Query 023967
Match_columns 274
No_of_seqs 138 out of 503
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 07:57:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023967.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023967hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0304 mRNA deadenylase subun 100.0 9.6E-89 2.1E-93 589.2 18.5 237 12-251 1-239 (239)
2 COG5228 POP2 mRNA deadenylase 100.0 3.7E-78 8E-83 524.1 12.9 257 8-269 15-272 (299)
3 PF04857 CAF1: CAF1 family rib 100.0 4.7E-65 1E-69 463.2 19.0 228 14-246 1-262 (262)
4 KOG1990 Poly(A)-specific exori 99.3 1.7E-12 3.7E-17 129.8 3.9 232 18-253 1-365 (564)
5 PRK07942 DNA polymerase III su 99.0 1.2E-08 2.5E-13 91.6 14.9 173 33-252 4-181 (232)
6 smart00479 EXOIII exonuclease 99.0 5.5E-08 1.2E-12 81.2 16.3 164 36-252 1-168 (169)
7 PRK05168 ribonuclease T; Provi 98.7 6.6E-07 1.4E-11 79.2 15.4 187 25-252 7-202 (211)
8 cd06131 DNA_pol_III_epsilon_Ec 98.7 6.4E-07 1.4E-11 75.4 14.4 163 37-247 1-166 (167)
9 cd06133 ERI-1_3'hExo_like DEDD 98.7 5.7E-07 1.2E-11 75.8 13.9 169 37-247 1-175 (176)
10 PRK09145 DNA polymerase III su 98.7 6.5E-07 1.4E-11 78.3 14.6 170 26-249 20-199 (202)
11 cd06134 RNaseT DEDDh 3'-5' exo 98.7 7.7E-07 1.7E-11 77.3 14.0 175 34-250 4-188 (189)
12 PRK05711 DNA polymerase III su 98.6 2.3E-06 4.9E-11 77.4 15.2 168 35-250 4-175 (240)
13 PRK07748 sporulation inhibitor 98.5 2.4E-06 5.3E-11 75.1 14.4 173 34-250 3-179 (207)
14 cd06130 DNA_pol_III_epsilon_li 98.5 2.4E-06 5.3E-11 70.7 13.1 151 37-245 1-155 (156)
15 PRK06195 DNA polymerase III su 98.4 6.5E-06 1.4E-10 76.9 15.0 160 36-252 2-165 (309)
16 PRK06807 DNA polymerase III su 98.4 5.7E-06 1.2E-10 77.6 14.3 163 35-251 8-172 (313)
17 PRK06063 DNA polymerase III su 98.4 1E-05 2.2E-10 75.9 15.3 163 34-252 14-180 (313)
18 PRK07247 DNA polymerase III su 98.4 8.3E-06 1.8E-10 71.5 13.6 160 36-251 6-169 (195)
19 PRK06310 DNA polymerase III su 98.4 6.5E-06 1.4E-10 74.7 12.8 169 31-251 3-174 (250)
20 PRK07740 hypothetical protein; 98.3 1.8E-05 4E-10 71.5 15.2 168 33-252 57-227 (244)
21 TIGR00573 dnaq exonuclease, DN 98.3 1.4E-05 3E-10 70.9 14.0 168 32-252 4-178 (217)
22 TIGR01406 dnaQ_proteo DNA poly 98.3 2.5E-05 5.4E-10 69.8 15.1 168 36-251 1-172 (225)
23 PRK09146 DNA polymerase III su 98.3 4E-05 8.7E-10 69.2 15.9 168 32-253 44-229 (239)
24 TIGR01298 RNaseT ribonuclease 98.3 4.3E-05 9.3E-10 67.0 15.0 177 33-252 6-193 (200)
25 cd06127 DEDDh DEDDh 3'-5' exon 98.2 1.4E-05 3E-10 64.9 10.5 155 38-245 1-159 (159)
26 cd06136 TREX1_2 DEDDh 3'-5' ex 98.2 4.8E-05 1E-09 65.3 14.0 168 37-246 1-176 (177)
27 PRK08517 DNA polymerase III su 98.2 5.7E-05 1.2E-09 69.0 14.9 167 32-252 65-232 (257)
28 PF00929 RNase_T: Exonuclease; 98.2 1.4E-06 3.1E-11 70.9 4.0 156 38-244 1-164 (164)
29 PRK08074 bifunctional ATP-depe 98.2 4.4E-05 9.6E-10 81.0 15.4 166 35-252 3-170 (928)
30 PRK06722 exonuclease; Provisio 98.1 0.00011 2.3E-09 68.0 15.7 169 34-248 4-178 (281)
31 PRK07246 bifunctional ATP-depe 98.1 8.4E-05 1.8E-09 78.0 16.2 162 34-252 6-171 (820)
32 TIGR01405 polC_Gram_pos DNA po 98.1 6.1E-05 1.3E-09 81.6 15.4 168 33-253 188-357 (1213)
33 PRK07883 hypothetical protein; 98.0 0.00012 2.5E-09 73.8 14.4 169 29-252 9-183 (557)
34 PRK07983 exodeoxyribonuclease 98.0 0.00022 4.8E-09 63.6 14.3 148 37-251 2-154 (219)
35 TIGR01407 dinG_rel DnaQ family 97.9 0.00037 8.1E-09 73.4 15.4 161 36-252 1-166 (850)
36 cd06138 ExoI_N N-terminal DEDD 97.8 0.00028 6E-09 60.8 11.8 166 39-243 2-181 (183)
37 cd06144 REX4_like DEDDh 3'-5' 97.7 0.00027 5.9E-09 59.1 10.0 69 158-244 79-151 (152)
38 PTZ00315 2'-phosphotransferase 97.7 0.0013 2.9E-08 66.1 16.2 174 35-251 56-255 (582)
39 PRK09182 DNA polymerase III su 97.7 0.0012 2.6E-08 61.4 13.8 155 36-248 38-198 (294)
40 PRK06309 DNA polymerase III su 97.6 0.0015 3.3E-08 58.5 13.9 160 36-252 3-167 (232)
41 PRK05601 DNA polymerase III su 97.6 0.00075 1.6E-08 64.6 11.7 176 31-248 42-246 (377)
42 PRK11779 sbcB exonuclease I; P 97.6 0.0011 2.3E-08 65.7 13.1 174 34-250 5-197 (476)
43 PRK00448 polC DNA polymerase I 97.6 0.0012 2.7E-08 72.8 14.6 168 32-252 416-585 (1437)
44 COG0847 DnaQ DNA polymerase II 97.6 0.0018 3.9E-08 57.8 13.0 163 35-250 13-181 (243)
45 cd06145 REX1_like DEDDh 3'-5' 97.3 0.0023 4.9E-08 53.5 9.3 69 156-244 76-149 (150)
46 cd06137 DEDDh_RNase DEDDh 3'-5 97.2 0.0029 6.4E-08 53.4 9.7 68 157-244 85-160 (161)
47 PRK05359 oligoribonuclease; Pr 96.9 0.024 5.2E-07 49.0 12.8 166 35-253 3-177 (181)
48 cd06149 ISG20 DEDDh 3'-5' exon 96.8 0.0099 2.1E-07 50.1 9.6 97 125-244 51-156 (157)
49 PF01612 DNA_pol_A_exo1: 3'-5' 95.7 0.21 4.5E-06 41.4 11.3 84 151-251 72-175 (176)
50 PRK05755 DNA polymerase I; Pro 95.4 0.25 5.5E-06 52.6 13.4 83 154-252 368-470 (880)
51 cd06141 WRN_exo DEDDy 3'-5' ex 95.0 0.59 1.3E-05 39.1 12.1 80 153-248 70-169 (170)
52 cd06146 mut-7_like_exo DEDDy 3 94.9 0.46 1E-05 41.2 11.4 87 152-248 78-192 (193)
53 COG0349 Rnd Ribonuclease D [Tr 94.7 0.24 5.2E-06 47.4 9.5 82 154-252 68-167 (361)
54 PRK10829 ribonuclease D; Provi 93.6 1.3 2.9E-05 42.6 12.4 85 153-253 71-172 (373)
55 cd06135 Orn DEDDh 3'-5' exonuc 93.5 1.9 4.1E-05 36.6 12.1 163 37-249 1-170 (173)
56 cd06129 RNaseD_like DEDDy 3'-5 92.8 3.3 7.1E-05 34.6 12.4 80 153-248 64-160 (161)
57 COG2176 PolC DNA polymerase II 82.6 2.8 6E-05 45.9 6.1 84 158-253 503-588 (1444)
58 PF10108 DNA_pol_B_exo2: Predi 81.3 5 0.00011 35.7 6.4 93 156-250 52-172 (209)
59 cd06139 DNA_polA_I_Ecoli_like_ 80.6 5.4 0.00012 33.4 6.3 84 154-253 65-172 (193)
60 PF13482 RNase_H_2: RNase_H su 74.4 1.3 2.9E-05 36.6 0.7 71 157-242 58-131 (164)
61 KOG1990 Poly(A)-specific exori 65.5 2.4 5.2E-05 43.1 0.5 153 10-165 101-262 (564)
62 cd05782 DNA_polB_like1_exo Unc 62.4 20 0.00043 31.5 5.7 68 158-226 95-170 (208)
63 COG3359 Predicted exonuclease 54.4 24 0.00051 32.5 4.8 76 158-246 158-237 (278)
64 TIGR01388 rnd ribonuclease D. 49.9 17 0.00036 34.9 3.4 83 154-252 68-167 (367)
65 COG5228 POP2 mRNA deadenylase 46.6 14 0.0003 33.4 2.0 94 162-269 197-298 (299)
66 cd00007 35EXOc 3'-5' exonuclea 46.6 62 0.0013 25.4 5.8 53 154-222 52-106 (155)
67 TIGR02841 spore_YyaC putative 41.0 28 0.00061 29.1 2.9 30 15-44 43-72 (140)
68 PF04405 ScdA_N: Domain of Unk 40.0 39 0.00084 23.6 3.1 32 115-146 12-52 (56)
69 cd05785 DNA_polB_like2_exo Unc 38.6 28 0.00062 30.5 2.8 69 158-226 76-169 (207)
70 KOG2249 3'-5' exonuclease [Rep 37.7 17 0.00036 33.7 1.2 54 197-251 207-266 (280)
71 TIGR01388 rnd ribonuclease D. 33.5 1.8E+02 0.0039 27.9 7.6 26 22-47 5-30 (367)
72 smart00474 35EXOc 3'-5' exonuc 31.5 2.7E+02 0.0058 22.1 7.4 80 154-250 73-170 (172)
73 KOG4013 Predicted Cu2+ homeost 31.5 61 0.0013 28.9 3.6 86 115-208 83-173 (255)
74 cd05776 DNA_polB_alpha_exo ina 28.3 64 0.0014 28.7 3.4 68 158-226 100-187 (234)
75 TIGR01229 rocF_arginase argina 27.1 2E+02 0.0043 26.6 6.5 68 15-84 196-272 (300)
76 PF13637 Ank_4: Ankyrin repeat 27.0 63 0.0014 21.3 2.4 29 115-143 13-41 (54)
77 PF06866 DUF1256: Protein of u 26.3 63 0.0014 27.7 2.8 31 15-45 67-97 (163)
78 PF13606 Ank_3: Ankyrin repeat 26.1 55 0.0012 19.4 1.8 17 115-131 14-30 (30)
79 PF12345 DUF3641: Protein of u 24.5 73 0.0016 26.5 2.7 32 121-152 16-48 (134)
80 PRK13772 formimidoylglutamase; 24.1 2.9E+02 0.0062 25.8 7.1 69 14-84 217-293 (314)
81 PF13967 RSN1_TM: Late exocyto 23.4 61 0.0013 26.9 2.2 64 188-252 20-90 (157)
82 cd06148 Egl_like_exo DEDDy 3'- 21.5 68 0.0015 27.6 2.1 86 152-253 61-179 (197)
83 PRK08446 coproporphyrinogen II 21.1 1.3E+02 0.0028 28.4 4.1 31 115-145 136-167 (350)
No 1
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=9.6e-89 Score=589.24 Aligned_cols=237 Identities=66% Similarity=1.132 Sum_probs=230.7
Q ss_pred eEEEcCcccHHHHHHHHHHHhhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCC
Q 023967 12 QIREVWNDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPT 91 (274)
Q Consensus 12 ~i~dVw~~Nf~~el~~I~~~i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~ 91 (274)
.|||||++|+++||..||++|++||||||||||||++.+|.+.++++.+++||.||+|||.+++||+|||+++++|++|.
T Consensus 1 ~ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p~ 80 (239)
T KOG0304|consen 1 FIREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNLPD 80 (239)
T ss_pred ChhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccCCCCCC
Confidence 37999999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCCeeeEEEeeeccCCCCccchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHH
Q 023967 92 CGTDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYL 171 (274)
Q Consensus 92 ~~~~~~~~~~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yL 171 (274)
.| .++|||||.+|+..+|+++++||+||+++|+||.|+.+.||+..+|+|+|++||++++++|+||||||+||||||
T Consensus 81 ~g---~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYL 157 (239)
T KOG0304|consen 81 CG---TDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYL 157 (239)
T ss_pred CC---CceeEEecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHH
Confidence 65 469999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhcc--ccccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHH
Q 023967 172 LKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNS--LHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRE 249 (274)
Q Consensus 172 lk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~--l~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~ 249 (274)
+|+||+++||++.++|.+.++++||.+||+|||++.|.+ +++||++||+.|+++|+|++|||||||+||+.+|+||++
T Consensus 158 lK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 158 LKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred HHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhhhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999955 899999999999999999999999999999999999998
Q ss_pred Hh
Q 023967 250 NF 251 (274)
Q Consensus 250 ~~ 251 (274)
.|
T Consensus 238 ~f 239 (239)
T KOG0304|consen 238 LF 239 (239)
T ss_pred cC
Confidence 64
No 2
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=3.7e-78 Score=524.13 Aligned_cols=257 Identities=49% Similarity=0.850 Sum_probs=241.3
Q ss_pred CCcceEEEcCcccHHHHHHHHHHHhhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCC
Q 023967 8 GDEIQIREVWNDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENG 87 (274)
Q Consensus 8 ~~~~~i~dVw~~Nf~~el~~I~~~i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g 87 (274)
+.-..|||||++|+..||..|+++|.+|++|+|||||||+++||.|.|+++.+++||.+|+|||.++|||+||++++++|
T Consensus 15 ~~~~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~G 94 (299)
T COG5228 15 PNYLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENG 94 (299)
T ss_pred cchHHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccC
Confidence 33456999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCeeeEEEeeeccCCCCccchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchh
Q 023967 88 NLPTCGTDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYD 167 (274)
Q Consensus 88 ~~p~~~~~~~~~~~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD 167 (274)
+.|. ..|||||||- |++.+||++++||++|+++|+||.||.+.||+..+|+|+|+.||||++++|+|||||++||
T Consensus 95 N~P~----~~sTWQFNF~-F~l~~dmya~ESieLL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~VtWitfHsaYD 169 (299)
T COG5228 95 NKPN----GPSTWQFNFE-FDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYD 169 (299)
T ss_pred CCCC----CCceeEEEEE-ecchhhhcchHHHHHHHHcCCChhhHhhcCCCHHHHHHHHhccCceeccceEEEEeecchh
Confidence 9984 5899999999 9999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhccccccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHH
Q 023967 168 FGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKL 247 (274)
Q Consensus 168 ~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~l~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l 247 (274)
||||+|+|++.|||+..++|..++++|||+.||+|++.+...+.+.||++++..|++.|.|++||||+||++|+..|++.
T Consensus 170 fgyLikilt~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~ 249 (299)
T COG5228 170 FGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLP 249 (299)
T ss_pred HHHHHHHHhcCCCCccHHHHHHHHHHHCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcch
Confidence 99999999999999999999999999999999999999999889999999999999999999999999999999999999
Q ss_pred HHHhcCCC-ccccccEEEecCCC
Q 023967 248 RENFFNGC-TEKYAGVLYGLGVE 269 (274)
Q Consensus 248 ~~~~~~~~-~~~~~g~i~Gl~~~ 269 (274)
|..+|++. -...-..+||++..
T Consensus 250 R~~~F~~sig~~ll~~L~g~~~~ 272 (299)
T COG5228 250 RFSIFTTSIGQSLLMLLSGCQLS 272 (299)
T ss_pred hhheecccccHHHHHHHhccccC
Confidence 99988642 23344445555444
No 3
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=100.00 E-value=4.7e-65 Score=463.16 Aligned_cols=228 Identities=37% Similarity=0.611 Sum_probs=201.7
Q ss_pred EEcCcccHHHHHHHHHHHhhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeee-cCCCCCCCC
Q 023967 14 REVWNDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFS-DENGNLPTC 92 (274)
Q Consensus 14 ~dVw~~Nf~~el~~I~~~i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~-~~~g~~p~~ 92 (274)
+|||++||+++++.|+++|++|+|||||+||||+..++.....+++++||+++|.||+.+++||+|||++ +++++.|.
T Consensus 1 m~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~- 79 (262)
T PF04857_consen 1 MEVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPS- 79 (262)
T ss_dssp EEE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEEC-
T ss_pred CcccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCc-
Confidence 6999999999999999999999999999999999998865578899999999999999999999999999 77888774
Q ss_pred CCCCeeeEEEeeeccCCCCccchhhhHHHHHHcCCCccchhhcCCChhHHH------HHHHHhcccc---cCceeEEeec
Q 023967 93 GTDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKKNNEKGIDVNRFG------ELLMSSGIVL---NDVVRWVTFH 163 (274)
Q Consensus 93 ~~~~~~~~~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~------e~l~~Sglv~---~~~~~wi~f~ 163 (274)
.+.+|+|||+.|+.+++.++++||+||++||||||+++++||+|..++ +.+..++++. ..+++||+||
T Consensus 80 ---~~~~~~~nf~~f~~~~~~~~~~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn 156 (262)
T PF04857_consen 80 ---SYNVWPFNFYLFPLDRDFSQASSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHN 156 (262)
T ss_dssp ---CEEEEEEEBSTTSTTTCEEEHHHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESS
T ss_pred ---eeEEEEeeeeccccccceecchhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeC
Confidence 589999999999999998899999999999999999999999999999 6677788875 4458999999
Q ss_pred cchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhccccccHHHHHHHcCCcc-----------------
Q 023967 164 SGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNSLHGGLNKLAELLEVER----------------- 226 (274)
Q Consensus 164 g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~l~~~L~~la~~L~v~r----------------- 226 (274)
|.||++||++.+++ |||+|+++|++.++.+||.|||||||++.+....++|+.|++.|++.|
T Consensus 157 ~~~Dl~~l~~~f~~-~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~ 235 (262)
T PF04857_consen 157 GLYDLMYLYKKFIG-PLPETLEEFKELLRELFPRIYDTKYLAEECPGKSTSLQELAEELGIRRNPSSISSPEGFPSYDEE 235 (262)
T ss_dssp THHHHHHHHHHHTT-S--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS-SSHHHHHHHTTSTT----EEE-TTS------
T ss_pred hHhHHHHHHHHhcC-CCCCCHHHHHHHHHHHCcccccHHHHHHhccccccCHHHHHHHhCCCcccccccccccccccccc
Confidence 99999999999997 999999999999999999999999999999877899999999999988
Q ss_pred ------CCC-CcccchhHHHHHHHHHH
Q 023967 227 ------VGI-CHQAGSDSLLTSCTFRK 246 (274)
Q Consensus 227 ------~g~-~HqAGsDs~lT~~~F~~ 246 (274)
.+. .||||+||||||.||++
T Consensus 236 ~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 236 KNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp -------SS-TTSHHHHHHHHHHHHHH
T ss_pred ccccccCCCCCCCcchHHHHHHHHHcC
Confidence 566 99999999999999986
No 4
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.28 E-value=1.7e-12 Score=129.80 Aligned_cols=232 Identities=18% Similarity=0.198 Sum_probs=159.4
Q ss_pred cccHHHHHHHHHHHhhhCCeeEEeccccccccCCC--CCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCC--C
Q 023967 18 NDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRPV--GAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTC--G 93 (274)
Q Consensus 18 ~~Nf~~el~~I~~~i~~~~fIAiDtEf~G~~~~~~--~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~--~ 93 (274)
+.|++. +..++..|+++.|+++|.|++|+...+. +.-.+++|.+|+++|.|+-.+.++|+|+|.|..++.-... +
T Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 79 (564)
T KOG1990|consen 1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMST 79 (564)
T ss_pred CCcccc-hhHHHhhcCHHHHHHHhhhhccceecccccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccC
Confidence 468889 9999999999999999999999988873 2236889999999999999999999999999987653321 0
Q ss_pred CCCeeeEEEeeeccCCCCccchhhhHHHHHHcCCCccch-----------hhcCCCh-----------------------
Q 023967 94 TDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKKN-----------NEKGIDV----------------------- 139 (274)
Q Consensus 94 ~~~~~~~~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~-----------~~~GI~~----------------------- 139 (274)
.....+|+.-.. ....+.+|+.+++.++.+++-++..- ...|+.+
T Consensus 80 ~~n~~~~~~g~~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~ 158 (564)
T KOG1990|consen 80 GGNFVVWSRGDS-ISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIP 158 (564)
T ss_pred CCceeeeecCcc-ccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhh
Confidence 011334443222 22224578888888888872211110 0112222
Q ss_pred ---------------------------------------------------------hHHHHHHHHhcc-----------
Q 023967 140 ---------------------------------------------------------NRFGELLMSSGI----------- 151 (274)
Q Consensus 140 ---------------------------------------------------------~~f~e~l~~Sgl----------- 151 (274)
..|++.++..|.
T Consensus 159 ~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~ 238 (564)
T KOG1990|consen 159 DYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADE 238 (564)
T ss_pred cccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHH
Confidence 012222222222
Q ss_pred ---cccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHh--hcc--ccccHHHHHHHcC-
Q 023967 152 ---VLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKF--CNS--LHGGLNKLAELLE- 223 (274)
Q Consensus 152 ---v~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~--~~~--l~~~L~~la~~L~- 223 (274)
+......-|.+++.+|+.|+.+-+.+ +||+++.+|.+. ...||.++|++.+++. ... +.+.+.+.+..-.
T Consensus 239 l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~-~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~ 316 (564)
T KOG1990|consen 239 LQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDS-SSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAK 316 (564)
T ss_pred HHHHHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhh-hhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcc
Confidence 12233355788899999999999987 999999999999 9999999999998882 222 4454444432111
Q ss_pred C-------------------ccCCCCcccchhHHHHHHHHHHHHHHhcC
Q 023967 224 V-------------------ERVGICHQAGSDSLLTSCTFRKLRENFFN 253 (274)
Q Consensus 224 v-------------------~r~g~~HqAGsDs~lT~~~F~~l~~~~~~ 253 (274)
. ..-+..|+++++++.++.++.+......+
T Consensus 317 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 365 (564)
T KOG1990|consen 317 KEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILA 365 (564)
T ss_pred cccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhh
Confidence 0 01256789999999999999998777664
No 5
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.00 E-value=1.2e-08 Score=91.59 Aligned_cols=173 Identities=21% Similarity=0.214 Sum_probs=116.6
Q ss_pred hhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCc
Q 023967 33 DKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDD 112 (274)
Q Consensus 33 ~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d 112 (274)
.+.+||++|+|-||+. | ..=.|||+|+..++.+|+.. ..|+.. .+.. .
