Query 025183
Match_columns 256
No_of_seqs 157 out of 462
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 03:24:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025183.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025183hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0304 mRNA deadenylase subun 100.0 6.7E-84 1.4E-88 558.4 16.5 213 15-234 1-239 (239)
2 COG5228 POP2 mRNA deadenylase 100.0 4.2E-74 9.2E-79 498.7 12.1 241 3-253 7-271 (299)
3 PF04857 CAF1: CAF1 family rib 100.0 3.9E-55 8.4E-60 394.8 17.5 205 17-229 1-262 (262)
4 KOG1990 Poly(A)-specific exori 99.2 4.7E-12 1E-16 125.7 1.8 209 21-235 1-364 (564)
5 PRK07942 DNA polymerase III su 98.8 1.1E-07 2.3E-12 84.8 14.3 153 36-235 4-181 (232)
6 smart00479 EXOIII exonuclease 98.8 3.9E-07 8.4E-12 75.2 15.0 146 39-235 1-168 (169)
7 PRK09145 DNA polymerase III su 98.7 4E-07 8.8E-12 79.0 14.0 152 30-232 21-199 (202)
8 cd06131 DNA_pol_III_epsilon_Ec 98.7 6.9E-07 1.5E-11 74.5 14.0 147 40-230 1-166 (167)
9 cd06134 RNaseT DEDDh 3'-5' exo 98.6 1.2E-06 2.5E-11 75.6 13.5 87 137-233 102-188 (189)
10 PRK05168 ribonuclease T; Provi 98.5 3.6E-06 7.8E-11 73.9 14.8 166 28-234 7-201 (211)
11 PRK06063 DNA polymerase III su 98.5 3.2E-06 7E-11 78.6 14.6 150 37-235 14-180 (313)
12 cd06133 ERI-1_3'hExo_like DEDD 98.5 3.5E-06 7.5E-11 70.3 13.4 150 40-230 1-175 (176)
13 PRK06310 DNA polymerase III su 98.5 2.9E-06 6.2E-11 76.5 13.7 154 34-234 3-174 (250)
14 PRK05711 DNA polymerase III su 98.5 3.4E-06 7.3E-11 75.8 13.9 152 38-233 4-175 (240)
15 PRK07748 sporulation inhibitor 98.4 5.7E-06 1.2E-10 72.2 13.2 80 140-233 96-179 (207)
16 PRK07740 hypothetical protein; 98.4 8E-06 1.7E-10 73.4 13.3 85 137-235 141-227 (244)
17 TIGR00573 dnaq exonuclease, DN 98.4 1.1E-05 2.3E-10 71.1 13.8 153 35-234 4-177 (217)
18 cd06130 DNA_pol_III_epsilon_li 98.3 1E-05 2.3E-10 66.2 12.2 77 137-228 77-155 (156)
19 PRK07247 DNA polymerase III su 98.3 9.1E-06 2E-10 70.8 11.4 81 137-233 84-168 (195)
20 PRK09146 DNA polymerase III su 98.3 2.1E-05 4.7E-10 70.5 13.9 84 137-237 129-230 (239)
21 TIGR01406 dnaQ_proteo DNA poly 98.3 2.3E-05 4.9E-10 69.6 13.9 151 39-233 1-171 (225)
22 PRK06807 DNA polymerase III su 98.3 2.1E-05 4.6E-10 73.3 13.8 146 38-234 8-172 (313)
23 cd06127 DEDDh DEDDh 3'-5' exon 98.2 9.4E-06 2E-10 65.2 9.7 138 41-228 1-159 (159)
24 PRK07883 hypothetical protein; 98.2 2.9E-05 6.3E-10 77.6 13.5 156 31-235 8-183 (557)
25 TIGR01298 RNaseT ribonuclease 98.1 6.6E-05 1.4E-09 65.4 13.7 89 137-235 105-193 (200)
26 PRK06195 DNA polymerase III su 98.1 4.9E-05 1.1E-09 70.5 13.4 82 137-235 80-165 (309)
27 PRK08517 DNA polymerase III su 98.1 0.00011 2.5E-09 66.6 14.5 83 138-234 148-231 (257)
28 PRK07246 bifunctional ATP-depe 98.1 6.7E-05 1.4E-09 78.1 14.5 82 137-235 86-171 (820)
29 PRK08074 bifunctional ATP-depe 98.1 6.5E-05 1.4E-09 79.1 14.6 150 38-235 3-170 (928)
30 PRK06722 exonuclease; Provisio 98.0 0.00013 2.9E-09 67.1 14.2 81 139-231 92-178 (281)
31 TIGR01407 dinG_rel DnaQ family 98.0 0.00011 2.3E-09 76.8 14.5 85 137-235 80-166 (850)
32 cd06136 TREX1_2 DEDDh 3'-5' ex 98.0 9.7E-05 2.1E-09 63.0 11.8 149 40-229 1-176 (177)
33 PRK07983 exodeoxyribonuclease 98.0 0.00021 4.6E-09 63.3 13.5 77 136-233 73-153 (219)
34 PRK06309 DNA polymerase III su 97.9 0.00042 9E-09 61.7 13.9 84 137-234 80-166 (232)
35 TIGR01405 polC_Gram_pos DNA po 97.9 0.00027 5.7E-09 76.3 14.7 151 36-235 188-356 (1213)
36 PRK05601 DNA polymerase III su 97.8 0.00041 8.9E-09 66.1 13.4 166 34-232 42-247 (377)
37 PF00929 RNase_T: Exonuclease; 97.8 3.2E-05 6.9E-10 62.1 4.5 143 41-227 1-164 (164)
38 PTZ00315 2'-phosphotransferase 97.7 0.0014 3.1E-08 65.6 15.6 152 39-233 57-254 (582)
39 PRK11779 sbcB exonuclease I; P 97.6 0.0012 2.7E-08 64.8 13.9 160 37-233 5-197 (476)
40 cd06144 REX4_like DEDDh 3'-5' 97.5 0.00026 5.6E-09 58.8 6.6 70 138-227 78-151 (152)
41 cd06138 ExoI_N N-terminal DEDD 97.5 0.0015 3.2E-08 55.9 11.3 146 42-226 2-181 (183)
42 PF01612 DNA_pol_A_exo1: 3'-5' 97.4 0.0039 8.5E-08 51.3 12.0 150 25-234 7-175 (176)
43 PRK00448 polC DNA polymerase I 97.3 0.0032 7E-08 69.1 13.7 152 34-235 415-585 (1437)
44 PRK09182 DNA polymerase III su 97.3 0.0056 1.2E-07 56.7 13.2 142 39-232 38-199 (294)
45 COG0847 DnaQ DNA polymerase II 97.1 0.0097 2.1E-07 52.5 11.9 148 38-233 13-181 (243)
46 cd06149 ISG20 DEDDh 3'-5' exon 96.8 0.0049 1.1E-07 51.6 7.6 71 137-227 77-156 (157)
47 PRK05755 DNA polymerase I; Pro 96.5 0.062 1.3E-06 56.7 14.4 86 133-235 366-470 (880)
48 PRK10829 ribonuclease D; Provi 96.5 0.03 6.5E-07 53.6 11.0 147 25-235 9-171 (373)
49 COG0349 Rnd Ribonuclease D [Tr 96.4 0.014 3E-07 55.5 8.1 144 26-235 5-167 (361)
50 cd06141 WRN_exo DEDDy 3'-5' ex 96.3 0.053 1.2E-06 45.1 10.5 146 25-231 4-169 (170)
51 PRK05359 oligoribonuclease; Pr 96.1 0.098 2.1E-06 44.9 11.1 77 140-236 100-177 (181)
52 cd06146 mut-7_like_exo DEDDy 3 96.0 0.13 2.7E-06 44.5 11.6 156 25-232 7-193 (193)
53 cd06129 RNaseD_like DEDDy 3'-5 95.6 0.12 2.7E-06 42.9 9.6 142 29-232 3-161 (161)
54 cd06135 Orn DEDDh 3'-5' exonuc 95.4 0.18 3.8E-06 42.7 10.1 76 139-233 95-171 (173)
55 TIGR01388 rnd ribonuclease D. 95.2 0.36 7.8E-06 46.0 12.3 147 25-235 5-167 (367)
56 cd06137 DEDDh_RNase DEDDh 3'-5 94.3 0.1 2.2E-06 43.7 5.5 69 138-227 85-160 (161)
57 cd06145 REX1_like DEDDh 3'-5' 93.5 0.21 4.5E-06 41.4 5.9 70 137-227 76-149 (150)
58 PF13482 RNase_H_2: RNase_H su 92.6 0.056 1.2E-06 44.6 1.3 75 137-227 57-133 (164)
59 cd06148 Egl_like_exo DEDDy 3'- 90.1 4.5 9.7E-05 34.8 10.6 87 132-235 60-178 (197)
60 PF10108 DNA_pol_B_exo2: Predi 87.7 2 4.3E-05 38.1 6.9 93 137-233 52-172 (209)
61 cd06139 DNA_polA_I_Ecoli_like_ 86.2 2 4.4E-05 35.7 5.9 84 135-235 65-171 (193)
62 COG2176 PolC DNA polymerase II 85.9 1.1 2.3E-05 48.7 4.8 87 137-237 501-589 (1444)
63 KOG2249 3'-5' exonuclease [Rep 84.3 2.9 6.4E-05 38.4 6.2 54 180-234 208-266 (280)
64 cd05782 DNA_polB_like1_exo Unc 83.5 2.9 6.3E-05 36.6 5.8 69 139-208 95-170 (208)
65 COG3359 Predicted exonuclease 77.2 5.8 0.00013 36.3 5.6 76 139-229 158-237 (278)
66 cd00007 35EXOc 3'-5' exonuclea 66.5 27 0.00059 27.2 6.8 55 133-204 50-106 (155)
67 COG5228 POP2 mRNA deadenylase 63.7 6.5 0.00014 35.5 2.8 100 142-254 196-298 (299)
68 cd05785 DNA_polB_like2_exo Unc 56.7 11 0.00024 32.9 3.1 70 139-208 76-169 (207)
69 cd06125 DnaQ_like_exo DnaQ-lik 56.7 18 0.00038 27.5 3.9 21 138-158 45-65 (96)
70 COG5018 KapD Inhibitor of the 55.7 78 0.0017 27.6 7.9 100 120-233 83-184 (210)
71 TIGR02841 spore_YyaC putative 55.3 12 0.00026 31.2 2.9 30 18-47 43-72 (140)
72 KOG2207 Predicted 3'-5' exonuc 48.7 84 0.0018 32.2 8.0 173 13-235 389-586 (617)
73 cd05781 DNA_polB_B3_exo DEDDy 45.0 28 0.00061 29.8 3.7 67 139-207 66-144 (188)
74 PF06866 DUF1256: Protein of u 40.1 26 0.00057 29.9 2.7 31 18-48 67-97 (163)
75 smart00474 35EXOc 3'-5' exonuc 39.8 1.9E+02 0.004 22.8 7.9 82 134-233 72-170 (172)
76 cd05780 DNA_polB_Kod1_like_exo 36.7 36 0.00078 29.1 3.1 69 139-208 74-156 (195)
77 KOG4013 Predicted Cu2+ homeost 36.6 19 0.00041 32.0 1.3 85 122-208 85-202 (255)
78 PF04297 UPF0122: Putative hel 32.6 26 0.00055 27.6 1.3 25 195-225 34-58 (101)
79 cd05160 DEDDy_DNA_polB_exo DED 30.9 52 0.0011 27.8 3.1 69 139-208 81-162 (199)
80 PF11959 DUF3473: Domain of un 29.2 79 0.0017 25.8 3.8 30 16-45 99-128 (133)
81 KOG4793 Three prime repair exo 29.0 46 0.00099 31.0 2.5 42 193-235 251-292 (318)
82 PF07176 DUF1400: Alpha/beta h 23.5 3.9E+02 0.0085 21.5 8.2 93 107-224 5-99 (127)
83 TIGR01229 rocF_arginase argina 22.6 2.4E+02 0.0053 25.8 6.2 68 18-88 196-272 (300)
84 PF13404 HTH_AsnC-type: AsnC-t 22.5 71 0.0015 20.8 1.9 28 181-208 4-31 (42)
85 PF00550 PP-binding: Phosphopa 22.0 1.8E+02 0.0039 19.5 4.1 37 198-234 5-45 (67)
86 COG5606 Uncharacterized conser 22.0 87 0.0019 24.2 2.5 31 198-228 45-81 (91)
87 KOG4355 Predicted Fe-S oxidore 21.6 44 0.00095 32.8 1.0 30 196-225 284-316 (547)
88 COG3155 ElbB Uncharacterized p 20.8 3.4E+02 0.0075 23.6 6.1 85 137-229 33-126 (217)
89 PF02954 HTH_8: Bacterial regu 20.8 72 0.0016 20.4 1.6 24 185-208 9-32 (42)
90 PF06056 Terminase_5: Putative 20.2 84 0.0018 22.0 2.0 26 182-208 1-27 (58)
No 1
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=6.7e-84 Score=558.36 Aligned_cols=213 Identities=56% Similarity=0.924 Sum_probs=205.2
Q ss_pred eEEeccccCHHHHHHHHHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCC
Q 025183 15 LIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLP 94 (256)
Q Consensus 15 ~v~dVw~~N~~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p 94 (256)
.|||||++|+++||.+||++|++||||||||||||++.+|.+.|+++. +++||.||+|||.+++||+|||++|++|++|
T Consensus 1 ~ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~~~f~s~~-d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p 79 (239)
T KOG0304|consen 1 FIREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPIGTFRSSD-DYHYQTLKCNVDNLKLIQLGLTLSDEKGNLP 79 (239)
T ss_pred ChhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecCccccCCh-HHHHHHHHhchhhhhhhheeeeeeccCCCCC
Confidence 479999999999999999999999999999999999999999998887 9999999999999999999999999999999
Q ss_pred CCCCCCCeeeEEEeeeecccccccCchhHHHHHHHcC------------------------ccccCCccEEeecchhhHH
Q 025183 95 DLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQG------------------------LVLNKDVTWVTFHSAYDFG 150 (256)
Q Consensus 95 ~~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~~L~~~G------------------------lv~~~~v~Wvtfhg~yDf~ 150 (256)
..| ..+|||||++|++.+|+++++||+||+++| ++++++|+|||||||||||
T Consensus 80 ~~g----~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfg 155 (239)
T KOG0304|consen 80 DCG----TDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFG 155 (239)
T ss_pred CCC----CceeEEecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHH
Confidence 664 469999999999999999999999999999 6889999999999999999
Q ss_pred HHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhcc--CCCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHH
Q 025183 151 YLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC--LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFL 228 (256)
Q Consensus 151 yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~--l~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~ 228 (256)
||+|+||+++||++.++|.+.++.+||. +||+|||++.|.+ +++||++||+.|+++| +|++||||||||||+++|+
T Consensus 156 YLlK~Lt~~~LP~~~~eF~~~v~~~fp~-vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~R-vG~~HqAGSDSlLT~~~F~ 233 (239)
T KOG0304|consen 156 YLLKILTGKPLPETEEEFFEIVRQLFPF-VYDVKYLMKFCEGLSLKGGLQRLADLLGLKR-VGIAHQAGSDSLLTARVFF 233 (239)
T ss_pred HHHHHHcCCCCcchHHHHHHHHHHHcch-hhhHHHHHHhhhhhhhhcCHHHHHHHhCCCe-eecccccCcHHHHHHHHHH
Confidence 9999999999999999999999999999 9999999999965 7999999999999999 9999999999999999999
Q ss_pred HHHHhh
Q 025183 229 KIKDKH 234 (256)
Q Consensus 229 kl~~~~ 234 (256)
||++.|
T Consensus 234 kl~~~f 239 (239)
T KOG0304|consen 234 KLKELF 239 (239)
T ss_pred HHHhcC
Confidence 999864
No 2
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=4.2e-74 Score=498.67 Aligned_cols=241 Identities=42% Similarity=0.691 Sum_probs=221.2
Q ss_pred CCCCCCCCCCCceEEeccccCHHHHHHHHHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeee
Q 025183 3 DVPPPQPPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQI 82 (256)
Q Consensus 3 ~~~~~~~~~~~~~v~dVw~~N~~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQl 82 (256)
+|+.-.++..-..|||||++|+..||..|+++|.+|++|+|||||||+++||.|.|+++. +++||.||+|||.++|||+
T Consensus 7 ~p~i~~dg~~~~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPiG~FkSs~-dyhYQtlraNVD~LkiIQl 85 (299)
T COG5228 7 MPPIFLDGPNYLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSV-DYHYQTLRANVDFLKIIQL 85 (299)
T ss_pred CCCccCCCcchHHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceeecccccccccc-hHHHHHHhcccchhhhhhe
Confidence 344334445567799999999999999999999999999999999999999999999998 9999999999999999999
Q ss_pred eeeeecCCCCCCCCCCCCCeeeEEEeeeecccccccCchhHHHHHHHcC------------------------ccccCCc
Q 025183 83 GLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQG------------------------LVLNKDV 138 (256)
Q Consensus 83 Glt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~~L~~~G------------------------lv~~~~v 138 (256)
||+++|++||.|.+ .+||||||. |++.+||++++||++|+++| ||+.++|
T Consensus 86 GlsLSDe~GN~P~~-----~sTWQFNF~-F~l~~dmya~ESieLL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~V 159 (299)
T COG5228 86 GLSLSDENGNKPNG-----PSTWQFNFE-FDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESV 159 (299)
T ss_pred eeeeccccCCCCCC-----CceeEEEEE-ecchhhhcchHHHHHHHHcCCChhhHhhcCCCHHHHHHHHhccCceeccce
Confidence 99999999999953 799999999 99999999999999999999 7889999
Q ss_pred cEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccCCCcHHHHHHHcCCcccCCCCCcchh
Q 025183 139 TWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGS 218 (256)
Q Consensus 139 ~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l~~gL~~vA~~L~v~r~~g~~hqAGs 218 (256)
||||||++||||||+|+||+.|||+..++|+++|++|||+ +||+||+.+.....+.|||+++..|++.| .|++|||||
T Consensus 160 tWitfHsaYDfgyLikilt~~plP~~~EdFy~~l~~yfP~-fYDik~v~ks~~~~~KglQei~ndlql~r-~g~QhQags 237 (299)
T COG5228 160 TWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPN-FYDIKLVYKSVLNNSKGLQEIKNDLQLQR-SGQQHQAGS 237 (299)
T ss_pred EEEEeecchhHHHHHHHHhcCCCCccHHHHHHHHHHHCcc-ccchHHHHHhhhhhhhHHHHhcCcHhhhc-cchhhhccc
Confidence 9999999999999999999999999999999999999999 99999999998888999999999999999 999999999
Q ss_pred hHHHHHHHHHHHHHhhCCCchhhhcccceEecCCC
Q 025183 219 DSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLEL 253 (256)
Q Consensus 219 dsllT~~~F~kl~~~~~~~~~~~~~~~g~l~Gl~~ 253 (256)
|||+|++.|++.|.++|..+++ ...-.+|||++.
T Consensus 238 daLlTa~~ff~~R~~~F~~sig-~~ll~~L~g~~~ 271 (299)
T COG5228 238 DALLTADEFFLPRFSIFTTSIG-QSLLMLLSGCQL 271 (299)
T ss_pred hhhhhhHHhcchhhheeccccc-HHHHHHHhcccc
Confidence 9999999999999999866543 344445555543
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=3.9e-55 Score=394.80 Aligned_cols=205 Identities=34% Similarity=0.588 Sum_probs=179.9
Q ss_pred EeccccCHHHHHHHHHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeee-cCCCCCCC
Q 025183 17 REVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLS-DEEGNLPD 95 (256)
Q Consensus 17 ~dVw~~N~~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~-~~~g~~p~ 95 (256)
+|||++||+++++.|+++|++|+|||||+||||+..++......+. ++||+++|.||+.+.+||+|||+| +++++.|.
T Consensus 1 m~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~~~~~t~-~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~ 79 (262)
T PF04857_consen 1 MEVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPRSRFDTP-EERYEKLRANVETFQIIQFGLTLFHDEDGNIPS 79 (262)
T ss_dssp EEE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-SHCSSHH-HHHHHHHHHHHTTBEEEEEEEEEETTTTSEEEC
T ss_pred CcccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCccccccH-HHHHHHHHHhhcccccceeeEEEeecccccCCc
Confidence 6999999999999999999999999999999999999875445554 999999999999999999999999 78888775
Q ss_pred CCCCCCeeeEEEeeeecccccccCchhHHHHHHHcC------------------------------cc---ccCCccEEe
Q 025183 96 LGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQG------------------------------LV---LNKDVTWVT 142 (256)
Q Consensus 96 ~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~~L~~~G------------------------------lv---~~~~v~Wvt 142 (256)
.+.+|+|||+.|+..++.++++||+||+++| ++ .+.+++||+
T Consensus 80 -----~~~~~~~nf~~f~~~~~~~~~~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vg 154 (262)
T PF04857_consen 80 -----SYNVWPFNFYLFPLDRDFSQASSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVG 154 (262)
T ss_dssp -----CEEEEEEEBSTTSTTTCEEEHHHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEE
T ss_pred -----eeEEEEeeeeccccccceecchhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEE
Confidence 3789999999999999988999999999999 11 134689999
Q ss_pred ecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccCCCcHHHHHHHcCCcc--------------
Q 025183 143 FHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVER-------------- 208 (256)
Q Consensus 143 fhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l~~gL~~vA~~L~v~r-------------- 208 (256)
|||+||++||++.++| +||+|+++|.+.++.+||. |||||||++.+....++|+.|++.|++.|
T Consensus 155 hn~~~Dl~~l~~~f~~-~LP~t~~eF~~~~~~~FP~-i~DtK~la~~~~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~ 232 (262)
T PF04857_consen 155 HNGLYDLMYLYKKFIG-PLPETLEEFKELLRELFPR-IYDTKYLAEECPGKSTSLQELAEELGIRRNPSSISSPEGFPSY 232 (262)
T ss_dssp SSTHHHHHHHHHHHTT-S--SSHHHHHHHHHHHSSS-EEEHHHHHTSTTTS-SSHHHHHHHTTSTT----EEE-TTS---
T ss_pred eChHhHHHHHHHHhcC-CCCCCHHHHHHHHHHHCcc-cccHHHHHHhccccccCHHHHHHHhCCCccccccccccccccc
Confidence 9999999999999998 9999999999999999999 99999999999877889999999999987
Q ss_pred --------cCCC-CCcchhhHHHHHHHHHH
Q 025183 209 --------VVGK-SHQAGSDSLLTLHAFLK 229 (256)
Q Consensus 209 --------~~g~-~hqAGsdsllT~~~F~k 229 (256)
..|. .|+||+||++|+.||.|
T Consensus 233 ~~~~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 233 DEEKNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp ----------SS-TTSHHHHHHHHHHHHHH
T ss_pred cccccccccCCCCCCCcchHHHHHHHHHcC
Confidence 2455 99999999999999986
No 4
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.19 E-value=4.7e-12 Score=125.73 Aligned_cols=209 Identities=20% Similarity=0.209 Sum_probs=156.3
Q ss_pred ccCHHHHHHHHHHHhhcCCeeEEeeccccccccCCC--CCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCC-C
Q 025183 21 EFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDS--NIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDL-G 97 (256)
Q Consensus 21 ~~N~~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~--~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~-~ 97 (256)
+.|++. +.+++..|+.+.|+++|.|++|+...+.+ .-.++. +.+|+++|.|+..+.++|+|+|.|.+++..... .
T Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~ 78 (564)
T KOG1990|consen 1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKAGSTFDTV-EAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMS 78 (564)
T ss_pred CCcccc-hhHHHhhcCHHHHHHHhhhhccceecccccccchhhh-HHHHHHHHhhhhhheeeccccchhHHHhhhHhhcc
Confidence 468999 99999999999999999999999888742 222343 999999999999999999999999987764322 1
Q ss_pred CCCCeeeEEEeeeecccccccCchhHHHHHHHc--C--------------------------------------------
Q 025183 98 SGSTYYIWEFNFKDFDIARHAHALDSVELLKRQ--G-------------------------------------------- 131 (256)
Q Consensus 98 ~~~~~~~wqFNF~~F~~~~d~~~~~Si~~L~~~--G-------------------------------------------- 131 (256)
++++..+|..-+. ....+.+|...++.++.++ +
T Consensus 79 ~~~n~~~~~~g~~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i 157 (564)
T KOG1990|consen 79 TGGNFVVWSRGDS-ISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKI 157 (564)
T ss_pred CCCceeeeecCcc-ccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhh
Confidence 1224566765443 3333678888888888888 3
Q ss_pred --------------------------------------------------------------------------------
Q 025183 132 -------------------------------------------------------------------------------- 131 (256)
Q Consensus 132 -------------------------------------------------------------------------------- 131 (256)
T Consensus 158 ~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~ 237 (564)
T KOG1990|consen 158 PDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMAD 237 (564)
T ss_pred hcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHH
Confidence
Q ss_pred -c--cccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhc--c--CCCcHHHHHHH-
Q 025183 132 -L--VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCT--C--LYGGLDRVCKA- 203 (256)
Q Consensus 132 -l--v~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~--~--l~~gL~~vA~~- 203 (256)
+ +......-|.+++.+|+.|+.|-+.+ +||+++++|... ...||. ++|++.++...+ . +.+.+.+.+..
T Consensus 238 ~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~-~~~fp~-~~~~~~~~~~~~~~~~~~~~t~~e~~~~~ 314 (564)
T KOG1990|consen 238 ELQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDS-SSMFPN-IEDTKRLAKLSEYQKLNLKATLLELARAK 314 (564)
T ss_pred HHHHHHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhh-hhhhhh-hHHHHHhhccccccchhhhhhHHHHHHHh
Confidence 2 22334455788899999999999998 999999999999 999999 899988887322 2 44444444332
Q ss_pred cCCc----c--------------cCCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 204 LGVE----R--------------VVGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 204 L~v~----r--------------~~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
.... + ..+..|+++++++.++.++.+.-....
T Consensus 315 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 364 (564)
T KOG1990|consen 315 AKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRIL 364 (564)
T ss_pred cccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhh
Confidence 1111 1 134567899999999999998766654
No 5
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=98.82 E-value=1.1e-07 Score=84.78 Aligned_cols=153 Identities=20% Similarity=0.268 Sum_probs=102.9
Q ss_pred hcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecccc
Q 025183 36 DRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIA 115 (256)
Q Consensus 36 ~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~ 115 (256)
.+.+||++|+|-||+... . =.|||+|+..++.+|+.. -.|+.. .+..
T Consensus 4 ~~~~~vv~D~ETTGl~p~-------~---------------d~Iieig~v~v~~~g~~~----------~~~~~l-v~P~ 50 (232)
T PRK07942 4 HPGPLAAFDLETTGVDPE-------T---------------ARIVTAALVVVDADGEVV----------ESREWL-ADPG 50 (232)
T ss_pred ccCcEEEEEeccCCCCCC-------C---------------CeeEEEEEEEEeCCCccc----------cceEEE-ECCC
Confidence 456899999999997311 0 138999999998777542 123333 3332
Q ss_pred cccCchhHH-------HHHHHcCc------------c---ccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHH
Q 025183 116 RHAHALDSV-------ELLKRQGL------------V---LNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVG 173 (256)
Q Consensus 116 ~d~~~~~Si-------~~L~~~Gl------------v---~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~ 173 (256)
. ..++++. +.|+++|. + +.++..+|+||+.||+++|-+.+...-+|.-
T Consensus 51 ~-~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~--------- 120 (232)
T PRK07942 51 V-EIPEEASAVHGITTEYARAHGRPAAEVLAEIADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSL--------- 120 (232)
T ss_pred C-CCCHHHHHHhCCCHHHHHhhCCCHHHHHHHHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCc---------
Confidence 2 2233322 34555551 1 1245578999999999999888753222211
Q ss_pred hhcCCcccchhHHHHhhccC---CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 174 VFFGEKVYDVKHLIRFCTCL---YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 174 ~~Fp~~vyD~K~la~~~~~l---~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
.+..++|+-.|++.+... +.+|+.+++.+|++. ...|.|-+|++.|+++|.+|.+++.
T Consensus 121 --~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~--~~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 121 --VPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRL--DNAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred --cCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCC--CCCCChHHHHHHHHHHHHHHHHHHH
Confidence 222367887777665332 246999999999986 4479999999999999999988764
No 6
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.77 E-value=3.9e-07 Score=75.22 Aligned_cols=146 Identities=21% Similarity=0.243 Sum_probs=97.9
Q ss_pred CeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeeccccccc
Q 025183 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (256)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~ 118 (256)
.||++|+|++|+... .-.|||+|....+.+. ....||.. .... ..
T Consensus 1 ~~v~~D~Ettg~~~~----------------------~~~Iieig~v~~~~~~-----------~~~~f~~~-v~p~-~~ 45 (169)
T smart00479 1 TLVVIDCETTGLDPG----------------------KDEIIEIAAVDVDGGR-----------IIVVFDTY-VKPD-RP 45 (169)
T ss_pred CEEEEEeeCCCCCCC----------------------CCeEEEEEEEEEECCE-----------eEEEEEEE-ECCC-CC
Confidence 489999999997422 1239999998877643 23456766 4432 22
Q ss_pred CchhHHHH-------HHHcC---------c--cccCCccEEeecc-hhhHHHHHHHhcC--CCCCCChHHHHHHHHhhcC
Q 025183 119 HALDSVEL-------LKRQG---------L--VLNKDVTWVTFHS-AYDFGYLVKCLTQ--RVLPEKLSEFVTRVGVFFG 177 (256)
Q Consensus 119 ~~~~Si~~-------L~~~G---------l--v~~~~v~Wvtfhg-~yDf~yL~k~l~~--~~LP~~~~~F~~~l~~~Fp 177 (256)
.++.+.+. |.+ | + .+. +-.+|++|+ .||+.+|.+.+.. .+.|. +
T Consensus 46 i~~~~~~~~Git~~~l~~-~~~~~~~~~~~~~~l~-~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~-------------~ 110 (169)
T smart00479 46 ITDYATEIHGITPEMLDD-APTFEEVLEELLEFLK-GKILVAGNALNFDLRFLKLEHPRLGIKDPP-------------K 110 (169)
T ss_pred CCHHHHHHhCCCHHHHhC-CCCHHHHHHHHHHHhc-CCEEEEeCCHHHhHHHHHHHHHHhCCCCCc-------------C
Confidence 22222221 111 2 0 112 235899999 8999999998753 33331 2
Q ss_pred CcccchhHHHHhhc-cCCCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 178 EKVYDVKHLIRFCT-CLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 178 ~~vyD~K~la~~~~-~l~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
..++|+.-+++... ....+|+.+++.+|++. .+..|-|-.|++.|+++|.+|++..+
T Consensus 111 ~~~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~-~~~~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 111 NPVIDTLKLARALNPGRKYSLKKLAERLGLEV-IGRAHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred CCeeEHHHHHHHHCCCCCCCHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHHHHHHHHhh
Confidence 22678876666542 23678999999999998 78789999999999999999987654
No 7
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.71 E-value=4e-07 Score=78.99 Aligned_cols=152 Identities=18% Similarity=0.236 Sum_probs=93.3
Q ss_pred HHHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEee
Q 025183 30 RIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNF 109 (256)
Q Consensus 30 ~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF 109 (256)
.+.+.....+||++|+|.+|+... .-.|||+|...++.+... ....|.+
T Consensus 21 ~~~~~~~~~~~vviD~ETTGl~~~----------------------~d~IieIgaV~~~~~~~~---------~~~~f~~ 69 (202)
T PRK09145 21 FLFEPPPPDEWVALDCETTGLDPR----------------------RAEIVSIAAVKIRGNRIL---------TSERLEL 69 (202)
T ss_pred HHhcCCCCCCEEEEEeECCCCCCC----------------------CCceEEEEEEEEECCEEe---------ecCceEE
Confidence 334444556999999999997311 013899999888743211 1123444
Q ss_pred eecccccccCchhHHHH-------HHHcCc--------cc--cCCccEEeecchhhHHHHHHHhc---CCCCCCChHHHH
Q 025183 110 KDFDIARHAHALDSVEL-------LKRQGL--------VL--NKDVTWVTFHSAYDFGYLVKCLT---QRVLPEKLSEFV 169 (256)
Q Consensus 110 ~~F~~~~d~~~~~Si~~-------L~~~Gl--------v~--~~~v~Wvtfhg~yDf~yL~k~l~---~~~LP~~~~~F~ 169 (256)
. .+... ...+.+.++ |+ .|. +. -.+-.||+++..||+.+|-+-+. +.++|..
T Consensus 70 ~-i~p~~-~i~~~~~~ihGIt~~~l~-~~~~~~~vl~~~~~~i~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~----- 141 (202)
T PRK09145 70 L-VRPPQ-SLSAESIKIHRLRHQDLE-DGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNP----- 141 (202)
T ss_pred E-ECCCC-CCCHhHhhhcCcCHHHHh-cCCCHHHHHHHHHHHHcCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCC-----
Confidence 4 33322 222333222 22 220 00 12346899998999999987653 4455432
Q ss_pred HHHHhhcCCcccchhHHHHh-----hcc--CCCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHH
Q 025183 170 TRVGVFFGEKVYDVKHLIRF-----CTC--LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKD 232 (256)
Q Consensus 170 ~~l~~~Fp~~vyD~K~la~~-----~~~--l~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~ 232 (256)
.+|+.-+... .+. ..-+|+.+++.+|++. .+ .|.|-+|++.|+++|.+|++
T Consensus 142 ----------~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~-~~-~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 142 ----------LIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPV-LG-RHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred ----------eeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCC-CC-CCCcHHHHHHHHHHHHHHHh
Confidence 4566444321 111 1348999999999987 44 59999999999999999865
No 8
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=98.68 E-value=6.9e-07 Score=74.48 Aligned_cols=147 Identities=23% Similarity=0.277 Sum_probs=94.8
Q ss_pred eeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecccccccC
Q 025183 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAH 119 (256)
Q Consensus 40 fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~ 119 (256)
||++|+|-||+..+ ..-.|||+|....+. +.. ...+|+.. .+.... .
T Consensus 1 ~v~~D~ETTGl~~~---------------------~~~~iieig~v~v~~-~~~---------~~~~~~~~-v~P~~~-i 47 (167)
T cd06131 1 QIVLDTETTGLDPR---------------------EGHRIIEIGCVELIN-RRL---------TGNTFHVY-INPERD-I 47 (167)
T ss_pred CEEEEeeCCCCCCC---------------------CCCeEEEEEEEEEEC-CcE---------eccEEEEE-ECCCCC-C
Confidence 79999999997320 011499999887654 221 12356665 444332 3
Q ss_pred chhHHHH-------HHHcC--------c--cccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccc
Q 025183 120 ALDSVEL-------LKRQG--------L--VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYD 182 (256)
Q Consensus 120 ~~~Si~~-------L~~~G--------l--v~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD 182 (256)
++.+.+. |+..+ + .++ +-.+|.+|+.||..+|-+-+....++.. ...|..++|
T Consensus 48 ~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~l~-~~~lv~hn~~fD~~~l~~~~~~~~~~~~---------~~~~~~~id 117 (167)
T cd06131 48 PEEAFKVHGITDEFLADKPKFAEIADEFLDFIR-GAELVIHNASFDVGFLNAELSLLGLGKK---------IIDFCRVID 117 (167)
T ss_pred CHHHHHHhCCCHHHHhcCCCHHHHHHHHHHHHC-CCeEEEeChHHhHHHHHHHHHHhCCCcc---------cccCCCceE
Confidence 4444322 23222 0 112 3358999999999999887653222211 012444789
Q ss_pred hhHHHHhh-ccCCCcHHHHHHHcCCcccCC-CCCcchhhHHHHHHHHHHH
Q 025183 183 VKHLIRFC-TCLYGGLDRVCKALGVERVVG-KSHQAGSDSLLTLHAFLKI 230 (256)
Q Consensus 183 ~K~la~~~-~~l~~gL~~vA~~L~v~r~~g-~~hqAGsdsllT~~~F~kl 230 (256)
+-.+++.. +....+|+.+++.+|++. .+ ..|.|-+|++.|+++|.+|
T Consensus 118 t~~~~~~~~~~~~~~L~~l~~~~~i~~-~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 118 TLALARKKFPGKPNSLDALCKRFGIDN-SHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred hHHHHHHHcCCCCCCHHHHHHHCCCCC-CCCCCCChHHHHHHHHHHHHHh
Confidence 87777653 334568999999999997 54 5899999999999999987
No 9
>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=98.60 E-value=1.2e-06 Score=75.61 Aligned_cols=87 Identities=22% Similarity=0.316 Sum_probs=64.6
Q ss_pred CccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccCCCcHHHHHHHcCCcccCCCCCcc
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQA 216 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l~~gL~~vA~~L~v~r~~g~~hqA 216 (256)
+-.+|+||..+|++||-+.+....++. ..+-|..++|+..|++.... ...|+.+++.+|++......|.|
T Consensus 102 ~~~lVaHna~FD~~fL~~~~~~~~~~~---------~~~~~~~~lDt~~la~~~~~-~~~L~~l~~~~gi~~~~~~~H~A 171 (189)
T cd06134 102 RAILVGHNAHFDLGFLNAAVARCKIKR---------NPFHPFSTFDTATLAGLAYG-QTVLAKACQAAGIEFDNKEAHSA 171 (189)
T ss_pred CCeEEEecchhhHHHHHHHHHHhCCCC---------CCCCCCcEEEHHHHHHHHhC-CCcHHHHHHHCCCCCCCCCCcCh
Confidence 347999999999999998875322210 01113337899999887532 23699999999998522468999
Q ss_pred hhhHHHHHHHHHHHHHh
Q 025183 217 GSDSLLTLHAFLKIKDK 233 (256)
Q Consensus 217 GsdsllT~~~F~kl~~~ 233 (256)
-+|++.|+++|.+|.++
T Consensus 172 l~DA~ata~lf~~l~~~ 188 (189)
T cd06134 172 LYDTQKTAELFCKIVNR 188 (189)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 99999999999999875
No 10
>PRK05168 ribonuclease T; Provisional
Probab=98.53 E-value=3.6e-06 Score=73.89 Aligned_cols=166 Identities=16% Similarity=0.206 Sum_probs=105.9
Q ss_pred HHHHHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecC--CCCCCCCCCCCCeeeE
Q 025183 28 FERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDE--EGNLPDLGSGSTYYIW 105 (256)
Q Consensus 28 ~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~--~g~~p~~~~~~~~~~w 105 (256)
+..|..-++...||++|+|-+|+.... + .|||+|....+. +|... ...
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~---------d-------------~IieIgaV~v~~d~~g~i~--------~~~ 56 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKT---------D-------------ALLEIAAVTLKMDEQGWLY--------PDE 56 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCC---------C-------------EEEEEeEEEEEecCCCcEe--------ccc
Confidence 456778889999999999999984321 1 299999887754 45421 123
Q ss_pred EEeeeecccc-cccCchhHHHH-------HHHcC----------------cc---ccCCccEEeecchhhHHHHHHHhcC
Q 025183 106 EFNFKDFDIA-RHAHALDSVEL-------LKRQG----------------LV---LNKDVTWVTFHSAYDFGYLVKCLTQ 158 (256)
Q Consensus 106 qFNF~~F~~~-~d~~~~~Si~~-------L~~~G----------------lv---~~~~v~Wvtfhg~yDf~yL~k~l~~ 158 (256)
+|... .+.. ....++.+++. +.+.| .+ ...+..+|++|..||++||-+.+..
T Consensus 57 ~f~~l-v~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r 135 (211)
T PRK05168 57 TLHFH-VEPFEGANLEPEALAFNGIDPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAER 135 (211)
T ss_pred eEEEE-ECCCCCCCCCHHHHhhcCCCchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHH
Confidence 45444 3321 11122222111 11222 00 0124579999999999999887643
Q ss_pred CCCCCChHHHHHHHHhhcCCcccchhHHHHhhccCCCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhh
Q 025183 159 RVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 234 (256)
Q Consensus 159 ~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~ 234 (256)
..+.. ..+.|..++||.-+++...+. ..|+.+++.+|++-.....|.|-+|++.|+++|.+|.+++
T Consensus 136 ~~~~~---------~~~~~~~~iDt~~lar~~~~~-~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 136 AGLKR---------NPFHPFSTFDTATLSGLALGQ-TVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred hCCCC---------CCCCCCcEeeHHHHHHHHcCC-CCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 22210 012343388999888765322 3799999999998511368999999999999999998876
No 11
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.50 E-value=3.2e-06 Score=78.62 Aligned_cols=150 Identities=19% Similarity=0.177 Sum_probs=97.2
Q ss_pred cCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeeccccc
Q 025183 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (256)
Q Consensus 37 ~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~ 116 (256)
..+||++|+|-+|+... .-.|||+|...++.+|+.- -.|... .+...
T Consensus 14 ~~~fvvlD~ETTGl~p~----------------------~d~IIeIgav~v~~~g~i~----------~~~~~l-v~P~~ 60 (313)
T PRK06063 14 PRGWAVVDVETSGFRPG----------------------QARIISLAVLGLDADGNVE----------QSVVTL-LNPGV 60 (313)
T ss_pred CCCEEEEEEECCCCCCC----------------------CCEEEEEEEEEEECCceee----------eEEEEE-ECcCC
Confidence 35899999999997321 1149999999998887532 223322 22211
Q ss_pred ccCch----hHHHHHHHcC--------c-cccCCccEEeecchhhHHHHHHHhc--CCCCCCChHHHHHHHHhhcCCccc
Q 025183 117 HAHAL----DSVELLKRQG--------L-VLNKDVTWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVTRVGVFFGEKVY 181 (256)
Q Consensus 117 d~~~~----~Si~~L~~~G--------l-v~~~~v~Wvtfhg~yDf~yL~k~l~--~~~LP~~~~~F~~~l~~~Fp~~vy 181 (256)
+..+. =+-+.|+.+. + -.-.+-.+|+||..||+++|-+.+- |.++|.. . .+
T Consensus 61 ~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~-------------~-~l 126 (313)
T PRK06063 61 DPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVD-------------Q-VM 126 (313)
T ss_pred CCCCeecCCCCHHHHhCCCCHHHHHHHHHHHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCCC-------------C-EE
Confidence 11100 0112222221 0 0113347899999999999988874 3344421 3 67
Q ss_pred chhHHHHhhc-cC-CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 182 DVKHLIRFCT-CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 182 D~K~la~~~~-~l-~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
|+.-+++... .+ ...|+.+|+.+|++. ...|.|-+|++.|+++|.++.+..-
T Consensus 127 dTl~lar~~~~~~~~~kL~~l~~~~gi~~--~~~H~Al~DA~ata~l~~~ll~~~~ 180 (313)
T PRK06063 127 CTVELARRLGLGLPNLRLETLAAHWGVPQ--QRPHDALDDARVLAGILRPSLERAR 180 (313)
T ss_pred ehHHHHHHhccCCCCCCHHHHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 8888887642 22 346999999999986 5679999999999999999877754
No 12
>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=98.50 E-value=3.5e-06 Score=70.31 Aligned_cols=150 Identities=21% Similarity=0.206 Sum_probs=95.3
Q ss_pred eeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeeccccc-cc
Q 025183 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR-HA 118 (256)
Q Consensus 40 fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~-d~ 118 (256)
||.+|+|.+|....... + ..-.|||+|....+.++.. ..-+|+.. ..... ..
T Consensus 1 ~vv~D~Ettg~~~~~~~----~-------------~~~~IieIgav~v~~~~~~---------~~~~f~~~-i~P~~~~~ 53 (176)
T cd06133 1 YLVIDFEATCWEGNSKP----D-------------YPNEIIEIGAVLVDVKTKE---------IIDTFSSY-VKPVINPK 53 (176)
T ss_pred CEEEEeeccccCCCCCC----C-------------CCcceEEEEEEEEEcCCCe---------EEeeeeee-ECCCcCCc
Confidence 79999999998543210 0 0124999999999887742 22345555 22222 23
Q ss_pred CchhHHHHHHHcCc--------------------cccCC--ccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhc
Q 025183 119 HALDSVELLKRQGL--------------------VLNKD--VTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFF 176 (256)
Q Consensus 119 ~~~~Si~~L~~~Gl--------------------v~~~~--v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~F 176 (256)
.++.+.+. +|+ .+++. ...++ ||.+|...+.+......... ...++
T Consensus 54 i~~~~~~i---~gIt~e~l~~~~~~~~vl~~~~~~l~~~~~~~~v~-~~~~d~~~l~~~~~~~~~~~--------~~~~~ 121 (176)
T cd06133 54 LSDFCTEL---TGITQEDVDNAPSFPEVLKEFLEWLGKNGKYAFVT-WGDWDLKDLLQNQCKYKIIN--------LPPFF 121 (176)
T ss_pred hhHHHHHh---cCcCHHHHhcCCCHHHHHHHHHHHHHhCCCeEEEe-ecHhhHHHHHHHHHHhcCCC--------Ccccc
Confidence 34433333 441 11222 44444 46899888877644211100 01122
Q ss_pred CCcccchhHHHHhhccC--CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHH
Q 025183 177 GEKVYDVKHLIRFCTCL--YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKI 230 (256)
Q Consensus 177 p~~vyD~K~la~~~~~l--~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl 230 (256)
.. .+|++.+++...+. ..+|.++|+.+|++. .+..|.|=+|++.|+++|.+|
T Consensus 122 ~~-~~D~~~~~~~~~~~~~~~~L~~l~~~~gi~~-~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 122 RQ-WIDLKKEFAKFYGLKKRTGLSKALEYLGLEF-EGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred cc-eEEHHHHHHHHhCCCCCCCHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHHHHh
Confidence 34 88999888876433 568999999999998 689999999999999999987
No 13
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=98.50 E-value=2.9e-06 Score=76.49 Aligned_cols=154 Identities=14% Similarity=0.141 Sum_probs=100.3
Q ss_pred HhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecc
Q 025183 34 LIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFD 113 (256)
Q Consensus 34 ~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~ 113 (256)
++++.+||.+|+|-+|+... . =.|||+|+..++.++ ...+|+.. .+
T Consensus 3 ~l~~~~~v~~D~ETTGl~~~-------~---------------d~IIEIa~v~v~~~~-----------~~~~~~~l-i~ 48 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDVK-------K---------------DRIIEFAAIRFTFDE-----------VIDSVEFL-IN 48 (250)
T ss_pred cccCCcEEEEEEeCCCCCCC-------C---------------CeEEEEEEEEEECCe-----------EEEEEEEE-EC
Confidence 46778999999999997321 0 138999988776432 23456665 44
Q ss_pred cccccCchhHHH-------HHHHcC--------c--cccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhc
Q 025183 114 IARHAHALDSVE-------LLKRQG--------L--VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFF 176 (256)
Q Consensus 114 ~~~d~~~~~Si~-------~L~~~G--------l--v~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~F 176 (256)
... ..+++++. .++.+. + .+.+.-.+|+|+..||..+|.+.+-...+|.. ..
