Query 027829
Match_columns 218
No_of_seqs 146 out of 366
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 15:50:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027829.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027829hhsearch_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 6E-77 1.3E-81 508.9 12.3 176 15-196 1-239 (239)
2 COG5228 POP2 mRNA deadenylase 100.0 3.7E-67 8.1E-72 450.7 7.5 203 4-215 6-271 (299)
3 PF04857 CAF1: CAF1 family rib 100.0 6E-41 1.3E-45 295.2 11.7 169 17-191 1-262 (262)
4 smart00479 EXOIII exonuclease 98.1 7.2E-05 1.6E-09 59.9 11.7 121 39-197 1-168 (169)
5 PRK07942 DNA polymerase III su 98.0 8.7E-05 1.9E-09 64.6 11.5 126 36-197 4-181 (232)
6 cd06131 DNA_pol_III_epsilon_Ec 97.9 0.00021 4.5E-09 58.0 10.9 118 40-192 1-166 (167)
7 PRK09145 DNA polymerase III su 97.7 0.0004 8.7E-09 58.8 10.4 36 157-194 164-199 (202)
8 PRK06063 DNA polymerase III su 97.5 0.0013 2.9E-08 59.9 11.0 126 37-197 14-180 (313)
9 cd06133 ERI-1_3'hExo_like DEDD 97.5 0.0021 4.6E-08 52.0 11.1 36 156-192 140-175 (176)
10 PRK07748 sporulation inhibitor 97.4 0.0017 3.7E-08 55.3 10.2 38 157-195 142-179 (207)
11 TIGR00573 dnaq exonuclease, DN 97.2 0.0046 1E-07 53.1 11.2 126 35-196 4-177 (217)
12 PRK08074 bifunctional ATP-depe 97.2 0.0035 7.6E-08 64.7 11.2 124 38-197 3-170 (928)
13 PRK06310 DNA polymerase III su 97.2 0.0049 1.1E-07 54.3 10.7 127 33-196 2-174 (250)
14 PRK07247 DNA polymerase III su 97.1 0.004 8.7E-08 53.1 9.4 35 158-195 134-168 (195)
15 cd06136 TREX1_2 DEDDh 3'-5' ex 97.1 0.0044 9.4E-08 51.6 9.3 127 40-191 1-176 (177)
16 cd06130 DNA_pol_III_epsilon_li 97.1 0.0043 9.3E-08 49.3 8.8 51 137-190 77-155 (156)
17 PRK05168 ribonuclease T; Provi 97.1 0.0062 1.3E-07 52.2 10.4 137 28-196 7-201 (211)
18 PRK08517 DNA polymerase III su 97.1 0.0078 1.7E-07 53.5 11.2 57 138-196 148-231 (257)
19 PRK06807 DNA polymerase III su 97.0 0.0064 1.4E-07 55.5 10.6 119 39-196 9-172 (313)
20 KOG1990 Poly(A)-specific exori 97.0 0.00013 2.9E-09 71.4 -0.6 107 21-130 1-110 (564)
21 TIGR01406 dnaQ_proteo DNA poly 97.0 0.011 2.4E-07 51.4 11.2 38 157-195 133-171 (225)
22 PRK05711 DNA polymerase III su 96.9 0.0086 1.9E-07 52.8 10.2 125 37-195 3-175 (240)
23 PRK07883 hypothetical protein; 96.8 0.0094 2E-07 58.4 10.6 129 32-197 9-183 (557)
24 PRK07740 hypothetical protein; 96.8 0.018 3.9E-07 50.6 11.4 59 137-197 141-227 (244)
25 PRK09146 DNA polymerase III su 96.8 0.015 3.2E-07 51.1 10.6 40 158-199 191-230 (239)
26 PRK06195 DNA polymerase III su 96.7 0.016 3.4E-07 52.6 10.2 58 137-197 80-165 (309)
27 TIGR01407 dinG_rel DnaQ family 96.5 0.022 4.7E-07 58.3 11.3 59 137-197 80-166 (850)
28 PRK07246 bifunctional ATP-depe 96.4 0.03 6.6E-07 57.3 11.3 60 136-197 85-171 (820)
29 cd06127 DEDDh DEDDh 3'-5' exon 96.2 0.021 4.5E-07 44.2 7.1 112 41-190 1-159 (159)
30 PRK07983 exodeoxyribonuclease 96.1 0.089 1.9E-06 45.7 11.1 61 136-196 73-154 (219)
31 PRK11779 sbcB exonuclease I; P 95.9 0.11 2.5E-06 50.1 11.6 125 37-195 5-197 (476)
32 TIGR01405 polC_Gram_pos DNA po 95.5 0.11 2.4E-06 55.4 10.8 125 36-197 188-356 (1213)
33 PRK09182 DNA polymerase III su 95.4 0.18 3.9E-06 45.8 10.6 121 39-193 38-198 (294)
34 PRK00448 polC DNA polymerase I 95.1 0.22 4.8E-06 54.0 11.9 125 35-197 416-585 (1437)
35 PRK05601 DNA polymerase III su 93.0 0.91 2E-05 42.8 10.0 38 158-195 201-248 (377)
36 COG0847 DnaQ DNA polymerase II 93.0 0.86 1.9E-05 39.1 9.2 58 138-195 96-181 (243)
37 cd06134 RNaseT DEDDh 3'-5' exo 92.6 0.19 4.2E-06 42.2 4.6 59 137-195 102-188 (189)
38 PF00929 RNase_T: Exonuclease; 92.4 0.18 3.8E-06 38.9 3.8 116 41-189 1-164 (164)
39 PRK06722 exonuclease; Provisio 89.8 0.45 9.8E-06 43.1 4.3 35 158-193 144-178 (281)
40 TIGR01298 RNaseT ribonuclease 89.0 0.56 1.2E-05 39.8 4.1 39 158-196 154-192 (200)
41 cd06144 REX4_like DEDDh 3'-5' 88.9 0.51 1.1E-05 38.1 3.6 51 138-189 78-151 (152)
42 cd06149 ISG20 DEDDh 3'-5' exon 86.4 0.81 1.8E-05 37.3 3.5 32 157-189 122-156 (157)
43 PRK05755 DNA polymerase I; Pro 84.5 7.2 0.00016 40.4 10.0 41 157-197 412-470 (880)
44 PRK06309 DNA polymerase III su 81.2 2.7 5.9E-05 36.4 4.7 38 157-196 129-166 (232)
45 PF01612 DNA_pol_A_exo1: 3'-5' 73.7 3.6 7.7E-05 32.6 3.1 26 25-50 7-32 (176)
46 PTZ00315 2'-phosphotransferase 72.4 5.4 0.00012 39.8 4.5 38 158-196 218-255 (582)
47 cd06138 ExoI_N N-terminal DEDD 71.1 4.1 9E-05 33.7 3.0 29 158-188 153-181 (183)
48 cd06137 DEDDh_RNase DEDDh 3'-5 64.1 9.1 0.0002 31.1 3.6 52 138-189 85-160 (161)
49 COG0349 Rnd Ribonuclease D [Tr 59.7 7.7 0.00017 36.5 2.7 25 26-50 5-29 (361)
50 PRK11572 copper homeostasis pr 59.2 8.1 0.00018 34.6 2.6 59 108-172 64-145 (248)
51 cd06146 mut-7_like_exo DEDDy 3 58.4 11 0.00023 31.8 3.1 25 25-49 7-33 (193)
52 cd06141 WRN_exo DEDDy 3'-5' ex 56.2 13 0.00028 29.8 3.2 26 25-50 4-30 (170)
53 TIGR02841 spore_YyaC putative 56.2 12 0.00027 30.7 3.0 31 17-47 42-72 (140)
54 cd06145 REX1_like DEDDh 3'-5' 54.6 17 0.00036 29.2 3.6 53 137-189 76-149 (150)
55 TIGR01388 rnd ribonuclease D. 54.5 12 0.00027 34.8 3.1 126 25-197 5-167 (367)
56 PRK10829 ribonuclease D; Provi 54.3 12 0.00027 35.1 3.1 126 25-197 9-171 (373)
57 PF13482 RNase_H_2: RNase_H su 49.7 13 0.00027 29.6 2.1 53 135-189 55-133 (164)
58 PF06866 DUF1256: Protein of u 41.1 27 0.00057 29.4 2.8 32 17-48 66-97 (163)
59 KOG4355 Predicted Fe-S oxidore 39.2 14 0.00031 35.5 1.0 29 158-186 284-315 (547)
60 KOG4793 Three prime repair exo 37.4 24 0.00053 32.3 2.2 41 156-197 252-292 (318)
61 PF04967 HTH_10: HTH DNA bindi 34.5 26 0.00056 24.0 1.5 17 154-170 21-37 (53)
62 PF08228 RNase_P_pop3: RNase P 32.2 37 0.0008 28.4 2.3 29 156-185 110-142 (158)
63 PF04297 UPF0122: Putative hel 30.7 26 0.00057 27.2 1.1 24 158-187 35-58 (101)
64 PHA02535 P terminase ATPase su 30.2 82 0.0018 31.6 4.7 27 20-46 440-469 (581)
65 PF04386 SspB: Stringent starv 29.9 59 0.0013 26.7 3.1 17 36-52 30-46 (155)
66 TIGR02724 phenyl_P_beta phenyl 29.7 64 0.0014 31.3 3.8 32 139-170 42-75 (472)
67 COG3142 CutC Uncharacterized p 28.7 48 0.001 29.6 2.5 84 105-194 61-166 (241)
68 PF13309 HTH_22: HTH domain 26.3 37 0.0008 23.7 1.2 17 154-170 40-56 (64)
69 PF11959 DUF3473: Domain of un 26.3 96 0.0021 24.9 3.7 31 15-45 98-128 (133)
70 cd06129 RNaseD_like DEDDy 3'-5 26.1 63 0.0014 25.9 2.7 38 156-193 108-160 (161)
71 PF11413 HIF-1: Hypoxia-induci 25.4 17 0.00036 22.9 -0.7 11 37-47 14-24 (34)
72 PF03213 Pox_P35: Poxvirus P35 24.2 43 0.00093 31.2 1.5 47 136-186 171-240 (325)
73 PF14549 P22_Cro: DNA-binding 22.2 57 0.0012 22.8 1.5 16 155-170 8-23 (60)
74 PF02954 HTH_8: Bacterial regu 21.9 57 0.0012 20.6 1.3 16 155-170 17-32 (42)
75 COG5228 POP2 mRNA deadenylase 21.6 54 0.0012 29.4 1.5 56 159-216 240-298 (299)
76 PRK14569 D-alanyl-alanine synt 21.6 1.4E+02 0.0029 26.6 4.1 44 135-191 56-99 (296)
77 COG5606 Uncharacterized conser 21.4 89 0.0019 23.9 2.5 31 159-189 44-80 (91)
78 PF08685 GON: GON domain; Int 21.3 53 0.0011 28.6 1.4 67 65-143 91-160 (201)
No 1
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=6e-77 Score=508.86 Aligned_cols=176 Identities=58% Similarity=0.977 Sum_probs=168.5
Q ss_pred eEEEeccccHHHHHHHHHHhhhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCC
Q 027829 15 LIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLP 94 (218)
Q Consensus 15 ~I~eVwa~NleeE~~~I~~~i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p 94 (218)
.||+||++|+++||++||++|++||||||||||||++++|.+.|+++. |++||+||+|||.+|+||+|||++|++|++|
T Consensus 1 ~ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~~~f~s~~-d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p 79 (239)
T KOG0304|consen 1 FIREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPIGTFRSSD-DYHYQTLKCNVDNLKLIQLGLTLSDEKGNLP 79 (239)
T ss_pred ChhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecCccccCCh-HHHHHHHHhchhhhhhhheeeeeeccCCCCC
Confidence 479999999999999999999999999999999999999999999888 9999999999999999999999999999999
Q ss_pred CCCCCCCceeEEEeeeeeccccCCCchhHHHHHHhcC------------------------ccccCCeeEEeeccccccc
Q 027829 95 DLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQG------------------------LVLNKDVTWVTFHSAYDFG 150 (218)
Q Consensus 95 ~~~~~~~~~~wqFNF~~Fd~~~d~~~~~SI~lL~~~G------------------------lv~~~~v~WvtFhg~yDfg 150 (218)
.+| .++|||||++||+.+|+++++||+||+++| ++++++|+|||||||||||
T Consensus 80 ~~g----~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfg 155 (239)
T KOG0304|consen 80 DCG----TDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFG 155 (239)
T ss_pred CCC----CceeEEecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHH
Confidence 775 469999999999999999999999999999 7889999999999999999
Q ss_pred -------------------------------------ccc--cccCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHH
Q 027829 151 -------------------------------------FCT--CLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLK 191 (218)
Q Consensus 151 -------------------------------------~~~--~l~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~k 191 (218)
+|. +++|||++||+.|+|+| +|++||||||||||+++|+|
T Consensus 156 YLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~R-vG~~HqAGSDSlLT~~~F~k 234 (239)
T KOG0304|consen 156 YLLKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKR-VGIAHQAGSDSLLTARVFFK 234 (239)
T ss_pred HHHHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhhhhcCHHHHHHHhCCCe-eecccccCcHHHHHHHHHHH
Confidence 574 48999999999999999 99999999999999999999
Q ss_pred HHHhh
Q 027829 192 IKDKH 196 (218)
Q Consensus 192 l~~~~ 196 (218)
||+.|
T Consensus 235 l~~~f 239 (239)
T KOG0304|consen 235 LKELF 239 (239)
T ss_pred HHhcC
Confidence 99864
No 2
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=3.7e-67 Score=450.72 Aligned_cols=203 Identities=45% Similarity=0.741 Sum_probs=181.4
Q ss_pred CCCCCC--CCCCceEEEeccccHHHHHHHHHHhhhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhccccccee
Q 027829 4 VPPPQP--PKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQ 81 (218)
Q Consensus 4 ~~~~~~--~~~~~~I~eVwa~NleeE~~~I~~~i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQ 81 (218)
+|||.- ++.-..||+||++||..||+.|+++|.+|++|+|||||||+++||.|.|+++. +++||+||||||.|||||
T Consensus 6 s~p~i~~dg~~~~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPiG~FkSs~-dyhYQtlraNVD~LkiIQ 84 (299)
T COG5228 6 SMPPIFLDGPNYLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSV-DYHYQTLRANVDFLKIIQ 84 (299)
T ss_pred CCCCccCCCcchHHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceeecccccccccc-hHHHHHHhcccchhhhhh
Confidence 455543 33345699999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred eeeeeecCCCCCCCCCCCCCceeEEEeeeeeccccCCCchhHHHHHHhcC------------------------ccccCC
Q 027829 82 IGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQG------------------------LVLNKD 137 (218)
Q Consensus 82 lGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~~d~~~~~SI~lL~~~G------------------------lv~~~~ 137 (218)
|||+++|++|+.|.+ .|||||||. |++++|||+++|||+|+++| ||+.++
T Consensus 85 lGlsLSDe~GN~P~~-----~sTWQFNF~-F~l~~dmya~ESieLL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~ 158 (299)
T COG5228 85 LGLSLSDENGNKPNG-----PSTWQFNFE-FDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDES 158 (299)
T ss_pred eeeeeccccCCCCCC-----CceeEEEEE-ecchhhhcchHHHHHHHHcCCChhhHhhcCCCHHHHHHHHhccCceeccc
Confidence 999999999999953 799999999 99999999999999999999 889999
Q ss_pred eeEEeecccccccc-------------------------------------cccccCcHHHHHHHhCccccCCCCCCchh
Q 027829 138 VTWVTFHSAYDFGF-------------------------------------CTCLYGGLDRVCKALGVERVVGKSHQAGS 180 (218)
Q Consensus 138 v~WvtFhg~yDfg~-------------------------------------~~~l~ggL~~vA~~L~v~r~~g~~hqAGs 180 (218)
|+|||||++||||+ +.+.+.||++++..|++.| .|.+|||||
T Consensus 159 VtWitfHsaYDfgyLikilt~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~~~~KglQei~ndlql~r-~g~QhQags 237 (299)
T COG5228 159 VTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQR-SGQQHQAGS 237 (299)
T ss_pred eEEEEeecchhHHHHHHHHhcCCCCccHHHHHHHHHHHCccccchHHHHHhhhhhhhHHHHhcCcHhhhc-cchhhhccc
Confidence 99999999999990 1234579999999999999 999999999
Q ss_pred HHHHHHHHHHHHHHhhCCCccccccccceEeccCC
Q 027829 181 DSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLEL 215 (218)
Q Consensus 181 dsllT~~~F~kl~~~~f~~~~~~~~~~g~l~Gl~~ 215 (218)
|||||++.|++.|.++|..+++ ...-.+|||++.