T Consensus 4 ~~~~~vv~D~ETTGl~--p-------------------~~d~Iieig~v~v~~~g~~~---------~~~~~l-v~P~-~ 51 (232)
T PRK07942 4 HPGPLAAFDLETTGVD--P-------------------ETARIVTAALVVVDADGEVV---------ESREWL-ADPG-V 51 (232)
T ss_pred ccCcEEEEEeccCCCC--C-------------------CCCeeEEEEEEEEeCCCccc---------cceEEE-ECCC-C
Confidence 3568999999999983 1 11248999999998666532 234433 3332 2
Q ss_pred cchhhhHHHHHHcCCCccchhhcCCChhH-HHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHH
Q 023967 113 IFASDSVELLHQCGIDFKKNNEKGIDVNR-FGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELI 191 (274)
Q Consensus 113 ~~~~~Si~fL~~~GfDFnk~~~~GI~~~~-f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l 191 (274)
.+.+++.+. |||.=..+..+|.+... +.+..-.-.-....+..+|+||..||+++|-+.+...-+|.-
T Consensus 52 ~i~~~a~~I---hGIt~e~l~~~g~~~~~vl~e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~-------- 120 (232)
T PRK07942 52 EIPEEASAV---HGITTEYARAHGRPAAEVLAEIADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSL-------- 120 (232)
T ss_pred CCCHHHHHH---hCCCHHHHHhhCCCHHHHHHHHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCc--------
Confidence 456666655 99999999989998643 222221100001234468999999999999887732222211
Q ss_pred HccCC-ccccchhhhHhhccc---cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 192 NMYFP-VVYDIKHLMKFCNSL---HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 192 ~~~FP-~iyDtK~l~~~~~~l---~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
.| .++|+-.|++.+... +-+|+.+++.+|++.. ..|.|-+|++.|+++|.+|.+++.
T Consensus 121 ---~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~~-~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 121 ---VPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRLD-NAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred ---cCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCCC-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 12 356887777665322 2379999999999854 479999999999999999988775
No 6
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.96 E-value=5.5e-08 Score=81.19 Aligned_cols=164 Identities=22% Similarity=0.215 Sum_probs=113.8
Q ss_pred CeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccch
Q 023967 36 NYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFA 115 (274)
Q Consensus 36 ~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~ 115 (274)
.||++|+|.+|+... .-.|+|+|....+.+. ....|+.+ ... ....+
T Consensus 1 ~~v~~D~Ettg~~~~---------------------~~~Iieig~v~~~~~~----------~~~~f~~~-v~p-~~~i~ 47 (169)
T smart00479 1 TLVVIDCETTGLDPG---------------------KDEIIEIAAVDVDGGR----------IIVVFDTY-VKP-DRPIT 47 (169)
T ss_pred CEEEEEeeCCCCCCC---------------------CCeEEEEEEEEEECCE----------eEEEEEEE-ECC-CCCCC
Confidence 389999999997421 1359999998877532 24567776 333 23344
Q ss_pred hhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeecc-chhHHHHHHHhC--CCCCCCChHHHHHHHH
Q 023967 116 SDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHS-GYDFGYLLKLLT--CRSLPDTQAGFFELIN 192 (274)
Q Consensus 116 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g-~yD~~yLlk~l~--~~~LP~~~~~F~~~l~ 192 (274)
+.+.+ -+|+.-+.+.. |.+..+..+.+.. .+ .+ -.+|++|+ .||+.+|-+.+. +.+.|..
T Consensus 48 ~~~~~---~~Git~~~l~~-~~~~~~~~~~~~~--~l-~~-~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~--------- 110 (169)
T smart00479 48 DYATE---IHGITPEMLDD-APTFEEVLEELLE--FL-KG-KILVAGNALNFDLRFLKLEHPRLGIKDPPK--------- 110 (169)
T ss_pred HHHHH---HhCCCHHHHhC-CCCHHHHHHHHHH--Hh-cC-CEEEEeCCHHHhHHHHHHHHHHhCCCCCcC---------
Confidence 55544 47888777654 8888765544432 12 12 25789999 999999988774 3333311
Q ss_pred ccCCccccchhhhHhh-ccccccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 193 MYFPVVYDIKHLMKFC-NSLHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 193 ~~FP~iyDtK~l~~~~-~~l~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
-..+|+.-+++.. +....+|+.+++.++++..+..|.|-.|+..|+++|.+|.+..+
T Consensus 111 ---~~~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 111 ---NPVIDTLKLARALNPGRKYSLKKLAERLGLEVIGRAHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred ---CCeeEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHHhh
Confidence 1266776666544 22367999999999999988889999999999999999987653
No 7
>PRK05168 ribonuclease T; Provisional
Probab=98.71 E-value=6.6e-07 Score=79.15 Aligned_cols=187 Identities=16% Similarity=0.188 Sum_probs=123.3
Q ss_pred HHHHHHHhhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecC--CCCCCCCCCCCeeeEEE
Q 023967 25 FALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDE--NGNLPTCGTDKFCIWQF 102 (274)
Q Consensus 25 l~~I~~~i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~--~g~~p~~~~~~~~~~~F 102 (274)
+.-|..-++...||++|+|-||+.... + .|||+|....+. +|.+. ....|
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~-----d----------------~IieIgaV~v~~d~~g~i~-------~~~~f 58 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKT-----D----------------ALLEIAAVTLKMDEQGWLY-------PDETL 58 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCC-----C----------------EEEEEeEEEEEecCCCcEe-------ccceE
Confidence 345777889999999999999985321 1 299999887764 34321 23456
Q ss_pred eeeccCCCCccchhhhHHHHHHcCCCccchhhcCCChhH-HHHHHHH--hccc--ccCceeEEeeccchhHHHHHHHhCC
Q 023967 103 NFREFNLIDDIFASDSVELLHQCGIDFKKNNEKGIDVNR-FGELLMS--SGIV--LNDVVRWVTFHSGYDFGYLLKLLTC 177 (274)
Q Consensus 103 NF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~-f~e~l~~--Sglv--~~~~~~wi~f~g~yD~~yLlk~l~~ 177 (274)
..+.-|.......+++++. ||+.=+...++|++... +.+.+-. ..+. ...+..+|+||-.||++||-+.+..
T Consensus 59 ~~lv~P~~~~~i~~~~~~i---hGIt~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r 135 (211)
T PRK05168 59 HFHVEPFEGANLEPEALAF---NGIDPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAER 135 (211)
T ss_pred EEEECCCCCCCCCHHHHhh---cCCCchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHH
Confidence 6662232233566676665 89865556677887643 2232211 1110 0124579999999999999887631
Q ss_pred CCCCCChHHHHHHHHccCC-ccccchhhhHhhccccccHHHHHHHcCCccC-CCCcccchhHHHHHHHHHHHHHHhc
Q 023967 178 RSLPDTQAGFFELINMYFP-VVYDIKHLMKFCNSLHGGLNKLAELLEVERV-GICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 178 ~~LP~~~~~F~~~l~~~FP-~iyDtK~l~~~~~~l~~~L~~la~~L~v~r~-g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
..+.. ..+.| .++||.-+++..... .+|..+++.+|++.. ...|.|-+|++.|+++|.+|.+++.
T Consensus 136 ~~~~~---------~~~~~~~~iDt~~lar~~~~~-~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 136 AGLKR---------NPFHPFSTFDTATLSGLALGQ-TVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred hCCCC---------CCCCCCcEeeHHHHHHHHcCC-CCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 11110 01123 478998888765222 379999999999854 3689999999999999999998874
No 8
>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=98.69 E-value=6.4e-07 Score=75.40 Aligned_cols=163 Identities=18% Similarity=0.186 Sum_probs=104.6
Q ss_pred eeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccchh
Q 023967 37 YIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFAS 116 (274)
Q Consensus 37 fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~~ 116 (274)
||++|+|-||+... +.-.|||+|....+. +. ....+|+.+ ..... ..++
T Consensus 1 ~v~~D~ETTGl~~~--------------------~~~~iieig~v~v~~-~~--------~~~~~~~~~-v~P~~-~i~~ 49 (167)
T cd06131 1 QIVLDTETTGLDPR--------------------EGHRIIEIGCVELIN-RR--------LTGNTFHVY-INPER-DIPE 49 (167)
T ss_pred CEEEEeeCCCCCCC--------------------CCCeEEEEEEEEEEC-Cc--------EeccEEEEE-ECCCC-CCCH
Confidence 79999999998320 123599999987653 22 122456665 33333 3566
Q ss_pred hhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCC
Q 023967 117 DSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFP 196 (274)
Q Consensus 117 ~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP 196 (274)
.+.+. ||+.=+.+... .+..+..+.+.. .+ .+ -.+|++|+.||..+|-+-+....++... ..|
T Consensus 50 ~~~~i---hGIt~e~l~~~-~~~~~v~~~l~~--~l-~~-~~lv~hn~~fD~~~l~~~~~~~~~~~~~---------~~~ 112 (167)
T cd06131 50 EAFKV---HGITDEFLADK-PKFAEIADEFLD--FI-RG-AELVIHNASFDVGFLNAELSLLGLGKKI---------IDF 112 (167)
T ss_pred HHHHH---hCCCHHHHhcC-CCHHHHHHHHHH--HH-CC-CeEEEeChHHhHHHHHHHHHHhCCCccc---------ccC
Confidence 66554 78777665443 333333333322 11 22 2589999999999887766421121110 013
Q ss_pred -ccccchhhhHhh-ccccccHHHHHHHcCCccCC-CCcccchhHHHHHHHHHHH
Q 023967 197 -VVYDIKHLMKFC-NSLHGGLNKLAELLEVERVG-ICHQAGSDSLLTSCTFRKL 247 (274)
Q Consensus 197 -~iyDtK~l~~~~-~~l~~~L~~la~~L~v~r~g-~~HqAGsDs~lT~~~F~~l 247 (274)
..+||-.+++.. .....+|+.+++.+|++..+ .+|.|-+|++.|+++|.+|
T Consensus 113 ~~~idt~~~~~~~~~~~~~~L~~l~~~~~i~~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 113 CRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCceEhHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHh
Confidence 467887666554 23456899999999999864 5899999999999999987
No 9
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=98.69 E-value=5.7e-07 Score=75.82 Aligned_cols=169 Identities=21% Similarity=0.208 Sum_probs=111.6
Q ss_pred eeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccchh
Q 023967 37 YIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFAS 116 (274)
Q Consensus 37 fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~~ 116 (274)
||.+|+|.+|...... .. ..-.|||||....+.++. ...-.|+.+.-|......++
T Consensus 1 ~vv~D~Ettg~~~~~~--------------~~--~~~~IieIgav~v~~~~~--------~~~~~f~~~i~P~~~~~i~~ 56 (176)
T cd06133 1 YLVIDFEATCWEGNSK--------------PD--YPNEIIEIGAVLVDVKTK--------EIIDTFSSYVKPVINPKLSD 56 (176)
T ss_pred CEEEEeeccccCCCCC--------------CC--CCcceEEEEEEEEEcCCC--------eEEeeeeeeECCCcCCchhH
Confidence 7999999999864321 00 112599999999987653 23456666644443335666
Q ss_pred hhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccC-ceeEEeeccchhHHHHHHHhCC---CCCCCChHHHHHHHH
Q 023967 117 DSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLND-VVRWVTFHSGYDFGYLLKLLTC---RSLPDTQAGFFELIN 192 (274)
Q Consensus 117 ~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~-~~~wi~f~g~yD~~yLlk~l~~---~~LP~~~~~F~~~l~ 192 (274)
.+.+. +|+..+.+. ++.+..+-.+.+.. .+.+. ....++ +|.+|...+.+-+.. .++|
T Consensus 57 ~~~~i---~gIt~e~l~-~~~~~~~vl~~~~~--~l~~~~~~~~v~-~~~~d~~~l~~~~~~~~~~~~~----------- 118 (176)
T cd06133 57 FCTEL---TGITQEDVD-NAPSFPEVLKEFLE--WLGKNGKYAFVT-WGDWDLKDLLQNQCKYKIINLP----------- 118 (176)
T ss_pred HHHHh---cCcCHHHHh-cCCCHHHHHHHHHH--HHHhCCCeEEEe-ecHhhHHHHHHHHHHhcCCCCc-----------
Confidence 66666 999998874 56766543332211 11111 233444 468898877765431 1111
Q ss_pred ccCCccccchhhhHhhccc--cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHH
Q 023967 193 MYFPVVYDIKHLMKFCNSL--HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKL 247 (274)
Q Consensus 193 ~~FP~iyDtK~l~~~~~~l--~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l 247 (274)
.++...+|++.+++..... ..+|.++++.+|++..+..|.|=+||..|+++|.+|
T Consensus 119 ~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 119 PFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred ccccceEEHHHHHHHHhCCCCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHh
Confidence 2345688998887766332 568999999999998889999999999999999987
No 10
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.68 E-value=6.5e-07 Score=78.33 Aligned_cols=170 Identities=15% Similarity=0.264 Sum_probs=107.3
Q ss_pred HHHHHHhhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeee
Q 023967 26 ALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFR 105 (274)
Q Consensus 26 ~~I~~~i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~ 105 (274)
..+.+.....+||++|+|.||+. |. .-.|||+|...++.+ .. .....|..+
T Consensus 20 ~~~~~~~~~~~~vviD~ETTGl~--~~-------------------~d~IieIgaV~~~~~-~~-------~~~~~f~~~ 70 (202)
T PRK09145 20 AFLFEPPPPDEWVALDCETTGLD--PR-------------------RAEIVSIAAVKIRGN-RI-------LTSERLELL 70 (202)
T ss_pred HHHhcCCCCCCEEEEEeECCCCC--CC-------------------CCceEEEEEEEEECC-EE-------eecCceEEE
Confidence 33444445579999999999983 20 125899999888743 21 122345555
Q ss_pred ccCCCCccchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHh---CCCCCCC
Q 023967 106 EFNLIDDIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLL---TCRSLPD 182 (274)
Q Consensus 106 ~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l---~~~~LP~ 182 (274)
.+... ...+.+.+. ||+.-..+ ++|.+..+.-+.+.. .+ .+-.||+++..||..+|.+-+ .+.++|.
T Consensus 71 -i~p~~-~i~~~~~~i---hGIt~~~l-~~~~~~~~vl~~~~~--~i--~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~ 140 (202)
T PRK09145 71 -VRPPQ-SLSAESIKI---HRLRHQDL-EDGLSEEEALRQLLA--FI--GNRPLVGYYLEFDVAMLNRYVRPLLGIPLPN 140 (202)
T ss_pred -ECCCC-CCCHhHhhh---cCcCHHHH-hcCCCHHHHHHHHHH--HH--cCCeEEEeCHHHHHHHHHHHHHHhcCCCCCC
Confidence 33332 345555554 77776655 456666543333322 11 123589999999999987765 2455654
Q ss_pred ChHHHHHHHHccCCccccchhhhHhh--cc-----ccccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHH
Q 023967 183 TQAGFFELINMYFPVVYDIKHLMKFC--NS-----LHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRE 249 (274)
Q Consensus 183 ~~~~F~~~l~~~FP~iyDtK~l~~~~--~~-----l~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~ 249 (274)
. .+|+.-+.... .. ..-+|+.+++.+|++..+ .|.|-+||+.|+.+|.+|.+
T Consensus 141 ~--------------~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~-~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 141 P--------------LIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVLG-RHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred C--------------eeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCCC-CCCcHHHHHHHHHHHHHHHh
Confidence 3 34554333211 11 124899999999998754 69999999999999999864
No 11
>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=98.65 E-value=7.7e-07 Score=77.32 Aligned_cols=175 Identities=18% Similarity=0.220 Sum_probs=115.4
Q ss_pred hCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecC--CCCCCCCCCCCeeeEEEeeeccCCCC
Q 023967 34 KYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDE--NGNLPTCGTDKFCIWQFNFREFNLID 111 (274)
Q Consensus 34 ~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~--~g~~p~~~~~~~~~~~FNF~~F~~~~ 111 (274)
.+.+|++|+|-||+.... + .|||+|...+.. +|.. ....+|++..-|...
T Consensus 4 ~~~~vv~D~ETTGl~~~~-----d----------------~Iieigav~v~~~~~~~i-------~~~~~f~~lv~P~~~ 55 (189)
T cd06134 4 GFLPVVVDVETGGFNPQT-----D----------------ALLEIAAVTLEMDEQGNL-------YPDETFHFHILPFEG 55 (189)
T ss_pred cceeEEEEecCCCCCCCC-----C----------------eEEEEEEEEEEECCCCce-------eccceEEEEEcCCCC
Confidence 467999999999985321 1 299999998864 3432 123466666233223
Q ss_pred ccchhhhHHHHHHcCCCccchhhcCCChhH-HHHHHHHh-cccc---cCceeEEeeccchhHHHHHHHhCCCCCCCChHH
Q 023967 112 DIFASDSVELLHQCGIDFKKNNEKGIDVNR-FGELLMSS-GIVL---NDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAG 186 (274)
Q Consensus 112 d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~-f~e~l~~S-glv~---~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~ 186 (274)
..+.+++++. |||.=+...+.|++... +.+.+-.- .++. .++-.+|+||..||.+||-+.+....++
T Consensus 56 ~~i~~~~~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~----- 127 (189)
T cd06134 56 ANLDPAALEF---NGIDPFHPFRFAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIK----- 127 (189)
T ss_pred CCCCHHHHhh---cCCCchhhhccccchHHHHHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCC-----
Confidence 3566666655 99886666778887653 33322110 1111 1234799999999999998876321111
Q ss_pred HHHHHHccC-C-ccccchhhhHhhccccccHHHHHHHcCCccC-CCCcccchhHHHHHHHHHHHHHH
Q 023967 187 FFELINMYF-P-VVYDIKHLMKFCNSLHGGLNKLAELLEVERV-GICHQAGSDSLLTSCTFRKLREN 250 (274)
Q Consensus 187 F~~~l~~~F-P-~iyDtK~l~~~~~~l~~~L~~la~~L~v~r~-g~~HqAGsDs~lT~~~F~~l~~~ 250 (274)
+..| | ..+||.-|++.... ...|+.+++.+|++.. ...|.|.+|++.|+++|.+|.++
T Consensus 128 -----~~~~~~~~~lDt~~la~~~~~-~~~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 128 -----RNPFHPFSTFDTATLAGLAYG-QTVLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred -----CCCCCCCcEEEHHHHHHHHhC-CCcHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 0112 2 36899888876532 2369999999999863 57899999999999999999875
No 12
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=98.57 E-value=2.3e-06 Score=77.42 Aligned_cols=168 Identities=14% Similarity=0.208 Sum_probs=110.7
Q ss_pred CCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccc
Q 023967 35 YNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIF 114 (274)
Q Consensus 35 ~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~ 114 (274)
-.||++|||-||+... ..=.|||||.-.... +. .....|+.+ .+..+ ..
T Consensus 4 ~r~vvlDtETTGldp~--------------------~~drIIEIGaV~v~~-~~--------~~~~~f~~~-i~P~~-~i 52 (240)
T PRK05711 4 MRQIVLDTETTGLNQR--------------------EGHRIIEIGAVELIN-RR--------LTGRNFHVY-IKPDR-LV 52 (240)
T ss_pred CeEEEEEeeCCCcCCC--------------------CCCeEEEEEEEEEEC-CE--------EeccEEEEE-ECcCC-cC
Confidence 4699999999998421 022599999876542 22 122456666 44333 35
Q ss_pred hhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC--CCCCCCChHHHHHHHH
Q 023967 115 ASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQAGFFELIN 192 (274)
Q Consensus 115 ~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~~~F~~~l~ 192 (274)
++++++. ||+.-+.+.. +-+..+..+.+.. .+ .+-.+|++|..||.+||-+-+. +.++|...
T Consensus 53 ~~~a~~V---HGIT~e~l~~-~p~f~ev~~~f~~--fi--~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~-------- 116 (240)
T PRK05711 53 DPEALAV---HGITDEFLAD-KPTFAEVADEFLD--FI--RGAELIIHNAPFDIGFMDYEFALLGRDIPKTN-------- 116 (240)
T ss_pred CHHHhhh---cCCCHHHHcC-CCCHHHHHHHHHH--Hh--CCCEEEEEccHHhHHHHHHHHHHhCCCCCccc--------
Confidence 6666554 7877666554 3333333322322 12 2235899999999999987662 33455321
Q ss_pred ccCCccccchhhhHhh-ccccccHHHHHHHcCCccCC-CCcccchhHHHHHHHHHHHHHH
Q 023967 193 MYFPVVYDIKHLMKFC-NSLHGGLNKLAELLEVERVG-ICHQAGSDSLLTSCTFRKLREN 250 (274)
Q Consensus 193 ~~FP~iyDtK~l~~~~-~~l~~~L~~la~~L~v~r~g-~~HqAGsDs~lT~~~F~~l~~~ 250 (274)
.+..++||--|++.. ++.+.+|+.+++.+|++..+ ..|.|-.||.+|+.+|.+|...
T Consensus 117 -~~~~~iDTl~lar~~~p~~~~~L~aL~~~~gi~~~~r~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 117 -TFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred -ccCceeeHHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCc
Confidence 134578888887765 34456999999999998754 4799999999999999999764
No 13
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=98.55 E-value=2.4e-06 Score=75.11 Aligned_cols=173 Identities=17% Similarity=0.096 Sum_probs=105.8
Q ss_pred hCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCcc
Q 023967 34 KYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDI 113 (274)
Q Consensus 34 ~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~ 113 (274)
.-.||++|+|.||+..+. +++. + .-.|||+|.-..+. |+. .-.|+-+.-|.....
T Consensus 3 ~~~~vvlD~EtTg~~~~~------~~~~-~--------~~eIIeIGaV~v~~-~~i---------~~~f~~lV~P~~~~~ 57 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKK------KPKG-F--------FPEIIEVGLVSVVG-CEV---------EDTFSSYVKPKTFPS 57 (207)
T ss_pred cceEEEEEeecCCcCCCC------CCCC-C--------CCceEEEeEEEEec-CcC---------hhhhcceECCCccCc
Confidence 357999999999975321 1110 0 01499999888763 332 123443322221113
Q ss_pred chhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC--CCCCCCChHHHHHHH
Q 023967 114 FASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQAGFFELI 191 (274)
Q Consensus 114 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~~~F~~~l 191 (274)
.++.+.++ +|+.=+.+ .+|.+..+.-+.+.. .+.+... +|..|+.+|+.+|-+-+. +-+.|.
T Consensus 58 i~~~~~~l---tGIt~~~l-~~ap~~~evl~~f~~--~~~~~~~-~iv~~~~fD~~fL~~~~~~~~~~~~~--------- 121 (207)
T PRK07748 58 LTERCKSF---LGITQEDV-DKGISFEELVEKLAE--YDKRCKP-TIVTWGNMDMKVLKHNCEKAGVPFPF--------- 121 (207)
T ss_pred cChhhhhh---cCcCHHHH-ccCCCHHHHHHHHHH--HhCcCCe-EEEEECHHHHHHHHHHHHHcCCCCcc---------
Confidence 45555555 88876666 467777654444332 1212123 444568999999988763 333331
Q ss_pred HccCCccccchhhhHhhcc--ccccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHH
Q 023967 192 NMYFPVVYDIKHLMKFCNS--LHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLREN 250 (274)
Q Consensus 192 ~~~FP~iyDtK~l~~~~~~--l~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~ 250 (274)
++..+|+..+.+.... -..+|..+++.+|++..+..|.|-+||+.|+.+|.+|.+.
