Query 023991
Match_columns 274
No_of_seqs 152 out of 507
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 08:08:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023991.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023991hhsearch_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 8.4E-89 1.8E-93 589.1 18.4 237 11-250 1-239 (239)
2 COG5228 POP2 mRNA deadenylase 100.0 4.5E-78 9.7E-83 523.1 12.0 256 9-269 17-273 (299)
3 PF04857 CAF1: CAF1 family rib 100.0 7.4E-65 1.6E-69 461.7 18.7 228 13-245 1-262 (262)
4 KOG1990 Poly(A)-specific exori 99.3 3.6E-12 7.9E-17 127.4 4.8 232 17-252 1-365 (564)
5 PRK07942 DNA polymerase III su 99.0 9.6E-09 2.1E-13 92.1 15.0 173 32-251 4-181 (232)
6 smart00479 EXOIII exonuclease 99.0 4.8E-08 1E-12 81.5 16.6 164 35-251 1-168 (169)
7 cd06134 RNaseT DEDDh 3'-5' exo 98.8 2.2E-07 4.8E-12 80.7 14.2 175 32-249 3-188 (189)
8 cd06133 ERI-1_3'hExo_like DEDD 98.7 4E-07 8.7E-12 76.8 13.9 172 36-246 1-175 (176)
9 PRK05168 ribonuclease T; Provi 98.7 6.5E-07 1.4E-11 79.1 15.7 185 25-251 8-202 (211)
10 PRK09145 DNA polymerase III su 98.7 8.5E-07 1.8E-11 77.6 15.2 170 25-248 20-199 (202)
11 cd06130 DNA_pol_III_epsilon_li 98.7 6.7E-07 1.5E-11 74.0 13.8 150 36-244 1-155 (156)
12 cd06131 DNA_pol_III_epsilon_Ec 98.7 7.4E-07 1.6E-11 75.0 14.1 163 36-246 1-166 (167)
13 PRK05711 DNA polymerase III su 98.6 1.2E-06 2.6E-11 79.1 14.7 169 33-249 3-175 (240)
14 PRK07748 sporulation inhibitor 98.6 1.8E-06 3.9E-11 76.0 14.2 173 33-249 3-179 (207)
15 PRK06195 DNA polymerase III su 98.5 3.6E-06 7.8E-11 78.6 15.0 160 35-251 2-165 (309)
16 PRK06807 DNA polymerase III su 98.5 4E-06 8.6E-11 78.6 14.7 161 34-250 8-172 (313)
17 TIGR00573 dnaq exonuclease, DN 98.5 7.4E-06 1.6E-10 72.6 15.5 168 31-251 4-178 (217)
18 PRK06310 DNA polymerase III su 98.5 4.3E-06 9.3E-11 75.9 14.0 170 30-251 3-175 (250)
19 PRK07740 hypothetical protein; 98.4 7.7E-06 1.7E-10 74.0 15.0 168 32-251 57-227 (244)
20 TIGR01406 dnaQ_proteo DNA poly 98.4 9.4E-06 2E-10 72.6 15.1 168 35-250 1-172 (225)
21 PRK07247 DNA polymerase III su 98.4 6E-06 1.3E-10 72.4 13.2 160 35-251 6-170 (195)
22 PRK06063 DNA polymerase III su 98.4 1E-05 2.3E-10 75.7 15.3 162 33-251 14-180 (313)
23 TIGR01298 RNaseT ribonuclease 98.4 1.6E-05 3.4E-10 69.8 14.6 177 32-251 6-193 (200)
24 PRK09146 DNA polymerase III su 98.3 2.6E-05 5.7E-10 70.4 16.1 169 30-252 43-229 (239)
25 cd06136 TREX1_2 DEDDh 3'-5' ex 98.3 2.2E-05 4.7E-10 67.4 13.9 168 36-245 1-176 (177)
26 cd06127 DEDDh DEDDh 3'-5' exon 98.3 1.1E-05 2.3E-10 65.7 10.4 155 37-244 1-159 (159)
27 PRK06722 exonuclease; Provisio 98.2 6E-05 1.3E-09 69.6 16.3 168 33-247 4-178 (281)
28 PRK08517 DNA polymerase III su 98.2 5.1E-05 1.1E-09 69.2 15.2 167 31-251 65-232 (257)
29 PF00929 RNase_T: Exonuclease; 98.2 2.5E-06 5.5E-11 69.5 4.9 156 37-243 1-164 (164)
30 PRK07246 bifunctional ATP-depe 98.1 7.2E-05 1.6E-09 78.4 16.4 162 33-251 6-171 (820)
31 PRK07883 hypothetical protein; 98.1 7.1E-05 1.5E-09 75.3 15.7 170 27-251 8-183 (557)
32 PRK08074 bifunctional ATP-depe 98.1 6.8E-05 1.5E-09 79.6 15.4 166 34-251 3-170 (928)
33 TIGR01405 polC_Gram_pos DNA po 98.1 9.3E-05 2E-09 80.2 15.9 168 32-252 188-357 (1213)
34 PRK07983 exodeoxyribonuclease 98.0 0.00018 3.8E-09 64.2 14.1 148 36-250 2-154 (219)
35 TIGR01407 dinG_rel DnaQ family 98.0 0.00015 3.2E-09 76.4 15.6 161 35-251 1-166 (850)
36 cd06138 ExoI_N N-terminal DEDD 98.0 0.00014 3.1E-09 62.6 12.1 165 38-242 2-181 (183)
37 PTZ00315 2'-phosphotransferase 98.0 0.00027 5.8E-09 71.0 15.5 175 34-251 56-256 (582)
38 PRK06309 DNA polymerase III su 97.9 0.00048 1E-08 61.7 14.0 160 35-251 3-167 (232)
39 PRK09182 DNA polymerase III su 97.8 0.00061 1.3E-08 63.4 13.9 155 35-247 38-198 (294)
40 cd06144 REX4_like DEDDh 3'-5' 97.8 0.00044 9.5E-09 57.8 11.6 69 157-243 79-151 (152)
41 PRK11779 sbcB exonuclease I; P 97.8 0.00042 9.2E-09 68.5 13.2 175 32-249 4-197 (476)
42 PRK05601 DNA polymerase III su 97.7 0.0006 1.3E-08 65.2 11.9 176 30-247 42-246 (377)
43 COG0847 DnaQ DNA polymerase II 97.6 0.0015 3.2E-08 58.3 13.9 163 34-249 13-181 (243)
44 PRK00448 polC DNA polymerase I 97.5 0.0017 3.8E-08 71.6 14.4 168 31-251 416-585 (1437)
45 cd06145 REX1_like DEDDh 3'-5' 97.4 0.0012 2.6E-08 55.2 9.6 69 155-243 76-149 (150)
46 cd06137 DEDDh_RNase DEDDh 3'-5 97.4 0.0022 4.7E-08 54.2 11.1 68 156-243 85-160 (161)
47 PRK05359 oligoribonuclease; Pr 97.3 0.0079 1.7E-07 52.0 13.3 166 34-252 3-177 (181)
48 cd06149 ISG20 DEDDh 3'-5' exon 97.0 0.0086 1.9E-07 50.4 10.0 70 156-243 78-156 (157)
49 PF01612 DNA_pol_A_exo1: 3'-5' 95.5 0.27 5.8E-06 40.6 11.4 83 151-250 73-175 (176)
50 PRK05755 DNA polymerase I; Pro 95.1 0.37 8E-06 51.3 13.6 83 153-251 368-470 (880)
51 COG0349 Rnd Ribonuclease D [Tr 94.8 0.18 3.9E-06 48.2 9.1 76 159-251 74-167 (361)
52 cd06141 WRN_exo DEDDy 3'-5' ex 94.8 0.37 8.1E-06 40.3 10.2 79 153-247 71-169 (170)
53 cd06135 Orn DEDDh 3'-5' exonuc 94.7 0.81 1.8E-05 38.9 12.1 164 36-249 1-171 (173)
54 cd06146 mut-7_like_exo DEDDy 3 94.2 0.87 1.9E-05 39.5 11.4 87 151-247 78-192 (193)
55 COG2176 PolC DNA polymerase II 93.2 0.6 1.3E-05 50.7 10.0 84 157-252 503-588 (1444)
56 PRK10829 ribonuclease D; Provi 92.2 3.2 7E-05 40.0 12.9 84 153-252 72-172 (373)
57 cd06148 Egl_like_exo DEDDy 3'- 88.5 11 0.00024 32.6 12.1 85 152-252 62-179 (197)
58 PF10108 DNA_pol_B_exo2: Predi 81.1 4.5 9.7E-05 36.0 6.1 93 155-249 52-172 (209)
59 cd06139 DNA_polA_I_Ecoli_like_ 77.5 8.4 0.00018 32.3 6.6 83 154-252 66-172 (193)
60 PF13482 RNase_H_2: RNase_H su 72.7 1.5 3.3E-05 36.2 0.7 71 156-241 58-131 (164)
61 cd05782 DNA_polB_like1_exo Unc 70.8 7.9 0.00017 34.0 4.9 68 157-225 95-170 (208)
62 KOG1990 Poly(A)-specific exori 62.5 2.7 5.7E-05 42.8 0.2 152 9-163 101-261 (564)
63 cd06129 RNaseD_like DEDDy 3'-5 62.1 15 0.00033 30.5 4.7 80 152-247 64-160 (161)
64 TIGR01388 rnd ribonuclease D. 47.3 18 0.00039 34.6 3.2 26 21-46 5-30 (367)
65 TIGR02841 spore_YyaC putative 44.5 23 0.0005 29.6 2.9 29 15-43 44-72 (140)
66 KOG4013 Predicted Cu2+ homeost 43.5 34 0.00073 30.4 3.9 86 114-207 83-173 (255)
67 TIGR01229 rocF_arginase argina 43.1 71 0.0015 29.6 6.3 68 14-83 196-272 (300)
68 COG3359 Predicted exonuclease 41.9 50 0.0011 30.4 4.8 76 157-245 158-237 (278)
69 cd00007 35EXOc 3'-5' exonuclea 41.7 96 0.0021 24.3 6.2 53 153-221 52-106 (155)
70 COG5228 POP2 mRNA deadenylase 38.9 26 0.00056 31.7 2.5 96 161-267 197-297 (299)
71 cd05785 DNA_polB_like2_exo Unc 38.4 25 0.00055 30.8 2.5 69 157-225 76-169 (207)
72 KOG2249 3'-5' exonuclease [Rep 38.3 15 0.00033 33.9 1.0 54 196-250 207-266 (280)
73 PF04405 ScdA_N: Domain of Unk 37.4 44 0.00094 23.3 3.0 32 114-145 12-52 (56)
74 PRK13772 formimidoylglutamase; 36.2 1.3E+02 0.0028 28.1 6.9 69 13-83 217-293 (314)
75 PF06866 DUF1256: Protein of u 29.4 51 0.0011 28.2 2.8 30 15-44 68-97 (163)
76 cd05776 DNA_polB_alpha_exo ina 29.4 60 0.0013 28.9 3.4 68 157-225 100-187 (234)
77 TIGR01388 rnd ribonuclease D. 28.0 2.6E+02 0.0057 26.7 7.7 83 153-251 68-167 (367)
78 PRK13775 formimidoylglutamase; 27.1 1.7E+02 0.0036 27.6 6.1 69 13-83 224-300 (328)
79 PF13606 Ank_3: Ankyrin repeat 25.9 58 0.0013 19.3 1.8 17 114-130 14-30 (30)
80 smart00474 35EXOc 3'-5' exonuc 25.5 3.4E+02 0.0074 21.5 7.6 80 153-249 73-170 (172)
81 PF13637 Ank_4: Ankyrin repeat 25.3 73 0.0016 21.0 2.5 29 114-142 13-41 (54)
82 PF02671 PAH: Paired amphipath 24.1 44 0.00096 21.9 1.2 34 180-213 1-34 (47)
83 PF12345 DUF3641: Protein of u 23.1 76 0.0016 26.3 2.6 32 120-151 16-48 (134)
84 PRK02190 agmatinase; Provision 22.9 2.5E+02 0.0053 26.0 6.3 66 15-83 199-271 (301)
85 PF00550 PP-binding: Phosphopa 22.3 1.9E+02 0.0042 19.5 4.3 36 216-251 6-46 (67)
86 PF02845 CUE: CUE domain; Int 22.0 1.3E+02 0.0028 19.2 3.1 30 187-217 5-34 (42)
87 PRK05264 transcriptional repre 21.8 61 0.0013 25.2 1.6 15 170-184 62-76 (105)
88 cd06129 RNaseD_like DEDDy 3'-5 20.9 90 0.002 25.7 2.7 22 25-46 3-25 (161)
89 cd00490 Met_repressor_MetJ Met 20.3 68 0.0015 24.7 1.6 15 170-184 61-75 (103)
90 TIGR01227 hutG formimidoylglut 20.1 3.2E+02 0.007 25.2 6.5 67 15-83 211-285 (307)
No 1
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=8.4e-89 Score=589.11 Aligned_cols=237 Identities=65% Similarity=1.124 Sum_probs=230.5
Q ss_pred eEEEcCcccHHHHHHHHHHHhhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCC
Q 023991 11 QIREVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPT 90 (274)
Q Consensus 11 ~v~eVw~~Nf~~e~~~I~~~i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~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 37999999999999999999999999999999999999999999899999999999999999999999999999999997
Q ss_pred CCCCCeeEEEeeecccCCCCCCCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHH
Q 023991 91 CGTDKYCVWQFNFREFDVNEDIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYL 170 (274)
Q Consensus 91 ~~~~~~~~w~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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 65 469999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc--ccCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHH
Q 023991 171 LKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS--LHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKE 248 (274)
Q Consensus 171 ~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~--l~~~L~~la~~L~~~r~~~~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 023991 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=4.5e-78 Score=523.15 Aligned_cols=256 Identities=48% Similarity=0.866 Sum_probs=241.8
Q ss_pred cceEEEcCcccHHHHHHHHHHHhhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCC
Q 023991 9 SIQIREVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNL 88 (274)
Q Consensus 9 ~~~v~eVw~~Nf~~e~~~I~~~i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~ 88 (274)
-..||+||++|+..||..|+.+|.+|++|+|||||||+++||+|.|+++.+++||.+|+|||.++|||+||++++++|+.
T Consensus 17 ~~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~ 96 (299)
T COG5228 17 YLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNK 96 (299)
T ss_pred hHHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCC
Confidence 45699999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCeeEEEeeecccCCCCCCCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHH
Q 023991 89 PTCGTDKYCVWQFNFREFDVNEDIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFG 168 (274)
Q Consensus 89 p~~~~~~~~~w~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~ 168 (274)
|. +.++|||||- |++.+||++++||++|+++|+||.||.+.||+..+|+|+|+.|||++.++|+|||||++||||
T Consensus 97 P~----~~sTWQFNF~-F~l~~dmya~ESieLL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~VtWitfHsaYDfg 171 (299)
T COG5228 97 PN----GPSTWQFNFE-FDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDFG 171 (299)
T ss_pred CC----CCceeEEEEE-ecchhhhcchHHHHHHHHcCCChhhHhhcCCCHHHHHHHHhccCceeccceEEEEeecchhHH
Confidence 83 6899999998 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhcccCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHH
Q 023991 169 YLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKE 248 (274)
Q Consensus 169 yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~l~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~ 248 (274)
||+|+|++.|||+.+++|.+++++|||+.||.|++.+...+.+.||++++..|++.|.|++||||+||++|+..|++.|.
T Consensus 172 yLikilt~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~ 251 (299)
T COG5228 172 YLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRF 251 (299)
T ss_pred HHHHHHhcCCCCccHHHHHHHHHHHCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhh
Confidence 99999999999999999999999999999999999999988899999999999999999999999999999999999999
Q ss_pred HhcCCC-ccccccEEeecCCCC
Q 023991 249 NFFSSS-LEKYAGVLYGLGVEN 269 (274)
Q Consensus 249 ~~~~~~-~~~~~g~i~Gl~~~~ 269 (274)
.+|+.. ....-..+||++...
