Query 024017
Match_columns 274
No_of_seqs 149 out of 485
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 08:19:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024017.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024017hhsearch_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 1.9E-91 4.2E-96 608.0 19.3 237 11-250 1-239 (239)
2 COG5228 POP2 mRNA deadenylase 100.0 2.5E-81 5.5E-86 545.8 14.0 264 1-269 7-273 (299)
3 PF04857 CAF1: CAF1 family rib 100.0 3E-64 6.4E-69 458.5 19.0 228 13-245 1-262 (262)
4 KOG1990 Poly(A)-specific exori 99.1 5E-11 1.1E-15 119.5 2.2 231 17-251 1-364 (564)
5 PRK07942 DNA polymerase III su 98.9 2.8E-08 6E-13 89.3 15.1 170 32-251 4-181 (232)
6 smart00479 EXOIII exonuclease 98.9 8E-08 1.7E-12 80.2 16.6 164 35-251 1-168 (169)
7 cd06133 ERI-1_3'hExo_like DEDD 98.8 2.8E-07 6.2E-12 77.7 14.1 172 36-246 1-175 (176)
8 PRK09145 DNA polymerase III su 98.7 7.8E-07 1.7E-11 78.0 15.7 171 24-248 19-199 (202)
9 cd06131 DNA_pol_III_epsilon_Ec 98.6 1.9E-06 4.2E-11 72.5 14.8 163 36-246 1-166 (167)
10 PRK07748 sporulation inhibitor 98.6 2.6E-06 5.6E-11 75.0 15.2 172 33-249 3-179 (207)
11 PRK05168 ribonuclease T; Provi 98.6 2.9E-06 6.3E-11 75.1 15.5 186 24-251 7-202 (211)
12 cd06134 RNaseT DEDDh 3'-5' exo 98.6 2.2E-06 4.7E-11 74.6 14.2 174 33-249 4-188 (189)
13 cd06130 DNA_pol_III_epsilon_li 98.5 3.2E-06 7E-11 70.0 13.7 151 36-244 1-155 (156)
14 PRK05711 DNA polymerase III su 98.4 8.2E-06 1.8E-10 73.9 15.3 169 33-249 3-175 (240)
15 PRK07740 hypothetical protein; 98.4 1.7E-05 3.7E-10 71.9 15.7 168 32-251 57-227 (244)
16 PRK06807 DNA polymerase III su 98.4 1.3E-05 2.9E-10 75.3 15.4 163 34-250 8-172 (313)
17 PRK06310 DNA polymerase III su 98.3 2.3E-05 5E-10 71.3 15.1 169 30-250 3-174 (250)
18 PRK06063 DNA polymerase III su 98.3 2.9E-05 6.2E-10 72.9 15.9 163 33-251 14-180 (313)
19 TIGR00573 dnaq exonuclease, DN 98.3 2.8E-05 6.1E-10 69.0 14.5 168 31-250 4-177 (217)
20 PRK07247 DNA polymerase III su 98.3 2.6E-05 5.6E-10 68.5 14.0 159 35-249 6-168 (195)
21 TIGR01406 dnaQ_proteo DNA poly 98.3 4.1E-05 8.9E-10 68.6 15.6 167 35-249 1-171 (225)
22 cd06127 DEDDh DEDDh 3'-5' exon 98.2 1.5E-05 3.2E-10 64.8 11.0 155 37-244 1-159 (159)
23 PRK06195 DNA polymerase III su 98.2 4.8E-05 1E-09 71.2 15.4 160 35-251 2-165 (309)
24 PRK09146 DNA polymerase III su 98.2 7E-05 1.5E-09 67.8 15.6 169 31-253 44-230 (239)
25 TIGR01298 RNaseT ribonuclease 98.2 9.2E-05 2E-09 65.0 15.4 178 32-251 6-193 (200)
26 cd06136 TREX1_2 DEDDh 3'-5' ex 98.1 9E-05 2E-09 63.7 13.4 168 36-245 1-176 (177)
27 PRK06722 exonuclease; Provisio 98.1 0.00014 3.1E-09 67.4 15.5 169 33-247 4-178 (281)
28 PRK08517 DNA polymerase III su 98.1 0.00019 4.1E-09 65.7 15.7 166 31-250 65-231 (257)
29 PRK07883 hypothetical protein; 98.1 0.00014 2.9E-09 73.5 15.7 171 28-251 9-183 (557)
30 PRK07246 bifunctional ATP-depe 98.0 0.00023 5E-09 74.8 16.6 162 33-251 6-171 (820)
31 TIGR01405 polC_Gram_pos DNA po 98.0 0.00022 4.7E-09 77.6 16.6 167 32-251 188-356 (1213)
32 TIGR01407 dinG_rel DnaQ family 97.9 0.00026 5.6E-09 74.7 16.1 163 35-251 1-166 (850)
33 PRK08074 bifunctional ATP-depe 97.9 0.00029 6.4E-09 75.0 16.4 166 34-251 3-170 (928)
34 PTZ00315 2'-phosphotransferase 97.9 0.00053 1.1E-08 69.1 16.5 172 35-249 57-254 (582)
35 cd06138 ExoI_N N-terminal DEDD 97.8 0.00029 6.2E-09 60.8 11.7 165 38-242 2-181 (183)
36 cd06144 REX4_like DEDDh 3'-5' 97.8 0.00015 3.2E-09 60.8 9.3 69 157-243 79-151 (152)
37 PRK07983 exodeoxyribonuclease 97.8 0.0011 2.4E-08 59.3 14.6 148 36-250 2-154 (219)
38 PF00929 RNase_T: Exonuclease; 97.7 2.4E-05 5.1E-10 63.7 3.3 156 37-243 1-164 (164)
39 PRK06309 DNA polymerase III su 97.7 0.0013 2.9E-08 58.9 14.3 162 35-251 3-167 (232)
40 PRK09182 DNA polymerase III su 97.7 0.00088 1.9E-08 62.5 13.5 155 35-247 38-198 (294)
41 PRK11779 sbcB exonuclease I; P 97.7 0.0019 4E-08 64.1 16.2 175 32-249 4-197 (476)
42 PRK00448 polC DNA polymerase I 97.5 0.002 4.3E-08 71.3 15.0 168 31-251 416-585 (1437)
43 COG0847 DnaQ DNA polymerase II 97.4 0.0062 1.3E-07 54.3 14.9 164 34-249 13-181 (243)
44 PRK05601 DNA polymerase III su 97.4 0.0024 5.2E-08 61.3 12.7 177 30-248 42-247 (377)
45 cd06145 REX1_like DEDDh 3'-5' 97.4 0.0013 2.9E-08 55.0 9.8 144 37-243 1-149 (150)
46 cd06137 DEDDh_RNase DEDDh 3'-5 97.1 0.0045 9.7E-08 52.3 9.7 68 156-243 85-160 (161)
47 cd06149 ISG20 DEDDh 3'-5' exon 96.8 0.012 2.7E-07 49.6 9.7 97 124-243 51-156 (157)
48 PRK05359 oligoribonuclease; Pr 96.4 0.094 2E-06 45.4 12.7 165 33-252 2-177 (181)
49 PF01612 DNA_pol_A_exo1: 3'-5' 95.2 0.7 1.5E-05 38.2 13.0 83 152-250 74-175 (176)
50 PRK05755 DNA polymerase I; Pro 95.1 0.42 9.2E-06 51.0 14.1 83 153-251 368-470 (880)
51 COG0349 Rnd Ribonuclease D [Tr 94.9 0.21 4.6E-06 47.9 9.9 82 153-251 68-167 (361)
52 cd06135 Orn DEDDh 3'-5' exonuc 94.4 0.78 1.7E-05 39.1 11.4 164 36-249 1-171 (173)
53 cd06141 WRN_exo DEDDy 3'-5' ex 94.3 1.1 2.5E-05 37.4 12.2 79 153-247 71-169 (170)
54 TIGR01388 rnd ribonuclease D. 93.5 3.7 7.9E-05 39.5 15.4 82 153-251 68-167 (367)
55 cd06146 mut-7_like_exo DEDDy 3 93.3 2.4 5.2E-05 36.8 12.6 86 152-247 79-192 (193)
56 PRK10829 ribonuclease D; Provi 92.4 2.2 4.9E-05 41.2 12.2 83 153-251 72-171 (373)
57 cd06129 RNaseD_like DEDDy 3'-5 91.6 4.5 9.8E-05 33.8 11.9 79 153-247 65-160 (161)
58 cd06148 Egl_like_exo DEDDy 3'- 89.6 7.2 0.00016 33.8 11.7 83 153-251 63-178 (197)
59 PF10108 DNA_pol_B_exo2: Predi 84.7 3.3 7.1E-05 37.0 6.7 92 156-249 53-172 (209)
60 KOG2249 3'-5' exonuclease [Rep 80.7 18 0.00038 33.6 9.9 58 192-250 201-266 (280)
61 cd06139 DNA_polA_I_Ecoli_like_ 76.8 21 0.00046 29.8 8.9 83 153-251 65-171 (193)
62 COG2176 PolC DNA polymerase II 73.1 5.8 0.00012 43.7 5.2 84 157-252 503-588 (1444)
63 PF13482 RNase_H_2: RNase_H su 70.9 1.8 4E-05 35.8 0.8 70 157-241 59-131 (164)
64 cd05782 DNA_polB_like1_exo Unc 53.5 29 0.00063 30.5 5.2 69 157-225 95-170 (208)
65 KOG1990 Poly(A)-specific exori 51.7 4.7 0.0001 41.1 -0.1 150 10-163 102-261 (564)
66 TIGR02841 spore_YyaC putative 47.5 20 0.00042 30.1 2.9 30 14-43 43-72 (140)
67 PF04405 ScdA_N: Domain of Unk 41.8 35 0.00076 23.9 3.1 33 114-146 12-53 (56)
68 KOG4013 Predicted Cu2+ homeost 41.8 95 0.0021 27.8 6.4 85 114-206 83-172 (255)
69 COG3359 Predicted exonuclease 39.4 31 0.00068 31.8 3.2 74 157-243 158-235 (278)
70 cd00007 35EXOc 3'-5' exonuclea 36.9 1.1E+02 0.0024 24.0 5.8 53 153-221 52-106 (155)
71 PF06866 DUF1256: Protein of u 32.5 43 0.00093 28.8 2.8 31 14-44 67-97 (163)
72 TIGR01229 rocF_arginase argina 29.9 1.5E+02 0.0033 27.4 6.3 68 14-83 196-272 (300)
73 PF13637 Ank_4: Ankyrin repeat 29.5 51 0.0011 21.8 2.3 29 114-142 13-41 (54)
74 PF07827 KNTase_C: KNTase C-te 29.3 54 0.0012 27.6 2.8 48 177-224 86-134 (143)
75 PF13606 Ank_3: Ankyrin repeat 27.7 48 0.001 19.8 1.7 17 114-130 14-30 (30)
76 PF12345 DUF3641: Protein of u 27.3 60 0.0013 27.0 2.7 32 120-151 16-48 (134)
77 KOG0626 Beta-glucosidase, lact 26.4 55 0.0012 33.2 2.8 65 56-139 84-150 (524)
78 PF02845 CUE: CUE domain; Int 26.1 1.4E+02 0.003 19.1 3.9 30 187-217 5-34 (42)
79 PF02954 HTH_8: Bacterial regu 24.3 70 0.0015 20.6 2.1 25 201-225 8-32 (42)
80 PRK13772 formimidoylglutamase; 23.5 2.8E+02 0.0061 25.9 6.9 69 13-83 217-293 (314)
81 smart00546 CUE Domain that may 23.0 1.7E+02 0.0037 18.7 3.8 30 187-217 6-35 (43)
82 PF08870 DUF1832: Domain of un 22.5 1.6E+02 0.0035 23.6 4.3 32 155-188 54-87 (113)
83 KOG2725 Cytochrome oxidase ass 21.7 70 0.0015 30.9 2.4 68 177-244 300-402 (411)
84 PF02671 PAH: Paired amphipath 21.5 83 0.0018 20.6 2.1 32 180-211 1-32 (47)
85 PF13857 Ank_5: Ankyrin repeat 21.2 87 0.0019 21.1 2.3 29 114-142 28-56 (56)
86 PF00550 PP-binding: Phosphopa 20.6 2.1E+02 0.0045 19.4 4.2 36 215-250 5-45 (67)
87 PF02257 RFX_DNA_binding: RFX 20.6 76 0.0017 24.3 2.0 29 169-197 33-61 (85)
88 PRK02190 agmatinase; Provision 20.2 3.2E+02 0.007 25.2 6.5 66 15-83 199-271 (301)
No 1
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=1.9e-91 Score=607.95 Aligned_cols=237 Identities=64% Similarity=1.133 Sum_probs=231.1
Q ss_pred eEEEcCcccHHHHHHHHHHHhhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCC
Q 024017 11 HIREVWNDNLEHEFSLIRDIVDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPK 90 (274)
Q Consensus 11 ~i~~Vw~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~ 90 (274)
.|||||++|+++||+.||++|++||||||||||||++.+|.+.++++.+++|+.||+|||.+++||+|||++|++|++|.
T Consensus 1 ~ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p~ 80 (239)
T KOG0304|consen 1 FIREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNLPD 80 (239)
T ss_pred ChhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccCCCCCC
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCCeeeEEEeeeecCCCCCccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHH
Q 024017 91 CGTDKYCLWQFNFREFSPDEDVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYL 170 (274)
Q Consensus 91 ~g~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl 170 (274)
+| ..+|||||.+|++.+|+++++||+||+++|+||.|++..||+..+|+|+|++||++++++|+||||||+||||||
T Consensus 81 ~g---~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYL 157 (239)
T KOG0304|consen 81 CG---TDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYL 157 (239)
T ss_pred CC---CceeEEecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHH
Confidence 75 569999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhh--ccccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHH
Q 024017 171 LKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNS--LHGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKD 248 (274)
Q Consensus 171 ~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~--l~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~ 248 (274)
+|+||+++||++..+|.+.++++||.+||+|+|++.|.+ +++||++||+.|+++|+|++|||||||+||+.+|+||++
T Consensus 158 lK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 158 LKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred HHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhhhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999965 899999999999999999999999999999999999998
Q ss_pred hh
Q 024017 249 NF 250 (274)
Q Consensus 249 ~~ 250 (274)
.|
T Consensus 238 ~f 239 (239)
T KOG0304|consen 238 LF 239 (239)
T ss_pred cC
Confidence 64
No 2
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=2.5e-81 Score=545.75 Aligned_cols=264 Identities=47% Similarity=0.821 Sum_probs=248.3
Q ss_pred CCCC--CCCCCceEEEcCcccHHHHHHHHHHHhhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeee
Q 024017 1 MSIL--PKSESIHIREVWNDNLEHEFSLIRDIVDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLG 78 (274)
Q Consensus 1 ~~~~--~~~~~~~i~~Vw~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlG 78 (274)
||++ +.++-..|||||++|+..||+.|+++|.+|++|+|||||||+++||.|.|+++.+++||.||+|||.++|||+|
T Consensus 7 ~p~i~~dg~~~~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlG 86 (299)
T COG5228 7 MPPIFLDGPNYLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLG 86 (299)
T ss_pred CCCccCCCcchHHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhhee
Confidence 6776 44445679999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCcee
Q 024017 79 LTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHW 158 (274)
Q Consensus 79 it~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~W 158 (274)
|++.|++|+.|. ..++|||||- |++.+|+++++||++|+++||||.||.+.||++.+|+|+|+.||||+.++|+|
T Consensus 87 lsLSDe~GN~P~----~~sTWQFNF~-F~l~~dmya~ESieLL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~VtW 161 (299)
T COG5228 87 LSLSDENGNKPN----GPSTWQFNFE-FDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTW 161 (299)
T ss_pred eeeccccCCCCC----CCceeEEEEE-ecchhhhcchHHHHHHHHcCCChhhHhhcCCCHHHHHHHHhccCceeccceEE
Confidence 999999999995 4899999998 99999999999999999999999999999999999999999999999999999
Q ss_pred EEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhhccccHHHHHHHcCCccCCCccccchhhHH
Q 024017 159 VTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNSLHGGLNKLAELLEVERIGICHQAGSDSLL 238 (274)
Q Consensus 159 vtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~l~~~L~~la~~L~v~r~g~~HqAGsDS~l 238 (274)
||||++||||||+|+||+.|||+.+++|.++|++|||+.||+|++.+...+.+.|||+++..|++.|.|++||||+||++
T Consensus 162 itfHsaYDfgyLikilt~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLl 241 (299)
T COG5228 162 ITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALL 241 (299)
T ss_pred EEeecchhHHHHHHHHhcCCCCccHHHHHHHHHHHCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhh
Confidence 99999999999999999999999999999999999999999999999988889999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCC-ccccccEEeecCCCC
Q 024017 239 TCCTFMKMKDNFFKGS-PEKYAGVLYGLGVEN 269 (274)
Q Consensus 239 T~~~F~~l~~~~~~~~-~~~~~~~i~Gl~~~~ 269 (274)
|+..|++.|..+|+.. ....-+.+||++...
T Consensus 242 Ta~~ff~~R~~~F~~sig~~ll~~L~g~~~~~ 273 (299)
T COG5228 242 TADEFFLPRFSIFTTSIGQSLLMLLSGCQLSK 273 (299)
T ss_pred hhHHhcchhhheecccccHHHHHHHhccccCC
Confidence 9999999999998654 445556666666543
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=3e-64 Score=458.49 Aligned_cols=228 Identities=36% Similarity=0.613 Sum_probs=201.7
Q ss_pred EEcCcccHHHHHHHHHHHhhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeee-cCCCCCCCC
Q 024017 13 REVWNDNLEHEFSLIRDIVDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFT-DENGNLPKC 91 (274)
Q Consensus 13 ~~Vw~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~-~~~g~~p~~ 91 (274)
+|||++||+++++.|+++|++|+|||||+||||+..++.....+++++||+++|.||+.+.+||+|||+| +++++.|.
T Consensus 1 m~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~- 79 (262)
T PF04857_consen 1 MEVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPS- 79 (262)
T ss_dssp EEE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEEC-
T ss_pred CcccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCc-
Confidence 6899999999999999999999999999999999998865567899999999999999999999999999 77888775
Q ss_pred CCCCeeeEEEeeeecCCCCCccchhhHHHHHHcCCCccchhhCCCChHHHH------HHHHHcCccc---CCCceeEEee
Q 024017 92 GTDKYCLWQFNFREFSPDEDVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFS------ELLMSSGIVL---NDSVHWVTFH 162 (274)
Q Consensus 92 g~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~------e~l~~sgLv~---~~~v~Wvtfh 162 (274)
.+.+|+|||+.|+..++.++++||+||++|||||||++++||+|..++ +.+..++++. ..++.||+++
T Consensus 80 ---~~~~~~~nf~~f~~~~~~~~~~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn 156 (262)
T PF04857_consen 80 ---SYNVWPFNFYLFPLDRDFSQASSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHN 156 (262)
T ss_dssp ---CEEEEEEEBSTTSTTTCEEEHHHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESS
T ss_pred ---eeEEEEeeeeccccccceecchhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeC
Confidence 589999999999999998899999999999999999999999999999 6677788775 3458999999
Q ss_pred cchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhhccccHHHHHHHcCCcc-----------------
Q 024017 163 SGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNSLHGGLNKLAELLEVER----------------- 225 (274)
Q Consensus 163 g~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~l~~~L~~la~~L~v~r----------------- 225 (274)
|.||++||++.++| |||+|+++|++.++.+||.||||||||+.+....++|+.|++.|++.|
T Consensus 157 ~~~Dl~~l~~~f~~-~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~ 235 (262)
T PF04857_consen 157 GLYDLMYLYKKFIG-PLPETLEEFKELLRELFPRIYDTKYLAEECPGKSTSLQELAEELGIRRNPSSISSPEGFPSYDEE 235 (262)
T ss_dssp THHHHHHHHHHHTT-S--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS-SSHHHHHHHTTSTT----EEE-TTS------
T ss_pred hHhHHHHHHHHhcC-CCCCCHHHHHHHHHHHCcccccHHHHHHhccccccCHHHHHHHhCCCcccccccccccccccccc
Confidence 99999999999998 999999999999999999999999999998867889999999999988
Q ss_pred ------CCC-ccccchhhHHHHHHHHH
Q 024017 226 ------IGI-CHQAGSDSLLTCCTFMK 245 (274)
Q Consensus 226 ------~g~-~HqAGsDS~lT~~~F~~ 245 (274)
.|. .||||+|||||+.||++
T Consensus 236 ~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 236 KNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp -------SS-TTSHHHHHHHHHHHHHH
T ss_pred ccccccCCCCCCCcchHHHHHHHHHcC
Confidence 666 99999999999999985
No 4
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.06 E-value=5e-11 Score=119.49 Aligned_cols=231 Identities=19% Similarity=0.211 Sum_probs=152.9
Q ss_pred cccHHHHHHHHHHHhhcCCeeEEeecccccccccC--CCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCC--C
Q 024017 17 NDNLEHEFSLIRDIVDDYPYIAMDTEFPGIVLRSI--GNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKC--G 92 (274)
Q Consensus 17 ~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~--~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~--g 92 (274)
+.|++. +..++..|+.+.|+++|.|++|+...|. +.-.++.+.+|+++|.|+-.+.++|+|+|.|.++++.-.. +
T Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 79 (564)
T KOG1990|consen 1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMST 79 (564)
T ss_pred CCcccc-hhHHHhhcCHHHHHHHhhhhccceecccccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccC
Confidence 468888 9999999999999999999999988873 2334789999999999999999999999999887654321 0
Q ss_pred CCCeeeEEEeeeecCCCCCccchhhHHHHHHcCCCccch-----------hhCCCChH-----------H----------
Q 024017 93 TDKYCLWQFNFREFSPDEDVYAYDSIKLLSRSGIDFKKN-----------KEKGVDAM-----------R---------- 140 (274)
Q Consensus 93 ~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~-----------~~~GI~~~-----------~---------- 140 (274)
.....+|..-+. ....+.+|+..++.++.+++-++..- -..|+.+. .
T Consensus 80 ~~n~~~~~~g~~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~ 158 (564)
T KOG1990|consen 80 GGNFVVWSRGDS-ISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIP 158 (564)
T ss_pred CCceeeeecCcc-ccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhh
Confidence 002344543222 22224578889999988872111100 00111110 0
Q ss_pred -----------------------------------------------------------HHHHHHHcCcc----------
Q 024017 141 -----------------------------------------------------------FSELLMSSGIV---------- 151 (274)
Q Consensus 141 -----------------------------------------------------------f~e~l~~sgLv---------- 151 (274)
|+..+...|..
T Consensus 159 ~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~ 238 (564)
T KOG1990|consen 159 DYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADE 238 (564)
T ss_pred cccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHH
Confidence 11111111111
Q ss_pred ----cCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHh--hh--ccccHHHHHHH-cC
Q 024017 152 ----LNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFC--NS--LHGGLNKLAEL-LE 222 (274)
Q Consensus 152 ----~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~--~~--l~~~L~~la~~-L~ 222 (274)
......-|...+.+|+.|+.|-+.+ +||+++.+|.+. ...||+++|++.++... .+ +.+.+.+.+.. ..
T Consensus 239 l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~-~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~ 316 (564)
T KOG1990|consen 239 LQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDS-SSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAK 316 (564)
T ss_pred HHHHHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhh-hhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcc
Confidence 1111122334567899999999998 999999999999 99999999999998832 22 34444443321 11
Q ss_pred ----C---------------ccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 223 ----V---------------ERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 223 ----v---------------~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
+ .+-...|+++++++.++.++.+......
T Consensus 317 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 364 (564)
T KOG1990|consen 317 KEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRIL 364 (564)
T ss_pred cccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhh
Confidence 1 1124568999999999999999877754
No 5
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=98.95 E-value=2.8e-08 Score=89.31 Aligned_cols=170 Identities=21% Similarity=0.246 Sum_probs=118.6
Q ss_pred hcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCC
Q 024017 32 DDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDED 111 (274)
Q Consensus 32 ~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d 111 (274)
.+.+||++|+|=||+... .=.|||+|+..++.+|+.. -.|+.. .+...
