Query 038950
Match_columns 297
No_of_seqs 168 out of 490
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 04:53:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038950.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038950hhsearch_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 2.7E-86 5.9E-91 589.6 16.9 228 6-238 1-238 (239)
2 COG5228 POP2 mRNA deadenylase 100.0 6.3E-75 1.4E-79 518.1 11.5 246 5-256 18-272 (299)
3 PF04857 CAF1: CAF1 family rib 100.0 1.2E-61 2.6E-66 448.6 18.2 223 8-234 1-262 (262)
4 KOG1990 Poly(A)-specific exori 99.2 1.1E-11 2.3E-16 126.7 2.5 219 12-236 1-360 (564)
5 PRK07942 DNA polymerase III su 98.8 1.6E-07 3.6E-12 85.9 15.1 170 27-237 4-178 (232)
6 smart00479 EXOIII exonuclease 98.8 3.2E-07 6.9E-12 77.7 15.8 161 30-236 1-164 (169)
7 cd06133 ERI-1_3'hExo_like DEDD 98.6 1.2E-06 2.5E-11 75.1 13.4 175 31-235 1-175 (176)
8 PRK09145 DNA polymerase III su 98.6 1.5E-06 3.3E-11 77.4 13.4 173 19-236 19-198 (202)
9 cd06134 RNaseT DEDDh 3'-5' exo 98.5 4.6E-06 9.9E-11 73.9 14.1 173 27-236 3-186 (189)
10 PRK07748 sporulation inhibitor 98.5 4.1E-06 9E-11 75.1 13.8 172 28-236 3-177 (207)
11 PRK05168 ribonuclease T; Provi 98.4 1.3E-05 2.9E-10 72.2 15.2 182 19-236 7-198 (211)
12 cd06131 DNA_pol_III_epsilon_Ec 98.4 1.2E-05 2.5E-10 68.9 13.8 164 31-236 1-167 (167)
13 cd06130 DNA_pol_III_epsilon_li 98.3 1.5E-05 3.2E-10 67.0 12.5 152 31-233 1-155 (156)
14 PRK07740 hypothetical protein; 98.3 1.2E-05 2.7E-10 74.1 12.6 166 27-236 57-223 (244)
15 TIGR00573 dnaq exonuclease, DN 98.3 2.2E-05 4.8E-10 70.9 13.9 168 26-236 4-174 (217)
16 PRK05711 DNA polymerase III su 98.2 3.4E-05 7.3E-10 71.3 14.7 167 28-236 3-173 (240)
17 PRK06807 DNA polymerase III su 98.1 4.3E-05 9.3E-10 73.2 13.6 162 29-237 8-170 (313)
18 PRK06063 DNA polymerase III su 98.1 6.6E-05 1.4E-09 71.9 13.8 160 28-236 14-176 (313)
19 cd06127 DEDDh DEDDh 3'-5' exon 98.1 4.8E-05 1E-09 62.6 10.5 157 32-233 1-159 (159)
20 PRK07247 DNA polymerase III su 98.0 0.0001 2.2E-09 66.1 12.9 157 30-236 6-166 (195)
21 PRK09146 DNA polymerase III su 98.0 0.00013 2.8E-09 67.3 14.0 171 26-241 44-230 (239)
22 PRK06195 DNA polymerase III su 97.9 0.00016 3.5E-09 68.9 13.4 157 30-236 2-161 (309)
23 TIGR01406 dnaQ_proteo DNA poly 97.9 0.00038 8.3E-09 63.5 15.2 166 30-236 1-169 (225)
24 TIGR01298 RNaseT ribonuclease 97.9 0.00033 7.2E-09 62.7 14.0 175 27-237 6-190 (200)
25 PRK06310 DNA polymerase III su 97.9 0.00016 3.5E-09 67.0 12.2 168 25-236 3-171 (250)
26 PRK06722 exonuclease; Provisio 97.8 0.00061 1.3E-08 64.5 14.7 171 28-236 4-178 (281)
27 PRK08517 DNA polymerase III su 97.7 0.00088 1.9E-08 62.5 14.3 165 26-237 65-229 (257)
28 PRK07883 hypothetical protein; 97.7 0.00048 1E-08 70.9 13.5 171 22-236 8-179 (557)
29 TIGR01407 dinG_rel DnaQ family 97.7 0.00067 1.5E-08 72.8 15.0 160 30-236 1-162 (850)
30 PRK08074 bifunctional ATP-depe 97.7 0.00076 1.6E-08 73.2 14.7 163 29-236 3-166 (928)
31 TIGR01405 polC_Gram_pos DNA po 97.7 0.00084 1.8E-08 74.6 14.8 164 27-236 188-352 (1213)
32 PRK05601 DNA polymerase III su 97.6 0.00047 1E-08 67.6 11.1 196 25-256 42-269 (377)
33 PRK07246 bifunctional ATP-depe 97.6 0.0012 2.6E-08 70.8 15.0 159 28-236 6-167 (820)
34 cd06138 ExoI_N N-terminal DEDD 97.6 0.00089 1.9E-08 58.8 11.5 166 33-231 2-181 (183)
35 PTZ00315 2'-phosphotransferase 97.5 0.0034 7.4E-08 64.7 15.8 173 30-236 57-252 (582)
36 PF00929 RNase_T: Exonuclease; 97.5 2.6E-05 5.6E-10 64.2 0.3 160 32-232 1-164 (164)
37 PRK11779 sbcB exonuclease I; P 97.4 0.0039 8.4E-08 63.2 14.5 175 27-236 4-195 (476)
38 cd06144 REX4_like DEDDh 3'-5' 97.3 0.0014 3.1E-08 55.8 8.9 72 143-232 79-151 (152)
39 cd06136 TREX1_2 DEDDh 3'-5' ex 97.3 0.0041 8.8E-08 54.5 12.0 157 31-234 1-176 (177)
40 PRK09182 DNA polymerase III su 97.0 0.016 3.4E-07 55.2 13.3 155 30-236 38-198 (294)
41 cd06149 ISG20 DEDDh 3'-5' exon 96.9 0.0043 9.3E-08 53.4 8.1 32 201-232 122-156 (157)
42 COG0847 DnaQ DNA polymerase II 96.9 0.036 7.8E-07 50.2 14.2 163 29-237 13-180 (243)
43 PRK00448 polC DNA polymerase I 96.8 0.015 3.3E-07 65.7 13.6 166 25-236 415-581 (1437)
44 cd06145 REX1_like DEDDh 3'-5' 96.8 0.0072 1.6E-07 51.6 8.7 70 142-232 77-149 (150)
45 PRK06309 DNA polymerase III su 96.8 0.034 7.4E-07 50.8 13.3 159 30-236 3-163 (232)
46 PRK07983 exodeoxyribonuclease 96.6 0.032 6.9E-07 50.9 11.6 147 31-238 2-153 (219)
47 COG0349 Rnd Ribonuclease D [Tr 95.6 0.052 1.1E-06 53.2 8.3 71 146-236 74-163 (361)
48 PRK05359 oligoribonuclease; Pr 95.5 0.23 4.9E-06 43.9 11.2 166 28-239 2-176 (181)
49 cd06141 WRN_exo DEDDy 3'-5' ex 94.0 0.99 2.1E-05 38.5 11.3 80 140-236 72-169 (170)
50 PRK10829 ribonuclease D; Provi 93.9 0.89 1.9E-05 44.9 12.1 75 143-236 74-167 (373)
51 PRK05755 DNA polymerase I; Pro 93.6 1.2 2.6E-05 48.4 13.6 75 145-237 373-467 (880)
52 cd06135 Orn DEDDh 3'-5' exonuc 92.9 1.1 2.4E-05 39.0 9.9 163 31-236 1-169 (173)
53 cd06146 mut-7_like_exo DEDDy 3 92.6 1.7 3.7E-05 38.5 10.9 158 16-236 7-192 (193)
54 cd06137 DEDDh_RNase DEDDh 3'-5 91.7 0.35 7.7E-06 41.5 5.2 69 144-232 86-160 (161)
55 TIGR01388 rnd ribonuclease D. 91.6 2.6 5.6E-05 41.3 11.8 143 16-236 5-163 (367)
56 PF01612 DNA_pol_A_exo1: 3'-5' 90.8 8.7 0.00019 32.0 13.0 83 134-236 72-172 (176)
57 cd06129 RNaseD_like DEDDy 3'-5 89.6 7.7 0.00017 33.0 11.6 79 140-236 66-160 (161)
58 PF13482 RNase_H_2: RNase_H su 81.6 0.75 1.6E-05 38.8 1.3 73 141-230 57-131 (164)
59 COG2176 PolC DNA polymerase II 76.2 3.6 7.9E-05 46.1 4.7 80 146-239 505-587 (1444)
60 cd06139 DNA_polA_I_Ecoli_like_ 55.3 43 0.00094 28.4 6.5 80 140-236 66-167 (193)
61 PF10108 DNA_pol_B_exo2: Predi 54.7 52 0.0011 30.1 7.1 94 141-238 52-172 (209)
62 cd05782 DNA_polB_like1_exo Unc 54.1 41 0.00089 30.2 6.4 70 142-214 94-170 (208)
63 TIGR02841 spore_YyaC putative 39.2 31 0.00068 29.7 3.0 29 10-38 44-72 (140)
64 COG5228 POP2 mRNA deadenylase 38.7 24 0.00052 32.9 2.4 102 140-256 187-298 (299)
65 KOG1990 Poly(A)-specific exori 37.5 13 0.00027 38.8 0.4 120 5-126 102-231 (564)
66 TIGR01229 rocF_arginase argina 31.9 1.4E+02 0.0031 28.2 6.5 69 8-76 195-272 (300)
67 COG3359 Predicted exonuclease 28.4 72 0.0016 30.3 3.7 75 143-232 158-235 (278)
68 PF06866 DUF1256: Protein of u 25.7 67 0.0014 28.3 2.9 30 10-39 68-97 (163)
69 PRK05264 transcriptional repre 25.0 49 0.0011 26.6 1.7 16 155-170 61-76 (105)
70 KOG4233 DNA-bridging protein B 24.2 1E+02 0.0022 24.3 3.3 41 140-182 19-70 (90)
71 cd05785 DNA_polB_like2_exo Unc 23.3 84 0.0018 28.2 3.2 70 143-214 76-169 (207)
72 cd00490 Met_repressor_MetJ Met 23.2 55 0.0012 26.2 1.7 16 155-170 60-75 (103)
73 KOG2249 3'-5' exonuclease [Rep 22.7 44 0.00096 31.8 1.3 14 31-44 107-120 (280)
74 PF05491 RuvB_C: Holliday junc 21.7 96 0.0021 24.0 2.7 31 184-214 9-39 (76)
75 cd00007 35EXOc 3'-5' exonuclea 21.5 2.8E+02 0.0061 21.9 5.8 54 140-210 53-106 (155)
76 cd05780 DNA_polB_Kod1_like_exo 21.2 81 0.0018 27.7 2.6 72 142-215 72-157 (195)
77 PF01340 MetJ: Met Apo-repress 21.1 44 0.00096 26.7 0.8 16 155-170 60-75 (104)
78 PRK08445 hypothetical protein; 20.7 1.9E+02 0.0041 28.1 5.3 86 169-257 108-210 (348)
No 1
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=2.7e-86 Score=589.60 Aligned_cols=228 Identities=45% Similarity=0.732 Sum_probs=221.8
Q ss_pred eeeeeccccHHHHHHHHHHHhhcCCeeEEeccccCcccCCC--CCCChhHHHHHHhhccccccceEEEeEEeccCCCcce
Q 038950 6 KILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTP--RNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISY 83 (297)
Q Consensus 6 ~i~eVw~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~--~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~ 83 (297)
.|||||++|+++||+.||++|++|+||||||||||++.+|. |+++.+++|+.||+|||.+++||+|||++|++|+.|+
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 47999999999999999999999999999999999999998 7799999999999999999999999999999999994
Q ss_pred ----eEEEeeecCCCCCCCCchhhHHHHHhcCCChhhhhhCCCCCcch--hhhhccccccCCCCceeEEeecchhHHHHH
Q 038950 84 ----TFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVF--APRFLEVLSKHRENLKWVTFHGLYDVAYLV 157 (297)
Q Consensus 84 ----~wqFNF~~Fd~~~d~~~~~SI~fL~~~GfDFnk~~~~GI~~~~F--ll~~SGLv~~~~~~~~Witfh~~yD~~yL~ 157 (297)
+|||||++|++.+|+++++||+||+++|+||.|+++.||+..+| ++++||++++ ++++|||||||||||||+
T Consensus 81 ~g~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~--~~V~WvTFhs~YDfgYLl 158 (239)
T KOG0304|consen 81 CGTDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLD--ENVTWVTFHSGYDFGYLL 158 (239)
T ss_pred CCCceeEEecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhcc--CceEEEEeeccchHHHHH
Confidence 99999999999999999999999999999999999999999999 9999999999 999999999999999999
Q ss_pred HHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccc--cCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHH
Q 038950 158 KIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQG--LQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEM 235 (297)
Q Consensus 158 k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~--l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl 235 (297)
|+||+++||++.++|.+.++.+||.+||+|||++.|.+ +++ ||++||+.|++.|+|.+|||||||+||+++|+||
T Consensus 159 K~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~l~~---GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl 235 (239)
T KOG0304|consen 159 KILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLSLKG---GLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKL 235 (239)
T ss_pred HHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhhhhc---CHHHHHHHhCCCeeecccccCcHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999965 777 9999999999999999999999999999999999
Q ss_pred HHh
Q 038950 236 KNR 238 (297)
Q Consensus 236 ~~~ 238 (297)
++.
T Consensus 236 ~~~ 238 (239)
T KOG0304|consen 236 KEL 238 (239)
T ss_pred Hhc
Confidence 853
No 2
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=6.3e-75 Score=518.14 Aligned_cols=246 Identities=37% Similarity=0.572 Sum_probs=236.0
Q ss_pred ceeeeeccccHHHHHHHHHHHhhcCCeeEEeccccCcccCCC--CCCChhHHHHHHhhccccccceEEEeEEeccCCCcc
Q 038950 5 SKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTP--RNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKIS 82 (297)
Q Consensus 5 ~~i~eVw~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~--~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p 82 (297)
..|||||++|+..||..|+++|.+|++|+|||||||+++||. |+++.+++||++|+|||.++|||+||++.|++|+.|
T Consensus 18 ~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P 97 (299)
T COG5228 18 LFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKP 97 (299)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCC
Confidence 358999999999999999999999999999999999999998 999999999999999999999999999999999998
Q ss_pred ---eeEEEeeecCCCCCCCCchhhHHHHHhcCCChhhhhhCCCCCcch--hhhhccccccCCCCceeEEeecchhHHHHH
Q 038950 83 ---YTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVF--APRFLEVLSKHRENLKWVTFHGLYDVAYLV 157 (297)
Q Consensus 83 ---~~wqFNF~~Fd~~~d~~~~~SI~fL~~~GfDFnk~~~~GI~~~~F--ll~~SGLv~~~~~~~~Witfh~~yD~~yL~ 157 (297)
.||||||- |++.+||++++||++|+++||||.||.+.||+..+| +++.||||+. ++++|||||++||||||+
T Consensus 98 ~~~sTWQFNF~-F~l~~dmya~ESieLL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~--e~VtWitfHsaYDfgyLi 174 (299)
T COG5228 98 NGPSTWQFNFE-FDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMD--ESVTWITFHSAYDFGYLI 174 (299)
T ss_pred CCCceeEEEEE-ecchhhhcchHHHHHHHHcCCChhhHhhcCCCHHHHHHHHhccCceec--cceEEEEeecchhHHHHH
Confidence 49999999 999999999999999999999999999999999999 9999999999 999999999999999999
Q ss_pred HHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH-
Q 038950 158 KIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK- 236 (297)
Q Consensus 158 k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~- 236 (297)
|+||+.|||+..++|..++++|||..||+||+.+...+.+. ||++++..|++.|.|++||||+||++|+..|++.+
T Consensus 175 kilt~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~~~~K---glQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~ 251 (299)
T COG5228 175 KILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSK---GLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRF 251 (299)
T ss_pred HHHhcCCCCccHHHHHHHHHHHCccccchHHHHHhhhhhhh---HHHHhcCcHhhhccchhhhccchhhhhhHHhcchhh
Confidence 99999999999999999999999999999999999877766 99999999999999999999999999999999999
Q ss_pred HhcCCc-ccccCceeecCCCC
Q 038950 237 NRYELE-ESAFDGFLYGMDSR 256 (297)
Q Consensus 237 ~~f~~~-~~~~~g~l~Gl~~~ 256 (297)
.+|..+ .......|||++..
T Consensus 252 ~~F~~sig~~ll~~L~g~~~~ 272 (299)
T COG5228 252 SIFTTSIGQSLLMLLSGCQLS 272 (299)
T ss_pred heecccccHHHHHHHhccccC
Confidence 899776 56677788888765
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=1.2e-61 Score=448.55 Aligned_cols=223 Identities=36% Similarity=0.601 Sum_probs=194.7
Q ss_pred eeeccccHHHHHHHHHHHhhcCCeeEEeccccCcccCCC--CCCChhHHHHHHhhccccccceEEEeEEe-ccCCCcc--
Q 038950 8 LNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTP--RNAPAVESYNDLKFNVDCTHLIQLGITLS-DKEGKIS-- 82 (297)
Q Consensus 8 ~eVw~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~--~~~t~eerY~~lk~nVd~~~iiQlGLt~~-~~~g~~p-- 82 (297)
+|||++||+++|+.|+++|++|+|||||+||||+..++. ..+++++||+++|.||+.+.+||+|||++ +++++.+
T Consensus 1 m~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~ 80 (262)
T PF04857_consen 1 MEVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSS 80 (262)
T ss_dssp EEE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECC
T ss_pred CcccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCce
Confidence 589999999999999999999999999999999999887 67789999999999999999999999999 7788876
Q ss_pred -eeEEEeeecCCCCCCCCchhhHHHHHhcCCChhhhhhCCCCCcchh--------hhhccccccC-CCCceeEEeecchh
Q 038950 83 -YTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFA--------PRFLEVLSKH-RENLKWVTFHGLYD 152 (297)
Q Consensus 83 -~~wqFNF~~Fd~~~d~~~~~SI~fL~~~GfDFnk~~~~GI~~~~Fl--------l~~SGLv~~~-~~~~~Witfh~~yD 152 (297)
.+|+|||+.|+.+++.++++||+||+++||||||++++||+|..+. +..++++... ..++.||++||+||
T Consensus 81 ~~~~~~nf~~f~~~~~~~~~~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~D 160 (262)
T PF04857_consen 81 YNVWPFNFYLFPLDRDFSQASSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYD 160 (262)
T ss_dssp EEEEEEEBSTTSTTTCEEEHHHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHH
T ss_pred eEEEEeeeeccccccceecchhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhH
Confidence 3999999999999998899999999999999999999999999983 5667777553 24689999999999
Q ss_pred HHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHHcCCcc------------------
Q 038950 153 VAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKR------------------ 214 (297)
Q Consensus 153 ~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r------------------ 214 (297)
++||+++|+| +||+|+++|++.++.+||.|||||||++.+....+ +|+.|++.|++.|
T Consensus 161 l~~l~~~f~~-~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~~~---~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~ 236 (262)
T PF04857_consen 161 LMYLYKKFIG-PLPETLEEFKELLRELFPRIYDTKYLAEECPGKST---SLQELAEELGIRRNPSSISSPEGFPSYDEEK 236 (262)
T ss_dssp HHHHHHHHTT-S--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS-S---SHHHHHHHTTSTT----EEE-TTS-------
T ss_pred HHHHHHHhcC-CCCCCHHHHHHHHHHHCcccccHHHHHHhcccccc---CHHHHHHHhCCCccccccccccccccccccc
Confidence 9999999997 99999999999999999999999999999875555 9999999999988
Q ss_pred -----cCC-CcccchHHHHHHHHHHH
Q 038950 215 -----HGG-AHHAGSDSLLTAAVFAE 234 (297)
Q Consensus 215 -----~g~-~HqAGsDSllT~~vF~k 234 (297)
.|. .|+||+|||+|+.||+|
T Consensus 237 ~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 237 NNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp ------SS-TTSHHHHHHHHHHHHHH
T ss_pred cccccCCCCCCCcchHHHHHHHHHcC
Confidence 566 99999999999999986
No 4
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.16 E-value=1.1e-11 Score=126.66 Aligned_cols=219 Identities=18% Similarity=0.133 Sum_probs=150.2
Q ss_pred cccHHHHHHHHHHHhhcCCeeEEeccccCcccCCC----CCCChhHHHHHHhhccccccceEEEeEEeccCCCcc-----
Q 038950 12 CENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTP----RNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKIS----- 82 (297)
Q Consensus 12 ~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~----~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p----- 82 (297)
+.|++. +..++..|+++.|+++|.|++|+...+. --++.|.+|++.|.|+..+.++|+|+|.|.+++...
T Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 79 (564)
T KOG1990|consen 1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMST 79 (564)
T ss_pred CCcccc-hhHHHhhcCHHHHHHHhhhhccceecccccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccC
Confidence 468899 9999999999999999999999988774 224789999999999999999999999999876543
Q ss_pred ----eeEEEeeecCCCCCCCCchhhHHHHHhcC--CChh---hhh------hCCCCCcc---------------------
Q 038950 83 ----YTFEFNFSDFDLKKDLHAGDSIQLLKDSG--LDFD---KIR------KDGIPRCV--------------------- 126 (297)
Q Consensus 83 ----~~wqFNF~~Fd~~~d~~~~~SI~fL~~~G--fDFn---k~~------~~GI~~~~--------------------- 126 (297)
.+|..-+. ....+.+|+..++.++.+++ ++=. +.. ..|+.+..
T Consensus 80 ~~n~~~~~~g~~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~ 158 (564)
T KOG1990|consen 80 GGNFVVWSRGDS-ISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIP 158 (564)
T ss_pred CCceeeeecCcc-ccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhh
Confidence 15554332 22335688999999998882 2111 000 11221111
Q ss_pred -----------------------------------hhhhhcc--------------------------ccccC----CC-
Q 038950 127 -----------------------------------FAPRFLE--------------------------VLSKH----RE- 140 (297)
Q Consensus 127 -----------------------------------Fll~~SG--------------------------Lv~~~----~~- 140 (297)
|.+..++ ..-.. ..
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 0001111 00000 01
Q ss_pred ------CceeEEeecc-hhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHh--ccc--cCCCcchHHHHHHH
Q 038950 141 ------NLKWVTFHGL-YDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGY--CQG--LQGLKLGLSKLARI 209 (297)
Q Consensus 141 ------~~~Witfh~~-yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~--~~~--l~~~~~~L~~la~~ 209 (297)
.-+-+.-||+ +|++|++|.|.+ +||+++++|.+. .+.||.++|+|-+++- +.. +.+ +.++.....