T Consensus 252 ~~F~~sig~~ll~~L~g~~~~~ 273 (299)
T COG5228 252 SIFTTSIGQSLLMLLSGCQLSK 273 (299)
T ss_pred heecccccHHHHHHHhccccCC
Confidence 988642 344455556655543
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=7.4e-65 Score=461.68 Aligned_cols=228 Identities=37% Similarity=0.594 Sum_probs=201.0
Q ss_pred EEcCcccHHHHHHHHHHHhhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeee-ecCCCCCCC
Q 023991 13 REVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFS-DENGNLPTC 91 (274)
Q Consensus 13 ~eVw~~Nf~~e~~~I~~~i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~-~~~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 6999999999999999999999999999999999999765467899999999999999999999999999 77787764
Q ss_pred CCCCeeEEEeeecccCCCCCCCchhHHHHHHHcCCCccchhhcCCchhHHH------HHHHHhcccc---cCCcceEEec
Q 023991 92 GTDKYCVWQFNFREFDVNEDIFANDSIELLKQSGINFTKNNEIGIDAMRFG------EFMMSSGIVL---SDSMHWVTFH 162 (274)
Q Consensus 92 ~~~~~~~w~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~------e~l~~Sgl~~---~~~v~wvtf~ 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 588999999999999998899999999999999999999999999999 6677788765 3458999999
Q ss_pred cchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhcccCcHHHHHHHcCCcc-----------------
Q 023991 163 SGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNSLHGGLNKLAELLEVER----------------- 225 (274)
Q Consensus 163 g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~l~~~L~~la~~L~~~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 99999999999997 999999999999999999999999999999877899999999999987
Q ss_pred ------CCC-CccchhhHHHHHHHHHH
Q 023991 226 ------VGI-CHQAGSDSLLTASTFRK 245 (274)
Q Consensus 226 ------~~~-~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 566 99999999999999986
No 4
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.26 E-value=3.6e-12 Score=127.35 Aligned_cols=232 Identities=20% Similarity=0.218 Sum_probs=159.0
Q ss_pred cccHHHHHHHHHHHhhcCCeeeEecccccccccCC--CCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCC--C
Q 023991 17 SDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRPV--GSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTC--G 92 (274)
Q Consensus 17 ~~Nf~~e~~~I~~~i~~~~fIAiDtEf~Gl~~~~~--~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~--~ 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 2336789999999999999999999999999987653321 1
Q ss_pred CCCeeEEEeeecccCCCCCCCchhHHHHHHHcCCCccch-----------hhcCCch-----------------------
Q 023991 93 TDKYCVWQFNFREFDVNEDIFANDSIELLKQSGINFTKN-----------NEIGIDA----------------------- 138 (274)
Q Consensus 93 ~~~~~~w~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~-----------~~~GI~~----------------------- 138 (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 112345553222 22224578888999988872211111 0112222
Q ss_pred ---------------------------------------------------------hHHHHHHHHhcc-----------
Q 023991 139 ---------------------------------------------------------MRFGEFMMSSGI----------- 150 (274)
Q Consensus 139 ---------------------------------------------------------~~f~e~l~~Sgl----------- 150 (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 011112222221
Q ss_pred ---cccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhh--hc--ccCcHHHHHHHcC-
Q 023991 151 ---VLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFC--NS--LHGGLNKLAELLE- 222 (274)
Q Consensus 151 ---~~~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~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 22233345678889999999999988 999999999999 99999999999988832 22 4444444432111
Q ss_pred C---------------c----cCCCCccchhhHHHHHHHHHHHHHHhcC
Q 023991 223 V---------------E----RVGICHQAGSDSLLTASTFRKLKENFFS 252 (274)
Q Consensus 223 ~---------------~----r~~~~HqAGsDs~lT~~~F~~l~~~~~~ 252 (274)
. + .-+..|+++++++.++.++.+......+
T Consensus 317 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 365 (564)
T KOG1990|consen 317 KEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILA 365 (564)
T ss_pred cccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhh
Confidence 0 0 1245789999999999999998777663
No 5
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.02 E-value=9.6e-09 Score=92.13 Aligned_cols=173 Identities=21% Similarity=0.242 Sum_probs=117.2
Q ss_pred hcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCC
Q 023991 32 DDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNED 111 (274)
Q Consensus 32 ~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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-ADPG-V 51 (232)
T ss_pred ccCcEEEEEeccCCCCCC---------------------CCeeEEEEEEEEeCCCccc---------cceEEE-ECCC-C
Confidence 456899999999998421 1139999999998766532 234443 3332 2
Q ss_pred CCchhHHHHHHHcCCCccchhhcCCchhH-HHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHH
Q 023991 112 IFANDSIELLKQSGINFTKNNEIGIDAMR-FGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLI 190 (274)
Q Consensus 112 ~~~~~Si~fL~~~GfDFnk~~~~GI~~~~-f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l 190 (274)
.+.+++.+. |||.=..+..+|.+... +.+..-.-.-...++..+|+||..||+++|-+.+...-+|.-
T Consensus 52 ~i~~~a~~I---hGIt~e~l~~~g~~~~~vl~e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~-------- 120 (232)
T PRK07942 52 EIPEEASAV---HGITTEYARAHGRPAAEVLAEIADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSL-------- 120 (232)
T ss_pred CCCHHHHHH---hCCCHHHHHhhCCCHHHHHHHHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCc--------
Confidence 456666665 99999998888998643 332221100011224468999999999999887732122211
Q ss_pred HhhCC-ccccchhhhHhhhcc---cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 191 RIYFP-TVYDIKHLMKFCNSL---HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 191 ~~~FP-~iyDtK~la~~~~~l---~~~L~~la~~L~~~r~~~~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 12 356887777765332 2379999999999855 479999999999999999988765
No 6
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.97 E-value=4.8e-08 Score=81.51 Aligned_cols=164 Identities=22% Similarity=0.229 Sum_probs=113.4
Q ss_pred CeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCc
Q 023991 35 PYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFA 114 (274)
Q Consensus 35 ~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 489999999997432 1349999998877532 24567776 333 23445
Q ss_pred hhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEecc-chhHHHHHHHhC--CCCCCCChHHHHHHHH
Q 023991 115 NDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHS-GYDFGYLLKLLT--CQNLPDTQVEFFNLIR 191 (274)
Q Consensus 115 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g-~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-KG-KILVAGNALNFDLRFLKLEHPRLGIKDPPK--------- 110 (169)
T ss_pred HHHHH---HhCCCHHHHhC-CCCHHHHHHHHHH--Hh-cC-CEEEEeCCHHHhHHHHHHHHHHhCCCCCcC---------
Confidence 55544 47887777654 8887655444432 12 12 25788998 999999988873 3333411
Q ss_pred hhCCccccchhhhHhhh-cccCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 192 IYFPTVYDIKHLMKFCN-SLHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 192 ~~FP~iyDtK~la~~~~-~l~~~L~~la~~L~~~r~~~~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 13667766665542 2356999999999999988889999999999999999987653
No 7
>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=98.77 E-value=2.2e-07 Score=80.70 Aligned_cols=175 Identities=20% Similarity=0.257 Sum_probs=116.5
Q ss_pred hcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecC--CCCCCCCCCCeeEEEeeecccCCC
Q 023991 32 DDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDEN--GNLPTCGTDKYCVWQFNFREFDVN 109 (274)
Q Consensus 32 ~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~--g~~p~~~~~~~~~w~FNF~~F~~~ 109 (274)
+.+.+|++|+|-||+.... + .|||+|...++.+ |.. ..+.+|+++ ++..
T Consensus 3 ~~~~~vv~D~ETTGl~~~~-----d----------------~Iieigav~v~~~~~~~i-------~~~~~f~~l-v~P~ 53 (189)
T cd06134 3 RGFLPVVVDVETGGFNPQT-----D----------------ALLEIAAVTLEMDEQGNL-------YPDETFHFH-ILPF 53 (189)
T ss_pred ccceeEEEEecCCCCCCCC-----C----------------eEEEEEEEEEEECCCCce-------eccceEEEE-EcCC
Confidence 3568999999999996431 1 2999999988753 332 133567766 4332
Q ss_pred -CCCCchhHHHHHHHcCCCccchhhcCCchhH-HHHHHHHh-cccc---cCCcceEEeccchhHHHHHHHhCCCCCCCCh
Q 023991 110 -EDIFANDSIELLKQSGINFTKNNEIGIDAMR-FGEFMMSS-GIVL---SDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQ 183 (274)
Q Consensus 110 -~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~-f~e~l~~S-gl~~---~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~ 183 (274)
...+.+++++. ||+.=+...+.|++... +.+.+-.- .++. .++-.+|++|..||++||-+.+....++
T Consensus 54 ~~~~i~~~~~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~--- 127 (189)
T cd06134 54 EGANLDPAALEF---NGIDPFHPFRFAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIK--- 127 (189)
T ss_pred CCCCCCHHHHhh---cCCCchhhhccccchHHHHHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCC---
Confidence 33566777665 89876666777886653 33322110 1110 1134799999999999998877321111
Q ss_pred HHHHHHHHhhC-C-ccccchhhhHhhhcccCcHHHHHHHcCCccC-CCCccchhhHHHHHHHHHHHHHH
Q 023991 184 VEFFNLIRIYF-P-TVYDIKHLMKFCNSLHGGLNKLAELLEVERV-GICHQAGSDSLLTASTFRKLKEN 249 (274)
Q Consensus 184 ~~F~~~l~~~F-P-~iyDtK~la~~~~~l~~~L~~la~~L~~~r~-~~~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 36899988877632 2379999999999853 56899999999999999999865
No 8
>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=98.72 E-value=4e-07 Score=76.76 Aligned_cols=172 Identities=19% Similarity=0.175 Sum_probs=111.4
Q ss_pred eeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCch
Q 023991 36 YVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFAN 115 (274)
Q Consensus 36 fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 7999999999865421 00 112499999999987664 13456766644433235667
Q ss_pred hHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccC-CcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhC
Q 023991 116 DSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSD-SMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYF 194 (274)
Q Consensus 116 ~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~-~v~wvtf~g~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 67666 999888874 56666532222211 01111 133444 46889887776543111100 01223
Q ss_pred CccccchhhhHhhhcc--cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHH
Q 023991 195 PTVYDIKHLMKFCNSL--HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKL 246 (274)
Q Consensus 195 P~iyDtK~la~~~~~l--~~~L~~la~~L~~~r~~~~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 5788998888776432 568999999999998889999999999999999987
No 9
>PRK05168 ribonuclease T; Provisional
Probab=98.72 E-value=6.5e-07 Score=79.14 Aligned_cols=185 Identities=15% Similarity=0.185 Sum_probs=123.2
Q ss_pred HHHHHHhhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeec--CCCCCCCCCCCeeEEEee
Q 023991 25 DLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDE--NGNLPTCGTDKYCVWQFN 102 (274)
Q Consensus 25 ~~I~~~i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~--~g~~p~~~~~~~~~w~FN 102 (274)
.-|..-++...||++|+|-||+.... + .|||+|....+. +|... ....|.
T Consensus 8 ~~~~~~~~~~~~vv~D~ETTGl~~~~-----d----------------~IieIgaV~v~~d~~g~i~-------~~~~f~ 59 (211)
T PRK05168 8 NPLKDRFRGFLPVVIDVETAGFNAKT-----D----------------ALLEIAAVTLKMDEQGWLY-------PDETLH 59 (211)
T ss_pred chHHHHhcCCceEEEEeeCCCCCCCC-----C----------------EEEEEeEEEEEecCCCcEe-------ccceEE
Confidence 45777889999999999999986431 1 399999888764 34321 234566
Q ss_pred ecccCCC-CCCCchhHHHHHHHcCCCccchhhcCCchhH-HHHHHHHhc-ccc---cCCcceEEeccchhHHHHHHHhCC
Q 023991 103 FREFDVN-EDIFANDSIELLKQSGINFTKNNEIGIDAMR-FGEFMMSSG-IVL---SDSMHWVTFHSGYDFGYLLKLLTC 176 (274)
Q Consensus 103 F~~F~~~-~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~-f~e~l~~Sg-l~~---~~~v~wvtf~g~yD~~yL~k~l~~ 176 (274)
.+ .+.. ...+.+++++. +|+.=+...+.|++... +.+.+-.-+ .+. .++..+|++|-.||++||-+.+.-
T Consensus 60 ~l-v~P~~~~~i~~~~~~i---hGIt~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r 135 (211)
T PRK05168 60 FH-VEPFEGANLEPEALAF---NGIDPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAER 135 (211)
T ss_pred EE-ECCCCCCCCCHHHHhh---cCCCchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHH
Confidence 66 4332 33566777665 88865555677887643 333222111 110 124579999999999999887631
Q ss_pred CCCCCChHHHHHHHHhhCC-ccccchhhhHhhhcccCcHHHHHHHcCCccC-CCCccchhhHHHHHHHHHHHHHHhc
Q 023991 177 QNLPDTQVEFFNLIRIYFP-TVYDIKHLMKFCNSLHGGLNKLAELLEVERV-GICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 177 ~~LP~~~~~F~~~l~~~FP-~iyDtK~la~~~~~l~~~L~~la~~L~~~r~-~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
..+.. ..+.| .++||.-+++..... ..|..+++.+|++.. ...|.|-+|++.|+++|.+|.+.+.
T Consensus 136 ~~~~~---------~~~~~~~~iDt~~lar~~~~~-~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 136 AGLKR---------NPFHPFSTFDTATLSGLALGQ-TVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred hCCCC---------CCCCCCcEeeHHHHHHHHcCC-CCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 11110 01123 478999888765322 379999999999754 3689999999999999999988764
No 10
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.68 E-value=8.5e-07 Score=77.57 Aligned_cols=170 Identities=14% Similarity=0.205 Sum_probs=106.5
Q ss_pred HHHHHHhhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeec
Q 023991 25 DLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFR 104 (274)
Q Consensus 25 ~~I~~~i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~ 104 (274)
..+.+.....+||++|+|.||+... .-.|||+|...++.+.. .....|..+
T Consensus 20 ~~~~~~~~~~~~vviD~ETTGl~~~---------------------~d~IieIgaV~~~~~~~--------~~~~~f~~~ 70 (202)
T PRK09145 20 AFLFEPPPPDEWVALDCETTGLDPR---------------------RAEIVSIAAVKIRGNRI--------LTSERLELL 70 (202)
T ss_pred HHHhcCCCCCCEEEEEeECCCCCCC---------------------CCceEEEEEEEEECCEE--------eecCceEEE
Confidence 3344444557999999999998421 11499999988874321 122345555
Q ss_pred ccCCCCCCCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHh---CCCCCCC
Q 023991 105 EFDVNEDIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLL---TCQNLPD 181 (274)
Q Consensus 105 ~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l---~~~~LP~ 181 (274)
.+.. ...++.+.+. ||+.-..+ ++|.+..+.-+.+.. .+ .+-.||+++..||..+|.+.+ .+.++|.
T Consensus 71 -i~p~-~~i~~~~~~i---hGIt~~~l-~~~~~~~~vl~~~~~--~i--~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~ 140 (202)
T PRK09145 71 -VRPP-QSLSAESIKI---HRLRHQDL-EDGLSEEEALRQLLA--FI--GNRPLVGYYLEFDVAMLNRYVRPLLGIPLPN 140 (202)
T ss_pred -ECCC-CCCCHhHhhh---cCcCHHHH-hcCCCHHHHHHHHHH--HH--cCCeEEEeCHHHHHHHHHHHHHHhcCCCCCC
Confidence 3333 2345555554 67665554 456665443323221 11 123589999899999987765 2455664
Q ss_pred ChHHHHHHHHhhCCccccchhhhHhh--hc-----ccCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHH
Q 023991 182 TQVEFFNLIRIYFPTVYDIKHLMKFC--NS-----LHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKE 248 (274)
Q Consensus 182 ~~~~F~~~l~~~FP~iyDtK~la~~~--~~-----l~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~ 248 (274)
. .+|+.-+.... .. .+-+|+.+++.+|++.. ..|.|-+||+.|+++|.+|.+
T Consensus 141 ~--------------~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 141 P--------------LIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVL-GRHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred C--------------eeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHh
Confidence 3 34554333211 11 13489999999999875 469999999999999999865
No 11
>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=98.68 E-value=6.7e-07 Score=74.02 Aligned_cols=150 Identities=21% Similarity=0.173 Sum_probs=99.6
Q ss_pred eeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCch
Q 023991 36 YVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFAN 115 (274)
Q Consensus 36 fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~d~~~~ 115 (274)
||++|+|.+|.. + -.|||+|...++ +|+ ..-+|+.+ ..... ...+
T Consensus 1 ~v~~D~Ettg~~--~---------------------~~ii~ig~v~~~-~~~---------~~~~~~~~-i~p~~-~~~~ 45 (156)
T cd06130 1 FVAIDFETANAD--R---------------------ASACSIGLVKVR-DGQ---------IVDTFYTL-IRPPT-RFDP 45 (156)
T ss_pred CEEEEEeCCCCC--C---------------------CceEEEEEEEEE-CCE---------EEEEEEEE-eCcCC-CCCh
Confidence 799999999842 1 128999998887 332 34567776 44333 4555
Q ss_pred hHHHHHHHcCCCccchhhcCCchhH-HHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHHHHHh
Q 023991 116 DSIELLKQSGINFTKNNEIGIDAMR-FGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFNLIRI 192 (274)
Q Consensus 116 ~Si~fL~~~GfDFnk~~~~GI~~~~-f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~~~~F~~~l~~ 192 (274)
++.++ +|+.-..+.. +.+..+ +.+++-. + + +..||+++..||+++|-+.+- |.+.|.
T Consensus 46 ~~~~i---~GIt~e~l~~-~~~~~~v~~~l~~~---l-~-~~~lv~hn~~fD~~~l~~~~~~~g~~~~~----------- 105 (156)
T cd06130 46 FNIAI---HGITPEDVAD-APTFPEVWPEIKPF---L-G-GSLVVAHNASFDRSVLRAALEAYGLPPPP----------- 105 (156)
T ss_pred hhccc---cCcCHHHHhc-CCCHHHHHHHHHHH---h-C-CCEEEEeChHHhHHHHHHHHHHcCCCCCC-----------
Confidence 55444 8887777653 444332 2222211 1 1 247899999999999987773 333331
Q ss_pred hCCccccchhhhHhh-hcc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHH
Q 023991 193 YFPTVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFR 244 (274)
Q Consensus 193 ~FP~iyDtK~la~~~-~~l-~~~L~~la~~L~~~r~~~~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 467887666664 222 3589999999999876 8999999999999885
No 12
>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=98.67 E-value=7.4e-07 Score=74.99 Aligned_cols=163 Identities=17% Similarity=0.198 Sum_probs=104.0
Q ss_pred eeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCch
Q 023991 36 YVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFAN 115 (274)
Q Consensus 36 fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~d~~~~ 115 (274)
||++|+|-||+... +.-.|||+|....+. +.. ...+|+.+ .+... ..++
T Consensus 1 ~v~~D~ETTGl~~~--------------------~~~~iieig~v~v~~-~~~--------~~~~~~~~-v~P~~-~i~~ 49 (167)
T cd06131 1 QIVLDTETTGLDPR--------------------EGHRIIEIGCVELIN-RRL--------TGNTFHVY-INPER-DIPE 49 (167)
T ss_pred CEEEEeeCCCCCCC--------------------CCCeEEEEEEEEEEC-CcE--------eccEEEEE-ECCCC-CCCH
Confidence 69999999998421 112599999987653 221 22456665 33332 3666
Q ss_pred hHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCC
Q 023991 116 DSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFP 195 (274)
Q Consensus 116 ~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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---HGITDEFLAD-KPKFAEIADEFLD--FI-RG-AELVIHNASFDVGFLNAELSLLGLGKKI---------IDF 112 (167)
T ss_pred HHHHH---hCCCHHHHhc-CCCHHHHHHHHHH--HH-CC-CeEEEeChHHhHHHHHHHHHHhCCCccc---------ccC
Confidence 66654 6776655444 3333332223221 11 22 3589999999999887776421121110 012
Q ss_pred -ccccchhhhHhhh-cccCcHHHHHHHcCCccCC-CCccchhhHHHHHHHHHHH
Q 023991 196 -TVYDIKHLMKFCN-SLHGGLNKLAELLEVERVG-ICHQAGSDSLLTASTFRKL 246 (274)
Q Consensus 196 -~iyDtK~la~~~~-~l~~~L~~la~~L~~~r~~-~~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 4678877776542 3456899999999999864 5899999999999999987
No 13
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=98.62 E-value=1.2e-06 Score=79.15 Aligned_cols=169 Identities=14% Similarity=0.213 Sum_probs=110.5
Q ss_pred cCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCC
Q 023991 33 DYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDI 112 (274)
Q Consensus 33 ~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 22 122456666 44433 4
Q ss_pred CchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHHHH
Q 023991 113 FANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFNLI 190 (274)
Q Consensus 113 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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 6766555443 3333322222221 12 2235899999999999987662 34455321
Q ss_pred HhhCCccccchhhhHhh-hcccCcHHHHHHHcCCccCC-CCccchhhHHHHHHHHHHHHHH
Q 023991 191 RIYFPTVYDIKHLMKFC-NSLHGGLNKLAELLEVERVG-ICHQAGSDSLLTASTFRKLKEN 249 (274)
Q Consensus 191 ~~~FP~iyDtK~la~~~-~~l~~~L~~la~~L~~~r~~-~~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 134578988888775 34456999999999998754 4799999999999999999764
No 14
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=98.57 E-value=1.8e-06 Score=75.95 Aligned_cols=173 Identities=16% Similarity=0.062 Sum_probs=104.1
Q ss_pred cCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCC
Q 023991 33 DYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDI 112 (274)
Q Consensus 33 ~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~d~ 112 (274)
..+||++|+|.||+..+.. +.... -.|||+|....+. |+. +-.|+-+.-|.....
T Consensus 3 ~~~~vvlD~EtTg~~~~~~-~~~~~--------------~eIIeIGaV~v~~-~~i---------~~~f~~lV~P~~~~~ 57 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKK-PKGFF--------------PEIIEVGLVSVVG-CEV---------EDTFSSYVKPKTFPS 57 (207)
T ss_pred cceEEEEEeecCCcCCCCC-CCCCC--------------CceEEEeEEEEec-CcC---------hhhhcceECCCccCc
Confidence 3579999999999754310 00000 1399999988763 332 223444422211113
Q ss_pred CchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHHHH
Q 023991 113 FANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFNLI 190 (274)
Q Consensus 113 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~~~~F~~~l 190 (274)
.++.+.++ +|+.=+.+ .+|.+..+..+.+.. .+-+... ++..|+.+|+.+|-+-+. +-+.|.