T Consensus 238 daLlTa~~ff~~R~~~F~~sig-~~ll~~L~g~~~ 271 (299)
T COG5228 238 DALLTADEFFLPRFSIFTTSIG-QSLLMLLSGCQL 271 (299)
T ss_pred hhhhhhHHhcchhhheeccccc-HHHHHHHhcccc
Confidence 9999999999999999976653 444555555544
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=6e-41 Score=295.24 Aligned_cols=169 Identities=33% Similarity=0.586 Sum_probs=144.3
Q ss_pred EEeccccHHHHHHHHHHhhhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeee-cCCCCCCC
Q 027829 17 REVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLS-DEEGNLPD 95 (218)
Q Consensus 17 ~eVwa~NleeE~~~I~~~i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~-~~~G~~p~ 95 (218)
+|||++||++||+.|+++|++++|||||+||||+..++......++ ++||+++|.||+.+++||+|||++ +++++.|.
T Consensus 1 m~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~~~~~t~-~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~ 79 (262)
T PF04857_consen 1 MEVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPRSRFDTP-EERYEKLRANVETFQIIQFGLTLFHDEDGNIPS 79 (262)
T ss_dssp EEE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-SHCSSHH-HHHHHHHHHHHTTBEEEEEEEEEETTTTSEEEC
T ss_pred CcccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCccccccH-HHHHHHHHHhhcccccceeeEEEeecccccCCc
Confidence 6899999999999999999999999999999999999886555566 999999999999999999999999 88988885
Q ss_pred CCCCCCceeEEEeeeeeccccCCCchhHHHHHHhcC------------------------------ccc---cCCeeEEe
Q 027829 96 LGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQG------------------------------LVL---NKDVTWVT 142 (218)
Q Consensus 96 ~~~~~~~~~wqFNF~~Fd~~~d~~~~~SI~lL~~~G------------------------------lv~---~~~v~Wvt 142 (218)
.+.+|+|||+.|+..++.++++||+||+++| ++. ..++.||+
T Consensus 80 -----~~~~~~~nf~~f~~~~~~~~~~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vg 154 (262)
T PF04857_consen 80 -----SYNVWPFNFYLFPLDRDFSQASSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVG 154 (262)
T ss_dssp -----CEEEEEEEBSTTSTTTCEEEHHHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEE
T ss_pred -----eeEEEEeeeeccccccceecchhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEE
Confidence 3789999999999999988999999999999 222 34689999
Q ss_pred eccccccc------------------------------------ccccccCcHHHHHHHhCccc----------------
Q 027829 143 FHSAYDFG------------------------------------FCTCLYGGLDRVCKALGVER---------------- 170 (218)
Q Consensus 143 Fhg~yDfg------------------------------------~~~~l~ggL~~vA~~L~v~r---------------- 170 (218)
+||.||++ .+....++|+.|++.|++.|
T Consensus 155 hn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~ 234 (262)
T PF04857_consen 155 HNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECPGKSTSLQELAEELGIRRNPSSISSPEGFPSYDE 234 (262)
T ss_dssp SSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS-SSHHHHHHHTTSTT----EEE-TTS-----
T ss_pred eChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhccccccCHHHHHHHhCCCccccccccccccccccc
Confidence 99999999 11224569999999999998
Q ss_pred ------cCCC-CCCchhHHHHHHHHHHH
Q 027829 171 ------VVGK-SHQAGSDSLLTLHAFLK 191 (218)
Q Consensus 171 ------~~g~-~hqAGsdsllT~~~F~k 191 (218)
..|. .|+||.||++|+.+|.|
T Consensus 235 ~~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 235 EKNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp --------SS-TTSHHHHHHHHHHHHHH
T ss_pred cccccccCCCCCCCcchHHHHHHHHHcC
Confidence 3466 99999999999999986
No 4
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.08 E-value=7.2e-05 Score=59.90 Aligned_cols=121 Identities=22% Similarity=0.282 Sum_probs=80.8
Q ss_pred CeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeeccccCC
Q 027829 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (218)
Q Consensus 39 ~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~~d~ 118 (218)
.||++|+|..|.... .-.|||+|....+.+. ....||.. ......
T Consensus 1 ~~v~~D~Ettg~~~~----------------------~~~Iieig~v~~~~~~-----------~~~~f~~~-v~p~~~- 45 (169)
T smart00479 1 TLVVIDCETTGLDPG----------------------KDEIIEIAAVDVDGGR-----------IIVVFDTY-VKPDRP- 45 (169)
T ss_pred CEEEEEeeCCCCCCC----------------------CCeEEEEEEEEEECCE-----------eEEEEEEE-ECCCCC-
Confidence 389999999995311 1249999998887753 23457766 444221
Q ss_pred CchhHHH-------HHHhcC---------c--cccCCeeEEeecc-ccccccc---------------------------
Q 027829 119 HALDSVE-------LLKRQG---------L--VLNKDVTWVTFHS-AYDFGFC--------------------------- 152 (218)
Q Consensus 119 ~~~~SI~-------lL~~~G---------l--v~~~~v~WvtFhg-~yDfg~~--------------------------- 152 (218)
.++.+.+ .|.+ | + .+.+ -.+|.+|+ .||+.+.
T Consensus 46 i~~~~~~~~Git~~~l~~-~~~~~~~~~~~~~~l~~-~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~ 123 (169)
T smart00479 46 ITDYATEIHGITPEMLDD-APTFEEVLEELLEFLKG-KILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARAL 123 (169)
T ss_pred CCHHHHHHhCCCHHHHhC-CCCHHHHHHHHHHHhcC-CEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHH
Confidence 1222211 1222 2 0 1123 35889999 9998810
Q ss_pred -ccccCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhhC
Q 027829 153 -TCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 153 -~~l~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~f 197 (218)
.....+|+.+++.+|++. .+..|-|-.|++.|.++|.+|++..+
T Consensus 124 ~~~~~~~L~~l~~~~~~~~-~~~~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 124 NPGRKYSLKKLAERLGLEV-IGRAHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred CCCCCCCHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHHHHHHHHhh
Confidence 011348999999999998 78789999999999999999987754
No 5
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=98.00 E-value=8.7e-05 Score=64.63 Aligned_cols=126 Identities=20% Similarity=0.356 Sum_probs=85.4
Q ss_pred hcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeeccc
Q 027829 36 DRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIA 115 (218)
Q Consensus 36 ~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~ 115 (218)
.+.+||++|||-+|+- |. . =.|||+|+...+.+|+... .|+.. .+..
T Consensus 4 ~~~~~vv~D~ETTGl~--p~------~--------------d~Iieig~v~v~~~g~~~~----------~~~~l-v~P~ 50 (232)
T PRK07942 4 HPGPLAAFDLETTGVD--PE------T--------------ARIVTAALVVVDADGEVVE----------SREWL-ADPG 50 (232)
T ss_pred ccCcEEEEEeccCCCC--CC------C--------------CeeEEEEEEEEeCCCcccc----------ceEEE-ECCC
Confidence 3568999999999962 10 0 1489999999987775431 23333 3333
Q ss_pred cCCCchh-------HHHHHHhcC------------cc---ccCCeeEEeecccccccc-------------cc-------
Q 027829 116 RHAHALD-------SVELLKRQG------------LV---LNKDVTWVTFHSAYDFGF-------------CT------- 153 (218)
Q Consensus 116 ~d~~~~~-------SI~lL~~~G------------lv---~~~~v~WvtFhg~yDfg~-------------~~------- 153 (218)
.. .+++ +-+.|+.+| .+ +.++..+|++++.||+++ +.
T Consensus 51 ~~-i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~ 129 (232)
T PRK07942 51 VE-IPEEASAVHGITTEYARAHGRPAAEVLAEIADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPY 129 (232)
T ss_pred CC-CCHHHHHHhCCCHHHHHhhCCCHHHHHHHHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHH
Confidence 22 2222 223555555 11 124567899999999981 10
Q ss_pred -------cc-c--CcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhhC
Q 027829 154 -------CL-Y--GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 154 -------~l-~--ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~f 197 (218)
.. + -.|+.+++.+|++. ..+|.|-+|++.|+++|.+|.+++.
T Consensus 130 ~l~~~~~~~~~~~~~L~~l~~~~gi~~--~~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 130 VIDKAVDRYRKGKRTLTALCEHYGVRL--DNAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred HHHhhhhcccCCCCCHHHHHHHcCCCC--CCCCChHHHHHHHHHHHHHHHHHHH
Confidence 01 1 26999999999986 4479999999999999999988774
No 6
>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=97.87 E-value=0.00021 Score=58.00 Aligned_cols=118 Identities=23% Similarity=0.311 Sum_probs=76.2
Q ss_pred eEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeeccccCCC
Q 027829 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAH 119 (218)
Q Consensus 40 yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~~d~~ 119 (218)
||++|+|-+|.-. +. .-.|||+|....+. |.. ...+|++. ...... .
T Consensus 1 ~v~~D~ETTGl~~-----------~~----------~~~iieig~v~v~~-~~~---------~~~~~~~~-v~P~~~-i 47 (167)
T cd06131 1 QIVLDTETTGLDP-----------RE----------GHRIIEIGCVELIN-RRL---------TGNTFHVY-INPERD-I 47 (167)
T ss_pred CEEEEeeCCCCCC-----------CC----------CCeEEEEEEEEEEC-CcE---------eccEEEEE-ECCCCC-C
Confidence 7999999999621 00 12589999886654 221 12356666 444432 3
Q ss_pred chhHH-------HHHHhcC--------c--cccCCeeEEeecccccccc---------------------c---------
Q 027829 120 ALDSV-------ELLKRQG--------L--VLNKDVTWVTFHSAYDFGF---------------------C--------- 152 (218)
Q Consensus 120 ~~~SI-------~lL~~~G--------l--v~~~~v~WvtFhg~yDfg~---------------------~--------- 152 (218)
++.+. +.|+..+ + .+.+ -.+|.+++.||..+ |
T Consensus 48 ~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~l~~-~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~ 126 (167)
T cd06131 48 PEEAFKVHGITDEFLADKPKFAEIADEFLDFIRG-AELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKF 126 (167)
T ss_pred CHHHHHHhCCCHHHHhcCCCHHHHHHHHHHHHCC-CeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHc
Confidence 33333 2333333 1 1123 34899999999871 0
Q ss_pred ccccCcHHHHHHHhCccccCC-CCCCchhHHHHHHHHHHHH
Q 027829 153 TCLYGGLDRVCKALGVERVVG-KSHQAGSDSLLTLHAFLKI 192 (218)
Q Consensus 153 ~~l~ggL~~vA~~L~v~r~~g-~~hqAGsdsllT~~~F~kl 192 (218)
.....+|+.+++.+|++. .+ .+|.|-+|++.|.++|.+|
T Consensus 127 ~~~~~~L~~l~~~~~i~~-~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 127 PGKPNSLDALCKRFGIDN-SHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCCCHHHHHHHCCCCC-CCCCCCChHHHHHHHHHHHHHh
Confidence 112348999999999997 54 4799999999999999987
No 7
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=97.70 E-value=0.0004 Score=58.77 Aligned_cols=36 Identities=25% Similarity=0.463 Sum_probs=32.1
Q ss_pred CcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHH
Q 027829 157 GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKD 194 (218)
Q Consensus 157 ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~ 194 (218)
-+|+.+++.+|++. .+ .|.|-+|++.|+++|.+|++
T Consensus 164 ~~L~~l~~~~gi~~-~~-~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 164 LRFDAILKHLDLPV-LG-RHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCHHHHHHHcCCCC-CC-CCCcHHHHHHHHHHHHHHHh
Confidence 38999999999987 44 69999999999999999875
No 8
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.47 E-value=0.0013 Score=59.89 Aligned_cols=126 Identities=21% Similarity=0.263 Sum_probs=79.9
Q ss_pred cCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeecccc
Q 027829 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (218)
Q Consensus 37 ~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~~ 116 (218)
..+||++|+|-+|.- | + .=.|||||...++.+|+.- -.|... .+...
T Consensus 14 ~~~fvvlD~ETTGl~--p---------~-----------~d~IIeIgav~v~~~g~i~----------~~~~~l-v~P~~ 60 (313)
T PRK06063 14 PRGWAVVDVETSGFR--P---------G-----------QARIISLAVLGLDADGNVE----------QSVVTL-LNPGV 60 (313)
T ss_pred CCCEEEEEEECCCCC--C---------C-----------CCEEEEEEEEEEECCceee----------eEEEEE-ECcCC
Confidence 358999999999962 1 1 1259999999998887642 122222 22221
Q ss_pred CCCch----hHHHHHHhcC--------cc-ccCCeeEEeecccccccc------------------cc-----cc-----
Q 027829 117 HAHAL----DSVELLKRQG--------LV-LNKDVTWVTFHSAYDFGF------------------CT-----CL----- 155 (218)
Q Consensus 117 d~~~~----~SI~lL~~~G--------lv-~~~~v~WvtFhg~yDfg~------------------~~-----~l----- 155 (218)
+..+. =+-+.|+.+. +. .-++-.+|+++..||.++ |. .+
T Consensus 61 ~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~ 140 (313)
T PRK06063 61 DPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLP 140 (313)
T ss_pred CCCCeecCCCCHHHHhCCCCHHHHHHHHHHHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCC
Confidence 11110 0112222222 00 013447899999999881 10 01
Q ss_pred cCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhhC
Q 027829 156 YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 156 ~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~f 197 (218)
.-.|+.+|+.+|++. ...|.|-+|++.|.++|.++.++.-
T Consensus 141 ~~kL~~l~~~~gi~~--~~~H~Al~DA~ata~l~~~ll~~~~ 180 (313)
T PRK06063 141 NLRLETLAAHWGVPQ--QRPHDALDDARVLAGILRPSLERAR 180 (313)
T ss_pred CCCHHHHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 126999999999986 5679999999999999999887764
No 9
>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=97.46 E-value=0.0021 Score=51.95 Aligned_cols=36 Identities=22% Similarity=0.340 Sum_probs=33.2
Q ss_pred cCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHH
Q 027829 156 YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKI 192 (218)
Q Consensus 156 ~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl 192 (218)
..+|.++|+.||++. .|..|.|=+|++.|+++|.+|
T Consensus 140 ~~~L~~l~~~~gi~~-~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 140 RTGLSKALEYLGLEF-EGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred CCCHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHHHHh
Confidence 348999999999999 688999999999999999987
No 10
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=97.39 E-value=0.0017 Score=55.31 Aligned_cols=38 Identities=29% Similarity=0.393 Sum_probs=34.9
Q ss_pred CcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHh
Q 027829 157 GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 195 (218)
Q Consensus 157 ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~ 195 (218)
-+|..+++.+|++- .|..|.|-+|++.|.++|.+|.+.
T Consensus 142 ~~L~~~~~~~gi~~-~~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 142 TGLWKAIEEYGKEG-TGKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred CCHHHHHHHcCCCC-CCCCcChHHHHHHHHHHHHHHHhC
Confidence 38999999999997 788899999999999999998876
No 11
>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=97.24 E-value=0.0046 Score=53.06 Aligned_cols=126 Identities=19% Similarity=0.259 Sum_probs=79.4
Q ss_pred hhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeecc
Q 027829 35 IDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDI 114 (218)
Q Consensus 35 i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~ 114 (218)
+..-.||++|+|-+|.- + +. .|||+|.......+. ..-+|... .+.
