Consensus 178 ~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (329)
-|..||.++.+|+..|.++..
T Consensus 161 -------------------~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 161 -------------------EATADALAAARVAWALARRFP 181 (232)
T ss_pred -------------------ChHHHHHHHHHHHHHHHHHHH
Confidence 155677777777777766554
No 33
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.82 E-value=0.0072 Score=45.60 Aligned_cols=42 Identities=33% Similarity=0.568 Sum_probs=36.0
Q ss_pred ccceeeccCCCcccceecccCCCCCcceeecccCceeeeeec
Q 020198 259 VDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKE 300 (329)
Q Consensus 259 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 300 (329)
|+++-+..+..+..+.-.+.+.|+-||++|||+|.+|.||+-
T Consensus 16 Pd~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 16 PDDVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred ccceEEEEEecCCeEEEEEEECcccccceecCCChhHHHHHH
Confidence 456777777778888999999999999999999999988764
No 34
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=94.81 E-value=0.018 Score=53.28 Aligned_cols=136 Identities=18% Similarity=0.160 Sum_probs=82.8
Q ss_pred ceEEeeecCccccccCCceeE---EEeecCCeeEEEecccc---------------hH----------HHHHhccccccc
Q 020198 49 QLVIGFDCEGVDLCRHGSLCI---MQLAFPDAIYLVDAIQG---------------GE----------TVVKACKPALES 100 (329)
Q Consensus 49 ~~~Ia~D~E~~~~~~~g~l~l---lQLa~~~~~~liD~~~l---------------~~----------~~~~~L~~lLed 100 (329)
..+||+|||.++.+..|+.++ ++|-...+-.++|-.-- .. .+-..+.++|.+
T Consensus 105 ~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL~g 184 (280)
T KOG2249|consen 105 TRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLLKG 184 (280)
T ss_pred ceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHHHhC
Confidence 359999999998876555444 33333333344553321 00 011344456765
Q ss_pred cceeeeeccccCccchhheecceeec-ccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHh
Q 020198 101 SYITKVIHDCKRDSEALYFQFGIKLH-NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLR 179 (329)
Q Consensus 101 ~~i~KV~hd~k~Dl~~L~~~~Gi~l~-~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~ 179 (329)
. +.|||+.+.|+.+|.-.+ +. -+-||.----|...-... .+.||..|.+ .+||.++-. +
T Consensus 185 R--IlVGHaLhnDl~~L~l~h---p~s~iRDTs~~~pl~k~~~~~-----~tpSLK~Lt~--~~Lg~~IQ~--------G 244 (280)
T KOG2249|consen 185 R--ILVGHALHNDLQALKLEH---PRSMIRDTSKYPPLMKLLSKK-----ATPSLKKLTE--ALLGKDIQV--------G 244 (280)
T ss_pred C--EEeccccccHHHHHhhhC---chhhhcccccCchHHHHhhcc-----CCccHHHHHH--HHhchhhhc--------c
Confidence 3 349999999999995322 33 367887644333321111 2579999999 999977631 1
Q ss_pred cCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhh
Q 020198 180 QDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQ 219 (329)
Q Consensus 180 ~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~ 219 (329)
+. + ..+||.+..+||.....+-++.
T Consensus 245 eH--s-------------SvEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 245 EH--S-------------SVEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred cc--C-------------cHHHHHHHHHHHHHHHHHHHHH
Confidence 10 1 3478999999999998776653
No 35
>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=94.70 E-value=0.01 Score=51.06 Aligned_cols=65 Identities=22% Similarity=0.146 Sum_probs=43.3
Q ss_pred hccccccccceeeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCcc
Q 020198 93 ACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (329)
Q Consensus 93 ~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l 168 (329)
.|..++.+.. .-|+||+.+|+..|.. . ...++||...+..+.+.... +...+|..|++ +|+|+++
T Consensus 76 ~~~~~i~~~~-vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~~~~~~~~~~----~~~~~L~~L~~--~~~~~~~ 140 (161)
T cd06137 76 ALWKFIDPDT-ILVGHSLQNDLDALRM-I---HTRVVDTAILTREAVKGPLA----KRQWSLRTLCR--DFLGLKI 140 (161)
T ss_pred HHHHhcCCCc-EEEeccHHHHHHHHhC-c---CCCeeEehhhhhhccCCCcC----CCCccHHHHHH--HHCCchh
Confidence 4555665533 3499999999999953 2 23578999887766543210 01368999998 7888665
No 36
>PRK07883 hypothetical protein; Validated
Probab=94.61 E-value=0.015 Score=60.05 Aligned_cols=141 Identities=16% Similarity=0.114 Sum_probs=84.3
Q ss_pred cccceEEeeecCccccccCCceeEEEeec----CCe-----eEEEeccc-----------chH----------HHHHhcc
Q 020198 46 SERQLVIGFDCEGVDLCRHGSLCIMQLAF----PDA-----IYLVDAIQ-----------GGE----------TVVKACK 95 (329)
Q Consensus 46 ~~~~~~Ia~D~E~~~~~~~g~l~llQLa~----~~~-----~~liD~~~-----------l~~----------~~~~~L~ 95 (329)
+.+...+.||+|+++++... -.+++|+. ++. ..+++|.. +.+ +++..+.
T Consensus 12 ~~~~~~Vv~D~ETTGl~p~~-~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f~ 90 (557)
T PRK07883 12 LRDVTFVVVDLETTGGSPAG-DAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFL 90 (557)
T ss_pred CcCCCEEEEEEecCCCCCCC-CeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHH
Confidence 45568899999999875321 23344442 221 23444421 110 2344555
Q ss_pred ccccccceeeeeccccCccchhhe---ecceee--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccch
Q 020198 96 PALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE 170 (329)
Q Consensus 96 ~lLed~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~ 170 (329)
.++.+. ..|+||+.+|...|.. .+|+.. ...+||+..+.-+-+.... ...+|.++++ ++|++...
T Consensus 91 ~fl~~~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~-----~~~~L~~L~~---~~gi~~~~ 160 (557)
T PRK07883 91 EFARGA--VLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEA-----PNVRLSTLAR---LFGATTTP 160 (557)
T ss_pred HHhcCC--EEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCC-----CCCCHHHHHH---HCCcccCC
Confidence 666653 3489999999998853 345554 2478998765543331111 1356888885 66766431
Q ss_pred hHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcc
Q 020198 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSL 221 (329)
Q Consensus 171 k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~ 221 (329)
. .-|..||.++..|+..+..++.+.|.
T Consensus 161 -~-----------------------H~Al~DA~ata~l~~~l~~~~~~~~~ 187 (557)
T PRK07883 161 -T-----------------------HRALDDARATVDVLHGLIERLGNLGV 187 (557)
T ss_pred -C-----------------------CCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 1 12667899999999999998876544
No 37
>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=94.58 E-value=0.0065 Score=43.84 Aligned_cols=36 Identities=31% Similarity=0.532 Sum_probs=32.9
Q ss_pred ecccCCCCCcceeecccCceeeeeecccceeEEecc
Q 020198 275 SILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
....||+.+.|++||+.|++|..|.+..+|.|.|.-
T Consensus 4 ~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~ 39 (61)
T cd02393 4 ETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED 39 (61)
T ss_pred EEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC
Confidence 356899999999999999999999999999999864
No 38
>PF13014 KH_3: KH domain
Probab=94.47 E-value=0.015 Score=38.70 Aligned_cols=27 Identities=48% Similarity=0.724 Sum_probs=25.5
Q ss_pred cceeecccCceeeeeecccceeEEecc
Q 020198 284 MGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
+|++||++|++|..|.+.++|.|.|--
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 588999999999999999999999977
No 39
>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=94.42 E-value=0.0057 Score=52.17 Aligned_cols=68 Identities=24% Similarity=0.166 Sum_probs=43.2
Q ss_pred HHHhccccccccceeeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccc
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~ 169 (329)
++..|..++.+ .+ .|+||+.+|+..|. .+.....++||.....+..+.. ....||+.|++ +++|+++.
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 45667777776 44 39999999999994 2332235778866433332210 12468999998 77887653
No 40
>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=94.37 E-value=0.014 Score=41.65 Aligned_cols=37 Identities=41% Similarity=0.585 Sum_probs=32.7
Q ss_pred cccCCCCCcceeecccCceeeeeecccceeEEeccCC
Q 020198 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAK 312 (329)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 312 (329)
+..||...++++||++|++|..|.+.+++.|.|...+
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~ 39 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG 39 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCC
Confidence 4568888899999999999999999999999998644
No 41
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=94.19 E-value=0.04 Score=60.14 Aligned_cols=141 Identities=17% Similarity=0.219 Sum_probs=95.3
Q ss_pred cccceEEeeecCccccc-cCCceeEEEeec-----C----CeeEEEeccc-----------ch----------HHHHHhc
Q 020198 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF-----P----DAIYLVDAIQ-----------GG----------ETVVKAC 94 (329)
Q Consensus 46 ~~~~~~Ia~D~E~~~~~-~~g~l~llQLa~-----~----~~~~liD~~~-----------l~----------~~~~~~L 94 (329)
+.++..+.||.|+++++ .+.. +||++. + .--++++|.. +. ++++..+
T Consensus 418 l~datyVVfDiETTGLs~~~d~--iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf 495 (1444)
T COG2176 418 LDDATYVVFDIETTGLSPVYDE--IIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKF 495 (1444)
T ss_pred cccccEEEEEeecCCcCcccch--hhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHH
Confidence 45678899999999986 4554 345543 1 1123333322 00 1355677
Q ss_pred cccccccceeeeeccccCccchhhee---cceee--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccc
Q 020198 95 KPALESSYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (329)
Q Consensus 95 ~~lLed~~i~KV~hd~k~Dl~~L~~~---~Gi~l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~ 169 (329)
+.++.|. ..|.||+.+|+..|... +|+.+ +.+.||.-.++.|+|...+| +|..|++ -||+.+.
