Query 023614
Match_columns 280
No_of_seqs 137 out of 442
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 05:21:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023614.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023614hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0304 mRNA deadenylase subun 100.0 6.9E-93 1.5E-97 620.7 19.2 237 15-258 1-239 (239)
2 COG5228 POP2 mRNA deadenylase 100.0 2.5E-81 5.4E-86 549.1 14.7 258 9-276 13-270 (299)
3 PF04857 CAF1: CAF1 family rib 100.0 1.9E-62 4.2E-67 448.6 19.0 229 17-253 1-262 (262)
4 PRK07942 DNA polymerase III su 98.9 3.3E-08 7.1E-13 89.3 15.8 171 36-259 4-181 (232)
5 smart00479 EXOIII exonuclease 98.9 9.7E-08 2.1E-12 80.0 17.0 164 39-259 1-168 (169)
6 KOG1990 Poly(A)-specific exori 98.9 8.7E-10 1.9E-14 111.2 4.1 234 21-260 1-365 (564)
7 cd06133 ERI-1_3'hExo_like DEDD 98.7 8E-07 1.7E-11 75.3 15.1 171 40-254 1-175 (176)
8 PRK09145 DNA polymerase III su 98.7 8E-07 1.7E-11 78.3 15.5 168 31-256 22-199 (202)
9 cd06131 DNA_pol_III_epsilon_Ec 98.7 1.2E-06 2.6E-11 74.1 15.4 164 40-254 1-166 (167)
10 cd06134 RNaseT DEDDh 3'-5' exo 98.7 7.7E-07 1.7E-11 77.8 14.3 177 37-257 4-188 (189)
11 PRK05168 ribonuclease T; Provi 98.6 2.6E-06 5.5E-11 75.9 15.6 187 28-259 7-202 (211)
12 PRK07748 sporulation inhibitor 98.6 3.2E-06 7E-11 74.8 15.5 172 37-257 3-179 (207)
13 cd06130 DNA_pol_III_epsilon_li 98.5 4.3E-06 9.4E-11 69.5 14.1 150 40-252 1-155 (156)
14 PRK05711 DNA polymerase III su 98.5 5.6E-06 1.2E-10 75.4 15.7 168 38-257 4-175 (240)
15 TIGR00573 dnaq exonuclease, DN 98.4 1.6E-05 3.5E-10 70.9 15.2 169 35-258 4-177 (217)
16 PRK07740 hypothetical protein; 98.4 1.7E-05 3.6E-10 72.3 15.4 169 36-259 57-227 (244)
17 PRK06310 DNA polymerase III su 98.3 2.3E-05 4.9E-10 71.7 15.6 169 34-258 3-174 (250)
18 cd06127 DEDDh DEDDh 3'-5' exon 98.3 9.6E-06 2.1E-10 66.2 11.9 156 41-252 1-159 (159)
19 PRK06063 DNA polymerase III su 98.3 2.3E-05 5.1E-10 73.9 15.6 163 37-259 14-180 (313)
20 TIGR01406 dnaQ_proteo DNA poly 98.3 3E-05 6.5E-10 69.8 15.2 167 39-257 1-171 (225)
21 PRK09146 DNA polymerase III su 98.2 4.9E-05 1.1E-09 69.1 15.6 169 35-261 44-230 (239)
22 PRK06807 DNA polymerase III su 98.2 5.9E-05 1.3E-09 71.3 15.5 162 39-258 9-172 (313)
23 TIGR01298 RNaseT ribonuclease 98.2 8.8E-05 1.9E-09 65.5 15.2 179 36-259 6-193 (200)
24 PRK07247 DNA polymerase III su 98.2 4.6E-05 1E-09 67.3 13.2 159 39-257 6-168 (195)
25 cd06136 TREX1_2 DEDDh 3'-5' ex 98.1 6.8E-05 1.5E-09 64.8 13.6 169 40-253 1-176 (177)
26 PRK06195 DNA polymerase III su 98.1 8.9E-05 1.9E-09 69.7 15.1 160 39-259 2-165 (309)
27 PRK08517 DNA polymerase III su 98.0 0.00023 5.1E-09 65.4 15.9 166 35-258 65-231 (257)
28 PRK08074 bifunctional ATP-depe 98.0 0.00013 2.8E-09 78.0 16.3 166 38-259 3-170 (928)
29 PRK07246 bifunctional ATP-depe 98.0 0.00021 4.5E-09 75.6 16.7 162 37-259 6-171 (820)
30 PRK07883 hypothetical protein; 98.0 0.00018 3.9E-09 73.0 15.4 171 32-259 9-183 (557)
31 TIGR01405 polC_Gram_pos DNA po 98.0 0.00023 5E-09 77.8 16.9 168 36-260 188-357 (1213)
32 PRK06722 exonuclease; Provisio 97.9 0.00048 1E-08 64.3 15.9 169 37-255 4-178 (281)
33 TIGR01407 dinG_rel DnaQ family 97.9 0.00035 7.5E-09 74.1 16.3 164 39-259 1-166 (850)
34 PRK11779 sbcB exonuclease I; P 97.8 0.00057 1.2E-08 68.1 14.9 180 36-257 4-197 (476)
35 cd06138 ExoI_N N-terminal DEDD 97.8 0.00047 1E-08 59.8 12.5 165 42-250 2-181 (183)
36 PF00929 RNase_T: Exonuclease; 97.8 3.5E-05 7.6E-10 62.9 4.8 157 41-251 1-164 (164)
37 PRK07983 exodeoxyribonuclease 97.7 0.0012 2.6E-08 59.4 14.0 149 40-258 2-154 (219)
38 PRK05601 DNA polymerase III su 97.7 0.0013 2.9E-08 63.4 14.7 180 34-257 42-248 (377)
39 PRK06309 DNA polymerase III su 97.7 0.0017 3.8E-08 58.5 14.5 161 39-258 3-166 (232)
40 PTZ00315 2'-phosphotransferase 97.6 0.0022 4.8E-08 65.1 16.5 171 39-257 57-254 (582)
41 PRK09182 DNA polymerase III su 97.6 0.0012 2.6E-08 62.0 13.6 155 39-255 38-198 (294)
42 cd06144 REX4_like DEDDh 3'-5' 97.5 0.00075 1.6E-08 56.8 9.9 69 163-251 79-151 (152)
43 PRK00448 polC DNA polymerase I 97.5 0.0023 5E-08 71.1 15.0 168 35-259 416-585 (1437)
44 COG0847 DnaQ DNA polymerase II 97.3 0.0058 1.3E-07 54.8 13.4 165 38-257 13-181 (243)
45 cd06137 DEDDh_RNase DEDDh 3'-5 97.2 0.0047 1E-07 52.4 10.4 69 162-251 85-160 (161)
46 cd06145 REX1_like DEDDh 3'-5' 96.9 0.011 2.3E-07 49.8 9.9 98 130-251 48-149 (150)
47 PRK05359 oligoribonuclease; Pr 96.7 0.042 9.2E-07 47.8 12.7 171 37-261 2-178 (181)
48 cd06149 ISG20 DEDDh 3'-5' exon 96.6 0.017 3.7E-07 49.0 9.5 97 130-251 51-156 (157)
49 PF01612 DNA_pol_A_exo1: 3'-5' 95.7 0.29 6.3E-06 40.6 12.2 84 157-258 73-175 (176)
50 COG0349 Rnd Ribonuclease D [Tr 95.6 0.091 2E-06 50.7 9.7 90 145-259 60-167 (361)
51 cd06135 Orn DEDDh 3'-5' exonuc 95.2 0.49 1.1E-05 40.5 12.4 165 40-257 1-171 (173)
52 cd06146 mut-7_like_exo DEDDy 3 95.1 0.75 1.6E-05 40.2 13.2 89 157-256 78-193 (193)
53 cd06141 WRN_exo DEDDy 3'-5' ex 94.5 1 2.2E-05 37.9 12.3 80 159-255 71-169 (170)
54 PRK05755 DNA polymerase I; Pro 94.5 0.82 1.8E-05 49.1 14.3 84 159-259 368-470 (880)
55 PRK10829 ribonuclease D; Provi 94.4 1.4 3E-05 42.9 14.3 84 159-259 72-171 (373)
56 TIGR01388 rnd ribonuclease D. 91.6 10 0.00022 36.7 15.6 84 159-259 68-167 (367)
57 cd06129 RNaseD_like DEDDy 3'-5 91.3 5.6 0.00012 33.4 12.2 81 159-256 65-161 (161)
58 COG2176 PolC DNA polymerase II 84.0 4 8.6E-05 45.1 8.0 85 163-261 503-589 (1444)
59 PF13482 RNase_H_2: RNase_H su 83.3 0.6 1.3E-05 38.9 1.4 73 162-250 58-132 (164)
60 PF10108 DNA_pol_B_exo2: Predi 81.2 5.6 0.00012 35.7 6.8 93 161-257 52-172 (209)