T Consensus 239 l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~-~~~fp~~~~~~~~~~~~~~~~~~~~~--t~~e~~~~~ 314 (564)
T KOG1990|consen 239 LQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDS-SSMFPNIEDTKRLAKLSEYQKLNLKA--TLLELARAK 314 (564)
T ss_pred HHHHHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhh-hhhhhhhHHHHHhhccccccchhhhh--hHHHHHHHh
Confidence 1144567777 999999999998 999999999999 9999999999988872 222 333 233332222
Q ss_pred cCCc-------------------ccCCCcccchHHHHHHHHHHHHH
Q 038950 210 LNVK-------------------RHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 210 L~v~-------------------r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
.... +.+..|+++++++.++.++.+..
T Consensus 315 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~ 360 (564)
T KOG1990|consen 315 AKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASA 360 (564)
T ss_pred cccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccch
Confidence 1111 12567889999999999999988
No 5
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=98.80 E-value=1.6e-07 Score=85.87 Aligned_cols=170 Identities=19% Similarity=0.260 Sum_probs=114.6
Q ss_pred hcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHH
Q 038950 27 NCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQL 106 (297)
Q Consensus 27 ~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~f 106 (297)
.+.+||++|+|-||+... .=.|||+|+..++.+|+.. -.|+.. .+... ...+++.+.
T Consensus 4 ~~~~~vv~D~ETTGl~p~-------------------~d~Iieig~v~v~~~g~~~--~~~~~l-v~P~~-~i~~~a~~I 60 (232)
T PRK07942 4 HPGPLAAFDLETTGVDPE-------------------TARIVTAALVVVDADGEVV--ESREWL-ADPGV-EIPEEASAV 60 (232)
T ss_pred ccCcEEEEEeccCCCCCC-------------------CCeeEEEEEEEEeCCCccc--cceEEE-ECCCC-CCCHHHHHH
Confidence 467899999999998421 1249999999998777643 234433 23222 345555554
Q ss_pred HHhcCCChhhhhhCCCCCcchhhhhcccc---ccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccC-c
Q 038950 107 LKDSGLDFDKIRKDGIPRCVFAPRFLEVL---SKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQ-S 182 (297)
Q Consensus 107 L~~~GfDFnk~~~~GI~~~~Fll~~SGLv---~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP-~ 182 (297)
+||.=..+..+|.+...-+......+ .. ++..+|++|..||+.+|-+.+....+|.- .+ .
T Consensus 61 ---hGIt~e~l~~~g~~~~~vl~e~~~~l~~~~~--~~~~lVahNa~FD~~fL~~~~~r~~~~~~-----------~~~~ 124 (232)
T PRK07942 61 ---HGITTEYARAHGRPAAEVLAEIADALREAWA--RGVPVVVFNAPYDLTVLDRELRRHGLPSL-----------VPGP 124 (232)
T ss_pred ---hCCCHHHHHhhCCCHHHHHHHHHHHHHHHhh--cCCEEEEeCcHhhHHHHHHHHHHcCCCCc-----------cCCc
Confidence 99999999888998654311111111 11 34567888888999999888753222211 22 2
Q ss_pred ccchhHHHHhcccc-CCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHHH
Q 038950 183 VFDIKVVAGYCQGL-QGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKN 237 (297)
Q Consensus 183 vyDtK~~a~~~~~l-~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~~ 237 (297)
++|+-.|++.+... .+ +..|+.+++.+|++.. ..|.|-+|++.|+++|.+|.+
T Consensus 125 ~iDt~~l~~~~~~~~~~-~~~L~~l~~~~gi~~~-~aH~Al~Da~ata~l~~~l~~ 178 (232)
T PRK07942 125 VIDPYVIDKAVDRYRKG-KRTLTALCEHYGVRLD-NAHEATADALAAARVAWALAR 178 (232)
T ss_pred EeeHHHHHhhhhcccCC-CCCHHHHHHHcCCCCC-CCCChHHHHHHHHHHHHHHHH
Confidence 67988888765432 23 3489999999999754 489999999999999999983
No 6
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.80 E-value=3.2e-07 Score=77.66 Aligned_cols=161 Identities=21% Similarity=0.195 Sum_probs=109.6
Q ss_pred CeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHh
Q 038950 30 NVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKD 109 (297)
Q Consensus 30 ~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~ 109 (297)
.||++|+|.+|+... .-.|+|+|....+.+. . ...|+.+ .... ...++.+. +-
T Consensus 1 ~~v~~D~Ettg~~~~-------------------~~~Iieig~v~~~~~~--~-~~~f~~~-v~p~-~~i~~~~~---~~ 53 (169)
T smart00479 1 TLVVIDCETTGLDPG-------------------KDEIIEIAAVDVDGGR--I-IVVFDTY-VKPD-RPITDYAT---EI 53 (169)
T ss_pred CEEEEEeeCCCCCCC-------------------CCeEEEEEEEEEECCE--e-EEEEEEE-ECCC-CCCCHHHH---HH
Confidence 489999999997532 2349999999888753 2 5667766 3332 23334333 34
Q ss_pred cCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeec-chhHHHHHHHhc--CCCCCCChHHHHHHHHhccCcccch
Q 038950 110 SGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHG-LYDVAYLVKIFT--NDALPPTAEAFSGVAALFFQSVFDI 186 (297)
Q Consensus 110 ~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~-~yD~~yL~k~l~--g~~LP~t~~eF~~~l~~~FP~vyDt 186 (297)
+|+.-+.+.. |.++...+......+ . +-.+|++|+ .+|+.+|-+.+. |.+.|.. -..+|+
T Consensus 54 ~Git~~~l~~-~~~~~~~~~~~~~~l-~---~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~------------~~~iD~ 116 (169)
T smart00479 54 HGITPEMLDD-APTFEEVLEELLEFL-K---GKILVAGNALNFDLRFLKLEHPRLGIKDPPK------------NPVIDT 116 (169)
T ss_pred hCCCHHHHhC-CCCHHHHHHHHHHHh-c---CCEEEEeCCHHHhHHHHHHHHHHhCCCCCcC------------CCeeEH
Confidence 7887777654 777665422222233 2 235788888 799999999885 2333311 126788
Q ss_pred hHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 187 KVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 187 K~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
.-+++...... ..+|+.+++.+|++..+..|-|-+|+..|+++|.+|.
T Consensus 117 ~~~~~~~~~~~--~~~L~~l~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~ 164 (169)
T smart00479 117 LKLARALNPGR--KYSLKKLAERLGLEVIGRAHRALDDARATAKLFKKLV 164 (169)
T ss_pred HHHHHHHCCCC--CCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHH
Confidence 77776543211 3499999999999998888999999999999999998
No 7
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=98.60 E-value=1.2e-06 Score=75.07 Aligned_cols=175 Identities=22% Similarity=0.221 Sum_probs=109.7
Q ss_pred eeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHhc
Q 038950 31 VLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDS 110 (297)
Q Consensus 31 fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~~ 110 (297)
||.+|+|.+|...... .. ..-.|||+|....+.++... .-.|+.+.-+......++.+.+. +
T Consensus 1 ~vv~D~Ettg~~~~~~------------~~--~~~~IieIgav~v~~~~~~~-~~~f~~~i~P~~~~~i~~~~~~i---~ 62 (176)
T cd06133 1 YLVIDFEATCWEGNSK------------PD--YPNEIIEIGAVLVDVKTKEI-IDTFSSYVKPVINPKLSDFCTEL---T 62 (176)
T ss_pred CEEEEeeccccCCCCC------------CC--CCcceEEEEEEEEEcCCCeE-EeeeeeeECCCcCCchhHHHHHh---c
Confidence 7999999999865321 00 11259999999999877533 33455542233223455555555 9
Q ss_pred CCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHH
Q 038950 111 GLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVA 190 (297)
Q Consensus 111 GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a 190 (297)
|+.-+.+. ++.++..-+-.....+.+. .....++ ||.+|...+.+.+....... ...++...+|++-++
T Consensus 63 gIt~e~l~-~~~~~~~vl~~~~~~l~~~-~~~~~v~-~~~~d~~~l~~~~~~~~~~~--------~~~~~~~~~D~~~~~ 131 (176)
T cd06133 63 GITQEDVD-NAPSFPEVLKEFLEWLGKN-GKYAFVT-WGDWDLKDLLQNQCKYKIIN--------LPPFFRQWIDLKKEF 131 (176)
T ss_pred CcCHHHHh-cCCCHHHHHHHHHHHHHhC-CCeEEEe-ecHhhHHHHHHHHHHhcCCC--------CcccccceEEHHHHH
Confidence 99988875 4555443221122222220 0123333 46789887777544211100 012344688999888
Q ss_pred HhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHH
Q 038950 191 GYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEM 235 (297)
Q Consensus 191 ~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl 235 (297)
+...+... +.+|.++++.+|++..+..|.|=+|+..|+++|.+|
T Consensus 132 ~~~~~~~~-~~~L~~l~~~~gi~~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 132 AKFYGLKK-RTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred HHHhCCCC-CCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHh
Confidence 76543322 458999999999998889999999999999999987
No 8
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.55 E-value=1.5e-06 Score=77.42 Aligned_cols=173 Identities=16% Similarity=0.228 Sum_probs=104.3
Q ss_pred HHHHHHHhhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCC
Q 038950 19 MRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDL 98 (297)
Q Consensus 19 l~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~ 98 (297)
+..+.+.....+||++|+|-+|+... .-.|||+|...++.+.. .....|.++ .+... .
T Consensus 19 ~~~~~~~~~~~~~vviD~ETTGl~~~-------------------~d~IieIgaV~~~~~~~-~~~~~f~~~-i~p~~-~ 76 (202)
T PRK09145 19 YAFLFEPPPPDEWVALDCETTGLDPR-------------------RAEIVSIAAVKIRGNRI-LTSERLELL-VRPPQ-S 76 (202)
T ss_pred HHHHhcCCCCCCEEEEEeECCCCCCC-------------------CCceEEEEEEEEECCEE-eecCceEEE-ECCCC-C
Confidence 33444444567999999999997421 12499999998875322 112344444 22222 2
Q ss_pred CchhhHHHHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhc---CCCCCCChHHHHHH
Q 038950 99 HAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFT---NDALPPTAEAFSGV 175 (297)
Q Consensus 99 ~~~~SI~fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~---g~~LP~t~~eF~~~ 175 (297)
..+.+.+. +|+.-..+ ++|.+...-+-.....+ ++-.||+++..+|..+|-+.+. |.++|..
T Consensus 77 i~~~~~~i---hGIt~~~l-~~~~~~~~vl~~~~~~i----~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~------- 141 (202)
T PRK09145 77 LSAESIKI---HRLRHQDL-EDGLSEEEALRQLLAFI----GNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNP------- 141 (202)
T ss_pred CCHhHhhh---cCcCHHHH-hcCCCHHHHHHHHHHHH----cCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCC-------
Confidence 34444443 67666554 34555444311112222 1335777766799999987653 4455532
Q ss_pred HHhccCcccchhHHHHh--ccccCC--CcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 176 AALFFQSVFDIKVVAGY--CQGLQG--LKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 176 l~~~FP~vyDtK~~a~~--~~~l~~--~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
.+|+.-+... ...+.. .+.+|+.+++.+|++.. ..|.|-+|++.|+++|.+|+
T Consensus 142 -------~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~-~~H~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 142 -------LIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVL-GRHDALNDAIMAALIFLRLR 198 (202)
T ss_pred -------eeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHH
Confidence 4566544321 111111 12489999999999874 46999999999999999986
No 9
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=98.47 E-value=4.6e-06 Score=73.91 Aligned_cols=173 Identities=18% Similarity=0.194 Sum_probs=110.9
Q ss_pred hcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEecc--CCCcceeEEEeeecCCCC-CCCCchhh
Q 038950 27 NCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDK--EGKISYTFEFNFSDFDLK-KDLHAGDS 103 (297)
Q Consensus 27 ~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~--~g~~p~~wqFNF~~Fd~~-~d~~~~~S 103 (297)
..+.+|++|+|-||+.... + .|||+|...++. +|.....-.|++. ++.. .....+++
T Consensus 3 ~~~~~vv~D~ETTGl~~~~------d-------------~Iieigav~v~~~~~~~i~~~~~f~~l-v~P~~~~~i~~~~ 62 (189)
T cd06134 3 RGFLPVVVDVETGGFNPQT------D-------------ALLEIAAVTLEMDEQGNLYPDETFHFH-ILPFEGANLDPAA 62 (189)
T ss_pred ccceeEEEEecCCCCCCCC------C-------------eEEEEEEEEEEECCCCceeccceEEEE-EcCCCCCCCCHHH
Confidence 3467899999999986421 1 299999998875 3442213345554 3332 23455555
Q ss_pred HHHHHhcCCChhhhhhCCCCCcch---hh-hhccccccC-CCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHh
Q 038950 104 IQLLKDSGLDFDKIRKDGIPRCVF---AP-RFLEVLSKH-RENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAAL 178 (297)
Q Consensus 104 I~fL~~~GfDFnk~~~~GI~~~~F---ll-~~SGLv~~~-~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~ 178 (297)
++. +||.=+...+.|++...- ++ ....++... .++..+|.+|..+|++||-+.+.-..++ ..
T Consensus 63 ~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~----------~~ 129 (189)
T cd06134 63 LEF---NGIDPFHPFRFAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIK----------RN 129 (189)
T ss_pred Hhh---cCCCchhhhccccchHHHHHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCC----------CC
Confidence 555 888766666777765542 11 011111000 0234677888889999999887521111 01
Q ss_pred cc-C-cccchhHHHHhccccCCCcchHHHHHHHcCCccc-CCCcccchHHHHHHHHHHHHH
Q 038950 179 FF-Q-SVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRH-GGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 179 ~F-P-~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~-g~~HqAGsDSllT~~vF~kl~ 236 (297)
.| | ..+||..|++... + ...|+.+++.+|++.. ...|.|.+|++.|+++|.+|.
T Consensus 130 ~~~~~~~lDt~~la~~~~---~-~~~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~ 186 (189)
T cd06134 130 PFHPFSTFDTATLAGLAY---G-QTVLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIV 186 (189)
T ss_pred CCCCCcEEEHHHHHHHHh---C-CCcHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHH
Confidence 12 2 2789999997653 2 2379999999999753 568999999999999999997
No 10
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=98.46 E-value=4.1e-06 Score=75.06 Aligned_cols=172 Identities=16% Similarity=0.136 Sum_probs=102.3
Q ss_pred cCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCC-CCCchhhHHH
Q 038950 28 CFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKK-DLHAGDSIQL 106 (297)
Q Consensus 28 ~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~-d~~~~~SI~f 106 (297)
.-.||++|+|.+|...+.. ++. + .-.|||+|....+. |+. .-.|+-+ ..... ....+.+.++
T Consensus 3 ~~~~vvlD~EtTg~~~~~~----~~~-~--------~~eIIeIGaV~v~~-~~i--~~~f~~l-V~P~~~~~i~~~~~~l 65 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKK----PKG-F--------FPEIIEVGLVSVVG-CEV--EDTFSSY-VKPKTFPSLTERCKSF 65 (207)
T ss_pred cceEEEEEeecCCcCCCCC----CCC-C--------CCceEEEeEEEEec-CcC--hhhhcce-ECCCccCccChhhhhh
Confidence 4579999999999753211 000 0 01399999988874 332 2223333 11111 1233334333
Q ss_pred HHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhc--CCCCCCChHHHHHHHHhccCccc
Q 038950 107 LKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFT--NDALPPTAEAFSGVAALFFQSVF 184 (297)
Q Consensus 107 L~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~--g~~LP~t~~eF~~~l~~~FP~vy 184 (297)
+||.=+.+ .+|.+...-+......+ . +.-.+++.|+.+|+.+|-+.+. |-+.|. +....
T Consensus 66 ---tGIt~~~l-~~ap~~~evl~~f~~~~-~--~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~------------~~~~~ 126 (207)
T PRK07748 66 ---LGITQEDV-DKGISFEELVEKLAEYD-K--RCKPTIVTWGNMDMKVLKHNCEKAGVPFPF------------KGQCR 126 (207)
T ss_pred ---cCcCHHHH-ccCCCHHHHHHHHHHHh-C--cCCeEEEEECHHHHHHHHHHHHHcCCCCcc------------cccce
Confidence 77765555 35666555422222233 2 2123444578899999988874 323231 12345
Q ss_pred chhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 185 DIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 185 DtK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
|+..+.+....... ..+|+.+++.+|++-.+..|.|-+||+.|+++|.+|.
T Consensus 127 dl~~~~~~~~~~~~-~~~L~~~~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~ 177 (207)
T PRK07748 127 DLSLEYKKFFGERN-QTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVE 177 (207)
T ss_pred eHHHHHHHHhCcCC-CCCHHHHHHHcCCCCCCCCcChHHHHHHHHHHHHHHH
Confidence 66555443322211 2489999999999988889999999999999999998
No 11
>PRK05168 ribonuclease T; Provisional
Probab=98.38 E-value=1.3e-05 Score=72.22 Aligned_cols=182 Identities=19% Similarity=0.235 Sum_probs=117.2
Q ss_pred HHHHHHHhhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEecc--CCCcceeEEEeeecCCCC-
Q 038950 19 MRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDK--EGKISYTFEFNFSDFDLK- 95 (297)
Q Consensus 19 l~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~--~g~~p~~wqFNF~~Fd~~- 95 (297)
+..|..-++...||++|+|-+|+.... + .|||+|....+. +|.......|... ....
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~------d-------------~IieIgaV~v~~d~~g~i~~~~~f~~l-v~P~~ 66 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKT------D-------------ALLEIAAVTLKMDEQGWLYPDETLHFH-VEPFE 66 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCC------C-------------EEEEEeEEEEEecCCCcEeccceEEEE-ECCCC
Confidence 456788899999999999999986432 1 399999888764 4543213456655 3332
Q ss_pred CCCCchhhHHHHHhcCCChhhhhhCCCCCcch---hhh-hcccccc-CCCCceeEEeecchhHHHHHHHhcCCCCCCChH
Q 038950 96 KDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVF---APR-FLEVLSK-HRENLKWVTFHGLYDVAYLVKIFTNDALPPTAE 170 (297)
Q Consensus 96 ~d~~~~~SI~fL~~~GfDFnk~~~~GI~~~~F---ll~-~SGLv~~-~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~ 170 (297)
.....+++++. +||.=+...+.|++...- ++. ....+.. ..++..+|++|..+|++||-+.+.-..+..
T Consensus 67 ~~~i~~~~~~i---hGIt~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~--- 140 (211)
T PRK05168 67 GANLEPEALAF---NGIDPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKR--- 140 (211)
T ss_pred CCCCCHHHHhh---cCCCchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCC---
Confidence 22455555554 888555556777765432 110 0111100 002456777777899999988874211110
Q ss_pred HHHHHHHhccC-cccchhHHHHhccccCCCcchHHHHHHHcCCccc-CCCcccchHHHHHHHHHHHHH
Q 038950 171 AFSGVAALFFQ-SVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRH-GGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 171 eF~~~l~~~FP-~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~-g~~HqAGsDSllT~~vF~kl~ 236 (297)
..+.| .++||.-+++... + ...|..+++.+|++-. ...|.|-+|++.|+++|.+|.
T Consensus 141 ------~~~~~~~~iDt~~lar~~~---~-~~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~ 198 (211)
T PRK05168 141 ------NPFHPFSTFDTATLSGLAL---G-QTVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIV 198 (211)
T ss_pred ------CCCCCCcEeeHHHHHHHHc---C-CCCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHH
Confidence 01223 3789998887542 2 2379999999998753 358999999999999999998
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=98.37 E-value=1.2e-05 Score=68.86 Aligned_cols=164 Identities=18% Similarity=0.224 Sum_probs=101.7
Q ss_pred eeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHhc
Q 038950 31 VLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDS 110 (297)
Q Consensus 31 fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~~ 110 (297)
||++|+|-||+..+ +.-.|||+|....+.+. .. ..+|+.. ..... ...+.+.+. +
T Consensus 1 ~v~~D~ETTGl~~~------------------~~~~iieig~v~v~~~~-~~-~~~~~~~-v~P~~-~i~~~~~~i---h 55 (167)
T cd06131 1 QIVLDTETTGLDPR------------------EGHRIIEIGCVELINRR-LT-GNTFHVY-INPER-DIPEEAFKV---H 55 (167)
T ss_pred CEEEEeeCCCCCCC------------------CCCeEEEEEEEEEECCc-Ee-ccEEEEE-ECCCC-CCCHHHHHH---h
Confidence 68999999998421 12259999998776422 22 3466665 33322 345555543 7
Q ss_pred CCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccC-cccchhHH
Q 038950 111 GLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQ-SVFDIKVV 189 (297)
Q Consensus 111 GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP-~vyDtK~~ 189 (297)
|+.=+.+...+ +...-+...-..+ + +-.+|.+|+.+|..+|-+.+-...++... ..| ..+||-.+
T Consensus 56 GIt~e~l~~~~-~~~~v~~~l~~~l-~---~~~lv~hn~~fD~~~l~~~~~~~~~~~~~---------~~~~~~idt~~~ 121 (167)
T cd06131 56 GITDEFLADKP-KFAEIADEFLDFI-R---GAELVIHNASFDVGFLNAELSLLGLGKKI---------IDFCRVIDTLAL 121 (167)
T ss_pred CCCHHHHhcCC-CHHHHHHHHHHHH-C---CCeEEEeChHHhHHHHHHHHHHhCCCccc---------ccCCCceEhHHH
Confidence 87776655432 2222111111122 2 23477777779999988776531121110 123 37899777
Q ss_pred HHhcc-ccCCCcchHHHHHHHcCCcccC-CCcccchHHHHHHHHHHHHH
Q 038950 190 AGYCQ-GLQGLKLGLSKLARILNVKRHG-GAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 190 a~~~~-~l~~~~~~L~~la~~L~v~r~g-~~HqAGsDSllT~~vF~kl~ 236 (297)
++... .. ..+|+.+++.+|++..+ ..|.|-+|++.|+++|.+|.
T Consensus 122 ~~~~~~~~---~~~L~~l~~~~~i~~~~~~~H~Al~Da~~~a~l~~~l~ 167 (167)
T cd06131 122 ARKKFPGK---PNSLDALCKRFGIDNSHRTLHGALLDAELLAEVYLELT 167 (167)
T ss_pred HHHHcCCC---CCCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHhC
Confidence 76532 22 23899999999999765 47999999999999999873
No 13
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=98.30 E-value=1.5e-05 Score=67.04 Aligned_cols=152 Identities=16% Similarity=0.127 Sum_probs=96.2
Q ss_pred eeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHhc
Q 038950 31 VLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDS 110 (297)
Q Consensus 31 fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~~ 110 (297)
||++|+|-+|.. + -.|||+|...++. |+. .-+|+.+ ....+ ...+++.+ -+
T Consensus 1 ~v~~D~Ettg~~--~-------------------~~ii~ig~v~~~~-~~~--~~~~~~~-i~p~~-~~~~~~~~---i~ 51 (156)
T cd06130 1 FVAIDFETANAD--R-------------------ASACSIGLVKVRD-GQI--VDTFYTL-IRPPT-RFDPFNIA---IH 51 (156)
T ss_pred CEEEEEeCCCCC--C-------------------CceEEEEEEEEEC-CEE--EEEEEEE-eCcCC-CCChhhcc---cc
Confidence 799999999842 1 1289999988873 433 3456665 33332 34444443 38
Q ss_pred CCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcC--CCCCCChHHHHHHHHhccCcccchhH
Q 038950 111 GLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTN--DALPPTAEAFSGVAALFFQSVFDIKV 188 (297)
Q Consensus 111 GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g--~~LP~t~~eF~~~l~~~FP~vyDtK~ 188 (297)
|+.-..+.. +.++..-+......+ + +..||++|..+|..+|-+.+-. .+.|. + ..+||.-
T Consensus 52 GIt~e~l~~-~~~~~~v~~~l~~~l-~---~~~lv~hn~~fD~~~l~~~~~~~g~~~~~------------~-~~idt~~ 113 (156)
T cd06130 52 GITPEDVAD-APTFPEVWPEIKPFL-G---GSLVVAHNASFDRSVLRAALEAYGLPPPP------------Y-QYLCTVR 113 (156)
T ss_pred CcCHHHHhc-CCCHHHHHHHHHHHh-C---CCEEEEeChHHhHHHHHHHHHHcCCCCCC------------C-CEEEHHH
Confidence 888777654 333222111111112 2 3456666668999999888752 22221 1 3678876
Q ss_pred HHHhcc-ccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHH
Q 038950 189 VAGYCQ-GLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFA 233 (297)
Q Consensus 189 ~a~~~~-~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~ 233 (297)
+++... .+. ..+|+.+++.+|++.. .|.|-+|+..|+++|.