T Consensus 49 P~~-~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~----------~~ 117 (250)
T PRK06310 49 PER-VVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKEGDYIVGHSVGFDLQVLSQESERIGETFL----------SK 117 (250)
T ss_pred cCC-CCCHhhhhccCcCHHHHhCCCCHHHHHHHHHHHhCCCCEEEEECHHHHHHHHHHHHHHcCCCcc----------cc
Confidence 332 22222221 111111 0 11233468998888999999988653222211 01
Q ss_pred CCcccchhHHHHhhccC-CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhh
Q 025183 177 GEKVYDVKHLIRFCTCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 234 (256)
Q Consensus 177 p~~vyD~K~la~~~~~l-~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~ 234 (256)
+..++||..+++..+.. ..+|+.+++.+|++. . .+|.|-+|++.|+.+|.+|.+++
T Consensus 118 ~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~-~-~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 118 HYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPY-D-GNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred CCcEEehHHHHHhcccCCCCCHHHHHHHCCCCC-C-CCcChHHHHHHHHHHHHHHHHhc
Confidence 23378998888865443 357999999999986 4 47999999999999999998765
No 14
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=98.49 E-value=3.4e-06 Score=75.82 Aligned_cols=152 Identities=20% Similarity=0.272 Sum_probs=99.4
Q ss_pred CCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecccccc
Q 025183 38 YPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH 117 (256)
Q Consensus 38 ~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d 117 (256)
-.||++|||-||+.... .=.|||+|...... +.. ..-.|+.+ .+...+
T Consensus 4 ~r~vvlDtETTGldp~~---------------------~drIIEIGaV~v~~-~~~---------~~~~f~~~-i~P~~~ 51 (240)
T PRK05711 4 MRQIVLDTETTGLNQRE---------------------GHRIIEIGAVELIN-RRL---------TGRNFHVY-IKPDRL 51 (240)
T ss_pred CeEEEEEeeCCCcCCCC---------------------CCeEEEEEEEEEEC-CEE---------eccEEEEE-ECcCCc
Confidence 47999999999974210 11499999876542 211 11246666 454332
Q ss_pred cCchhHHH-------HHHHcC---------ccccCCccEEeecchhhHHHHHHHhc--CCCCCCChHHHHHHHHhhcCCc
Q 025183 118 AHALDSVE-------LLKRQG---------LVLNKDVTWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVTRVGVFFGEK 179 (256)
Q Consensus 118 ~~~~~Si~-------~L~~~G---------lv~~~~v~Wvtfhg~yDf~yL~k~l~--~~~LP~~~~~F~~~l~~~Fp~~ 179 (256)
.++++++ +|+..- +-.-.+-.+|.+|..||+++|-+-+- |..+|... .+..
T Consensus 52 -i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~---------~~~~- 120 (240)
T PRK05711 52 -VDPEALAVHGITDEFLADKPTFAEVADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTN---------TFCK- 120 (240)
T ss_pred -CCHHHhhhcCCCHHHHcCCCCHHHHHHHHHHHhCCCEEEEEccHHhHHHHHHHHHHhCCCCCccc---------ccCc-
Confidence 3333322 222222 00113446899999999999987764 33455321 1234
Q ss_pred ccchhHHHHhh-ccCCCcHHHHHHHcCCcccCC-CCCcchhhHHHHHHHHHHHHHh
Q 025183 180 VYDVKHLIRFC-TCLYGGLDRVCKALGVERVVG-KSHQAGSDSLLTLHAFLKIKDK 233 (256)
Q Consensus 180 vyD~K~la~~~-~~l~~gL~~vA~~L~v~r~~g-~~hqAGsdsllT~~~F~kl~~~ 233 (256)
++|+--|++.. ++.+.+|+.+++.+|++. .+ ..|.|-+|+.+|+++|.+|...
T Consensus 121 ~iDTl~lar~~~p~~~~~L~aL~~~~gi~~-~~r~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 121 VTDTLAMARRMFPGKRNSLDALCKRYGIDN-SHRTLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred eeeHHHHHHHHcCCCCCCHHHHHHHCCCCC-CCCCCCCHHHHHHHHHHHHHHHHCc
Confidence 88998888764 455668999999999987 44 4799999999999999999764
No 15
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=98.42 E-value=5.7e-06 Score=72.21 Aligned_cols=80 Identities=20% Similarity=0.168 Sum_probs=58.2
Q ss_pred EEeecchhhHHHHHHHhc--CCCCCCChHHHHHHHHhhcCCcccchhHHHHhhcc--CCCcHHHHHHHcCCcccCCCCCc
Q 025183 140 WVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC--LYGGLDRVCKALGVERVVGKSHQ 215 (256)
Q Consensus 140 Wvtfhg~yDf~yL~k~l~--~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~--l~~gL~~vA~~L~v~r~~g~~hq 215 (256)
+|..|+.+|+.+|-+.+. |-+.|. +.. ..|+..+.+.... -..+|..+++.+|++- .+..|.
T Consensus 96 ~iv~~~~fD~~fL~~~~~~~~~~~~~------------~~~-~~dl~~~~~~~~~~~~~~~L~~~~~~~gi~~-~~~~H~ 161 (207)
T PRK07748 96 TIVTWGNMDMKVLKHNCEKAGVPFPF------------KGQ-CRDLSLEYKKFFGERNQTGLWKAIEEYGKEG-TGKHHC 161 (207)
T ss_pred EEEEECHHHHHHHHHHHHHcCCCCcc------------ccc-ceeHHHHHHHHhCcCCCCCHHHHHHHcCCCC-CCCCcC
Confidence 344578999999988875 323231 122 5566555443321 1358999999999997 788999
Q ss_pred chhhHHHHHHHHHHHHHh
Q 025183 216 AGSDSLLTLHAFLKIKDK 233 (256)
Q Consensus 216 AGsdsllT~~~F~kl~~~ 233 (256)
|-+|++.|+++|.+|.+.
T Consensus 162 Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 162 ALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred hHHHHHHHHHHHHHHHhC
Confidence 999999999999998876
No 16
>PRK07740 hypothetical protein; Provisional
Probab=98.37 E-value=8e-06 Score=73.37 Aligned_cols=85 Identities=19% Similarity=0.207 Sum_probs=64.6
Q ss_pred CccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccC--CCcHHHHHHHcCCcccCCCCC
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCL--YGGLDRVCKALGVERVVGKSH 214 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l--~~gL~~vA~~L~v~r~~g~~h 214 (256)
+-.+|+||..+|+.+|-+.+... + ..-|+..+.|+..+++..... ..+|+.+++.+|++. .+ .|
T Consensus 141 ~~~lVahna~fD~~fL~~~~~~~-~-----------~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~-~~-~H 206 (244)
T PRK07740 141 AGVLVAHHAGHDKAFLRHALWRT-Y-----------RQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPI-PR-RH 206 (244)
T ss_pred CCEEEEeCHHHHHHHHHHHHHHh-c-----------CCCcCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCC-CC-CC
Confidence 34799999999999998776421 1 111334488998888765422 457999999999987 55 49
Q ss_pred cchhhHHHHHHHHHHHHHhhC
Q 025183 215 QAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 215 qAGsdsllT~~~F~kl~~~~~ 235 (256)
.|-+|++.|+++|.++.....
T Consensus 207 ~Al~Da~ata~l~~~ll~~~~ 227 (244)
T PRK07740 207 HALGDALMTAKLWAILLVEAQ 227 (244)
T ss_pred CcHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999877654
No 17
>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=98.37 E-value=1.1e-05 Score=71.07 Aligned_cols=153 Identities=17% Similarity=0.235 Sum_probs=95.4
Q ss_pred hhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeeccc
Q 025183 35 IDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDI 114 (256)
Q Consensus 35 i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~ 114 (256)
+....||++|+|-+|+... . .|||+|.......+. ...+|... .+.
T Consensus 4 l~~~~fvv~D~ETTGl~~~---------------------~--~IIeIgav~v~~~~~----------~~~~f~~l-i~P 49 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAG---------------------H--DIIEIGAVEIINRRI----------TGNKFHTY-IKP 49 (217)
T ss_pred EEecCEEEEEecCCCCCCC---------------------C--CEEEEEEEEEECCCE----------eeeEEEEE-ECc
Confidence 4567899999999997311 0 289999988543321 22345555 333
Q ss_pred ccccCchhHHH-------HHHHcC--------c-cccCCccEEeecchhhHHHHHHHhcC-CCCCCChHHHHHHHHhhcC
Q 025183 115 ARHAHALDSVE-------LLKRQG--------L-VLNKDVTWVTFHSAYDFGYLVKCLTQ-RVLPEKLSEFVTRVGVFFG 177 (256)
Q Consensus 115 ~~d~~~~~Si~-------~L~~~G--------l-v~~~~v~Wvtfhg~yDf~yL~k~l~~-~~LP~~~~~F~~~l~~~Fp 177 (256)
.. ..++.++. .|+... + -.-++-.+|+++..||+.+|-+.+-. ...|. .+
T Consensus 50 ~~-~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~------------~~ 116 (217)
T TIGR00573 50 DR-PIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVEP------------KT 116 (217)
T ss_pred CC-CCCHHHHhhcCCCHHHHcCCCCHHHHHHHHHHHhCCCEEEEeccHHHHHHHHHHHHHhcCCCC------------Cc
Confidence 22 23333332 222222 0 01134578999999999999887652 11111 11
Q ss_pred CcccchhHHHHhh-ccC---CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhh
Q 025183 178 EKVYDVKHLIRFC-TCL---YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 234 (256)
Q Consensus 178 ~~vyD~K~la~~~-~~l---~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~ 234 (256)
..+.|+.-+++.. +.+ +.+|+.+++.+|++..-...|.|-+|+.+|+++|.+|.+..
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 2256665555543 222 34799999999998621368999999999999999998874
No 18
>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=98.33 E-value=1e-05 Score=66.21 Aligned_cols=77 Identities=23% Similarity=0.215 Sum_probs=57.1
Q ss_pred CccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhh-ccC-CCcHHHHHHHcCCcccCCCCC
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFC-TCL-YGGLDRVCKALGVERVVGKSH 214 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~-~~l-~~gL~~vA~~L~v~r~~g~~h 214 (256)
+..||++|..||+++|-+.+-...++.. +...+|+.-+++.. +.+ ..+|+.+++.+|++. . .|
T Consensus 77 ~~~lv~hn~~fD~~~l~~~~~~~g~~~~------------~~~~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~-~--~H 141 (156)
T cd06130 77 GSLVVAHNASFDRSVLRAALEAYGLPPP------------PYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIEL-N--HH 141 (156)
T ss_pred CCEEEEeChHHhHHHHHHHHHHcCCCCC------------CCCEEEHHHHHHHHhccCCCCCHHHHHHHcCCCc-c--Cc
Confidence 3579999999999999888753222111 22377887666654 333 347999999999987 4 89
Q ss_pred cchhhHHHHHHHHH
Q 025183 215 QAGSDSLLTLHAFL 228 (256)
Q Consensus 215 qAGsdsllT~~~F~ 228 (256)
.|-+|++.|+++|.
T Consensus 142 ~Al~Da~~ta~l~~ 155 (156)
T cd06130 142 DALEDARACAEILL 155 (156)
T ss_pred CchHHHHHHHHHHh
Confidence 99999999999885
No 19
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=98.29 E-value=9.1e-06 Score=70.81 Aligned_cols=81 Identities=16% Similarity=0.272 Sum_probs=54.2
Q ss_pred CccEEeecch-hhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHh--hccC-CCcHHHHHHHcCCcccCCC
Q 025183 137 DVTWVTFHSA-YDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRF--CTCL-YGGLDRVCKALGVERVVGK 212 (256)
Q Consensus 137 ~v~Wvtfhg~-yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~--~~~l-~~gL~~vA~~L~v~r~~g~ 212 (256)
+-.||++|.. +|+.+|-+. |.+++.. +....||+++..+. .+++ .-.|+.||+.+|++. .
T Consensus 84 ~~~lVaHNa~~fD~~fL~~~--g~~~~~~-----------~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~---~ 147 (195)
T PRK07247 84 ELPLIGYNAQKSDLPILAEN--GLDLSDQ-----------YQVDLYDEAFERRSSDLNGIANLKLQTVADFLGIKG---R 147 (195)
T ss_pred CCeEEEEeCcHhHHHHHHHc--CCCcCCC-----------ceeehHHHHHHhhccccCCCCCCCHHHHHHhcCCCC---C
Confidence 4469999876 899998653 4343321 11113444332221 1222 247999999999985 3
Q ss_pred CCcchhhHHHHHHHHHHHHHh
Q 025183 213 SHQAGSDSLLTLHAFLKIKDK 233 (256)
Q Consensus 213 ~hqAGsdsllT~~~F~kl~~~ 233 (256)
.|.|-+|++.|+.+|.+|.+.
T Consensus 148 ~HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 148 GHNSLEDARMTARVYESFLES 168 (195)
T ss_pred CcCCHHHHHHHHHHHHHHHhh
Confidence 699999999999999998775
No 20
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=98.28 E-value=2.1e-05 Score=70.50 Aligned_cols=84 Identities=17% Similarity=0.092 Sum_probs=62.5
Q ss_pred CccEEeecchhhHHHHHHHhcC---CCCCCChHHHHHHHHhhcCCcccchhHHHHhh-cc--------C------CCcHH
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQ---RVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFC-TC--------L------YGGLD 198 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~---~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~-~~--------l------~~gL~ 198 (256)
+-.+|++|..+|.++|-+.+.. .++|. . ++||-.+++.. +. + .-.|+
T Consensus 129 ~~~lVaHna~FD~~fL~~~l~~~~~~~~~~--------------~-~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~ 193 (239)
T PRK09146 129 GKVVVVHYRRIERDFLDQALRNRIGEGIEF--------------P-VIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLA 193 (239)
T ss_pred CCEEEEECHHHHHHHHHHHHHHhcCCCCCC--------------c-eechHHHHHHHcccccccccchhccCCCCCCCHH
Confidence 3468999999999999988752 22222 2 56776666553 11 1 12599
Q ss_pred HHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhhCCC
Q 025183 199 RVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGN 237 (256)
Q Consensus 199 ~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~~~~ 237 (256)
.+++.+|++. ...|.|-+|++.|+++|.++.+.+++.
T Consensus 194 ~l~~~~gl~~--~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 194 DSRLRYGLPA--YSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred HHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 9999999985 556999999999999999999888744
No 21
>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=98.28 E-value=2.3e-05 Score=69.62 Aligned_cols=151 Identities=21% Similarity=0.214 Sum_probs=96.2
Q ss_pred CeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeeccccccc
Q 025183 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (256)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~ 118 (256)
.||.+|||-||+.... .=.||++|...... +. + ..-.|+.+ .+...+
T Consensus 1 r~vvlD~ETTGl~p~~---------------------~d~IIEIgav~~~~-~~-~--------~~~~f~~~-i~P~~~- 47 (225)
T TIGR01406 1 RQIILDTETTGLDPKG---------------------GHRIVEIGAVELVN-RM-L--------TGDNFHVY-VNPERD- 47 (225)
T ss_pred CEEEEEeeCCCcCCCC---------------------CCeEEEEEEEEEEC-Cc-E--------ecceEEEE-ECcCCC-
Confidence 4899999999973210 01499999875542 21 1 11246666 444332
Q ss_pred CchhHH-------HHHHHcC---------ccccCCccEEeecchhhHHHHHHHhc--CCCCCCChHHHHHHHHhhcCCcc
Q 025183 119 HALDSV-------ELLKRQG---------LVLNKDVTWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVTRVGVFFGEKV 180 (256)
Q Consensus 119 ~~~~Si-------~~L~~~G---------lv~~~~v~Wvtfhg~yDf~yL~k~l~--~~~LP~~~~~F~~~l~~~Fp~~v 180 (256)
..+++. ++|+... +-.-.+-.+|.+|..||++||-+-+- |..+|.- ..+ ..+
T Consensus 48 i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~---------~~~-~~~ 117 (225)
T TIGR01406 48 MPAEAAKVHGITDEFLADKPKFKEIADEFLDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKI---------GEF-CRV 117 (225)
T ss_pred CCHHHHhccCCCHHHHhCCCCHHHHHHHHHHHhCCCEEEEEecHHHHHHHHHHHHHhCCCCccc---------ccC-CCE
Confidence 233333 2232222 00113446899999999999988764 2111110 001 238
Q ss_pred cchhHHHHhh-ccCCCcHHHHHHHcCCcccCC-CCCcchhhHHHHHHHHHHHHHh
Q 025183 181 YDVKHLIRFC-TCLYGGLDRVCKALGVERVVG-KSHQAGSDSLLTLHAFLKIKDK 233 (256)
Q Consensus 181 yD~K~la~~~-~~l~~gL~~vA~~L~v~r~~g-~~hqAGsdsllT~~~F~kl~~~ 233 (256)
+|+--|++.. ++.+.+|+.+++.+|++. .+ ..|-|-.|+.+|+++|.+|...
T Consensus 118 iDTl~lar~~~p~~~~~L~~L~~~~gi~~-~~r~~H~Al~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 118 IDTLAMARERFPGQRNSLDALCKRFKVDN-SHRTLHGALLDAHLLAEVYLALTGG 171 (225)
T ss_pred EEHHHHHHHHcCCCCCCHHHHHHhcCCCC-CCCCCcCHHHHHHHHHHHHHHHHcC
Confidence 8998888764 455678999999999997 55 4799999999999999999775
No 22
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=98.26 E-value=2.1e-05 Score=73.26 Aligned_cols=146 Identities=17% Similarity=0.166 Sum_probs=95.8
Q ss_pred CCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecccccc
Q 025183 38 YPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH 117 (256)
Q Consensus 38 ~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d 117 (256)
.+||++|+|.+|+... .-.|||+|...++ +|+ ...+|+.. ......
T Consensus 8 ~~~Vv~DlETTGl~p~----------------------~~eIIEIgaV~v~-~g~----------i~~~f~~l-VkP~~~ 53 (313)
T PRK06807 8 LDYVVIDFETTGFNPY----------------------NDKIIQVAAVKYR-NHE----------LVDQFVSY-VNPERP 53 (313)
T ss_pred CCEEEEEEECCCCCCC----------------------CCeEEEEEEEEEE-CCE----------EEEEEEEE-ECcCCC
Confidence 3899999999997321 1159999998886 332 34567766 444332
Q ss_pred cCchhH-------HHHHHHcC--------c--cccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcc
Q 025183 118 AHALDS-------VELLKRQG--------L--VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKV 180 (256)
Q Consensus 118 ~~~~~S-------i~~L~~~G--------l--v~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~v 180 (256)
+ .+.+ -+.|+... + .++++ .+|++++.||+.+|-+.+-...+|.. ... +
T Consensus 54 I-~~~a~~ihGIT~e~l~~~~~~~evl~~f~~fl~~~-~lVaHNa~FD~~fL~~~~~~~gl~~~-----------~~~-~ 119 (313)
T PRK06807 54 I-PDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN-VIVAHNASFDMRFLKSNVNMLGLPEP-----------KNK-V 119 (313)
T ss_pred C-CHhhhccCCCCHHHHhCCCCHHHHHHHHHHHHcCC-eEEEEcHHHHHHHHHHHHHHcCCCCC-----------CCC-E
Confidence 2 2221 12222221 0 11223 57999999999999998753233211 012 6
Q ss_pred cchhHHHHhhc-cCC-CcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhh
Q 025183 181 YDVKHLIRFCT-CLY-GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 234 (256)
Q Consensus 181 yD~K~la~~~~-~l~-~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~ 234 (256)
+|+-.+++... .+. .+|+.+++.+|++. ..|.|=.|++.|+++|.+|...-
T Consensus 120 iDtl~la~~~~~~~~~~kL~~L~~~lgi~~---~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 120 IDTVFLAKKYMKHAPNHKLETLKRMLGIRL---SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred eeHHHHHHHHhCCCCCCCHHHHHHHcCCCC---CCcChHHHHHHHHHHHHHHHHhh
Confidence 78777766543 332 37999999999985 68999999999999999987764
No 23
>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=98.24 E-value=9.4e-06 Score=65.20 Aligned_cols=138 Identities=21% Similarity=0.238 Sum_probs=89.1
Q ss_pred eEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecccccccCc
Q 025183 41 ISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHA 120 (256)
Q Consensus 41 IAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~~ 120 (256)
|.+|+|.+|+... .-.|||+|...++.+++. ...||.+ +....++ .
T Consensus 1 v~~D~Ettg~~~~----------------------~~~iiei~~v~~~~~~~~----------~~~~~~~-i~p~~~~-~ 46 (159)
T cd06127 1 VVFDTETTGLDPK----------------------KDRIIEIGAVKVDGGIEI----------VERFETL-VNPGRPI-P 46 (159)
T ss_pred CeEEeeCCCcCCC----------------------CCeEEEEEEEEEECCcCh----------hhhhhee-eCcCCcC-C
Confidence 5799999997421 123999999999987432 2345555 3333221 1
Q ss_pred hhH-------HHHHHHcC---------c--cccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccc
Q 025183 121 LDS-------VELLKRQG---------L--VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYD 182 (256)
Q Consensus 121 ~~S-------i~~L~~~G---------l--v~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD 182 (256)
+.. -+.+. +| + .+.+ -.||++++.+|..+|.+.+.... ...++...+|
T Consensus 47 ~~~~~~~gi~~~~~~-~~~~~~~~~~~~~~~l~~-~~~v~~n~~fD~~~l~~~~~~~~------------~~~~~~~~iD 112 (159)
T cd06127 47 PEATAIHGITDEMLA-DAPPFEEVLPEFLEFLGG-RVLVAHNASFDLRFLNRELRRLG------------GPPLPNPWID 112 (159)
T ss_pred HhheeccCCCHHHHh-cCCCHHHHHHHHHHHHCC-CEEEEeCcHhhHHHHHHHHHHhC------------CCCCCCCeeE
Confidence 111 11222 22 0 1223 57999999999999998876311 2233445889
Q ss_pred hhHHHHhhccC--CCcHHHH-HHHcCCcccCCCCCcchhhHHHHHHHHH
Q 025183 183 VKHLIRFCTCL--YGGLDRV-CKALGVERVVGKSHQAGSDSLLTLHAFL 228 (256)
Q Consensus 183 ~K~la~~~~~l--~~gL~~v-A~~L~v~r~~g~~hqAGsdsllT~~~F~ 228 (256)
++-+++..-.. ..+|..+ ++.+++.. +..|.|=+|++.|.++|.
T Consensus 113 t~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 113 TLRLARRLLPGLRSHRLGLLLAERYGIPL--EGAHRALADALATAELLL 159 (159)
T ss_pred HHHHHHHHcCCCCcCchHHHHHHHcCCCC--CCCCCcHHHHHHHHHHhC
Confidence 98888765432 2467777 88888864 688999999999999883
No 24
>PRK07883 hypothetical protein; Validated
Probab=98.17 E-value=2.9e-05 Score=77.55 Aligned_cols=156 Identities=17% Similarity=0.163 Sum_probs=101.2
Q ss_pred HHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeee
Q 025183 31 IRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFK 110 (256)
Q Consensus 31 I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~ 110 (256)
+..-+.+.+||++|+|.+|+... .-.|||+|.-.++ +|+ ...+|+..
T Consensus 8 ~~~~~~~~~~Vv~D~ETTGl~p~----------------------~~~IIEIgaV~v~-~g~----------iv~~f~~l 54 (557)
T PRK07883 8 LGTPLRDVTFVVVDLETTGGSPA----------------------GDAITEIGAVKVR-GGE----------VLGEFATL 54 (557)
T ss_pred hCCCCcCCCEEEEEEecCCCCCC----------------------CCeEEEEEEEEEE-CCE----------EEEEEEEE
Confidence 34457788999999999998311 1249999998886 231 34466665
Q ss_pred ecccccccCchhHHHH-------HHHcC---------ccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHh
Q 025183 111 DFDIARHAHALDSVEL-------LKRQG---------LVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGV 174 (256)
Q Consensus 111 ~F~~~~d~~~~~Si~~-------L~~~G---------lv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~ 174 (256)
.+.... .++.+... |.... .-.-.+-.+|+|++.||+.+|-+.+....+|.