61 cd06139 DNA_polA_I_Ecoli_like_ 73.9 16 0.00034 30.7 7.3 85 159-260 65-172 (193)
62 cd05782 DNA_polB_like1_exo Unc 63.0 7.6 0.00017 34.4 3.2 69 163-232 95-170 (208)
63 KOG2207 Predicted 3'-5' exonuc 60.3 31 0.00067 35.7 7.2 173 23-259 396-586 (617)
64 TIGR02841 spore_YyaC putative 56.6 11 0.00023 31.8 2.8 30 18-47 43-72 (140)
65 PF04405 ScdA_N: Domain of Unk 50.5 28 0.00061 24.6 3.7 33 120-152 12-53 (56)
66 COG5228 POP2 mRNA deadenylase 47.5 22 0.00047 32.6 3.4 99 167-278 197-298 (299)
67 cd00007 35EXOc 3'-5' exonuclea 43.0 1E+02 0.0023 24.2 6.6 53 159-228 52-106 (155)
68 PF06866 DUF1256: Protein of u 40.7 25 0.00054 30.4 2.6 31 18-48 67-97 (163)
69 COG3359 Predicted exonuclease 39.9 58 0.0013 30.3 5.0 76 163-253 158-237 (278)
70 PF13637 Ank_4: Ankyrin repeat 32.0 44 0.00096 22.3 2.4 29 120-148 13-41 (54)
71 cd06125 DnaQ_like_exo DnaQ-lik 31.9 88 0.0019 23.9 4.3 20 162-181 45-64 (96)
72 PF12345 DUF3641: Protein of u 28.0 59 0.0013 27.3 2.8 33 125-157 15-48 (134)
73 KOG1990 Poly(A)-specific exori 27.9 34 0.00073 35.2 1.7 142 14-169 102-261 (564)
74 COG5018 KapD Inhibitor of the 26.1 1E+02 0.0022 27.2 4.0 81 163-257 100-184 (210)
75 PF02671 PAH: Paired amphipath 23.0 68 0.0015 21.2 1.9 33 186-219 1-33 (47)
76 PF13606 Ank_3: Ankyrin repeat 22.9 69 0.0015 19.2 1.8 18 119-136 13-30 (30)
77 KOG2249 3'-5' exonuclease [Rep 21.8 46 0.00099 31.1 1.1 14 40-53 107-120 (280)
78 PRK05264 transcriptional repre 21.8 61 0.0013 25.5 1.7 16 175-190 61-76 (105)
79 PF04386 SspB: Stringent starv 21.3 53 0.0011 27.9 1.4 16 37-52 31-46 (155)
80 PF13857 Ank_5: Ankyrin repeat 21.0 94 0.002 21.1 2.4 29 120-148 28-56 (56)
81 TIGR01229 rocF_arginase argina 20.2 2E+02 0.0044 26.7 5.2 68 18-88 196-272 (300)
82 cd00490 Met_repressor_MetJ Met 20.1 69 0.0015 25.0 1.6 15 175-189 60-74 (103)
No 1
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=6.9e-93 Score=620.73 Aligned_cols=237 Identities=58% Similarity=0.937 Sum_probs=230.6
Q ss_pred eEEecCccCHHHHHHHHHHHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCC
Q 023614 15 LIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLP 94 (280)
Q Consensus 15 ~i~eVw~~Nl~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p 94 (280)
.|||||++|+++||++||++|++||||||||||||++.+|.+.|+++. +++|+.||+|||.+++||+|||++|++|++|
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 379999999999999999999999999999999999999999999887 9999999999999999999999999999999
Q ss_pred CCCCCCCceEEEEeccccCcCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHH
Q 023614 95 DLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFG 174 (280)
Q Consensus 95 ~~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~g 174 (280)
.+| ..+|||||++|++.+|+++++||+||+++||||.|++++||+..+|+|+|++||++++++|+||||||+||||
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 764 5799999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcc--ccchHHHHHHHcCCCccCCCccchhhhHHHHHHHHH
Q 023614 175 YLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC--LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFL 252 (280)
Q Consensus 175 yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~--l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~ 252 (280)
||+|+||+++||++.++|.+.++++||. +||+|||++.|.+ +++||++||+.|+|+| +|++|||||||+||+.+|+
T Consensus 156 YLlK~Lt~~~LP~~~~eF~~~v~~~fp~-vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~R-vG~~HqAGSDSlLT~~~F~ 233 (239)
T KOG0304|consen 156 YLLKILTGKPLPETEEEFFEIVRQLFPF-VYDVKYLMKFCEGLSLKGGLQRLADLLGLKR-VGIAHQAGSDSLLTARVFF 233 (239)
T ss_pred HHHHHHcCCCCcchHHHHHHHHHHHcch-hhhHHHHHHhhhhhhhhcCHHHHHHHhCCCe-eecccccCcHHHHHHHHHH
Confidence 9999999999999999999999999999 9999999999965 8999999999999999 9999999999999999999
Q ss_pred HHHHhh
Q 023614 253 KIKDKH 258 (280)
Q Consensus 253 ~l~~~~ 258 (280)
||++.|
T Consensus 234 kl~~~f 239 (239)
T KOG0304|consen 234 KLKELF 239 (239)
T ss_pred HHHhcC
Confidence 999864
No 2
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=2.5e-81 Score=549.10 Aligned_cols=258 Identities=44% Similarity=0.741 Sum_probs=241.6
Q ss_pred CCCCCceEEecCccCHHHHHHHHHHHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeecc
Q 023614 9 PPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSD 88 (280)
Q Consensus 9 ~~~~~~~i~eVw~~Nl~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~ 88 (280)
++..-..||+||++||..||+.|+++|++|++|+|||||||+++||.|.|+++. +++||.||+|||.++|||+||+++|
T Consensus 13 dg~~~~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPiG~FkSs~-dyhYQtlraNVD~LkiIQlGlsLSD 91 (299)
T COG5228 13 DGPNYLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSV-DYHYQTLRANVDFLKIIQLGLSLSD 91 (299)
T ss_pred CCcchHHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceeecccccccccc-hHHHHHHhcccchhhhhheeeeecc
Confidence 444456799999999999999999999999999999999999999999999998 9999999999999999999999999
Q ss_pred CCCCCCCCCCCCCceEEEEeccccCcCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEec
Q 023614 89 EEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFH 168 (280)
Q Consensus 89 ~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfh 168 (280)
++|+.|.+ .+||||||- |++.+||++++||++|+++||||.||.+.||++.+|+|+|+.||||+.++|+|||||
T Consensus 92 e~GN~P~~-----~sTWQFNF~-F~l~~dmya~ESieLL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~VtWitfH 165 (299)
T COG5228 92 ENGNKPNG-----PSTWQFNFE-FDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFH 165 (299)
T ss_pred ccCCCCCC-----CceeEEEEE-ecchhhhcchHHHHHHHHcCCChhhHhhcCCCHHHHHHHHhccCceeccceEEEEee