T Consensus 4 ~~~~~vv~D~ETTGl~p~---------------------~d~Iieig~v~v~~~g~~~---------~~~~~l-v~P~~- 51 (232)
T PRK07942 4 HPGPLAAFDLETTGVDPE---------------------TARIVTAALVVVDADGEVV---------ESREWL-ADPGV- 51 (232)
T ss_pred ccCcEEEEEeccCCCCCC---------------------CCeeEEEEEEEEeCCCccc---------cceEEE-ECCCC-
Confidence 467899999999998421 1139999999998767532 234444 44433
Q ss_pred ccchhhHHHHHHcCCCccchhhCCCChHH----HHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHH
Q 024017 112 VYAYDSIKLLSRSGIDFKKNKEKGVDAMR----FSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFF 187 (274)
Q Consensus 112 ~~~~~Si~fL~~~G~DF~k~~~~GI~~~~----f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~ 187 (274)
.+.+++.+. |||.=..+..+|.+... |.+.+.. .. .....+|+++..||+++|-+.+...-+|.-
T Consensus 52 ~i~~~a~~I---hGIt~e~l~~~g~~~~~vl~e~~~~l~~--~~-~~~~~lVahNa~FD~~fL~~~~~r~~~~~~----- 120 (232)
T PRK07942 52 EIPEEASAV---HGITTEYARAHGRPAAEVLAEIADALRE--AW-ARGVPVVVFNAPYDLTVLDRELRRHGLPSL----- 120 (232)
T ss_pred CCCHHHHHH---hCCCHHHHHhhCCCHHHHHHHHHHHHHH--Hh-hcCCEEEEeCcHhhHHHHHHHHHHcCCCCc-----
Confidence 456666666 99999999999998643 3333321 11 123478999999999999777642222211
Q ss_pred HHHHhhCC-CcccHHHHHHHhhhc---cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 188 DLIKMYFP-TLYDIKHLMKFCNSL---HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 188 ~~l~~~FP-~iyD~K~la~~~~~l---~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
.| .++|+-.|++.+... +-+|+.+++.+|++.. .+|.|-+|++.|+++|.+|.+.+.
T Consensus 121 ------~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~~-~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 121 ------VPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRLD-NAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred ------cCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCCC-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 22 366888888765432 2379999999999855 489999999999999999988764
No 6
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.94 E-value=8e-08 Score=80.23 Aligned_cols=164 Identities=20% Similarity=0.213 Sum_probs=115.4
Q ss_pred CeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccc
Q 024017 35 PYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYA 114 (274)
Q Consensus 35 ~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~ 114 (274)
.||++|+|.+|+... .-.|||+|....+.+. ....|+.+ ... ....+
T Consensus 1 ~~v~~D~Ettg~~~~---------------------~~~Iieig~v~~~~~~----------~~~~f~~~-v~p-~~~i~ 47 (169)
T smart00479 1 TLVVIDCETTGLDPG---------------------KDEIIEIAAVDVDGGR----------IIVVFDTY-VKP-DRPIT 47 (169)
T ss_pred CEEEEEeeCCCCCCC---------------------CCeEEEEEEEEEECCE----------eEEEEEEE-ECC-CCCCC
Confidence 489999999997532 1249999998887632 24567777 444 23444
Q ss_pred hhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeec-chhHHHHHHHhc--CCCCCCCHHHHHHHHH
Q 024017 115 YDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHS-GYDFGYLLKLLT--CKDLPETQACFFDLIK 191 (274)
Q Consensus 115 ~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg-~yD~~yl~k~l~--~~~LP~~~~~F~~~l~ 191 (274)
+.+.+ -+|+.-+.+.. |.++....+.+.. ++ ... .+|++|+ .+|+.+|-+.+. |.+.|..
T Consensus 48 ~~~~~---~~Git~~~l~~-~~~~~~~~~~~~~--~l-~~~-~~v~~n~~~fD~~~L~~~~~~~~~~~~~~--------- 110 (169)
T smart00479 48 DYATE---IHGITPEMLDD-APTFEEVLEELLE--FL-KGK-ILVAGNALNFDLRFLKLEHPRLGIKDPPK--------- 110 (169)
T ss_pred HHHHH---HhCCCHHHHhC-CCCHHHHHHHHHH--Hh-cCC-EEEEeCCHHHhHHHHHHHHHHhCCCCCcC---------
Confidence 54444 47888777765 8888765555443 22 222 5788999 999999987774 2333311
Q ss_pred hhCCCcccHHHHHHHhh-hccccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 192 MYFPTLYDIKHLMKFCN-SLHGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 192 ~~FP~iyD~K~la~~~~-~l~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
-...|+.-+++... ....+|+.+++.++++..+..|.|-.|+..|+++|.+|.+..+
T Consensus 111 ---~~~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 111 ---NPVIDTLKLARALNPGRKYSLKKLAERLGLEVIGRAHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred ---CCeeEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHHhh
Confidence 12568877766542 2356899999999999988889999999999999999987643
No 7
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=98.76 E-value=2.8e-07 Score=77.74 Aligned_cols=172 Identities=17% Similarity=0.138 Sum_probs=111.9
Q ss_pred eeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccch
Q 024017 36 YIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYAY 115 (274)
Q Consensus 36 fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~~ 115 (274)
||.+|+|.+|...... .. ..=.|||+|....+.++. ...-.|+.+.-+......++
T Consensus 1 ~vv~D~Ettg~~~~~~--------------~~--~~~~IieIgav~v~~~~~--------~~~~~f~~~i~P~~~~~i~~ 56 (176)
T cd06133 1 YLVIDFEATCWEGNSK--------------PD--YPNEIIEIGAVLVDVKTK--------EIIDTFSSYVKPVINPKLSD 56 (176)
T ss_pred CEEEEeeccccCCCCC--------------CC--CCcceEEEEEEEEEcCCC--------eEEeeeeeeECCCcCCchhH
Confidence 7999999999865321 00 112499999999987653 13445666633332235666
Q ss_pred hhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCC-CceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhC
Q 024017 116 DSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLND-SVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYF 194 (274)
Q Consensus 116 ~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~-~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~F 194 (274)
.+.+. +|+.-+.+. ++.++....+.+.. .+.+. ....++ +|.+|...+.+......... ...++
T Consensus 57 ~~~~i---~gIt~e~l~-~~~~~~~vl~~~~~--~l~~~~~~~~v~-~~~~d~~~l~~~~~~~~~~~--------~~~~~ 121 (176)
T cd06133 57 FCTEL---TGITQEDVD-NAPSFPEVLKEFLE--WLGKNGKYAFVT-WGDWDLKDLLQNQCKYKIIN--------LPPFF 121 (176)
T ss_pred HHHHh---cCcCHHHHh-cCCCHHHHHHHHHH--HHHhCCCeEEEe-ecHhhHHHHHHHHHHhcCCC--------Ccccc
Confidence 66666 999998875 56776643333221 11111 133444 46788887766443111100 11223
Q ss_pred CCcccHHHHHHHhhhc--cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHH
Q 024017 195 PTLYDIKHLMKFCNSL--HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKM 246 (274)
Q Consensus 195 P~iyD~K~la~~~~~l--~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l 246 (274)
...+|++.+++..... ..+|.++++.+|++..+..|.|=+|+..|+++|.+|
T Consensus 122 ~~~~D~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 122 RQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred cceEEHHHHHHHHhCCCCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHh
Confidence 4678999888876433 568999999999999999999999999999999987
No 8
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.70 E-value=7.8e-07 Score=77.96 Aligned_cols=171 Identities=15% Similarity=0.271 Sum_probs=109.8
Q ss_pred HHHHHHHhhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEee
Q 024017 24 FSLIRDIVDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNF 103 (274)
Q Consensus 24 l~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF 103 (274)
+..+.+.....+||++|+|-||+... .-.|||+|...++.+ .. .....|.+
T Consensus 19 ~~~~~~~~~~~~~vviD~ETTGl~~~---------------------~d~IieIgaV~~~~~-~~-------~~~~~f~~ 69 (202)
T PRK09145 19 YAFLFEPPPPDEWVALDCETTGLDPR---------------------RAEIVSIAAVKIRGN-RI-------LTSERLEL 69 (202)
T ss_pred HHHHhcCCCCCCEEEEEeECCCCCCC---------------------CCceEEEEEEEEECC-EE-------eecCceEE
Confidence 33444444567999999999998421 114999999988743 21 12234555
Q ss_pred eecCCCCCccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHh---cCCCCC
Q 024017 104 REFSPDEDVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLL---TCKDLP 180 (274)
Q Consensus 104 ~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l---~~~~LP 180 (274)
+ .+... ...+.+.+. ||+.-..+ ++|.+.....+.+.. .+ . +-.||+++..+|..+|-+-+ .+.++|
T Consensus 70 ~-i~p~~-~i~~~~~~i---hGIt~~~l-~~~~~~~~vl~~~~~--~i-~-~~~lv~hn~~fD~~fL~~~~~~~~~~~~~ 139 (202)
T PRK09145 70 L-VRPPQ-SLSAESIKI---HRLRHQDL-EDGLSEEEALRQLLA--FI-G-NRPLVGYYLEFDVAMLNRYVRPLLGIPLP 139 (202)
T ss_pred E-ECCCC-CCCHhHhhh---cCcCHHHH-hcCCCHHHHHHHHHH--HH-c-CCeEEEeCHHHHHHHHHHHHHHhcCCCCC
Confidence 5 44432 345555554 77776665 467776654444332 11 1 23688888899999986554 345555
Q ss_pred CCHHHHHHHHHhhCCCcccHHHHHHHh--hhc-----cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHH
Q 024017 181 ETQACFFDLIKMYFPTLYDIKHLMKFC--NSL-----HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKD 248 (274)
Q Consensus 181 ~~~~~F~~~l~~~FP~iyD~K~la~~~--~~l-----~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~ 248 (274)
.. .+|+.-+.... ..+ .-+|+.+++.+|++.. ..|.|-+||+.|+++|.+|++
T Consensus 140 ~~--------------~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 140 NP--------------LIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVL-GRHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CC--------------eeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHh
Confidence 43 34555443211 111 2489999999999875 469999999999999999865
No 9
>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=98.61 E-value=1.9e-06 Score=72.53 Aligned_cols=163 Identities=17% Similarity=0.212 Sum_probs=106.5
Q ss_pred eeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccch
Q 024017 36 YIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYAY 115 (274)
Q Consensus 36 fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~~ 115 (274)
||++|+|=||+..+ ..-.|||+|....+. +. ....+|+.+ .+... ...+
T Consensus 1 ~v~~D~ETTGl~~~--------------------~~~~iieig~v~v~~-~~--------~~~~~~~~~-v~P~~-~i~~ 49 (167)
T cd06131 1 QIVLDTETTGLDPR--------------------EGHRIIEIGCVELIN-RR--------LTGNTFHVY-INPER-DIPE 49 (167)
T ss_pred CEEEEeeCCCCCCC--------------------CCCeEEEEEEEEEEC-Cc--------EeccEEEEE-ECCCC-CCCH
Confidence 79999999998421 112499999987754 22 123467766 44443 3566
Q ss_pred hhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCC
Q 024017 116 DSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFP 195 (274)
Q Consensus 116 ~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP 195 (274)
.+.+. |||.=+.+... .+.....+.+.. .+ .+. .+|.+++.+|..+|-+-+....++... ..|
T Consensus 50 ~~~~i---hGIt~e~l~~~-~~~~~v~~~l~~--~l-~~~-~lv~hn~~fD~~~l~~~~~~~~~~~~~---------~~~ 112 (167)
T cd06131 50 EAFKV---HGITDEFLADK-PKFAEIADEFLD--FI-RGA-ELVIHNASFDVGFLNAELSLLGLGKKI---------IDF 112 (167)
T ss_pred HHHHH---hCCCHHHHhcC-CCHHHHHHHHHH--HH-CCC-eEEEeChHHhHHHHHHHHHHhCCCccc---------ccC
Confidence 66654 78777665543 344443333332 12 222 589999999999987766432121110 023
Q ss_pred -CcccHHHHHHHhh-hccccHHHHHHHcCCccCC-CccccchhhHHHHHHHHHH
Q 024017 196 -TLYDIKHLMKFCN-SLHGGLNKLAELLEVERIG-ICHQAGSDSLLTCCTFMKM 246 (274)
Q Consensus 196 -~iyD~K~la~~~~-~l~~~L~~la~~L~v~r~g-~~HqAGsDS~lT~~~F~~l 246 (274)
..+||-.+++... ....+|+.+++.+|++..+ .+|.|-+|++.|+++|.+|
T Consensus 113 ~~~idt~~~~~~~~~~~~~~L~~l~~~~~i~~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 113 CRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCceEhHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHh
Confidence 3678877776542 3445899999999999865 5899999999999999987
No 10
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=98.57 E-value=2.6e-06 Score=75.04 Aligned_cols=172 Identities=18% Similarity=0.091 Sum_probs=107.9
Q ss_pred cCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCC-
Q 024017 33 DYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDED- 111 (274)
Q Consensus 33 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d- 111 (274)
+.+||++|+|.||+..+.. +.... -.|||+|....+. |+. .-.|+-+ ..+...
T Consensus 3 ~~~~vvlD~EtTg~~~~~~-~~~~~--------------~eIIeIGaV~v~~-~~i---------~~~f~~l-V~P~~~~ 56 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKK-PKGFF--------------PEIIEVGLVSVVG-CEV---------EDTFSSY-VKPKTFP 56 (207)
T ss_pred cceEEEEEeecCCcCCCCC-CCCCC--------------CceEEEeEEEEec-CcC---------hhhhcce-ECCCccC
Confidence 4579999999999753210 00000 1399999988873 332 2234444 333222
Q ss_pred ccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhc--CCCCCCCHHHHHHH
Q 024017 112 VYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLT--CKDLPETQACFFDL 189 (274)
Q Consensus 112 ~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~--~~~LP~~~~~F~~~ 189 (274)
..++.+.++ +||.=+.+ ..|.+.....+.+.. .+.+....++ .|+.+|+.+|-+.+. |-+.|.
T Consensus 57 ~i~~~~~~l---tGIt~~~l-~~ap~~~evl~~f~~--~~~~~~~~iv-~~~~fD~~fL~~~~~~~~~~~~~-------- 121 (207)
T PRK07748 57 SLTERCKSF---LGITQEDV-DKGISFEELVEKLAE--YDKRCKPTIV-TWGNMDMKVLKHNCEKAGVPFPF-------- 121 (207)
T ss_pred ccChhhhhh---cCcCHHHH-ccCCCHHHHHHHHHH--HhCcCCeEEE-EECHHHHHHHHHHHHHcCCCCcc--------
Confidence 345555555 88876666 468887665544433 2212133444 468999999977764 323331
Q ss_pred HHhhCCCcccHHHHHHHhhh--ccccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHh
Q 024017 190 IKMYFPTLYDIKHLMKFCNS--LHGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDN 249 (274)
Q Consensus 190 l~~~FP~iyD~K~la~~~~~--l~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~ 249 (274)
+....|+..+.+.... -..+|..+++.+|++-.+..|.|-+||+.|+.+|.+|.+.
T Consensus 122 ----~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 122 ----KGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred ----cccceeHHHHHHHHhCcCCCCCHHHHHHHcCCCCCCCCcChHHHHHHHHHHHHHHHhC
Confidence 1234566554443321 1258999999999998888999999999999999998876
No 11
>PRK05168 ribonuclease T; Provisional
Probab=98.57 E-value=2.9e-06 Score=75.15 Aligned_cols=186 Identities=16% Similarity=0.207 Sum_probs=123.2
Q ss_pred HHHHHHHhhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecC--CCCCCCCCCCCeeeEEE
Q 024017 24 FSLIRDIVDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDE--NGNLPKCGTDKYCLWQF 101 (274)
Q Consensus 24 l~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~--~g~~p~~g~~~~~~wqF 101 (274)
+.-|..-++...||++|+|=||+.... + .|||+|....+. +|... ....|
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~-----d----------------~IieIgaV~v~~d~~g~i~-------~~~~f 58 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKT-----D----------------ALLEIAAVTLKMDEQGWLY-------PDETL 58 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCC-----C----------------EEEEEeEEEEEecCCCcEe-------ccceE
Confidence 445777788999999999999986431 0 299999888764 34321 23456
Q ss_pred eeeecCCC-CCccchhhHHHHHHcCCCccchhhCCCChHH-HHHHHHHcC-ccc---CCCceeEEeecchhHHHHHHHhc
Q 024017 102 NFREFSPD-EDVYAYDSIKLLSRSGIDFKKNKEKGVDAMR-FSELLMSSG-IVL---NDSVHWVTFHSGYDFGYLLKLLT 175 (274)
Q Consensus 102 NF~~F~~~-~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~-f~e~l~~sg-Lv~---~~~v~Wvtfhg~yD~~yl~k~l~ 175 (274)
..+ .+.. .-...+++++. +||.=+...+.|++... +.+.+..-+ .+. .++..+|+++..+|++||-+.+.
T Consensus 59 ~~l-v~P~~~~~i~~~~~~i---hGIt~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~ 134 (211)
T PRK05168 59 HFH-VEPFEGANLEPEALAF---NGIDPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAE 134 (211)
T ss_pred EEE-ECCCCCCCCCHHHHhh---cCCCchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHH
Confidence 666 4442 23466676665 89965555677887543 222221100 000 02357999999999999977663
Q ss_pred CCCCCCCHHHHHHHHHhhCC-CcccHHHHHHHhhhccccHHHHHHHcCCccCC-CccccchhhHHHHHHHHHHHHhhc
Q 024017 176 CKDLPETQACFFDLIKMYFP-TLYDIKHLMKFCNSLHGGLNKLAELLEVERIG-ICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 176 ~~~LP~~~~~F~~~l~~~FP-~iyD~K~la~~~~~l~~~L~~la~~L~v~r~g-~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
-..+.. ..+.| .++||.-|++..-.. .+|..+++.+|++-.+ ..|.|-+|++.|+++|.+|.+.+-
T Consensus 135 r~~~~~---------~~~~~~~~iDt~~lar~~~~~-~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 135 RAGLKR---------NPFHPFSTFDTATLSGLALGQ-TVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred HhCCCC---------CCCCCCcEeeHHHHHHHHcCC-CCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 211110 01123 478999998755322 3799999999997543 689999999999999999988763
No 12
>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=98.56 E-value=2.2e-06 Score=74.61 Aligned_cols=174 Identities=19% Similarity=0.226 Sum_probs=115.3
Q ss_pred cCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecC--CCCCCCCCCCCeeeEEEeeeecCCC-
Q 024017 33 DYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDE--NGNLPKCGTDKYCLWQFNFREFSPD- 109 (274)
Q Consensus 33 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~--~g~~p~~g~~~~~~wqFNF~~F~~~- 109 (274)
.+.+|++|+|=||+.... + .|||+|...++. +|... ..-+|++. ++..
T Consensus 4 ~~~~vv~D~ETTGl~~~~-----d----------------~Iieigav~v~~~~~~~i~-------~~~~f~~l-v~P~~ 54 (189)
T cd06134 4 GFLPVVVDVETGGFNPQT-----D----------------ALLEIAAVTLEMDEQGNLY-------PDETFHFH-ILPFE 54 (189)
T ss_pred cceeEEEEecCCCCCCCC-----C----------------eEEEEEEEEEEECCCCcee-------ccceEEEE-EcCCC
Confidence 467899999999986431 0 299999998864 34321 23456766 4443
Q ss_pred CCccchhhHHHHHHcCCCccchhhCCCChHH-HHHHHHHc-Cccc---CCCceeEEeecchhHHHHHHHhcCCCCCCCHH
Q 024017 110 EDVYAYDSIKLLSRSGIDFKKNKEKGVDAMR-FSELLMSS-GIVL---NDSVHWVTFHSGYDFGYLLKLLTCKDLPETQA 184 (274)
Q Consensus 110 ~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~-f~e~l~~s-gLv~---~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~ 184 (274)
.....+++++. |||.=+...+.|++... +.+.+-.- .++. ..+-.+|.+|..+|++||-+.+....++
T Consensus 55 ~~~i~~~~~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~---- 127 (189)
T cd06134 55 GANLDPAALEF---NGIDPFHPFRFAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIK---- 127 (189)
T ss_pred CCCCCHHHHhh---cCCCchhhhccccchHHHHHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCC----
Confidence 33566677666 89886666777886542 22221110 0110 0124799999999999998776421111
Q ss_pred HHHHHHHhhC-C-CcccHHHHHHHhhhccccHHHHHHHcCCccC-CCccccchhhHHHHHHHHHHHHh
Q 024017 185 CFFDLIKMYF-P-TLYDIKHLMKFCNSLHGGLNKLAELLEVERI-GICHQAGSDSLLTCCTFMKMKDN 249 (274)
Q Consensus 185 ~F~~~l~~~F-P-~iyD~K~la~~~~~l~~~L~~la~~L~v~r~-g~~HqAGsDS~lT~~~F~~l~~~ 249 (274)
...+ | .++||..|++.... ...|+.+++.+|++.. ...|.|.+|++.|+++|.+|.++
T Consensus 128 ------~~~~~~~~~lDt~~la~~~~~-~~~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 128 ------RNPFHPFSTFDTATLAGLAYG-QTVLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred ------CCCCCCCcEEEHHHHHHHHhC-CCcHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 0112 2 36899999876532 2369999999999853 46899999999999999999875
No 13
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=98.52 E-value=3.2e-06 Score=69.99 Aligned_cols=151 Identities=18% Similarity=0.175 Sum_probs=100.8
Q ss_pred eeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccch
Q 024017 36 YIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYAY 115 (274)
Q Consensus 36 fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~~ 115 (274)
||++|+|-+|.. + -.|||+|...++. |+ ..-+|+.+ ..... ...+
T Consensus 1 ~v~~D~Ettg~~--~---------------------~~ii~ig~v~~~~-~~---------~~~~~~~~-i~p~~-~~~~ 45 (156)
T cd06130 1 FVAIDFETANAD--R---------------------ASACSIGLVKVRD-GQ---------IVDTFYTL-IRPPT-RFDP 45 (156)
T ss_pred CEEEEEeCCCCC--C---------------------CceEEEEEEEEEC-CE---------EEEEEEEE-eCcCC-CCCh
Confidence 799999999832 1 1279999988873 32 24567776 54443 4555
Q ss_pred hhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcC--CCCCCCHHHHHHHHHhh
Q 024017 116 DSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTC--KDLPETQACFFDLIKMY 193 (274)
Q Consensus 116 ~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~--~~LP~~~~~F~~~l~~~ 193 (274)
++.++ +|+.-..+.. +.++..-.+.+.. .+ +. -.||+++..+|.++|-+.+-. .+.|.
T Consensus 46 ~~~~i---~GIt~e~l~~-~~~~~~v~~~l~~--~l-~~-~~lv~hn~~fD~~~l~~~~~~~g~~~~~------------ 105 (156)
T cd06130 46 FNIAI---HGITPEDVAD-APTFPEVWPEIKP--FL-GG-SLVVAHNASFDRSVLRAALEAYGLPPPP------------ 105 (156)
T ss_pred hhccc---cCcCHHHHhc-CCCHHHHHHHHHH--Hh-CC-CEEEEeChHHhHHHHHHHHHHcCCCCCC------------
Confidence 66544 8888887764 4444432222221 11 22 478889999999999776642 22221
Q ss_pred CCCcccHHHHHHHhh-hc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHH
Q 024017 194 FPTLYDIKHLMKFCN-SL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFM 244 (274)
Q Consensus 194 FP~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~ 244 (274)
+ ..+|+.-+++..- .+ ..+|+.+++.+|++.. .|.|-+|+..|+.+|.
T Consensus 106 ~-~~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~~--~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 106 Y-QYLCTVRLARRVWPLLPNHKLNTVAEHLGIELN--HHDALEDARACAEILL 155 (156)
T ss_pred C-CEEEHHHHHHHHhccCCCCCHHHHHHHcCCCcc--CcCchHHHHHHHHHHh
Confidence 1 3678877766542 22 2489999999999876 9999999999999885
No 14
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=98.44 E-value=8.2e-06 Score=73.93 Aligned_cols=169 Identities=15% Similarity=0.241 Sum_probs=113.1
Q ss_pred cCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCc
Q 024017 33 DYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDV 112 (274)
Q Consensus 33 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~ 112 (274)
.-.||++|||=||+.... .=.|||+|...... +. .....|+.+ .+..+ .
T Consensus 3 ~~r~vvlDtETTGldp~~--------------------~drIIEIGaV~v~~-~~--------~~~~~f~~~-i~P~~-~ 51 (240)
T PRK05711 3 IMRQIVLDTETTGLNQRE--------------------GHRIIEIGAVELIN-RR--------LTGRNFHVY-IKPDR-L 51 (240)
T ss_pred CCeEEEEEeeCCCcCCCC--------------------CCeEEEEEEEEEEC-CE--------EeccEEEEE-ECcCC-c
Confidence 347999999999985320 12499999876652 21 123456776 55543 3
Q ss_pred cchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhc--CCCCCCCHHHHHHHH
Q 024017 113 YAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLT--CKDLPETQACFFDLI 190 (274)
Q Consensus 113 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~--~~~LP~~~~~F~~~l 190 (274)
..+++++. |||.-..+.. +-++....+.+.. .+ .+-.+|.++..+|++||-+-+. |.++|...