T Consensus 4 l~~~~fvv~D~ETTGl~----------~-~~------------~IIeIgav~v~~~~~----------~~~~f~~l-i~P 49 (217)
T TIGR00573 4 LVLDTETTGDNETTGLY----------A-GH------------DIIEIGAVEIINRRI----------TGNKFHTY-IKP 49 (217)
T ss_pred EEecCEEEEEecCCCCC----------C-CC------------CEEEEEEEEEECCCE----------eeeEEEEE-ECc
Confidence 34568999999999952 1 10 289999988543332 12245444 333
Q ss_pred ccCCCchhHH-------HHHHhcC--------c-cccCCeeEEeecccccccc------------------cc-------
Q 027829 115 ARHAHALDSV-------ELLKRQG--------L-VLNKDVTWVTFHSAYDFGF------------------CT------- 153 (218)
Q Consensus 115 ~~d~~~~~SI-------~lL~~~G--------l-v~~~~v~WvtFhg~yDfg~------------------~~------- 153 (218)
... .++.++ +.|+... + -.-++-.+|+++..||+.+ |.
T Consensus 50 ~~~-i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~ 128 (217)
T TIGR00573 50 DRP-IDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQY 128 (217)
T ss_pred CCC-CCHHHHhhcCCCHHHHcCCCCHHHHHHHHHHHhCCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHH
Confidence 322 232222 2232222 0 0013456899999999881 10
Q ss_pred ---cc---cCcHHHHHHHhCccccCC-CCCCchhHHHHHHHHHHHHHHhh
Q 027829 154 ---CL---YGGLDRVCKALGVERVVG-KSHQAGSDSLLTLHAFLKIKDKH 196 (218)
Q Consensus 154 ---~l---~ggL~~vA~~L~v~r~~g-~~hqAGsdsllT~~~F~kl~~~~ 196 (218)
.+ ..+|+.+++.+|++. -. .+|.|-+|+..|+++|.+|.+..
T Consensus 129 ~~~~~~~~~~~L~~l~~~~gl~~-~~~~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 129 ARPEFPGKRNTLDALCKRYEITN-SHRALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred HHHhCCCCCCCHHHHHHHcCCCC-CCcccCCHHHHHHHHHHHHHHHHhcc
Confidence 11 237999999999986 32 58999999999999999998774
No 12
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.15 E-value=0.0035 Score=64.68 Aligned_cols=124 Identities=23% Similarity=0.314 Sum_probs=80.5
Q ss_pred CCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeeccccC
Q 027829 38 YPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH 117 (218)
Q Consensus 38 ~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~~d 117 (218)
-.||++|+|.+|.- | ... =.|||+|....+ +|+ .+=.|+.. .+....
T Consensus 3 ~~~vvvD~ETTG~~--p---------~~~----------d~IIeigav~v~-~~~----------i~~~f~~~-v~P~~~ 49 (928)
T PRK08074 3 KRFVVVDLETTGNS--P---------KKG----------DKIIQIAAVVVE-DGE----------ILERFSSF-VNPERP 49 (928)
T ss_pred CCEEEEEEeCCCCC--C---------CCC----------CcEEEEEEEEEE-CCE----------EEEEEEEE-ECcCCC
Confidence 47999999999852 1 100 169999999985 342 22345555 444332
Q ss_pred CCchhHH-------HHHHhcC---------ccccCCeeEEeeccccccccc---------------------------cc
Q 027829 118 AHALDSV-------ELLKRQG---------LVLNKDVTWVTFHSAYDFGFC---------------------------TC 154 (218)
Q Consensus 118 ~~~~~SI-------~lL~~~G---------lv~~~~v~WvtFhg~yDfg~~---------------------------~~ 154 (218)
.++... +.|+..- .-+-++-.+|+++..||+.+. +.
T Consensus 50 -i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~~l~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~ 128 (928)
T PRK08074 50 -IPPFITELTGISEEMVKQAPLFEDVAPEIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPT 128 (928)
T ss_pred -CCHHHhhcCCCCHHHHhcCCCHHHHHHHHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCC
Confidence 222211 1122211 011246679999999999821 01
Q ss_pred c-cCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhhC
Q 027829 155 L-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 155 l-~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~f 197 (218)
+ .-+|..+|+.||++. +.+|.|-+|++.|+++|.+|.++..
T Consensus 129 ~~~~~L~~l~~~l~i~~--~~~H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 129 AESYKLRDLSEELGLEH--DQPHRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred CCCCCHHHHHHhCCCCC--CCCCChHHHHHHHHHHHHHHHHHHH
Confidence 1 127999999999986 6789999999999999999988764
No 13
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.15 E-value=0.0049 Score=54.34 Aligned_cols=127 Identities=16% Similarity=0.218 Sum_probs=80.8
Q ss_pred HhhhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeee
Q 027829 33 ALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDF 112 (218)
Q Consensus 33 ~~i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~F 112 (218)
+++++-+||.+|||-+|+... . =.|||+|+--.+.++ ...+|+.. .
T Consensus 2 ~~l~~~~~v~~D~ETTGl~~~----------~------------d~IIEIa~v~v~~~~-----------~~~~~~~l-i 47 (250)
T PRK06310 2 SLLKDTEFVCLDCETTGLDVK----------K------------DRIIEFAAIRFTFDE-----------VIDSVEFL-I 47 (250)
T ss_pred CcccCCcEEEEEEeCCCCCCC----------C------------CeEEEEEEEEEECCe-----------EEEEEEEE-E
Confidence 356778999999999996211 1 138899887775432 23456665 4
Q ss_pred ccccCCCchhHH-------HHHHhcC--------c--cccCCeeEEeecccccccc--------------------cc--
Q 027829 113 DIARHAHALDSV-------ELLKRQG--------L--VLNKDVTWVTFHSAYDFGF--------------------CT-- 153 (218)
Q Consensus 113 d~~~d~~~~~SI-------~lL~~~G--------l--v~~~~v~WvtFhg~yDfg~--------------------~~-- 153 (218)
+.... .+.+++ +.++.+. + .+.+.-.+|+++..||..+ |.
T Consensus 48 ~P~~~-I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~ 126 (250)
T PRK06310 48 NPERV-VSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLR 126 (250)
T ss_pred CcCCC-CCHhhhhccCcCHHHHhCCCCHHHHHHHHHHHhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHH
Confidence 44322 222221 1122221 0 0123346888888899771 10
Q ss_pred ---cc----cCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhh
Q 027829 154 ---CL----YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 196 (218)
Q Consensus 154 ---~l----~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~ 196 (218)
.+ ...|+.+++.+|++. . .+|.|-+|++.|..+|.+|.+++
T Consensus 127 lar~~~~~~~~~L~~l~~~~g~~~-~-~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 127 LAKEYGDSPNNSLEALAVHFNVPY-D-GNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred HHHhcccCCCCCHHHHHHHCCCCC-C-CCcChHHHHHHHHHHHHHHHHhc
Confidence 01 247999999999986 4 47999999999999999998765
No 14
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=97.10 E-value=0.004 Score=53.13 Aligned_cols=35 Identities=20% Similarity=0.371 Sum_probs=31.6
Q ss_pred cHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHh
Q 027829 158 GLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 195 (218)
Q Consensus 158 gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~ 195 (218)
.|..||+.||++. ..|.|-+|++.|+++|.+|.+.
T Consensus 134 ~L~~La~~~gi~~---~~HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 134 KLQTVADFLGIKG---RGHNSLEDARMTARVYESFLES 168 (195)
T ss_pred CHHHHHHhcCCCC---CCcCCHHHHHHHHHHHHHHHhh
Confidence 6999999999985 3699999999999999998765
No 15
>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=97.09 E-value=0.0044 Score=51.60 Aligned_cols=127 Identities=20% Similarity=0.276 Sum_probs=76.6
Q ss_pred eEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCC--CCCCceeEEEeeeeeccccC
Q 027829 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLG--SGSTYYIWEFNFKDFDIARH 117 (218)
Q Consensus 40 yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~--~~~~~~~wqFNF~~Fd~~~d 117 (218)
||++|||-+|.-. +. . + +|||+|..-.+.++...... +.-...+-+|++. .+..+.
T Consensus 1 ~vv~D~ETTGl~~-~~-----~--d-------------~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~l-v~P~~~ 58 (177)
T cd06136 1 FVFLDLETTGLPK-HN-----R--P-------------EITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLC-FNPGRA 58 (177)
T ss_pred CeEEeeecCCCCC-CC-----C--C-------------ceEEEEEEEEecccccccccccccccceeeeeeEE-eCCCCc
Confidence 7999999999731 00 0 1 48999998887665322100 0000123356666 555432
Q ss_pred CCchhH-------HHHHHhcCc------------c--ccCCeeEEeecc-ccccccc-----------------------
Q 027829 118 AHALDS-------VELLKRQGL------------V--LNKDVTWVTFHS-AYDFGFC----------------------- 152 (218)
Q Consensus 118 ~~~~~S-------I~lL~~~Gl------------v--~~~~v~WvtFhg-~yDfg~~----------------------- 152 (218)
+ .+.+ =+.|+.++- + +.+....|++++ .+|+.+.
T Consensus 59 I-~~~a~~IhGIt~e~l~~~~~~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l 137 (177)
T cd06136 59 I-SPGASEITGLSNDLLEHKAPFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPA 137 (177)
T ss_pred C-ChhHHHHhCcCHHHHhcCCCccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHH
Confidence 2 2221 134444440 0 123467899998 7999821
Q ss_pred -ccccCcHHHHHHH-hCccccCCCCCCchhHHHHHHHHHHH
Q 027829 153 -TCLYGGLDRVCKA-LGVERVVGKSHQAGSDSLLTLHAFLK 191 (218)
Q Consensus 153 -~~l~ggL~~vA~~-L~v~r~~g~~hqAGsdsllT~~~F~k 191 (218)
+.+...|+.+++. +|++. ..+|.|-+|++.|+++|++
T Consensus 138 ~r~~~~~L~~l~~~~~~~~~--~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 138 FRELDQSLGSLYKRLFGQEP--KNSHTAEGDVLALLKCALH 176 (177)
T ss_pred HhhhHhhHHHHHHHHhCCCc--ccccchHHHHHHHHHHHhh
Confidence 1123488999885 78885 5579999999999999985
No 16
>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=97.08 E-value=0.0043 Score=49.29 Aligned_cols=51 Identities=24% Similarity=0.271 Sum_probs=40.7
Q ss_pred CeeEEeeccccccccc---------------------------ccc-cCcHHHHHHHhCccccCCCCCCchhHHHHHHHH
Q 027829 137 DVTWVTFHSAYDFGFC---------------------------TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 188 (218)
Q Consensus 137 ~v~WvtFhg~yDfg~~---------------------------~~l-~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~ 188 (218)
+..||+++..||+++. +.+ ..+|+.+++.+|++. . +|.|-+|++.|++.
T Consensus 77 ~~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~-~--~H~Al~Da~~ta~l 153 (156)
T cd06130 77 GSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIEL-N--HHDALEDARACAEI 153 (156)
T ss_pred CCEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHHHHcCCCc-c--CcCchHHHHHHHHH
Confidence 3579999999999821 111 138999999999987 4 89999999999998
Q ss_pred HH
Q 027829 189 FL 190 (218)
Q Consensus 189 F~ 190 (218)
|.
T Consensus 154 ~~ 155 (156)
T cd06130 154 LL 155 (156)
T ss_pred Hh
Confidence 84
No 17
>PRK05168 ribonuclease T; Provisional
Probab=97.08 E-value=0.0062 Score=52.24 Aligned_cols=137 Identities=17% Similarity=0.220 Sum_probs=85.0
Q ss_pred HHHHHHhhhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecC--CCCCCCCCCCCCceeE
Q 027829 28 FERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDE--EGNLPDLGSGSTYYIW 105 (218)
Q Consensus 28 ~~~I~~~i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~--~G~~p~~~~~~~~~~w 105 (218)
+.-|..-+....||++|+|-+|..... + .|||+|...... +|.+.. ..
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~---------d-------------~IieIgaV~v~~d~~g~i~~--------~~ 56 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKT---------D-------------ALLEIAAVTLKMDEQGWLYP--------DE 56 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCC---------C-------------EEEEEeEEEEEecCCCcEec--------cc
Confidence 455677788899999999999973211 1 399999887653 454321 12
Q ss_pred EEeeeeecccc-CCCchhHHH-------HHHhcC----------------ccc---cCCeeEEeecccccccccc-----
Q 027829 106 EFNFKDFDIAR-HAHALDSVE-------LLKRQG----------------LVL---NKDVTWVTFHSAYDFGFCT----- 153 (218)
Q Consensus 106 qFNF~~Fd~~~-d~~~~~SI~-------lL~~~G----------------lv~---~~~v~WvtFhg~yDfg~~~----- 153 (218)
.|... .+... -...+.+++ .+.+.| .+. .++..+|++|..||+++..
T Consensus 57 ~f~~l-v~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r 135 (211)
T PRK05168 57 TLHFH-VEPFEGANLEPEALAFNGIDPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAER 135 (211)
T ss_pred eEEEE-ECCCCCCCCCHHHHhhcCCCchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHH
Confidence 34444 32211 112222211 111222 000 1246799999999988210
Q ss_pred ---------------------ccc--CcHHHHHHHhCccccCC-CCCCchhHHHHHHHHHHHHHHhh
Q 027829 154 ---------------------CLY--GGLDRVCKALGVERVVG-KSHQAGSDSLLTLHAFLKIKDKH 196 (218)
Q Consensus 154 ---------------------~l~--ggL~~vA~~L~v~r~~g-~~hqAGsdsllT~~~F~kl~~~~ 196 (218)
.++ ..|..+++.+|++- .+ ..|.|-+|++.|.++|.+|.+++
T Consensus 136 ~~~~~~~~~~~~~iDt~~lar~~~~~~~L~~l~~~~gl~~-~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 136 AGLKRNPFHPFSTFDTATLSGLALGQTVLAKACQAAGIEF-DNKEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred hCCCCCCCCCCcEeeHHHHHHHHcCCCCHHHHHHHCCCCC-CCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 011 26888899999874 33 58999999999999999998875
No 18
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=97.06 E-value=0.0078 Score=53.51 Aligned_cols=57 Identities=25% Similarity=0.354 Sum_probs=46.5
Q ss_pred eeEEeecccccccc------------------c---------ccccCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHH
Q 027829 138 VTWVTFHSAYDFGF------------------C---------TCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFL 190 (218)
Q Consensus 138 v~WvtFhg~yDfg~------------------~---------~~l~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~ 190 (218)
-.||+++..+|+++ | ..-+-||+.+++.+|++. . ..|.|-+|++.|+++|.