T Consensus 114 ~~~~~~~~~~--~~~L~~l~~~~g~~~~--~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 114 LARRVWPLLP--NHKLNTVAEHLGIELN--HHDALEDARACAEILL 155 (156)
T ss_pred HHHHHhccCC--CCCHHHHHHHcCCCcc--CcCchHHHHHHHHHHh
Confidence 766532 333 3589999999999865 9999999999999884
No 14
>PRK07740 hypothetical protein; Provisional
Probab=98.28 E-value=1.2e-05 Score=74.13 Aligned_cols=166 Identities=17% Similarity=0.198 Sum_probs=101.6
Q ss_pred hcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHH
Q 038950 27 NCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQL 106 (297)
Q Consensus 27 ~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~f 106 (297)
.+.+||.+|+|.||+.... .=.|||+|....+. |... .-.|... ..... ...+.+.+
T Consensus 57 ~~~~~vv~D~ETTGl~p~~------------------~deIIeIgaV~~~~-~~i~-~~~f~~l-v~P~~-~i~~~~~~- 113 (244)
T PRK07740 57 TDLPFVVFDLETTGFSPQQ------------------GDEILSIGAVKTKG-GEVE-TDTFYSL-VKPKR-PIPEHILE- 113 (244)
T ss_pred cCCCEEEEEEeCCCCCCCC------------------CCeEEEEEEEEEEC-CEEE-EEEEEEE-eCcCC-CCChhhee-
Confidence 3468999999999975210 02489999988874 3221 2334433 12221 23333322
Q ss_pred HHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhcc-Ccccc
Q 038950 107 LKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFF-QSVFD 185 (297)
Q Consensus 107 L~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~F-P~vyD 185 (297)
-+|+.=..+. +|.+...-+......+ ++-.+|++|..+|+.+|-+.+.. .+. .-| ..+.|
T Consensus 114 --ltGIt~e~l~-~ap~~~evl~~f~~fi----~~~~lVahna~fD~~fL~~~~~~-~~~-----------~~~~~~~iD 174 (244)
T PRK07740 114 --LTGITAEDVA-FAPPLAEVLHRFYAFI----GAGVLVAHHAGHDKAFLRHALWR-TYR-----------QPFTHRLID 174 (244)
T ss_pred --ccCCCHHHHh-CCCCHHHHHHHHHHHh----CCCEEEEeCHHHHHHHHHHHHHH-hcC-----------CCcCCCeec
Confidence 2666655443 3443332211111222 23467877777999999887752 110 112 35889
Q ss_pred hhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 186 IKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 186 tK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
|..+++....... ..+|+.+++.+|++..+ .|.|-+|++.|+.+|.++.
T Consensus 175 t~~l~r~l~~~~~-~~sL~~l~~~~gi~~~~-~H~Al~Da~ata~l~~~ll 223 (244)
T PRK07740 175 TMFLTKLLAHERD-FPTLDDALAYYGIPIPR-RHHALGDALMTAKLWAILL 223 (244)
T ss_pred hHHHHHHHcCCCC-CCCHHHHHHHCCcCCCC-CCCcHHHHHHHHHHHHHHH
Confidence 9988876543221 34899999999998655 5999999999999999997
No 15
>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=98.27 E-value=2.2e-05 Score=70.91 Aligned_cols=168 Identities=18% Similarity=0.215 Sum_probs=104.7
Q ss_pred hhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHH
Q 038950 26 LNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQ 105 (297)
Q Consensus 26 i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~ 105 (297)
+....||++|+|-+|+... . .|||+|.......+.. ..+|..+..+ . ....+.+++
T Consensus 4 l~~~~fvv~D~ETTGl~~~-------------------~-~IIeIgav~v~~~~~~--~~~f~~li~P-~-~~i~~~a~~ 59 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAG-------------------H-DIIEIGAVEIINRRIT--GNKFHTYIKP-D-RPIDPDAIK 59 (217)
T ss_pred EEecCEEEEEecCCCCCCC-------------------C-CEEEEEEEEEECCCEe--eeEEEEEECc-C-CCCCHHHHh
Confidence 4567899999999997421 1 2999999986544332 2445544222 2 234555554
Q ss_pred HHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCC-CCCCChHHHHHHHHhccCccc
Q 038950 106 LLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTND-ALPPTAEAFSGVAALFFQSVF 184 (297)
Q Consensus 106 fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~-~LP~t~~eF~~~l~~~FP~vy 184 (297)
. +|+.-..+... -+...-+......+ ++-.+|+++..+|+.+|-+.+... ..|. ....+.
T Consensus 60 i---hGIt~e~l~~~-p~~~ev~~~~~~~~----~~~~lVaHNa~FD~~fL~~~~~r~~~~~~-----------~~~~~~ 120 (217)
T TIGR00573 60 I---HGITDDMLKDK-PDFKEIAEDFADYI----RGAELVIHNASFDVGFLNYEFSKLYKVEP-----------KTNDVI 120 (217)
T ss_pred h---cCCCHHHHcCC-CCHHHHHHHHHHHh----CCCEEEEeccHHHHHHHHHHHHHhcCCCC-----------Ccccee
Confidence 3 88887776543 22221111111222 234677777779999998877510 1100 011356
Q ss_pred chhHHHHhcc-ccCCCcchHHHHHHHcCCccc-CCCcccchHHHHHHHHHHHHH
Q 038950 185 DIKVVAGYCQ-GLQGLKLGLSKLARILNVKRH-GGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 185 DtK~~a~~~~-~l~~~~~~L~~la~~L~v~r~-g~~HqAGsDSllT~~vF~kl~ 236 (297)
||.-+++... .+.+.+.+|+.+++.+|++.. ...|.|-+|+.+|+++|.+|.
T Consensus 121 dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~~~H~Al~DA~~ta~l~~~l~ 174 (217)
T TIGR00573 121 DTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMT 174 (217)
T ss_pred cHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHH
Confidence 7766665532 333323489999999999864 368999999999999999998
No 16
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=98.24 E-value=3.4e-05 Score=71.32 Aligned_cols=167 Identities=17% Similarity=0.262 Sum_probs=104.7
Q ss_pred cCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHH
Q 038950 28 CFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLL 107 (297)
Q Consensus 28 ~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL 107 (297)
.-.||++|||-||+.... .=.|||+|...... +. +....|+.+ .+..+ ...+++++.
T Consensus 3 ~~r~vvlDtETTGldp~~------------------~drIIEIGaV~v~~-~~-~~~~~f~~~-i~P~~-~i~~~a~~V- 59 (240)
T PRK05711 3 IMRQIVLDTETTGLNQRE------------------GHRIIEIGAVELIN-RR-LTGRNFHVY-IKPDR-LVDPEALAV- 59 (240)
T ss_pred CCeEEEEEeeCCCcCCCC------------------CCeEEEEEEEEEEC-CE-EeccEEEEE-ECcCC-cCCHHHhhh-
Confidence 347999999999985320 22599999876653 22 212345655 33332 344555444
Q ss_pred HhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhc--CCCCCCChHHHHHHHHhccCcccc
Q 038950 108 KDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFT--NDALPPTAEAFSGVAALFFQSVFD 185 (297)
Q Consensus 108 ~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~--g~~LP~t~~eF~~~l~~~FP~vyD 185 (297)
|||.-..+... -++..-+-.....+ ++-.+|.+|..+|+++|-+-+- |.++|... .+..++|
T Consensus 60 --HGIT~e~l~~~-p~f~ev~~~f~~fi----~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~---------~~~~~iD 123 (240)
T PRK05711 60 --HGITDEFLADK-PTFAEVADEFLDFI----RGAELIIHNAPFDIGFMDYEFALLGRDIPKTN---------TFCKVTD 123 (240)
T ss_pred --cCCCHHHHcCC-CCHHHHHHHHHHHh----CCCEEEEEccHHhHHHHHHHHHHhCCCCCccc---------ccCceee
Confidence 77776655442 22111111111122 2345676666699999988774 33455321 1335889
Q ss_pred hhHHHHhc-cccCCCcchHHHHHHHcCCcccCC-CcccchHHHHHHHHHHHHH
Q 038950 186 IKVVAGYC-QGLQGLKLGLSKLARILNVKRHGG-AHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 186 tK~~a~~~-~~l~~~~~~L~~la~~L~v~r~g~-~HqAGsDSllT~~vF~kl~ 236 (297)
|--|++.. ++.+ .+|+.|++.+|++..+. .|.|-+|+.+|+++|.+|.
T Consensus 124 Tl~lar~~~p~~~---~~L~aL~~~~gi~~~~r~~H~AL~DA~~~A~v~~~l~ 173 (240)
T PRK05711 124 TLAMARRMFPGKR---NSLDALCKRYGIDNSHRTLHGALLDAEILAEVYLAMT 173 (240)
T ss_pred HHHHHHHHcCCCC---CCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 98888764 2323 38999999999987554 6999999999999999997
No 17
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=98.15 E-value=4.3e-05 Score=73.24 Aligned_cols=162 Identities=20% Similarity=0.236 Sum_probs=102.5
Q ss_pred CCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHH
Q 038950 29 FNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLK 108 (297)
Q Consensus 29 ~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~ 108 (297)
-+||++|+|.+|+... .-.|||+|...++ +|+. ..+|+.. ...... ..+.+. +
T Consensus 8 ~~~Vv~DlETTGl~p~-------------------~~eIIEIgaV~v~-~g~i--~~~f~~l-VkP~~~-I~~~a~---~ 60 (313)
T PRK06807 8 LDYVVIDFETTGFNPY-------------------NDKIIQVAAVKYR-NHEL--VDQFVSY-VNPERP-IPDRIT---S 60 (313)
T ss_pred CCEEEEEEECCCCCCC-------------------CCeEEEEEEEEEE-CCEE--EEEEEEE-ECcCCC-CCHhhh---c
Confidence 4799999999998521 1259999998886 4432 4567665 333322 223322 3
Q ss_pred hcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhH
Q 038950 109 DSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKV 188 (297)
Q Consensus 109 ~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~ 188 (297)
-+|+.-..+. ++.+...-+-..-..+ . +-.+|+.++.+|+.+|.+.+--..+|.. ....+||-.
T Consensus 61 ihGIT~e~l~-~~~~~~evl~~f~~fl-~---~~~lVaHNa~FD~~fL~~~~~~~gl~~~-----------~~~~iDtl~ 124 (313)
T PRK06807 61 LTGITNYRVS-DAPTIEEVLPLFLAFL-H---TNVIVAHNASFDMRFLKSNVNMLGLPEP-----------KNKVIDTVF 124 (313)
T ss_pred cCCCCHHHHh-CCCCHHHHHHHHHHHH-c---CCeEEEEcHHHHHHHHHHHHHHcCCCCC-----------CCCEeeHHH
Confidence 3777755543 3433222111111122 2 2246676667999999998842222211 113678877
Q ss_pred HHHhcc-ccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHHH
Q 038950 189 VAGYCQ-GLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKN 237 (297)
Q Consensus 189 ~a~~~~-~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~~ 237 (297)
+++... .+.+ .+|+.+++.+|++. ..|.|=.|++.|+++|.++..
T Consensus 125 la~~~~~~~~~--~kL~~L~~~lgi~~--~~H~Al~DA~~ta~l~~~l~~ 170 (313)
T PRK06807 125 LAKKYMKHAPN--HKLETLKRMLGIRL--SSHNAFDDCITCAAVYQKCAS 170 (313)
T ss_pred HHHHHhCCCCC--CCHHHHHHHcCCCC--CCcChHHHHHHHHHHHHHHHH
Confidence 777543 3333 38999999999997 789999999999999999983
No 18
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.10 E-value=6.6e-05 Score=71.88 Aligned_cols=160 Identities=20% Similarity=0.200 Sum_probs=99.3
Q ss_pred cCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHH
Q 038950 28 CFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLL 107 (297)
Q Consensus 28 ~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL 107 (297)
.-+||++|+|-+|+... .=.|||+|...++.+|+.. ..|... .+...+ +.++.
T Consensus 14 ~~~fvvlD~ETTGl~p~-------------------~d~IIeIgav~v~~~g~i~--~~~~~l-v~P~~~---~~~~~-- 66 (313)
T PRK06063 14 PRGWAVVDVETSGFRPG-------------------QARIISLAVLGLDADGNVE--QSVVTL-LNPGVD---PGPTH-- 66 (313)
T ss_pred CCCEEEEEEECCCCCCC-------------------CCEEEEEEEEEEECCceee--eEEEEE-ECcCCC---CCCee--
Confidence 35799999999998421 1259999999999888643 333332 222211 22221
Q ss_pred HhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhc--CCCCCCChHHHHHHHHhccCcccc
Q 038950 108 KDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFT--NDALPPTAEAFSGVAALFFQSVFD 185 (297)
Q Consensus 108 ~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~--g~~LP~t~~eF~~~l~~~FP~vyD 185 (297)
=|||.=..+... -++...+.....++ ++-.+|++|..+|+.+|.+.+- |.++|. ...+|
T Consensus 67 -IhGIt~e~l~~a-p~f~ev~~~l~~~l----~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~-------------~~~ld 127 (313)
T PRK06063 67 -VHGLTAEMLEGQ-PQFADIAGEVAELL----RGRTLVAHNVAFDYSFLAAEAERAGAELPV-------------DQVMC 127 (313)
T ss_pred -cCCCCHHHHhCC-CCHHHHHHHHHHHc----CCCEEEEeCHHHHHHHHHHHHHHcCCCCCC-------------CCEEe
Confidence 155554444321 11111111111122 2335666666699999988874 333342 13679
Q ss_pred hhHHHHhcc-ccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 186 IKVVAGYCQ-GLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 186 tK~~a~~~~-~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
|.-+++... .+.. ..|+.|++.+|++. ...|.|-+|+..|+++|.++.
T Consensus 128 Tl~lar~~~~~~~~--~kL~~l~~~~gi~~-~~~H~Al~DA~ata~l~~~ll 176 (313)
T PRK06063 128 TVELARRLGLGLPN--LRLETLAAHWGVPQ-QRPHDALDDARVLAGILRPSL 176 (313)
T ss_pred hHHHHHHhccCCCC--CCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHH
Confidence 888887643 3332 37999999999985 568999999999999999987
No 19
>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=98.05 E-value=4.8e-05 Score=62.57 Aligned_cols=157 Identities=21% Similarity=0.221 Sum_probs=95.3
Q ss_pred eEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHhcC
Q 038950 32 LSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSG 111 (297)
Q Consensus 32 IAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~~G 111 (297)
|.+|+|-+|+.. ..-.|||+|...++.+++. ...||.+ +....+ ..+.+.+. +|
T Consensus 1 v~~D~Ettg~~~-------------------~~~~iiei~~v~~~~~~~~--~~~~~~~-i~p~~~-~~~~~~~~---~g 54 (159)
T cd06127 1 VVFDTETTGLDP-------------------KKDRIIEIGAVKVDGGIEI--VERFETL-VNPGRP-IPPEATAI---HG 54 (159)
T ss_pred CeEEeeCCCcCC-------------------CCCeEEEEEEEEEECCcCh--hhhhhee-eCcCCc-CCHhheec---cC
Confidence 579999999752 2335999999999987433 3445555 332222 22222221 55
Q ss_pred CChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccC-cccchhHHH
Q 038950 112 LDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQ-SVFDIKVVA 190 (297)
Q Consensus 112 fDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP-~vyDtK~~a 190 (297)
+.-+.. +.|.+...-+.....++ + +..||++++.+|..+|-+.+.... ...++ ..+||+-++
T Consensus 55 i~~~~~-~~~~~~~~~~~~~~~~l-~---~~~~v~~n~~fD~~~l~~~~~~~~------------~~~~~~~~iDt~~~~ 117 (159)
T cd06127 55 ITDEML-ADAPPFEEVLPEFLEFL-G---GRVLVAHNASFDLRFLNRELRRLG------------GPPLPNPWIDTLRLA 117 (159)
T ss_pred CCHHHH-hcCCCHHHHHHHHHHHH-C---CCEEEEeCcHhhHHHHHHHHHHhC------------CCCCCCCeeEHHHHH
Confidence 554443 35554443211111122 2 345667666799999988876211 12233 488999888
Q ss_pred HhccccCCCcchHHHH-HHHcCCcccCCCcccchHHHHHHHHHH
Q 038950 191 GYCQGLQGLKLGLSKL-ARILNVKRHGGAHHAGSDSLLTAAVFA 233 (297)
Q Consensus 191 ~~~~~l~~~~~~L~~l-a~~L~v~r~g~~HqAGsDSllT~~vF~ 233 (297)
+..-.... ..+|..+ ++.+++.. +..|.|-+|+..|+++|.
T Consensus 118 ~~~~~~~~-~~~l~~~~~~~~~~~~-~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 118 RRLLPGLR-SHRLGLLLAERYGIPL-EGAHRALADALATAELLL 159 (159)
T ss_pred HHHcCCCC-cCchHHHHHHHcCCCC-CCCCCcHHHHHHHHHHhC
Confidence 76543322 2477777 78888754 689999999999999873
No 20
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=98.03 E-value=0.0001 Score=66.10 Aligned_cols=157 Identities=21% Similarity=0.235 Sum_probs=88.1
Q ss_pred CeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHh
Q 038950 30 NVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKD 109 (297)
Q Consensus 30 ~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~ 109 (297)
.||++|+|.+|+.. . + .|||+|...++. |.. +..|..+ ..... .....+.+ -
T Consensus 6 ~~vvlD~EtTGl~~------~------------~--eIIeIgaV~v~~-g~~--~~~f~~l-v~P~~-~i~~~~~~---l 57 (195)
T PRK07247 6 TYIAFDLEFNTVNG------V------------S--HIIQVSAVKYDD-HKE--VDSFDSY-VYTDV-PLQSFING---L 57 (195)
T ss_pred eEEEEEeeCCCCCC------C------------C--eEEEEEEEEEEC-CEE--EEEEEEE-ECCCC-CCCcccee---c
Confidence 79999999999731 0 1 499999998874 322 3456554 22211 12222211 1
Q ss_pred cCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecc-hhHHHHHHHhcCCCCCCChHHHHHHHHhccC-cccchh
Q 038950 110 SGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGL-YDVAYLVKIFTNDALPPTAEAFSGVAALFFQ-SVFDIK 187 (297)
Q Consensus 110 ~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~-yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP-~vyDtK 187 (297)
+||.=..+. ++.+...-+......+ + +..||.+|.. +|+.+|-+. |.+++.. +. ..+|+.
T Consensus 58 hGIt~~~v~-~ap~~~evl~~f~~f~-~---~~~lVaHNa~~fD~~fL~~~--g~~~~~~-----------~~idt~~~~ 119 (195)
T PRK07247 58 TGITADKIA-DAPKVEEVLAAFKEFV-G---ELPLIGYNAQKSDLPILAEN--GLDLSDQ-----------YQVDLYDEA 119 (195)
T ss_pred CCCCHHHHh-CCCCHHHHHHHHHHHH-C---CCeEEEEeCcHhHHHHHHHc--CCCcCCC-----------ceeehHHHH
Confidence 555544442 2322211111111222 2 3357766655 899988653 3333321 11 134444
Q ss_pred HHHHh--ccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 188 VVAGY--CQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 188 ~~a~~--~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
+..+. .++++. -.|+.||+.+|++. ..|.|-+|++.|+.+|.+|.
T Consensus 120 ~~~~~~~~~~~~~--~~L~~La~~~gi~~--~~HrAl~DA~~ta~v~~~ll 166 (195)
T PRK07247 120 FERRSSDLNGIAN--LKLQTVADFLGIKG--RGHNSLEDARMTARVYESFL 166 (195)
T ss_pred HHhhccccCCCCC--CCHHHHHHhcCCCC--CCcCCHHHHHHHHHHHHHHH
Confidence 32221 112222 37999999999984 47999999999999999987
No 21
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=98.03 E-value=0.00013 Score=67.29 Aligned_cols=171 Identities=15% Similarity=0.188 Sum_probs=103.0
Q ss_pred hhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHH
Q 038950 26 LNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQ 105 (297)
Q Consensus 26 i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~ 105 (297)
+.+.+|+++|+|-||+... .=.|||+|...++.+.-.. ...|... .+... ...+++.+
T Consensus 44 ~~~~~~vviD~ETTGl~p~-------------------~d~IieIg~v~v~~~~i~~-~~~~~~l-i~P~~-~i~~~~~~ 101 (239)
T PRK09146 44 LSEVPFVALDFETTGLDAE-------------------QDAIVSIGLVPFTLQRIRC-RQARHWV-VKPRR-PLEEESVV 101 (239)
T ss_pred cccCCEEEEEeECCCCCCC-------------------CCcEEEEEEEEEECCeEee-cceEEEE-ECCCC-CCChhhhh
Confidence 4578999999999998532 1249999999887533211 2233332 22221 23444443
Q ss_pred HHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhc---CCCCCCChHHHHHHHHhccCc
Q 038950 106 LLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFT---NDALPPTAEAFSGVAALFFQS 182 (297)
Q Consensus 106 fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~---g~~LP~t~~eF~~~l~~~FP~ 182 (297)
. +||.-..+. .|-+...-+-.....+ ++-.+|+.|..+|.++|-+.+. +.++|. .
T Consensus 102 I---hGIt~e~l~-~ap~~~evl~~l~~~~----~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~--------------~ 159 (239)
T PRK09146 102 I---HGITHSELQ-DAPDLERILDELLEAL----AGKVVVVHYRRIERDFLDQALRNRIGEGIEF--------------P 159 (239)
T ss_pred h---cCCCHHHHh-CCCCHHHHHHHHHHHh----CCCEEEEECHHHHHHHHHHHHHHhcCCCCCC--------------c
Confidence 3 777665543 3433222111111111 2335777667799999988875 222221 2
Q ss_pred ccchhHHHHhcc-c--------cCC---CcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH-HhcCC
Q 038950 183 VFDIKVVAGYCQ-G--------LQG---LKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK-NRYEL 241 (297)
Q Consensus 183 vyDtK~~a~~~~-~--------l~~---~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~-~~f~~ 241 (297)
++||-.+++..- . +.+ ....|+.+++.+|++. ...|.|-+|++.|+++|.++. ++++.