T Consensus 496 ~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh-------~Lg~l~k---k~~v~le 563 (1444)
T COG2176 496 REFIGDS--ILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSH-------RLGTLCK---KLGVELE 563 (1444)
T ss_pred HHHhcCc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhc-------chHHHHH---HhCccHH
Confidence 7788764 34999999999988532 55554 45999999999999987665 5788886 4466552
Q ss_pred hhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcchhe
Q 020198 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYL 224 (329)
Q Consensus 170 ~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~~ 224 (329)
.. .-|--|+.++-.++-.+.+.+.+.|...+
T Consensus 564 -~h-----------------------HRA~yDaeat~~vf~~f~~~~ke~Gi~~l 594 (1444)
T COG2176 564 -RH-----------------------HRADYDAEATAKVFFVFLKDLKEKGITNL 594 (1444)
T ss_pred -Hh-----------------------hhhhhhHHHHHHHHHHHHHHHHHhchhhH
Confidence 21 12556889999999999999998765544
No 42
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=94.02 E-value=0.053 Score=58.54 Aligned_cols=133 Identities=18% Similarity=0.131 Sum_probs=79.3
Q ss_pred cceEEeeecCccccccCCceeEEEeec----CCe-----eEEEeccc-----------ch----------HHHHHhcccc
Q 020198 48 RQLVIGFDCEGVDLCRHGSLCIMQLAF----PDA-----IYLVDAIQ-----------GG----------ETVVKACKPA 97 (329)
Q Consensus 48 ~~~~Ia~D~E~~~~~~~g~l~llQLa~----~~~-----~~liD~~~-----------l~----------~~~~~~L~~l 97 (329)
....++||+|+++.+..+ .++||+. ++. ..++.|.. +. .+++..+..+
T Consensus 6 ~~~~vvvD~ETTGl~~~d--~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~ 83 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNA--SIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDL 83 (820)
T ss_pred CCCEEEEEEecCCcCCCC--eEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHH
Confidence 346889999999875333 3556653 221 12344321 00 1234556666
Q ss_pred ccccceeeeeccccCccchhhee---cceee-cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHH
Q 020198 98 LESSYITKVIHDCKRDSEALYFQ---FGIKL-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEE 173 (329)
Q Consensus 98 Led~~i~KV~hd~k~Dl~~L~~~---~Gi~l-~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~ 173 (329)
+.+.- .|+||+.+|+..|.+. .|..+ ...+||.-.+..+-+... ..+|.+|++ ++|++... .+
T Consensus 84 l~~~~--lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~-------~~~L~~L~~---~lgl~~~~-~H 150 (820)
T PRK07246 84 IEDCI--FVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLE-------KYSLSHLSR---ELNIDLAD-AH 150 (820)
T ss_pred hCCCE--EEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCC-------CCCHHHHHH---HcCCCCCC-CC
Confidence 76643 4999999999988543 35544 347899887776655322 256888886 56765431 11
Q ss_pred HHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhh
Q 020198 174 VRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (329)
Q Consensus 174 ~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (329)
-|..||.++..|+..|..++.+
T Consensus 151 -----------------------~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 151 -----------------------TAIADARATAELFLKLLQKIES 172 (820)
T ss_pred -----------------------CHHHHHHHHHHHHHHHHHHHhh
Confidence 1445666677777776666644
No 43
>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=93.89 E-value=0.033 Score=47.75 Aligned_cols=88 Identities=19% Similarity=0.206 Sum_probs=52.6
Q ss_pred HHHhccccccccceeeeeccccCccchhhee---ccee-----ecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCC
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIK-----LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADP 161 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~---~Gi~-----l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~ 161 (329)
+...|.+++++.. .|+||+.+|+..|.+. +|+. ....+||+..++.+.+.. ..+|+++++
T Consensus 71 v~~~l~~~l~~~~--lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~--------~~~L~~l~~-- 138 (167)
T cd06131 71 IADEFLDFIRGAE--LVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGK--------PNSLDALCK-- 138 (167)
T ss_pred HHHHHHHHHCCCe--EEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCC--------CCCHHHHHH--
Confidence 3455666666543 4899999999888543 2332 134789987665443321 246888886
Q ss_pred cccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHH
Q 020198 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (329)
Q Consensus 162 ~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L 212 (329)
++|++...+. ..-|..||..+.+|+..|
T Consensus 139 -~~~i~~~~~~----------------------~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 139 -RFGIDNSHRT----------------------LHGALLDAELLAEVYLEL 166 (167)
T ss_pred -HCCCCCCCCC----------------------CCChHHHHHHHHHHHHHh
Confidence 5576542110 112667788777777654
No 44
>PRK00468 hypothetical protein; Provisional
Probab=93.89 E-value=0.014 Score=44.05 Aligned_cols=45 Identities=29% Similarity=0.452 Sum_probs=35.4
Q ss_pred ccceeeccCCCcccceecccCCCCCcceeecccCceeeeeecccc
Q 020198 259 VDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCN 303 (329)
Q Consensus 259 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 (329)
|+++.+.....++.+.-...++|.-+|++|||+|.+|.||..-.+
T Consensus 16 Pe~v~V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 16 PDAVQVNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCeEEEEEEeCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 456666655666668888999999999999999999988765433
No 45
>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=93.82 E-value=0.014 Score=50.21 Aligned_cols=69 Identities=22% Similarity=0.105 Sum_probs=39.4
Q ss_pred HHHhccccccccceeeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCC-CeeeeeecccCCcccCCcc
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPD-DYISFVGLLADPRYCGISY 168 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~-~~~sL~~L~~~~~~Lg~~l 168 (329)
+...+..++.+. ..|+||+++|+..|... .....+.||.....+.... .+++ ..++|..|++ +|++..+
T Consensus 67 v~~~l~~~l~~~--vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~----~~p~~~~~~L~~L~~--~~~~~~i 136 (157)
T cd06149 67 AQKEILKILKGK--VVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKA----GFPENCRVSLKVLAK--RLLHRDI 136 (157)
T ss_pred HHHHHHHHcCCC--EEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhc----CCcccCChhHHHHHH--HHcChhh
Confidence 445666677643 35999999999988432 1223467875422111100 0011 2368999998 7776544
No 46
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=93.32 E-value=0.059 Score=49.71 Aligned_cols=90 Identities=20% Similarity=0.224 Sum_probs=56.3
Q ss_pred HHhccccccccceeeeeccccCccchhhee---cceee------cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCC
Q 020198 91 VKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKL------HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADP 161 (329)
Q Consensus 91 ~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~---~Gi~l------~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~ 161 (329)
+..+..++.+.. .|+||+.+|+..|.+. +|..+ ..++||...++.+.+.. ..+|..|++
T Consensus 77 ~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~--------~~~L~aL~~-- 144 (240)
T PRK05711 77 ADEFLDFIRGAE--LIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGK--------RNSLDALCK-- 144 (240)
T ss_pred HHHHHHHhCCCE--EEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCC--------CCCHHHHHH--
Confidence 345555666543 4899999999887532 33221 34789988776655431 247899987
Q ss_pred cccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHH
Q 020198 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (329)
Q Consensus 162 ~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~ 215 (329)
+ +|++... |. ..-|-.||..+..+|..|...
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 4654321 00 111667889998998888654
No 47
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=93.14 E-value=0.054 Score=49.38 Aligned_cols=92 Identities=20% Similarity=0.196 Sum_probs=57.9
Q ss_pred HHHhccccccccceeeeeccccCccchhhee---cc--ee-e---cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccC
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FG--IK-L---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLAD 160 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~---~G--i~-l---~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~ 160 (329)
++..|..++.+.. .|+||+.+|+..|.+. +| +. + ..++||+..++.+-+. ...+|++|++
T Consensus 72 v~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~--------~~~~L~~L~~- 140 (225)
T TIGR01406 72 IADEFLDFIGGSE--LVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPG--------QRNSLDALCK- 140 (225)
T ss_pred HHHHHHHHhCCCE--EEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCC--------CCCCHHHHHH-
Confidence 3445556666543 3899999999888532 44 22 1 3588998877655443 1357888886
Q ss_pred CcccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHh
Q 020198 161 PRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKL 216 (329)
Q Consensus 161 ~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L 216 (329)
.+|++.... . ..-|..||..+..+|..|....
T Consensus 141 --~~gi~~~~r-----------------~-----~H~Al~DA~~~a~v~~~l~~~~ 172 (225)
T TIGR01406 141 --RFKVDNSHR-----------------T-----LHGALLDAHLLAEVYLALTGGQ 172 (225)
T ss_pred --hcCCCCCCC-----------------C-----CcCHHHHHHHHHHHHHHHHcCC
Confidence 456553210 0 0116678999999998886543
No 48
>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=92.99 E-value=0.044 Score=48.96 Aligned_cols=85 Identities=15% Similarity=0.175 Sum_probs=57.5
Q ss_pred eeeeccccCccchhhee---ccee---e--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHH
Q 020198 104 TKVIHDCKRDSEALYFQ---FGIK---L--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVR 175 (329)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~---~Gi~---l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~ 175 (329)
.-|+||+.+|+..|.+. +|.. . ...+||...++.+.+. .+|+.+++ ++|++.... +
T Consensus 107 ~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~~----------~~L~~l~~---~~gi~~~~~-~-- 170 (200)
T TIGR01298 107 ILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYGQ----------TVLAKACQ---AAGXDFDST-Q-- 170 (200)
T ss_pred EEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcCc----------ccHHHHHH---HcCCCcccc-c--
Confidence 45999999999988532 3332 1 2378998876654321 35777775 457654211 1
Q ss_pred HHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcchh
Q 020198 176 VLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWY 223 (329)
Q Consensus 176 ~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~ 223 (329)
..-|..||..+..|+..|..++.+.+.|.
T Consensus 171 -------------------~H~Al~Da~ata~lf~~l~~~~~~~~~~~ 199 (200)
T TIGR01298 171 -------------------AHSALYDTEKTAELFCEIVNRWKRLGGWP 199 (200)
T ss_pred -------------------hhhhHHhHHHHHHHHHHHHHHHHHccCCC
Confidence 11266789999999999999999888875
No 49
>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=92.88 E-value=0.029 Score=47.77 Aligned_cols=65 Identities=23% Similarity=0.209 Sum_probs=41.5
Q ss_pred HHHhccccccccceeeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCcc
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l 168 (329)
+...+.+++.+.. ..|+||+++|+..|.. . ...++||...++...+.. ...+|..|++ +|++..+
T Consensus 65 v~~~~~~fl~~~~-vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~r~~~~~~-------~~~~L~~L~~--~~~~~~i 129 (150)
T cd06145 65 VQKKLLSLISPDT-ILVGHSLENDLKALKL-I---HPRVIDTAILFPHPRGPP-------YKPSLKNLAK--KYLGRDI 129 (150)
T ss_pred HHHHHHHHhCCCC-EEEEcChHHHHHHhhc-c---CCCEEEcHHhccccCCCC-------CChhHHHHHH--HHCCcce
Confidence 3445666665223 3599999999999953 2 134789986554332221 1357999998 7877544
No 50
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=92.85 E-value=0.1 Score=58.44 Aligned_cols=137 Identities=16% Similarity=0.233 Sum_probs=87.6
Q ss_pred ccceEEeeecCccccc-cCCceeEEEeec----CCe-----eEEEeccc-----------ch----------HHHHHhcc
Q 020198 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-----IYLVDAIQ-----------GG----------ETVVKACK 95 (329)
Q Consensus 47 ~~~~~Ia~D~E~~~~~-~~g~l~llQLa~----~~~-----~~liD~~~-----------l~----------~~~~~~L~ 95 (329)
.+...+.||+|+++++ ...+ +++|+. .+. ..++.|.. +. .+++..+.
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~--IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~ 265 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDE--IIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFK 265 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCe--EEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHH
Confidence 4568899999999875 3333 344442 121 12333321 00 13445666
Q ss_pred ccccccceeeeeccccCccchhhe---ecceee--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccch
Q 020198 96 PALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQE 170 (329)
Q Consensus 96 ~lLed~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~ 170 (329)
.++.+. ..|+||+.+|...|.+ .+|+.. ...+||+..++.+.+... ..+|++|++ .+|+++..
T Consensus 266 ~fl~~~--iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k-------~~kL~~Lak---~lgi~~~~ 333 (1213)
T TIGR01405 266 EFFKDS--ILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYK-------SHRLGNICK---KLGVDLDD 333 (1213)
T ss_pred HHhCCC--eEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCC-------CCCHHHHHH---HcCCCCCC
Confidence 677653 3499999999988853 245542 358999998887765432 257888886 45776541
Q ss_pred hHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcc
Q 020198 171 KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSL 221 (329)
Q Consensus 171 k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~ 221 (329)
. ..|..||.++..++..|.+++.+.|.
T Consensus 334 -~-----------------------HrAl~DA~aTa~I~~~ll~~l~~~~i 360 (1213)
T TIGR01405 334 -H-----------------------HRADYDAEATAKVFKVMVEQLKEKGI 360 (1213)
T ss_pred -C-----------------------cCHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 1 22667899999999999988877543
No 51
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=92.58 E-value=0.095 Score=48.55 Aligned_cols=133 Identities=18% Similarity=0.235 Sum_probs=77.9
Q ss_pred ccceEEeeecCccccc-cCCceeEEEeec----CC-----eeEEEeccc-c----------hH----------HHHHhcc
Q 020198 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PD-----AIYLVDAIQ-G----------GE----------TVVKACK 95 (329)
Q Consensus 47 ~~~~~Ia~D~E~~~~~-~~g~l~llQLa~----~~-----~~~liD~~~-l----------~~----------~~~~~L~ 95 (329)
.+...+.||+|+++.. ...+ +++|+. .+ ...++.|.. + .+ ++...+.
T Consensus 5 ~~~~~v~~D~ETTGl~~~~d~--IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~ 82 (250)
T PRK06310 5 KDTEFVCLDCETTGLDVKKDR--IIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIK 82 (250)
T ss_pred cCCcEEEEEEeCCCCCCCCCe--EEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHH
Confidence 4467899999999875 3333 344432 12 223455431 1 00 2334555
Q ss_pred ccccccceeeeeccccCccchhhee---cceee----cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCcc
Q 020198 96 PALESSYITKVIHDCKRDSEALYFQ---FGIKL----HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (329)
Q Consensus 96 ~lLed~~i~KV~hd~k~Dl~~L~~~---~Gi~l----~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l 168 (329)
.++.+.. ..|+||+.+|...|... .|+.. ..++||+-.++.+... ...+|+.|++ ++|++.