T Consensus 122 ---~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 122 ---KGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred ---cccceeHHHHHHHHhCcCCCCCHHHHHHHcCCCCCCCCcChHHHHHHHHHHHHHHHhC
Confidence 1234455444333211 1348999999999998888999999999999999998876
No 14
>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=98.53 E-value=2.4e-06 Score=70.67 Aligned_cols=151 Identities=17% Similarity=0.143 Sum_probs=99.3
Q ss_pred eeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccchh
Q 023967 37 YIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFAS 116 (274)
Q Consensus 37 fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~~ 116 (274)
||++|+|.+|.. + -.|||+|...++ +|+ ..-+|+.+ ..... ...+
T Consensus 1 ~v~~D~Ettg~~--~---------------------~~ii~ig~v~~~-~~~---------~~~~~~~~-i~p~~-~~~~ 45 (156)
T cd06130 1 FVAIDFETANAD--R---------------------ASACSIGLVKVR-DGQ---------IVDTFYTL-IRPPT-RFDP 45 (156)
T ss_pred CEEEEEeCCCCC--C---------------------CceEEEEEEEEE-CCE---------EEEEEEEE-eCcCC-CCCh
Confidence 799999999831 1 127999998886 332 33567766 44333 4455
Q ss_pred hhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC--CCCCCCChHHHHHHHHcc
Q 023967 117 DSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQAGFFELINMY 194 (274)
Q Consensus 117 ~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~~~F~~~l~~~ 194 (274)
++.++ ||+.-.++.. +.+..+--+.+.. .+ + +-.||+++..||.++|-+.+- |.+.|+
T Consensus 46 ~~~~i---~GIt~e~l~~-~~~~~~v~~~l~~--~l-~-~~~lv~hn~~fD~~~l~~~~~~~g~~~~~------------ 105 (156)
T cd06130 46 FNIAI---HGITPEDVAD-APTFPEVWPEIKP--FL-G-GSLVVAHNASFDRSVLRAALEAYGLPPPP------------ 105 (156)
T ss_pred hhccc---cCcCHHHHhc-CCCHHHHHHHHHH--Hh-C-CCEEEEeChHHhHHHHHHHHHHcCCCCCC------------
Confidence 55443 8888887654 4444332222221 11 1 247999999999999987763 223221
Q ss_pred CCccccchhhhHhh-ccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHH
Q 023967 195 FPVVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFR 245 (274)
Q Consensus 195 FP~iyDtK~l~~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~ 245 (274)
+ ..+||.-+++.. +.+ ..+|+.+++.+|++.. .|.|-+|+..|+.+|.
T Consensus 106 ~-~~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~~--~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 106 Y-QYLCTVRLARRVWPLLPNHKLNTVAEHLGIELN--HHDALEDARACAEILL 155 (156)
T ss_pred C-CEEEHHHHHHHHhccCCCCCHHHHHHHcCCCcc--CcCchHHHHHHHHHHh
Confidence 1 367887666654 233 3589999999999876 9999999999999885
No 15
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=98.44 E-value=6.5e-06 Score=76.88 Aligned_cols=160 Identities=16% Similarity=0.212 Sum_probs=104.6
Q ss_pred CeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccch
Q 023967 36 NYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFA 115 (274)
Q Consensus 36 ~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~ 115 (274)
.||++|+|-||.. . | .|||+|+..++ +|+ ....|+.+ .+.....+.
T Consensus 2 ~~vviD~ETTg~~-------~--------------d--~IieIgav~v~-~g~---------i~~~f~~l-v~P~~~~~~ 47 (309)
T PRK06195 2 NFVAIDFETANEK-------R--------------N--SPCSIGIVVVK-DGE---------IVEKVHYL-IKPKEMRFM 47 (309)
T ss_pred cEEEEEEeCCCCC-------C--------------C--ceEEEEEEEEE-CCE---------EEEEEEEE-ECCCCCCCC
Confidence 6999999988631 0 1 37999998886 332 23456655 444333445
Q ss_pred hhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC--CCCCCCChHHHHHHHHc
Q 023967 116 SDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQAGFFELINM 193 (274)
Q Consensus 116 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~~~F~~~l~~ 193 (274)
+.+++ =|||.=+.+...+ +..+.-+.+.. .+ .+-.+|+||+.||.++|-+-+. +.+.|.
T Consensus 48 ~~~~~---IhGIT~e~v~~ap-~f~ev~~~~~~--fl--~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~----------- 108 (309)
T PRK06195 48 PINIG---IHGIRPHMVEDEL-EFDKIWEKIKH--YF--NNNLVIAHNASFDISVLRKTLELYNIPMPS----------- 108 (309)
T ss_pred hhhee---ccCcCHHHHhCCC-CHHHHHHHHHH--Hh--CCCEEEEECcHHHHHHHHHHHHHhCCCCCC-----------
Confidence 55553 3888777766543 33322112111 11 1236899999999999987663 333331
Q ss_pred cCCccccchhhhHhh-ccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 194 YFPVVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 194 ~FP~iyDtK~l~~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
...+||--+++.. +.+ .-+|+.+++.+|++. ..|.|-+||+.|+++|.+|.+..-
T Consensus 109 --~~~idT~~lar~l~~~~~~~~L~~L~~~~gi~~--~~H~Al~DA~ata~l~~~l~~~~~ 165 (309)
T PRK06195 109 --FEYICTMKLAKNFYSNIDNARLNTVNNFLGYEF--KHHDALADAMACSNILLNISKELN 165 (309)
T ss_pred --CCEEEHHHHHHHHcCCCCcCCHHHHHHHcCCCC--cccCCHHHHHHHHHHHHHHHHHhc
Confidence 1356776666654 344 357999999999973 589999999999999999987753
No 16
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=98.43 E-value=5.7e-06 Score=77.59 Aligned_cols=163 Identities=18% Similarity=0.192 Sum_probs=107.4
Q ss_pred CCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccc
Q 023967 35 YNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIF 114 (274)
Q Consensus 35 ~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~ 114 (274)
.+||++|+|.+|+... .-.|||+|...++ +|+ ...+|+.. ...... .
T Consensus 8 ~~~Vv~DlETTGl~p~---------------------~~eIIEIgaV~v~-~g~---------i~~~f~~l-VkP~~~-I 54 (313)
T PRK06807 8 LDYVVIDFETTGFNPY---------------------NDKIIQVAAVKYR-NHE---------LVDQFVSY-VNPERP-I 54 (313)
T ss_pred CCEEEEEEECCCCCCC---------------------CCeEEEEEEEEEE-CCE---------EEEEEEEE-ECcCCC-C
Confidence 4899999999998421 1269999998886 332 45677766 443332 3
Q ss_pred hhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHcc
Q 023967 115 ASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMY 194 (274)
Q Consensus 115 ~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~ 194 (274)
.+.+. +-||+.-..+. ++.+..+-.+.+.. .+ .. -.+|++++.||..+|.+.+....+|..
T Consensus 55 ~~~a~---~ihGIT~e~l~-~~~~~~evl~~f~~--fl-~~-~~lVaHNa~FD~~fL~~~~~~~gl~~~----------- 115 (313)
T PRK06807 55 PDRIT---SLTGITNYRVS-DAPTIEEVLPLFLA--FL-HT-NVIVAHNASFDMRFLKSNVNMLGLPEP----------- 115 (313)
T ss_pred CHhhh---ccCCCCHHHHh-CCCCHHHHHHHHHH--HH-cC-CeEEEEcHHHHHHHHHHHHHHcCCCCC-----------
Confidence 44443 34888766653 45454433222222 12 12 257999999999999988732222210
Q ss_pred CCccccchhhhHhh-cccc-ccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHh
Q 023967 195 FPVVYDIKHLMKFC-NSLH-GGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENF 251 (274)
Q Consensus 195 FP~iyDtK~l~~~~-~~l~-~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~ 251 (274)
...++||-.+++.. +.+. -+|+.+++.+|++. .+|.|=.|++.|+.+|.+|....
T Consensus 116 ~~~~iDtl~la~~~~~~~~~~kL~~L~~~lgi~~--~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 116 KNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRL--SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred CCCEeeHHHHHHHHhCCCCCCCHHHHHHHcCCCC--CCcChHHHHHHHHHHHHHHHHhh
Confidence 12366877766654 2332 37999999999997 78999999999999999987765
No 17
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.40 E-value=1e-05 Score=75.85 Aligned_cols=163 Identities=18% Similarity=0.150 Sum_probs=103.8
Q ss_pred hCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCcc
Q 023967 34 KYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDI 113 (274)
Q Consensus 34 ~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~ 113 (274)
..+||++|+|-||+. | +.=.|||+|...++.+|+. ...|... .+...+
T Consensus 14 ~~~fvvlD~ETTGl~--p-------------------~~d~IIeIgav~v~~~g~i---------~~~~~~l-v~P~~~- 61 (313)
T PRK06063 14 PRGWAVVDVETSGFR--P-------------------GQARIISLAVLGLDADGNV---------EQSVVTL-LNPGVD- 61 (313)
T ss_pred CCCEEEEEEECCCCC--C-------------------CCCEEEEEEEEEEECCcee---------eeEEEEE-ECcCCC-
Confidence 358999999999983 1 1125999999999877753 2334333 332221
Q ss_pred chhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC--CCCCCCChHHHHHHH
Q 023967 114 FASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQAGFFELI 191 (274)
Q Consensus 114 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~~~F~~~l 191 (274)
+.++. =|||.=..+... -+..+..+.+.. ++ .+-.+|+||..||.++|-+.+. +.++|.
T Consensus 62 --~~~~~---IhGIt~e~l~~a-p~f~ev~~~l~~--~l--~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~--------- 122 (313)
T PRK06063 62 --PGPTH---VHGLTAEMLEGQ-PQFADIAGEVAE--LL--RGRTLVAHNVAFDYSFLAAEAERAGAELPV--------- 122 (313)
T ss_pred --CCCee---cCCCCHHHHhCC-CCHHHHHHHHHH--Hc--CCCEEEEeCHHHHHHHHHHHHHHcCCCCCC---------
Confidence 22221 155544443321 112222222221 11 2336899999999999988763 344442
Q ss_pred HccCCccccchhhhHhh-ccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 192 NMYFPVVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 192 ~~~FP~iyDtK~l~~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
...+||.-+++.. ..+ .-.|+.+++.+|++. ...|.|-+|+..|+++|.++.+...
T Consensus 123 ----~~~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~-~~~H~Al~DA~ata~l~~~ll~~~~ 180 (313)
T PRK06063 123 ----DQVMCTVELARRLGLGLPNLRLETLAAHWGVPQ-QRPHDALDDARVLAGILRPSLERAR 180 (313)
T ss_pred ----CCEEehHHHHHHhccCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 1367887777765 223 346999999999985 5679999999999999999887765
No 18
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=98.39 E-value=8.3e-06 Score=71.52 Aligned_cols=160 Identities=19% Similarity=0.190 Sum_probs=92.3
Q ss_pred CeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccch
Q 023967 36 NYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFA 115 (274)
Q Consensus 36 ~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~ 115 (274)
.||++|+|.+|+. + .+ .|||+|...++. |. .+..|..+.-|. . ..+
T Consensus 6 ~~vvlD~EtTGl~--~----~~----------------eIIeIgaV~v~~-g~---------~~~~f~~lv~P~-~-~i~ 51 (195)
T PRK07247 6 TYIAFDLEFNTVN--G----VS----------------HIIQVSAVKYDD-HK---------EVDSFDSYVYTD-V-PLQ 51 (195)
T ss_pred eEEEEEeeCCCCC--C----CC----------------eEEEEEEEEEEC-CE---------EEEEEEEEECCC-C-CCC
Confidence 7999999999973 1 11 599999988873 32 234566553332 1 222
Q ss_pred hhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccc-hhHHHHHHHhCCCCCCCChHHHHHHHHcc
Q 023967 116 SDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSG-YDFGYLLKLLTCRSLPDTQAGFFELINMY 194 (274)
Q Consensus 116 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~-yD~~yLlk~l~~~~LP~~~~~F~~~l~~~ 194 (274)
..+.+ -|||.=..+. ++.+..+--+.+.. .+ . +-.||++|.. +|+.+|-+. |.+++....
T Consensus 52 ~~~~~---lhGIt~~~v~-~ap~~~evl~~f~~--f~-~-~~~lVaHNa~~fD~~fL~~~--g~~~~~~~~--------- 112 (195)
T PRK07247 52 SFING---LTGITADKIA-DAPKVEEVLAAFKE--FV-G-ELPLIGYNAQKSDLPILAEN--GLDLSDQYQ--------- 112 (195)
T ss_pred cccee---cCCCCHHHHh-CCCCHHHHHHHHHH--HH-C-CCeEEEEeCcHhHHHHHHHc--CCCcCCCce---------
Confidence 22222 1555544443 23332221111111 11 2 2358999876 899998653 444432110
Q ss_pred CCccccchhhhHh--hccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHh
Q 023967 195 FPVVYDIKHLMKF--CNSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENF 251 (274)
Q Consensus 195 FP~iyDtK~l~~~--~~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~ 251 (274)
. ..||+.+..+. .+++ +-+|+.||+.+|++. ..|.|-+||+.|+.+|.+|.+.-
T Consensus 113 i-dt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~--~~HrAl~DA~~ta~v~~~ll~~~ 169 (195)
T PRK07247 113 V-DLYDEAFERRSSDLNGIANLKLQTVADFLGIKG--RGHNSLEDARMTARVYESFLESD 169 (195)
T ss_pred e-ehHHHHHHhhccccCCCCCCCHHHHHHhcCCCC--CCcCCHHHHHHHHHHHHHHHhhc
Confidence 0 12333322111 1122 247999999999984 47999999999999999987763
No 19
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=98.37 E-value=6.5e-06 Score=74.73 Aligned_cols=169 Identities=17% Similarity=0.179 Sum_probs=109.0
Q ss_pred HhhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCC
Q 023967 31 IVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLI 110 (274)
Q Consensus 31 ~i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~ 110 (274)
++++..||.+|+|-||+... .=.|||+|+..++.++ ...+|+.+ .+..
T Consensus 3 ~l~~~~~v~~D~ETTGl~~~---------------------~d~IIEIa~v~v~~~~----------~~~~~~~l-i~P~ 50 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDVK---------------------KDRIIEFAAIRFTFDE----------VIDSVEFL-INPE 50 (250)
T ss_pred cccCCcEEEEEEeCCCCCCC---------------------CCeEEEEEEEEEECCe----------EEEEEEEE-ECcC
Confidence 56778999999999998421 1238999998876431 33556665 4433
Q ss_pred CccchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC--CCCCCCChHHHH
Q 023967 111 DDIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQAGFF 188 (274)
Q Consensus 111 ~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~~~F~ 188 (274)
. ....++. +-||+--..+... -+..+..+.+.. .+ .+.-.+|+|+..||..+|.+.+. +.+.|..
T Consensus 51 ~-~I~~~a~---~ihgIt~e~v~~~-p~~~ev~~~~~~--fl-~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~----- 117 (250)
T PRK06310 51 R-VVSAESQ---RIHHISDAMLRDK-PKIAEVFPQIKG--FF-KEGDYIVGHSVGFDLQVLSQESERIGETFLSK----- 117 (250)
T ss_pred C-CCCHhhh---hccCcCHHHHhCC-CCHHHHHHHHHH--Hh-CCCCEEEEECHHHHHHHHHHHHHHcCCCcccc-----
Confidence 2 3444443 3366654444322 233332222222 11 22246899999999999988763 3332211
Q ss_pred HHHHccCCccccchhhhHhhccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHh
Q 023967 189 ELINMYFPVVYDIKHLMKFCNSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENF 251 (274)
Q Consensus 189 ~~l~~~FP~iyDtK~l~~~~~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~ 251 (274)
--.++||..+++..... +.+|+.+++.+|++..+ +|.|-+|++.|+.+|.+|.+.+
T Consensus 118 ------~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~~~-aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 118 ------HYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDG-NHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred ------CCcEEehHHHHHhcccCCCCCHHHHHHHCCCCCCC-CcChHHHHHHHHHHHHHHHHhc
Confidence 01477888887765433 46899999999988554 7999999999999999998765
No 20
>PRK07740 hypothetical protein; Provisional
Probab=98.35 E-value=1.8e-05 Score=71.54 Aligned_cols=168 Identities=17% Similarity=0.157 Sum_probs=106.7
Q ss_pred hhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCc
Q 023967 33 DKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDD 112 (274)
Q Consensus 33 ~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d 112 (274)
.+.+||.+|+|.||+. |. . .=.|||+|....+. |.. ....|... .+.+ .
T Consensus 57 ~~~~~vv~D~ETTGl~--p~-----~-------------~deIIeIgaV~~~~-~~i--------~~~~f~~l-v~P~-~ 105 (244)
T PRK07740 57 TDLPFVVFDLETTGFS--PQ-----Q-------------GDEILSIGAVKTKG-GEV--------ETDTFYSL-VKPK-R 105 (244)
T ss_pred cCCCEEEEEEeCCCCC--CC-----C-------------CCeEEEEEEEEEEC-CEE--------EEEEEEEE-eCcC-C
Confidence 3458999999999974 21 0 12489999888762 221 13345443 2222 2
Q ss_pred cchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCC-CCCCChHHHHHHH
Q 023967 113 IFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCR-SLPDTQAGFFELI 191 (274)
Q Consensus 113 ~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~-~LP~~~~~F~~~l 191 (274)
..++.+.++ +|+.=..+ .+|.+..+-.+.+.. .+ . +-.+|+||..+|+.+|-+.+... ..|
T Consensus 106 ~i~~~~~~l---tGIt~e~l-~~ap~~~evl~~f~~--fi-~-~~~lVahna~fD~~fL~~~~~~~~~~~---------- 167 (244)
T PRK07740 106 PIPEHILEL---TGITAEDV-AFAPPLAEVLHRFYA--FI-G-AGVLVAHHAGHDKAFLRHALWRTYRQP---------- 167 (244)
T ss_pred CCChhheec---cCCCHHHH-hCCCCHHHHHHHHHH--Hh-C-CCEEEEeCHHHHHHHHHHHHHHhcCCC----------
Confidence 344444333 67665554 345555433222222 11 1 23699999999999988766311 111
Q ss_pred HccCCccccchhhhHhhcc-c-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 192 NMYFPVVYDIKHLMKFCNS-L-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 192 ~~~FP~iyDtK~l~~~~~~-l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
+...+.||..+++.... . ..+|+.+++.+|++..+. |.|-+|++.|+.+|.++.....
T Consensus 168 --~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~~~~-H~Al~Da~ata~l~~~ll~~~~ 227 (244)
T PRK07740 168 --FTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRR-HHALGDALMTAKLWAILLVEAQ 227 (244)
T ss_pred --cCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCCCCC-CCcHHHHHHHHHHHHHHHHHHH
Confidence 11367888888776532 2 457999999999987664 9999999999999999987765
No 21
>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=98.34 E-value=1.4e-05 Score=70.86 Aligned_cols=168 Identities=15% Similarity=0.156 Sum_probs=108.5
Q ss_pred hhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCC
Q 023967 32 VDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLID 111 (274)
Q Consensus 32 i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~ 111 (274)
+....||++|+|-||+. |. . .|||+|.......+. ...+|..+..|.
T Consensus 4 l~~~~fvv~D~ETTGl~--~~------------------~--~IIeIgav~v~~~~~---------~~~~f~~li~P~-- 50 (217)
T TIGR00573 4 LVLDTETTGDNETTGLY--AG------------------H--DIIEIGAVEIINRRI---------TGNKFHTYIKPD-- 50 (217)
T ss_pred EEecCEEEEEecCCCCC--CC------------------C--CEEEEEEEEEECCCE---------eeeEEEEEECcC--
Confidence 45678999999999984 20 1 299999998643321 234565553332
Q ss_pred ccchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCC--CCCCCChHHHHH
Q 023967 112 DIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTC--RSLPDTQAGFFE 189 (274)
Q Consensus 112 d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~--~~LP~~~~~F~~ 189 (274)
...++.++.. ||+.-..+... -+..+-.+.+.. .+ ++-.+|+++..||..+|-+-+.. .+.|.
T Consensus 51 ~~i~~~a~~i---hGIt~e~l~~~-p~~~ev~~~~~~--~~--~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~------- 115 (217)
T TIGR00573 51 RPIDPDAIKI---HGITDDMLKDK-PDFKEIAEDFAD--YI--RGAELVIHNASFDVGFLNYEFSKLYKVEPK------- 115 (217)
T ss_pred CCCCHHHHhh---cCCCHHHHcCC-CCHHHHHHHHHH--Hh--CCCEEEEeccHHHHHHHHHHHHHhcCCCCC-------
Confidence 3456666544 88888777554 333332222222 11 12368999999999999887631 11110
Q ss_pred HHHccCCccccchhhhHhh-ccc---cccHHHHHHHcCCccC-CCCcccchhHHHHHHHHHHHHHHhc
Q 023967 190 LINMYFPVVYDIKHLMKFC-NSL---HGGLNKLAELLEVERV-GICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 190 ~l~~~FP~iyDtK~l~~~~-~~l---~~~L~~la~~L~v~r~-g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
...+.||.-+++.. +.+ +.+|+.+++.+|++.. ...|.|-+|+.+|+.+|.+|.+...
T Consensus 116 -----~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~~~H~Al~DA~~ta~l~~~l~~~~~ 178 (217)
T TIGR00573 116 -----TNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQT 178 (217)
T ss_pred -----ccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHHhcch
Confidence 12355665555544 222 3479999999999864 3689999999999999999988754
No 22
>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=98.32 E-value=2.5e-05 Score=69.85 Aligned_cols=168 Identities=16% Similarity=0.166 Sum_probs=107.0
Q ss_pred CeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccch
Q 023967 36 NYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFA 115 (274)
Q Consensus 36 ~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~ 115 (274)
.+|.+|||-||+.... .=.|||+|...... +. .....|+.+ .+..+ ...
T Consensus 1 r~vvlD~ETTGl~p~~--------------------~d~IIEIgav~~~~-~~--------~~~~~f~~~-i~P~~-~i~ 49 (225)
T TIGR01406 1 RQIILDTETTGLDPKG--------------------GHRIVEIGAVELVN-RM--------LTGDNFHVY-VNPER-DMP 49 (225)
T ss_pred CEEEEEeeCCCcCCCC--------------------CCeEEEEEEEEEEC-Cc--------EecceEEEE-ECcCC-CCC
Confidence 3799999999984210 02499999775542 21 122456666 44333 345
Q ss_pred hhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC--CCCCCCChHHHHHHHHc
Q 023967 116 SDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQAGFFELINM 193 (274)
Q Consensus 116 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~~~F~~~l~~ 193 (274)
+++.+. ||+.-..+... .+..+-.+.+.. .+ .+..+|++|..||.+||-.-+. +..+|.- .
T Consensus 50 ~~a~~v---hGIt~e~l~~~-p~f~ev~~~f~~--fi--~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~---------~ 112 (225)
T TIGR01406 50 AEAAKV---HGITDEFLADK-PKFKEIADEFLD--FI--GGSELVIHNAAFDVGFLNYELERLGPTIKKI---------G 112 (225)
T ss_pred HHHHhc---cCCCHHHHhCC-CCHHHHHHHHHH--Hh--CCCEEEEEecHHHHHHHHHHHHHhCCCCccc---------c
Confidence 555544 78777666543 443332222222 11 1236899999999999987663 2111110 0
Q ss_pred cCCccccchhhhHhh-ccccccHHHHHHHcCCccCC-CCcccchhHHHHHHHHHHHHHHh
Q 023967 194 YFPVVYDIKHLMKFC-NSLHGGLNKLAELLEVERVG-ICHQAGSDSLLTSCTFRKLRENF 251 (274)
Q Consensus 194 ~FP~iyDtK~l~~~~-~~l~~~L~~la~~L~v~r~g-~~HqAGsDs~lT~~~F~~l~~~~ 251 (274)
.+-.++||--|++.. +..+.+|+.+++.+|++..+ ..|-|-.||.+|+.+|.+|...-
T Consensus 113 ~~~~~iDTl~lar~~~p~~~~~L~~L~~~~gi~~~~r~~H~Al~DA~~~a~v~~~l~~~~ 172 (225)
T TIGR01406 113 EFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAHLLAEVYLALTGGQ 172 (225)
T ss_pred cCCCEEEHHHHHHHHcCCCCCCHHHHHHhcCCCCCCCCCcCHHHHHHHHHHHHHHHHcCC
Confidence 112578888777764 34456999999999999865 47999999999999999997743
No 23
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=98.29 E-value=4e-05 Score=69.20 Aligned_cols=168 Identities=15% Similarity=0.141 Sum_probs=107.3
Q ss_pred hhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCC
Q 023967 32 VDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLID 111 (274)
Q Consensus 32 i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~ 111 (274)
+.+.+|+++|+|-||+..+ .=.|||+|....+.+ .. .....|... .+...