T Consensus 160 ~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl~~-~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 160 VIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGLPA-YSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred eechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 568877776531 1 111 1236999999999885 456999999999999999998 66543
No 22
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=97.95 E-value=0.00016 Score=68.87 Aligned_cols=157 Identities=14% Similarity=0.157 Sum_probs=98.6
Q ss_pred CeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHh
Q 038950 30 NVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKD 109 (297)
Q Consensus 30 ~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~ 109 (297)
.||++|+|-+|.. + | .|||+|+..++ +|+. .-.|+.. .+.......+.+++ =
T Consensus 2 ~~vviD~ETTg~~-----~--------------d--~IieIgav~v~-~g~i--~~~f~~l-v~P~~~~~~~~~~~---I 53 (309)
T PRK06195 2 NFVAIDFETANEK-----R--------------N--SPCSIGIVVVK-DGEI--VEKVHYL-IKPKEMRFMPINIG---I 53 (309)
T ss_pred cEEEEEEeCCCCC-----C--------------C--ceEEEEEEEEE-CCEE--EEEEEEE-ECCCCCCCChhhee---c
Confidence 6999999998631 0 1 38999999886 3432 3445554 33332234455543 3
Q ss_pred cCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcC--CCCCCChHHHHHHHHhccCcccchh
Q 038950 110 SGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTN--DALPPTAEAFSGVAALFFQSVFDIK 187 (297)
Q Consensus 110 ~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g--~~LP~t~~eF~~~l~~~FP~vyDtK 187 (297)
+||.=..+...+ ++..-+-.....+ .+-.+|++|..+|+++|-+.+.. .+.|. ...+||-
T Consensus 54 hGIT~e~v~~ap-~f~ev~~~~~~fl----~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~-------------~~~idT~ 115 (309)
T PRK06195 54 HGIRPHMVEDEL-EFDKIWEKIKHYF----NNNLVIAHNASFDISVLRKTLELYNIPMPS-------------FEYICTM 115 (309)
T ss_pred cCcCHHHHhCCC-CHHHHHHHHHHHh----CCCEEEEECcHHHHHHHHHHHHHhCCCCCC-------------CCEEEHH
Confidence 888777665532 3222111111111 23345666666999999887642 23331 1367887
Q ss_pred HHHHhc-cccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 188 VVAGYC-QGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 188 ~~a~~~-~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
-+++.. +.+.. .+|+.|++.+|++ ...|.|-+|++.|+++|.+|.
T Consensus 116 ~lar~l~~~~~~--~~L~~L~~~~gi~--~~~H~Al~DA~ata~l~~~l~ 161 (309)
T PRK06195 116 KLAKNFYSNIDN--ARLNTVNNFLGYE--FKHHDALADAMACSNILLNIS 161 (309)
T ss_pred HHHHHHcCCCCc--CCHHHHHHHcCCC--CcccCCHHHHHHHHHHHHHHH
Confidence 777654 33432 3899999999997 258999999999999999998
No 23
>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=97.94 E-value=0.00038 Score=63.53 Aligned_cols=166 Identities=17% Similarity=0.194 Sum_probs=100.1
Q ss_pred CeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHh
Q 038950 30 NVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKD 109 (297)
Q Consensus 30 ~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~ 109 (297)
.+|.+|||-||+.... .=.|||+|...... +. +..-.|..+ .+... ...+++.+.
T Consensus 1 r~vvlD~ETTGl~p~~------------------~d~IIEIgav~~~~-~~-~~~~~f~~~-i~P~~-~i~~~a~~v--- 55 (225)
T TIGR01406 1 RQIILDTETTGLDPKG------------------GHRIVEIGAVELVN-RM-LTGDNFHVY-VNPER-DMPAEAAKV--- 55 (225)
T ss_pred CEEEEEeeCCCcCCCC------------------CCeEEEEEEEEEEC-Cc-EecceEEEE-ECcCC-CCCHHHHhc---
Confidence 4899999999985321 12499999875543 22 112345555 33322 234444433
Q ss_pred cCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhc--CCCCCCChHHHHHHHHhccCcccchh
Q 038950 110 SGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFT--NDALPPTAEAFSGVAALFFQSVFDIK 187 (297)
Q Consensus 110 ~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~--g~~LP~t~~eF~~~l~~~FP~vyDtK 187 (297)
+||.-..+... .++..-+-..-..+ ++-.+|.+|..+|++||-+.+- |..+|. + .-+-.++||-
T Consensus 56 hGIt~e~l~~~-p~f~ev~~~f~~fi----~~~~lVaHNa~FD~~fL~~el~r~g~~~~~----~-----~~~~~~iDTl 121 (225)
T TIGR01406 56 HGITDEFLADK-PKFKEIADEFLDFI----GGSELVIHNAAFDVGFLNYELERLGPTIKK----I-----GEFCRVIDTL 121 (225)
T ss_pred cCCCHHHHhCC-CCHHHHHHHHHHHh----CCCEEEEEecHHHHHHHHHHHHHhCCCCcc----c-----ccCCCEEEHH
Confidence 77776666543 22211111011122 2335666666699999988764 211111 0 0112478998
Q ss_pred HHHHhccccCCCcchHHHHHHHcCCcccCC-CcccchHHHHHHHHHHHHH
Q 038950 188 VVAGYCQGLQGLKLGLSKLARILNVKRHGG-AHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 188 ~~a~~~~~l~~~~~~L~~la~~L~v~r~g~-~HqAGsDSllT~~vF~kl~ 236 (297)
-|++..- .+.+.+|+.+++.+|++..+. .|-|-.|+.+|+++|.+|.
T Consensus 122 ~lar~~~--p~~~~~L~~L~~~~gi~~~~r~~H~Al~DA~~~a~v~~~l~ 169 (225)
T TIGR01406 122 AMARERF--PGQRNSLDALCKRFKVDNSHRTLHGALLDAHLLAEVYLALT 169 (225)
T ss_pred HHHHHHc--CCCCCCHHHHHHhcCCCCCCCCCcCHHHHHHHHHHHHHHHH
Confidence 8887642 122238999999999987654 7999999999999999997
No 24
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=97.91 E-value=0.00033 Score=62.68 Aligned_cols=175 Identities=19% Similarity=0.238 Sum_probs=106.7
Q ss_pred hcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEecc--CCCcceeEEEeeecCCCCCCCCchhhH
Q 038950 27 NCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDK--EGKISYTFEFNFSDFDLKKDLHAGDSI 104 (297)
Q Consensus 27 ~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~--~g~~p~~wqFNF~~Fd~~~d~~~~~SI 104 (297)
..+.||++|+|-+|+.... =.||++|...... +|.......|.+...+...-...++++
T Consensus 6 ~~~~~vv~D~ETTGl~~~~-------------------d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~ 66 (200)
T TIGR01298 6 RGYLPVVVDVETGGFNAKT-------------------DALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEAL 66 (200)
T ss_pred cCCeeEEEEeeCCCCCCCC-------------------CeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHH
Confidence 4578999999999985321 1399999888764 343321344555512222234556665
Q ss_pred HHHHhcCCChhhhhhCCCCCcch---hh-hhccccccC-CCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhc
Q 038950 105 QLLKDSGLDFDKIRKDGIPRCVF---AP-RFLEVLSKH-RENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALF 179 (297)
Q Consensus 105 ~fL~~~GfDFnk~~~~GI~~~~F---ll-~~SGLv~~~-~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~ 179 (297)
+. +||.=++..+++.+...- ++ .....+... .++-..|.+|..+|+.+|-+.+....++. ..
T Consensus 67 ~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~----------~~ 133 (200)
T TIGR01298 67 EF---TGIDLDHPLRGAVSEYEALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKR----------NP 133 (200)
T ss_pred Hc---cCCChhhhhhcCcchHHHHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCC----------CC
Confidence 44 888877666667654431 10 000011000 01233555555699999988874211110 01
Q ss_pred c-C-cccchhHHHHhccccCCCcchHHHHHHHcCCccc-CCCcccchHHHHHHHHHHHHHH
Q 038950 180 F-Q-SVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRH-GGAHHAGSDSLLTAAVFAEMKN 237 (297)
Q Consensus 180 F-P-~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~-g~~HqAGsDSllT~~vF~kl~~ 237 (297)
+ | .++||--+++... + ...|+.+++.+|++.. ...|.|-+|++.|+++|.+|..
T Consensus 134 ~~~~~~lDTl~lar~~~---~-~~~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~ 190 (200)
T TIGR01298 134 FHPFSTFDTATLAGLAY---G-QTVLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVN 190 (200)
T ss_pred CCCCcEEEHHHHHHHHc---C-cccHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHH
Confidence 1 1 2779988886542 2 2379999999999853 4689999999999999999983
No 25
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.91 E-value=0.00016 Score=67.01 Aligned_cols=168 Identities=17% Similarity=0.108 Sum_probs=101.7
Q ss_pred HhhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhH
Q 038950 25 LLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSI 104 (297)
Q Consensus 25 ~i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI 104 (297)
++++..||.+|+|-+|+.... =.|||+|+..++.++. ..+|+.. .+... ....+++
T Consensus 3 ~l~~~~~v~~D~ETTGl~~~~-------------------d~IIEIa~v~v~~~~~---~~~~~~l-i~P~~-~I~~~a~ 58 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDVKK-------------------DRIIEFAAIRFTFDEV---IDSVEFL-INPER-VVSAESQ 58 (250)
T ss_pred cccCCcEEEEEEeCCCCCCCC-------------------CeEEEEEEEEEECCeE---EEEEEEE-ECcCC-CCCHhhh
Confidence 567789999999999974211 2399999988875432 3456655 33322 2333333
Q ss_pred HHHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhcc-Ccc
Q 038950 105 QLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFF-QSV 183 (297)
Q Consensus 105 ~fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~F-P~v 183 (297)
+-|||--..+... -+....+-.....+ . +.-.+|.++..||..+|-+.+-...+|.. .. -.+
T Consensus 59 ---~ihgIt~e~v~~~-p~~~ev~~~~~~fl-~--~~~~lvghn~~FD~~~L~~~~~r~g~~~~----------~~~~~~ 121 (250)
T PRK06310 59 ---RIHHISDAMLRDK-PKIAEVFPQIKGFF-K--EGDYIVGHSVGFDLQVLSQESERIGETFL----------SKHYYI 121 (250)
T ss_pred ---hccCcCHHHHhCC-CCHHHHHHHHHHHh-C--CCCEEEEECHHHHHHHHHHHHHHcCCCcc----------ccCCcE
Confidence 2366554444322 11111110111111 2 22345665556999999988742222211 01 137
Q ss_pred cchhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 184 FDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 184 yDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
+||..+++..+... +.+|+.+++.+|++.. ..|.|-+|++.|+.+|.+|.
T Consensus 122 iDtl~lar~~~~~~--~~~L~~l~~~~g~~~~-~aH~Al~Da~at~~vl~~l~ 171 (250)
T PRK06310 122 IDTLRLAKEYGDSP--NNSLEALAVHFNVPYD-GNHRAMKDVEINIKVFKHLC 171 (250)
T ss_pred EehHHHHHhcccCC--CCCHHHHHHHCCCCCC-CCcChHHHHHHHHHHHHHHH
Confidence 89988887654332 2389999999998754 47999999999999999988
No 26
>PRK06722 exonuclease; Provisional
Probab=97.82 E-value=0.00061 Score=64.54 Aligned_cols=171 Identities=15% Similarity=0.090 Sum_probs=97.8
Q ss_pred cCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccC-CCcceeEEEeeecCCCCCCCCchhhHHH
Q 038950 28 CFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKE-GKISYTFEFNFSDFDLKKDLHAGDSIQL 106 (297)
Q Consensus 28 ~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~-g~~p~~wqFNF~~Fd~~~d~~~~~SI~f 106 (297)
...||++|+|.+|.... +-+.-.|||+|....+.. ++. +-.|+.+ .... ....+.+.++
T Consensus 4 ~~~~vViD~ETT~~p~~----------------~~~~deIIEIGAVkV~~g~i~I--vd~F~sL-V~P~-~~I~~~i~~L 63 (281)
T PRK06722 4 ATHFIVFDIERNFRPYK----------------SEDPSEIVDIGAVKIEASTMKV--IGEFSEL-VKPG-ARLTRHTTKL 63 (281)
T ss_pred CCEEEEEEeeCCCCCCC----------------CCCCCeEEEEEEEEEECCceeE--EeeEEEE-ECCC-CcCCHhHhhh
Confidence 46799999999852111 011224999999888752 232 3445554 2221 1233333332
Q ss_pred HHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhc--CCCCCCChHHHHHHHHhccCccc
Q 038950 107 LKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFT--NDALPPTAEAFSGVAALFFQSVF 184 (297)
Q Consensus 107 L~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~--g~~LP~t~~eF~~~l~~~FP~vy 184 (297)
+||.=+.+ +.|.+...-+-.....+ .+-.+++.|+.+|..+|-+.+. |.+.|.-. +-..+
T Consensus 64 ---TGIT~emV-~~AP~f~eVl~ef~~fi----g~~~lvahna~FD~~FL~~~l~~~gi~~p~~~----------~~~~i 125 (281)
T PRK06722 64 ---TGITKKDL-IGVEKFPQIIEKFIQFI----GEDSIFVTWGKEDYRFLSHDCTLHSVECPCME----------KERRI 125 (281)
T ss_pred ---cCCCHHHH-cCCCCHHHHHHHHHHHH----CCCcEEEEEeHHHHHHHHHHHHHcCCCCCccc----------ccchh
Confidence 55554444 22333222111111222 1234677788899999999774 43444311 00134
Q ss_pred chhHHHHh-ccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 185 DIKVVAGY-CQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 185 DtK~~a~~-~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
|+.-++.. .+.+.....+|+.+++.+|++..|..|.|-+||..|+++|.+|.
T Consensus 126 dl~~la~~~~~~l~~~~~sL~~l~~~lgL~~~g~~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 126 DLQKFVFQAYEELFEHTPSLQSAVEQLGLIWEGKQHRALADAENTANILLKAY 178 (281)
T ss_pred HHHHHHHHHhhhhccCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHh
Confidence 55433321 22221112379999999999988899999999999999999986
No 27
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=97.74 E-value=0.00088 Score=62.52 Aligned_cols=165 Identities=16% Similarity=0.155 Sum_probs=100.4
Q ss_pred hhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHH
Q 038950 26 LNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQ 105 (297)
Q Consensus 26 i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~ 105 (297)
+.+..||++|+|-+|..... -.|||+|...++ +|+.. -+|..+..+. ...+.+.+
T Consensus 65 ~~~~~~vv~DiETTG~~~~~-------------------~~IIEIGAv~v~-~g~i~--~~f~~~v~p~---~ip~~~~~ 119 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKK-------------------HQIIEIGAVKVK-NGEII--DRFESFVKAK---EVPEYITE 119 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCC-------------------CeEEEEEEEEEE-CCEEE--EEEEEEECCC---CCChhhhh
Confidence 46788999999999964321 159999999986 34332 2344332221 22222222
Q ss_pred HHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccc
Q 038950 106 LLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFD 185 (297)
Q Consensus 106 fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyD 185 (297)
-+|+.=..+. .|.+...-+...-..+ . +-.||+++..+|.++|-+.+....+|. +.....|
T Consensus 120 ---itGIt~e~l~-~ap~~~evl~~f~~fl-~---~~v~VaHNa~FD~~fL~~~l~r~g~~~-----------~~~~~ld 180 (257)
T PRK08517 120 ---LTGITYEDLE-NAPSLKEVLEEFRLFL-G---DSVFVAHNVNFDYNFISRSLEEIGLGP-----------LLNRKLC 180 (257)
T ss_pred ---hcCcCHHHHc-CCCCHHHHHHHHHHHH-C---CCeEEEECHHHHHHHHHHHHHHcCCCC-----------CCCCcEe
Confidence 2777666654 2433332211111112 2 335888777799999988775322222 1122456
Q ss_pred hhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHHH
Q 038950 186 IKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKN 237 (297)
Q Consensus 186 tK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~~ 237 (297)
|--+++.+-.. .+.+|+.+++.+|++.. ..|.|-+|++.|+++|.++..
T Consensus 181 tl~la~~~~~~--~~~~L~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~ 229 (257)
T PRK08517 181 TIDLAKRTIES--PRYGLSFLKELLGIEIE-VHHRAYADALAAYEIFKICLL 229 (257)
T ss_pred hHHHHHHHccC--CCCCHHHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHH
Confidence 65555543211 23489999999999864 789999999999999999984
No 28
>PRK07883 hypothetical protein; Validated
Probab=97.73 E-value=0.00048 Score=70.86 Aligned_cols=171 Identities=19% Similarity=0.171 Sum_probs=104.9
Q ss_pred HHHHhhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCch
Q 038950 22 LDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAG 101 (297)
Q Consensus 22 I~~~i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~ 101 (297)
+..-+.+.+||++|+|.+|+... .-.|||+|.-.++. |+. ..+|+.. .+... ...+
T Consensus 8 ~~~~~~~~~~Vv~D~ETTGl~p~-------------------~~~IIEIgaV~v~~-g~i--v~~f~~l-V~P~~-~i~~ 63 (557)
T PRK07883 8 LGTPLRDVTFVVVDLETTGGSPA-------------------GDAITEIGAVKVRG-GEV--LGEFATL-VNPGR-PIPP 63 (557)
T ss_pred hCCCCcCCCEEEEEEecCCCCCC-------------------CCeEEEEEEEEEEC-CEE--EEEEEEE-ECCCC-CCCh
Confidence 34557789999999999998421 12599999999873 332 3455554 33322 2344
Q ss_pred hhHHHHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccC
Q 038950 102 DSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQ 181 (297)
Q Consensus 102 ~SI~fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP 181 (297)
.+.+. +|+.=..+ +++.+...-+......+ ++...|+++..+|+.+|-+.+....+|.. -.
T Consensus 64 ~~~~i---tGIt~e~l-~~ap~~~evl~~f~~fl----~~~~lVaHNa~FD~~fL~~~~~r~g~~~~-----------~~ 124 (557)
T PRK07883 64 FITVL---TGITTAMV-AGAPPIEEVLPAFLEFA----RGAVLVAHNAPFDIGFLRAAAARCGYPWP-----------GP 124 (557)
T ss_pred hHHhh---cCCCHHHH-hCCCCHHHHHHHHHHHh----cCCEEEEeCcHHHHHHHHHHHHHcCCCCC-----------CC
Confidence 44332 77755443 34443332211111222 23345665556999999888753222210 01
Q ss_pred cccchhHHHHhccc-cCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 182 SVFDIKVVAGYCQG-LQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 182 ~vyDtK~~a~~~~~-l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
..+||-.+++..-. ......+|+.+++.+|++. ...|-|-+|++.|+.+|.++.
T Consensus 125 ~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~-~~~H~Al~DA~ata~l~~~l~ 179 (557)
T PRK07883 125 PVLCTVRLARRVLPRDEAPNVRLSTLARLFGATT-TPTHRALDDARATVDVLHGLI 179 (557)
T ss_pred CcEecHHHHHHhcccCCCCCCCHHHHHHHCCccc-CCCCCHHHHHHHHHHHHHHHH
Confidence 35788777765321 1111347999999999985 456999999999999999998
No 29
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=97.72 E-value=0.00067 Score=72.84 Aligned_cols=160 Identities=19% Similarity=0.225 Sum_probs=97.4
Q ss_pred CeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHh
Q 038950 30 NVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKD 109 (297)
Q Consensus 30 ~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~ 109 (297)
.||++|+|-+|+.... =.|||+|...++ +|+. .-+|... .+... ...+.+.+ -
T Consensus 1 ~~vvvD~ETTG~~~~~-------------------~~IIeig~v~v~-~~~i--~~~f~~~-v~P~~-~i~~~~~~---l 53 (850)
T TIGR01407 1 RYAVVDLETTGTQLSF-------------------DKIIQIGIVVVE-DGEI--VDTFHTD-VNPNE-PIPPFIQE---L 53 (850)
T ss_pred CEEEEEEECCCCCCCC-------------------CeEEEEEEEEEE-CCEE--EEEEEEE-eCCCC-CCChhhhh---h
Confidence 4899999999974211 239999999985 4443 2334443 22222 22333222 2
Q ss_pred cCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccC-cccchhH
Q 038950 110 SGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQ-SVFDIKV 188 (297)
Q Consensus 110 ~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP-~vyDtK~ 188 (297)
+|+.-+.+.. +-++...+.....++ ++-.+|++|..+|+.+|-+.+....+| .+| ..+||--
T Consensus 54 tGIt~e~l~~-ap~~~ev~~~l~~~l----~~~~~VahN~~fD~~fL~~~~~~~g~~------------~~~~~~iDt~~ 116 (850)
T TIGR01407 54 TGISDNMLQQ-APYFSQVAQEIYDLL----EDGIFVAHNVHFDLNFLAKALKDCGYE------------PLPKPRIDTVE 116 (850)
T ss_pred cCcCHHHHhC-CCCHHHHHHHHHHHh----CCCEEEEeCcHHHHHHHHHHHHHcCCC------------CCCCCeEeHHH
Confidence 7777555543 222221111111122 233577777779999999887522222 112 2678766
Q ss_pred HHHhcc-ccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 189 VAGYCQ-GLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 189 ~a~~~~-~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
+++... ... +.+|+.+++.+|++. ..+|.|-+|+..|+++|.+|.
T Consensus 117 l~~~~~p~~~--~~~L~~l~~~~gi~~-~~~H~Al~DA~ata~l~~~l~ 162 (850)
T TIGR01407 117 LAQIFFPTEE--SYQLSELSEALGLTH-ENPHRADSDAQATAELLLLLF 162 (850)
T ss_pred HHHHhcCCCC--CCCHHHHHHHCCCCC-CCCCChHHHHHHHHHHHHHHH
Confidence 665542 222 248999999999985 468999999999999999998
No 30
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.68 E-value=0.00076 Score=73.20 Aligned_cols=163 Identities=19% Similarity=0.260 Sum_probs=99.7
Q ss_pred CCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHH
Q 038950 29 FNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLK 108 (297)
Q Consensus 29 ~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~ 108 (297)
-.||++|+|-+|..... .-.|||+|....+ +|+. .-.|+.. .+... ...+.+.+ |
T Consensus 3 ~~~vvvD~ETTG~~p~~------------------~d~IIeigav~v~-~~~i--~~~f~~~-v~P~~-~i~~~~~~-l- 57 (928)
T PRK08074 3 KRFVVVDLETTGNSPKK------------------GDKIIQIAAVVVE-DGEI--LERFSSF-VNPER-PIPPFITE-L- 57 (928)
T ss_pred CCEEEEEEeCCCCCCCC------------------CCcEEEEEEEEEE-CCEE--EEEEEEE-ECcCC-CCCHHHhh-c-
Confidence 46999999999964221 0159999999995 4443 2344443 23222 23333222 2
Q ss_pred hcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhH
Q 038950 109 DSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKV 188 (297)
Q Consensus 109 ~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~ 188 (297)
+||+=..+. .+.++...+-..-.++ ++..+|+++..+|+.+|-+.+...-+|.. -...+||=.