T Consensus 52 i~~~a~~V---HGIT~e~l~~-~p~f~ev~~~f~~--fi--~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~------- 116 (240)
T PRK05711 52 VDPEALAV---HGITDEFLAD-KPTFAEVADEFLD--FI--RGAELIIHNAPFDIGFMDYEFALLGRDIPKTN------- 116 (240)
T ss_pred CCHHHhhh---cCCCHHHHcC-CCCHHHHHHHHHH--Hh--CCCEEEEEccHHhHHHHHHHHHHhCCCCCccc-------
Confidence 56666555 7777666554 3444444443332 22 2236899999999999966553 33455321
Q ss_pred HhhCCCcccHHHHHHHh-hhccccHHHHHHHcCCccCC-CccccchhhHHHHHHHHHHHHh
Q 024017 191 KMYFPTLYDIKHLMKFC-NSLHGGLNKLAELLEVERIG-ICHQAGSDSLLTCCTFMKMKDN 249 (274)
Q Consensus 191 ~~~FP~iyD~K~la~~~-~~l~~~L~~la~~L~v~r~g-~~HqAGsDS~lT~~~F~~l~~~ 249 (274)
.+..++||--|++.. ++.+.+|+.|++.+|++..+ ..|.|-.|+.+|+.+|.+|...
T Consensus 117 --~~~~~iDTl~lar~~~p~~~~~L~aL~~~~gi~~~~r~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 117 --TFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred --ccCceeeHHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCc
Confidence 134578998888765 34456899999999998765 4699999999999999999865
No 15
>PRK07740 hypothetical protein; Provisional
Probab=98.38 E-value=1.7e-05 Score=71.85 Aligned_cols=168 Identities=18% Similarity=0.191 Sum_probs=108.5
Q ss_pred hcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCC
Q 024017 32 DDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDED 111 (274)
Q Consensus 32 ~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d 111 (274)
.+.+||.+|+|-||+.... .=.|||+|....+. |.. ..-.|... .+...
T Consensus 57 ~~~~~vv~D~ETTGl~p~~--------------------~deIIeIgaV~~~~-~~i--------~~~~f~~l-v~P~~- 105 (244)
T PRK07740 57 TDLPFVVFDLETTGFSPQQ--------------------GDEILSIGAVKTKG-GEV--------ETDTFYSL-VKPKR- 105 (244)
T ss_pred cCCCEEEEEEeCCCCCCCC--------------------CCeEEEEEEEEEEC-CEE--------EEEEEEEE-eCcCC-
Confidence 3568999999999975210 01489999888773 221 13345444 33332
Q ss_pred ccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCC-CCCCCHHHHHHHH
Q 024017 112 VYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCK-DLPETQACFFDLI 190 (274)
Q Consensus 112 ~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~-~LP~~~~~F~~~l 190 (274)
..++.+.++ +|+.=..+. +|.+...-.+.+.. .+ .. -.+|+++..+|.+||-+.+... ..|
T Consensus 106 ~i~~~~~~l---tGIt~e~l~-~ap~~~evl~~f~~--fi-~~-~~lVahna~fD~~fL~~~~~~~~~~~---------- 167 (244)
T PRK07740 106 PIPEHILEL---TGITAEDVA-FAPPLAEVLHRFYA--FI-GA-GVLVAHHAGHDKAFLRHALWRTYRQP---------- 167 (244)
T ss_pred CCChhheec---cCCCHHHHh-CCCCHHHHHHHHHH--Hh-CC-CEEEEeCHHHHHHHHHHHHHHhcCCC----------
Confidence 344444333 777665543 46665543333332 12 22 3799999999999987765321 111
Q ss_pred HhhCCCcccHHHHHHHhhh-c-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 191 KMYFPTLYDIKHLMKFCNS-L-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 191 ~~~FP~iyD~K~la~~~~~-l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
+...+.||..+++.... . ..+|+.+++.+|++..+ .|.|-+|++.|+.+|.++.....
T Consensus 168 --~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~~~-~H~Al~Da~ata~l~~~ll~~~~ 227 (244)
T PRK07740 168 --FTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPR-RHHALGDALMTAKLWAILLVEAQ 227 (244)
T ss_pred --cCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCCCC-CCCcHHHHHHHHHHHHHHHHHHH
Confidence 11357799888876542 2 35799999999998765 49999999999999999877754
No 16
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=98.37 E-value=1.3e-05 Score=75.25 Aligned_cols=163 Identities=19% Similarity=0.189 Sum_probs=109.8
Q ss_pred CCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCcc
Q 024017 34 YPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVY 113 (274)
Q Consensus 34 ~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~ 113 (274)
.+||++|+|.+|+... .-.|||+|...++ +| ....+|+.. ..+... .
T Consensus 8 ~~~Vv~DlETTGl~p~---------------------~~eIIEIgaV~v~-~g---------~i~~~f~~l-VkP~~~-I 54 (313)
T PRK06807 8 LDYVVIDFETTGFNPY---------------------NDKIIQVAAVKYR-NH---------ELVDQFVSY-VNPERP-I 54 (313)
T ss_pred CCEEEEEEECCCCCCC---------------------CCeEEEEEEEEEE-CC---------EEEEEEEEE-ECcCCC-C
Confidence 3899999999998521 1259999998886 33 245678876 555443 3
Q ss_pred chhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhh
Q 024017 114 AYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMY 193 (274)
Q Consensus 114 ~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~ 193 (274)
.+.+. +-+|+.-..+ .++.+.....+.+.. ++ ..+ .+|++++.+|..+|-+.+....+|..
T Consensus 55 ~~~a~---~ihGIT~e~l-~~~~~~~evl~~f~~--fl-~~~-~lVaHNa~FD~~fL~~~~~~~gl~~~----------- 115 (313)
T PRK06807 55 PDRIT---SLTGITNYRV-SDAPTIEEVLPLFLA--FL-HTN-VIVAHNASFDMRFLKSNVNMLGLPEP----------- 115 (313)
T ss_pred CHhhh---ccCCCCHHHH-hCCCCHHHHHHHHHH--HH-cCC-eEEEEcHHHHHHHHHHHHHHcCCCCC-----------
Confidence 44443 3488876554 345555443333332 12 223 57888999999999887742222211
Q ss_pred CCCcccHHHHHHHhh-hcc-ccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhh
Q 024017 194 FPTLYDIKHLMKFCN-SLH-GGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNF 250 (274)
Q Consensus 194 FP~iyD~K~la~~~~-~l~-~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~ 250 (274)
...+.||-.+++..- .+. .+|+.+++.+|++. .+|.|=.|++.|+.+|.+|...-
T Consensus 116 ~~~~iDtl~la~~~~~~~~~~kL~~L~~~lgi~~--~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 116 KNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRL--SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred CCCEeeHHHHHHHHhCCCCCCCHHHHHHHcCCCC--CCcChHHHHHHHHHHHHHHHHhh
Confidence 113668877777543 233 37999999999997 79999999999999999987764
No 17
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=98.32 E-value=2.3e-05 Score=71.26 Aligned_cols=169 Identities=15% Similarity=0.170 Sum_probs=110.0
Q ss_pred HhhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCC
Q 024017 30 IVDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPD 109 (274)
Q Consensus 30 ~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~ 109 (274)
++++.+||.+|+|=+|+.... =.|||+|+..++.+ ....+|+.+ .+..
T Consensus 3 ~l~~~~~v~~D~ETTGl~~~~---------------------d~IIEIa~v~v~~~----------~~~~~~~~l-i~P~ 50 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDVKK---------------------DRIIEFAAIRFTFD----------EVIDSVEFL-INPE 50 (250)
T ss_pred cccCCcEEEEEEeCCCCCCCC---------------------CeEEEEEEEEEECC----------eEEEEEEEE-ECcC
Confidence 467789999999999984211 13899999888643 134567776 5544
Q ss_pred CCccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcC--CCCCCCHHHHH
Q 024017 110 EDVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTC--KDLPETQACFF 187 (274)
Q Consensus 110 ~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~--~~LP~~~~~F~ 187 (274)
. ...++++. -|||--..... .-+.....+.+.. .+ .+.-.+|.++..||.++|-+.+.. .+.|...
T Consensus 51 ~-~I~~~a~~---ihgIt~e~v~~-~p~~~ev~~~~~~--fl-~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~---- 118 (250)
T PRK06310 51 R-VVSAESQR---IHHISDAMLRD-KPKIAEVFPQIKG--FF-KEGDYIVGHSVGFDLQVLSQESERIGETFLSKH---- 118 (250)
T ss_pred C-CCCHhhhh---ccCcCHHHHhC-CCCHHHHHHHHHH--Hh-CCCCEEEEECHHHHHHHHHHHHHHcCCCccccC----
Confidence 3 34444443 36655444432 2333333333332 12 222368888889999999877642 2222110
Q ss_pred HHHHhhCCCcccHHHHHHHhhhc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhh
Q 024017 188 DLIKMYFPTLYDIKHLMKFCNSL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNF 250 (274)
Q Consensus 188 ~~l~~~FP~iyD~K~la~~~~~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~ 250 (274)
-.+.||..+++..... ..+|+.+++.+|++.. .+|.|-+|++.|+.+|.+|.+.+
T Consensus 119 -------~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~~-~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 119 -------YYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYD-GNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred -------CcEEehHHHHHhcccCCCCCHHHHHHHCCCCCC-CCcChHHHHHHHHHHHHHHHHhc
Confidence 1367998888865433 3589999999999865 48999999999999999998765
No 18
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.30 E-value=2.9e-05 Score=72.95 Aligned_cols=163 Identities=15% Similarity=0.152 Sum_probs=105.3
Q ss_pred cCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCc
Q 024017 33 DYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDV 112 (274)
Q Consensus 33 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~ 112 (274)
.-+||++|+|=+|+... .=.|||+|...++.+|+. ...|... .+...+
T Consensus 14 ~~~fvvlD~ETTGl~p~---------------------~d~IIeIgav~v~~~g~i---------~~~~~~l-v~P~~~- 61 (313)
T PRK06063 14 PRGWAVVDVETSGFRPG---------------------QARIISLAVLGLDADGNV---------EQSVVTL-LNPGVD- 61 (313)
T ss_pred CCCEEEEEEECCCCCCC---------------------CCEEEEEEEEEEECCcee---------eeEEEEE-ECcCCC-
Confidence 35899999999998421 124999999999877753 2334443 333322
Q ss_pred cchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhc--CCCCCCCHHHHHHHH
Q 024017 113 YAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLT--CKDLPETQACFFDLI 190 (274)
Q Consensus 113 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~--~~~LP~~~~~F~~~l 190 (274)
+.++.. |||.=..+.. .-++....+.+.. ++ .+-.+|+++..+|++||-+.+. |.++|.
T Consensus 62 --~~~~~I---hGIt~e~l~~-ap~f~ev~~~l~~--~l--~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~--------- 122 (313)
T PRK06063 62 --PGPTHV---HGLTAEMLEG-QPQFADIAGEVAE--LL--RGRTLVAHNVAFDYSFLAAEAERAGAELPV--------- 122 (313)
T ss_pred --CCCeec---CCCCHHHHhC-CCCHHHHHHHHHH--Hc--CCCEEEEeCHHHHHHHHHHHHHHcCCCCCC---------
Confidence 222221 5555444432 1222223333322 12 2237899999999999977663 334442
Q ss_pred HhhCCCcccHHHHHHHhh-hc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 191 KMYFPTLYDIKHLMKFCN-SL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 191 ~~~FP~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
...+||.-+++... .+ .-.|+.|++.+|++. ...|.|-+|+..|+++|.++.+...
T Consensus 123 ----~~~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~-~~~H~Al~DA~ata~l~~~ll~~~~ 180 (313)
T PRK06063 123 ----DQVMCTVELARRLGLGLPNLRLETLAAHWGVPQ-QRPHDALDDARVLAGILRPSLERAR 180 (313)
T ss_pred ----CCEEehHHHHHHhccCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 13578888887652 22 346999999999985 4689999999999999999887754
No 19
>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=98.28 E-value=2.8e-05 Score=68.99 Aligned_cols=168 Identities=17% Similarity=0.217 Sum_probs=109.7
Q ss_pred hhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCC
Q 024017 31 VDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDE 110 (274)
Q Consensus 31 i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~ 110 (274)
+....||++|+|=||+... . .|||+|.......+. ...+|..+ .+..
T Consensus 4 l~~~~fvv~D~ETTGl~~~--------------------~--~IIeIgav~v~~~~~---------~~~~f~~l-i~P~- 50 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAG--------------------H--DIIEIGAVEIINRRI---------TGNKFHTY-IKPD- 50 (217)
T ss_pred EEecCEEEEEecCCCCCCC--------------------C--CEEEEEEEEEECCCE---------eeeEEEEE-ECcC-
Confidence 4567999999999998421 0 299999998653321 23456665 3333
Q ss_pred CccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcC-CCCCCCHHHHHHH
Q 024017 111 DVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTC-KDLPETQACFFDL 189 (274)
Q Consensus 111 d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~-~~LP~~~~~F~~~ 189 (274)
....+.+++. +|+.-..+... -++....+.+.. .+ ++-.+|+++..+|..||-+.+.. ...|..
T Consensus 51 ~~i~~~a~~i---hGIt~e~l~~~-p~~~ev~~~~~~--~~--~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~------- 115 (217)
T TIGR00573 51 RPIDPDAIKI---HGITDDMLKDK-PDFKEIAEDFAD--YI--RGAELVIHNASFDVGFLNYEFSKLYKVEPK------- 115 (217)
T ss_pred CCCCHHHHhh---cCCCHHHHcCC-CCHHHHHHHHHH--Hh--CCCEEEEeccHHHHHHHHHHHHHhcCCCCC-------
Confidence 3456666644 88888777554 344444333332 12 12378999999999999776531 011000
Q ss_pred HHhhCCCcccHHHHHHHhh-hc---cccHHHHHHHcCCccCC-CccccchhhHHHHHHHHHHHHhh
Q 024017 190 IKMYFPTLYDIKHLMKFCN-SL---HGGLNKLAELLEVERIG-ICHQAGSDSLLTCCTFMKMKDNF 250 (274)
Q Consensus 190 l~~~FP~iyD~K~la~~~~-~l---~~~L~~la~~L~v~r~g-~~HqAGsDS~lT~~~F~~l~~~~ 250 (274)
...+.|+.-+++... .+ +.+|+.+++.+|++... .+|.|-+|+.+|+.+|.+|.+..
T Consensus 116 ----~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 116 ----TNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred ----ccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHHhcc
Confidence 013557666665542 22 34799999999998643 68999999999999999998874
No 20
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=98.28 E-value=2.6e-05 Score=68.51 Aligned_cols=159 Identities=19% Similarity=0.219 Sum_probs=93.3
Q ss_pred CeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccc
Q 024017 35 PYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYA 114 (274)
Q Consensus 35 ~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~ 114 (274)
.||++|+|.+|+. + .+ .|||+|..-++. |. .+..|..+ ..+.. ...
T Consensus 6 ~~vvlD~EtTGl~--~----~~----------------eIIeIgaV~v~~-g~---------~~~~f~~l-v~P~~-~i~ 51 (195)
T PRK07247 6 TYIAFDLEFNTVN--G----VS----------------HIIQVSAVKYDD-HK---------EVDSFDSY-VYTDV-PLQ 51 (195)
T ss_pred eEEEEEeeCCCCC--C----CC----------------eEEEEEEEEEEC-CE---------EEEEEEEE-ECCCC-CCC
Confidence 7999999999973 1 00 499999988873 32 24567666 33322 223
Q ss_pred hhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecc-hhHHHHHHHhcCCCCCCCHHHHHHHHHhh
Q 024017 115 YDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSG-YDFGYLLKLLTCKDLPETQACFFDLIKMY 193 (274)
Q Consensus 115 ~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~-yD~~yl~k~l~~~~LP~~~~~F~~~l~~~ 193 (274)
+.+.+. +||.=..+. ++.+.....+.+.. .+ . +-.||.++.. +|+.+|-+. |.+++....
T Consensus 52 ~~~~~l---hGIt~~~v~-~ap~~~evl~~f~~--f~-~-~~~lVaHNa~~fD~~fL~~~--g~~~~~~~~--------- 112 (195)
T PRK07247 52 SFINGL---TGITADKIA-DAPKVEEVLAAFKE--FV-G-ELPLIGYNAQKSDLPILAEN--GLDLSDQYQ--------- 112 (195)
T ss_pred ccceec---CCCCHHHHh-CCCCHHHHHHHHHH--HH-C-CCeEEEEeCcHhHHHHHHHc--CCCcCCCce---------
Confidence 222221 555544443 23333322222221 12 2 3368888876 899998653 434332110
Q ss_pred CCCcccHHHHHHH--hhhc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHh
Q 024017 194 FPTLYDIKHLMKF--CNSL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDN 249 (274)
Q Consensus 194 FP~iyD~K~la~~--~~~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~ 249 (274)
. ..||+.+..+. .+++ .-.|+.||+.+|++. ..|.|-+|++.|+.+|.+|.+.
T Consensus 113 i-dt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~--~~HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 113 V-DLYDEAFERRSSDLNGIANLKLQTVADFLGIKG--RGHNSLEDARMTARVYESFLES 168 (195)
T ss_pred e-ehHHHHHHhhccccCCCCCCCHHHHHHhcCCCC--CCcCCHHHHHHHHHHHHHHHhh
Confidence 0 12344332211 1122 247999999999984 5799999999999999998776
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=98.27 E-value=4.1e-05 Score=68.57 Aligned_cols=167 Identities=15% Similarity=0.185 Sum_probs=108.6
Q ss_pred CeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccc
Q 024017 35 PYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYA 114 (274)
Q Consensus 35 ~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~ 114 (274)
.+|.+|||=||+.... .=.|||+|...... +. + ..-.|+.+ .+..+ ...
T Consensus 1 r~vvlD~ETTGl~p~~--------------------~d~IIEIgav~~~~-~~-~-------~~~~f~~~-i~P~~-~i~ 49 (225)
T TIGR01406 1 RQIILDTETTGLDPKG--------------------GHRIVEIGAVELVN-RM-L-------TGDNFHVY-VNPER-DMP 49 (225)
T ss_pred CEEEEEeeCCCcCCCC--------------------CCeEEEEEEEEEEC-Cc-E-------ecceEEEE-ECcCC-CCC
Confidence 4899999999985321 02499999875542 21 1 22356776 55543 345
Q ss_pred hhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhc--CCCCCCCHHHHHHHHHh
Q 024017 115 YDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLT--CKDLPETQACFFDLIKM 192 (274)
Q Consensus 115 ~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~--~~~LP~~~~~F~~~l~~ 192 (274)
+++.+. |||.-..+.. +.++....+.+.. .+ .+-.+|.++..+|.+||-.-+. |..+|.- .
T Consensus 50 ~~a~~v---hGIt~e~l~~-~p~f~ev~~~f~~--fi--~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~---------~ 112 (225)
T TIGR01406 50 AEAAKV---HGITDEFLAD-KPKFKEIADEFLD--FI--GGSELVIHNAAFDVGFLNYELERLGPTIKKI---------G 112 (225)
T ss_pred HHHHhc---cCCCHHHHhC-CCCHHHHHHHHHH--Hh--CCCEEEEEecHHHHHHHHHHHHHhCCCCccc---------c
Confidence 555544 7887766654 3454444333332 12 1236889999999999976653 2111110 0
Q ss_pred hCCCcccHHHHHHHh-hhccccHHHHHHHcCCccCCC-ccccchhhHHHHHHHHHHHHh
Q 024017 193 YFPTLYDIKHLMKFC-NSLHGGLNKLAELLEVERIGI-CHQAGSDSLLTCCTFMKMKDN 249 (274)
Q Consensus 193 ~FP~iyD~K~la~~~-~~l~~~L~~la~~L~v~r~g~-~HqAGsDS~lT~~~F~~l~~~ 249 (274)
-+-.++||--|++.. ++.+.+|+.|++.+|++..+. .|-|-.||.+|+.+|.+|...
T Consensus 113 ~~~~~iDTl~lar~~~p~~~~~L~~L~~~~gi~~~~r~~H~Al~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 113 EFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAHLLAEVYLALTGG 171 (225)
T ss_pred cCCCEEEHHHHHHHHcCCCCCCHHHHHHhcCCCCCCCCCcCHHHHHHHHHHHHHHHHcC
Confidence 112478998888764 344568999999999988664 799999999999999999775
No 22
>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=1.5e-05 Score=64.82 Aligned_cols=155 Identities=17% Similarity=0.172 Sum_probs=101.7
Q ss_pred eEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccchh
Q 024017 37 IAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYAYD 116 (274)
Q Consensus 37 IAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~~~ 116 (274)
|.+|+|-+|+.. ..-.|||+|...++.+++ ....||.+ +....+ ..+.
T Consensus 1 v~~D~Ettg~~~---------------------~~~~iiei~~v~~~~~~~---------~~~~~~~~-i~p~~~-~~~~ 48 (159)
T cd06127 1 VVFDTETTGLDP---------------------KKDRIIEIGAVKVDGGIE---------IVERFETL-VNPGRP-IPPE 48 (159)
T ss_pred CeEEeeCCCcCC---------------------CCCeEEEEEEEEEECCcC---------hhhhhhee-eCcCCc-CCHh
Confidence 579999999853 123499999999997633 23456666 444333 2233
Q ss_pred hHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCC-
Q 024017 117 SIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFP- 195 (274)
Q Consensus 117 Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP- 195 (274)
+.+. +|+.-+.. ..|.+.....+.+.. ++ .+ -.||++++.+|..+|.+.+.... ...++
T Consensus 49 ~~~~---~gi~~~~~-~~~~~~~~~~~~~~~--~l-~~-~~~v~~n~~fD~~~l~~~~~~~~------------~~~~~~ 108 (159)
T cd06127 49 ATAI---HGITDEML-ADAPPFEEVLPEFLE--FL-GG-RVLVAHNASFDLRFLNRELRRLG------------GPPLPN 108 (159)
T ss_pred heec---cCCCHHHH-hcCCCHHHHHHHHHH--HH-CC-CEEEEeCcHhhHHHHHHHHHHhC------------CCCCCC
Confidence 3222 67666554 477777655555443 22 22 47899999999999887765211 12223
Q ss_pred CcccHHHHHHHhhhc--cccHHHH-HHHcCCccCCCccccchhhHHHHHHHH
Q 024017 196 TLYDIKHLMKFCNSL--HGGLNKL-AELLEVERIGICHQAGSDSLLTCCTFM 244 (274)
Q Consensus 196 ~iyD~K~la~~~~~l--~~~L~~l-a~~L~v~r~g~~HqAGsDS~lT~~~F~ 244 (274)
..+||+.+++..-.. ..+|..+ ++.++++. ...|.|=+|++.|+.+|.
T Consensus 109 ~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 109 PWIDTLRLARRLLPGLRSHRLGLLLAERYGIPL-EGAHRALADALATAELLL 159 (159)
T ss_pred CeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCC-CCCCCcHHHHHHHHHHhC
Confidence 488998888765422 2367777 77788754 689999999999999873
No 23
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=98.22 E-value=4.8e-05 Score=71.20 Aligned_cols=160 Identities=16% Similarity=0.220 Sum_probs=106.7
Q ss_pred CeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccc
Q 024017 35 PYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYA 114 (274)
Q Consensus 35 ~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~ 114 (274)
.||++|+|=+|.. + | .|||+|+..++ +|+ ...+|+.+ .+.......
T Consensus 2 ~~vviD~ETTg~~-------~--------------d--~IieIgav~v~-~g~---------i~~~f~~l-v~P~~~~~~ 47 (309)
T PRK06195 2 NFVAIDFETANEK-------R--------------N--SPCSIGIVVVK-DGE---------IVEKVHYL-IKPKEMRFM 47 (309)
T ss_pred cEEEEEEeCCCCC-------C--------------C--ceEEEEEEEEE-CCE---------EEEEEEEE-ECCCCCCCC
Confidence 6999999988631 0 1 37999999886 332 23456666 555443455
Q ss_pred hhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhc--CCCCCCCHHHHHHHHHh
Q 024017 115 YDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLT--CKDLPETQACFFDLIKM 192 (274)
Q Consensus 115 ~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~--~~~LP~~~~~F~~~l~~ 192 (274)
+.+++ =|||.=+.....+ ++....+.+.. .+ . +-.+|++++.+|.+||-+.+. +.+.|.