T Consensus 148 ~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~~~lgi~~-~-~~HrAl~DA~ata~ll~ 225 (257)
T PRK08517 148 SVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEI-E-VHHRAYADALAAYEIFK 225 (257)
T ss_pred CeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHHHHcCcCC-C-CCCChHHHHHHHHHHHH
Confidence 35999999999882 1 112348999999999997 3 68999999999999999
Q ss_pred HHHHhh
Q 027829 191 KIKDKH 196 (218)
Q Consensus 191 kl~~~~ 196 (218)
++.+.+
T Consensus 226 ~ll~~~ 231 (257)
T PRK08517 226 ICLLNL 231 (257)
T ss_pred HHHHHh
Confidence 988765
No 19
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=97.03 E-value=0.0064 Score=55.54 Aligned_cols=119 Identities=16% Similarity=0.152 Sum_probs=78.2
Q ss_pred CeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeeccccCC
Q 027829 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (218)
Q Consensus 39 ~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~~d~ 118 (218)
+||++|+|.+|.-. . .-.|||+|....+ +|+ ...+|+.. ......+
T Consensus 9 ~~Vv~DlETTGl~p-----------~-----------~~eIIEIgaV~v~-~g~----------i~~~f~~l-VkP~~~I 54 (313)
T PRK06807 9 DYVVIDFETTGFNP-----------Y-----------NDKIIQVAAVKYR-NHE----------LVDQFVSY-VNPERPI 54 (313)
T ss_pred CEEEEEEECCCCCC-----------C-----------CCeEEEEEEEEEE-CCE----------EEEEEEEE-ECcCCCC
Confidence 79999999998621 1 1268999998886 332 34567766 5544332
Q ss_pred CchhH-------HHHHHhcC--------c--cccCCeeEEeecccccccc------------------c---------cc
Q 027829 119 HALDS-------VELLKRQG--------L--VLNKDVTWVTFHSAYDFGF------------------C---------TC 154 (218)
Q Consensus 119 ~~~~S-------I~lL~~~G--------l--v~~~~v~WvtFhg~yDfg~------------------~---------~~ 154 (218)
.+.+ -+.|.... + .+.++ .+|+.++.||+.+ | +.
T Consensus 55 -~~~a~~ihGIT~e~l~~~~~~~evl~~f~~fl~~~-~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~ 132 (313)
T PRK06807 55 -PDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN-VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKH 132 (313)
T ss_pred -CHhhhccCCCCHHHHhCCCCHHHHHHHHHHHHcCC-eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCC
Confidence 1211 12233222 0 11233 4788899999881 0 11
Q ss_pred cc-CcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhh
Q 027829 155 LY-GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 196 (218)
Q Consensus 155 l~-ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~ 196 (218)
+. -+|+.+|+.||++. .+|-|=.|++.|+++|.+|...-
T Consensus 133 ~~~~kL~~L~~~lgi~~---~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 133 APNHKLETLKRMLGIRL---SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred CCCCCHHHHHHHcCCCC---CCcChHHHHHHHHHHHHHHHHhh
Confidence 11 27999999999996 58999999999999999987664
No 20
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=97.01 E-value=0.00013 Score=71.40 Aligned_cols=107 Identities=17% Similarity=0.180 Sum_probs=83.1
Q ss_pred cccHHHHHHHHHHhhhcCCeEEEeccccceeecCC--CCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCC-C
Q 027829 21 EFNLISEFERIRALIDRYPIISMDTEFPGVVVRPD--SNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDL-G 97 (218)
Q Consensus 21 a~NleeE~~~I~~~i~~~~yIAmDtEFPGvv~~p~--~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~-~ 97 (218)
+.|++. ..+++..|+++-++++|.|+.|+...+. +.--.+. +.+|+++|.|+-.+.++|+|+|++-.++..... .
T Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~ 78 (564)
T KOG1990|consen 1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKAGSTFDTV-EAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMS 78 (564)
T ss_pred CCcccc-hhHHHhhcCHHHHHHHhhhhccceecccccccchhhh-HHHHHHHHhhhhhheeeccccchhHHHhhhHhhcc
Confidence 468899 9999999999999999999999988874 2222345 999999999999999999999999887765533 1
Q ss_pred CCCCceeEEEeeeeeccccCCCchhHHHHHHhc
Q 027829 98 SGSTYYIWEFNFKDFDIARHAHALDSVELLKRQ 130 (218)
Q Consensus 98 ~~~~~~~wqFNF~~Fd~~~d~~~~~SI~lL~~~ 130 (218)
++++..+|..-+. +..-+.+|...++.++.++
T Consensus 79 ~~~n~~~~~~g~~-~s~~~~~~~~~~~~~~~~~ 110 (564)
T KOG1990|consen 79 TGGNFVVWSRGDS-ISSPEFLCQRSPVDFVARQ 110 (564)
T ss_pred CCCceeeeecCcc-ccCCccceeecchhhhhhh
Confidence 2234667775444 3333567888888888888
No 21
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=96.99 E-value=0.011 Score=51.36 Aligned_cols=38 Identities=26% Similarity=0.420 Sum_probs=33.6
Q ss_pred CcHHHHHHHhCccccCCC-CCCchhHHHHHHHHHHHHHHh
Q 027829 157 GGLDRVCKALGVERVVGK-SHQAGSDSLLTLHAFLKIKDK 195 (218)
Q Consensus 157 ggL~~vA~~L~v~r~~g~-~hqAGsdsllT~~~F~kl~~~ 195 (218)
.+|+.+++.+|++. .+. .|-|-.|+.+|+++|.+|...
T Consensus 133 ~~L~~L~~~~gi~~-~~r~~H~Al~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 133 NSLDALCKRFKVDN-SHRTLHGALLDAHLLAEVYLALTGG 171 (225)
T ss_pred CCHHHHHHhcCCCC-CCCCCcCHHHHHHHHHHHHHHHHcC
Confidence 48999999999997 554 799999999999999999764
No 22
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.94 E-value=0.0086 Score=52.77 Aligned_cols=125 Identities=21% Similarity=0.329 Sum_probs=79.1
Q ss_pred cCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeecccc
Q 027829 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (218)
Q Consensus 37 ~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~~ 116 (218)
.-.||++|||-+|.-.. . .=.|||||..-... +. + ..-.|+.+ .+..+
T Consensus 3 ~~r~vvlDtETTGldp~-----------~----------~drIIEIGaV~v~~-~~-~--------~~~~f~~~-i~P~~ 50 (240)
T PRK05711 3 IMRQIVLDTETTGLNQR-----------E----------GHRIIEIGAVELIN-RR-L--------TGRNFHVY-IKPDR 50 (240)
T ss_pred CCeEEEEEeeCCCcCCC-----------C----------CCeEEEEEEEEEEC-CE-E--------eccEEEEE-ECcCC
Confidence 34799999999996311 0 12589999866542 21 1 11246666 55544
Q ss_pred CCCchhHH-------HHHHhcC--------cc-ccCCeeEEeecccccccc------------------cc---------
Q 027829 117 HAHALDSV-------ELLKRQG--------LV-LNKDVTWVTFHSAYDFGF------------------CT--------- 153 (218)
Q Consensus 117 d~~~~~SI-------~lL~~~G--------lv-~~~~v~WvtFhg~yDfg~------------------~~--------- 153 (218)
++ .++++ ++|+..- ++ .-++-.+|.++..||+++ |.
T Consensus 51 ~i-~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar 129 (240)
T PRK05711 51 LV-DPEALAVHGITDEFLADKPTFAEVADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMAR 129 (240)
T ss_pred cC-CHHHhhhcCCCHHHHcCCCCHHHHHHHHHHHhCCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHH
Confidence 32 33332 2333222 00 013445899999999881 21
Q ss_pred ----cccCcHHHHHHHhCccccCCC-CCCchhHHHHHHHHHHHHHHh
Q 027829 154 ----CLYGGLDRVCKALGVERVVGK-SHQAGSDSLLTLHAFLKIKDK 195 (218)
Q Consensus 154 ----~l~ggL~~vA~~L~v~r~~g~-~hqAGsdsllT~~~F~kl~~~ 195 (218)
+...+|+.+++.+|++. .+. .|.|-.|+.+|+++|.+|...
T Consensus 130 ~~~p~~~~~L~aL~~~~gi~~-~~r~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 130 RMFPGKRNSLDALCKRYGIDN-SHRTLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred HHcCCCCCCHHHHHHHCCCCC-CCCCCCCHHHHHHHHHHHHHHHHCc
Confidence 12348999999999987 443 699999999999999999754
No 23
>PRK07883 hypothetical protein; Validated
Probab=96.84 E-value=0.0094 Score=58.42 Aligned_cols=129 Identities=19% Similarity=0.237 Sum_probs=84.1
Q ss_pred HHhhhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeee
Q 027829 32 RALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKD 111 (218)
Q Consensus 32 ~~~i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~ 111 (218)
..-+.+.+||++|+|.+|.- | + .-.|||||.-.++. | ...-+|+..
T Consensus 9 ~~~~~~~~~Vv~D~ETTGl~--p---------~-----------~~~IIEIgaV~v~~-g----------~iv~~f~~l- 54 (557)
T PRK07883 9 GTPLRDVTFVVVDLETTGGS--P---------A-----------GDAITEIGAVKVRG-G----------EVLGEFATL- 54 (557)
T ss_pred CCCCcCCCEEEEEEecCCCC--C---------C-----------CCeEEEEEEEEEEC-C----------EEEEEEEEE-
Confidence 34567789999999999972 1 1 12589999988863 2 134456665
Q ss_pred eccccCCCchhHHH-------HHHhcC---------ccccCCeeEEeecccccccc------------------cc----
Q 027829 112 FDIARHAHALDSVE-------LLKRQG---------LVLNKDVTWVTFHSAYDFGF------------------CT---- 153 (218)
Q Consensus 112 Fd~~~d~~~~~SI~-------lL~~~G---------lv~~~~v~WvtFhg~yDfg~------------------~~---- 153 (218)
.+....+ .+.+.+ .|.... +-.-.+-..|++++.||+.+ |.
T Consensus 55 V~P~~~i-~~~~~~itGIt~e~l~~ap~~~evl~~f~~fl~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~la 133 (557)
T PRK07883 55 VNPGRPI-PPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLA 133 (557)
T ss_pred ECCCCCC-ChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHhcCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHH
Confidence 5443322 222221 222111 00113456788888999881 11
Q ss_pred -------cc-cCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhhC
Q 027829 154 -------CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 154 -------~l-~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~f 197 (218)
.. .-+|..+|+.+|++. ...|-|-+|++.|+++|.++.+.+.
T Consensus 134 r~l~~~~~~~~~~L~~L~~~~gi~~--~~~H~Al~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 134 RRVLPRDEAPNVRLSTLARLFGATT--TPTHRALDDARATVDVLHGLIERLG 183 (557)
T ss_pred HHhcccCCCCCCCHHHHHHHCCccc--CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 11 126999999999986 4579999999999999999988875
No 24
>PRK07740 hypothetical protein; Provisional
Probab=96.84 E-value=0.018 Score=50.60 Aligned_cols=59 Identities=20% Similarity=0.184 Sum_probs=46.7
Q ss_pred CeeEEeeccccccccc---------------------------ccc-cCcHHHHHHHhCccccCCCCCCchhHHHHHHHH
Q 027829 137 DVTWVTFHSAYDFGFC---------------------------TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 188 (218)
Q Consensus 137 ~v~WvtFhg~yDfg~~---------------------------~~l-~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~ 188 (218)
+-.+|+++..+|+.+. +.. ..+|+.+++.+|++. .| .|.|-+|++.|+++
T Consensus 141 ~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~-~~-~H~Al~Da~ata~l 218 (244)
T PRK07740 141 AGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPI-PR-RHHALGDALMTAKL 218 (244)
T ss_pred CCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCC-CC-CCCcHHHHHHHHHH
Confidence 3479999999999821 001 247999999999987 45 59999999999999
Q ss_pred HHHHHHhhC
Q 027829 189 FLKIKDKHF 197 (218)
Q Consensus 189 F~kl~~~~f 197 (218)
|.++.+...
T Consensus 219 ~~~ll~~~~ 227 (244)
T PRK07740 219 WAILLVEAQ 227 (244)
T ss_pred HHHHHHHHH
Confidence 999877654
No 25
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.80 E-value=0.015 Score=51.12 Aligned_cols=40 Identities=20% Similarity=0.199 Sum_probs=35.2
Q ss_pred cHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhhCCC
Q 027829 158 GLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGN 199 (218)
Q Consensus 158 gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~f~~ 199 (218)
.|+.+++.+|++. ..+|.|-+|++.|+++|.++.+.+++.
T Consensus 191 ~L~~l~~~~gl~~--~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 191 RLADSRLRYGLPA--YSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred CHHHHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 5889999999986 557999999999999999999888754
No 26
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.68 E-value=0.016 Score=52.57 Aligned_cols=58 Identities=22% Similarity=0.371 Sum_probs=45.8
Q ss_pred CeeEEeecccccccc------------------c---------ccc-cCcHHHHHHHhCccccCCCCCCchhHHHHHHHH
Q 027829 137 DVTWVTFHSAYDFGF------------------C---------TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 188 (218)
Q Consensus 137 ~v~WvtFhg~yDfg~------------------~---------~~l-~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~ 188 (218)
+-.+|++++.||.++ | +.+ .-+|+.+++.+|++- ..|.|-+|++.|+++
T Consensus 80 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~~gi~~---~~H~Al~DA~ata~l 156 (309)
T PRK06195 80 NNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEF---KHHDALADAMACSNI 156 (309)
T ss_pred CCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHHcCCCC---cccCCHHHHHHHHHH
Confidence 456899999999881 1 111 237999999999973 479999999999999
Q ss_pred HHHHHHhhC
Q 027829 189 FLKIKDKHF 197 (218)
Q Consensus 189 F~kl~~~~f 197 (218)
|.+|.+..-
T Consensus 157 ~~~l~~~~~ 165 (309)
T PRK06195 157 LLNISKELN 165 (309)
T ss_pred HHHHHHHhc
Confidence 999987753
No 27
>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=96.55 E-value=0.022 Score=58.27 Aligned_cols=59 Identities=25% Similarity=0.334 Sum_probs=47.0
Q ss_pred CeeEEeeccccccccc---------------------------ccc-cCcHHHHHHHhCccccCCCCCCchhHHHHHHHH
Q 027829 137 DVTWVTFHSAYDFGFC---------------------------TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 188 (218)
Q Consensus 137 ~v~WvtFhg~yDfg~~---------------------------~~l-~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~ 188 (218)
+-.+|+++..||+.+. +.. .-+|..+|+.||++. ..+|.|-+|+..|+++
T Consensus 80 ~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~--~~~H~Al~DA~ata~l 157 (850)
T TIGR01407 80 DGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTH--ENPHRADSDAQATAEL 157 (850)
T ss_pred CCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCC--CCCCChHHHHHHHHHH
Confidence 3459999999999821 001 238999999999986 4579999999999999
Q ss_pred HHHHHHhhC
Q 027829 189 FLKIKDKHF 197 (218)
Q Consensus 189 F~kl~~~~f 197 (218)
|.+|.+++-
T Consensus 158 ~~~l~~~~~ 166 (850)
T TIGR01407 158 LLLLFEKME 166 (850)
T ss_pred HHHHHHHHH
Confidence 999988763
No 28
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.42 E-value=0.03 Score=57.27 Aligned_cols=60 Identities=23% Similarity=0.332 Sum_probs=47.7
Q ss_pred CCeeEEeeccccccccc--------------------------ccc-cCcHHHHHHHhCccccCCCCCCchhHHHHHHHH
Q 027829 136 KDVTWVTFHSAYDFGFC--------------------------TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 188 (218)
Q Consensus 136 ~~v~WvtFhg~yDfg~~--------------------------~~l-~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~ 188 (218)
++-.+|+.+..+|+++. +.+ .-+|+.+|+.||++. ..+|.|-+|++.|+++
T Consensus 85 ~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~--~~~H~Al~DA~ata~L 162 (820)
T PRK07246 85 EDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRELNIDL--ADAHTAIADARATAEL 162 (820)
T ss_pred CCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHHcCCCC--CCCCCHHHHHHHHHHH
Confidence 34568999999998721 111 238999999999986 4679999999999999
Q ss_pred HHHHHHhhC
Q 027829 189 FLKIKDKHF 197 (218)
Q Consensus 189 F~kl~~~~f 197 (218)
|.+|.+++.
T Consensus 163 ~~~l~~~l~ 171 (820)
T PRK07246 163 FLKLLQKIE 171 (820)
T ss_pred HHHHHHHHh
Confidence 999988764
No 29
>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=96.21 E-value=0.021 Score=44.21 Aligned_cols=112 Identities=21% Similarity=0.282 Sum_probs=70.4
Q ss_pred EEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeeccccCCCc
Q 027829 41 ISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHA 120 (218)
Q Consensus 41 IAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~~d~~~ 120 (218)
|.+|+|.+|.-. ..-.|||+|....+.+++. ...||.. +....+. .