T Consensus 58 -tGIt~~~l~-~ap~f~ev~~~l~~~l----~~~~~VaHN~~FD~~fL~~~~~~~g~~~~-----------~~~~iDt~~ 120 (928)
T PRK08074 58 -TGISEEMVK-QAPLFEDVAPEIVELL----EGAYFVAHNVHFDLNFLNEELERAGYTEI-----------HCPKLDTVE 120 (928)
T ss_pred -CCCCHHHHh-cCCCHHHHHHHHHHHh----CCCeEEEEChHHHHHHHHHHHHHcCCCCC-----------CCCeeeHHH
Confidence 777766544 3333222211111122 24467776666999999887753222211 013678766
Q ss_pred HHHhc-cccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 189 VAGYC-QGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 189 ~a~~~-~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
+++.. +.+.+ .+|+.|++.||++ .+.+|.|-+|++.|+++|.+|.
T Consensus 121 la~~~~p~~~~--~~L~~l~~~l~i~-~~~~H~Al~DA~ata~l~~~l~ 166 (928)
T PRK08074 121 LARILLPTAES--YKLRDLSEELGLE-HDQPHRADSDAEVTAELFLQLL 166 (928)
T ss_pred HHHHhcCCCCC--CCHHHHHHhCCCC-CCCCCChHHHHHHHHHHHHHHH
Confidence 66543 23332 3799999999987 4688999999999999999998
No 31
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=97.66 E-value=0.00084 Score=74.56 Aligned_cols=164 Identities=20% Similarity=0.268 Sum_probs=108.3
Q ss_pred hcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHH
Q 038950 27 NCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQL 106 (297)
Q Consensus 27 ~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~f 106 (297)
++..||++|+|-||+.... =.|||+|....+. |+. .-.|++. .+.. ....+.+.+
T Consensus 188 ~~~~~VVfDiETTGL~~~~-------------------d~IIEIGAVkv~~-g~i--id~f~~~-V~P~-~~I~~~~~~- 242 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQY-------------------DEIIEFGAVKVKN-GRI--IDKFQFF-IKPH-EPLSAFVTE- 242 (1213)
T ss_pred cCCcEEEEEeEecCCCCCC-------------------CeEEEEEEEEEEC-CeE--EEEEEEE-ECCC-CCCCHHHHH-
Confidence 7789999999999985321 1599999999874 432 3345554 2222 234444433
Q ss_pred HHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccch
Q 038950 107 LKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDI 186 (297)
Q Consensus 107 L~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDt 186 (297)
-+|+.-..+. +|.+...-+-.....+ ++-.+|+++..+|+.+|-+.+....+|. +-..++||
T Consensus 243 --ltGIT~e~L~-~ap~~~evl~~f~~fl----~~~iLVaHNa~FD~~fL~~~~~r~g~~~-----------~~~~~IDT 304 (1213)
T TIGR01405 243 --LTGITQDMLE-NAPEIEEVLEKFKEFF----KDSILVAHNASFDIGFLNTNFEKVGLEP-----------LENPVIDT 304 (1213)
T ss_pred --HhCCCHHHHh-CCCCHHHHHHHHHHHh----CCCeEEEEChHHHHHHHHHHHHHcCCCc-----------cCCCEeEH
Confidence 3788777653 4554443211111122 2345666565699999998875323331 11247899
Q ss_pred hHHHHhcc-ccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 187 KVVAGYCQ-GLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 187 K~~a~~~~-~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
--+++... .++ +.+|+.|++.+|++..+ .|.|-+|+..|+++|.+|.
T Consensus 305 l~lar~l~p~~k--~~kL~~Lak~lgi~~~~-~HrAl~DA~aTa~I~~~ll 352 (1213)
T TIGR01405 305 LELARALNPEYK--SHRLGNICKKLGVDLDD-HHRADYDAEATAKVFKVMV 352 (1213)
T ss_pred HHHHHHHhccCC--CCCHHHHHHHcCCCCCC-CcCHHHHHHHHHHHHHHHH
Confidence 88887653 343 24899999999998755 8999999999999999998
No 32
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=97.64 E-value=0.00047 Score=67.55 Aligned_cols=196 Identities=12% Similarity=0.173 Sum_probs=110.5
Q ss_pred HhhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhH
Q 038950 25 LLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSI 104 (297)
Q Consensus 25 ~i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI 104 (297)
.+++.+||++|+|-||+.... =.||+||.-.++.+|+.. ..|... .+...+.. +.
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~-------------------drIIeIgAV~i~~~g~iv--e~f~tL-VnP~~~~~---p~ 96 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPST-------------------SRLITIDAVTLTADGEEV--EHFHAV-LNPGEDPG---PF 96 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCC-------------------CeEEEEEEEEEEcCCEEE--EEEEEE-ECcCCCCC---Cc
Confidence 467789999999999985321 139999999888888643 444443 23322211 11
Q ss_pred HHHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcC--CCC-----CCChHHH-----
Q 038950 105 QLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTN--DAL-----PPTAEAF----- 172 (297)
Q Consensus 105 ~fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g--~~L-----P~t~~eF----- 172 (297)
.=+||.=+.+.. |.++..-+-....++ ++-.||..|..+|++||.+-+.- ..+ |... .+
T Consensus 97 ---~LHGIT~e~La~-AP~f~eVl~el~~fL----~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r-~~~~~~~ 167 (377)
T PRK05601 97 ---HLHGLSAEEFAQ-GKRFSQILKPLDRLI----DGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNR-GNRRGGR 167 (377)
T ss_pred ---cccCCCHHHHhc-CCCHHHHHHHHHHHh----CCCEEEEECcHHHHHHHHHHHHHhhhhhhhccccccc-ccccccc
Confidence 125555444432 333333221122233 34467775556999999887631 100 0000 00
Q ss_pred ----HHHHHhccCc-ccchhHHHHhcc-ccCCCcchHHHHHHHcCCcc---------cCCCcccch--HHHHHHHHHHHH
Q 038950 173 ----SGVAALFFQS-VFDIKVVAGYCQ-GLQGLKLGLSKLARILNVKR---------HGGAHHAGS--DSLLTAAVFAEM 235 (297)
Q Consensus 173 ----~~~l~~~FP~-vyDtK~~a~~~~-~l~~~~~~L~~la~~L~v~r---------~g~~HqAGs--DSllT~~vF~kl 235 (297)
...-+...|. ++||=-+++... .+.. -.|+.||+.+|++. -...|.|=+ |+.|++..|+++
T Consensus 168 ~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~--~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 168 GRRRQRVGHIPKPVVIVDTLATARRQGVALDD--IRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred cccccccCCCCCCCCEEEhHHHHHHHcCCCCC--CCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 0001123443 889977887654 4443 37999999999864 255666654 999999999997
Q ss_pred H-H--hcCCcccccCceeecCCCC
Q 038950 236 K-N--RYELEESAFDGFLYGMDSR 256 (297)
Q Consensus 236 ~-~--~f~~~~~~~~g~l~Gl~~~ 256 (297)
+ . .-....+....--+|+...
T Consensus 246 ~~~~~l~~~~p~~l~a~~fglq~s 269 (377)
T PRK05601 246 RASGPLSSIDPEDLRADKFGLQRS 269 (377)
T ss_pred hccCCccccChhhhhccccCcccc
Confidence 4 1 1111123334445777644
No 33
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.62 E-value=0.0012 Score=70.83 Aligned_cols=159 Identities=22% Similarity=0.268 Sum_probs=98.0
Q ss_pred cCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHH
Q 038950 28 CFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLL 107 (297)
Q Consensus 28 ~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL 107 (297)
...||++|+|-||+..+ + .|||+|....+ +|+. .-.|... .+.. ....+.+.+.
T Consensus 6 ~~~~vvvD~ETTGl~~~------------------d--~IIeIgaV~v~-~g~i--~~~f~~l-v~P~-~~i~~~~~~l- 59 (820)
T PRK07246 6 LRKYAVVDLEATGAGPN------------------A--SIIQVGIVIIE-GGEI--IDSYTTD-VNPH-EPLDEHIKHL- 59 (820)
T ss_pred CCCEEEEEEecCCcCCC------------------C--eEEEEEEEEEE-CCEE--EEEEEEE-eCcC-CCCCHhHhhc-
Confidence 46899999999997310 1 49999999885 3433 2334433 2222 1223322222
Q ss_pred HhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhc--CCCCCCChHHHHHHHHhccCcccc
Q 038950 108 KDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFT--NDALPPTAEAFSGVAALFFQSVFD 185 (297)
Q Consensus 108 ~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~--g~~LP~t~~eF~~~l~~~FP~vyD 185 (297)
+||.=..+. ++.+...-+-.....+ ++-.+|++|..+|+++|-+.+. |-+++. ..+|
T Consensus 60 --tGIt~e~l~-~ap~~~ev~~~~~~~l----~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~--------------~~iD 118 (820)
T PRK07246 60 --TGITDQQLA-QAPDFSQVARHIYDLI----EDCIFVAHNVKFDANLLAEALFLEGYELRT--------------PRVD 118 (820)
T ss_pred --CCCCHHHHh-cCCCHHHHHHHHHHHh----CCCEEEEECcHHHHHHHHHHHHHcCCCCCC--------------Ccee
Confidence 677665543 3333222211111122 2445677666799999988763 333321 1357
Q ss_pred hhHHHHhcc-ccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 186 IKVVAGYCQ-GLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 186 tK~~a~~~~-~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
|--+++..- .+. +-+|+.+++.+|++. ...|.|-+|+..|+++|.+|.
T Consensus 119 T~~la~~~~p~~~--~~~L~~L~~~lgl~~-~~~H~Al~DA~ata~L~~~l~ 167 (820)
T PRK07246 119 TVELAQVFFPTLE--KYSLSHLSRELNIDL-ADAHTAIADARATAELFLKLL 167 (820)
T ss_pred HHHHHHHHhCCCC--CCCHHHHHHHcCCCC-CCCCCHHHHHHHHHHHHHHHH
Confidence 777776532 232 248999999999985 468999999999999999998
No 34
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=97.60 E-value=0.00089 Score=58.80 Aligned_cols=166 Identities=18% Similarity=0.192 Sum_probs=94.3
Q ss_pred EEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCC-CCchhhHHHHHhcC
Q 038950 33 SIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKD-LHAGDSIQLLKDSG 111 (297)
Q Consensus 33 AiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d-~~~~~SI~fL~~~G 111 (297)
-+|+|-||+... .=.|||+|.-.++.++... ..|++. ...+.. ...++++. -+|
T Consensus 2 ~~D~ETTGl~~~-------------------~d~Iieig~v~v~~~~~~~--~~~~~~-v~p~~~~~~~~~a~~---ihG 56 (183)
T cd06138 2 FYDYETFGLNPS-------------------FDQILQFAAIRTDENFNEI--EPFNIF-CRLPPDVLPSPEALI---VTG 56 (183)
T ss_pred EEEeecCCCCCC-------------------CCceEEEEEEEECCCCCCc--cceeEE-EeCCCCCCCCHHHHH---HhC
Confidence 489999998531 1149999999888765432 445554 323222 33444443 488
Q ss_pred CChhhhhhCCCCCcchhhhhccccccCCCCceeEEeec-chhHHHHHHHhcCC---CCCCC------hHHHHHHHH---h
Q 038950 112 LDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHG-LYDVAYLVKIFTND---ALPPT------AEAFSGVAA---L 178 (297)
Q Consensus 112 fDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~-~yD~~yL~k~l~g~---~LP~t------~~eF~~~l~---~ 178 (297)
|.=..+...|.+....+-.....+.+ ++..+|++|+ .+|.++|-+.+... +++.+ .-+.....+ .
T Consensus 57 It~e~l~~~~~~~~~~l~~~~~~~~~--~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~ 134 (183)
T cd06138 57 ITPQQLLKEGLSEYEFIAKIHRLFNT--PGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYA 134 (183)
T ss_pred CCHHHHHhcCCCHHHHHHHHHHHHcc--CCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHh
Confidence 88777777677655442222223322 2445787776 59999998887521 22111 111122222 1
Q ss_pred ccCcccchhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHH
Q 038950 179 FFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAV 231 (297)
Q Consensus 179 ~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~v 231 (297)
++|..++. .+.-.+++ +-.|+.+++.+|++. ...|-|-+|++.|+++
T Consensus 135 ~~~~~~~~---~~~~~~~~--~~~L~~l~~~~gi~~-~~~H~Al~Da~~ta~l 181 (183)
T cd06138 135 LRPDGIVW---PKNDDGKP--SFKLEDLAQANGIEH-SNAHDALSDVEATIAL 181 (183)
T ss_pred hChhhccC---ccccCCCc--chhHHHHHHHCCCCc-cccccHHHHHHHHHHH
Confidence 22221110 00000111 237999999999986 6689999999999874
No 35
>PTZ00315 2'-phosphotransferase; Provisional
Probab=97.50 E-value=0.0034 Score=64.75 Aligned_cols=173 Identities=15% Similarity=0.096 Sum_probs=100.9
Q ss_pred CeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEecc-CCCcceeEEEeeecCCCCCCCCchhhHHHHH
Q 038950 30 NVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDK-EGKISYTFEFNFSDFDLKKDLHAGDSIQLLK 108 (297)
Q Consensus 30 ~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~-~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~ 108 (297)
.||++|+|.+|...... +.-.||++|...++. +|+. ...|..+.-+.......+...++
T Consensus 57 ~~IV~DlETTgl~~~~~----------------~~dEIIEIGaV~Vd~~ng~I--i~~F~~yVkP~~~p~Ls~fct~L-- 116 (582)
T PTZ00315 57 AYVVLDFEATCEADRRI----------------EDAEVIEFPMVLVDARTATP--VAEFQRYVRPVKNPVLSRFCTEL-- 116 (582)
T ss_pred eEEEEEEecCCCCCCCC----------------CCCceEEEEEEEEEccCCEE--EEEEEEEECCCCCCCCChhHhhh--
Confidence 68999999999642210 122499999999984 5543 45665552232211233333333
Q ss_pred hcCCChhhhhhCCCCCcch------hhhhccccccCCCCceeEEeec-chhHH-HHHHHhc--C-CCCCCChHHHHHHHH
Q 038950 109 DSGLDFDKIRKDGIPRCVF------APRFLEVLSKHRENLKWVTFHG-LYDVA-YLVKIFT--N-DALPPTAEAFSGVAA 177 (297)
Q Consensus 109 ~~GfDFnk~~~~GI~~~~F------ll~~SGLv~~~~~~~~Witfh~-~yD~~-yL~k~l~--g-~~LP~t~~eF~~~l~ 177 (297)
+||.=+. .+++.++..- .+..+++.-. .+....+..|+ .+|+. +|-+.+. + ..+|.
T Consensus 117 -TGITqe~-V~~Ap~F~eVl~ef~~fL~~~~~~e~-~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~---------- 183 (582)
T PTZ00315 117 -TGITQSM-VSRADPFPVVYCEALQFLAEAGLGDA-PPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPL---------- 183 (582)
T ss_pred -cCcCHHH-HhcCCCHHHHHHHHHHHHhccccccc-cccCceEEEeccHHHHHHHHHHHHHHhhhcCCCc----------
Confidence 5655333 3445544442 1111111100 01123444455 49995 6766553 2 24443
Q ss_pred hccCcccchh-HHHHhc-ccc--------CC-CcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 178 LFFQSVFDIK-VVAGYC-QGL--------QG-LKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 178 ~~FP~vyDtK-~~a~~~-~~l--------~~-~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
.|...+|+| ++++.. ++. +. .+.+|+.+++.+|++-.|..|.|=.|+.-|+++|.+|.
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 344566764 666642 211 01 12489999999999999999999999999999999998
No 36
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=97.50 E-value=2.6e-05 Score=64.22 Aligned_cols=160 Identities=20% Similarity=0.168 Sum_probs=88.9
Q ss_pred eEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHhcC
Q 038950 32 LSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSG 111 (297)
Q Consensus 32 IAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~~G 111 (297)
|.+|+|++|... +.-.|||+|.-..+.+.... .-.|+.+..+.........+ .+-+|
T Consensus 1 v~~D~Ettg~~~-------------------~~~~iieig~v~~~~~~~~~-~~~~~~~i~p~~~~~i~~~~---~~~~g 57 (164)
T PF00929_consen 1 VVFDTETTGLDP-------------------RQDEIIEIGAVKVDDDENEE-VESFNSLIRPEEPPKISPWA---TKVHG 57 (164)
T ss_dssp EEEEEEESSSTT-------------------TTCTEEEEEEEEEETTTTEE-EEEEEEEBEHSSHCSSEHHH---HHHHH
T ss_pred cEEEeEcCCCCC-------------------CCCeEEEEEEEEeeCCcccc-ceeeeecccccccccCCHHH---eeecC
Confidence 689999999864 23359999999888866422 44566552222222233333 33356
Q ss_pred CChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccC---cccchhH
Q 038950 112 LDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQ---SVFDIKV 188 (297)
Q Consensus 112 fDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP---~vyDtK~ 188 (297)
+.-..+...+-... -+......+ + +...|+..+..+|.+++.+.+. ..+...+| .++|+.-
T Consensus 58 It~~~l~~~~~~~~-~~~~~~~~~-~--~~~~~v~~n~~fd~~~l~~~~~------------~~~~~~~~~~~~~~~~~~ 121 (164)
T PF00929_consen 58 ITQEDLEDAPSFEE-ALDEFEEFL-K--KNDILVGHNASFDIGFLRREDK------------RFLGKPIPKPNPFIDTLE 121 (164)
T ss_dssp HCHHHHHCHCEHHH-HHHHHHHHH-H--HHTEEEETTCCHEEESSHHHHH------------HHHHHHHHHHHHECEEEE
T ss_pred CcccccccCCcHHH-HHHhhhhhh-h--cccccccccccchhhHHHHhhh------------hcccccccccchhhhhhH
Confidence 65555444332111 100011112 1 1335555555788766655544 11111111 2334332
Q ss_pred HHHh-ccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHH
Q 038950 189 VAGY-CQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVF 232 (297)
Q Consensus 189 ~a~~-~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF 232 (297)
+.+. .+.... .+|+++++.++++..+..|.|-+|++.|+.+|
T Consensus 122 ~~~~~~~~~~~--~~l~~l~~~~~~~~~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 122 LARALFPNRKK--YSLDDLAEYFGIPFDGTAHDALDDARATAELF 164 (164)
T ss_dssp EHHHHHHHHHH--HSHHHHHHHTTSSSTSTTTSHHHHHHHHHHHH
T ss_pred HHHHHhhcccc--CCHHHHHHHcCCCCCCCCcChHHHHHHHhCcC
Confidence 2222 111211 38999999999999888999999999999987
No 37
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.40 E-value=0.0039 Score=63.17 Aligned_cols=175 Identities=19% Similarity=0.170 Sum_probs=107.9
Q ss_pred hcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCC-CCchhhHH
Q 038950 27 NCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKD-LHAGDSIQ 105 (297)
Q Consensus 27 ~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d-~~~~~SI~ 105 (297)
....||.+|+|-||+..+. + .|||+|.--++.+++.. ...|+++ .....+ ...++|+
T Consensus 4 ~~~~fvv~D~ETTGLdP~~--D-----------------rIIeiAaVrvd~~~~~i-~e~~~~~-~~P~~~~lp~p~a~- 61 (476)
T PRK11779 4 MQPTFLWHDYETFGANPAL--D-----------------RPAQFAGIRTDADLNII-GEPLVFY-CKPADDYLPSPEAV- 61 (476)
T ss_pred CCCcEEEEEEECCCCCCCC--C-----------------eeEEEEEEEEeCCCcee-cceeEEE-EcCCcCcCCCHHHH-
Confidence 3567999999999986321 1 39999999888765432 2456665 334333 2345553
Q ss_pred HHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeec-chhHHHHHHHhcCCCCCCChHHHHHHHHhccC---
Q 038950 106 LLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHG-LYDVAYLVKIFTNDALPPTAEAFSGVAALFFQ--- 181 (297)
Q Consensus 106 fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~-~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP--- 181 (297)
.-+||-=+.+...|++...++....+.+.. ++..+|.+|+ .+|..++-+.+.. .+-++. .+. ++
T Consensus 62 --~IhGIT~e~l~~~g~~e~e~~~~i~~~l~~--~~~~lVGhNni~FD~eflr~~~~r-~~~d~y------~~~-~~~~n 129 (476)
T PRK11779 62 --LITGITPQEALEKGLPEAEFAARIHAEFSQ--PGTCILGYNNIRFDDEVTRYIFYR-NFYDPY------ARE-WQNGN 129 (476)
T ss_pred --HHhCCCHHHHHhcCCCHHHHHHHHHHHHhc--CCCEEEEeCchhhcHHHHHHHHHh-ccchHH------HHH-hcCCC
Confidence 448998888888898777763333333322 3334555555 4999999888862 211111 111 11
Q ss_pred ---cccchhHHHHhc-c---ccC----C-CcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 182 ---SVFDIKVVAGYC-Q---GLQ----G-LKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 182 ---~vyDtK~~a~~~-~---~l~----~-~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
.+.|+-.++... + .+. | .+..|+.|++.+|++. +.+|.|=+|++.|+.++.+|+
T Consensus 130 ~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~L~~~~gI~~-~~AHdALsDa~aT~~la~~l~ 195 (476)
T PRK11779 130 SRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEH-ENAHDAMSDVYATIAMAKLIK 195 (476)
T ss_pred CccCHHHHHHHHHHhccccccCcccccCCCCCcHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHH
Confidence 123332222211 0 000 1 1247999999999874 678999999999999999998
No 38
>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=97.32 E-value=0.0014 Score=55.83 Aligned_cols=72 Identities=19% Similarity=0.173 Sum_probs=44.9
Q ss_pred eeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHH-cCCcccCCCccc
Q 038950 143 KWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARI-LNVKRHGGAHHA 221 (297)
Q Consensus 143 ~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~-L~v~r~g~~HqA 221 (297)
.+|..|..+|+.+|- ...|. ..+.||--+..........+-+|+.|++. ||++..+..|.|
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 466666679998773 12222 12455532222211110113489999997 688755568999
Q ss_pred chHHHHHHHHH
Q 038950 222 GSDSLLTAAVF 232 (297)
Q Consensus 222 GsDSllT~~vF 232 (297)
.+|++.|+++|
T Consensus 141 l~DA~at~~l~ 151 (152)
T cd06144 141 VEDARAAMRLY 151 (152)
T ss_pred HHHHHHHHHHh
Confidence 99999999987
No 39
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=97.31 E-value=0.0041 Score=54.45 Aligned_cols=157 Identities=15% Similarity=0.178 Sum_probs=95.2
Q ss_pred eeEEeccccCccc-CCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcce----------eEEEeeecCCCCCCCC
Q 038950 31 VLSIDTEFPGFLR-NTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISY----------TFEFNFSDFDLKKDLH 99 (297)
Q Consensus 31 fIAiDtEFpGv~~-~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~----------~wqFNF~~Fd~~~d~~ 99 (297)
||++|+|=||+.. +. =.|||+|....+.++...+ +-.|++. .+... ..