T Consensus 58 i~~~~~~l---tGIt~~~l-~~ap~~~evl~~f~~--~~~~~~~-~iv~~~~fD~~fL~~~~~~~~~~~~~--------- 121 (207)
T PRK07748 58 LTERCKSF---LGITQEDV-DKGISFEELVEKLAE--YDKRCKP-TIVTWGNMDMKVLKHNCEKAGVPFPF--------- 121 (207)
T ss_pred cChhhhhh---cCcCHHHH-ccCCCHHHHHHHHHH--HhCcCCe-EEEEECHHHHHHHHHHHHHcCCCCcc---------
Confidence 44555544 77765555 457776544333322 1111122 444568899999988773 333331
Q ss_pred HhhCCccccchhhhHhhhc--ccCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHH
Q 023991 191 RIYFPTVYDIKHLMKFCNS--LHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKEN 249 (274)
Q Consensus 191 ~~~FP~iyDtK~la~~~~~--l~~~L~~la~~L~~~r~~~~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 1234455444333211 1248999999999998888999999999999999998876
No 15
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=98.50 E-value=3.6e-06 Score=78.59 Aligned_cols=160 Identities=18% Similarity=0.194 Sum_probs=104.2
Q ss_pred CeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCc
Q 023991 35 PYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFA 114 (274)
Q Consensus 35 ~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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----------------------NSPCSIGIVVVK-DGE---------IVEKVHYL-IKPKEMRFM 47 (309)
T ss_pred cEEEEEEeCCCCC-C----------------------CceEEEEEEEEE-CCE---------EEEEEEEE-ECCCCCCCC
Confidence 6999999998631 0 127999999886 333 23556665 444333455
Q ss_pred hhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHHHHHh
Q 023991 115 NDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFNLIRI 192 (274)
Q Consensus 115 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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--NNNLVIAHNASFDISVLRKTLELYNIPMPS----------- 108 (309)
T ss_pred hhhee---ccCcCHHHHhCCC-CHHHHHHHHHH--Hh--CCCEEEEECcHHHHHHHHHHHHHhCCCCCC-----------
Confidence 55553 3777766665532 33221111111 11 1236899999999999987763 334332
Q ss_pred hCCccccchhhhHhh-hcc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 193 YFPTVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 193 ~FP~iyDtK~la~~~-~~l-~~~L~~la~~L~~~r~~~~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 --FEYICTMKLAKNFYSNIDNARLNTVNNFLGYEF--KHHDALADAMACSNILLNISKELN 165 (309)
T ss_pred --CCEEEHHHHHHHHcCCCCcCCHHHHHHHcCCCC--cccCCHHHHHHHHHHHHHHHHHhc
Confidence 1356777666654 333 358999999999973 589999999999999999987654
No 16
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=98.48 E-value=4e-06 Score=78.58 Aligned_cols=161 Identities=19% Similarity=0.165 Sum_probs=106.5
Q ss_pred CCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCC
Q 023991 34 YPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIF 113 (274)
Q Consensus 34 ~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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-NHE---------LVDQFVSY-VNPERP-I 54 (313)
T ss_pred CCEEEEEEECCCCCCC---------------------CCeEEEEEEEEEE-CCE---------EEEEEEEE-ECcCCC-C
Confidence 3899999999998421 1259999998886 332 45677776 443332 3
Q ss_pred chhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHHHHH
Q 023991 114 ANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFNLIR 191 (274)
Q Consensus 114 ~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~~~~F~~~l~ 191 (274)
.+.+. +-+|+.-..+ .++.+..+-.+.+.. ++ .+ -.+|++++.||..+|.+.+. |.+.|.
T Consensus 55 ~~~a~---~ihGIT~e~l-~~~~~~~evl~~f~~--fl-~~-~~lVaHNa~FD~~fL~~~~~~~gl~~~~---------- 116 (313)
T PRK06807 55 PDRIT---SLTGITNYRV-SDAPTIEEVLPLFLA--FL-HT-NVIVAHNASFDMRFLKSNVNMLGLPEPK---------- 116 (313)
T ss_pred CHhhh---ccCCCCHHHH-hCCCCHHHHHHHHHH--HH-cC-CeEEEEcHHHHHHHHHHHHHHcCCCCCC----------
Confidence 44443 3377775554 345444332222222 11 12 25799999999999998873 332221
Q ss_pred hhCCccccchhhhHhhh-ccc-CcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHh
Q 023991 192 IYFPTVYDIKHLMKFCN-SLH-GGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENF 250 (274)
Q Consensus 192 ~~FP~iyDtK~la~~~~-~l~-~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~~ 250 (274)
..++||-.+++..- .+. -+|+.+++.+|++. .+|.|=.|++.|+++|.+|...-
T Consensus 117 ---~~~iDtl~la~~~~~~~~~~kL~~L~~~lgi~~--~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 117 ---NKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRL--SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred ---CCEeeHHHHHHHHhCCCCCCCHHHHHHHcCCCC--CCcChHHHHHHHHHHHHHHHHhh
Confidence 23667777766542 232 37999999999997 78999999999999999987765
No 17
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.47 E-value=7.4e-06 Score=72.60 Aligned_cols=168 Identities=15% Similarity=0.172 Sum_probs=108.1
Q ss_pred hhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCC
Q 023991 31 VDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNE 110 (274)
Q Consensus 31 i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~ 110 (274)
+....||++|+|-||+... . .|||+|.......+. ...+|..+..| .
T Consensus 4 l~~~~fvv~D~ETTGl~~~--------------------~--~IIeIgav~v~~~~~---------~~~~f~~li~P-~- 50 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAG--------------------H--DIIEIGAVEIINRRI---------TGNKFHTYIKP-D- 50 (217)
T ss_pred EEecCEEEEEecCCCCCCC--------------------C--CEEEEEEEEEECCCE---------eeeEEEEEECc-C-
Confidence 4567999999999998421 0 299999998653322 23456555333 2
Q ss_pred CCCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHH
Q 023991 111 DIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFN 188 (274)
Q Consensus 111 d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~~~~F~~ 188 (274)
...++.++.. +|+.-..+... -+..+-.+.+.. .+ ++-.+|+++..||..+|-+.+. +.+.|.
T Consensus 51 ~~i~~~a~~i---hGIt~e~l~~~-p~~~ev~~~~~~--~~--~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~------- 115 (217)
T TIGR00573 51 RPIDPDAIKI---HGITDDMLKDK-PDFKEIAEDFAD--YI--RGAELVIHNASFDVGFLNYEFSKLYKVEPK------- 115 (217)
T ss_pred CCCCHHHHhh---cCCCHHHHcCC-CCHHHHHHHHHH--Hh--CCCEEEEeccHHHHHHHHHHHHHhcCCCCC-------
Confidence 3456666544 78777776543 333322222221 11 2236899999999999987763 111111
Q ss_pred HHHhhCCccccchhhhHhhh-cc---cCcHHHHHHHcCCccC-CCCccchhhHHHHHHHHHHHHHHhc
Q 023991 189 LIRIYFPTVYDIKHLMKFCN-SL---HGGLNKLAELLEVERV-GICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 189 ~l~~~FP~iyDtK~la~~~~-~l---~~~L~~la~~L~~~r~-~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
...+.||.-+++... .+ +.+|+.+++.+|++.. ..+|.|-+|+.+|+.+|.+|.+..-
T Consensus 116 -----~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~~~H~Al~DA~~ta~l~~~l~~~~~ 178 (217)
T TIGR00573 116 -----TNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQT 178 (217)
T ss_pred -----ccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHHhcch
Confidence 024556665555542 22 3479999999999864 3689999999999999999988754
No 18
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=98.46 E-value=4.3e-06 Score=75.87 Aligned_cols=170 Identities=16% Similarity=0.183 Sum_probs=108.6
Q ss_pred HhhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCC
Q 023991 30 IVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVN 109 (274)
Q Consensus 30 ~i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~ 109 (274)
+++...||.+|||-||+.... =.|||+|+..++.++ ...+|+.+ .+..
T Consensus 3 ~l~~~~~v~~D~ETTGl~~~~---------------------d~IIEIa~v~v~~~~----------~~~~~~~l-i~P~ 50 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDVKK---------------------DRIIEFAAIRFTFDE----------VIDSVEFL-INPE 50 (250)
T ss_pred cccCCcEEEEEEeCCCCCCCC---------------------CeEEEEEEEEEECCe----------EEEEEEEE-ECcC
Confidence 467789999999999984221 139999998886432 34566665 4433
Q ss_pred CCCCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHH
Q 023991 110 EDIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFF 187 (274)
Q Consensus 110 ~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~~~~F~ 187 (274)
. ...+++.. -||+--..+.. .-+..+..+.+.. .+ .+.-.+|+++..||..+|.+.+. +.+.|..
T Consensus 51 ~-~I~~~a~~---ihgIt~e~v~~-~p~~~ev~~~~~~--fl-~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~----- 117 (250)
T PRK06310 51 R-VVSAESQR---IHHISDAMLRD-KPKIAEVFPQIKG--FF-KEGDYIVGHSVGFDLQVLSQESERIGETFLSK----- 117 (250)
T ss_pred C-CCCHhhhh---ccCcCHHHHhC-CCCHHHHHHHHHH--Hh-CCCCEEEEECHHHHHHHHHHHHHHcCCCcccc-----
Confidence 2 34444443 25554333322 2222222222221 11 22246899988999999988763 3333211
Q ss_pred HHHHhhCCccccchhhhHhhhcc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 188 NLIRIYFPTVYDIKHLMKFCNSL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 188 ~~l~~~FP~iyDtK~la~~~~~l-~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
--.++||..+++..... +.+|+.+++.+|++..+ +|.|-+|++.|+.+|.+|.+.+-
T Consensus 118 ------~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~~~-aH~Al~Da~at~~vl~~l~~~~~ 175 (250)
T PRK06310 118 ------HYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDG-NHRAMKDVEINIKVFKHLCKRFR 175 (250)
T ss_pred ------CCcEEehHHHHHhcccCCCCCHHHHHHHCCCCCCC-CcChHHHHHHHHHHHHHHHHhcc
Confidence 01477888888765433 35899999999997554 79999999999999999987653
No 19
>PRK07740 hypothetical protein; Provisional
Probab=98.44 E-value=7.7e-06 Score=73.97 Aligned_cols=168 Identities=18% Similarity=0.204 Sum_probs=105.9
Q ss_pred hcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCC
Q 023991 32 DDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNED 111 (274)
Q Consensus 32 ~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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-VKPK-R 105 (244)
T ss_pred cCCCEEEEEEeCCCCCCCC--------------------CCeEEEEEEEEEEC-CEE--------EEEEEEEE-eCcC-C
Confidence 4458999999999975210 02489999888762 221 13445444 2222 2
Q ss_pred CCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCC-CCCCChHHHHHHH
Q 023991 112 IFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQ-NLPDTQVEFFNLI 190 (274)
Q Consensus 112 ~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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---TGITAEDV-AFAPPLAEVLHRFYA--FI--GAGVLVAHHAGHDKAFLRHALWRTYRQP---------- 167 (244)
T ss_pred CCChhheec---cCCCHHHH-hCCCCHHHHHHHHHH--Hh--CCCEEEEeCHHHHHHHHHHHHHHhcCCC----------
Confidence 344444333 66655443 345554432222221 11 123799999999999988766311 111
Q ss_pred HhhCCccccchhhhHhhhcc--cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 191 RIYFPTVYDIKHLMKFCNSL--HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 191 ~~~FP~iyDtK~la~~~~~l--~~~L~~la~~L~~~r~~~~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 --FTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRR-HHALGDALMTAKLWAILLVEAQ 227 (244)
T ss_pred --cCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCCCCC-CCcHHHHHHHHHHHHHHHHHHH
Confidence 113678888888765322 358999999999987654 9999999999999999877654
No 20
>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=98.43 E-value=9.4e-06 Score=72.56 Aligned_cols=168 Identities=15% Similarity=0.166 Sum_probs=106.4
Q ss_pred CeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCc
Q 023991 35 PYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFA 114 (274)
Q Consensus 35 ~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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--------LTGDNFHVY-VNPER-DMP 49 (225)
T ss_pred CEEEEEeeCCCcCCCC--------------------CCeEEEEEEEEEEC-Cc--------EecceEEEE-ECcCC-CCC
Confidence 4899999999985321 02499999875542 21 122356666 44333 345
Q ss_pred hhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHHHHHh
Q 023991 115 NDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFNLIRI 192 (274)
Q Consensus 115 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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 6776655543 3343322222221 11 2236899999999999987762 3111110 0
Q ss_pred hCCccccchhhhHhh-hcccCcHHHHHHHcCCccCC-CCccchhhHHHHHHHHHHHHHHh
Q 023991 193 YFPTVYDIKHLMKFC-NSLHGGLNKLAELLEVERVG-ICHQAGSDSLLTASTFRKLKENF 250 (274)
Q Consensus 193 ~FP~iyDtK~la~~~-~~l~~~L~~la~~L~~~r~~-~~HqAGsDs~lT~~~F~~l~~~~ 250 (274)
.+-.++||--|++.. +..+.+|+.|++.+|++..+ ..|-|-.||.+|+.+|.+|...-
T Consensus 113 ~~~~~iDTl~lar~~~p~~~~~L~~L~~~~gi~~~~r~~H~Al~DA~~~a~v~~~l~~~~ 172 (225)
T TIGR01406 113 EFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAHLLAEVYLALTGGQ 172 (225)
T ss_pred cCCCEEEHHHHHHHHcCCCCCCHHHHHHhcCCCCCCCCCcCHHHHHHHHHHHHHHHHcCC
Confidence 112578888887764 33456999999999998765 47999999999999999997743
No 21
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=98.41 E-value=6e-06 Score=72.38 Aligned_cols=160 Identities=20% Similarity=0.220 Sum_probs=91.4
Q ss_pred CeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCc
Q 023991 35 PYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFA 114 (274)
Q Consensus 35 ~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~d~~~ 114 (274)
.||++|+|.||+. + .+ .|||+|..-.+. |. .+..|..+.-|.. ...
T Consensus 6 ~~vvlD~EtTGl~--~----~~----------------eIIeIgaV~v~~-g~---------~~~~f~~lv~P~~--~i~ 51 (195)
T PRK07247 6 TYIAFDLEFNTVN--G----VS----------------HIIQVSAVKYDD-HK---------EVDSFDSYVYTDV--PLQ 51 (195)
T ss_pred eEEEEEeeCCCCC--C----CC----------------eEEEEEEEEEEC-CE---------EEEEEEEEECCCC--CCC
Confidence 7999999999973 1 11 499999988873 32 2455666533321 222
Q ss_pred hhHHHHHHHcCCCccchhhcCCchhHHHHHHHHh-cccccCCcceEEeccc-hhHHHHHHHhCCCCCCCChHHHHHHHHh
Q 023991 115 NDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSS-GIVLSDSMHWVTFHSG-YDFGYLLKLLTCQNLPDTQVEFFNLIRI 192 (274)
Q Consensus 115 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~S-gl~~~~~v~wvtf~g~-yD~~yL~k~l~~~~LP~~~~~F~~~l~~ 192 (274)
+.+... +|+.=..+. ++.+ |.+.+..- ..+ . +-.||+++.. +|+.+|-+. |.+++....
T Consensus 52 ~~~~~l---hGIt~~~v~-~ap~---~~evl~~f~~f~-~-~~~lVaHNa~~fD~~fL~~~--g~~~~~~~~-------- 112 (195)
T PRK07247 52 SFINGL---TGITADKIA-DAPK---VEEVLAAFKEFV-G-ELPLIGYNAQKSDLPILAEN--GLDLSDQYQ-------- 112 (195)
T ss_pred ccceec---CCCCHHHHh-CCCC---HHHHHHHHHHHH-C-CCeEEEEeCcHhHHHHHHHc--CCCcCCCce--------
Confidence 222211 444433332 2322 22222211 111 2 3358988875 899998653 444432110
Q ss_pred hCCccccchhhhHh--hhcc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 193 YFPTVYDIKHLMKF--CNSL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 193 ~FP~iyDtK~la~~--~~~l-~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
. ..||+.+..+. ..++ +-.|+.||+.+|++. ..|.|-+|++.|+.+|.+|.+.--
T Consensus 113 -i-dt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~--~~HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 113 -V-DLYDEAFERRSSDLNGIANLKLQTVADFLGIKG--RGHNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred -e-ehHHHHHHhhccccCCCCCCCHHHHHHhcCCCC--CCcCCHHHHHHHHHHHHHHHhhcc
Confidence 0 12333322111 1122 247999999999984 479999999999999999877633
No 22
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.40 E-value=1e-05 Score=75.74 Aligned_cols=162 Identities=18% Similarity=0.183 Sum_probs=103.0
Q ss_pred cCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCC
Q 023991 33 DYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDI 112 (274)
Q Consensus 33 ~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 2334433 332221
Q ss_pred CchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHh-cccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHHH
Q 023991 113 FANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSS-GIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFNL 189 (274)
Q Consensus 113 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~S-gl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~~~~F~~~ 189 (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-QPQ---FADIAGEVAELL--RGRTLVAHNVAFDYSFLAAEAERAGAELPV-------- 122 (313)
T ss_pred --CCCeec---CCCCHHHHhC-CCC---HHHHHHHHHHHc--CCCEEEEeCHHHHHHHHHHHHHHcCCCCCC--------
Confidence 222211 4443333221 111 33222110 111 2336899999999999988773 444442
Q ss_pred HHhhCCccccchhhhHhhh-cc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 190 IRIYFPTVYDIKHLMKFCN-SL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 190 l~~~FP~iyDtK~la~~~~-~l-~~~L~~la~~L~~~r~~~~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 13678888887652 22 337999999999985 4679999999999999999877765
No 23
>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=98.36 E-value=1.6e-05 Score=69.80 Aligned_cols=177 Identities=17% Similarity=0.213 Sum_probs=114.8
Q ss_pred hcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecC--CCCCCCCCCCeeEEEeeecccCCC
Q 023991 32 DDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDEN--GNLPTCGTDKYCVWQFNFREFDVN 109 (274)
Q Consensus 32 ~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~--g~~p~~~~~~~~~w~FNF~~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 4578999999999986321 13999998887643 321 12345666633322
Q ss_pred CCCCchhHHHHHHHcCCCccchhhcCCchhH-HHHHHHHh-----cccccCCcceEEeccchhHHHHHHHhCCCCCCCCh
Q 023991 110 EDIFANDSIELLKQSGINFTKNNEIGIDAMR-FGEFMMSS-----GIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQ 183 (274)
Q Consensus 110 ~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~-f~e~l~~S-----gl~~~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~ 183 (274)
.-...++++.. ||+.=++..+++.+... +.+.+-.- +..+ .+-..|++|-.||+.||-+.+-...++.
T Consensus 58 ~~~i~~~a~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~lVaHNa~FD~~fL~~~~~r~~~~~-- 131 (200)
T TIGR01298 58 GANIQPEALEF---TGIDLDHPLRGAVSEYEALHEIFKVVRKAMKASGC-QRAILVGHNANFDLGFLNAAVERTSLKR-- 131 (200)
T ss_pred CCCCCHHHHHc---cCCChhhhhhcCcchHHHHHHHHHHHHHHHHhccc-CCCEEEEECchhhHHHHHHHHHHhCCCC--
Confidence 34567777655 88887766677776543 33332210 1111 2335899999999999988763111110
Q ss_pred HHHHHHHHhhC-C-ccccchhhhHhhhcccCcHHHHHHHcCCccC-CCCccchhhHHHHHHHHHHHHHHhc
Q 023991 184 VEFFNLIRIYF-P-TVYDIKHLMKFCNSLHGGLNKLAELLEVERV-GICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 184 ~~F~~~l~~~F-P-~iyDtK~la~~~~~l~~~L~~la~~L~~~r~-~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
..+ | ..+||--+++.... ..+|..+++.+|++.. ...|.|-+|++.|+++|.+|.+.+.
