Query psy6037
Match_columns 286
No_of_seqs 145 out of 443
Neff 5.9
Searched_HMMs 46136
Date Sat Aug 17 00:54:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6037.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6037hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0304|consensus 100.0 2.8E-93 6.1E-98 629.6 19.5 236 13-249 1-239 (239)
2 COG5228 POP2 mRNA deadenylase 100.0 1.3E-84 2.8E-89 575.9 15.9 275 4-281 6-284 (299)
3 PF04857 CAF1: CAF1 family rib 100.0 5.2E-63 1.1E-67 454.8 18.7 227 15-244 1-262 (262)
4 PRK07942 DNA polymerase III su 99.0 2.9E-08 6.3E-13 90.2 15.7 170 34-250 4-181 (232)
5 smart00479 EXOIII exonuclease 98.9 1.2E-07 2.6E-12 79.7 17.1 165 37-250 1-168 (169)
6 KOG1990|consensus 98.9 5.4E-10 1.2E-14 113.5 3.0 229 19-252 1-366 (564)
7 cd06133 ERI-1_3'hExo_like DEDD 98.7 1.2E-06 2.7E-11 74.4 15.0 168 38-245 1-175 (176)
8 PRK09145 DNA polymerase III su 98.6 1.2E-06 2.5E-11 77.6 15.1 171 26-247 19-199 (202)
9 PRK05168 ribonuclease T; Provi 98.6 2.3E-06 5.1E-11 76.6 15.6 185 26-250 7-202 (211)
10 cd06131 DNA_pol_III_epsilon_Ec 98.6 2.7E-06 5.8E-11 72.3 14.3 163 38-245 1-166 (167)
11 cd06134 RNaseT DEDDh 3'-5' exo 98.5 3.5E-06 7.6E-11 74.1 14.0 174 35-248 4-188 (189)
12 PRK07748 sporulation inhibitor 98.4 9.9E-06 2.1E-10 72.1 15.6 172 35-248 3-179 (207)
13 cd06130 DNA_pol_III_epsilon_li 98.4 9.4E-06 2E-10 67.8 13.9 151 38-243 1-155 (156)
14 PRK05711 DNA polymerase III su 98.4 1.5E-05 3.2E-10 73.2 15.8 169 36-248 4-175 (240)
15 PRK06807 DNA polymerase III su 98.3 1.7E-05 3.8E-10 75.4 15.7 163 36-249 8-172 (313)
16 TIGR00573 dnaq exonuclease, DN 98.3 2.5E-05 5.4E-10 70.1 15.2 169 33-249 4-177 (217)
17 PRK07740 hypothetical protein; 98.3 2.9E-05 6.3E-10 71.2 15.8 171 33-251 56-228 (244)
18 cd06127 DEDDh DEDDh 3'-5' exon 98.3 1.7E-05 3.6E-10 64.9 11.6 155 39-243 1-159 (159)
19 PRK06063 DNA polymerase III su 98.2 6.1E-05 1.3E-09 71.6 15.7 166 35-252 14-182 (313)
20 PRK06310 DNA polymerase III su 98.2 5.8E-05 1.3E-09 69.5 14.8 170 32-249 3-174 (250)
21 PRK09146 DNA polymerase III su 98.2 8.4E-05 1.8E-09 68.1 15.7 170 33-252 44-230 (239)
22 PRK06195 DNA polymerase III su 98.2 6.8E-05 1.5E-09 70.9 15.2 161 37-250 2-165 (309)
23 PRK07247 DNA polymerase III su 98.1 6.4E-05 1.4E-09 66.9 13.3 159 37-248 6-168 (195)
24 TIGR01406 dnaQ_proteo DNA poly 98.1 0.00016 3.5E-09 65.6 15.9 168 37-248 1-171 (225)
25 PRK08074 bifunctional ATP-depe 98.1 9.8E-05 2.1E-09 79.5 16.5 166 36-250 3-170 (928)
26 PRK08517 DNA polymerase III su 98.0 0.00023 4.9E-09 66.0 15.9 166 33-249 65-231 (257)
27 PRK06722 exonuclease; Provisio 98.0 0.00026 5.7E-09 66.5 16.1 170 35-246 4-178 (281)
28 TIGR01298 RNaseT ribonuclease 98.0 0.00027 5.9E-09 62.8 14.6 176 35-250 7-193 (200)
29 TIGR01407 dinG_rel DnaQ family 98.0 0.00023 5.1E-09 75.8 16.6 163 37-250 1-166 (850)
30 TIGR01405 polC_Gram_pos DNA po 98.0 0.00024 5.2E-09 78.2 16.7 170 34-253 188-359 (1213)
31 cd06136 TREX1_2 DEDDh 3'-5' ex 98.0 0.00016 3.5E-09 62.9 12.5 166 38-244 1-176 (177)
32 PRK07883 hypothetical protein; 97.9 0.00025 5.4E-09 72.4 15.2 173 30-252 9-185 (557)
33 PRK07246 bifunctional ATP-depe 97.9 0.00033 7.1E-09 74.5 16.6 164 35-251 6-172 (820)
34 cd06138 ExoI_N N-terminal DEDD 97.9 0.0003 6.5E-09 61.4 12.9 166 40-241 2-181 (183)
35 PF00929 RNase_T: Exonuclease; 97.9 1.4E-05 3E-10 65.4 4.2 155 39-242 1-164 (164)
36 PTZ00315 2'-phosphotransferase 97.8 0.0014 3E-08 67.1 17.5 172 37-248 57-254 (582)
37 PRK07983 exodeoxyribonuclease 97.6 0.0022 4.8E-08 58.0 15.1 148 38-249 2-154 (219)
38 PRK11779 sbcB exonuclease I; P 97.6 0.0022 4.7E-08 64.5 16.2 174 35-248 5-197 (476)
39 PRK05601 DNA polymerase III su 97.6 0.00087 1.9E-08 65.2 12.8 200 32-269 42-269 (377)
40 PRK00448 polC DNA polymerase I 97.5 0.0024 5.2E-08 71.5 16.0 172 32-253 415-588 (1437)
41 COG0847 DnaQ DNA polymerase II 97.5 0.0047 1E-07 55.7 15.3 165 36-248 13-181 (243)
42 PRK09182 DNA polymerase III su 97.5 0.0039 8.4E-08 58.9 14.4 156 37-246 38-198 (294)
43 cd06144 REX4_like DEDDh 3'-5' 97.4 0.0014 3E-08 55.5 10.0 146 39-242 1-151 (152)
44 PRK06309 DNA polymerase III su 97.4 0.0099 2.1E-07 54.0 15.8 161 37-249 3-166 (232)
45 cd06145 REX1_like DEDDh 3'-5' 97.1 0.0069 1.5E-07 51.3 10.5 144 39-242 1-149 (150)
46 PRK05359 oligoribonuclease; Pr 97.0 0.026 5.7E-07 49.5 13.5 165 36-252 3-178 (181)
47 cd06137 DEDDh_RNase DEDDh 3'-5 96.8 0.0093 2E-07 51.0 9.0 68 154-242 85-160 (161)
48 cd06149 ISG20 DEDDh 3'-5' exon 96.5 0.029 6.3E-07 47.9 9.8 97 122-242 51-156 (157)
49 COG0349 Rnd Ribonuclease D [Tr 96.1 0.027 5.8E-07 54.7 8.6 146 24-251 5-168 (361)
50 cd06146 mut-7_like_exo DEDDy 3 95.7 0.21 4.5E-06 44.1 11.7 157 23-247 7-193 (193)
51 PRK05755 DNA polymerase I; Pro 95.1 0.37 8E-06 52.0 13.7 84 151-251 368-471 (880)
52 PF01612 DNA_pol_A_exo1: 3'-5' 94.9 0.41 8.9E-06 39.9 10.8 83 149-249 73-175 (176)
53 PRK10829 ribonuclease D; Provi 94.1 0.28 6E-06 48.0 8.9 83 151-250 72-171 (373)
54 cd06135 Orn DEDDh 3'-5' exonuc 93.4 1.9 4.1E-05 37.2 12.0 164 38-248 1-171 (173)
55 cd06141 WRN_exo DEDDy 3'-5' ex 93.2 1.4 3.1E-05 37.2 10.8 145 23-246 4-169 (170)
56 TIGR01388 rnd ribonuclease D. 92.6 5.2 0.00011 38.9 15.1 145 23-250 5-167 (367)
57 cd06148 Egl_like_exo DEDDy 3'- 88.8 8.5 0.00019 33.8 11.7 85 150-251 62-179 (197)
58 PF10108 DNA_pol_B_exo2: Predi 85.0 2.8 6E-05 38.0 6.5 103 154-260 53-182 (209)
59 PF13482 RNase_H_2: RNase_H su 82.3 0.57 1.2E-05 39.3 0.9 70 155-240 59-131 (164)
60 COG2176 PolC DNA polymerase II 81.1 4.6 9.9E-05 45.1 7.2 86 155-253 503-590 (1444)
61 COG5228 POP2 mRNA deadenylase 74.5 1.8 3.8E-05 39.9 1.6 97 159-267 197-296 (299)
62 cd06139 DNA_polA_I_Ecoli_like_ 67.3 19 0.0004 30.5 6.4 84 151-251 65-172 (193)
63 KOG2207|consensus 57.8 26 0.00057 36.5 6.3 41 209-249 529-585 (617)
64 cd06129 RNaseD_like DEDDy 3'-5 57.4 33 0.00071 28.9 6.0 79 151-246 65-160 (161)
65 KOG4013|consensus 54.6 29 0.00062 31.6 5.3 84 113-205 84-172 (255)
66 COG3359 Predicted exonuclease 50.7 19 0.00041 33.8 3.7 75 155-243 158-236 (278)
67 PF04405 ScdA_N: Domain of Unk 48.9 31 0.00068 24.7 3.8 33 112-144 12-53 (56)
68 PRK14345 lipoate-protein ligas 45.0 14 0.00031 34.0 2.0 193 11-233 11-228 (234)
69 KOG1990|consensus 45.0 9.6 0.00021 39.4 0.9 123 12-137 102-230 (564)
70 TIGR02841 spore_YyaC putative 40.7 27 0.00059 29.8 2.8 30 16-45 43-72 (140)
71 PF12345 DUF3641: Protein of u 40.2 26 0.00055 29.7 2.6 33 117-149 15-48 (134)
72 cd05782 DNA_polB_like1_exo Unc 40.1 57 0.0012 29.0 5.0 69 155-224 95-170 (208)
73 KOG4233|consensus 36.6 54 0.0012 25.5 3.6 41 151-195 18-70 (90)
74 cd00007 35EXOc 3'-5' exonuclea 31.9 1.8E+02 0.004 22.9 6.4 53 151-220 52-106 (155)
75 PF08228 RNase_P_pop3: RNase P 26.4 53 0.0011 28.5 2.4 30 210-239 110-143 (158)
76 PF06866 DUF1256: Protein of u 26.3 59 0.0013 28.4 2.7 31 16-46 67-97 (163)
77 PF08870 DUF1832: Domain of un 25.6 1.3E+02 0.0027 24.6 4.3 36 152-190 53-90 (113)
78 PF04386 SspB: Stringent starv 21.9 62 0.0013 27.7 1.9 16 35-50 31-46 (155)
79 KOG0638|consensus 21.6 25 0.00055 34.1 -0.5 72 114-192 275-353 (381)
80 TIGR01229 rocF_arginase argina 20.9 2.9E+02 0.0064 25.8 6.5 68 16-85 196-272 (300)
81 cd06129 RNaseD_like DEDDy 3'-5 20.8 90 0.002 26.2 2.7 22 27-48 3-25 (161)
No 1
>KOG0304|consensus
Probab=100.00 E-value=2.8e-93 Score=629.58 Aligned_cols=236 Identities=61% Similarity=1.065 Sum_probs=230.0
Q ss_pred cEEeccccCHHHHHHHHHHHhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCC
Q psy6037 13 GIREVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPP 92 (286)
Q Consensus 13 ~i~dVw~~N~~ee~~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~ 92 (286)
.|||||++|+++||+.||++|++||||||||||||++++|++.|+++.+++|+.||+|||.+++||+|||++|++|+.|.
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 48999999999999999999999999999999999999999999999999999999999999999999999999999995
Q ss_pred CCcceEEEEEE-ecCCCcccchhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHH
Q psy6037 93 GPFTTWQFNFK-FDLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKL 171 (286)
Q Consensus 93 ~~~~~wqFNF~-F~~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~ 171 (286)
...++|||||. |+..+|+++++||+||+++||||.|+++.||+..+|+|+|++||++++++|+||||||+||||||+|+
T Consensus 81 ~g~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~ 160 (239)
T KOG0304|consen 81 CGTDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKI 160 (239)
T ss_pred CCCceeEEecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHHHHH
Confidence 54789999999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhcc--ccccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHh
Q psy6037 172 LMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKN--LKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELF 249 (286)
Q Consensus 172 lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~--l~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~ 249 (286)
||++ +||++.++|.+.++++||.+||+|||++.|.+ +++||++||+.|+++|+|++||||||||||+++|+||++.|
T Consensus 161 Lt~~-~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~~f 239 (239)
T KOG0304|consen 161 LTGK-PLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKELF 239 (239)
T ss_pred HcCC-CCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhhhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHhcC
Confidence 9998 99999999999999999999999999999965 89999999999999999999999999999999999999864
No 2
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=1.3e-84 Score=575.93 Aligned_cols=275 Identities=45% Similarity=0.789 Sum_probs=262.3
Q ss_pred ccccccCccc----EEeccccCHHHHHHHHHHHhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceee
Q psy6037 4 SVNAINEKYG----IREVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQI 79 (286)
Q Consensus 4 ~~~~~~~~~~----i~dVw~~N~~ee~~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQl 79 (286)
|-.++-.+++ |||||++|+..||+.|+++|.+|++|+|||||||+++||+|.|+++.+++||+||+|||.++|||+
T Consensus 6 s~p~i~~dg~~~~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQl 85 (299)
T COG5228 6 SMPPIFLDGPNYLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQL 85 (299)
T ss_pred CCCCccCCCcchHHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhhe
Confidence 3344444555 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEe
Q psy6037 80 GLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSF 159 (286)
Q Consensus 80 Gitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtf 159 (286)
||+++|++|+.|.+ .+||||||.|++.+||+++|||++|+++||||.||.+.||++.+|+|+|+.||||+.++|+||||
T Consensus 86 GlsLSDe~GN~P~~-~sTWQFNF~F~l~~dmya~ESieLL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~VtWitf 164 (299)
T COG5228 86 GLSLSDENGNKPNG-PSTWQFNFEFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITF 164 (299)
T ss_pred eeeeccccCCCCCC-CceeEEEEEecchhhhcchHHHHHHHHcCCChhhHhhcCCCHHHHHHHHhccCceeccceEEEEe
Confidence 99999999999976 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhccccccHHHHHhHcCCccCCCCcccchhhHHHH
Q psy6037 160 HSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTG 239 (286)
Q Consensus 160 hg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~l~ggL~~lA~~L~v~r~g~~HqAGsDSllT~ 239 (286)
|++||||||+|+||+. |||+..++|+++|++|||+.||+|++.+.+..++.||++++..|++.|.|.+||||||||+|+
T Consensus 165 HsaYDfgyLikilt~~-plP~~~EdFy~~l~~yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa 243 (299)
T COG5228 165 HSAYDFGYLIKILTND-PLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTA 243 (299)
T ss_pred ecchhHHHHHHHHhcC-CCCccHHHHHHHHHHHCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhh
Confidence 9999999999999998 999999999999999999999999999999899999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCCCCcccccceEEecCCCCCCCCCCCcccc
Q psy6037 240 RVFFKMRELFFEDAIDDDKYCGHIYGLGPAGWNGHTNGNAEN 281 (286)
Q Consensus 240 ~~F~~l~~~~~~~~~~~~~~~g~i~Gl~~~~~~~~~~~~~~~ 281 (286)
..|++.|..+|...++ ......+||++..-.+-|.++|.+.
T Consensus 244 ~~ff~~R~~~F~~sig-~~ll~~L~g~~~~~~sl~~~~~~t~ 284 (299)
T COG5228 244 DEFFLPRFSIFTTSIG-QSLLMLLSGCQLSKLSLHKFPNGTD 284 (299)
T ss_pred HHhcchhhheeccccc-HHHHHHHhccccCCchheeCCCccc
Confidence 9999999999998874 4678899999999999998888764
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=5.2e-63 Score=454.82 Aligned_cols=227 Identities=40% Similarity=0.660 Sum_probs=201.0
Q ss_pred EeccccCHHHHHHHHHHHhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeee-cCCCCCCCC
Q psy6037 15 REVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFF-DSKSCTPPG 93 (286)
Q Consensus 15 ~dVw~~N~~ee~~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~-~~~g~~p~~ 93 (286)
+|||++||+++|+.|+++|++|+|||||+||||+..++.....+++++||+++|.||+.+.+||+|||+| +++++.|..
T Consensus 1 m~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~ 80 (262)
T PF04857_consen 1 MEVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSS 80 (262)
T ss_dssp EEE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECC
T ss_pred CcccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCce
Confidence 6999999999999999999999999999999999998875567789999999999999999999999999 788887765
Q ss_pred CcceEEEEEE-ecCCCcccchhHHHHHHHcCCChhhhhhCCCChHHHH------HHHHhcCcccc---CCccEEEeecch
Q psy6037 94 PFTTWQFNFK-FDLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFA------ELLTTSGVVLN---DKVKWLSFHSGY 163 (286)
Q Consensus 94 ~~~~wqFNF~-F~~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~F~------ell~~SgLv~~---~~v~Wvtfhg~y 163 (286)
+.+|+|||+ |+...+.++++||+||+++||||||++++||||..++ +.+..++++.. .+++||+|||+|
T Consensus 81 -~~~~~~nf~~f~~~~~~~~~~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~ 159 (262)
T PF04857_consen 81 -YNVWPFNFYLFPLDRDFSQASSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLY 159 (262)
T ss_dssp -EEEEEEEBSTTSTTTCEEEHHHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHH
T ss_pred -eEEEEeeeeccccccceecchhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHh
Confidence 889999999 9999998999999999999999999999999999999 66777888864 358999999999
Q ss_pred hHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhccccccHHHHHhHcCCcc-------------------
Q psy6037 164 DFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQLDLSR------------------- 224 (286)
Q Consensus 164 D~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~l~ggL~~lA~~L~v~r------------------- 224 (286)
|++||+++|+| |||+++++|.+.++.+||.+||||||++.+....++|+.|++.|++.|
T Consensus 160 Dl~~l~~~f~~--~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~ 237 (262)
T PF04857_consen 160 DLMYLYKKFIG--PLPETLEEFKELLRELFPRIYDTKYLAEECPGKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKN 237 (262)
T ss_dssp HHHHHHHHHTT--S--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS-SSHHHHHHHTTSTT----EEE-TTS--------
T ss_pred HHHHHHHHhcC--CCCCCHHHHHHHHHHHCcccccHHHHHHhccccccCHHHHHHHhCCCcccccccccccccccccccc
Confidence 99999999999 899999999999999999999999999998777889999999999998
Q ss_pred ----CCC-CcccchhhHHHHHHHHH
Q psy6037 225 ----IGP-QHQAGSDSLLTGRVFFK 244 (286)
Q Consensus 225 ----~g~-~HqAGsDSllT~~~F~~ 244 (286)
.|. .|+||+||+||+.+|.|
T Consensus 238 ~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 238 NFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp -----SS-TTSHHHHHHHHHHHHHH
T ss_pred ccccCCCCCCCcchHHHHHHHHHcC
Confidence 676 99999999999999986
No 4
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=98.95 E-value=2.9e-08 Score=90.18 Aligned_cols=170 Identities=21% Similarity=0.250 Sum_probs=118.8
Q ss_pred hhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccch
Q psy6037 34 NTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQ 113 (286)
Q Consensus 34 ~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~ 113 (286)
.+.+||++|+|=||+.. ..=.|||+|+..++.+|.. +-.|+...+... .+.+
T Consensus 4 ~~~~~vv~D~ETTGl~p---------------------~~d~Iieig~v~v~~~g~~------~~~~~~lv~P~~-~i~~ 55 (232)
T PRK07942 4 HPGPLAAFDLETTGVDP---------------------ETARIVTAALVVVDADGEV------VESREWLADPGV-EIPE 55 (232)
T ss_pred ccCcEEEEEeccCCCCC---------------------CCCeeEEEEEEEEeCCCcc------ccceEEEECCCC-CCCH
Confidence 35689999999999832 1114999999999876753 234555545443 3556
Q ss_pred hHHHHHHHcCCChhhhhhCCCChH----HHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHH
Q psy6037 114 DSIDLLQNSGIQFQRHKEEGIEPA----DFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQ 189 (286)
Q Consensus 114 ~SI~fL~~~G~DF~k~~~~GI~~~----~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l 189 (286)
++.+. |||.=..+...|.|.. +|.+.+.. +. .++..+|+||..||+++|-+.+... .+|.-
T Consensus 56 ~a~~I---hGIt~e~l~~~g~~~~~vl~e~~~~l~~--~~-~~~~~lVahNa~FD~~fL~~~~~r~-~~~~~-------- 120 (232)
T PRK07942 56 EASAV---HGITTEYARAHGRPAAEVLAEIADALRE--AW-ARGVPVVVFNAPYDLTVLDRELRRH-GLPSL-------- 120 (232)
T ss_pred HHHHH---hCCCHHHHHhhCCCHHHHHHHHHHHHHH--Hh-hcCCEEEEeCcHhhHHHHHHHHHHc-CCCCc--------
Confidence 66555 9999999999999864 23333322 11 1244789999999999998877542 23221
Q ss_pred HhhcC-CccchhHHHHhhccc---cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhc
Q psy6037 190 RLFFK-SIYDVKYLMKSCKNL---KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFF 250 (286)
Q Consensus 190 ~~~FP-~iYD~K~l~~~~~~l---~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~ 250 (286)
.| .++|+-.|++.+... +-.|+.+++.+|++..+ +|.|-+|++.|+.+|.+|.+.+.
T Consensus 121 ---~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~~~-aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 121 ---VPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRLDN-AHEATADALAAARVAWALARRFP 181 (232)
T ss_pred ---cCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCCCC-CCChHHHHHHHHHHHHHHHHHHH
Confidence 12 256877777654322 23699999999998654 89999999999999999988764
No 5
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.92 E-value=1.2e-07 Score=79.74 Aligned_cols=165 Identities=21% Similarity=0.213 Sum_probs=115.7
Q ss_pred CeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHH
Q psy6037 37 NYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSI 116 (286)
Q Consensus 37 ~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI 116 (286)
.||++|+|.+|+... .-.|||+|....+.+. ....|+.+.... ...++.+.
T Consensus 1 ~~v~~D~Ettg~~~~---------------------~~~Iieig~v~~~~~~-------~~~~f~~~v~p~-~~i~~~~~ 51 (169)
T smart00479 1 TLVVIDCETTGLDPG---------------------KDEIIEIAAVDVDGGR-------IIVVFDTYVKPD-RPITDYAT 51 (169)
T ss_pred CEEEEEeeCCCCCCC---------------------CCeEEEEEEEEEECCE-------eEEEEEEEECCC-CCCCHHHH
Confidence 389999999997431 1349999998877642 256788776653 23444444
Q ss_pred HHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeec-chhHHHHHHHHhCC-CCCCCChHHHHHHHHhhcC
Q psy6037 117 DLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHS-GYDFGYLLKLLMGT-RSLPSEEAEFFELQRLFFK 194 (286)
Q Consensus 117 ~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg-~yD~gyL~K~lt~~-~~LP~~~~~F~~~l~~~FP 194 (286)
+-+|+.-+.+.. |.++.+..+.+.. ++ .+. .+|++|+ .+|+.+|-+.+... .+.|.. -
T Consensus 52 ---~~~Git~~~l~~-~~~~~~~~~~~~~--~l-~~~-~~v~~n~~~fD~~~L~~~~~~~~~~~~~~------------~ 111 (169)
T smart00479 52 ---EIHGITPEMLDD-APTFEEVLEELLE--FL-KGK-ILVAGNALNFDLRFLKLEHPRLGIKDPPK------------N 111 (169)
T ss_pred ---HHhCCCHHHHhC-CCCHHHHHHHHHH--Hh-cCC-EEEEeCCHHHhHHHHHHHHHHhCCCCCcC------------C
Confidence 447998887765 8888765544433 22 222 5789999 99999998877532 133311 1
Q ss_pred CccchhHHHHhhc-cccccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhc
Q psy6037 195 SIYDVKYLMKSCK-NLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFF 250 (286)
Q Consensus 195 ~iYD~K~l~~~~~-~l~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~ 250 (286)
...|+.-+++... ....+|+.+++.+|++..+..|-|-.|++.|+.+|.+|++..+
T Consensus 112 ~~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 112 PVIDTLKLARALNPGRKYSLKKLAERLGLEVIGRAHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred CeeEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHHhh
Confidence 2567766655432 2256899999999999988889999999999999999987654
No 6
>KOG1990|consensus
Probab=98.91 E-value=5.4e-10 Score=113.49 Aligned_cols=229 Identities=20% Similarity=0.242 Sum_probs=157.9
Q ss_pred ccCHHHHHHHHHHHhhhCCeeeeeccccccccccC--CCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCC------
Q psy6037 19 ARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPL--GDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCT------ 90 (286)
Q Consensus 19 ~~N~~ee~~~I~~~i~~~~fIAiDtEFpGv~~~p~--~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~------ 90 (286)
+.|++. +.+++..|+.+.|+++|.|++|+...|. +.-.++.+.+|+++|.|+..+.++|+|+|+|..+++.
T Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 79 (564)
T KOG1990|consen 1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMST 79 (564)
T ss_pred CCcccc-hhHHHhhcCHHHHHHHhhhhccceecccccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccC
Confidence 468888 8999999999999999999999988772 3344578999999999999999999999999876542
Q ss_pred CCCCcceEEEEEEecCCCcccchhHHHHHHHc--CCChh---hhh------hCCCChH----------------------
Q psy6037 91 PPGPFTTWQFNFKFDLQEDMYAQDSIDLLQNS--GIQFQ---RHK------EEGIEPA---------------------- 137 (286)
Q Consensus 91 p~~~~~~wqFNF~F~~~~d~~~~~SI~fL~~~--G~DF~---k~~------~~GI~~~---------------------- 137 (286)
|.. ..+|...+.+.....+|+..++.++.++ +++=. ... ..|+.+.
T Consensus 80 ~~n-~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~ 158 (564)
T KOG1990|consen 80 GGN-FVVWSRGDSISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIP 158 (564)
T ss_pred CCc-eeeeecCccccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhh
Confidence 111 3466655444444678889999998887 22111 000 1111110
Q ss_pred ----------------------------------------------------------HHHHHHHhcCc-----------
Q psy6037 138 ----------------------------------------------------------DFAELLTTSGV----------- 148 (286)
Q Consensus 138 ----------------------------------------------------------~F~ell~~SgL----------- 148 (286)
.|+..+...|.
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 01122222222
Q ss_pred ---cccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHh--hcc--ccccHHHHHhH-c
Q psy6037 149 ---VLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKS--CKN--LKGGLQEVAEQ-L 220 (286)
Q Consensus 149 ---v~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~--~~~--l~ggL~~lA~~-L 220 (286)
+...+..-|..++.+|+.|+.|-|.+ +||+++++|.+. ...||.++|+|-++.- +.. +.+.+.+.+.. .
T Consensus 239 l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~--~lp~~l~~f~~~-~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~ 315 (564)
T KOG1990|consen 239 LQELLLTGKVLVLHNKLLDVMYRYKNFLS--PLPSTLEEFTDS-SSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKA 315 (564)
T ss_pred HHHHHhcCCeEEeeccceeeeeehhhccc--ccchhHHHhhhh-hhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhc
Confidence 22223344567789999999999999 899999999999 9999999999998872 222 44444443332 1
Q ss_pred C----Cc---------------cCCCCcccchhhHHHHHHHHHHHHHhcCC
Q psy6037 221 D----LS---------------RIGPQHQAGSDSLLTGRVFFKMRELFFED 252 (286)
Q Consensus 221 ~----v~---------------r~g~~HqAGsDSllT~~~F~~l~~~~~~~ 252 (286)
. +. +....|+++++++.++.++.+........
T Consensus 316 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 366 (564)
T KOG1990|consen 316 KKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAK 366 (564)
T ss_pred ccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhc
Confidence 1 11 11346889999999999998877665543
No 7
>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=98.65 E-value=1.2e-06 Score=74.43 Aligned_cols=168 Identities=21% Similarity=0.238 Sum_probs=112.1
Q ss_pred eeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCC-cccchhHH
Q psy6037 38 YIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQE-DMYAQDSI 116 (286)
Q Consensus 38 fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~-d~~~~~SI 116 (286)
||.+|+|.+|...... ... .-.|||+|....+.++.. ..-.|+.+..... ...++.+.
T Consensus 1 ~vv~D~Ettg~~~~~~--------------~~~--~~~IieIgav~v~~~~~~-----~~~~f~~~i~P~~~~~i~~~~~ 59 (176)
T cd06133 1 YLVIDFEATCWEGNSK--------------PDY--PNEIIEIGAVLVDVKTKE-----IIDTFSSYVKPVINPKLSDFCT 59 (176)
T ss_pred CEEEEeeccccCCCCC--------------CCC--CcceEEEEEEEEEcCCCe-----EEeeeeeeECCCcCCchhHHHH
Confidence 7899999999865321 001 125999999999887642 3455666554444 35566666
Q ss_pred HHHHHcCCChhhhhhCCCChHH----HHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhh
Q psy6037 117 DLLQNSGIQFQRHKEEGIEPAD----FAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLF 192 (286)
Q Consensus 117 ~fL~~~G~DF~k~~~~GI~~~~----F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~ 192 (286)
+. +||.-+.+. .+.++.+ |.+.+.... ....++ +|.+|...+.+.+... ..+. ...+
T Consensus 60 ~i---~gIt~e~l~-~~~~~~~vl~~~~~~l~~~~-----~~~~v~-~~~~d~~~l~~~~~~~-~~~~--------~~~~ 120 (176)
T cd06133 60 EL---TGITQEDVD-NAPSFPEVLKEFLEWLGKNG-----KYAFVT-WGDWDLKDLLQNQCKY-KIIN--------LPPF 120 (176)
T ss_pred Hh---cCcCHHHHh-cCCCHHHHHHHHHHHHHhCC-----CeEEEe-ecHhhHHHHHHHHHHh-cCCC--------Cccc
Confidence 65 999999985 5576653 333332221 133444 4688988877654432 1110 0122
Q ss_pred cCCccchhHHHHhhccc--cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHH
Q psy6037 193 FKSIYDVKYLMKSCKNL--KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKM 245 (286)
Q Consensus 193 FP~iYD~K~l~~~~~~l--~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l 245 (286)
+...+|++.+++..... ..+|..+++.+|++..+..|-|=+|++.|+.+|.+|
T Consensus 121 ~~~~~D~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 121 FRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred ccceEEHHHHHHHHhCCCCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHh
Confidence 34677988888765433 568999999999999899999999999999999987
No 8
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.64 E-value=1.2e-06 Score=77.64 Aligned_cols=171 Identities=16% Similarity=0.316 Sum_probs=109.4
Q ss_pred HHHHHHHhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEec
Q psy6037 26 FVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFD 105 (286)
Q Consensus 26 ~~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~ 105 (286)
+..+.+.....+||++|+|-+|+... .-.|||+|...++.+.. .....|.++.+
T Consensus 19 ~~~~~~~~~~~~~vviD~ETTGl~~~---------------------~d~IieIgaV~~~~~~~-----~~~~~f~~~i~ 72 (202)
T PRK09145 19 YAFLFEPPPPDEWVALDCETTGLDPR---------------------RAEIVSIAAVKIRGNRI-----LTSERLELLVR 72 (202)
T ss_pred HHHHhcCCCCCCEEEEEeECCCCCCC---------------------CCceEEEEEEEEECCEE-----eecCceEEEEC
Confidence 33344444556999999999997311 12599999988875321 12345666655
Q ss_pred CCCcccchhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHh---CCCCCCCCh
Q psy6037 106 LQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLM---GTRSLPSEE 182 (286)
Q Consensus 106 ~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt---~~~~LP~~~ 182 (286)
... ...+.+.++ +|+.-..+. .|.+..+..+.+.. .+. +-.||+++..+|..+|-+-+. +. ++|...
T Consensus 73 p~~-~i~~~~~~i---hGIt~~~l~-~~~~~~~vl~~~~~--~i~--~~~lv~hn~~fD~~fL~~~~~~~~~~-~~~~~~ 142 (202)
T PRK09145 73 PPQ-SLSAESIKI---HRLRHQDLE-DGLSEEEALRQLLA--FIG--NRPLVGYYLEFDVAMLNRYVRPLLGI-PLPNPL 142 (202)
T ss_pred CCC-CCCHhHhhh---cCcCHHHHh-cCCCHHHHHHHHHH--HHc--CCeEEEeCHHHHHHHHHHHHHHhcCC-CCCCCe
Confidence 543 345555554 888777664 67776543333332 111 235899888999999977653 33 566432
Q ss_pred HHHHHHHHhhcCCccchhHHHHh-----h-cc-ccccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHH
Q psy6037 183 AEFFELQRLFFKSIYDVKYLMKS-----C-KN-LKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRE 247 (286)
Q Consensus 183 ~~F~~~l~~~FP~iYD~K~l~~~-----~-~~-l~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~ 247 (286)
+|+.-+... . .. ..-+|+.+++.+|++..+ .|.|-+|++.|+.+|.+|++
T Consensus 143 --------------id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~-~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 143 --------------IEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVLG-RHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred --------------eeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCCC-CCCcHHHHHHHHHHHHHHHh
Confidence 344333211 0 11 124899999999998754 69999999999999999865
No 9
>PRK05168 ribonuclease T; Provisional
Probab=98.59 E-value=2.3e-06 Score=76.63 Aligned_cols=185 Identities=14% Similarity=0.213 Sum_probs=124.4
Q ss_pred HHHHHHHhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecC--CCCCCCCCcceEEEEEE
Q psy6037 26 FVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDS--KSCTPPGPFTTWQFNFK 103 (286)
Q Consensus 26 ~~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~--~g~~p~~~~~~wqFNF~ 103 (286)
+..|..-++...||++|+|=+|+.... | .|||+|....+. +|.. ....+|...
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~-------------------d--~IieIgaV~v~~d~~g~i----~~~~~f~~l 61 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKT-------------------D--ALLEIAAVTLKMDEQGWL----YPDETLHFH 61 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCC-------------------C--EEEEEeEEEEEecCCCcE----eccceEEEE
Confidence 456778888999999999999986422 0 399999887754 3432 124567777
Q ss_pred ecCC-CcccchhHHHHHHHcCCChhhhhhCCCChHH-HHHH---HHh--cCccccCCccEEEeecchhHHHHHHHHhCCC
Q psy6037 104 FDLQ-EDMYAQDSIDLLQNSGIQFQRHKEEGIEPAD-FAEL---LTT--SGVVLNDKVKWLSFHSGYDFGYLLKLLMGTR 176 (286)
Q Consensus 104 F~~~-~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~-F~el---l~~--SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~ 176 (286)
.+.. .-...+++++. +||.=+...+.|++... +.+. +.. ++..+ ++..+|++|-.+|++||-+.+...
T Consensus 62 v~P~~~~~i~~~~~~i---hGIt~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~-~~~~lVaHNa~FD~~fL~~~~~r~- 136 (211)
T PRK05168 62 VEPFEGANLEPEALAF---NGIDPDNPLRGAVSEKEALHEIFKMVRKGIKASGC-NRAILVAHNAHFDLSFLMAAAERA- 136 (211)
T ss_pred ECCCCCCCCCHHHHhh---cCCCchhhhhcCCChHHHHHHHHHHHHHHHHhccc-CCceEEEeccHHhHHHHHHHHHHh-
Confidence 6653 23466666655 99966656677887542 2222 221 00011 245799999999999998776432
Q ss_pred CCCCChHHHHHHHHhhcC-CccchhHHHHhhccccccHHHHHhHcCCccCC-CCcccchhhHHHHHHHHHHHHHhc
Q psy6037 177 SLPSEEAEFFELQRLFFK-SIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIG-PQHQAGSDSLLTGRVFFKMRELFF 250 (286)
Q Consensus 177 ~LP~~~~~F~~~l~~~FP-~iYD~K~l~~~~~~l~ggL~~lA~~L~v~r~g-~~HqAGsDSllT~~~F~~l~~~~~ 250 (286)
.+.. ..+.| .++||.-|++..... ..|..+++.+|++-.+ ..|.|-+|++.|+++|.+|.+++-
T Consensus 137 ~~~~---------~~~~~~~~iDt~~lar~~~~~-~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 137 GLKR---------NPFHPFSTFDTATLSGLALGQ-TVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred CCCC---------CCCCCCcEeeHHHHHHHHcCC-CCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 2210 01123 478998888754322 3699999999998543 589999999999999999988764
No 10
>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=98.55 E-value=2.7e-06 Score=72.33 Aligned_cols=163 Identities=18% Similarity=0.226 Sum_probs=106.8
Q ss_pred eeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHHH
Q psy6037 38 YIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSID 117 (286)
Q Consensus 38 fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI~ 117 (286)
||.+|+|=+|+..+ ..-.|||+|....+. +.. ...+|+...+.... ..+.+.+
T Consensus 1 ~v~~D~ETTGl~~~--------------------~~~~iieig~v~v~~-~~~-----~~~~~~~~v~P~~~-i~~~~~~ 53 (167)
T cd06131 1 QIVLDTETTGLDPR--------------------EGHRIIEIGCVELIN-RRL-----TGNTFHVYINPERD-IPEEAFK 53 (167)
T ss_pred CEEEEeeCCCCCCC--------------------CCCeEEEEEEEEEEC-CcE-----eccEEEEEECCCCC-CCHHHHH
Confidence 68999999998420 112599999987654 221 23467776665543 5666655
Q ss_pred HHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcC-Cc
Q psy6037 118 LLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFK-SI 196 (286)
Q Consensus 118 fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP-~i 196 (286)
. +||.=+.+... .+..+..+.+.. .+ .+. .+|.+|+.+|+.+|-+-+-.- .++... ..| ..
T Consensus 54 i---hGIt~e~l~~~-~~~~~v~~~l~~--~l-~~~-~lv~hn~~fD~~~l~~~~~~~-~~~~~~---------~~~~~~ 115 (167)
T cd06131 54 V---HGITDEFLADK-PKFAEIADEFLD--FI-RGA-ELVIHNASFDVGFLNAELSLL-GLGKKI---------IDFCRV 115 (167)
T ss_pred H---hCCCHHHHhcC-CCHHHHHHHHHH--HH-CCC-eEEEeChHHhHHHHHHHHHHh-CCCccc---------ccCCCc
Confidence 4 78887776554 344433333332 12 222 589999999999987766531 121110 022 46
Q ss_pred cchhHHHHhhc-cccccHHHHHhHcCCccCC-CCcccchhhHHHHHHHHHH
Q psy6037 197 YDVKYLMKSCK-NLKGGLQEVAEQLDLSRIG-PQHQAGSDSLLTGRVFFKM 245 (286)
Q Consensus 197 YD~K~l~~~~~-~l~ggL~~lA~~L~v~r~g-~~HqAGsDSllT~~~F~~l 245 (286)
+|+-.+++... ....+|+.+++.+|++..+ .+|-|-+|++.|+.+|.+|
T Consensus 116 idt~~~~~~~~~~~~~~L~~l~~~~~i~~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 116 IDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred eEhHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHh
Confidence 78866665432 3456899999999999875 4799999999999999887
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=98.50 E-value=3.5e-06 Score=74.14 Aligned_cols=174 Identities=14% Similarity=0.189 Sum_probs=114.9
Q ss_pred hCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecC--CCCCCCCCcceEEEEEEecCC-Cccc
Q psy6037 35 TYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDS--KSCTPPGPFTTWQFNFKFDLQ-EDMY 111 (286)
Q Consensus 35 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~--~g~~p~~~~~~wqFNF~F~~~-~d~~ 111 (286)
.+.+|++|+|=+|+.... =.|||+|...++. +|.. ...-+|++.++.. ....
T Consensus 4 ~~~~vv~D~ETTGl~~~~---------------------d~Iieigav~v~~~~~~~i----~~~~~f~~lv~P~~~~~i 58 (189)
T cd06134 4 GFLPVVVDVETGGFNPQT---------------------DALLEIAAVTLEMDEQGNL----YPDETFHFHILPFEGANL 58 (189)
T ss_pred cceeEEEEecCCCCCCCC---------------------CeEEEEEEEEEEECCCCce----eccceEEEEEcCCCCCCC
Confidence 467899999999986421 0299999998864 3432 1234666666653 2345
Q ss_pred chhHHHHHHHcCCChhhhhhCCCChHH-HHHHHHh-cCccc---cCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHH
Q psy6037 112 AQDSIDLLQNSGIQFQRHKEEGIEPAD-FAELLTT-SGVVL---NDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFF 186 (286)
Q Consensus 112 ~~~SI~fL~~~G~DF~k~~~~GI~~~~-F~ell~~-SgLv~---~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~ 186 (286)
.+++++. +||.=+...+.|++... +.+++-. ..++. ..+-.+|++|..+|++||-+.+..- .++
T Consensus 59 ~~~~~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~-~~~------- 127 (189)
T cd06134 59 DPAALEF---NGIDPFHPFRFAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARC-KIK------- 127 (189)
T ss_pred CHHHHhh---cCCCchhhhccccchHHHHHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHh-CCC-------
Confidence 6666555 99986666777876542 3322211 00110 0134799999999999998877532 221
Q ss_pred HHHHhhc-C-CccchhHHHHhhccccccHHHHHhHcCCccC-CCCcccchhhHHHHHHHHHHHHH
Q psy6037 187 ELQRLFF-K-SIYDVKYLMKSCKNLKGGLQEVAEQLDLSRI-GPQHQAGSDSLLTGRVFFKMREL 248 (286)
Q Consensus 187 ~~l~~~F-P-~iYD~K~l~~~~~~l~ggL~~lA~~L~v~r~-g~~HqAGsDSllT~~~F~~l~~~ 248 (286)
+..+ | .++||..|++..... -.|+.+++.+|++.. ...|.|.+|++.|+.+|.+|.++
T Consensus 128 ---~~~~~~~~~lDt~~la~~~~~~-~~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 128 ---RNPFHPFSTFDTATLAGLAYGQ-TVLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred ---CCCCCCCcEEEHHHHHHHHhCC-CcHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 0111 2 368998888765321 269999999999853 46899999999999999999875
No 12
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=98.44 E-value=9.9e-06 Score=72.12 Aligned_cols=172 Identities=18% Similarity=0.129 Sum_probs=106.5
Q ss_pred hCCeeeeecccccccccc-CCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCc-ccc
Q psy6037 35 TYNYIGIDTEFPGVVAKP-LGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQED-MYA 112 (286)
Q Consensus 35 ~~~fIAiDtEFpGv~~~p-~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d-~~~ 112 (286)
.-+||++|+|.+|...+. +..+. + .|||+|....+. |+. .-.|+-+.+.... ...
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~--------------~--eIIeIGaV~v~~-~~i------~~~f~~lV~P~~~~~i~ 59 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFF--------------P--EIIEVGLVSVVG-CEV------EDTFSSYVKPKTFPSLT 59 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCC--------------C--ceEEEeEEEEec-CcC------hhhhcceECCCccCccC
Confidence 457999999999975421 00000 1 499999988864 332 2234444443322 344
Q ss_pred hhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCC-CCCCCChHHHHHHHHh
Q psy6037 113 QDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGT-RSLPSEEAEFFELQRL 191 (286)
Q Consensus 113 ~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~-~~LP~~~~~F~~~l~~ 191 (286)
+.+.++ +||.=+.+. .|.+..+..+.+.. .+-+....++ .|+.+|+.+|-+-+.-. .+.|.
T Consensus 60 ~~~~~l---tGIt~~~l~-~ap~~~evl~~f~~--~~~~~~~~iv-~~~~fD~~fL~~~~~~~~~~~~~----------- 121 (207)
T PRK07748 60 ERCKSF---LGITQEDVD-KGISFEELVEKLAE--YDKRCKPTIV-TWGNMDMKVLKHNCEKAGVPFPF----------- 121 (207)
T ss_pred hhhhhh---cCcCHHHHc-cCCCHHHHHHHHHH--HhCcCCeEEE-EECHHHHHHHHHHHHHcCCCCcc-----------
Confidence 444444 888877764 68887654444433 2212133444 57899999998877532 12231
Q ss_pred hcCCccchhHHHHhhc--cccccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHH
Q psy6037 192 FFKSIYDVKYLMKSCK--NLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMREL 248 (286)
Q Consensus 192 ~FP~iYD~K~l~~~~~--~l~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~ 248 (286)
++...|+..+.+... .-..+|..+++.+|++-.+..|-|-+||+.|+.+|.+|.+.
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 112344444333221 11247999999999998888999999999999999999876
No 13
>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=98.41 E-value=9.4e-06 Score=67.78 Aligned_cols=151 Identities=17% Similarity=0.163 Sum_probs=100.6
Q ss_pred eeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHHH
Q psy6037 38 YIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSID 117 (286)
Q Consensus 38 fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI~ 117 (286)
||++|+|-+|.. + -.|||+|...++. |+ ..-+|+.++.... ...+++.+
T Consensus 1 ~v~~D~Ettg~~--~---------------------~~ii~ig~v~~~~-~~------~~~~~~~~i~p~~-~~~~~~~~ 49 (156)
T cd06130 1 FVAIDFETANAD--R---------------------ASACSIGLVKVRD-GQ------IVDTFYTLIRPPT-RFDPFNIA 49 (156)
T ss_pred CEEEEEeCCCCC--C---------------------CceEEEEEEEEEC-CE------EEEEEEEEeCcCC-CCChhhcc
Confidence 799999999731 1 0279999988863 43 2456777766554 44555543
Q ss_pred HHHHcCCChhhhhhCCCChHH-HHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCC-CCCCCChHHHHHHHHhhcCC
Q psy6037 118 LLQNSGIQFQRHKEEGIEPAD-FAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGT-RSLPSEEAEFFELQRLFFKS 195 (286)
Q Consensus 118 fL~~~G~DF~k~~~~GI~~~~-F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~-~~LP~~~~~F~~~l~~~FP~ 195 (286)
-+||.-..+.. +.++.+ +.+++.- + + +-.||+++..+|+++|-+.+-.. .+.|+ + .
T Consensus 50 ---i~GIt~e~l~~-~~~~~~v~~~l~~~---l-~-~~~lv~hn~~fD~~~l~~~~~~~g~~~~~------------~-~ 107 (156)
T cd06130 50 ---IHGITPEDVAD-APTFPEVWPEIKPF---L-G-GSLVVAHNASFDRSVLRAALEAYGLPPPP------------Y-Q 107 (156)
T ss_pred ---ccCcCHHHHhc-CCCHHHHHHHHHHH---h-C-CCEEEEeChHHhHHHHHHHHHHcCCCCCC------------C-C
Confidence 49998888764 444433 3333211 1 2 24789999999999998777542 12221 1 3
Q ss_pred ccchhHHHHhh-ccc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHH
Q psy6037 196 IYDVKYLMKSC-KNL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFF 243 (286)
Q Consensus 196 iYD~K~l~~~~-~~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~ 243 (286)
.+|+.-+++.. ..+ ..+|+.+++.+|++.. +|-|-+|++.|+..|.
T Consensus 108 ~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~~--~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 108 YLCTVRLARRVWPLLPNHKLNTVAEHLGIELN--HHDALEDARACAEILL 155 (156)
T ss_pred EEEHHHHHHHHhccCCCCCHHHHHHHcCCCcc--CcCchHHHHHHHHHHh
Confidence 56776665543 222 2589999999999876 9999999999999874
No 14
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=98.39 E-value=1.5e-05 Score=73.21 Aligned_cols=169 Identities=16% Similarity=0.234 Sum_probs=111.6
Q ss_pred CCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhH
Q psy6037 36 YNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDS 115 (286)
Q Consensus 36 ~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~S 115 (286)
-.||++|||=||+.... .-.|||||...... +. .....|..+.+... ...+++
T Consensus 4 ~r~vvlDtETTGldp~~--------------------~drIIEIGaV~v~~-~~-----~~~~~f~~~i~P~~-~i~~~a 56 (240)
T PRK05711 4 MRQIVLDTETTGLNQRE--------------------GHRIIEIGAVELIN-RR-----LTGRNFHVYIKPDR-LVDPEA 56 (240)
T ss_pred CeEEEEEeeCCCcCCCC--------------------CCeEEEEEEEEEEC-CE-----EeccEEEEEECcCC-cCCHHH
Confidence 47999999999985310 22599999876543 22 12245677776644 345666
Q ss_pred HHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCC-CCCCCChHHHHHHHHhhcC
Q psy6037 116 IDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGT-RSLPSEEAEFFELQRLFFK 194 (286)
Q Consensus 116 I~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~-~~LP~~~~~F~~~l~~~FP 194 (286)
++. |||.-..+... -++.+-.+.+.. .+ .+-.+|.+|..+|++||-+-+-.- .++|... .+.