Confidence 99999963 799999999 999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhccccchHHHHHHHcCCCccCCCccchhhhHHHHH
Q 023614 169 SAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTL 248 (280)
Q Consensus 169 g~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~ 248 (280)
++||||||+|+||+.|||+.+++|...|++|||. .||+|++.+....++.||++++..|++.| .|.+||||+||++|+
T Consensus 166 saYDfgyLikilt~~plP~~~EdFy~~l~~yfP~-fYDik~v~ks~~~~~KglQei~ndlql~r-~g~QhQagsdaLlTa 243 (299)
T COG5228 166 SAYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPN-FYDIKLVYKSVLNNSKGLQEIKNDLQLQR-SGQQHQAGSDALLTA 243 (299)
T ss_pred cchhHHHHHHHHhcCCCCccHHHHHHHHHHHCcc-ccchHHHHHhhhhhhhHHHHhcCcHhhhc-cchhhhccchhhhhh
Confidence 9999999999999999999999999999999999 99999999999889999999999999999 999999999999999
Q ss_pred HHHHHHHHhhCCCccccccccceEecCC
Q 023614 249 HAFLKIKDKHFGNEYELQKYANVLHGLE 276 (280)
Q Consensus 249 ~~F~~l~~~~~~~~~~~~~~~g~i~Gl~ 276 (280)
..|++.|.++|..+++ ...-..|||++
T Consensus 244 ~~ff~~R~~~F~~sig-~~ll~~L~g~~ 270 (299)
T COG5228 244 DEFFLPRFSIFTTSIG-QSLLMLLSGCQ 270 (299)
T ss_pred HHhcchhhheeccccc-HHHHHHHhccc
Confidence 9999999998865532 33333444443
No 3
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=100.00 E-value=1.9e-62 Score=448.65 Aligned_cols=229 Identities=35% Similarity=0.579 Sum_probs=199.3
Q ss_pred EecCccCHHHHHHHHHHHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeec-cCCCCCCC
Q 023614 17 REVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLS-DEEGNLPD 95 (280)
Q Consensus 17 ~eVw~~Nl~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~-~~~g~~p~ 95 (280)
+|||++||+++++.|+++|++|+|||||+||||+..++......+. ++||+++|.||+.+.+||+|||+| +++++.|.
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 6999999999999999999999999999999999998865444555 999999999999999999999999 78888775
Q ss_pred CCCCCCceEEEEeccccCcCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHH------HHHHHcccccC---CCceEEE
Q 023614 96 LGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFA------ELLMSSGLVLN---KDVTWVT 166 (280)
Q Consensus 96 ~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~------e~l~~Sglv~~---~~v~Wvt 166 (280)
.+.+|+|||+.|+.+++.++++||+||++|||||||+.++||+|..++ +.+..++++.. .++.||+
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 478999999999999998899999999999999999999999999999 66777888753 3589999
Q ss_pred eccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhccccchHHHHHHHcCCCc--------------
Q 023614 167 FHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVER-------------- 232 (280)
Q Consensus 167 fhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~L~v~r-------------- 232 (280)
++|.||++||++.++| |||+|+++|++.++.+||. |||||||++.+....++|+.|++.|++.|
T Consensus 155 hn~~~Dl~~l~~~f~~-~LP~t~~eF~~~~~~~FP~-i~DtK~la~~~~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~ 232 (262)
T PF04857_consen 155 HNGLYDLMYLYKKFIG-PLPETLEEFKELLRELFPR-IYDTKYLAEECPGKSTSLQELAEELGIRRNPSSISSPEGFPSY 232 (262)
T ss_dssp SSTHHHHHHHHHHHTT-S--SSHHHHHHHHHHHSSS-EEEHHHHHTSTTTS-SSHHHHHHHTTSTT----EEE-TTS---
T ss_pred eChHhHHHHHHHHhcC-CCCCCHHHHHHHHHHHCcc-cccHHHHHHhccccccCHHHHHHHhCCCccccccccccccccc
Confidence 9999999999999998 9999999999999999999 99999999999877889999999999887
Q ss_pred --------cCCC-ccchhhhHHHHHHHHHH
Q 023614 233 --------VVGK-SHQAGSDSLLTLHAFLK 253 (280)
Q Consensus 233 --------~~g~-~hqAGsDs~lT~~~F~~ 253 (280)
..|. .|+||+|||||+.||+|
T Consensus 233 ~~~~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 233 DEEKNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp ----------SS-TTSHHHHHHHHHHHHHH
T ss_pred cccccccccCCCCCCCcchHHHHHHHHHcC
Confidence 2455 99999999999999986
No 4
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=98.95 E-value=3.3e-08 Score=89.28 Aligned_cols=171 Identities=20% Similarity=0.263 Sum_probs=118.5
Q ss_pred hhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcC
Q 023614 36 DRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIA 115 (280)
Q Consensus 36 ~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~ 115 (280)
.+.+||++|+|-||+... . =.|||+|+..++.+|+.. -.|+.. .+..
T Consensus 4 ~~~~~vv~D~ETTGl~p~-------~---------------d~Iieig~v~v~~~g~~~----------~~~~~l-v~P~ 50 (232)
T PRK07942 4 HPGPLAAFDLETTGVDPE-------T---------------ARIVTAALVVVDADGEVV----------ESREWL-ADPG 50 (232)
T ss_pred ccCcEEEEEeccCCCCCC-------C---------------CeeEEEEEEEEeCCCccc----------cceEEE-ECCC
Confidence 456899999999998321 0 138999999998767542 123333 3333
Q ss_pred cCCCchhHHHHHHHcCCCchhhhhcCCChHH----HHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHH
Q 023614 116 RHAHALDSVELLKRQGIDFEKNREFGIDSVR----FAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSE 191 (280)
Q Consensus 116 ~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~----f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~ 191 (280)
. ...+++.+. |||.=..+..+|.+... |.+.+.. .. ..+..+|+++..||+++|-+-+...-+|.-
T Consensus 51 ~-~i~~~a~~I---hGIt~e~l~~~g~~~~~vl~e~~~~l~~--~~-~~~~~lVahNa~FD~~fL~~~~~r~~~~~~--- 120 (232)
T PRK07942 51 V-EIPEEASAV---HGITTEYARAHGRPAAEVLAEIADALRE--AW-ARGVPVVVFNAPYDLTVLDRELRRHGLPSL--- 120 (232)
T ss_pred C-CCCHHHHHH---hCCCHHHHHhhCCCHHHHHHHHHHHHHH--Hh-hcCCEEEEeCcHhhHHHHHHHHHHcCCCCc---
Confidence 2 356666666 99999999999998643 3333221 11 224478999999999999877753222211
Q ss_pred HHHHHhhhcCCCccchHHHHHhhccc---cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 192 FVTRVGVFFGEKVYDVKHLIRFCTCL---YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 192 F~~~l~~~Fp~~iyD~K~la~~~~~l---~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
.+..++|+-.|++.+... +..|+.+++.+|++. . .+|.|-+|++.|+++|.+|.+.+.