T Consensus 44 ~~~~~~vviD~ETTGl~p~---------------------~d~IieIg~v~v~~~-~i-------~~~~~~~~l-i~P~~ 93 (239)
T PRK09146 44 LSEVPFVALDFETTGLDAE---------------------QDAIVSIGLVPFTLQ-RI-------RCRQARHWV-VKPRR 93 (239)
T ss_pred cccCCEEEEEeECCCCCCC---------------------CCcEEEEEEEEEECC-eE-------eecceEEEE-ECCCC
Confidence 4567999999999998421 124999999888642 21 123344443 33222
Q ss_pred ccchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC---CCCCCCChHHHH
Q 023967 112 DIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT---CRSLPDTQAGFF 188 (274)
Q Consensus 112 d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~---~~~LP~~~~~F~ 188 (274)
.+.+++... |||.-..+ ..|-+..+-.+.+... + .+-.+|++|..||.++|-+.+. +.++|..
T Consensus 94 -~i~~~~~~I---hGIt~e~l-~~ap~~~evl~~l~~~--~--~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~----- 159 (239)
T PRK09146 94 -PLEEESVVI---HGITHSEL-QDAPDLERILDELLEA--L--AGKVVVVHYRRIERDFLDQALRNRIGEGIEFP----- 159 (239)
T ss_pred -CCChhhhhh---cCCCHHHH-hCCCCHHHHHHHHHHH--h--CCCEEEEECHHHHHHHHHHHHHHhcCCCCCCc-----
Confidence 345555443 77776665 3355544333333221 1 2236899999999999988763 2333322
Q ss_pred HHHHccCCccccchhhhHhh-cc--------c------cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhcC
Q 023967 189 ELINMYFPVVYDIKHLMKFC-NS--------L------HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFFN 253 (274)
Q Consensus 189 ~~l~~~FP~iyDtK~l~~~~-~~--------l------~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~~ 253 (274)
++||--+++.. +. + .-.|+.+++.+|++. ...|.|-+|++.|+.+|.++.+.+++
T Consensus 160 ---------~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl~~-~~~H~Al~DA~ata~l~~~~~~~~~~ 229 (239)
T PRK09146 160 ---------VIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGLPA-YSPHHALTDAIATAELLQAQIAHHFS 229 (239)
T ss_pred ---------eechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHHcC
Confidence 45665555543 11 1 126999999999985 45699999999999999999888764
No 24
>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=98.26 E-value=4.3e-05 Score=67.05 Aligned_cols=177 Identities=18% Similarity=0.198 Sum_probs=114.1
Q ss_pred hhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCC--CCCCCCCCCCeeeEEEeeeccCCC
Q 023967 33 DKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDEN--GNLPTCGTDKFCIWQFNFREFNLI 110 (274)
Q Consensus 33 ~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~--g~~p~~~~~~~~~~~FNF~~F~~~ 110 (274)
..+.||++|+|-||+.... =.||++|......+ |.. .....|.++..+..
T Consensus 6 ~~~~~vv~D~ETTGl~~~~---------------------d~IieIgav~v~~~~~g~i-------~~~~~f~~~v~p~p 57 (200)
T TIGR01298 6 RGYLPVVVDVETGGFNAKT---------------------DALLEIAAITLKMDEQGWL-------FPDTTLHFHVEPFE 57 (200)
T ss_pred cCCeeEEEEeeCCCCCCCC---------------------CeEEEEEEEEEEEcCCCcE-------eecceeEEEEcCCC
Confidence 3578999999999985221 13899998877543 321 12345666633333
Q ss_pred CccchhhhHHHHHHcCCCccchhhcCCChhH-HHHHHHHh-----cccccCceeEEeeccchhHHHHHHHhCCCCCCCCh
Q 023967 111 DDIFASDSVELLHQCGIDFKKNNEKGIDVNR-FGELLMSS-----GIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQ 184 (274)
Q Consensus 111 ~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~-f~e~l~~S-----glv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~ 184 (274)
.....++++.. |||.=++..+++.+... +.+.+-.- +..+ .+-..|++|-.||..||-+.+-...++.
T Consensus 58 ~~~i~~~a~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~lVaHNa~FD~~fL~~~~~r~~~~~-- 131 (200)
T TIGR01298 58 GANIQPEALEF---TGIDLDHPLRGAVSEYEALHEIFKVVRKAMKASGC-QRAILVGHNANFDLGFLNAAVERTSLKR-- 131 (200)
T ss_pred CCCCCHHHHHc---cCCChhhhhhcCcchHHHHHHHHHHHHHHHHhccc-CCCEEEEECchhhHHHHHHHHHHhCCCC--
Confidence 34566777655 89887776777776543 33332210 1111 2336899999999999988763111110
Q ss_pred HHHHHHHHccC-C-ccccchhhhHhhccccccHHHHHHHcCCccC-CCCcccchhHHHHHHHHHHHHHHhc
Q 023967 185 AGFFELINMYF-P-VVYDIKHLMKFCNSLHGGLNKLAELLEVERV-GICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 185 ~~F~~~l~~~F-P-~iyDtK~l~~~~~~l~~~L~~la~~L~v~r~-g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
..+ | .++||--+++.... ..+|..+++.+|++.. ...|.|-+|++.|+++|.+|.+++.
T Consensus 132 --------~~~~~~~~lDTl~lar~~~~-~~~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 132 --------NPFHPFSTFDTATLAGLAYG-QTVLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred --------CCCCCCcEEEHHHHHHHHcC-cccHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 001 1 26788777765421 2369999999999863 4789999999999999999988764
No 25
>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=98.22 E-value=1.4e-05 Score=64.94 Aligned_cols=155 Identities=17% Similarity=0.129 Sum_probs=99.3
Q ss_pred eEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccchhh
Q 023967 38 IAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFASD 117 (274)
Q Consensus 38 IAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~~~ 117 (274)
|.+|+|.+|+.. ..-.|+|+|...++.+++ ....||.+ +....+ ..+.
T Consensus 1 v~~D~Ettg~~~---------------------~~~~iiei~~v~~~~~~~---------~~~~~~~~-i~p~~~-~~~~ 48 (159)
T cd06127 1 VVFDTETTGLDP---------------------KKDRIIEIGAVKVDGGIE---------IVERFETL-VNPGRP-IPPE 48 (159)
T ss_pred CeEEeeCCCcCC---------------------CCCeEEEEEEEEEECCcC---------hhhhhhee-eCcCCc-CCHh
Confidence 579999999842 234599999999987633 23456665 333322 2233
Q ss_pred hHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccC-C
Q 023967 118 SVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYF-P 196 (274)
Q Consensus 118 Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~F-P 196 (274)
+.+. +|+.-+.. .+|.+.....+.+.. .+ .+ -.||++++.+|..+|.+.+.... ...+ .
T Consensus 49 ~~~~---~gi~~~~~-~~~~~~~~~~~~~~~--~l-~~-~~~v~~n~~fD~~~l~~~~~~~~------------~~~~~~ 108 (159)
T cd06127 49 ATAI---HGITDEML-ADAPPFEEVLPEFLE--FL-GG-RVLVAHNASFDLRFLNRELRRLG------------GPPLPN 108 (159)
T ss_pred heec---cCCCHHHH-hcCCCHHHHHHHHHH--HH-CC-CEEEEeCcHhhHHHHHHHHHHhC------------CCCCCC
Confidence 2222 66665554 467776654444432 11 12 47999999999999888774211 1122 2
Q ss_pred ccccchhhhHhhccc--cccHHHH-HHHcCCccCCCCcccchhHHHHHHHHH
Q 023967 197 VVYDIKHLMKFCNSL--HGGLNKL-AELLEVERVGICHQAGSDSLLTSCTFR 245 (274)
Q Consensus 197 ~iyDtK~l~~~~~~l--~~~L~~l-a~~L~v~r~g~~HqAGsDs~lT~~~F~ 245 (274)
..+||+.+++..-.. ..+|..+ ++.++++. +..|.|-+|+..|+.||.
T Consensus 109 ~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 109 PWIDTLRLARRLLPGLRSHRLGLLLAERYGIPL-EGAHRALADALATAELLL 159 (159)
T ss_pred CeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCC-CCCCCcHHHHHHHHHHhC
Confidence 588888887765322 2357776 77788754 688999999999999873
No 26
>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=98.21 E-value=4.8e-05 Score=65.33 Aligned_cols=168 Identities=17% Similarity=0.130 Sum_probs=101.9
Q ss_pred eeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCC---CCCCeeeEEEeeeccCCCCcc
Q 023967 37 YIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTC---GTDKFCIWQFNFREFNLIDDI 113 (274)
Q Consensus 37 fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~---~~~~~~~~~FNF~~F~~~~d~ 113 (274)
||++|+|-||+.. + ..=.|||+|.-..+.++..... ....-.+..|+.. .+... .
T Consensus 1 ~vv~D~ETTGl~~-~-------------------~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~l-v~P~~-~ 58 (177)
T cd06136 1 FVFLDLETTGLPK-H-------------------NRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLC-FNPGR-A 58 (177)
T ss_pred CeEEeeecCCCCC-C-------------------CCCceEEEEEEEEecccccccccccccccceeeeeeEE-eCCCC-c
Confidence 7999999999942 1 0013999999988765432210 0001134567666 44433 3
Q ss_pred chhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHh-cccccCceeEEeecc-chhHHHHHHHhC--CCCCCCChHHHHH
Q 023967 114 FASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSS-GIVLNDVVRWVTFHS-GYDFGYLLKLLT--CRSLPDTQAGFFE 189 (274)
Q Consensus 114 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~S-glv~~~~~~wi~f~g-~yD~~yLlk~l~--~~~LP~~~~~F~~ 189 (274)
..+++... |||.=..+...|-......+.+..- +. ..+....|+||+ .||+.+|-+-+. +.++|..
T Consensus 59 I~~~a~~I---hGIt~e~l~~~~~~~~~~~~~l~~f~~~-~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~------ 128 (177)
T cd06136 59 ISPGASEI---TGLSNDLLEHKAPFDSDTANLIKLFLRR-QPKPICLVAHNGNRFDFPILRSELERLGTKLPDD------ 128 (177)
T ss_pred CChhHHHH---hCcCHHHHhcCCCccHHHHHHHHHHHHh-cCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCC------
Confidence 45556554 8888888877763222222322110 11 123457899998 799999977763 3333311
Q ss_pred HHHccCCccccchhhhHhhccccccHHHHHHH-cCCccCCCCcccchhHHHHHHHHHH
Q 023967 190 LINMYFPVVYDIKHLMKFCNSLHGGLNKLAEL-LEVERVGICHQAGSDSLLTSCTFRK 246 (274)
Q Consensus 190 ~l~~~FP~iyDtK~l~~~~~~l~~~L~~la~~-L~v~r~g~~HqAGsDs~lT~~~F~~ 246 (274)
+...||--+++.... +|+++++. +|++. ...|.|-+|+..|++||++
T Consensus 129 ------~~~iDtl~l~r~~~~---~L~~l~~~~~~~~~-~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 129 ------ILCVDSLPAFRELDQ---SLGSLYKRLFGQEP-KNSHTAEGDVLALLKCALH 176 (177)
T ss_pred ------CEEEEeHHHHhhhHh---hHHHHHHHHhCCCc-ccccchHHHHHHHHHHHhh
Confidence 123466555554322 89999875 78774 4569999999999999975
No 27
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=98.20 E-value=5.7e-05 Score=68.98 Aligned_cols=167 Identities=22% Similarity=0.224 Sum_probs=105.4
Q ss_pred hhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCC
Q 023967 32 VDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLID 111 (274)
Q Consensus 32 i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~ 111 (274)
+.+..||.+|+|-+|.... .-.|||+|...++ +|+ ..-+|..+..+.
T Consensus 65 ~~~~~~vv~DiETTG~~~~---------------------~~~IIEIGAv~v~-~g~---------i~~~f~~~v~p~-- 111 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPK---------------------KHQIIEIGAVKVK-NGE---------IIDRFESFVKAK-- 111 (257)
T ss_pred CCCCCEEEEEEeCCCCCCC---------------------CCeEEEEEEEEEE-CCE---------EEEEEEEEECCC--
Confidence 4678999999999996321 0259999999886 332 223455443332
Q ss_pred ccchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHH
Q 023967 112 DIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELI 191 (274)
Q Consensus 112 d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l 191 (274)
...+.+.+. +|+.=..+. .+.+..+-.+.+.. . +.+ -.||+++..||.++|-+.+....+|.
T Consensus 112 -~ip~~~~~i---tGIt~e~l~-~ap~~~evl~~f~~--f-l~~-~v~VaHNa~FD~~fL~~~l~r~g~~~--------- 173 (257)
T PRK08517 112 -EVPEYITEL---TGITYEDLE-NAPSLKEVLEEFRL--F-LGD-SVFVAHNVNFDYNFISRSLEEIGLGP--------- 173 (257)
T ss_pred -CCChhhhhh---cCcCHHHHc-CCCCHHHHHHHHHH--H-HCC-CeEEEECHHHHHHHHHHHHHHcCCCC---------
Confidence 233333332 777766654 35554433222221 1 122 36999999999999887664222221
Q ss_pred HccCCccccchhhhHhh-ccccccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 192 NMYFPVVYDIKHLMKFC-NSLHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 192 ~~~FP~iyDtK~l~~~~-~~l~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
+.+...||--+++.. ..-+-+|+.+++.+|++.. ..|.|-+||..|+.+|.++.+.+-
T Consensus 174 --~~~~~ldtl~la~~~~~~~~~~L~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 174 --LLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIE-VHHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred --CCCCcEehHHHHHHHccCCCCCHHHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHhH
Confidence 112345554444433 2234589999999999865 789999999999999999987663
No 28
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=98.19 E-value=1.4e-06 Score=70.89 Aligned_cols=156 Identities=20% Similarity=0.182 Sum_probs=97.7
Q ss_pred eEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccchhh
Q 023967 38 IAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFASD 117 (274)
Q Consensus 38 IAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~~~ 117 (274)
|.+|||++|+.. +.-.|||||.-..+.+.. ...-.|+.+..|.......+.
T Consensus 1 v~~D~Ettg~~~---------------------~~~~iieig~v~~~~~~~--------~~~~~~~~~i~p~~~~~i~~~ 51 (164)
T PF00929_consen 1 VVFDTETTGLDP---------------------RQDEIIEIGAVKVDDDEN--------EEVESFNSLIRPEEPPKISPW 51 (164)
T ss_dssp EEEEEEESSSTT---------------------TTCTEEEEEEEEEETTTT--------EEEEEEEEEBEHSSHCSSEHH
T ss_pred cEEEeEcCCCCC---------------------CCCeEEEEEEEEeeCCcc--------ccceeeeecccccccccCCHH
Confidence 689999999853 334599999988876542 144567766344333234555
Q ss_pred hHHHHHHcCCCccchhhcCCChhH---HHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHcc
Q 023967 118 SVELLHQCGIDFKKNNEKGIDVNR---FGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMY 194 (274)
Q Consensus 118 Si~fL~~~GfDFnk~~~~GI~~~~---f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~ 194 (274)
+.+ -+|+.-..+...+-.... |.+.+ .+...|++++..+|.+++.+.+. ..++..
T Consensus 52 ~~~---~~gIt~~~l~~~~~~~~~~~~~~~~~-------~~~~~~v~~n~~fd~~~l~~~~~------------~~~~~~ 109 (164)
T PF00929_consen 52 ATK---VHGITQEDLEDAPSFEEALDEFEEFL-------KKNDILVGHNASFDIGFLRREDK------------RFLGKP 109 (164)
T ss_dssp HHH---HHHHCHHHHHCHCEHHHHHHHHHHHH-------HHHTEEEETTCCHEEESSHHHHH------------HHHHHH
T ss_pred Hee---ecCCcccccccCCcHHHHHHhhhhhh-------hcccccccccccchhhHHHHhhh------------hccccc
Confidence 433 366666665555432221 22222 22346888887888766655442 111221
Q ss_pred C---CccccchhhhHhh-cccc-ccHHHHHHHcCCccCCCCcccchhHHHHHHHH
Q 023967 195 F---PVVYDIKHLMKFC-NSLH-GGLNKLAELLEVERVGICHQAGSDSLLTSCTF 244 (274)
Q Consensus 195 F---P~iyDtK~l~~~~-~~l~-~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F 244 (274)
+ ..++|+.-+.+.. ++.. .+|.++++.++++..+.+|.|-+|++.|+.+|
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 110 IPKPNPFIDTLELARALFPNRKKYSLDDLAEYFGIPFDGTAHDALDDARATAELF 164 (164)
T ss_dssp HHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTSSSTSTTTSHHHHHHHHHHHH
T ss_pred ccccchhhhhhHHHHHHhhccccCCHHHHHHHcCCCCCCCCcChHHHHHHHhCcC
Confidence 2 2355665444443 3333 48999999999999888999999999999987
No 29
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.16 E-value=4.4e-05 Score=81.05 Aligned_cols=166 Identities=19% Similarity=0.206 Sum_probs=105.7
Q ss_pred CCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccc
Q 023967 35 YNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIF 114 (274)
Q Consensus 35 ~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~ 114 (274)
-.||++|+|.||+.... .-.|||+|....+ +|+ ..-.|+.+ .+... ..
T Consensus 3 ~~~vvvD~ETTG~~p~~--------------------~d~IIeigav~v~-~~~---------i~~~f~~~-v~P~~-~i 50 (928)
T PRK08074 3 KRFVVVDLETTGNSPKK--------------------GDKIIQIAAVVVE-DGE---------ILERFSSF-VNPER-PI 50 (928)
T ss_pred CCEEEEEEeCCCCCCCC--------------------CCcEEEEEEEEEE-CCE---------EEEEEEEE-ECcCC-CC
Confidence 46999999999973211 0159999999985 333 33456655 33332 34
Q ss_pred hhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHcc
Q 023967 115 ASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMY 194 (274)
Q Consensus 115 ~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~ 194 (274)
.+.+.+. +||+=..+. ++.+..+..+.+.. ++ ++..+|+|+..||+.+|-+-+...-+|..
T Consensus 51 ~~~~~~l---tGIt~~~l~-~ap~f~ev~~~l~~--~l--~~~~~VaHN~~FD~~fL~~~~~~~g~~~~----------- 111 (928)
T PRK08074 51 PPFITEL---TGISEEMVK-QAPLFEDVAPEIVE--LL--EGAYFVAHNVHFDLNFLNEELERAGYTEI----------- 111 (928)
T ss_pred CHHHhhc---CCCCHHHHh-cCCCHHHHHHHHHH--Hh--CCCeEEEEChHHHHHHHHHHHHHcCCCCC-----------
Confidence 4444333 777766644 44444443333322 11 24579999999999999886642222210
Q ss_pred CCccccchhhhHhh-ccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 195 FPVVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 195 FP~iyDtK~l~~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
-...+||=-+++.. +.+ .-+|+.+++.++++. ..+|.|-+||..|+.+|.+|.++..
T Consensus 112 ~~~~iDt~~la~~~~p~~~~~~L~~l~~~l~i~~-~~~H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 112 HCPKLDTVELARILLPTAESYKLRDLSEELGLEH-DQPHRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred CCCeeeHHHHHHHhcCCCCCCCHHHHHHhCCCCC-CCCCChHHHHHHHHHHHHHHHHHHH
Confidence 01345654444442 222 237999999999874 5789999999999999999988775
No 30
>PRK06722 exonuclease; Provisional
Probab=98.14 E-value=0.00011 Score=68.03 Aligned_cols=169 Identities=17% Similarity=0.123 Sum_probs=98.6
Q ss_pred hCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCcc
Q 023967 34 KYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDI 113 (274)
Q Consensus 34 ~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~ 113 (274)
...||++|+|.+|. |. . +-+.-.|||||....+. |.. ..+..|+-+.-|. ..
T Consensus 4 ~~~~vViD~ETT~~---p~---~------------~~~~deIIEIGAVkV~~-g~i-------~Ivd~F~sLV~P~--~~ 55 (281)
T PRK06722 4 ATHFIVFDIERNFR---PY---K------------SEDPSEIVDIGAVKIEA-STM-------KVIGEFSELVKPG--AR 55 (281)
T ss_pred CCEEEEEEeeCCCC---CC---C------------CCCCCeEEEEEEEEEEC-Cce-------eEEeeEEEEECCC--Cc
Confidence 35799999999852 21 0 01223499999988864 211 2345666663332 23
Q ss_pred chhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC--CCCCCCChHHHHHHH
Q 023967 114 FASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQAGFFELI 191 (274)
Q Consensus 114 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~~~F~~~l 191 (274)
.++.+.++ +||.=+.+. .+.+..+.-+.+.. .+ .+ -.+|++|+.+|.++|-+-+. +.+.|.-..
T Consensus 56 I~~~i~~L---TGIT~emV~-~AP~f~eVl~ef~~--fi-g~-~~lvahna~FD~~FL~~~l~~~gi~~p~~~~------ 121 (281)
T PRK06722 56 LTRHTTKL---TGITKKDLI-GVEKFPQIIEKFIQ--FI-GE-DSIFVTWGKEDYRFLSHDCTLHSVECPCMEK------ 121 (281)
T ss_pred CCHhHhhh---cCCCHHHHc-CCCCHHHHHHHHHH--HH-CC-CcEEEEEeHHHHHHHHHHHHHcCCCCCcccc------
Confidence 44444444 666555542 33333322111111 11 11 24677889999999998763 334443110
Q ss_pred HccCCccccchhhhHh-hccc---cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHH
Q 023967 192 NMYFPVVYDIKHLMKF-CNSL---HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLR 248 (274)
Q Consensus 192 ~~~FP~iyDtK~l~~~-~~~l---~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~ 248 (274)
-..+|+.-++.. .+.+ .-+|+.+++.+|++..|..|.|-+||.+|+.+|.+|.
T Consensus 122 ----~~~idl~~la~~~~~~l~~~~~sL~~l~~~lgL~~~g~~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 122 ----ERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIWEGKQHRALADAENTANILLKAY 178 (281)
T ss_pred ----cchhHHHHHHHHHhhhhccCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHh
Confidence 012333222211 1111 1269999999999988999999999999999999986
No 31
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.12 E-value=8.4e-05 Score=77.99 Aligned_cols=162 Identities=20% Similarity=0.264 Sum_probs=105.8
Q ss_pred hCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCcc
Q 023967 34 KYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDI 113 (274)
Q Consensus 34 ~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~ 113 (274)
...||++|+|-||+. + + + .|||+|..... +|+ ..-.|... .+.. ..
T Consensus 6 ~~~~vvvD~ETTGl~--~---------------~---d--~IIeIgaV~v~-~g~---------i~~~f~~l-v~P~-~~ 51 (820)
T PRK07246 6 LRKYAVVDLEATGAG--P---------------N---A--SIIQVGIVIIE-GGE---------IIDSYTTD-VNPH-EP 51 (820)
T ss_pred CCCEEEEEEecCCcC--C---------------C---C--eEEEEEEEEEE-CCE---------EEEEEEEE-eCcC-CC
Confidence 468999999999972 1 0 1 49999998875 332 33456555 2322 23
Q ss_pred chhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC--CCCCCCChHHHHHHH
Q 023967 114 FASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQAGFFELI 191 (274)
Q Consensus 114 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~~~F~~~l 191 (274)
..+.+.+. +||.=..+. ++.+..+....+.. .+ .+-.+|+||..||+++|-+.+. |-++|..