T Consensus 132 --------~~~~~~~~lDTl~lar~~~~-~~~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 132 --------NPFHPFSTFDTATLAGLAYG-QTVLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred --------CCCCCCcEEEHHHHHHHHcC-cccHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 001 1 36788777765421 2369999999999853 4789999999999999999988764
No 24
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=98.35 E-value=2.6e-05 Score=70.39 Aligned_cols=169 Identities=17% Similarity=0.177 Sum_probs=106.9
Q ss_pred HhhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCC
Q 023991 30 IVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVN 109 (274)
Q Consensus 30 ~i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~ 109 (274)
-+.+.+|+++|+|-||+..+ .=.|||+|....+.+ .. .....|... .+..
T Consensus 43 ~~~~~~~vviD~ETTGl~p~---------------------~d~IieIg~v~v~~~-~i-------~~~~~~~~l-i~P~ 92 (239)
T PRK09146 43 PLSEVPFVALDFETTGLDAE---------------------QDAIVSIGLVPFTLQ-RI-------RCRQARHWV-VKPR 92 (239)
T ss_pred CcccCCEEEEEeECCCCCCC---------------------CCcEEEEEEEEEECC-eE-------eecceEEEE-ECCC
Confidence 35567999999999998532 114999999888743 21 122344443 3332
Q ss_pred CCCCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC---CCCCCCChHHH
Q 023991 110 EDIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT---CQNLPDTQVEF 186 (274)
Q Consensus 110 ~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~---~~~LP~~~~~F 186 (274)
. .+.+++... |||.-..+ ..|-+..+-.+.+... + .+-.+|++|..||.++|-+.+. +.++|.
T Consensus 93 ~-~i~~~~~~I---hGIt~e~l-~~ap~~~evl~~l~~~--~--~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~----- 158 (239)
T PRK09146 93 R-PLEEESVVI---HGITHSEL-QDAPDLERILDELLEA--L--AGKVVVVHYRRIERDFLDQALRNRIGEGIEF----- 158 (239)
T ss_pred C-CCChhhhhh---cCCCHHHH-hCCCCHHHHHHHHHHH--h--CCCEEEEECHHHHHHHHHHHHHHhcCCCCCC-----
Confidence 2 345555444 77665554 3354443322222221 1 2236899999999999988763 233332
Q ss_pred HHHHHhhCCccccchhhhHhhh---------cc------cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 187 FNLIRIYFPTVYDIKHLMKFCN---------SL------HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 187 ~~~l~~~FP~iyDtK~la~~~~---------~l------~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
.++||-.+++..- .+ .-.|+.+++.+|++. ..+|.|-+|++.|+++|.++.+.++
T Consensus 159 ---------~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl~~-~~~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 159 ---------PVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGLPA-YSPHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred ---------ceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHHc
Confidence 2456666655531 01 126999999999985 4569999999999999999988876
Q ss_pred C
Q 023991 252 S 252 (274)
Q Consensus 252 ~ 252 (274)
.
T Consensus 229 ~ 229 (239)
T PRK09146 229 S 229 (239)
T ss_pred C
Confidence 4
No 25
>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=98.30 E-value=2.2e-05 Score=67.43 Aligned_cols=168 Identities=16% Similarity=0.148 Sum_probs=101.6
Q ss_pred eeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCC---CCCCeeEEEeeecccCCCCCC
Q 023991 36 YVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTC---GTDKYCVWQFNFREFDVNEDI 112 (274)
Q Consensus 36 fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~---~~~~~~~w~FNF~~F~~~~d~ 112 (274)
||++|+|-||+.... . =.|||+|....+.++..... ....-.+..|+.. .+..+ .
T Consensus 1 ~vv~D~ETTGl~~~~----~----------------d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~l-v~P~~-~ 58 (177)
T cd06136 1 FVFLDLETTGLPKHN----R----------------PEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLC-FNPGR-A 58 (177)
T ss_pred CeEEeeecCCCCCCC----C----------------CceEEEEEEEEecccccccccccccccceeeeeeEE-eCCCC-c
Confidence 799999999995210 0 13999999988865432100 0001134567766 44432 4
Q ss_pred CchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHh-cccccCCcceEEecc-chhHHHHHHHhC--CCCCCCChHHHHH
Q 023991 113 FANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSS-GIVLSDSMHWVTFHS-GYDFGYLLKLLT--CQNLPDTQVEFFN 188 (274)
Q Consensus 113 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~S-gl~~~~~v~wvtf~g-~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---TGLSNDLLEHKAPFDSDTANLIKLFLRR-QPKPICLVAHNGNRFDFPILRSELERLGTKLPDD------ 128 (177)
T ss_pred CChhHHHH---hCcCHHHHhcCCCccHHHHHHHHHHHHh-cCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCC------
Confidence 45566554 8888777777663222222222110 11 122356899998 799999977763 3333311
Q ss_pred HHHhhCCccccchhhhHhhhcccCcHHHHHHH-cCCccCCCCccchhhHHHHHHHHHH
Q 023991 189 LIRIYFPTVYDIKHLMKFCNSLHGGLNKLAEL-LEVERVGICHQAGSDSLLTASTFRK 245 (274)
Q Consensus 189 ~l~~~FP~iyDtK~la~~~~~l~~~L~~la~~-L~~~r~~~~HqAGsDs~lT~~~F~~ 245 (274)
+...||-.+++.... +|+.|++. +|++. ..+|.|-+|+..|++||++
T Consensus 129 ------~~~iDtl~l~r~~~~---~L~~l~~~~~~~~~-~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 129 ------ILCVDSLPAFRELDQ---SLGSLYKRLFGQEP-KNSHTAEGDVLALLKCALH 176 (177)
T ss_pred ------CEEEEeHHHHhhhHh---hHHHHHHHHhCCCc-ccccchHHHHHHHHHHHhh
Confidence 123466555554422 89999885 78774 4569999999999999975
No 26
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=98.25 E-value=1.1e-05 Score=65.67 Aligned_cols=155 Identities=18% Similarity=0.133 Sum_probs=98.8
Q ss_pred eeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCchh
Q 023991 37 VAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFAND 116 (274)
Q Consensus 37 IAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 579999999852 123499999999997633 23456665 333332 2333
Q ss_pred HHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhC-C
Q 023991 117 SIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYF-P 195 (274)
Q Consensus 117 Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~F-P 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 66555443 466666544443332 11 12 47899999999999888874211 1122 3
Q ss_pred ccccchhhhHhhhcc--cCcHHHH-HHHcCCccCCCCccchhhHHHHHHHHH
Q 023991 196 TVYDIKHLMKFCNSL--HGGLNKL-AELLEVERVGICHQAGSDSLLTASTFR 244 (274)
Q Consensus 196 ~iyDtK~la~~~~~l--~~~L~~l-a~~L~~~r~~~~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 688998887775322 2367777 77788754 688999999999999873
No 27
>PRK06722 exonuclease; Provisional
Probab=98.24 E-value=6e-05 Score=69.65 Aligned_cols=168 Identities=15% Similarity=0.099 Sum_probs=97.2
Q ss_pred cCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCC
Q 023991 33 DYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDI 112 (274)
Q Consensus 33 ~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~d~ 112 (274)
...||++|+|.+|. |.. +-+.-.|||+|....+. |.. ..+..|+-+.-|. ..
T Consensus 4 ~~~~vViD~ETT~~---p~~---------------~~~~deIIEIGAVkV~~-g~i-------~Ivd~F~sLV~P~--~~ 55 (281)
T PRK06722 4 ATHFIVFDIERNFR---PYK---------------SEDPSEIVDIGAVKIEA-STM-------KVIGEFSELVKPG--AR 55 (281)
T ss_pred CCEEEEEEeeCCCC---CCC---------------CCCCCeEEEEEEEEEEC-Cce-------eEEeeEEEEECCC--Cc
Confidence 35799999999852 210 01122499999988874 221 1345676663332 23
Q ss_pred CchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHh-cccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHHH
Q 023991 113 FANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSS-GIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFNL 189 (274)
Q Consensus 113 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~S-gl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~~~~F~~~ 189 (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-IGVEKF---PQIIEKFIQFI-GE-DSIFVTWGKEDYRFLSHDCTLHSVECPCMEK----- 121 (281)
T ss_pred CCHhHhhh---cCCCHHHH-cCCCCH---HHHHHHHHHHH-CC-CcEEEEEeHHHHHHHHHHHHHcCCCCCcccc-----
Confidence 44444444 55543333 223333 3332211 111 11 24677889999999998763 444443110
Q ss_pred HHhhCCccccchhhhHh-hhcc---cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHH
Q 023991 190 IRIYFPTVYDIKHLMKF-CNSL---HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLK 247 (274)
Q Consensus 190 l~~~FP~iyDtK~la~~-~~~l---~~~L~~la~~L~~~r~~~~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 012233222211 1111 1269999999999988899999999999999999986
No 28
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=98.22 E-value=5.1e-05 Score=69.24 Aligned_cols=167 Identities=22% Similarity=0.226 Sum_probs=104.5
Q ss_pred hhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCC
Q 023991 31 VDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNE 110 (274)
Q Consensus 31 i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 56789999999999964221 159999999886 332 234455543332
Q ss_pred CCCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHH
Q 023991 111 DIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLI 190 (274)
Q Consensus 111 d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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~~~--------- 173 (257)
T PRK08517 112 -EVPEYITEL---TGITYEDLE-NAPSLKEVLEEFRL---FLGD-SVFVAHNVNFDYNFISRSLEEIGLGP--------- 173 (257)
T ss_pred -CCChhhhhh---cCcCHHHHc-CCCCHHHHHHHHHH---HHCC-CeEEEECHHHHHHHHHHHHHHcCCCC---------
Confidence 233333322 676655543 34444332222221 1122 36999999999999987764222221
Q ss_pred HhhCCccccchhhhHhh-hcccCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 191 RIYFPTVYDIKHLMKFC-NSLHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 191 ~~~FP~iyDtK~la~~~-~~l~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
+.+...||--+++.. ..-+-+|+.+++.+|++.. .+|.|-+||..|+++|.++.+.+-
T Consensus 174 --~~~~~ldtl~la~~~~~~~~~~L~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 174 --LLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIE-VHHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred --CCCCcEehHHHHHHHccCCCCCHHHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHhH
Confidence 112334554455443 2234589999999999865 789999999999999999887653
No 29
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=98.17 E-value=2.5e-06 Score=69.45 Aligned_cols=156 Identities=22% Similarity=0.237 Sum_probs=97.3
Q ss_pred eeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCchh
Q 023991 37 VAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFAND 116 (274)
Q Consensus 37 IAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~d~~~~~ 116 (274)
|.+|||++|+..+ .-.|||+|.-..+.+.. ...-.|+.+..+.......+.
T Consensus 1 v~~D~Ettg~~~~---------------------~~~iieig~v~~~~~~~--------~~~~~~~~~i~p~~~~~i~~~ 51 (164)
T PF00929_consen 1 VVFDTETTGLDPR---------------------QDEIIEIGAVKVDDDEN--------EEVESFNSLIRPEEPPKISPW 51 (164)
T ss_dssp EEEEEEESSSTTT---------------------TCTEEEEEEEEEETTTT--------EEEEEEEEEBEHSSHCSSEHH
T ss_pred cEEEeEcCCCCCC---------------------CCeEEEEEEEEeeCCcc--------ccceeeeecccccccccCCHH
Confidence 6799999998642 23499999988886543 134567766444333345555
Q ss_pred HHHHHHHcCCCccchhhcCCchhH---HHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhh
Q 023991 117 SIELLKQSGINFTKNNEIGIDAMR---FGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIY 193 (274)
Q Consensus 117 Si~fL~~~GfDFnk~~~~GI~~~~---f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~ 193 (274)
+.+. +|+.-..+...+-.... |.+.+ .+...|++++..+|.+++.+.+. +.+...
T Consensus 52 ~~~~---~gIt~~~l~~~~~~~~~~~~~~~~~-------~~~~~~v~~n~~fd~~~l~~~~~------------~~~~~~ 109 (164)
T PF00929_consen 52 ATKV---HGITQEDLEDAPSFEEALDEFEEFL-------KKNDILVGHNASFDIGFLRREDK------------RFLGKP 109 (164)
T ss_dssp HHHH---HHHCHHHHHCHCEHHHHHHHHHHHH-------HHHTEEEETTCCHEEESSHHHHH------------HHHHHH
T ss_pred Heee---cCCcccccccCCcHHHHHHhhhhhh-------hcccccccccccchhhHHHHhhh------------hccccc
Confidence 5433 66665555554432221 22222 12246788877888776665542 111221
Q ss_pred C---CccccchhhhHhh-hccc-CcHHHHHHHcCCccCCCCccchhhHHHHHHHH
Q 023991 194 F---PTVYDIKHLMKFC-NSLH-GGLNKLAELLEVERVGICHQAGSDSLLTASTF 243 (274)
Q Consensus 194 F---P~iyDtK~la~~~-~~l~-~~L~~la~~L~~~r~~~~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 2 2455655554443 3333 48999999999999888999999999999987
No 30
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.14 E-value=7.2e-05 Score=78.43 Aligned_cols=162 Identities=20% Similarity=0.267 Sum_probs=104.7
Q ss_pred cCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCC
Q 023991 33 DYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDI 112 (274)
Q Consensus 33 ~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~d~ 112 (274)
...||++|+|-||+. +. + .|||+|..... +|+ .+-.|..+ .+.. ..
T Consensus 6 ~~~~vvvD~ETTGl~--~~------------------d--~IIeIgaV~v~-~g~---------i~~~f~~l-v~P~-~~ 51 (820)
T PRK07246 6 LRKYAVVDLEATGAG--PN------------------A--SIIQVGIVIIE-GGE---------IIDSYTTD-VNPH-EP 51 (820)
T ss_pred CCCEEEEEEecCCcC--CC------------------C--eEEEEEEEEEE-CCE---------EEEEEEEE-eCcC-CC
Confidence 468999999999973 10 1 39999999875 332 34456555 2322 23
Q ss_pred CchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHHHH
Q 023991 113 FANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFNLI 190 (274)
Q Consensus 113 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~~~~F~~~l 190 (274)
+.+.+.+. +|+.=..+. ++.+..+-...+.. ++ .+-.+|++|..||+++|-+.+. |-++|..
T Consensus 52 i~~~~~~l---tGIt~e~l~-~ap~~~ev~~~~~~--~l--~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~-------- 115 (820)
T PRK07246 52 LDEHIKHL---TGITDQQLA-QAPDFSQVARHIYD--LI--EDCIFVAHNVKFDANLLAEALFLEGYELRTP-------- 115 (820)
T ss_pred CCHhHhhc---CCCCHHHHh-cCCCHHHHHHHHHH--Hh--CCCEEEEECcHHHHHHHHHHHHHcCCCCCCC--------
Confidence 44444333 666655543 34444433333322 11 2346899999999999988763 3344322
Q ss_pred HhhCCccccchhhhHhh-hcc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 191 RIYFPTVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 191 ~~~FP~iyDtK~la~~~-~~l-~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
.+||--+++.. +.+ +-+|+.+++.+|++.. .+|.|-+||..|+.+|.+|.+.+.
T Consensus 116 ------~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~~-~~H~Al~DA~ata~L~~~l~~~l~ 171 (820)
T PRK07246 116 ------RVDTVELAQVFFPTLEKYSLSHLSRELNIDLA-DAHTAIADARATAELFLKLLQKIE 171 (820)
T ss_pred ------ceeHHHHHHHHhCCCCCCCHHHHHHHcCCCCC-CCCCHHHHHHHHHHHHHHHHHHHh
Confidence 24665555543 222 3489999999999854 679999999999999999988765
No 31
>PRK07883 hypothetical protein; Validated
Probab=98.14 E-value=7.1e-05 Score=75.31 Aligned_cols=170 Identities=17% Similarity=0.157 Sum_probs=110.8
Q ss_pred HHHHhhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeeccc
Q 023991 27 IRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREF 106 (274)
Q Consensus 27 I~~~i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F 106 (274)
+..-+.+..||++|+|.||+... .-.|||+|.-.++ +|+ .+.+|+.. .
T Consensus 8 ~~~~~~~~~~Vv~D~ETTGl~p~---------------------~~~IIEIgaV~v~-~g~---------iv~~f~~l-V 55 (557)
T PRK07883 8 LGTPLRDVTFVVVDLETTGGSPA---------------------GDAITEIGAVKVR-GGE---------VLGEFATL-V 55 (557)
T ss_pred hCCCCcCCCEEEEEEecCCCCCC---------------------CCeEEEEEEEEEE-CCE---------EEEEEEEE-E
Confidence 34557789999999999998421 1249999999886 232 34567665 4
Q ss_pred CCCCCCCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCCCCCChH
Q 023991 107 DVNEDIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQV 184 (274)
Q Consensus 107 ~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~~~ 184 (274)
+... ...+.+... +|+.=.. ..++.+..+..+.+.. ++ . +-.+|+++..||+.+|-..+. |.+.|.
T Consensus 56 ~P~~-~i~~~~~~i---tGIt~e~-l~~ap~~~evl~~f~~--fl-~-~~~lVaHNa~FD~~fL~~~~~r~g~~~~~--- 123 (557)
T PRK07883 56 NPGR-PIPPFITVL---TGITTAM-VAGAPPIEEVLPAFLE--FA-R-GAVLVAHNAPFDIGFLRAAAARCGYPWPG--- 123 (557)
T ss_pred CCCC-CCChhHHhh---cCCCHHH-HhCCCCHHHHHHHHHH--Hh-c-CCEEEEeCcHHHHHHHHHHHHHcCCCCCC---
Confidence 4332 345555433 7765433 3344444332222221 11 1 346888999999999988774 333221
Q ss_pred HHHHHHHhhCCccccchhhhHhh-h--cc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 185 EFFNLIRIYFPTVYDIKHLMKFC-N--SL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 185 ~F~~~l~~~FP~iyDtK~la~~~-~--~l-~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
+..+||-.+++.. . .. .-+|..+++.+|++.. ..|.|-+|+..|+.+|.++.+...
T Consensus 124 ----------~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 124 ----------PPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTT-PTHRALDDARATVDVLHGLIERLG 183 (557)
T ss_pred ----------CCcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccC-CCCCHHHHHHHHHHHHHHHHHHHH
Confidence 2356887776654 2 22 3479999999999854 469999999999999999888775
No 32
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.10 E-value=6.8e-05 Score=79.63 Aligned_cols=166 Identities=20% Similarity=0.229 Sum_probs=104.5
Q ss_pred CCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCC
Q 023991 34 YPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIF 113 (274)
Q Consensus 34 ~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 46999999999974221 0 159999999985 343 34456665 33332 34
Q ss_pred chhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhh
Q 023991 114 ANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIY 193 (274)
Q Consensus 114 ~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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 4443333 777655543 34444333322222 11 24579999999999999887642222210
Q ss_pred CCccccchhhhHhh-hcc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 194 FPTVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 194 FP~iyDtK~la~~~-~~l-~~~L~~la~~L~~~r~~~~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 01345655454443 122 237999999999874 5789999999999999999988765
No 33
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=98.07 E-value=9.3e-05 Score=80.19 Aligned_cols=168 Identities=22% Similarity=0.264 Sum_probs=115.1
Q ss_pred hcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCC
Q 023991 32 DDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNED 111 (274)
Q Consensus 32 ~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~d 111 (274)
+...||++|+|-||+.... =.|||+|....+. |+ ..-.|+++ .+. ..