T Consensus 57 ~~V---HGIT~e~l~~~-p~f~ev~~~f~~--fi--~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~---------~~~ 119 (240)
T PRK05711 57 LAV---HGITDEFLADK-PTFAEVADEFLD--FI--RGAELIIHNAPFDIGFMDYEFALLGRDIPKTN---------TFC 119 (240)
T ss_pred hhh---cCCCHHHHcCC-CCHHHHHHHHHH--Hh--CCCEEEEEccHHhHHHHHHHHHHhCCCCCccc---------ccC
Confidence 554 88887776553 344333333332 12 123589999999999997765321 1455321 123
Q ss_pred CccchhHHHHhh-ccccccHHHHHhHcCCccCCC-CcccchhhHHHHHHHHHHHHH
Q psy6037 195 SIYDVKYLMKSC-KNLKGGLQEVAEQLDLSRIGP-QHQAGSDSLLTGRVFFKMREL 248 (286)
Q Consensus 195 ~iYD~K~l~~~~-~~l~ggL~~lA~~L~v~r~g~-~HqAGsDSllT~~~F~~l~~~ 248 (286)
.+.||--|++.. .+.+.+|+.|++.+|++..+. .|.|-.|+.+|+.+|.+|...
T Consensus 120 ~~iDTl~lar~~~p~~~~~L~aL~~~~gi~~~~r~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 120 KVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred ceeeHHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCc
Confidence 577887777654 234458999999999987654 699999999999999999753
No 15
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=98.35 E-value=1.7e-05 Score=75.36 Aligned_cols=163 Identities=18% Similarity=0.214 Sum_probs=108.6
Q ss_pred CCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhH
Q psy6037 36 YNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDS 115 (286)
Q Consensus 36 ~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~S 115 (286)
-+||++|+|.+|+... .-.|||+|...++ +|+ ...+|+........+ .+.+
T Consensus 8 ~~~Vv~DlETTGl~p~---------------------~~eIIEIgaV~v~-~g~------i~~~f~~lVkP~~~I-~~~a 58 (313)
T PRK06807 8 LDYVVIDFETTGFNPY---------------------NDKIIQVAAVKYR-NHE------LVDQFVSYVNPERPI-PDRI 58 (313)
T ss_pred CCEEEEEEECCCCCCC---------------------CCeEEEEEEEEEE-CCE------EEEEEEEEECcCCCC-CHhh
Confidence 3799999999998421 1269999998886 343 367788776655432 3433
Q ss_pred HHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCC
Q psy6037 116 IDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKS 195 (286)
Q Consensus 116 I~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~ 195 (286)
. +-+||.-..+. .+.+..+-.+.+.. ++ .++ .+|++++.+|+.+|-+-+-.- .+|.- .+.
T Consensus 59 ~---~ihGIT~e~l~-~~~~~~evl~~f~~--fl-~~~-~lVaHNa~FD~~fL~~~~~~~-gl~~~-----------~~~ 118 (313)
T PRK06807 59 T---SLTGITNYRVS-DAPTIEEVLPLFLA--FL-HTN-VIVAHNASFDMRFLKSNVNML-GLPEP-----------KNK 118 (313)
T ss_pred h---ccCCCCHHHHh-CCCCHHHHHHHHHH--HH-cCC-eEEEEcHHHHHHHHHHHHHHc-CCCCC-----------CCC
Confidence 3 44888866654 45554433333322 11 223 578999999999998877432 23311 012
Q ss_pred ccchhHHHHhhc-ccc-ccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHh
Q psy6037 196 IYDVKYLMKSCK-NLK-GGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELF 249 (286)
Q Consensus 196 iYD~K~l~~~~~-~l~-ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~ 249 (286)
+.||-.+++..- .+. .+|+.+++.+|++. .+|-|=.|++.|+.+|.+|...-
T Consensus 119 ~iDtl~la~~~~~~~~~~kL~~L~~~lgi~~--~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 119 VIDTVFLAKKYMKHAPNHKLETLKRMLGIRL--SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred EeeHHHHHHHHhCCCCCCCHHHHHHHcCCCC--CCcChHHHHHHHHHHHHHHHHhh
Confidence 557766665432 222 37999999999997 78999999999999999987654
No 16
>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=98.31 E-value=2.5e-05 Score=70.09 Aligned_cols=169 Identities=15% Similarity=0.224 Sum_probs=108.3
Q ss_pred hhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccc
Q psy6037 33 INTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYA 112 (286)
Q Consensus 33 i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~ 112 (286)
+..-.||++|+|=+|+... . .|||+|.......+. ...+|..+.+... ...
T Consensus 4 l~~~~fvv~D~ETTGl~~~--------------------~--~IIeIgav~v~~~~~------~~~~f~~li~P~~-~i~ 54 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAG--------------------H--DIIEIGAVEIINRRI------TGNKFHTYIKPDR-PID 54 (217)
T ss_pred EEecCEEEEEecCCCCCCC--------------------C--CEEEEEEEEEECCCE------eeeEEEEEECcCC-CCC
Confidence 4567899999999997421 1 299999988544322 2345665555443 456
Q ss_pred hhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhh
Q psy6037 113 QDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLF 192 (286)
Q Consensus 113 ~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~ 192 (286)
+.+++. +||.-..+... -++.+-.+.+.. .+ ++-.+|+++..+|+.||-+.+-.-...|...
T Consensus 55 ~~a~~i---hGIt~e~l~~~-p~~~ev~~~~~~--~~--~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~---------- 116 (217)
T TIGR00573 55 PDAIKI---HGITDDMLKDK-PDFKEIAEDFAD--YI--RGAELVIHNASFDVGFLNYEFSKLYKVEPKT---------- 116 (217)
T ss_pred HHHHhh---cCCCHHHHcCC-CCHHHHHHHHHH--Hh--CCCEEEEeccHHHHHHHHHHHHHhcCCCCCc----------
Confidence 666544 89988887654 344333333322 12 1236899999999999987764210111111
Q ss_pred cCCccchhHHHHhhc----cccccHHHHHhHcCCccCC-CCcccchhhHHHHHHHHHHHHHh
Q psy6037 193 FKSIYDVKYLMKSCK----NLKGGLQEVAEQLDLSRIG-PQHQAGSDSLLTGRVFFKMRELF 249 (286)
Q Consensus 193 FP~iYD~K~l~~~~~----~l~ggL~~lA~~L~v~r~g-~~HqAGsDSllT~~~F~~l~~~~ 249 (286)
+.+.|+.-+++... +-+.+|+.+++.+|++... ..|-|-+|+.+|+.+|.+|.+..
T Consensus 117 -~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 117 -NDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred -cceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHHhcc
Confidence 12345544444321 1234799999999998753 68999999999999999998764
No 17
>PRK07740 hypothetical protein; Provisional
Probab=98.31 E-value=2.9e-05 Score=71.21 Aligned_cols=171 Identities=16% Similarity=0.161 Sum_probs=109.9
Q ss_pred hhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccc
Q psy6037 33 INTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYA 112 (286)
Q Consensus 33 i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~ 112 (286)
+.+.+||.+|+|-+|+.... . =.|||+|....+. +.. ..-.|....+... ..+
T Consensus 56 ~~~~~~vv~D~ETTGl~p~~------------------~--deIIeIgaV~~~~-~~i-----~~~~f~~lv~P~~-~i~ 108 (244)
T PRK07740 56 LTDLPFVVFDLETTGFSPQQ------------------G--DEILSIGAVKTKG-GEV-----ETDTFYSLVKPKR-PIP 108 (244)
T ss_pred ccCCCEEEEEEeCCCCCCCC------------------C--CeEEEEEEEEEEC-CEE-----EEEEEEEEeCcCC-CCC
Confidence 34568999999999974210 1 2489999988773 221 1334554444433 334
Q ss_pred hhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhh
Q psy6037 113 QDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLF 192 (286)
Q Consensus 113 ~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~ 192 (286)
+.+. +-+||.=..+. .|.+..+-.+.+.. .+ . +-.+|+++..+|+.||-+.+......| +
T Consensus 109 ~~~~---~ltGIt~e~l~-~ap~~~evl~~f~~--fi-~-~~~lVahna~fD~~fL~~~~~~~~~~~------------~ 168 (244)
T PRK07740 109 EHIL---ELTGITAEDVA-FAPPLAEVLHRFYA--FI-G-AGVLVAHHAGHDKAFLRHALWRTYRQP------------F 168 (244)
T ss_pred hhhe---eccCCCHHHHh-CCCCHHHHHHHHHH--Hh-C-CCEEEEeCHHHHHHHHHHHHHHhcCCC------------c
Confidence 4433 33787766654 46665533223322 12 2 237999999999999987775321111 1
Q ss_pred cCCccchhHHHHhhccc--cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhcC
Q psy6037 193 FKSIYDVKYLMKSCKNL--KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFE 251 (286)
Q Consensus 193 FP~iYD~K~l~~~~~~l--~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~~ 251 (286)
...+.||..+++....- ..+|+.+++.+|++..+. |.|-+|++.|+.+|.++......
T Consensus 169 ~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~~~~-H~Al~Da~ata~l~~~ll~~~~~ 228 (244)
T PRK07740 169 THRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRR-HHALGDALMTAKLWAILLVEAQQ 228 (244)
T ss_pred CCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCCCCC-CCcHHHHHHHHHHHHHHHHHHHH
Confidence 13567888777654321 357999999999987664 89999999999999999877654
No 18
>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=98.25 E-value=1.7e-05 Score=64.93 Aligned_cols=155 Identities=16% Similarity=0.156 Sum_probs=102.7
Q ss_pred eeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHHHH
Q psy6037 39 IGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSIDL 118 (286)
Q Consensus 39 IAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI~f 118 (286)
|.+|+|-+|+.. ..-.|||+|...++.+++ ....||.++....+ ..+.+.+.
T Consensus 1 v~~D~Ettg~~~---------------------~~~~iiei~~v~~~~~~~------~~~~~~~~i~p~~~-~~~~~~~~ 52 (159)
T cd06127 1 VVFDTETTGLDP---------------------KKDRIIEIGAVKVDGGIE------IVERFETLVNPGRP-IPPEATAI 52 (159)
T ss_pred CeEEeeCCCcCC---------------------CCCeEEEEEEEEEECCcC------hhhhhheeeCcCCc-CCHhheec
Confidence 578999999752 233599999999998733 35566766655443 23333332
Q ss_pred HHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcC-Ccc
Q psy6037 119 LQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFK-SIY 197 (286)
Q Consensus 119 L~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP-~iY 197 (286)
+|+.-+.. ..|.+...-.+.+.. ++ .+ -.||++++.+|..+|-+.+... . ...+| ...
T Consensus 53 ---~gi~~~~~-~~~~~~~~~~~~~~~--~l-~~-~~~v~~n~~fD~~~l~~~~~~~-~------------~~~~~~~~i 111 (159)
T cd06127 53 ---HGITDEML-ADAPPFEEVLPEFLE--FL-GG-RVLVAHNASFDLRFLNRELRRL-G------------GPPLPNPWI 111 (159)
T ss_pred ---cCCCHHHH-hcCCCHHHHHHHHHH--HH-CC-CEEEEeCcHhhHHHHHHHHHHh-C------------CCCCCCCee
Confidence 77766665 477777654444433 12 22 4789999999999998877642 1 11222 577
Q ss_pred chhHHHHhhccc--cccHHHH-HhHcCCccCCCCcccchhhHHHHHHHH
Q psy6037 198 DVKYLMKSCKNL--KGGLQEV-AEQLDLSRIGPQHQAGSDSLLTGRVFF 243 (286)
Q Consensus 198 D~K~l~~~~~~l--~ggL~~l-A~~L~v~r~g~~HqAGsDSllT~~~F~ 243 (286)
|++.+++..... ..+|..+ ++.++++. +..|-|=+|++.|+.+|.
T Consensus 112 Dt~~~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 112 DTLRLARRLLPGLRSHRLGLLLAERYGIPL-EGAHRALADALATAELLL 159 (159)
T ss_pred EHHHHHHHHcCCCCcCchHHHHHHHcCCCC-CCCCCcHHHHHHHHHHhC
Confidence 888777654322 2367776 77888864 678999999999999873
No 19
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.20 E-value=6.1e-05 Score=71.60 Aligned_cols=166 Identities=14% Similarity=0.157 Sum_probs=107.5
Q ss_pred hCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchh
Q psy6037 35 TYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQD 114 (286)
Q Consensus 35 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~ 114 (286)
.-+||++|+|=+|+... .=.|||+|...++.+|+. ...|....+...+ +.
T Consensus 14 ~~~fvvlD~ETTGl~p~---------------------~d~IIeIgav~v~~~g~i------~~~~~~lv~P~~~---~~ 63 (313)
T PRK06063 14 PRGWAVVDVETSGFRPG---------------------QARIISLAVLGLDADGNV------EQSVVTLLNPGVD---PG 63 (313)
T ss_pred CCCEEEEEEECCCCCCC---------------------CCEEEEEEEEEEECCcee------eeEEEEEECcCCC---CC
Confidence 35899999999997421 125999999999887753 3445544444322 22
Q ss_pred HHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCC-CCCCCChHHHHHHHHhhc
Q psy6037 115 SIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGT-RSLPSEEAEFFELQRLFF 193 (286)
Q Consensus 115 SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~-~~LP~~~~~F~~~l~~~F 193 (286)
++. =|||.=..+... -++.+..+.|.. ++ . +-.+|++|..+|++||-+.+-.- .++|.
T Consensus 64 ~~~---IhGIt~e~l~~a-p~f~ev~~~l~~--~l-~-~~~lVaHNa~FD~~fL~~~~~r~g~~~~~------------- 122 (313)
T PRK06063 64 PTH---VHGLTAEMLEGQ-PQFADIAGEVAE--LL-R-GRTLVAHNVAFDYSFLAAEAERAGAELPV------------- 122 (313)
T ss_pred Cee---cCCCCHHHHhCC-CCHHHHHHHHHH--Hc-C-CCEEEEeCHHHHHHHHHHHHHHcCCCCCC-------------
Confidence 222 267665555422 222233233322 12 2 33789999999999998776421 13342
Q ss_pred CCccchhHHHHhhc-cc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhcCC
Q psy6037 194 KSIYDVKYLMKSCK-NL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFED 252 (286)
Q Consensus 194 P~iYD~K~l~~~~~-~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~~~ 252 (286)
...+||.-+++... .+ .-.|+.|++.+|++. ...|-|-+|++.|+.+|.++.+.....
T Consensus 123 ~~~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~-~~~H~Al~DA~ata~l~~~ll~~~~~~ 182 (313)
T PRK06063 123 DQVMCTVELARRLGLGLPNLRLETLAAHWGVPQ-QRPHDALDDARVLAGILRPSLERARER 182 (313)
T ss_pred CCEEehHHHHHHhccCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHHHhc
Confidence 13568777776542 22 236999999999985 468999999999999999998876544
No 20
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=98.18 E-value=5.8e-05 Score=69.47 Aligned_cols=170 Identities=16% Similarity=0.175 Sum_probs=110.8
Q ss_pred HhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCccc
Q psy6037 32 LINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMY 111 (286)
Q Consensus 32 ~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~ 111 (286)
++++-+||.+|+|=+|+... .=.|||+|+..++.++ ...+|+..++... ..
T Consensus 3 ~l~~~~~v~~D~ETTGl~~~---------------------~d~IIEIa~v~v~~~~-------~~~~~~~li~P~~-~I 53 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDVK---------------------KDRIIEFAAIRFTFDE-------VIDSVEFLINPER-VV 53 (250)
T ss_pred cccCCcEEEEEEeCCCCCCC---------------------CCeEEEEEEEEEECCe-------EEEEEEEEECcCC-CC
Confidence 56778999999999997421 1238999998776431 3556777766543 34
Q ss_pred chhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHh
Q psy6037 112 AQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRL 191 (286)
Q Consensus 112 ~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~ 191 (286)
.++++ +-|||--...... -+..+..+.+.. .+ .+.-.+|+++..||..+|-+.+-.- .+|...
T Consensus 54 ~~~a~---~ihgIt~e~v~~~-p~~~ev~~~~~~--fl-~~~~~lvghn~~FD~~~L~~~~~r~-g~~~~~--------- 116 (250)
T PRK06310 54 SAESQ---RIHHISDAMLRDK-PKIAEVFPQIKG--FF-KEGDYIVGHSVGFDLQVLSQESERI-GETFLS--------- 116 (250)
T ss_pred CHhhh---hccCcCHHHHhCC-CCHHHHHHHHHH--Hh-CCCCEEEEECHHHHHHHHHHHHHHc-CCCccc---------
Confidence 44444 3477765555433 333333333332 11 2223688888899999998876432 222110
Q ss_pred hc-CCccchhHHHHhhccc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHh
Q psy6037 192 FF-KSIYDVKYLMKSCKNL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELF 249 (286)
Q Consensus 192 ~F-P~iYD~K~l~~~~~~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~ 249 (286)
. -.+.||..+++..... ...|+.+++.+|++..+ +|-|-+|++.|+.+|..|.+.+
T Consensus 117 -~~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~~~-aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 117 -KHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDG-NHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred -cCCcEEehHHHHHhcccCCCCCHHHHHHHCCCCCCC-CcChHHHHHHHHHHHHHHHHhc
Confidence 1 1366887777754333 35799999999998654 7999999999999999998765
No 21
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=98.18 E-value=8.4e-05 Score=68.08 Aligned_cols=170 Identities=14% Similarity=0.163 Sum_probs=109.5
Q ss_pred hhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccc
Q psy6037 33 INTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYA 112 (286)
Q Consensus 33 i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~ 112 (286)
+.+.+|+++|+|=||+... .=.|||+|....+... . .....|....+... .+.
T Consensus 44 ~~~~~~vviD~ETTGl~p~---------------------~d~IieIg~v~v~~~~-i----~~~~~~~~li~P~~-~i~ 96 (239)
T PRK09146 44 LSEVPFVALDFETTGLDAE---------------------QDAIVSIGLVPFTLQR-I----RCRQARHWVVKPRR-PLE 96 (239)
T ss_pred cccCCEEEEEeECCCCCCC---------------------CCcEEEEEEEEEECCe-E----eecceEEEEECCCC-CCC
Confidence 4577999999999998531 1249999998886532 1 12344554444443 344
Q ss_pred hhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhC--CCCCCCChHHHHHHHH
Q psy6037 113 QDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMG--TRSLPSEEAEFFELQR 190 (286)
Q Consensus 113 ~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~--~~~LP~~~~~F~~~l~ 190 (286)
++++.. |||.-..+. .|-+..+-.+.+... + . +-.+|++|..+|.+||-+.+.. +.++|..
T Consensus 97 ~~~~~I---hGIt~e~l~-~ap~~~evl~~l~~~--~-~-~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~--------- 159 (239)
T PRK09146 97 EESVVI---HGITHSELQ-DAPDLERILDELLEA--L-A-GKVVVVHYRRIERDFLDQALRNRIGEGIEFP--------- 159 (239)
T ss_pred hhhhhh---cCCCHHHHh-CCCCHHHHHHHHHHH--h-C-CCEEEEECHHHHHHHHHHHHHHhcCCCCCCc---------
Confidence 555443 888877764 355554332333221 1 2 2368999999999999887752 1133222
Q ss_pred hhcCCccchhHHHHhhc---------cc------cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhcCC
Q psy6037 191 LFFKSIYDVKYLMKSCK---------NL------KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFED 252 (286)
Q Consensus 191 ~~FP~iYD~K~l~~~~~---------~l------~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~~~ 252 (286)
++||-.|++..- .+ .-.|+.+++.+|++. ..+|.|-+|++.|+.+|.++.+.++..
T Consensus 160 -----~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl~~-~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 160 -----VIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGLPA-YSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred -----eechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 346655554421 01 125999999999984 456999999999999999999888754
No 22
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=98.16 E-value=6.8e-05 Score=70.95 Aligned_cols=161 Identities=19% Similarity=0.206 Sum_probs=106.7
Q ss_pred CeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHH
Q psy6037 37 NYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSI 116 (286)
Q Consensus 37 ~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI 116 (286)
.||++|+|=+|.. + | .|||+|+..++ +|+ ..-+|+...+.......+.++
T Consensus 2 ~~vviD~ETTg~~-------~--------------d--~IieIgav~v~-~g~------i~~~f~~lv~P~~~~~~~~~~ 51 (309)
T PRK06195 2 NFVAIDFETANEK-------R--------------N--SPCSIGIVVVK-DGE------IVEKVHYLIKPKEMRFMPINI 51 (309)
T ss_pred cEEEEEEeCCCCC-------C--------------C--ceEEEEEEEEE-CCE------EEEEEEEEECCCCCCCChhhe
Confidence 6999999987520 0 1 37999998886 333 245677666665444566665
Q ss_pred HHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCC-CCCCCChHHHHHHHHhhcCC
Q psy6037 117 DLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGT-RSLPSEEAEFFELQRLFFKS 195 (286)
Q Consensus 117 ~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~-~~LP~~~~~F~~~l~~~FP~ 195 (286)
+ =|||.=..+...+ ++.+..+.+.. .+ . +-.+|++|+.+|++||-+.+..- .+.|. ..
T Consensus 52 ~---IhGIT~e~v~~ap-~f~ev~~~~~~--fl-~-~~~lVaHNa~FD~~fL~~~~~r~~~~~~~-------------~~ 110 (309)
T PRK06195 52 G---IHGIRPHMVEDEL-EFDKIWEKIKH--YF-N-NNLVIAHNASFDISVLRKTLELYNIPMPS-------------FE 110 (309)
T ss_pred e---ccCcCHHHHhCCC-CHHHHHHHHHH--Hh-C-CCEEEEECcHHHHHHHHHHHHHhCCCCCC-------------CC
Confidence 3 4898888876643 44332222221 11 1 23688999999999998766432 13331 12
Q ss_pred ccchhHHHHhh-ccc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhc
Q psy6037 196 IYDVKYLMKSC-KNL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFF 250 (286)
Q Consensus 196 iYD~K~l~~~~-~~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~ 250 (286)
.+||--+++.. ..+ ..+|..|++.+|++ ..+|.|-+|++.|+.+|.+|.+...
T Consensus 111 ~idT~~lar~l~~~~~~~~L~~L~~~~gi~--~~~H~Al~DA~ata~l~~~l~~~~~ 165 (309)
T PRK06195 111 YICTMKLAKNFYSNIDNARLNTVNNFLGYE--FKHHDALADAMACSNILLNISKELN 165 (309)
T ss_pred EEEHHHHHHHHcCCCCcCCHHHHHHHcCCC--CcccCCHHHHHHHHHHHHHHHHHhc
Confidence 45776666543 233 34799999999997 3589999999999999999988754
No 23
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=98.12 E-value=6.4e-05 Score=66.88 Aligned_cols=159 Identities=20% Similarity=0.254 Sum_probs=94.8
Q ss_pred CeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHH
Q psy6037 37 NYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSI 116 (286)
Q Consensus 37 ~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI 116 (286)
.||++|+|.+|+. +. + .|||+|..-++. |. .+..|..+..... ...+.+.
T Consensus 6 ~~vvlD~EtTGl~--~~------------------~--eIIeIgaV~v~~-g~------~~~~f~~lv~P~~-~i~~~~~ 55 (195)
T PRK07247 6 TYIAFDLEFNTVN--GV------------------S--HIIQVSAVKYDD-HK------EVDSFDSYVYTDV-PLQSFIN 55 (195)
T ss_pred eEEEEEeeCCCCC--CC------------------C--eEEEEEEEEEEC-CE------EEEEEEEEECCCC-CCCccce
Confidence 7999999999973 10 0 599999988874 32 2556776655433 2222222
Q ss_pred HHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecc-hhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCC
Q psy6037 117 DLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSG-YDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKS 195 (286)
Q Consensus 117 ~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~-yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~ 195 (286)
. -+||.=..+.. +.+..+-.+.+.. .+ . +-.||.+|.. +|+.+|-+. |. +++... .+ .
T Consensus 56 ~---lhGIt~~~v~~-ap~~~evl~~f~~--f~-~-~~~lVaHNa~~fD~~fL~~~--g~-~~~~~~-----~i-----d 114 (195)
T PRK07247 56 G---LTGITADKIAD-APKVEEVLAAFKE--FV-G-ELPLIGYNAQKSDLPILAEN--GL-DLSDQY-----QV-----D 114 (195)
T ss_pred e---cCCCCHHHHhC-CCCHHHHHHHHHH--HH-C-CCeEEEEeCcHhHHHHHHHc--CC-CcCCCc-----ee-----e
Confidence 2 26766665543 4443322222221 12 2 3368888875 899998653 32 333210 00 1
Q ss_pred ccchhHHHHh--hccc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHH
Q psy6037 196 IYDVKYLMKS--CKNL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMREL 248 (286)
Q Consensus 196 iYD~K~l~~~--~~~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~ 248 (286)
+||+++..+. ..++ .-.|..||+.+|++. ..|.|-+|+++|+.+|.+|.+.