T Consensus 48 ~~~~~---IhGIT~e~v~~ap-~f~ev~~~~~~--fl-~-~~~lVaHNa~FD~~fL~~~~~r~~~~~~~----------- 108 (309)
T PRK06195 48 PINIG---IHGIRPHMVEDEL-EFDKIWEKIKH--YF-N-NNLVIAHNASFDISVLRKTLELYNIPMPS----------- 108 (309)
T ss_pred hhhee---ccCcCHHHHhCCC-CHHHHHHHHHH--Hh-C-CCEEEEECcHHHHHHHHHHHHHhCCCCCC-----------
Confidence 66654 3888877776643 44332222221 11 1 237889999999999977653 233331
Q ss_pred hCCCcccHHHHHHHh-hhc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 193 YFPTLYDIKHLMKFC-NSL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 193 ~FP~iyD~K~la~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
...+||--+++.. +.+ ..+|+.|++.+|++ ...|.|-+|++.|+++|.+|.+...
T Consensus 109 --~~~idT~~lar~l~~~~~~~~L~~L~~~~gi~--~~~H~Al~DA~ata~l~~~l~~~~~ 165 (309)
T PRK06195 109 --FEYICTMKLAKNFYSNIDNARLNTVNNFLGYE--FKHHDALADAMACSNILLNISKELN 165 (309)
T ss_pred --CCEEEHHHHHHHHcCCCCcCCHHHHHHHcCCC--CcccCCHHHHHHHHHHHHHHHHHhc
Confidence 1356887777754 334 35799999999997 3589999999999999999987753
No 24
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=98.21 E-value=7e-05 Score=67.76 Aligned_cols=169 Identities=15% Similarity=0.174 Sum_probs=110.4
Q ss_pred hhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCC
Q 024017 31 VDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDE 110 (274)
Q Consensus 31 i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~ 110 (274)
+.+.+|+++|+|=||+... .=.|||+|...++.+ .. .....|... .+..+
T Consensus 44 ~~~~~~vviD~ETTGl~p~---------------------~d~IieIg~v~v~~~-~i-------~~~~~~~~l-i~P~~ 93 (239)
T PRK09146 44 LSEVPFVALDFETTGLDAE---------------------QDAIVSIGLVPFTLQ-RI-------RCRQARHWV-VKPRR 93 (239)
T ss_pred cccCCEEEEEeECCCCCCC---------------------CCcEEEEEEEEEECC-eE-------eecceEEEE-ECCCC
Confidence 4578999999999998532 114999999988753 21 122344444 33433
Q ss_pred CccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhc---CCCCCCCHHHHH
Q 024017 111 DVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLT---CKDLPETQACFF 187 (274)
Q Consensus 111 d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~---~~~LP~~~~~F~ 187 (274)
.+.+++... |||.-..+ ..|-+.....+.+... + . +-.+|+++..+|.+||-+.+. +.++|.
T Consensus 94 -~i~~~~~~I---hGIt~e~l-~~ap~~~evl~~l~~~--~-~-~~~lVaHna~FD~~fL~~~l~~~~~~~~~~------ 158 (239)
T PRK09146 94 -PLEEESVVI---HGITHSEL-QDAPDLERILDELLEA--L-A-GKVVVVHYRRIERDFLDQALRNRIGEGIEF------ 158 (239)
T ss_pred -CCChhhhhh---cCCCHHHH-hCCCCHHHHHHHHHHH--h-C-CCEEEEECHHHHHHHHHHHHHHhcCCCCCC------
Confidence 345555544 77776665 3465555444343331 1 2 236899999999999977764 223222
Q ss_pred HHHHhhCCCcccHHHHHHHhh-h--------c------cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhcC
Q 024017 188 DLIKMYFPTLYDIKHLMKFCN-S--------L------HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFFK 252 (274)
Q Consensus 188 ~~l~~~FP~iyD~K~la~~~~-~--------l------~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~~ 252 (274)
.++||-.+++..- . + .-.|+.+++.+|++. ...|.|-+|++.|+.+|.++.+.+++
T Consensus 159 --------~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl~~-~~~H~Al~DA~ata~l~~~~~~~~~~ 229 (239)
T PRK09146 159 --------PVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGLPA-YSPHHALTDAIATAELLQAQIAHHFS 229 (239)
T ss_pred --------ceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHHcC
Confidence 2467777766531 1 1 126999999999985 45799999999999999999888764
Q ss_pred C
Q 024017 253 G 253 (274)
Q Consensus 253 ~ 253 (274)
.
T Consensus 230 ~ 230 (239)
T PRK09146 230 P 230 (239)
T ss_pred C
Confidence 3
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=98.18 E-value=9.2e-05 Score=65.05 Aligned_cols=178 Identities=16% Similarity=0.214 Sum_probs=114.1
Q ss_pred hcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCC--CCCCCCCCCCeeeEEEeeeecCCC
Q 024017 32 DDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDEN--GNLPKCGTDKYCLWQFNFREFSPD 109 (274)
Q Consensus 32 ~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~--g~~p~~g~~~~~~wqFNF~~F~~~ 109 (274)
..+.||++|+|=||+.... =.||++|..-...+ |.. ....+|+++..+..
T Consensus 6 ~~~~~vv~D~ETTGl~~~~---------------------d~IieIgav~v~~~~~g~i-------~~~~~f~~~v~p~p 57 (200)
T TIGR01298 6 RGYLPVVVDVETGGFNAKT---------------------DALLEIAAITLKMDEQGWL-------FPDTTLHFHVEPFE 57 (200)
T ss_pred cCCeeEEEEeeCCCCCCCC---------------------CeEEEEEEEEEEEcCCCcE-------eecceeEEEEcCCC
Confidence 3578999999999986421 03899998887543 322 12345666623222
Q ss_pred CCccchhhHHHHHHcCCCccchhhCCCChHH-HHHHHHHc-----CcccCCCceeEEeecchhHHHHHHHhcCCCCCCCH
Q 024017 110 EDVYAYDSIKLLSRSGIDFKKNKEKGVDAMR-FSELLMSS-----GIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQ 183 (274)
Q Consensus 110 ~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~-f~e~l~~s-----gLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~ 183 (274)
.-...+++++. |||.=++..+++++... +.+.+..- +..+ .+-..|.++-.+|++||-+.+....++..
T Consensus 58 ~~~i~~~a~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~lVaHNa~FD~~fL~~~~~r~~~~~~- 132 (200)
T TIGR01298 58 GANIQPEALEF---TGIDLDHPLRGAVSEYEALHEIFKVVRKAMKASGC-QRAILVGHNANFDLGFLNAAVERTSLKRN- 132 (200)
T ss_pred CCCCCHHHHHc---cCCChhhhhhcCcchHHHHHHHHHHHHHHHHhccc-CCCEEEEECchhhHHHHHHHHHHhCCCCC-
Confidence 34567777655 88887776777776543 23322110 1111 23368889999999999777632111100
Q ss_pred HHHHHHHHhhCC-CcccHHHHHHHhhhccccHHHHHHHcCCccC-CCccccchhhHHHHHHHHHHHHhhc
Q 024017 184 ACFFDLIKMYFP-TLYDIKHLMKFCNSLHGGLNKLAELLEVERI-GICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 184 ~~F~~~l~~~FP-~iyD~K~la~~~~~l~~~L~~la~~L~v~r~-g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
.+-| .+.||--+++..-. ..+|..+++.+|++.. -..|.|-+|++.|+++|.+|.+.+.
T Consensus 133 --------~~~~~~~lDTl~lar~~~~-~~~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 133 --------PFHPFSTFDTATLAGLAYG-QTVLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred --------CCCCCcEEEHHHHHHHHcC-cccHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 0011 26788888775421 2369999999999853 3789999999999999999988753
No 26
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=98.10 E-value=9e-05 Score=63.74 Aligned_cols=168 Identities=16% Similarity=0.156 Sum_probs=103.2
Q ss_pred eeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCC---CCCCeeeEEEeeeecCCCCCc
Q 024017 36 YIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKC---GTDKYCLWQFNFREFSPDEDV 112 (274)
Q Consensus 36 fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~---g~~~~~~wqFNF~~F~~~~d~ 112 (274)
||++|+|=||+.. +. + =.|||+|.-..+.++..... ....-.+-+|++. .+..+ .
T Consensus 1 ~vv~D~ETTGl~~-~~---~----------------d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~l-v~P~~-~ 58 (177)
T cd06136 1 FVFLDLETTGLPK-HN---R----------------PEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLC-FNPGR-A 58 (177)
T ss_pred CeEEeeecCCCCC-CC---C----------------CceEEEEEEEEecccccccccccccccceeeeeeEE-eCCCC-c
Confidence 7999999999952 10 0 13999999988865432200 0000134567776 55543 3
Q ss_pred cchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHc-CcccCCCceeEEeec-chhHHHHHHHhc--CCCCCCCHHHHHH
Q 024017 113 YAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSS-GIVLNDSVHWVTFHS-GYDFGYLLKLLT--CKDLPETQACFFD 188 (274)
Q Consensus 113 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~s-gLv~~~~v~Wvtfhg-~yD~~yl~k~l~--~~~LP~~~~~F~~ 188 (274)
..+++... |||.=..+...|-......+.+..- +.. ......|++++ .+|+.||-+-+. |.++|..
T Consensus 59 I~~~a~~I---hGIt~e~l~~~~~~~~~~~~~l~~f~~~~-~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~------ 128 (177)
T cd06136 59 ISPGASEI---TGLSNDLLEHKAPFDSDTANLIKLFLRRQ-PKPICLVAHNGNRFDFPILRSELERLGTKLPDD------ 128 (177)
T ss_pred CChhHHHH---hCcCHHHHhcCCCccHHHHHHHHHHHHhc-CCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCC------
Confidence 45666555 8888888888763222222322110 111 22357889998 799999976664 3333311
Q ss_pred HHHhhCCCcccHHHHHHHhhhccccHHHHHHH-cCCccCCCccccchhhHHHHHHHHH
Q 024017 189 LIKMYFPTLYDIKHLMKFCNSLHGGLNKLAEL-LEVERIGICHQAGSDSLLTCCTFMK 245 (274)
Q Consensus 189 ~l~~~FP~iyD~K~la~~~~~l~~~L~~la~~-L~v~r~g~~HqAGsDS~lT~~~F~~ 245 (274)
+...||-.+++... .+|+.|++. +|++. ..+|.|-+|+..|++||++
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 12347666665443 289999885 77764 4679999999999999975
No 27
>PRK06722 exonuclease; Provisional
Probab=98.09 E-value=0.00014 Score=67.39 Aligned_cols=169 Identities=17% Similarity=0.166 Sum_probs=100.6
Q ss_pred cCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCc
Q 024017 33 DYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDV 112 (274)
Q Consensus 33 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~ 112 (274)
...||++|+|-+|. |. . +-+.-.|||+|....+. |.. ..+..|+-+ ..+. ..
T Consensus 4 ~~~~vViD~ETT~~---p~---~------------~~~~deIIEIGAVkV~~-g~i-------~Ivd~F~sL-V~P~-~~ 55 (281)
T PRK06722 4 ATHFIVFDIERNFR---PY---K------------SEDPSEIVDIGAVKIEA-STM-------KVIGEFSEL-VKPG-AR 55 (281)
T ss_pred CCEEEEEEeeCCCC---CC---C------------CCCCCeEEEEEEEEEEC-Cce-------eEEeeEEEE-ECCC-Cc
Confidence 35799999999852 21 0 01122499999988874 221 134567766 3333 24
Q ss_pred cchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhc--CCCCCCCHHHHHHHH
Q 024017 113 YAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLT--CKDLPETQACFFDLI 190 (274)
Q Consensus 113 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~--~~~LP~~~~~F~~~l 190 (274)
.++.+.++ +||.=+.. ..+.+.....+.+.. .+ .+. .+|+.|+.+|.+||-+-+. |.+.|....
T Consensus 56 I~~~i~~L---TGIT~emV-~~AP~f~eVl~ef~~--fi-g~~-~lvahna~FD~~FL~~~l~~~gi~~p~~~~------ 121 (281)
T PRK06722 56 LTRHTTKL---TGITKKDL-IGVEKFPQIIEKFIQ--FI-GED-SIFVTWGKEDYRFLSHDCTLHSVECPCMEK------ 121 (281)
T ss_pred CCHhHhhh---cCCCHHHH-cCCCCHHHHHHHHHH--HH-CCC-cEEEEEeHHHHHHHHHHHHHcCCCCCcccc------
Confidence 44455444 66655444 334444332222221 11 222 4667788999999987664 334443110
Q ss_pred HhhCCCcccHHHHHHH-hhhc---cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHH
Q 024017 191 KMYFPTLYDIKHLMKF-CNSL---HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMK 247 (274)
Q Consensus 191 ~~~FP~iyD~K~la~~-~~~l---~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~ 247 (274)
-+.+|+.-++.. .+.+ ..+|+.+++.+|++..|..|.|-+||..|+.+|.+|.
T Consensus 122 ----~~~idl~~la~~~~~~l~~~~~sL~~l~~~lgL~~~g~~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 122 ----ERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIWEGKQHRALADAENTANILLKAY 178 (281)
T ss_pred ----cchhHHHHHHHHHhhhhccCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHh
Confidence 012344333321 1222 1379999999999988999999999999999999986
No 28
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=98.07 E-value=0.00019 Score=65.68 Aligned_cols=166 Identities=21% Similarity=0.231 Sum_probs=107.0
Q ss_pred hhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCC
Q 024017 31 VDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDE 110 (274)
Q Consensus 31 i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~ 110 (274)
+.+..||++|+|=+|..... -.|||+|...++ +|+ ..-+|..+..+.
T Consensus 65 ~~~~~~vv~DiETTG~~~~~---------------------~~IIEIGAv~v~-~g~---------i~~~f~~~v~p~-- 111 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKK---------------------HQIIEIGAVKVK-NGE---------IIDRFESFVKAK-- 111 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCC---------------------CeEEEEEEEEEE-CCE---------EEEEEEEEECCC--
Confidence 46789999999999964321 159999999886 332 223455553332
Q ss_pred CccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHH
Q 024017 111 DVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLI 190 (274)
Q Consensus 111 d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l 190 (274)
...+.+.+. +|+.=..+. .+.+.....+.+.. .+ ... .||+++..+|.++|-+.+....+|.-
T Consensus 112 -~ip~~~~~i---tGIt~e~l~-~ap~~~evl~~f~~--fl-~~~-v~VaHNa~FD~~fL~~~l~r~g~~~~-------- 174 (257)
T PRK08517 112 -EVPEYITEL---TGITYEDLE-NAPSLKEVLEEFRL--FL-GDS-VFVAHNVNFDYNFISRSLEEIGLGPL-------- 174 (257)
T ss_pred -CCChhhhhh---cCcCHHHHc-CCCCHHHHHHHHHH--HH-CCC-eEEEECHHHHHHHHHHHHHHcCCCCC--------
Confidence 233333332 777766654 35555543333332 11 223 69999999999999776643222221
Q ss_pred HhhCCCcccHHHHHHHh-hhccccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhh
Q 024017 191 KMYFPTLYDIKHLMKFC-NSLHGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNF 250 (274)
Q Consensus 191 ~~~FP~iyD~K~la~~~-~~l~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~ 250 (274)
.+...||--+++.. ..-+-||+.+++.+|++.. .+|.|-+|++.|+.+|.++.+.+
T Consensus 175 ---~~~~ldtl~la~~~~~~~~~~L~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 175 ---LNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIE-VHHRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred ---CCCcEehHHHHHHHccCCCCCHHHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHh
Confidence 12234655555443 2234589999999999865 78999999999999999998765
No 29
>PRK07883 hypothetical protein; Validated
Probab=98.05 E-value=0.00014 Score=73.46 Aligned_cols=171 Identities=16% Similarity=0.131 Sum_probs=112.2
Q ss_pred HHHhhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecC
Q 024017 28 RDIVDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFS 107 (274)
Q Consensus 28 ~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~ 107 (274)
..-+.+.+||++|+|-||+... .-.|||+|.-.++. |+ ...+|+.. .+
T Consensus 9 ~~~~~~~~~Vv~D~ETTGl~p~---------------------~~~IIEIgaV~v~~-g~---------iv~~f~~l-V~ 56 (557)
T PRK07883 9 GTPLRDVTFVVVDLETTGGSPA---------------------GDAITEIGAVKVRG-GE---------VLGEFATL-VN 56 (557)
T ss_pred CCCCcCCCEEEEEEecCCCCCC---------------------CCeEEEEEEEEEEC-CE---------EEEEEEEE-EC
Confidence 4457788999999999998421 12499999998863 22 34567766 55
Q ss_pred CCCCccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHH
Q 024017 108 PDEDVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFF 187 (274)
Q Consensus 108 ~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~ 187 (274)
... ...+.+.+. +|+.=..+ .++.+.....+.+.. ++ . +-.+|++++.+|+.+|-+.+...-+|..
T Consensus 57 P~~-~i~~~~~~i---tGIt~e~l-~~ap~~~evl~~f~~--fl-~-~~~lVaHNa~FD~~fL~~~~~r~g~~~~----- 122 (557)
T PRK07883 57 PGR-PIPPFITVL---TGITTAMV-AGAPPIEEVLPAFLE--FA-R-GAVLVAHNAPFDIGFLRAAAARCGYPWP----- 122 (557)
T ss_pred CCC-CCChhHHhh---cCCCHHHH-hCCCCHHHHHHHHHH--Hh-c-CCEEEEeCcHHHHHHHHHHHHHcCCCCC-----
Confidence 433 345555433 77755443 455555443333322 11 1 2367888889999999777653222210
Q ss_pred HHHHhhCCCcccHHHHHHHhh---hc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 188 DLIKMYFPTLYDIKHLMKFCN---SL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 188 ~~l~~~FP~iyD~K~la~~~~---~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
-+...||-.+++..- .. ..+|..+++.+|++.. ..|.|-+|++.|+.+|.++.....
T Consensus 123 ------~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 123 ------GPPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTT-PTHRALDDARATVDVLHGLIERLG 183 (557)
T ss_pred ------CCCcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccC-CCCCHHHHHHHHHHHHHHHHHHHH
Confidence 013568877776532 22 2479999999999864 579999999999999999888764
No 30
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.99 E-value=0.00023 Score=74.84 Aligned_cols=162 Identities=19% Similarity=0.272 Sum_probs=107.8
Q ss_pred cCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCc
Q 024017 33 DYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDV 112 (274)
Q Consensus 33 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~ 112 (274)
...||++|+|-||+..+ | .|||+|...++ +|+ ..-.|... .++. ..
T Consensus 6 ~~~~vvvD~ETTGl~~~--------------------d--~IIeIgaV~v~-~g~---------i~~~f~~l-v~P~-~~ 51 (820)
T PRK07246 6 LRKYAVVDLEATGAGPN--------------------A--SIIQVGIVIIE-GGE---------IIDSYTTD-VNPH-EP 51 (820)
T ss_pred CCCEEEEEEecCCcCCC--------------------C--eEEEEEEEEEE-CCE---------EEEEEEEE-eCcC-CC
Confidence 46899999999997310 1 39999999885 332 33455555 3333 23
Q ss_pred cchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhc--CCCCCCCHHHHHHHH
Q 024017 113 YAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLT--CKDLPETQACFFDLI 190 (274)
Q Consensus 113 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~--~~~LP~~~~~F~~~l 190 (274)
..+.+.+. +||.=.... ++.+....+..+.. ++ .+-.+|+++..+|++||-+.+. |-++|.
T Consensus 52 i~~~~~~l---tGIt~e~l~-~ap~~~ev~~~~~~--~l--~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~--------- 114 (820)
T PRK07246 52 LDEHIKHL---TGITDQQLA-QAPDFSQVARHIYD--LI--EDCIFVAHNVKFDANLLAEALFLEGYELRT--------- 114 (820)
T ss_pred CCHhHhhc---CCCCHHHHh-cCCCHHHHHHHHHH--Hh--CCCEEEEECcHHHHHHHHHHHHHcCCCCCC---------
Confidence 44444433 777766554 45555554444432 12 2346899999999999987663 333332
Q ss_pred HhhCCCcccHHHHHHHh-hhc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 191 KMYFPTLYDIKHLMKFC-NSL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 191 ~~~FP~iyD~K~la~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
| ..||--+++.. +.+ .-+|+.+++.+|++.. .+|.|-+|+..|+.+|.+|.+...
T Consensus 115 ----~-~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~~-~~H~Al~DA~ata~L~~~l~~~l~ 171 (820)
T PRK07246 115 ----P-RVDTVELAQVFFPTLEKYSLSHLSRELNIDLA-DAHTAIADARATAELFLKLLQKIE 171 (820)
T ss_pred ----C-ceeHHHHHHHHhCCCCCCCHHHHHHHcCCCCC-CCCCHHHHHHHHHHHHHHHHHHHh
Confidence 1 24776666653 222 3489999999999864 689999999999999999988764
No 31
>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=97.98 E-value=0.00022 Score=77.58 Aligned_cols=167 Identities=20% Similarity=0.262 Sum_probs=117.1
Q ss_pred hcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCC
Q 024017 32 DDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDED 111 (274)
Q Consensus 32 ~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d 111 (274)
++.+||++|+|-||+.... =.|||+|....+. |+ ..-.|+++ .++. .
T Consensus 188 ~~~~~VVfDiETTGL~~~~---------------------d~IIEIGAVkv~~-g~---------iid~f~~~-V~P~-~ 234 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQY---------------------DEIIEFGAVKVKN-GR---------IIDKFQFF-IKPH-E 234 (1213)
T ss_pred cCCcEEEEEeEecCCCCCC---------------------CeEEEEEEEEEEC-Ce---------EEEEEEEE-ECCC-C
Confidence 6789999999999985321 1599999999874 32 34467776 4443 3
Q ss_pred ccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHH
Q 024017 112 VYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIK 191 (274)
Q Consensus 112 ~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~ 191 (274)
..++.+.++ +||.-+.+. +|.+.....+.+.. .+ ++-.+|+++..+|++||-+.+...-+|.
T Consensus 235 ~I~~~~~~l---tGIT~e~L~-~ap~~~evl~~f~~--fl--~~~iLVaHNa~FD~~fL~~~~~r~g~~~---------- 296 (1213)
T TIGR01405 235 PLSAFVTEL---TGITQDMLE-NAPEIEEVLEKFKE--FF--KDSILVAHNASFDIGFLNTNFEKVGLEP---------- 296 (1213)
T ss_pred CCCHHHHHH---hCCCHHHHh-CCCCHHHHHHHHHH--Hh--CCCeEEEEChHHHHHHHHHHHHHcCCCc----------
Confidence 455555544 888877764 57776554433332 11 2247899999999999987764323331
Q ss_pred hhCCCcccHHHHHHHhh-hc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 192 MYFPTLYDIKHLMKFCN-SL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 192 ~~FP~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
+-..+.||--+++... .+ .-+|+.|++.+|++..+ +|.|-.|+..|+.+|.+|.+...
T Consensus 297 -~~~~~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~~~-~HrAl~DA~aTa~I~~~ll~~l~ 356 (1213)
T TIGR01405 297 -LENPVIDTLELARALNPEYKSHRLGNICKKLGVDLDD-HHRADYDAEATAKVFKVMVEQLK 356 (1213)
T ss_pred -cCCCEeEHHHHHHHHhccCCCCCHHHHHHHcCCCCCC-CcCHHHHHHHHHHHHHHHHHHHH
Confidence 0124779888887653 33 34899999999998766 89999999999999999987764
No 32
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=97.95 E-value=0.00026 Score=74.69 Aligned_cols=163 Identities=20% Similarity=0.239 Sum_probs=105.1
Q ss_pred CeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccc
Q 024017 35 PYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYA 114 (274)
Q Consensus 35 ~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~ 114 (274)
.||++|+|-||+.... =.|||+|...++ +|+ ..-+|... .++.. ...