T Consensus 1 v~~D~Ettg~~~----------------------~~~~iiei~~v~~~~~~~~----------~~~~~~~-i~p~~~~-~ 46 (159)
T cd06127 1 VVFDTETTGLDP----------------------KKDRIIEIGAVKVDGGIEI----------VERFETL-VNPGRPI-P 46 (159)
T ss_pred CeEEeeCCCcCC----------------------CCCeEEEEEEEEEECCcCh----------hhhhhee-eCcCCcC-C
Confidence 578999988631 1235899999999987432 2345555 4443322 1
Q ss_pred hhH-------HHHHHhcC---------c--cccCCeeEEeecccccccc------------------c---------cc-
Q 027829 121 LDS-------VELLKRQG---------L--VLNKDVTWVTFHSAYDFGF------------------C---------TC- 154 (218)
Q Consensus 121 ~~S-------I~lL~~~G---------l--v~~~~v~WvtFhg~yDfg~------------------~---------~~- 154 (218)
+.. -+.+. .| + .+. +-.||++++.+|..+ | +.
T Consensus 47 ~~~~~~~gi~~~~~~-~~~~~~~~~~~~~~~l~-~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~ 124 (159)
T cd06127 47 PEATAIHGITDEMLA-DAPPFEEVLPEFLEFLG-GRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGL 124 (159)
T ss_pred HhheeccCCCHHHHh-cCCCHHHHHHHHHHHHC-CCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCC
Confidence 111 12222 22 1 112 367999999999771 0 00
Q ss_pred ccCcHHHH-HHHhCccccCCCCCCchhHHHHHHHHHH
Q 027829 155 LYGGLDRV-CKALGVERVVGKSHQAGSDSLLTLHAFL 190 (218)
Q Consensus 155 l~ggL~~v-A~~L~v~r~~g~~hqAGsdsllT~~~F~ 190 (218)
-..+|..+ ++.+++.. +.+|.|-+|++.|.++|.
T Consensus 125 ~~~~l~~~~~~~~~~~~--~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 125 RSHRLGLLLAERYGIPL--EGAHRALADALATAELLL 159 (159)
T ss_pred CcCchHHHHHHHcCCCC--CCCCCcHHHHHHHHHHhC
Confidence 12367777 88899865 678999999999999984
No 30
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=96.11 E-value=0.089 Score=45.69 Aligned_cols=61 Identities=15% Similarity=0.144 Sum_probs=47.4
Q ss_pred CCeeEEeecccccccc---------c---------ccccCcHHHHHHHhCcccc---CCCCCCchhHHHHHHHHHHHHHH
Q 027829 136 KDVTWVTFHSAYDFGF---------C---------TCLYGGLDRVCKALGVERV---VGKSHQAGSDSLLTLHAFLKIKD 194 (218)
Q Consensus 136 ~~v~WvtFhg~yDfg~---------~---------~~l~ggL~~vA~~L~v~r~---~g~~hqAGsdsllT~~~F~kl~~ 194 (218)
.+-.+|.++..||.++ | +.+.-+|+.+++.+++... ...+|.|-+|++.|.++|.+|.+
T Consensus 73 ~~~~lVaHNa~FD~~~L~~~~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 73 GSEWYVAHNASFDRRVLPEMPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred CCCEEEEeCcHhhHHHHhCcCCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 4557899999999882 2 2345679999999998531 24689999999999999999886
Q ss_pred hh
Q 027829 195 KH 196 (218)
Q Consensus 195 ~~ 196 (218)
.+
T Consensus 153 ~~ 154 (219)
T PRK07983 153 TS 154 (219)
T ss_pred Hc
Confidence 43
No 31
>PRK11779 sbcB exonuclease I; Provisional
Probab=95.85 E-value=0.11 Score=50.15 Aligned_cols=125 Identities=19% Similarity=0.090 Sum_probs=82.6
Q ss_pred cCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeecccc
Q 027829 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (218)
Q Consensus 37 ~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~~ 116 (218)
...||.+|+|-+|.-.+ . | .|||+|.--.+.+++. ..-.|+++ .....
T Consensus 5 ~~~fvv~D~ETTGLdP~--------~-D-------------rIIeiAaVrvd~~~~~---------i~e~~~~~-~~P~~ 52 (476)
T PRK11779 5 QPTFLWHDYETFGANPA--------L-D-------------RPAQFAGIRTDADLNI---------IGEPLVFY-CKPAD 52 (476)
T ss_pred CCcEEEEEEECCCCCCC--------C-C-------------eeEEEEEEEEeCCCce---------ecceeEEE-EcCCc
Confidence 45799999999997321 0 1 3899999888776532 12246666 44444
Q ss_pred CC-CchhHHH-------HHHhcC------------ccccCCeeEEeecc-cccccc----------c-------------
Q 027829 117 HA-HALDSVE-------LLKRQG------------LVLNKDVTWVTFHS-AYDFGF----------C------------- 152 (218)
Q Consensus 117 d~-~~~~SI~-------lL~~~G------------lv~~~~v~WvtFhg-~yDfg~----------~------------- 152 (218)
+. -.++++. .|+.+| .+..++-.+|.+|. .||..+ +
T Consensus 53 ~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~ 132 (476)
T PRK11779 53 DYLPSPEAVLITGITPQEALEKGLPEAEFAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRW 132 (476)
T ss_pred CcCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCcc
Confidence 32 2344433 555666 12223445788875 588851 0
Q ss_pred ---------cc---------------ccCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHh
Q 027829 153 ---------TC---------------LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 195 (218)
Q Consensus 153 ---------~~---------------l~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~ 195 (218)
.. -.-.|+.|++.+|++. +.+|-|=+|++.|..++.+|++.
T Consensus 133 D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~L~~~~gI~~--~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 133 DLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEH--ENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CHHHHHHHHHHhccccccCcccccCCCCCcHHHHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHHh
Confidence 00 0125899999999986 67899999999999999999977
No 32
>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=95.47 E-value=0.11 Score=55.45 Aligned_cols=125 Identities=22% Similarity=0.316 Sum_probs=81.6
Q ss_pred hcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeeccc
Q 027829 36 DRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIA 115 (218)
Q Consensus 36 ~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~ 115 (218)
+..+||++|+|.+|.-.. . + .|||+|....+. |+ ..=.|++. .+..
T Consensus 188 ~~~~~VVfDiETTGL~~~--------~-d-------------~IIEIGAVkv~~-g~----------iid~f~~~-V~P~ 233 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQ--------Y-D-------------EIIEFGAVKVKN-GR----------IIDKFQFF-IKPH 233 (1213)
T ss_pred cCCcEEEEEeEecCCCCC--------C-C-------------eEEEEEEEEEEC-Ce----------EEEEEEEE-ECCC
Confidence 677999999999996311 1 1 599999988864 32 22346665 3333
Q ss_pred cCCCchhHH-------HHHHhcC---------ccccCCeeEEeecccccccccc--------------------------
Q 027829 116 RHAHALDSV-------ELLKRQG---------LVLNKDVTWVTFHSAYDFGFCT-------------------------- 153 (218)
Q Consensus 116 ~d~~~~~SI-------~lL~~~G---------lv~~~~v~WvtFhg~yDfg~~~-------------------------- 153 (218)
.. .++.+. +.|+..- +-.-++-.+|+....||+.+..
T Consensus 234 ~~-I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~ 312 (1213)
T TIGR01405 234 EP-LSAFVTELTGITQDMLENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALN 312 (1213)
T ss_pred CC-CCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHh
Confidence 22 222221 2222211 0001345788988889988210
Q ss_pred -cc-cCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhhC
Q 027829 154 -CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 154 -~l-~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~f 197 (218)
.+ .-+|+.||+.||++. .+ +|.|-.|+..|+++|.+|.+...
T Consensus 313 p~~k~~kL~~Lak~lgi~~-~~-~HrAl~DA~aTa~I~~~ll~~l~ 356 (1213)
T TIGR01405 313 PEYKSHRLGNICKKLGVDL-DD-HHRADYDAEATAKVFKVMVEQLK 356 (1213)
T ss_pred ccCCCCCHHHHHHHcCCCC-CC-CcCHHHHHHHHHHHHHHHHHHHH
Confidence 11 238999999999997 44 89999999999999999987765
No 33
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=95.40 E-value=0.18 Score=45.78 Aligned_cols=121 Identities=18% Similarity=0.217 Sum_probs=76.9
Q ss_pred CeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecC--CCCCCCCCCCCCceeEEEeeeeecccc
Q 027829 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDE--EGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (218)
Q Consensus 39 ~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~--~G~~p~~~~~~~~~~wqFNF~~Fd~~~ 116 (218)
.+|++|||-+|.-.. .=+|||||+..++. +|++- ...-.|++. .+...
T Consensus 38 ~~vvlD~ETTGLd~~----------------------~d~IIEIg~V~v~~~~~g~i~-------~v~~~~~~l-v~P~~ 87 (294)
T PRK09182 38 LGVILDTETTGLDPR----------------------KDEIIEIGMVAFEYDDDGRIG-------DVLDTFGGL-QQPSR 87 (294)
T ss_pred eEEEEEeeCCCCCCC----------------------CCeEEEEEEEEEEecCCCcee-------eeeeEEEEE-eCCCC
Confidence 579999999996321 11489999999874 45432 123456666 44433
Q ss_pred CCCchhHH-------HHHHhcCc-------cccCCeeEEeecccccccc--------------cc---------cc-cCc
Q 027829 117 HAHALDSV-------ELLKRQGL-------VLNKDVTWVTFHSAYDFGF--------------CT---------CL-YGG 158 (218)
Q Consensus 117 d~~~~~SI-------~lL~~~Gl-------v~~~~v~WvtFhg~yDfg~--------------~~---------~l-~gg 158 (218)
. .++++. +.++.++. .+...--.|+++..+|..| |. .+ .-.
T Consensus 88 ~-I~~~~t~IhGIt~e~v~~~~~~~~~l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~k 166 (294)
T PRK09182 88 P-IPPEITRLTGITDEMVAGQTIDPAAVDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTK 166 (294)
T ss_pred C-CCHHHHHhcCCCHHHHhcCCCcHHHHHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCC
Confidence 2 233222 33444441 1123346789999999872 21 01 126
Q ss_pred HHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHH
Q 027829 159 LDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIK 193 (218)
Q Consensus 159 L~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~ 193 (218)
|+.+|+.+| . ...+|.|-+|++.|+++|.++.
T Consensus 167 L~~La~~~g--~-~~~aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 167 LGYLAGQAG--F-FHEGHRAVDDCQALLELLARPL 198 (294)
T ss_pred HHHHHHHcC--C-CCCCcChHHHHHHHHHHHHHHH
Confidence 999999999 3 4567999999999999999754
No 34
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=95.15 E-value=0.22 Score=54.05 Aligned_cols=125 Identities=22% Similarity=0.307 Sum_probs=80.5
Q ss_pred hhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeecc
Q 027829 35 IDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDI 114 (218)
Q Consensus 35 i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~ 114 (218)
+.+.+||++|+|.+|.-. .|. .|||+|....+ +|. ..-.|+.. .+.
T Consensus 416 L~~~~~VVfDLETTGL~~-------------~~d---------eIIEIgAV~V~-~G~----------iie~F~~~-V~P 461 (1437)
T PRK00448 416 LKDATYVVFDVETTGLSA-------------VYD---------EIIEIGAVKIK-NGE----------IIDKFEFF-IKP 461 (1437)
T ss_pred hccCcEEEEEhhhcCCCC-------------chh---------hhheeeeEEEe-CCe----------EeeeEEEE-ECC
Confidence 446789999999998521 121 58888887775 332 23345665 444
Q ss_pred ccCCCchhHH-------HHHHhcC--------ccc--cCCeeEEeeccccccccc-------------------------
Q 027829 115 ARHAHALDSV-------ELLKRQG--------LVL--NKDVTWVTFHSAYDFGFC------------------------- 152 (218)
Q Consensus 115 ~~d~~~~~SI-------~lL~~~G--------lv~--~~~v~WvtFhg~yDfg~~------------------------- 152 (218)
... ..+.+. +.|+ .+ .+. -++..+|+..+.||+++.
T Consensus 462 ~~~-I~~~~~~LTGIT~e~L~-~aps~~EaL~~f~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~ 539 (1437)
T PRK00448 462 GHP-LSAFTTELTGITDDMVK-DAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRF 539 (1437)
T ss_pred CCC-CCHHHHHHhCCCHHHHc-CCCCHHHHHHHHHHHhCCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHH
Confidence 321 122111 2222 12 011 245678999999998721
Q ss_pred --c-cccCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhhC
Q 027829 153 --T-CLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 153 --~-~l~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~f 197 (218)
+ .-.-+|+.+|+.+|+.. .+ .|-|-.|++.|+++|.+|.+...
T Consensus 540 l~p~~k~~kL~~LAk~lGL~~-~~-~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 540 LYPELKSHRLNTLAKKFGVEL-EH-HHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred HcCccccccHHHHHHHcCCCC-CC-CcChHHHHHHHHHHHHHHHHHHH
Confidence 0 11247999999999997 44 59999999999999999988765
No 35
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=93.01 E-value=0.91 Score=42.85 Aligned_cols=38 Identities=16% Similarity=0.365 Sum_probs=29.8
Q ss_pred cHHHHHHHhCcccc--------CCCCCCchh--HHHHHHHHHHHHHHh
Q 027829 158 GLDRVCKALGVERV--------VGKSHQAGS--DSLLTLHAFLKIKDK 195 (218)
Q Consensus 158 gL~~vA~~L~v~r~--------~g~~hqAGs--dsllT~~~F~kl~~~ 195 (218)
.|..||+.|||+.. .-..|.|=+ |++|+.+.|+++++.
T Consensus 201 rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~ 248 (377)
T PRK05601 201 RIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS 248 (377)
T ss_pred CHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc
Confidence 78999999999651 245666665 999999999998544
No 36
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=92.95 E-value=0.86 Score=39.08 Aligned_cols=58 Identities=28% Similarity=0.367 Sum_probs=46.4
Q ss_pred eeEEeeccccccccc---------------------------cc-ccCcHHHHHHHhCccccCCCCCCchhHHHHHHHHH
Q 027829 138 VTWVTFHSAYDFGFC---------------------------TC-LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAF 189 (218)
Q Consensus 138 v~WvtFhg~yDfg~~---------------------------~~-l~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F 189 (218)
-.+|+..-++|.+++ .+ -..+|+.+|+.+||.+.....|.|-.|++.+...|
T Consensus 96 ~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~~~a~~~ 175 (243)
T COG0847 96 RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDALALAELF 175 (243)
T ss_pred CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHHHcCCCcCCcCCcchHHHHHHHHHHH
Confidence 678888888888821 12 24589999999999974345688999999999999
Q ss_pred HHHHHh
Q 027829 190 LKIKDK 195 (218)
Q Consensus 190 ~kl~~~ 195 (218)
.++...