T Consensus 1 ~vv~D~ETTGl~~~~~-------------------d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~l-v~P~~-~I 59 (177)
T cd06136 1 FVFLDLETTGLPKHNR-------------------PEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLC-FNPGR-AI 59 (177)
T ss_pred CeEEeeecCCCCCCCC-------------------CceEEEEEEEEecccccccccccccccceeeeeeEE-eCCCC-cC
Confidence 7999999999852 11 1499999999886543221 2345554 34332 23
Q ss_pred chhhHHHHHhcCCChhhhhhCCCCCcc-h---hhhhccccccCCCCceeEEeec-chhHHHHHHHhc--CCCCCCChHHH
Q 038950 100 AGDSIQLLKDSGLDFDKIRKDGIPRCV-F---APRFLEVLSKHRENLKWVTFHG-LYDVAYLVKIFT--NDALPPTAEAF 172 (297)
Q Consensus 100 ~~~SI~fL~~~GfDFnk~~~~GI~~~~-F---ll~~SGLv~~~~~~~~Witfh~-~yD~~yL~k~l~--g~~LP~t~~eF 172 (297)
.+++... +||.=..+...|- ... . +....+.. . +....|++++ .+|+.+|-+.+. |.++|..
T Consensus 60 ~~~a~~I---hGIt~e~l~~~~~-~~~~~~~~l~~f~~~~-~--~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~---- 128 (177)
T cd06136 60 SPGASEI---TGLSNDLLEHKAP-FDSDTANLIKLFLRRQ-P--KPICLVAHNGNRFDFPILRSELERLGTKLPDD---- 128 (177)
T ss_pred ChhHHHH---hCcCHHHHhcCCC-ccHHHHHHHHHHHHhc-C--CCCEEEEcCCcccCHHHHHHHHHHcCCCCCCC----
Confidence 4444443 8888877777662 221 1 11111111 1 2334555554 599999988874 3232211
Q ss_pred HHHHHhccCcccchhHHHHhccccCCCcchHHHHHHH-cCCcccCCCcccchHHHHHHHHHHH
Q 038950 173 SGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARI-LNVKRHGGAHHAGSDSLLTAAVFAE 234 (297)
Q Consensus 173 ~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~-L~v~r~g~~HqAGsDSllT~~vF~k 234 (297)
....||--+++... . +|+.|++. +|++. ...|.|-+|+..|++||++
T Consensus 129 --------~~~iDtl~l~r~~~---~---~L~~l~~~~~~~~~-~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 129 --------ILCVDSLPAFRELD---Q---SLGSLYKRLFGQEP-KNSHTAEGDVLALLKCALH 176 (177)
T ss_pred --------CEEEEeHHHHhhhH---h---hHHHHHHHHhCCCc-ccccchHHHHHHHHHHHhh
Confidence 12347766665432 2 79999885 67764 5579999999999999975
No 40
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=96.99 E-value=0.016 Score=55.24 Aligned_cols=155 Identities=15% Similarity=0.173 Sum_probs=91.4
Q ss_pred CeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEecc--CCCcc-eeEEEeeecCCCCCCCCchhhHHH
Q 038950 30 NVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDK--EGKIS-YTFEFNFSDFDLKKDLHAGDSIQL 106 (297)
Q Consensus 30 ~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~--~g~~p-~~wqFNF~~Fd~~~d~~~~~SI~f 106 (297)
.+|++|||-||+.... =.|||||+..++. +|+.- ....|+.. .+... ...+++...
T Consensus 38 ~~vvlD~ETTGLd~~~-------------------d~IIEIg~V~v~~~~~g~i~~v~~~~~~l-v~P~~-~I~~~~t~I 96 (294)
T PRK09182 38 LGVILDTETTGLDPRK-------------------DEIIEIGMVAFEYDDDGRIGDVLDTFGGL-QQPSR-PIPPEITRL 96 (294)
T ss_pred eEEEEEeeCCCCCCCC-------------------CeEEEEEEEEEEecCCCceeeeeeEEEEE-eCCCC-CCCHHHHHh
Confidence 6799999999985321 1499999999985 45432 14556665 33322 334444433
Q ss_pred HHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhc---CCCCCCChHHHHHHHHhccCcc
Q 038950 107 LKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFT---NDALPPTAEAFSGVAALFFQSV 183 (297)
Q Consensus 107 L~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~---g~~LP~t~~eF~~~l~~~FP~v 183 (297)
+||.=......+++...+. .++ . ..-..|++|..+|..||-+.+. +.+...+...
T Consensus 97 ---hGIt~e~v~~~~~~~~~l~----~fl-~--~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~------------ 154 (294)
T PRK09182 97 ---TGITDEMVAGQTIDPAAVD----ALI-A--PADLIIAHNAGFDRPFLERFSPVFATKPWACSVSE------------ 154 (294)
T ss_pred ---cCCCHHHHhcCCCcHHHHH----HHh-c--CCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHH------------
Confidence 7776666666665433331 011 2 1223445555699999877542 1122222111
Q ss_pred cchhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 184 FDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 184 yDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
.|-+ -.++. +..|+.|++.+| .....|.|.+|++.|+++|.++.
T Consensus 155 i~~~-----~~~~~--~~kL~~La~~~g--~~~~aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 155 IDWS-----ARGFE--GTKLGYLAGQAG--FFHEGHRAVDDCQALLELLARPL 198 (294)
T ss_pred Hhhc-----cccCC--CCCHHHHHHHcC--CCCCCcChHHHHHHHHHHHHHHH
Confidence 0100 01222 247999999999 34568999999999999999653
No 41
>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=96.92 E-value=0.0043 Score=53.41 Aligned_cols=32 Identities=22% Similarity=0.336 Sum_probs=26.6
Q ss_pred chHHHHHHHc---CCcccCCCcccchHHHHHHHHH
Q 038950 201 LGLSKLARIL---NVKRHGGAHHAGSDSLLTAAVF 232 (297)
Q Consensus 201 ~~L~~la~~L---~v~r~g~~HqAGsDSllT~~vF 232 (297)
-+|+.|++.+ +++..+..|.|-+||..|+++|
T Consensus 122 ~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 122 VSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELY 156 (157)
T ss_pred hhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHh
Confidence 4899999999 4554456799999999999987
No 42
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=96.88 E-value=0.036 Score=50.25 Aligned_cols=163 Identities=20% Similarity=0.274 Sum_probs=101.1
Q ss_pred CCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHH
Q 038950 29 FNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLK 108 (297)
Q Consensus 29 ~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~ 108 (297)
..||++|+|-+|... ..-.||++|.-....+.... .+ |..+ .+. +..+.+++...
T Consensus 13 ~~~vv~D~ETtg~~~-------------------~~~~iieIgav~~~~~~i~~-~~-~~~~-v~P-~~~i~~~~~~i-- 67 (243)
T COG0847 13 TRFVVIDLETTGLNP-------------------KKDRIIEIGAVTLEDGRIVE-RS-FHTL-VNP-ERPIPPEIFKI-- 67 (243)
T ss_pred CcEEEEecccCCCCC-------------------CCCceEEEEeEEEECCeeec-ce-eEEE-ECC-CCCCChhhhhh--
Confidence 689999999999864 33459999998887754332 11 3333 122 22334444433
Q ss_pred hcCCChhhhhhCCCCCcch-hhhhccccccCCCCceeEEeecchhHHHHHHHhc--CCCCCCChHHHHHHHHhccCcccc
Q 038950 109 DSGLDFDKIRKDGIPRCVF-APRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFT--NDALPPTAEAFSGVAALFFQSVFD 185 (297)
Q Consensus 109 ~~GfDFnk~~~~GI~~~~F-ll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~--g~~LP~t~~eF~~~l~~~FP~vyD 185 (297)
+||....+... |...- +-....++ + +.-.+|+.+-++|.+++-+.+. +.+.| -..++|
T Consensus 68 -~git~e~l~~~--p~~~~v~~~~~~~i-~--~~~~~Vahna~fD~~fl~~~~~~~~~~~~-------------~~~~~~ 128 (243)
T COG0847 68 -HGITDEMLADA--PKFAEVLPEFLDFI-G--GLRLLVAHNAAFDVGFLRVESERLGIEIP-------------GDPVLD 128 (243)
T ss_pred -cCCCHHHHhcC--CCHHHHHHHHHHHH-C--CCCeEEEEchhhcHHHHHHHHHHcCCCcc-------------cCceeh
Confidence 66666666655 11111 11111122 2 2245555555699999987765 33333 223667
Q ss_pred hhHHHHhc-cccCCCcchHHHHHHHcCCccc-CCCcccchHHHHHHHHHHHHHH
Q 038950 186 IKVVAGYC-QGLQGLKLGLSKLARILNVKRH-GGAHHAGSDSLLTAAVFAEMKN 237 (297)
Q Consensus 186 tK~~a~~~-~~l~~~~~~L~~la~~L~v~r~-g~~HqAGsDSllT~~vF~kl~~ 237 (297)
|--+++.. ++.. +.+|+.+++.+|+++- ...|.|-.|+++|+.+|.++..
T Consensus 129 t~~~~r~~~~~~~--~~~L~~l~~~~gi~~~~~~~H~Al~Da~~~a~~~~~~~~ 180 (243)
T COG0847 129 TLALARRHFPGFD--RSSLDALAERLGIDRNPFHPHRALFDALALAELFLLLQT 180 (243)
T ss_pred HHHHHHHHcCCCc--cchHHHHHHHcCCCcCCcCCcchHHHHHHHHHHHHHHHh
Confidence 76666653 3322 3489999999999984 5568899999999999999984
No 43
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=96.84 E-value=0.015 Score=65.75 Aligned_cols=166 Identities=20% Similarity=0.255 Sum_probs=100.3
Q ss_pred HhhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhH
Q 038950 25 LLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSI 104 (297)
Q Consensus 25 ~i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI 104 (297)
.+.+..||++|+|-+|+.... =.|||+|....+ +|.. ...|+.+ .+.. ....+.+.
T Consensus 415 ~L~~~~~VVfDLETTGL~~~~-------------------deIIEIgAV~V~-~G~i--ie~F~~~-V~P~-~~I~~~~~ 470 (1437)
T PRK00448 415 DLKDATYVVFDVETTGLSAVY-------------------DEIIEIGAVKIK-NGEI--IDKFEFF-IKPG-HPLSAFTT 470 (1437)
T ss_pred hhccCcEEEEEhhhcCCCCch-------------------hhhheeeeEEEe-CCeE--eeeEEEE-ECCC-CCCCHHHH
Confidence 355688999999999975321 158999988776 4433 3445554 3322 22333333
Q ss_pred HHHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCccc
Q 038950 105 QLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVF 184 (297)
Q Consensus 105 ~fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vy 184 (297)
++ +|+.=..+. .+.+...-+......+ ++..+|++++.+|+++|-+.+..--+|. +-....
T Consensus 471 ~L---TGIT~e~L~-~aps~~EaL~~f~~fi----gg~vLVAHNa~FD~~fL~~~l~rlgl~~-----------l~~~~I 531 (1437)
T PRK00448 471 EL---TGITDDMVK-DAPSIEEVLPKFKEFC----GDSILVAHNASFDVGFINTNYEKLGLEK-----------IKNPVI 531 (1437)
T ss_pred HH---hCCCHHHHc-CCCCHHHHHHHHHHHh----CCCEEEEeCccccHHHHHHHHHHcCCcc-----------ccccce
Confidence 32 555544444 3443333211111111 3456777667799999877665211221 111356
Q ss_pred chhHHHHhcc-ccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 185 DIKVVAGYCQ-GLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 185 DtK~~a~~~~-~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
||--+++... ... +.+|+.+|+.+|+...+ .|-|-+|++.|+.+|.+|.
T Consensus 532 DTLelar~l~p~~k--~~kL~~LAk~lGL~~~~-~HrAl~DA~aTa~lf~~ll 581 (1437)
T PRK00448 532 DTLELSRFLYPELK--SHRLNTLAKKFGVELEH-HHRADYDAEATAYLLIKFL 581 (1437)
T ss_pred eHHHHHHHHcCccc--cccHHHHHHHcCCCCCC-CcChHHHHHHHHHHHHHHH
Confidence 7765655432 222 34899999999998755 5999999999999999998
No 44
>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=96.83 E-value=0.0072 Score=51.55 Aligned_cols=70 Identities=19% Similarity=0.101 Sum_probs=47.1
Q ss_pred ceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHHcCCccc---CCC
Q 038950 142 LKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRH---GGA 218 (297)
Q Consensus 142 ~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~---g~~ 218 (297)
..+|..|..+|+.+|-. .-+.++||-.+++....... +-+|+.|++.+....+ +..
T Consensus 77 ~vlVgHn~~fD~~fL~~--------------------~~~~~iDT~~l~r~~~~~~~-~~~L~~L~~~~~~~~i~~~~~~ 135 (150)
T cd06145 77 TILVGHSLENDLKALKL--------------------IHPRVIDTAILFPHPRGPPY-KPSLKNLAKKYLGRDIQQGEGG 135 (150)
T ss_pred CEEEEcChHHHHHHhhc--------------------cCCCEEEcHHhccccCCCCC-ChhHHHHHHHHCCcceeCCCCC
Confidence 34555445599998732 12568999888765432111 2389999988643322 567
Q ss_pred cccchHHHHHHHHH
Q 038950 219 HHAGSDSLLTAAVF 232 (297)
Q Consensus 219 HqAGsDSllT~~vF 232 (297)
|.|-+|++.|+.+|
T Consensus 136 H~Al~DA~~t~~l~ 149 (150)
T cd06145 136 HDSVEDARAALELV 149 (150)
T ss_pred CCcHHHHHHHHHHh
Confidence 99999999999877
No 45
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.79 E-value=0.034 Score=50.79 Aligned_cols=159 Identities=18% Similarity=0.203 Sum_probs=91.3
Q ss_pred CeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHh
Q 038950 30 NVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKD 109 (297)
Q Consensus 30 ~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~ 109 (297)
.+|.+|||-||+.... =.|||+|. .+. .. .-.|+-. ++... ...+++++.
T Consensus 3 ~~vv~D~ETTGl~~~~-------------------d~IIeig~--v~~--~~--~~~f~~l-v~P~~-~I~~~a~~I--- 52 (232)
T PRK06309 3 ALIFYDTETTGTQIDK-------------------DRIIEIAA--YNG--VT--SESFQTL-VNPEI-PIPAEASKI--- 52 (232)
T ss_pred cEEEEEeeCCCCCCCC-------------------CEEEEEEE--EcC--cc--ccEEEEE-eCCCC-CCChhHHhh---
Confidence 5899999999985321 13999997 332 11 1234433 23322 234444333
Q ss_pred cCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeec-chhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhH
Q 038950 110 SGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHG-LYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKV 188 (297)
Q Consensus 110 ~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~-~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~ 188 (297)
+||.=+...... +...-+.....++ + +.-.+|++++ .+|..+|-+.+-...++.. .-..+||--
T Consensus 53 hGIt~e~v~~~p-~f~ev~~~~~~fi-~--~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~-----------~~~~iDt~~ 117 (232)
T PRK06309 53 HGITTDEVADAP-KFPEAYQKFIEFC-G--TDNILVAHNNDAFDFPLLRKECRRHGLEPP-----------TLRTIDSLK 117 (232)
T ss_pred cCCCHHHHhCCC-CHHHHHHHHHHHH-c--CCCEEEEeCCHHHHHHHHHHHHHHcCCCCC-----------CCcEEeHHH
Confidence 666555544422 1111110111122 2 2334455553 4999999988752222211 013678877
Q ss_pred HHHhcc-ccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 189 VAGYCQ-GLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 189 ~a~~~~-~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
+++... .+. +.+|+.+++.+|++. +.+|-|-+|++.|+++|.+|.
T Consensus 118 l~~~~~~~~~--~~~L~~l~~~~~~~~-~~aH~Al~Da~~t~~vl~~l~ 163 (232)
T PRK06309 118 WAQKYRPDLP--KHNLQYLRQVYGFEE-NQAHRALDDVITLHRVFSALV 163 (232)
T ss_pred HHHHHcCCCC--CCCHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHH
Confidence 776542 332 237999999998764 568999999999999999988
No 46
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=96.60 E-value=0.032 Score=50.93 Aligned_cols=147 Identities=15% Similarity=0.094 Sum_probs=87.6
Q ss_pred eeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCCchhhHHHHHhc
Q 038950 31 VLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDS 110 (297)
Q Consensus 31 fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~~~~SI~fL~~~ 110 (297)
++.+|||-+|+. + .|||+|..-+. +|+. +..|+.. .+... .....+++. +
T Consensus 2 ~~vlD~ETTGl~--~--------------------~IieIg~v~v~-~~~i--~~~~~~l-v~P~~-~i~~~~~~i---h 51 (219)
T PRK07983 2 LRVIDTETCGLQ--G--------------------GIVEIASVDVI-DGKI--VNPMSHL-VRPDR-PISPQAMAI---H 51 (219)
T ss_pred eEEEEEECCCCC--C--------------------CCEEEEEEEEE-CCEE--EEEEEEE-ECcCC-CCCHHHhhc---C
Confidence 789999999973 1 19999987665 4443 3344443 23222 233333332 5
Q ss_pred CCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHH
Q 038950 111 GLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVA 190 (297)
Q Consensus 111 GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a 190 (297)
||.=.... |-|...-.+.. +. ++..+|.+|..+|.++|-+ .-...+||--++
T Consensus 52 gIt~e~v~--~ap~~~ev~~~--~~----~~~~lVaHNa~FD~~~L~~--------------------~~~~~idTl~la 103 (219)
T PRK07983 52 RITEAMVA--DKPWIEDVIPH--YY----GSEWYVAHNASFDRRVLPE--------------------MPGEWICTMKLA 103 (219)
T ss_pred CCCHHHHc--CCCCHHHHHHH--Hc----CCCEEEEeCcHhhHHHHhC--------------------cCCCcEeHHHHH
Confidence 55433321 11211101111 11 2334555556699988621 012468998888
Q ss_pred Hhcc-ccCCCcchHHHHHHHcCCcc----cCCCcccchHHHHHHHHHHHHHHh
Q 038950 191 GYCQ-GLQGLKLGLSKLARILNVKR----HGGAHHAGSDSLLTAAVFAEMKNR 238 (297)
Q Consensus 191 ~~~~-~l~~~~~~L~~la~~L~v~r----~g~~HqAGsDSllT~~vF~kl~~~ 238 (297)
+... +++. +|+.|++.+++.. ....|.|-+|+++|+.+|.+|.+.
T Consensus 104 r~l~p~~~~---~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 104 RRLWPGIKY---SNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred HHHccCCCC---CHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 7643 4443 8899999998753 246899999999999999998843
No 47
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=95.59 E-value=0.052 Score=53.17 Aligned_cols=71 Identities=21% Similarity=0.444 Sum_probs=47.2
Q ss_pred Eeecc-hhHHHHHHHhcCCCCCCChHHHHHHHHhccC-cccchhHHHHhccccCCCcchHHHHHHH-cCCcccCCCcc--
Q 038950 146 TFHGL-YDVAYLVKIFTNDALPPTAEAFSGVAALFFQ-SVFDIKVVAGYCQGLQGLKLGLSKLARI-LNVKRHGGAHH-- 220 (297)
Q Consensus 146 tfh~~-yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP-~vyDtK~~a~~~~~l~~~~~~L~~la~~-L~v~r~g~~Hq-- 220 (297)
.||++ .|+..|.+.|- .-| .+||||..++.|+ +.. +-||..+.++ +|+. +-+.||
T Consensus 74 IfHaa~~DL~~l~~~~g-----------------~~p~plfdTqiAa~l~g-~~~-~~gl~~Lv~~ll~v~-ldK~~q~S 133 (361)
T COG0349 74 IFHAARFDLEVLLNLFG-----------------LLPTPLFDTQIAAKLAG-FGT-SHGLADLVEELLGVE-LDKSEQRS 133 (361)
T ss_pred eeccccccHHHHHHhcC-----------------CCCCchhHHHHHHHHhC-Ccc-cccHHHHHHHHhCCc-cccccccc
Confidence 78887 99998888873 334 4999999999996 322 3489888765 4654 322222
Q ss_pred --------------cchHHHHHHHHHHHHH
Q 038950 221 --------------AGSDSLLTAAVFAEMK 236 (297)
Q Consensus 221 --------------AGsDSllT~~vF~kl~ 236 (297)
|-+|...=...+-+|.