T Consensus 1 ~~vvvD~ETTG~~~~~---------------------~~IIeig~v~v~-~~~---------i~~~f~~~-v~P~~-~i~ 47 (850)
T TIGR01407 1 RYAVVDLETTGTQLSF---------------------DKIIQIGIVVVE-DGE---------IVDTFHTD-VNPNE-PIP 47 (850)
T ss_pred CEEEEEEECCCCCCCC---------------------CeEEEEEEEEEE-CCE---------EEEEEEEE-eCCCC-CCC
Confidence 4899999999975211 139999999985 333 23456665 44433 334
Q ss_pred hhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhC
Q 024017 115 YDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYF 194 (274)
Q Consensus 115 ~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~F 194 (274)
+.+.+ -+||.-+... .+-++...++.+.. ++ . +-.||+++..+|+.+|-+-+...-+|. +
T Consensus 48 ~~~~~---ltGIt~e~l~-~ap~~~ev~~~l~~--~l-~-~~~~VahN~~fD~~fL~~~~~~~g~~~------------~ 107 (850)
T TIGR01407 48 PFIQE---LTGISDNMLQ-QAPYFSQVAQEIYD--LL-E-DGIFVAHNVHFDLNFLAKALKDCGYEP------------L 107 (850)
T ss_pred hhhhh---hcCcCHHHHh-CCCCHHHHHHHHHH--Hh-C-CCEEEEeCcHHHHHHHHHHHHHcCCCC------------C
Confidence 44433 3777755554 34444444444332 22 2 236899999999999987664222221 1
Q ss_pred C-CcccHHHHHHHhh-hc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 195 P-TLYDIKHLMKFCN-SL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 195 P-~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
| ..+||--+++..- .. .-+|+.|++.+|++.. .+|.|-+|+..|+.+|.+|.+.+-
T Consensus 108 ~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 108 PKPRIDTVELAQIFFPTEESYQLSELSEALGLTHE-NPHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred CCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCC-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 2 2567766665442 12 3479999999999864 589999999999999999988763
No 33
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.94 E-value=0.00029 Score=74.99 Aligned_cols=166 Identities=20% Similarity=0.261 Sum_probs=108.5
Q ss_pred CCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCcc
Q 024017 34 YPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVY 113 (274)
Q Consensus 34 ~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~ 113 (274)
-.||++|+|-||+.... + -.|||+|....+ +|+ ..-.|+.+ .+... ..
T Consensus 3 ~~~vvvD~ETTG~~p~~-~-------------------d~IIeigav~v~-~~~---------i~~~f~~~-v~P~~-~i 50 (928)
T PRK08074 3 KRFVVVDLETTGNSPKK-G-------------------DKIIQIAAVVVE-DGE---------ILERFSSF-VNPER-PI 50 (928)
T ss_pred CCEEEEEEeCCCCCCCC-C-------------------CcEEEEEEEEEE-CCE---------EEEEEEEE-ECcCC-CC
Confidence 47999999999974221 0 159999999995 332 23456665 44433 34
Q ss_pred chhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhh
Q 024017 114 AYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMY 193 (274)
Q Consensus 114 ~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~ 193 (274)
.+.+.+. +||+=..+. ++.++...++.+.. ++ ++-.+|+++..+|+.||-+-+...-+|..
T Consensus 51 ~~~~~~l---tGIt~~~l~-~ap~f~ev~~~l~~--~l--~~~~~VaHN~~FD~~fL~~~~~~~g~~~~----------- 111 (928)
T PRK08074 51 PPFITEL---TGISEEMVK-QAPLFEDVAPEIVE--LL--EGAYFVAHNVHFDLNFLNEELERAGYTEI----------- 111 (928)
T ss_pred CHHHhhc---CCCCHHHHh-cCCCHHHHHHHHHH--Hh--CCCeEEEEChHHHHHHHHHHHHHcCCCCC-----------
Confidence 4444333 787766544 45555554444433 22 24578999999999999776643222211
Q ss_pred CCCcccHHHHHHHh-hhc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 194 FPTLYDIKHLMKFC-NSL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 194 FP~iyD~K~la~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
-...+||--+++.. +.+ .-+|+.|++.|+++. +.+|.|-+|++.|+.+|.+|.+...
T Consensus 112 ~~~~iDt~~la~~~~p~~~~~~L~~l~~~l~i~~-~~~H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 112 HCPKLDTVELARILLPTAESYKLRDLSEELGLEH-DQPHRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred CCCeeeHHHHHHHhcCCCCCCCHHHHHHhCCCCC-CCCCChHHHHHHHHHHHHHHHHHHH
Confidence 01356776666543 222 237999999999874 5889999999999999999988764
No 34
>PTZ00315 2'-phosphotransferase; Provisional
Probab=97.90 E-value=0.00053 Score=69.13 Aligned_cols=172 Identities=15% Similarity=0.163 Sum_probs=109.5
Q ss_pred CeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecC-CCCCCCCCCCCeeeEEEeeeecCCCCCcc
Q 024017 35 PYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDE-NGNLPKCGTDKYCLWQFNFREFSPDEDVY 113 (274)
Q Consensus 35 ~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~-~g~~p~~g~~~~~~wqFNF~~F~~~~d~~ 113 (274)
.||++|+|-||...... +.-.||++|...++. +|+ .+..|..+.-+......
T Consensus 57 ~~IV~DlETTgl~~~~~------------------~~dEIIEIGaV~Vd~~ng~---------Ii~~F~~yVkP~~~p~L 109 (582)
T PTZ00315 57 AYVVLDFEATCEADRRI------------------EDAEVIEFPMVLVDARTAT---------PVAEFQRYVRPVKNPVL 109 (582)
T ss_pred eEEEEEEecCCCCCCCC------------------CCCceEEEEEEEEEccCCE---------EEEEEEEEECCCCCCCC
Confidence 68999999999642210 122499999999984 332 45677777333322245
Q ss_pred chhhHHHHHHcCCCccchhhCCCChHH----HHHHHHHcCccc---CCCceeEEeecchhHH-HHHHHhc--C-CCCCCC
Q 024017 114 AYDSIKLLSRSGIDFKKNKEKGVDAMR----FSELLMSSGIVL---NDSVHWVTFHSGYDFG-YLLKLLT--C-KDLPET 182 (274)
Q Consensus 114 ~~~Si~fL~~~G~DF~k~~~~GI~~~~----f~e~l~~sgLv~---~~~v~Wvtfhg~yD~~-yl~k~l~--~-~~LP~~ 182 (274)
.+...++ +||.=+.. .++.++.. |.+.+..+++.. +.+ ..|...|.+|+. +|.+-+. + ..+|.
T Consensus 110 s~fct~L---TGITqe~V-~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~-~~vah~g~fDl~~fL~~e~~~~~~~g~p~- 183 (582)
T PTZ00315 110 SRFCTEL---TGITQSMV-SRADPFPVVYCEALQFLAEAGLGDAPPLRS-YCVVTCGDWDLKTMLPSQMRVSGQQGTPL- 183 (582)
T ss_pred ChhHhhh---cCcCHHHH-hcCCCHHHHHHHHHHHHhccccccccccCc-eEEEeccHHHHHHHHHHHHHHhhhcCCCc-
Confidence 5555555 66664333 55666554 334443333221 112 344566899995 7755442 1 24443
Q ss_pred HHHHHHHHHhhCCCcccHH-HHHHHh-hh-----------c-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHH
Q 024017 183 QACFFDLIKMYFPTLYDIK-HLMKFC-NS-----------L-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKD 248 (274)
Q Consensus 183 ~~~F~~~l~~~FP~iyD~K-~la~~~-~~-----------l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~ 248 (274)
.|...+|+| ++++.. ++ + ..+|+.+++.+|++-.|..|.|=.||..|+.+|.+|.+
T Consensus 184 ----------~f~~widLk~~lar~l~p~~~~~~~~~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~ 253 (582)
T PTZ00315 184 ----------SFQRWCNLKKYMSQLGFGNGSGCGGGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLR 253 (582)
T ss_pred ----------ccceEEEhHHHHHHHhCccccccccccccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHH
Confidence 344566764 666643 11 1 24899999999999999999999999999999999987
Q ss_pred h
Q 024017 249 N 249 (274)
Q Consensus 249 ~ 249 (274)
.
T Consensus 254 ~ 254 (582)
T PTZ00315 254 R 254 (582)
T ss_pred c
Confidence 6
No 35
>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=97.83 E-value=0.00029 Score=60.82 Aligned_cols=165 Identities=19% Similarity=0.144 Sum_probs=97.6
Q ss_pred EEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCC-ccchh
Q 024017 38 AMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDED-VYAYD 116 (274)
Q Consensus 38 AiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d-~~~~~ 116 (274)
-+|+|=||+.... | .|||+|.-.++.++.. ...|++. ...... ...++
T Consensus 2 ~~D~ETTGl~~~~-------------------d--~Iieig~v~v~~~~~~---------~~~~~~~-v~p~~~~~~~~~ 50 (183)
T cd06138 2 FYDYETFGLNPSF-------------------D--QILQFAAIRTDENFNE---------IEPFNIF-CRLPPDVLPSPE 50 (183)
T ss_pred EEEeecCCCCCCC-------------------C--ceEEEEEEEECCCCCC---------ccceeEE-EeCCCCCCCCHH
Confidence 4799999985311 1 3899999888765432 2456666 433332 34555
Q ss_pred hHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeec-chhHHHHHHHhcC---CCCCCC------HHHH
Q 024017 117 SIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHS-GYDFGYLLKLLTC---KDLPET------QACF 186 (274)
Q Consensus 117 Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg-~yD~~yl~k~l~~---~~LP~~------~~~F 186 (274)
++. -|||.=..+...|.+.....+.+.. .+..++..+|++|+ .+|.+||-+.+.. .+++.+ .-+.
T Consensus 51 a~~---ihGIt~e~l~~~~~~~~~~l~~~~~--~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dt 125 (183)
T cd06138 51 ALI---VTGITPQQLLKEGLSEYEFIAKIHR--LFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDL 125 (183)
T ss_pred HHH---HhCCCHHHHHhcCCCHHHHHHHHHH--HHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCcccccc
Confidence 544 4999888887778887665544433 22123346888885 6999999776642 122211 1122
Q ss_pred HHHHHh---hCCCcccHHHHHHHhhhc-cccHHHHHHHcCCccCCCccccchhhHHHHHH
Q 024017 187 FDLIKM---YFPTLYDIKHLMKFCNSL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCT 242 (274)
Q Consensus 187 ~~~l~~---~FP~iyD~K~la~~~~~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~ 242 (274)
...++. ++|..++.... -.++ .-+|+.+++.+|++. ..+|.|-+|++.|+++
T Consensus 126 l~l~r~~~~~~~~~~~~~~~---~~~~~~~~L~~l~~~~gi~~-~~~H~Al~Da~~ta~l 181 (183)
T cd06138 126 LDVVRAYYALRPDGIVWPKN---DDGKPSFKLEDLAQANGIEH-SNAHDALSDVEATIAL 181 (183)
T ss_pred HHHHHHHHhhChhhccCccc---cCCCcchhHHHHHHHCCCCc-cccccHHHHHHHHHHH
Confidence 222222 22321110000 0012 236999999999986 5789999999999864
No 36
>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=97.80 E-value=0.00015 Score=60.79 Aligned_cols=69 Identities=19% Similarity=0.129 Sum_probs=46.7
Q ss_pred eeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhh---hccccHHHHHHH-cCCccCCCcccc
Q 024017 157 HWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCN---SLHGGLNKLAEL-LEVERIGICHQA 232 (274)
Q Consensus 157 ~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~---~l~~~L~~la~~-L~v~r~g~~HqA 232 (274)
.+|.++..+|+++|- .+.|. ..+.||-.+..... ...-+|+.|++. ||++.....|.|
T Consensus 79 vlVgHn~~fD~~~L~-----~~~~~-------------~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~A 140 (152)
T cd06144 79 ILVGHALKNDLKVLK-----LDHPK-------------KLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSS 140 (152)
T ss_pred EEEEcCcHHHHHHhc-----CcCCC-------------ccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcCc
Confidence 688888999999873 12222 12445533322221 123589999997 698765578999
Q ss_pred chhhHHHHHHH
Q 024017 233 GSDSLLTCCTF 243 (274)
Q Consensus 233 GsDS~lT~~~F 243 (274)
.+||+.|+++|
T Consensus 141 l~DA~at~~l~ 151 (152)
T cd06144 141 VEDARAAMRLY 151 (152)
T ss_pred HHHHHHHHHHh
Confidence 99999999987
No 37
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=97.76 E-value=0.0011 Score=59.30 Aligned_cols=148 Identities=12% Similarity=0.091 Sum_probs=95.5
Q ss_pred eeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccch
Q 024017 36 YIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYAY 115 (274)
Q Consensus 36 fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~~ 115 (274)
|+.+|||=+|+. + .|||+|..-+. +|+ .+.+|+.. .+... ..++
T Consensus 2 ~~vlD~ETTGl~--~----------------------~IieIg~v~v~-~~~---------i~~~~~~l-v~P~~-~i~~ 45 (219)
T PRK07983 2 LRVIDTETCGLQ--G----------------------GIVEIASVDVI-DGK---------IVNPMSHL-VRPDR-PISP 45 (219)
T ss_pred eEEEEEECCCCC--C----------------------CCEEEEEEEEE-CCE---------EEEEEEEE-ECcCC-CCCH
Confidence 789999999973 1 08999987665 333 23455555 44433 3445
Q ss_pred hhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCC
Q 024017 116 DSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFP 195 (274)
Q Consensus 116 ~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP 195 (274)
.+++. |||.=.... |-|. |.+.+-. +. ..-.+|.++..+|.++|-+ + -.
T Consensus 46 ~~~~i---hgIt~e~v~--~ap~--~~ev~~~--~~--~~~~lVaHNa~FD~~~L~~------~--------------~~ 94 (219)
T PRK07983 46 QAMAI---HRITEAMVA--DKPW--IEDVIPH--YY--GSEWYVAHNASFDRRVLPE------M--------------PG 94 (219)
T ss_pred HHhhc---CCCCHHHHc--CCCC--HHHHHHH--Hc--CCCEEEEeCcHhhHHHHhC------c--------------CC
Confidence 55443 555433332 1121 3333332 21 3347889999999998721 1 12
Q ss_pred CcccHHHHHHHh-hhccccHHHHHHHcCCcc----CCCccccchhhHHHHHHHHHHHHhh
Q 024017 196 TLYDIKHLMKFC-NSLHGGLNKLAELLEVER----IGICHQAGSDSLLTCCTFMKMKDNF 250 (274)
Q Consensus 196 ~iyD~K~la~~~-~~l~~~L~~la~~L~v~r----~g~~HqAGsDS~lT~~~F~~l~~~~ 250 (274)
..+||--+|+.. +++..+|+.|++.+++.. ...+|.|-+|++.|+.+|.+|.+..
T Consensus 95 ~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 95 EWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred CcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHc
Confidence 467888888754 456678999999998753 2468999999999999999988653
No 38
>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=97.73 E-value=2.4e-05 Score=63.66 Aligned_cols=156 Identities=21% Similarity=0.223 Sum_probs=92.8
Q ss_pred eEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccchh
Q 024017 37 IAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYAYD 116 (274)
Q Consensus 37 IAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~~~ 116 (274)
|.+|||++|+.. +.-.|||+|.-.++.+.. ...-.|+.+..+.......+.
T Consensus 1 v~~D~Ettg~~~---------------------~~~~iieig~v~~~~~~~--------~~~~~~~~~i~p~~~~~i~~~ 51 (164)
T PF00929_consen 1 VVFDTETTGLDP---------------------RQDEIIEIGAVKVDDDEN--------EEVESFNSLIRPEEPPKISPW 51 (164)
T ss_dssp EEEEEEESSSTT---------------------TTCTEEEEEEEEEETTTT--------EEEEEEEEEBEHSSHCSSEHH
T ss_pred cEEEeEcCCCCC---------------------CCCeEEEEEEEEeeCCcc--------ccceeeeecccccccccCCHH
Confidence 679999999864 223499999988886542 134567776333322234444
Q ss_pred hHHHHHHcCCCccchhhCCCChHH---HHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhh
Q 024017 117 SIKLLSRSGIDFKKNKEKGVDAMR---FSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMY 193 (274)
Q Consensus 117 Si~fL~~~G~DF~k~~~~GI~~~~---f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~ 193 (274)
+.+ -+|+.-..+...+-.... |.+.+. +...||..+..+|.+++.+.+. ..+...
T Consensus 52 ~~~---~~gIt~~~l~~~~~~~~~~~~~~~~~~-------~~~~~v~~n~~fd~~~l~~~~~------------~~~~~~ 109 (164)
T PF00929_consen 52 ATK---VHGITQEDLEDAPSFEEALDEFEEFLK-------KNDILVGHNASFDIGFLRREDK------------RFLGKP 109 (164)
T ss_dssp HHH---HHHHCHHHHHCHCEHHHHHHHHHHHHH-------HHTEEEETTCCHEEESSHHHHH------------HHHHHH
T ss_pred Hee---ecCCcccccccCCcHHHHHHhhhhhhh-------cccccccccccchhhHHHHhhh------------hccccc
Confidence 433 366666665554432221 222222 1236666666777766544432 111111
Q ss_pred CC---CcccHHHHHHH-hhhcc-ccHHHHHHHcCCccCCCccccchhhHHHHHHH
Q 024017 194 FP---TLYDIKHLMKF-CNSLH-GGLNKLAELLEVERIGICHQAGSDSLLTCCTF 243 (274)
Q Consensus 194 FP---~iyD~K~la~~-~~~l~-~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F 243 (274)
+| .+.|+.-+.+. .+... .+|..+++.++++..+.+|.|-+|++.|+.+|
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 110 IPKPNPFIDTLELARALFPNRKKYSLDDLAEYFGIPFDGTAHDALDDARATAELF 164 (164)
T ss_dssp HHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTSSSTSTTTSHHHHHHHHHHHH
T ss_pred ccccchhhhhhHHHHHHhhccccCCHHHHHHHcCCCCCCCCcChHHHHHHHhCcC
Confidence 11 23344333222 22233 48999999999999988999999999999987
No 39
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.70 E-value=0.0013 Score=58.94 Aligned_cols=162 Identities=17% Similarity=0.181 Sum_probs=99.0
Q ss_pred CeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccc
Q 024017 35 PYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYA 114 (274)
Q Consensus 35 ~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~ 114 (274)
.+|.+|||=||+.... =.|||+|. ++ +.. .-.|+-. ++... ...
T Consensus 3 ~~vv~D~ETTGl~~~~---------------------d~IIeig~--v~--~~~---------~~~f~~l-v~P~~-~I~ 46 (232)
T PRK06309 3 ALIFYDTETTGTQIDK---------------------DRIIEIAA--YN--GVT---------SESFQTL-VNPEI-PIP 46 (232)
T ss_pred cEEEEEeeCCCCCCCC---------------------CEEEEEEE--Ec--Ccc---------ccEEEEE-eCCCC-CCC
Confidence 5899999999985321 13999997 32 211 1234444 44433 345
Q ss_pred hhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeec-chhHHHHHHHhcCCCCCCCHHHHHHHHHhh
Q 024017 115 YDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHS-GYDFGYLLKLLTCKDLPETQACFFDLIKMY 193 (274)
Q Consensus 115 ~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg-~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~ 193 (274)
+++++. |||.=+...... +.....+.+.. ++ .+.-.+|++++ .+|..+|-+.+....+|...
T Consensus 47 ~~a~~I---hGIt~e~v~~~p-~f~ev~~~~~~--fi-~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~---------- 109 (232)
T PRK06309 47 AEASKI---HGITTDEVADAP-KFPEAYQKFIE--FC-GTDNILVAHNNDAFDFPLLRKECRRHGLEPPT---------- 109 (232)
T ss_pred hhHHhh---cCCCHHHHhCCC-CHHHHHHHHHH--HH-cCCCEEEEeCCHHHHHHHHHHHHHHcCCCCCC----------
Confidence 555443 666555544432 33222222221 11 22336777774 69999998776422222110
Q ss_pred CCCcccHHHHHHHh-hhc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 194 FPTLYDIKHLMKFC-NSL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 194 FP~iyD~K~la~~~-~~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
-..+||--+++.. +++ ..+|+.+++.++++. ..+|-|-+|++.|+.+|.+|.+.+-
T Consensus 110 -~~~iDt~~l~~~~~~~~~~~~L~~l~~~~~~~~-~~aH~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 110 -LRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEE-NQAHRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred -CcEEeHHHHHHHHcCCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 1356887777654 233 357999999999764 5699999999999999999887753
No 40
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=97.69 E-value=0.00088 Score=62.50 Aligned_cols=155 Identities=17% Similarity=0.179 Sum_probs=100.6
Q ss_pred CeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecC--CCCCCCCCCCCeeeEEEeeeecCCCCCc
Q 024017 35 PYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDE--NGNLPKCGTDKYCLWQFNFREFSPDEDV 112 (274)
Q Consensus 35 ~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~--~g~~p~~g~~~~~~wqFNF~~F~~~~d~ 112 (274)
.+|++|||=||+.... =.|||+|+..++. +|+.- .....|+.. .+... .
T Consensus 38 ~~vvlD~ETTGLd~~~---------------------d~IIEIg~V~v~~~~~g~i~------~v~~~~~~l-v~P~~-~ 88 (294)
T PRK09182 38 LGVILDTETTGLDPRK---------------------DEIIEIGMVAFEYDDDGRIG------DVLDTFGGL-QQPSR-P 88 (294)
T ss_pred eEEEEEeeCCCCCCCC---------------------CeEEEEEEEEEEecCCCcee------eeeeEEEEE-eCCCC-C
Confidence 6899999999986321 1399999999985 34421 234567776 44433 3
Q ss_pred cchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhc---CCCCCCCHHHHHHH
Q 024017 113 YAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLT---CKDLPETQACFFDL 189 (274)
Q Consensus 113 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~---~~~LP~~~~~F~~~ 189 (274)
..+++... +||.=......+++...+.+.+-. .-..|+++..+|.+||-+.+. +.+...+....
T Consensus 89 I~~~~t~I---hGIt~e~v~~~~~~~~~l~~fl~~-------~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i--- 155 (294)
T PRK09182 89 IPPEITRL---TGITDEMVAGQTIDPAAVDALIAP-------ADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEI--- 155 (294)
T ss_pred CCHHHHHh---cCCCHHHHhcCCCcHHHHHHHhcC-------CCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHH---
Confidence 45555544 888877777777776666554422 125688999999999866532 12222221110
Q ss_pred HHhhCCCcccHHHHHHHhhhc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHH
Q 024017 190 IKMYFPTLYDIKHLMKFCNSL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMK 247 (274)
Q Consensus 190 l~~~FP~iyD~K~la~~~~~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~ 247 (274)
| . ...++ .-.|+.|++.+|. ....|.|-+|++.|+.+|.++.
T Consensus 156 ---------~--~---~~~~~~~~kL~~La~~~g~--~~~aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 156 ---------D--W---SARGFEGTKLGYLAGQAGF--FHEGHRAVDDCQALLELLARPL 198 (294)
T ss_pred ---------h--h---ccccCCCCCHHHHHHHcCC--CCCCcChHHHHHHHHHHHHHHH
Confidence 1 0 00112 2469999999993 4578999999999999999754
No 41
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.68 E-value=0.0019 Score=64.13 Aligned_cols=175 Identities=17% Similarity=0.129 Sum_probs=112.4
Q ss_pred hcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCC
Q 024017 32 DDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDED 111 (274)
Q Consensus 32 ~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d 111 (274)
....||.+|+|=||+.... + .|||+|.--.+.+++ .....|+++ .....+
T Consensus 4 ~~~~fvv~D~ETTGLdP~~-----D----------------rIIeiAaVrvd~~~~--------~i~e~~~~~-~~P~~~ 53 (476)
T PRK11779 4 MQPTFLWHDYETFGANPAL-----D----------------RPAQFAGIRTDADLN--------IIGEPLVFY-CKPADD 53 (476)
T ss_pred CCCcEEEEEEECCCCCCCC-----C----------------eeEEEEEEEEeCCCc--------eecceeEEE-EcCCcC
Confidence 3568999999999986321 0 399999998886543 123457776 555544
Q ss_pred -ccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeec-chhHHHHHHHhcCCCCCCCHHHHHHH
Q 024017 112 -VYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHS-GYDFGYLLKLLTCKDLPETQACFFDL 189 (274)
Q Consensus 112 -~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg-~yD~~yl~k~l~~~~LP~~~~~F~~~ 189 (274)
+..++|+ .-+||-=+.+...|++...+.+.+.. .+..++..+|.+|. .+|..++-+.+... +-++ .