T Consensus 83 ~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~--------~~~~L~~l~~---~~g~~~ 150 (250)
T PRK06310 83 GFFKEGD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDS--------PNNSLEALAV---HFNVPY 150 (250)
T ss_pred HHhCCCC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccC--------CCCCHHHHHH---HCCCCC
Confidence 5665533 35999999999888532 34433 3478998776654321 1246888876 457654
Q ss_pred chhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhh
Q 020198 169 QEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (329)
Q Consensus 169 ~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (329)
.. .+ -|..||.++..++..+.+++.
T Consensus 151 ~~-aH-----------------------~Al~Da~at~~vl~~l~~~~~ 175 (250)
T PRK06310 151 DG-NH-----------------------RAMKDVEINIKVFKHLCKRFR 175 (250)
T ss_pred CC-Cc-----------------------ChHHHHHHHHHHHHHHHHhcc
Confidence 31 11 156788888888888876654
No 52
>smart00322 KH K homology RNA-binding domain.
Probab=92.57 E-value=0.061 Score=38.05 Aligned_cols=38 Identities=34% Similarity=0.458 Sum_probs=32.9
Q ss_pred ecccCCCCCcceeecccCceeeeeecccceeEEeccCC
Q 020198 275 SILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAK 312 (329)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 312 (329)
....||+..++.+||++|++|..|.+.+++.|.+...+
T Consensus 5 ~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~ 42 (69)
T smart00322 5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG 42 (69)
T ss_pred EEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC
Confidence 34567888999999999999999999999999997543
No 53
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=91.83 E-value=0.2 Score=54.95 Aligned_cols=108 Identities=18% Similarity=0.073 Sum_probs=64.0
Q ss_pred ceEEeeecCccccccCCceeEEEeec----CCe-----eEEEeccc-----------ch----------HHHHHhccccc
Q 020198 49 QLVIGFDCEGVDLCRHGSLCIMQLAF----PDA-----IYLVDAIQ-----------GG----------ETVVKACKPAL 98 (329)
Q Consensus 49 ~~~Ia~D~E~~~~~~~g~l~llQLa~----~~~-----~~liD~~~-----------l~----------~~~~~~L~~lL 98 (329)
...+.||+|+++......-.+|||+. .++ ..+|.|.. +. .++...|..++
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~~l 82 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELL 82 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHHHHh
Confidence 35788999998765221123566653 221 12444421 00 12345566677
Q ss_pred cccceeeeeccccCccchhhee---cceee--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCcc
Q 020198 99 ESSYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (329)
Q Consensus 99 ed~~i~KV~hd~k~Dl~~L~~~---~Gi~l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l 168 (329)
++. ..|+||+.+|...|.+. .|+.. ...+||+-.+..+-+... ..+|.+|++ ++|+..
T Consensus 83 ~~~--~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~-------~~~L~~l~~---~l~i~~ 145 (928)
T PRK08074 83 EGA--YFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAE-------SYKLRDLSE---ELGLEH 145 (928)
T ss_pred CCC--eEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCC-------CCCHHHHHH---hCCCCC
Confidence 654 34999999999988542 45443 347899877776655422 246888886 567654
No 54
>PRK02821 hypothetical protein; Provisional
Probab=91.78 E-value=0.028 Score=42.61 Aligned_cols=46 Identities=24% Similarity=0.387 Sum_probs=36.2
Q ss_pred ccceeeccCCCcccceecccCCCCCcceeecccCceeeeeecccce
Q 020198 259 VDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCNA 304 (329)
Q Consensus 259 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 304 (329)
++++.+..+..++...-...++|.-+|++|||+|.+|.||..-.+|
T Consensus 17 Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 17 PDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 4566666666666677888899999999999999999888765554
No 55
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=91.54 E-value=0.17 Score=48.47 Aligned_cols=91 Identities=20% Similarity=0.181 Sum_probs=56.2
Q ss_pred HHHhccccccccceeeeeccccCccchhhee---ccee-e-cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCccc
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIK-L-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~---~Gi~-l-~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (329)
++..+..++.+..+ |+||+.+|+..|.+. +|+. + ...+||+..+..+.+... ..+|.+|++ ++
T Consensus 78 vl~~f~~fl~~~~l--VaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~-------~~kL~~L~~---~l 145 (313)
T PRK06807 78 VLPLFLAFLHTNVI--VAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAP-------NHKLETLKR---ML 145 (313)
T ss_pred HHHHHHHHHcCCeE--EEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCC-------CCCHHHHHH---Hc
Confidence 34455555655433 999999999988643 3442 2 347899886665544321 246888875 66
Q ss_pred CCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhh
Q 020198 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (329)
Q Consensus 165 g~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (329)
|+.. + .+ -|-.||.++..++..+.....
T Consensus 146 gi~~-~-~H-----------------------~Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 146 GIRL-S-SH-----------------------NAFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred CCCC-C-Cc-----------------------ChHHHHHHHHHHHHHHHHhhh
Confidence 7654 1 11 144677777777777776664
No 56
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=91.48 E-value=0.28 Score=45.21 Aligned_cols=141 Identities=15% Similarity=0.146 Sum_probs=76.2
Q ss_pred cccceEEeeecCccccc-cCCceeEEEeec----CCe-------eEEEeccc-----------ch----------HHHHH
Q 020198 46 SERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-------IYLVDAIQ-----------GG----------ETVVK 92 (329)
Q Consensus 46 ~~~~~~Ia~D~E~~~~~-~~g~l~llQLa~----~~~-------~~liD~~~-----------l~----------~~~~~ 92 (329)
+.+...++||+|+++++ ..++ +++|+. ++. ..++.|.. +. .+++.
T Consensus 44 ~~~~~~vviD~ETTGl~p~~d~--IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~ 121 (239)
T PRK09146 44 LSEVPFVALDFETTGLDAEQDA--IVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILD 121 (239)
T ss_pred cccCCEEEEEeECCCCCCCCCc--EEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHH
Confidence 34567899999999876 3343 334432 121 23444421 00 02334
Q ss_pred hccccccccceeeeeccccCccchhhee----cceee-cccchhHHHHHHHHhHhcCC---CCC---CCeeeeeecccCC
Q 020198 93 ACKPALESSYITKVIHDCKRDSEALYFQ----FGIKL-HNVVDTQIAYSLIEEQEGRK---RSP---DDYISFVGLLADP 161 (329)
Q Consensus 93 ~L~~lLed~~i~KV~hd~k~Dl~~L~~~----~Gi~l-~~vfDt~lA~~LL~~~~~~~---~l~---~~~~sL~~L~~~~ 161 (329)
.+...+.+. ..|+||+.+|...|.+. .+..+ ..++||+-.++-+.+..... .+. ....+|.++++
T Consensus 122 ~l~~~~~~~--~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~-- 197 (239)
T PRK09146 122 ELLEALAGK--VVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRL-- 197 (239)
T ss_pred HHHHHhCCC--EEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHH--
Confidence 444445443 34899999999988543 23333 34889998776554321000 000 01234555554
Q ss_pred cccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhh
Q 020198 162 RYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (329)
Q Consensus 162 ~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (329)
.+|++... ..-|..||.++..|+..+..+..
T Consensus 198 -~~gl~~~~------------------------~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 198 -RYGLPAYS------------------------PHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred -HcCCCCCC------------------------CCCcHHHHHHHHHHHHHHHHHHc
Confidence 34543210 11266788888888888877664
No 57
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=91.23 E-value=0.25 Score=46.05 Aligned_cols=133 Identities=17% Similarity=0.074 Sum_probs=77.8
Q ss_pred ccceEEeeecCccccc-cCCceeEEEeec----CCe-----eEEEecccch--------------------HHHHHhccc
Q 020198 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF----PDA-----IYLVDAIQGG--------------------ETVVKACKP 96 (329)
Q Consensus 47 ~~~~~Ia~D~E~~~~~-~~g~l~llQLa~----~~~-----~~liD~~~l~--------------------~~~~~~L~~ 96 (329)
.+...+.||+|+.+.. ..++ +++|+. .++ ..++.+..+. .+++..+..
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 3333 444442 221 1233332110 134456666
Q ss_pred cccccceeeeeccccCccchhhe---ecceee--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchh
Q 020198 97 ALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK 171 (329)
Q Consensus 97 lLed~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k 171 (329)
++.+. ..|+||+.+|...|.+ ++|... ...+||+-.+..+-+. ...+|++|++ ++|++.. .
T Consensus 144 fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~--------~~~~L~~L~~---~lgi~~~-~ 209 (257)
T PRK08517 144 FLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES--------PRYGLSFLKE---LLGIEIE-V 209 (257)
T ss_pred HHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccC--------CCCCHHHHHH---HcCcCCC-C
Confidence 77654 3589999999988753 344432 3467876544322111 1256888875 6676543 1
Q ss_pred HHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhh
Q 020198 172 EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (329)
Q Consensus 172 ~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (329)
.+ -|-.||.++.+|+..+..++..
T Consensus 210 ~H-----------------------rAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 210 HH-----------------------RAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred CC-----------------------ChHHHHHHHHHHHHHHHHHhHH
Confidence 11 1557888888898888877753
No 58
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=90.71 E-value=0.26 Score=48.13 Aligned_cols=140 Identities=11% Similarity=0.131 Sum_probs=81.0
Q ss_pred ccceEEeeecCccccc-cCCceeEEEeec-----CC-----eeEEEeccc---------ch----------HHHHHhccc
Q 020198 47 ERQLVIGFDCEGVDLC-RHGSLCIMQLAF-----PD-----AIYLVDAIQ---------GG----------ETVVKACKP 96 (329)
Q Consensus 47 ~~~~~Ia~D~E~~~~~-~~g~l~llQLa~-----~~-----~~~liD~~~---------l~----------~~~~~~L~~ 96 (329)
.+...++||+|+.+++ ..++ +|+|+. .+ -..+|++.. +. .+++..|.+
T Consensus 44 ~~~~fVvlDiETTGLdp~~dr--IIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~~ 121 (377)
T PRK05601 44 EAAPFVAVSIQTSGIHPSTSR--LITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLDR 121 (377)
T ss_pred CCCCEEEEEEECCCCCCCCCe--EEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHHH
Confidence 4568999999999986 3443 343321 11 122444322 10 135566777
Q ss_pred cccccceeeeeccccCccchhheec-------------------------------ceee-cccchhHHHHHHHHhHhcC
Q 020198 97 ALESSYITKVIHDCKRDSEALYFQF-------------------------------GIKL-HNVVDTQIAYSLIEEQEGR 144 (329)
Q Consensus 97 lLed~~i~KV~hd~k~Dl~~L~~~~-------------------------------Gi~l-~~vfDt~lA~~LL~~~~~~ 144 (329)
++.+. ..|+||+.+|+..|.+.+ ++.+ ..++||.-.++.+.+...+
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 77754 349999999999875422 1222 2479998888887765333
Q ss_pred CCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHH
Q 020198 145 KRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (329)
Q Consensus 145 ~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L 212 (329)
++|.+|++ ++|+..+.- ..+.-+ ..+| .. ..+-.|+.++-.||..+
T Consensus 200 -------~rL~~La~---~lGi~~p~~--~A~~~R------a~~p--~~--~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 200 -------IRIRGVAH---TLGLDAPAA--EASVER------AQVP--HR--QLCREETLLVARLYFAL 245 (377)
T ss_pred -------CCHHHHHH---HhCCCCCch--hhhhhh------hcCC--hh--hhhhHHHHHHHHHHHHh
Confidence 46888886 678876531 110000 0111 11 11235888888888776
No 59
>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=90.42 E-value=0.011 Score=42.11 Aligned_cols=35 Identities=40% Similarity=0.690 Sum_probs=31.2
Q ss_pred cccCCCCCcceeecccCceeeeeecccceeEEecc
Q 020198 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
+..||+...|++||++|++|..|.+.+++.|.|-.