T Consensus 121 --------~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~-~-~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 121 --------VPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRL-D-NAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred --------cCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCC-C-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 222267888887765332 246999999999986 3 479999999999999999988774
No 5
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.93 E-value=9.7e-08 Score=80.03 Aligned_cols=164 Identities=20% Similarity=0.210 Sum_probs=115.2
Q ss_pred CeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCC
Q 023614 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (280)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~ 118 (280)
.||++|+|.+|+... .-.|||+|....+.+. ....||.+ ... ...
T Consensus 1 ~~v~~D~Ettg~~~~----------------------~~~Iieig~v~~~~~~-----------~~~~f~~~-v~p-~~~ 45 (169)
T smart00479 1 TLVVIDCETTGLDPG----------------------KDEIIEIAAVDVDGGR-----------IIVVFDTY-VKP-DRP 45 (169)
T ss_pred CEEEEEeeCCCCCCC----------------------CCeEEEEEEEEEECCE-----------eEEEEEEE-ECC-CCC
Confidence 489999999997421 1239999988877642 23457766 444 223
Q ss_pred CchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEecc-chhHHHHHHHhhC--CCCCCCHHHHHHH
Q 023614 119 HALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHS-AYDFGYLVKCLTQ--RVLPEKLSEFVTR 195 (280)
Q Consensus 119 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg-~yD~gyL~k~l~~--~~LP~~~~~F~~~ 195 (280)
.++.+.+ -+||.-+.+.. |.++....+.+.. .+ .+. .+|++|+ .+|+.+|-+.+.. .+.|.
T Consensus 46 i~~~~~~---~~Git~~~l~~-~~~~~~~~~~~~~--~l-~~~-~~v~~n~~~fD~~~L~~~~~~~~~~~~~-------- 109 (169)
T smart00479 46 ITDYATE---IHGITPEMLDD-APTFEEVLEELLE--FL-KGK-ILVAGNALNFDLRFLKLEHPRLGIKDPP-------- 109 (169)
T ss_pred CCHHHHH---HhCCCHHHHhC-CCCHHHHHHHHHH--Hh-cCC-EEEEeCCHHHhHHHHHHHHHHhCCCCCc--------
Confidence 4454444 47998888765 8888765554432 22 222 5788999 8999999887753 33331
Q ss_pred HhhhcCCCccchHHHHHhhc-cccchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 196 VGVFFGEKVYDVKHLIRFCT-CLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 196 l~~~Fp~~iyD~K~la~~~~-~l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
+..+.|+.-+++... ....+|+.+++.++++. .+..|.|-.|+..|+++|.+|.+..+
T Consensus 110 -----~~~~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~-~~~~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 110 -----KNPVIDTLKLARALNPGRKYSLKKLAERLGLEV-IGRAHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred -----CCCeeEHHHHHHHHCCCCCCCHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHHHHHHHHhh
Confidence 122678877776542 23578999999999998 78789999999999999999987653
No 6
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=98.90 E-value=8.7e-10 Score=111.21 Aligned_cols=234 Identities=19% Similarity=0.208 Sum_probs=154.1
Q ss_pred ccCHHHHHHHHHHHhhhCCeeEeeeccccccccCCC--CCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCC-C
Q 023614 21 EFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDS--NIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDL-G 97 (280)
Q Consensus 21 ~~Nl~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~--~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~-~ 97 (280)
+.|++. +.+++..|+++.|+++|.|++|+...+.. .--.+. +.+|+++|.|+-.+.++|+|+|.|..++.-... .
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 468888 99999999999999999999999888732 112344 999999999999999999999999876643211 0
Q ss_pred CCCCceEEEEeccccCcCcCCCchhHHHHHHHcCCCchhh-----------hhcCCChH-----------H---------
Q 023614 98 SGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKN-----------REFGIDSV-----------R--------- 146 (280)
Q Consensus 98 ~~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~-----------~~~GI~~~-----------~--------- 146 (280)
++++..+|..-+. ....+.+|+..++.++.+++-++..- -..|+.+. .
T Consensus 79 ~~~n~~~~~~g~~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i 157 (564)
T KOG1990|consen 79 TGGNFVVWSRGDS-ISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKI 157 (564)
T ss_pred CCCceeeeecCcc-ccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhh
Confidence 1113456664333 23335688888998888872111110 01111111 0
Q ss_pred ------------------------------------------------------------HHHHHHHccc----------
Q 023614 147 ------------------------------------------------------------FAELLMSSGL---------- 156 (280)
Q Consensus 147 ------------------------------------------------------------f~e~l~~Sgl---------- 156 (280)
|+..+...|.
T Consensus 158 ~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~ 237 (564)
T KOG1990|consen 158 PDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMAD 237 (564)
T ss_pred hcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHH
Confidence 1111111221
Q ss_pred ----ccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhh--cc--ccchHHHHHHH-
Q 023614 157 ----VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFC--TC--LYGGLDRVCKA- 227 (280)
Q Consensus 157 ----v~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~--~~--l~~~L~~la~~- 227 (280)
+......-|...+.+|+.|+.|-+.+ +||+++++|.+. ...||. ++|++.++... .. +.+.+.+.+..
T Consensus 238 ~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~-~~~fp~-~~~~~~~~~~~~~~~~~~~~t~~e~~~~~ 314 (564)
T KOG1990|consen 238 ELQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDS-SSMFPN-IEDTKRLAKLSEYQKLNLKATLLELARAK 314 (564)
T ss_pred HHHHHHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhh-hhhhhh-hHHHHHhhccccccchhhhhhHHHHHHHh
Confidence 11112233445567899999999998 999999999999 999999 99999888822 22 44444444331
Q ss_pred cC----CCc--------------cCCCccchhhhHHHHHHHHHHHHHhhCC
Q 023614 228 LG----VER--------------VVGKSHQAGSDSLLTLHAFLKIKDKHFG 260 (280)
Q Consensus 228 L~----v~r--------------~~g~~hqAGsDs~lT~~~F~~l~~~~~~ 260 (280)
.. +++ .....|+++++++.++.++.+.-+....
T Consensus 315 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 365 (564)
T KOG1990|consen 315 AKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILA 365 (564)
T ss_pred cccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhh
Confidence 11 111 1345689999999999999998777553
No 7
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=98.70 E-value=8e-07 Score=75.30 Aligned_cols=171 Identities=18% Similarity=0.158 Sum_probs=110.7
Q ss_pred eeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCc-CC
Q 023614 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR-HA 118 (280)
Q Consensus 40 fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~-d~ 118 (280)
||.+|+|.+|...... . + ..-.|||+|....+.++.. ..-.|+.+ ..... ..
T Consensus 1 ~vv~D~Ettg~~~~~~---~-~-------------~~~~IieIgav~v~~~~~~---------~~~~f~~~-i~P~~~~~ 53 (176)
T cd06133 1 YLVIDFEATCWEGNSK---P-D-------------YPNEIIEIGAVLVDVKTKE---------IIDTFSSY-VKPVINPK 53 (176)
T ss_pred CEEEEeeccccCCCCC---C-C-------------CCcceEEEEEEEEEcCCCe---------EEeeeeee-ECCCcCCc
Confidence 7999999999854321 0 0 0114999999999887642 23345555 33333 35
Q ss_pred CchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCC-CceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHh
Q 023614 119 HALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNK-DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVG 197 (280)
Q Consensus 119 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~-~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~ 197 (280)
.++.+.+. +||..+.+. ++.++..-.+.+.. .+.+. ....+++ |.+|...+.+......... ..