T Consensus 115 t~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~--~~HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 115 LYDEAFERRSSDLNGIANLKLQTVADFLGIKG--RGHNSLEDARMTARVYESFLES 168 (195)
T ss_pred hHHHHHHhhccccCCCCCCCHHHHHHhcCCCC--CCcCCHHHHHHHHHHHHHHHhh
Confidence 2343322111 0122 246999999999984 4799999999999999999775
No 24
>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=98.11 E-value=0.00016 Score=65.56 Aligned_cols=168 Identities=16% Similarity=0.204 Sum_probs=107.7
Q ss_pred CeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHH
Q psy6037 37 NYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSI 116 (286)
Q Consensus 37 ~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI 116 (286)
.+|.+|||=||+.... .=.|||+|...... +. + ..-.|..+.+...+ ..++++
T Consensus 1 r~vvlD~ETTGl~p~~--------------------~d~IIEIgav~~~~-~~-~----~~~~f~~~i~P~~~-i~~~a~ 53 (225)
T TIGR01406 1 RQIILDTETTGLDPKG--------------------GHRIVEIGAVELVN-RM-L----TGDNFHVYVNPERD-MPAEAA 53 (225)
T ss_pred CEEEEEeeCCCcCCCC--------------------CCeEEEEEEEEEEC-Cc-E----ecceEEEEECcCCC-CCHHHH
Confidence 4799999999984321 12599999875542 21 1 12356766665543 355554
Q ss_pred HHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCC-CCCCChHHHHHHHHhhcCC
Q psy6037 117 DLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTR-SLPSEEAEFFELQRLFFKS 195 (286)
Q Consensus 117 ~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~-~LP~~~~~F~~~l~~~FP~ 195 (286)
+. |||.-..+... .++.+-.+.+.. .+ . +-.+|.+|..+|++||-+-+-.-. .+|.- . -+-.
T Consensus 54 ~v---hGIt~e~l~~~-p~f~ev~~~f~~--fi-~-~~~lVaHNa~FD~~fL~~el~r~g~~~~~~-~--------~~~~ 116 (225)
T TIGR01406 54 KV---HGITDEFLADK-PKFKEIADEFLD--FI-G-GSELVIHNAAFDVGFLNYELERLGPTIKKI-G--------EFCR 116 (225)
T ss_pred hc---cCCCHHHHhCC-CCHHHHHHHHHH--Hh-C-CCEEEEEecHHHHHHHHHHHHHhCCCCccc-c--------cCCC
Confidence 43 88887777643 444333333322 12 1 236899999999999987663210 11110 0 0124
Q ss_pred ccchhHHHHhh-ccccccHHHHHhHcCCccCCC-CcccchhhHHHHHHHHHHHHH
Q psy6037 196 IYDVKYLMKSC-KNLKGGLQEVAEQLDLSRIGP-QHQAGSDSLLTGRVFFKMREL 248 (286)
Q Consensus 196 iYD~K~l~~~~-~~l~ggL~~lA~~L~v~r~g~-~HqAGsDSllT~~~F~~l~~~ 248 (286)
++||--|++.. .+.+.+|+.+++.+|++..+. .|-|-.|+.+|+.+|.+|...
T Consensus 117 ~iDTl~lar~~~p~~~~~L~~L~~~~gi~~~~r~~H~Al~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 117 VIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAHLLAEVYLALTGG 171 (225)
T ss_pred EEEHHHHHHHHcCCCCCCHHHHHHhcCCCCCCCCCcCHHHHHHHHHHHHHHHHcC
Confidence 67887777653 234568999999999998765 699999999999999999663
No 25
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.09 E-value=9.8e-05 Score=79.45 Aligned_cols=166 Identities=19% Similarity=0.215 Sum_probs=107.0
Q ss_pred CCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhH
Q psy6037 36 YNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDS 115 (286)
Q Consensus 36 ~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~S 115 (286)
-.||++|+|-+|..... .-.|||+|....+ +|+ .+-.|+.+.+.... ..+..
T Consensus 3 ~~~vvvD~ETTG~~p~~--------------------~d~IIeigav~v~-~~~------i~~~f~~~v~P~~~-i~~~~ 54 (928)
T PRK08074 3 KRFVVVDLETTGNSPKK--------------------GDKIIQIAAVVVE-DGE------ILERFSSFVNPERP-IPPFI 54 (928)
T ss_pred CCEEEEEEeCCCCCCCC--------------------CCcEEEEEEEEEE-CCE------EEEEEEEEECcCCC-CCHHH
Confidence 46999999999963211 0159999999985 343 24456666665433 34443
Q ss_pred HHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCC
Q psy6037 116 IDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKS 195 (286)
Q Consensus 116 I~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~ 195 (286)
.++ +||+=..+. .+.++.+..+.+.. ++ ++-.+|+++..+|+.||-+-+... -+|... ..
T Consensus 55 ~~l---tGIt~~~l~-~ap~f~ev~~~l~~--~l--~~~~~VaHN~~FD~~fL~~~~~~~-g~~~~~-----------~~ 114 (928)
T PRK08074 55 TEL---TGISEEMVK-QAPLFEDVAPEIVE--LL--EGAYFVAHNVHFDLNFLNEELERA-GYTEIH-----------CP 114 (928)
T ss_pred hhc---CCCCHHHHh-cCCCHHHHHHHHHH--Hh--CCCeEEEEChHHHHHHHHHHHHHc-CCCCCC-----------CC
Confidence 333 888876654 44555444434333 12 245799999999999998866532 233210 12
Q ss_pred ccchhHHHHhh-ccc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhc
Q psy6037 196 IYDVKYLMKSC-KNL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFF 250 (286)
Q Consensus 196 iYD~K~l~~~~-~~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~ 250 (286)
.+||=-+++.. ..+ .-+|..|++.||++. +.+|.|-+|++.|+.+|.+|.+...
T Consensus 115 ~iDt~~la~~~~p~~~~~~L~~l~~~l~i~~-~~~H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 115 KLDTVELARILLPTAESYKLRDLSEELGLEH-DQPHRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred eeeHHHHHHHhcCCCCCCCHHHHHHhCCCCC-CCCCChHHHHHHHHHHHHHHHHHHH
Confidence 34554444332 111 236999999999874 5789999999999999999988764
No 26
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=98.04 E-value=0.00023 Score=65.98 Aligned_cols=166 Identities=17% Similarity=0.188 Sum_probs=105.6
Q ss_pred hhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccc
Q psy6037 33 INTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYA 112 (286)
Q Consensus 33 i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~ 112 (286)
+.+..||.+|+|=+|..... -.|||+|...++ +|+. .-+|..+.... ...
T Consensus 65 ~~~~~~vv~DiETTG~~~~~---------------------~~IIEIGAv~v~-~g~i------~~~f~~~v~p~--~ip 114 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKK---------------------HQIIEIGAVKVK-NGEI------IDRFESFVKAK--EVP 114 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCC---------------------CeEEEEEEEEEE-CCEE------EEEEEEEECCC--CCC
Confidence 35778999999999964211 159999998886 3332 33455444332 233
Q ss_pred hhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhh
Q psy6037 113 QDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLF 192 (286)
Q Consensus 113 ~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~ 192 (286)
+.+.+ -+||.=..+.. +.+..+-.+.+.. . +.+. .||+++..+|+++|-+.+... .+|.-
T Consensus 115 ~~~~~---itGIt~e~l~~-ap~~~evl~~f~~--f-l~~~-v~VaHNa~FD~~fL~~~l~r~-g~~~~----------- 174 (257)
T PRK08517 115 EYITE---LTGITYEDLEN-APSLKEVLEEFRL--F-LGDS-VFVAHNVNFDYNFISRSLEEI-GLGPL----------- 174 (257)
T ss_pred hhhhh---hcCcCHHHHcC-CCCHHHHHHHHHH--H-HCCC-eEEEECHHHHHHHHHHHHHHc-CCCCC-----------
Confidence 33333 38888777653 5555433222222 1 1223 699999999999997766542 33321
Q ss_pred cCCccchhHHHHhh-ccccccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHh
Q psy6037 193 FKSIYDVKYLMKSC-KNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELF 249 (286)
Q Consensus 193 FP~iYD~K~l~~~~-~~l~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~ 249 (286)
.+...||--+++.. ..-+-||+.+++.+|++.. .+|-|-+|++.|+.+|.++.+.+
T Consensus 175 ~~~~ldtl~la~~~~~~~~~~L~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 175 LNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIE-VHHRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred CCCcEehHHHHHHHccCCCCCHHHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHh
Confidence 11233443344332 2234579999999999865 78999999999999999998765
No 27
>PRK06722 exonuclease; Provisional
Probab=98.03 E-value=0.00026 Score=66.51 Aligned_cols=170 Identities=19% Similarity=0.182 Sum_probs=99.9
Q ss_pred hCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchh
Q psy6037 35 TYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQD 114 (286)
Q Consensus 35 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~ 114 (286)
...||++|+|-+|. |.. +-+.-.|||+|....+. |.. ..+-.|.-+.+... ..++.
T Consensus 4 ~~~~vViD~ETT~~---p~~---------------~~~~deIIEIGAVkV~~-g~i----~Ivd~F~sLV~P~~-~I~~~ 59 (281)
T PRK06722 4 ATHFIVFDIERNFR---PYK---------------SEDPSEIVDIGAVKIEA-STM----KVIGEFSELVKPGA-RLTRH 59 (281)
T ss_pred CCEEEEEEeeCCCC---CCC---------------CCCCCeEEEEEEEEEEC-Cce----eEEeeEEEEECCCC-cCCHh
Confidence 35799999999852 210 11123499999988865 221 12556776655442 34444
Q ss_pred HHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCC-CCCCCChHHHHHHHHhhc
Q psy6037 115 SIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGT-RSLPSEEAEFFELQRLFF 193 (286)
Q Consensus 115 SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~-~~LP~~~~~F~~~l~~~F 193 (286)
+.++ +||.=+.+. .+.+..+-.+.+.. .+ .+. .+|+.|+.+|.+||-+-+..- .+.|.-..
T Consensus 60 i~~L---TGIT~emV~-~AP~f~eVl~ef~~--fi-g~~-~lvahna~FD~~FL~~~l~~~gi~~p~~~~---------- 121 (281)
T PRK06722 60 TTKL---TGITKKDLI-GVEKFPQIIEKFIQ--FI-GED-SIFVTWGKEDYRFLSHDCTLHSVECPCMEK---------- 121 (281)
T ss_pred Hhhh---cCCCHHHHc-CCCCHHHHHHHHHH--HH-CCC-cEEEEEeHHHHHHHHHHHHHcCCCCCcccc----------
Confidence 4444 777655553 34443322222211 11 122 467788999999999876532 13333110
Q ss_pred CCccchhHHHHh-hccc---cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHH
Q psy6037 194 KSIYDVKYLMKS-CKNL---KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMR 246 (286)
Q Consensus 194 P~iYD~K~l~~~-~~~l---~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~ 246 (286)
-..+|+.-++.. ...+ ..+|..+++.+|++..|..|.|-+||++|+..|.+|.
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 011233222211 1111 1369999999999988999999999999999999986
No 28
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=97.98 E-value=0.00027 Score=62.78 Aligned_cols=176 Identities=16% Similarity=0.249 Sum_probs=113.1
Q ss_pred hCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCC--CCCCCCCcceEEEEEEecCC-Cccc
Q psy6037 35 TYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSK--SCTPPGPFTTWQFNFKFDLQ-EDMY 111 (286)
Q Consensus 35 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~--g~~p~~~~~~wqFNF~F~~~-~d~~ 111 (286)
.+.||++|+|=+|+.... | .||++|..-...+ |.. ....+|.+.+... .-..
T Consensus 7 ~~~~vv~D~ETTGl~~~~-------------------d--~IieIgav~v~~~~~g~i----~~~~~f~~~v~p~p~~~i 61 (200)
T TIGR01298 7 GYLPVVVDVETGGFNAKT-------------------D--ALLEIAAITLKMDEQGWL----FPDTTLHFHVEPFEGANI 61 (200)
T ss_pred CCeeEEEEeeCCCCCCCC-------------------C--eEEEEEEEEEEEcCCCcE----eecceeEEEEcCCCCCCC
Confidence 578999999999975321 1 3899998877543 322 1235577665543 3356
Q ss_pred chhHHHHHHHcCCChhhhhhCCCChHH-HHHHHHh-----cCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHH
Q psy6037 112 AQDSIDLLQNSGIQFQRHKEEGIEPAD-FAELLTT-----SGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEF 185 (286)
Q Consensus 112 ~~~SI~fL~~~G~DF~k~~~~GI~~~~-F~ell~~-----SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F 185 (286)
.++++.. +||.=++..+.+.+... +.+.+.. .+... .+-..|++|-.+|+.||-+.+-.. .++...
T Consensus 62 ~~~a~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~lVaHNa~FD~~fL~~~~~r~-~~~~~~--- 133 (200)
T TIGR01298 62 QPEALEF---TGIDLDHPLRGAVSEYEALHEIFKVVRKAMKASGC-QRAILVGHNANFDLGFLNAAVERT-SLKRNP--- 133 (200)
T ss_pred CHHHHHc---cCCChhhhhhcCcchHHHHHHHHHHHHHHHHhccc-CCCEEEEECchhhHHHHHHHHHHh-CCCCCC---
Confidence 6666655 99987776777776532 3333221 01111 233688999999999998877432 121100
Q ss_pred HHHHHhhcC-CccchhHHHHhhccccccHHHHHhHcCCccC-CCCcccchhhHHHHHHHHHHHHHhc
Q psy6037 186 FELQRLFFK-SIYDVKYLMKSCKNLKGGLQEVAEQLDLSRI-GPQHQAGSDSLLTGRVFFKMRELFF 250 (286)
Q Consensus 186 ~~~l~~~FP-~iYD~K~l~~~~~~l~ggL~~lA~~L~v~r~-g~~HqAGsDSllT~~~F~~l~~~~~ 250 (286)
+-| .+.||--|++..-. ...|..+++.+|++.. -..|-|-+|++.|+.+|.+|.+.+-
T Consensus 134 ------~~~~~~lDTl~lar~~~~-~~~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 134 ------FHPFSTFDTATLAGLAYG-QTVLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred ------CCCCcEEEHHHHHHHHcC-cccHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 001 25677667664321 1369999999999854 3689999999999999999988764
No 29
>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=97.98 E-value=0.00023 Score=75.81 Aligned_cols=163 Identities=20% Similarity=0.207 Sum_probs=104.4
Q ss_pred CeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHH
Q psy6037 37 NYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSI 116 (286)
Q Consensus 37 ~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI 116 (286)
.||++|+|-+|+... .=.|||+|...++ +|+ ..-+|....+... ...+.+.
T Consensus 1 ~~vvvD~ETTG~~~~---------------------~~~IIeig~v~v~-~~~------i~~~f~~~v~P~~-~i~~~~~ 51 (850)
T TIGR01407 1 RYAVVDLETTGTQLS---------------------FDKIIQIGIVVVE-DGE------IVDTFHTDVNPNE-PIPPFIQ 51 (850)
T ss_pred CEEEEEEECCCCCCC---------------------CCeEEEEEEEEEE-CCE------EEEEEEEEeCCCC-CCChhhh
Confidence 489999999997421 1239999999885 343 2345666655543 3334333
Q ss_pred HHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcC-C
Q psy6037 117 DLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFK-S 195 (286)
Q Consensus 117 ~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP-~ 195 (286)
+-+||.-+.+.. +-++.+..+.+.. ++ . +-.||+++..+|+.+|-+-+... .+|. +| .
T Consensus 52 ---~ltGIt~e~l~~-ap~~~ev~~~l~~--~l-~-~~~~VahN~~fD~~fL~~~~~~~-g~~~------------~~~~ 110 (850)
T TIGR01407 52 ---ELTGISDNMLQQ-APYFSQVAQEIYD--LL-E-DGIFVAHNVHFDLNFLAKALKDC-GYEP------------LPKP 110 (850)
T ss_pred ---hhcCcCHHHHhC-CCCHHHHHHHHHH--Hh-C-CCEEEEeCcHHHHHHHHHHHHHc-CCCC------------CCCC
Confidence 238888666553 4444443333333 12 2 23699999999999998876532 2221 11 2
Q ss_pred ccchhHHHHhhc-cc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhc
Q psy6037 196 IYDVKYLMKSCK-NL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFF 250 (286)
Q Consensus 196 iYD~K~l~~~~~-~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~ 250 (286)
.+||--+++..- .. .-+|..|++.+|++.. .+|.|-+|+..|+.+|.+|.+.+-
T Consensus 111 ~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 111 RIDTVELAQIFFPTEESYQLSELSEALGLTHE-NPHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred eEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCC-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 345544443321 11 2479999999999864 589999999999999999988764
No 30
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=97.96 E-value=0.00024 Score=78.23 Aligned_cols=170 Identities=18% Similarity=0.228 Sum_probs=118.3
Q ss_pred hhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccch
Q psy6037 34 NTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQ 113 (286)
Q Consensus 34 ~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~ 113 (286)
+..+||++|+|-+|+.... =.|||+|....+. |+ ..-.|++..+... ...+
T Consensus 188 ~~~~~VVfDiETTGL~~~~---------------------d~IIEIGAVkv~~-g~------iid~f~~~V~P~~-~I~~ 238 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQY---------------------DEIIEFGAVKVKN-GR------IIDKFQFFIKPHE-PLSA 238 (1213)
T ss_pred cCCcEEEEEeEecCCCCCC---------------------CeEEEEEEEEEEC-Ce------EEEEEEEEECCCC-CCCH
Confidence 6789999999999985321 1599999998874 32 2456776655543 3455
Q ss_pred hHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhc
Q psy6037 114 DSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFF 193 (286)
Q Consensus 114 ~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~F 193 (286)
.+.+ -+||.-+.+. .|.+..+-.+.+.. .+ . +-.+|+++..+|++||-+.+..- .+|.- -
T Consensus 239 ~~~~---ltGIT~e~L~-~ap~~~evl~~f~~--fl-~-~~iLVaHNa~FD~~fL~~~~~r~-g~~~~-----------~ 298 (1213)
T TIGR01405 239 FVTE---LTGITQDMLE-NAPEIEEVLEKFKE--FF-K-DSILVAHNASFDIGFLNTNFEKV-GLEPL-----------E 298 (1213)
T ss_pred HHHH---HhCCCHHHHh-CCCCHHHHHHHHHH--Hh-C-CCeEEEEChHHHHHHHHHHHHHc-CCCcc-----------C
Confidence 5544 4899888764 57766543333332 11 1 33789999999999998877643 33321 1
Q ss_pred CCccchhHHHHhhc-cc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhcCCC
Q psy6037 194 KSIYDVKYLMKSCK-NL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFEDA 253 (286)
Q Consensus 194 P~iYD~K~l~~~~~-~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~~~~ 253 (286)
..+.||--+++... .+ .-+|..||+.+|++..+ +|-|-.|+..|+.+|.+|.+.+.+.+
T Consensus 299 ~~~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~~~-~HrAl~DA~aTa~I~~~ll~~l~~~~ 359 (1213)
T TIGR01405 299 NPVIDTLELARALNPEYKSHRLGNICKKLGVDLDD-HHRADYDAEATAKVFKVMVEQLKEKG 359 (1213)
T ss_pred CCEeEHHHHHHHHhccCCCCCHHHHHHHcCCCCCC-CcCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 24668877776542 23 35899999999999766 89999999999999999988776543
No 31
>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=97.96 E-value=0.00016 Score=62.90 Aligned_cols=166 Identities=14% Similarity=0.148 Sum_probs=102.9
Q ss_pred eeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCC------CCcceEEEEEEecCCCccc
Q psy6037 38 YIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPP------GPFTTWQFNFKFDLQEDMY 111 (286)
Q Consensus 38 fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~------~~~~~wqFNF~F~~~~d~~ 111 (286)
||.+|+|=||+.. + ..=.|||+|.-..+.++.... ..-.+-+|+...+... ..
T Consensus 1 ~vv~D~ETTGl~~-~-------------------~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~-~I 59 (177)
T cd06136 1 FVFLDLETTGLPK-H-------------------NRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGR-AI 59 (177)
T ss_pred CeEEeeecCCCCC-C-------------------CCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCC-cC
Confidence 7899999999842 1 001499999998876543211 0012456777777654 34
Q ss_pred chhHHHHHHHcCCChhhhhhCCCChHHHHHHHHh-cCccccCCccEEEeec-chhHHHHHHHHhCC-CCCCCChHHHHHH
Q psy6037 112 AQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTT-SGVVLNDKVKWLSFHS-GYDFGYLLKLLMGT-RSLPSEEAEFFEL 188 (286)
Q Consensus 112 ~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~-SgLv~~~~v~Wvtfhg-~yD~gyL~K~lt~~-~~LP~~~~~F~~~ 188 (286)
.+++... +||.=..+...+-......+.+.. .+. ..+....|++++ .+|+.||-+-+..- .++|..
T Consensus 60 ~~~a~~I---hGIt~e~l~~~~~~~~~~~~~l~~f~~~-~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~------- 128 (177)
T cd06136 60 SPGASEI---TGLSNDLLEHKAPFDSDTANLIKLFLRR-QPKPICLVAHNGNRFDFPILRSELERLGTKLPDD------- 128 (177)
T ss_pred ChhHHHH---hCcCHHHHhcCCCccHHHHHHHHHHHHh-cCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCC-------
Confidence 5555444 999988888877322222232221 010 123457899998 79999997776432 122211
Q ss_pred HHhhcCCccchhHHHHhhccccccHHHHHhH-cCCccCCCCcccchhhHHHHHHHHH
Q psy6037 189 QRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQ-LDLSRIGPQHQAGSDSLLTGRVFFK 244 (286)
Q Consensus 189 l~~~FP~iYD~K~l~~~~~~l~ggL~~lA~~-L~v~r~g~~HqAGsDSllT~~~F~~ 244 (286)
+.+.||-.+++... .+|+.|++. +|++. ..+|.|-+|++.|+++|++
T Consensus 129 -----~~~iDtl~l~r~~~---~~L~~l~~~~~~~~~-~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 129 -----ILCVDSLPAFRELD---QSLGSLYKRLFGQEP-KNSHTAEGDVLALLKCALH 176 (177)
T ss_pred -----CEEEEeHHHHhhhH---hhHHHHHHHHhCCCc-ccccchHHHHHHHHHHHhh
Confidence 11236544544322 289999885 78874 4579999999999999975
No 32
>PRK07883 hypothetical protein; Validated
Probab=97.93 E-value=0.00025 Score=72.42 Aligned_cols=173 Identities=13% Similarity=0.077 Sum_probs=113.6
Q ss_pred HHHhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCc
Q psy6037 30 RSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQED 109 (286)
Q Consensus 30 ~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d 109 (286)
..-+.+.+||.+|+|-+|+... .-.|||+|.-.++. |+ ...+|....+....
T Consensus 9 ~~~~~~~~~Vv~D~ETTGl~p~---------------------~~~IIEIgaV~v~~-g~------iv~~f~~lV~P~~~ 60 (557)
T PRK07883 9 GTPLRDVTFVVVDLETTGGSPA---------------------GDAITEIGAVKVRG-GE------VLGEFATLVNPGRP 60 (557)
T ss_pred CCCCcCCCEEEEEEecCCCCCC---------------------CCeEEEEEEEEEEC-CE------EEEEEEEEECCCCC
Confidence 3446778999999999998321 12599999988863 32 35677776665443
Q ss_pred ccchhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHH
Q psy6037 110 MYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQ 189 (286)
Q Consensus 110 ~~~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l 189 (286)
..+.+.+ -+||.=..+ ..+.+.....+.+.. ++ . +-.+|++++.+|+.+|-+.+... .+|.-
T Consensus 61 -i~~~~~~---itGIt~e~l-~~ap~~~evl~~f~~--fl-~-~~~lVaHNa~FD~~fL~~~~~r~-g~~~~-------- 122 (557)
T PRK07883 61 -IPPFITV---LTGITTAMV-AGAPPIEEVLPAFLE--FA-R-GAVLVAHNAPFDIGFLRAAAARC-GYPWP-------- 122 (557)
T ss_pred -CChhHHh---hcCCCHHHH-hCCCCHHHHHHHHHH--Hh-c-CCEEEEeCcHHHHHHHHHHHHHc-CCCCC--------
Confidence 3455543 388866554 445555433333322 11 1 23688888999999998777543 23210
Q ss_pred HhhcCCccchhHHHHhhc---cc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhcCC
Q psy6037 190 RLFFKSIYDVKYLMKSCK---NL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFED 252 (286)
Q Consensus 190 ~~~FP~iYD~K~l~~~~~---~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~~~ 252 (286)
.+...||-.+++..- .. .-+|..+++.+|++.. ..|-|-+|++.|+.+|.++.+.+...
T Consensus 123 ---~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~~~ 185 (557)
T PRK07883 123 ---GPPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTT-PTHRALDDARATVDVLHGLIERLGNL 185 (557)
T ss_pred ---CCCcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccC-CCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 013457766665431 22 2479999999999854 46999999999999999998887543
No 33
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.93 E-value=0.00033 Score=74.55 Aligned_cols=164 Identities=20% Similarity=0.258 Sum_probs=106.7
Q ss_pred hCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchh
Q psy6037 35 TYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQD 114 (286)
Q Consensus 35 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~ 114 (286)
...||++|+|-||+. | . | .|||+|....+ +|+ ..-.|....+... ...+.