T Consensus 3 ~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~ 37 (60)
T PF00013_consen 3 RIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPD 37 (60)
T ss_dssp EEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEES
T ss_pred EEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcC
Confidence 45677788899999999999999999999999954
No 60
>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=90.21 E-value=0.6 Score=41.37 Aligned_cols=105 Identities=16% Similarity=0.145 Sum_probs=62.1
Q ss_pred HHHHhccccccc--cceeeeecccc-Cccchhhee---cceeec------------------------ccchhHHHHHHH
Q 020198 89 TVVKACKPALES--SYITKVIHDCK-RDSEALYFQ---FGIKLH------------------------NVVDTQIAYSLI 138 (329)
Q Consensus 89 ~~~~~L~~lLed--~~i~KV~hd~k-~Dl~~L~~~---~Gi~l~------------------------~vfDt~lA~~LL 138 (329)
+++..+..++.. |.+ -++||.. +|+..|..+ +|+... ..+|++....-
T Consensus 58 ~lL~~F~~~i~~~dpdi-ivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~- 135 (195)
T cd05780 58 EMIKRFIEIVKEKDPDV-IYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARR- 135 (195)
T ss_pred HHHHHHHHHHHHcCCCE-EEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHh-
Confidence 455555555554 765 4899975 799887532 344311 15676654321
Q ss_pred HhHhcCCCCCCCeeeeeecccCCcccCCccchh--HHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHH
Q 020198 139 EEQEGRKRSPDDYISFVGLLADPRYCGISYQEK--EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHN 211 (329)
Q Consensus 139 ~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k--~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~ 211 (329)
. ..+ ...+|..+++ ++||.+-.+. +++.. -|...+--...++|+-.||..+++|...
T Consensus 136 --~---~~l--~sy~L~~v~~--~~Lg~~k~d~~~~~i~~-------~~~~~~~~~~l~~Y~~~D~~lt~~L~~~ 194 (195)
T cd05780 136 --T---LNL--TRYTLERVYE--ELFGIEKEDVPGEEIAE-------AWDSGENLERLFRYSMEDAKYTYEIGKE 194 (195)
T ss_pred --h---CCC--CcCcHHHHHH--HHhCCCCCcCCHHHHHH-------HHhCCCchHHHHHHhHHHHHHHHHHHhh
Confidence 1 111 2467888888 8998653221 22221 2333322366799999999999998765
No 61
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=90.19 E-value=0.34 Score=44.23 Aligned_cols=99 Identities=16% Similarity=0.105 Sum_probs=60.5
Q ss_pred Hhccccccccceeeeecc-ccCccchhhee---cceee--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccC
Q 020198 92 KACKPALESSYITKVIHD-CKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCG 165 (329)
Q Consensus 92 ~~L~~lLed~~i~KV~hd-~k~Dl~~L~~~---~Gi~l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg 165 (329)
..+..++.+. ...|+|| ..+|...|.+. +|+.. ...+||+-.+..+.+... ..+|..+++ ++|
T Consensus 71 ~~~~~fi~~~-~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~-------~~~L~~l~~---~~~ 139 (232)
T PRK06309 71 QKFIEFCGTD-NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLP-------KHNLQYLRQ---VYG 139 (232)
T ss_pred HHHHHHHcCC-CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCC-------CCCHHHHHH---HcC
Confidence 3444555443 2349999 48999888532 44442 357899876665543211 245777775 446
Q ss_pred CccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcchhee
Q 020198 166 ISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLA 225 (329)
Q Consensus 166 ~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~~~ 225 (329)
++.. .. .-|..||.++..++..+..++..+.++.+.
T Consensus 140 ~~~~-~a-----------------------H~Al~Da~~t~~vl~~l~~~~~~~~l~~l~ 175 (232)
T PRK06309 140 FEEN-QA-----------------------HRALDDVITLHRVFSALVGDLSPQQVYDLL 175 (232)
T ss_pred CCCC-CC-----------------------CCcHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence 5432 11 116678999999999998887655444444
No 62
>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=90.11 E-value=0.32 Score=42.47 Aligned_cols=53 Identities=28% Similarity=0.327 Sum_probs=35.4
Q ss_pred eeeeeccc-cCccchhhee---cceeec---ccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccc
Q 020198 103 ITKVIHDC-KRDSEALYFQ---FGIKLH---NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (329)
Q Consensus 103 i~KV~hd~-k~Dl~~L~~~---~Gi~l~---~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~ 169 (329)
..-|+||+ .+|+..|.+. +|+.+. ..+||+-.++.+.+ +|++|++ +++|++..
T Consensus 99 ~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~------------~L~~l~~--~~~~~~~~ 158 (177)
T cd06136 99 ICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ------------SLGSLYK--RLFGQEPK 158 (177)
T ss_pred CEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh------------hHHHHHH--HHhCCCcc
Confidence 35699998 8999988532 454431 25798876665543 3788887 67777653
No 63
>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=90.06 E-value=0.55 Score=41.39 Aligned_cols=102 Identities=18% Similarity=0.107 Sum_probs=60.2
Q ss_pred HHHHhccccccc--cceeeeeccc-cCccchhhe---ecceee-----------------------c-ccchhHHHHHHH
Q 020198 89 TVVKACKPALES--SYITKVIHDC-KRDSEALYF---QFGIKL-----------------------H-NVVDTQIAYSLI 138 (329)
Q Consensus 89 ~~~~~L~~lLed--~~i~KV~hd~-k~Dl~~L~~---~~Gi~l-----------------------~-~vfDt~lA~~LL 138 (329)
+++..+..++.+ |.+ -|+||. .+|+..|.. .+|+.. + ..+|+.....-.
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 345555555554 444 499999 789988753 245444 1 257877654432
Q ss_pred HhHhcCCCCCCCeeeeeecccCCcccCCccchh--HHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHH
Q 020198 139 EEQEGRKRSPDDYISFVGLLADPRYCGISYQEK--EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (329)
Q Consensus 139 ~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k--~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~ 209 (329)
.. . ...+|+++++ .+|+..-.+- ..... ..|.. -....++|+-.||..+++|+
T Consensus 144 ~~-l-------~sy~L~~v~~--~~l~~~k~~~~~~~~~~------~~~~~--~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 144 FK-L-------KSYTLDAVAE--ELLGEGKEKVDGEIIED------AEWEE--DPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred cC-c-------ccCCHHHHHH--HHhCCCCCcCCHHHHhh------ccCcc--hHHHHHHHHHHHHHHHHHhh
Confidence 21 1 1367999998 8887532211 11110 01322 13567999999999998875
No 64
>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=89.83 E-value=0.35 Score=40.61 Aligned_cols=67 Identities=19% Similarity=0.095 Sum_probs=42.9
Q ss_pred HHHhccccccccceeeeeccccCccchhhe---ecceee--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCccc
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYF---QFGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~---~~Gi~l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (329)
++..|..++++. ..|+||+.+|...|.+ .+|+.. ...+||+..+..+.+... ..+|..+++ ++
T Consensus 67 v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~-------~~~L~~l~~---~~ 134 (156)
T cd06130 67 VWPEIKPFLGGS--LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLP-------NHKLNTVAE---HL 134 (156)
T ss_pred HHHHHHHHhCCC--EEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCC-------CCCHHHHHH---Hc
Confidence 445666777763 4599999999998853 245543 347899876655443211 256888885 56
Q ss_pred CCcc
Q 020198 165 GISY 168 (329)
Q Consensus 165 g~~l 168 (329)
|+..
T Consensus 135 g~~~ 138 (156)
T cd06130 135 GIEL 138 (156)
T ss_pred CCCc
Confidence 6544
No 65
>PRK01064 hypothetical protein; Provisional
Probab=89.79 E-value=0.078 Score=40.32 Aligned_cols=45 Identities=24% Similarity=0.344 Sum_probs=35.1
Q ss_pred ccceeeccCCCcccceecccCCCCCcceeecccCceeeeeecccc
Q 020198 259 VDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCN 303 (329)
Q Consensus 259 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 (329)
++++.+........+.-...+.+..+|++|||+|.+|.||..-.+
T Consensus 16 Pe~V~V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 16 PEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CCeEEEEEEeCCCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 345555544556668888999999999999999999998876544
No 66
>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=89.59 E-value=0.044 Score=48.02 Aligned_cols=64 Identities=17% Similarity=0.099 Sum_probs=41.9
Q ss_pred HhccccccccceeeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccc
Q 020198 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169 (329)
Q Consensus 92 ~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~ 169 (329)
..|..++... ...|||+..+|+.+|.- -..-..+.||.+...+ ... +..||..|++ +|||..+.
T Consensus 93 ~~l~~li~~~-tILVGHsL~nDL~aL~l--~hp~~~viDTa~l~~~---~~~------r~~sLk~La~--~~L~~~IQ 156 (174)
T cd06143 93 LKLRLLVDLG-CIFVGHGLAKDFRVINI--QVPKEQVIDTVELFHL---PGQ------RKLSLRFLAW--YLLGEKIQ 156 (174)
T ss_pred HHHHHHcCCC-CEEEeccchhHHHHhcC--cCCCcceEEcHHhccC---CCC------CChhHHHHHH--HHcCCccc
Confidence 4455556433 34599999999999842 1112368899764321 111 2478999999 99998774
No 67
>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=88.87 E-value=0.38 Score=52.25 Aligned_cols=68 Identities=19% Similarity=0.127 Sum_probs=44.7
Q ss_pred HHHhccccccccceeeeeccccCccchhhee---cceee--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCccc
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~---~Gi~l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (329)
+...+..++.+. ..|+||+.+|...|.+. .|+.+ ...+||+-.+..+.+... ..+|.+|++ ++
T Consensus 70 v~~~l~~~l~~~--~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~-------~~~L~~l~~---~~ 137 (850)
T TIGR01407 70 VAQEIYDLLEDG--IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEE-------SYQLSELSE---AL 137 (850)
T ss_pred HHHHHHHHhCCC--EEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCC-------CCCHHHHHH---HC
Confidence 345566667654 35999999999888532 45542 357899887776655322 256888886 56
Q ss_pred CCccc
Q 020198 165 GISYQ 169 (329)
Q Consensus 165 g~~l~ 169 (329)
|++..
T Consensus 138 gi~~~ 142 (850)
T TIGR01407 138 GLTHE 142 (850)
T ss_pred CCCCC
Confidence 76653
No 68
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=87.07 E-value=0.94 Score=40.27 Aligned_cols=93 Identities=14% Similarity=0.110 Sum_probs=51.6
Q ss_pred HHHhccccccccceeeeeccccCccchhhee----cceeec-ccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCccc
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ----FGIKLH-NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~----~Gi~l~-~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (329)
++..+..++.+. ..|+||+.+|...|.+. +|..+. ..+|++-..+-..... ... .....+|+++++ ++
T Consensus 101 vl~~~~~~i~~~--~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~-~~~-~~~~~~L~~l~~---~~ 173 (202)
T PRK09145 101 ALRQLLAFIGNR--PLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERH-LPD-AYIDLRFDAILK---HL 173 (202)
T ss_pred HHHHHHHHHcCC--eEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhcc-CCC-cccCCCHHHHHH---Hc
Confidence 345555666653 35999999999888543 234333 4678764332111100 000 001357888885 55
Q ss_pred CCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHH
Q 020198 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMM 213 (329)
Q Consensus 165 g~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~ 213 (329)
|++... .+ -|..||.++..||..|.
T Consensus 174 gi~~~~-~H-----------------------~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 174 DLPVLG-RH-----------------------DALNDAIMAALIFLRLR 198 (202)
T ss_pred CCCCCC-CC-----------------------CcHHHHHHHHHHHHHHH
Confidence 765421 11 15578888888887774
No 69
>PRK05168 ribonuclease T; Provisional
Probab=86.70 E-value=0.17 Score=45.57 Aligned_cols=87 Identities=21% Similarity=0.276 Sum_probs=57.3
Q ss_pred eeeeeccccCccchhhe---eccee---e--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHH
Q 020198 103 ITKVIHDCKRDSEALYF---QFGIK---L--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEV 174 (329)
Q Consensus 103 i~KV~hd~k~Dl~~L~~---~~Gi~---l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~ 174 (329)
...|+||+.+|+..|.+ ++|+. . ..++||...+..+.+. .+|..+++ ++|+++....