T Consensus 176 ~~~~~~ 181 (243)
T COG0847 176 LLLQTG 181 (243)
T ss_pred HHHHhc
Confidence 998874
No 37
>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=92.60 E-value=0.19 Score=42.18 Aligned_cols=59 Identities=29% Similarity=0.427 Sum_probs=45.4
Q ss_pred CeeEEeecccccccccc--------------------------ccc--CcHHHHHHHhCccccCCCCCCchhHHHHHHHH
Q 027829 137 DVTWVTFHSAYDFGFCT--------------------------CLY--GGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 188 (218)
Q Consensus 137 ~v~WvtFhg~yDfg~~~--------------------------~l~--ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~ 188 (218)
+-.+|.+|..+|+++.+ .+. -.|+.+++.+|++......|.|.+|++.|.++
T Consensus 102 ~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~~~~L~~l~~~~gi~~~~~~~H~Al~DA~ata~l 181 (189)
T cd06134 102 RAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAGIEFDNKEAHSALYDTQKTAEL 181 (189)
T ss_pred CCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhCCCcHHHHHHHCCCCCCCCCCcChHHHHHHHHHH
Confidence 35799999999998210 011 26888999999974124579999999999999
Q ss_pred HHHHHHh
Q 027829 189 FLKIKDK 195 (218)
Q Consensus 189 F~kl~~~ 195 (218)
|.+|.++
T Consensus 182 f~~l~~~ 188 (189)
T cd06134 182 FCKIVNR 188 (189)
T ss_pred HHHHHHh
Confidence 9999875
No 38
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=92.35 E-value=0.18 Score=38.93 Aligned_cols=116 Identities=24% Similarity=0.259 Sum_probs=74.5
Q ss_pred EEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCceeEEEeeeeeccccC-CC
Q 027829 41 ISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH-AH 119 (218)
Q Consensus 41 IAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~wqFNF~~Fd~~~d-~~ 119 (218)
|.+|||+.|.-. +.-.|||||.-..+.+... ..=.|+.. ...... ..
T Consensus 1 v~~D~Ettg~~~----------------------~~~~iieig~v~~~~~~~~---------~~~~~~~~-i~p~~~~~i 48 (164)
T PF00929_consen 1 VVFDTETTGLDP----------------------RQDEIIEIGAVKVDDDENE---------EVESFNSL-IRPEEPPKI 48 (164)
T ss_dssp EEEEEEESSSTT----------------------TTCTEEEEEEEEEETTTTE---------EEEEEEEE-BEHSSHCSS
T ss_pred cEEEeEcCCCCC----------------------CCCeEEEEEEEEeeCCccc---------cceeeeec-ccccccccC
Confidence 679999998632 1234899999888876531 22346665 222222 22
Q ss_pred chhH-------HHHHHhcC----------ccccCCeeEEeecccccccc------------c-----------------c
Q 027829 120 ALDS-------VELLKRQG----------LVLNKDVTWVTFHSAYDFGF------------C-----------------T 153 (218)
Q Consensus 120 ~~~S-------I~lL~~~G----------lv~~~~v~WvtFhg~yDfg~------------~-----------------~ 153 (218)
.+.+ -+.|+..+ -.+.+...||.....+|.++ + +
T Consensus 49 ~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~~~~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 128 (164)
T PF00929_consen 49 SPWATKVHGITQEDLEDAPSFEEALDEFEEFLKKNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFP 128 (164)
T ss_dssp EHHHHHHHHHCHHHHHCHCEHHHHHHHHHHHHHHHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHH
T ss_pred CHHHeeecCCcccccccCCcHHHHHHhhhhhhhcccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhh
Confidence 2222 23344444 12233567777777888871 1 0
Q ss_pred ccc-CcHHHHHHHhCccccCCCCCCchhHHHHHHHHH
Q 027829 154 CLY-GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAF 189 (218)
Q Consensus 154 ~l~-ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F 189 (218)
.+. .+|.++|+.++++. .+.+|-|-+|++.|+++|
T Consensus 129 ~~~~~~l~~l~~~~~~~~-~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 129 NRKKYSLDDLAEYFGIPF-DGTAHDALDDARATAELF 164 (164)
T ss_dssp HHHHHSHHHHHHHTTSSS-TSTTTSHHHHHHHHHHHH
T ss_pred ccccCCHHHHHHHcCCCC-CCCCcChHHHHHHHhCcC
Confidence 122 28999999999999 788999999999999987
No 39
>PRK06722 exonuclease; Provisional
Probab=89.81 E-value=0.45 Score=43.08 Aligned_cols=35 Identities=31% Similarity=0.354 Sum_probs=32.8
Q ss_pred cHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHH
Q 027829 158 GLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIK 193 (218)
Q Consensus 158 gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~ 193 (218)
+|+.+++.+|++. .|..|.|-+|++.|++.|.+|.
T Consensus 144 sL~~l~~~lgL~~-~g~~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 144 SLQSAVEQLGLIW-EGKQHRALADAENTANILLKAY 178 (281)
T ss_pred CHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHHHHHh
Confidence 6999999999997 7889999999999999999975
No 40
>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=88.95 E-value=0.56 Score=39.82 Aligned_cols=39 Identities=26% Similarity=0.331 Sum_probs=33.0
Q ss_pred cHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhh
Q 027829 158 GLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 196 (218)
Q Consensus 158 gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~ 196 (218)
.|..+++.+|++...-..|.|-+|++.|.++|.+|.+++
T Consensus 154 ~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 154 VLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred cHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHH
Confidence 689999999997411357999999999999999998775
No 41
>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=88.86 E-value=0.51 Score=38.06 Aligned_cols=51 Identities=16% Similarity=0.184 Sum_probs=38.7
Q ss_pred eeEEeecccccccccc----------------------cccCcHHHHHHH-hCccccCCCCCCchhHHHHHHHHH
Q 027829 138 VTWVTFHSAYDFGFCT----------------------CLYGGLDRVCKA-LGVERVVGKSHQAGSDSLLTLHAF 189 (218)
Q Consensus 138 v~WvtFhg~yDfg~~~----------------------~l~ggL~~vA~~-L~v~r~~g~~hqAGsdsllT~~~F 189 (218)
-.+|..|..+|+.+.+ .-.-+|+.+|+. ||++. .+..|.|.+|++.|+++|
T Consensus 78 ~vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~-~~~~H~Al~DA~at~~l~ 151 (152)
T cd06144 78 RILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDI-QEGEHSSVEDARAAMRLY 151 (152)
T ss_pred CEEEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCccc-CCCCcCcHHHHHHHHHHh
Confidence 3578888899988210 012389999997 69975 346799999999999987
No 42
>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=86.42 E-value=0.81 Score=37.30 Aligned_cols=32 Identities=19% Similarity=0.264 Sum_probs=27.1
Q ss_pred CcHHHHHHHh---CccccCCCCCCchhHHHHHHHHH
Q 027829 157 GGLDRVCKAL---GVERVVGKSHQAGSDSLLTLHAF 189 (218)
Q Consensus 157 ggL~~vA~~L---~v~r~~g~~hqAGsdsllT~~~F 189 (218)
-+|+.+|+.+ +++. .+..|.|-+|++.|++.|
T Consensus 122 ~~L~~L~~~~~~~~i~~-~~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 122 VSLKVLAKRLLHRDIQV-GRQGHSSVEDARATMELY 156 (157)
T ss_pred hhHHHHHHHHcChhhcC-CCCCcCcHHHHHHHHHHh
Confidence 3899999999 5654 356799999999999887
No 43
>PRK05755 DNA polymerase I; Provisional
Probab=84.51 E-value=7.2 Score=40.37 Aligned_cols=41 Identities=29% Similarity=0.394 Sum_probs=29.8
Q ss_pred CcHHHHHHHh-Cccc-----cCC------------CCCCchhHHHHHHHHHHHHHHhhC
Q 027829 157 GGLDRVCKAL-GVER-----VVG------------KSHQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 157 ggL~~vA~~L-~v~r-----~~g------------~~hqAGsdsllT~~~F~kl~~~~f 197 (218)
-||+.+++.+ |+.- ..| ..|.|..|+.+|++.|.+|++.+-
T Consensus 412 ~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 412 HGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred CCHHHHHHHHhCCCccchHHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5899998776 5541 001 235799999999999999998754
No 44
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=81.17 E-value=2.7 Score=36.41 Aligned_cols=38 Identities=18% Similarity=0.265 Sum_probs=33.6
Q ss_pred CcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhh
Q 027829 157 GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 196 (218)
Q Consensus 157 ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~ 196 (218)
..|+.+++.+|++. ..+|-|-+|++.|+++|.+|.+.+
T Consensus 129 ~~L~~l~~~~~~~~--~~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 129 HNLQYLRQVYGFEE--NQAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred CCHHHHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHHHH
Confidence 37999999999875 668999999999999999988765
No 45
>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=73.74 E-value=3.6 Score=32.57 Aligned_cols=26 Identities=23% Similarity=0.359 Sum_probs=22.3
Q ss_pred HHHHHHHHHhhhcCCeEEEeccccce
Q 027829 25 ISEFERIRALIDRYPIISMDTEFPGV 50 (218)
Q Consensus 25 eeE~~~I~~~i~~~~yIAmDtEFPGv 50 (218)
++|+..+.+-+.+.++||+|+|.+|.
T Consensus 7 ~~~l~~~~~~l~~~~~~a~D~E~~~~ 32 (176)
T PF01612_consen 7 EEELEEAIKKLKNAKVLAFDTETTGL 32 (176)
T ss_dssp HHHHHHHHHHHTTTSEEEEEEEEETS
T ss_pred HHHHHHHHHHHcCCCeEEEEEEECCC
Confidence 56788888888899999999998765
No 46
>PTZ00315 2'-phosphotransferase; Provisional
Probab=72.43 E-value=5.4 Score=39.80 Aligned_cols=38 Identities=13% Similarity=0.206 Sum_probs=35.5
Q ss_pred cHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhh
Q 027829 158 GLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 196 (218)
Q Consensus 158 gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~ 196 (218)
+|+.+++.+|++- .|..|.|=.|+.-|+++|.+|.+.-
T Consensus 218 ~L~~al~~lgL~~-eGr~HrAlDDA~ntA~L~~~Ll~~g 255 (582)
T PTZ00315 218 DMPDMLQMLGLPL-QGRHHSGIDDCRNIAAVLCELLRRG 255 (582)
T ss_pred CHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHHHHHHHcC
Confidence 7999999999998 8999999999999999999988763
No 47
>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=71.07 E-value=4.1 Score=33.75 Aligned_cols=29 Identities=31% Similarity=0.401 Sum_probs=25.1
Q ss_pred cHHHHHHHhCccccCCCCCCchhHHHHHHHH
Q 027829 158 GLDRVCKALGVERVVGKSHQAGSDSLLTLHA 188 (218)
Q Consensus 158 gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~ 188 (218)
.|+.+++.+|++. ..+|-|-+|++.|++.
T Consensus 153 ~L~~l~~~~gi~~--~~~H~Al~Da~~ta~l 181 (183)
T cd06138 153 KLEDLAQANGIEH--SNAHDALSDVEATIAL 181 (183)
T ss_pred hHHHHHHHCCCCc--cccccHHHHHHHHHHH
Confidence 3999999999986 6679999999999764
No 48
>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=64.10 E-value=9.1 Score=31.07 Aligned_cols=52 Identities=19% Similarity=0.231 Sum_probs=37.5
Q ss_pred eeEEeeccccccccc------------------ccc----cCcHHHHHHH-hCccccC-CCCCCchhHHHHHHHHH
Q 027829 138 VTWVTFHSAYDFGFC------------------TCL----YGGLDRVCKA-LGVERVV-GKSHQAGSDSLLTLHAF 189 (218)
Q Consensus 138 v~WvtFhg~yDfg~~------------------~~l----~ggL~~vA~~-L~v~r~~-g~~hqAGsdsllT~~~F 189 (218)
-..|..+..+|+.+. ..+ .-+|+.+++. ||++-+. ...|.|-+|++.|+++|
T Consensus 85 ~vlVgHn~~fD~~fL~~~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 85 TILVGHSLQNDLDALRMIHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREVV 160 (161)
T ss_pred cEEEeccHHHHHHHHhCcCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCCCCcHHHHHHHHHHh
Confidence 457777777888721 112 3589999987 7876423 45799999999999876
No 49
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=59.68 E-value=7.7 Score=36.53 Aligned_cols=25 Identities=28% Similarity=0.328 Sum_probs=19.2
Q ss_pred HHHHHHHHhhhcCCeEEEeccccce
Q 027829 26 SEFERIRALIDRYPIISMDTEFPGV 50 (218)
Q Consensus 26 eE~~~I~~~i~~~~yIAmDtEFPGv 50 (218)
++++.+-..+..+++|||||||-|.
T Consensus 5 ~~l~~~~~~~~~~~~iAiDTEf~r~ 29 (361)
T COG0349 5 DLLAAACALLRGSKAIAIDTEFMRL 29 (361)
T ss_pred hHHHHHHHHhcCCCceEEecccccc
Confidence 3455566667788999999999764
No 50
>PRK11572 copper homeostasis protein CutC; Provisional
Probab=59.22 E-value=8.1 Score=34.55 Aligned_cols=59 Identities=27% Similarity=0.501 Sum_probs=36.6
Q ss_pred eeeeeccccCCCchhHHHHHHhcC---ccc--------------------cCCeeEEeecccccccccccccCcHHHHHH
Q 027829 108 NFKDFDIARHAHALDSVELLKRQG---LVL--------------------NKDVTWVTFHSAYDFGFCTCLYGGLDRVCK 164 (218)
Q Consensus 108 NF~~Fd~~~d~~~~~SI~lL~~~G---lv~--------------------~~~v~WvtFhg~yDfg~~~~l~ggL~~vA~ 164 (218)
+|. |+..+--.-.+.|+.+++.| +|+ ..++. +|||-++|.. ......|+.+++
T Consensus 64 dF~-Ys~~E~~~M~~di~~~~~~GadGvV~G~L~~dg~vD~~~~~~Li~~a~~~~-vTFHRAfD~~--~d~~~al~~l~~ 139 (248)
T PRK11572 64 DFC-YSDGEFAAMLEDIATVRELGFPGLVTGVLDVDGHVDMPRMRKIMAAAGPLA-VTFHRAFDMC--ANPLNALKQLAD 139 (248)
T ss_pred CCC-CCHHHHHHHHHHHHHHHHcCCCEEEEeeECCCCCcCHHHHHHHHHHhcCCc-eEEechhhcc--CCHHHHHHHHHH
Confidence 355 54333223344688888888 111 12344 5999999965 445567888777
Q ss_pred HhCccccC
Q 027829 165 ALGVERVV 172 (218)
Q Consensus 165 ~L~v~r~~ 172 (218)
. |+.| |
T Consensus 140 l-G~~r-I 145 (248)
T PRK11572 140 L-GVAR-I 145 (248)
T ss_pred c-CCCE-E
Confidence 6 9999 5
No 51
>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=58.44 E-value=11 Score=31.77 Aligned_cols=25 Identities=16% Similarity=0.329 Sum_probs=20.5
Q ss_pred HHHHHHHHHh--hhcCCeEEEeccccc
Q 027829 25 ISEFERIRAL--IDRYPIISMDTEFPG 49 (218)
Q Consensus 25 eeE~~~I~~~--i~~~~yIAmDtEFPG 49 (218)
.+|+..+.+. +.+.+.|++|||+..
T Consensus 7 ~~el~~~~~~~~l~~~~vig~D~Ew~~ 33 (193)
T cd06146 7 EEELEALLLALSLEAGRVVGIDSEWKP 33 (193)
T ss_pred HHHHHHHHHHHhhccCCEEEEECccCC
Confidence 4677777777 899999999999853
No 52
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=56.24 E-value=13 Score=29.84 Aligned_cols=26 Identities=15% Similarity=0.196 Sum_probs=20.3
Q ss_pred HHHHHHHHHhhh-cCCeEEEeccccce
Q 027829 25 ISEFERIRALID-RYPIISMDTEFPGV 50 (218)
Q Consensus 25 eeE~~~I~~~i~-~~~yIAmDtEFPGv 50 (218)
++++..+.+.+. +.+.|++|||+.+.
T Consensus 4 ~~~~~~~~~~~~~~~~~ig~D~E~~~~ 30 (170)
T cd06141 4 AQDAEEAVKELLGKEKVVGFDTEWRPS 30 (170)
T ss_pred HHHHHHHHHHHhcCCCEEEEeCccCCc
Confidence 456666666666 99999999999753
No 53
>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=56.15 E-value=12 Score=30.70 Aligned_cols=31 Identities=23% Similarity=0.193 Sum_probs=27.6
Q ss_pred EEeccccHHHHHHHHHHhhhcCCeEEEeccc
Q 027829 17 REVFEFNLISEFERIRALIDRYPIISMDTEF 47 (218)
Q Consensus 17 ~eVwa~NleeE~~~I~~~i~~~~yIAmDtEF 47 (218)
.-|.|-||+|-++.|.+.-++...||||.-.