T Consensus 134 DW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~ 163 (361)
T COG0349 134 DWLARPLSEAQLEYAAADVEYLLPLYDKLT 163 (361)
T ss_pred ccccCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555566666
No 48
>PRK05359 oligoribonuclease; Provisional
Probab=95.45 E-value=0.23 Score=43.86 Aligned_cols=166 Identities=14% Similarity=0.142 Sum_probs=86.8
Q ss_pred cCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCC--CCCchhhHH
Q 038950 28 CFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKK--DLHAGDSIQ 105 (297)
Q Consensus 28 ~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~--d~~~~~SI~ 105 (297)
.-.||++|+|-||+.... + .|||+|.-..+.+.+.- .-.|++....... +...+.+.+
T Consensus 2 ~~~~vvlD~ETTGLdp~~------d-------------~IieIgaV~~~~~~~~~-~~~~~~~i~~~~~~l~~~~~~~~~ 61 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPER------D-------------RIIEIATIVTDADLNIL-AEGPVIAIHQSDEALAAMDEWNTR 61 (181)
T ss_pred CCcEEEEEeecCCCCCCC------C-------------eEEEEEEEEEcCCceEc-ccceEEEECCCHHHhhccChHHHH
Confidence 347999999999985321 1 29999999886654322 1224433112111 011222222
Q ss_pred HHHhcCCChhhhhhCCCCCcch---hh-hhccccccCCCCceeEEeec-chhHHHHHHHhcCCCCCCChHHHHHHHHhcc
Q 038950 106 LLKDSGLDFDKIRKDGIPRCVF---AP-RFLEVLSKHRENLKWVTFHG-LYDVAYLVKIFTNDALPPTAEAFSGVAALFF 180 (297)
Q Consensus 106 fL~~~GfDFnk~~~~GI~~~~F---ll-~~SGLv~~~~~~~~Witfh~-~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~F 180 (297)
.-..+|+. ++..+.|.+.... ++ ...|-+.. ...+++.|+ .+|..||-+.+- .+...+
T Consensus 62 ih~~tGIt-~~~l~~~~~~~e~~~~~l~fl~~~~~~---~~~~l~g~~v~FD~~FL~~~~~-------------~~~~~l 124 (181)
T PRK05359 62 THTRSGLI-DRVRASTVSEAEAEAQTLEFLKQWVPA---GKSPLCGNSIGQDRRFLARYMP-------------ELEAYF 124 (181)
T ss_pred hcccccCc-HHHHhcCCCHHHHHHHHHHHHHHhcCC---CCCceeecchhhCHHHHHHHHH-------------HhcccC
Confidence 21123666 5566667766654 11 11122212 234677777 699999988763 112222
Q ss_pred C-cccchhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH-Hhc
Q 038950 181 Q-SVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK-NRY 239 (297)
Q Consensus 181 P-~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~-~~f 239 (297)
. .+.|+--+.+.++.+.. .+ ..++.+ ...|.|=+|.+-|.+++...+ .++
T Consensus 125 ~~~~~Dv~tl~~l~r~~~P---~~-----~~~~~~-~~~HRal~D~~~s~~~~~~~~~~~~ 176 (181)
T PRK05359 125 HYRNLDVSTLKELARRWKP---EI-----LNGFKK-QGTHRALADIRESIAELKYYREHFF 176 (181)
T ss_pred CCcccchhHHHHHHHHhCh---hh-----hhCCCC-cCCcccHHHHHHHHHHHHHHHHHhc
Confidence 2 13443211111222222 11 013333 345999999999999999888 444
No 49
>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=94.02 E-value=0.99 Score=38.45 Aligned_cols=80 Identities=14% Similarity=0.108 Sum_probs=53.7
Q ss_pred CCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHHc-CCcc----
Q 038950 140 ENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARIL-NVKR---- 214 (297)
Q Consensus 140 ~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L-~v~r---- 214 (297)
++++.|.++...|+..|.+.+- .. +.+++|+..++..+..... +.||+.+++.+ |..-
T Consensus 72 ~~i~kv~~~~k~D~~~L~~~~g-~~---------------~~~~~Dl~~aa~ll~~~~~-~~~l~~l~~~~l~~~~~k~k 134 (170)
T cd06141 72 PSILKVGVGIKGDARKLARDFG-IE---------------VRGVVDLSHLAKRVGPRRK-LVSLARLVEEVLGLPLSKPK 134 (170)
T ss_pred CCeeEEEeeeHHHHHHHHhHcC-CC---------------CCCeeeHHHHHHHhCCCcC-CccHHHHHHHHcCcccCCCC
Confidence 5666776666688887755442 11 3357899998887764322 24899998875 4321
Q ss_pred -------------cCCCcccchHHHHHHHHHHHHH
Q 038950 215 -------------HGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 215 -------------~g~~HqAGsDSllT~~vF~kl~ 236 (297)
..+-|-|..|++++..++.+|+
T Consensus 135 ~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 135 KVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 1234668999999999998874
No 50
>PRK10829 ribonuclease D; Provisional
Probab=93.90 E-value=0.89 Score=44.86 Aligned_cols=75 Identities=15% Similarity=0.252 Sum_probs=51.7
Q ss_pred eeE-Eeecc-hhHHHHHHHhcCCCCCCChHHHHHHHHhccC-cccchhHHHHhccccCCCcchHHHHHHH-cCCcc----
Q 038950 143 KWV-TFHGL-YDVAYLVKIFTNDALPPTAEAFSGVAALFFQ-SVFDIKVVAGYCQGLQGLKLGLSKLARI-LNVKR---- 214 (297)
Q Consensus 143 ~Wi-tfh~~-yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP-~vyDtK~~a~~~~~l~~~~~~L~~la~~-L~v~r---- 214 (297)
.|+ +|||+ +|+..|.+.+ | ..| .++||...+..++ ... +.||..|.+. ||+.-
T Consensus 74 ~ivKV~H~~~~Dl~~l~~~~-g----------------~~p~~~fDTqiaa~~lg-~~~-~~gl~~Lv~~~lgv~ldK~~ 134 (373)
T PRK10829 74 QVTKFLHAGSEDLEVFLNAF-G----------------ELPQPLIDTQILAAFCG-RPL-SCGFASMVEEYTGVTLDKSE 134 (373)
T ss_pred CeEEEEeChHhHHHHHHHHc-C----------------CCcCCeeeHHHHHHHcC-CCc-cccHHHHHHHHhCCccCccc
Confidence 455 57776 9999887744 2 233 4999999998885 221 2489887654 67641
Q ss_pred --------c---CCCcccchHHHHHHHHHHHHH
Q 038950 215 --------H---GGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 215 --------~---g~~HqAGsDSllT~~vF~kl~ 236 (297)
. .+.+=|..|+.....+|-+|+
T Consensus 135 ~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~ 167 (373)
T PRK10829 135 SRTDWLARPLSERQCEYAAADVFYLLPIAAKLM 167 (373)
T ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 223447889999999999988
No 51
>PRK05755 DNA polymerase I; Provisional
Probab=93.62 E-value=1.2 Score=48.45 Aligned_cols=75 Identities=23% Similarity=0.190 Sum_probs=50.3
Q ss_pred EEeecc-hhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHHc-CCccc-------
Q 038950 145 VTFHGL-YDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARIL-NVKRH------- 215 (297)
Q Consensus 145 itfh~~-yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L-~v~r~------- 215 (297)
+++|++ +|+.+|.+. |.++| +.++||+.++..+..-.+ .||+.+++.. |..-+
T Consensus 373 kV~HNakfDl~~L~~~--gi~~~--------------~~~~DT~iAa~Ll~~~~~--~~L~~L~~~ylg~~~~~~~~~~g 434 (880)
T PRK05755 373 KVGQNLKYDLHVLARY--GIELR--------------GIAFDTMLASYLLDPGRR--HGLDSLAERYLGHKTISFEEVAG 434 (880)
T ss_pred EEEeccHhHHHHHHhC--CCCcC--------------CCcccHHHHHHHcCCCCC--CCHHHHHHHHhCCCccchHHhcC
Confidence 345655 999988752 43332 358899988877642111 3899988765 44411
Q ss_pred -----------CCCcccchHHHHHHHHHHHHHH
Q 038950 216 -----------GGAHHAGSDSLLTAAVFAEMKN 237 (297)
Q Consensus 216 -----------g~~HqAGsDSllT~~vF~kl~~ 237 (297)
...|-|..|+.+|..+|.+|..
T Consensus 435 k~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~ 467 (880)
T PRK05755 435 KQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKP 467 (880)
T ss_pred CCCCccccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1236688999999999999983
No 52
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=92.91 E-value=1.1 Score=38.95 Aligned_cols=163 Identities=14% Similarity=0.202 Sum_probs=81.4
Q ss_pred eeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCCCCCC---chhhHHHH
Q 038950 31 VLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLH---AGDSIQLL 107 (297)
Q Consensus 31 fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~~d~~---~~~SI~fL 107 (297)
+|.+|+|-+|+.... =.|||+|.-.++.++... ...|+.. .+.....- ...+.+.-
T Consensus 1 lv~iD~ETTGl~p~~-------------------d~IieIgaV~~~~~~~~i-~~~f~~~-i~p~~~~~~~~~~~~~~ih 59 (173)
T cd06135 1 LVWIDLEMTGLDPEK-------------------DRILEIACIITDGDLNII-AEGPELV-IHQPDEVLDGMDEWCTEMH 59 (173)
T ss_pred CEEEEEecCCCCCCC-------------------CeeEEEEEEEEeCCCcee-cCceeEE-ECCCHHHhhhccHHHHHcc
Confidence 578999999985311 139999999887653222 2344443 22221110 01111111
Q ss_pred HhcCCChhhhhhCCCCCcchhhhhccccccC-CCCceeEEeec-chhHHHHHHHhcCCCCCCChHHHHHHHHhcc-Cccc
Q 038950 108 KDSGLDFDKIRKDGIPRCVFAPRFLEVLSKH-RENLKWVTFHG-LYDVAYLVKIFTNDALPPTAEAFSGVAALFF-QSVF 184 (297)
Q Consensus 108 ~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~-~~~~~Witfh~-~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~F-P~vy 184 (297)
.-+|+. ++....|.+....+......+.+. +.+-.+++.|+ .+|+.+|-+.+.. + ...+ ....
T Consensus 60 ~~tgIt-~~~l~~~~~~~~vl~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~---------~----~~~~~~~~~ 125 (173)
T cd06135 60 TKSGLT-ERVRASTVTLAQAEAELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPE---------L----EEYLHYRIL 125 (173)
T ss_pred cccccH-HHHHhCCCCHHHHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHH---------H----hccCCcchh
Confidence 112443 222344443333211111112110 02345677888 7999999887751 0 1122 2356
Q ss_pred chhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH
Q 038950 185 DIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 185 DtK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~ 236 (297)
|+.-+.+..+.+.. .+.+ +++. .+..|.|=+|+.-|+..+....
T Consensus 126 D~~~l~~l~~~l~p---~~~~----~~~~-~~~~HrAl~Da~~~~~~~~~~~ 169 (173)
T cd06135 126 DVSSIKELARRWYP---EIYR----KAPK-KKGTHRALDDIRESIAELKYYR 169 (173)
T ss_pred hHHHHHHHHHHhCc---Hhhh----cCCC-CCCCcchHHHHHHHHHHHHHHH
Confidence 76332222222222 2222 2333 3567999999999999887765
No 53
>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=92.61 E-value=1.7 Score=38.50 Aligned_cols=158 Identities=20% Similarity=0.195 Sum_probs=87.5
Q ss_pred HHHHHHHHHH--hhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCC
Q 038950 16 EIVMRFLDKL--LNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFD 93 (297)
Q Consensus 16 ~~el~~I~~~--i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd 93 (297)
.+|+..+.+. +.+.+.|++|+|+.+....+ .-....+||+.- .++ ++-|... .
T Consensus 7 ~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~~---------------~~~~v~LiQiat-----~~~---~~lid~~--~ 61 (193)
T cd06146 7 EEELEALLLALSLEAGRVVGIDSEWKPSFLGD---------------SDPRVAILQLAT-----EDE---VFLLDLL--A 61 (193)
T ss_pred HHHHHHHHHHHhhccCCEEEEECccCCCccCC---------------CCCCceEEEEec-----CCC---EEEEEch--h
Confidence 3566666666 89999999999997643211 123567899882 121 4433222 1
Q ss_pred CCCCCCchhh-HHHHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHH
Q 038950 94 LKKDLHAGDS-IQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAF 172 (297)
Q Consensus 94 ~~~d~~~~~S-I~fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF 172 (297)
+.. ...+. .++|+ .++.+ +++.=|.+....|+..|.+.+-. ++. . +
T Consensus 62 ~~~--~~~~~~~~~L~------------------------~ll~d--~~i~KVg~~~~~D~~~L~~~~~~--~~~-~--~ 108 (193)
T cd06146 62 LEN--LESEDWDRLLK------------------------RLFED--PDVLKLGFGFKQDLKALSASYPA--LKC-M--F 108 (193)
T ss_pred ccc--cchHHHHHHHH------------------------HHhCC--CCeeEEEechHHHHHHHHHhcCc--ccc-c--c
Confidence 110 00111 11221 13334 45444444444999998876642 110 0 0
Q ss_pred HHHHHhccCcccchhHHHHhcccc---------CCCcchHHHHHHHc-CCcc------------c---CCCcccchHHHH
Q 038950 173 SGVAALFFQSVFDIKVVAGYCQGL---------QGLKLGLSKLARIL-NVKR------------H---GGAHHAGSDSLL 227 (297)
Q Consensus 173 ~~~l~~~FP~vyDtK~~a~~~~~l---------~~~~~~L~~la~~L-~v~r------------~---g~~HqAGsDSll 227 (297)
...-+++|+..+++..... ...+.||+.+++.+ |+.- . .+.+-|..|++.
T Consensus 109 -----~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~ 183 (193)
T cd06146 109 -----ERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYC 183 (193)
T ss_pred -----ccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHH
Confidence 0123599999888764321 11235899988764 4321 0 234558999999
Q ss_pred HHHHHHHHH
Q 038950 228 TAAVFAEMK 236 (297)
Q Consensus 228 T~~vF~kl~ 236 (297)
..++|-+|.
T Consensus 184 l~~l~~~L~ 192 (193)
T cd06146 184 LLEVFDKLL 192 (193)
T ss_pred HHHHHHHHh
Confidence 999998875
No 54
>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=91.67 E-value=0.35 Score=41.49 Aligned_cols=69 Identities=22% Similarity=0.208 Sum_probs=48.2
Q ss_pred eEEeec-chhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccc-cCC-CcchHHHHHHH-cCCcc-c-CC
Q 038950 144 WVTFHG-LYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQG-LQG-LKLGLSKLARI-LNVKR-H-GG 217 (297)
Q Consensus 144 Witfh~-~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~-l~~-~~~~L~~la~~-L~v~r-~-g~ 217 (297)
-++.|| .+|+.+|-. ..+.+.||-.|++.... ..+ .+.+|+.|++. +|++- . ..
T Consensus 86 vlVgHn~~fD~~fL~~--------------------~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~ 145 (161)
T cd06137 86 ILVGHSLQNDLDALRM--------------------IHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGE 145 (161)
T ss_pred EEEeccHHHHHHHHhC--------------------cCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCC
Confidence 344555 499988732 13468899999987542 210 13589999987 67653 2 45
Q ss_pred CcccchHHHHHHHHH
Q 038950 218 AHHAGSDSLLTAAVF 232 (297)
Q Consensus 218 ~HqAGsDSllT~~vF 232 (297)
.|.|-.|+..|+++|
T Consensus 146 ~H~A~~DA~at~~l~ 160 (161)
T cd06137 146 GHDSLEDALAAREVV 160 (161)
T ss_pred CCCcHHHHHHHHHHh
Confidence 799999999999887
No 55
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=91.61 E-value=2.6 Score=41.35 Aligned_cols=143 Identities=22% Similarity=0.316 Sum_probs=80.9
Q ss_pred HHHHHHHHHHhhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcceeEEEeeecCCCC
Q 038950 16 EIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLK 95 (297)
Q Consensus 16 ~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~~wqFNF~~Fd~~ 95 (297)
.+++..+.+.+..++.||+||||..... | -..+-+||+.- .++ ++- ||.-
T Consensus 5 ~~~l~~~~~~l~~~~~ia~DtE~~~~~~-----------y------~~~l~LiQia~----~~~----~~l-----iD~~ 54 (367)
T TIGR01388 5 DDELATVCEAVRTFPFVALDTEFVRERT-----------F------WPQLGLIQVAD----GEQ----LAL-----IDPL 54 (367)
T ss_pred HHHHHHHHHHHhcCCEEEEeccccCCCC-----------C------CCcceEEEEee----CCe----EEE-----EeCC
Confidence 3567777777888999999999976421 1 11245888862 111 332 3331
Q ss_pred CCCCchhhHHHHHhcCCChhhhhhCCCCCcchhhhhccccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHH
Q 038950 96 KDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGV 175 (297)
Q Consensus 96 ~d~~~~~SI~fL~~~GfDFnk~~~~GI~~~~Fll~~SGLv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~ 175 (297)
.. .|.+.+. .++.+ +++.+|.+...+|+..|.+... .+|
T Consensus 55 ~~--------------~~~~~L~--------------~lL~d--~~i~KV~h~~k~Dl~~L~~~~~--~~~--------- 93 (367)
T TIGR01388 55 VI--------------IDWSPLK--------------ELLRD--ESVVKVLHAASEDLEVFLNLFG--ELP--------- 93 (367)
T ss_pred Cc--------------ccHHHHH--------------HHHCC--CCceEEEeecHHHHHHHHHHhC--CCC---------
Confidence 10 0111111 13345 5778887666699887755432 222
Q ss_pred HHhccCcccchhHHHHhccccCCCcchHHHHHHH-cCCccc-C-----------CC---cccchHHHHHHHHHHHHH
Q 038950 176 AALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARI-LNVKRH-G-----------GA---HHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 176 l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~-L~v~r~-g-----------~~---HqAGsDSllT~~vF~kl~ 236 (297)
..++||...+..++.-. +.||+.+++. ||+.-. + .. +-|..|+.....++-+|+
T Consensus 94 -----~~~fDtqlAa~lL~~~~--~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~ 163 (367)
T TIGR01388 94 -----QPLFDTQIAAAFCGFGM--SMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLM 163 (367)
T ss_pred -----CCcccHHHHHHHhCCCC--CccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 15789998887775221 2389888765 465411 0 00 125667766666677776
No 56
>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=90.77 E-value=8.7 Score=32.02 Aligned_cols=83 Identities=23% Similarity=0.389 Sum_probs=51.3
Q ss_pred ccccCCCCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHH-cC-
Q 038950 134 VLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARI-LN- 211 (297)
Q Consensus 134 Lv~~~~~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~-L~- 211 (297)
++.+ ++++.|.++..+|+..|.+.+- ....+++|| .++..+-+-.. +.||+.+++. +|
T Consensus 72 ll~~--~~i~kv~~n~~~D~~~L~~~~~----------------i~~~~~~D~-~l~~~~l~~~~-~~~L~~L~~~~l~~ 131 (176)
T PF01612_consen 72 LLED--PNIIKVGHNAKFDLKWLYRSFG----------------IDLKNVFDT-MLAAYLLDPTR-SYSLKDLAEEYLGN 131 (176)
T ss_dssp HHTT--TTSEEEESSHHHHHHHHHHHHT----------------S--SSEEEH-HHHHHHTTTST-TSSHHHHHHHHHSE
T ss_pred HHhC--CCccEEEEEEechHHHHHHHhc----------------cccCCccch-hhhhhcccccc-cccHHHHHHHHhhh
Confidence 4445 6777777666699999988722 234468999 55555432221 1489998765 45
Q ss_pred Ccc-----cCC-----------CcccchHHHHHHHHHHHHH
Q 038950 212 VKR-----HGG-----------AHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 212 v~r-----~g~-----------~HqAGsDSllT~~vF~kl~ 236 (297)
... .+. ..=|+.|+..|.+.+-+|.
T Consensus 132 ~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~ 172 (176)
T PF01612_consen 132 IDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLK 172 (176)
T ss_dssp EE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHH
T ss_pred ccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHH
Confidence 221 111 1226779999999999887
No 57
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=89.56 E-value=7.7 Score=33.01 Aligned_cols=79 Identities=15% Similarity=0.163 Sum_probs=51.7
Q ss_pred CCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHH-cCCcc----
Q 038950 140 ENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARI-LNVKR---- 214 (297)
Q Consensus 140 ~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~-L~v~r---- 214 (297)
+++..|.+....|+..|.+.+ |.. +.+++||..++..+..-. +.||+.+++. ||+.-
T Consensus 66 ~~i~Kvg~~~k~D~~~L~~~~-gi~---------------~~~~~D~~~aa~ll~~~~--~~~L~~l~~~~lg~~l~K~~ 127 (161)
T cd06129 66 PSIVKALHGIEGDLWKLLRDF-GEK---------------LQRLFDTTIAANLKGLPE--RWSLASLVEHFLGKTLDKSI 127 (161)
T ss_pred CCEEEEEeccHHHHHHHHHHc-CCC---------------cccHhHHHHHHHHhCCCC--CchHHHHHHHHhCCCCCccc
Confidence 566666666668877766542 211 224689988887664221 2389998876 46531
Q ss_pred -----------cCCCcccchHHHHHHHHHHHHH
Q 038950 215 -----------HGGAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 215 -----------~g~~HqAGsDSllT~~vF~kl~ 236 (297)
..+.+-|..|++....+|-+|+
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 1234568999999999999885
No 58
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=81.59 E-value=0.75 Score=38.81 Aligned_cols=73 Identities=21% Similarity=0.352 Sum_probs=38.9
Q ss_pred CceeEEeecc-hhHHHHHHHhcCCCCCCChHHHHHHHHhccC-cccchhHHHHhccccCCCcchHHHHHHHcCCcccCCC
Q 038950 141 NLKWVTFHGL-YDVAYLVKIFTNDALPPTAEAFSGVAALFFQ-SVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGA 218 (297)
Q Consensus 141 ~~~Witfh~~-yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP-~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~ 218 (297)
.-.+|+|||. ||+.+|-+.+-.-.+|. + ...|+..+++.... . +.+|..||+.||+.|- ..
T Consensus 57 ~~~iv~yng~~FD~p~L~~~~~~~~~~~-------------~~~~iDl~~~~~~~~~-~--~~~Lk~ve~~lg~~~~-~~ 119 (164)
T PF13482_consen 57 ADNIVTYNGKNFDIPFLKRRAKRYGLPP-------------PFNHIDLLKIIKKHFL-E--SYSLKNVEKFLGIERR-DD 119 (164)
T ss_dssp T--EEESSTTTTHHHHHHHHH-HHHH---------------GGGEEEHHHHHT-TTS-C--CTT--SHHH----------
T ss_pred CCeEEEEeCcccCHHHHHHHHHHcCCCc-------------ccchhhHHHHHHhccC-C--CCCHHHHhhhcccccc-cC
Confidence 4579999985 99999999984323443 3 37799888865432 2 3489999999999983 23
Q ss_pred cccchHHHHHHH
Q 038950 219 HHAGSDSLLTAA 230 (297)
Q Consensus 219 HqAGsDSllT~~ 230 (297)
...|+++...-.
T Consensus 120 ~~~G~~~~~~~~ 131 (164)
T PF13482_consen 120 DISGSESVKLYK 131 (164)
T ss_dssp --HHHHHHHHHH
T ss_pred CCCHHHHHHHHH
Confidence 356777666543
No 59
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=76.17 E-value=3.6 Score=46.13 Aligned_cols=80 Identities=24% Similarity=0.277 Sum_probs=58.9
Q ss_pred Eeecc-hhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhcc-ccCCCcchHHHHHHHcCCcccCCCcccch
Q 038950 146 TFHGL-YDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQ-GLQGLKLGLSKLARILNVKRHGGAHHAGS 223 (297)
Q Consensus 146 tfh~~-yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~-~l~~~~~~L~~la~~L~v~r~g~~HqAGs 223 (297)
+-||+ +|++||-.-+---.||+-. . .+.||=-+|+... .++. -+|..|++.|++.- ...|-|-+
T Consensus 505 VAHNasFD~gFl~~~~~k~~~~~~~----------~-pvIDTL~lar~L~P~~ks--h~Lg~l~kk~~v~l-e~hHRA~y 570 (1444)
T COG2176 505 VAHNASFDMGFLNTNYEKYGLEPLT----------N-PVIDTLELARALNPEFKS--HRLGTLCKKLGVEL-ERHHRADY 570 (1444)
T ss_pred EeccCccchhHHHHHHHHhCCcccc----------C-chhhHHHHHHHhChhhhh--cchHHHHHHhCccH-HHhhhhhh
Confidence 44665 9999997766521111110 1 3779999998764 4443 48999999999987 77899999
Q ss_pred HHHHHHHHHHHHH-Hhc
Q 038950 224 DSLLTAAVFAEMK-NRY 239 (297)
Q Consensus 224 DSllT~~vF~kl~-~~f 239 (297)
||-.|+.+|++|. ...
T Consensus 571 Daeat~~vf~~f~~~~k 587 (1444)
T COG2176 571 DAEATAKVFFVFLKDLK 587 (1444)
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 9999999999998 544
No 60
>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=55.33 E-value=43 Score=28.38 Aligned_cols=80 Identities=23% Similarity=0.225 Sum_probs=50.1
Q ss_pred CCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHHc-CCccc---
Q 038950 140 ENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARIL-NVKRH--- 215 (297)
Q Consensus 140 ~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L-~v~r~--- 215 (297)
.+++.|+++..+|+..|.+. |-++| +.++||..++..+..-.+ +.+|+++++.+ +..-+
T Consensus 66 ~~~~~v~hn~k~d~~~l~~~--gi~~~--------------~~~~Dt~l~a~ll~p~~~-~~~l~~l~~~~l~~~~~~~~ 128 (193)
T cd06139 66 PSIKKVGQNLKFDLHVLANH--GIELR--------------GPAFDTMLASYLLNPGRR-RHGLDDLAERYLGHKTISFE 128 (193)
T ss_pred CCCcEEeeccHHHHHHHHHC--CCCCC--------------CCcccHHHHHHHhCCCCC-CCCHHHHHHHHhCCCCccHH
Confidence 34567777777999988653 32221 247899988887653221 23888888764 33200
Q ss_pred ---C---------------CCcccchHHHHHHHHHHHHH
Q 038950 216 ---G---------------GAHHAGSDSLLTAAVFAEMK 236 (297)
Q Consensus 216 ---g---------------~~HqAGsDSllT~~vF~kl~ 236 (297)
| ..|-|..|+.++..++-+|.