T Consensus 115 ~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~----------~~L~~l~~---~~gl~~~~~~-- 179 (211)
T PRK05168 115 AILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQ----------TVLAKACQ---AAGIEFDNKE-- 179 (211)
T ss_pred ceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCC----------CCHHHHHH---HCCCCCCCCC--
Confidence 45699999999988753 24432 1 1378997766654321 24777775 4566542110
Q ss_pred HHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcchhe
Q 020198 175 RVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYL 224 (329)
Q Consensus 175 ~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~~ 224 (329)
..-|..||..+.+|+..|..++.+.|.|.+
T Consensus 180 --------------------~H~Al~DA~ata~l~~~l~~~~~~~~~~~~ 209 (211)
T PRK05168 180 --------------------AHSALYDTEKTAELFCEIVNRWKRLGGWPL 209 (211)
T ss_pred --------------------CCChHHHHHHHHHHHHHHHHHHHHccCCCC
Confidence 011667899999999999999988777654
No 70
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=85.28 E-value=1 Score=40.17 Aligned_cols=95 Identities=15% Similarity=0.156 Sum_probs=53.7
Q ss_pred HHHhccccccccceeeeecccc-Cccchhheecceeecc--cchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCC
Q 020198 90 VVKACKPALESSYITKVIHDCK-RDSEALYFQFGIKLHN--VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGI 166 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k-~Dl~~L~~~~Gi~l~~--vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~ 166 (329)
++..+..++.+.. .|+||+. +|+..|. ..|..+.+ .+||.-..+..... ..+.+ ..++|.+|++ ++|+
T Consensus 74 vl~~f~~f~~~~~--lVaHNa~~fD~~fL~-~~g~~~~~~~~idt~~~~~~~~~~-~~~~~--~~~~L~~La~---~~gi 144 (195)
T PRK07247 74 VLAAFKEFVGELP--LIGYNAQKSDLPILA-ENGLDLSDQYQVDLYDEAFERRSS-DLNGI--ANLKLQTVAD---FLGI 144 (195)
T ss_pred HHHHHHHHHCCCe--EEEEeCcHhHHHHHH-HcCCCcCCCceeehHHHHHHhhcc-ccCCC--CCCCHHHHHH---hcCC
Confidence 4456666776543 4999995 8999995 46766543 34543111111100 00001 1356888885 6676
Q ss_pred ccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhh
Q 020198 167 SYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (329)
Q Consensus 167 ~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (329)
+.. .+ | |..||.++..++..|...-+.
T Consensus 145 ~~~--~H--------------r---------Al~DA~~ta~v~~~ll~~~~~ 171 (195)
T PRK07247 145 KGR--GH--------------N---------SLEDARMTARVYESFLESDQN 171 (195)
T ss_pred CCC--Cc--------------C---------CHHHHHHHHHHHHHHHhhccc
Confidence 531 11 1 557888888888888765544
No 71
>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=85.21 E-value=1.1 Score=37.93 Aligned_cols=146 Identities=18% Similarity=0.172 Sum_probs=65.5
Q ss_pred EeeecCccccc-cCCceeEEEeec--CCe-eEEEecccch---H-HHHHhccccccccceeeeecc-ccCccchhhee--
Q 020198 52 IGFDCEGVDLC-RHGSLCIMQLAF--PDA-IYLVDAIQGG---E-TVVKACKPALESSYITKVIHD-CKRDSEALYFQ-- 120 (329)
Q Consensus 52 Ia~D~E~~~~~-~~g~l~llQLa~--~~~-~~liD~~~l~---~-~~~~~L~~lLed~~i~KV~hd-~k~Dl~~L~~~-- 120 (329)
+.||+|+.++. ..+.+.++.++. .++ .++.+...-. . .+.+.+ ..+.+.... |+|| ..+|...|.+.
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~-~~l~~~~~i-v~yng~~FD~p~L~~~~~ 78 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFF-ELLDEADNI-VTYNGKNFDIPFLKRRAK 78 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH---HHHHTT--E-EESSTTTTHHHHHHHHH-
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHH-HHHhcCCeE-EEEeCcccCHHHHHHHHH
Confidence 45899998875 356777888775 332 2233222111 1 122333 344444433 6666 56799998643
Q ss_pred -ccee-ecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchh----HHHHHHHhcCCCCccccchHHHH
Q 020198 121 -FGIK-LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK----EEVRVLLRQDPQFWTYRPLTELM 194 (329)
Q Consensus 121 -~Gi~-l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k----~~~~~l~~~~~~~W~~RPLs~~q 194 (329)
+++. ..+.+|++-..+-... ...||..+.. ++|..-.+. .+...++....... .....+..
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 3444 3457888764421111 1356787775 577654311 11111111100000 12245778
Q ss_pred HHhhcccceehHHHHHHH
Q 020198 195 VRAAADDVRFLPYIYHNM 212 (329)
Q Consensus 195 l~YAA~Da~~Ll~L~~~L 212 (329)
+.|.-.|+..+.+|++.|
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 999999999999999886
No 72
>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=82.44 E-value=0.31 Score=35.04 Aligned_cols=34 Identities=21% Similarity=0.333 Sum_probs=27.9
Q ss_pred ceecccCCCCCcceeecccCceeeeeecccceeE
Q 020198 273 ILSILDVPPGKMGRIIGRRGSSILAIKESCNAEI 306 (329)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 306 (329)
-....-|+++.+|.+||++|.+|..+.+.++-.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I 58 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKI 58 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCe
Confidence 4566778899999999999999998877766443
No 73
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=81.98 E-value=0.72 Score=52.66 Aligned_cols=95 Identities=16% Similarity=0.191 Sum_probs=63.0
Q ss_pred HhccccccccceeeeeccccCccchhh---eeccee-e-cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCC
Q 020198 92 KACKPALESSYITKVIHDCKRDSEALY---FQFGIK-L-HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGI 166 (329)
Q Consensus 92 ~~L~~lLed~~i~KV~hd~k~Dl~~L~---~~~Gi~-l-~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~ 166 (329)
..+..++.+ ...|+||+.+|...|. +.+|+. + ...+||+-.++.+.+... ..+|..|++ .+|+
T Consensus 491 ~~f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k-------~~kL~~LAk---~lGL 558 (1437)
T PRK00448 491 PKFKEFCGD--SILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELK-------SHRLNTLAK---KFGV 558 (1437)
T ss_pred HHHHHHhCC--CEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccc-------cccHHHHHH---HcCC
Confidence 344444443 4569999999987663 235653 2 347899888777665322 357888886 4576
Q ss_pred ccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcch
Q 020198 167 SYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLW 222 (329)
Q Consensus 167 ~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~ 222 (329)
.... . .-|-.||.++..|+..|.+++.+.|..
T Consensus 559 ~~~~-~-----------------------HrAl~DA~aTa~lf~~ll~~l~~~gi~ 590 (1437)
T PRK00448 559 ELEH-H-----------------------HRADYDAEATAYLLIKFLKDLKEKGIT 590 (1437)
T ss_pred CCCC-C-----------------------cChHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 5532 1 126678999999999999988765443
No 74
>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=81.53 E-value=2.5 Score=37.96 Aligned_cols=144 Identities=17% Similarity=0.209 Sum_probs=74.2
Q ss_pred ceEEeeecCccccc--c-----CCceeEEEeecC--Ce-eEEEecccc-hHHHHHhccccccc--cceeeeeccc-cCcc
Q 020198 49 QLVIGFDCEGVDLC--R-----HGSLCIMQLAFP--DA-IYLVDAIQG-GETVVKACKPALES--SYITKVIHDC-KRDS 114 (329)
Q Consensus 49 ~~~Ia~D~E~~~~~--~-----~g~l~llQLa~~--~~-~~liD~~~l-~~~~~~~L~~lLed--~~i~KV~hd~-k~Dl 114 (329)
-..++||+|..+.. . ...-.++||+.. ++ ..++..... ..+++..+...+.+ |.+ .++||. .+|+
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 36788999885431 1 123456777752 21 122211111 12455555555554 565 379998 7898
Q ss_pred chhhe---ecceee------------------------------c-c-cchhHHHHHHHHhHhcCCCCCCCeeeeeeccc
Q 020198 115 EALYF---QFGIKL------------------------------H-N-VVDTQIAYSLIEEQEGRKRSPDDYISFVGLLA 159 (329)
Q Consensus 115 ~~L~~---~~Gi~l------------------------------~-~-vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~ 159 (329)
..|.. .+|+.. . . ++|++.+..-.+.. .+.+ ...+|..+++
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 87642 234332 0 1 36766643321111 1111 1357888886
Q ss_pred CCcccCCc----cc-hhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHH
Q 020198 160 DPRYCGIS----YQ-EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIY 209 (329)
Q Consensus 160 ~~~~Lg~~----l~-~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~ 209 (329)
.+ |.. .+ ...++.. .|...+ +..++|+..||..++.|+
T Consensus 164 --~~-g~~~~~k~d~~~~~I~~-------l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 164 --HF-GLASPDRTYIDGRQIAE-------VWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred --Hh-cccCCCcCCCCHHHHHH-------HHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 44 321 11 0122221 354442 678999999999998875
No 75
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=80.26 E-value=0.66 Score=44.29 Aligned_cols=95 Identities=15% Similarity=0.170 Sum_probs=59.5
Q ss_pred HHHhccccccccceeeeeccccCccchhhee---cceee--cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCccc
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKL--HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYC 164 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~---~Gi~l--~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~L 164 (329)
++..|..++.+. ..|+||+.+|+..|.+. +|+.. ...+||+..+.-+-+... ..+|.+|++ .+
T Consensus 70 v~~~~~~fl~~~--~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~-------~~~L~~L~~---~~ 137 (309)
T PRK06195 70 IWEKIKHYFNNN--LVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNID-------NARLNTVNN---FL 137 (309)
T ss_pred HHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCC-------cCCHHHHHH---Hc
Confidence 345566666543 35999999999888532 44443 247899876654433321 245777775 45
Q ss_pred CCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcc
Q 020198 165 GISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSL 221 (329)
Q Consensus 165 g~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~ 221 (329)
|+... . .-|..||.++.+|+..|.+++...+.
T Consensus 138 gi~~~--~-----------------------H~Al~DA~ata~l~~~l~~~~~~~~~ 169 (309)
T PRK06195 138 GYEFK--H-----------------------HDALADAMACSNILLNISKELNSKDI 169 (309)
T ss_pred CCCCc--c-----------------------cCCHHHHHHHHHHHHHHHHHhccCCH
Confidence 65431 1 12667888888888888887765443
No 76
>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=78.02 E-value=0.65 Score=41.01 Aligned_cols=77 Identities=21% Similarity=0.205 Sum_probs=49.0
Q ss_pred eeeeccccCccchhhe---eccee-----ecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHH
Q 020198 104 TKVIHDCKRDSEALYF---QFGIK-----LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVR 175 (329)
Q Consensus 104 ~KV~hd~k~Dl~~L~~---~~Gi~-----l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~ 175 (329)
..|+||+.+|+..|.+ .+|+. ....+||...+..+.+. .+|+.+++ ++|+++....
T Consensus 104 ~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~~----------~~L~~l~~---~~gi~~~~~~--- 167 (189)
T cd06134 104 ILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQ----------TVLAKACQ---AAGIEFDNKE--- 167 (189)
T ss_pred eEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhCC----------CcHHHHHH---HCCCCCCCCC---
Confidence 4699999999988853 35551 12479998877765432 24777776 4576542100
Q ss_pred HHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHH
Q 020198 176 VLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215 (329)
Q Consensus 176 ~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~ 215 (329)
..-|..||..+.+|+..|.++
T Consensus 168 -------------------~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 168 -------------------AHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred -------------------CcChHHHHHHHHHHHHHHHHh
Confidence 011567888888888877653
No 77
>PRK12704 phosphodiesterase; Provisional
Probab=75.46 E-value=0.8 Score=46.99 Aligned_cols=43 Identities=33% Similarity=0.629 Sum_probs=36.7
Q ss_pred CCcccceecccCCCCCc-ceeecccCceeeeeecccceeEEecc
Q 020198 268 VPEEEILSILDVPPGKM-GRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 268 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
.+-|..-++..+|-.-| ||+|||.|.||+++...++++|.|--
T Consensus 205 ~~~e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd 248 (520)
T PRK12704 205 HVAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD 248 (520)
T ss_pred hhhhhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC
Confidence 44555677888877777 99999999999999999999999954
No 78
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=75.31 E-value=0.75 Score=38.84 Aligned_cols=92 Identities=21% Similarity=0.240 Sum_probs=58.8
Q ss_pred HHHhccccccccceeeeeccc-cCccchhhee---cceee---cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCc
Q 020198 90 VVKACKPALESSYITKVIHDC-KRDSEALYFQ---FGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPR 162 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~-k~Dl~~L~~~---~Gi~l---~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~ 162 (329)
+...+..++.+.. .|+||+ ++|+..|... +|+.. ...+||+..++...+.. ..+|..+++
T Consensus 70 ~~~~~~~~l~~~~--~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~--------~~~L~~l~~--- 136 (169)
T smart00479 70 VLEELLEFLKGKI--LVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR--------KYSLKKLAE--- 136 (169)
T ss_pred HHHHHHHHhcCCE--EEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC--------CCCHHHHHH---
Confidence 4456666776643 377888 9999988642 34332 23689977666554321 257888886
Q ss_pred ccCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhh
Q 020198 163 YCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLN 217 (329)
Q Consensus 163 ~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~ 217 (329)
++|++.... ...|..||..+.+|+..+.+++.