T Consensus 188 ~~~~~VVfDiETTGL~~~~---------------------d~IIEIGAVkv~~-g~---------iid~f~~~-V~P-~~ 234 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQY---------------------DEIIEFGAVKVKN-GR---------IIDKFQFF-IKP-HE 234 (1213)
T ss_pred cCCcEEEEEeEecCCCCCC---------------------CeEEEEEEEEEEC-Ce---------EEEEEEEE-ECC-CC
Confidence 6789999999999985321 1599999998873 32 34567766 332 23
Q ss_pred CCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHH
Q 023991 112 IFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIR 191 (274)
Q Consensus 112 ~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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---TGITQDML-ENAPEIEEVLEKFKE--FF--KDSILVAHNASFDIGFLNTNFEKVGLEP---------- 296 (1213)
T ss_pred CCCHHHHHH---hCCCHHHH-hCCCCHHHHHHHHHH--Hh--CCCeEEEEChHHHHHHHHHHHHHcCCCc----------
Confidence 455555443 88877765 456665443222222 11 2347899999999999988764222221
Q ss_pred hhCCccccchhhhHhhh-cc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhcC
Q 023991 192 IYFPTVYDIKHLMKFCN-SL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFFS 252 (274)
Q Consensus 192 ~~FP~iyDtK~la~~~~-~l-~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~~~~ 252 (274)
+-..++||--+++... .+ .-+|+.|++.+|++..+ +|.|-.|+..|+.+|.+|.+....
T Consensus 297 -~~~~~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~~~-~HrAl~DA~aTa~I~~~ll~~l~~ 357 (1213)
T TIGR01405 297 -LENPVIDTLELARALNPEYKSHRLGNICKKLGVDLDD-HHRADYDAEATAKVFKVMVEQLKE 357 (1213)
T ss_pred -cCCCEeEHHHHHHHHhccCCCCCHHHHHHHcCCCCCC-CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 1135778888877653 33 34899999999998765 899999999999999999877653
No 34
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=98.02 E-value=0.00018 Score=64.23 Aligned_cols=148 Identities=13% Similarity=0.083 Sum_probs=94.8
Q ss_pred eeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCch
Q 023991 36 YVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFAN 115 (274)
Q Consensus 36 fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 09999987665 443 23455554 44332 3455
Q ss_pred hHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCC
Q 023991 116 DSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFP 195 (274)
Q Consensus 116 ~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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--Y--YGSEWYVAHNASFDRRVLPE------MP--------------G 94 (219)
T ss_pred HHhhc---CCCCHHHHc--CCCC--HHHHHHH--H--cCCCEEEEeCcHhhHHHHhC------cC--------------C
Confidence 55443 554333221 1111 3443322 1 13347899999999988731 11 2
Q ss_pred ccccchhhhHhh-hcccCcHHHHHHHcCCcc----CCCCccchhhHHHHHHHHHHHHHHh
Q 023991 196 TVYDIKHLMKFC-NSLHGGLNKLAELLEVER----VGICHQAGSDSLLTASTFRKLKENF 250 (274)
Q Consensus 196 ~iyDtK~la~~~-~~l~~~L~~la~~L~~~r----~~~~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 467887777654 445678899999998753 2468999999999999999988643
No 35
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=98.01 E-value=0.00015 Score=76.39 Aligned_cols=161 Identities=24% Similarity=0.249 Sum_probs=101.3
Q ss_pred CeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCc
Q 023991 35 PYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFA 114 (274)
Q Consensus 35 ~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 139999999885 343 23456555 33332 334
Q ss_pred hhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC--CCC-CCCChHHHHHHHH
Q 023991 115 NDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQN-LPDTQVEFFNLIR 191 (274)
Q Consensus 115 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~-LP~~~~~F~~~l~ 191 (274)
+.+.+ -+|+.-+.+. .+-++.+..+.+.. ++ . +-.+|+++..||+.+|-+.+. |.+ +|.
T Consensus 48 ~~~~~---ltGIt~e~l~-~ap~~~ev~~~l~~--~l-~-~~~~VahN~~fD~~fL~~~~~~~g~~~~~~---------- 109 (850)
T TIGR01407 48 PFIQE---LTGISDNMLQ-QAPYFSQVAQEIYD--LL-E-DGIFVAHNVHFDLNFLAKALKDCGYEPLPK---------- 109 (850)
T ss_pred hhhhh---hcCcCHHHHh-CCCCHHHHHHHHHH--Hh-C-CCEEEEeCcHHHHHHHHHHHHHcCCCCCCC----------
Confidence 44333 2676654443 33333332222222 11 2 235999999999999988773 222 222
Q ss_pred hhCCccccchhhhHhhh-cc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 192 IYFPTVYDIKHLMKFCN-SL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 192 ~~FP~iyDtK~la~~~~-~l-~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
..+||--+++..- .. .-+|..|++.+|++.. .+|.|-+|+..|+.+|.+|.+.+.
T Consensus 110 ----~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 110 ----PRIDTVELAQIFFPTEESYQLSELSEALGLTHE-NPHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred ----CeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCC-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 3456554554431 11 3489999999999864 579999999999999999988765
No 36
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=97.96 E-value=0.00014 Score=62.64 Aligned_cols=165 Identities=18% Similarity=0.127 Sum_probs=96.2
Q ss_pred eEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCC-CCCchh
Q 023991 38 AMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNE-DIFAND 116 (274)
Q Consensus 38 AiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~-d~~~~~ 116 (274)
-+|+|-||+.... =.|||+|.-..+.++.. ...|++. ..... ....++
T Consensus 2 ~~D~ETTGl~~~~---------------------d~Iieig~v~v~~~~~~---------~~~~~~~-v~p~~~~~~~~~ 50 (183)
T cd06138 2 FYDYETFGLNPSF---------------------DQILQFAAIRTDENFNE---------IEPFNIF-CRLPPDVLPSPE 50 (183)
T ss_pred EEEeecCCCCCCC---------------------CceEEEEEEEECCCCCC---------ccceeEE-EeCCCCCCCCHH
Confidence 4899999985321 13899999888765432 2456665 32332 244555
Q ss_pred HHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEecc-chhHHHHHHHhCC---CCCCCC------hHHH
Q 023991 117 SIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHS-GYDFGYLLKLLTC---QNLPDT------QVEF 186 (274)
Q Consensus 117 Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g-~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 4888877776667776554333332 12123345899885 6999999877632 222211 1122
Q ss_pred HHHHHh---hCCccccchhhhHhhhcc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHH
Q 023991 187 FNLIRI---YFPTVYDIKHLMKFCNSL-HGGLNKLAELLEVERVGICHQAGSDSLLTAST 242 (274)
Q Consensus 187 ~~~l~~---~FP~iyDtK~la~~~~~l-~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~ 242 (274)
....+. ++|..++.- ..-.++ +-+|+.+++.+|++. ..+|.|-+|++.|+++
T Consensus 126 l~l~r~~~~~~~~~~~~~---~~~~~~~~~~L~~l~~~~gi~~-~~~H~Al~Da~~ta~l 181 (183)
T cd06138 126 LDVVRAYYALRPDGIVWP---KNDDGKPSFKLEDLAQANGIEH-SNAHDALSDVEATIAL 181 (183)
T ss_pred HHHHHHHHhhChhhccCc---cccCCCcchhHHHHHHHCCCCc-cccccHHHHHHHHHHH
Confidence 222222 224211110 000012 236999999999986 5679999999999874
No 37
>PTZ00315 2'-phosphotransferase; Provisional
Probab=97.95 E-value=0.00027 Score=71.01 Aligned_cols=175 Identities=18% Similarity=0.165 Sum_probs=109.5
Q ss_pred CCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeec-CCCCCCCCCCCeeEEEeeecccCCCCCC
Q 023991 34 YPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDE-NGNLPTCGTDKYCVWQFNFREFDVNEDI 112 (274)
Q Consensus 34 ~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~-~g~~p~~~~~~~~~w~FNF~~F~~~~d~ 112 (274)
-.||++|+|.||..... . +.-.||++|...++. +|+ .+..|..+.-|.....
T Consensus 56 d~~IV~DlETTgl~~~~----~--------------~~dEIIEIGaV~Vd~~ng~---------Ii~~F~~yVkP~~~p~ 108 (582)
T PTZ00315 56 DAYVVLDFEATCEADRR----I--------------EDAEVIEFPMVLVDARTAT---------PVAEFQRYVRPVKNPV 108 (582)
T ss_pred CeEEEEEEecCCCCCCC----C--------------CCCceEEEEEEEEEccCCE---------EEEEEEEEECCCCCCC
Confidence 36999999999964221 0 112499999999984 343 4567766633332224
Q ss_pred CchhHHHHHHHcCCCccchhhcCCchhH----HHHHHHHhcccc---cCCcceEEeccchhHH-HHHHHhC--C-CCCCC
Q 023991 113 FANDSIELLKQSGINFTKNNEIGIDAMR----FGEFMMSSGIVL---SDSMHWVTFHSGYDFG-YLLKLLT--C-QNLPD 181 (274)
Q Consensus 113 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~----f~e~l~~Sgl~~---~~~v~wvtf~g~yD~~-yL~k~l~--~-~~LP~ 181 (274)
.++.+.++ +||.=+. ..++.++.+ |.+.+..+++.. +.+ ..|...|.+|+. +|.+-+. + ..+|.
T Consensus 109 Ls~fct~L---TGITqe~-V~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~-~~vah~g~fDl~~fL~~e~~~~~~~g~p~ 183 (582)
T PTZ00315 109 LSRFCTEL---TGITQSM-VSRADPFPVVYCEALQFLAEAGLGDAPPLRS-YCVVTCGDWDLKTMLPSQMRVSGQQGTPL 183 (582)
T ss_pred CChhHhhh---cCcCHHH-HhcCCCHHHHHHHHHHHHhccccccccccCc-eEEEeccHHHHHHHHHHHHHHhhhcCCCc
Confidence 55555554 6665333 344555543 333333332211 111 345677999995 7766553 1 24553
Q ss_pred ChHHHHHHHHhhCCccccch-hhhHhh-hc-----------c-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHH
Q 023991 182 TQVEFFNLIRIYFPTVYDIK-HLMKFC-NS-----------L-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLK 247 (274)
Q Consensus 182 ~~~~F~~~l~~~FP~iyDtK-~la~~~-~~-----------l-~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~ 247 (274)
.|...+|+| ++++.. ++ + .-+|+.+++.+|++..|..|.|=.||..|+++|.+|.
T Consensus 184 -----------~f~~widLk~~lar~l~p~~~~~~~~~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll 252 (582)
T PTZ00315 184 -----------SFQRWCNLKKYMSQLGFGNGSGCGGGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELL 252 (582)
T ss_pred -----------ccceEEEhHHHHHHHhCccccccccccccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHH
Confidence 345566654 666643 11 2 2489999999999999999999999999999999998
Q ss_pred HHhc
Q 023991 248 ENFF 251 (274)
Q Consensus 248 ~~~~ 251 (274)
+.-.
T Consensus 253 ~~g~ 256 (582)
T PTZ00315 253 RRGL 256 (582)
T ss_pred HcCC
Confidence 7633
No 38
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.85 E-value=0.00048 Score=61.69 Aligned_cols=160 Identities=16% Similarity=0.165 Sum_probs=96.9
Q ss_pred CeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCCc
Q 023991 35 PYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFA 114 (274)
Q Consensus 35 ~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 4899999999985321 13999997 22 211 1234444 33332 345
Q ss_pred hhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEecc-chhHHHHHHHhC--CCCCCCChHHHHHHHH
Q 023991 115 NDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHS-GYDFGYLLKLLT--CQNLPDTQVEFFNLIR 191 (274)
Q Consensus 115 ~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g-~yD~~yL~k~l~--~~~LP~~~~~F~~~l~ 191 (274)
+++++. ||+.=+...... +..+..+.+. .+ +...-.+|++++ .||..+|.+.+. +.+.|.
T Consensus 47 ~~a~~I---hGIt~e~v~~~p-~f~ev~~~~~--~f-i~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~---------- 109 (232)
T PRK06309 47 AEASKI---HGITTDEVADAP-KFPEAYQKFI--EF-CGTDNILVAHNNDAFDFPLLRKECRRHGLEPPT---------- 109 (232)
T ss_pred hhHHhh---cCCCHHHHhCCC-CHHHHHHHHH--HH-HcCCCEEEEeCCHHHHHHHHHHHHHHcCCCCCC----------
Confidence 555443 555544433322 2222111111 11 122346888884 699999988773 322221
Q ss_pred hhCCccccchhhhHhh-hcc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 192 IYFPTVYDIKHLMKFC-NSL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 192 ~~FP~iyDtK~la~~~-~~l-~~~L~~la~~L~~~r~~~~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 1356887676654 233 358999999999764 5689999999999999999887764
No 39
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=97.78 E-value=0.00061 Score=63.42 Aligned_cols=155 Identities=17% Similarity=0.156 Sum_probs=99.1
Q ss_pred CeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecC--CCCCCCCCCCeeEEEeeecccCCCCCC
Q 023991 35 PYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDEN--GNLPTCGTDKYCVWQFNFREFDVNEDI 112 (274)
Q Consensus 35 ~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~--g~~p~~~~~~~~~w~FNF~~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-QQPS-RP 88 (294)
T ss_pred eEEEEEeeCCCCCCCC---------------------CeEEEEEEEEEEecCCCcee------eeeeEEEEE-eCCC-CC
Confidence 6899999999986321 13999999999853 4421 134567765 4333 24
Q ss_pred CchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhC---CCCCCCChHHHHHH
Q 023991 113 FANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLT---CQNLPDTQVEFFNL 189 (274)
Q Consensus 113 ~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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 888777776667766666554322 235789999999999876541 12222221110
Q ss_pred HHhhCCccccchhhhHhhhcc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHH
Q 023991 190 IRIYFPTVYDIKHLMKFCNSL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLK 247 (274)
Q Consensus 190 l~~~FP~iyDtK~la~~~~~l-~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~ 247 (274)
|-+ ...+ +-.|+.|++.+| .....|.|.+|++.|+.+|.++.
T Consensus 156 ---------~~~-----~~~~~~~kL~~La~~~g--~~~~aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 156 ---------DWS-----ARGFEGTKLGYLAGQAG--FFHEGHRAVDDCQALLELLARPL 198 (294)
T ss_pred ---------hhc-----cccCCCCCHHHHHHHcC--CCCCCcChHHHHHHHHHHHHHHH
Confidence 100 0111 247999999999 34578999999999999999643
No 40
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=97.77 E-value=0.00044 Score=57.80 Aligned_cols=69 Identities=17% Similarity=0.135 Sum_probs=47.7
Q ss_pred ceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc---ccCcHHHHHHH-cCCccCCCCccc
Q 023991 157 HWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS---LHGGLNKLAEL-LEVERVGICHQA 232 (274)
Q Consensus 157 ~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~---l~~~L~~la~~-L~~~r~~~~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 589999999998874 12222 135565443333221 23489999997 698765568999
Q ss_pred hhhHHHHHHHH
Q 023991 233 GSDSLLTASTF 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 41
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.77 E-value=0.00042 Score=68.47 Aligned_cols=175 Identities=15% Similarity=0.123 Sum_probs=109.4
Q ss_pred hcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCC
Q 023991 32 DDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNED 111 (274)
Q Consensus 32 ~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~d 111 (274)
....||.+|+|-||+..+ .+ .|||+|.--.+.+++. ....|+++ .....+
T Consensus 4 ~~~~fvv~D~ETTGLdP~-----~D----------------rIIeiAaVrvd~~~~~--------i~e~~~~~-~~P~~~ 53 (476)
T PRK11779 4 MQPTFLWHDYETFGANPA-----LD----------------RPAQFAGIRTDADLNI--------IGEPLVFY-CKPADD 53 (476)
T ss_pred CCCcEEEEEEECCCCCCC-----CC----------------eeEEEEEEEEeCCCce--------ecceeEEE-EcCCcC
Confidence 346799999999998632 11 3999999988765431 23457776 444443
Q ss_pred -CCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEecc-chhHHHHHHHhCCCCCCCChHHHHHH
Q 023991 112 -IFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHS-GYDFGYLLKLLTCQNLPDTQVEFFNL 189 (274)
Q Consensus 112 -~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g-~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---LITGITPQEALEKGLPEAEFAARIHAE--FSQPGTCILGYNNIRFDDEVTRYIFY-RNFYDPY------ 121 (476)
T ss_pred cCCCHHHH---HHhCCCHHHHHhcCCCHHHHHHHHHHH--HhcCCCEEEEeCchhhcHHHHHHHHH-hccchHH------
Confidence 3455554 448988888888898877666555431 1122335788876 599998888773 1111111
Q ss_pred HHhhC-C----ccccchhhhHhh-h----------c-ccCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHH
Q 023991 190 IRIYF-P----TVYDIKHLMKFC-N----------S-LHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKEN 249 (274)
Q Consensus 190 l~~~F-P----~iyDtK~la~~~-~----------~-l~~~L~~la~~L~~~r~~~~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 11100 0 122222222111 0 1 1236999999999974 56799999999999999999876
No 42
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=97.65 E-value=0.0006 Score=65.15 Aligned_cols=176 Identities=15% Similarity=0.204 Sum_probs=102.0
Q ss_pred HhhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCC
Q 023991 30 IVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVN 109 (274)
Q Consensus 30 ~i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 1399999998887775 34556555 4433
Q ss_pred CCCCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhCC--CCCCC-ChHHH
Q 023991 110 EDIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTC--QNLPD-TQVEF 186 (274)
Q Consensus 110 ~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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 3221 11 114443333322 3333322222211 12 23469999999999999886510 00000 00000
Q ss_pred H------------HHHHhhCC-ccccchhhhHhhh-cc-cCcHHHHHHHcCCcc---------CCCCccchh--hHHHHH
Q 023991 187 F------------NLIRIYFP-TVYDIKHLMKFCN-SL-HGGLNKLAELLEVER---------VGICHQAGS--DSLLTA 240 (274)
Q Consensus 187 ~------------~~l~~~FP-~iyDtK~la~~~~-~l-~~~L~~la~~L~~~r---------~~~~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 00011223 5788877777763 33 347999999999864 345666654 999999
Q ss_pred HHHHHHH
Q 023991 241 STFRKLK 247 (274)
Q Consensus 241 ~~F~~l~ 247 (274)
.+|.+++
T Consensus 240 ~l~~~~~ 246 (377)
T PRK05601 240 RLYFALR 246 (377)
T ss_pred HHHHHhh
Confidence 9999974
No 43
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=97.65 E-value=0.0015 Score=58.30 Aligned_cols=163 Identities=20% Similarity=0.229 Sum_probs=102.6
Q ss_pred CCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCC
Q 023991 34 YPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIF 113 (274)
Q Consensus 34 ~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~d~~ 113 (274)
..||.+|+|-||... ..=.+||+|...+..+.... ..|..+.-| +..+
T Consensus 13 ~~~vv~D~ETtg~~~---------------------~~~~iieIgav~~~~~~i~~---------~~~~~~v~P--~~~i 60 (243)
T COG0847 13 TRFVVIDLETTGLNP---------------------KKDRIIEIGAVTLEDGRIVE---------RSFHTLVNP--ERPI 60 (243)
T ss_pred CcEEEEecccCCCCC---------------------CCCceEEEEeEEEECCeeec---------ceeEEEECC--CCCC
Confidence 689999999999864 22359999998887653321 114444222 3334
Q ss_pred chhHHHHHHHcCCCccchhhcCCchhHHHHHHHHh-cccccCCcceEEeccchhHHHHHHHhC--CCCCCCChHHHHHHH
Q 023991 114 ANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSS-GIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDTQVEFFNLI 190 (274)
Q Consensus 114 ~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~S-gl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~~~~F~~~l 190 (274)
.+++... +||....+... . .|.+.+-.- .++ .+.-.+|+++-.+|.++|-..+. +.+.|
T Consensus 61 ~~~~~~i---~git~e~l~~~-p---~~~~v~~~~~~~i-~~~~~~Vahna~fD~~fl~~~~~~~~~~~~---------- 122 (243)
T COG0847 61 PPEIFKI---HGITDEMLADA-P---KFAEVLPEFLDFI-GGLRLLVAHNAAFDVGFLRVESERLGIEIP---------- 122 (243)
T ss_pred Chhhhhh---cCCCHHHHhcC-C---CHHHHHHHHHHHH-CCCCeEEEEchhhcHHHHHHHHHHcCCCcc----------
Confidence 4555443 55555554444 1 122222111 111 22147899999999999976663 33433
Q ss_pred HhhCCccccchhhhHhh-hc-ccCcHHHHHHHcCCcc-CCCCccchhhHHHHHHHHHHHHHH
Q 023991 191 RIYFPTVYDIKHLMKFC-NS-LHGGLNKLAELLEVER-VGICHQAGSDSLLTASTFRKLKEN 249 (274)
Q Consensus 191 ~~~FP~iyDtK~la~~~-~~-l~~~L~~la~~L~~~r-~~~~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 12344555555443 23 3568999999999997 456699999999999999999874
No 44
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=97.50 E-value=0.0017 Score=71.57 Aligned_cols=168 Identities=22% Similarity=0.229 Sum_probs=107.3
Q ss_pred hhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCC
Q 023991 31 VDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNE 110 (274)
Q Consensus 31 i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 148899987765 332 34566666 4432
Q ss_pred CCCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHH
Q 023991 111 DIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLI 190 (274)
Q Consensus 111 d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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-DAPSIEEVLPKFKEF----CGDSILVAHNASFDVGFINTNYEKLGLEK--------- 525 (1437)
T ss_pred CCCCHHHHHH---hCCCHHHHc-CCCCHHHHHHHHHHH----hCCCEEEEeCccccHHHHHHHHHHcCCcc---------
Confidence 2344444443 566554444 455555433333320 12357899999999999876653211221
Q ss_pred HhhCCccccchhhhHhhh-cc-cCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhc
Q 023991 191 RIYFPTVYDIKHLMKFCN-SL-HGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 191 ~~~FP~iyDtK~la~~~~-~l-~~~L~~la~~L~~~r~~~~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 1123456655554432 22 35899999999998765 59999999999999999988765
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=0.0012 Score=55.21 Aligned_cols=69 Identities=17% Similarity=0.069 Sum_probs=50.4
Q ss_pred CcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc-c-cCcHHHHHHHc-CCcc-C-CCC
Q 023991 155 SMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS-L-HGGLNKLAELL-EVER-V-GIC 229 (274)
Q Consensus 155 ~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~-l-~~~L~~la~~L-~~~r-~-~~~ 229 (274)
+-.+|+++-.+|+.+|-. .-+.++||-.+++.... . +-+|+.|++.+ +..- . +..