T Consensus 42 ~PVHA~NL~e~l~~I~~~~~~~~iIAIDAcL 72 (140)
T TIGR02841 42 EPVHAKNLEEKLKIIKKKHPNPFIIAIDACL 72 (140)
T ss_pred CCcccccHHHHHHHHHHhCCCCeEEEEECcc
Confidence 3488999999999999999999999999754
No 54
>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=54.56 E-value=17 Score=29.23 Aligned_cols=53 Identities=17% Similarity=0.120 Sum_probs=35.9
Q ss_pred CeeEEeeccccccccc--------------cccc-----CcHHHHHHHh-CccccC-CCCCCchhHHHHHHHHH
Q 027829 137 DVTWVTFHSAYDFGFC--------------TCLY-----GGLDRVCKAL-GVERVV-GKSHQAGSDSLLTLHAF 189 (218)
Q Consensus 137 ~v~WvtFhg~yDfg~~--------------~~l~-----ggL~~vA~~L-~v~r~~-g~~hqAGsdsllT~~~F 189 (218)
+-.+|..+-.+|+.+. +.+. -+|+.+|+.+ +..-.. +..|.|-+|++.|++.|
T Consensus 76 ~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 76 DTILVGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELV 149 (150)
T ss_pred CCEEEEcChHHHHHHhhccCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHh
Confidence 4457777777777721 1111 3899999886 432111 46799999999999887
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=54.46 E-value=12 Score=34.80 Aligned_cols=126 Identities=23% Similarity=0.306 Sum_probs=70.8
Q ss_pred HHHHHHHHHhhhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCcee
Q 027829 25 ISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYI 104 (218)
Q Consensus 25 eeE~~~I~~~i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~ 104 (218)
.+|+..+-+.+...+.||+||||-.. ..| -..+-+|||.- .+ .+
T Consensus 5 ~~~l~~~~~~l~~~~~ia~DtE~~~~--------------~~y------~~~l~LiQia~----~~------------~~ 48 (367)
T TIGR01388 5 DDELATVCEAVRTFPFVALDTEFVRE--------------RTF------WPQLGLIQVAD----GE------------QL 48 (367)
T ss_pred HHHHHHHHHHHhcCCEEEEeccccCC--------------CCC------CCcceEEEEee----CC------------eE
Confidence 46777777777889999999998532 112 11356888861 11 11
Q ss_pred EEEeeeeeccccCCCchhHHHHHHhcCccccCCeeEEeeccccccc---------------------ccc-cccCcHHHH
Q 027829 105 WEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFG---------------------FCT-CLYGGLDRV 162 (218)
Q Consensus 105 wqFNF~~Fd~~~d~~~~~SI~lL~~~Glv~~~~v~WvtFhg~yDfg---------------------~~~-~l~ggL~~v 162 (218)
|- ||.-.. .. ++.|.. ++.++++.+|.+...+|+- +++ ....||..+
T Consensus 49 ----~l-iD~~~~-~~---~~~L~~--lL~d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~~~l~~L 117 (367)
T TIGR01388 49 ----AL-IDPLVI-ID---WSPLKE--LLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKL 117 (367)
T ss_pred ----EE-EeCCCc-cc---HHHHHH--HHCCCCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCCCccHHHH
Confidence 22 433211 11 222221 3446678888777777665 121 123489988
Q ss_pred HHH-hCccccCC-----------CC---CCchhHHHHHHHHHHHHHHhhC
Q 027829 163 CKA-LGVERVVG-----------KS---HQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 163 A~~-L~v~r~~g-----------~~---hqAGsdsllT~~~F~kl~~~~f 197 (218)
++. ||+.-.-| .. +-|..|+......|-+|++..-
T Consensus 118 v~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 118 VQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLE 167 (367)
T ss_pred HHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 866 46642001 00 1267778777788888877653
No 56
>PRK10829 ribonuclease D; Provisional
Probab=54.28 E-value=12 Score=35.12 Aligned_cols=126 Identities=23% Similarity=0.296 Sum_probs=73.4
Q ss_pred HHHHHHHHHhhhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCCCCCCCCCcee
Q 027829 25 ISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYI 104 (218)
Q Consensus 25 eeE~~~I~~~i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p~~~~~~~~~~ 104 (218)
.+++..+-+.+..++.||+||||-.. ..|. ..+-+|||. + |. .+
T Consensus 9 ~~~L~~~~~~l~~~~~lalDtEf~~~--------------~ty~------~~l~LiQl~----~--~~----------~~ 52 (373)
T PRK10829 9 DDALASVCEAARAFPAIALDTEFVRT--------------RTYY------PQLGLIQLY----D--GE----------QL 52 (373)
T ss_pred HHHHHHHHHHHhcCCeEEEecccccC--------------ccCC------CceeEEEEe----c--CC----------ce
Confidence 35666666668999999999998431 1121 246789987 1 21 11
Q ss_pred EEEeeeeeccccCCCchhHHHHHHhcCccccCCeeEEeeccccccc---------------------ccc-cccCcHHHH
Q 027829 105 WEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFG---------------------FCT-CLYGGLDRV 162 (218)
Q Consensus 105 wqFNF~~Fd~~~d~~~~~SI~lL~~~Glv~~~~v~WvtFhg~yDfg---------------------~~~-~l~ggL~~v 162 (218)
|- +|.-. ....+.|+. ++-|+++.-|-+.+.+|+- +++ +..-||..+
T Consensus 53 ----~L-iD~l~----~~d~~~L~~--ll~~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~~~gl~~L 121 (373)
T PRK10829 53 ----SL-IDPLG----ITDWSPFKA--LLRDPQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASM 121 (373)
T ss_pred ----EE-EecCC----ccchHHHHH--HHcCCCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCccccHHHH
Confidence 22 44321 111223322 4446676667666777776 121 112478887
Q ss_pred H-HHhCccc------------cCC--CCCCchhHHHHHHHHHHHHHHhhC
Q 027829 163 C-KALGVER------------VVG--KSHQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 163 A-~~L~v~r------------~~g--~~hqAGsdsllT~~~F~kl~~~~f 197 (218)
. +.|||.- +.. .-+-|..|+.....+|-+|++..-
T Consensus 122 v~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 122 VEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred HHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6 5678742 111 112388899999999999888654
No 57
>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=49.73 E-value=13 Score=29.62 Aligned_cols=53 Identities=28% Similarity=0.450 Sum_probs=25.3
Q ss_pred cCCeeEEeecc-ccccccc------------------------ccccC-cHHHHHHHhCccccCCCCCCchhHHHHHHHH
Q 027829 135 NKDVTWVTFHS-AYDFGFC------------------------TCLYG-GLDRVCKALGVERVVGKSHQAGSDSLLTLHA 188 (218)
Q Consensus 135 ~~~v~WvtFhg-~yDfg~~------------------------~~l~g-gL~~vA~~L~v~r~~g~~hqAGsdsllT~~~ 188 (218)
.+.-.+|+||| .||+.+. ....+ +|..||+.||+.| - .....|+++....+-
T Consensus 55 ~~~~~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~~~~~Lk~ve~~lg~~~-~-~~~~~G~~~~~~~~~ 132 (164)
T PF13482_consen 55 DEADNIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFLESYSLKNVEKFLGIER-R-DDDISGSESVKLYKE 132 (164)
T ss_dssp HTT--EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TTSCCTT--SHHH-------------HHHHHHHHHH-
T ss_pred hcCCeEEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhccCCCCCHHHHhhhccccc-c-cCCCCHHHHHHHHHH
Confidence 34457999997 7898811 01234 8999999999999 2 223588888877654
Q ss_pred H
Q 027829 189 F 189 (218)
Q Consensus 189 F 189 (218)
|
T Consensus 133 ~ 133 (164)
T PF13482_consen 133 Y 133 (164)
T ss_dssp -
T ss_pred H
Confidence 4
No 58
>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=41.11 E-value=27 Score=29.44 Aligned_cols=32 Identities=22% Similarity=0.238 Sum_probs=28.2
Q ss_pred EEeccccHHHHHHHHHHhhhcCCeEEEecccc
Q 027829 17 REVFEFNLISEFERIRALIDRYPIISMDTEFP 48 (218)
Q Consensus 17 ~eVwa~NleeE~~~I~~~i~~~~yIAmDtEFP 48 (218)
.-|.|-||+|-++.|.+.-++.-.||||.-..
T Consensus 66 ~PVHA~NL~e~l~~I~~~~~~~~IIAIDAcLG 97 (163)
T PF06866_consen 66 EPVHALNLEETLNEIKKKHPNPFIIAIDACLG 97 (163)
T ss_pred CCcchhhHHHHHHHHHHHCCCCeEEEEECCCC
Confidence 34889999999999999989999999997663
No 59
>KOG4355 consensus Predicted Fe-S oxidoreductase [General function prediction only]
Probab=39.17 E-value=14 Score=35.55 Aligned_cols=29 Identities=38% Similarity=0.359 Sum_probs=23.0
Q ss_pred cHHHHHHHhCccccCCC---CCCchhHHHHHH
Q 027829 158 GLDRVCKALGVERVVGK---SHQAGSDSLLTL 186 (218)
Q Consensus 158 gL~~vA~~L~v~r~~g~---~hqAGsdsllT~ 186 (218)
-|+.+|..|..+|.-.- +-|+||||+||-
T Consensus 284 hl~e~a~vlrhp~vYsflhvpvqsgsdsvl~e 315 (547)
T KOG4355|consen 284 HLEEAAFVLRHPRVYSFLHVPVQSGSDSVLTE 315 (547)
T ss_pred HHHHHHHHhcCCeEEEEEecccccCchhHHHH
Confidence 57899999999994332 359999999985
No 60
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=37.44 E-value=24 Score=32.33 Aligned_cols=41 Identities=22% Similarity=0.225 Sum_probs=36.9
Q ss_pred cCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhhC
Q 027829 156 YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 197 (218)
Q Consensus 156 ~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~f 197 (218)
...|+.+|..-...| .+.+|||=||-+++.+.|-+++..+.
T Consensus 252 vs~le~Lat~~~~~p-~l~ahra~~Dv~~~~k~~q~~~idll 292 (318)
T KOG4793|consen 252 VSSLEALATYYSLTP-ELDAHRALSDVLLLSKVFQKLTIDLL 292 (318)
T ss_pred chhHHHHHHHhhcCc-ccchhhhccccchhhhHHHHhhhhhh
Confidence 457999999999999 89999999999999999999887654
No 61
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=34.49 E-value=26 Score=23.98 Aligned_cols=17 Identities=18% Similarity=0.286 Sum_probs=14.2
Q ss_pred cccCcHHHHHHHhCccc
Q 027829 154 CLYGGLDRVCKALGVER 170 (218)
Q Consensus 154 ~l~ggL~~vA~~L~v~r 170 (218)
.-.-.|++||+.|||.+
T Consensus 21 PR~~tl~elA~~lgis~ 37 (53)
T PF04967_consen 21 PRRITLEELAEELGISK 37 (53)
T ss_pred CCcCCHHHHHHHhCCCH
Confidence 34568999999999987
No 62
>PF08228 RNase_P_pop3: RNase P subunit Pop3; InterPro: IPR013241 This family of fungal proteins form a subunit of RNase P, the ribonucleoprotein enzyme that cleaves the leader sequence of precursor tRNAs to generate mature tRNAs. The structure of Pop3 has been assigned the L7Ae/L30e fold []. This RNA-binding fold is also present in human RNase P subunit Rpp38, raising the possibility that Pop3p and Rpp38 are functional homologues.
Probab=32.19 E-value=37 Score=28.37 Aligned_cols=29 Identities=38% Similarity=0.639 Sum_probs=21.5
Q ss_pred cCcHHHHHHHhCccccCCC----CCCchhHHHHH
Q 027829 156 YGGLDRVCKALGVERVVGK----SHQAGSDSLLT 185 (218)
Q Consensus 156 ~ggL~~vA~~L~v~r~~g~----~hqAGsdsllT 185 (218)
+|..+++|+.||++| +|. .+..|+++|..
T Consensus 110 kgs~~rLs~aLgi~r-~g~l~v~~~~~~~~~L~~ 142 (158)
T PF08228_consen 110 KGSEARLSEALGIPR-VGILAVRADAPGAKSLVD 142 (158)
T ss_pred hhHHHHHHHHhCCCC-ccEEEEecCCcccHHHHH
Confidence 688999999999999 554 45555555543
No 63
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=30.70 E-value=26 Score=27.17 Aligned_cols=24 Identities=33% Similarity=0.490 Sum_probs=17.2
Q ss_pred cHHHHHHHhCccccCCCCCCchhHHHHHHH
Q 027829 158 GLDRVCKALGVERVVGKSHQAGSDSLLTLH 187 (218)
Q Consensus 158 gL~~vA~~L~v~r~~g~~hqAGsdsllT~~ 187 (218)
+|..||+.+||.| ||-+|++--+.
T Consensus 35 SlsEIAe~~~iSR------qaV~d~ikr~~ 58 (101)
T PF04297_consen 35 SLSEIAEELGISR------QAVYDSIKRAE 58 (101)
T ss_dssp -HHHHHHHCTS-H------HHHHHHHHHHH
T ss_pred CHHHHHHHHCCCH------HHHHHHHHHHH
Confidence 7999999999999 47777665443
No 64
>PHA02535 P terminase ATPase subunit; Provisional
Probab=30.22 E-value=82 Score=31.61 Aligned_cols=27 Identities=22% Similarity=0.465 Sum_probs=23.9
Q ss_pred ccc-cHHHHHHHHHHhhhcCC--eEEEecc
Q 027829 20 FEF-NLISEFERIRALIDRYP--IISMDTE 46 (218)
Q Consensus 20 wa~-NleeE~~~I~~~i~~~~--yIAmDtE 46 (218)
|+. ++++..+.|+++.++|+ ||+||+-
T Consensus 440 ~~g~~f~~QA~~I~~l~~rynV~~I~ID~T 469 (581)
T PHA02535 440 WRGLDFAEQAAEIRKLTEKYNVTYIGIDAT 469 (581)
T ss_pred EcCCCHHHHHHHHHHHHHHcCceEEEEcCC
Confidence 544 89999999999999999 9999964
No 65
>PF04386 SspB: Stringent starvation protein B; InterPro: IPR007481 Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB is a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA []. However, more recent work has cast doubt on the importance of SspB in wild-type cells []. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates [].; PDB: 2NYS_A 2QAZ_D 2QAS_A 1OX9_A 1OX8_A 1YFN_C 1TWB_B 1OU9_C 1OU8_B 1ZSZ_B ....
Probab=29.91 E-value=59 Score=26.74 Aligned_cols=17 Identities=53% Similarity=1.017 Sum_probs=12.3
Q ss_pred hcCCeEEEeccccceee
Q 027829 36 DRYPIISMDTEFPGVVV 52 (218)
Q Consensus 36 ~~~~yIAmDtEFPGvv~ 52 (218)
+..|||.+||..|||..
T Consensus 30 ~~tpyI~v~t~~pgV~v 46 (155)
T PF04386_consen 30 DHTPYITVDTDYPGVQV 46 (155)
T ss_dssp T--EEEEEETTSTT-BS
T ss_pred CCeEEEEEEeCCCCCCC
Confidence 35599999999999754
No 66
>TIGR02724 phenyl_P_beta phenylphosphate carboxylase, beta subunit. Members of this protein family are the beta subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. This beta subunit is homologous to the alpha subunit and, more broadly, to UbiD family decarboxylases.