T Consensus 52 i~~~~~~l---tGIt~e~l~-~ap~~~ev~~~~~~--~l--~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~-------- 115 (820)
T PRK07246 52 LDEHIKHL---TGITDQQLA-QAPDFSQVARHIYD--LI--EDCIFVAHNVKFDANLLAEALFLEGYELRTP-------- 115 (820)
T ss_pred CCHhHhhc---CCCCHHHHh-cCCCHHHHHHHHHH--Hh--CCCEEEEECcHHHHHHHHHHHHHcCCCCCCC--------
Confidence 34444333 777766654 34455444333332 11 2346999999999999988663 3344322
Q ss_pred HccCCccccchhhhHhh-ccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 192 NMYFPVVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 192 ~~~FP~iyDtK~l~~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
.+||--+++.. +.+ +-+|+.+++.+|++.. .+|.|-+||..|+.+|.+|.+.+.
T Consensus 116 ------~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~~-~~H~Al~DA~ata~L~~~l~~~l~ 171 (820)
T PRK07246 116 ------RVDTVELAQVFFPTLEKYSLSHLSRELNIDLA-DAHTAIADARATAELFLKLLQKIE 171 (820)
T ss_pred ------ceeHHHHHHHHhCCCCCCCHHHHHHHcCCCCC-CCCCHHHHHHHHHHHHHHHHHHHh
Confidence 24665555543 222 3489999999999854 679999999999999999988765
No 32
>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=98.11 E-value=6.1e-05 Score=81.64 Aligned_cols=168 Identities=20% Similarity=0.251 Sum_probs=115.7
Q ss_pred hhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCc
Q 023967 33 DKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDD 112 (274)
Q Consensus 33 ~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d 112 (274)
+...||++|+|-||+.... =.|||+|....+. |+ ..-.|++. .+. ..
T Consensus 188 ~~~~~VVfDiETTGL~~~~---------------------d~IIEIGAVkv~~-g~---------iid~f~~~-V~P-~~ 234 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQY---------------------DEIIEFGAVKVKN-GR---------IIDKFQFF-IKP-HE 234 (1213)
T ss_pred cCCcEEEEEeEecCCCCCC---------------------CeEEEEEEEEEEC-Ce---------EEEEEEEE-ECC-CC
Confidence 6789999999999984221 1699999998863 32 34557666 332 23
Q ss_pred cchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHH
Q 023967 113 IFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELIN 192 (274)
Q Consensus 113 ~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~ 192 (274)
..++.+.++ +|+.-+.+. +|.+..+.-+.+.. .+ ++-.+|+++..||+.+|-+-+....+|.
T Consensus 235 ~I~~~~~~l---tGIT~e~L~-~ap~~~evl~~f~~--fl--~~~iLVaHNa~FD~~fL~~~~~r~g~~~---------- 296 (1213)
T TIGR01405 235 PLSAFVTEL---TGITQDMLE-NAPEIEEVLEKFKE--FF--KDSILVAHNASFDIGFLNTNFEKVGLEP---------- 296 (1213)
T ss_pred CCCHHHHHH---hCCCHHHHh-CCCCHHHHHHHHHH--Hh--CCCeEEEEChHHHHHHHHHHHHHcCCCc----------
Confidence 455555444 888877764 57666543333322 11 2347899999999999988764222221
Q ss_pred ccCCccccchhhhHhhc-cc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhcC
Q 023967 193 MYFPVVYDIKHLMKFCN-SL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFFN 253 (274)
Q Consensus 193 ~~FP~iyDtK~l~~~~~-~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~~ 253 (274)
+-..++||--+++... .+ .-+|+.|++.+|++..+ +|.|-.||..|+.+|.+|.+.+.+
T Consensus 297 -~~~~~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~~~-~HrAl~DA~aTa~I~~~ll~~l~~ 357 (1213)
T TIGR01405 297 -LENPVIDTLELARALNPEYKSHRLGNICKKLGVDLDD-HHRADYDAEATAKVFKVMVEQLKE 357 (1213)
T ss_pred -cCCCEeEHHHHHHHHhccCCCCCHHHHHHHcCCCCCC-CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 1135778877777652 33 34899999999998766 899999999999999999887653
No 33
>PRK07883 hypothetical protein; Validated
Probab=98.02 E-value=0.00012 Score=73.84 Aligned_cols=169 Identities=17% Similarity=0.159 Sum_probs=110.8
Q ss_pred HHHhhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccC
Q 023967 29 REIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFN 108 (274)
Q Consensus 29 ~~~i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~ 108 (274)
..-+.+..||++|+|.||+. | +.-.|||||.-.++ +|+ ...+|+.. .+
T Consensus 9 ~~~~~~~~~Vv~D~ETTGl~--p-------------------~~~~IIEIgaV~v~-~g~---------iv~~f~~l-V~ 56 (557)
T PRK07883 9 GTPLRDVTFVVVDLETTGGS--P-------------------AGDAITEIGAVKVR-GGE---------VLGEFATL-VN 56 (557)
T ss_pred CCCCcCCCEEEEEEecCCCC--C-------------------CCCeEEEEEEEEEE-CCE---------EEEEEEEE-EC
Confidence 44577899999999999983 2 11359999998886 222 34566665 44
Q ss_pred CCCccchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCC--CCCCCChHH
Q 023967 109 LIDDIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTC--RSLPDTQAG 186 (274)
Q Consensus 109 ~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~--~~LP~~~~~ 186 (274)
... ...+.+... ||+.=..+ .++.+..+..+.+.. .+ . +-.+|+|++.||+.+|-..+.. .+.|.
T Consensus 57 P~~-~i~~~~~~i---tGIt~e~l-~~ap~~~evl~~f~~--fl-~-~~~lVaHNa~FD~~fL~~~~~r~g~~~~~---- 123 (557)
T PRK07883 57 PGR-PIPPFITVL---TGITTAMV-AGAPPIEEVLPAFLE--FA-R-GAVLVAHNAPFDIGFLRAAAARCGYPWPG---- 123 (557)
T ss_pred CCC-CCChhHHhh---cCCCHHHH-hCCCCHHHHHHHHHH--Hh-c-CCEEEEeCcHHHHHHHHHHHHHcCCCCCC----
Confidence 332 344554433 77765443 345544433222221 11 1 3468899999999999887743 22221
Q ss_pred HHHHHHccCCccccchhhhHhh-c--cc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 187 FFELINMYFPVVYDIKHLMKFC-N--SL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 187 F~~~l~~~FP~iyDtK~l~~~~-~--~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
+..+||--+++.. + .. .-+|..+++.+|++.. ..|.|-+|+..|+.+|.++.+...
T Consensus 124 ---------~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 124 ---------PPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTT-PTHRALDDARATVDVLHGLIERLG 183 (557)
T ss_pred ---------CCcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccC-CCCCHHHHHHHHHHHHHHHHHHHH
Confidence 2356886666653 2 22 3479999999999864 469999999999999999888875
No 34
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=97.99 E-value=0.00022 Score=63.62 Aligned_cols=148 Identities=11% Similarity=0.047 Sum_probs=95.0
Q ss_pred eeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccchh
Q 023967 37 YIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFAS 116 (274)
Q Consensus 37 fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~~ 116 (274)
|+.+|||-||+. + .|||+|..-+. +|+ .+.+|+.. .+... ..+.
T Consensus 2 ~~vlD~ETTGl~--~----------------------~IieIg~v~v~-~~~---------i~~~~~~l-v~P~~-~i~~ 45 (219)
T PRK07983 2 LRVIDTETCGLQ--G----------------------GIVEIASVDVI-DGK---------IVNPMSHL-VRPDR-PISP 45 (219)
T ss_pred eEEEEEECCCCC--C----------------------CCEEEEEEEEE-CCE---------EEEEEEEE-ECcCC-CCCH
Confidence 789999999973 1 08999987665 343 23455554 44332 3445
Q ss_pred hhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCC
Q 023967 117 DSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFP 196 (274)
Q Consensus 117 ~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP 196 (274)
.+++. |||.=..+. |-+. |.+.+-. + ...-.+|+||..||..+|-. ++ .
T Consensus 46 ~~~~i---hgIt~e~v~--~ap~--~~ev~~~--~--~~~~~lVaHNa~FD~~~L~~------~~--------------~ 94 (219)
T PRK07983 46 QAMAI---HRITEAMVA--DKPW--IEDVIPH--Y--YGSEWYVAHNASFDRRVLPE------MP--------------G 94 (219)
T ss_pred HHhhc---CCCCHHHHc--CCCC--HHHHHHH--H--cCCCEEEEeCcHhhHHHHhC------cC--------------C
Confidence 55443 665443332 1121 3333322 1 23447899999999988731 11 2
Q ss_pred ccccchhhhHhh-ccccccHHHHHHHcCCcc----CCCCcccchhHHHHHHHHHHHHHHh
Q 023967 197 VVYDIKHLMKFC-NSLHGGLNKLAELLEVER----VGICHQAGSDSLLTSCTFRKLRENF 251 (274)
Q Consensus 197 ~iyDtK~l~~~~-~~l~~~L~~la~~L~v~r----~g~~HqAGsDs~lT~~~F~~l~~~~ 251 (274)
..+||=-+++.. +++.-+|+.|++.++++. ....|.|-+|++.|+.+|.+|.+..
T Consensus 95 ~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 95 EWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred CcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHc
Confidence 457777777654 455678899999998753 2568999999999999999988643
No 35
>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=97.85 E-value=0.00037 Score=73.42 Aligned_cols=161 Identities=21% Similarity=0.234 Sum_probs=101.9
Q ss_pred CeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccch
Q 023967 36 NYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFA 115 (274)
Q Consensus 36 ~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~ 115 (274)
.||++|+|-||+. |. .=.|||+|...++ +|+ ..-+|... .+... ...
T Consensus 1 ~~vvvD~ETTG~~--~~-------------------~~~IIeig~v~v~-~~~---------i~~~f~~~-v~P~~-~i~ 47 (850)
T TIGR01407 1 RYAVVDLETTGTQ--LS-------------------FDKIIQIGIVVVE-DGE---------IVDTFHTD-VNPNE-PIP 47 (850)
T ss_pred CEEEEEEECCCCC--CC-------------------CCeEEEEEEEEEE-CCE---------EEEEEEEE-eCCCC-CCC
Confidence 3899999999974 20 0239999999885 333 23455555 33322 334
Q ss_pred hhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC--CCC-CCCChHHHHHHHH
Q 023967 116 SDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRS-LPDTQAGFFELIN 192 (274)
Q Consensus 116 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~-LP~~~~~F~~~l~ 192 (274)
+.+.+ -+|+.-+.+. .+-+..+..+.+.. ++ . +-.||+||..||+.+|-+-+. |.+ +|.
T Consensus 48 ~~~~~---ltGIt~e~l~-~ap~~~ev~~~l~~--~l-~-~~~~VahN~~fD~~fL~~~~~~~g~~~~~~---------- 109 (850)
T TIGR01407 48 PFIQE---LTGISDNMLQ-QAPYFSQVAQEIYD--LL-E-DGIFVAHNVHFDLNFLAKALKDCGYEPLPK---------- 109 (850)
T ss_pred hhhhh---hcCcCHHHHh-CCCCHHHHHHHHHH--Hh-C-CCEEEEeCcHHHHHHHHHHHHHcCCCCCCC----------
Confidence 44333 3777755554 33333333333222 11 2 235999999999999988763 222 332
Q ss_pred ccCCccccchhhhHhh-ccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 193 MYFPVVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 193 ~~FP~iyDtK~l~~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
..+||--+++.. +.. .-+|..+++.+|++.. .+|.|-+|+..|+.+|.+|.+.+.
T Consensus 110 ----~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 110 ----PRIDTVELAQIFFPTEESYQLSELSEALGLTHE-NPHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred ----CeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCC-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 245654444433 112 3479999999999864 579999999999999999988765
No 36
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=97.84 E-value=0.00028 Score=60.82 Aligned_cols=166 Identities=18% Similarity=0.086 Sum_probs=96.8
Q ss_pred EEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccchhhh
Q 023967 39 AMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFASDS 118 (274)
Q Consensus 39 AiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~~~S 118 (274)
-+|+|-||+... .=.|||+|.-.++.++.. ...|++..-+.......+++
T Consensus 2 ~~D~ETTGl~~~---------------------~d~Iieig~v~v~~~~~~---------~~~~~~~v~p~~~~~~~~~a 51 (183)
T cd06138 2 FYDYETFGLNPS---------------------FDQILQFAAIRTDENFNE---------IEPFNIFCRLPPDVLPSPEA 51 (183)
T ss_pred EEEeecCCCCCC---------------------CCceEEEEEEEECCCCCC---------ccceeEEEeCCCCCCCCHHH
Confidence 489999998421 114899999888765432 24566652222222345555
Q ss_pred HHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeecc-chhHHHHHHHhCC---CCCCCC------hHHHH
Q 023967 119 VELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHS-GYDFGYLLKLLTC---RSLPDT------QAGFF 188 (274)
Q Consensus 119 i~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g-~yD~~yLlk~l~~---~~LP~~------~~~F~ 188 (274)
+. -|||.=+.+...|.+..+..+.+.. .+..++..+|++|+ .||.+||-+-+.. .+++.+ .-+..
T Consensus 52 ~~---ihGIt~e~l~~~~~~~~~~l~~~~~--~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl 126 (183)
T cd06138 52 LI---VTGITPQQLLKEGLSEYEFIAKIHR--LFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLL 126 (183)
T ss_pred HH---HhCCCHHHHHhcCCCHHHHHHHHHH--HHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccH
Confidence 44 4999888887778876654444332 12123345899985 6999999877632 222211 11222
Q ss_pred HHHHc---cCCccccchhhhHhhccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHH
Q 023967 189 ELINM---YFPVVYDIKHLMKFCNSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCT 243 (274)
Q Consensus 189 ~~l~~---~FP~iyDtK~l~~~~~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~ 243 (274)
..++. ++|..++.- ..-.++ +-+|+.+++.+|++. ...|.|-+|++.|+.+
T Consensus 127 ~l~r~~~~~~~~~~~~~---~~~~~~~~~~L~~l~~~~gi~~-~~~H~Al~Da~~ta~l 181 (183)
T cd06138 127 DVVRAYYALRPDGIVWP---KNDDGKPSFKLEDLAQANGIEH-SNAHDALSDVEATIAL 181 (183)
T ss_pred HHHHHHHhhChhhccCc---cccCCCcchhHHHHHHHCCCCc-cccccHHHHHHHHHHH
Confidence 22222 223211110 000012 236999999999986 5679999999999874
No 37
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=97.75 E-value=0.00027 Score=59.08 Aligned_cols=69 Identities=17% Similarity=0.125 Sum_probs=47.7
Q ss_pred eEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhcc---ccccHHHHHHH-cCCccCCCCccc
Q 023967 158 RWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNS---LHGGLNKLAEL-LEVERVGICHQA 233 (274)
Q Consensus 158 ~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~---l~~~L~~la~~-L~v~r~g~~HqA 233 (274)
.+|++|..+|+++|- .+.|. ..++||-.+...... -+-+|+.|++. ||++.....|.|
T Consensus 79 vlVgHn~~fD~~~L~-----~~~~~-------------~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~A 140 (152)
T cd06144 79 ILVGHALKNDLKVLK-----LDHPK-------------KLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSS 140 (152)
T ss_pred EEEEcCcHHHHHHhc-----CcCCC-------------ccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcCc
Confidence 589999999998873 12222 135565433322221 23489999997 698765568999
Q ss_pred chhHHHHHHHH
Q 023967 234 GSDSLLTSCTF 244 (274)
Q Consensus 234 GsDs~lT~~~F 244 (274)
.+||+.|+++|
T Consensus 141 l~DA~at~~l~ 151 (152)
T cd06144 141 VEDARAAMRLY 151 (152)
T ss_pred HHHHHHHHHHh
Confidence 99999999987
No 38
>PTZ00315 2'-phosphotransferase; Provisional
Probab=97.73 E-value=0.0013 Score=66.12 Aligned_cols=174 Identities=14% Similarity=0.136 Sum_probs=110.5
Q ss_pred CCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecC-CCCCCCCCCCCeeeEEEeeeccCCCCcc
Q 023967 35 YNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDE-NGNLPTCGTDKFCIWQFNFREFNLIDDI 113 (274)
Q Consensus 35 ~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~-~g~~p~~~~~~~~~~~FNF~~F~~~~d~ 113 (274)
-.||++|+|.||..... . +.-.||++|...++. +|+ ....|..+.-|.....
T Consensus 56 d~~IV~DlETTgl~~~~----~--------------~~dEIIEIGaV~Vd~~ng~---------Ii~~F~~yVkP~~~p~ 108 (582)
T PTZ00315 56 DAYVVLDFEATCEADRR----I--------------EDAEVIEFPMVLVDARTAT---------PVAEFQRYVRPVKNPV 108 (582)
T ss_pred CeEEEEEEecCCCCCCC----C--------------CCCceEEEEEEEEEccCCE---------EEEEEEEEECCCCCCC
Confidence 36999999999963211 0 123599999999974 333 3466766634432224
Q ss_pred chhhhHHHHHHcCCCccchhhcCCChhH----HHHHHHHhcccc---cCceeEEeeccchhHH-HHHHHhC--C-CCCCC
Q 023967 114 FASDSVELLHQCGIDFKKNNEKGIDVNR----FGELLMSSGIVL---NDVVRWVTFHSGYDFG-YLLKLLT--C-RSLPD 182 (274)
Q Consensus 114 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~----f~e~l~~Sglv~---~~~~~wi~f~g~yD~~-yLlk~l~--~-~~LP~ 182 (274)
.++.+.++ +||.=+.+ .++.+..+ |.+.+..+++.. +.+ ..|+.+|.+|+. +|.+-+. + ..+|.
T Consensus 109 Ls~fct~L---TGITqe~V-~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~-~~vah~g~fDl~~fL~~e~~~~~~~g~p~ 183 (582)
T PTZ00315 109 LSRFCTEL---TGITQSMV-SRADPFPVVYCEALQFLAEAGLGDAPPLRS-YCVVTCGDWDLKTMLPSQMRVSGQQGTPL 183 (582)
T ss_pred CChhHhhh---cCcCHHHH-hcCCCHHHHHHHHHHHHhccccccccccCc-eEEEeccHHHHHHHHHHHHHHhhhcCCCc
Confidence 56666655 67664443 44665543 333333333221 112 356677999995 7766543 1 24553
Q ss_pred ChHHHHHHHHccCCccccch-hhhHhh-cc-----------c-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHH
Q 023967 183 TQAGFFELINMYFPVVYDIK-HLMKFC-NS-----------L-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLR 248 (274)
Q Consensus 183 ~~~~F~~~l~~~FP~iyDtK-~l~~~~-~~-----------l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~ 248 (274)
.|...+|+| ++++.. ++ + .-+|+.+.+.+|++..|..|.|=.||..|+.+|.+|.
T Consensus 184 -----------~f~~widLk~~lar~l~p~~~~~~~~~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll 252 (582)
T PTZ00315 184 -----------SFQRWCNLKKYMSQLGFGNGSGCGGGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELL 252 (582)
T ss_pred -----------ccceEEEhHHHHHHHhCccccccccccccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHH
Confidence 345566764 666543 21 2 2489999999999999999999999999999999998
Q ss_pred HHh
Q 023967 249 ENF 251 (274)
Q Consensus 249 ~~~ 251 (274)
+.-
T Consensus 253 ~~g 255 (582)
T PTZ00315 253 RRG 255 (582)
T ss_pred HcC
Confidence 763
No 39
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=97.66 E-value=0.0012 Score=61.44 Aligned_cols=155 Identities=16% Similarity=0.131 Sum_probs=99.6
Q ss_pred CeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecC--CCCCCCCCCCCeeeEEEeeeccCCCCcc
Q 023967 36 NYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDE--NGNLPTCGTDKFCIWQFNFREFNLIDDI 113 (274)
Q Consensus 36 ~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~--~g~~p~~~~~~~~~~~FNF~~F~~~~d~ 113 (274)
.+|.+|||-||+... .=.|||||+-.++. +|++- .....|+.. .+... .
T Consensus 38 ~~vvlD~ETTGLd~~---------------------~d~IIEIg~V~v~~~~~g~i~------~v~~~~~~l-v~P~~-~ 88 (294)
T PRK09182 38 LGVILDTETTGLDPR---------------------KDEIIEIGMVAFEYDDDGRIG------DVLDTFGGL-QQPSR-P 88 (294)
T ss_pred eEEEEEeeCCCCCCC---------------------CCeEEEEEEEEEEecCCCcee------eeeeEEEEE-eCCCC-C
Confidence 689999999998521 12499999999975 34421 234567665 43332 3
Q ss_pred chhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhC---CCCCCCChHHHHHH
Q 023967 114 FASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLT---CRSLPDTQAGFFEL 190 (274)
Q Consensus 114 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~---~~~LP~~~~~F~~~ 190 (274)
..+++... |||.=+.+...+++...+.+.+-. .-..|+||..||..||-+.+- ..+...+...
T Consensus 89 I~~~~t~I---hGIt~e~v~~~~~~~~~l~~fl~~-------~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~---- 154 (294)
T PRK09182 89 IPPEITRL---TGITDEMVAGQTIDPAAVDALIAP-------ADLIIAHNAGFDRPFLERFSPVFATKPWACSVSE---- 154 (294)
T ss_pred CCHHHHHh---cCCCHHHHhcCCCcHHHHHHHhcC-------CCEEEEeCHHHHHHHHHHHHHhccCCcccccHHH----
Confidence 45555444 888877777777776666554321 235799999999999876541 1111111110
Q ss_pred HHccCCccccchhhhHhhccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHH
Q 023967 191 INMYFPVVYDIKHLMKFCNSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLR 248 (274)
Q Consensus 191 l~~~FP~iyDtK~l~~~~~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~ 248 (274)
+|-+ ...+ +-.|+.|+..+| .....|.|.+|++.|+.+|.+..
T Consensus 155 --------i~~~-----~~~~~~~kL~~La~~~g--~~~~aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 155 --------IDWS-----ARGFEGTKLGYLAGQAG--FFHEGHRAVDDCQALLELLARPL 198 (294)
T ss_pred --------Hhhc-----cccCCCCCHHHHHHHcC--CCCCCcChHHHHHHHHHHHHHHH
Confidence 0100 0112 246999999999 34578999999999999999653
No 40
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.65 E-value=0.0015 Score=58.51 Aligned_cols=160 Identities=17% Similarity=0.156 Sum_probs=97.8
Q ss_pred CeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccch
Q 023967 36 NYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFA 115 (274)
Q Consensus 36 ~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~~ 115 (274)
.+|.+|||-||+.... =.|||+|. .+ +. ..-.|+-. ++... ...
T Consensus 3 ~~vv~D~ETTGl~~~~---------------------d~IIeig~--v~--~~---------~~~~f~~l-v~P~~-~I~ 46 (232)
T PRK06309 3 ALIFYDTETTGTQIDK---------------------DRIIEIAA--YN--GV---------TSESFQTL-VNPEI-PIP 46 (232)
T ss_pred cEEEEEeeCCCCCCCC---------------------CEEEEEEE--Ec--Cc---------cccEEEEE-eCCCC-CCC
Confidence 4899999999984210 13899997 22 21 11234444 33332 345
Q ss_pred hhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeecc-chhHHHHHHHhC--CCCCCCChHHHHHHHH
Q 023967 116 SDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHS-GYDFGYLLKLLT--CRSLPDTQAGFFELIN 192 (274)
Q Consensus 116 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g-~yD~~yLlk~l~--~~~LP~~~~~F~~~l~ 192 (274)
+++++. ||+.=+.+.... +..+..+.+.. + +...-.+|++++ .||..+|.+.+. +.+.|.