T Consensus 76 ~~vlVgHn~~fD~~fL~~--------------------~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~ 135 (150)
T cd06145 76 DTILVGHSLENDLKALKL--------------------IHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGG 135 (150)
T ss_pred CCEEEEcChHHHHHHhhc--------------------cCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCC
Confidence 346899999999998732 12568899888776421 2 34899999876 4322 1 467
Q ss_pred ccchhhHHHHHHHH
Q 023991 230 HQAGSDSLLTASTF 243 (274)
Q Consensus 230 HqAGsDs~lT~~~F 243 (274)
|.|-+||+.|+.+|
T Consensus 136 H~Al~DA~~t~~l~ 149 (150)
T cd06145 136 HDSVEDARAALELV 149 (150)
T ss_pred CCcHHHHHHHHHHh
Confidence 99999999999877
No 46
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=97.41 E-value=0.0022 Score=54.16 Aligned_cols=68 Identities=19% Similarity=0.102 Sum_probs=52.2
Q ss_pred cceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhh-cc----cCcHHHHHHH-cCCccC--C
Q 023991 156 MHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCN-SL----HGGLNKLAEL-LEVERV--G 227 (274)
Q Consensus 156 v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~-~l----~~~L~~la~~-L~~~r~--~ 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 46888888999988732 1357889999998763 23 3589999987 687542 4
Q ss_pred CCccchhhHHHHHHHH
Q 023991 228 ICHQAGSDSLLTASTF 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
>PRK05359 oligoribonuclease; Provisional
Probab=97.28 E-value=0.0079 Score=51.96 Aligned_cols=166 Identities=14% Similarity=0.165 Sum_probs=94.7
Q ss_pred CCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCC--C
Q 023991 34 YPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNE--D 111 (274)
Q Consensus 34 ~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~F~~~~--d 111 (274)
-.||++|+|.||+.... + .|||+|.-..+.+.+. ..-.|+....+... +
T Consensus 3 ~~~vvlD~ETTGLdp~~-----d----------------~IieIgaV~~~~~~~~--------~~~~~~~~i~~~~~~l~ 53 (181)
T PRK05359 3 DNLIWIDLEMTGLDPER-----D----------------RIIEIATIVTDADLNI--------LAEGPVIAIHQSDEALA 53 (181)
T ss_pred CcEEEEEeecCCCCCCC-----C----------------eEEEEEEEEEcCCceE--------cccceEEEECCCHHHhh
Confidence 47999999999985321 1 2999999977654321 11234444232211 1
Q ss_pred CCchhHHHHHHHcCCCccchhhcCCchhHHHHHHHH--hcccccCCcceEEeccchhHHHHHHHhC--CCCCCCC---hH
Q 023991 112 IFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMS--SGIVLSDSMHWVTFHSGYDFGYLLKLLT--CQNLPDT---QV 184 (274)
Q Consensus 112 ~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~--Sgl~~~~~v~wvtf~g~yD~~yL~k~l~--~~~LP~~---~~ 184 (274)
...+.+...-..+|+. ++....|.+..+..+.+.. .+.+.......+.++-.||..||-+.+- +.+|+.. ..
T Consensus 54 ~~~~~~~~ih~~tGIt-~~~l~~~~~~~e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~ 132 (181)
T PRK05359 54 AMDEWNTRTHTRSGLI-DRVRASTVSEAEAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVS 132 (181)
T ss_pred ccChHHHHhcccccCc-HHHHhcCCCHHHHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchh
Confidence 1223333322234776 5666777777655444332 1222222223344444789999988872 3444432 22
Q ss_pred HHHHHHHhhCCccccchhhhHhhhcccCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHHhcC
Q 023991 185 EFFNLIRIYFPTVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFFS 252 (274)
Q Consensus 185 ~F~~~l~~~FP~iyDtK~la~~~~~l~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~~~~ 252 (274)
..+++.+.++|..| .++++.+ .|.|=+|++-|.+++...+..++.
T Consensus 133 tl~~l~r~~~P~~~----------------------~~~~~~~-~HRal~D~~~s~~~~~~~~~~~~~ 177 (181)
T PRK05359 133 TLKELARRWKPEIL----------------------NGFKKQG-THRALADIRESIAELKYYREHFFK 177 (181)
T ss_pred HHHHHHHHhChhhh----------------------hCCCCcC-CcccHHHHHHHHHHHHHHHHHhcc
Confidence 33355555556531 1444443 599999999999999998887763
No 48
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=96.95 E-value=0.0086 Score=50.41 Aligned_cols=70 Identities=17% Similarity=0.096 Sum_probs=44.6
Q ss_pred cceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhh--hHh---hhcc-cCcHHHHHHHc---CCccC
Q 023991 156 MHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHL--MKF---CNSL-HGGLNKLAELL---EVERV 226 (274)
Q Consensus 156 v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~l--a~~---~~~l-~~~L~~la~~L---~~~r~ 226 (274)
-.+|+++-.+|+++|-.. ..|. .+.||=.+ ++. .++. +-+|+.|++.+ +++..
T Consensus 78 ~vlV~Hn~~~D~~~l~~~----~~~~--------------~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~ 139 (157)
T cd06149 78 KVVVGHAIHNDFKALKYF----HPKH--------------MTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVG 139 (157)
T ss_pred CEEEEeCcHHHHHHhccc----CCCc--------------CEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCC
Confidence 368888888899877522 1111 23455322 211 1122 24899999999 45544
Q ss_pred CCCccchhhHHHHHHHH
Q 023991 227 GICHQAGSDSLLTASTF 243 (274)
Q Consensus 227 ~~~HqAGsDs~lT~~~F 243 (274)
+..|.|-+||..|+++|
T Consensus 140 ~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 140 RQGHSSVEDARATMELY 156 (157)
T ss_pred CCCcCcHHHHHHHHHHh
Confidence 56799999999999887
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=95.50 E-value=0.27 Score=40.65 Aligned_cols=83 Identities=20% Similarity=0.299 Sum_probs=55.5
Q ss_pred cccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhcc-c-CcHHHHHHHc-C-Ccc-
Q 023991 151 VLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNSL-H-GGLNKLAELL-E-VER- 225 (274)
Q Consensus 151 ~~~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~l-~-~~L~~la~~L-~-~~r- 225 (274)
+.++++..|.|+..+|+..|.+.+ + ...++++|| .++..+-+. . -||..+++.+ | ...
T Consensus 73 l~~~~i~kv~~n~~~D~~~L~~~~-~---------------i~~~~~~D~-~l~~~~l~~~~~~~L~~L~~~~l~~~~~~ 135 (176)
T PF01612_consen 73 LEDPNIIKVGHNAKFDLKWLYRSF-G---------------IDLKNVFDT-MLAAYLLDPTRSYSLKDLAEEYLGNIDLD 135 (176)
T ss_dssp HTTTTSEEEESSHHHHHHHHHHHH-T---------------S--SSEEEH-HHHHHHTTTSTTSSHHHHHHHHHSEEE-G
T ss_pred HhCCCccEEEEEEechHHHHHHHh-c---------------cccCCccch-hhhhhcccccccccHHHHHHHHhhhccCc
Confidence 446788899999999999988873 2 223478999 555554222 2 5899987554 5 211
Q ss_pred ----CC--C---------CccchhhHHHHHHHHHHHHHHh
Q 023991 226 ----VG--I---------CHQAGSDSLLTASTFRKLKENF 250 (274)
Q Consensus 226 ----~~--~---------~HqAGsDs~lT~~~F~~l~~~~ 250 (274)
.+ . ..=|+.|+.+|.++|-+|.+..
T Consensus 136 ~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 136 KKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp HCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred HHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 11 1 1238889999999999998754
No 50
>PRK05755 DNA polymerase I; Provisional
Probab=95.14 E-value=0.37 Score=51.29 Aligned_cols=83 Identities=19% Similarity=0.207 Sum_probs=58.4
Q ss_pred cCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc-ccCcHHHHHHHc-CCccC----
Q 023991 153 SDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS-LHGGLNKLAELL-EVERV---- 226 (274)
Q Consensus 153 ~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~-l~~~L~~la~~L-~~~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 445667888889999988752 54443 457898887777642 235888887765 44310
Q ss_pred --------------CCCccchhhHHHHHHHHHHHHHHhc
Q 023991 227 --------------GICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 227 --------------~~~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 1236699999999999999988764
No 51
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=94.80 E-value=0.18 Score=48.25 Aligned_cols=76 Identities=26% Similarity=0.368 Sum_probs=50.2
Q ss_pred EEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc-ccCcHHHHHHH-cCCccCCCCc------
Q 023991 159 VTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS-LHGGLNKLAEL-LEVERVGICH------ 230 (274)
Q Consensus 159 vtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~-l~~~L~~la~~-L~~~r~~~~H------ 230 (274)
|-|++.+|+..|.+.+ .-+| +.+||||..++.|+- .+-||..+.+. +|++ +.+.|
T Consensus 74 IfHaa~~DL~~l~~~~--g~~p--------------~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~-ldK~~q~SDW~ 136 (361)
T COG0349 74 IFHAARFDLEVLLNLF--GLLP--------------TPLFDTQIAAKLAGFGTSHGLADLVEELLGVE-LDKSEQRSDWL 136 (361)
T ss_pred eeccccccHHHHHHhc--CCCC--------------CchhHHHHHHHHhCCcccccHHHHHHHHhCCc-ccccccccccc
Confidence 4444677999988886 2444 479999999999952 26689887654 4654 22222
Q ss_pred ----------cchhhHHHHHHHHHHHHHHhc
Q 023991 231 ----------QAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 231 ----------qAGsDs~lT~~~F~~l~~~~~ 251 (274)
=|-+|-..=..++-+|.+...
T Consensus 137 ~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~ 167 (361)
T COG0349 137 ARPLSEAQLEYAAADVEYLLPLYDKLTEELA 167 (361)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 155666666666777766655
No 52
>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=94.78 E-value=0.37 Score=40.30 Aligned_cols=79 Identities=22% Similarity=0.127 Sum_probs=56.1
Q ss_pred cCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhcc--cCcHHHHHHHc-CCcc----
Q 023991 153 SDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNSL--HGGLNKLAELL-EVER---- 225 (274)
Q Consensus 153 ~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~l--~~~L~~la~~L-~~~r---- 225 (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 4567788888888888776543 322 34678999988888543 35999998875 4321
Q ss_pred -------------CCCCccchhhHHHHHHHHHHHH
Q 023991 226 -------------VGICHQAGSDSLLTASTFRKLK 247 (274)
Q Consensus 226 -------------~~~~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 1234669999999999998885
No 53
>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=94.66 E-value=0.81 Score=38.92 Aligned_cols=164 Identities=13% Similarity=0.159 Sum_probs=81.7
Q ss_pred eeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCCCCCCCCCCCeeEEEeeecccCCCCCCC--
Q 023991 36 YVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIF-- 113 (274)
Q Consensus 36 fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g~~p~~~~~~~~~w~FNF~~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 1399999998875422 123445554 33222110
Q ss_pred -chhHHHHHHHcCCCccchhhcCCchhHHHHHHHH--hcccccCCcceEEecc-chhHHHHHHHhCCCCCCCChHHHHHH
Q 023991 114 -ANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMS--SGIVLSDSMHWVTFHS-GYDFGYLLKLLTCQNLPDTQVEFFNL 189 (274)
Q Consensus 114 -~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~--Sgl~~~~~v~wvtf~g-~yD~~yL~k~l~~~~LP~~~~~F~~~ 189 (274)
.+.+.+.-.-+|+. ++....|.+..+..+.+.. .+.+ ..+-..+..|+ .||+++|-+.+..
T Consensus 51 ~~~~~~~ih~~tgIt-~~~l~~~~~~~~vl~~~~~f~~~~~-~~~~~~lvgh~~~FD~~fL~~~~~~------------- 115 (173)
T cd06135 51 MDEWCTEMHTKSGLT-ERVRASTVTLAQAEAELLEFIKKYV-PKGKSPLAGNSVHQDRRFLDKYMPE------------- 115 (173)
T ss_pred ccHHHHHcccccccH-HHHHhCCCCHHHHHHHHHHHHHHhc-CCCCCceeecchhhCHHHHHHHHHH-------------
Confidence 11122211223443 2233445444432222221 0111 11223566666 8999999887631
Q ss_pred HHhhC-CccccchhhhHhhhcccCcHHHHHHHcCCccCCCCccchhhHHHHHHHHHHHHHH
Q 023991 190 IRIYF-PTVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKEN 249 (274)
Q Consensus 190 l~~~F-P~iyDtK~la~~~~~l~~~L~~la~~L~~~r~~~~HqAGsDs~lT~~~F~~l~~~ 249 (274)
....+ ....|+..+.+..+.+...+.+ ++++ .+..|.|=+|+.-|...+...++.
T Consensus 116 ~~~~~~~~~~D~~~l~~l~~~l~p~~~~----~~~~-~~~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 116 LEEYLHYRILDVSSIKELARRWYPEIYR----KAPK-KKGTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred HhccCCcchhhHHHHHHHHHHhCcHhhh----cCCC-CCCCcchHHHHHHHHHHHHHHHHH
Confidence 01112 2345653322222222222221 2333 346799999999999988876653
No 54
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=94.19 E-value=0.87 Score=39.50 Aligned_cols=87 Identities=21% Similarity=0.132 Sum_probs=56.6
Q ss_pred cccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc------------ccCcHHHHH
Q 023991 151 VLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS------------LHGGLNKLA 218 (274)
Q Consensus 151 ~~~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~------------l~~~L~~la 218 (274)
+.++++.=|.++...|+..|.+.+. . ++. . + ....+++|+..+++.... -.-||..++
T Consensus 78 l~d~~i~KVg~~~~~D~~~L~~~~~-~-~~~-~--~-----~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~ 147 (193)
T cd06146 78 FEDPDVLKLGFGFKQDLKALSASYP-A-LKC-M--F-----ERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLV 147 (193)
T ss_pred hCCCCeeEEEechHHHHHHHHHhcC-c-ccc-c--c-----ccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHH
Confidence 3456666677777889999887652 1 111 0 0 012479999988887531 235899988
Q ss_pred HHc-CCc------------c---CCCCccchhhHHHHHHHHHHHH
Q 023991 219 ELL-EVE------------R---VGICHQAGSDSLLTASTFRKLK 247 (274)
Q Consensus 219 ~~L-~~~------------r---~~~~HqAGsDs~lT~~~F~~l~ 247 (274)
+.+ |++ | ....+-|..|++....+|.+|.
T Consensus 148 ~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 148 QEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 754 432 1 1234559999999999999985
No 55
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=93.15 E-value=0.6 Score=50.71 Aligned_cols=84 Identities=24% Similarity=0.254 Sum_probs=62.0
Q ss_pred ceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhh-ccc-CcHHHHHHHcCCccCCCCccchh
Q 023991 157 HWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCN-SLH-GGLNKLAELLEVERVGICHQAGS 234 (274)
Q Consensus 157 ~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~-~l~-~~L~~la~~L~~~r~~~~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 ILVAHNASFDMGFLNTNYEKYGLEPL-T----------NPVIDTLELARALNPEFKSHRLGTLCKKLGVEL-ERHHRADY 570 (1444)
T ss_pred EEEeccCccchhHHHHHHHHhCCccc-c----------CchhhHHHHHHHhChhhhhcchHHHHHHhCccH-HHhhhhhh
Confidence 46888889999998765521111110 0 13568877777764 443 48999999999986 67899999
Q ss_pred hHHHHHHHHHHHHHHhcC
Q 023991 235 DSLLTASTFRKLKENFFS 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 999999999999887764
No 56
>PRK10829 ribonuclease D; Provisional
Probab=92.17 E-value=3.2 Score=39.99 Aligned_cols=84 Identities=20% Similarity=0.298 Sum_probs=57.7
Q ss_pred cCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhh-cccCcHHHHHH-HcCCcc-----
Q 023991 153 SDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCN-SLHGGLNKLAE-LLEVER----- 225 (274)
Q Consensus 153 ~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~-~l~~~L~~la~-~L~~~r----- 225 (274)
++++.-|.|++.+|+..|.+.+ |. .| ..++||...+..++ +..-||..|.+ .||+.-
T Consensus 72 ~~~ivKV~H~~~~Dl~~l~~~~-g~-~p--------------~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~ 135 (373)
T PRK10829 72 DPQVTKFLHAGSEDLEVFLNAF-GE-LP--------------QPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSES 135 (373)
T ss_pred CCCeEEEEeChHhHHHHHHHHc-CC-Cc--------------CCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCcccc
Confidence 4554445666778999987754 31 12 37999999998885 33468988754 557641
Q ss_pred --------C--CCCccchhhHHHHHHHHHHHHHHhcC
Q 023991 226 --------V--GICHQAGSDSLLTASTFRKLKENFFS 252 (274)
Q Consensus 226 --------~--~~~HqAGsDs~lT~~~F~~l~~~~~~ 252 (274)
. ...+=|..|+.....+|-+|++....