T Consensus 6 ~~~~vvvD~ETTGl~--~-----------------~-d--~IIeIgaV~v~-~g~------i~~~f~~lv~P~~-~i~~~ 55 (820)
T PRK07246 6 LRKYAVVDLEATGAG--P-----------------N-A--SIIQVGIVIIE-GGE------IIDSYTTDVNPHE-PLDEH 55 (820)
T ss_pred CCCEEEEEEecCCcC--C-----------------C-C--eEEEEEEEEEE-CCE------EEEEEEEEeCcCC-CCCHh
Confidence 468999999999962 1 0 2 49999999875 333 2445555555443 23333
Q ss_pred HHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCC-CCCCCChHHHHHHHHhhc
Q psy6037 115 SIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGT-RSLPSEEAEFFELQRLFF 193 (286)
Q Consensus 115 SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~-~~LP~~~~~F~~~l~~~F 193 (286)
+... +||.=..+. .+.+..+-.+.+.. ++ .+-.+|++|..+|++||-+.+... .++|.
T Consensus 56 ~~~l---tGIt~e~l~-~ap~~~ev~~~~~~--~l--~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~------------- 114 (820)
T PRK07246 56 IKHL---TGITDQQLA-QAPDFSQVARHIYD--LI--EDCIFVAHNVKFDANLLAEALFLEGYELRT------------- 114 (820)
T ss_pred Hhhc---CCCCHHHHh-cCCCHHHHHHHHHH--Hh--CCCEEEEECcHHHHHHHHHHHHHcCCCCCC-------------
Confidence 3333 888876665 45555544444333 12 234689999999999998876421 13332
Q ss_pred CCccchhHHHHhhc-cc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhcC
Q psy6037 194 KSIYDVKYLMKSCK-NL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFE 251 (286)
Q Consensus 194 P~iYD~K~l~~~~~-~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~~ 251 (286)
| ..||--+++..- .+ .-+|..+++.+|++.. .+|.|-+|++.|+.+|.+|.+.+..
T Consensus 115 ~-~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~~-~~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 115 P-RVDTVELAQVFFPTLEKYSLSHLSRELNIDLA-DAHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred C-ceeHHHHHHHHhCCCCCCCHHHHHHHcCCCCC-CCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 1 235555554321 12 2479999999999854 6799999999999999999887643
No 34
>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=97.88 E-value=0.0003 Score=61.36 Aligned_cols=166 Identities=16% Similarity=0.112 Sum_probs=100.1
Q ss_pred eeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCc-ccchhHHHH
Q psy6037 40 GIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQED-MYAQDSIDL 118 (286)
Q Consensus 40 AiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d-~~~~~SI~f 118 (286)
-+|+|=||+... .=.|||+|.-.++.++.. ...|++....... ...++++.
T Consensus 2 ~~D~ETTGl~~~---------------------~d~Iieig~v~v~~~~~~------~~~~~~~v~p~~~~~~~~~a~~- 53 (183)
T cd06138 2 FYDYETFGLNPS---------------------FDQILQFAAIRTDENFNE------IEPFNIFCRLPPDVLPSPEALI- 53 (183)
T ss_pred EEEeecCCCCCC---------------------CCceEEEEEEEECCCCCC------ccceeEEEeCCCCCCCCHHHHH-
Confidence 479999998421 114899999888766542 2556666544432 34455543
Q ss_pred HHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeec-chhHHHHHHHHhCC--CCCCC------ChHHHHHHH
Q psy6037 119 LQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHS-GYDFGYLLKLLMGT--RSLPS------EEAEFFELQ 189 (286)
Q Consensus 119 L~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg-~yD~gyL~K~lt~~--~~LP~------~~~~F~~~l 189 (286)
-+||.=+.+...|.+..+..+.+.. .+..++-.+|++|+ .+|.+||-+.+... .+++. ..-+.+.+.
T Consensus 54 --ihGIt~e~l~~~~~~~~~~l~~~~~--~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~ 129 (183)
T cd06138 54 --VTGITPQQLLKEGLSEYEFIAKIHR--LFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVV 129 (183)
T ss_pred --HhCCCHHHHHhcCCCHHHHHHHHHH--HHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHH
Confidence 5999988887778887655444433 12123446899886 69999998877532 12211 111223333
Q ss_pred Hh---hcCCccchhHHHHhhccc-cccHHHHHhHcCCccCCCCcccchhhHHHHHH
Q psy6037 190 RL---FFKSIYDVKYLMKSCKNL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRV 241 (286)
Q Consensus 190 ~~---~FP~iYD~K~l~~~~~~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~ 241 (286)
+. ++|..++.-.. -.++ .-.|+.+++.+|++. ..+|-|-+|++.|+..
T Consensus 130 r~~~~~~~~~~~~~~~---~~~~~~~~L~~l~~~~gi~~-~~~H~Al~Da~~ta~l 181 (183)
T cd06138 130 RAYYALRPDGIVWPKN---DDGKPSFKLEDLAQANGIEH-SNAHDALSDVEATIAL 181 (183)
T ss_pred HHHHhhChhhccCccc---cCCCcchhHHHHHHHCCCCc-cccccHHHHHHHHHHH
Confidence 32 23432111000 0112 236999999999986 5679999999999763
No 35
>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=97.88 E-value=1.4e-05 Score=65.43 Aligned_cols=155 Identities=21% Similarity=0.230 Sum_probs=95.9
Q ss_pred eeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCC-cccchhHHH
Q psy6037 39 IGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQE-DMYAQDSID 117 (286)
Q Consensus 39 IAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~-d~~~~~SI~ 117 (286)
|.+|+|++|... +.-.|||+|.-..+.+.. ...-.|+.+..... ....+.+
T Consensus 1 v~~D~Ettg~~~---------------------~~~~iieig~v~~~~~~~-----~~~~~~~~~i~p~~~~~i~~~~-- 52 (164)
T PF00929_consen 1 VVFDTETTGLDP---------------------RQDEIIEIGAVKVDDDEN-----EEVESFNSLIRPEEPPKISPWA-- 52 (164)
T ss_dssp EEEEEEESSSTT---------------------TTCTEEEEEEEEEETTTT-----EEEEEEEEEBEHSSHCSSEHHH--
T ss_pred cEEEeEcCCCCC---------------------CCCeEEEEEEEEeeCCcc-----ccceeeeecccccccccCCHHH--
Confidence 679999999854 223499999988877653 13566777643332 2344444
Q ss_pred HHHHcCCChhhhhhCCCChH---HHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcC
Q psy6037 118 LLQNSGIQFQRHKEEGIEPA---DFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFK 194 (286)
Q Consensus 118 fL~~~G~DF~k~~~~GI~~~---~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP 194 (286)
.+-+|+.-..+...+-... .|.+.+.. ...||.++..+|.+++.+.+. +.++..+|
T Consensus 53 -~~~~gIt~~~l~~~~~~~~~~~~~~~~~~~-------~~~~v~~n~~fd~~~l~~~~~-------------~~~~~~~~ 111 (164)
T PF00929_consen 53 -TKVHGITQEDLEDAPSFEEALDEFEEFLKK-------NDILVGHNASFDIGFLRREDK-------------RFLGKPIP 111 (164)
T ss_dssp -HHHHHHCHHHHHCHCEHHHHHHHHHHHHHH-------HTEEEETTCCHEEESSHHHHH-------------HHHHHHHH
T ss_pred -eeecCCcccccccCCcHHHHHHhhhhhhhc-------ccccccccccchhhHHHHhhh-------------hccccccc
Confidence 3447777777666553332 23333321 236777777788766544333 22222121
Q ss_pred ---CccchhHHHHh-hcccc-ccHHHHHhHcCCccCCCCcccchhhHHHHHHH
Q psy6037 195 ---SIYDVKYLMKS-CKNLK-GGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVF 242 (286)
Q Consensus 195 ---~iYD~K~l~~~-~~~l~-ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F 242 (286)
.+.|+.-+.+. ..... .+|..+++.++++..+.+|-|-+|++.|+.+|
T Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 112 KPNPFIDTLELARALFPNRKKYSLDDLAEYFGIPFDGTAHDALDDARATAELF 164 (164)
T ss_dssp HHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTSSSTSTTTSHHHHHHHHHHHH
T ss_pred ccchhhhhhHHHHHHhhccccCCHHHHHHHcCCCCCCCCcChHHHHHHHhCcC
Confidence 23444333222 22233 48999999999999988999999999999887
No 36
>PTZ00315 2'-phosphotransferase; Provisional
Probab=97.78 E-value=0.0014 Score=67.11 Aligned_cols=172 Identities=15% Similarity=0.196 Sum_probs=111.4
Q ss_pred CeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecC-CCCCCCCCcceEEEEEEecCCC-cccchh
Q psy6037 37 NYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDS-KSCTPPGPFTTWQFNFKFDLQE-DMYAQD 114 (286)
Q Consensus 37 ~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~-~g~~p~~~~~~wqFNF~F~~~~-d~~~~~ 114 (286)
.||++|.|.+|...... +.-.||++|...++. +|+ .+..|..+..... ....+.
T Consensus 57 ~~IV~DlETTgl~~~~~------------------~~dEIIEIGaV~Vd~~ng~------Ii~~F~~yVkP~~~p~Ls~f 112 (582)
T PTZ00315 57 AYVVLDFEATCEADRRI------------------EDAEVIEFPMVLVDARTAT------PVAEFQRYVRPVKNPVLSRF 112 (582)
T ss_pred eEEEEEEecCCCCCCCC------------------CCCceEEEEEEEEEccCCE------EEEEEEEEECCCCCCCCChh
Confidence 68999999999632110 122599999999984 443 3577777755543 245555
Q ss_pred HHHHHHHcCCChhhhhhCCCChH----HHHHHHHhcCccc---cCCccEEEeecchhHH-HHHHHHh--CCCCCCCChHH
Q psy6037 115 SIDLLQNSGIQFQRHKEEGIEPA----DFAELLTTSGVVL---NDKVKWLSFHSGYDFG-YLLKLLM--GTRSLPSEEAE 184 (286)
Q Consensus 115 SI~fL~~~G~DF~k~~~~GI~~~----~F~ell~~SgLv~---~~~v~Wvtfhg~yD~g-yL~K~lt--~~~~LP~~~~~ 184 (286)
..++ +||.=+.+ ..+.++. +|.+.|..+++.. +.+ ..|+..|.+|+. ||.+-+. +...+|.
T Consensus 113 ct~L---TGITqe~V-~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~-~~vah~g~fDl~~fL~~e~~~~~~~g~p~---- 183 (582)
T PTZ00315 113 CTEL---TGITQSMV-SRADPFPVVYCEALQFLAEAGLGDAPPLRS-YCVVTCGDWDLKTMLPSQMRVSGQQGTPL---- 183 (582)
T ss_pred Hhhh---cCcCHHHH-hcCCCHHHHHHHHHHHHhccccccccccCc-eEEEeccHHHHHHHHHHHHHHhhhcCCCc----
Confidence 5554 77764444 4566654 3445554443321 112 345567999995 7766553 1114553
Q ss_pred HHHHHHhhcCCccchh-HHHHhhc------------cc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHH
Q psy6037 185 FFELQRLFFKSIYDVK-YLMKSCK------------NL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMREL 248 (286)
Q Consensus 185 F~~~l~~~FP~iYD~K-~l~~~~~------------~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~ 248 (286)
.|...+|+| ++++..- .+ .-+|..+++.+|++-.|.+|.|=.|+.-|+.+|.+|.+.
T Consensus 184 -------~f~~widLk~~lar~l~p~~~~~~~~~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~ 254 (582)
T PTZ00315 184 -------SFQRWCNLKKYMSQLGFGNGSGCGGGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRR 254 (582)
T ss_pred -------ccceEEEhHHHHHHHhCccccccccccccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHc
Confidence 244555664 6665421 12 247999999999999999999999999999999999775
No 37
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=97.65 E-value=0.0022 Score=58.03 Aligned_cols=148 Identities=12% Similarity=0.059 Sum_probs=96.3
Q ss_pred eeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHHH
Q psy6037 38 YIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSID 117 (286)
Q Consensus 38 fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI~ 117 (286)
++.+|||=+|+. + .|||+|..-+. +|. .+-+|+...+... ..++.+++
T Consensus 2 ~~vlD~ETTGl~--~----------------------~IieIg~v~v~-~~~------i~~~~~~lv~P~~-~i~~~~~~ 49 (219)
T PRK07983 2 LRVIDTETCGLQ--G----------------------GIVEIASVDVI-DGK------IVNPMSHLVRPDR-PISPQAMA 49 (219)
T ss_pred eEEEEEECCCCC--C----------------------CCEEEEEEEEE-CCE------EEEEEEEEECcCC-CCCHHHhh
Confidence 788999999973 1 09999987664 343 2445665555544 34455444
Q ss_pred HHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCcc
Q psy6037 118 LLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIY 197 (286)
Q Consensus 118 fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iY 197 (286)
. |||.=.... |-|+ |.+.+.. +. ..-.+|++|-.+|.++|- .++ ...+
T Consensus 50 i---hgIt~e~v~--~ap~--~~ev~~~--~~--~~~~lVaHNa~FD~~~L~-------~~~--------------~~~i 97 (219)
T PRK07983 50 I---HRITEAMVA--DKPW--IEDVIPH--YY--GSEWYVAHNASFDRRVLP-------EMP--------------GEWI 97 (219)
T ss_pred c---CCCCHHHHc--CCCC--HHHHHHH--Hc--CCCEEEEeCcHhhHHHHh-------CcC--------------CCcE
Confidence 3 666554442 2232 4444333 21 234789999999999872 111 1356
Q ss_pred chhHHHHhh-ccccccHHHHHhHcCCcc----CCCCcccchhhHHHHHHHHHHHHHh
Q psy6037 198 DVKYLMKSC-KNLKGGLQEVAEQLDLSR----IGPQHQAGSDSLLTGRVFFKMRELF 249 (286)
Q Consensus 198 D~K~l~~~~-~~l~ggL~~lA~~L~v~r----~g~~HqAGsDSllT~~~F~~l~~~~ 249 (286)
||--+++.. .+++.+|+.|++.+++.. ...+|.|-+|++.|+.+|.+|.+..
T Consensus 98 dTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 98 CTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred eHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHc
Confidence 777777643 345677899999998753 2468999999999999999998643
No 38
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.64 E-value=0.0022 Score=64.51 Aligned_cols=174 Identities=17% Similarity=0.150 Sum_probs=112.5
Q ss_pred hCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcc-cch
Q psy6037 35 TYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDM-YAQ 113 (286)
Q Consensus 35 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~-~~~ 113 (286)
...||.+|+|=+|+.... | .|||+|.-..+.+++. ....|+++.....+. ..+
T Consensus 5 ~~~fvv~D~ETTGLdP~~-------------------D--rIIeiAaVrvd~~~~~-----i~e~~~~~~~P~~~~lp~p 58 (476)
T PRK11779 5 QPTFLWHDYETFGANPAL-------------------D--RPAQFAGIRTDADLNI-----IGEPLVFYCKPADDYLPSP 58 (476)
T ss_pred CCcEEEEEEECCCCCCCC-------------------C--eeEEEEEEEEeCCCce-----ecceeEEEEcCCcCcCCCH
Confidence 467999999999985311 1 3999999988876532 234677776665543 355
Q ss_pred hHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeec-chhHHHHHHHHhCCCCCCCChHHHHHHHHhh
Q psy6037 114 DSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHS-GYDFGYLLKLLMGTRSLPSEEAEFFELQRLF 192 (286)
Q Consensus 114 ~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg-~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~ 192 (286)
+|+ .-+||-=+.+...|++..++.+.+.. .+..++-.+|.+|. .+|..+|-+.+... +-+.+ .+.+
T Consensus 59 ~a~---~IhGIT~e~l~~~g~~e~e~~~~i~~--~l~~~~~~lVGhNni~FD~eflr~~~~r~--~~d~y------~~~~ 125 (476)
T PRK11779 59 EAV---LITGITPQEALEKGLPEAEFAARIHA--EFSQPGTCILGYNNIRFDDEVTRYIFYRN--FYDPY------AREW 125 (476)
T ss_pred HHH---HHhCCCHHHHHhcCCCHHHHHHHHHH--HHhcCCCEEEEeCchhhcHHHHHHHHHhc--cchHH------HHHh
Confidence 553 45999999999999987777666543 12123445777776 59999988887642 21111 1110
Q ss_pred c-C-CccchhHHHHhhc--------------cc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHH
Q psy6037 193 F-K-SIYDVKYLMKSCK--------------NL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMREL 248 (286)
Q Consensus 193 F-P-~iYD~K~l~~~~~--------------~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~ 248 (286)
- + ...|+=-+++.+. +. .-.|+.|++.+|++. +.+|-|=+|++.|+.++.+|++.
T Consensus 126 ~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~L~~~~gI~~-~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 126 QNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEH-ENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred cCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHh
Confidence 0 0 0112211111110 11 136999999999984 56899999999999999999876
No 39
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=97.63 E-value=0.00087 Score=65.22 Aligned_cols=200 Identities=15% Similarity=0.208 Sum_probs=119.0
Q ss_pred HhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCccc
Q psy6037 32 LINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMY 111 (286)
Q Consensus 32 ~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~ 111 (286)
.+++.+||++|+|=||+.... =.||+||.-.++.+|.. +..|...++...+..
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~---------------------drIIeIgAV~i~~~g~i------ve~f~tLVnP~~~~~ 94 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPST---------------------SRLITIDAVTLTADGEE------VEHFHAVLNPGEDPG 94 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCC---------------------CeEEEEEEEEEEcCCEE------EEEEEEEECcCCCCC
Confidence 467789999999999984311 14999999888877752 566666666554432
Q ss_pred chhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCC-CCC-----CCChH--
Q psy6037 112 AQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGT-RSL-----PSEEA-- 183 (286)
Q Consensus 112 ~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~-~~L-----P~~~~-- 183 (286)
. . .=|||.=+.+.. |.++.+..+.|.. ++ ++-.||++|-.+|++||-+-+.-. ..+ |....
T Consensus 95 p---~---~LHGIT~e~La~-AP~f~eVl~el~~--fL--~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~ 163 (377)
T PRK05601 95 P---F---HLHGLSAEEFAQ-GKRFSQILKPLDR--LI--DGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNR 163 (377)
T ss_pred C---c---cccCCCHHHHhc-CCCHHHHHHHHHH--Hh--CCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccc
Confidence 1 1 237776666644 6665554444433 22 234799999999999998755210 000 00000
Q ss_pred ----HH--HHHHHhhcC-CccchhHHHHhhc-ccc-ccHHHHHhHcCCcc---------CCCCcccch--hhHHHHHHHH
Q psy6037 184 ----EF--FELQRLFFK-SIYDVKYLMKSCK-NLK-GGLQEVAEQLDLSR---------IGPQHQAGS--DSLLTGRVFF 243 (286)
Q Consensus 184 ----~F--~~~l~~~FP-~iYD~K~l~~~~~-~l~-ggL~~lA~~L~v~r---------~g~~HqAGs--DSllT~~~F~ 243 (286)
.= ...-+...| .++||=-+++... .+. -.|..||+.+|++. -...|.|=+ |++|+...|+
T Consensus 164 ~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~ 243 (377)
T PRK05601 164 RGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYF 243 (377)
T ss_pred cccccccccccCCCCCCCCEEEhHHHHHHHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHH
Confidence 00 000011234 4678866666553 332 46999999999864 345666664 9999999999
Q ss_pred HHHHHhcCCCCCcccccceEEecCCC
Q psy6037 244 KMRELFFEDAIDDDKYCGHIYGLGPA 269 (286)
Q Consensus 244 ~l~~~~~~~~~~~~~~~g~i~Gl~~~ 269 (286)
++++.--=.+.+.+.+..--+|+.-+
T Consensus 244 ~~~~~~~l~~~~p~~l~a~~fglq~s 269 (377)
T PRK05601 244 ALRASGPLSSIDPEDLRADKFGLQRS 269 (377)
T ss_pred HhhccCCccccChhhhhccccCcccc
Confidence 98543100122234555556777644
No 40
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=97.52 E-value=0.0024 Score=71.54 Aligned_cols=172 Identities=16% Similarity=0.168 Sum_probs=112.7
Q ss_pred HhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCccc
Q psy6037 32 LINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMY 111 (286)
Q Consensus 32 ~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~ 111 (286)
.+.+.+||++|+|-+|+.... =.|||+|....+ +|. ..-.|..+++... ..
T Consensus 415 ~L~~~~~VVfDLETTGL~~~~---------------------deIIEIgAV~V~-~G~------iie~F~~~V~P~~-~I 465 (1437)
T PRK00448 415 DLKDATYVVFDVETTGLSAVY---------------------DEIIEIGAVKIK-NGE------IIDKFEFFIKPGH-PL 465 (1437)
T ss_pred hhccCcEEEEEhhhcCCCCch---------------------hhhheeeeEEEe-CCe------EeeeEEEEECCCC-CC
Confidence 345688999999999974311 158999987775 342 2456777666543 33
Q ss_pred chhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHh
Q psy6037 112 AQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRL 191 (286)
Q Consensus 112 ~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~ 191 (286)
.+.+.++ +||.=..+. .+.+..+-.+.+.. + -.+..+|++++.+|+++|-+.+-.- -+|+-
T Consensus 466 ~~~~~~L---TGIT~e~L~-~aps~~EaL~~f~~--f--igg~vLVAHNa~FD~~fL~~~l~rl-gl~~l---------- 526 (1437)
T PRK00448 466 SAFTTEL---TGITDDMVK-DAPSIEEVLPKFKE--F--CGDSILVAHNASFDVGFINTNYEKL-GLEKI---------- 526 (1437)
T ss_pred CHHHHHH---hCCCHHHHc-CCCCHHHHHHHHHH--H--hCCCEEEEeCccccHHHHHHHHHHc-CCccc----------
Confidence 4444333 677766666 57776654444443 0 1245789999999999987665432 23220
Q ss_pred hcCCccchhHHHHhhc-c-ccccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhcCCC
Q psy6037 192 FFKSIYDVKYLMKSCK-N-LKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFEDA 253 (286)
Q Consensus 192 ~FP~iYD~K~l~~~~~-~-l~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~~~~ 253 (286)
-....|+--+++... . -..+|+.||+.+|++..+ .|-|-+|++.|+.+|.+|.+.+...+
T Consensus 527 -~~~~IDTLelar~l~p~~k~~kL~~LAk~lGL~~~~-~HrAl~DA~aTa~lf~~ll~~l~~~g 588 (1437)
T PRK00448 527 -KNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEH-HHRADYDAEATAYLLIKFLKDLKEKG 588 (1437)
T ss_pred -cccceeHHHHHHHHcCccccccHHHHHHHcCCCCCC-CcChHHHHHHHHHHHHHHHHHHHHcC
Confidence 112446544444321 1 235799999999998766 59999999999999999988875443
No 41
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=97.51 E-value=0.0047 Score=55.67 Aligned_cols=165 Identities=18% Similarity=0.220 Sum_probs=105.0
Q ss_pred CCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhH
Q psy6037 36 YNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDS 115 (286)
Q Consensus 36 ~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~S 115 (286)
..||.+|+|-+|... ..-.||++|.-.+..+.... -.|..+.+. ...+.+++
T Consensus 13 ~~~vv~D~ETtg~~~---------------------~~~~iieIgav~~~~~~i~~------~~~~~~v~P-~~~i~~~~ 64 (243)
T COG0847 13 TRFVVIDLETTGLNP---------------------KKDRIIEIGAVTLEDGRIVE------RSFHTLVNP-ERPIPPEI 64 (243)
T ss_pred CcEEEEecccCCCCC---------------------CCCceEEEEeEEEECCeeec------ceeEEEECC-CCCCChhh
Confidence 689999999999854 33359999998776653221 114444444 33344555
Q ss_pred HHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCC-CCCCCChHHHHHHHHhhcC
Q psy6037 116 IDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGT-RSLPSEEAEFFELQRLFFK 194 (286)
Q Consensus 116 I~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~-~~LP~~~~~F~~~l~~~FP 194 (286)
... +||....+... .....-.+.+.. ++ ++.-.+|+++-++|.+||-+.+... .+.| ..