T Consensus 54 ~lp~p~a~---~IhGIT~e~l~~~g~~e~e~~~~i~~--~l~~~~~~lVGhNni~FD~eflr~~~~r~-~~d~------y 121 (476)
T PRK11779 54 YLPSPEAV---LITGITPQEALEKGLPEAEFAARIHA--EFSQPGTCILGYNNIRFDDEVTRYIFYRN-FYDP------Y 121 (476)
T ss_pred cCCCHHHH---HHhCCCHHHHHhcCCCHHHHHHHHHH--HHhcCCCEEEEeCchhhcHHHHHHHHHhc-cchH------H
Confidence 3355554 44999988888899987776666543 22123335677775 59999988877411 1111 1
Q ss_pred HHhhC-C----CcccHHHHHHHhh-----------hc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHh
Q 024017 190 IKMYF-P----TLYDIKHLMKFCN-----------SL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDN 249 (274)
Q Consensus 190 l~~~F-P----~iyD~K~la~~~~-----------~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~ 249 (274)
.+.+- + .+.|+-.++.... +. .-.|+.|++.+|++. ..+|.|=+|++.|+.++.+|++.
T Consensus 122 ~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~L~~~~gI~~-~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 122 AREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEH-ENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHh
Confidence 11110 0 1223333322210 11 136999999999974 57899999999999999999876
No 42
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=97.51 E-value=0.002 Score=71.30 Aligned_cols=168 Identities=21% Similarity=0.263 Sum_probs=111.1
Q ss_pred hhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCC
Q 024017 31 VDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDE 110 (274)
Q Consensus 31 i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~ 110 (274)
+.+..||++|+|-+|+.... =.|||+|....+ +|. ....|+.+ .+..
T Consensus 416 L~~~~~VVfDLETTGL~~~~---------------------deIIEIgAV~V~-~G~---------iie~F~~~-V~P~- 462 (1437)
T PRK00448 416 LKDATYVVFDVETTGLSAVY---------------------DEIIEIGAVKIK-NGE---------IIDKFEFF-IKPG- 462 (1437)
T ss_pred hccCcEEEEEhhhcCCCCch---------------------hhhheeeeEEEe-CCe---------EeeeEEEE-ECCC-
Confidence 45688999999999975321 158899987775 332 34567776 5443
Q ss_pred CccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHH
Q 024017 111 DVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLI 190 (274)
Q Consensus 111 d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l 190 (274)
....+.+.++ +|+.=..+. .+.+.....+.+.. + -.+..+|++++.+|+++|-+.+..--+|.
T Consensus 463 ~~I~~~~~~L---TGIT~e~L~-~aps~~EaL~~f~~--f--igg~vLVAHNa~FD~~fL~~~l~rlgl~~--------- 525 (1437)
T PRK00448 463 HPLSAFTTEL---TGITDDMVK-DAPSIEEVLPKFKE--F--CGDSILVAHNASFDVGFINTNYEKLGLEK--------- 525 (1437)
T ss_pred CCCCHHHHHH---hCCCHHHHc-CCCCHHHHHHHHHH--H--hCCCEEEEeCccccHHHHHHHHHHcCCcc---------
Confidence 2344444444 677665555 56666655544443 1 12357899999999999866654222221
Q ss_pred HhhCCCcccHHHHHHHhh-hc-cccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhc
Q 024017 191 KMYFPTLYDIKHLMKFCN-SL-HGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 191 ~~~FP~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
+-....||--+++... .. ..+|+.||+.+|+...+ .|.|-+||+.|+.+|.+|.+...
T Consensus 526 --l~~~~IDTLelar~l~p~~k~~kL~~LAk~lGL~~~~-~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 526 --IKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEH-HHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred --ccccceeHHHHHHHHcCccccccHHHHHHHcCCCCCC-CcChHHHHHHHHHHHHHHHHHHH
Confidence 1113557766655432 22 35799999999998765 59999999999999999988764
No 43
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=97.43 E-value=0.0062 Score=54.35 Aligned_cols=164 Identities=18% Similarity=0.221 Sum_probs=105.9
Q ss_pred CCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCcc
Q 024017 34 YPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVY 113 (274)
Q Consensus 34 ~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~ 113 (274)
..||.+|+|-+|... ..-.||++|.-.+..+.... -.|..+ .+. ...+
T Consensus 13 ~~~vv~D~ETtg~~~---------------------~~~~iieIgav~~~~~~i~~---------~~~~~~-v~P-~~~i 60 (243)
T COG0847 13 TRFVVIDLETTGLNP---------------------KKDRIIEIGAVTLEDGRIVE---------RSFHTL-VNP-ERPI 60 (243)
T ss_pred CcEEEEecccCCCCC---------------------CCCceEEEEeEEEECCeeec---------ceeEEE-ECC-CCCC
Confidence 689999999999864 22358999998887643221 114444 333 3335
Q ss_pred chhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhc--CCCCCCCHHHHHHHHH
Q 024017 114 AYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLT--CKDLPETQACFFDLIK 191 (274)
Q Consensus 114 ~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~--~~~LP~~~~~F~~~l~ 191 (274)
.+++... +||....+... .......+.+.. ++ ++.-.+|+++-++|.+||-+.+. +.+.|
T Consensus 61 ~~~~~~i---~git~e~l~~~-p~~~~v~~~~~~--~i-~~~~~~Vahna~fD~~fl~~~~~~~~~~~~----------- 122 (243)
T COG0847 61 PPEIFKI---HGITDEMLADA-PKFAEVLPEFLD--FI-GGLRLLVAHNAAFDVGFLRVESERLGIEIP----------- 122 (243)
T ss_pred Chhhhhh---cCCCHHHHhcC-CCHHHHHHHHHH--HH-CCCCeEEEEchhhcHHHHHHHHHHcCCCcc-----------
Confidence 5555444 66666665555 222222222211 12 22148899999999999965543 33433
Q ss_pred hhCCCcccHHHHHHHh-hh-ccccHHHHHHHcCCcc-CCCccccchhhHHHHHHHHHHHHh
Q 024017 192 MYFPTLYDIKHLMKFC-NS-LHGGLNKLAELLEVER-IGICHQAGSDSLLTCCTFMKMKDN 249 (274)
Q Consensus 192 ~~FP~iyD~K~la~~~-~~-l~~~L~~la~~L~v~r-~g~~HqAGsDS~lT~~~F~~l~~~ 249 (274)
...++|+--+++.. ++ -..+|+.+++.+|+++ ....|.|-.|+++++.+|.++...
T Consensus 123 --~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 123 --GDPVLDTLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred --cCceehHHHHHHHHcCCCccchHHHHHHHcCCCcCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 22355666666553 34 3568999999999998 356699999999999999999874
No 44
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=97.43 E-value=0.0024 Score=61.29 Aligned_cols=177 Identities=14% Similarity=0.221 Sum_probs=107.3
Q ss_pred HhhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCC
Q 024017 30 IVDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPD 109 (274)
Q Consensus 30 ~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~ 109 (274)
.+++.+||++|+|=||+.... =.||++|.-.++.+|+ .+..|... .+..
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~---------------------drIIeIgAV~i~~~g~---------ive~f~tL-VnP~ 90 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPST---------------------SRLITIDAVTLTADGE---------EVEHFHAV-LNPG 90 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCC---------------------CeEEEEEEEEEEcCCE---------EEEEEEEE-ECcC
Confidence 467789999999999985321 1389999998887774 34556665 5554
Q ss_pred CCccchhhHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcC--CCCCC-CHHHH
Q 024017 110 EDVYAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTC--KDLPE-TQACF 186 (274)
Q Consensus 110 ~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~--~~LP~-~~~~F 186 (274)
.+.. +. .=|||.=+.+.. |.++....+.|.. ++ .+-.||+.+..+|++||-+-+.- ..+.. +....
T Consensus 91 ~~~~---p~---~LHGIT~e~La~-AP~f~eVl~el~~--fL--~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~ 159 (377)
T PRK05601 91 EDPG---PF---HLHGLSAEEFAQ-GKRFSQILKPLDR--LI--DGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRN 159 (377)
T ss_pred CCCC---Cc---cccCCCHHHHhc-CCCHHHHHHHHHH--Hh--CCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccc
Confidence 4322 11 126665555533 5555544444332 22 23479999999999999775421 00000 00000
Q ss_pred H------------HHHHhhCC-CcccHHHHHHHhh-hc-cccHHHHHHHcCCcc---------CCCccccch--hhHHHH
Q 024017 187 F------------DLIKMYFP-TLYDIKHLMKFCN-SL-HGGLNKLAELLEVER---------IGICHQAGS--DSLLTC 240 (274)
Q Consensus 187 ~------------~~l~~~FP-~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r---------~g~~HqAGs--DS~lT~ 240 (274)
. ..-+...| .++||=-+++... .+ .-.|+.||+.+|++. -...|.|=+ |+.++.
T Consensus 160 r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~ 239 (377)
T PRK05601 160 RGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVA 239 (377)
T ss_pred cccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHH
Confidence 0 00011234 4789988887663 34 357999999999865 234565554 999999
Q ss_pred HHHHHHHH
Q 024017 241 CTFMKMKD 248 (274)
Q Consensus 241 ~~F~~l~~ 248 (274)
..|+++++
T Consensus 240 ~l~~~~~~ 247 (377)
T PRK05601 240 RLYFALRA 247 (377)
T ss_pred HHHHHhhc
Confidence 99999743
No 45
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=97.43 E-value=0.0013 Score=55.04 Aligned_cols=144 Identities=19% Similarity=0.164 Sum_probs=86.0
Q ss_pred eEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCccchh
Q 024017 37 IAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVYAYD 116 (274)
Q Consensus 37 IAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~~~~ 116 (274)
+|||||++|+..+ -.|+++|+- +.+|+. .|+-+ .++. ..+...
T Consensus 1 ~~iD~E~~g~~~g----------------------~ei~~i~~v--~~~~~~-----------~f~~l-v~P~-~~i~~~ 43 (150)
T cd06145 1 FALDCEMCYTTDG----------------------LELTRVTVV--DENGKV-----------VLDEL-VKPD-GEIVDY 43 (150)
T ss_pred CEEeeeeeeecCC----------------------CEEEEEEEE--eCCCCE-----------EEEEe-ECCC-Cccchh
Confidence 6899999998642 127777776 334431 24544 3332 233333
Q ss_pred hHHHHHHcCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCC
Q 024017 117 SIKLLSRSGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPT 196 (274)
Q Consensus 117 Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~ 196 (274)
..++ +||.=..+...+.+.....+.+.. ++ .++-.+|..+-.+|+.+|-. .-+.
T Consensus 44 ~t~i---tGIt~~~l~~a~~~~~~v~~~~~~--fl-~~~~vlVgHn~~fD~~fL~~--------------------~~~~ 97 (150)
T cd06145 44 NTRF---SGITEEMLENVTTTLEDVQKKLLS--LI-SPDTILVGHSLENDLKALKL--------------------IHPR 97 (150)
T ss_pred ccCc---CCCCHHHhccCCCCHHHHHHHHHH--Hh-CCCCEEEEcChHHHHHHhhc--------------------cCCC
Confidence 3333 555544444443344333322222 22 22347888888999998732 1256
Q ss_pred cccHHHHHHHhhh-c-cccHHHHHHHcCCccC---CCccccchhhHHHHHHH
Q 024017 197 LYDIKHLMKFCNS-L-HGGLNKLAELLEVERI---GICHQAGSDSLLTCCTF 243 (274)
Q Consensus 197 iyD~K~la~~~~~-l-~~~L~~la~~L~v~r~---g~~HqAGsDS~lT~~~F 243 (274)
++||-.+++.... . +-+|+.|++.+....+ +..|.|-+|++.|+..|
T Consensus 98 ~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 98 VIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELV 149 (150)
T ss_pred EEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHh
Confidence 8899888775432 1 3489999988633222 57899999999999877
No 46
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=97.10 E-value=0.0045 Score=52.33 Aligned_cols=68 Identities=18% Similarity=0.071 Sum_probs=51.3
Q ss_pred ceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhh-hc----cccHHHHHHH-cCCccC--C
Q 024017 156 VHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCN-SL----HGGLNKLAEL-LEVERI--G 227 (274)
Q Consensus 156 v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~-~l----~~~L~~la~~-L~v~r~--g 227 (274)
-.+|.++..+|+.+|-. ..+.+.||-.|++... .. .-+|+.|++. +|++-. .
T Consensus 85 ~vlVgHn~~fD~~fL~~--------------------~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~ 144 (161)
T cd06137 85 TILVGHSLQNDLDALRM--------------------IHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGG 144 (161)
T ss_pred cEEEeccHHHHHHHHhC--------------------cCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCC
Confidence 36777878899998732 1356889999988764 33 3589999987 686542 4
Q ss_pred CccccchhhHHHHHHH
Q 024017 228 ICHQAGSDSLLTCCTF 243 (274)
Q Consensus 228 ~~HqAGsDS~lT~~~F 243 (274)
..|.|-.||..|+++|
T Consensus 145 ~~H~A~~DA~at~~l~ 160 (161)
T cd06137 145 EGHDSLEDALAAREVV 160 (161)
T ss_pred CCCCcHHHHHHHHHHh
Confidence 6799999999999887
No 47
>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=96.79 E-value=0.012 Score=49.58 Aligned_cols=97 Identities=16% Similarity=0.084 Sum_probs=56.1
Q ss_pred cCCCccchhhCCCChHHHHHHHHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHH
Q 024017 124 SGIDFKKNKEKGVDAMRFSELLMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHL 203 (274)
Q Consensus 124 ~G~DF~k~~~~GI~~~~f~e~l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~l 203 (274)
+||.-+.+. ++.+.....+.+.. ++ ++-.+|.++-.+|+++|-.. ..|. .+.||-.+
T Consensus 51 ~GIt~~~l~-~a~~~~~v~~~l~~--~l--~~~vlV~Hn~~~D~~~l~~~----~~~~--------------~~~Dt~~l 107 (157)
T cd06149 51 SGIRRQHLV-NATPFAVAQKEILK--IL--KGKVVVGHAIHNDFKALKYF----HPKH--------------MTRDTSTI 107 (157)
T ss_pred CCCCHHHHh-cCCCHHHHHHHHHH--Hc--CCCEEEEeCcHHHHHHhccc----CCCc--------------CEEECccc
Confidence 666655553 45655544433332 22 23367887778898877421 1111 12344221
Q ss_pred --HHH---hhhc-cccHHHHHHHc---CCccCCCccccchhhHHHHHHH
Q 024017 204 --MKF---CNSL-HGGLNKLAELL---EVERIGICHQAGSDSLLTCCTF 243 (274)
Q Consensus 204 --a~~---~~~l-~~~L~~la~~L---~v~r~g~~HqAGsDS~lT~~~F 243 (274)
++. .+.. +-+|+.|++.+ +++..+..|.|-+||..|+++|
T Consensus 108 ~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 108 PLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELY 156 (157)
T ss_pred ccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHh
Confidence 211 1122 24899999998 4554466899999999999887
No 48
>PRK05359 oligoribonuclease; Provisional
Probab=96.38 E-value=0.094 Score=45.38 Aligned_cols=165 Identities=16% Similarity=0.183 Sum_probs=92.9
Q ss_pred cCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCc
Q 024017 33 DYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDV 112 (274)
Q Consensus 33 ~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~ 112 (274)
.-+||++|+|-||+.... + .|||+|.-..+.+.+. ..-.|++... .+...
T Consensus 2 ~~~~vvlD~ETTGLdp~~-----d----------------~IieIgaV~~~~~~~~--------~~~~~~~~i~-~~~~~ 51 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPER-----D----------------RIIEIATIVTDADLNI--------LAEGPVIAIH-QSDEA 51 (181)
T ss_pred CCcEEEEEeecCCCCCCC-----C----------------eEEEEEEEEEcCCceE--------cccceEEEEC-CCHHH
Confidence 357999999999985321 0 2899999988654331 1123555422 22211
Q ss_pred ---cchhhHHHHHHcCCCccchhhCCCChHHHHHHHHH--cCcccCCCceeEEeec-chhHHHHHHHhc--CCCCCCC--
Q 024017 113 ---YAYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMS--SGIVLNDSVHWVTFHS-GYDFGYLLKLLT--CKDLPET-- 182 (274)
Q Consensus 113 ---~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~--sgLv~~~~v~Wvtfhg-~yD~~yl~k~l~--~~~LP~~-- 182 (274)
..+.+...-..+|+. +...+.|.+.....+.+.. .+.+.... .+++.|+ .+|.+||-+.+- +.+|+..
T Consensus 52 l~~~~~~~~~ih~~tGIt-~~~l~~~~~~~e~~~~~l~fl~~~~~~~~-~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~ 129 (181)
T PRK05359 52 LAAMDEWNTRTHTRSGLI-DRVRASTVSEAEAEAQTLEFLKQWVPAGK-SPLCGNSIGQDRRFLARYMPELEAYFHYRNL 129 (181)
T ss_pred hhccChHHHHhcccccCc-HHHHhcCCCHHHHHHHHHHHHHHhcCCCC-CceeecchhhCHHHHHHHHHHhcccCCCccc
Confidence 223333322234777 5666778877765544332 12222222 3445555 789999977653 2333322
Q ss_pred -HHHHHHHHHhhCCCcccHHHHHHHhhhccccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHhhcC
Q 024017 183 -QACFFDLIKMYFPTLYDIKHLMKFCNSLHGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDNFFK 252 (274)
Q Consensus 183 -~~~F~~~l~~~FP~iyD~K~la~~~~~l~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~~~~ 252 (274)
....+++.+.++|..| .++++.+ .|.|=+|++-|.+++...++.++.
T Consensus 130 Dv~tl~~l~r~~~P~~~----------------------~~~~~~~-~HRal~D~~~s~~~~~~~~~~~~~ 177 (181)
T PRK05359 130 DVSTLKELARRWKPEIL----------------------NGFKKQG-THRALADIRESIAELKYYREHFFK 177 (181)
T ss_pred chhHHHHHHHHhChhhh----------------------hCCCCcC-CcccHHHHHHHHHHHHHHHHHhcc
Confidence 1122233444444321 2444443 599999999999999999888764
No 49
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=95.22 E-value=0.7 Score=38.17 Aligned_cols=83 Identities=17% Similarity=0.271 Sum_probs=54.0
Q ss_pred cCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhhcc-ccHHHHHHH-cC-Ccc---
Q 024017 152 LNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNSLH-GGLNKLAEL-LE-VER--- 225 (274)
Q Consensus 152 ~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~l~-~~L~~la~~-L~-v~r--- 225 (274)
.+++++.|.++..+|+-.|.+.+ ....++++||..++.....-. .||..+++. +| ...
T Consensus 74 ~~~~i~kv~~n~~~D~~~L~~~~----------------~i~~~~~~D~~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~ 137 (176)
T PF01612_consen 74 EDPNIIKVGHNAKFDLKWLYRSF----------------GIDLKNVFDTMLAAYLLDPTRSYSLKDLAEEYLGNIDLDKK 137 (176)
T ss_dssp TTTTSEEEESSHHHHHHHHHHHH----------------TS--SSEEEHHHHHHHTTTSTTSSHHHHHHHHHSEEE-GHC
T ss_pred hCCCccEEEEEEechHHHHHHHh----------------ccccCCccchhhhhhcccccccccHHHHHHHHhhhccCcHH
Confidence 36788889988899999888762 233446889944444433222 589998866 45 211
Q ss_pred --CC--C---------ccccchhhHHHHHHHHHHHHhh
Q 024017 226 --IG--I---------CHQAGSDSLLTCCTFMKMKDNF 250 (274)
Q Consensus 226 --~g--~---------~HqAGsDS~lT~~~F~~l~~~~ 250 (274)
.+ . ..=|+.|+.+|.++|-+|....
T Consensus 138 ~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 138 EQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp CTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred HhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 11 1 1237889999999999988753
No 50
>PRK05755 DNA polymerase I; Provisional
Probab=95.15 E-value=0.42 Score=50.96 Aligned_cols=83 Identities=19% Similarity=0.197 Sum_probs=58.4
Q ss_pred CCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhh-hccccHHHHHHHc-CCccC----
Q 024017 153 NDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCN-SLHGGLNKLAELL-EVERI---- 226 (274)
Q Consensus 153 ~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~-~l~~~L~~la~~L-~v~r~---- 226 (274)
++.+..|+++.-+|+.+|.+. |.++| +.++||+.++..+. +..-||+.+++.. ++.-+
T Consensus 368 d~~v~kV~HNakfDl~~L~~~--gi~~~--------------~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~~ 431 (880)
T PRK05755 368 DPAIKKVGQNLKYDLHVLARY--GIELR--------------GIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFEE 431 (880)
T ss_pred CCCCcEEEeccHhHHHHHHhC--CCCcC--------------CCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchHH
Confidence 455667888888999988752 44433 35789988887765 2235888888774 44310
Q ss_pred --------------CCccccchhhHHHHHHHHHHHHhhc
Q 024017 227 --------------GICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 227 --------------g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
...|.|..|+.+|..+|.+|....-
T Consensus 432 ~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 432 VAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred hcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1236799999999999999988753
No 51
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=94.89 E-value=0.21 Score=47.89 Aligned_cols=82 Identities=26% Similarity=0.347 Sum_probs=50.3
Q ss_pred CCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhh-hccccHHHHHHH-cCCccCCCcc
Q 024017 153 NDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCN-SLHGGLNKLAEL-LEVERIGICH 230 (274)
Q Consensus 153 ~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~-~l~~~L~~la~~-L~v~r~g~~H 230 (274)
+++|.=|-+.+..|+.-|.+.+- -+| +.+||||..++.|. ..+-||..+.++ +|++ +.+.|
T Consensus 68 d~~v~KIfHaa~~DL~~l~~~~g--~~p--------------~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~-ldK~~ 130 (361)
T COG0349 68 DPNVVKIFHAARFDLEVLLNLFG--LLP--------------TPLFDTQIAAKLAGFGTSHGLADLVEELLGVE-LDKSE 130 (361)
T ss_pred CCceeeeeccccccHHHHHHhcC--CCC--------------CchhHHHHHHHHhCCcccccHHHHHHHHhCCc-ccccc
Confidence 34433344445688887777752 222 25889999999996 336789998876 4665 44433
Q ss_pred c----------------cchhhHHHHHHHHHHHHhhc
Q 024017 231 Q----------------AGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 231 q----------------AGsDS~lT~~~F~~l~~~~~ 251 (274)
| |-+|-..=...+-+|.+..-
T Consensus 131 q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~ 167 (361)
T COG0349 131 QRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELA 167 (361)
T ss_pred cccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3 44555555555666665543
No 52
>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=94.39 E-value=0.78 Score=39.09 Aligned_cols=164 Identities=13% Similarity=0.141 Sum_probs=85.8
Q ss_pred eeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCCCcc--
Q 024017 36 YIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDEDVY-- 113 (274)
Q Consensus 36 fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~d~~-- 113 (274)
+|.+|+|=||+.... =.|||+|.-.++.++. .....|+.. .+....+-
T Consensus 1 lv~iD~ETTGl~p~~---------------------d~IieIgaV~~~~~~~--------~i~~~f~~~-i~p~~~~~~~ 50 (173)
T cd06135 1 LVWIDLEMTGLDPEK---------------------DRILEIACIITDGDLN--------IIAEGPELV-IHQPDEVLDG 50 (173)
T ss_pred CEEEEEecCCCCCCC---------------------CeeEEEEEEEEeCCCc--------eecCceeEE-ECCCHHHhhh
Confidence 578999999986321 1399999998875421 123445555 44432211
Q ss_pred -chhhHHHHHHcCCCccchhhCCCChHHHHHHHHHc--CcccCCCceeEEeec-chhHHHHHHHhcCCCCCCCHHHHHHH
Q 024017 114 -AYDSIKLLSRSGIDFKKNKEKGVDAMRFSELLMSS--GIVLNDSVHWVTFHS-GYDFGYLLKLLTCKDLPETQACFFDL 189 (274)
Q Consensus 114 -~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~s--gLv~~~~v~Wvtfhg-~yD~~yl~k~l~~~~LP~~~~~F~~~ 189 (274)
.+.+.+.-.-+|+. +.....|.+.....+.+..- +.+ ..+-.+|..|+ .+|++||-+.+.. +
T Consensus 51 ~~~~~~~ih~~tgIt-~~~l~~~~~~~~vl~~~~~f~~~~~-~~~~~~lvgh~~~FD~~fL~~~~~~---------~--- 116 (173)
T cd06135 51 MDEWCTEMHTKSGLT-ERVRASTVTLAQAEAELLEFIKKYV-PKGKSPLAGNSVHQDRRFLDKYMPE---------L--- 116 (173)
T ss_pred ccHHHHHcccccccH-HHHHhCCCCHHHHHHHHHHHHHHhc-CCCCCceeecchhhCHHHHHHHHHH---------H---
Confidence 11122221223544 22335555554433333210 111 11224566777 8999999776631 0
Q ss_pred HHhhC-CCcccHHHHHHHhhhccccHHHHHHHcCCccCCCccccchhhHHHHHHHHHHHHh
Q 024017 190 IKMYF-PTLYDIKHLMKFCNSLHGGLNKLAELLEVERIGICHQAGSDSLLTCCTFMKMKDN 249 (274)
Q Consensus 190 l~~~F-P~iyD~K~la~~~~~l~~~L~~la~~L~v~r~g~~HqAGsDS~lT~~~F~~l~~~ 249 (274)
...+ ....|+..+.+..+.+...+.+ +++. .+..|.|=+|+.-|...+...++.