T Consensus 136 ~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~ 172 (373)
T PRK10829 136 RTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEA 172 (373)
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 12344899999999999999887663
No 57
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=88.54 E-value=11 Score=32.57 Aligned_cols=85 Identities=18% Similarity=0.146 Sum_probs=54.1
Q ss_pred ccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhcc-c--------CcHHHHHHH-c
Q 023991 152 LSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNSL-H--------GGLNKLAEL-L 221 (274)
Q Consensus 152 ~~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~l-~--------~~L~~la~~-L 221 (274)
.++++..|.|....|...|.+.+ |-.+ .+++||..++..+..- . .||..+++. |
T Consensus 62 e~~~i~Kv~h~~k~D~~~L~~~~-gi~~---------------~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l 125 (197)
T cd06148 62 ESKKILKVIHDCRRDSDALYHQY-GIKL---------------NNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYL 125 (197)
T ss_pred cCCCccEEEEechhHHHHHHHhc-Cccc---------------cceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhh
Confidence 35677888888888887765443 3221 2468887666555321 1 377777665 3
Q ss_pred CCc--------------------c-C--CCCccchhhHHHHHHHHHHHHHHhcC
Q 023991 222 EVE--------------------R-V--GICHQAGSDSLLTASTFRKLKENFFS 252 (274)
Q Consensus 222 ~~~--------------------r-~--~~~HqAGsDs~lT~~~F~~l~~~~~~ 252 (274)
+++ | . ....=|..|++....+|.+|+..+..
T Consensus 126 ~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~ 179 (197)
T cd06148 126 YISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALIS 179 (197)
T ss_pred CCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 432 1 1 12234999999999999999887754
No 58
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=81.15 E-value=4.5 Score=36.00 Aligned_cols=93 Identities=22% Similarity=0.225 Sum_probs=55.0
Q ss_pred CcceEEecc-chhHHHHHHHh--CCCCCCCChHHHH----HHHHhhCCccccchhhhHhh-hcccCcHHHHHHHcCCccC
Q 023991 155 SMHWVTFHS-GYDFGYLLKLL--TCQNLPDTQVEFF----NLIRIYFPTVYDIKHLMKFC-NSLHGGLNKLAELLEVERV 226 (274)
Q Consensus 155 ~v~wvtf~g-~yD~~yL~k~l--~~~~LP~~~~~F~----~~l~~~FP~iyDtK~la~~~-~~l~~~L~~la~~L~~~r~ 226 (274)
.-.+|+|+| ++|+-+|..-. +|-++|.-++.=. ...+.|--.-.|+.-+-..- ..-+.+|..||..||++-
T Consensus 52 ~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~~~sLd~la~~lgiPg- 130 (209)
T PF10108_consen 52 NPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKARTSLDELAALLGIPG- 130 (209)
T ss_pred CCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccccCCHHHHHHHcCCCC-
Confidence 346999995 79999987433 5778886444211 01111111123332111111 122568999999999973
Q ss_pred CCCccch--------------------hhHHHHHHHHHHHHHH
Q 023991 227 GICHQAG--------------------SDSLLTASTFRKLKEN 249 (274)
Q Consensus 227 ~~~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 222233 3899999999998764
No 59
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=77.53 E-value=8.4 Score=32.26 Aligned_cols=83 Identities=22% Similarity=0.227 Sum_probs=55.3
Q ss_pred CCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc-c-cCcHHHHHHHc-CCccC----
Q 023991 154 DSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS-L-HGGLNKLAELL-EVERV---- 226 (274)
Q Consensus 154 ~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~-l-~~~L~~la~~L-~~~r~---- 226 (274)
.+++.|+++..+|+.+|.+. |-++| +.++||..++..+.. . ..+|+++++.+ +..-+
T Consensus 66 ~~~~~v~hn~k~d~~~l~~~--gi~~~--------------~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~ 129 (193)
T cd06139 66 PSIKKVGQNLKFDLHVLANH--GIELR--------------GPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFED 129 (193)
T ss_pred CCCcEEeeccHHHHHHHHHC--CCCCC--------------CCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHH
Confidence 45678999999999887643 43332 256888888877743 2 35788887764 32200
Q ss_pred --C---------------CCccchhhHHHHHHHHHHHHHHhcC
Q 023991 227 --G---------------ICHQAGSDSLLTASTFRKLKENFFS 252 (274)
Q Consensus 227 --~---------------~~HqAGsDs~lT~~~F~~l~~~~~~ 252 (274)
+ ..|-|..|+.++..++.+|.....+
T Consensus 130 ~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 130 LVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred HcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 0 1224788899999999998887653
No 60
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=72.66 E-value=1.5 Score=36.23 Aligned_cols=71 Identities=23% Similarity=0.328 Sum_probs=37.8
Q ss_pred cceEEecc-chhHHHHHHHhCCCCCCCChHHHHHHHHhhCC-ccccchhhhHhhhcccC-cHHHHHHHcCCccCCCCccc
Q 023991 156 MHWVTFHS-GYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFP-TVYDIKHLMKFCNSLHG-GLNKLAELLEVERVGICHQA 232 (274)
Q Consensus 156 v~wvtf~g-~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP-~iyDtK~la~~~~~l~~-~L~~la~~L~~~r~~~~HqA 232 (274)
-.+|+||| .||+.+|-+.+..-.+|. | ...|+..+++.... .+ +|..||+.||.+|. .....
T Consensus 58 ~~iv~yng~~FD~p~L~~~~~~~~~~~-------------~~~~iDl~~~~~~~~~-~~~~Lk~ve~~lg~~~~-~~~~~ 122 (164)
T PF13482_consen 58 DNIVTYNGKNFDIPFLKRRAKRYGLPP-------------PFNHIDLLKIIKKHFL-ESYSLKNVEKFLGIERR-DDDIS 122 (164)
T ss_dssp --EEESSTTTTHHHHHHHHH-HHHH---------------GGGEEEHHHHHT-TTS-CCTT--SHHH------------H
T ss_pred CeEEEEeCcccCHHHHHHHHHHcCCCc-------------ccchhhHHHHHHhccC-CCCCHHHHhhhcccccc-cCCCC
Confidence 36999996 789999999983323343 3 56788777765433 55 89999999999873 22346
Q ss_pred hhhHHHHHH
Q 023991 233 GSDSLLTAS 241 (274)
Q Consensus 233 GsDs~lT~~ 241 (274)
|+++.-.-.
T Consensus 123 G~~~~~~~~ 131 (164)
T PF13482_consen 123 GSESVKLYK 131 (164)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 777665543
No 61
>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=70.78 E-value=7.9 Score=34.03 Aligned_cols=68 Identities=22% Similarity=0.223 Sum_probs=42.7
Q ss_pred ceEEecc-chhHHHHHHHh--CCCCCCCChHHHHHHHHhhC----CccccchhhhHhhhcc-cCcHHHHHHHcCCcc
Q 023991 157 HWVTFHS-GYDFGYLLKLL--TCQNLPDTQVEFFNLIRIYF----PTVYDIKHLMKFCNSL-HGGLNKLAELLEVER 225 (274)
Q Consensus 157 ~wvtf~g-~yD~~yL~k~l--~~~~LP~~~~~F~~~l~~~F----P~iyDtK~la~~~~~l-~~~L~~la~~L~~~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 RLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDW-NYRNRYSERHLDLMDLLAFYGARARASLDLLAKLLGIPG 170 (208)
T ss_pred EEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchh-hccCcCCCCcccHHHHHhccCccCCCCHHHHHHHhCCCC
Confidence 6899997 79999998754 4666665443221111 111 1266766555443332 458999999999964
No 62
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=62.53 E-value=2.7 Score=42.79 Aligned_cols=152 Identities=6% Similarity=-0.054 Sum_probs=88.3
Q ss_pred cceEEEcCcc--cHHHHHHHHHHHhhcCCeeeEecccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeeecCC
Q 023991 9 SIQIREVWSD--NLELEFDLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSDENG 86 (274)
Q Consensus 9 ~~~v~eVw~~--Nf~~e~~~I~~~i~~~~fIAiDtEf~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~~~g 86 (274)
.+.+..+-+. |....++.....+.+..+.+++.|+.++...+ ......+..+++++.-.....++-+|+...--.-
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~ 178 (564)
T KOG1990|consen 101 RSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSD--RLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSI 178 (564)
T ss_pred ecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCC--CccchhhhchhhhhcccChhccCCCCChhhhhhH
Confidence 4455566666 78888777777778889999999999987553 2233456777777777766666666665443211
Q ss_pred CCCCCCCCCeeEEEeeecccCCCCCCCchhHHHHHHHcCCCccchhhcCCchhH-------HHHHHHHhcccccCCcceE
Q 023991 87 NLPTCGTDKYCVWQFNFREFDVNEDIFANDSIELLKQSGINFTKNNEIGIDAMR-------FGEFMMSSGIVLSDSMHWV 159 (274)
Q Consensus 87 ~~p~~~~~~~~~w~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~-------f~e~l~~Sgl~~~~~v~wv 159 (274)
+........+.+..++-..++.......+..+++..++.+++ ..+.+|+.... +.+...+.+++...+.-.+
T Consensus 179 ~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k-~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~d 257 (564)
T KOG1990|consen 179 ESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAK-ILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLD 257 (564)
T ss_pred HHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHH-HHHHhcchhhhccchHHHHHHHHhcCCeEEeecccee
Confidence 110000001233333222255444556677777777777777 66667776642 2233344456555554455
Q ss_pred Eecc
Q 023991 160 TFHS 163 (274)
Q Consensus 160 tf~g 163 (274)
.++-
T Consensus 258 v~y~ 261 (564)
T KOG1990|consen 258 VMYR 261 (564)
T ss_pred eeee
Confidence 5544
No 63
>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=62.13 E-value=15 Score=30.50 Aligned_cols=80 Identities=16% Similarity=0.058 Sum_probs=54.3
Q ss_pred ccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc-ccCcHHHHHHH-cCCcc----
Q 023991 152 LSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS-LHGGLNKLAEL-LEVER---- 225 (274)
Q Consensus 152 ~~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~-l~~~L~~la~~-L~~~r---- 225 (274)
.++++..|+++...|+..|.+.. +-+ +.+++||..++..+.. -+.||+.+++. ||++-
T Consensus 64 ~d~~i~Kvg~~~k~D~~~L~~~~-gi~---------------~~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~ 127 (161)
T cd06129 64 ENPSIVKALHGIEGDLWKLLRDF-GEK---------------LQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSI 127 (161)
T ss_pred CCCCEEEEEeccHHHHHHHHHHc-CCC---------------cccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccc
Confidence 34567778887777877765532 322 2356898888777643 24589998876 46531
Q ss_pred -----------CCCCccchhhHHHHHHHHHHHH
Q 023991 226 -----------VGICHQAGSDSLLTASTFRKLK 247 (274)
Q Consensus 226 -----------~~~~HqAGsDs~lT~~~F~~l~ 247 (274)
....+-|..|++....+|-+|+
T Consensus 128 ~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 128 SCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred eeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 1234569999999999999986
No 64
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=47.33 E-value=18 Score=34.64 Aligned_cols=26 Identities=35% Similarity=0.588 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhhcCCeeeEecccccc
Q 023991 21 ELEFDLIRKIVDDYPYVAMDTEFPGI 46 (274)
Q Consensus 21 ~~e~~~I~~~i~~~~fIAiDtEf~Gl 46 (274)
.+++..+.+.+..++.||+||||...
T Consensus 5 ~~~l~~~~~~l~~~~~ia~DtE~~~~ 30 (367)
T TIGR01388 5 DDELATVCEAVRTFPFVALDTEFVRE 30 (367)
T ss_pred HHHHHHHHHHHhcCCEEEEeccccCC
Confidence 35677777778889999999999765
No 65
>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=44.51 E-value=23 Score=29.55 Aligned_cols=29 Identities=28% Similarity=0.361 Sum_probs=26.9
Q ss_pred cCcccHHHHHHHHHHHhhcCCeeeEeccc
Q 023991 15 VWSDNLELEFDLIRKIVDDYPYVAMDTEF 43 (274)
Q Consensus 15 Vw~~Nf~~e~~~I~~~i~~~~fIAiDtEf 43 (274)
|.+-|++|.++.|.+.-++.-.||+|.-.
T Consensus 44 VHA~NL~e~l~~I~~~~~~~~iIAIDAcL 72 (140)
T TIGR02841 44 VHAKNLEEKLKIIKKKHPNPFIIAIDACL 72 (140)
T ss_pred cccccHHHHHHHHHHhCCCCeEEEEECcc
Confidence 78999999999999999999999999755
No 66
>KOG4013 consensus Predicted Cu2+ homeostasis protein CutC [Inorganic ion transport and metabolism]
Probab=43.54 E-value=34 Score=30.45 Aligned_cols=86 Identities=23% Similarity=0.292 Sum_probs=54.4
Q ss_pred chhHHHHHHHcC---CCccchhhcC-CchhHHHHHHHHhcccccCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHH
Q 023991 114 ANDSIELLKQSG---INFTKNNEIG-IDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNL 189 (274)
Q Consensus 114 ~~~Si~fL~~~G---fDFnk~~~~G-I~~~~f~e~l~~Sgl~~~~~v~wvtf~g~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 466788999875 5588877776 4444333444343 3357999999999864333321100 02468888
Q ss_pred HHhhC-CccccchhhhHhh
Q 023991 190 IRIYF-PTVYDIKHLMKFC 207 (274)
Q Consensus 190 l~~~F-P~iyDtK~la~~~ 207 (274)
|..=| |.-.|--|+.+++
T Consensus 155 LtSG~~psAldGv~~i~~l 173 (255)
T KOG4013|consen 155 LTSGQEPSALDGVYIIREL 173 (255)
T ss_pred hhcCCCcccccchHHHHHH
Confidence 88888 7766766666655
No 67
>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=43.11 E-value=71 Score=29.56 Aligned_cols=68 Identities=7% Similarity=-0.040 Sum_probs=46.6
Q ss_pred EcCcccHHHHHHHHHHHhhcCC---eeeEec------ccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeee
Q 023991 14 EVWSDNLELEFDLIRKIVDDYP---YVAMDT------EFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSD 83 (274)
Q Consensus 14 eVw~~Nf~~e~~~I~~~i~~~~---fIAiDt------Ef~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~ 83 (274)
+|++...++.+..+.+.++..+ ||++|+ .+||+.... +..-+..+--+.++.-....+++=+.|+=++
T Consensus 196 ~i~~~g~~~v~~~~~~~l~~~~~~vyvS~DiDvlDps~aPgv~tp~--pgGl~~~e~~~~l~~i~~~~~v~g~DivE~~ 272 (300)
T TIGR01229 196 EIDELGIGKVVEETLEYLKAEDGPIHLSLDVDGLDPSLAPATGTPV--VGGLTFREGLLIMEMLYETGLLTALDVVEVN 272 (300)
T ss_pred HHhhhhHHHHHHHHHHHHhcCCCeEEEEEeccccCcccCCCCCCCC--CCCCCHHHHHHHHHHHHhcCCEEEEEEEEEC
Confidence 4556666777888888886655 999997 678876542 2234677777888877766667656655444
No 68
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=41.90 E-value=50 Score=30.41 Aligned_cols=76 Identities=17% Similarity=0.275 Sum_probs=49.4
Q ss_pred ceEEecc-chhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhh-c--ccCcHHHHHHHcCCccCCCCccc
Q 023991 157 HWVTFHS-GYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCN-S--LHGGLNKLAELLEVERVGICHQA 232 (274)
Q Consensus 157 ~wvtf~g-~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~-~--l~~~L~~la~~L~~~r~~~~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 6999998 579988886433 345544332 3467777777763 2 3679999999999998431 24
Q ss_pred hhhHHHHHHHHHH
Q 023991 233 GSDSLLTASTFRK 245 (274)
Q Consensus 233 GsDs~lT~~~F~~ 245 (274)
|+|+-..-.-|.+
T Consensus 225 G~~~p~lyr~~~~ 237 (278)
T COG3359 225 GYDGPELYRLYRR 237 (278)
T ss_pred CcchHHHHHHHHH
Confidence 5666555544443
No 69
>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=41.71 E-value=96 Score=24.25 Aligned_cols=53 Identities=19% Similarity=0.244 Sum_probs=34.3
Q ss_pred cCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc-c-cCcHHHHHHHc
Q 023991 153 SDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS-L-HGGLNKLAELL 221 (274)
Q Consensus 153 ~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~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 445667778777787776543 21222 367899888877743 2 34899988775
No 70
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=38.85 E-value=26 Score=31.74 Aligned_cols=96 Identities=21% Similarity=0.198 Sum_probs=60.1
Q ss_pred eccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhcccCcHHHHHHHcCCccCCCCccchhhHHHHH
Q 023991 161 FHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTA 240 (274)
Q Consensus 161 f~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~l~~~L~~la~~L~~~r~~~~HqAGsDs~lT~ 240 (274)
|...||+.|++|...+ +-.-+.+++..+...= ...+.+.-.-.|.. |+.+..+|.......+-.++|..
T Consensus 197 fP~fYDik~v~ks~~~--~~KglQei~ndlql~r--------~g~QhQagsdaLlT-a~~ff~~R~~~F~~sig~~ll~~ 265 (299)
T COG5228 197 FPNFYDIKLVYKSVLN--NSKGLQEIKNDLQLQR--------SGQQHQAGSDALLT-ADEFFLPRFSIFTTSIGQSLLML 265 (299)
T ss_pred CccccchHHHHHhhhh--hhhHHHHhcCcHhhhc--------cchhhhccchhhhh-hHHhcchhhheecccccHHHHHH
Confidence 7788999999977532 2233444444332110 00111101123433 88999999777777777888888
Q ss_pred HHHHHHHHHhc---C--CCccccccEEeecCC
Q 023991 241 STFRKLKENFF---S--SSLEKYAGVLYGLGV 267 (274)
Q Consensus 241 ~~F~~l~~~~~---~--~~~~~~~g~i~Gl~~ 267 (274)
..++.+++.-. + .++.++.|+|||+..
T Consensus 266 L~g~~~~~~sl~~~~~~t~f~~~~g~~~gi~~ 297 (299)
T COG5228 266 LSGCQLSKLSLHKFPNGTDFAKYQGVIYGIDG 297 (299)
T ss_pred HhccccCCchheeCCCcccHhhcCCcccCCCC
Confidence 88888776543 2 257899999999854
No 71
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=38.35 E-value=25 Score=30.81 Aligned_cols=69 Identities=16% Similarity=0.112 Sum_probs=38.9
Q ss_pred ceEEecc-chhHHHHHHHhCCCCCCCChHHHHH-------------HH---Hh--hCCc-cccchhhhHhh----hccc-
Q 023991 157 HWVTFHS-GYDFGYLLKLLTCQNLPDTQVEFFN-------------LI---RI--YFPT-VYDIKHLMKFC----NSLH- 211 (274)
Q Consensus 157 ~wvtf~g-~yD~~yL~k~l~~~~LP~~~~~F~~-------------~l---~~--~FP~-iyDtK~la~~~----~~l~- 211 (274)
.++++++ +||+.||.+-...-.+|.++..... .. .. ..++ +.|+-.+.+.. ..+.
T Consensus 76 ii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~s 155 (207)
T cd05785 76 VIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPS 155 (207)
T ss_pred EEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCC
Confidence 5778998 8999999987632222222111100 00 01 1123 47887766642 1342
Q ss_pred CcHHHHHHHcCCcc
Q 023991 212 GGLNKLAELLEVER 225 (274)
Q Consensus 212 ~~L~~la~~L~~~r 225 (274)
-+|+.||+.+|+..