T Consensus 137 ~~~~~~~~~-----------------------~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 137 RLGLEVIGR-----------------------AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred HCCCCCCCC-----------------------CcCcHHHHHHHHHHHHHHHHHhh
Confidence 455543210 13377899999999998877653
No 79
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=74.91 E-value=0.82 Score=46.85 Aligned_cols=43 Identities=33% Similarity=0.629 Sum_probs=36.4
Q ss_pred CCcccceecccCCCCCc-ceeecccCceeeeeecccceeEEecc
Q 020198 268 VPEEEILSILDVPPGKM-GRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 268 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
..-|..-++..+|-.-| ||+|||.|.||+++...+++++.|--
T Consensus 199 ~~~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd 242 (514)
T TIGR03319 199 HVAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD 242 (514)
T ss_pred hhhhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC
Confidence 44455677788877777 99999999999999999999999954
No 80
>PRK00106 hypothetical protein; Provisional
Probab=73.11 E-value=0.97 Score=46.44 Aligned_cols=43 Identities=28% Similarity=0.591 Sum_probs=36.3
Q ss_pred CCcccceecccCCCCCc-ceeecccCceeeeeecccceeEEecc
Q 020198 268 VPEEEILSILDVPPGKM-GRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 268 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
..-|.--++..+|-.-| ||+|||.|.||+++...+++++.|--
T Consensus 220 ~~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 263 (535)
T PRK00106 220 YVTEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD 263 (535)
T ss_pred hhhhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC
Confidence 44455577888877777 99999999999999999999999853
No 81
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=72.44 E-value=0.3 Score=36.25 Aligned_cols=42 Identities=21% Similarity=0.401 Sum_probs=30.8
Q ss_pred eeeccCCCcccceecccCCCCCcceeecccCceeeeeecccc
Q 020198 262 LIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCN 303 (329)
Q Consensus 262 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 (329)
+.+.-....++..-..++.+...|++|||+|.++.||.--++
T Consensus 18 v~v~~~~~~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 18 VEVTIEIEEDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp -EEEEEEETTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred EEEEEEEcCCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 333333445556777888888899999999999998866555
No 82
>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=70.30 E-value=2 Score=35.38 Aligned_cols=30 Identities=30% Similarity=0.554 Sum_probs=28.1
Q ss_pred CCcceeecccCceeeeeecccceeEEeccC
Q 020198 282 GKMGRIIGRRGSSILAIKESCNAEILIGGA 311 (329)
Q Consensus 282 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 311 (329)
+.+|++||-+|.+|..|.+..+|.|.|-|-
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~ 44 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGK 44 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecC
Confidence 568999999999999999999999999984
No 83
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=68.42 E-value=2.7 Score=43.21 Aligned_cols=46 Identities=28% Similarity=0.491 Sum_probs=35.7
Q ss_pred ccCCCCCcceeecccCceeeeeecccceeEEeccC---CCCCCccceeE
Q 020198 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGA---KGPPDKDESLH 322 (329)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~ 322 (329)
.-||++|.|+||||.|-+|-.|-+...|-+=+==. ..|+.|.|+|-
T Consensus 322 ~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~Ir 370 (600)
T KOG1676|consen 322 MKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIR 370 (600)
T ss_pred EeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEe
Confidence 35899999999999999999999998886544322 34566788763
No 84
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=67.24 E-value=0.88 Score=48.82 Aligned_cols=93 Identities=18% Similarity=0.181 Sum_probs=64.6
Q ss_pred cccccceeeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHH
Q 020198 97 ALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRV 176 (329)
Q Consensus 97 lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~ 176 (329)
+|-+-.+.-|||+.++|...+ + .-+....++||.+... ++.+ +.+||.-|+- .+||.++-.-.
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvI-N-i~Vp~~QiiDTv~lf~-~~s~--------R~LSLrfLa~--~lLg~~IQ~~~---- 1071 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVI-N-IHVPEEQIIDTVTLFR-LGSQ--------RMLSLRFLAW--ELLGETIQMEA---- 1071 (1118)
T ss_pred HHHHcCcEEEcccccccceEE-E-EecChhhheeeeEEEe-cccc--------cEEEHHHHHH--HHhcchhhccc----
Confidence 566777889999999999877 3 3333344999987432 2221 2589999998 89987653111
Q ss_pred HHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHhhhhcchheee
Q 020198 177 LLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAV 226 (329)
Q Consensus 177 l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L~~~g~~~~~~ 226 (329)
.| ..+||+..+.||++.. +|+++|+.+-..
T Consensus 1072 ------HD-------------SIeDA~taLkLYk~Yl-~lkeq~~~~~~l 1101 (1118)
T KOG1275|consen 1072 ------HD-------------SIEDARTALKLYKKYL-KLKEQGKLESEL 1101 (1118)
T ss_pred ------cc-------------cHHHHHHHHHHHHHHH-HHHHhhHHHHHH
Confidence 11 3478999999999985 678888776655
No 85
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=64.94 E-value=1.5 Score=40.32 Aligned_cols=36 Identities=36% Similarity=0.740 Sum_probs=32.7
Q ss_pred ecccCCCCCcceeecccCceeeeeecccceeEEecc
Q 020198 275 SILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
-...|||.+.+++||.+|..|..|.+.++++|.||-
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~ 182 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ 182 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC
Confidence 346789999999999999999999999999999985
No 86
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=64.22 E-value=2.8 Score=38.47 Aligned_cols=36 Identities=39% Similarity=0.814 Sum_probs=31.8
Q ss_pred ecccCCCCCcceeecccCceeeeeecccceeEEecc
Q 020198 275 SILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
....|+|.+.+|+||++|+-+.-+++..+.+|++|=
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~ 183 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec
Confidence 356789999999999999999888898999999884
No 87
>PRK12705 hypothetical protein; Provisional
Probab=61.77 E-value=2.2 Score=43.56 Aligned_cols=43 Identities=30% Similarity=0.591 Sum_probs=35.5
Q ss_pred CCcccceecccCCCCCc-ceeecccCceeeeeecccceeEEecc
Q 020198 268 VPEEEILSILDVPPGKM-GRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 268 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
..-|.--++..+|-.-| |++|||.|.+|+++...++.++.|--
T Consensus 193 ~~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 193 TASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred hhhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 34445577888877777 99999999999999999999998853
No 88
>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=60.75 E-value=2.4 Score=35.28 Aligned_cols=68 Identities=18% Similarity=0.209 Sum_probs=34.7
Q ss_pred CccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCCCccccchH
Q 020198 112 RDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLT 191 (329)
Q Consensus 112 ~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~~W~~RPLs 191 (329)
.|+.++...-|+.+..--|-++.+||+++.++. ...+++ +|+|- +|...
T Consensus 71 K~LAv~a~~~G~~v~PGDDPlLlAYLlDPsNt~---------p~~var--RY~~~-----------------~W~~d--- 119 (138)
T PF09281_consen 71 KDLAVHALREGVVVEPGDDPLLLAYLLDPSNTN---------PEGVAR--RYLGG-----------------EWPED--- 119 (138)
T ss_dssp HHHHHHHHHTT----B---HHHHHHHH-TT--S---------HHHHHH--HH-TS--------------------SS---
T ss_pred HHHHHHHHhcCcccCCCCCcchhhhhcCccCCC---------hHHHHH--HhcCC-----------------CCCcc---
Confidence 445554445788877777999999999997532 456666 77653 45433
Q ss_pred HHHHHhhcccceehHHHHHHHHHHh
Q 020198 192 ELMVRAAADDVRFLPYIYHNMMKKL 216 (329)
Q Consensus 192 ~~ql~YAA~Da~~Ll~L~~~L~~~L 216 (329)
|+..+.+.-+|+..|..+|
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 4445555667777776654
No 89
>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=59.90 E-value=2.6 Score=34.54 Aligned_cols=49 Identities=16% Similarity=0.000 Sum_probs=32.7
Q ss_pred HHHhccccccccceeeeeccccCccchhheecc-----eeecccchhHHHHHHHHh
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQFG-----IKLHNVVDTQIAYSLIEE 140 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~G-----i~l~~vfDt~lA~~LL~~ 140 (329)
+...+..++++ -..|+||+.+|...|.+.+. ......+||+..+..+.+
T Consensus 69 ~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~ 122 (159)
T cd06127 69 VLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLP 122 (159)
T ss_pred HHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcC
Confidence 44566667766 34599999999998865433 222458899976655443
No 90
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=59.51 E-value=5.8 Score=42.51 Aligned_cols=108 Identities=17% Similarity=0.164 Sum_probs=60.6
Q ss_pred eeeeeccccCccchhheecceeecc--cchhHHHHHHHH----hHh----------------cCC---------CCC-CC
Q 020198 103 ITKVIHDCKRDSEALYFQFGIKLHN--VVDTQIAYSLIE----EQE----------------GRK---------RSP-DD 150 (329)
Q Consensus 103 i~KV~hd~k~Dl~~L~~~~Gi~l~~--vfDt~lA~~LL~----~~~----------------~~~---------~l~-~~ 150 (329)
-+.||||..+|-..+..+|.|.-.. ++|||-++-... .++ .++ .|. ..
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 4569999999998887788876543 679997653221 110 000 000 00
Q ss_pred eeeeeecccCCcccCCc-cchhHHHHHHHhcCCCCccccchH---HHHHHhhcccceehHHHHHHHHHHhhh
Q 020198 151 YISFVGLLADPRYCGIS-YQEKEEVRVLLRQDPQFWTYRPLT---ELMVRAAADDVRFLPYIYHNMMKKLNQ 218 (329)
Q Consensus 151 ~~sL~~L~~~~~~Lg~~-l~~k~~~~~l~~~~~~~W~~RPLs---~~ql~YAA~Da~~Ll~L~~~L~~~L~~ 218 (329)
..||.++.. -++|.. ++ |+. +..|-+. ...++- .+.+.|+|.|++++.+++..+.....+
T Consensus 322 ~NSL~dVhk--~~c~~~~Ld-Kt~-Rd~Fvs~----~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fle 385 (1075)
T KOG3657|consen 322 LNSLVDVHK--FHCGIDALD-KTP-RDSFVSG----TKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLE 385 (1075)
T ss_pred hHHHHHHHH--hhCCCCccc-cch-HHhhhcC----cHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHH
Confidence 124445555 566665 44 221 1111110 001111 445899999999999988887776554
No 91
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=55.38 E-value=3.5 Score=30.85 Aligned_cols=29 Identities=24% Similarity=0.501 Sum_probs=23.6
Q ss_pred cccCCCCCcceeecccCceeeeeecccce
Q 020198 276 ILDVPPGKMGRIIGRRGSSILAIKESCNA 304 (329)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 304 (329)
..++.+..+|+.|||+|.++-||---.|.