T Consensus 65 ~~i---~git~e~l~~~-p~~~~v~~~~~~--~i-~~~~~~Vahna~fD~~fl~~~~~~~~~~~~-------------~~ 124 (243)
T COG0847 65 FKI---HGITDEMLADA-PKFAEVLPEFLD--FI-GGLRLLVAHNAAFDVGFLRVESERLGIEIP-------------GD 124 (243)
T ss_pred hhh---cCCCHHHHhcC-CCHHHHHHHHHH--HH-CCCCeEEEEchhhcHHHHHHHHHHcCCCcc-------------cC
Confidence 444 77777777766 222222222211 11 2214789999999999997655532 1333 12
Q ss_pred CccchhHHHHhh-cc-ccccHHHHHhHcCCccC-CCCcccchhhHHHHHHHHHHHHH
Q psy6037 195 SIYDVKYLMKSC-KN-LKGGLQEVAEQLDLSRI-GPQHQAGSDSLLTGRVFFKMREL 248 (286)
Q Consensus 195 ~iYD~K~l~~~~-~~-l~ggL~~lA~~L~v~r~-g~~HqAGsDSllT~~~F~~l~~~ 248 (286)
.++|+--+++.. .+ -+.+|+.+++.+|+++- ...|.|-.|+++++..|.++...
T Consensus 125 ~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 125 PVLDTLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred ceehHHHHHHHHcCCCccchHHHHHHHcCCCcCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 344554444432 22 34679999999999984 45688999999999999999874
No 42
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=97.45 E-value=0.0039 Score=58.95 Aligned_cols=156 Identities=18% Similarity=0.164 Sum_probs=101.6
Q ss_pred CeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecC--CCCCCCCCcceEEEEEEecCCCcccchh
Q psy6037 37 NYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDS--KSCTPPGPFTTWQFNFKFDLQEDMYAQD 114 (286)
Q Consensus 37 ~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~--~g~~p~~~~~~wqFNF~F~~~~d~~~~~ 114 (286)
.+|.+|||=||+... .=.|||||+..++. +|..- .....|+...+... ...++
T Consensus 38 ~~vvlD~ETTGLd~~---------------------~d~IIEIg~V~v~~~~~g~i~---~v~~~~~~lv~P~~-~I~~~ 92 (294)
T PRK09182 38 LGVILDTETTGLDPR---------------------KDEIIEIGMVAFEYDDDGRIG---DVLDTFGGLQQPSR-PIPPE 92 (294)
T ss_pred eEEEEEeeCCCCCCC---------------------CCeEEEEEEEEEEecCCCcee---eeeeEEEEEeCCCC-CCCHH
Confidence 679999999998531 11499999999875 35431 13466777666543 34555
Q ss_pred HHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCC--CCCCCChHHHHHHHHhh
Q psy6037 115 SIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGT--RSLPSEEAEFFELQRLF 192 (286)
Q Consensus 115 SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~--~~LP~~~~~F~~~l~~~ 192 (286)
+... +||.=......+++...+.+.+.. .-..|++|..+|..||-+.+..- .+...+... +
T Consensus 93 ~t~I---hGIt~e~v~~~~~~~~~l~~fl~~-------~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~----i--- 155 (294)
T PRK09182 93 ITRL---TGITDEMVAGQTIDPAAVDALIAP-------ADLIIAHNAGFDRPFLERFSPVFATKPWACSVSE----I--- 155 (294)
T ss_pred HHHh---cCCCHHHHhcCCCcHHHHHHHhcC-------CCEEEEeCHHHHHHHHHHHHHhccCCcccccHHH----H---
Confidence 5443 899888888888877666665432 12568999999999997754210 011111110 0
Q ss_pred cCCccchhHHHHhhccc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHH
Q psy6037 193 FKSIYDVKYLMKSCKNL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMR 246 (286)
Q Consensus 193 FP~iYD~K~l~~~~~~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~ 246 (286)
|-+ ...+ .-.|+.|++.+|. ....|-|.+|++.|+.+|.++.
T Consensus 156 -----~~~-----~~~~~~~kL~~La~~~g~--~~~aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 156 -----DWS-----ARGFEGTKLGYLAGQAGF--FHEGHRAVDDCQALLELLARPL 198 (294)
T ss_pred -----hhc-----cccCCCCCHHHHHHHcCC--CCCCcChHHHHHHHHHHHHHHH
Confidence 100 0111 2469999999993 4568999999999999999654
No 43
>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=97.42 E-value=0.0014 Score=55.54 Aligned_cols=146 Identities=16% Similarity=0.201 Sum_probs=83.2
Q ss_pred eeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeee-eeeecCCCCCCCCCcceEEEEEEecCCCcccchhHHH
Q psy6037 39 IGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIG-LTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSID 117 (286)
Q Consensus 39 IAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlG-itl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI~ 117 (286)
|++|+|.+|+..+ + .++|++ +++.+.+|+. . |+.+++... ...+.+++
T Consensus 1 v~lD~EttGl~~~------------------~----~~~~i~~v~~v~~~~~~------~--~~~~v~P~~-~i~~~~~~ 49 (152)
T cd06144 1 VALDCEMVGVGPD------------------G----SESALARVSIVNEDGNV------V--YDTYVKPQE-PVTDYRTA 49 (152)
T ss_pred CEEEEEeecccCC------------------C----CEEEEEEEEEEeCCCCE------E--EEEEECCCC-CCCccccc
Confidence 6899999998421 1 355664 4555665542 2 666655542 23333333
Q ss_pred HHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCcc
Q psy6037 118 LLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIY 197 (286)
Q Consensus 118 fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iY 197 (286)
. +||.=..+. .+.+..+-.+.+.. ++ .. -.+|.+|..+|+++|- . +.|.. .+.
T Consensus 50 i---hGIt~~~v~-~a~~~~~~~~~l~~--~l-~~-~vlVgHn~~fD~~~L~-----~-~~~~~-------------~~~ 102 (152)
T cd06144 50 V---SGIRPEHLK-DAPDFEEVQKKVAE--LL-KG-RILVGHALKNDLKVLK-----L-DHPKK-------------LIR 102 (152)
T ss_pred C---CCCCHHHHc-CCCCHHHHHHHHHH--Hh-CC-CEEEEcCcHHHHHHhc-----C-cCCCc-------------cEE
Confidence 3 566554443 34444332222221 22 22 3689989999999883 1 33331 233
Q ss_pred chhHHHHhhc---cccccHHHHHhH-cCCccCCCCcccchhhHHHHHHH
Q psy6037 198 DVKYLMKSCK---NLKGGLQEVAEQ-LDLSRIGPQHQAGSDSLLTGRVF 242 (286)
Q Consensus 198 D~K~l~~~~~---~l~ggL~~lA~~-L~v~r~g~~HqAGsDSllT~~~F 242 (286)
|+-.+..... ...-+|+.||+. ||++..+.+|.|.+|++.|+++|
T Consensus 103 dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~at~~l~ 151 (152)
T cd06144 103 DTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151 (152)
T ss_pred EeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcCcHHHHHHHHHHh
Confidence 4422221111 123589999997 69875557899999999999887
No 44
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.39 E-value=0.0099 Score=53.97 Aligned_cols=161 Identities=17% Similarity=0.187 Sum_probs=99.4
Q ss_pred CeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHH
Q psy6037 37 NYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSI 116 (286)
Q Consensus 37 ~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI 116 (286)
.+|.+|||=||+.... =.|||+|. .+ +. ..-.|+-.++.... ..++++
T Consensus 3 ~~vv~D~ETTGl~~~~---------------------d~IIeig~--v~--~~------~~~~f~~lv~P~~~-I~~~a~ 50 (232)
T PRK06309 3 ALIFYDTETTGTQIDK---------------------DRIIEIAA--YN--GV------TSESFQTLVNPEIP-IPAEAS 50 (232)
T ss_pred cEEEEEeeCCCCCCCC---------------------CEEEEEEE--Ec--Cc------cccEEEEEeCCCCC-CChhHH
Confidence 4899999999984211 14999997 22 11 12245555555443 455554
Q ss_pred HHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeec-chhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCC
Q psy6037 117 DLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHS-GYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKS 195 (286)
Q Consensus 117 ~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg-~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~ 195 (286)
+. |||.=+...... +..+..+.+.. ++ .+.-.+|++++ .+|..+|-+.+-.. .+|... -.
T Consensus 51 ~I---hGIt~e~v~~~p-~f~ev~~~~~~--fi-~~~~~lVaHN~~~FD~~~L~~e~~r~-g~~~~~-----------~~ 111 (232)
T PRK06309 51 KI---HGITTDEVADAP-KFPEAYQKFIE--FC-GTDNILVAHNNDAFDFPLLRKECRRH-GLEPPT-----------LR 111 (232)
T ss_pred hh---cCCCHHHHhCCC-CHHHHHHHHHH--HH-cCCCEEEEeCCHHHHHHHHHHHHHHc-CCCCCC-----------Cc
Confidence 43 777766665533 33222222221 11 22336788884 69999998877532 222110 13
Q ss_pred ccchhHHHHhh-ccc-cccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHh
Q psy6037 196 IYDVKYLMKSC-KNL-KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELF 249 (286)
Q Consensus 196 iYD~K~l~~~~-~~l-~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~ 249 (286)
.+||--+++.. .++ ..+|+.+++.+|++. ..+|-|-+|++.|+.+|.+|.+.+
T Consensus 112 ~iDt~~l~~~~~~~~~~~~L~~l~~~~~~~~-~~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 112 TIDSLKWAQKYRPDLPKHNLQYLRQVYGFEE-NQAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred EEeHHHHHHHHcCCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHH
Confidence 56776666543 222 357999999999774 568999999999999999998765
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=97.07 E-value=0.0069 Score=51.31 Aligned_cols=144 Identities=13% Similarity=0.123 Sum_probs=86.7
Q ss_pred eeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcccchhHHHH
Q psy6037 39 IGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSIDL 118 (286)
Q Consensus 39 IAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~~~~SI~f 118 (286)
+|||+|++|+..+ -.|+++|+. +.+|+. .|+-+.+... .+.+...++
T Consensus 1 ~~iD~E~~g~~~g----------------------~ei~~i~~v--~~~~~~--------~f~~lv~P~~-~i~~~~t~i 47 (150)
T cd06145 1 FALDCEMCYTTDG----------------------LELTRVTVV--DENGKV--------VLDELVKPDG-EIVDYNTRF 47 (150)
T ss_pred CEEeeeeeeecCC----------------------CEEEEEEEE--eCCCCE--------EEEEeECCCC-ccchhccCc
Confidence 6899999997531 127777776 444431 2555454432 223333332
Q ss_pred HHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccc
Q psy6037 119 LQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYD 198 (286)
Q Consensus 119 L~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD 198 (286)
+||.=..+...+.+..+..+.+.. ++ .++-.+|.++-.+|+.+|-+ .-|.++|
T Consensus 48 ---tGIt~~~l~~a~~~~~~v~~~~~~--fl-~~~~vlVgHn~~fD~~fL~~---------------------~~~~~iD 100 (150)
T cd06145 48 ---SGITEEMLENVTTTLEDVQKKLLS--LI-SPDTILVGHSLENDLKALKL---------------------IHPRVID 100 (150)
T ss_pred ---CCCCHHHhccCCCCHHHHHHHHHH--Hh-CCCCEEEEcChHHHHHHhhc---------------------cCCCEEE
Confidence 676665655544444433323222 12 22347889889999999831 1256788
Q ss_pred hhHHHHhhcc--ccccHHHHHhHcCCccC---CCCcccchhhHHHHHHH
Q psy6037 199 VKYLMKSCKN--LKGGLQEVAEQLDLSRI---GPQHQAGSDSLLTGRVF 242 (286)
Q Consensus 199 ~K~l~~~~~~--l~ggL~~lA~~L~v~r~---g~~HqAGsDSllT~~~F 242 (286)
|-.+++.... .+-+|+.|++.+....+ +..|-|-+|++.|+..|
T Consensus 101 T~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 101 TAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELV 149 (150)
T ss_pred cHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHh
Confidence 8777765321 12489999988633222 46799999999999876
No 46
>PRK05359 oligoribonuclease; Provisional
Probab=96.96 E-value=0.026 Score=49.48 Aligned_cols=165 Identities=20% Similarity=0.167 Sum_probs=95.7
Q ss_pred CCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCcc---cc
Q psy6037 36 YNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDM---YA 112 (286)
Q Consensus 36 ~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~---~~ 112 (286)
-+||++|+|-||+.... | .|||+|.-..+.+.+. ..-.|++........ ..
T Consensus 3 ~~~vvlD~ETTGLdp~~-------------------d--~IieIgaV~~~~~~~~-----~~~~~~~~i~~~~~~l~~~~ 56 (181)
T PRK05359 3 DNLIWIDLEMTGLDPER-------------------D--RIIEIATIVTDADLNI-----LAEGPVIAIHQSDEALAAMD 56 (181)
T ss_pred CcEEEEEeecCCCCCCC-------------------C--eEEEEEEEEEcCCceE-----cccceEEEECCCHHHhhccC
Confidence 47999999999985321 1 2899999987665432 122355443322211 12
Q ss_pred hhHHHHHHHcCCChhhhhhCCCChHHHHHHHHh--cCccccCCccEEEeec-chhHHHHHHHHh--CCCCCCCCh---HH
Q psy6037 113 QDSIDLLQNSGIQFQRHKEEGIEPADFAELLTT--SGVVLNDKVKWLSFHS-GYDFGYLLKLLM--GTRSLPSEE---AE 184 (286)
Q Consensus 113 ~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~--SgLv~~~~v~Wvtfhg-~yD~gyL~K~lt--~~~~LP~~~---~~ 184 (286)
+.+...-..+|+. ++....|.+..+..+.+.. .+.+.. .-.+++.|+ .+|..||-+.+- +. +|+... ..
T Consensus 57 ~~~~~ih~~tGIt-~~~l~~~~~~~e~~~~~l~fl~~~~~~-~~~~l~g~~v~FD~~FL~~~~~~~~~-~l~~~~~Dv~t 133 (181)
T PRK05359 57 EWNTRTHTRSGLI-DRVRASTVSEAEAEAQTLEFLKQWVPA-GKSPLCGNSIGQDRRFLARYMPELEA-YFHYRNLDVST 133 (181)
T ss_pred hHHHHhcccccCc-HHHHhcCCCHHHHHHHHHHHHHHhcCC-CCCceeecchhhCHHHHHHHHHHhcc-cCCCcccchhH
Confidence 2333322234777 5666778887654444332 122222 223455555 789999988763 22 343222 12
Q ss_pred HHHHHHhhcCCccchhHHHHhhccccccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHHhcCC
Q psy6037 185 FFELQRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFED 252 (286)
Q Consensus 185 F~~~l~~~FP~iYD~K~l~~~~~~l~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~~~~~ 252 (286)
.+++.+.++|..| .++++.+ .|.|=+|.+-|.+++...++.++..
T Consensus 134 l~~l~r~~~P~~~----------------------~~~~~~~-~HRal~D~~~s~~~~~~~~~~~~~~ 178 (181)
T PRK05359 134 LKELARRWKPEIL----------------------NGFKKQG-THRALADIRESIAELKYYREHFFKL 178 (181)
T ss_pred HHHHHHHhChhhh----------------------hCCCCcC-CcccHHHHHHHHHHHHHHHHHhccC
Confidence 2344444555431 2444444 5999999999999999999988753
No 47
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=96.78 E-value=0.0093 Score=50.99 Aligned_cols=68 Identities=18% Similarity=0.203 Sum_probs=50.7
Q ss_pred ccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhc-cc----cccHHHHHhH-cCCccC--
Q psy6037 154 VKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCK-NL----KGGLQEVAEQ-LDLSRI-- 225 (286)
Q Consensus 154 v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~-~l----~ggL~~lA~~-L~v~r~-- 225 (286)
-.+|.++-.+|+.+|-. ..|.+.||-.|++... .+ .-+|+.|++. +|++-.
T Consensus 85 ~vlVgHn~~fD~~fL~~---------------------~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~ 143 (161)
T cd06137 85 TILVGHSLQNDLDALRM---------------------IHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGG 143 (161)
T ss_pred cEEEeccHHHHHHHHhC---------------------cCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCC
Confidence 36788888899999821 0356779988887653 22 3589999987 787632
Q ss_pred CCCcccchhhHHHHHHH
Q psy6037 226 GPQHQAGSDSLLTGRVF 242 (286)
Q Consensus 226 g~~HqAGsDSllT~~~F 242 (286)
...|-|-.|+..|+..|
T Consensus 144 ~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 144 GEGHDSLEDALAAREVV 160 (161)
T ss_pred CCCCCcHHHHHHHHHHh
Confidence 46799999999999876
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=96.45 E-value=0.029 Score=47.90 Aligned_cols=97 Identities=16% Similarity=0.114 Sum_probs=57.0
Q ss_pred cCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhH
Q psy6037 122 SGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKY 201 (286)
Q Consensus 122 ~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~ 201 (286)
+||.-+.+. .+.+...-.+.+.. ++ . +-.+|.++-.+|+.+|-.. ..|. .+-||=.
T Consensus 51 ~GIt~~~l~-~a~~~~~v~~~l~~--~l-~-~~vlV~Hn~~~D~~~l~~~-----~~~~--------------~~~Dt~~ 106 (157)
T cd06149 51 SGIRRQHLV-NATPFAVAQKEILK--IL-K-GKVVVGHAIHNDFKALKYF-----HPKH--------------MTRDTST 106 (157)
T ss_pred CCCCHHHHh-cCCCHHHHHHHHHH--Hc-C-CCEEEEeCcHHHHHHhccc-----CCCc--------------CEEECcc
Confidence 777766664 46666544444332 23 2 3368888878999887311 1111 1223321
Q ss_pred H--HHhh---ccc-cccHHHHHhHc---CCccCCCCcccchhhHHHHHHH
Q psy6037 202 L--MKSC---KNL-KGGLQEVAEQL---DLSRIGPQHQAGSDSLLTGRVF 242 (286)
Q Consensus 202 l--~~~~---~~l-~ggL~~lA~~L---~v~r~g~~HqAGsDSllT~~~F 242 (286)
+ ++.. ... +-+|+.|++.+ +++..+..|.|-+||+.|+..|
T Consensus 107 l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 107 IPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELY 156 (157)
T ss_pred cccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHh
Confidence 1 1111 111 24799999998 4554466899999999999877
No 49
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=96.10 E-value=0.027 Score=54.72 Aligned_cols=146 Identities=24% Similarity=0.308 Sum_probs=89.9
Q ss_pred HHHHHHHHHhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEE
Q psy6037 24 EEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFK 103 (286)
Q Consensus 24 ee~~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~ 103 (286)
+++..+-..+..+++|||||||-|.... =+.+-+|||. +.++. +
T Consensus 5 ~~l~~~~~~~~~~~~iAiDTEf~r~~t~-------------------~p~LcLIQi~----~~e~~--------~----- 48 (361)
T COG0349 5 DLLAAACALLRGSKAIAIDTEFMRLRTY-------------------YPRLCLIQIS----DGEGA--------S----- 48 (361)
T ss_pred hHHHHHHHHhcCCCceEEeccccccccc-------------------CCceEEEEEe----cCCCc--------e-----
Confidence 4556666677889999999999887432 1245688874 22221 0
Q ss_pred ecCCCcccchhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChH
Q psy6037 104 FDLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEA 183 (286)
Q Consensus 104 F~~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~ 183 (286)
.||.... +.+..-|.++|....++ =|-+.+..|+.-|.+.+ | -+|
T Consensus 49 -------------------lIdpl~~---~~d~~~l~~Ll~d~~v~------KIfHaa~~DL~~l~~~~-g--~~p---- 93 (361)
T COG0349 49 -------------------LIDPLAG---ILDLPPLVALLADPNVV------KIFHAARFDLEVLLNLF-G--LLP---- 93 (361)
T ss_pred -------------------Eeccccc---ccccchHHHHhcCCcee------eeeccccccHHHHHHhc-C--CCC----
Confidence 1111110 23344576776554433 24444669999888877 3 233
Q ss_pred HHHHHHHhhcCCccchhHHHHhhc-cccccHHHHHhH-cCCccCCCCcc----------------cchhhHHHHHHHHHH
Q psy6037 184 EFFELQRLFFKSIYDVKYLMKSCK-NLKGGLQEVAEQ-LDLSRIGPQHQ----------------AGSDSLLTGRVFFKM 245 (286)
Q Consensus 184 ~F~~~l~~~FP~iYD~K~l~~~~~-~l~ggL~~lA~~-L~v~r~g~~Hq----------------AGsDSllT~~~F~~l 245 (286)
+.+||||..++.|. +.+-||..+.++ +||+ +.+.|| |-+|-..=...+-+|
T Consensus 94 ----------~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~-ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L 162 (361)
T COG0349 94 ----------TPLFDTQIAAKLAGFGTSHGLADLVEELLGVE-LDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKL 162 (361)
T ss_pred ----------CchhHHHHHHHHhCCcccccHHHHHHHHhCCc-ccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 26899999999995 336789998865 6776 444444 445655556667777
Q ss_pred HHHhcC
Q psy6037 246 RELFFE 251 (286)
Q Consensus 246 ~~~~~~ 251 (286)
.+..-.
T Consensus 163 ~~~L~~ 168 (361)
T COG0349 163 TEELAR 168 (361)
T ss_pred HHHHHH
Confidence 665543
No 50
>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=95.66 E-value=0.21 Score=44.08 Aligned_cols=157 Identities=20% Similarity=0.232 Sum_probs=91.1
Q ss_pred HHHHHHHHHH--hhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEE
Q psy6037 23 QEEFVHIRSL--INTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQF 100 (286)
Q Consensus 23 ~ee~~~I~~~--i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqF 100 (286)
.+|+..+.+. +.+.+.|++|+|+.+....+ .-..+.+|||.- .+ .++-|
T Consensus 7 ~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~~-----------------~~~~v~LiQiat-----~~-------~~~li 57 (193)
T cd06146 7 EEELEALLLALSLEAGRVVGIDSEWKPSFLGD-----------------SDPRVAILQLAT-----ED-------EVFLL 57 (193)
T ss_pred HHHHHHHHHHHhhccCCEEEEECccCCCccCC-----------------CCCCceEEEEec-----CC-------CEEEE
Confidence 3566776666 89999999999997543321 123467899982 11 23333
Q ss_pred EEEecCCCcccchhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCC
Q psy6037 101 NFKFDLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPS 180 (286)
Q Consensus 101 NF~F~~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~ 180 (286)
-. .... +-+...+.+.|.. ++.++++.=|.++...|+..|.+-+.. ++.
T Consensus 58 d~----~~~~----------------------~~~~~~~~~~L~~--ll~d~~i~KVg~~~~~D~~~L~~~~~~---~~~ 106 (193)
T cd06146 58 DL----LALE----------------------NLESEDWDRLLKR--LFEDPDVLKLGFGFKQDLKALSASYPA---LKC 106 (193)
T ss_pred Ec----hhcc----------------------ccchHHHHHHHHH--HhCCCCeeEEEechHHHHHHHHHhcCc---ccc
Confidence 22 1100 0011222222222 334566666667777999999875542 111
Q ss_pred ChHHHHHHHHhhcCCccchhHHHHhhc------------cccccHHHHHhH-cCCc------------cCCC---Ccccc
Q psy6037 181 EEAEFFELQRLFFKSIYDVKYLMKSCK------------NLKGGLQEVAEQ-LDLS------------RIGP---QHQAG 232 (286)
Q Consensus 181 ~~~~F~~~l~~~FP~iYD~K~l~~~~~------------~l~ggL~~lA~~-L~v~------------r~g~---~HqAG 232 (286)
. + ...-+++|+..++.... .-..||..+++. ||++ |.=. .+-|.
T Consensus 107 -~--~-----~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA 178 (193)
T cd06146 107 -M--F-----ERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAA 178 (193)
T ss_pred -c--c-----ccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHH
Confidence 0 0 01137899988887543 124589999876 4543 1112 24499
Q ss_pred hhhHHHHHHHHHHHH
Q psy6037 233 SDSLLTGRVFFKMRE 247 (286)
Q Consensus 233 sDSllT~~~F~~l~~ 247 (286)
.|++.....|-+|.+
T Consensus 179 ~Da~~l~~l~~~L~~ 193 (193)
T cd06146 179 LDAYCLLEVFDKLLE 193 (193)
T ss_pred HHHHHHHHHHHHHhC
Confidence 999999999998863
No 51
>PRK05755 DNA polymerase I; Provisional
Probab=95.11 E-value=0.37 Score=51.96 Aligned_cols=84 Identities=19% Similarity=0.222 Sum_probs=56.3
Q ss_pred cCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhcc-ccccHHHHHhHc-CCcc----
Q psy6037 151 NDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKN-LKGGLQEVAEQL-DLSR---- 224 (286)
Q Consensus 151 ~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~-l~ggL~~lA~~L-~v~r---- 224 (286)
++.+..|+++.-+|+.+|.+. |- ++| +.++||..++..+.. ..-||+.+++.. |+.-
T Consensus 368 d~~v~kV~HNakfDl~~L~~~--gi-~~~--------------~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~ 430 (880)
T PRK05755 368 DPAIKKVGQNLKYDLHVLARY--GI-ELR--------------GIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFE 430 (880)
T ss_pred CCCCcEEEeccHhHHHHHHhC--CC-CcC--------------CCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchH
Confidence 455667888888999998752 42 433 356788777766532 225788877664 4431
Q ss_pred ---------CC-----CCcccchhhHHHHHHHHHHHHHhcC
Q psy6037 225 ---------IG-----PQHQAGSDSLLTGRVFFKMRELFFE 251 (286)
Q Consensus 225 ---------~g-----~~HqAGsDSllT~~~F~~l~~~~~~ 251 (286)
.. ..|.|..|+.+|...|.+|++.+-.