T Consensus 156 ysL~~Va~~~g~~~ 169 (207)
T cd05785 156 YGLKAVAKHFGLAS 169 (207)
T ss_pred CCHHHHHHHhcccC
Confidence 38999999987643
No 72
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=38.34 E-value=15 Score=33.92 Aligned_cols=54 Identities=22% Similarity=0.317 Sum_probs=39.9
Q ss_pred ccccchhhhHhhh----cccCcHHHHHHH-cCCcc-CCCCccchhhHHHHHHHHHHHHHHh
Q 023991 196 TVYDIKHLMKFCN----SLHGGLNKLAEL-LEVER-VGICHQAGSDSLLTASTFRKLKENF 250 (274)
Q Consensus 196 ~iyDtK~la~~~~----~l~~~L~~la~~-L~~~r-~~~~HqAGsDs~lT~~~F~~l~~~~ 250 (274)
-|.||-+.--.++ ...-||.+|++. ||.+- .|. |..=-|+--|++.|.+++...
T Consensus 207 ~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~Ge-HsSvEDA~AtM~LY~~vk~qw 266 (280)
T KOG2249|consen 207 MIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGE-HSSVEDARATMELYKRVKVQW 266 (280)
T ss_pred hhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccc-cCcHHHHHHHHHHHHHHHHHH
Confidence 3788876555443 235689999874 57665 455 999999999999999988764
No 73
>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=37.38 E-value=44 Score=23.34 Aligned_cols=32 Identities=22% Similarity=0.378 Sum_probs=23.5
Q ss_pred chhHHHHHHHcCCCc---------cchhhcCCchhHHHHHH
Q 023991 114 ANDSIELLKQSGINF---------TKNNEIGIDAMRFGEFM 145 (274)
Q Consensus 114 ~~~Si~fL~~~GfDF---------nk~~~~GI~~~~f~e~l 145 (274)
.+.+.+.++++|||| ....+.||+...+-+.|
T Consensus 12 ~p~~a~vf~~~gIDfCCgG~~~L~eA~~~~~ld~~~vl~~L 52 (56)
T PF04405_consen 12 DPRAARVFRKYGIDFCCGGNRSLEEACEEKGLDPEEVLEEL 52 (56)
T ss_pred ChHHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHH
Confidence 467888999999999 34456777777765554
No 74
>PRK13772 formimidoylglutamase; Provisional
Probab=36.22 E-value=1.3e+02 Score=28.12 Aligned_cols=69 Identities=13% Similarity=0.161 Sum_probs=47.2
Q ss_pred EEcCcccHHHHHHHHHHHhhcCC--eeeEec------ccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeee
Q 023991 13 REVWSDNLELEFDLIRKIVDDYP--YVAMDT------EFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSD 83 (274)
Q Consensus 13 ~eVw~~Nf~~e~~~I~~~i~~~~--fIAiDt------Ef~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~ 83 (274)
.|++..++++.+..|++.++..+ ||++|. ..||+..... ..-+..+-.+.+|.-.+.-+++=+.|+-++
T Consensus 217 ~e~~~~g~~~~~~~i~~~l~~~~~vylS~DiD~lDps~aPGvgtP~p--gGlt~~e~~~il~~l~~~~~v~g~DvvEv~ 293 (314)
T PRK13772 217 VDMQERHLDARLAELDALLDAADHVYLTIDLDVLPAAVAPGVSAPAA--YGVPLPVVEEIVLHVRASGKLRVADLAEYN 293 (314)
T ss_pred hhhhhcCHHHHHHHHHHHHhcCCeEEEEEEecCcCcccCCCCCCCCC--CCCCHHHHHHHHHHHHhcCCeeEEEEEEEC
Confidence 45666778888888888887544 889997 4778765522 234778888888876665566655555444
No 75
>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=29.43 E-value=51 Score=28.22 Aligned_cols=30 Identities=27% Similarity=0.224 Sum_probs=27.4
Q ss_pred cCcccHHHHHHHHHHHhhcCCeeeEecccc
Q 023991 15 VWSDNLELEFDLIRKIVDDYPYVAMDTEFP 44 (274)
Q Consensus 15 Vw~~Nf~~e~~~I~~~i~~~~fIAiDtEf~ 44 (274)
|.+-|+++.++.|.+.-++.-.||+|.-..
T Consensus 68 VHA~NL~e~l~~I~~~~~~~~IIAIDAcLG 97 (163)
T PF06866_consen 68 VHALNLEETLNEIKKKHPNPFIIAIDACLG 97 (163)
T ss_pred cchhhHHHHHHHHHHHCCCCeEEEEECCCC
Confidence 889999999999999989999999998663
No 76
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=29.37 E-value=60 Score=28.88 Aligned_cols=68 Identities=22% Similarity=0.223 Sum_probs=40.1
Q ss_pred ceEEecc-chhHHHHHHHhCCCCCCCChHHHHHH---------------HHhhCC-c-cccchhhhHhhhcccC-cHHHH
Q 023991 157 HWVTFHS-GYDFGYLLKLLTCQNLPDTQVEFFNL---------------IRIYFP-T-VYDIKHLMKFCNSLHG-GLNKL 217 (274)
Q Consensus 157 ~wvtf~g-~yD~~yL~k~l~~~~LP~~~~~F~~~---------------l~~~FP-~-iyDtK~la~~~~~l~~-~L~~l 217 (274)
-.++++. ++|+.||++-+..-.+| .+..+-.. .+..++ + +.|+.-.++..-.+.+ +|++|
T Consensus 100 iivG~Ni~~fdl~~L~~R~~~l~i~-~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~~k~~~~~~sY~L~~v 178 (234)
T cd05776 100 VLVGHDLEGFDLDVLLSRIQELKVP-HWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLSAKELIRCKSYDLTEL 178 (234)
T ss_pred EEEeeccCCCCHHHHHHHHHHhCCC-ccccccccccccCccccccccccccccccCchhhccHHHHHHHhCCCCCChHHH
Confidence 3566664 89999999887422222 11111111 122333 2 7788887776633443 89999
Q ss_pred HH-HcCCcc
Q 023991 218 AE-LLEVER 225 (274)
Q Consensus 218 a~-~L~~~r 225 (274)
|+ .||.+|
T Consensus 179 a~~~Lg~~k 187 (234)
T cd05776 179 SQQVLGIER 187 (234)
T ss_pred HHHHhCcCc
Confidence 98 778766
No 77
>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=28.02 E-value=2.6e+02 Score=26.71 Aligned_cols=83 Identities=25% Similarity=0.331 Sum_probs=54.3
Q ss_pred cCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc-ccCcHHHHHHH-cCCccCC---
Q 023991 153 SDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS-LHGGLNKLAEL-LEVERVG--- 227 (274)
Q Consensus 153 ~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~-l~~~L~~la~~-L~~~r~~--- 227 (274)
++++.+|+|+..+|+..|.+.. ..+| ..++||...+..++. ...||..+++. ||++-..
T Consensus 68 d~~i~KV~h~~k~Dl~~L~~~~--~~~~--------------~~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~ 131 (367)
T TIGR01388 68 DESVVKVLHAASEDLEVFLNLF--GELP--------------QPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSES 131 (367)
T ss_pred CCCceEEEeecHHHHHHHHHHh--CCCC--------------CCcccHHHHHHHhCCCCCccHHHHHHHHcCCCCCcccc
Confidence 4577889888888988775542 2334 267899988877742 24589988765 4553100
Q ss_pred ---------C---CccchhhHHHHHHHHHHHHHHhc
Q 023991 228 ---------I---CHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 228 ---------~---~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
. .+-|..|+.....++-+|++...
T Consensus 132 ~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 132 RTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLE 167 (367)
T ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0 11277788777888888877664
No 78
>PRK13775 formimidoylglutamase; Provisional
Probab=27.08 E-value=1.7e+02 Score=27.56 Aligned_cols=69 Identities=12% Similarity=0.197 Sum_probs=44.3
Q ss_pred EEcCcccHHHHHHHHHHHhhcCC--eeeEec------ccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeee
Q 023991 13 REVWSDNLELEFDLIRKIVDDYP--YVAMDT------EFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSD 83 (274)
Q Consensus 13 ~eVw~~Nf~~e~~~I~~~i~~~~--fIAiDt------Ef~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~ 83 (274)
.+|++.+.++.+..+.+.++..+ ||++|. ..||+..... ..-+..+-.+.+|.-+..-+++=+.|+=++
T Consensus 224 ~~i~~~g~~~v~~~~~~~~~~~~~vyvS~DiD~lDps~aPGtgtP~p--gGLt~~e~~~il~~l~~~~~vvg~DivEv~ 300 (328)
T PRK13775 224 QDIYQMGHQKVCRAIDRFLEGQERVYLTIDMDCFSVGAAPGVSAIQS--LGVDPNLAVLVLQHIAASGKLVGFDVVEVS 300 (328)
T ss_pred HHhhhcCHHHHHHHHHHHHhcCCeEEEEEEcCccCcccCCCCCCCCC--CCCCHHHHHHHHHHHHhCCCEEEEEEEEEC
Confidence 35555566666777777776555 999997 5677765422 234677777788886665566655555443
No 79
>PF13606 Ank_3: Ankyrin repeat
Probab=25.89 E-value=58 Score=19.30 Aligned_cols=17 Identities=12% Similarity=0.270 Sum_probs=14.6
Q ss_pred chhHHHHHHHcCCCccc
Q 023991 114 ANDSIELLKQSGINFTK 130 (274)
Q Consensus 114 ~~~Si~fL~~~GfDFnk 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 80
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=25.52 E-value=3.4e+02 Score=21.46 Aligned_cols=80 Identities=18% Similarity=0.208 Sum_probs=46.7
Q ss_pred cCCcceEEeccchhHHHHHHHhCCCCCCCChHHHHHHHHhhCCccccchhhhHhhhc-cc-CcHHHHHHHc-CCc--c-C
Q 023991 153 SDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRIYFPTVYDIKHLMKFCNS-LH-GGLNKLAELL-EVE--R-V 226 (274)
Q Consensus 153 ~~~v~wvtf~g~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~FP~iyDtK~la~~~~~-l~-~~L~~la~~L-~~~--r-~ 226 (274)
+++++-|+++..+|+..|.+ .|-+++ +++||..++..+.. -. .+|+++++.+ +.+ . .
T Consensus 73 ~~~~~kv~~d~k~~~~~L~~--~gi~~~---------------~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~ 135 (172)
T smart00474 73 DETITKVGHNAKFDLHVLAR--FGIELE---------------NIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEE 135 (172)
T ss_pred CCCceEEEechHHHHHHHHH--CCCccc---------------chhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCccc
Confidence 34567788877778777654 354443 24788777665432 22 4788887664 332 1 0
Q ss_pred CC--------Cc----cchhhHHHHHHHHHHHHHH
Q 023991 227 GI--------CH----QAGSDSLLTASTFRKLKEN 249 (274)
Q Consensus 227 ~~--------~H----qAGsDs~lT~~~F~~l~~~ 249 (274)
+. .. .|..|++.+...+-+|.+.
T Consensus 136 ~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~ 170 (172)
T smart00474 136 QKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKE 170 (172)
T ss_pred CccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 10 11 2677777777777776654
No 81
>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=25.34 E-value=73 Score=20.95 Aligned_cols=29 Identities=17% Similarity=0.399 Sum_probs=20.6
Q ss_pred chhHHHHHHHcCCCccchhhcCCchhHHH
Q 023991 114 ANDSIELLKQSGINFTKNNEIGIDAMRFG 142 (274)
Q Consensus 114 ~~~Si~fL~~~GfDFnk~~~~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 57789999999999999999998886554
No 82
>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=24.09 E-value=44 Score=21.88 Aligned_cols=34 Identities=18% Similarity=0.305 Sum_probs=26.2
Q ss_pred CCChHHHHHHHHhhCCccccchhhhHhhhcccCc
Q 023991 180 PDTQVEFFNLIRIYFPTVYDIKHLMKFCNSLHGG 213 (274)
Q Consensus 180 P~~~~~F~~~l~~~FP~iyDtK~la~~~~~l~~~ 213 (274)
|+.+++|++.++.+=-...|.+-+.+.+..|-++
T Consensus 1 p~~Y~~FL~il~~y~~~~~~~~~v~~~v~~Ll~~ 34 (47)
T PF02671_consen 1 PEVYNEFLKILNDYKKGRISRSEVIEEVSELLRG 34 (47)
T ss_dssp HHHHHHHHHHHHHHHCTCSCHHHHHHHHHHHTTT
T ss_pred ChHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcc
Confidence 6678999999999888788887777776655444
No 83
>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=23.11 E-value=76 Score=26.33 Aligned_cols=32 Identities=34% Similarity=0.502 Sum_probs=26.3
Q ss_pred HHHHcCCCccchhhc-CCchhHHHHHHHHhccc
Q 023991 120 LLKQSGINFTKNNEI-GIDAMRFGEFMMSSGIV 151 (274)
Q Consensus 120 fL~~~GfDFnk~~~~-GI~~~~f~e~l~~Sgl~ 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 446789999999875 58899999999888753
No 84
>PRK02190 agmatinase; Provisional
Probab=22.86 E-value=2.5e+02 Score=25.96 Aligned_cols=66 Identities=18% Similarity=0.282 Sum_probs=43.0
Q ss_pred cCcccHHHHHHHHHHHhhcCC-eeeEec------ccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeee
Q 023991 15 VWSDNLELEFDLIRKIVDDYP-YVAMDT------EFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSD 83 (274)
Q Consensus 15 Vw~~Nf~~e~~~I~~~i~~~~-fIAiDt------Ef~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~ 83 (274)
|++...++.+..+.+.+...+ ||++|. ..||+..... ..-+..+-...++. +...+++=+.|+-++
T Consensus 199 ~~~~g~~~~~~~~~~~l~~~~vyiSiDiDvlDps~aPg~~~p~p--gGl~~~e~~~il~~-i~~~~vvg~DivE~~ 271 (301)
T PRK02190 199 VNDRGVDAIIAQIKQIVGDMPVYLTFDIDCLDPAFAPGTGTPVI--GGLTSAQALKILRG-LKGLNIVGMDVVEVA 271 (301)
T ss_pred hhccCHHHHHHHHHHHhCCCEEEEEEeecccCcccCCCCCCCCC--CCcCHHHHHHHHHH-HhcCCeEEEEeeeec
Confidence 455567777788888876554 999998 6777765422 23467777777776 333566666666554
No 85
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=22.29 E-value=1.9e+02 Score=19.51 Aligned_cols=36 Identities=31% Similarity=0.340 Sum_probs=26.9
Q ss_pred HHHHHcCCcc--C---CCCccchhhHHHHHHHHHHHHHHhc
Q 023991 216 KLAELLEVER--V---GICHQAGSDSLLTASTFRKLKENFF 251 (274)
Q Consensus 216 ~la~~L~~~r--~---~~~HqAGsDs~lT~~~F~~l~~~~~ 251 (274)
-+++.++++. + ....+.|.||+...+.-.++.+.|-
T Consensus 6 ~~~~~l~~~~~~i~~~~~~~~lG~DSl~~~~l~~~l~~~~g 46 (67)
T PF00550_consen 6 IIAEVLGVDPEEIDPDTDFFDLGLDSLDAIELVSELEEEFG 46 (67)
T ss_dssp HHHHHHTSSGGCTSTTSBTTTTTSSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHCcCHhhCCCCCCHHHhCCchHHHHHHHHHHHHHHc
Confidence 4667777543 2 3455799999999999888988874
No 86
>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=22.04 E-value=1.3e+02 Score=19.15 Aligned_cols=30 Identities=13% Similarity=0.283 Sum_probs=18.1
Q ss_pred HHHHHhhCCccccchhhhHhhhcccCcHHHH
Q 023991 187 FNLIRIYFPTVYDIKHLMKFCNSLHGGLNKL 217 (274)
Q Consensus 187 ~~~l~~~FP~iyDtK~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 5555555554444555443
No 87
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=21.78 E-value=61 Score=25.15 Aligned_cols=15 Identities=40% Similarity=0.552 Sum_probs=11.8
Q ss_pred HHHHhCCCCCCCChH
Q 023991 170 LLKLLTCQNLPDTQV 184 (274)
Q Consensus 170 L~k~l~~~~LP~~~~ 184 (274)
++..+||+|||.+.+
T Consensus 62 FLHA~TGQPLP~D~D 76 (105)
T PRK05264 62 FLHAFTGQPLPDDED 76 (105)
T ss_pred HHHHHcCCCCCChhh
Confidence 467789999998753
No 88
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=20.87 E-value=90 Score=25.74 Aligned_cols=22 Identities=23% Similarity=0.267 Sum_probs=16.8
Q ss_pred HHHHHHhh-cCCeeeEecccccc
Q 023991 25 DLIRKIVD-DYPYVAMDTEFPGI 46 (274)
Q Consensus 25 ~~I~~~i~-~~~fIAiDtEf~Gl 46 (274)
..+.+.+. +.+.|++|||+...
T Consensus 3 ~~~~~~l~~~~~~ig~D~E~~~~ 25 (161)
T cd06129 3 SSLCEDLSMDGDVIAFDMEWPPG 25 (161)
T ss_pred HHHHHHHhcCCCEEEEECCccCC
Confidence 34455566 99999999999754
No 89
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=20.30 E-value=68 Score=24.74 Aligned_cols=15 Identities=40% Similarity=0.510 Sum_probs=11.7
Q ss_pred HHHHhCCCCCCCChH
Q 023991 170 LLKLLTCQNLPDTQV 184 (274)
Q Consensus 170 L~k~l~~~~LP~~~~ 184 (274)
++..+||+|||.+.+
T Consensus 61 FLHAfTGQPLP~D~D 75 (103)
T cd00490 61 FLHAFTGQPLPDDAD 75 (103)
T ss_pred HHHHhcCCCCCChhh
Confidence 467789999998743
No 90
>TIGR01227 hutG formimidoylglutamase. Formiminoglutamase, the fourth enzyme of histidine degradation, is similar to arginases and agmatinases. It is often encoded near other enzymes of the histidine degredation pathway: histidine ammonia-lyase, urocanate hydratase, and imidazolonepropionase.
Probab=20.09 E-value=3.2e+02 Score=25.25 Aligned_cols=67 Identities=13% Similarity=0.094 Sum_probs=40.9
Q ss_pred cCcccHHHHHHHHHHHhhcCC--eeeEec------ccccccccCCCCCCCCHHHHHHHHHhcccccceeeeeeeeee
Q 023991 15 VWSDNLELEFDLIRKIVDDYP--YVAMDT------EFPGIALRPVGSFKSSYEYHYQTLKSNVDMLKLIQLGLTFSD 83 (274)
Q Consensus 15 Vw~~Nf~~e~~~I~~~i~~~~--fIAiDt------Ef~Gl~~~~~~~~~~t~~~rY~~lr~nv~~~~iiQlGlt~~~ 83 (274)
|+..+.+.....++..++..+ ||++|+ ..||+..... ..-+..+-.+.+|.-....+++=+.|+=++
T Consensus 211 i~~~~~~~i~~~~~~~~~~~~~vyvs~DiDvlDps~aPgtg~p~p--gGLt~~e~~~il~~l~~~~~vvg~DvvE~~ 285 (307)
T TIGR01227 211 LRPGLLPTIKDILPVFLDKVDHIYLTVDMDVLDAAHAPGVSAPAP--GGLYPDELLELVKRIAASDKVRGAEIAEVN 285 (307)
T ss_pred hhhcCHHHHHHHHHHHHhCCCeEEEEEEecccChhhCCCCCCCCC--CCCCHHHHHHHHHHHhcCCCEEEEEEEEEC
Confidence 333444445555565555555 999998 5678765422 234778888888876665566655555443
Done!