T Consensus 55 -V~P~~~-i~~~~~~itGIt~e~l~~ap~~~evl~~f~~fl~~~~lVaHNa~FD~~fL~~~~~r~g~~~----------- 121 (557)
T PRK07883 55 -VNPGRP-IPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPW----------- 121 (557)
T ss_pred -ECCCCC-CChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHhcCCEEEEeCcHHHHHHHHHHHHHcCCCC-----------
Confidence 444322 23332221 11111 00112456889889999999988876433321
Q ss_pred hcCCcccchhHHHHhh-c--cC-CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 175 FFGEKVYDVKHLIRFC-T--CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 175 ~Fp~~vyD~K~la~~~-~--~l-~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
.+...+|+-.+++.. + .. ..+|+.+|+.+|++. ...|-|-+|++.|+++|.++.+.+.
T Consensus 122 -~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~--~~~H~Al~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 122 -PGPPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATT--TPTHRALDDARATVDVLHGLIERLG 183 (557)
T ss_pred -CCCCcEecHHHHHHhcccCCCCCCCHHHHHHHCCccc--CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 111266887666653 2 22 347999999999986 4469999999999999999988874
No 25
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=98.14 E-value=6.6e-05 Score=65.37 Aligned_cols=89 Identities=20% Similarity=0.289 Sum_probs=63.1
Q ss_pred CccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccCCCcHHHHHHHcCCcccCCCCCcc
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQA 216 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l~~gL~~vA~~L~v~r~~g~~hqA 216 (256)
+-..|++|-.+|+.+|-+.+-...++.. .+-|..+.|+--+++.... ..+|..+++.+|++......|.|
T Consensus 105 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~---------~~~~~~~lDTl~lar~~~~-~~~L~~l~~~~gi~~~~~~~H~A 174 (200)
T TIGR01298 105 RAILVGHNANFDLGFLNAAVERTSLKRN---------PFHPFSTFDTATLAGLAYG-QTVLAKACQAAGXDFDSTQAHSA 174 (200)
T ss_pred CCEEEEECchhhHHHHHHHHHHhCCCCC---------CCCCCcEEEHHHHHHHHcC-cccHHHHHHHcCCCccccchhhh
Confidence 3468999999999999888742111110 0012226788877775432 23699999999998512368999
Q ss_pred hhhHHHHHHHHHHHHHhhC
Q 025183 217 GSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 217 GsdsllT~~~F~kl~~~~~ 235 (256)
-+|++.|+++|.+|.+++-
T Consensus 175 l~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 175 LYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred HHhHHHHHHHHHHHHHHHH
Confidence 9999999999999988753
No 26
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=98.13 E-value=4.9e-05 Score=70.47 Aligned_cols=82 Identities=22% Similarity=0.244 Sum_probs=62.3
Q ss_pred CccEEeecchhhHHHHHHHhcC--CCCCCChHHHHHHHHhhcCCcccchhHHHHhh-ccC-CCcHHHHHHHcCCcccCCC
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQ--RVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFC-TCL-YGGLDRVCKALGVERVVGK 212 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~--~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~-~~l-~~gL~~vA~~L~v~r~~g~ 212 (256)
+-.+|++|+.||+++|-+-+.. .+.|. .. .+|+--+++.. +++ ..+|+.+++.+|++- .
T Consensus 80 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~-------------~~-~idT~~lar~l~~~~~~~~L~~L~~~~gi~~---~ 142 (309)
T PRK06195 80 NNLVIAHNASFDISVLRKTLELYNIPMPS-------------FE-YICTMKLAKNFYSNIDNARLNTVNNFLGYEF---K 142 (309)
T ss_pred CCEEEEECcHHHHHHHHHHHHHhCCCCCC-------------CC-EEEHHHHHHHHcCCCCcCCHHHHHHHcCCCC---c
Confidence 3478999999999999887643 23331 12 67887666654 344 357999999999973 4
Q ss_pred CCcchhhHHHHHHHHHHHHHhhC
Q 025183 213 SHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 213 ~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
.|.|-+|++.|+++|.+|.+..-
T Consensus 143 ~H~Al~DA~ata~l~~~l~~~~~ 165 (309)
T PRK06195 143 HHDALADAMACSNILLNISKELN 165 (309)
T ss_pred ccCCHHHHHHHHHHHHHHHHHhc
Confidence 79999999999999999988753
No 27
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=98.09 E-value=0.00011 Score=66.59 Aligned_cols=83 Identities=18% Similarity=0.206 Sum_probs=61.2
Q ss_pred ccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhh-ccCCCcHHHHHHHcCCcccCCCCCcc
Q 025183 138 VTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFC-TCLYGGLDRVCKALGVERVVGKSHQA 216 (256)
Q Consensus 138 v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~-~~l~~gL~~vA~~L~v~r~~g~~hqA 216 (256)
-.||++|..+|+++|-+.+....+|.- ... ..|+--+++.+ +.-+-||+.+++.+|++. ...|.|
T Consensus 148 ~v~VaHNa~FD~~fL~~~l~r~g~~~~-----------~~~-~ldtl~la~~~~~~~~~~L~~L~~~lgi~~--~~~HrA 213 (257)
T PRK08517 148 SVFVAHNVNFDYNFISRSLEEIGLGPL-----------LNR-KLCTIDLAKRTIESPRYGLSFLKELLGIEI--EVHHRA 213 (257)
T ss_pred CeEEEECHHHHHHHHHHHHHHcCCCCC-----------CCC-cEehHHHHHHHccCCCCCHHHHHHHcCcCC--CCCCCh
Confidence 369999999999999887654333321 112 45654455443 333568999999999987 378999
Q ss_pred hhhHHHHHHHHHHHHHhh
Q 025183 217 GSDSLLTLHAFLKIKDKH 234 (256)
Q Consensus 217 GsdsllT~~~F~kl~~~~ 234 (256)
-+|++.|+++|.++.+.+
T Consensus 214 l~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 214 YADALAAYEIFKICLLNL 231 (257)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 999999999999988765
No 28
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.08 E-value=6.7e-05 Score=78.12 Aligned_cols=82 Identities=23% Similarity=0.276 Sum_probs=62.4
Q ss_pred CccEEeecchhhHHHHHHHhc--CCCCCCChHHHHHHHHhhcCCcccchhHHHHhh-ccC-CCcHHHHHHHcCCcccCCC
Q 025183 137 DVTWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFC-TCL-YGGLDRVCKALGVERVVGK 212 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~--~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~-~~l-~~gL~~vA~~L~v~r~~g~ 212 (256)
+-.+|++|..+|+++|-+.+. |-++|. . .+||-.+++.. +.+ +-+|+.+|+.+|++. ..
T Consensus 86 ~~~lVaHN~~FD~~fL~~~~~~~g~~~~~--------------~-~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~--~~ 148 (820)
T PRK07246 86 DCIFVAHNVKFDANLLAEALFLEGYELRT--------------P-RVDTVELAQVFFPTLEKYSLSHLSRELNIDL--AD 148 (820)
T ss_pred CCEEEEECcHHHHHHHHHHHHHcCCCCCC--------------C-ceeHHHHHHHHhCCCCCCCHHHHHHHcCCCC--CC
Confidence 456999999999999988764 333321 1 35666666553 222 358999999999986 46
Q ss_pred CCcchhhHHHHHHHHHHHHHhhC
Q 025183 213 SHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 213 ~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
.|.|-+|+..|+++|.+|.+.+.
T Consensus 149 ~H~Al~DA~ata~L~~~l~~~l~ 171 (820)
T PRK07246 149 AHTAIADARATAELFLKLLQKIE 171 (820)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHh
Confidence 79999999999999999988764
No 29
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.08 E-value=6.5e-05 Score=79.13 Aligned_cols=150 Identities=22% Similarity=0.260 Sum_probs=96.4
Q ss_pred CCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecccccc
Q 025183 38 YPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH 117 (256)
Q Consensus 38 ~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d 117 (256)
-.||++|+|.+|..... . -.|||+|....+ +|+ .+-+|+.. .+....
T Consensus 3 ~~~vvvD~ETTG~~p~~------~---------------d~IIeigav~v~-~~~----------i~~~f~~~-v~P~~~ 49 (928)
T PRK08074 3 KRFVVVDLETTGNSPKK------G---------------DKIIQIAAVVVE-DGE----------ILERFSSF-VNPERP 49 (928)
T ss_pred CCEEEEEEeCCCCCCCC------C---------------CcEEEEEEEEEE-CCE----------EEEEEEEE-ECcCCC
Confidence 47999999999963111 0 149999999985 342 23345555 343322
Q ss_pred cCchhHHHH-------HHHcC---------ccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCccc
Q 025183 118 AHALDSVEL-------LKRQG---------LVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVY 181 (256)
Q Consensus 118 ~~~~~Si~~-------L~~~G---------lv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vy 181 (256)
.++...++ |+..- .-+-++..+|+|+..||+.+|-+-+...-+|.. +...+
T Consensus 50 -i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~~l~~~~~VaHN~~FD~~fL~~~~~~~g~~~~------------~~~~i 116 (928)
T PRK08074 50 -IPPFITELTGISEEMVKQAPLFEDVAPEIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEI------------HCPKL 116 (928)
T ss_pred -CCHHHhhcCCCCHHHHhcCCCHHHHHHHHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCCC------------CCCee
Confidence 22222211 11111 011245689999999999999887654333321 12266
Q ss_pred chhHHHHhh-ccC-CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 182 DVKHLIRFC-TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 182 D~K~la~~~-~~l-~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
||=-+++.. +.+ .-+|+.+|+.||++. +.+|.|-+|++.|+++|.+|.++..
T Consensus 117 Dt~~la~~~~p~~~~~~L~~l~~~l~i~~--~~~H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 117 DTVELARILLPTAESYKLRDLSEELGLEH--DQPHRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred eHHHHHHHhcCCCCCCCHHHHHHhCCCCC--CCCCChHHHHHHHHHHHHHHHHHHH
Confidence 776665543 222 347999999999985 6889999999999999999988764
No 30
>PRK06722 exonuclease; Provisional
Probab=98.05 E-value=0.00013 Score=67.09 Aligned_cols=81 Identities=21% Similarity=0.167 Sum_probs=56.5
Q ss_pred cEEeecchhhHHHHHHHhc--CCCCCCChHHHHHHHHhhcCCcccchhHHHHh-hccC---CCcHHHHHHHcCCcccCCC
Q 025183 139 TWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRF-CTCL---YGGLDRVCKALGVERVVGK 212 (256)
Q Consensus 139 ~Wvtfhg~yDf~yL~k~l~--~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~-~~~l---~~gL~~vA~~L~v~r~~g~ 212 (256)
.+|..|+.+|.++|-+-+. |.+.|.-. +-. .+|+.-++.. .+.+ ..+|+.+++.+|++. .|.
T Consensus 92 ~lvahna~FD~~FL~~~l~~~gi~~p~~~----------~~~-~idl~~la~~~~~~l~~~~~sL~~l~~~lgL~~-~g~ 159 (281)
T PRK06722 92 SIFVTWGKEDYRFLSHDCTLHSVECPCME----------KER-RIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIW-EGK 159 (281)
T ss_pred cEEEEEeHHHHHHHHHHHHHcCCCCCccc----------ccc-hhHHHHHHHHHhhhhccCCCCHHHHHHHCCCCC-CCC
Confidence 5677889999999999765 33344311 001 2344333221 1111 236999999999997 789
Q ss_pred CCcchhhHHHHHHHHHHHH
Q 025183 213 SHQAGSDSLLTLHAFLKIK 231 (256)
Q Consensus 213 ~hqAGsdsllT~~~F~kl~ 231 (256)
.|.|-+||..|++.|.+|.
T Consensus 160 ~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 160 QHRALADAENTANILLKAY 178 (281)
T ss_pred CcCcHHHHHHHHHHHHHHh
Confidence 9999999999999999976
No 31
>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=98.01 E-value=0.00011 Score=76.83 Aligned_cols=85 Identities=22% Similarity=0.272 Sum_probs=62.7
Q ss_pred CccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhc-cC-CCcHHHHHHHcCCcccCCCCC
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCT-CL-YGGLDRVCKALGVERVVGKSH 214 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~-~l-~~gL~~vA~~L~v~r~~g~~h 214 (256)
+-.||++|..||+.+|-+-+....+|. +|...+|+--+++... .. .-+|+.+++.+|++. ..+|
T Consensus 80 ~~~~VahN~~fD~~fL~~~~~~~g~~~------------~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~--~~~H 145 (850)
T TIGR01407 80 DGIFVAHNVHFDLNFLAKALKDCGYEP------------LPKPRIDTVELAQIFFPTEESYQLSELSEALGLTH--ENPH 145 (850)
T ss_pred CCEEEEeCcHHHHHHHHHHHHHcCCCC------------CCCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCC--CCCC
Confidence 346999999999999998775322221 1333667665555432 12 347999999999986 4579
Q ss_pred cchhhHHHHHHHHHHHHHhhC
Q 025183 215 QAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 215 qAGsdsllT~~~F~kl~~~~~ 235 (256)
.|-+|+..|+++|.+|.+.+-
T Consensus 146 ~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 146 RADSDAQATAELLLLLFEKME 166 (850)
T ss_pred ChHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999988763
No 32
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=98.01 E-value=9.7e-05 Score=62.98 Aligned_cols=149 Identities=21% Similarity=0.262 Sum_probs=89.8
Q ss_pred eeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCC--CCCCeeeEEEeeeecccccc
Q 025183 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLG--SGSTYYIWEFNFKDFDIARH 117 (256)
Q Consensus 40 fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~--~~~~~~~wqFNF~~F~~~~d 117 (256)
||++|+|-||+... . . =.|||+|.-..+.++...... +.....+-+|+.. .+....
T Consensus 1 ~vv~D~ETTGl~~~-~-----~---------------d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~l-v~P~~~ 58 (177)
T cd06136 1 FVFLDLETTGLPKH-N-----R---------------PEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLC-FNPGRA 58 (177)
T ss_pred CeEEeeecCCCCCC-C-----C---------------CceEEEEEEEEecccccccccccccccceeeeeeEE-eCCCCc
Confidence 79999999998421 0 0 138999999887654322000 0000123456666 554422
Q ss_pred cCchhHH-------HHHHHcCc------------c--ccCCccEEeecc-hhhHHHHHHHhcC--CCCCCChHHHHHHHH
Q 025183 118 AHALDSV-------ELLKRQGL------------V--LNKDVTWVTFHS-AYDFGYLVKCLTQ--RVLPEKLSEFVTRVG 173 (256)
Q Consensus 118 ~~~~~Si-------~~L~~~Gl------------v--~~~~v~Wvtfhg-~yDf~yL~k~l~~--~~LP~~~~~F~~~l~ 173 (256)
..+.+. +.|+.++. + +.+....|+||+ .+|+.+|-+-+.. .++|..
T Consensus 59 -I~~~a~~IhGIt~e~l~~~~~~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~--------- 128 (177)
T cd06136 59 -ISPGASEITGLSNDLLEHKAPFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDD--------- 128 (177)
T ss_pred -CChhHHHHhCcCHHHHhcCCCccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCC---------
Confidence 222222 23444330 0 122457899998 7999999887753 333311
Q ss_pred hhcCCcccchhHHHHhhccCCCcHHHHHHH-cCCcccCCCCCcchhhHHHHHHHHHH
Q 025183 174 VFFGEKVYDVKHLIRFCTCLYGGLDRVCKA-LGVERVVGKSHQAGSDSLLTLHAFLK 229 (256)
Q Consensus 174 ~~Fp~~vyD~K~la~~~~~l~~gL~~vA~~-L~v~r~~g~~hqAGsdsllT~~~F~k 229 (256)
....|+-.+++... .+|+.+++. +|++. ...|.|-+|++.|++||++
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 11347655555432 289999885 78885 5579999999999999975
No 33
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=97.96 E-value=0.00021 Score=63.33 Aligned_cols=77 Identities=14% Similarity=0.060 Sum_probs=59.8
Q ss_pred CCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHh-hccCCCcHHHHHHHcCCcc---cCC
Q 025183 136 KDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRF-CTCLYGGLDRVCKALGVER---VVG 211 (256)
Q Consensus 136 ~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~-~~~l~~gL~~vA~~L~v~r---~~g 211 (256)
..-.+|+||..||.++|-+ ++...+||--+++. .++++.+|+.+++.+++.. ...
T Consensus 73 ~~~~lVaHNa~FD~~~L~~---------------------~~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~ 131 (219)
T PRK07983 73 GSEWYVAHNASFDRRVLPE---------------------MPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGL 131 (219)
T ss_pred CCCEEEEeCcHhhHHHHhC---------------------cCCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCC
Confidence 3457899999999998731 22337898888875 4566778999999999753 124
Q ss_pred CCCcchhhHHHHHHHHHHHHHh
Q 025183 212 KSHQAGSDSLLTLHAFLKIKDK 233 (256)
Q Consensus 212 ~~hqAGsdsllT~~~F~kl~~~ 233 (256)
..|.|-+|+++|+++|.+|.+.
T Consensus 132 ~aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 132 HHHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred CCCcHHHHHHHHHHHHHHHHHH
Confidence 6899999999999999998864
No 34
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.88 E-value=0.00042 Score=61.66 Aligned_cols=84 Identities=20% Similarity=0.207 Sum_probs=62.4
Q ss_pred CccEEeecc-hhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhh-ccC-CCcHHHHHHHcCCcccCCCC
Q 025183 137 DVTWVTFHS-AYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFC-TCL-YGGLDRVCKALGVERVVGKS 213 (256)
Q Consensus 137 ~v~Wvtfhg-~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~-~~l-~~gL~~vA~~L~v~r~~g~~ 213 (256)
.-.+|++++ .||..+|.+.+-...+|.. +...+|+--+++.. +++ ..+|+.+++.+|++. +.+
T Consensus 80 ~~~lVaHN~~~FD~~~L~~e~~r~g~~~~------------~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~~~~~--~~a 145 (232)
T PRK06309 80 DNILVAHNNDAFDFPLLRKECRRHGLEPP------------TLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEE--NQA 145 (232)
T ss_pred CCEEEEeCCHHHHHHHHHHHHHHcCCCCC------------CCcEEeHHHHHHHHcCCCCCCCHHHHHHHcCCCC--CCC
Confidence 446888885 6999999988753222211 12277887777653 333 457999999999875 568
Q ss_pred CcchhhHHHHHHHHHHHHHhh
Q 025183 214 HQAGSDSLLTLHAFLKIKDKH 234 (256)
Q Consensus 214 hqAGsdsllT~~~F~kl~~~~ 234 (256)
|-|-+|++.|+++|.+|.+.+
T Consensus 146 H~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 146 HRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred CCcHHHHHHHHHHHHHHHHHH
Confidence 999999999999999988765
No 35
>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=97.87 E-value=0.00027 Score=76.28 Aligned_cols=151 Identities=23% Similarity=0.293 Sum_probs=101.8
Q ss_pred hcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecccc
Q 025183 36 DRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIA 115 (256)
Q Consensus 36 ~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~ 115 (256)
+...||++|+|.||+.... + .|||+|....+. |+ ..-+|++. .+..
T Consensus 188 ~~~~~VVfDiETTGL~~~~---------d-------------~IIEIGAVkv~~-g~----------iid~f~~~-V~P~ 233 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQY---------D-------------EIIEFGAVKVKN-GR----------IIDKFQFF-IKPH 233 (1213)
T ss_pred cCCcEEEEEeEecCCCCCC---------C-------------eEEEEEEEEEEC-Ce----------EEEEEEEE-ECCC
Confidence 6779999999999974221 1 499999998863 32 23356665 3333
Q ss_pred cccCchhHHH-------HHHHcC---------ccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCc
Q 025183 116 RHAHALDSVE-------LLKRQG---------LVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEK 179 (256)
Q Consensus 116 ~d~~~~~Si~-------~L~~~G---------lv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~ 179 (256)
. ..++.+.+ .|+..- +-.-++-.+|+++..||+.+|-+.+....+|. ++..
T Consensus 234 ~-~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~------------~~~~ 300 (1213)
T TIGR01405 234 E-PLSAFVTELTGITQDMLENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEP------------LENP 300 (1213)
T ss_pred C-CCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCc------------cCCC
Confidence 2 22332222 222111 00113457899999999999998865433332 1233
Q ss_pred ccchhHHHHhhc-cC-CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 180 VYDVKHLIRFCT-CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 180 vyD~K~la~~~~-~l-~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
++||--+++... ++ ..+|+.||+.+|++. .+ .|.|-.|+..|+++|.+|.+.+.
T Consensus 301 ~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~-~~-~HrAl~DA~aTa~I~~~ll~~l~ 356 (1213)
T TIGR01405 301 VIDTLELARALNPEYKSHRLGNICKKLGVDL-DD-HHRADYDAEATAKVFKVMVEQLK 356 (1213)
T ss_pred EeEHHHHHHHHhccCCCCCHHHHHHHcCCCC-CC-CcCHHHHHHHHHHHHHHHHHHHH
Confidence 789988887653 33 358999999999997 44 89999999999999999988765
No 36
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=97.81 E-value=0.00041 Score=66.05 Aligned_cols=166 Identities=14% Similarity=0.177 Sum_probs=98.7
Q ss_pred HhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecc
Q 025183 34 LIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFD 113 (256)
Q Consensus 34 ~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~ 113 (256)
.+++.+||++|+|-||+... + =.||++|.-.++.+|+. +..|... .+
T Consensus 42 ~~~~~~fVvlDiETTGLdp~-------~---------------drIIeIgAV~i~~~g~i----------ve~f~tL-Vn 88 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPS-------T---------------SRLITIDAVTLTADGEE----------VEHFHAV-LN 88 (377)
T ss_pred CCCCCCEEEEEEECCCCCCC-------C---------------CeEEEEEEEEEEcCCEE----------EEEEEEE-EC
Confidence 46778999999999998321 1 13899999988888742 3445555 44
Q ss_pred cccccCchh----HHHHHHHcC--------c-cccCCccEEeecchhhHHHHHHHhcC--CCC-----CCChH------H
Q 025183 114 IARHAHALD----SVELLKRQG--------L-VLNKDVTWVTFHSAYDFGYLVKCLTQ--RVL-----PEKLS------E 167 (256)
Q Consensus 114 ~~~d~~~~~----Si~~L~~~G--------l-v~~~~v~Wvtfhg~yDf~yL~k~l~~--~~L-----P~~~~------~ 167 (256)
...+..... +=+.|++.- + -+-++-.||++|..+|++||.+-+.- ..+ |.... .
T Consensus 89 P~~~~~p~~LHGIT~e~La~AP~f~eVl~el~~fL~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~ 168 (377)
T PRK05601 89 PGEDPGPFHLHGLSAEEFAQGKRFSQILKPLDRLIDGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRG 168 (377)
T ss_pred cCCCCCCccccCCCHHHHhcCCCHHHHHHHHHHHhCCCEEEEECcHHHHHHHHHHHHHhhhhhhhccccccccccccccc
Confidence 433222110 111222211 0 11134579999999999999886521 000 00000 0
Q ss_pred H--HHHHHhhcCCcccchhHHHHhhc-cC-CCcHHHHHHHcCCccc--------CCCCCcchh--hHHHHHHHHHHHHH
Q 025183 168 F--VTRVGVFFGEKVYDVKHLIRFCT-CL-YGGLDRVCKALGVERV--------VGKSHQAGS--DSLLTLHAFLKIKD 232 (256)
Q Consensus 168 F--~~~l~~~Fp~~vyD~K~la~~~~-~l-~~gL~~vA~~L~v~r~--------~g~~hqAGs--dsllT~~~F~kl~~ 232 (256)
= ...-...+|..++||=-+++... .+ .-.|..||+.+|++.+ ....|.|=+ |++|+...|+++++
T Consensus 169 ~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~ 247 (377)
T PRK05601 169 RRRQRVGHIPKPVVIVDTLATARRQGVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRA 247 (377)
T ss_pred ccccccCCCCCCCCEEEhHHHHHHHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhc
Confidence 0 00001234544889977777763 44 3579999999999651 245566664 99999999999744
No 37
>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=97.76 E-value=3.2e-05 Score=62.12 Aligned_cols=143 Identities=22% Similarity=0.209 Sum_probs=84.9
Q ss_pred eEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecccccccCc
Q 025183 41 ISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHA 120 (256)
Q Consensus 41 IAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~~ 120 (256)
|.+|+|++|...+ .-.+||+|.-..+.+... ..-.||....+.......