T Consensus 431 ~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~~ 471 (880)
T PRK05755 431 EVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLLE 471 (880)
T ss_pred HhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 11 2366999999999999999887543
No 52
>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=94.92 E-value=0.41 Score=39.92 Aligned_cols=83 Identities=18% Similarity=0.383 Sum_probs=53.4
Q ss_pred cccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhccc-c-ccHHHHHhH-cC-Cc-
Q psy6037 149 VLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKNL-K-GGLQEVAEQ-LD-LS- 223 (286)
Q Consensus 149 v~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~l-~-ggL~~lA~~-L~-v~- 223 (286)
+.+++++.|.++..+|+..|.+.+ | ...++++|+ .++..+.+- . -||..+++. || ..
T Consensus 73 l~~~~i~kv~~n~~~D~~~L~~~~-~----------------i~~~~~~D~-~l~~~~l~~~~~~~L~~L~~~~l~~~~~ 134 (176)
T PF01612_consen 73 LEDPNIIKVGHNAKFDLKWLYRSF-G----------------IDLKNVFDT-MLAAYLLDPTRSYSLKDLAEEYLGNIDL 134 (176)
T ss_dssp HTTTTSEEEESSHHHHHHHHHHHH-T----------------S--SSEEEH-HHHHHHTTTSTTSSHHHHHHHHHSEEE-
T ss_pred HhCCCccEEEEEEechHHHHHHHh-c----------------cccCCccch-hhhhhcccccccccHHHHHHHHhhhccC
Confidence 346788889888889999988762 1 223467888 444443222 2 588888765 45 21
Q ss_pred ----cCC--C---------CcccchhhHHHHHHHHHHHHHh
Q psy6037 224 ----RIG--P---------QHQAGSDSLLTGRVFFKMRELF 249 (286)
Q Consensus 224 ----r~g--~---------~HqAGsDSllT~~~F~~l~~~~ 249 (286)
+.+ . ..=|+.|+..|...|-+|+.++
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 1 1228889999999999998753
No 53
>PRK10829 ribonuclease D; Provisional
Probab=94.08 E-value=0.28 Score=48.01 Aligned_cols=83 Identities=17% Similarity=0.217 Sum_probs=56.0
Q ss_pred cCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhc-cccccHHHHHhH-cCCc-----
Q psy6037 151 NDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCK-NLKGGLQEVAEQ-LDLS----- 223 (286)
Q Consensus 151 ~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~-~l~ggL~~lA~~-L~v~----- 223 (286)
++++.-|-|.+.+|+..|.+.+ |- .-..++||...+..++ +..-||..|.+. ||+.
T Consensus 72 ~~~ivKV~H~~~~Dl~~l~~~~-g~----------------~p~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~ 134 (373)
T PRK10829 72 DPQVTKFLHAGSEDLEVFLNAF-GE----------------LPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSE 134 (373)
T ss_pred CCCeEEEEeChHhHHHHHHHHc-CC----------------CcCCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCccc
Confidence 4554445555679999986633 21 1126889999888885 334689997765 7874
Q ss_pred -cC------CCC---cccchhhHHHHHHHHHHHHHhc
Q psy6037 224 -RI------GPQ---HQAGSDSLLTGRVFFKMRELFF 250 (286)
Q Consensus 224 -r~------g~~---HqAGsDSllT~~~F~~l~~~~~ 250 (286)
|. =.. +=|..|......+|-+|++.+-
T Consensus 135 ~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 135 SRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11 122 3389999999999999988765
No 54
>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=93.39 E-value=1.9 Score=37.21 Aligned_cols=164 Identities=16% Similarity=0.113 Sum_probs=86.3
Q ss_pred eeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEEEecCCCccc---chh
Q psy6037 38 YIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMY---AQD 114 (286)
Q Consensus 38 fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF~F~~~~d~~---~~~ 114 (286)
+|.+|+|=+|+.... + .|||+|.-.++.++. .....|....+....+- .+.
T Consensus 1 lv~iD~ETTGl~p~~-------------------d--~IieIgaV~~~~~~~-----~i~~~f~~~i~p~~~~~~~~~~~ 54 (173)
T cd06135 1 LVWIDLEMTGLDPEK-------------------D--RILEIACIITDGDLN-----IIAEGPELVIHQPDEVLDGMDEW 54 (173)
T ss_pred CEEEEEecCCCCCCC-------------------C--eeEEEEEEEEeCCCc-----eecCceeEEECCCHHHhhhccHH
Confidence 578999999985311 1 399999998865432 12345666554433211 112
Q ss_pred HHHHHHHcCCChhhhhhCCCChHHHHHHHHh--cCccccCCccEEEeec-chhHHHHHHHHhCCCCCCCChHHHHHHHHh
Q psy6037 115 SIDLLQNSGIQFQRHKEEGIEPADFAELLTT--SGVVLNDKVKWLSFHS-GYDFGYLLKLLMGTRSLPSEEAEFFELQRL 191 (286)
Q Consensus 115 SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~--SgLv~~~~v~Wvtfhg-~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~ 191 (286)
+.+.-..+|+.= +....|.+..+..+.+.. .+.+ ..+-.+|..|+ .+|+.||-+.+..- ..
T Consensus 55 ~~~ih~~tgIt~-~~l~~~~~~~~vl~~~~~f~~~~~-~~~~~~lvgh~~~FD~~fL~~~~~~~--------------~~ 118 (173)
T cd06135 55 CTEMHTKSGLTE-RVRASTVTLAQAEAELLEFIKKYV-PKGKSPLAGNSVHQDRRFLDKYMPEL--------------EE 118 (173)
T ss_pred HHHcccccccHH-HHHhCCCCHHHHHHHHHHHHHHhc-CCCCCceeecchhhCHHHHHHHHHHH--------------hc
Confidence 222222246552 333556655443322221 0111 11224566777 89999997766421 11
Q ss_pred hc-CCccchhHHHHhhccccccHHHHHhHcCCccCCCCcccchhhHHHHHHHHHHHHH
Q psy6037 192 FF-KSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMREL 248 (286)
Q Consensus 192 ~F-P~iYD~K~l~~~~~~l~ggL~~lA~~L~v~r~g~~HqAGsDSllT~~~F~~l~~~ 248 (286)
.+ ....|+..+.+....+...+.+ ++++ .+..|-|=+|++-|+..+...++.
T Consensus 119 ~~~~~~~D~~~l~~l~~~l~p~~~~----~~~~-~~~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 119 YLHYRILDVSSIKELARRWYPEIYR----KAPK-KKGTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred cCCcchhhHHHHHHHHHHhCcHhhh----cCCC-CCCCcchHHHHHHHHHHHHHHHHH
Confidence 11 2345654333222223333322 3443 355799999999999988777653
No 55
>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=93.16 E-value=1.4 Score=37.19 Aligned_cols=145 Identities=15% Similarity=0.205 Sum_probs=89.3
Q ss_pred HHHHHHHHHHhh-hCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEE
Q psy6037 23 QEEFVHIRSLIN-TYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFN 101 (286)
Q Consensus 23 ~ee~~~I~~~i~-~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFN 101 (286)
++++..+.+.+. +.+.|++|||+.+.... .--..+.+||+. + ++ .++-|.
T Consensus 4 ~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~-----------------~~~~~~~liQl~-~-----~~------~~~l~~ 54 (170)
T cd06141 4 AQDAEEAVKELLGKEKVVGFDTEWRPSFRK-----------------GKRNKVALLQLA-T-----ES------RCLLFQ 54 (170)
T ss_pred HHHHHHHHHHHhcCCCEEEEeCccCCccCC-----------------CCCCCceEEEEe-c-----CC------cEEEEE
Confidence 455666666666 99999999999865331 012235578876 1 11 233333
Q ss_pred EEecCCCcccchhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCC
Q psy6037 102 FKFDLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSE 181 (286)
Q Consensus 102 F~F~~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~ 181 (286)
.. . + ..++ ..+.++| .++++..|.++.-.|+..|.+.+ |- .
T Consensus 55 ~~----~-------~---------------~~~~-~~l~~ll------~~~~i~kv~~~~k~D~~~L~~~~-g~-~---- 95 (170)
T cd06141 55 LA----H-------M---------------DKLP-PSLKQLL------EDPSILKVGVGIKGDARKLARDF-GI-E---- 95 (170)
T ss_pred hh----h-------h---------------hccc-HHHHHHh------cCCCeeEEEeeeHHHHHHHHhHc-CC-C----
Confidence 21 1 0 1233 3454444 34577788888888888875433 21 1
Q ss_pred hHHHHHHHHhhcCCccchhHHHHhhccc--cccHHHHHhHc-CCc-----cC------------CCCcccchhhHHHHHH
Q psy6037 182 EAEFFELQRLFFKSIYDVKYLMKSCKNL--KGGLQEVAEQL-DLS-----RI------------GPQHQAGSDSLLTGRV 241 (286)
Q Consensus 182 ~~~F~~~l~~~FP~iYD~K~l~~~~~~l--~ggL~~lA~~L-~v~-----r~------------g~~HqAGsDSllT~~~ 241 (286)
..+++|+..++..+... ..||+.+++.+ |++ ++ ..-|-|..|+++...+
T Consensus 96 -----------~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l 164 (170)
T cd06141 96 -----------VRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYASLEL 164 (170)
T ss_pred -----------CCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 33568999888877543 35999999874 542 11 1135699999999999
Q ss_pred HHHHH
Q psy6037 242 FFKMR 246 (286)
Q Consensus 242 F~~l~ 246 (286)
+.+|+
T Consensus 165 ~~~l~ 169 (170)
T cd06141 165 YRKLL 169 (170)
T ss_pred HHHHh
Confidence 98885
No 56
>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=92.61 E-value=5.2 Score=38.94 Aligned_cols=145 Identities=21% Similarity=0.311 Sum_probs=86.9
Q ss_pred HHHHHHHHHHhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCCCCCCCcceEEEEE
Q psy6037 23 QEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNF 102 (286)
Q Consensus 23 ~ee~~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~~p~~~~~~wqFNF 102 (286)
.+++..+.+.+...+.||+||||..... + -..+-+||+.- ++ .++
T Consensus 5 ~~~l~~~~~~l~~~~~ia~DtE~~~~~~-----y--------------~~~l~LiQia~------~~------~~~---- 49 (367)
T TIGR01388 5 DDELATVCEAVRTFPFVALDTEFVRERT-----F--------------WPQLGLIQVAD------GE------QLA---- 49 (367)
T ss_pred HHHHHHHHHHHhcCCEEEEeccccCCCC-----C--------------CCcceEEEEee------CC------eEE----
Confidence 3677777777888999999999976421 1 11245889862 11 122
Q ss_pred EecCCCcccchhHHHHHHHcCCChhhhhhCCCChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCCh
Q psy6037 103 KFDLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEE 182 (286)
Q Consensus 103 ~F~~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~ 182 (286)
.||.-. ..+...+.++| .++++.+|.|+..+|+..|.+.. + .+|.
T Consensus 50 liD~~~------------------------~~~~~~L~~lL------~d~~i~KV~h~~k~Dl~~L~~~~-~--~~~~-- 94 (367)
T TIGR01388 50 LIDPLV------------------------IIDWSPLKELL------RDESVVKVLHAASEDLEVFLNLF-G--ELPQ-- 94 (367)
T ss_pred EEeCCC------------------------cccHHHHHHHH------CCCCceEEEeecHHHHHHHHHHh-C--CCCC--
Confidence 233210 01223444443 35678899888889988775432 2 3442
Q ss_pred HHHHHHHHhhcCCccchhHHHHhhcc-ccccHHHHHhH-cCCccCCCC-------------c---ccchhhHHHHHHHHH
Q psy6037 183 AEFFELQRLFFKSIYDVKYLMKSCKN-LKGGLQEVAEQ-LDLSRIGPQ-------------H---QAGSDSLLTGRVFFK 244 (286)
Q Consensus 183 ~~F~~~l~~~FP~iYD~K~l~~~~~~-l~ggL~~lA~~-L~v~r~g~~-------------H---qAGsDSllT~~~F~~ 244 (286)
.++||...+..++. ...||..+++. ||++ +.+. . -|..|+......+-+
T Consensus 95 ------------~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~-l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~ 161 (367)
T TIGR01388 95 ------------PLFDTQIAAAFCGFGMSMGYAKLVQEVLGVE-LDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAK 161 (367)
T ss_pred ------------CcccHHHHHHHhCCCCCccHHHHHHHHcCCC-CCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 56899877766642 24589888766 5654 1111 1 266777777777777
Q ss_pred HHHHhc
Q psy6037 245 MRELFF 250 (286)
Q Consensus 245 l~~~~~ 250 (286)
|++.+-
T Consensus 162 L~~~L~ 167 (367)
T TIGR01388 162 LMERLE 167 (367)
T ss_pred HHHHHH
Confidence 776653
No 57
>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=88.77 E-value=8.5 Score=33.80 Aligned_cols=85 Identities=15% Similarity=0.152 Sum_probs=52.4
Q ss_pred ccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhccc---------cccHHHHHhH-
Q psy6037 150 LNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKNL---------KGGLQEVAEQ- 219 (286)
Q Consensus 150 ~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~l---------~ggL~~lA~~- 219 (286)
.++++..|.|..-.|...|.+-+ |- . | .+++||..++..+..- ..||..+++.
T Consensus 62 e~~~i~Kv~h~~k~D~~~L~~~~-gi-~-~--------------~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~ 124 (197)
T cd06148 62 ESKKILKVIHDCRRDSDALYHQY-GI-K-L--------------NNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKY 124 (197)
T ss_pred cCCCccEEEEechhHHHHHHHhc-Cc-c-c--------------cceeeHHHHHHHHHHHhcCCccccccccHHHHHHHh
Confidence 35678888888888887764422 21 1 1 1357876555443211 1377777765
Q ss_pred cCCc--------------------cCCCCcc---cchhhHHHHHHHHHHHHHhcC
Q psy6037 220 LDLS--------------------RIGPQHQ---AGSDSLLTGRVFFKMRELFFE 251 (286)
Q Consensus 220 L~v~--------------------r~g~~Hq---AGsDSllT~~~F~~l~~~~~~ 251 (286)
|+++ |.=...| |..|++.....|.+|++.+-+
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 4442 2112223 999999999999999887644
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=85.02 E-value=2.8 Score=38.01 Aligned_cols=103 Identities=21% Similarity=0.310 Sum_probs=59.9
Q ss_pred ccEEEeec-chhHHHHH-HHHhCCCCCCCChHHHH----HHHHhhcCCccchhHHHHhh-ccccccHHHHHhHcCCccCC
Q psy6037 154 VKWLSFHS-GYDFGYLL-KLLMGTRSLPSEEAEFF----ELQRLFFKSIYDVKYLMKSC-KNLKGGLQEVAEQLDLSRIG 226 (286)
Q Consensus 154 v~Wvtfhg-~yD~gyL~-K~lt~~~~LP~~~~~F~----~~l~~~FP~iYD~K~l~~~~-~~l~ggL~~lA~~L~v~r~g 226 (286)
-++|+|+| ++|+-||. |+|..+-++|.-.+.=- .-...|--.-.|+.-+.... ..-+.+|..||..||+| |
T Consensus 53 p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~~~sLd~la~~lgiP--g 130 (209)
T PF10108_consen 53 PQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKARTSLDELAALLGIP--G 130 (209)
T ss_pred CeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccccCCHHHHHHHcCCC--C
Confidence 37899997 79999965 56666547776433211 01111111133443222221 23356899999999997 2
Q ss_pred CCc----------ccc----------hhhHHHHHHHHHHHHHhcCCCCCccccc
Q psy6037 227 PQH----------QAG----------SDSLLTGRVFFKMRELFFEDAIDDDKYC 260 (286)
Q Consensus 227 ~~H----------qAG----------sDSllT~~~F~~l~~~~~~~~~~~~~~~ 260 (286)
+.- ++| .|.+-|..+|.++... .+.++.+.|.
T Consensus 131 K~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~--~G~l~~~~y~ 182 (209)
T PF10108_consen 131 KDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELL--RGRLSPEDYQ 182 (209)
T ss_pred CCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHh--hCCCCHHHHH
Confidence 222 223 6899999999998654 3444444443
No 59
>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=82.28 E-value=0.57 Score=39.27 Aligned_cols=70 Identities=19% Similarity=0.307 Sum_probs=38.5
Q ss_pred cEEEeec-chhHHHHHHHHhCCCCCCCChHHHHHHHHhhcC-CccchhHHHHhhccccc-cHHHHHhHcCCccCCCCccc
Q psy6037 155 KWLSFHS-GYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFK-SIYDVKYLMKSCKNLKG-GLQEVAEQLDLSRIGPQHQA 231 (286)
Q Consensus 155 ~Wvtfhg-~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP-~iYD~K~l~~~~~~l~g-gL~~lA~~L~v~r~g~~HqA 231 (286)
.+|+||| .||+.+|-+.+-.- .+|. | ...|+..+++.... .+ +|..||+.||..|. .....
T Consensus 59 ~iv~yng~~FD~p~L~~~~~~~-~~~~-------------~~~~iDl~~~~~~~~~-~~~~Lk~ve~~lg~~~~-~~~~~ 122 (164)
T PF13482_consen 59 NIVTYNGKNFDIPFLKRRAKRY-GLPP-------------PFNHIDLLKIIKKHFL-ESYSLKNVEKFLGIERR-DDDIS 122 (164)
T ss_dssp -EEESSTTTTHHHHHHHHH-HH-HH---------------GGGEEEHHHHHT-TTS-CCTT--SHHH------------H
T ss_pred eEEEEeCcccCHHHHHHHHHHc-CCCc-------------ccchhhHHHHHHhccC-CCCCHHHHhhhcccccc-cCCCC
Confidence 6999997 68999999988332 3444 3 46688877765433 55 89999999999984 23356
Q ss_pred chhhHHHHH
Q psy6037 232 GSDSLLTGR 240 (286)
Q Consensus 232 GsDSllT~~ 240 (286)
|+++...-.
T Consensus 123 G~~~~~~~~ 131 (164)
T PF13482_consen 123 GSESVKLYK 131 (164)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 787766643
No 60
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=81.07 E-value=4.6 Score=45.06 Aligned_cols=86 Identities=20% Similarity=0.279 Sum_probs=62.7
Q ss_pred cEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhc-ccc-ccHHHHHhHcCCccCCCCcccc
Q psy6037 155 KWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCK-NLK-GGLQEVAEQLDLSRIGPQHQAG 232 (286)
Q Consensus 155 ~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~-~l~-ggL~~lA~~L~v~r~g~~HqAG 232 (286)
.-|+++..+|+|||-.-+-.- .||+-. .| +.||=-|++... .++ -+|..|++.|++.- ...|-|-
T Consensus 503 IlVAHNasFD~gFl~~~~~k~-~~~~~~----------~p-vIDTL~lar~L~P~~ksh~Lg~l~kk~~v~l-e~hHRA~ 569 (1444)
T COG2176 503 ILVAHNASFDMGFLNTNYEKY-GLEPLT----------NP-VIDTLELARALNPEFKSHRLGTLCKKLGVEL-ERHHRAD 569 (1444)
T ss_pred EEEeccCccchhHHHHHHHHh-CCcccc----------Cc-hhhHHHHHHHhChhhhhcchHHHHHHhCccH-HHhhhhh
Confidence 567888899999985443321 122110 12 448877777664 343 58999999999986 6788999
Q ss_pred hhhHHHHHHHHHHHHHhcCCC
Q psy6037 233 SDSLLTGRVFFKMRELFFEDA 253 (286)
Q Consensus 233 sDSllT~~~F~~l~~~~~~~~ 253 (286)
+||-.|+.+|+.|.+.+.+.+
T Consensus 570 yDaeat~~vf~~f~~~~ke~G 590 (1444)
T COG2176 570 YDAEATAKVFFVFLKDLKEKG 590 (1444)
T ss_pred hhHHHHHHHHHHHHHHHHHhc
Confidence 999999999999998876543
No 61
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=74.47 E-value=1.8 Score=39.89 Aligned_cols=97 Identities=23% Similarity=0.208 Sum_probs=65.7
Q ss_pred eecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhccccccHHHHHhHcCCccCCCCcccchhhHHH
Q psy6037 159 FHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLT 238 (286)
Q Consensus 159 fhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~l~ggL~~lA~~L~v~r~g~~HqAGsDSllT 238 (286)
|-..||+-|++|.... +..-++|+...|... ....+...-...|-. |+.+..+|...-...+-.++|.
T Consensus 197 fP~fYDik~v~ks~~~---~~KglQei~ndlql~--------r~g~QhQagsdaLlT-a~~ff~~R~~~F~~sig~~ll~ 264 (299)
T COG5228 197 FPNFYDIKLVYKSVLN---NSKGLQEIKNDLQLQ--------RSGQQHQAGSDALLT-ADEFFLPRFSIFTTSIGQSLLM 264 (299)
T ss_pred CccccchHHHHHhhhh---hhhHHHHhcCcHhhh--------ccchhhhccchhhhh-hHHhcchhhheecccccHHHHH
Confidence 5578999999987664 344455555544321 011111111123544 8999999988877788889998
Q ss_pred HHHHHHHHHH---hcCCCCCcccccceEEecC
Q psy6037 239 GRVFFKMREL---FFEDAIDDDKYCGHIYGLG 267 (286)
Q Consensus 239 ~~~F~~l~~~---~~~~~~~~~~~~g~i~Gl~ 267 (286)
...++.+++. .|+++.++.++.|+|||+.
T Consensus 265 ~L~g~~~~~~sl~~~~~~t~f~~~~g~~~gi~ 296 (299)
T COG5228 265 LLSGCQLSKLSLHKFPNGTDFAKYQGVIYGID 296 (299)
T ss_pred HHhccccCCchheeCCCcccHhhcCCcccCCC
Confidence 8888888765 4566677899999999985
No 62
>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=67.26 E-value=19 Score=30.47 Aligned_cols=84 Identities=18% Similarity=0.240 Sum_probs=52.6
Q ss_pred cCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhcc-c-cccHHHHHhHc-CCc----
Q psy6037 151 NDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKN-L-KGGLQEVAEQL-DLS---- 223 (286)
Q Consensus 151 ~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~-l-~ggL~~lA~~L-~v~---- 223 (286)
+.++++|+++..+|+.+|.+. |- ++| +.++||..++..+.. . ..+|+.+++.+ +..
T Consensus 65 ~~~~~~v~hn~k~d~~~l~~~--gi-~~~--------------~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~ 127 (193)
T cd06139 65 DPSIKKVGQNLKFDLHVLANH--GI-ELR--------------GPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISF 127 (193)
T ss_pred CCCCcEEeeccHHHHHHHHHC--CC-CCC--------------CCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccH
Confidence 345678999999999988642 32 332 145777777665532 2 34677777653 321
Q ss_pred --------------cCC---CCcccchhhHHHHHHHHHHHHHhcC
Q psy6037 224 --------------RIG---PQHQAGSDSLLTGRVFFKMRELFFE 251 (286)
Q Consensus 224 --------------r~g---~~HqAGsDSllT~~~F~~l~~~~~~ 251 (286)
+.. ..|-|..|+..+...+-+|.+..-+
T Consensus 128 ~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 128 EDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred HHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 000 1124788899999999998887643
No 63
>KOG2207|consensus
Probab=57.75 E-value=26 Score=36.50 Aligned_cols=41 Identities=22% Similarity=0.289 Sum_probs=29.2
Q ss_pred ccccHHHHHhH-cCCc------------cCCCCcc---cchhhHHHHHHHHHHHHHh
Q psy6037 209 LKGGLQEVAEQ-LDLS------------RIGPQHQ---AGSDSLLTGRVFFKMRELF 249 (286)
Q Consensus 209 l~ggL~~lA~~-L~v~------------r~g~~Hq---AGsDSllT~~~F~~l~~~~ 249 (286)
..+||..|+.. ||.. |.=..|| ||-|+....++|.++.++-
T Consensus 529 ~~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv 585 (617)
T KOG2207|consen 529 ATKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVV 585 (617)
T ss_pred hhhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhc
Confidence 35678887765 3432 2224677 9999999999999998764
No 64
>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=57.42 E-value=33 Score=28.87 Aligned_cols=79 Identities=16% Similarity=0.107 Sum_probs=52.8
Q ss_pred cCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhcc-ccccHHHHHhH-cCCcc----
Q psy6037 151 NDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKN-LKGGLQEVAEQ-LDLSR---- 224 (286)
Q Consensus 151 ~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~-l~ggL~~lA~~-L~v~r---- 224 (286)
++++..|.++...|+..|.+.. |- + +.+++|+..++..... .+.||+.+++. ||++-
T Consensus 65 d~~i~Kvg~~~k~D~~~L~~~~-gi-~---------------~~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~ 127 (161)
T cd06129 65 NPSIVKALHGIEGDLWKLLRDF-GE-K---------------LQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSI 127 (161)
T ss_pred CCCEEEEEeccHHHHHHHHHHc-CC-C---------------cccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccc
Confidence 5677788877778887775532 21 1 2245788877776542 24589999887 57531
Q ss_pred --------CC---CCcccchhhHHHHHHHHHHH
Q psy6037 225 --------IG---PQHQAGSDSLLTGRVFFKMR 246 (286)
Q Consensus 225 --------~g---~~HqAGsDSllT~~~F~~l~ 246 (286)
.= ..+-|..|++....+|-+|+
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 10 13459999999999998885
No 65
>KOG4013|consensus
Probab=54.57 E-value=29 Score=31.59 Aligned_cols=84 Identities=20% Similarity=0.361 Sum_probs=51.9
Q ss_pred hhHHHHHHHcCCC---hhhhhhCC-CChHHHHHHHHhcCccccCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHH
Q psy6037 113 QDSIDLLQNSGIQ---FQRHKEEG-IEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFEL 188 (286)
Q Consensus 113 ~~SI~fL~~~G~D---F~k~~~~G-I~~~~F~ell~~SgLv~~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~ 188 (286)
-+-|++|+.+|-| |..+-..| |+...-..++..++ --.||||-++|++|=+|..... -| -.-.|.+.