T Consensus 47 ~~a~~I---hGIt~e~v~~~p-~f~ev~~~~~~--f-i~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~---------- 109 (232)
T PRK06309 47 AEASKI---HGITTDEVADAP-KFPEAYQKFIE--F-CGTDNILVAHNNDAFDFPLLRKECRRHGLEPPT---------- 109 (232)
T ss_pred hhHHhh---cCCCHHHHhCCC-CHHHHHHHHHH--H-HcCCCEEEEeCCHHHHHHHHHHHHHHcCCCCCC----------
Confidence 555443 666655544432 22222112211 1 123346888885 699999988773 222221
Q ss_pred ccCCccccchhhhHhh-ccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 193 MYFPVVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 193 ~~FP~iyDtK~l~~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
-..+||--+++.. +++ ..+|+.+++.++++. ..+|-|-+|++.|+.+|.+|.+.+.
T Consensus 110 ---~~~iDt~~l~~~~~~~~~~~~L~~l~~~~~~~~-~~aH~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 110 ---LRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEE-NQAHRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred ---CcEEeHHHHHHHHcCCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 1356876666654 333 457999999999774 5689999999999999999887763
No 41
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=97.60 E-value=0.00075 Score=64.56 Aligned_cols=176 Identities=14% Similarity=0.188 Sum_probs=102.2
Q ss_pred HhhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCC
Q 023967 31 IVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLI 110 (274)
Q Consensus 31 ~i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~ 110 (274)
.+++.+||++|+|-||+.... =.||+||.-.+..+|+ .+..|... .+..
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~---------------------drIIeIgAV~i~~~g~---------ive~f~tL-VnP~ 90 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPST---------------------SRLITIDAVTLTADGE---------EVEHFHAV-LNPG 90 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCC---------------------CeEEEEEEEEEEcCCE---------EEEEEEEE-ECcC
Confidence 467789999999999984210 1389999888887764 23555555 4433
Q ss_pred CccchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCC--CCC-----CCC
Q 023967 111 DDIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTC--RSL-----PDT 183 (274)
Q Consensus 111 ~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~--~~L-----P~~ 183 (274)
.+.. +. .=|||.=+.+.. |.+..+..+.+.. ++ ++-.||++|..||++||.+-+.- ..+ |..
T Consensus 91 ~~~~---p~---~LHGIT~e~La~-AP~f~eVl~el~~--fL--~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~ 159 (377)
T PRK05601 91 EDPG---PF---HLHGLSAEEFAQ-GKRFSQILKPLDR--LI--DGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRN 159 (377)
T ss_pred CCCC---Cc---cccCCCHHHHhc-CCCHHHHHHHHHH--Hh--CCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccc
Confidence 3221 11 125544444422 4444333332221 11 23369999999999999885410 000 000
Q ss_pred hH-------HHH-HHHHccCC-ccccchhhhHhh-ccc-cccHHHHHHHcCCcc---------CCCCcccch--hHHHHH
Q 023967 184 QA-------GFF-ELINMYFP-VVYDIKHLMKFC-NSL-HGGLNKLAELLEVER---------VGICHQAGS--DSLLTS 241 (274)
Q Consensus 184 ~~-------~F~-~~l~~~FP-~iyDtK~l~~~~-~~l-~~~L~~la~~L~v~r---------~g~~HqAGs--Ds~lT~ 241 (274)
.. .=. ..-+...| .++||=-+++.+ ..+ .-.|..||+.+|++. ...+|.|=+ |+.++.
T Consensus 160 r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~ 239 (377)
T PRK05601 160 RGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVA 239 (377)
T ss_pred cccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHH
Confidence 00 000 00011223 477886666665 334 347999999999864 356676664 999999
Q ss_pred HHHHHHH
Q 023967 242 CTFRKLR 248 (274)
Q Consensus 242 ~~F~~l~ 248 (274)
.+|.+++
T Consensus 240 ~l~~~~~ 246 (377)
T PRK05601 240 RLYFALR 246 (377)
T ss_pred HHHHHhh
Confidence 9999974
No 42
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.59 E-value=0.0011 Score=65.67 Aligned_cols=174 Identities=16% Similarity=0.120 Sum_probs=109.5
Q ss_pred hCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCc-
Q 023967 34 KYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDD- 112 (274)
Q Consensus 34 ~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d- 112 (274)
...||.+|+|-||+... .+ .|||+|.--.+.+++ ....+|+++ .....+
T Consensus 5 ~~~fvv~D~ETTGLdP~-----~D----------------rIIeiAaVrvd~~~~--------~i~e~~~~~-~~P~~~~ 54 (476)
T PRK11779 5 QPTFLWHDYETFGANPA-----LD----------------RPAQFAGIRTDADLN--------IIGEPLVFY-CKPADDY 54 (476)
T ss_pred CCcEEEEEEECCCCCCC-----CC----------------eeEEEEEEEEeCCCc--------eecceeEEE-EcCCcCc
Confidence 46799999999998522 11 389999988876543 223467776 444443
Q ss_pred cchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeecc-chhHHHHHHHhCCCCCCCChHHHHHHH
Q 023967 113 IFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHS-GYDFGYLLKLLTCRSLPDTQAGFFELI 191 (274)
Q Consensus 113 ~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g-~yD~~yLlk~l~~~~LP~~~~~F~~~l 191 (274)
...++++ .-|||-=+.+..+|++..++.+.+..- +..++-.+|++|+ .||..++-+.+. ..+-+++ .
T Consensus 55 lp~p~a~---~IhGIT~e~l~~~g~~e~e~~~~i~~~--l~~~~~~lVGhNni~FD~eflr~~~~-r~~~d~y------~ 122 (476)
T PRK11779 55 LPSPEAV---LITGITPQEALEKGLPEAEFAARIHAE--FSQPGTCILGYNNIRFDDEVTRYIFY-RNFYDPY------A 122 (476)
T ss_pred CCCHHHH---HHhCCCHHHHHhcCCCHHHHHHHHHHH--HhcCCCEEEEeCchhhcHHHHHHHHH-hccchHH------H
Confidence 3355554 449999888888999877766665431 1123345788876 599998888763 1111111 1
Q ss_pred HccC-C----ccccchhhhHhh-c----------c-ccccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHH
Q 023967 192 NMYF-P----VVYDIKHLMKFC-N----------S-LHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLREN 250 (274)
Q Consensus 192 ~~~F-P----~iyDtK~l~~~~-~----------~-l~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~ 250 (274)
+.+= + .+.|+--++... + + -+-.|+.|++.+|++. ..+|.|=+|++.|+.++.+|++.
T Consensus 123 ~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~L~~~~gI~~-~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 123 REWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEH-ENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHh
Confidence 1100 0 122222221111 0 1 1236999999999974 56799999999999999999876
No 43
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=97.58 E-value=0.0012 Score=72.76 Aligned_cols=168 Identities=21% Similarity=0.239 Sum_probs=108.4
Q ss_pred hhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCC
Q 023967 32 VDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLID 111 (274)
Q Consensus 32 i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~ 111 (274)
+.+..||++|+|.+|+... + =.|||+|....+ +|. ....|+.+ .+..
T Consensus 416 L~~~~~VVfDLETTGL~~~------------~---------deIIEIgAV~V~-~G~---------iie~F~~~-V~P~- 462 (1437)
T PRK00448 416 LKDATYVVFDVETTGLSAV------------Y---------DEIIEIGAVKIK-NGE---------IIDKFEFF-IKPG- 462 (1437)
T ss_pred hccCcEEEEEhhhcCCCCc------------h---------hhhheeeeEEEe-CCe---------EeeeEEEE-ECCC-
Confidence 4568899999999997421 1 158889887765 332 34566666 4432
Q ss_pred ccchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHH
Q 023967 112 DIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELI 191 (274)
Q Consensus 112 d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l 191 (274)
....+.+.++ +|+.=..+. ++.+..+..+.+..- ..+..+|++++.||+++|-+.+..--+|+
T Consensus 463 ~~I~~~~~~L---TGIT~e~L~-~aps~~EaL~~f~~f----igg~vLVAHNa~FD~~fL~~~l~rlgl~~--------- 525 (1437)
T PRK00448 463 HPLSAFTTEL---TGITDDMVK-DAPSIEEVLPKFKEF----CGDSILVAHNASFDVGFINTNYEKLGLEK--------- 525 (1437)
T ss_pred CCCCHHHHHH---hCCCHHHHc-CCCCHHHHHHHHHHH----hCCCEEEEeCccccHHHHHHHHHHcCCcc---------
Confidence 2344444444 677665555 566665544443331 12357899999999999876653211221
Q ss_pred HccCCccccchhhhHhh-ccc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 192 NMYFPVVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 192 ~~~FP~iyDtK~l~~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
+-...+||--+++.. +.. +-+|+.+|+.+|++..+ .|.|-+||+.|+.+|.+|.+...
T Consensus 526 --l~~~~IDTLelar~l~p~~k~~kL~~LAk~lGL~~~~-~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 526 --IKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEH-HHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred --ccccceeHHHHHHHHcCccccccHHHHHHHcCCCCCC-CcChHHHHHHHHHHHHHHHHHHH
Confidence 112345665444443 222 35799999999998765 59999999999999999988775
No 44
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=97.56 E-value=0.0018 Score=57.80 Aligned_cols=163 Identities=19% Similarity=0.216 Sum_probs=103.2
Q ss_pred CCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccc
Q 023967 35 YNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIF 114 (274)
Q Consensus 35 ~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~ 114 (274)
..||.+|+|-+|... ..=.+|++|.-.+..+.... ..|..+.-| +..+
T Consensus 13 ~~~vv~D~ETtg~~~---------------------~~~~iieIgav~~~~~~i~~---------~~~~~~v~P--~~~i 60 (243)
T COG0847 13 TRFVVIDLETTGLNP---------------------KKDRIIEIGAVTLEDGRIVE---------RSFHTLVNP--ERPI 60 (243)
T ss_pred CcEEEEecccCCCCC---------------------CCCceEEEEeEEEECCeeec---------ceeEEEECC--CCCC
Confidence 689999999999853 33458999998887543221 124444222 3334
Q ss_pred hhhhHHHHHHcCCCccchhhcCCChhHHHHHHHHh-cccccCceeEEeeccchhHHHHHHHhC--CCCCCCChHHHHHHH
Q 023967 115 ASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMSS-GIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQAGFFELI 191 (274)
Q Consensus 115 ~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~S-glv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~~~F~~~l 191 (274)
.+++... +||....+... .. |.+.+-.- .++ .+.-.+|+++-.+|.++|-.-+. +.+.|
T Consensus 61 ~~~~~~i---~git~e~l~~~-p~---~~~v~~~~~~~i-~~~~~~Vahna~fD~~fl~~~~~~~~~~~~---------- 122 (243)
T COG0847 61 PPEIFKI---HGITDEMLADA-PK---FAEVLPEFLDFI-GGLRLLVAHNAAFDVGFLRVESERLGIEIP---------- 122 (243)
T ss_pred Chhhhhh---cCCCHHHHhcC-CC---HHHHHHHHHHHH-CCCCeEEEEchhhcHHHHHHHHHHcCCCcc----------
Confidence 4454443 66666655555 22 22222111 111 22247899999999999977663 33333
Q ss_pred HccCCccccchhhhHhh-cc-ccccHHHHHHHcCCcc-CCCCcccchhHHHHHHHHHHHHHH
Q 023967 192 NMYFPVVYDIKHLMKFC-NS-LHGGLNKLAELLEVER-VGICHQAGSDSLLTSCTFRKLREN 250 (274)
Q Consensus 192 ~~~FP~iyDtK~l~~~~-~~-l~~~L~~la~~L~v~r-~g~~HqAGsDs~lT~~~F~~l~~~ 250 (274)
-..++||--+++.. .+ -..+|+.+++.+|+++ ....|.|-.|+++++.+|.++...
T Consensus 123 ---~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 123 ---GDPVLDTLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred ---cCceehHHHHHHHHcCCCccchHHHHHHHcCCCcCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 12345555555443 33 4568999999999997 456699999999999999999874
No 45
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=97.25 E-value=0.0023 Score=53.54 Aligned_cols=69 Identities=17% Similarity=0.031 Sum_probs=50.4
Q ss_pred ceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhc-cc-cccHHHHHHHcCCccC---CCC
Q 023967 156 VVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCN-SL-HGGLNKLAELLEVERV---GIC 230 (274)
Q Consensus 156 ~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~-~l-~~~L~~la~~L~v~r~---g~~ 230 (274)
+-.+|+++-.+|+.+|-. .-|.++||-.+++... .. +-+|+.|++.+....+ +..
T Consensus 76 ~~vlVgHn~~fD~~fL~~--------------------~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~ 135 (150)
T cd06145 76 DTILVGHSLENDLKALKL--------------------IHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGG 135 (150)
T ss_pred CCEEEEcChHHHHHHhhc--------------------cCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCC
Confidence 346899999999998742 1256889987776542 22 3489999987643222 567
Q ss_pred cccchhHHHHHHHH
Q 023967 231 HQAGSDSLLTSCTF 244 (274)
Q Consensus 231 HqAGsDs~lT~~~F 244 (274)
|.|-+||..|+.+|
T Consensus 136 H~Al~DA~~t~~l~ 149 (150)
T cd06145 136 HDSVEDARAALELV 149 (150)
T ss_pred CCcHHHHHHHHHHh
Confidence 99999999999877
No 46
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=97.22 E-value=0.0029 Score=53.36 Aligned_cols=68 Identities=19% Similarity=0.081 Sum_probs=52.4
Q ss_pred eeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhc-cc----cccHHHHHHH-cCCccC--C
Q 023967 157 VRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCN-SL----HGGLNKLAEL-LEVERV--G 228 (274)
Q Consensus 157 ~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~-~l----~~~L~~la~~-L~v~r~--g 228 (274)
-.+|+++..+|+.+|-. ..|.++||-.|++... .+ +-+|..|++. +|++-. .
T Consensus 85 ~vlVgHn~~fD~~fL~~--------------------~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~ 144 (161)
T cd06137 85 TILVGHSLQNDLDALRM--------------------IHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGG 144 (161)
T ss_pred cEEEeccHHHHHHHHhC--------------------cCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCC
Confidence 46889999999998732 1356889998888763 33 4589999986 686542 4
Q ss_pred CCcccchhHHHHHHHH
Q 023967 229 ICHQAGSDSLLTSCTF 244 (274)
Q Consensus 229 ~~HqAGsDs~lT~~~F 244 (274)
..|.|-.||..|+++|
T Consensus 145 ~~H~A~~DA~at~~l~ 160 (161)
T cd06137 145 EGHDSLEDALAAREVV 160 (161)
T ss_pred CCCCcHHHHHHHHHHh
Confidence 6799999999999887
No 47
>PRK05359 oligoribonuclease; Provisional
Probab=96.92 E-value=0.024 Score=49.00 Aligned_cols=166 Identities=14% Similarity=0.152 Sum_probs=94.8
Q ss_pred CCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCC--c
Q 023967 35 YNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLID--D 112 (274)
Q Consensus 35 ~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~--d 112 (274)
-.||++|+|.||+... .+ .|||+|.-..+.+.+. ..-.|+....+... +
T Consensus 3 ~~~vvlD~ETTGLdp~-----~d----------------~IieIgaV~~~~~~~~--------~~~~~~~~i~~~~~~l~ 53 (181)
T PRK05359 3 DNLIWIDLEMTGLDPE-----RD----------------RIIEIATIVTDADLNI--------LAEGPVIAIHQSDEALA 53 (181)
T ss_pred CcEEEEEeecCCCCCC-----CC----------------eEEEEEEEEEcCCceE--------cccceEEEECCCHHHhh
Confidence 4799999999998422 11 1899999977654321 11235544233211 1
Q ss_pred cchhhhHHHHHHcCCCccchhhcCCChhHHHHHHHH--hcccccCceeEEeeccchhHHHHHHHhC--CCCCCCCh---H
Q 023967 113 IFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMS--SGIVLNDVVRWVTFHSGYDFGYLLKLLT--CRSLPDTQ---A 185 (274)
Q Consensus 113 ~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~--Sglv~~~~~~wi~f~g~yD~~yLlk~l~--~~~LP~~~---~ 185 (274)
...+.+...-..+|+. +.....|.+..+..+.+.. .+.+.......+.++-.||..||-+.+- +.+|+... .
T Consensus 54 ~~~~~~~~ih~~tGIt-~~~l~~~~~~~e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~ 132 (181)
T PRK05359 54 AMDEWNTRTHTRSGLI-DRVRASTVSEAEAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVS 132 (181)
T ss_pred ccChHHHHhcccccCc-HHHHhcCCCHHHHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchh
Confidence 1223333322234776 5666777877665544432 1223222333344444899999988762 33444322 1
Q ss_pred HHHHHHHccCCccccchhhhHhhccccccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhcC
Q 023967 186 GFFELINMYFPVVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFFN 253 (274)
Q Consensus 186 ~F~~~l~~~FP~iyDtK~l~~~~~~l~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~~ 253 (274)
..+++.+.++|..| .++++.+ .|.|=+|++-|.+++...++.++.
T Consensus 133 tl~~l~r~~~P~~~----------------------~~~~~~~-~HRal~D~~~s~~~~~~~~~~~~~ 177 (181)
T PRK05359 133 TLKELARRWKPEIL----------------------NGFKKQG-THRALADIRESIAELKYYREHFFK 177 (181)
T ss_pred HHHHHHHHhChhhh----------------------hCCCCcC-CcccHHHHHHHHHHHHHHHHHhcc
Confidence 22345555555431 1444443 599999999999999999887763
No 48
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=96.85 E-value=0.0099 Score=50.07 Aligned_cols=97 Identities=15% Similarity=0.078 Sum_probs=56.8
Q ss_pred cCCCccchhhcCCChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhh
Q 023967 125 CGIDFKKNNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHL 204 (274)
Q Consensus 125 ~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l 204 (274)
||+.-+.+. ++.+..+-.+.+.. .+ ++-.+|+++-.+|+++|-.. +.|. .+.||=.+
T Consensus 51 ~GIt~~~l~-~a~~~~~v~~~l~~--~l--~~~vlV~Hn~~~D~~~l~~~----~~~~--------------~~~Dt~~l 107 (157)
T cd06149 51 SGIRRQHLV-NATPFAVAQKEILK--IL--KGKVVVGHAIHNDFKALKYF----HPKH--------------MTRDTSTI 107 (157)
T ss_pred CCCCHHHHh-cCCCHHHHHHHHHH--Hc--CCCEEEEeCcHHHHHHhccc----CCCc--------------CEEECccc
Confidence 566555543 45555443333322 22 23468998888999877522 1111 24455322
Q ss_pred --hHh---hccc-cccHHHHHHHc---CCccCCCCcccchhHHHHHHHH
Q 023967 205 --MKF---CNSL-HGGLNKLAELL---EVERVGICHQAGSDSLLTSCTF 244 (274)
Q Consensus 205 --~~~---~~~l-~~~L~~la~~L---~v~r~g~~HqAGsDs~lT~~~F 244 (274)
++. .++. +-+|+.|++.+ +++..+..|.|-+||..|+++|
T Consensus 108 ~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 108 PLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELY 156 (157)
T ss_pred ccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHh
Confidence 211 1222 24899999999 4554456799999999999887
No 49
>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=95.67 E-value=0.21 Score=41.37 Aligned_cols=84 Identities=18% Similarity=0.269 Sum_probs=56.3
Q ss_pred ccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhccc-c-ccHHHHHHHc-C-Ccc
Q 023967 151 IVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNSL-H-GGLNKLAELL-E-VER 226 (274)
Q Consensus 151 lv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~l-~-~~L~~la~~L-~-v~r 226 (274)
++.++++..|+|+..+|+..|.+.+ + ...++++|| .++..+-+. . -||..++..+ | ...
T Consensus 72 ll~~~~i~kv~~n~~~D~~~L~~~~-~---------------i~~~~~~D~-~l~~~~l~~~~~~~L~~L~~~~l~~~~~ 134 (176)
T PF01612_consen 72 LLEDPNIIKVGHNAKFDLKWLYRSF-G---------------IDLKNVFDT-MLAAYLLDPTRSYSLKDLAEEYLGNIDL 134 (176)
T ss_dssp HHTTTTSEEEESSHHHHHHHHHHHH-T---------------S--SSEEEH-HHHHHHTTTSTTSSHHHHHHHHHSEEE-
T ss_pred HHhCCCccEEEEEEechHHHHHHHh-c---------------cccCCccch-hhhhhcccccccccHHHHHHHHhhhccC
Confidence 3457788999999999999998863 2 222478999 555554322 2 5899987554 5 211
Q ss_pred -----CCC-----------CcccchhHHHHHHHHHHHHHHh
Q 023967 227 -----VGI-----------CHQAGSDSLLTSCTFRKLRENF 251 (274)
Q Consensus 227 -----~g~-----------~HqAGsDs~lT~~~F~~l~~~~ 251 (274)
.+. ..=|+.|+.+|.++|-+|.++.
T Consensus 135 ~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 135 DKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred cHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 111 1238889999999999998764
No 50
>PRK05755 DNA polymerase I; Provisional
Probab=95.42 E-value=0.25 Score=52.57 Aligned_cols=83 Identities=18% Similarity=0.210 Sum_probs=58.6
Q ss_pred cCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhc-cccccHHHHHHHc-CCccC----
Q 023967 154 NDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCN-SLHGGLNKLAELL-EVERV---- 227 (274)
Q Consensus 154 ~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~-~l~~~L~~la~~L-~v~r~---- 227 (274)
++.+..|+|+..+|+.+|.+ .|.++| +.++||..++..+. +..-||+.+++.+ +++.+
T Consensus 368 d~~v~kV~HNakfDl~~L~~--~gi~~~--------------~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~~ 431 (880)
T PRK05755 368 DPAIKKVGQNLKYDLHVLAR--YGIELR--------------GIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFEE 431 (880)
T ss_pred CCCCcEEEeccHhHHHHHHh--CCCCcC--------------CCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchHH
Confidence 45566789999999998876 254443 45788888776663 2235888887665 44310
Q ss_pred --------------CCCcccchhHHHHHHHHHHHHHHhc
Q 023967 228 --------------GICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 228 --------------g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
...|-|..|+.+|..+|.+|...+.