T Consensus 1 v~~D~Ettg~~~~----------------------~~~iieig~v~~~~~~~~---------~~~~~~~~i~p~~~~~i~ 49 (164)
T PF00929_consen 1 VVFDTETTGLDPR----------------------QDEIIEIGAVKVDDDENE---------EVESFNSLIRPEEPPKIS 49 (164)
T ss_dssp EEEEEEESSSTTT----------------------TCTEEEEEEEEEETTTTE---------EEEEEEEEBEHSSHCSSE
T ss_pred cEEEeEcCCCCCC----------------------CCeEEEEEEEEeeCCccc---------cceeeeecccccccccCC
Confidence 6799999998541 123899999888877631 233566652222222233
Q ss_pred hhHHH-------HHHHcC----------ccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcC--Cccc
Q 025183 121 LDSVE-------LLKRQG----------LVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFG--EKVY 181 (256)
Q Consensus 121 ~~Si~-------~L~~~G----------lv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp--~~vy 181 (256)
+.+.+ .|+..+ -.+++...||+++..+|.+++.+.+.. .+...+| ..++
T Consensus 50 ~~~~~~~gIt~~~l~~~~~~~~~~~~~~~~~~~~~~~v~~n~~fd~~~l~~~~~~------------~~~~~~~~~~~~~ 117 (164)
T PF00929_consen 50 PWATKVHGITQEDLEDAPSFEEALDEFEEFLKKNDILVGHNASFDIGFLRREDKR------------FLGKPIPKPNPFI 117 (164)
T ss_dssp HHHHHHHHHCHHHHHCHCEHHHHHHHHHHHHHHHTEEEETTCCHEEESSHHHHHH------------HHHHHHHHHHHEC
T ss_pred HHHeeecCCcccccccCCcHHHHHHhhhhhhhcccccccccccchhhHHHHhhhh------------cccccccccchhh
Confidence 33322 233333 112334578888777888777666441 1111111 1133
Q ss_pred chhHHHHh-hccCC-CcHHHHHHHcCCcccCCCCCcchhhHHHHHHHH
Q 025183 182 DVKHLIRF-CTCLY-GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAF 227 (256)
Q Consensus 182 D~K~la~~-~~~l~-~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F 227 (256)
|+.-+.+. .+... .+|.++++.++++. .+..|.|-+|++.|+++|
T Consensus 118 ~~~~~~~~~~~~~~~~~l~~l~~~~~~~~-~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 118 DTLELARALFPNRKKYSLDDLAEYFGIPF-DGTAHDALDDARATAELF 164 (164)
T ss_dssp EEEEEHHHHHHHHHHHSHHHHHHHTTSSS-TSTTTSHHHHHHHHHHHH
T ss_pred hhhHHHHHHhhccccCCHHHHHHHcCCCC-CCCCcChHHHHHHHhCcC
Confidence 33222222 22222 48999999999998 777999999999999987
No 38
>PTZ00315 2'-phosphotransferase; Provisional
Probab=97.68 E-value=0.0014 Score=65.57 Aligned_cols=152 Identities=16% Similarity=0.163 Sum_probs=95.2
Q ss_pred CeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecC-CCCCCCCCCCCCeeeEEEeeeecccccc
Q 025183 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDE-EGNLPDLGSGSTYYIWEFNFKDFDIARH 117 (256)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~-~g~~p~~~~~~~~~~wqFNF~~F~~~~d 117 (256)
.||++|+|.+|..... .. .-.||++|...++. +|+ .+.+|..+.-+....
T Consensus 57 ~~IV~DlETTgl~~~~---~~----------------~dEIIEIGaV~Vd~~ng~----------Ii~~F~~yVkP~~~p 107 (582)
T PTZ00315 57 AYVVLDFEATCEADRR---IE----------------DAEVIEFPMVLVDARTAT----------PVAEFQRYVRPVKNP 107 (582)
T ss_pred eEEEEEEecCCCCCCC---CC----------------CCceEEEEEEEEEccCCE----------EEEEEEEEECCCCCC
Confidence 6899999999963211 00 12499999999984 442 345666552221111
Q ss_pred cC------------------------chhHHHHHHHcCccc---cCCccEEeecchhhHH-HHHHHhc--C-CCCCCChH
Q 025183 118 AH------------------------ALDSVELLKRQGLVL---NKDVTWVTFHSAYDFG-YLVKCLT--Q-RVLPEKLS 166 (256)
Q Consensus 118 ~~------------------------~~~Si~~L~~~Glv~---~~~v~Wvtfhg~yDf~-yL~k~l~--~-~~LP~~~~ 166 (256)
.. -++-++||.++++.- +.+ ..|...|.+|+. +|-+-+. + ..+|.
T Consensus 108 ~Ls~fct~LTGITqe~V~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~-~~vah~g~fDl~~fL~~e~~~~~~~g~p~--- 183 (582)
T PTZ00315 108 VLSRFCTELTGITQSMVSRADPFPVVYCEALQFLAEAGLGDAPPLRS-YCVVTCGDWDLKTMLPSQMRVSGQQGTPL--- 183 (582)
T ss_pred CCChhHhhhcCcCHHHHhcCCCHHHHHHHHHHHHhccccccccccCc-eEEEeccHHHHHHHHHHHHHHhhhcCCCc---
Confidence 11 122334444443211 111 245666899995 7766543 2 24553
Q ss_pred HHHHHHHhhcCCcccchh-HHHHhh-cc-----------C-CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHH
Q 025183 167 EFVTRVGVFFGEKVYDVK-HLIRFC-TC-----------L-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKD 232 (256)
Q Consensus 167 ~F~~~l~~~Fp~~vyD~K-~la~~~-~~-----------l-~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~ 232 (256)
+|.. .+|+| ++++.. ++ + ..+|+.+++.+|++- .|..|.|=.|+.-|+++|.+|.+
T Consensus 184 --------~f~~-widLk~~lar~l~p~~~~~~~~~~~~~~~~~L~~al~~lgL~~-eGr~HrAlDDA~ntA~L~~~Ll~ 253 (582)
T PTZ00315 184 --------SFQR-WCNLKKYMSQLGFGNGSGCGGGATPPLGPSDMPDMLQMLGLPL-QGRHHSGIDDCRNIAAVLCELLR 253 (582)
T ss_pred --------ccce-EEEhHHHHHHHhCccccccccccccccCCcCHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHHHHHHH
Confidence 3444 67774 666643 21 1 247999999999998 89999999999999999999887
Q ss_pred h
Q 025183 233 K 233 (256)
Q Consensus 233 ~ 233 (256)
.
T Consensus 254 ~ 254 (582)
T PTZ00315 254 R 254 (582)
T ss_pred c
Confidence 6
No 39
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.62 E-value=0.0012 Score=64.84 Aligned_cols=160 Identities=18% Similarity=0.049 Sum_probs=95.6
Q ss_pred cCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeeccccc
Q 025183 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (256)
Q Consensus 37 ~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~ 116 (256)
...||.+|+|-||+.... + .|||+|.-..+.+++. ..-.|+++ .....
T Consensus 5 ~~~fvv~D~ETTGLdP~~---------D-------------rIIeiAaVrvd~~~~~---------i~e~~~~~-~~P~~ 52 (476)
T PRK11779 5 QPTFLWHDYETFGANPAL---------D-------------RPAQFAGIRTDADLNI---------IGEPLVFY-CKPAD 52 (476)
T ss_pred CCcEEEEEEECCCCCCCC---------C-------------eeEEEEEEEEeCCCce---------ecceeEEE-EcCCc
Confidence 567999999999984220 1 3899999888876532 12246665 34433
Q ss_pred c-cCchhHHH-------HHHHcCc------------cccCCccEEeecc-hhhHHHHHHHhcCCCCCCChHHHHHHHHhh
Q 025183 117 H-AHALDSVE-------LLKRQGL------------VLNKDVTWVTFHS-AYDFGYLVKCLTQRVLPEKLSEFVTRVGVF 175 (256)
Q Consensus 117 d-~~~~~Si~-------~L~~~Gl------------v~~~~v~Wvtfhg-~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~ 175 (256)
+ +..++++. .|+.+|+ +..++..+|.||+ .||.+++-+.+...-++.-..+ .....
T Consensus 53 ~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~---~~~~n 129 (476)
T PRK11779 53 DYLPSPEAVLITGITPQEALEKGLPEAEFAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYARE---WQNGN 129 (476)
T ss_pred CcCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHH---hcCCC
Confidence 3 23444443 4556661 2223445888886 4999999888752111100000 00000
Q ss_pred cCCcccchhHHHHhh-c----------c-CCCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHh
Q 025183 176 FGEKVYDVKHLIRFC-T----------C-LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 233 (256)
Q Consensus 176 Fp~~vyD~K~la~~~-~----------~-l~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~ 233 (256)
.+.++.|+-.++... + + -+-.|+.|++.+|++. +.+|.|=+|++.|+.++.+|++.
T Consensus 130 ~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~L~~~~gI~~--~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 130 SRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEH--ENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CccCHHHHHHHHHHhccccccCcccccCCCCCcHHHHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHHh
Confidence 011133333322211 0 1 1246999999999985 67899999999999999999877
No 40
>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=97.52 E-value=0.00026 Score=58.76 Aligned_cols=70 Identities=16% Similarity=0.168 Sum_probs=47.3
Q ss_pred ccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhc---cCCCcHHHHHHH-cCCcccCCCC
Q 025183 138 VTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCT---CLYGGLDRVCKA-LGVERVVGKS 213 (256)
Q Consensus 138 v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~---~l~~gL~~vA~~-L~v~r~~g~~ 213 (256)
-.+|++|..+|+++|- ...|. ..++|+--+..... .-+-+|+.||+. ||++. .+..
T Consensus 78 ~vlVgHn~~fD~~~L~-----~~~~~--------------~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~-~~~~ 137 (152)
T cd06144 78 RILVGHALKNDLKVLK-----LDHPK--------------KLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDI-QEGE 137 (152)
T ss_pred CEEEEcCcHHHHHHhc-----CcCCC--------------ccEEEeEEeeccccccCCCChhHHHHHHHHcCccc-CCCC
Confidence 4689999999999884 12222 11455432222211 124589999997 69875 3467
Q ss_pred CcchhhHHHHHHHH
Q 025183 214 HQAGSDSLLTLHAF 227 (256)
Q Consensus 214 hqAGsdsllT~~~F 227 (256)
|.|.+|++.|+++|
T Consensus 138 H~Al~DA~at~~l~ 151 (152)
T cd06144 138 HSSVEDARAAMRLY 151 (152)
T ss_pred cCcHHHHHHHHHHh
Confidence 99999999999987
No 41
>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=97.50 E-value=0.0015 Score=55.89 Aligned_cols=146 Identities=17% Similarity=0.120 Sum_probs=81.8
Q ss_pred EEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecccccc-cCc
Q 025183 42 SMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH-AHA 120 (256)
Q Consensus 42 AiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d-~~~ 120 (256)
-+|+|-||+... . =.|||+|.-.++.+++.. ..|++. ..+... ...
T Consensus 2 ~~D~ETTGl~~~-------~---------------d~Iieig~v~v~~~~~~~----------~~~~~~-v~p~~~~~~~ 48 (183)
T cd06138 2 FYDYETFGLNPS-------F---------------DQILQFAAIRTDENFNEI----------EPFNIF-CRLPPDVLPS 48 (183)
T ss_pred EEEeecCCCCCC-------C---------------CceEEEEEEEECCCCCCc----------cceeEE-EeCCCCCCCC
Confidence 489999997421 0 138999998887765422 345555 322221 233
Q ss_pred hhHH-------HHHHHcC------------ccccCCccEEeecc-hhhHHHHHHHhcCC---CCCCCh------HHHHHH
Q 025183 121 LDSV-------ELLKRQG------------LVLNKDVTWVTFHS-AYDFGYLVKCLTQR---VLPEKL------SEFVTR 171 (256)
Q Consensus 121 ~~Si-------~~L~~~G------------lv~~~~v~Wvtfhg-~yDf~yL~k~l~~~---~LP~~~------~~F~~~ 171 (256)
++++ +.|+++| .+..+...+|++|+ .+|.+||-+-+... +++.+. -+.+..
T Consensus 49 ~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l 128 (183)
T cd06138 49 PEALIVTGITPQQLLKEGLSEYEFIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDV 128 (183)
T ss_pred HHHHHHhCCCHHHHHhcCCCHHHHHHHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHH
Confidence 3332 3455544 12223456899986 69999998877532 222111 111222
Q ss_pred HHh---hcCCcccchhHHHHhhccC-CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHH
Q 025183 172 VGV---FFGEKVYDVKHLIRFCTCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 226 (256)
Q Consensus 172 l~~---~Fp~~vyD~K~la~~~~~l-~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~ 226 (256)
++. ++|. .++.. ..-.++ ...|+.+++.+|++. ...|-|-+|++.|+++
T Consensus 129 ~r~~~~~~~~-~~~~~---~~~~~~~~~~L~~l~~~~gi~~--~~~H~Al~Da~~ta~l 181 (183)
T cd06138 129 VRAYYALRPD-GIVWP---KNDDGKPSFKLEDLAQANGIEH--SNAHDALSDVEATIAL 181 (183)
T ss_pred HHHHHhhChh-hccCc---cccCCCcchhHHHHHHHCCCCc--cccccHHHHHHHHHHH
Confidence 222 2232 11100 000012 235999999999986 6679999999999864
No 42
>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=97.37 E-value=0.0039 Score=51.28 Aligned_cols=150 Identities=18% Similarity=0.288 Sum_probs=88.3
Q ss_pred HHHHHHHHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeee
Q 025183 25 ISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYI 104 (256)
Q Consensus 25 ~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~ 104 (256)
++++..+.+.+.+.+.||+|+|.+|...... . ... .+|++...++ +
T Consensus 7 ~~~l~~~~~~l~~~~~~a~D~E~~~~~~~~~-----~-------------~~~----~~iq~~~~~~------------~ 52 (176)
T PF01612_consen 7 EEELEEAIKKLKNAKVLAFDTETTGLDPYSY-----N-------------PKI----ALIQLATGEG------------C 52 (176)
T ss_dssp HHHHHHHHHHHTTTSEEEEEEEEETSTSTTS-----S-------------EEE----EEEEEEESCE------------E
T ss_pred HHHHHHHHHHHcCCCeEEEEEEECCCCcccc-----C-------------CeE----EEEEEecCCC------------c
Confidence 4677788888889999999999988643211 0 112 2333333221 1
Q ss_pred EEEeeeecccccccCchhHHHHHHHcCccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchh
Q 025183 105 WEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVK 184 (256)
Q Consensus 105 wqFNF~~F~~~~d~~~~~Si~~L~~~Glv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K 184 (256)
|-+ ...+..... -++.|++ ++-+++++.|.|+..+|+..|.+.+ |-. ..+ ++|+
T Consensus 53 ~i~--~~~~~~~~~----~~~~l~~--ll~~~~i~kv~~n~~~D~~~L~~~~-~i~---------------~~~-~~D~- 106 (176)
T PF01612_consen 53 YII--DPIDLGDNW----ILDALKE--LLEDPNIIKVGHNAKFDLKWLYRSF-GID---------------LKN-VFDT- 106 (176)
T ss_dssp EEE--CGTTSTTTT----HHHHHHH--HHTTTTSEEEESSHHHHHHHHHHHH-TS-----------------SS-EEEH-
T ss_pred eee--eeccccccc----hHHHHHH--HHhCCCccEEEEEEechHHHHHHHh-ccc---------------cCC-ccch-
Confidence 211 001111111 2333332 4557889999988899999999972 211 234 9999
Q ss_pred HHHHhhccCC--CcHHHHHHH-cC-Cccc----CC--C---------CCcchhhHHHHHHHHHHHHHhh
Q 025183 185 HLIRFCTCLY--GGLDRVCKA-LG-VERV----VG--K---------SHQAGSDSLLTLHAFLKIKDKH 234 (256)
Q Consensus 185 ~la~~~~~l~--~gL~~vA~~-L~-v~r~----~g--~---------~hqAGsdsllT~~~F~kl~~~~ 234 (256)
.++..+.+.. .||+.+++. || .... .+ . ..=|+.|+..|.+.|.+|++..
T Consensus 107 ~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 107 MLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp HHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred hhhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 5555543332 589999877 56 2221 11 1 1236779999999999998764
No 43
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=97.33 E-value=0.0032 Score=69.10 Aligned_cols=152 Identities=22% Similarity=0.286 Sum_probs=95.8
Q ss_pred HhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecc
Q 025183 34 LIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFD 113 (256)
Q Consensus 34 ~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~ 113 (256)
.+.+..||++|+|.+|+... + =.|||+|....+ +|. ..-.|+.. .+
T Consensus 415 ~L~~~~~VVfDLETTGL~~~-------------~---------deIIEIgAV~V~-~G~----------iie~F~~~-V~ 460 (1437)
T PRK00448 415 DLKDATYVVFDVETTGLSAV-------------Y---------DEIIEIGAVKIK-NGE----------IIDKFEFF-IK 460 (1437)
T ss_pred hhccCcEEEEEhhhcCCCCc-------------h---------hhhheeeeEEEe-CCe----------EeeeEEEE-EC
Confidence 34567899999999997321 1 147889887765 332 23456665 44
Q ss_pred cccccCchhHH-------HHHHHcC--------cc--ccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhc
Q 025183 114 IARHAHALDSV-------ELLKRQG--------LV--LNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFF 176 (256)
Q Consensus 114 ~~~d~~~~~Si-------~~L~~~G--------lv--~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~F 176 (256)
... ..++.+. +.|+ .+ .+ ...+..+|++++.||+++|-+.+-.--+|. +
T Consensus 461 P~~-~I~~~~~~LTGIT~e~L~-~aps~~EaL~~f~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~------------l 526 (1437)
T PRK00448 461 PGH-PLSAFTTELTGITDDMVK-DAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEK------------I 526 (1437)
T ss_pred CCC-CCCHHHHHHhCCCHHHHc-CCCCHHHHHHHHHHHhCCCEEEEeCccccHHHHHHHHHHcCCcc------------c
Confidence 332 2222221 1222 12 01 124567899999999999977655322221 1
Q ss_pred CCcccchhHHHHhhc-cC-CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 177 GEKVYDVKHLIRFCT-CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 177 p~~vyD~K~la~~~~-~l-~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
.....|+--+++... .. ..+|+.+|+.+|+.. .+ .|-|-+|++.|+++|.+|.+...
T Consensus 527 ~~~~IDTLelar~l~p~~k~~kL~~LAk~lGL~~-~~-~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 527 KNPVIDTLELSRFLYPELKSHRLNTLAKKFGVEL-EH-HHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred cccceeHHHHHHHHcCccccccHHHHHHHcCCCC-CC-CcChHHHHHHHHHHHHHHHHHHH
Confidence 122567655554432 22 457999999999987 44 59999999999999999988765
No 44
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=97.29 E-value=0.0056 Score=56.67 Aligned_cols=142 Identities=17% Similarity=0.173 Sum_probs=85.4
Q ss_pred CeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecC--CCCCCCCCCCCCeeeEEEeeeeccccc
Q 025183 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDE--EGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (256)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~--~g~~p~~~~~~~~~~wqFNF~~F~~~~ 116 (256)
.+|++|||-||+.... =.|||+|+..++. +|+.- ...-.|+.. .+...
T Consensus 38 ~~vvlD~ETTGLd~~~----------------------d~IIEIg~V~v~~~~~g~i~-------~v~~~~~~l-v~P~~ 87 (294)
T PRK09182 38 LGVILDTETTGLDPRK----------------------DEIIEIGMVAFEYDDDGRIG-------DVLDTFGGL-QQPSR 87 (294)
T ss_pred eEEEEEeeCCCCCCCC----------------------CeEEEEEEEEEEecCCCcee-------eeeeEEEEE-eCCCC
Confidence 5899999999984321 1399999999875 45431 133456666 44433
Q ss_pred ccCchhHH-------HHHHHcCc-------cccCCccEEeecchhhHHHHHHHhcC---CCCCCChHHHHHHHHhhcCCc
Q 025183 117 HAHALDSV-------ELLKRQGL-------VLNKDVTWVTFHSAYDFGYLVKCLTQ---RVLPEKLSEFVTRVGVFFGEK 179 (256)
Q Consensus 117 d~~~~~Si-------~~L~~~Gl-------v~~~~v~Wvtfhg~yDf~yL~k~l~~---~~LP~~~~~F~~~l~~~Fp~~ 179 (256)
..++++. +.++.++. .+...-..|+||..||..||-+.+.. .+...+...
T Consensus 88 -~I~~~~t~IhGIt~e~v~~~~~~~~~l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~------------ 154 (294)
T PRK09182 88 -PIPPEITRLTGITDEMVAGQTIDPAAVDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSE------------ 154 (294)
T ss_pred -CCCHHHHHhcCCCHHHHhcCCCcHHHHHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHH------------
Confidence 2233332 23344341 11223367899999999999775421 111111110
Q ss_pred ccchhHHHHhhccC-CCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHH
Q 025183 180 VYDVKHLIRFCTCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKD 232 (256)
Q Consensus 180 vyD~K~la~~~~~l-~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~ 232 (256)
.|.+ -.++ ...|+.||+.+| . ....|.|-+|++.|+++|.++..
T Consensus 155 -i~~~-----~~~~~~~kL~~La~~~g--~-~~~aHrAl~Da~Ata~ll~~~l~ 199 (294)
T PRK09182 155 -IDWS-----ARGFEGTKLGYLAGQAG--F-FHEGHRAVDDCQALLELLARPLP 199 (294)
T ss_pred -Hhhc-----cccCCCCCHHHHHHHcC--C-CCCCcChHHHHHHHHHHHHHHHh
Confidence 0100 0112 346999999999 2 35679999999999999997543
No 45
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=97.06 E-value=0.0097 Score=52.54 Aligned_cols=148 Identities=22% Similarity=0.266 Sum_probs=95.5
Q ss_pred CCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEEeeeecccccc
Q 025183 38 YPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH 117 (256)
Q Consensus 38 ~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d 117 (256)
..||.+|+|-+|... ..-.+|++|.-.+..+..... .|... .+. ..
T Consensus 13 ~~~vv~D~ETtg~~~----------------------~~~~iieIgav~~~~~~i~~~----------~~~~~-v~P-~~ 58 (243)
T COG0847 13 TRFVVIDLETTGLNP----------------------KKDRIIEIGAVTLEDGRIVER----------SFHTL-VNP-ER 58 (243)
T ss_pred CcEEEEecccCCCCC----------------------CCCceEEEEeEEEECCeeecc----------eeEEE-ECC-CC
Confidence 689999999999854 112488999887766533211 13333 222 11
Q ss_pred cCchhH-------HHHHHHc---C------c-cccCCccEEeecchhhHHHHHHHhcC--CCCCCChHHHHHHHHhhcCC
Q 025183 118 AHALDS-------VELLKRQ---G------L-VLNKDVTWVTFHSAYDFGYLVKCLTQ--RVLPEKLSEFVTRVGVFFGE 178 (256)
Q Consensus 118 ~~~~~S-------i~~L~~~---G------l-v~~~~v~Wvtfhg~yDf~yL~k~l~~--~~LP~~~~~F~~~l~~~Fp~ 178 (256)
.+.+++ -+.|+.+ . + ..++.-.+|+++-++|.++|-+.+.. .+.| +.