T Consensus 117 -~~~~~~~~~D~~~l~~l~~~l~p~~~~----~~~~-~~~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 117 -EEYLHYRILDVSSIKELARRWYPEIYR----KAPK-KKGTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred -hccCCcchhhHHHHHHHHHHhCcHhhh----cCCC-CCCCcchHHHHHHHHHHHHHHHHH
Confidence 1122 2356764433322233333322 3333 356799999999999988877653
No 53
>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=94.33 E-value=1.1 Score=37.41 Aligned_cols=79 Identities=18% Similarity=0.089 Sum_probs=56.0
Q ss_pred CCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhhc--cccHHHHHHHc-CCccC---
Q 024017 153 NDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNSL--HGGLNKLAELL-EVERI--- 226 (274)
Q Consensus 153 ~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~l--~~~L~~la~~L-~v~r~--- 226 (274)
+++++.|.++...|+..|.+.. |-. +.+++|+..++..+... ..||+.+++.+ +++-.
T Consensus 71 ~~~i~kv~~~~k~D~~~L~~~~-g~~---------------~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k 134 (170)
T cd06141 71 DPSILKVGVGIKGDARKLARDF-GIE---------------VRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPK 134 (170)
T ss_pred CCCeeEEEeeeHHHHHHHHhHc-CCC---------------CCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCC
Confidence 5667788888888888775543 221 33578999999888643 35899999875 43211
Q ss_pred --------------CCccccchhhHHHHHHHHHHH
Q 024017 227 --------------GICHQAGSDSLLTCCTFMKMK 247 (274)
Q Consensus 227 --------------g~~HqAGsDS~lT~~~F~~l~ 247 (274)
...|-|..|+++...+|.+|+
T Consensus 135 ~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 135 KVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 134679999999999998885
No 54
>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=93.51 E-value=3.7 Score=39.49 Aligned_cols=82 Identities=26% Similarity=0.399 Sum_probs=53.7
Q ss_pred CCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhh-hccccHHHHHHH-cCCccCCCc-
Q 024017 153 NDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCN-SLHGGLNKLAEL-LEVERIGIC- 229 (274)
Q Consensus 153 ~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~-~l~~~L~~la~~-L~v~r~g~~- 229 (274)
++++.+|.++..+|+..|.+.. ..+|. .++||...+..+. +...||+.+++. ||+. +.+.
T Consensus 68 d~~i~KV~h~~k~Dl~~L~~~~--~~~~~--------------~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~-l~K~~ 130 (367)
T TIGR01388 68 DESVVKVLHAASEDLEVFLNLF--GELPQ--------------PLFDTQIAAAFCGFGMSMGYAKLVQEVLGVE-LDKSE 130 (367)
T ss_pred CCCceEEEeecHHHHHHHHHHh--CCCCC--------------CcccHHHHHHHhCCCCCccHHHHHHHHcCCC-CCccc
Confidence 5678899888889988765442 22332 5789998888775 234589998876 4553 1111
Q ss_pred ---------------cccchhhHHHHHHHHHHHHhhc
Q 024017 230 ---------------HQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 230 ---------------HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
+-|..|+.....++-+|+...-
T Consensus 131 ~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 131 SRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLE 167 (367)
T ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1266777777777777776653
No 55
>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=93.26 E-value=2.4 Score=36.84 Aligned_cols=86 Identities=19% Similarity=0.085 Sum_probs=55.7
Q ss_pred cCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhh------------ccccHHHHHH
Q 024017 152 LNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNS------------LHGGLNKLAE 219 (274)
Q Consensus 152 ~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~------------l~~~L~~la~ 219 (274)
.++++.=|.+....|+..|.+-+. . ++. . + ...-+++|+..++..... -..||+.+++
T Consensus 79 ~d~~i~KVg~~~~~D~~~L~~~~~-~-~~~-~--~-----~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~ 148 (193)
T cd06146 79 EDPDVLKLGFGFKQDLKALSASYP-A-LKC-M--F-----ERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQ 148 (193)
T ss_pred CCCCeeEEEechHHHHHHHHHhcC-c-ccc-c--c-----ccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHH
Confidence 356666666777799998877553 1 110 0 0 011368999988886542 2358999987
Q ss_pred Hc-CCcc---------------CCCccccchhhHHHHHHHHHHH
Q 024017 220 LL-EVER---------------IGICHQAGSDSLLTCCTFMKMK 247 (274)
Q Consensus 220 ~L-~v~r---------------~g~~HqAGsDS~lT~~~F~~l~ 247 (274)
.+ |++- ....+-|..|++....+|-+|.
T Consensus 149 ~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 149 EVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 64 4321 0123569999999999999886
No 56
>PRK10829 ribonuclease D; Provisional
Probab=92.43 E-value=2.2 Score=41.18 Aligned_cols=83 Identities=19% Similarity=0.201 Sum_probs=56.9
Q ss_pred CCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhh-hccccHHHHHHH-cCCccC----
Q 024017 153 NDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCN-SLHGGLNKLAEL-LEVERI---- 226 (274)
Q Consensus 153 ~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~-~l~~~L~~la~~-L~v~r~---- 226 (274)
++++.-|-+.+.+|+..|.+.+ |. .-..++||...|..+. +..-||..|.+. ||+.-.
T Consensus 72 ~~~ivKV~H~~~~Dl~~l~~~~-g~---------------~p~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~ 135 (373)
T PRK10829 72 DPQVTKFLHAGSEDLEVFLNAF-GE---------------LPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSES 135 (373)
T ss_pred CCCeEEEEeChHhHHHHHHHHc-CC---------------CcCCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCcccc
Confidence 5555455556679999887654 21 1125889999998885 334689988765 666321
Q ss_pred -----------CCccccchhhHHHHHHHHHHHHhhc
Q 024017 227 -----------GICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 227 -----------g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
...+=|..|+.....+|-+|++..-
T Consensus 136 ~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 136 RTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1234488899999999999888764
No 57
>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=91.64 E-value=4.5 Score=33.77 Aligned_cols=79 Identities=18% Similarity=0.078 Sum_probs=54.1
Q ss_pred CCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhh-ccccHHHHHHH-cCCccC----
Q 024017 153 NDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNS-LHGGLNKLAEL-LEVERI---- 226 (274)
Q Consensus 153 ~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~-l~~~L~~la~~-L~v~r~---- 226 (274)
++++..|.+....|+..|.+.. |.. +.+++|+..++..+.. ...||+.+++. ||+.-.
T Consensus 65 d~~i~Kvg~~~k~D~~~L~~~~-gi~---------------~~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~ 128 (161)
T cd06129 65 NPSIVKALHGIEGDLWKLLRDF-GEK---------------LQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSIS 128 (161)
T ss_pred CCCEEEEEeccHHHHHHHHHHc-CCC---------------cccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccce
Confidence 5677778777778877765532 221 2246799888887652 24589999887 465321
Q ss_pred -----------CCccccchhhHHHHHHHHHHH
Q 024017 227 -----------GICHQAGSDSLLTCCTFMKMK 247 (274)
Q Consensus 227 -----------g~~HqAGsDS~lT~~~F~~l~ 247 (274)
...+-|..|++....+|-+|+
T Consensus 129 ~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 129 CADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred eccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 134569999999999999986
No 58
>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=89.62 E-value=7.2 Score=33.83 Aligned_cols=83 Identities=16% Similarity=0.137 Sum_probs=53.0
Q ss_pred CCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhh-cc--------ccHHHHHHH-cC
Q 024017 153 NDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNS-LH--------GGLNKLAEL-LE 222 (274)
Q Consensus 153 ~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~-l~--------~~L~~la~~-L~ 222 (274)
++++..|.+..-.|...|.+-+ |-. ..+++||..++..+.. .. .||+.+++. |+
T Consensus 63 ~~~i~Kv~h~~k~D~~~L~~~~-gi~---------------~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~ 126 (197)
T cd06148 63 SKKILKVIHDCRRDSDALYHQY-GIK---------------LNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLY 126 (197)
T ss_pred CCCccEEEEechhHHHHHHHhc-Ccc---------------ccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhC
Confidence 5678888888888888764432 221 1135788776665542 11 377777766 34
Q ss_pred Cc--------------------c-C--CCccccchhhHHHHHHHHHHHHhhc
Q 024017 223 VE--------------------R-I--GICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 223 v~--------------------r-~--g~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
++ | . ....=|..|++....+|.+|++..-
T Consensus 127 ~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~ 178 (197)
T cd06148 127 ISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALI 178 (197)
T ss_pred CChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhh
Confidence 32 1 1 1123489999999999999988764
No 59
>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=84.74 E-value=3.3 Score=36.99 Aligned_cols=92 Identities=22% Similarity=0.310 Sum_probs=57.4
Q ss_pred ceeEEeec-chhHHHH-HHHh-cCCCCCCCHHH----HHHHHHhhCCCcccHHHHHHHh-hhccccHHHHHHHcCCccCC
Q 024017 156 VHWVTFHS-GYDFGYL-LKLL-TCKDLPETQAC----FFDLIKMYFPTLYDIKHLMKFC-NSLHGGLNKLAELLEVERIG 227 (274)
Q Consensus 156 v~Wvtfhg-~yD~~yl-~k~l-~~~~LP~~~~~----F~~~l~~~FP~iyD~K~la~~~-~~l~~~L~~la~~L~v~r~g 227 (274)
-++|+|+| ++|+-|| .++| .|-++|.-... +....+.|--.-.|+.-+-... ..-+.+|..||..||+|-
T Consensus 53 p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~~~sLd~la~~lgiPg-- 130 (209)
T PF10108_consen 53 PQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKARTSLDELAALLGIPG-- 130 (209)
T ss_pred CeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccccCCHHHHHHHcCCCC--
Confidence 47899997 7999998 4444 46677764432 1111222221244654333222 123578999999999973
Q ss_pred Cccccc--------------------hhhHHHHHHHHHHHHh
Q 024017 228 ICHQAG--------------------SDSLLTCCTFMKMKDN 249 (274)
Q Consensus 228 ~~HqAG--------------------sDS~lT~~~F~~l~~~ 249 (274)
+.--.| .|.+-|..+|.|+...
T Consensus 131 K~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~ 172 (209)
T PF10108_consen 131 KDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELL 172 (209)
T ss_pred CCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 333233 3999999999998765
No 60
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=80.72 E-value=18 Score=33.62 Aligned_cols=58 Identities=21% Similarity=0.288 Sum_probs=41.2
Q ss_pred hhCCC--cccHHHHHHHhh----hccccHHHHHHH-cCCcc-CCCccccchhhHHHHHHHHHHHHhh
Q 024017 192 MYFPT--LYDIKHLMKFCN----SLHGGLNKLAEL-LEVER-IGICHQAGSDSLLTCCTFMKMKDNF 250 (274)
Q Consensus 192 ~~FP~--iyD~K~la~~~~----~l~~~L~~la~~-L~v~r-~g~~HqAGsDS~lT~~~F~~l~~~~ 250 (274)
..-|. |.||-+.--.++ ....||-+|++. ||.+= .|. |-.=-|+-.|+..|.+++...
T Consensus 201 l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~Ge-HsSvEDA~AtM~LY~~vk~qw 266 (280)
T KOG2249|consen 201 LEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGE-HSSVEDARATMELYKRVKVQW 266 (280)
T ss_pred hhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccc-cCcHHHHHHHHHHHHHHHHHH
Confidence 33364 888855433332 345699999987 66654 344 999999999999999988764
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=76.85 E-value=21 Score=29.77 Aligned_cols=83 Identities=22% Similarity=0.218 Sum_probs=54.8
Q ss_pred CCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhh-c-cccHHHHHHHc-CCccC---
Q 024017 153 NDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNS-L-HGGLNKLAELL-EVERI--- 226 (274)
Q Consensus 153 ~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~-l-~~~L~~la~~L-~v~r~--- 226 (274)
+.++++|+++..+|+.+|.+. |-++| +.++||..++..+.. . ..+|+++++.+ +..-+
T Consensus 65 ~~~~~~v~hn~k~d~~~l~~~--gi~~~--------------~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~ 128 (193)
T cd06139 65 DPSIKKVGQNLKFDLHVLANH--GIELR--------------GPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFE 128 (193)
T ss_pred CCCCcEEeeccHHHHHHHHHC--CCCCC--------------CCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHH
Confidence 345678888889999987542 33322 246799888887752 2 45888888764 33200
Q ss_pred ---C---------------CccccchhhHHHHHHHHHHHHhhc
Q 024017 227 ---G---------------ICHQAGSDSLLTCCTFMKMKDNFF 251 (274)
Q Consensus 227 ---g---------------~~HqAGsDS~lT~~~F~~l~~~~~ 251 (274)
| ..|-|..|+.+|..++-+|....-
T Consensus 129 ~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~ 171 (193)
T cd06139 129 DLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLK 171 (193)
T ss_pred HHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1 122478889999999999887753
No 62
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=73.07 E-value=5.8 Score=43.69 Aligned_cols=84 Identities=21% Similarity=0.237 Sum_probs=61.0
Q ss_pred eeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhh-hcc-ccHHHHHHHcCCccCCCccccch
Q 024017 157 HWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCN-SLH-GGLNKLAELLEVERIGICHQAGS 234 (274)
Q Consensus 157 ~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~-~l~-~~L~~la~~L~v~r~g~~HqAGs 234 (274)
.-|+.+..+|+|||-.-+.--.||+-. . -+.||=-||+.+. .++ -+|..|++.|++.- ...|-|-+
T Consensus 503 IlVAHNasFD~gFl~~~~~k~~~~~~~----------~-pvIDTL~lar~L~P~~ksh~Lg~l~kk~~v~l-e~hHRA~y 570 (1444)
T COG2176 503 ILVAHNASFDMGFLNTNYEKYGLEPLT----------N-PVIDTLELARALNPEFKSHRLGTLCKKLGVEL-ERHHRADY 570 (1444)
T ss_pred EEEeccCccchhHHHHHHHHhCCcccc----------C-chhhHHHHHHHhChhhhhcchHHHHHHhCccH-HHhhhhhh
Confidence 567788889999984332211111110 1 2558888888764 443 58999999999987 67899999
Q ss_pred hhHHHHHHHHHHHHhhcC
Q 024017 235 DSLLTCCTFMKMKDNFFK 252 (274)
Q Consensus 235 DS~lT~~~F~~l~~~~~~ 252 (274)
||-.|+.+|+.|.+...+
T Consensus 571 Daeat~~vf~~f~~~~ke 588 (1444)
T COG2176 571 DAEATAKVFFVFLKDLKE 588 (1444)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 999999999999888653
No 63
>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=70.95 E-value=1.8 Score=35.79 Aligned_cols=70 Identities=23% Similarity=0.337 Sum_probs=37.9
Q ss_pred eeEEeec-chhHHHHHHHhcCCCCCCCHHHHHHHHHhhCC-CcccHHHHHHHhhhccc-cHHHHHHHcCCccCCCccccc
Q 024017 157 HWVTFHS-GYDFGYLLKLLTCKDLPETQACFFDLIKMYFP-TLYDIKHLMKFCNSLHG-GLNKLAELLEVERIGICHQAG 233 (274)
Q Consensus 157 ~Wvtfhg-~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP-~iyD~K~la~~~~~l~~-~L~~la~~L~v~r~g~~HqAG 233 (274)
.+|+||| .||+.+|-+.+..-.+|. | ...|+..+++.... .+ +|..||+.||+.|- ...-.|
T Consensus 59 ~iv~yng~~FD~p~L~~~~~~~~~~~-------------~~~~iDl~~~~~~~~~-~~~~Lk~ve~~lg~~~~-~~~~~G 123 (164)
T PF13482_consen 59 NIVTYNGKNFDIPFLKRRAKRYGLPP-------------PFNHIDLLKIIKKHFL-ESYSLKNVEKFLGIERR-DDDISG 123 (164)
T ss_dssp -EEESSTTTTHHHHHHHHH-HHHH---------------GGGEEEHHHHHT-TTS-CCTT--SHHH------------HH
T ss_pred eEEEEeCcccCHHHHHHHHHHcCCCc-------------ccchhhHHHHHHhccC-CCCCHHHHhhhcccccc-cCCCCH
Confidence 7999997 789999988883223333 3 36698888765433 44 89999999999883 233567
Q ss_pred hhhHHHHH
Q 024017 234 SDSLLTCC 241 (274)
Q Consensus 234 sDS~lT~~ 241 (274)
+++.-.-.
T Consensus 124 ~~~~~~~~ 131 (164)
T PF13482_consen 124 SESVKLYK 131 (164)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 77666543
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=53.51 E-value=29 Score=30.52 Aligned_cols=69 Identities=22% Similarity=0.272 Sum_probs=41.7
Q ss_pred eeEEeec-chhHHHHHH-H-hcCCCCCCCHHHHHHHH---HhhCCCcccHHHHHHHhhhc-cccHHHHHHHcCCcc
Q 024017 157 HWVTFHS-GYDFGYLLK-L-LTCKDLPETQACFFDLI---KMYFPTLYDIKHLMKFCNSL-HGGLNKLAELLEVER 225 (274)
Q Consensus 157 ~Wvtfhg-~yD~~yl~k-~-l~~~~LP~~~~~F~~~l---~~~FP~iyD~K~la~~~~~l-~~~L~~la~~L~v~r 225 (274)
.+|+|+| ++|+-||.+ . ..|-++|.......+.- ..+-.+.+|+-.+.+..... ..+|..||+.||+++
T Consensus 95 ~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~L~~va~~lG~~~ 170 (208)
T cd05782 95 RLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARARASLDLLAKLLGIPG 170 (208)
T ss_pred EEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCccCCCCHHHHHHHhCCCC
Confidence 6899998 899999954 3 23555664332211110 11111366876666544332 458999999999965
No 65
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=51.67 E-value=4.7 Score=41.09 Aligned_cols=150 Identities=10% Similarity=0.006 Sum_probs=87.0
Q ss_pred ceEEEcCcc--cHHHHHHHHHHHhhcCCeeEEeecccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeecCCCC
Q 024017 10 IHIREVWND--NLEHEFSLIRDIVDDYPYIAMDTEFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTDENGN 87 (274)
Q Consensus 10 ~~i~~Vw~~--N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~ 87 (274)
+++..+-+. |....++.......+..+.++++|+.++...+ ......+..+++++.-.....++-+|..-.--.-+
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~ 179 (564)
T KOG1990|consen 102 SPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSD--RLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIE 179 (564)
T ss_pred cchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCC--CccchhhhchhhhhcccChhccCCCCChhhhhhHH
Confidence 344445555 68888777777777889999999999987543 23345677788888877777777777654421111
Q ss_pred CCCCCCCCeeeE-EEeeeecCCCCCccchhhHHHHHHcCCCccchhhCCCChHH----HHHH--HHHc-CcccCCCceeE
Q 024017 88 LPKCGTDKYCLW-QFNFREFSPDEDVYAYDSIKLLSRSGIDFKKNKEKGVDAMR----FSEL--LMSS-GIVLNDSVHWV 159 (274)
Q Consensus 88 ~p~~g~~~~~~w-qFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~----f~e~--l~~s-gLv~~~~v~Wv 159 (274)
........+.+. .|++- ++.......+..+++..++.+++ ..+.+|+.... ..++ +..+ +++..++.--.
T Consensus 180 ~~~~r~~~~~~p~~~~~~-~~~~~~~~~~~~~~~~~k~~~~k-~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~d 257 (564)
T KOG1990|consen 180 STLLRRLGYKLPPHFALG-RSRKLQGLAVAMVSFWEKHEFAK-ILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLD 257 (564)
T ss_pred HHHHHHhcccccccceeh-hccccccchhHHHHHHHHHHHHH-HHHHhcchhhhccchHHHHHHHHhcCCeEEeecccee
Confidence 000000011121 23333 55555566777777777777777 77777777653 2222 3444 45545554444
Q ss_pred Eeec
Q 024017 160 TFHS 163 (274)
Q Consensus 160 tfhg 163 (274)
.+|.
T Consensus 258 v~y~ 261 (564)
T KOG1990|consen 258 VMYR 261 (564)
T ss_pred eeee
Confidence 4443
No 66
>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=47.51 E-value=20 Score=30.10 Aligned_cols=30 Identities=27% Similarity=0.339 Sum_probs=27.1
Q ss_pred EcCcccHHHHHHHHHHHhhcCCeeEEeecc
Q 024017 14 EVWNDNLEHEFSLIRDIVDDYPYIAMDTEF 43 (274)
Q Consensus 14 ~Vw~~N~~~el~~I~~~i~~~~fIAiDtEF 43 (274)
-|.+-|+++.++.|.+.-++.-.||||.-.
T Consensus 43 PVHA~NL~e~l~~I~~~~~~~~iIAIDAcL 72 (140)
T TIGR02841 43 PVHAKNLEEKLKIIKKKHPNPFIIAIDACL 72 (140)
T ss_pred CcccccHHHHHHHHHHhCCCCeEEEEECcc
Confidence 488999999999999999999999999765
No 67
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=41.83 E-value=35 Score=23.95 Aligned_cols=33 Identities=30% Similarity=0.460 Sum_probs=24.4
Q ss_pred chhhHHHHHHcCCCc---------cchhhCCCChHHHHHHHH
Q 024017 114 AYDSIKLLSRSGIDF---------KKNKEKGVDAMRFSELLM 146 (274)
Q Consensus 114 ~~~Si~fL~~~G~DF---------~k~~~~GI~~~~f~e~l~ 146 (274)
.+.+.+.+.++|||| ......||++..+.+.|-
T Consensus 12 ~p~~a~vf~~~gIDfCCgG~~~L~eA~~~~~ld~~~vl~~L~ 53 (56)
T PF04405_consen 12 DPRAARVFRKYGIDFCCGGNRSLEEACEEKGLDPEEVLEELN 53 (56)
T ss_pred ChHHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHH
Confidence 467888999999999 345567777777666553
No 68
>KOG4013 consensus Predicted Cu2+ homeostasis protein CutC [Inorganic ion transport and metabolism]
Probab=41.77 E-value=95 Score=27.81 Aligned_cols=85 Identities=20% Similarity=0.243 Sum_probs=51.7
Q ss_pred chhhHHHHHHcCCC---ccchhhCCCChHHHHHH-HHHcCcccCCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHH
Q 024017 114 AYDSIKLLSRSGID---FKKNKEKGVDAMRFSEL-LMSSGIVLNDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDL 189 (274)
Q Consensus 114 ~~~Si~fL~~~G~D---F~k~~~~GI~~~~f~e~-l~~sgLv~~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~ 189 (274)
.-+-|++|+++|-| |..+-..|=--..-..- +..+ .-..||||-++|++|=+|......| -.-.|...