Probab=29.70 E-value=64 Score=31.30 Aligned_cols=32 Identities=25% Similarity=0.364 Sum_probs=26.2
Q ss_pred eEEeecc--cccccccccccCcHHHHHHHhCccc
Q 027829 139 TWVTFHS--AYDFGFCTCLYGGLDRVCKALGVER 170 (218)
Q Consensus 139 ~WvtFhg--~yDfg~~~~l~ggL~~vA~~L~v~r 170 (218)
..+-|+. ||++-.+.++.|+++++|..||++.
T Consensus 42 pA~LF~nv~g~~~pv~~n~~~s~~r~a~~LG~~~ 75 (472)
T TIGR02724 42 PALLFESIKGYDTPVFTGAFATTKRLAIMLGLPH 75 (472)
T ss_pred CeEEEeCCCCCCCceEEcCCCCHHHHHHHcCCCc
Confidence 4677776 6777767789999999999999975
No 67
>COG3142 CutC Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]
Probab=28.66 E-value=48 Score=29.58 Aligned_cols=84 Identities=27% Similarity=0.409 Sum_probs=47.5
Q ss_pred EEEeeeeeccccCCCchhHHHHHHhcC---ccc--------------cCCeeE-----EeecccccccccccccCcHHHH
Q 027829 105 WEFNFKDFDIARHAHALDSVELLKRQG---LVL--------------NKDVTW-----VTFHSAYDFGFCTCLYGGLDRV 162 (218)
Q Consensus 105 wqFNF~~Fd~~~d~~~~~SI~lL~~~G---lv~--------------~~~v~W-----vtFhg~yDfg~~~~l~ggL~~v 162 (218)
...||. |+-.+--.-.+-|+..++-| +|+ .+=+.| ||||-++|. |.+-.--|+.+
T Consensus 61 RgGdFv-Y~~~E~~iM~~DI~~~~~lG~~GVV~G~lt~dg~iD~~~le~Li~aA~gL~vTFHrAFD~--~~d~~~ale~l 137 (241)
T COG3142 61 RGGDFV-YSDDELEIMLEDIRLARELGVQGVVLGALTADGNIDMPRLEKLIEAAGGLGVTFHRAFDE--CPDPLEALEQL 137 (241)
T ss_pred CCCCcc-cChHHHHHHHHHHHHHHHcCCCcEEEeeecCCCccCHHHHHHHHHHccCCceeeehhhhh--cCCHHHHHHHH
Confidence 346777 66433223344678888877 222 111223 899999995 43333456666
Q ss_pred HHHhCccccCCCCCCchhHHHHHHHHHHHHHH
Q 027829 163 CKALGVERVVGKSHQAGSDSLLTLHAFLKIKD 194 (218)
Q Consensus 163 A~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~ 194 (218)
++ ||++| |=+.-|+ ++++.......+|.+
T Consensus 138 i~-~Gv~R-ILTsGg~-~sa~eg~~~l~~li~ 166 (241)
T COG3142 138 IE-LGVER-ILTSGGK-ASALEGLDLLKRLIE 166 (241)
T ss_pred HH-CCCcE-EecCCCc-CchhhhHHHHHHHHH
Confidence 54 79999 6443344 445555555555544
No 68
>PF13309 HTH_22: HTH domain
Probab=26.34 E-value=37 Score=23.72 Aligned_cols=17 Identities=35% Similarity=0.657 Sum_probs=15.6
Q ss_pred cccCcHHHHHHHhCccc
Q 027829 154 CLYGGLDRVCKALGVER 170 (218)
Q Consensus 154 ~l~ggL~~vA~~L~v~r 170 (218)
.++|+.+.||+.|||.|
T Consensus 40 ~lKgav~~vA~~L~iS~ 56 (64)
T PF13309_consen 40 LLKGAVEYVAEKLGISR 56 (64)
T ss_pred ccCcHHHHHHHHHCCCH
Confidence 47899999999999998
No 69
>PF11959 DUF3473: Domain of unknown function (DUF3473); InterPro: IPR022560 This domain, found in bacteria and archaea, is functionally uncharacterised. It is about 130 amino acids in length and is found C-terminal to PF01522 from PFAM. It contains two completely conserved residues (P and H) that may be functionally important.
Probab=26.25 E-value=96 Score=24.89 Aligned_cols=31 Identities=19% Similarity=0.086 Sum_probs=26.6
Q ss_pred eEEEeccccHHHHHHHHHHhhhcCCeEEEec
Q 027829 15 LIREVFEFNLISEFERIRALIDRYPIISMDT 45 (218)
Q Consensus 15 ~I~eVwa~NleeE~~~I~~~i~~~~yIAmDt 45 (218)
.-+=.+-.|++.-.++++.+++++.|..|+.
T Consensus 98 ~~rf~~y~~l~~~~~rl~~Ll~~f~f~t~~~ 128 (133)
T PF11959_consen 98 KSRFRHYNNLDRMEKRLDRLLSDFRFGTMRE 128 (133)
T ss_pred ceeEEEEcCHHHHHHHHHHHHhhCceEEHHH
Confidence 3345788999999999999999999998873
No 70
>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=26.05 E-value=63 Score=25.92 Aligned_cols=38 Identities=18% Similarity=0.210 Sum_probs=26.1
Q ss_pred cCcHHHHHHH-hCccc------------cC--CCCCCchhHHHHHHHHHHHHH
Q 027829 156 YGGLDRVCKA-LGVER------------VV--GKSHQAGSDSLLTLHAFLKIK 193 (218)
Q Consensus 156 ~ggL~~vA~~-L~v~r------------~~--g~~hqAGsdsllT~~~F~kl~ 193 (218)
..||+.+++. ||+.- +. ...+-|..|+....++|.+|+
T Consensus 108 ~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 108 RWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred CchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3489999887 47642 11 112348889999999998886
No 71
>PF11413 HIF-1: Hypoxia-inducible factor-1; InterPro: IPR021537 Hypoxia-inducible factors (HIFs) are transcription factors that respond to changes in available oxygen in the cellular environment. Specifically, they respond to decreases in oxygen, mediating the effects of hypoxia []. HIFs are heterodimers, composed of an alpha and a beta subunit. At least 3 different alpha subunits are known to exist, termed HIF-1, -2 and -3 alpha. Beta subunits, meanwhile, are constitutively-expressed aryl hydrocarbon receptor nuclear translocators (ARNTs). In addition to their role in hypoxia, HIFs have been shown to be involved in a range of processes, including angiogenesis, metal transport, mitochondrial function and cell growth []. This entry represents HIF alpha subunits.; PDB: 3HQU_S 1LQB_D 1LM8_H 3HQR_S.
Probab=25.41 E-value=17 Score=22.94 Aligned_cols=11 Identities=45% Similarity=0.776 Sum_probs=6.1
Q ss_pred cCCeEEEeccc
Q 027829 37 RYPIISMDTEF 47 (218)
Q Consensus 37 ~~~yIAmDtEF 47 (218)
-+|||.||-.|
T Consensus 14 LAPYIpMddDF 24 (34)
T PF11413_consen 14 LAPYIPMDDDF 24 (34)
T ss_dssp TSBB--SS--E
T ss_pred hcCccccCccc
Confidence 68999999777
No 72
>PF03213 Pox_P35: Poxvirus P35 protein; InterPro: IPR004900 The Poxvirus P35 protein is an immunodominant envelope protein. It binds to heparan sulphate on the cell surface to provide virion attachment to target cell [].; GO: 0019031 viral envelope
Probab=24.21 E-value=43 Score=31.15 Aligned_cols=47 Identities=19% Similarity=0.288 Sum_probs=32.0
Q ss_pred CCeeEEeecccccccc-----------------c--c----cccCcHHHHHHHhCccccCCCCCCchhHHHHHH
Q 027829 136 KDVTWVTFHSAYDFGF-----------------C--T----CLYGGLDRVCKALGVERVVGKSHQAGSDSLLTL 186 (218)
Q Consensus 136 ~~v~WvtFhg~yDfg~-----------------~--~----~l~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~ 186 (218)
.+-.--+|-|||||-+ . + +|.--+.++.+.||+.|+| .+||+..++=
T Consensus 171 ~~p~~~~Y~GGyD~SLsAYIIr~~~a~kl~~~i~~~~Gvst~l~~Ei~rlE~~l~inR~V----l~~s~~yV~h 240 (325)
T PF03213_consen 171 GNPSMYSYTGGYDVSLSAYIIRVSTAKKLYNEIIKNGGVSTSLSFEIYRLENRLGINRQV----LNDSSKYVHH 240 (325)
T ss_pred cCcceeeecCccceeeEEEEEEhHHHHHHHHHHHhCCCCccceeeeHHHHHhhhCchhhh----hcCccceeec
Confidence 3556789999999981 0 1 2333468999999999953 3666655543
No 73
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=22.19 E-value=57 Score=22.78 Aligned_cols=16 Identities=44% Similarity=0.856 Sum_probs=13.4
Q ss_pred ccCcHHHHHHHhCccc
Q 027829 155 LYGGLDRVCKALGVER 170 (218)
Q Consensus 155 l~ggL~~vA~~L~v~r 170 (218)
..||..+||+.|||.+
T Consensus 8 ~~G~~~~lAkalGVs~ 23 (60)
T PF14549_consen 8 YFGGQSKLAKALGVSP 23 (60)
T ss_dssp HHSSHHHHHHHHTS-H
T ss_pred HHCCHHHHHHHHCCCH
Confidence 3589999999999998
No 74
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=21.94 E-value=57 Score=20.60 Aligned_cols=16 Identities=25% Similarity=0.567 Sum_probs=12.1
Q ss_pred ccCcHHHHHHHhCccc
Q 027829 155 LYGGLDRVCKALGVER 170 (218)
Q Consensus 155 l~ggL~~vA~~L~v~r 170 (218)
..|...+.|+.|||.|
T Consensus 17 ~~gn~~~aA~~Lgisr 32 (42)
T PF02954_consen 17 CGGNVSKAARLLGISR 32 (42)
T ss_dssp TTT-HHHHHHHHTS-H
T ss_pred hCCCHHHHHHHHCCCH
Confidence 3467899999999998
No 75
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=21.59 E-value=54 Score=29.44 Aligned_cols=56 Identities=20% Similarity=0.183 Sum_probs=40.8
Q ss_pred HHHHHHHhCccccCCCCCCchhHHHHHHHHHHHHHHhhC---CCccccccccceEeccCCC
Q 027829 159 LDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF---GNEYELQKYANVLHGLELL 216 (218)
Q Consensus 159 L~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~kl~~~~f---~~~~~~~~~~g~l~Gl~~~ 216 (218)
|.. |+.+..+| .-.-.-.+-.+||..--+..+++.-. .+.-+..++.|++||+..+
T Consensus 240 LlT-a~~ff~~R-~~~F~~sig~~ll~~L~g~~~~~~sl~~~~~~t~f~~~~g~~~gi~~~ 298 (299)
T COG5228 240 LLT-ADEFFLPR-FSIFTTSIGQSLLMLLSGCQLSKLSLHKFPNGTDFAKYQGVIYGIDGD 298 (299)
T ss_pred hhh-hHHhcchh-hheecccccHHHHHHHhccccCCchheeCCCcccHhhcCCcccCCCCC
Confidence 444 89999999 44444566678888888877776643 4445778999999999653
No 76
>PRK14569 D-alanyl-alanine synthetase A; Provisional
Probab=21.57 E-value=1.4e+02 Score=26.57 Aligned_cols=44 Identities=16% Similarity=0.198 Sum_probs=31.5
Q ss_pred cCCeeEEeecccccccccccccCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHH
Q 027829 135 NKDVTWVTFHSAYDFGFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLK 191 (218)
Q Consensus 135 ~~~v~WvtFhg~yDfg~~~~l~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~k 191 (218)
..++-|..+||.+ +.-|-++.+.+.+|++- +| |++....-|.-|
T Consensus 56 ~~d~vf~~lhG~~------ge~~~i~~~le~~gip~-~G------s~~~a~~l~~DK 99 (296)
T PRK14569 56 KPDKCFVALHGED------GENGRVSALLEMLEIKH-TS------SSMKSSVITMDK 99 (296)
T ss_pred CCCEEEEeCCCCC------CCChHHHHHHHHcCCCe-eC------CCHHHHHHHHCH
Confidence 4688899999887 45567899999999998 44 444444444444
No 77
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=21.43 E-value=89 Score=23.88 Aligned_cols=31 Identities=29% Similarity=0.371 Sum_probs=24.8
Q ss_pred HHHHHHHhCcccc------CCCCCCchhHHHHHHHHH
Q 027829 159 LDRVCKALGVERV------VGKSHQAGSDSLLTLHAF 189 (218)
Q Consensus 159 L~~vA~~L~v~r~------~g~~hqAGsdsllT~~~F 189 (218)
-.++|+.|||+|+ -|..|-++-|.|+|+-++
T Consensus 44 Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~ 80 (91)
T COG5606 44 QAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLAR 80 (91)
T ss_pred HHHHHHHhCCCCchHHHHHhcchhHhhHHHHHHHHHH
Confidence 4689999999984 377788888888887554
No 78
>PF08685 GON: GON domain; InterPro: IPR012314 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. The ADAMTSs (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) are a family of zinc dependent metalloproteinases that play important roles in a variety of normal and pathological conditions. These enzymes show a complex domain organisation including signal sequence, propeptide, metalloproteinase domain (see PDOC50215 from PROSITEDOC), disintegrin-like domain (see PDOC00351 from PROSITEDOC), central TS-1 motif (see PDOC50092 from PROSITEDOC), cysteine-rich region, and a variable number of TS-like repeats at the C-terminal region. The GON domain is an approximately 200-residue module, whose presence is the hallmark of a subfamily of structurally and evolutionarily related ADAMTSs, called GON- ADAMTSs. The GON domain is characterised by the presence of several conserved cysteine residues and is likely to be globular [], []. Some proteins known to contain a GON domain are listed below: Mammalian ADAMTS-9 Mammalian ADAMTS-20 Caenorhabditis elegans gon-1, a protease required for gonadal morphogenesis Proteins containing the GON domain belong to MEROPS peptidase subfamily M12B (adamalysin, clan MA).; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding
Probab=21.34 E-value=53 Score=28.61 Aligned_cols=67 Identities=21% Similarity=0.446 Sum_probs=45.0
Q ss_pred cchHHHhhhcccccceeeeeeeecCC-CCCCCCCCCCCceeEEEeeeeeccccCCCchh--HHHHHHhcCccccCCeeEE
Q 027829 65 ANYNGLKANVDLLNLIQIGLTLSDEE-GNLPDLGSGSTYYIWEFNFKDFDIARHAHALD--SVELLKRQGLVLNKDVTWV 141 (218)
Q Consensus 65 ~~Y~~lk~NVd~l~iIQlGit~~~~~-G~~p~~~~~~~~~~wqFNF~~Fd~~~d~~~~~--SI~lL~~~Glv~~~~v~Wv 141 (218)
-+|.+||-|+..|+||--=.||+.-. |+.-..|+.+.+ |+.. -|++. ||+| +.-|+.+.++++|+
T Consensus 91 T~F~KvRid~~tl~I~~~D~tFa~t~~G~~v~~~tAGDC---------yS~~--~CpqG~FsIdL-~GTgf~vs~~~~W~ 158 (201)
T PF08685_consen 91 TRFSKVRIDPSTLRIITNDFTFARTTGGNPVPFGTAGDC---------YSAA--RCPQGRFSIDL-RGTGFRVSPDTKWV 158 (201)
T ss_pred eEEEEEEEcccccEEEeCCceEeeccCCcccCccccccc---------cccC--CCCCceEEEee-CCCceEecCCCEEE
Confidence 46999999999999999999999987 544334544332 2222 23332 4543 44557788999998
Q ss_pred ee
Q 027829 142 TF 143 (218)
Q Consensus 142 tF 143 (218)
+-
T Consensus 159 ~~ 160 (201)
T PF08685_consen 159 TQ 160 (201)
T ss_pred eC
Confidence 73
Done!