T Consensus 54 i~~~~~~i---~gIt~e~l~-~~~~~~~vl~~~~~--~l~~~~~~~~v~~-~~~d~~~l~~~~~~~~~~~--------~~ 118 (176)
T cd06133 54 LSDFCTEL---TGITQEDVD-NAPSFPEVLKEFLE--WLGKNGKYAFVTW-GDWDLKDLLQNQCKYKIIN--------LP 118 (176)
T ss_pred hhHHHHHh---cCcCHHHHh-cCCCHHHHHHHHHH--HHHhCCCeEEEee-cHhhHHHHHHHHHHhcCCC--------Cc
Confidence 66666666 999999985 55776643332221 11111 2344444 6789887776544211100 01
Q ss_pred hhcCCCccchHHHHHhhccc--cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHH
Q 023614 198 VFFGEKVYDVKHLIRFCTCL--YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKI 254 (280)
Q Consensus 198 ~~Fp~~iyD~K~la~~~~~l--~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l 254 (280)
.++.. .+|++.+++...+. ..+|.++++.+|++. .+..|.|=+|+..|+++|.+|
T Consensus 119 ~~~~~-~~D~~~~~~~~~~~~~~~~L~~l~~~~gi~~-~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 119 PFFRQ-WIDLKKEFAKFYGLKKRTGLSKALEYLGLEF-EGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred ccccc-eEEHHHHHHHHhCCCCCCCHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHHHHh
Confidence 12334 88999888876543 568999999999999 688999999999999999987
No 8
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.69 E-value=8e-07 Score=78.26 Aligned_cols=168 Identities=15% Similarity=0.205 Sum_probs=107.5
Q ss_pred HHHHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEecc
Q 023614 31 IRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFK 110 (280)
Q Consensus 31 I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~ 110 (280)
+.+.....+||++|+|-+|+... .-.|||+|...++.+... ....|.++
T Consensus 22 ~~~~~~~~~~vviD~ETTGl~~~----------------------~d~IieIgaV~~~~~~~~---------~~~~f~~~ 70 (202)
T PRK09145 22 LFEPPPPDEWVALDCETTGLDPR----------------------RAEIVSIAAVKIRGNRIL---------TSERLELL 70 (202)
T ss_pred HhcCCCCCCEEEEEeECCCCCCC----------------------CCceEEEEEEEEECCEEe---------ecCceEEE
Confidence 33333456999999999997321 013899999888743211 12235454
Q ss_pred ccCcCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhh---CCCCCC
Q 023614 111 DFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLT---QRVLPE 187 (280)
Q Consensus 111 ~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~---~~~LP~ 187 (280)
..... ...+.+.++ ||+.-+.+. +|.+.....+.+.. .+ . +-.||+++..||..+|-+-+. +.++|.
T Consensus 71 -i~p~~-~i~~~~~~i---hGIt~~~l~-~~~~~~~vl~~~~~--~i-~-~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~ 140 (202)
T PRK09145 71 -VRPPQ-SLSAESIKI---HRLRHQDLE-DGLSEEEALRQLLA--FI-G-NRPLVGYYLEFDVAMLNRYVRPLLGIPLPN 140 (202)
T ss_pred -ECCCC-CCCHhHhhh---cCcCHHHHh-cCCCHHHHHHHHHH--HH-c-CCeEEEeCHHHHHHHHHHHHHHhcCCCCCC
Confidence 34432 345566554 888777664 67776654433332 11 1 236899888999999876553 445553
Q ss_pred CHHHHHHHHhhhcCCCccchHHHHHhh-----cc-c-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHH
Q 023614 188 KLSEFVTRVGVFFGEKVYDVKHLIRFC-----TC-L-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKD 256 (280)
Q Consensus 188 ~~~~F~~~l~~~Fp~~iyD~K~la~~~-----~~-l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~ 256 (280)
. .+|+..+.... +. . .-+|+.+++.+|++. .+ .|.|-+|++.|+.+|.+|++
T Consensus 141 ~---------------~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~-~~-~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 141 P---------------LIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPV-LG-RHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred C---------------eeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCC-CC-CCCcHHHHHHHHHHHHHHHh
Confidence 2 55665443211 11 1 348999999999987 44 69999999999999999865
No 9
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=98.67 E-value=1.2e-06 Score=74.12 Aligned_cols=164 Identities=23% Similarity=0.246 Sum_probs=106.4
Q ss_pred eeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCCC
Q 023614 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAH 119 (280)
Q Consensus 40 fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~ 119 (280)
||++|+|-||+... . .-.|||+|....+. +.. ...+|+.. ..... ..
T Consensus 1 ~v~~D~ETTGl~~~-------~--------------~~~iieig~v~v~~-~~~---------~~~~~~~~-v~P~~-~i 47 (167)
T cd06131 1 QIVLDTETTGLDPR-------E--------------GHRIIEIGCVELIN-RRL---------TGNTFHVY-INPER-DI 47 (167)
T ss_pred CEEEEeeCCCCCCC-------C--------------CCeEEEEEEEEEEC-CcE---------eccEEEEE-ECCCC-CC
Confidence 79999999998320 0 11499999887654 221 22356665 44433 35
Q ss_pred chhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhh
Q 023614 120 ALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVF 199 (280)
Q Consensus 120 ~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~ 199 (280)
++.+.+. |||.=+.+...+ +.....+.|.. .+ .+ -.+|.+++.||..+|-+-+....++.. ..
T Consensus 48 ~~~~~~i---hGIt~e~l~~~~-~~~~v~~~l~~--~l-~~-~~lv~hn~~fD~~~l~~~~~~~~~~~~---------~~ 110 (167)
T cd06131 48 PEEAFKV---HGITDEFLADKP-KFAEIADEFLD--FI-RG-AELVIHNASFDVGFLNAELSLLGLGKK---------II 110 (167)
T ss_pred CHHHHHH---hCCCHHHHhcCC-CHHHHHHHHHH--HH-CC-CeEEEeChHHhHHHHHHHHHHhCCCcc---------cc
Confidence 6666654 788877765543 34333333332 12 22 358999999999999777653212111 01
Q ss_pred cCCCccchHHHHHhhc-cccchHHHHHHHcCCCccCC-CccchhhhHHHHHHHHHHH
Q 023614 200 FGEKVYDVKHLIRFCT-CLYGGLDRVCKALGVERVVG-KSHQAGSDSLLTLHAFLKI 254 (280)
Q Consensus 200 Fp~~iyD~K~la~~~~-~l~~~L~~la~~L~v~r~~g-~~hqAGsDs~lT~~~F~~l 254 (280)
.|...+||-.+++... ....+|+.+++.+|++. .+ .+|.|-+|++.|+.+|.+|
T Consensus 111 ~~~~~idt~~~~~~~~~~~~~~L~~l~~~~~i~~-~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 111 DFCRVIDTLALARKKFPGKPNSLDALCKRFGIDN-SHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred cCCCceEhHHHHHHHcCCCCCCHHHHHHHCCCCC-CCCCCCChHHHHHHHHHHHHHh
Confidence 2334789877776542 34568999999999998 55 4799999999999999987
No 10
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=98.66 E-value=7.7e-07 Score=77.84 Aligned_cols=177 Identities=20% Similarity=0.258 Sum_probs=115.2
Q ss_pred hCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccC--CCCCCCCCCCCCceEEEEeccccCc
Q 023614 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDE--EGNLPDLGSGSTYYIWEFNFKDFDI 114 (280)
Q Consensus 37 ~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~--~g~~p~~~~~~~~~~wqFNF~~F~~ 114 (280)
.+.+|++|+|-||+.... + .|||+|...++. +|... ..-+|++. ++.