T Consensus 59 ~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~i~~~~~~Vahna~fD~~fl~~~~~~~~~~~~--------------~~ 124 (243)
T COG0847 59 PIPPEIFKIHGITDEMLADAPKFAEVLPEFLDFIGGLRLLVAHNAAFDVGFLRVESERLGIEIP--------------GD 124 (243)
T ss_pred CCChhhhhhcCCCHHHHhcCCCHHHHHHHHHHHHCCCCeEEEEchhhcHHHHHHHHHHcCCCcc--------------cC
Confidence 122222 2223332 1 0 11232578999999999999877553 3433 22
Q ss_pred cccchhHHHHhh-cc-CCCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHh
Q 025183 179 KVYDVKHLIRFC-TC-LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 233 (256)
Q Consensus 179 ~vyD~K~la~~~-~~-l~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~ 233 (256)
.++|+--+++.. ++ -..+|+.+|+.+|+++.....|.|-.|+++|+..|.++...
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 267776666664 44 35689999999999974345689999999999999998874
No 46
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=96.85 E-value=0.0049 Score=51.60 Aligned_cols=71 Identities=18% Similarity=0.083 Sum_probs=45.8
Q ss_pred CccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhH---HHHh--hccC-CCcHHHHHHHc---CCc
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKH---LIRF--CTCL-YGGLDRVCKAL---GVE 207 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~---la~~--~~~l-~~gL~~vA~~L---~v~ 207 (256)
+-.+|++|-.+|+.+|-.. ..| ..+.||-. +.+. .+.. +-+|+.||+.+ +++
T Consensus 77 ~~vlV~Hn~~~D~~~l~~~----~~~---------------~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~ 137 (157)
T cd06149 77 GKVVVGHAIHNDFKALKYF----HPK---------------HMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQ 137 (157)
T ss_pred CCEEEEeCcHHHHHHhccc----CCC---------------cCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhc
Confidence 4468888888999887532 111 11334421 1111 1122 35899999998 566
Q ss_pred ccCCCCCcchhhHHHHHHHH
Q 025183 208 RVVGKSHQAGSDSLLTLHAF 227 (256)
Q Consensus 208 r~~g~~hqAGsdsllT~~~F 227 (256)
. .+..|.|-+||+.|++.|
T Consensus 138 ~-~~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 138 V-GRQGHSSVEDARATMELY 156 (157)
T ss_pred C-CCCCcCcHHHHHHHHHHh
Confidence 5 466899999999999987
No 47
>PRK05755 DNA polymerase I; Provisional
Probab=96.47 E-value=0.062 Score=56.66 Aligned_cols=86 Identities=20% Similarity=0.204 Sum_probs=61.0
Q ss_pred cccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhcc-CCCcHHHHHHHc-CCccc-
Q 025183 133 VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC-LYGGLDRVCKAL-GVERV- 209 (256)
Q Consensus 133 v~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~-l~~gL~~vA~~L-~v~r~- 209 (256)
+-++.+..|+|+.-+|+.+|.+. |-++| +. ++||..++..+.. ...||+.+++.. |+.-.
T Consensus 366 L~d~~v~kV~HNakfDl~~L~~~--gi~~~--------------~~-~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~ 428 (880)
T PRK05755 366 LEDPAIKKVGQNLKYDLHVLARY--GIELR--------------GI-AFDTMLASYLLDPGRRHGLDSLAERYLGHKTIS 428 (880)
T ss_pred HhCCCCcEEEeccHhHHHHHHhC--CCCcC--------------CC-cccHHHHHHHcCCCCCCCHHHHHHHHhCCCccc
Confidence 34556677888888999998863 44433 23 8999998887752 236899998874 55410
Q ss_pred ----------------CCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 210 ----------------VGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 210 ----------------~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
....|.|..|+.+|..+|.+|++.+-
T Consensus 429 ~~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 429 FEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred hHHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 01236789999999999999988754
No 48
>PRK10829 ribonuclease D; Provisional
Probab=96.47 E-value=0.03 Score=53.58 Aligned_cols=147 Identities=20% Similarity=0.246 Sum_probs=92.4
Q ss_pred HHHHHHHHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeee
Q 025183 25 ISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYI 104 (256)
Q Consensus 25 ~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~ 104 (256)
.+++..+.+.+..++.||+||||-+... +. ..+-+||+. +|+ .+
T Consensus 9 ~~~L~~~~~~l~~~~~lalDtEf~~~~t-----y~---------------~~l~LiQl~------~~~----------~~ 52 (373)
T PRK10829 9 DDALASVCEAARAFPAIALDTEFVRTRT-----YY---------------PQLGLIQLY------DGE----------QL 52 (373)
T ss_pred HHHHHHHHHHHhcCCeEEEecccccCcc-----CC---------------CceeEEEEe------cCC----------ce
Confidence 3566666666899999999999865311 11 134588887 121 12
Q ss_pred EEEeeeecccccccCchhHHHHHHHcCccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchh
Q 025183 105 WEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVK 184 (256)
Q Consensus 105 wqFNF~~F~~~~d~~~~~Si~~L~~~Glv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K 184 (256)
+ .+|.-. ...++.|.. ++-++++.-|.|.+.+|+..|.+.+ |. .|..++||.
T Consensus 53 ~-----LiD~l~----~~d~~~L~~--ll~~~~ivKV~H~~~~Dl~~l~~~~-g~----------------~p~~~fDTq 104 (373)
T PRK10829 53 S-----LIDPLG----ITDWSPFKA--LLRDPQVTKFLHAGSEDLEVFLNAF-GE----------------LPQPLIDTQ 104 (373)
T ss_pred E-----EEecCC----ccchHHHHH--HHcCCCeEEEEeChHhHHHHHHHHc-CC----------------CcCCeeeHH
Confidence 2 133211 111222322 4445665555555669999997754 31 244499999
Q ss_pred HHHHhhc-cCCCcHHHHHHH-cCCcc------------c--CCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 185 HLIRFCT-CLYGGLDRVCKA-LGVER------------V--VGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 185 ~la~~~~-~l~~gL~~vA~~-L~v~r------------~--~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
..+..++ +..-||..+.+. ||+.- + ..+.+=|..|+.....+|-+|++..-
T Consensus 105 iaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 105 ILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred HHHHHcCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9998886 335689987766 78842 1 12344578899999999999888764
No 49
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=96.39 E-value=0.014 Score=55.54 Aligned_cols=144 Identities=27% Similarity=0.331 Sum_probs=86.4
Q ss_pred HHHHHHHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeE
Q 025183 26 SEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIW 105 (256)
Q Consensus 26 ~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~w 105 (256)
+++..+...+..+.+|||||||-|.... . +.+-+||+. +.++ ++
T Consensus 5 ~~l~~~~~~~~~~~~iAiDTEf~r~~t~-----~---------------p~LcLIQi~----~~e~------------~~ 48 (361)
T COG0349 5 DLLAAACALLRGSKAIAIDTEFMRLRTY-----Y---------------PRLCLIQIS----DGEG------------AS 48 (361)
T ss_pred hHHHHHHHHhcCCCceEEeccccccccc-----C---------------CceEEEEEe----cCCC------------ce
Confidence 4556666777889999999999886322 1 235577763 2222 11
Q ss_pred EEeeeecccccccCch-hHHHHHHHcCccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchh
Q 025183 106 EFNFKDFDIARHAHAL-DSVELLKRQGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVK 184 (256)
Q Consensus 106 qFNF~~F~~~~d~~~~-~Si~~L~~~Glv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K 184 (256)
- .|.-...... .-..+| -+++|+=|-+++..|+..|.+.+ | -+| ..+||||
T Consensus 49 l-----Idpl~~~~d~~~l~~Ll------~d~~v~KIfHaa~~DL~~l~~~~-g-~~p---------------~plfdTq 100 (361)
T COG0349 49 L-----IDPLAGILDLPPLVALL------ADPNVVKIFHAARFDLEVLLNLF-G-LLP---------------TPLFDTQ 100 (361)
T ss_pred E-----ecccccccccchHHHHh------cCCceeeeeccccccHHHHHHhc-C-CCC---------------CchhHHH
Confidence 1 1111101111 112222 34444444444669999999987 3 333 3399999
Q ss_pred HHHHhhcc-CCCcHHHHHHH-cCCcccCCCCCc----------------chhhHHHHHHHHHHHHHhhC
Q 025183 185 HLIRFCTC-LYGGLDRVCKA-LGVERVVGKSHQ----------------AGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 185 ~la~~~~~-l~~gL~~vA~~-L~v~r~~g~~hq----------------AGsdsllT~~~F~kl~~~~~ 235 (256)
..++.|.. .+.||.++.++ +||. +.+.|| |-+|...=...+.+|.+..-
T Consensus 101 iAa~l~g~~~~~gl~~Lv~~ll~v~--ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~ 167 (361)
T COG0349 101 IAAKLAGFGTSHGLADLVEELLGVE--LDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELA 167 (361)
T ss_pred HHHHHhCCcccccHHHHHHHHhCCc--ccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999963 37799988876 6775 233333 44577666777777777654
No 50
>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=96.32 E-value=0.053 Score=45.10 Aligned_cols=146 Identities=17% Similarity=0.157 Sum_probs=91.5
Q ss_pred HHHHHHHHHHhh-cCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCee
Q 025183 25 ISEFERIRALID-RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYY 103 (256)
Q Consensus 25 ~~e~~~I~~~i~-~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~ 103 (256)
++++..+.+.+. +.+.|++|||+.+..... . -....+||+. + + ..
T Consensus 4 ~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~~---~---------------~~~~~liQl~-~-----~----------~~ 49 (170)
T cd06141 4 AQDAEEAVKELLGKEKVVGFDTEWRPSFRKG---K---------------RNKVALLQLA-T-----E----------SR 49 (170)
T ss_pred HHHHHHHHHHHhcCCCEEEEeCccCCccCCC---C---------------CCCceEEEEe-c-----C----------Cc
Confidence 456666666666 999999999998653320 0 1224577776 1 1 12
Q ss_pred eEEEeeeecccccccCchhHHHHHHHcCccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccch
Q 025183 104 IWEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDV 183 (256)
Q Consensus 104 ~wqFNF~~F~~~~d~~~~~Si~~L~~~Glv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~ 183 (256)
++-|... .....+..+ ++ ++.+++++.|+|+.-.|+..|.+.+ |-. +.+ ++|+
T Consensus 50 ~~l~~~~-----~~~~~~~~l---~~--ll~~~~i~kv~~~~k~D~~~L~~~~-g~~---------------~~~-~~Dl 102 (170)
T cd06141 50 CLLFQLA-----HMDKLPPSL---KQ--LLEDPSILKVGVGIKGDARKLARDF-GIE---------------VRG-VVDL 102 (170)
T ss_pred EEEEEhh-----hhhcccHHH---HH--HhcCCCeeEEEeeeHHHHHHHHhHc-CCC---------------CCC-eeeH
Confidence 3333322 111111222 11 3445678888888889999886553 322 234 8999
Q ss_pred hHHHHhhccC--CCcHHHHHHHc-CCcc----------------cCCCCCcchhhHHHHHHHHHHHH
Q 025183 184 KHLIRFCTCL--YGGLDRVCKAL-GVER----------------VVGKSHQAGSDSLLTLHAFLKIK 231 (256)
Q Consensus 184 K~la~~~~~l--~~gL~~vA~~L-~v~r----------------~~g~~hqAGsdsllT~~~F~kl~ 231 (256)
..++..+..- ..||+.+++.+ |+.- ...+.|-|..|+++...+|.+|+
T Consensus 103 ~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 103 SHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999888643 35999999884 5522 02345678999999999999886
No 51
>PRK05359 oligoribonuclease; Provisional
Probab=96.06 E-value=0.098 Score=44.88 Aligned_cols=77 Identities=16% Similarity=0.210 Sum_probs=45.6
Q ss_pred EEeecc-hhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccCCCcHHHHHHHcCCcccCCCCCcchh
Q 025183 140 WVTFHS-AYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGS 218 (256)
Q Consensus 140 Wvtfhg-~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l~~gL~~vA~~L~v~r~~g~~hqAGs 218 (256)
+++.|+ .+|..||-+-+- .+...+..++.|+--+.+.+..+...+ ..++++ . ..|.|=+
T Consensus 100 ~l~g~~v~FD~~FL~~~~~-------------~~~~~l~~~~~Dv~tl~~l~r~~~P~~-----~~~~~~-~-~~HRal~ 159 (181)
T PRK05359 100 PLCGNSIGQDRRFLARYMP-------------ELEAYFHYRNLDVSTLKELARRWKPEI-----LNGFKK-Q-GTHRALA 159 (181)
T ss_pred ceeecchhhCHHHHHHHHH-------------HhcccCCCcccchhHHHHHHHHhChhh-----hhCCCC-c-CCcccHH
Confidence 445555 799999988763 122233333445322211111122222 125555 3 4599999
Q ss_pred hHHHHHHHHHHHHHhhCC
Q 025183 219 DSLLTLHAFLKIKDKHFG 236 (256)
Q Consensus 219 dsllT~~~F~kl~~~~~~ 236 (256)
|.+-|.+++...++.++.
T Consensus 160 D~~~s~~~~~~~~~~~~~ 177 (181)
T PRK05359 160 DIRESIAELKYYREHFFK 177 (181)
T ss_pred HHHHHHHHHHHHHHHhcc
Confidence 999999999999998874
No 52
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=95.99 E-value=0.13 Score=44.48 Aligned_cols=156 Identities=19% Similarity=0.201 Sum_probs=95.7
Q ss_pred HHHHHHHHHH--hhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCe
Q 025183 25 ISEFERIRAL--IDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTY 102 (256)
Q Consensus 25 ~~e~~~I~~~--i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~ 102 (256)
.+|+..+... +.+.+.|++|||+.+....+ .-..+.+||+.- .+
T Consensus 7 ~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~~------------------~~~~v~LiQiat-----~~----------- 52 (193)
T cd06146 7 EEELEALLLALSLEAGRVVGIDSEWKPSFLGD------------------SDPRVAILQLAT-----ED----------- 52 (193)
T ss_pred HHHHHHHHHHHhhccCCEEEEECccCCCccCC------------------CCCCceEEEEec-----CC-----------
Confidence 4567777777 89999999999987543221 012456889872 11
Q ss_pred eeEEEeeeeccccccc-Cchh-HHHHHHHcCccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcc
Q 025183 103 YIWEFNFKDFDIARHA-HALD-SVELLKRQGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKV 180 (256)
Q Consensus 103 ~~wqFNF~~F~~~~d~-~~~~-Si~~L~~~Glv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~v 180 (256)
.++-| |+.... ...+ -.++|++ ++-++++.=|.|+...|+..|.+.+.. ++. . ..-|.++
T Consensus 53 ~~~li-----d~~~~~~~~~~~~~~~L~~--ll~d~~i~KVg~~~~~D~~~L~~~~~~--~~~-~--------~~~~~~v 114 (193)
T cd06146 53 EVFLL-----DLLALENLESEDWDRLLKR--LFEDPDVLKLGFGFKQDLKALSASYPA--LKC-M--------FERVQNV 114 (193)
T ss_pred CEEEE-----EchhccccchHHHHHHHHH--HhCCCCeeEEEechHHHHHHHHHhcCc--ccc-c--------cccCCce
Confidence 23323 322111 1111 2233333 455677777877788999999886542 111 0 0114559
Q ss_pred cchhHHHHhhcc------------CCCcHHHHHHH-cCCcc--------------cCCCCCcchhhHHHHHHHHHHHHH
Q 025183 181 YDVKHLIRFCTC------------LYGGLDRVCKA-LGVER--------------VVGKSHQAGSDSLLTLHAFLKIKD 232 (256)
Q Consensus 181 yD~K~la~~~~~------------l~~gL~~vA~~-L~v~r--------------~~g~~hqAGsdsllT~~~F~kl~~ 232 (256)
+|+..+++.... -..||+.+++. ||++- ...+.+-|..|++...++|-+|++
T Consensus 115 ~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 115 LDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred EEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 999998886531 23589999987 45531 123456788999999999999863
No 53
>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=95.60 E-value=0.12 Score=42.93 Aligned_cols=142 Identities=15% Similarity=0.156 Sum_probs=89.6
Q ss_pred HHHHHHhh-cCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeeeEEE
Q 025183 29 ERIRALID-RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEF 107 (256)
Q Consensus 29 ~~I~~~i~-~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqF 107 (256)
..+.+.+. +.+.|++|||+..... |. ..+.+||+.-. + ..++-|
T Consensus 3 ~~~~~~l~~~~~~ig~D~E~~~~~~--------------~~------~~~~liQl~~~-----~----------~~~~l~ 47 (161)
T cd06129 3 SSLCEDLSMDGDVIAFDMEWPPGRR--------------YY------GEVALIQLCVS-----E----------EKCYLF 47 (161)
T ss_pred HHHHHHHhcCCCEEEEECCccCCCC--------------CC------CceEEEEEEEC-----C----------CCEEEE
Confidence 34555566 9999999999975421 10 24668888732 1 123433
Q ss_pred eeeecccccccCchhHHHHHHHcCccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHH
Q 025183 108 NFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLI 187 (256)
Q Consensus 108 NF~~F~~~~d~~~~~Si~~L~~~Glv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la 187 (256)
... ... ..+.++.- ++.+++++.|.++...|+..|.+. .|-. +.+ ++|+..++
T Consensus 48 d~~--~~~---~~~~~L~~-----lL~d~~i~Kvg~~~k~D~~~L~~~-~gi~---------------~~~-~~D~~~aa 100 (161)
T cd06129 48 DPL--SLS---VDWQGLKM-----LLENPSIVKALHGIEGDLWKLLRD-FGEK---------------LQR-LFDTTIAA 100 (161)
T ss_pred ecc--cCc---cCHHHHHH-----HhCCCCEEEEEeccHHHHHHHHHH-cCCC---------------ccc-HhHHHHHH
Confidence 332 111 12333322 344677888888888998887664 2322 123 78999888
Q ss_pred Hhhcc-CCCcHHHHHHH-cCCcc------------c--CCCCCcchhhHHHHHHHHHHHHH
Q 025183 188 RFCTC-LYGGLDRVCKA-LGVER------------V--VGKSHQAGSDSLLTLHAFLKIKD 232 (256)
Q Consensus 188 ~~~~~-l~~gL~~vA~~-L~v~r------------~--~g~~hqAGsdsllT~~~F~kl~~ 232 (256)
..... .+.||+.+++. ||+.- + ..+.+-|..|++....+|.+|++
T Consensus 101 ~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 101 NLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLRN 161 (161)
T ss_pred HHhCCCCCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 87753 24599999987 57632 1 23456788999999999999863
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=95.43 E-value=0.18 Score=42.73 Aligned_cols=76 Identities=14% Similarity=0.202 Sum_probs=46.9
Q ss_pred cEEeecc-hhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccCCCcHHHHHHHcCCcccCCCCCcch
Q 025183 139 TWVTFHS-AYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAG 217 (256)
Q Consensus 139 ~Wvtfhg-~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l~~gL~~vA~~L~v~r~~g~~hqAG 217 (256)
..+..|+ .+|+++|-+.+.. ...++.....|+.-+.+....+...+.+ +++.. +..|.|=
T Consensus 95 ~~lvgh~~~FD~~fL~~~~~~-------------~~~~~~~~~~D~~~l~~l~~~l~p~~~~----~~~~~--~~~HrAl 155 (173)
T cd06135 95 SPLAGNSVHQDRRFLDKYMPE-------------LEEYLHYRILDVSSIKELARRWYPEIYR----KAPKK--KGTHRAL 155 (173)
T ss_pred CceeecchhhCHHHHHHHHHH-------------HhccCCcchhhHHHHHHHHHHhCcHhhh----cCCCC--CCCcchH
Confidence 4566777 7999999887641 1122333356763332222222233322 45554 6679999
Q ss_pred hhHHHHHHHHHHHHHh
Q 025183 218 SDSLLTLHAFLKIKDK 233 (256)
Q Consensus 218 sdsllT~~~F~kl~~~ 233 (256)
+|++-|...+..+++-
T Consensus 156 ~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 156 DDIRESIAELKYYREN 171 (173)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999887764
No 55
>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=95.17 E-value=0.36 Score=45.99 Aligned_cols=147 Identities=22% Similarity=0.307 Sum_probs=89.5
Q ss_pred HHHHHHHHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCCeee
Q 025183 25 ISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYI 104 (256)
Q Consensus 25 ~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~ 104 (256)
.+++..+.+.+...+.||+||||..... +. ..+-+||+.- |+ .+
T Consensus 5 ~~~l~~~~~~l~~~~~ia~DtE~~~~~~-----y~---------------~~l~LiQia~------~~----------~~ 48 (367)
T TIGR01388 5 DDELATVCEAVRTFPFVALDTEFVRERT-----FW---------------PQLGLIQVAD------GE----------QL 48 (367)
T ss_pred HHHHHHHHHHHhcCCEEEEeccccCCCC-----CC---------------CcceEEEEee------CC----------eE
Confidence 3677777777888999999999875411 11 1245888862 11 12
Q ss_pred EEEeeeecccccccCchhHHHHHHHcCccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchh
Q 025183 105 WEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVK 184 (256)
Q Consensus 105 wqFNF~~F~~~~d~~~~~Si~~L~~~Glv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K 184 (256)
+- +|.-.. .. ++.|.. ++.++++++|.|+..+|+..|.+.. ..+| ..++||.
T Consensus 49 ~l-----iD~~~~-~~---~~~L~~--lL~d~~i~KV~h~~k~Dl~~L~~~~--~~~~---------------~~~fDtq 100 (367)
T TIGR01388 49 AL-----IDPLVI-ID---WSPLKE--LLRDESVVKVLHAASEDLEVFLNLF--GELP---------------QPLFDTQ 100 (367)
T ss_pred EE-----EeCCCc-cc---HHHHHH--HHCCCCceEEEeecHHHHHHHHHHh--CCCC---------------CCcccHH
Confidence 21 333211 11 222221 4446788899888889999876542 2333 2389999
Q ss_pred HHHHhhcc-CCCcHHHHHHH-cCCcccCC--------------CCCcchhhHHHHHHHHHHHHHhhC
Q 025183 185 HLIRFCTC-LYGGLDRVCKA-LGVERVVG--------------KSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 185 ~la~~~~~-l~~gL~~vA~~-L~v~r~~g--------------~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
..+..++. ...||+.+++. ||+.-.-+ +.+-|..|+......|-+|++..-
T Consensus 101 lAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 101 IAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLE 167 (367)
T ss_pred HHHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88887752 34589998876 56642101 011266777777788888877654
No 56
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=94.27 E-value=0.1 Score=43.66 Aligned_cols=69 Identities=22% Similarity=0.219 Sum_probs=52.4
Q ss_pred ccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhc-cC----CCcHHHHHHH-cCCcccC-
Q 025183 138 VTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCT-CL----YGGLDRVCKA-LGVERVV- 210 (256)
Q Consensus 138 v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~-~l----~~gL~~vA~~-L~v~r~~- 210 (256)
-.+|++|..+|+.+|-.. .+. +.||-.|++... .. +-+|+.|++. +|++-..
T Consensus 85 ~vlVgHn~~fD~~fL~~~--------------------~~~-~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~ 143 (161)
T cd06137 85 TILVGHSLQNDLDALRMI--------------------HTR-VVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGG 143 (161)
T ss_pred cEEEeccHHHHHHHHhCc--------------------CCC-eeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCC
Confidence 468888888999998321 245 889999988754 32 4589999987 7876422
Q ss_pred CCCCcchhhHHHHHHHH
Q 025183 211 GKSHQAGSDSLLTLHAF 227 (256)
Q Consensus 211 g~~hqAGsdsllT~~~F 227 (256)
...|.|-.|+..|+++|
T Consensus 144 ~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 144 GEGHDSLEDALAAREVV 160 (161)
T ss_pred CCCCCcHHHHHHHHHHh
Confidence 46799999999999887
No 57
>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=93.47 E-value=0.21 Score=41.35 Aligned_cols=70 Identities=19% Similarity=0.119 Sum_probs=50.7
Q ss_pred CccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhcc-C-CCcHHHHHHHc-CCcccC-CC
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC-L-YGGLDRVCKAL-GVERVV-GK 212 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~-l-~~gL~~vA~~L-~v~r~~-g~ 212 (256)
+-.+|++|..+|+.+|-. .-+. ++||-.+++.... . +-+|+.|++.+ +..-.. +.