T Consensus 84 ~~Dv~llk~~GAdGfVFGaLt~dgsid~~~C~si~~~~r------plPVTFHRAfD~~~D~k~~lE~-~l--~~lGF~rv 154 (255)
T KOG4013|consen 84 MEDVELLKKAGADGFVFGALTSDGSIDRTSCQSIIETAR------PLPVTFHRAFDVAYDWKTCLED-AL--LDLGFKRV 154 (255)
T ss_pred HHHHHHHHHcCCCceEEeecCCCCCcCHHHHHHHHHhcC------CCceeeeeehhhhcCHHHHHHH-HH--HHhhHHHH
Confidence 4668888887654 77777776 55544344444432 2579999999999977644321 00 01248888
Q ss_pred HHhhc-CCccchhHHHHh
Q psy6037 189 QRLFF-KSIYDVKYLMKS 205 (286)
Q Consensus 189 l~~~F-P~iYD~K~l~~~ 205 (286)
|.-=| |.--|--|+.++
T Consensus 155 LtSG~~psAldGv~~i~~ 172 (255)
T KOG4013|consen 155 LTSGQEPSALDGVYIIRE 172 (255)
T ss_pred hhcCCCcccccchHHHHH
Confidence 87666 765555555444
No 66
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=50.70 E-value=19 Score=33.75 Aligned_cols=75 Identities=17% Similarity=0.223 Sum_probs=50.1
Q ss_pred cEEEeec-chhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhc--c-ccccHHHHHhHcCCccCCCCcc
Q psy6037 155 KWLSFHS-GYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCK--N-LKGGLQEVAEQLDLSRIGPQHQ 230 (286)
Q Consensus 155 ~Wvtfhg-~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~--~-l~ggL~~lA~~L~v~r~g~~Hq 230 (286)
.||||+| ++|.-|+-++..+ .+|.+++. .=||.=|-++... - ..+||..|-+.||+.|... .
T Consensus 158 ~lvsfNGkaFD~PfikR~v~~--~~el~l~~----------~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~R~ed--t 223 (278)
T COG3359 158 MLVSFNGKAFDIPFIKRMVRD--RLELSLEF----------GHFDLYHPSRRLWKHLLPRCGLKTVERILGIRREED--T 223 (278)
T ss_pred eEEEecCcccCcHHHHHHHhc--ccccCccc----------cchhhhhhhhhhhhccCCCCChhhHHHHhCcccccc--C
Confidence 8999999 5999999885555 46655432 3457766666552 1 2578999999999999541 1
Q ss_pred cchhhHHHHHHHH
Q psy6037 231 AGSDSLLTGRVFF 243 (286)
Q Consensus 231 AGsDSllT~~~F~ 243 (286)
-|+++-..-..|.
T Consensus 224 dG~~~p~lyr~~~ 236 (278)
T COG3359 224 DGYDGPELYRLYR 236 (278)
T ss_pred CCcchHHHHHHHH
Confidence 2556555544443
No 67
>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=48.85 E-value=31 Score=24.66 Aligned_cols=33 Identities=24% Similarity=0.549 Sum_probs=25.6
Q ss_pred chhHHHHHHHcCCCh---------hhhhhCCCChHHHHHHHH
Q psy6037 112 AQDSIDLLQNSGIQF---------QRHKEEGIEPADFAELLT 144 (286)
Q Consensus 112 ~~~SI~fL~~~G~DF---------~k~~~~GI~~~~F~ell~ 144 (286)
.|.+.+.++++|||| ....+.||++..+.+.|.
T Consensus 12 ~p~~a~vf~~~gIDfCCgG~~~L~eA~~~~~ld~~~vl~~L~ 53 (56)
T PF04405_consen 12 DPRAARVFRKYGIDFCCGGNRSLEEACEEKGLDPEEVLEELN 53 (56)
T ss_pred ChHHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHH
Confidence 367889999999999 455678888887766654
No 68
>PRK14345 lipoate-protein ligase B; Provisional
Probab=45.02 E-value=14 Score=33.95 Aligned_cols=193 Identities=13% Similarity=0.052 Sum_probs=97.0
Q ss_pred cccEEeccccCHHHHHHHHHHHhhh-----CCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeee-
Q psy6037 11 KYGIREVWARNVQEEFVHIRSLINT-----YNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFF- 84 (286)
Q Consensus 11 ~~~i~dVw~~N~~ee~~~I~~~i~~-----~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~- 84 (286)
...|++--.-.+++.+...+++.++ -+=.-+=.|+|-+..--.. .. ++.. +.. |+.++
T Consensus 11 ~~~~~~lG~~~Y~~~~~~Q~~l~~~~~~~~~~d~llllEH~pVyT~Gr~---~~-~~~l--~~~----------~i~v~~ 74 (234)
T PRK14345 11 PIEVRRLGLVDYQEAWDLQRELADARVAGEGPDTLLLLEHPAVYTAGKR---TE-PHER--PTD----------GTPVVD 74 (234)
T ss_pred ceEEEECCCcCHHHHHHHHHHHHHHHhcCCCCCEEEEEcCCCCccCCCC---CC-cccc--ccC----------CCcEEE
Confidence 3567888888999999998887653 1122345677766542211 11 1111 011 23333
Q ss_pred -cCCCCCCCCCcceEEEEEEecCCC--c------ccchhHHHHHHHcCCChh-hhhhCCCChH--H--HHHHHHhcCccc
Q psy6037 85 -DSKSCTPPGPFTTWQFNFKFDLQE--D------MYAQDSIDLLQNSGIQFQ-RHKEEGIEPA--D--FAELLTTSGVVL 150 (286)
Q Consensus 85 -~~~g~~p~~~~~~wqFNF~F~~~~--d------~~~~~SI~fL~~~G~DF~-k~~~~GI~~~--~--F~ell~~SgLv~ 150 (286)
+.-|+.-....--..--+-+|+.. + ..+..-|+.|++.|+.=. +-..-||=.. . -.+++.+-|+-.
T Consensus 75 tdRGG~iTyHGPGQLV~YpIldL~~~~~v~~yv~~LE~~vI~~l~~~gi~a~~~~~~~GVWv~~~~~~~~~KIaaIGv~v 154 (234)
T PRK14345 75 VDRGGKITWHGPGQLVGYPIIKLAEPLDVVDYVRRLEEALIAVCADLGLNAGRVDGRSGVWVPADGGRPDRKIAAIGIRV 154 (234)
T ss_pred ecCCCceeEeCCCeEEEEEEEecCCCCCHHHHHHHHHHHHHHHHHHcCCceeecCCCCeEEECCCCCCCcceEEEEEeee
Confidence 333443211000111111144432 2 334566788887776422 1122232110 0 123555566643
Q ss_pred cCCccEEEeecc-----hhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhccccccHHHHHhHcCCccC
Q psy6037 151 NDKVKWLSFHSG-----YDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRI 225 (286)
Q Consensus 151 ~~~v~Wvtfhg~-----yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~l~ggL~~lA~~L~v~r~ 225 (286)
. +|||+||. -|+.++-++.-++ |++..-+= |....+.--+++-+.... ++++++.|+....
T Consensus 155 ~---r~vT~HG~ALNV~~DL~~F~~IvPCG--l~~~~vTS---l~~~~g~~~~~~~v~~~l------~~~f~~~f~~~~~ 220 (234)
T PRK14345 155 S---RGVTMHGFALNCDNDLAAFDAIVPCG--ISDAGVTT---LSAELGRTVTVAEVVDPV------AAALCDALDGRLP 220 (234)
T ss_pred c---cceeecceEEEeCCChHHhceEEeCC--CCCCcEEe---hhHhhCCCCCHHHHHHHH------HHHHHHHhCcccc
Confidence 3 69999994 7999988888775 66543221 111122222444443332 3566777777665
Q ss_pred CCCcccch
Q psy6037 226 GPQHQAGS 233 (286)
Q Consensus 226 g~~HqAGs 233 (286)
...|+-||
T Consensus 221 ~~~~~~~~ 228 (234)
T PRK14345 221 VRDHSPGS 228 (234)
T ss_pred cCCCcccc
Confidence 67799886
No 69
>KOG1990|consensus
Probab=44.98 E-value=9.6 Score=39.39 Aligned_cols=123 Identities=6% Similarity=-0.052 Sum_probs=77.0
Q ss_pred ccEEecccc--CHHHHHHHHHHHhhhCCeeeeeccccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeecCCCC
Q psy6037 12 YGIREVWAR--NVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSC 89 (286)
Q Consensus 12 ~~i~dVw~~--N~~ee~~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~~~g~ 89 (286)
+++..+-+. |....++..........+.+|++|+.++...+. .....+..+++++.-.....++-+|..-.--.-+
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~ 179 (564)
T KOG1990|consen 102 SPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDR--LSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIE 179 (564)
T ss_pred cchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCC--ccchhhhchhhhhcccChhccCCCCChhhhhhHH
Confidence 445556666 788888887888888999999999999876432 2334567777777777666666666553321100
Q ss_pred CCCC---Cc-ceEEEEEEecCCCcccchhHHHHHHHcCCChhhhhhCCCChH
Q psy6037 90 TPPG---PF-TTWQFNFKFDLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPA 137 (286)
Q Consensus 90 ~p~~---~~-~~wqFNF~F~~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~ 137 (286)
.+.. .+ ..-.|++.++.......+..+++..++.+++ ....+|+...
T Consensus 180 ~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k-~~~~rg~~~~ 230 (564)
T KOG1990|consen 180 STLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAK-ILIKRGVLET 230 (564)
T ss_pred HHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHH-HHHHhcchhh
Confidence 0000 01 1122444466666666777777777777777 6677777764
No 70
>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=40.66 E-value=27 Score=29.80 Aligned_cols=30 Identities=27% Similarity=0.284 Sum_probs=27.2
Q ss_pred eccccCHHHHHHHHHHHhhhCCeeeeeccc
Q psy6037 16 EVWARNVQEEFVHIRSLINTYNYIGIDTEF 45 (286)
Q Consensus 16 dVw~~N~~ee~~~I~~~i~~~~fIAiDtEF 45 (286)
-|.+-|++|.++.|.+.-++.-.||||.-.
T Consensus 43 PVHA~NL~e~l~~I~~~~~~~~iIAIDAcL 72 (140)
T TIGR02841 43 PVHAKNLEEKLKIIKKKHPNPFIIAIDACL 72 (140)
T ss_pred CcccccHHHHHHHHHHhCCCCeEEEEECcc
Confidence 388999999999999999999999999765
No 71
>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=40.15 E-value=26 Score=29.73 Aligned_cols=33 Identities=24% Similarity=0.337 Sum_probs=27.1
Q ss_pred HHHHHcCCChhhhhhCC-CChHHHHHHHHhcCcc
Q psy6037 117 DLLQNSGIQFQRHKEEG-IEPADFAELLTTSGVV 149 (286)
Q Consensus 117 ~fL~~~G~DF~k~~~~G-I~~~~F~ell~~SgLv 149 (286)
++.++.||.||.+..-- +|..+|++.|.++|..
T Consensus 15 ~L~~~~GI~Fn~L~titNmPI~RF~~~L~~~g~~ 48 (134)
T PF12345_consen 15 ELKERFGIVFNNLFTITNMPIGRFGSFLERSGNL 48 (134)
T ss_pred HHHHhcCceecchhhhhcCcHHHHHHHHHHccCH
Confidence 34578899999998754 8999999999987744
No 72
>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=40.12 E-value=57 Score=29.04 Aligned_cols=69 Identities=19% Similarity=0.159 Sum_probs=42.0
Q ss_pred cEEEeec-chhHHHHHH-HHhCCCCCCCChHHHHHHHHhhc----CCccchhHHHHhhccc-cccHHHHHhHcCCcc
Q psy6037 155 KWLSFHS-GYDFGYLLK-LLMGTRSLPSEEAEFFELQRLFF----KSIYDVKYLMKSCKNL-KGGLQEVAEQLDLSR 224 (286)
Q Consensus 155 ~Wvtfhg-~yD~gyL~K-~lt~~~~LP~~~~~F~~~l~~~F----P~iYD~K~l~~~~~~l-~ggL~~lA~~L~v~r 224 (286)
.+|+|+| ++|+-||.+ ++..+-++|......-+.. .|. ...+|+-.+.+....+ ..+|..||+.||+++
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 799999776 4443335565433221111 111 1266776665544332 458999999999964
No 73
>KOG4233|consensus
Probab=36.60 E-value=54 Score=25.51 Aligned_cols=41 Identities=29% Similarity=0.485 Sum_probs=30.7
Q ss_pred cCCccEEEeec----------chhHHHHH--HHHhCCCCCCCChHHHHHHHHhhcCC
Q psy6037 151 NDKVKWLSFHS----------GYDFGYLL--KLLMGTRSLPSEEAEFFELQRLFFKS 195 (286)
Q Consensus 151 ~~~v~Wvtfhg----------~yD~gyL~--K~lt~~~~LP~~~~~F~~~l~~~FP~ 195 (286)
+++|+|++--| |+|-+|.+ +-| -|-.+++.|.++|+.-+..
T Consensus 18 eK~V~~laGIg~~lg~~L~~~GfdkAYvllGQfL----llkKdE~lF~~Wlk~~~ga 70 (90)
T KOG4233|consen 18 EKDVTWLAGIGETLGIKLVDAGFDKAYVLLGQFL----LLKKDEDLFQEWLKETCGA 70 (90)
T ss_pred CCcceeeccccHHhhhhHHhccccHHHHHHHHHH----HhcccHHHHHHHHHHHcCc
Confidence 67999998644 78999943 222 3567899999999988763
No 74
>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=31.89 E-value=1.8e+02 Score=22.88 Aligned_cols=53 Identities=15% Similarity=0.246 Sum_probs=31.6
Q ss_pred cCCccEEEeecchhHHHHHHHHhCCCCCCCChHHHHHHHHhhcCCccchhHHHHhhcc-c-cccHHHHHhHc
Q psy6037 151 NDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKN-L-KGGLQEVAEQL 220 (286)
Q Consensus 151 ~~~v~Wvtfhg~yD~gyL~K~lt~~~~LP~~~~~F~~~l~~~FP~iYD~K~l~~~~~~-l-~ggL~~lA~~L 220 (286)
+++++-|.++..+|+..|.+.. . .+| +.++||..++..... . ..+|+.+++.+
T Consensus 52 ~~~~~~v~~~~k~d~~~L~~~~--~-~~~--------------~~~~D~~~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 52 DEDITKVGHDAKFDLVVLARDG--I-ELP--------------GNIFDTMLAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred CCCCcEEeccHHHHHHHHHHCC--C-CCC--------------CCcccHHHHHHHhCCCCCcCCHHHHHHHH
Confidence 4456667777677777765421 1 222 256788777766542 2 34788888774
No 75
>PF08228 RNase_P_pop3: RNase P subunit Pop3; InterPro: IPR013241 This family of fungal proteins form a subunit of RNase P, the ribonucleoprotein enzyme that cleaves the leader sequence of precursor tRNAs to generate mature tRNAs. The structure of Pop3 has been assigned the L7Ae/L30e fold []. This RNA-binding fold is also present in human RNase P subunit Rpp38, raising the possibility that Pop3p and Rpp38 are functional homologues.
Probab=26.42 E-value=53 Score=28.52 Aligned_cols=30 Identities=30% Similarity=0.521 Sum_probs=23.5
Q ss_pred cccHHHHHhHcCCccCC----CCcccchhhHHHH
Q psy6037 210 KGGLQEVAEQLDLSRIG----PQHQAGSDSLLTG 239 (286)
Q Consensus 210 ~ggL~~lA~~L~v~r~g----~~HqAGsDSllT~ 239 (286)
+|+.++||+.||++|+| ..+..|.++|...
T Consensus 110 kgs~~rLs~aLgi~r~g~l~v~~~~~~~~~L~~~ 143 (158)
T PF08228_consen 110 KGSEARLSEALGIPRVGILAVRADAPGAKSLVDL 143 (158)
T ss_pred hhHHHHHHHHhCCCCccEEEEecCCcccHHHHHH
Confidence 57899999999999998 3666667676543
No 76
>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=26.32 E-value=59 Score=28.42 Aligned_cols=31 Identities=26% Similarity=0.214 Sum_probs=27.6
Q ss_pred eccccCHHHHHHHHHHHhhhCCeeeeecccc
Q psy6037 16 EVWARNVQEEFVHIRSLINTYNYIGIDTEFP 46 (286)
Q Consensus 16 dVw~~N~~ee~~~I~~~i~~~~fIAiDtEFp 46 (286)
-|.+-|++|.++.|.+.-++.-.||||.-+.
T Consensus 67 PVHA~NL~e~l~~I~~~~~~~~IIAIDAcLG 97 (163)
T PF06866_consen 67 PVHALNLEETLNEIKKKHPNPFIIAIDACLG 97 (163)
T ss_pred CcchhhHHHHHHHHHHHCCCCeEEEEECCCC
Confidence 3889999999999999888888999998774
No 77
>PF08870 DUF1832: Domain of unknown function (DUF1832); InterPro: IPR014969 This entry describes the DndE protein encoded by an operon associated with a sulphur-containing modification to DNA []. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is a putative carboxylase homologous to NCAIR synthetases.
Probab=25.64 E-value=1.3e+02 Score=24.59 Aligned_cols=36 Identities=31% Similarity=0.534 Sum_probs=24.4
Q ss_pred CCccEEEeecchhHHH--HHHHHhCCCCCCCChHHHHHHHH
Q psy6037 152 DKVKWLSFHSGYDFGY--LLKLLMGTRSLPSEEAEFFELQR 190 (286)
Q Consensus 152 ~~v~Wvtfhg~yD~gy--L~K~lt~~~~LP~~~~~F~~~l~ 190 (286)
.++.|-||-|.|+--| |+|...|. ++ +.++|.+.++
T Consensus 53 ~e~~~~t~~Ge~~~~~~~ll~q~~g~-~~--d~~~l~~~~~ 90 (113)
T PF08870_consen 53 LELNWKTFTGEYDDIYEALLKQRYGP-EL--DDEELPKYFK 90 (113)
T ss_pred eEEeeeeecCchHHHHHHHHHHHhCC-CC--CHHHHHHHHH
Confidence 3568999999999888 66666653 44 5566654443
No 78
>PF04386 SspB: Stringent starvation protein B; InterPro: IPR007481 Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB is a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA []. However, more recent work has cast doubt on the importance of SspB in wild-type cells []. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates [].; PDB: 2NYS_A 2QAZ_D 2QAS_A 1OX9_A 1OX8_A 1YFN_C 1TWB_B 1OU9_C 1OU8_B 1ZSZ_B ....
Probab=21.90 E-value=62 Score=27.73 Aligned_cols=16 Identities=44% Similarity=0.872 Sum_probs=12.1
Q ss_pred hCCeeeeecccccccc
Q psy6037 35 TYNYIGIDTEFPGVVA 50 (286)
Q Consensus 35 ~~~fIAiDtEFpGv~~ 50 (286)
..+||.+||..||+..
T Consensus 31 ~tpyI~v~t~~pgV~v 46 (155)
T PF04386_consen 31 HTPYITVDTDYPGVQV 46 (155)
T ss_dssp --EEEEEETTSTT-BS
T ss_pred CeEEEEEEeCCCCCCC
Confidence 3599999999999765
No 79
>KOG0638|consensus
Probab=21.64 E-value=25 Score=34.06 Aligned_cols=72 Identities=25% Similarity=0.312 Sum_probs=47.8
Q ss_pred hHHHHHHHcCCChhhhhhCCCChH---HHHHHHHhcCccccCCccEEEe-ecchh---HHHHHHHHhCCCCCCCChHHHH
Q psy6037 114 DSIDLLQNSGIQFQRHKEEGIEPA---DFAELLTTSGVVLNDKVKWLSF-HSGYD---FGYLLKLLMGTRSLPSEEAEFF 186 (286)
Q Consensus 114 ~SI~fL~~~G~DF~k~~~~GI~~~---~F~ell~~SgLv~~~~v~Wvtf-hg~yD---~gyL~K~lt~~~~LP~~~~~F~ 186 (286)
++|+-|+..|.+|- -||.. ...|.|..|.++..++++-+.= +=..| =|||++++|. ||-+...=|+
T Consensus 275 ~Ai~~lr~rG~eFL-----s~Ps~YYqnl~erl~~~~~~vked~~~l~el~ILvD~De~gyLLQIFTK--plqdrpTlFl 347 (381)
T KOG0638|consen 275 EAIRGLRARGGEFL-----SPPSTYYQNLKERLSTSIRKVKEDIKLLEELGILVDFDENGYLLQIFTK--PLQDRPTLFL 347 (381)
T ss_pred HHHHHHHhcCCccc-----cCCHHHHHhHHHHhhhhhhhhhccHHHHHHcCeEEecCCCcEEeeeecc--ccCCCchHHH
Confidence 67889999999996 36643 4455555444444333322211 11223 3899999997 8999999999
Q ss_pred HHHHhh
Q psy6037 187 ELQRLF 192 (286)
Q Consensus 187 ~~l~~~ 192 (286)
+.++..
T Consensus 348 EiIQR~ 353 (381)
T KOG0638|consen 348 EIIQRQ 353 (381)
T ss_pred HHHHHh
Confidence 998764
No 80
>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=20.95 E-value=2.9e+02 Score=25.82 Aligned_cols=68 Identities=7% Similarity=0.034 Sum_probs=44.7
Q ss_pred eccccCHHHHHHHHHHHhhhC---Ceeeeec------cccccccccCCCCCCChHHHHHHHHhhhhcccceeeeeeeec
Q psy6037 16 EVWARNVQEEFVHIRSLINTY---NYIGIDT------EFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFD 85 (286)
Q Consensus 16 dVw~~N~~ee~~~I~~~i~~~---~fIAiDt------EFpGv~~~p~~~~~~t~e~~Y~~lr~nVd~l~iIQlGitl~~ 85 (286)
+|++...++.+..+.+.+... -||++|. ..||+.....+- -+..+-.+.++.-....+++-+.|+=++
T Consensus 196 ~i~~~g~~~v~~~~~~~l~~~~~~vyvS~DiDvlDps~aPgv~tp~pgG--l~~~e~~~~l~~i~~~~~v~g~DivE~~ 272 (300)
T TIGR01229 196 EIDELGIGKVVEETLEYLKAEDGPIHLSLDVDGLDPSLAPATGTPVVGG--LTFREGLLIMEMLYETGLLTALDVVEVN 272 (300)
T ss_pred HHhhhhHHHHHHHHHHHHhcCCCeEEEEEeccccCcccCCCCCCCCCCC--CCHHHHHHHHHHHHhcCCEEEEEEEEEC
Confidence 455666777788888888654 4999985 567876533322 2456777778777666677766666444
No 81
>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=20.81 E-value=90 Score=26.15 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=17.1
Q ss_pred HHHHHHhh-hCCeeeeecccccc
Q psy6037 27 VHIRSLIN-TYNYIGIDTEFPGV 48 (286)
Q Consensus 27 ~~I~~~i~-~~~fIAiDtEFpGv 48 (286)
..+.+.+. +.+.|++|||+...
T Consensus 3 ~~~~~~l~~~~~~ig~D~E~~~~ 25 (161)
T cd06129 3 SSLCEDLSMDGDVIAFDMEWPPG 25 (161)
T ss_pred HHHHHHHhcCCCEEEEECCccCC
Confidence 45556666 99999999999754
Done!