T Consensus 4 ~~~~vv~D~ETTGl~~~~---------d-------------~Iieigav~v~~~~~~~i~--------~~~~f~~l-v~P 52 (189)
T cd06134 4 GFLPVVVDVETGGFNPQT---------D-------------ALLEIAAVTLEMDEQGNLY--------PDETFHFH-ILP 52 (189)
T ss_pred cceeEEEEecCCCCCCCC---------C-------------eEEEEEEEEEEECCCCcee--------ccceEEEE-EcC
Confidence 467899999999985321 1 289999998864 34321 22345555 444
Q ss_pred C-cCCCchhHHHHHHHcCCCchhhhhcCCChHH-HHHHHHHcc-ccc---CCCceEEEeccchhHHHHHHHhhCCCCCCC
Q 023614 115 A-RHAHALDSVELLKRQGIDFEKNREFGIDSVR-FAELLMSSG-LVL---NKDVTWVTFHSAYDFGYLVKCLTQRVLPEK 188 (280)
Q Consensus 115 ~-~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~-f~e~l~~Sg-lv~---~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~ 188 (280)
. .....+++++. |||.=+...+.|++... +.+.+-.-+ ++. ..+-.+|++|..+|++||-+.+....++.
T Consensus 53 ~~~~~i~~~~~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~- 128 (189)
T cd06134 53 FEGANLDPAALEF---NGIDPFHPFRFAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKR- 128 (189)
T ss_pred CCCCCCCHHHHhh---cCCCchhhhccccchHHHHHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCC-
Confidence 2 23466666666 99986666777886543 333221100 110 11347999999999999988775211110
Q ss_pred HHHHHHHHhhhcCCCccchHHHHHhhccccchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHh
Q 023614 189 LSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 257 (280)
Q Consensus 189 ~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~ 257 (280)
..+-|...+||..|++...+ ...|+.+++.+|++......|.|-+|++.|+++|.+|.++
T Consensus 129 --------~~~~~~~~lDt~~la~~~~~-~~~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 129 --------NPFHPFSTFDTATLAGLAYG-QTVLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred --------CCCCCCcEEEHHHHHHHHhC-CCcHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 00112237899999886633 2369999999999852246799999999999999999875
No 11
>PRK05168 ribonuclease T; Provisional
Probab=98.58 E-value=2.6e-06 Score=75.90 Aligned_cols=187 Identities=16% Similarity=0.216 Sum_probs=123.1
Q ss_pred HHHHHHHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccC--CCCCCCCCCCCCceEE
Q 023614 28 FERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDE--EGNLPDLGSGSTYYIW 105 (280)
Q Consensus 28 ~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~--~g~~p~~~~~~~~~~w 105 (280)
+.-|..-++...||++|+|-+|+.... + .|||+|....+. +|... ...
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~---------d-------------~IieIgaV~v~~d~~g~i~--------~~~ 56 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKT---------D-------------ALLEIAAVTLKMDEQGWLY--------PDE 56 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCC---------C-------------EEEEEeEEEEEecCCCcEe--------ccc
Confidence 345777788999999999999985321 1 299999887754 45421 223
Q ss_pred EEeccccCcC-cCCCchhHHHHHHHcCCCchhhhhcCCChHH-HHHHHHHcc-ccc---CCCceEEEeccchhHHHHHHH
Q 023614 106 EFNFKDFDIA-RHAHALDSVELLKRQGIDFEKNREFGIDSVR-FAELLMSSG-LVL---NKDVTWVTFHSAYDFGYLVKC 179 (280)
Q Consensus 106 qFNF~~F~~~-~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~-f~e~l~~Sg-lv~---~~~v~Wvtfhg~yD~gyL~k~ 179 (280)
.|..+ .... .-...+++++. |||.=+...+.|++... +.+.+..-+ .+. .++..+|+++-.+|++||-+-
T Consensus 57 ~f~~l-v~P~~~~~i~~~~~~i---hGIt~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~ 132 (211)
T PRK05168 57 TLHFH-VEPFEGANLEPEALAF---NGIDPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAA 132 (211)
T ss_pred eEEEE-ECCCCCCCCCHHHHhh---cCCCchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHH
Confidence 45555 4442 23466666665 99965556677887543 233222110 110 124579999999999999777
Q ss_pred hhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhccccchHHHHHHHcCCCccCC-CccchhhhHHHHHHHHHHHHHhh
Q 023614 180 LTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVG-KSHQAGSDSLLTLHAFLKIKDKH 258 (280)
Q Consensus 180 l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~L~v~r~~g-~~hqAGsDs~lT~~~F~~l~~~~ 258 (280)
+....+.. ..+.|..++||.-|++...+. ..|..+++.+|++- .+ ..|.|-+|++.|+++|.+|.+.+
T Consensus 133 ~~r~~~~~---------~~~~~~~~iDt~~lar~~~~~-~~L~~l~~~~gl~~-~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 133 AERAGLKR---------NPFHPFSTFDTATLSGLALGQ-TVLAKACQAAGIEF-DNKEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred HHHhCCCC---------CCCCCCcEeeHHHHHHHHcCC-CCHHHHHHHCCCCC-CCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 64211110 012332378999998765332 36999999999985 33 58999999999999999998876
Q ss_pred C
Q 023614 259 F 259 (280)
Q Consensus 259 ~ 259 (280)
-
T Consensus 202 ~ 202 (211)
T PRK05168 202 K 202 (211)
T ss_pred H
Confidence 3
No 12
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=98.56 E-value=3.2e-06 Score=74.82 Aligned_cols=172 Identities=19% Similarity=0.139 Sum_probs=107.5
Q ss_pred hCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCc
Q 023614 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (280)
Q Consensus 37 ~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~ 116 (280)
+-+||++|+|.+|...+.. + +... + .|||+|....+. |+. .-.|+-+ ..+..
T Consensus 3 ~~~~vvlD~EtTg~~~~~~-----~--~~~~-------~--eIIeIGaV~v~~-~~i----------~~~f~~l-V~P~~ 54 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKK-----P--KGFF-------P--EIIEVGLVSVVG-CEV----------EDTFSSY-VKPKT 54 (207)
T ss_pred cceEEEEEeecCCcCCCCC-----C--CCCC-------C--ceEEEeEEEEec-CcC----------hhhhcce-ECCCc
Confidence 4579999999999743211 0 1000 1 399999988863 332 1123333 22222
Q ss_pred C-CCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhh--CCCCCCCHHHHH
Q 023614 117 H-AHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFV 193 (280)
Q Consensus 117 d-~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~--~~~LP~~~~~F~ 193 (280)
. ..++.+.++ +||.=+.+. .|.+.....+.|.. .+.+....++ .|+.+|+++|-+-+. |-+.|.
T Consensus 55 ~~~i~~~~~~l---tGIt~~~l~-~ap~~~evl~~f~~--~~~~~~~~iv-~~~~fD~~fL~~~~~~~~~~~~~------ 121 (207)
T PRK07748 55 FPSLTERCKSF---LGITQEDVD-KGISFEELVEKLAE--YDKRCKPTIV-TWGNMDMKVLKHNCEKAGVPFPF------ 121 (207)
T ss_pred cCccChhhhhh---cCcCHHHHc-cCCCHHHHHHHHHH--HhCcCCeEEE-EECHHHHHHHHHHHHHcCCCCcc------
Confidence 1 345555555 888877764 68887665444433 2212133455 468899999988775 223331
Q ss_pred HHHhhhcCCCccchHHHHHhhcc--ccchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHh
Q 023614 194 TRVGVFFGEKVYDVKHLIRFCTC--LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 257 (280)
Q Consensus 194 ~~l~~~Fp~~iyD~K~la~~~~~--l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~ 257 (280)
+.. ..|+..+.+.... -..+|..+++.+|++. .+..|.|-+||+.|+.+|.+|.+.