T Consensus 76 ~~vlVgHn~~fD~~fL~~--------------------~~~~-~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~ 134 (150)
T cd06145 76 DTILVGHSLENDLKALKL--------------------IHPR-VIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEG 134 (150)
T ss_pred CCEEEEcChHHHHHHhhc--------------------cCCC-EEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCC
Confidence 457899999999999742 1145 8899888765321 2 34899999886 432212 46
Q ss_pred CCcchhhHHHHHHHH
Q 025183 213 SHQAGSDSLLTLHAF 227 (256)
Q Consensus 213 ~hqAGsdsllT~~~F 227 (256)
.|.|-+|++.|++.|
T Consensus 135 ~H~Al~DA~~t~~l~ 149 (150)
T cd06145 135 GHDSVEDARAALELV 149 (150)
T ss_pred CCCcHHHHHHHHHHh
Confidence 799999999999887
No 58
>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=92.61 E-value=0.056 Score=44.56 Aligned_cols=75 Identities=24% Similarity=0.325 Sum_probs=41.0
Q ss_pred CccEEeecc-hhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccCCC-cHHHHHHHcCCcccCCCCC
Q 025183 137 DVTWVTFHS-AYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYG-GLDRVCKALGVERVVGKSH 214 (256)
Q Consensus 137 ~v~Wvtfhg-~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l~~-gL~~vA~~L~v~r~~g~~h 214 (256)
.-.+|+||| .||+.+|-+.+..-.+|. +....|+...++.... .+ +|..||+.||+.| . ...
T Consensus 57 ~~~iv~yng~~FD~p~L~~~~~~~~~~~-------------~~~~iDl~~~~~~~~~-~~~~Lk~ve~~lg~~~-~-~~~ 120 (164)
T PF13482_consen 57 ADNIVTYNGKNFDIPFLKRRAKRYGLPP-------------PFNHIDLLKIIKKHFL-ESYSLKNVEKFLGIER-R-DDD 120 (164)
T ss_dssp T--EEESSTTTTHHHHHHHHH-HHHH---------------GGGEEEHHHHHT-TTS-CCTT--SHHH------------
T ss_pred CCeEEEEeCcccCHHHHHHHHHHcCCCc-------------ccchhhHHHHHHhccC-CCCCHHHHhhhccccc-c-cCC
Confidence 347999997 599999999984333444 4447899888876543 44 8999999999998 2 223
Q ss_pred cchhhHHHHHHHH
Q 025183 215 QAGSDSLLTLHAF 227 (256)
Q Consensus 215 qAGsdsllT~~~F 227 (256)
..|+++....+-|
T Consensus 121 ~~G~~~~~~~~~~ 133 (164)
T PF13482_consen 121 ISGSESVKLYKEY 133 (164)
T ss_dssp -HHHHHHHHHH--
T ss_pred CCHHHHHHHHHHH
Confidence 5788877775543
No 59
>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=90.06 E-value=4.5 Score=34.84 Aligned_cols=87 Identities=16% Similarity=0.061 Sum_probs=57.7
Q ss_pred ccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccC---------CCcHHHHHH
Q 025183 132 LVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCL---------YGGLDRVCK 202 (256)
Q Consensus 132 lv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l---------~~gL~~vA~ 202 (256)
++-++++.+|.|..-+|...|.+.+ |-. +.+++||..++..+..- ..||+.+++
T Consensus 60 iLe~~~i~Kv~h~~k~D~~~L~~~~-gi~----------------~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~ 122 (197)
T cd06148 60 ILESKKILKVIHDCRRDSDALYHQY-GIK----------------LNNVFDTQVADALLQEQETGGFNPDRVISLVQLLD 122 (197)
T ss_pred HhcCCCccEEEEechhHHHHHHHhc-Ccc----------------ccceeeHHHHHHHHHHHhcCCccccccccHHHHHH
Confidence 4446788899888889988875432 322 22378888766655321 137888877
Q ss_pred H-cCCc--------------------cc--CCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 203 A-LGVE--------------------RV--VGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 203 ~-L~v~--------------------r~--~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
. |+++ |+ .....=|..|+.....+|.+|++.+-
T Consensus 123 ~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~ 178 (197)
T cd06148 123 KYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALI 178 (197)
T ss_pred HhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhh
Confidence 6 4552 11 12334588899999999999988764
No 60
>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=87.73 E-value=2 Score=38.07 Aligned_cols=93 Identities=20% Similarity=0.266 Sum_probs=55.9
Q ss_pred CccEEeecch-hhHHHHHHH--hcCCCCCCChHHHH----HHHHhhcCCcccchhHHHHhh-ccCCCcHHHHHHHcCCcc
Q 025183 137 DVTWVTFHSA-YDFGYLVKC--LTQRVLPEKLSEFV----TRVGVFFGEKVYDVKHLIRFC-TCLYGGLDRVCKALGVER 208 (256)
Q Consensus 137 ~v~Wvtfhg~-yDf~yL~k~--l~~~~LP~~~~~F~----~~l~~~Fp~~vyD~K~la~~~-~~l~~gL~~vA~~L~v~r 208 (256)
+-++|||+|. +|+-||..= ..|-++|.-.+.=- ...+.|--. -.|+.-+-... ..-+.+|..+|..||++-
T Consensus 52 ~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~-H~DLmd~l~~~g~~~~~sLd~la~~lgiPg 130 (209)
T PF10108_consen 52 NPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSER-HLDLMDLLSFYGAKARTSLDELAALLGIPG 130 (209)
T ss_pred CCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcc-cccHHHHHhccCccccCCHHHHHHHcCCCC
Confidence 4579999965 999999763 33567776443200 001111111 34544332222 123568999999999974
Q ss_pred cCCCCCcch--------------------hhHHHHHHHHHHHHHh
Q 025183 209 VVGKSHQAG--------------------SDSLLTLHAFLKIKDK 233 (256)
Q Consensus 209 ~~g~~hqAG--------------------sdsllT~~~F~kl~~~ 233 (256)
+....| +|.+-|.++|.|+...
T Consensus 131 ---K~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~ 172 (209)
T PF10108_consen 131 ---KDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELL 172 (209)
T ss_pred ---CCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 223334 3899999999998654
No 61
>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=86.22 E-value=2 Score=35.74 Aligned_cols=84 Identities=20% Similarity=0.222 Sum_probs=57.4
Q ss_pred cCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhcc-C-CCcHHHHHHHc-CCcc---
Q 025183 135 NKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC-L-YGGLDRVCKAL-GVER--- 208 (256)
Q Consensus 135 ~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~-l-~~gL~~vA~~L-~v~r--- 208 (256)
+.++++|+++..+|+..|.+. |-++ +..++|+..++..+.. . +.+|+.+++.+ +..-
T Consensus 65 ~~~~~~v~hn~k~d~~~l~~~--gi~~---------------~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~ 127 (193)
T cd06139 65 DPSIKKVGQNLKFDLHVLANH--GIEL---------------RGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISF 127 (193)
T ss_pred CCCCcEEeeccHHHHHHHHHC--CCCC---------------CCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccH
Confidence 445788999999999998653 3332 3337899988887753 3 45899988874 4320
Q ss_pred --cCC---------------CCCcchhhHHHHHHHHHHHHHhhC
Q 025183 209 --VVG---------------KSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 209 --~~g---------------~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
..| ..|.|..|+.+|...+-+|++..-
T Consensus 128 ~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~ 171 (193)
T cd06139 128 EDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLK 171 (193)
T ss_pred HHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 001 122478889999999999988764
No 62
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=85.94 E-value=1.1 Score=48.73 Aligned_cols=87 Identities=25% Similarity=0.328 Sum_probs=66.4
Q ss_pred CccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhc-cC-CCcHHHHHHHcCCcccCCCCC
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCT-CL-YGGLDRVCKALGVERVVGKSH 214 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~-~l-~~gL~~vA~~L~v~r~~g~~h 214 (256)
+-.-|+++..+|++||-.-+---.||+-.. . +.||=-+|+... .+ +.+|..|++.|+|.- ...|
T Consensus 501 d~IlVAHNasFD~gFl~~~~~k~~~~~~~~-----------p-vIDTL~lar~L~P~~ksh~Lg~l~kk~~v~l--e~hH 566 (1444)
T COG2176 501 DSILVAHNASFDMGFLNTNYEKYGLEPLTN-----------P-VIDTLELARALNPEFKSHRLGTLCKKLGVEL--ERHH 566 (1444)
T ss_pred CcEEEeccCccchhHHHHHHHHhCCccccC-----------c-hhhHHHHHHHhChhhhhcchHHHHHHhCccH--HHhh
Confidence 335688888899999987765322222211 2 678888888764 44 468999999999986 7889
Q ss_pred cchhhHHHHHHHHHHHHHhhCCC
Q 025183 215 QAGSDSLLTLHAFLKIKDKHFGN 237 (256)
Q Consensus 215 qAGsdsllT~~~F~kl~~~~~~~ 237 (256)
.|-+||-.|+.+|+.|.+...+.
T Consensus 567 RA~yDaeat~~vf~~f~~~~ke~ 589 (1444)
T COG2176 567 RADYDAEATAKVFFVFLKDLKEK 589 (1444)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHh
Confidence 99999999999999998887643
No 63
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=84.27 E-value=2.9 Score=38.40 Aligned_cols=54 Identities=20% Similarity=0.305 Sum_probs=40.5
Q ss_pred ccchhHHHHhhc----cCCCcHHHHHHH-cCCcccCCCCCcchhhHHHHHHHHHHHHHhh
Q 025183 180 VYDVKHLIRFCT----CLYGGLDRVCKA-LGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 234 (256)
Q Consensus 180 vyD~K~la~~~~----~l~~gL~~vA~~-L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~ 234 (256)
+.||.+.--++. ....||.+|++. ||.+=..|. |-.=-|+-.|++.|.+++...
T Consensus 208 iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~Ge-HsSvEDA~AtM~LY~~vk~qw 266 (280)
T KOG2249|consen 208 IRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGE-HSSVEDARATMELYKRVKVQW 266 (280)
T ss_pred hcccccCchHHHHhhccCCccHHHHHHHHhchhhhccc-cCcHHHHHHHHHHHHHHHHHH
Confidence 777755433322 446789999988 777664566 999999999999999988764
No 64
>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=83.47 E-value=2.9 Score=36.56 Aligned_cols=69 Identities=19% Similarity=0.241 Sum_probs=43.2
Q ss_pred cEEeecc-hhhHHHHHHH--hcCCCCCCChHHHHHH---HHhhcCCcccchhHHHHhhcc-CCCcHHHHHHHcCCcc
Q 025183 139 TWVTFHS-AYDFGYLVKC--LTQRVLPEKLSEFVTR---VGVFFGEKVYDVKHLIRFCTC-LYGGLDRVCKALGVER 208 (256)
Q Consensus 139 ~Wvtfhg-~yDf~yL~k~--l~~~~LP~~~~~F~~~---l~~~Fp~~vyD~K~la~~~~~-l~~gL~~vA~~L~v~r 208 (256)
.+|+|+| ++|+-||.+= ..|-++|......-.. ...+-.+ .+|+-.+.+.... -..+|..||+.||+++
T Consensus 95 ~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~-h~DL~~~~~~~~~~~~~~L~~va~~lG~~~ 170 (208)
T cd05782 95 RLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSER-HLDLMDLLAFYGARARASLDLLAKLLGIPG 170 (208)
T ss_pred EEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCC-cccHHHHHhccCccCCCCHHHHHHHhCCCC
Confidence 6899998 5999999885 3355556543321110 0111123 6787766655433 2458999999999965
No 65
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=77.19 E-value=5.8 Score=36.26 Aligned_cols=76 Identities=21% Similarity=0.273 Sum_probs=53.9
Q ss_pred cEEeecch-hhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhcc---CCCcHHHHHHHcCCcccCCCCC
Q 025183 139 TWVTFHSA-YDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC---LYGGLDRVCKALGVERVVGKSH 214 (256)
Q Consensus 139 ~Wvtfhg~-yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~---l~~gL~~vA~~L~v~r~~g~~h 214 (256)
-||||+|. +|.-|+-++.. ..+|.+.+ .+=||+=|.++..-. ..+||..|-+.||+.|....
T Consensus 158 ~lvsfNGkaFD~PfikR~v~-~~~el~l~-----------~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~R~edt-- 223 (278)
T COG3359 158 MLVSFNGKAFDIPFIKRMVR-DRLELSLE-----------FGHFDLYHPSRRLWKHLLPRCGLKTVERILGIRREEDT-- 223 (278)
T ss_pred eEEEecCcccCcHHHHHHHh-cccccCcc-----------ccchhhhhhhhhhhhccCCCCChhhHHHHhCccccccC--
Confidence 79999987 99999998544 34555533 335788888777631 26789999999999994333
Q ss_pred cchhhHHHHHHHHHH
Q 025183 215 QAGSDSLLTLHAFLK 229 (256)
Q Consensus 215 qAGsdsllT~~~F~k 229 (256)
-|+++-..-+.|.+
T Consensus 224 -dG~~~p~lyr~~~~ 237 (278)
T COG3359 224 -DGYDGPELYRLYRR 237 (278)
T ss_pred -CCcchHHHHHHHHH
Confidence 56776666555554
No 66
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=66.54 E-value=27 Score=27.23 Aligned_cols=55 Identities=18% Similarity=0.199 Sum_probs=37.1
Q ss_pred cccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhcc-C-CCcHHHHHHHc
Q 025183 133 VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC-L-YGGLDRVCKAL 204 (256)
Q Consensus 133 v~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~-l-~~gL~~vA~~L 204 (256)
+.+++++-|+++..+|+..|.+. +..+ +..++|+..++..... . +.+|+.+++.+
T Consensus 50 l~~~~~~~v~~~~k~d~~~L~~~--~~~~---------------~~~~~D~~~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 50 LEDEDITKVGHDAKFDLVVLARD--GIEL---------------PGNIFDTMLAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred HcCCCCcEEeccHHHHHHHHHHC--CCCC---------------CCCcccHHHHHHHhCCCCCcCCHHHHHHHH
Confidence 33456677888878888887654 2122 3338999888887653 2 35899999885
No 67
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=63.70 E-value=6.5 Score=35.47 Aligned_cols=100 Identities=18% Similarity=0.145 Sum_probs=62.4
Q ss_pred eecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccCCCcHHHHHHHcCCcccCCCCCcchhhHH
Q 025183 142 TFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSL 221 (256)
Q Consensus 142 tfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l~~gL~~vA~~L~v~r~~g~~hqAGsdsl 221 (256)
-|-.-||+-|++|...+ +-.-++++...|...= ...+...-.-.|.. |+.+..+| .......+-.++
T Consensus 196 yfP~fYDik~v~ks~~~--~~KglQei~ndlql~r---------~g~QhQagsdaLlT-a~~ff~~R-~~~F~~sig~~l 262 (299)
T COG5228 196 YFPNFYDIKLVYKSVLN--NSKGLQEIKNDLQLQR---------SGQQHQAGSDALLT-ADEFFLPR-FSIFTTSIGQSL 262 (299)
T ss_pred HCccccchHHHHHhhhh--hhhHHHHhcCcHhhhc---------cchhhhccchhhhh-hHHhcchh-hheecccccHHH
Confidence 35577999999987553 1222344433332210 00000001123544 89999999 666666777788
Q ss_pred HHHHHHHHHHHhh---CCCchhhhcccceEecCCCC
Q 025183 222 LTLHAFLKIKDKH---FGNEYELQKYANVLHGLELL 254 (256)
Q Consensus 222 lT~~~F~kl~~~~---~~~~~~~~~~~g~l~Gl~~~ 254 (256)
|....+..+++.. |+++.+++++.|++||+..+
T Consensus 263 l~~L~g~~~~~~sl~~~~~~t~f~~~~g~~~gi~~~ 298 (299)
T COG5228 263 LMLLSGCQLSKLSLHKFPNGTDFAKYQGVIYGIDGD 298 (299)
T ss_pred HHHHhccccCCchheeCCCcccHhhcCCcccCCCCC
Confidence 8888888877763 35556789999999999654
No 68
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=56.75 E-value=11 Score=32.89 Aligned_cols=70 Identities=21% Similarity=0.266 Sum_probs=40.8
Q ss_pred cEEeecc-hhhHHHHHHHhcCCCCCCChHHHHH-------------H----HH-hhcCCcccchhHHHHhh----ccC-C
Q 025183 139 TWVTFHS-AYDFGYLVKCLTQRVLPEKLSEFVT-------------R----VG-VFFGEKVYDVKHLIRFC----TCL-Y 194 (256)
Q Consensus 139 ~Wvtfhg-~yDf~yL~k~l~~~~LP~~~~~F~~-------------~----l~-~~Fp~~vyD~K~la~~~----~~l-~ 194 (256)
.+++||+ ++|+.||.+-...-.++.++...-. . .. ...++-+.|+-.+.+.. ..+ +
T Consensus 76 ii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~s 155 (207)
T cd05785 76 VIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPS 155 (207)
T ss_pred EEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCC
Confidence 6789998 7999999987653233332111100 0 00 11223247987766642 123 2
Q ss_pred CcHHHHHHHcCCcc
Q 025183 195 GGLDRVCKALGVER 208 (256)
Q Consensus 195 ~gL~~vA~~L~v~r 208 (256)
-+|+.||+.+|+..
T Consensus 156 ysL~~Va~~~g~~~ 169 (207)
T cd05785 156 YGLKAVAKHFGLAS 169 (207)
T ss_pred CCHHHHHHHhcccC
Confidence 37999999998754
No 69
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=56.74 E-value=18 Score=27.49 Aligned_cols=21 Identities=14% Similarity=0.322 Sum_probs=17.6
Q ss_pred ccEEeecchhhHHHHHHHhcC
Q 025183 138 VTWVTFHSAYDFGYLVKCLTQ 158 (256)
Q Consensus 138 v~Wvtfhg~yDf~yL~k~l~~ 158 (256)
..||++|+.+|+.||.+-+..
T Consensus 45 ~v~V~hn~~fD~~fL~~~~~~ 65 (96)
T cd06125 45 AILVGHNGSFDLPFLNNRCAE 65 (96)
T ss_pred CEEEEeCcHHhHHHHHHHHHH
Confidence 478999999999999888753
No 70
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=55.67 E-value=78 Score=27.62 Aligned_cols=100 Identities=19% Similarity=0.209 Sum_probs=69.1
Q ss_pred chhHHHHHHHcCccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhccC--CCcH
Q 025183 120 ALDSVELLKRQGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCL--YGGL 197 (256)
Q Consensus 120 ~~~Si~~L~~~Glv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~l--~~gL 197 (256)
-.+-+.+|+++.-=.+ -+|++- |.||..-|.+--.-..+|+..-+ +. ..|+|.--+..-+. ..||
T Consensus 83 ~E~f~r~L~~h~Pr~~--~~wa~w-G~~Dm~~l~q~~~~~~~~p~~~k---------gp-~vdl~~~yk~v~~~pr~tgl 149 (210)
T COG5018 83 FEDFIRKLNEHDPRKN--STWATW-GNMDMKVLKQNCMFNHIPPFPFK---------GP-MVDLSLEYKNVFGDPRLTGL 149 (210)
T ss_pred HHHHHHHHHhcCcccC--Cccccc-cchhHHHHHHHHHhcCCCCcccc---------Cc-cchHHHHHHHHhcCCccccH
Confidence 3456677777762222 278764 78999988876443455522111 23 55666655555433 2589
Q ss_pred HHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHh
Q 025183 198 DRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 233 (256)
Q Consensus 198 ~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~ 233 (256)
...++.-|..- .|..|.|=-|+.-|.+.|.++...
T Consensus 150 n~ale~~G~sf-~G~~HraldDArn~~rl~klv~~~ 184 (210)
T COG5018 150 NKALEEYGDSF-TGTHHRALDDARNAYRLFKLVEQD 184 (210)
T ss_pred HHHHHHhcccc-CCchhhhHHHHHHHHHHHHHHcch
Confidence 99999999998 899999999999999999887654
No 71
>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=55.32 E-value=12 Score=31.18 Aligned_cols=30 Identities=23% Similarity=0.195 Sum_probs=27.0
Q ss_pred eccccCHHHHHHHHHHHhhcCCeeEEeecc
Q 025183 18 EVFEFNLISEFERIRALIDRYPIISMDTEF 47 (256)
Q Consensus 18 dVw~~N~~~e~~~I~~~i~~~~fIAiDtEF 47 (256)
-|.+.|+++.++.|.+.-++.-.||||.-.
T Consensus 43 PVHA~NL~e~l~~I~~~~~~~~iIAIDAcL 72 (140)
T TIGR02841 43 PVHAKNLEEKLKIIKKKHPNPFIIAIDACL 72 (140)
T ss_pred CcccccHHHHHHHHHHhCCCCeEEEEECcc
Confidence 489999999999999998998999999754
No 72
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=48.70 E-value=84 Score=32.20 Aligned_cols=173 Identities=16% Similarity=0.089 Sum_probs=94.6
Q ss_pred CceEEeccccCHHHHHHHHHHHhhcCCeeEEeeccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeecCCCC
Q 025183 13 RILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGN 92 (256)
Q Consensus 13 ~~~v~dVw~~N~~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~~~g~ 92 (256)
.-.|+-|...+.-.-+- +.++.+...||.+|.|++--...+ + ..+.|+|++.-
T Consensus 389 ~~~i~~V~~e~El~~l~-l~~l~~e~~yVGiDsEwkps~~v~------d-------------sk~~IlQif~~------- 441 (617)
T KOG2207|consen 389 VESIGMVGNEKELRDLL-LESLSEELRYVGIDSEWKPSKKVS------D-------------SKLAILQIFFK------- 441 (617)
T ss_pred ccceeeeCCHHHHHHHH-HHHhhhcCEEEEEccccCcccCCC------h-------------hHHHHHHHHhc-------
Confidence 34455555444333333 336677789999999997641111 1 13457777642
Q ss_pred CCCCCCCCCeeeEEEeeeecccccccCchhHHHHHHHcCccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHH
Q 025183 93 LPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRV 172 (256)
Q Consensus 93 ~p~~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~~L~~~Glv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l 172 (256)
-++|-.+.- ..+..++ ++=-+..++|.-++++.=|.|.=.-|+--|-. .+| .|-..+
T Consensus 442 ---------~~v~Lidc~----~l~~~~s-e~w~~~~s~if~s~~i~kvGf~~~eDL~~l~~-----s~p----a~~~q~ 498 (617)
T KOG2207|consen 442 ---------DCVYLIDCV----KLENLAS-EIWHLLLSQIFESKSILKVGFSMREDLEVLEA-----SSP----ALRFQM 498 (617)
T ss_pred ---------CeEEEeehH----HhhhchH-HHHHHHHHHHccCCceeeeecchhhhHHHHHh-----hhh----hhhhcc
Confidence 478876654 2222233 33344455566667766665554444433332 122 233333
Q ss_pred HhhcCCcccchhHHHHhh----------ccCCCcHHHHHHH-cCCcc----cC-------CCCC---cchhhHHHHHHHH
Q 025183 173 GVFFGEKVYDVKHLIRFC----------TCLYGGLDRVCKA-LGVER----VV-------GKSH---QAGSDSLLTLHAF 227 (256)
Q Consensus 173 ~~~Fp~~vyD~K~la~~~----------~~l~~gL~~vA~~-L~v~r----~~-------g~~h---qAGsdsllT~~~F 227 (256)
...=+..+|+++-+++.. +...+||+.|+.. ||+.- .. =..| -||-|+....++|
T Consensus 499 ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~if 578 (617)
T KOG2207|consen 499 KIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIF 578 (617)
T ss_pred cccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHH
Confidence 333333355555555543 2335689998877 34421 01 1223 3788999999999
Q ss_pred HHHHHhhC
Q 025183 228 LKIKDKHF 235 (256)
Q Consensus 228 ~kl~~~~~ 235 (256)
.+++++.-
T Consensus 579 kkv~~vv~ 586 (617)
T KOG2207|consen 579 KKVCSVVE 586 (617)
T ss_pred HHHHhhcc
Confidence 99988753
No 73
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=44.99 E-value=28 Score=29.79 Aligned_cols=67 Identities=21% Similarity=0.222 Sum_probs=37.0
Q ss_pred cEEeecch-hhHHHHHHHhc--CCCCCCC--------hHHHHHHHHhhcCCcccchhHHHHhhccC-CCcHHHHHHHcCC
Q 025183 139 TWVTFHSA-YDFGYLVKCLT--QRVLPEK--------LSEFVTRVGVFFGEKVYDVKHLIRFCTCL-YGGLDRVCKALGV 206 (256)
Q Consensus 139 ~Wvtfhg~-yDf~yL~k~l~--~~~LP~~--------~~~F~~~l~~~Fp~~vyD~K~la~~~~~l-~~gL~~vA~~L~v 206 (256)
..++|+|. +|+.||++=.. |-+++-. ...|-. . ..-++-..|+-.+.+.-..+ .-+|+.||+.||+
T Consensus 66 ~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~-~-~i~Gr~~iDl~~~~~~~~~l~~y~L~~Va~~Lg~ 143 (188)
T cd05781 66 IIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGH-Y-SITGRLNVDLYDFAEEIPEVKVKTLENVAEYLGV 143 (188)
T ss_pred EEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcce-E-eeeeEEEEEhHHHHHhhCCCCCCCHHHHHHHHCC
Confidence 46788966 99999987644 3222210 000000 0 00111156765555544334 3479999999999
Q ss_pred c
Q 025183 207 E 207 (256)
Q Consensus 207 ~ 207 (256)
.