T Consensus 27 ~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 27 EVNISGDDIGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred EEEEecCCCCeEECCCCccHHHHHHHHHH
Confidence 46777788899999999999888766653
No 92
>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=55.31 E-value=9.5 Score=34.48 Aligned_cols=106 Identities=16% Similarity=0.074 Sum_probs=63.8
Q ss_pred HHHHhccccccccceeeeecccc-Cccchhhe---ecceeeccc-------------------chhHHHHHHHHhHhcCC
Q 020198 89 TVVKACKPALESSYITKVIHDCK-RDSEALYF---QFGIKLHNV-------------------VDTQIAYSLIEEQEGRK 145 (329)
Q Consensus 89 ~~~~~L~~lLed~~i~KV~hd~k-~Dl~~L~~---~~Gi~l~~v-------------------fDt~lA~~LL~~~~~~~ 145 (329)
+++..+...++......|+||.+ +|+..|.. .+||.+... +|||-. +.+.+ ++
T Consensus 39 ~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~--l~~~g-~~- 114 (209)
T PF10108_consen 39 ELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDL--LSFYG-AK- 114 (209)
T ss_pred HHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHH--HhccC-cc-
Confidence 45566666676555556999975 89988743 267765332 454432 22222 11
Q ss_pred CCCCCeeeeeecccCCcccCCccch----hHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHH
Q 020198 146 RSPDDYISFVGLLADPRYCGISYQE----KEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMK 214 (329)
Q Consensus 146 ~l~~~~~sL~~L~~~~~~Lg~~l~~----k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~ 214 (329)
...||+.|+. .||++- | -.++.. -|..-.+ ++...|+-.||..+..||-.+..
T Consensus 115 ----~~~sLd~la~---~lgiPg-K~~idGs~V~~-------~y~~g~i-~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 115 ----ARTSLDELAA---LLGIPG-KDDIDGSQVAE-------LYQEGDI-DEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred ----ccCCHHHHHH---HcCCCC-CCCCCHHHHHH-------HHHcCCH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 1467888884 888652 1 122222 2443344 44689999999999999887753
No 93
>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=55.16 E-value=29 Score=30.51 Aligned_cols=144 Identities=17% Similarity=0.190 Sum_probs=74.5
Q ss_pred eEEeeecCccccc-----cCCceeEEEeecC-CeeEEEecccc-hHHHHHhccccccc--cceeeeeccc-cCccchhhe
Q 020198 50 LVIGFDCEGVDLC-----RHGSLCIMQLAFP-DAIYLVDAIQG-GETVVKACKPALES--SYITKVIHDC-KRDSEALYF 119 (329)
Q Consensus 50 ~~Ia~D~E~~~~~-----~~g~l~llQLa~~-~~~~liD~~~l-~~~~~~~L~~lLed--~~i~KV~hd~-k~Dl~~L~~ 119 (329)
..++||.|+.+.. ..+.+..|+++.. +...++-.... ..+++..+..++.. |.+. ++||. .+|+..|..
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~i-~gyN~~~FDlpyl~~ 82 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDII-VGYNSNAFDWPYLVE 82 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCEE-EecCCCcCcHHHHHH
Confidence 5688999987321 1345555555542 33333311111 22445555555553 5543 78985 588877642
Q ss_pred ---ecceeec----------------------ccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCc-cchh--
Q 020198 120 ---QFGIKLH----------------------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGIS-YQEK-- 171 (329)
Q Consensus 120 ---~~Gi~l~----------------------~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~-l~~k-- 171 (329)
.+|+.+. -.+|+.-... .. ..+ ...+|+++++ +||.. -++|
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 3454331 0345444221 11 111 2367887775 57752 1111
Q ss_pred ---HHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHH
Q 020198 172 ---EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 (329)
Q Consensus 172 ---~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L 212 (329)
.+... -|....-......|+..|+..++.|+..+
T Consensus 152 ~~~~~i~~-------~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 152 IEWYRIYE-------YWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred CCHHHHHH-------HHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 12211 34432123677999999999999998753
No 94
>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=48.07 E-value=29 Score=31.05 Aligned_cols=129 Identities=12% Similarity=0.069 Sum_probs=69.9
Q ss_pred cCCceeEEEeec---CCeeEEE-ecccc-hHHHHHhccccccccceeeeeccc-cCccchhhe---ecceeec-------
Q 020198 63 RHGSLCIMQLAF---PDAIYLV-DAIQG-GETVVKACKPALESSYITKVIHDC-KRDSEALYF---QFGIKLH------- 126 (329)
Q Consensus 63 ~~g~l~llQLa~---~~~~~li-D~~~l-~~~~~~~L~~lLed~~i~KV~hd~-k~Dl~~L~~---~~Gi~l~------- 126 (329)
..++++.|.++. .++.+.+ ..... ..+++..+...+++.....|+||. .+|+..|.. .+|+.+.
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 356777777765 3333322 11111 124555555566652224589998 699988853 2566321
Q ss_pred -----------ccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCcc--c-hhHHHHHHHhcCCCCccccchHH
Q 020198 127 -----------NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY--Q-EKEEVRVLLRQDPQFWTYRPLTE 192 (329)
Q Consensus 127 -----------~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l--~-~k~~~~~l~~~~~~~W~~RPLs~ 192 (329)
..+|++-...-.+ . ....+|+.+++ +||.+- + .-.++. ..|.... -+
T Consensus 129 ~~~~y~~r~~~~h~DL~~~~~~~~----~----~~~~~L~~va~---~lG~~~K~d~~G~~v~-------~~y~~g~-~~ 189 (208)
T cd05782 129 KDWNYRNRYSERHLDLMDLLAFYG----A----RARASLDLLAK---LLGIPGKMDVDGSQVW-------ELYAEGK-LD 189 (208)
T ss_pred chhhccCcCCCCcccHHHHHhccC----c----cCCCCHHHHHH---HhCCCCCcCCCHHHHH-------HHHHcCC-hH
Confidence 1457665432111 1 01367887764 677621 1 011221 1355444 35
Q ss_pred HHHHhhcccceehHHHHH
Q 020198 193 LMVRAAADDVRFLPYIYH 210 (329)
Q Consensus 193 ~ql~YAA~Da~~Ll~L~~ 210 (329)
...+|+..||..+..||.
T Consensus 190 ~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 190 EIAEYCETDVLNTYLLYL 207 (208)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 678999999999988874
No 95
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=46.70 E-value=3.3 Score=43.97 Aligned_cols=35 Identities=31% Similarity=0.487 Sum_probs=31.7
Q ss_pred cccCCCCCcceeecccCceeeeeecccceeEEecc
Q 020198 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
...|+|.|++.+||.+|.+|.+|.+..++.|-|--
T Consensus 554 ~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d 588 (684)
T TIGR03591 554 TIKINPDKIRDVIGPGGKVIREITEETGAKIDIED 588 (684)
T ss_pred EEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec
Confidence 46789999999999999999999999999998853
No 96
>PRK13763 putative RNA-processing protein; Provisional
Probab=45.27 E-value=5.2 Score=35.19 Aligned_cols=28 Identities=36% Similarity=0.496 Sum_probs=26.0
Q ss_pred CcceeecccCceeeeeecccceeEEecc
Q 020198 283 KMGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 283 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
..|++||++|.++.+|.+.+++.|.|-+
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~ 132 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYG 132 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcC
Confidence 4699999999999999999999999975
No 97
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=44.41 E-value=6.5 Score=35.03 Aligned_cols=93 Identities=15% Similarity=0.104 Sum_probs=54.1
Q ss_pred HHHhccccccccceeeeeccccCccchhhee---cceee---cccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcc
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKL---HNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRY 163 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~---~Gi~l---~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~ 163 (329)
++..|..++.+.... ++|++.+|+..|.+. +|+.. ....|++.....+-+.. ...+|.++++ +
T Consensus 82 vl~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~-------~~~~L~~~~~---~ 150 (207)
T PRK07748 82 LVEKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGER-------NQTGLWKAIE---E 150 (207)
T ss_pred HHHHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcC-------CCCCHHHHHH---H
Confidence 456677777763222 556678999888532 45542 23667776544332211 1357888885 5
Q ss_pred cCCccchhHHHHHHHhcCCCCccccchHHHHHHhhcccceehHHHHHHHHHHh
Q 020198 164 CGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKL 216 (329)
Q Consensus 164 Lg~~l~~k~~~~~l~~~~~~~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L 216 (329)
+|++..... .-|..||..+..|+..|....
T Consensus 151 ~gi~~~~~~-----------------------H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 151 YGKEGTGKH-----------------------HCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred cCCCCCCCC-----------------------cChHHHHHHHHHHHHHHHhCc
Confidence 676532111 115678888888888877653
No 98
>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=40.62 E-value=5.8 Score=34.58 Aligned_cols=28 Identities=36% Similarity=0.466 Sum_probs=26.0
Q ss_pred CcceeecccCceeeeeecccceeEEecc
Q 020198 283 KMGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 283 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
..|++||+.|.++.+|....++.|.|.+
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~ 126 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG 126 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC
Confidence 4699999999999999999999999975
No 99
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=40.03 E-value=6.8 Score=41.70 Aligned_cols=36 Identities=33% Similarity=0.581 Sum_probs=32.1
Q ss_pred ecccCCCCCcceeecccCceeeeeecccceeEEecc
Q 020198 275 SILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
....|+|.|++.+||-+|.+|..|.+..++.|-|--
T Consensus 580 ~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d 615 (719)
T TIGR02696 580 ITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED 615 (719)
T ss_pred EEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec
Confidence 356789999999999999999999999999988754
No 100
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=39.57 E-value=12 Score=33.95 Aligned_cols=79 Identities=14% Similarity=-0.046 Sum_probs=48.5
Q ss_pred eeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCccchhHHHHHHHhcCCC
Q 020198 104 TKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQ 183 (329)
Q Consensus 104 ~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l~~k~~~~~l~~~~~~ 183 (329)
..|+||+.+|...|.. .+ ...+||+-.++.+-++. ..++..|++ ++|+......
T Consensus 76 ~lVaHNa~FD~~~L~~-~~---~~~idTl~lar~l~p~~--------~~~l~~L~~---~~~l~~~~~~----------- 129 (219)
T PRK07983 76 WYVAHNASFDRRVLPE-MP---GEWICTMKLARRLWPGI--------KYSNMALYK---SRKLNVQTPP----------- 129 (219)
T ss_pred EEEEeCcHhhHHHHhC-cC---CCcEeHHHHHHHHccCC--------CCCHHHHHH---HcCCCCCCCC-----------
Confidence 4599999999998842 22 35789998887665542 134666664 4554431000
Q ss_pred CccccchHHHHHHhhcccceehHHHHHHHHHHh
Q 020198 184 FWTYRPLTELMVRAAADDVRFLPYIYHNMMKKL 216 (329)
Q Consensus 184 ~W~~RPLs~~ql~YAA~Da~~Ll~L~~~L~~~L 216 (329)
.. ...-|..||.++..|+..+.+..
T Consensus 130 ~~--------~aHrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 130 GL--------HHHRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred CC--------CCCcHHHHHHHHHHHHHHHHHHc
Confidence 00 01226678888888888877543
No 101
>PRK00228 hypothetical protein; Validated
Probab=39.47 E-value=21 Score=31.71 Aligned_cols=44 Identities=23% Similarity=0.431 Sum_probs=28.8
Q ss_pred CCCcceeecccCc-eeeee-----------ecccceeEEeccCCCCCCccceeEeee
Q 020198 281 PGKMGRIIGRRGS-SILAI-----------KESCNAEILIGGAKGPPDKDESLHVHC 325 (329)
Q Consensus 281 ~~~~~~~~~~~~~-~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 325 (329)
-|.||++|.|-.. ++-.+ ....+..+++|||-.| ++.|+||.+.
T Consensus 39 ~Ga~GlIlNrp~~~~l~~ll~~~~~~~~~~~~~~~~~v~~GGPV~~-~~~~~Lh~~~ 94 (191)
T PRK00228 39 NGAMGLVINRPSELDVAEVLPQLDILATPPEIRLDQPVFLGGPVQT-DRGFVLHSPR 94 (191)
T ss_pred CCceEEEEcCCCCCCHHHHHHHhcccccCcccccCCeEEeCCCccC-CcEEEEEECC
Confidence 4778888887532 12111 1122467999998885 7899999773
No 102
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=38.89 E-value=4.3 Score=34.25 Aligned_cols=32 Identities=25% Similarity=0.468 Sum_probs=26.0
Q ss_pred ecccCCCCCcceeecccCceeeeeecccceeE
Q 020198 275 SILDVPPGKMGRIIGRRGSSILAIKESCNAEI 306 (329)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 306 (329)
....|+++.+|++||++|.+|.++.+-++-.+
T Consensus 101 ~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~ 132 (140)
T PRK08406 101 AYVEVAPEDKGIAIGKNGKNIERAKDLAKRHF 132 (140)
T ss_pred EEEEECccccchhhCCCCHHHHHHHHHhCCcc
Confidence 34678899999999999999998877666544
No 103
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=36.35 E-value=9.2 Score=26.79 Aligned_cols=30 Identities=30% Similarity=0.525 Sum_probs=22.0
Q ss_pred cccCCCCCcceeecccCceeeeeeccccee
Q 020198 276 ILDVPPGKMGRIIGRRGSSILAIKESCNAE 305 (329)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 305 (329)
..-+..+..|++||++|.+|.++....+--
T Consensus 28 ~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~ 57 (68)
T cd02409 28 IIVVARGQPGLVIGKKGQNIRALQKLLQKL 57 (68)
T ss_pred EEEECCCCCceEECCCCccHHHHHHHHHHH
Confidence 334444467999999999999887766533
No 104
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=36.15 E-value=19 Score=36.73 Aligned_cols=40 Identities=33% Similarity=0.462 Sum_probs=36.3
Q ss_pred ceecccCCCCCcceeecccCceeeeeecccceeEEeccCC
Q 020198 273 ILSILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAK 312 (329)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 312 (329)
+-.++=||....|.+||+.|+.|.+|.+.-+|.|-|.+..