T Consensus 122 ------~~~-~~dl~~~~~~~~~~~~~~~L~~~~~~~gi~~-~~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 122 ------KGQ-CRDLSLEYKKFFGERNQTGLWKAIEEYGKEG-TGKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred ------ccc-ceeHHHHHHHHhCcCCCCCHHHHHHHcCCCC-CCCCcChHHHHHHHHHHHHHHHhC
Confidence 122 5566555443322 1358999999999998 788999999999999999998876
No 13
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=98.50 E-value=4.3e-06 Score=69.53 Aligned_cols=150 Identities=20% Similarity=0.198 Sum_probs=100.7
Q ss_pred eeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCCC
Q 023614 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAH 119 (280)
Q Consensus 40 fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~ 119 (280)
||++|+|-+|.. + + .|||+|...++. |+ ..-+|+.+ +.... ..
T Consensus 1 ~v~~D~Ettg~~---------~--~-------------~ii~ig~v~~~~-~~----------~~~~~~~~-i~p~~-~~ 43 (156)
T cd06130 1 FVAIDFETANAD---------R--A-------------SACSIGLVKVRD-GQ----------IVDTFYTL-IRPPT-RF 43 (156)
T ss_pred CEEEEEeCCCCC---------C--C-------------ceEEEEEEEEEC-CE----------EEEEEEEE-eCcCC-CC
Confidence 799999999731 1 1 279999988863 32 23456666 44433 44
Q ss_pred chhHHHHHHHcCCCchhhhhcCCChHH-HHHHHHHcccccCCCceEEEeccchhHHHHHHHhhC--CCCCCCHHHHHHHH
Q 023614 120 ALDSVELLKRQGIDFEKNREFGIDSVR-FAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQ--RVLPEKLSEFVTRV 196 (280)
Q Consensus 120 ~~~Si~fL~~~G~DF~k~~~~GI~~~~-f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~--~~LP~~~~~F~~~l 196 (280)
.+++.++ +||.-..+.. +.++.. +.+++.- + + +..||+++..+|+++|-+.+-. .+.|
T Consensus 44 ~~~~~~i---~GIt~e~l~~-~~~~~~v~~~l~~~---l-~-~~~lv~hn~~fD~~~l~~~~~~~g~~~~---------- 104 (156)
T cd06130 44 DPFNIAI---HGITPEDVAD-APTFPEVWPEIKPF---L-G-GSLVVAHNASFDRSVLRAALEAYGLPPP---------- 104 (156)
T ss_pred Chhhccc---cCcCHHHHhc-CCCHHHHHHHHHHH---h-C-CCEEEEeChHHhHHHHHHHHHHcCCCCC----------
Confidence 5555544 9998888764 444433 3333221 1 2 2478999999999999877753 2222
Q ss_pred hhhcCCCccchHHHHHhh-ccc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHH
Q 023614 197 GVFFGEKVYDVKHLIRFC-TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFL 252 (280)
Q Consensus 197 ~~~Fp~~iyD~K~la~~~-~~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~ 252 (280)
+...+|+.-+++.. +.+ ..+|+.+++.+|++. . .|.|-+|++.|+++|.
T Consensus 105 ----~~~~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~-~--~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 105 ----PYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIEL-N--HHDALEDARACAEILL 155 (156)
T ss_pred ----CCCEEEHHHHHHHHhccCCCCCHHHHHHHcCCCc-c--CcCchHHHHHHHHHHh
Confidence 22277887776654 233 357999999999987 4 8999999999999885
No 14
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=98.50 E-value=5.6e-06 Score=75.41 Aligned_cols=168 Identities=19% Similarity=0.260 Sum_probs=112.0
Q ss_pred CCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcC
Q 023614 38 YPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH 117 (280)
Q Consensus 38 ~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d 117 (280)
-.||++|||-||+.... .=.|||+|...... +. .....|+.+ .+..+
T Consensus 4 ~r~vvlDtETTGldp~~---------------------~drIIEIGaV~v~~-~~---------~~~~~f~~~-i~P~~- 50 (240)
T PRK05711 4 MRQIVLDTETTGLNQRE---------------------GHRIIEIGAVELIN-RR---------LTGRNFHVY-IKPDR- 50 (240)
T ss_pred CeEEEEEeeCCCcCCCC---------------------CCeEEEEEEEEEEC-CE---------EeccEEEEE-ECcCC-
Confidence 47999999999984210 11499999876542 22 122346666 55533
Q ss_pred CCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhh--CCCCCCCHHHHHHH
Q 023614 118 AHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVTR 195 (280)
Q Consensus 118 ~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~--~~~LP~~~~~F~~~ 195 (280)
...+++++. |||.-+.+.. +-++....+.+.. .+ . +-.+|.++..||++||-+-+- |.++|...
T Consensus 51 ~i~~~a~~V---HGIT~e~l~~-~p~f~ev~~~f~~--fi-~-~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~------ 116 (240)
T PRK05711 51 LVDPEALAV---HGITDEFLAD-KPTFAEVADEFLD--FI-R-GAELIIHNAPFDIGFMDYEFALLGRDIPKTN------ 116 (240)
T ss_pred cCCHHHhhh---cCCCHHHHcC-CCCHHHHHHHHHH--Hh-C-CCEEEEEccHHhHHHHHHHHHHhCCCCCccc------
Confidence 356666555 7888776655 3344433333332 12 2 236899999999999976653 33455321
Q ss_pred HhhhcCCCccchHHHHHhh-ccccchHHHHHHHcCCCccCCC-ccchhhhHHHHHHHHHHHHHh
Q 023614 196 VGVFFGEKVYDVKHLIRFC-TCLYGGLDRVCKALGVERVVGK-SHQAGSDSLLTLHAFLKIKDK 257 (280)
Q Consensus 196 l~~~Fp~~iyD~K~la~~~-~~l~~~L~~la~~L~v~r~~g~-~hqAGsDs~lT~~~F~~l~~~ 257 (280)
.+.. +.||--|++.. ++.+.+|+.|++.+|++. .+. .|.|-.|+.+|+.+|.+|...
T Consensus 117 ---~~~~-~iDTl~lar~~~p~~~~~L~aL~~~~gi~~-~~r~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 117 ---TFCK-VTDTLAMARRMFPGKRNSLDALCKRYGIDN-SHRTLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred ---ccCc-eeeHHHHHHHHcCCCCCCHHHHHHHCCCCC-CCCCCCCHHHHHHHHHHHHHHHHCc
Confidence 1334 88998888765 345668999999999987 444 699999999999999999764
No 15
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.37 E-value=1.6e-05 Score=70.88 Aligned_cols=169 Identities=17% Similarity=0.218 Sum_probs=109.2
Q ss_pred hhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCc
Q 023614 35 IDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDI 114 (280)
Q Consensus 35 i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~ 114 (280)
+....||++|+|-+|+. | + . .|||+|.......+. ...+|..+ .+.