T Consensus 129 ~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~ 167 (193)
T cd06139 129 DLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLK 167 (193)
T ss_pred HHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 11237778888888888887
No 61
>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=54.75 E-value=52 Score=30.09 Aligned_cols=94 Identities=16% Similarity=0.251 Sum_probs=55.3
Q ss_pred CceeEEeecc-hhHHHHHHH-h-cCCCCCCChHHHH----HHHHhccCcccchhHHHHhccccCCCcchHHHHHHHcCCc
Q 038950 141 NLKWVTFHGL-YDVAYLVKI-F-TNDALPPTAEAFS----GVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVK 213 (297)
Q Consensus 141 ~~~Witfh~~-yD~~yL~k~-l-~g~~LP~t~~eF~----~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~ 213 (297)
..++|+|+|. +|+-+|..- + .|-++|.-.+.=- .-.+.|--.-.|+.=+-...+ -+ .+.+|..||..||++
T Consensus 52 ~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g-~~-~~~sLd~la~~lgiP 129 (209)
T PF10108_consen 52 NPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYG-AK-ARTSLDELAALLGIP 129 (209)
T ss_pred CCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccC-cc-ccCCHHHHHHHcCCC
Confidence 4678998875 999998654 3 4677776444211 001111111345543332221 11 245899999999987
Q ss_pred ccCCCc----------cc----------chHHHHHHHHHHHHHHh
Q 038950 214 RHGGAH----------HA----------GSDSLLTAAVFAEMKNR 238 (297)
Q Consensus 214 r~g~~H----------qA----------GsDSllT~~vF~kl~~~ 238 (297)
- +.- ++ =.|.+-|..+|.|+...
T Consensus 130 g--K~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~ 172 (209)
T PF10108_consen 130 G--KDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELL 172 (209)
T ss_pred C--CCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3 211 12 25789999999999743
No 62
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=54.09 E-value=41 Score=30.18 Aligned_cols=70 Identities=16% Similarity=0.202 Sum_probs=42.7
Q ss_pred ceeEEeecc-hhHHHHHHHh--cCCCCCCChHHHHHHHHhcc----CcccchhHHHHhccccCCCcchHHHHHHHcCCcc
Q 038950 142 LKWVTFHGL-YDVAYLVKIF--TNDALPPTAEAFSGVAALFF----QSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKR 214 (297)
Q Consensus 142 ~~Witfh~~-yD~~yL~k~l--~g~~LP~t~~eF~~~l~~~F----P~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r 214 (297)
-.+|+|+|. +|+-||.+-. .|-++|.......+.. .+. ...+|+--+.+.....+ +.+|+.||+.||+++
T Consensus 94 p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~-~y~~r~~~~h~DL~~~~~~~~~~~--~~~L~~va~~lG~~~ 170 (208)
T cd05782 94 PRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDW-NYRNRYSERHLDLMDLLAFYGARA--RASLDLLAKLLGIPG 170 (208)
T ss_pred CEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchh-hccCcCCCCcccHHHHHhccCccC--CCCHHHHHHHhCCCC
Confidence 367888884 9999998853 4555665443221111 111 12668766665443222 348999999999964
No 63
>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=39.24 E-value=31 Score=29.66 Aligned_cols=29 Identities=21% Similarity=0.277 Sum_probs=26.7
Q ss_pred eccccHHHHHHHHHHHhhcCCeeEEeccc
Q 038950 10 VWCENFEIVMRFLDKLLNCFNVLSIDTEF 38 (297)
Q Consensus 10 Vw~~N~~~el~~I~~~i~~~~fIAiDtEF 38 (297)
|.+-|++|.+..|.+.-++.-.||||.-.
T Consensus 44 VHA~NL~e~l~~I~~~~~~~~iIAIDAcL 72 (140)
T TIGR02841 44 VHAKNLEEKLKIIKKKHPNPFIIAIDACL 72 (140)
T ss_pred cccccHHHHHHHHHHhCCCCeEEEEECcc
Confidence 78999999999999999999999999855
No 64
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=38.73 E-value=24 Score=32.94 Aligned_cols=102 Identities=20% Similarity=0.251 Sum_probs=61.9
Q ss_pred CCceeE---EeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhcc-ccCCCcchHHHHHHHcCCccc
Q 038950 140 ENLKWV---TFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQ-GLQGLKLGLSKLARILNVKRH 215 (297)
Q Consensus 140 ~~~~Wi---tfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~-~l~~~~~~L~~la~~L~v~r~ 215 (297)
++.-|+ -|-+-||+-|++|...+ +-.-++||...+.. .+... .-.| +-.|.. |+.+...|.
T Consensus 187 EdFy~~l~~yfP~fYDik~v~ks~~~--~~KglQei~ndlql-----------~r~g~QhQag-sdaLlT-a~~ff~~R~ 251 (299)
T COG5228 187 EDFYWWLHQYFPNFYDIKLVYKSVLN--NSKGLQEIKNDLQL-----------QRSGQQHQAG-SDALLT-ADEFFLPRF 251 (299)
T ss_pred HHHHHHHHHHCccccchHHHHHhhhh--hhhHHHHhcCcHhh-----------hccchhhhcc-chhhhh-hHHhcchhh
Confidence 344444 36777999999987652 23334444443221 11111 1112 123433 888999997
Q ss_pred CCCcccchHHHHHHHHHHHHH-H---hcCCc--ccccCceeecCCCC
Q 038950 216 GGAHHAGSDSLLTAAVFAEMK-N---RYELE--ESAFDGFLYGMDSR 256 (297)
Q Consensus 216 g~~HqAGsDSllT~~vF~kl~-~---~f~~~--~~~~~g~l~Gl~~~ 256 (297)
......+-.++|....++.++ . -|.+. ..++.|++||+..+
T Consensus 252 ~~F~~sig~~ll~~L~g~~~~~~sl~~~~~~t~f~~~~g~~~gi~~~ 298 (299)
T COG5228 252 SIFTTSIGQSLLMLLSGCQLSKLSLHKFPNGTDFAKYQGVIYGIDGD 298 (299)
T ss_pred heecccccHHHHHHHhccccCCchheeCCCcccHhhcCCcccCCCCC
Confidence 666666668888888888887 2 23333 78999999999643
No 65
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=37.49 E-value=13 Score=38.83 Aligned_cols=120 Identities=10% Similarity=-0.124 Sum_probs=77.1
Q ss_pred ceeeeeccc--cHHHHHHHHHHHhhcCCeeEEeccccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEeccCCCcc
Q 038950 5 SKILNVWCE--NFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKIS 82 (297)
Q Consensus 5 ~~i~eVw~~--N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p 82 (297)
+.+..+-+. |....++.....+.+..+.++++|+.++..........+..+++++.-.....++-+|..-.--.-+..
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~ 181 (564)
T KOG1990|consen 102 SPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIEST 181 (564)
T ss_pred cchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHH
Confidence 344444555 677787777777888999999999999986655444567788888888877777777766543322221
Q ss_pred -----e--eEE-EeeecCCCCCCCCchhhHHHHHhcCCChhhhhhCCCCCcc
Q 038950 83 -----Y--TFE-FNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCV 126 (297)
Q Consensus 83 -----~--~wq-FNF~~Fd~~~d~~~~~SI~fL~~~GfDFnk~~~~GI~~~~ 126 (297)
+ +-. |++- ++-.........+++..++.+++ ..+++|+....
T Consensus 182 ~~r~~~~~~p~~~~~~-~~~~~~~~~~~~~~~~~k~~~~k-~~~~rg~~~~~ 231 (564)
T KOG1990|consen 182 LLRRLGYKLPPHFALG-RSRKLQGLAVAMVSFWEKHEFAK-ILIKRGVLETR 231 (564)
T ss_pred HHHHhcccccccceeh-hccccccchhHHHHHHHHHHHHH-HHHHhcchhhh
Confidence 0 111 2222 33334455666677777777766 66666666655
No 66
>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=31.89 E-value=1.4e+02 Score=28.20 Aligned_cols=69 Identities=13% Similarity=-0.014 Sum_probs=46.1
Q ss_pred eeeccccHHHHHHHHHHHhhcCC---eeEEec------cccCcccCCCCCCChhHHHHHHhhccccccceEEEeEEec
Q 038950 8 LNVWCENFEIVMRFLDKLLNCFN---VLSIDT------EFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSD 76 (297)
Q Consensus 8 ~eVw~~N~~~el~~I~~~i~~~~---fIAiDt------EFpGv~~~p~~~~t~eerY~~lk~nVd~~~iiQlGLt~~~ 76 (297)
.+|++...++.+..+.+.+...+ ||++|. ..||+......--+..|--+.++.-....+++=+.|+=++
T Consensus 195 ~~i~~~g~~~v~~~~~~~l~~~~~~vyvS~DiDvlDps~aPgv~tp~pgGl~~~e~~~~l~~i~~~~~v~g~DivE~~ 272 (300)
T TIGR01229 195 HEIDELGIGKVVEETLEYLKAEDGPIHLSLDVDGLDPSLAPATGTPVVGGLTFREGLLIMEMLYETGLLTALDVVEVN 272 (300)
T ss_pred HHHhhhhHHHHHHHHHHHHhcCCCeEEEEEeccccCcccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCEEEEEEEEEC
Confidence 35566667777888888886544 999997 6788754333333567777777777666677656655544
No 67
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=28.39 E-value=72 Score=30.26 Aligned_cols=75 Identities=24% Similarity=0.422 Sum_probs=48.5
Q ss_pred eeEEeecc-hhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccc--cCCCcchHHHHHHHcCCcccCCCc
Q 038950 143 KWVTFHGL-YDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQG--LQGLKLGLSKLARILNVKRHGGAH 219 (297)
Q Consensus 143 ~Witfh~~-yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~--l~~~~~~L~~la~~L~v~r~g~~H 219 (297)
-|+||+|. +|.-|+-++.. ..+|.+++. .=||.=|.++..+. |. +-||..|.+.||+.|...
T Consensus 158 ~lvsfNGkaFD~PfikR~v~-~~~el~l~~----------~H~DL~h~~RRlwk~~l~--~c~Lk~VEr~LGi~R~ed-- 222 (278)
T COG3359 158 MLVSFNGKAFDIPFIKRMVR-DRLELSLEF----------GHFDLYHPSRRLWKHLLP--RCGLKTVERILGIRREED-- 222 (278)
T ss_pred eEEEecCcccCcHHHHHHHh-cccccCccc----------cchhhhhhhhhhhhccCC--CCChhhHHHHhCcccccc--
Confidence 79999997 99999987554 345544432 24577777776651 22 228999999999999431
Q ss_pred ccchHHHHHHHHH
Q 038950 220 HAGSDSLLTAAVF 232 (297)
Q Consensus 220 qAGsDSllT~~vF 232 (297)
.-|+|+-..-.-|
T Consensus 223 tdG~~~p~lyr~~ 235 (278)
T COG3359 223 TDGYDGPELYRLY 235 (278)
T ss_pred CCCcchHHHHHHH
Confidence 2355555443333
No 68
>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=25.66 E-value=67 Score=28.34 Aligned_cols=30 Identities=20% Similarity=0.144 Sum_probs=27.0
Q ss_pred eccccHHHHHHHHHHHhhcCCeeEEecccc
Q 038950 10 VWCENFEIVMRFLDKLLNCFNVLSIDTEFP 39 (297)
Q Consensus 10 Vw~~N~~~el~~I~~~i~~~~fIAiDtEFp 39 (297)
|.+-|++|.+..|.+.-++.-.||||.-..
T Consensus 68 VHA~NL~e~l~~I~~~~~~~~IIAIDAcLG 97 (163)
T PF06866_consen 68 VHALNLEETLNEIKKKHPNPFIIAIDACLG 97 (163)
T ss_pred cchhhHHHHHHHHHHHCCCCeEEEEECCCC
Confidence 789999999999999888889999998763
No 69
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=24.99 E-value=49 Score=26.63 Aligned_cols=16 Identities=25% Similarity=0.544 Sum_probs=13.1
Q ss_pred HHHHHhcCCCCCCChH
Q 038950 155 YLVKIFTNDALPPTAE 170 (297)
Q Consensus 155 yL~k~l~g~~LP~t~~ 170 (297)
-+++-+||+|||.+.+
T Consensus 61 AFLHA~TGQPLP~D~D 76 (105)
T PRK05264 61 AFLHAFTGQPLPDDED 76 (105)
T ss_pred HHHHHHcCCCCCChhh
Confidence 3678899999999854
No 70
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=24.23 E-value=1e+02 Score=24.27 Aligned_cols=41 Identities=20% Similarity=0.334 Sum_probs=31.0
Q ss_pred CCceeEEeec----------chhHHHHH-HHhcCCCCCCChHHHHHHHHhccCc
Q 038950 140 ENLKWVTFHG----------LYDVAYLV-KIFTNDALPPTAEAFSGVAALFFQS 182 (297)
Q Consensus 140 ~~~~Witfh~----------~yD~~yL~-k~l~g~~LP~t~~eF~~~l~~~FP~ 182 (297)
++++|+.-=| |+|-+|.+ -.+. -|-.+++.|.+++.+-++.
T Consensus 19 K~V~~laGIg~~lg~~L~~~GfdkAYvllGQfL--llkKdE~lF~~Wlk~~~ga 70 (90)
T KOG4233|consen 19 KDVTWLAGIGETLGIKLVDAGFDKAYVLLGQFL--LLKKDEDLFQEWLKETCGA 70 (90)
T ss_pred CcceeeccccHHhhhhHHhccccHHHHHHHHHH--HhcccHHHHHHHHHHHcCc
Confidence 6899997544 68999854 2332 5678999999999998864
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=23.30 E-value=84 Score=28.19 Aligned_cols=70 Identities=16% Similarity=0.195 Sum_probs=37.7
Q ss_pred eeEEeec-chhHHHHHHHhcCCCCCCChH-------------HHHHHH-----HhccCc-ccchhHHHHhc----cccCC
Q 038950 143 KWVTFHG-LYDVAYLVKIFTNDALPPTAE-------------AFSGVA-----ALFFQS-VFDIKVVAGYC----QGLQG 198 (297)
Q Consensus 143 ~Witfh~-~yD~~yL~k~l~g~~LP~t~~-------------eF~~~l-----~~~FP~-vyDtK~~a~~~----~~l~~ 198 (297)
.++++++ ++|+.||.+-..--.++.++. .+.... -...++ +.|+-.+.+.. ..+..
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 4556666 599999988764222222111 010000 012234 58997766642 12332
Q ss_pred CcchHHHHHHHcCCcc
Q 038950 199 LKLGLSKLARILNVKR 214 (297)
Q Consensus 199 ~~~~L~~la~~L~v~r 214 (297)
-+|+.||+.+|+..
T Consensus 156 --ysL~~Va~~~g~~~ 169 (207)
T cd05785 156 --YGLKAVAKHFGLAS 169 (207)
T ss_pred --CCHHHHHHHhcccC
Confidence 38999999987643
No 72
>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=23.24 E-value=55 Score=26.19 Aligned_cols=16 Identities=31% Similarity=0.594 Sum_probs=13.0
Q ss_pred HHHHHhcCCCCCCChH
Q 038950 155 YLVKIFTNDALPPTAE 170 (297)
Q Consensus 155 yL~k~l~g~~LP~t~~ 170 (297)
-+++-+||+|||.+.+
T Consensus 60 AFLHAfTGQPLP~D~D 75 (103)
T cd00490 60 AFLHAFTGQPLPDDAD 75 (103)
T ss_pred HHHHHhcCCCCCChhh
Confidence 3678899999998753
No 73
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=22.67 E-value=44 Score=31.83 Aligned_cols=14 Identities=29% Similarity=0.477 Sum_probs=0.0
Q ss_pred eeEEeccccCcccC
Q 038950 31 VLSIDTEFPGFLRN 44 (297)
Q Consensus 31 fIAiDtEFpGv~~~ 44 (297)
+||||+||-|+..+
T Consensus 107 ~vAmDCEMVG~Gp~ 120 (280)
T KOG2249|consen 107 VVAMDCEMVGVGPD 120 (280)
T ss_pred EEEEeeeEeccCCC
No 74
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=21.65 E-value=96 Score=23.98 Aligned_cols=31 Identities=23% Similarity=0.388 Sum_probs=22.4
Q ss_pred cchhHHHHhccccCCCcchHHHHHHHcCCcc
Q 038950 184 FDIKVVAGYCQGLQGLKLGLSKLARILNVKR 214 (297)
Q Consensus 184 yDtK~~a~~~~~l~~~~~~L~~la~~L~v~r 214 (297)
.|.||+-.-...++|..-||+.||..|+.++
T Consensus 9 ~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~ 39 (76)
T PF05491_consen 9 LDRRYLKTLIENFKGGPVGLDTLAAALGEDK 39 (76)
T ss_dssp HHHHHHHHHHHCSTTS-B-HHHHHHHTTS-H
T ss_pred HHHHHHHHHHHHcCCCCeeHHHHHHHHCCCH
Confidence 4788888777767765669999999998875
No 75
>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=21.50 E-value=2.8e+02 Score=21.91 Aligned_cols=54 Identities=24% Similarity=0.311 Sum_probs=31.3
Q ss_pred CCceeEEeecchhHHHHHHHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHHc
Q 038950 140 ENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARIL 210 (297)
Q Consensus 140 ~~~~Witfh~~yD~~yL~k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L 210 (297)
++++-|+++..+|+..|.+... .+| +.++||..++.....-.. +.+|+++++.+
T Consensus 53 ~~~~~v~~~~k~d~~~L~~~~~--~~~--------------~~~~D~~~~ayll~~~~~-~~~l~~l~~~~ 106 (155)
T cd00007 53 EDITKVGHDAKFDLVVLARDGI--ELP--------------GNIFDTMLAAYLLNPGEG-SHSLDDLAKEY 106 (155)
T ss_pred CCCcEEeccHHHHHHHHHHCCC--CCC--------------CCcccHHHHHHHhCCCCC-cCCHHHHHHHH
Confidence 3444555544577776654321 111 257899888877653221 13899998875
No 76
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=21.23 E-value=81 Score=27.69 Aligned_cols=72 Identities=15% Similarity=0.095 Sum_probs=39.3
Q ss_pred ceeEEeecc--hhHHHHHHHhc--CCCCCCChH-------HHH-HHHHhccCc-ccchhHHHHhccccCCCcchHHHHHH
Q 038950 142 LKWVTFHGL--YDVAYLVKIFT--NDALPPTAE-------AFS-GVAALFFQS-VFDIKVVAGYCQGLQGLKLGLSKLAR 208 (297)
Q Consensus 142 ~~Witfh~~--yD~~yL~k~l~--g~~LP~t~~-------eF~-~~l~~~FP~-vyDtK~~a~~~~~l~~~~~~L~~la~ 208 (297)
..-++-||+ +|+.||.+-.. |-++|-... .+- .....+-++ +.|+..+++....+.. -+|+.||+
T Consensus 72 pdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~l~s--y~L~~v~~ 149 (195)
T cd05780 72 PDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTR--YTLERVYE 149 (195)
T ss_pred CCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCCCCc--CcHHHHHH
Confidence 343444443 99999988753 333332110 000 000112244 8898777766444443 38999987
Q ss_pred -HcCCccc
Q 038950 209 -ILNVKRH 215 (297)
Q Consensus 209 -~L~v~r~ 215 (297)
.||..|.
T Consensus 150 ~~Lg~~k~ 157 (195)
T cd05780 150 ELFGIEKE 157 (195)
T ss_pred HHhCCCCC
Confidence 6788764
No 77
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=21.12 E-value=44 Score=26.74 Aligned_cols=16 Identities=25% Similarity=0.555 Sum_probs=7.3
Q ss_pred HHHHHhcCCCCCCChH
Q 038950 155 YLVKIFTNDALPPTAE 170 (297)
Q Consensus 155 yL~k~l~g~~LP~t~~ 170 (297)
-+++-|||+|||.+.+
T Consensus 60 AFLHAfTGQPLP~D~d 75 (104)
T PF01340_consen 60 AFLHAFTGQPLPTDDD 75 (104)
T ss_dssp HHHHHHH------TTG
T ss_pred HHHHHhcCCCCCChhh
Confidence 4678899999998854
No 78
>PRK08445 hypothetical protein; Provisional
Probab=20.74 E-value=1.9e+02 Score=28.10 Aligned_cols=86 Identities=14% Similarity=0.151 Sum_probs=46.5
Q ss_pred hHHHHHHHHhccCccc-------chhHHHHhccccCCCcchHHHHHHHcCCccc-CCCcccchHHHHH--------HHHH
Q 038950 169 AEAFSGVAALFFQSVF-------DIKVVAGYCQGLQGLKLGLSKLARILNVKRH-GGAHHAGSDSLLT--------AAVF 232 (297)
Q Consensus 169 ~~eF~~~l~~~FP~vy-------DtK~~a~~~~~l~~~~~~L~~la~~L~v~r~-g~~HqAGsDSllT--------~~vF 232 (297)
+.+..+.+++.||.+= .++++++.+. +.. ..-|++|.+ .|+.++ |...+.++|..+. .+.+
T Consensus 108 ~~~l~~~Ik~~~p~i~~~a~s~~ei~~~a~~~~-~~~-~e~L~~Lke-AGl~~~~g~glE~~~d~v~~~~~pk~~t~~~~ 184 (348)
T PRK08445 108 YENLVSHIAQKYPTITIHGFSAVEIDYIAKISK-ISI-KEVLERLQA-KGLSSIPGAGAEILSDRVRDIIAPKKLDSDRW 184 (348)
T ss_pred HHHHHHHHHHHCCCcEEEEccHHHHHHHHHHhC-CCH-HHHHHHHHH-cCCCCCCCCceeeCCHHHHHhhCCCCCCHHHH
Confidence 3456667888898421 2356665332 110 012333333 477775 5566666665553 2223
Q ss_pred HHHHHhc-CCcccccCceeecCCCCC
Q 038950 233 AEMKNRY-ELEESAFDGFLYGMDSRI 257 (297)
Q Consensus 233 ~kl~~~f-~~~~~~~~g~l~Gl~~~~ 257 (297)
.+..+.. +-......|.|||++.+.
T Consensus 185 i~~i~~a~~~Gi~~~sg~i~G~~Et~ 210 (348)
T PRK08445 185 LEVHRQAHLIGMKSTATMMFGTVEND 210 (348)
T ss_pred HHHHHHHHHcCCeeeeEEEecCCCCH
Confidence 3322222 333788999999998653
Done!