T Consensus 432 ~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 432 VAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred hcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1236799999999999999998764
No 51
>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=95.03 E-value=0.59 Score=39.11 Aligned_cols=80 Identities=20% Similarity=0.077 Sum_probs=56.9
Q ss_pred ccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhccc--cccHHHHHHHc-CCcc---
Q 023967 153 LNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNSL--HGGLNKLAELL-EVER--- 226 (274)
Q Consensus 153 ~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~l--~~~L~~la~~L-~v~r--- 226 (274)
.++++..|+|+...|+..|.+.. |-. +.+++|+..++..+..- ..||+.+++.+ +++-
T Consensus 70 ~~~~i~kv~~~~k~D~~~L~~~~-g~~---------------~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~ 133 (170)
T cd06141 70 EDPSILKVGVGIKGDARKLARDF-GIE---------------VRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKP 133 (170)
T ss_pred cCCCeeEEEeeeHHHHHHHHhHc-CCC---------------CCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCC
Confidence 35567788888889988876543 322 33578999988887543 35899998775 4321
Q ss_pred --------------CCCCcccchhHHHHHHHHHHHH
Q 023967 227 --------------VGICHQAGSDSLLTSCTFRKLR 248 (274)
Q Consensus 227 --------------~g~~HqAGsDs~lT~~~F~~l~ 248 (274)
..+-|-|..|+++...++.+|+
T Consensus 134 k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 134 KKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 1245669999999999998885
No 52
>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=94.91 E-value=0.46 Score=41.25 Aligned_cols=87 Identities=21% Similarity=0.080 Sum_probs=57.4
Q ss_pred cccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhcc------------ccccHHHHH
Q 023967 152 VLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNS------------LHGGLNKLA 219 (274)
Q Consensus 152 v~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~------------l~~~L~~la 219 (274)
+.++++.=|.|+...|+..|.+.+. . ++. . + ...-+++|+..+++.... -.-||+.++
T Consensus 78 l~d~~i~KVg~~~~~D~~~L~~~~~-~-~~~-~--~-----~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~ 147 (193)
T cd06146 78 FEDPDVLKLGFGFKQDLKALSASYP-A-LKC-M--F-----ERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLV 147 (193)
T ss_pred hCCCCeeEEEechHHHHHHHHHhcC-c-ccc-c--c-----ccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHH
Confidence 3466777788888899999887652 1 110 0 0 012479999988876531 235899987
Q ss_pred HHc-CCcc---------------CCCCcccchhHHHHHHHHHHHH
Q 023967 220 ELL-EVER---------------VGICHQAGSDSLLTSCTFRKLR 248 (274)
Q Consensus 220 ~~L-~v~r---------------~g~~HqAGsDs~lT~~~F~~l~ 248 (274)
+.+ |++- ..+.+-|..|++....+|-+|.
T Consensus 148 ~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 148 QEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 654 4321 1234559999999999999885
No 53
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=94.65 E-value=0.24 Score=47.44 Aligned_cols=82 Identities=28% Similarity=0.353 Sum_probs=52.9
Q ss_pred cCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhcc-ccccHHHHHH-HcCCccCCCCc
Q 023967 154 NDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNS-LHGGLNKLAE-LLEVERVGICH 231 (274)
Q Consensus 154 ~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~-l~~~L~~la~-~L~v~r~g~~H 231 (274)
++++.=|-|++.+|+..|.+.+ +-+| +.+||||..++.|+- .+-||..+.+ .+|++ +.+.|
T Consensus 68 d~~v~KIfHaa~~DL~~l~~~~--g~~p--------------~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~-ldK~~ 130 (361)
T COG0349 68 DPNVVKIFHAARFDLEVLLNLF--GLLP--------------TPLFDTQIAAKLAGFGTSHGLADLVEELLGVE-LDKSE 130 (361)
T ss_pred CCceeeeeccccccHHHHHHhc--CCCC--------------CchhHHHHHHHHhCCcccccHHHHHHHHhCCc-ccccc
Confidence 3344336666789999999976 2344 469999999999952 2678888764 44664 22222
Q ss_pred c----------------cchhHHHHHHHHHHHHHHhc
Q 023967 232 Q----------------AGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 232 q----------------AGsDs~lT~~~F~~l~~~~~ 252 (274)
| |-+|-..=..++-+|.+...
T Consensus 131 q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~ 167 (361)
T COG0349 131 QRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELA 167 (361)
T ss_pred cccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2 55565555666666666654
No 54
>PRK10829 ribonuclease D; Provisional
Probab=93.56 E-value=1.3 Score=42.65 Aligned_cols=85 Identities=21% Similarity=0.257 Sum_probs=59.8
Q ss_pred ccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhc-cccccHHHHH-HHcCCcc----
Q 023967 153 LNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCN-SLHGGLNKLA-ELLEVER---- 226 (274)
Q Consensus 153 ~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~-~l~~~L~~la-~~L~v~r---- 226 (274)
.++++.-|.|++.+|+..|.+.+ |. .| ..++||...+..++ +.+-||..|. +.||++-
T Consensus 71 ~~~~ivKV~H~~~~Dl~~l~~~~-g~-~p--------------~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~ 134 (373)
T PRK10829 71 RDPQVTKFLHAGSEDLEVFLNAF-GE-LP--------------QPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSE 134 (373)
T ss_pred cCCCeEEEEeChHhHHHHHHHHc-CC-Cc--------------CCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCccc
Confidence 35565566777889999987754 31 12 36999999998885 3356888875 5567641
Q ss_pred ---------C--CCCcccchhHHHHHHHHHHHHHHhcC
Q 023967 227 ---------V--GICHQAGSDSLLTSCTFRKLRENFFN 253 (274)
Q Consensus 227 ---------~--g~~HqAGsDs~lT~~~F~~l~~~~~~ 253 (274)
. ...+=|..|+.....+|-+|.+.+..
T Consensus 135 ~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~ 172 (373)
T PRK10829 135 SRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEA 172 (373)
T ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 13344999999999999999887663
No 55
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=93.47 E-value=1.9 Score=36.62 Aligned_cols=163 Identities=13% Similarity=0.156 Sum_probs=81.2
Q ss_pred eeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeccCCCCccc--
Q 023967 37 YIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIF-- 114 (274)
Q Consensus 37 fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~~~FNF~~F~~~~d~~-- 114 (274)
+|.+|+|-||+... . =.|||+|.-.++.+.. .....|... .+....+-
T Consensus 1 lv~iD~ETTGl~p~-----~----------------d~IieIgaV~~~~~~~--------~i~~~f~~~-i~p~~~~~~~ 50 (173)
T cd06135 1 LVWIDLEMTGLDPE-----K----------------DRILEIACIITDGDLN--------IIAEGPELV-IHQPDEVLDG 50 (173)
T ss_pred CEEEEEecCCCCCC-----C----------------CeeEEEEEEEEeCCCc--------eecCceeEE-ECCCHHHhhh
Confidence 57899999998521 0 1399999998864321 123445554 33322110
Q ss_pred -hhhhHHHHHHcCCCccchhhcCCChhHHHHHHHH--hcccccCceeEEeecc-chhHHHHHHHhCCCCCCCChHHHHHH
Q 023967 115 -ASDSVELLHQCGIDFKKNNEKGIDVNRFGELLMS--SGIVLNDVVRWVTFHS-GYDFGYLLKLLTCRSLPDTQAGFFEL 190 (274)
Q Consensus 115 -~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~--Sglv~~~~~~wi~f~g-~yD~~yLlk~l~~~~LP~~~~~F~~~ 190 (274)
.+.+.+...-+|+. +.....|.+..+..+.+.. .+.+ ..+-..+..|+ .||+++|-+.+..
T Consensus 51 ~~~~~~~ih~~tgIt-~~~l~~~~~~~~vl~~~~~f~~~~~-~~~~~~lvgh~~~FD~~fL~~~~~~------------- 115 (173)
T cd06135 51 MDEWCTEMHTKSGLT-ERVRASTVTLAQAEAELLEFIKKYV-PKGKSPLAGNSVHQDRRFLDKYMPE------------- 115 (173)
T ss_pred ccHHHHHcccccccH-HHHHhCCCCHHHHHHHHHHHHHHhc-CCCCCceeecchhhCHHHHHHHHHH-------------
Confidence 11112211223544 2233445544433322221 0111 11223556666 8999999886631
Q ss_pred HHccC-CccccchhhhHhhccccccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHH
Q 023967 191 INMYF-PVVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRE 249 (274)
Q Consensus 191 l~~~F-P~iyDtK~l~~~~~~l~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~ 249 (274)
....+ ....|+..+.+..+.+...+.+ ++++ .+..|.|=+|+.-|+..+...++
T Consensus 116 ~~~~~~~~~~D~~~l~~l~~~l~p~~~~----~~~~-~~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 116 LEEYLHYRILDVSSIKELARRWYPEIYR----KAPK-KKGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred HhccCCcchhhHHHHHHHHHHhCcHhhh----cCCC-CCCCcchHHHHHHHHHHHHHHHH
Confidence 01112 2355653332222222222211 2333 35679999999999998877655
No 56
>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=92.79 E-value=3.3 Score=34.57 Aligned_cols=80 Identities=16% Similarity=0.042 Sum_probs=55.4
Q ss_pred ccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhcc-ccccHHHHHHHc-CCcc----
Q 023967 153 LNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNS-LHGGLNKLAELL-EVER---- 226 (274)
Q Consensus 153 ~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~-l~~~L~~la~~L-~v~r---- 226 (274)
.++++..|+++...|+..|.+.. +-+ +.+++||..++..+.. -+.||+.+++.+ |++-
T Consensus 64 ~d~~i~Kvg~~~k~D~~~L~~~~-gi~---------------~~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~ 127 (161)
T cd06129 64 ENPSIVKALHGIEGDLWKLLRDF-GEK---------------LQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSI 127 (161)
T ss_pred CCCCEEEEEeccHHHHHHHHHHc-CCC---------------cccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccc
Confidence 35677788888888887776532 322 2356899888777643 245899998764 6531
Q ss_pred -----------CCCCcccchhHHHHHHHHHHHH
Q 023967 227 -----------VGICHQAGSDSLLTSCTFRKLR 248 (274)
Q Consensus 227 -----------~g~~HqAGsDs~lT~~~F~~l~ 248 (274)
..+.|-|..|++....+|-+|+
T Consensus 128 ~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 128 SCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred eeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 1244569999999999999886
No 57
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=82.57 E-value=2.8 Score=45.90 Aligned_cols=84 Identities=23% Similarity=0.231 Sum_probs=62.2
Q ss_pred eEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhc-ccc-ccHHHHHHHcCCccCCCCcccch
Q 023967 158 RWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCN-SLH-GGLNKLAELLEVERVGICHQAGS 235 (274)
Q Consensus 158 ~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~-~l~-~~L~~la~~L~v~r~g~~HqAGs 235 (274)
..|+++..||.+||-.-+---.||+-. -.+.||=-|++.+. .++ -+|..|++.|++.- ...|-|-+
T Consensus 503 IlVAHNasFD~gFl~~~~~k~~~~~~~-----------~pvIDTL~lar~L~P~~ksh~Lg~l~kk~~v~l-e~hHRA~y 570 (1444)
T COG2176 503 ILVAHNASFDMGFLNTNYEKYGLEPLT-----------NPVIDTLELARALNPEFKSHRLGTLCKKLGVEL-ERHHRADY 570 (1444)
T ss_pred EEEeccCccchhHHHHHHHHhCCcccc-----------CchhhHHHHHHHhChhhhhcchHHHHHHhCccH-HHhhhhhh
Confidence 568899999999986654211111000 13667777777763 443 48999999999987 78899999
Q ss_pred hHHHHHHHHHHHHHHhcC
Q 023967 236 DSLLTSCTFRKLRENFFN 253 (274)
Q Consensus 236 Ds~lT~~~F~~l~~~~~~ 253 (274)
||-.|+.+|+.|.+.+.+
T Consensus 571 Daeat~~vf~~f~~~~ke 588 (1444)
T COG2176 571 DAEATAKVFFVFLKDLKE 588 (1444)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 999999999999888764
No 58
>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=81.26 E-value=5 Score=35.72 Aligned_cols=93 Identities=23% Similarity=0.221 Sum_probs=54.9
Q ss_pred ceeEEeecc-chhHHHHHHHh--CCCCCCCChHHHH----HHHHccCCccccchhhhHhh-ccccccHHHHHHHcCCccC
Q 023967 156 VVRWVTFHS-GYDFGYLLKLL--TCRSLPDTQAGFF----ELINMYFPVVYDIKHLMKFC-NSLHGGLNKLAELLEVERV 227 (274)
Q Consensus 156 ~~~wi~f~g-~yD~~yLlk~l--~~~~LP~~~~~F~----~~l~~~FP~iyDtK~l~~~~-~~l~~~L~~la~~L~v~r~ 227 (274)
.-++|+|+| ++|+-+|..-. +|-++|.-+..=. ...+.|--.-.|+.-+...- ..-+.+|..||..||+|-
T Consensus 52 ~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~~~sLd~la~~lgiPg- 130 (209)
T PF10108_consen 52 NPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKARTSLDELAALLGIPG- 130 (209)
T ss_pred CCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccccCCHHHHHHHcCCCC-
Confidence 347999996 69998876543 5777776444211 01111111123333221111 123568999999999982
Q ss_pred CCCcccc--------------------hhHHHHHHHHHHHHHH
Q 023967 228 GICHQAG--------------------SDSLLTSCTFRKLREN 250 (274)
Q Consensus 228 g~~HqAG--------------------sDs~lT~~~F~~l~~~ 250 (274)
+.--.| .|.+-|..+|.|+...
T Consensus 131 -K~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~ 172 (209)
T PF10108_consen 131 -KDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELL 172 (209)
T ss_pred -CCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 322233 4789999999998664
No 59
>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=80.59 E-value=5.4 Score=33.43 Aligned_cols=84 Identities=19% Similarity=0.208 Sum_probs=55.2
Q ss_pred cCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhcc-c-cccHHHHHHHc-CCccC---
Q 023967 154 NDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNS-L-HGGLNKLAELL-EVERV--- 227 (274)
Q Consensus 154 ~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~-l-~~~L~~la~~L-~v~r~--- 227 (274)
+.++++|+++..+|+.+|.+. |-++| +.++||..++..+.. . ..+|+++++.+ +..-+
T Consensus 65 ~~~~~~v~hn~k~d~~~l~~~--gi~~~--------------~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~ 128 (193)
T cd06139 65 DPSIKKVGQNLKFDLHVLANH--GIELR--------------GPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFE 128 (193)
T ss_pred CCCCcEEeeccHHHHHHHHHC--CCCCC--------------CCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHH
Confidence 345678999999999988652 43333 246888888777632 2 34788887664 32200
Q ss_pred ---C---------------CCcccchhHHHHHHHHHHHHHHhcC
Q 023967 228 ---G---------------ICHQAGSDSLLTSCTFRKLRENFFN 253 (274)
Q Consensus 228 ---g---------------~~HqAGsDs~lT~~~F~~l~~~~~~ 253 (274)
| ..|-|..|+.++..++-+|......
T Consensus 129 ~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 129 DLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred HHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 0 1224888899999999998887643
No 60
>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=74.41 E-value=1.3 Score=36.60 Aligned_cols=71 Identities=23% Similarity=0.299 Sum_probs=37.7
Q ss_pred eeEEeecc-chhHHHHHHHhCCCCCCCChHHHHHHHHccCC-ccccchhhhHhhccccc-cHHHHHHHcCCccCCCCccc
Q 023967 157 VRWVTFHS-GYDFGYLLKLLTCRSLPDTQAGFFELINMYFP-VVYDIKHLMKFCNSLHG-GLNKLAELLEVERVGICHQA 233 (274)
Q Consensus 157 ~~wi~f~g-~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP-~iyDtK~l~~~~~~l~~-~L~~la~~L~v~r~g~~HqA 233 (274)
-.+|+||| .||+.+|-+.+..-.+|. | ..+|+...++.... .+ +|..||+.||.+|- ...-.
T Consensus 58 ~~iv~yng~~FD~p~L~~~~~~~~~~~-------------~~~~iDl~~~~~~~~~-~~~~Lk~ve~~lg~~~~-~~~~~ 122 (164)
T PF13482_consen 58 DNIVTYNGKNFDIPFLKRRAKRYGLPP-------------PFNHIDLLKIIKKHFL-ESYSLKNVEKFLGIERR-DDDIS 122 (164)
T ss_dssp --EEESSTTTTHHHHHHHHH-HHHH---------------GGGEEEHHHHHT-TTS-CCTT--SHHH------------H
T ss_pred CeEEEEeCcccCHHHHHHHHHHcCCCc-------------ccchhhHHHHHHhccC-CCCCHHHHhhhcccccc-cCCCC
Confidence 36999997 699999999883323443 3 46688777755433 44 89999999999873 22347
Q ss_pred chhHHHHHH
Q 023967 234 GSDSLLTSC 242 (274)
Q Consensus 234 GsDs~lT~~ 242 (274)
|+++...-.
T Consensus 123 G~~~~~~~~ 131 (164)
T PF13482_consen 123 GSESVKLYK 131 (164)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 777766543
No 61
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=65.52 E-value=2.4 Score=43.12 Aligned_cols=153 Identities=9% Similarity=-0.066 Sum_probs=90.4
Q ss_pred cceEEEcCcc--cHHHHHHHHHHHhhhCCeeEEeccccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeecCCC
Q 023967 10 EIQIREVWND--NLEEEFALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSDENG 87 (274)
Q Consensus 10 ~~~i~dVw~~--Nf~~el~~I~~~i~~~~fIAiDtEf~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~~~g 87 (274)
.+++..+-++ |....++.-...+.+..+.+++.|+.++...+ ......+..+++++.-.....++-+|+.-.--.-
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~ 178 (564)
T KOG1990|consen 101 RSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSD--RLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSI 178 (564)
T ss_pred ecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCC--CccchhhhchhhhhcccChhccCCCCChhhhhhH
Confidence 3445555556 78888777778888899999999999987553 2333456677777776666666666655432111
Q ss_pred CCCCCCCCCeeeEEEeeeccCCCCccchhhhHHHHHHcCCCccchhhcCCChhH-------HHHHHHHhcccccCceeEE
Q 023967 88 NLPTCGTDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKKNNEKGIDVNR-------FGELLMSSGIVLNDVVRWV 160 (274)
Q Consensus 88 ~~p~~~~~~~~~~~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~-------f~e~l~~Sglv~~~~~~wi 160 (274)
+........+.+.+++-..++..........+++..+|.+++ .++.+|+.... +.+...+.+++..++.-.+
T Consensus 179 ~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k-~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~d 257 (564)
T KOG1990|consen 179 ESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAK-ILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLD 257 (564)
T ss_pred HHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHH-HHHHhcchhhhccchHHHHHHHHhcCCeEEeecccee
Confidence 100000001233333222255555566677777777777777 67777777742 2233445566666665555
Q ss_pred eeccc
Q 023967 161 TFHSG 165 (274)
Q Consensus 161 ~f~g~ 165 (274)
.++-+
T Consensus 258 v~y~~ 262 (564)
T KOG1990|consen 258 VMYRY 262 (564)
T ss_pred eeeeh
Confidence 55543
No 62
>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=62.38 E-value=20 Score=31.49 Aligned_cols=68 Identities=25% Similarity=0.289 Sum_probs=42.6
Q ss_pred eEEeecc-chhHHHHHHHh--CCCCCCCChHHHHHHHHcc---C-CccccchhhhHhhccc-cccHHHHHHHcCCcc
Q 023967 158 RWVTFHS-GYDFGYLLKLL--TCRSLPDTQAGFFELINMY---F-PVVYDIKHLMKFCNSL-HGGLNKLAELLEVER 226 (274)
Q Consensus 158 ~wi~f~g-~yD~~yLlk~l--~~~~LP~~~~~F~~~l~~~---F-P~iyDtK~l~~~~~~l-~~~L~~la~~L~v~r 226 (274)
.+|+||| +||+-||.+-. +|-++|.......... .+ + ...+|+-.+.+....+ +.+|..+|+.||+++
T Consensus 95 ~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~-~y~~r~~~~h~DL~~~~~~~~~~~~~~L~~va~~lG~~~ 170 (208)
T cd05782 95 RLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDW-NYRNRYSERHLDLMDLLAFYGARARASLDLLAKLLGIPG 170 (208)
T ss_pred EEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchh-hccCcCCCCcccHHHHHhccCccCCCCHHHHHHHhCCCC
Confidence 6899998 79999998754 4566665443221110 11 1 1266776555544332 458999999999964
No 63
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=54.37 E-value=24 Score=32.49 Aligned_cols=76 Identities=17% Similarity=0.263 Sum_probs=49.7
Q ss_pred eEEeeccc-hhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhc-c--ccccHHHHHHHcCCccCCCCccc
Q 023967 158 RWVTFHSG-YDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCN-S--LHGGLNKLAELLEVERVGICHQA 233 (274)
Q Consensus 158 ~wi~f~g~-yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~-~--l~~~L~~la~~L~v~r~g~~HqA 233 (274)
-||||+|. ||.-|+-++.. ..+|.+.+. .=||.=|.++.+. . .+++|..|.+.||+.|.. -.-
T Consensus 158 ~lvsfNGkaFD~PfikR~v~-~~~el~l~~----------~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~R~e--dtd 224 (278)
T COG3359 158 MLVSFNGKAFDIPFIKRMVR-DRLELSLEF----------GHFDLYHPSRRLWKHLLPRCGLKTVERILGIRREE--DTD 224 (278)
T ss_pred eEEEecCcccCcHHHHHHHh-cccccCccc----------cchhhhhhhhhhhhccCCCCChhhHHHHhCccccc--cCC
Confidence 69999985 99999887443 345544332 2456666666552 2 367999999999999942 125
Q ss_pred chhHHHHHHHHHH
Q 023967 234 GSDSLLTSCTFRK 246 (274)
Q Consensus 234 GsDs~lT~~~F~~ 246 (274)
|+|+...-.-|.+
T Consensus 225 G~~~p~lyr~~~~ 237 (278)
T COG3359 225 GYDGPELYRLYRR 237 (278)
T ss_pred CcchHHHHHHHHH
Confidence 6666666555544
No 64
>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=49.89 E-value=17 Score=34.91 Aligned_cols=83 Identities=25% Similarity=0.298 Sum_probs=50.3
Q ss_pred cCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhcc-ccccHHHHHHH-cCCccCC---
Q 023967 154 NDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNS-LHGGLNKLAEL-LEVERVG--- 228 (274)
Q Consensus 154 ~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~-l~~~L~~la~~-L~v~r~g--- 228 (274)
++++.+|.|+..+|+-.|.+.. ..+| ..++||...+..++. ...||..+++. ||++-..
T Consensus 68 d~~i~KV~h~~k~Dl~~L~~~~--~~~~--------------~~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~ 131 (367)
T TIGR01388 68 DESVVKVLHAASEDLEVFLNLF--GELP--------------QPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSES 131 (367)
T ss_pred CCCceEEEeecHHHHHHHHHHh--CCCC--------------CCcccHHHHHHHhCCCCCccHHHHHHHHcCCCCCcccc
Confidence 4567788888888887765532 2333 257888877776642 23478887655 3543100
Q ss_pred ------------CCcccchhHHHHHHHHHHHHHHhc
Q 023967 229 ------------ICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 229 ------------~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
..+-|..|+.....++-+|++.+.