T Consensus 83 ~~~Dv~llk~~GAdGfVFGaLt~dgsid~~~C~si~~~~------rplPVTFHRAfD~~~D~k~~lE~~l--~~lGF~rv 154 (255)
T KOG4013|consen 83 NMEDVELLKKAGADGFVFGALTSDGSIDRTSCQSIIETA------RPLPVTFHRAFDVAYDWKTCLEDAL--LDLGFKRV 154 (255)
T ss_pred HHHHHHHHHHcCCCceEEeecCCCCCcCHHHHHHHHHhc------CCCceeeeeehhhhcCHHHHHHHHH--HHhhHHHH
Confidence 45678899987644 88887777333333333 3332 2357999999999986654431100 02468888
Q ss_pred HHhhC-CCcccHHHHHHH
Q 024017 190 IKMYF-PTLYDIKHLMKF 206 (274)
Q Consensus 190 l~~~F-P~iyD~K~la~~ 206 (274)
|..=| |.-.|--|+..+
T Consensus 155 LtSG~~psAldGv~~i~~ 172 (255)
T KOG4013|consen 155 LTSGQEPSALDGVYIIRE 172 (255)
T ss_pred hhcCCCcccccchHHHHH
Confidence 88777 764454444443
No 69
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=39.38 E-value=31 Score=31.78 Aligned_cols=74 Identities=18% Similarity=0.298 Sum_probs=49.1
Q ss_pred eeEEeec-chhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhh--c-cccHHHHHHHcCCccCCCcccc
Q 024017 157 HWVTFHS-GYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNS--L-HGGLNKLAELLEVERIGICHQA 232 (274)
Q Consensus 157 ~Wvtfhg-~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~--l-~~~L~~la~~L~v~r~g~~HqA 232 (274)
-||||+| ++|.-|+-++.. ..+|.+.+. .=||.-|-++.+.+ + .+||..|.+.||+.|..- --
T Consensus 158 ~lvsfNGkaFD~PfikR~v~-~~~el~l~~----------~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~R~ed--td 224 (278)
T COG3359 158 MLVSFNGKAFDIPFIKRMVR-DRLELSLEF----------GHFDLYHPSRRLWKHLLPRCGLKTVERILGIRREED--TD 224 (278)
T ss_pred eEEEecCcccCcHHHHHHHh-cccccCccc----------cchhhhhhhhhhhhccCCCCChhhHHHHhCcccccc--CC
Confidence 8999998 699999887544 345554432 24587777777642 2 578999999999999421 23
Q ss_pred chhhHHHHHHH
Q 024017 233 GSDSLLTCCTF 243 (274)
Q Consensus 233 GsDS~lT~~~F 243 (274)
|+++-..-.-|
T Consensus 225 G~~~p~lyr~~ 235 (278)
T COG3359 225 GYDGPELYRLY 235 (278)
T ss_pred CcchHHHHHHH
Confidence 55554444333
No 70
>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=36.89 E-value=1.1e+02 Score=23.95 Aligned_cols=53 Identities=19% Similarity=0.267 Sum_probs=33.3
Q ss_pred CCCceeEEeecchhHHHHHHHhcCCCCCCCHHHHHHHHHhhCCCcccHHHHHHHhhh-c-cccHHHHHHHc
Q 024017 153 NDSVHWVTFHSGYDFGYLLKLLTCKDLPETQACFFDLIKMYFPTLYDIKHLMKFCNS-L-HGGLNKLAELL 221 (274)
Q Consensus 153 ~~~v~Wvtfhg~yD~~yl~k~l~~~~LP~~~~~F~~~l~~~FP~iyD~K~la~~~~~-l-~~~L~~la~~L 221 (274)
+++++-|.++..+|+..|.+. +..+| +.++||..++..+.. . ..+|+.+++.+
T Consensus 52 ~~~~~~v~~~~k~d~~~L~~~--~~~~~--------------~~~~D~~~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 52 DEDITKVGHDAKFDLVVLARD--GIELP--------------GNIFDTMLAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred CCCCcEEeccHHHHHHHHHHC--CCCCC--------------CCcccHHHHHHHhCCCCCcCCHHHHHHHH
Confidence 445566777667777766443 11111 257899888887752 2 34899998875
No 71
>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=32.49 E-value=43 Score=28.80 Aligned_cols=31 Identities=26% Similarity=0.198 Sum_probs=27.6
Q ss_pred EcCcccHHHHHHHHHHHhhcCCeeEEeeccc
Q 024017 14 EVWNDNLEHEFSLIRDIVDDYPYIAMDTEFP 44 (274)
Q Consensus 14 ~Vw~~N~~~el~~I~~~i~~~~fIAiDtEFp 44 (274)
-|.+-|+++.++.|.+.-++.-.||||.-..
T Consensus 67 PVHA~NL~e~l~~I~~~~~~~~IIAIDAcLG 97 (163)
T PF06866_consen 67 PVHALNLEETLNEIKKKHPNPFIIAIDACLG 97 (163)
T ss_pred CcchhhHHHHHHHHHHHCCCCeEEEEECCCC
Confidence 4889999999999999888888899998764
No 72
>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=29.90 E-value=1.5e+02 Score=27.41 Aligned_cols=68 Identities=9% Similarity=0.015 Sum_probs=45.0
Q ss_pred EcCcccHHHHHHHHHHHhhcCC---eeEEee------cccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeec
Q 024017 14 EVWNDNLEHEFSLIRDIVDDYP---YIAMDT------EFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTD 83 (274)
Q Consensus 14 ~Vw~~N~~~el~~I~~~i~~~~---fIAiDt------EFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~ 83 (274)
+|++...++.+..+.+.+...+ ||++|. ..||+.....+ -.+..|--+.+|.-....+++-+.|+=++
T Consensus 196 ~i~~~g~~~v~~~~~~~l~~~~~~vyvS~DiDvlDps~aPgv~tp~pg--Gl~~~e~~~~l~~i~~~~~v~g~DivE~~ 272 (300)
T TIGR01229 196 EIDELGIGKVVEETLEYLKAEDGPIHLSLDVDGLDPSLAPATGTPVVG--GLTFREGLLIMEMLYETGLLTALDVVEVN 272 (300)
T ss_pred HHhhhhHHHHHHHHHHHHhcCCCeEEEEEeccccCcccCCCCCCCCCC--CCCHHHHHHHHHHHHhcCCEEEEEEEEEC
Confidence 4555566677888878876544 999996 46777543222 23677777888877766677666666554
No 73
>PF13637 Ank_4: Ankyrin repeats (many copies); PDB: 3B95_A 3B7B_A 3F6Q_A 2KBX_A 3IXE_A 2DWZ_C 2DVW_A 3AJI_A 1S70_B 2HE0_A ....
Probab=29.50 E-value=51 Score=21.83 Aligned_cols=29 Identities=24% Similarity=0.515 Sum_probs=21.0
Q ss_pred chhhHHHHHHcCCCccchhhCCCChHHHH
Q 024017 114 AYDSIKLLSRSGIDFKKNKEKGVDAMRFS 142 (274)
Q Consensus 114 ~~~Si~fL~~~G~DF~k~~~~GI~~~~f~ 142 (274)
+.+.+++|.++|.|.|..-+.|-++...|
T Consensus 13 ~~~~~~~Ll~~~~din~~d~~g~t~lh~A 41 (54)
T PF13637_consen 13 NLEIVKLLLEHGADINAQDEDGRTPLHYA 41 (54)
T ss_dssp -HHHHHHHHHTTSGTT-B-TTS--HHHHH
T ss_pred CHHHHHHHHHCCCCCCCCCCCCCCHHHHH
Confidence 56789999999999999999999987665
No 74
>PF07827 KNTase_C: KNTase C-terminal domain; InterPro: IPR012481 Kanamycin nucleotidyltransferase (KNTase) is involved in conferring resistance to aminoglycoside antibiotics and catalyses the transfer of a nucleoside monophosphate group from a nucleotide to kanamycin. This enzyme is dimeric with each subunit being composed of two domains. The C-terminal domain contains five alpha helices, four of which are organised into an up-and-down alpha helical bundle. Residues found in this domain may contribute to this enzyme's active site []. ; GO: 0016779 nucleotidyltransferase activity, 0046677 response to antibiotic; PDB: 1KNY_A.
Probab=29.29 E-value=54 Score=27.57 Aligned_cols=48 Identities=23% Similarity=0.333 Sum_probs=33.7
Q ss_pred CCCCCCHHHHHHHHHhhC-CCcccHHHHHHHhhhccccHHHHHHHcCCc
Q 024017 177 KDLPETQACFFDLIKMYF-PTLYDIKHLMKFCNSLHGGLNKLAELLEVE 224 (274)
Q Consensus 177 ~~LP~~~~~F~~~l~~~F-P~iyD~K~la~~~~~l~~~L~~la~~L~v~ 224 (274)
-.||+-.+.|.+++..+- +.+=|.+.|.+.|..+-.||+..|+++|+.
T Consensus 86 l~Lp~rP~Gyd~l~~lvm~G~L~d~~~i~~~cE~~W~Gl~~Wa~~hg~~ 134 (143)
T PF07827_consen 86 LSLPSRPSGYDELAQLVMSGQLTDPEKIYESCEALWTGLVKWAAEHGYT 134 (143)
T ss_dssp TTSSS--TTHHHHHHHHHHTB---HHHHHHHHHHHHHHHHHHHHHHT--
T ss_pred hcCCCCCccHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHcCeE
Confidence 367777777776665554 678899999999998999999999998863
No 75
>PF13606 Ank_3: Ankyrin repeat
Probab=27.74 E-value=48 Score=19.77 Aligned_cols=17 Identities=24% Similarity=0.380 Sum_probs=14.6
Q ss_pred chhhHHHHHHcCCCccc
Q 024017 114 AYDSIKLLSRSGIDFKK 130 (274)
Q Consensus 114 ~~~Si~fL~~~G~DF~k 130 (274)
+.+-+++|.++|.|.|.
T Consensus 14 ~~e~v~~Ll~~gadvn~ 30 (30)
T PF13606_consen 14 NIEIVKYLLEHGADVNA 30 (30)
T ss_pred CHHHHHHHHHcCCCCCC
Confidence 67889999999999874
No 76
>PF12345 DUF3641: Protein of unknown function (DUF3641) ; InterPro: IPR024521 This domain is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. It is found in association with an N-terminal radical_SAM domain (Pfam:PF04055 from PFAM).
Probab=27.28 E-value=60 Score=27.03 Aligned_cols=32 Identities=31% Similarity=0.342 Sum_probs=26.8
Q ss_pred HHHHcCCCccchhhC-CCChHHHHHHHHHcCcc
Q 024017 120 LLSRSGIDFKKNKEK-GVDAMRFSELLMSSGIV 151 (274)
Q Consensus 120 fL~~~G~DF~k~~~~-GI~~~~f~e~l~~sgLv 151 (274)
+..+.||.||.+..- -+|..+|++.|.++|..
T Consensus 16 L~~~~GI~Fn~L~titNmPI~RF~~~L~~~g~~ 48 (134)
T PF12345_consen 16 LKERFGIVFNNLFTITNMPIGRFGSFLERSGNL 48 (134)
T ss_pred HHHhcCceecchhhhhcCcHHHHHHHHHHccCH
Confidence 446889999999874 48889999999998866
No 77
>KOG0626 consensus Beta-glucosidase, lactase phlorizinhydrolase, and related proteins [Carbohydrate transport and metabolism]
Probab=26.45 E-value=55 Score=33.17 Aligned_cols=65 Identities=17% Similarity=0.260 Sum_probs=42.8
Q ss_pred CChHHHHHHHHhcccccceeeeeeeeecCCCCCCCCCCCCeeeEEEeeeecCCCC--CccchhhHHHHHHcCCCccchhh
Q 024017 56 SSSEYNYQNLKVNVDLLKLIQLGLTFTDENGNLPKCGTDKYCLWQFNFREFSPDE--DVYAYDSIKLLSRSGIDFKKNKE 133 (274)
Q Consensus 56 ~t~e~rY~~lr~nvd~~~iiQlGit~~~~~g~~p~~g~~~~~~wqFNF~~F~~~~--d~~~~~Si~fL~~~G~DF~k~~~ 133 (274)
+.+-+-|..-|+-|+.++ ++|++.|.- -..|. +++|..+ .-++++.|+|=..= -+++++
T Consensus 84 dva~D~Yh~ykeDv~Lmk--~lgv~afRF-----------SIsWS---RIlP~G~~~~gVN~~Gi~fY~~L---I~eL~~ 144 (524)
T KOG0626|consen 84 DVAVDFYHRYKEDVKLMK--ELGVDAFRF-----------SISWS---RILPNGRLTGGVNEAGIQFYNNL---IDELLA 144 (524)
T ss_pred CeechhhhhhHHHHHHHH--HcCCCeEEE-----------EeehH---hhCCCCCcCCCcCHHHHHHHHHH---HHHHHH
Confidence 445567888888888764 677776653 24554 4566665 45888888874432 356777
Q ss_pred CCCChH
Q 024017 134 KGVDAM 139 (274)
Q Consensus 134 ~GI~~~ 139 (274)
+||.+.
T Consensus 145 nGI~P~ 150 (524)
T KOG0626|consen 145 NGIEPF 150 (524)
T ss_pred cCCeEE
Confidence 788773
No 78
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=26.13 E-value=1.4e+02 Score=19.09 Aligned_cols=30 Identities=17% Similarity=0.317 Sum_probs=18.7
Q ss_pred HHHHHhhCCCcccHHHHHHHhhhccccHHHH
Q 024017 187 FDLIKMYFPTLYDIKHLMKFCNSLHGGLNKL 217 (274)
Q Consensus 187 ~~~l~~~FP~iyD~K~la~~~~~l~~~L~~l 217 (274)
.+.++.+||.+ |...+...+....+.++..
T Consensus 5 v~~L~~mFP~~-~~~~I~~~L~~~~~~ve~a 34 (42)
T PF02845_consen 5 VQQLQEMFPDL-DREVIEAVLQANNGDVEAA 34 (42)
T ss_dssp HHHHHHHSSSS--HHHHHHHHHHTTTTHHHH
T ss_pred HHHHHHHCCCC-CHHHHHHHHHHcCCCHHHH
Confidence 46789999986 6666666554444555543
No 79
>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=24.35 E-value=70 Score=20.61 Aligned_cols=25 Identities=24% Similarity=0.347 Sum_probs=16.9
Q ss_pred HHHHHHhhhccccHHHHHHHcCCcc
Q 024017 201 KHLMKFCNSLHGGLNKLAELLEVER 225 (274)
Q Consensus 201 K~la~~~~~l~~~L~~la~~L~v~r 225 (274)
.+|...+....|.....|+.||+.|
T Consensus 8 ~~i~~aL~~~~gn~~~aA~~Lgisr 32 (42)
T PF02954_consen 8 QLIRQALERCGGNVSKAARLLGISR 32 (42)
T ss_dssp HHHHHHHHHTTT-HHHHHHHHTS-H
T ss_pred HHHHHHHHHhCCCHHHHHHHHCCCH
Confidence 4555555555677999999999977
No 80
>PRK13772 formimidoylglutamase; Provisional
Probab=23.54 E-value=2.8e+02 Score=25.90 Aligned_cols=69 Identities=13% Similarity=0.114 Sum_probs=45.7
Q ss_pred EEcCcccHHHHHHHHHHHhhcC--CeeEEeec------ccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeec
Q 024017 13 REVWNDNLEHEFSLIRDIVDDY--PYIAMDTE------FPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTD 83 (274)
Q Consensus 13 ~~Vw~~N~~~el~~I~~~i~~~--~fIAiDtE------FpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~ 83 (274)
.+++..++++.+..+.+.+... -||++|.. .||+.....+. .+..|-.+.+|.-...-+++=+.|+-++
T Consensus 217 ~e~~~~g~~~~~~~i~~~l~~~~~vylS~DiD~lDps~aPGvgtP~pgG--lt~~e~~~il~~l~~~~~v~g~DvvEv~ 293 (314)
T PRK13772 217 VDMQERHLDARLAELDALLDAADHVYLTIDLDVLPAAVAPGVSAPAAYG--VPLPVVEEIVLHVRASGKLRVADLAEYN 293 (314)
T ss_pred hhhhhcCHHHHHHHHHHHHhcCCeEEEEEEecCcCcccCCCCCCCCCCC--CCHHHHHHHHHHHHhcCCeeEEEEEEEC
Confidence 3556667778888888888644 58899864 56765432222 3677888888876665566656665554
No 81
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=22.98 E-value=1.7e+02 Score=18.71 Aligned_cols=30 Identities=20% Similarity=0.327 Sum_probs=16.9
Q ss_pred HHHHHhhCCCcccHHHHHHHhhhccccHHHH
Q 024017 187 FDLIKMYFPTLYDIKHLMKFCNSLHGGLNKL 217 (274)
Q Consensus 187 ~~~l~~~FP~iyD~K~la~~~~~l~~~L~~l 217 (274)
.+.|+.+||.+ |...+...+....|.++..
T Consensus 6 v~~L~~mFP~l-~~~~I~~~L~~~~g~ve~~ 35 (43)
T smart00546 6 LHDLKDMFPNL-DEEVIKAVLEANNGNVEAT 35 (43)
T ss_pred HHHHHHHCCCC-CHHHHHHHHHHcCCCHHHH
Confidence 56788999986 4444444343333445443
No 82
>PF08870 DUF1832: Domain of unknown function (DUF1832); InterPro: IPR014969 This entry describes the DndE protein encoded by an operon associated with a sulphur-containing modification to DNA []. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is a putative carboxylase homologous to NCAIR synthetases.
Probab=22.50 E-value=1.6e+02 Score=23.56 Aligned_cols=32 Identities=31% Similarity=0.439 Sum_probs=20.9
Q ss_pred CceeEEeecchhHHH--HHHHhcCCCCCCCHHHHHH
Q 024017 155 SVHWVTFHSGYDFGY--LLKLLTCKDLPETQACFFD 188 (274)
Q Consensus 155 ~v~Wvtfhg~yD~~y--l~k~l~~~~LP~~~~~F~~ 188 (274)
++.|.||.|.|+--| |++...|.++ +.++|.+
T Consensus 54 e~~~~t~~Ge~~~~~~~ll~q~~g~~~--d~~~l~~ 87 (113)
T PF08870_consen 54 ELNWKTFTGEYDDIYEALLKQRYGPEL--DDEELPK 87 (113)
T ss_pred EEeeeeecCchHHHHHHHHHHHhCCCC--CHHHHHH
Confidence 469999999998887 3555554433 4444443
No 83
>KOG2725 consensus Cytochrome oxidase assembly factor COX15 [Posttranslational modification, protein turnover, chaperones]
Probab=21.70 E-value=70 Score=30.92 Aligned_cols=68 Identities=25% Similarity=0.326 Sum_probs=43.3
Q ss_pred CCCCCCHHHHHHHHHhhC--CC--cccHHHHHHHhhhccccHHHHH-----------------------HHcCCc-----
Q 024017 177 KDLPETQACFFDLIKMYF--PT--LYDIKHLMKFCNSLHGGLNKLA-----------------------ELLEVE----- 224 (274)
Q Consensus 177 ~~LP~~~~~F~~~l~~~F--P~--iyD~K~la~~~~~l~~~L~~la-----------------------~~L~v~----- 224 (274)
.-+||+.=+|....+-+| |. =+|-+.+|...--...++--++ ..|||-
T Consensus 300 ~wipd~~f~r~piwrN~~ENp~tVQ~~HRila~tt~~ai~~~~~~~rr~~lpkr~k~ai~~~v~~v~~QatLGv~TLl~y 379 (411)
T KOG2725|consen 300 SWIPDDMFTRSPIWRNFFENPTTVQFDHRILAITTVTAITALYLITRRAPLPKRTKMAINVTVAVVTTQATLGVSTLLYY 379 (411)
T ss_pred ccCccccccccHHHHHhhcCCceEEeehhhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhhhhheeeeee
Confidence 678999999999999999 53 4666666654211111111122 234432
Q ss_pred -c--CCCccccchhhHHHHHHHH
Q 024017 225 -R--IGICHQAGSDSLLTCCTFM 244 (274)
Q Consensus 225 -r--~g~~HqAGsDS~lT~~~F~ 244 (274)
+ .+..|||||=++||+..-+
T Consensus 380 VPv~Laa~HQaGsLalLt~aL~l 402 (411)
T KOG2725|consen 380 VPVPLAAAHQAGSLALLTSALWL 402 (411)
T ss_pred ccchhHhhhhcchHHHHHHHHHH
Confidence 2 3679999999999986543
No 84
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=21.52 E-value=83 Score=20.63 Aligned_cols=32 Identities=16% Similarity=0.235 Sum_probs=25.4
Q ss_pred CCCHHHHHHHHHhhCCCcccHHHHHHHhhhcc
Q 024017 180 PETQACFFDLIKMYFPTLYDIKHLMKFCNSLH 211 (274)
Q Consensus 180 P~~~~~F~~~l~~~FP~iyD~K~la~~~~~l~ 211 (274)
|+.+++|++.++.|=-...|.+-+.+.+..+-
T Consensus 1 p~~Y~~FL~il~~y~~~~~~~~~v~~~v~~Ll 32 (47)
T PF02671_consen 1 PEVYNEFLKILNDYKKGRISRSEVIEEVSELL 32 (47)
T ss_dssp HHHHHHHHHHHHHHHCTCSCHHHHHHHHHHHT
T ss_pred ChHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 66789999999999877888888777776543
No 85
>PF13857 Ank_5: Ankyrin repeats (many copies); PDB: 1SW6_A 3EHR_B 3EHQ_A.
Probab=21.23 E-value=87 Score=21.09 Aligned_cols=29 Identities=17% Similarity=0.440 Sum_probs=17.4
Q ss_pred chhhHHHHHHcCCCccchhhCCCChHHHH
Q 024017 114 AYDSIKLLSRSGIDFKKNKEKGVDAMRFS 142 (274)
Q Consensus 114 ~~~Si~fL~~~G~DF~k~~~~GI~~~~f~ 142 (274)
..+.+++|.+.|.|.+..-.+|-.+...|
T Consensus 28 ~~~~v~~Ll~~g~d~~~~d~~G~Tpl~~A 56 (56)
T PF13857_consen 28 HSEVVRLLLQNGADPNAKDKDGQTPLHYA 56 (56)
T ss_dssp -HHHHHHHHHCT--TT---TTS--HHHH-
T ss_pred cHHHHHHHHHCcCCCCCCcCCCCCHHHhC
Confidence 57889999999999999999998776543
No 86
>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=20.60 E-value=2.1e+02 Score=19.38 Aligned_cols=36 Identities=28% Similarity=0.342 Sum_probs=26.7
Q ss_pred HHHHHHcCCcc--C---CCccccchhhHHHHHHHHHHHHhh
Q 024017 215 NKLAELLEVER--I---GICHQAGSDSLLTCCTFMKMKDNF 250 (274)
Q Consensus 215 ~~la~~L~v~r--~---g~~HqAGsDS~lT~~~F~~l~~~~ 250 (274)
+-+++.++++. + ......|.||+...+.-.++.+.|
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 34566677543 3 335589999999999999998886
No 87
>PF02257 RFX_DNA_binding: RFX DNA-binding domain; InterPro: IPR003150 RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1DP7_P 2KW3_A.
Probab=20.59 E-value=76 Score=24.27 Aligned_cols=29 Identities=34% Similarity=0.357 Sum_probs=17.3
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHHhhCCCc
Q 024017 169 YLLKLLTCKDLPETQACFFDLIKMYFPTL 197 (274)
Q Consensus 169 yl~k~l~~~~LP~~~~~F~~~l~~~FP~i 197 (274)
|+--+=...--|-+.+.|-++++..||++
T Consensus 33 Y~~~C~~~~~~pln~AsFGKlir~vFP~l 61 (85)
T PF02257_consen 33 YLSFCEKNGIKPLNAASFGKLIRQVFPNL 61 (85)
T ss_dssp HHHHHHHTT-----HHHHHHHHHHHSTT-
T ss_pred HHHHHHHhCCCCCchHHHHHHHHHHcCCC
Confidence 44333334566789999999999999975
No 88
>PRK02190 agmatinase; Provisional
Probab=20.17 E-value=3.2e+02 Score=25.24 Aligned_cols=66 Identities=23% Similarity=0.344 Sum_probs=41.5
Q ss_pred cCcccHHHHHHHHHHHhhcCC-eeEEee------cccccccccCCCCCCChHHHHHHHHhcccccceeeeeeeeec
Q 024017 15 VWNDNLEHEFSLIRDIVDDYP-YIAMDT------EFPGIVLRSIGNFKSSSEYNYQNLKVNVDLLKLIQLGLTFTD 83 (274)
Q Consensus 15 Vw~~N~~~el~~I~~~i~~~~-fIAiDt------EFpGv~~~p~~~~~~t~e~rY~~lr~nvd~~~iiQlGit~~~ 83 (274)
|++...++.+..+.+.+...+ ||++|. ..||+.....+ -.+..+-...++. +...+++=+.|+-++
T Consensus 199 ~~~~g~~~~~~~~~~~l~~~~vyiSiDiDvlDps~aPg~~~p~pg--Gl~~~e~~~il~~-i~~~~vvg~DivE~~ 271 (301)
T PRK02190 199 VNDRGVDAIIAQIKQIVGDMPVYLTFDIDCLDPAFAPGTGTPVIG--GLTSAQALKILRG-LKGLNIVGMDVVEVA 271 (301)
T ss_pred hhccCHHHHHHHHHHHhCCCEEEEEEeecccCcccCCCCCCCCCC--CcCHHHHHHHHHH-HhcCCeEEEEeeeec
Confidence 445556677788888776544 999986 45666543222 2367777888876 344566666666554
Done!