T Consensus 144 ~ 144 (188)
T cd05781 144 M 144 (188)
T ss_pred C
Confidence 6
No 74
>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=40.14 E-value=26 Score=29.90 Aligned_cols=31 Identities=23% Similarity=0.241 Sum_probs=27.4
Q ss_pred eccccCHHHHHHHHHHHhhcCCeeEEeeccc
Q 025183 18 EVFEFNLISEFERIRALIDRYPIISMDTEFP 48 (256)
Q Consensus 18 dVw~~N~~~e~~~I~~~i~~~~fIAiDtEFp 48 (256)
-|.+.|+++.++.|.+.-++.-.||||.-+.
T Consensus 67 PVHA~NL~e~l~~I~~~~~~~~IIAIDAcLG 97 (163)
T PF06866_consen 67 PVHALNLEETLNEIKKKHPNPFIIAIDACLG 97 (163)
T ss_pred CcchhhHHHHHHHHHHHCCCCeEEEEECCCC
Confidence 4899999999999999888888899998663
No 75
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=39.78 E-value=1.9e+02 Score=22.83 Aligned_cols=82 Identities=22% Similarity=0.239 Sum_probs=49.0
Q ss_pred ccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHhhcc-CC-CcHHHHHHHc-CCcc--
Q 025183 134 LNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC-LY-GGLDRVCKAL-GVER-- 208 (256)
Q Consensus 134 ~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~~~~-l~-~gL~~vA~~L-~v~r-- 208 (256)
-+++++-|+++.-+|+..|.+ .|-+++ + ++|+..++..... -. .+|+++++.+ +..-
T Consensus 72 ~~~~~~kv~~d~k~~~~~L~~--~gi~~~---------------~-~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~ 133 (172)
T smart00474 72 EDETITKVGHNAKFDLHVLAR--FGIELE---------------N-IFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDK 133 (172)
T ss_pred cCCCceEEEechHHHHHHHHH--CCCccc---------------c-hhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCc
Confidence 345677888888888888765 454432 2 5777777664432 22 4788887763 4431
Q ss_pred cCCC--------CC----cchhhHHHHHHHHHHHHHh
Q 025183 209 VVGK--------SH----QAGSDSLLTLHAFLKIKDK 233 (256)
Q Consensus 209 ~~g~--------~h----qAGsdsllT~~~F~kl~~~ 233 (256)
..+. .. .|..|+..+.+.+-+|.+.
T Consensus 134 ~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~ 170 (172)
T smart00474 134 EEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKE 170 (172)
T ss_pred ccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0111 11 2666777777777777654
No 76
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=36.70 E-value=36 Score=29.06 Aligned_cols=69 Identities=25% Similarity=0.279 Sum_probs=41.4
Q ss_pred cEEeecch-hhHHHHHHHhc--CCCCCCChH---------HHHHHHHhhcCCcccchhHHHHhhccCC-CcHHHHHH-Hc
Q 025183 139 TWVTFHSA-YDFGYLVKCLT--QRVLPEKLS---------EFVTRVGVFFGEKVYDVKHLIRFCTCLY-GGLDRVCK-AL 204 (256)
Q Consensus 139 ~Wvtfhg~-yDf~yL~k~l~--~~~LP~~~~---------~F~~~l~~~Fp~~vyD~K~la~~~~~l~-~gL~~vA~-~L 204 (256)
.+++|+|. +|+.||++=.. |-++|-... .+.. ...+-++-+.|+..+++....+. -+|+.||+ .|
T Consensus 74 iivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~-~~~i~Gr~~lDl~~~~~~~~~l~sy~L~~v~~~~L 152 (195)
T cd05780 74 VIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNN-ASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELF 152 (195)
T ss_pred EEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceee-eeccCCeEEEeHHHHHHhhCCCCcCcHHHHHHHHh
Confidence 48999975 99999998654 333332110 0000 01122333788877776644443 47999988 58
Q ss_pred CCcc
Q 025183 205 GVER 208 (256)
Q Consensus 205 ~v~r 208 (256)
|.++
T Consensus 153 g~~k 156 (195)
T cd05780 153 GIEK 156 (195)
T ss_pred CCCC
Confidence 9887
No 77
>KOG4013 consensus Predicted Cu2+ homeostasis protein CutC [Inorganic ion transport and metabolism]
Probab=36.55 E-value=19 Score=31.98 Aligned_cols=85 Identities=28% Similarity=0.352 Sum_probs=49.6
Q ss_pred hHHHHHHHcC---ccc-------------------cCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhc-CC
Q 025183 122 DSVELLKRQG---LVL-------------------NKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFF-GE 178 (256)
Q Consensus 122 ~Si~~L~~~G---lv~-------------------~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~F-p~ 178 (256)
+-+++|++.| +|+ -.+--.||||-++|++|=-|......| -.-.|.+.|..=| |.
T Consensus 85 ~Dv~llk~~GAdGfVFGaLt~dgsid~~~C~si~~~~rplPVTFHRAfD~~~D~k~~lE~~l--~~lGF~rvLtSG~~ps 162 (255)
T KOG4013|consen 85 EDVELLKKAGADGFVFGALTSDGSIDRTSCQSIIETARPLPVTFHRAFDVAYDWKTCLEDAL--LDLGFKRVLTSGQEPS 162 (255)
T ss_pred HHHHHHHHcCCCceEEeecCCCCCcCHHHHHHHHHhcCCCceeeeeehhhhcCHHHHHHHHH--HHhhHHHHhhcCCCcc
Confidence 4788999998 221 224457999999999986655332100 0235777776655 32
Q ss_pred ---cccchhHHHHhhcc----CCC-c--HHHHHHHcCCcc
Q 025183 179 ---KVYDVKHLIRFCTC----LYG-G--LDRVCKALGVER 208 (256)
Q Consensus 179 ---~vyD~K~la~~~~~----l~~-g--L~~vA~~L~v~r 208 (256)
|+|=++-|.+...+ +.| | -..|++.|...+
T Consensus 163 AldGv~~i~~lie~hkg~i~VmpG~Gi~~sNl~~ile~s~ 202 (255)
T KOG4013|consen 163 ALDGVYIIRELIELHKGKIDVMPGCGINSSNLANILEWSK 202 (255)
T ss_pred cccchHHHHHHHHHhcCCEEEecCCCcchHHHHHHHhhcc
Confidence 35555555555442 333 3 345666665555
No 78
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=32.57 E-value=26 Score=27.63 Aligned_cols=25 Identities=32% Similarity=0.412 Sum_probs=18.3
Q ss_pred CcHHHHHHHcCCcccCCCCCcchhhHHHHHH
Q 025183 195 GGLDRVCKALGVERVVGKSHQAGSDSLLTLH 225 (256)
Q Consensus 195 ~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~ 225 (256)
-||.++|+.+||.| ||=+|++=-+.
T Consensus 34 lSlsEIAe~~~iSR------qaV~d~ikr~~ 58 (101)
T PF04297_consen 34 LSLSEIAEELGISR------QAVYDSIKRAE 58 (101)
T ss_dssp --HHHHHHHCTS-H------HHHHHHHHHHH
T ss_pred CCHHHHHHHHCCCH------HHHHHHHHHHH
Confidence 47999999999999 78888765544
No 79
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=30.88 E-value=52 Score=27.75 Aligned_cols=69 Identities=22% Similarity=0.119 Sum_probs=39.9
Q ss_pred cEEeecc-hhhHHHHHHHhc--CCCCC-------CCh--HHHHHHHHhhcCCcccchhHHHHhhccCC-CcHHHHHHHcC
Q 025183 139 TWVTFHS-AYDFGYLVKCLT--QRVLP-------EKL--SEFVTRVGVFFGEKVYDVKHLIRFCTCLY-GGLDRVCKALG 205 (256)
Q Consensus 139 ~Wvtfhg-~yDf~yL~k~l~--~~~LP-------~~~--~~F~~~l~~~Fp~~vyD~K~la~~~~~l~-~gL~~vA~~L~ 205 (256)
.+++|++ ++|+.||.+=+. |-++. ... ..+.. -..+-++-+.|+-.+++....+. -+|+.||+.+.
T Consensus 81 iivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~-~~~~~gr~~~D~~~~~r~~~~l~sy~L~~v~~~~l 159 (199)
T cd05160 81 ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTE-RIAVKGRVVFDLLAAYKRDFKLKSYTLDAVAEELL 159 (199)
T ss_pred EEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCccc-ceeeeccEeeehHHHHHHhcCcccCCHHHHHHHHh
Confidence 5899999 899999998654 22221 000 00000 00111333779877776654343 47999999765
Q ss_pred Ccc
Q 025183 206 VER 208 (256)
Q Consensus 206 v~r 208 (256)
..+
T Consensus 160 ~~~ 162 (199)
T cd05160 160 GEG 162 (199)
T ss_pred CCC
Confidence 444
No 80
>PF11959 DUF3473: Domain of unknown function (DUF3473); InterPro: IPR022560 This domain, found in bacteria and archaea, is functionally uncharacterised. It is about 130 amino acids in length and is found C-terminal to PF01522 from PFAM. It contains two completely conserved residues (P and H) that may be functionally important.
Probab=29.20 E-value=79 Score=25.83 Aligned_cols=30 Identities=20% Similarity=0.112 Sum_probs=26.1
Q ss_pred EEeccccCHHHHHHHHHHHhhcCCeeEEee
Q 025183 16 IREVFEFNLISEFERIRALIDRYPIISMDT 45 (256)
Q Consensus 16 v~dVw~~N~~~e~~~I~~~i~~~~fIAiDt 45 (256)
-+=.+-.|++...++|+.+|+++.|..|+.
T Consensus 99 ~rf~~y~~l~~~~~rl~~Ll~~f~f~t~~~ 128 (133)
T PF11959_consen 99 SRFRHYNNLDRMEKRLDRLLSDFRFGTMRE 128 (133)
T ss_pred eeEEEEcCHHHHHHHHHHHHhhCceEEHHH
Confidence 345788999999999999999999998874
No 81
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=28.99 E-value=46 Score=31.01 Aligned_cols=42 Identities=24% Similarity=0.252 Sum_probs=36.6
Q ss_pred CCCcHHHHHHHcCCcccCCCCCcchhhHHHHHHHHHHHHHhhC
Q 025183 193 LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 235 (256)
Q Consensus 193 l~~gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~~ 235 (256)
....|+.+|..-...| .+.+|+|-+|.+++..+|-++...+.
T Consensus 251 ~vs~le~Lat~~~~~p-~l~ahra~~Dv~~~~k~~q~~~idll 292 (318)
T KOG4793|consen 251 LVSSLEALATYYSLTP-ELDAHRALSDVLLLSKVFQKLTIDLL 292 (318)
T ss_pred cchhHHHHHHHhhcCc-ccchhhhccccchhhhHHHHhhhhhh
Confidence 3457999999999998 89999999999999999999876654
No 82
>PF07176 DUF1400: Alpha/beta hydrolase of unknown function (DUF1400); InterPro: IPR010802 This domain is specific to cyanobacterial proteins, its function and the function of the proteins it is associated with, are uncharacterised.
Probab=23.54 E-value=3.9e+02 Score=21.46 Aligned_cols=93 Identities=15% Similarity=0.293 Sum_probs=62.9
Q ss_pred EeeeecccccccCchhHHHHHHHcCccccCCccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHH
Q 025183 107 FNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHL 186 (256)
Q Consensus 107 FNF~~F~~~~d~~~~~Si~~L~~~Glv~~~~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~l 186 (256)
..|+ |..-.-..+-++++-.++.|-+. -+|+.++++++ |++.+++.+.|+.=++- |...+
T Consensus 5 I~~~-yg~~~~si~V~dLe~fa~tG~~~------------~~L~~~~~ll~----~~~~~~lr~~L~~~~~~---~~~~~ 64 (127)
T PF07176_consen 5 ITFR-YGPFQRSISVSDLETFAETGEIS------------PELAFYLNLLS----PQQRQQLRELLNTPIPI---DPVFL 64 (127)
T ss_pred EEEE-ECCceeeeeHHHHHHHHHcCCCC------------HHHHHHHHhcC----HhhHHHHHHHHcCCCCC---CHHHH
Confidence 3444 44333356777888888888553 47888888886 66788999999987765 77777
Q ss_pred HHhhccCCC--cHHHHHHHcCCcccCCCCCcchhhHHHHH
Q 025183 187 IRFCTCLYG--GLDRVCKALGVERVVGKSHQAGSDSLLTL 224 (256)
Q Consensus 187 a~~~~~l~~--gL~~vA~~L~v~r~~g~~hqAGsdsllT~ 224 (256)
.+......| -|+++++.+..+. + ++|..++-++
T Consensus 65 ~~lL~S~~G~~lL~~lg~vi~~~~--~---~~g~~ALr~A 99 (127)
T PF07176_consen 65 SQLLNSPIGERLLDQLGKVIRTPS--G---SNGQQALRSA 99 (127)
T ss_pred HHHhCChHHHHHHHHHHHHhcCCC--C---cccHHHHHHH
Confidence 666643333 2899999887665 2 4566555544
No 83
>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=22.57 E-value=2.4e+02 Score=25.78 Aligned_cols=68 Identities=10% Similarity=-0.018 Sum_probs=43.2
Q ss_pred eccccCHHHHHHHHHHHhhcCC---eeEEee------ccccccccCCCCCCCCChhhhHHHHHhcccccceeeeeeeeec
Q 025183 18 EVFEFNLISEFERIRALIDRYP---IISMDT------EFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSD 88 (256)
Q Consensus 18 dVw~~N~~~e~~~I~~~i~~~~---fIAiDt------EFpGv~~~~~~~~~~~~~e~rY~~lk~nvd~~~iiQlGlt~~~ 88 (256)
+|++...++.+..+.+.+...+ ||++|. .+||+.....+- .+. .|--+.++.-....+++-+.|+=++
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--LTF-REGLLIMEMLYETGLLTALDVVEVN 272 (300)
T ss_pred HHhhhhHHHHHHHHHHHHhcCCCeEEEEEeccccCcccCCCCCCCCCCC--CCH-HHHHHHHHHHHhcCCEEEEEEEEEC
Confidence 4556666777888888886544 999997 577875543221 122 6666777776666667656655444
No 84
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=22.50 E-value=71 Score=20.75 Aligned_cols=28 Identities=18% Similarity=0.112 Sum_probs=19.3
Q ss_pred cchhHHHHhhccCCCcHHHHHHHcCCcc
Q 025183 181 YDVKHLIRFCTCLYGGLDRVCKALGVER 208 (256)
Q Consensus 181 yD~K~la~~~~~l~~gL~~vA~~L~v~r 208 (256)
.|.|-+.....+-+-+..+||+.+|+.+
T Consensus 4 ~D~~Il~~Lq~d~r~s~~~la~~lglS~ 31 (42)
T PF13404_consen 4 LDRKILRLLQEDGRRSYAELAEELGLSE 31 (42)
T ss_dssp HHHHHHHHHHH-TTS-HHHHHHHHTS-H
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCcCH
Confidence 3666666666566778999999999987
No 85
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=22.03 E-value=1.8e+02 Score=19.54 Aligned_cols=37 Identities=19% Similarity=0.302 Sum_probs=27.3
Q ss_pred HHHHHHcCCccc----CCCCCcchhhHHHHHHHHHHHHHhh
Q 025183 198 DRVCKALGVERV----VGKSHQAGSDSLLTLHAFLKIKDKH 234 (256)
Q Consensus 198 ~~vA~~L~v~r~----~g~~hqAGsdsllT~~~F~kl~~~~ 234 (256)
+-+++.|+++.. .......|-||+...+.-.++++.|
T Consensus 5 ~~~~~~l~~~~~~i~~~~~~~~lG~DSl~~~~l~~~l~~~~ 45 (67)
T PF00550_consen 5 EIIAEVLGVDPEEIDPDTDFFDLGLDSLDAIELVSELEEEF 45 (67)
T ss_dssp HHHHHHHTSSGGCTSTTSBTTTTTSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHCcCHhhCCCCCCHHHhCCchHHHHHHHHHHHHHH
Confidence 456777776431 2334579999999999999998886
No 86
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=22.02 E-value=87 Score=24.18 Aligned_cols=31 Identities=29% Similarity=0.376 Sum_probs=25.4
Q ss_pred HHHHHHcCCccc------CCCCCcchhhHHHHHHHHH
Q 025183 198 DRVCKALGVERV------VGKSHQAGSDSLLTLHAFL 228 (256)
Q Consensus 198 ~~vA~~L~v~r~------~g~~hqAGsdsllT~~~F~ 228 (256)
.++|+.|||+|+ .|..|-++-|.|+|+.++.
T Consensus 45 ~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~ 81 (91)
T COG5606 45 AQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARA 81 (91)
T ss_pred HHHHHHhCCCCchHHHHHhcchhHhhHHHHHHHHHHc
Confidence 579999999984 5788889999999987543
No 87
>KOG4355 consensus Predicted Fe-S oxidoreductase [General function prediction only]
Probab=21.62 E-value=44 Score=32.75 Aligned_cols=30 Identities=37% Similarity=0.332 Sum_probs=22.6
Q ss_pred cHHHHHHHcCCcccCCC---CCcchhhHHHHHH
Q 025183 196 GLDRVCKALGVERVVGK---SHQAGSDSLLTLH 225 (256)
Q Consensus 196 gL~~vA~~L~v~r~~g~---~hqAGsdsllT~~ 225 (256)
-|+++|..|..+|.-.- +-|.||||+||..
T Consensus 284 hl~e~a~vlrhp~vYsflhvpvqsgsdsvl~em 316 (547)
T KOG4355|consen 284 HLEEAAFVLRHPRVYSFLHVPVQSGSDSVLTEM 316 (547)
T ss_pred HHHHHHHHhcCCeEEEEEecccccCchhHHHHH
Confidence 47888888888884333 3499999999863
No 88
>COG3155 ElbB Uncharacterized protein involved in an early stage of isoprenoid biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.83 E-value=3.4e+02 Score=23.56 Aligned_cols=85 Identities=18% Similarity=0.179 Sum_probs=55.6
Q ss_pred CccEEeecchhhHHHHHHHhcCCCCCCChHHHHHHHHhhcCCcccchhHHHHh-hcc--CCCc------HHHHHHHcCCc
Q 025183 137 DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRF-CTC--LYGG------LDRVCKALGVE 207 (256)
Q Consensus 137 ~v~Wvtfhg~yDf~yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~vyD~K~la~~-~~~--l~~g------L~~vA~~L~v~ 207 (256)
.-.|+.|.-..-=...+..|||..+|+|..-..+..|.-=+. |-|+.-.--. ... ..|| |...|.
T Consensus 33 GA~~~cFAP~~~Q~hViNHlTGE~m~EtRNVLvEsARIaRG~-i~~l~~a~~e~~DALivPGGFGAAKNLsdFA~----- 106 (217)
T COG3155 33 GAQAVCFAPDKQQVHVINHLTGEAMPETRNVLVESARIARGE-IRPLAQADAEELDALIVPGGFGAAKNLSDFAS----- 106 (217)
T ss_pred CceeEEecCCchhhhhhhhccccccchhhhHHHHHHHHhhcc-ccchhhcCHHhcceeeccCccchhhhhHHHhc-----
Confidence 357888877766777899999999999999998888876555 5554332111 111 1343 444443
Q ss_pred ccCCCCCcchhhHHHHHHHHHH
Q 025183 208 RVVGKSHQAGSDSLLTLHAFLK 229 (256)
Q Consensus 208 r~~g~~hqAGsdsllT~~~F~k 229 (256)
.|.+.+--+|.+-.++.|.+
T Consensus 107 --kGaeC~v~pDv~al~~a~~~ 126 (217)
T COG3155 107 --KGAECSVDPDLKALAQAMHQ 126 (217)
T ss_pred --cCccceeCHHHHHHHHHHHH
Confidence 46666677777777776655
No 89
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=20.79 E-value=72 Score=20.43 Aligned_cols=24 Identities=17% Similarity=0.295 Sum_probs=15.6
Q ss_pred HHHHhhccCCCcHHHHHHHcCCcc
Q 025183 185 HLIRFCTCLYGGLDRVCKALGVER 208 (256)
Q Consensus 185 ~la~~~~~l~~gL~~vA~~L~v~r 208 (256)
+|........|.....|+.||+.|
T Consensus 9 ~i~~aL~~~~gn~~~aA~~Lgisr 32 (42)
T PF02954_consen 9 LIRQALERCGGNVSKAARLLGISR 32 (42)
T ss_dssp HHHHHHHHTTT-HHHHHHHHTS-H
T ss_pred HHHHHHHHhCCCHHHHHHHHCCCH
Confidence 444444444567999999999998
No 90
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=20.23 E-value=84 Score=21.96 Aligned_cols=26 Identities=35% Similarity=0.537 Sum_probs=18.7
Q ss_pred chhHHHHhhccCCC-cHHHHHHHcCCcc
Q 025183 182 DVKHLIRFCTCLYG-GLDRVCKALGVER 208 (256)
Q Consensus 182 D~K~la~~~~~l~~-gL~~vA~~L~v~r 208 (256)
|+|.-|+..- +.| +..+||+.||+++
T Consensus 1 e~k~~A~~LY-~~G~~~~eIA~~Lg~~~ 27 (58)
T PF06056_consen 1 EVKEQARSLY-LQGWSIKEIAEELGVPR 27 (58)
T ss_pred CHHHHHHHHH-HcCCCHHHHHHHHCCCh
Confidence 4566666552 344 4899999999987
Done!