T Consensus 132 ~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 132 RTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLE 167 (367)
T ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 011266777777777777776654
No 65
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=46.62 E-value=14 Score=33.43 Aligned_cols=94 Identities=22% Similarity=0.256 Sum_probs=61.4
Q ss_pred eccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhccc-cc--cHHHHHHHcCCccCCCCcccchhHH
Q 023967 162 FHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNSL-HG--GLNKLAELLEVERVGICHQAGSDSL 238 (274)
Q Consensus 162 f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~l-~~--~L~~la~~L~v~r~g~~HqAGsDs~ 238 (274)
|..-||+.|++|... .+-.-++|+...+... +.-..- .| +|.. |+.+..+|.......+-.++
T Consensus 197 fP~fYDik~v~ks~~--~~~KglQei~ndlql~-----------r~g~QhQagsdaLlT-a~~ff~~R~~~F~~sig~~l 262 (299)
T COG5228 197 FPNFYDIKLVYKSVL--NNSKGLQEIKNDLQLQ-----------RSGQQHQAGSDALLT-ADEFFLPRFSIFTTSIGQSL 262 (299)
T ss_pred CccccchHHHHHhhh--hhhhHHHHhcCcHhhh-----------ccchhhhccchhhhh-hHHhcchhhheecccccHHH
Confidence 678899999998653 2233344444433211 110001 12 3443 89999999888888888889
Q ss_pred HHHHHHHHHHHHhc----CC-CccccccEEEecCCC
Q 023967 239 LTSCTFRKLRENFF----NG-CTEKYAGVLYGLGVE 269 (274)
Q Consensus 239 lT~~~F~~l~~~~~----~~-~~~~~~g~i~Gl~~~ 269 (274)
|....++.+++.-. ++ ++.++.|+|||+..+
T Consensus 263 l~~L~g~~~~~~sl~~~~~~t~f~~~~g~~~gi~~~ 298 (299)
T COG5228 263 LMLLSGCQLSKLSLHKFPNGTDFAKYQGVIYGIDGD 298 (299)
T ss_pred HHHHhccccCCchheeCCCcccHhhcCCcccCCCCC
Confidence 98888888776533 22 579999999999654
No 66
>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=46.61 E-value=62 Score=25.39 Aligned_cols=53 Identities=19% Similarity=0.214 Sum_probs=34.7
Q ss_pred cCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhcc-c-cccHHHHHHHc
Q 023967 154 NDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNS-L-HGGLNKLAELL 222 (274)
Q Consensus 154 ~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~-l-~~~L~~la~~L 222 (274)
++.++-|+++..+|...|.+. +..+| +.++||..++..+.. . ..+|+++++.+
T Consensus 52 ~~~~~~v~~~~k~d~~~L~~~--~~~~~--------------~~~~D~~~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 52 DEDITKVGHDAKFDLVVLARD--GIELP--------------GNIFDTMLAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred CCCCcEEeccHHHHHHHHHHC--CCCCC--------------CCcccHHHHHHHhCCCCCcCCHHHHHHHH
Confidence 455667888888888776543 22222 357899888777632 2 34898888775
No 67
>TIGR02841 spore_YyaC putative sporulation protein YyaC. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, also called YyaC, is a member of that panel and is otherwise uncharacterized. The second round of PSI-BLAST shows many similarities to the germination protease GPR, which is found in exactly the same set of organisms and has a known role in the sporulation/germination process.
Probab=40.98 E-value=28 Score=29.08 Aligned_cols=30 Identities=30% Similarity=0.369 Sum_probs=27.5
Q ss_pred EcCcccHHHHHHHHHHHhhhCCeeEEeccc
Q 023967 15 EVWNDNLEEEFALIREIVDKYNYIAMDTEF 44 (274)
Q Consensus 15 dVw~~Nf~~el~~I~~~i~~~~fIAiDtEf 44 (274)
-|.+-|++|.+..|.+.-++.-.||+|.-.
T Consensus 43 PVHA~NL~e~l~~I~~~~~~~~iIAIDAcL 72 (140)
T TIGR02841 43 PVHAKNLEEKLKIIKKKHPNPFIIAIDACL 72 (140)
T ss_pred CcccccHHHHHHHHHHhCCCCeEEEEECcc
Confidence 488999999999999999999999999765
No 68
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=39.96 E-value=39 Score=23.63 Aligned_cols=32 Identities=31% Similarity=0.521 Sum_probs=24.2
Q ss_pred hhhhHHHHHHcCCCc---------cchhhcCCChhHHHHHH
Q 023967 115 ASDSVELLHQCGIDF---------KKNNEKGIDVNRFGELL 146 (274)
Q Consensus 115 ~~~Si~fL~~~GfDF---------nk~~~~GI~~~~f~e~l 146 (274)
.+.+.+.++++|||| ....+.||+...+-+.|
T Consensus 12 ~p~~a~vf~~~gIDfCCgG~~~L~eA~~~~~ld~~~vl~~L 52 (56)
T PF04405_consen 12 DPRAARVFRKYGIDFCCGGNRSLEEACEEKGLDPEEVLEEL 52 (56)
T ss_pred ChHHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHH
Confidence 467888999999999 34566788877766554
No 69
>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=38.63 E-value=28 Score=30.51 Aligned_cols=69 Identities=16% Similarity=0.112 Sum_probs=39.0
Q ss_pred eEEeecc-chhHHHHHHHhCCCCCCCChHHHHH-------------HH---Hc--cCCc-cccchhhhHhh----cccc-
Q 023967 158 RWVTFHS-GYDFGYLLKLLTCRSLPDTQAGFFE-------------LI---NM--YFPV-VYDIKHLMKFC----NSLH- 212 (274)
Q Consensus 158 ~wi~f~g-~yD~~yLlk~l~~~~LP~~~~~F~~-------------~l---~~--~FP~-iyDtK~l~~~~----~~l~- 212 (274)
.+++||+ ++|+.||.+-...--+|.++..... -. .. ..++ +.|+-.+.+.. ..+.
T Consensus 76 ii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~s 155 (207)
T cd05785 76 VIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPS 155 (207)
T ss_pred EEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCC
Confidence 6789998 8999999887632222222111100 00 01 1123 47887766642 2342
Q ss_pred ccHHHHHHHcCCcc
Q 023967 213 GGLNKLAELLEVER 226 (274)
Q Consensus 213 ~~L~~la~~L~v~r 226 (274)
-+|+.||+.+|+..
T Consensus 156 ysL~~Va~~~g~~~ 169 (207)
T cd05785 156 YGLKAVAKHFGLAS 169 (207)
T ss_pred CCHHHHHHHhcccC
Confidence 38999999987643
No 70
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=37.74 E-value=17 Score=33.68 Aligned_cols=54 Identities=20% Similarity=0.303 Sum_probs=39.6
Q ss_pred ccccchhhhHhhc----cccccHHHHHHH-cCCcc-CCCCcccchhHHHHHHHHHHHHHHh
Q 023967 197 VVYDIKHLMKFCN----SLHGGLNKLAEL-LEVER-VGICHQAGSDSLLTSCTFRKLRENF 251 (274)
Q Consensus 197 ~iyDtK~l~~~~~----~l~~~L~~la~~-L~v~r-~g~~HqAGsDs~lT~~~F~~l~~~~ 251 (274)
.+.||-+.--.++ ...-||-+|++. ||.+= +|. |-.=-||-.|+..|-+++...
T Consensus 207 ~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~Ge-HsSvEDA~AtM~LY~~vk~qw 266 (280)
T KOG2249|consen 207 MIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGE-HSSVEDARATMELYKRVKVQW 266 (280)
T ss_pred hhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccc-cCcHHHHHHHHHHHHHHHHHH
Confidence 3788866544443 345689999854 56664 455 999999999999999987764
No 71
>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=33.49 E-value=1.8e+02 Score=27.85 Aligned_cols=26 Identities=35% Similarity=0.638 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhhhCCeeEEecccccc
Q 023967 22 EEEFALIREIVDKYNYIAMDTEFPGV 47 (274)
Q Consensus 22 ~~el~~I~~~i~~~~fIAiDtEf~G~ 47 (274)
.+++..+.+.+..++.||+||||...
T Consensus 5 ~~~l~~~~~~l~~~~~ia~DtE~~~~ 30 (367)
T TIGR01388 5 DDELATVCEAVRTFPFVALDTEFVRE 30 (367)
T ss_pred HHHHHHHHHHHhcCCEEEEeccccCC
Confidence 36777888888899999999999764
No 72
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=31.47 E-value=2.7e+02 Score=22.13 Aligned_cols=80 Identities=18% Similarity=0.159 Sum_probs=47.5
Q ss_pred cCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhcc-cc-ccHHHHHHHc-CCcc---C
Q 023967 154 NDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNS-LH-GGLNKLAELL-EVER---V 227 (274)
Q Consensus 154 ~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~-l~-~~L~~la~~L-~v~r---~ 227 (274)
+++++-|+++..+|+..|.+ .|-+++ +++||..++..+.. -. .+|+++++.+ +.+. .
T Consensus 73 ~~~~~kv~~d~k~~~~~L~~--~gi~~~---------------~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~ 135 (172)
T smart00474 73 DETITKVGHNAKFDLHVLAR--FGIELE---------------NIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEE 135 (172)
T ss_pred CCCceEEEechHHHHHHHHH--CCCccc---------------chhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCccc
Confidence 44567788888888877764 354443 34788777665422 22 4788887664 3321 1
Q ss_pred CC--------Cc----ccchhHHHHHHHHHHHHHH
Q 023967 228 GI--------CH----QAGSDSLLTSCTFRKLREN 250 (274)
Q Consensus 228 g~--------~H----qAGsDs~lT~~~F~~l~~~ 250 (274)
+. .. .|..|++.+...+-+|.+.
T Consensus 136 ~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~ 170 (172)
T smart00474 136 QKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKE 170 (172)
T ss_pred CccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 10 11 2677777777777777654
No 73
>KOG4013 consensus Predicted Cu2+ homeostasis protein CutC [Inorganic ion transport and metabolism]
Probab=31.47 E-value=61 Score=28.90 Aligned_cols=86 Identities=24% Similarity=0.313 Sum_probs=54.5
Q ss_pred hhhhHHHHHHcC---CCccchhhcC-CChhHHHHHHHHhcccccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHH
Q 023967 115 ASDSVELLHQCG---IDFKKNNEKG-IDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFEL 190 (274)
Q Consensus 115 ~~~Si~fL~~~G---fDFnk~~~~G-I~~~~f~e~l~~Sglv~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~ 190 (274)
..+-+++|+++| |=|..+-.+| |+-..-..++..++- ..||||-++|++|=-|.+....| -.-.|...
T Consensus 83 ~~~Dv~llk~~GAdGfVFGaLt~dgsid~~~C~si~~~~rp------lPVTFHRAfD~~~D~k~~lE~~l--~~lGF~rv 154 (255)
T KOG4013|consen 83 NMEDVELLKKAGADGFVFGALTSDGSIDRTSCQSIIETARP------LPVTFHRAFDVAYDWKTCLEDAL--LDLGFKRV 154 (255)
T ss_pred HHHHHHHHHHcCCCceEEeecCCCCCcCHHHHHHHHHhcCC------CceeeeeehhhhcCHHHHHHHHH--HHhhHHHH
Confidence 567789999985 5588888777 444444444444433 47999999999864333221100 02468888
Q ss_pred HHccC-CccccchhhhHhh
Q 023967 191 INMYF-PVVYDIKHLMKFC 208 (274)
Q Consensus 191 l~~~F-P~iyDtK~l~~~~ 208 (274)
|..=| |.-.|-=|+..++
T Consensus 155 LtSG~~psAldGv~~i~~l 173 (255)
T KOG4013|consen 155 LTSGQEPSALDGVYIIREL 173 (255)
T ss_pred hhcCCCcccccchHHHHHH
Confidence 88888 7666665555544
No 74
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=28.26 E-value=64 Score=28.70 Aligned_cols=68 Identities=21% Similarity=0.194 Sum_probs=40.0
Q ss_pred eEEeecc-chhHHHHHHHhCCCCCCCChHHHHHH---------------HHccCC-c-cccchhhhHhhccccc-cHHHH
Q 023967 158 RWVTFHS-GYDFGYLLKLLTCRSLPDTQAGFFEL---------------INMYFP-V-VYDIKHLMKFCNSLHG-GLNKL 218 (274)
Q Consensus 158 ~wi~f~g-~yD~~yLlk~l~~~~LP~~~~~F~~~---------------l~~~FP-~-iyDtK~l~~~~~~l~~-~L~~l 218 (274)
-.++++. ++|+.||++-+..-.+| .+..+-.. .+..++ + +.|+.-.++..-.+.+ +|++|
T Consensus 100 iivG~Ni~~fdl~~L~~R~~~l~i~-~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~~k~~~~~~sY~L~~v 178 (234)
T cd05776 100 VLVGHDLEGFDLDVLLSRIQELKVP-HWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLSAKELIRCKSYDLTEL 178 (234)
T ss_pred EEEeeccCCCCHHHHHHHHHHhCCC-ccccccccccccCccccccccccccccccCchhhccHHHHHHHhCCCCCChHHH
Confidence 4566664 89999999877422222 11111111 123333 2 7788888776634543 79999
Q ss_pred HH-HcCCcc
Q 023967 219 AE-LLEVER 226 (274)
Q Consensus 219 a~-~L~v~r 226 (274)
|+ .||.+|
T Consensus 179 a~~~Lg~~k 187 (234)
T cd05776 179 SQQVLGIER 187 (234)
T ss_pred HHHHhCcCc
Confidence 97 778766
No 75
>TIGR01229 rocF_arginase arginase. This model helps resolve arginases from known and putative agmatinases, formiminoglutamases, and other related proteins of unknown specifity. The pathway from arginine to the polyamine putrescine may procede by hydrolysis to remove urea (arginase) followed by decarboxylation (ornithine decarboxylase), or by decarboxylation first (arginine decarboxylase) followed by removal of urea (agmatinase).
Probab=27.08 E-value=2e+02 Score=26.60 Aligned_cols=68 Identities=9% Similarity=-0.071 Sum_probs=44.7
Q ss_pred EcCcccHHHHHHHHHHHhhhCC---eeEEec------cccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeec
Q 023967 15 EVWNDNLEEEFALIREIVDKYN---YIAMDT------EFPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSD 84 (274)
Q Consensus 15 dVw~~Nf~~el~~I~~~i~~~~---fIAiDt------Ef~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~ 84 (274)
+|++...++.+..+.+.+...+ ||++|. .+||+.... +..-+..+--+.++.-....+++=+.|+=++
T Consensus 196 ~i~~~g~~~v~~~~~~~l~~~~~~vyvS~DiDvlDps~aPgv~tp~--pgGl~~~e~~~~l~~i~~~~~v~g~DivE~~ 272 (300)
T TIGR01229 196 EIDELGIGKVVEETLEYLKAEDGPIHLSLDVDGLDPSLAPATGTPV--VGGLTFREGLLIMEMLYETGLLTALDVVEVN 272 (300)
T ss_pred HHhhhhHHHHHHHHHHHHhcCCCeEEEEEeccccCcccCCCCCCCC--CCCCCHHHHHHHHHHHHhcCCEEEEEEEEEC
Confidence 4556666677888888886655 999996 567775432 2234667777777776666667655555443
No 76
>PF13637 Ank_4: Ankyrin repeats (many copies); PDB: 3B95_A 3B7B_A 3F6Q_A 2KBX_A 3IXE_A 2DWZ_C 2DVW_A 3AJI_A 1S70_B 2HE0_A ....
Probab=27.04 E-value=63 Score=21.30 Aligned_cols=29 Identities=24% Similarity=0.393 Sum_probs=20.8
Q ss_pred hhhhHHHHHHcCCCccchhhcCCChhHHH
Q 023967 115 ASDSVELLHQCGIDFKKNNEKGIDVNRFG 143 (274)
Q Consensus 115 ~~~Si~fL~~~GfDFnk~~~~GI~~~~f~ 143 (274)
+.+.+++|.++|.|.|..-++|-++..++
T Consensus 13 ~~~~~~~Ll~~~~din~~d~~g~t~lh~A 41 (54)
T PF13637_consen 13 NLEIVKLLLEHGADINAQDEDGRTPLHYA 41 (54)
T ss_dssp -HHHHHHHHHTTSGTT-B-TTS--HHHHH
T ss_pred CHHHHHHHHHCCCCCCCCCCCCCCHHHHH
Confidence 57789999999999999999998887654
No 77
>PF06866 DUF1256: Protein of unknown function (DUF1256); InterPro: IPR009665 This family consists of several uncharacterised bacterial proteins, which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown.
Probab=26.33 E-value=63 Score=27.72 Aligned_cols=31 Identities=29% Similarity=0.219 Sum_probs=28.0
Q ss_pred EcCcccHHHHHHHHHHHhhhCCeeEEecccc
Q 023967 15 EVWNDNLEEEFALIREIVDKYNYIAMDTEFP 45 (274)
Q Consensus 15 dVw~~Nf~~el~~I~~~i~~~~fIAiDtEf~ 45 (274)
-|.+-|+++.+..|.+.-++.-.||+|.-..
T Consensus 67 PVHA~NL~e~l~~I~~~~~~~~IIAIDAcLG 97 (163)
T PF06866_consen 67 PVHALNLEETLNEIKKKHPNPFIIAIDACLG 97 (163)
T ss_pred CcchhhHHHHHHHHHHHCCCCeEEEEECCCC
Confidence 4899999999999999989999999998763
No 78
>PF13606 Ank_3: Ankyrin repeat
Probab=26.14 E-value=55 Score=19.41 Aligned_cols=17 Identities=24% Similarity=0.333 Sum_probs=14.5
Q ss_pred hhhhHHHHHHcCCCccc
Q 023967 115 ASDSVELLHQCGIDFKK 131 (274)
Q Consensus 115 ~~~Si~fL~~~GfDFnk 131 (274)
+.+-+++|.++|.|.|.
T Consensus 14 ~~e~v~~Ll~~gadvn~ 30 (30)
T PF13606_consen 14 NIEIVKYLLEHGADVNA 30 (30)
T ss_pred CHHHHHHHHHcCCCCCC
Confidence 57889999999999874
No 79
>PF12345 DUF3641: Protein of unknown function (DUF3641) ; InterPro: IPR024521 This domain is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. It is found in association with an N-terminal radical_SAM domain (Pfam:PF04055 from PFAM).
Probab=24.50 E-value=73 Score=26.45 Aligned_cols=32 Identities=31% Similarity=0.488 Sum_probs=26.2
Q ss_pred HHHHcCCCccchhhc-CCChhHHHHHHHHhccc
Q 023967 121 LLHQCGIDFKKNNEK-GIDVNRFGELLMSSGIV 152 (274)
Q Consensus 121 fL~~~GfDFnk~~~~-GI~~~~f~e~l~~Sglv 152 (274)
+..+.||.||.++.- -+|-.+|++.|..+|..
T Consensus 16 L~~~~GI~Fn~L~titNmPI~RF~~~L~~~g~~ 48 (134)
T PF12345_consen 16 LKERFGIVFNNLFTITNMPIGRFGSFLERSGNL 48 (134)
T ss_pred HHHhcCceecchhhhhcCcHHHHHHHHHHccCH
Confidence 346789999999874 48889999999888765
No 80
>PRK13772 formimidoylglutamase; Provisional
Probab=24.14 E-value=2.9e+02 Score=25.79 Aligned_cols=69 Identities=17% Similarity=0.173 Sum_probs=45.6
Q ss_pred EEcCcccHHHHHHHHHHHhhhC--CeeEEecc------ccccccCCCCCCCCChhHHHHHHHhcccccceeeeeeeeec
Q 023967 14 REVWNDNLEEEFALIREIVDKY--NYIAMDTE------FPGVVLRPVGAFKNINDYNYQTLKDNVDMLKLIQLGLTFSD 84 (274)
Q Consensus 14 ~dVw~~Nf~~el~~I~~~i~~~--~fIAiDtE------f~G~~~~~~~~~~~t~e~~Y~~lr~nv~~~~iiQlGlt~~~ 84 (274)
.|++..++++.+..|.+.++.. -||++|.- .||+.... +..-+..+-.+.++.-.+.-+++=+.|+-++
T Consensus 217 ~e~~~~g~~~~~~~i~~~l~~~~~vylS~DiD~lDps~aPGvgtP~--pgGlt~~e~~~il~~l~~~~~v~g~DvvEv~ 293 (314)
T PRK13772 217 VDMQERHLDARLAELDALLDAADHVYLTIDLDVLPAAVAPGVSAPA--AYGVPLPVVEEIVLHVRASGKLRVADLAEYN 293 (314)
T ss_pred hhhhhcCHHHHHHHHHHHHhcCCeEEEEEEecCcCcccCCCCCCCC--CCCCCHHHHHHHHHHHHhcCCeeEEEEEEEC
Confidence 4566677888888888888754 48899964 67765442 2233677777888776665566655555443
No 81
>PF13967 RSN1_TM: Late exocytosis, associated with Golgi transport
Probab=23.40 E-value=61 Score=26.88 Aligned_cols=64 Identities=16% Similarity=0.300 Sum_probs=45.4
Q ss_pred HHHHHccCCccccchhhhHh----hc--cc-cccHHHHHHHcCCccCCCCcccchhHHHHHHHHHHHHHHhc
Q 023967 188 FELINMYFPVVYDIKHLMKF----CN--SL-HGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252 (274)
Q Consensus 188 ~~~l~~~FP~iyDtK~l~~~----~~--~l-~~~L~~la~~L~v~r~g~~HqAGsDs~lT~~~F~~l~~~~~ 252 (274)
...+|.-+|.+|-.|..... .. .. +|-+.=+-..++++.....+.+|-||++-.+ |+||.-+++
T Consensus 20 F~~lR~~~~~iY~pR~~~~~~~~~~~~~~~~~g~f~Wi~~~~~~~d~~i~~~~GlDa~~flr-flr~~~~~f 90 (157)
T PF13967_consen 20 FCILRKRFPRIYQPRSYLPHPEPERPPPLPSRGFFGWIKPVFKISDDEILRHCGLDAYVFLR-FLRMLIKIF 90 (157)
T ss_pred HHHHHhccHHhcccccccCCcccccCCCCCCCCchHHHHHHHcCCHHHHHHHcCCCHHHHHH-HHHHHHHHH
Confidence 45667778889988877641 11 12 3446667777788777778899999999998 777776554
No 82
>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=21.52 E-value=68 Score=27.64 Aligned_cols=86 Identities=14% Similarity=0.081 Sum_probs=54.5
Q ss_pred cccCceeEEeeccchhHHHHHHHhCCCCCCCChHHHHHHHHccCCccccchhhhHhhccc---------cccHHHHHHHc
Q 023967 152 VLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELINMYFPVVYDIKHLMKFCNSL---------HGGLNKLAELL 222 (274)
Q Consensus 152 v~~~~~~wi~f~g~yD~~yLlk~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l~~~~~~l---------~~~L~~la~~L 222 (274)
+.++++..|.|+...|...|.+.+ |-.+ .+++||..++..+..- ..||..+++.+
T Consensus 61 Le~~~i~Kv~h~~k~D~~~L~~~~-gi~~---------------~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~ 124 (197)
T cd06148 61 LESKKILKVIHDCRRDSDALYHQY-GIKL---------------NNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKY 124 (197)
T ss_pred hcCCCccEEEEechhHHHHHHHhc-Cccc---------------cceeeHHHHHHHHHHHhcCCccccccccHHHHHHHh
Confidence 345677889988888888775433 3221 2468887665555321 13677776553
Q ss_pred -CCc--------------------c-C--CCCcccchhHHHHHHHHHHHHHHhcC
Q 023967 223 -EVE--------------------R-V--GICHQAGSDSLLTSCTFRKLRENFFN 253 (274)
Q Consensus 223 -~v~--------------------r-~--g~~HqAGsDs~lT~~~F~~l~~~~~~ 253 (274)
+++ | . ....=|..|++....+|.+|++.+..
T Consensus 125 l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~ 179 (197)
T cd06148 125 LYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALIS 179 (197)
T ss_pred hCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 432 1 1 12234999999999999999887753
No 83
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=21.08 E-value=1.3e+02 Score=28.39 Aligned_cols=31 Identities=10% Similarity=0.085 Sum_probs=22.9
Q ss_pred hhhhHHHHHHcCCC-ccchhhcCCChhHHHHH
Q 023967 115 ASDSVELLHQCGID-FKKNNEKGIDVNRFGEL 145 (274)
Q Consensus 115 ~~~Si~fL~~~GfD-Fnk~~~~GI~~~~f~e~ 145 (274)
..++++.+++.||+ .+--.--|+|.+...+.
T Consensus 136 ~~~ai~~lr~~g~~~v~iDli~GlPgqt~~~~ 167 (350)
T PRK08446 136 IIKAIENAKKAGFENISIDLIYDTPLDNKKLL 167 (350)
T ss_pred HHHHHHHHHHcCCCEEEEEeecCCCCCCHHHH
Confidence 46689999999996 67667778887654443
Done!