T Consensus 338 v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~ 377 (485)
T KOG2190|consen 338 VTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKE 377 (485)
T ss_pred eeeeeccCccccceeecccccchHHHHHhcCCceEEcccc
Confidence 6677788888899999999999999999999999999855
No 105
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=35.56 E-value=8.4 Score=32.50 Aligned_cols=31 Identities=29% Similarity=0.509 Sum_probs=24.5
Q ss_pred CCCCCcceeecccCceeeeeecccceeEEec
Q 020198 279 VPPGKMGRIIGRRGSSILAIKESCNAEILIG 309 (329)
Q Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 309 (329)
|++|.+|..||.+|+.|.+|.+..+-.|=|-
T Consensus 38 V~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 38 VKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred EeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 4578899999999999999987776444443
No 106
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=29.72 E-value=35 Score=31.96 Aligned_cols=46 Identities=28% Similarity=0.468 Sum_probs=38.0
Q ss_pred ccCCCCCcceeecccCceeeeeecccceeEEecc-CCCCCCccceeE
Q 020198 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILIGG-AKGPPDKDESLH 322 (329)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 322 (329)
.-||..--|.+|||.|..|--|.+...|.|-|-. -.|-||++..|.
T Consensus 319 vtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitIt 365 (390)
T KOG2192|consen 319 VTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT 365 (390)
T ss_pred EecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEe
Confidence 3344333578999999999999999999999998 578999988774
No 107
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=29.16 E-value=4.3 Score=30.21 Aligned_cols=29 Identities=31% Similarity=0.566 Sum_probs=23.7
Q ss_pred cCCCCCcceeecccCceeeeeecccceeE
Q 020198 278 DVPPGKMGRIIGRRGSSILAIKESCNAEI 306 (329)
Q Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 306 (329)
-+-.++.|.+||++|++|..|.+...-++
T Consensus 30 ~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 30 VIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp EEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred EEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 34467789999999999999988877665
No 108
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=28.39 E-value=16 Score=32.60 Aligned_cols=29 Identities=41% Similarity=0.540 Sum_probs=26.6
Q ss_pred cceeecccCceeeeeecccceeEEeccCC
Q 020198 284 MGRIIGRRGSSILAIKESCNAEILIGGAK 312 (329)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 312 (329)
.||+||+.|.+-.+|....++.|.++|..
T Consensus 113 kgRIIG~~GkTr~~IE~lt~~~I~V~g~t 141 (194)
T COG1094 113 KGRIIGREGKTRRAIEELTGVYISVYGKT 141 (194)
T ss_pred hceeeCCCchHHHHHHHHhCCeEEEeCcE
Confidence 49999999999999999999999999853
No 109
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=27.10 E-value=16 Score=34.21 Aligned_cols=37 Identities=35% Similarity=0.596 Sum_probs=30.6
Q ss_pred ceeecccCceeeeeecccce--eEEeccCCCCCCcccee
Q 020198 285 GRIIGRRGSSILAIKESCNA--EILIGGAKGPPDKDESL 321 (329)
Q Consensus 285 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~ 321 (329)
|-+|||.|++|-.+.+.|.| .||.|-..+--|||.++
T Consensus 135 g~iigrngskikelrekcsarlkift~c~p~stdrv~l~ 173 (390)
T KOG2192|consen 135 GGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLI 173 (390)
T ss_pred cceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEe
Confidence 66799999999999999986 46778777778887654
No 110
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=26.88 E-value=21 Score=36.44 Aligned_cols=39 Identities=33% Similarity=0.547 Sum_probs=33.6
Q ss_pred ceecccCCCCCcceeecccCceeeeeecccceeEEeccC
Q 020198 273 ILSILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGA 311 (329)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 311 (329)
+-=++=||...+|-+||++|..|-.|.+.++|-|.|-+.
T Consensus 138 v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~ 176 (485)
T KOG2190|consen 138 VTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD 176 (485)
T ss_pred eEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC
Confidence 344455778889999999999999999999999999875
No 111
>PRK06722 exonuclease; Provisional
Probab=25.84 E-value=26 Score=33.08 Aligned_cols=69 Identities=13% Similarity=0.057 Sum_probs=37.3
Q ss_pred HHHhccccccccceeeeeccccCccchhhee---cceeec-----ccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCC
Q 020198 90 VVKACKPALESSYITKVIHDCKRDSEALYFQ---FGIKLH-----NVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADP 161 (329)
Q Consensus 90 ~~~~L~~lLed~~i~KV~hd~k~Dl~~L~~~---~Gi~l~-----~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~ 161 (329)
++..+..++.+..+ |+|++.+|...|.+. +|+... ..+|++-.++-+-+.... ...||..+++
T Consensus 80 Vl~ef~~fig~~~l--vahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~-----~~~sL~~l~~-- 150 (281)
T PRK06722 80 IIEKFIQFIGEDSI--FVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFE-----HTPSLQSAVE-- 150 (281)
T ss_pred HHHHHHHHHCCCcE--EEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhcc-----CCCCHHHHHH--
Confidence 44566666765433 677889999888643 444321 135665322211111001 1257888885
Q ss_pred cccCCcc
Q 020198 162 RYCGISY 168 (329)
Q Consensus 162 ~~Lg~~l 168 (329)
++|++.
T Consensus 151 -~lgL~~ 156 (281)
T PRK06722 151 -QLGLIW 156 (281)
T ss_pred -HCCCCC
Confidence 667664
No 112
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=25.15 E-value=27 Score=34.53 Aligned_cols=64 Identities=23% Similarity=0.226 Sum_probs=41.0
Q ss_pred HhccccccccceeeeeccccCccchhheecceeecccchhHHHHHHHHhHhcCCCCCCCeeeeeecccCCcccCCcc
Q 020198 92 KACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISY 168 (329)
Q Consensus 92 ~~L~~lLed~~i~KV~hd~k~Dl~~L~~~~Gi~l~~vfDt~lA~~LL~~~~~~~~l~~~~~sL~~L~~~~~~Lg~~l 168 (329)
..|+.++....| -|||..-.|+.+|...| ..+.||.+. +....+... ...||..|++ .|||..+
T Consensus 285 ~~l~~~~~~~TI-LVGHSLenDL~aLKl~H----~~ViDTa~l---f~~~~g~~~---~k~sLk~L~~--~~L~~~I 348 (380)
T KOG2248|consen 285 KELLELISKNTI-LVGHSLENDLKALKLDH----PSVIDTAVL---FKHPTGPYP---FKSSLKNLAK--SYLGKLI 348 (380)
T ss_pred HHHHhhcCcCcE-EEeechhhHHHHHhhhC----CceeeeeEE---EecCCCCcc---chHHHHHHHH--HHHHHHH
Confidence 456666655555 49999999999995322 357899853 333322111 1357888998 8887544
No 113
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=25.04 E-value=36 Score=34.58 Aligned_cols=27 Identities=37% Similarity=0.609 Sum_probs=26.1
Q ss_pred cceeecccCceeeeeecccceeEEecc
Q 020198 284 MGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
+|++||=+|.+.-.|.+.++|.|.|=|
T Consensus 155 vGLiiGPRG~TqK~lE~etgAKI~IRG 181 (554)
T KOG0119|consen 155 VGLIIGPRGNTQKRLERETGAKIAIRG 181 (554)
T ss_pred eEEEecCCccHHHHHHHHhCCeEEEec
Confidence 699999999999999999999999988
No 114
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=24.98 E-value=63 Score=32.30 Aligned_cols=43 Identities=26% Similarity=0.489 Sum_probs=35.6
Q ss_pred CCC-cceeecccCceeeeeecc--cceeEEeccCCCCCCccceeEe
Q 020198 281 PGK-MGRIIGRRGSSILAIKES--CNAEILIGGAKGPPDKDESLHV 323 (329)
Q Consensus 281 ~~~-~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 323 (329)
|++ .|.+||..|++|..|.++ |+.+++==.-+|--||+..+|-
T Consensus 206 ptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~ 251 (584)
T KOG2193|consen 206 PTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHS 251 (584)
T ss_pred ccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEec
Confidence 455 699999999999999886 5577777778899999988884
No 115
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=24.94 E-value=33 Score=34.21 Aligned_cols=44 Identities=23% Similarity=0.547 Sum_probs=35.9
Q ss_pred ceecccCCCCCcceeecccCceeeeeecccceeEEeccCCCCCC
Q 020198 273 ILSILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPD 316 (329)
Q Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 316 (329)
|....+||..-.|||||.+|.+++.+-.-..||+.|---.-|..
T Consensus 493 lethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdE 536 (584)
T KOG2193|consen 493 LETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDE 536 (584)
T ss_pred eeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCc
Confidence 45667887777899999999999999999999999876554433
No 116
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=24.11 E-value=31 Score=35.74 Aligned_cols=36 Identities=31% Similarity=0.482 Sum_probs=31.4
Q ss_pred eecccCCCCCcceeecccCceeeeeecccceeEEec
Q 020198 274 LSILDVPPGKMGRIIGRRGSSILAIKESCNAEILIG 309 (329)
Q Consensus 274 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 309 (329)
-.+.+||..++|.+||+.|-+|..|--...+.|-|=
T Consensus 231 ~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfk 266 (600)
T KOG1676|consen 231 TREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFK 266 (600)
T ss_pred eeEEeccccceeeEEecCchHHHHHhhccCceeEee
Confidence 456789999999999999999999988888888763
No 117
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=23.71 E-value=15 Score=29.53 Aligned_cols=26 Identities=23% Similarity=0.460 Sum_probs=20.6
Q ss_pred CCCCcceeecccCceeeeeeccccee
Q 020198 280 PPGKMGRIIGRRGSSILAIKESCNAE 305 (329)
Q Consensus 280 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 305 (329)
-.++.|++||++|++|-+|++.....
T Consensus 68 ~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 68 HTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred EeCCCCcccCCchHHHHHHHHHHHHH
Confidence 34556899999999999888776654
No 118
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=23.40 E-value=27 Score=31.59 Aligned_cols=27 Identities=37% Similarity=0.655 Sum_probs=25.9
Q ss_pred cceeecccCceeeeeecccceeEEecc
Q 020198 284 MGRIIGRRGSSILAIKESCNAEILIGG 310 (329)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (329)
+|+.||-+|++..-+.+-.+|.|+|-|
T Consensus 165 VGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 165 VGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred eEEEecCCcchHHHHHHHhCCeEEEec
Confidence 699999999999999999999999988
No 119
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=22.90 E-value=23 Score=30.02 Aligned_cols=32 Identities=28% Similarity=0.498 Sum_probs=24.9
Q ss_pred ccCCCCCcceeecccCceeeeeecccceeEEe
Q 020198 277 LDVPPGKMGRIIGRRGSSILAIKESCNAEILI 308 (329)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 308 (329)
+=|.+|.+|..||.+|+.|.+|.+..+=.|=|
T Consensus 37 fvV~~g~vG~~IG~~G~rIk~i~el~gekIdV 68 (141)
T TIGR01952 37 FVVKEGEMGAAIGKGGENVKRLEELIGKSIEL 68 (141)
T ss_pred EEEcCCCccccCCCCchHHHHHHHhcCCeeEE
Confidence 34568899999999999999997766644433
Done!