T Consensus 4 l~~~~fvv~D~ETTGl~--~---------~----------~--~IIeIgav~v~~~~~----------~~~~f~~l-i~P 49 (217)
T TIGR00573 4 LVLDTETTGDNETTGLY--A---------G----------H--DIIEIGAVEIINRRI----------TGNKFHTY-IKP 49 (217)
T ss_pred EEecCEEEEEecCCCCC--C---------C----------C--CEEEEEEEEEECCCE----------eeeEEEEE-ECc
Confidence 45678999999999973 1 1 0 189999988543321 22345555 333
Q ss_pred CcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhC-CCCCCCHHHHH
Q 023614 115 ARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQ-RVLPEKLSEFV 193 (280)
Q Consensus 115 ~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~-~~LP~~~~~F~ 193 (280)
. ...++.+++. |||.-..+... -++....+.+.. .+ . +-.+|+++..||+.+|-+-+.. ...|
T Consensus 50 ~-~~i~~~a~~i---hGIt~e~l~~~-p~~~ev~~~~~~--~~-~-~~~lVaHNa~FD~~fL~~~~~r~~~~~------- 113 (217)
T TIGR00573 50 D-RPIDPDAIKI---HGITDDMLKDK-PDFKEIAEDFAD--YI-R-GAELVIHNASFDVGFLNYEFSKLYKVE------- 113 (217)
T ss_pred C-CCCCHHHHhh---cCCCHHHHcCC-CCHHHHHHHHHH--Hh-C-CCEEEEeccHHHHHHHHHHHHHhcCCC-------
Confidence 3 3456666644 89888887654 344433333332 12 1 2478999999999999776642 1110
Q ss_pred HHHhhhcCCCccchHHHHHhhc-cc---cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhh
Q 023614 194 TRVGVFFGEKVYDVKHLIRFCT-CL---YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 258 (280)
Q Consensus 194 ~~l~~~Fp~~iyD~K~la~~~~-~l---~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~ 258 (280)
..+..+.|+.-+++... .+ +.+|+.+++.+|++.....+|.|-+|+.+|+.+|.+|.+..
T Consensus 114 -----~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 114 -----PKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred -----CCccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHHhcc
Confidence 11122667666655442 22 34799999999998721268999999999999999998874
No 16
>PRK07740 hypothetical protein; Provisional
Probab=98.36 E-value=1.7e-05 Score=72.31 Aligned_cols=169 Identities=18% Similarity=0.216 Sum_probs=108.8
Q ss_pred hhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcC
Q 023614 36 DRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIA 115 (280)
Q Consensus 36 ~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~ 115 (280)
.+.+||.+|+|.+|+... . . =.|||+|....+. |.. ..-.|... ....
T Consensus 57 ~~~~~vv~D~ETTGl~p~-------~------------~--deIIeIgaV~~~~-~~i---------~~~~f~~l-v~P~ 104 (244)
T PRK07740 57 TDLPFVVFDLETTGFSPQ-------Q------------G--DEILSIGAVKTKG-GEV---------ETDTFYSL-VKPK 104 (244)
T ss_pred cCCCEEEEEEeCCCCCCC-------C------------C--CeEEEEEEEEEEC-CEE---------EEEEEEEE-eCcC
Confidence 356899999999997421 0 0 1389999888763 211 12234433 2332
Q ss_pred cCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHH
Q 023614 116 RHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTR 195 (280)
Q Consensus 116 ~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~ 195 (280)
. ..++.+.++ +||.=..+. +|.+...-.+.+.. .+ . +-.+|+++..+|++||-+.+...
T Consensus 105 ~-~i~~~~~~l---tGIt~e~l~-~ap~~~evl~~f~~--fi-~-~~~lVahna~fD~~fL~~~~~~~------------ 163 (244)
T PRK07740 105 R-PIPEHILEL---TGITAEDVA-FAPPLAEVLHRFYA--FI-G-AGVLVAHHAGHDKAFLRHALWRT------------ 163 (244)
T ss_pred C-CCChhheec---cCCCHHHHh-CCCCHHHHHHHHHH--Hh-C-CCEEEEeCHHHHHHHHHHHHHHh------------
Confidence 2 344444333 787766654 46665543333332 12 2 23799999999999997766421
Q ss_pred HhhhcCCCccchHHHHHhhcc-c-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 196 VGVFFGEKVYDVKHLIRFCTC-L-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 196 l~~~Fp~~iyD~K~la~~~~~-l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
+..-++.++.||..+++.... . ..+|+.+++.+|++. .+ .|.|-+|++.|+.+|.++.....
T Consensus 164 ~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~-~~-~H~Al~Da~ata~l~~~ll~~~~ 227 (244)
T PRK07740 164 YRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPI-PR-RHHALGDALMTAKLWAILLVEAQ 227 (244)
T ss_pred cCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCC-CC-CCCcHHHHHHHHHHHHHHHHHHH
Confidence 011123338899888876642 2 457999999999987 55 49999999999999999977754
No 17
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=98.34 E-value=2.3e-05 Score=71.70 Aligned_cols=169 Identities=14% Similarity=0.122 Sum_probs=111.0
Q ss_pred HhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccC
Q 023614 34 LIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFD 113 (280)
Q Consensus 34 ~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~ 113 (280)
++++-+||.+|+|-+|+... . =.|||+|+..++.++ ...+|+.+ ++
T Consensus 3 ~l~~~~~v~~D~ETTGl~~~-------~---------------d~IIEIa~v~v~~~~-----------~~~~~~~l-i~ 48 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDVK-------K---------------DRIIEFAAIRFTFDE-----------VIDSVEFL-IN 48 (250)
T ss_pred cccCCcEEEEEEeCCCCCCC-------C---------------CeEEEEEEEEEECCe-----------EEEEEEEE-EC
Confidence 46778999999999997321 1 138999988776432 33456665 44
Q ss_pred cCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhC--CCCCCCHHH
Q 023614 114 IARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQ--RVLPEKLSE 191 (280)
Q Consensus 114 ~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~--~~LP~~~~~ 191 (280)
... ...+++++ -|||--...... -+.....+.+.. .+ .+.-.+|+++..||.++|-+.+-. .+.|.
T Consensus 49 P~~-~I~~~a~~---ihgIt~e~v~~~-p~~~ev~~~~~~--fl-~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~---- 116 (250)
T PRK06310 49 PER-VVSAESQR---IHHISDAMLRDK-PKIAEVFPQIKG--FF-KEGDYIVGHSVGFDLQVLSQESERIGETFLS---- 116 (250)
T ss_pred cCC-CCCHhhhh---ccCcCHHHHhCC-CCHHHHHHHHHH--Hh-CCCCEEEEECHHHHHHHHHHHHHHcCCCccc----
Confidence 433 34444443 377665555432 333333333332 11 222478888889999999887643 22221
Q ss_pred HHHHHhhhcCCCccchHHHHHhhccc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhh
Q 023614 192 FVTRVGVFFGEKVYDVKHLIRFCTCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 258 (280)
Q Consensus 192 F~~~l~~~Fp~~iyD~K~la~~~~~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~ 258 (280)
.+..+.||..+++..... ...|+.+++.+|++. . .+|.|-+|++.|+.+|.+|.+.+
T Consensus 117 --------~~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~-~-~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 117 --------KHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPY-D-GNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred --------cCCcEEehHHHHHhcccCCCCCHHHHHHHCCCCC-C-CCcChHHHHHHHHHHHHHHHHhc
Confidence 112378998888865443 367999999999986 4 47999999999999999998765
No 18
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=98.33 E-value=9.6e-06 Score=66.19 Aligned_cols=156 Identities=19% Similarity=0.174 Sum_probs=103.4
Q ss_pred eEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCCCc
Q 023614 41 ISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHA 120 (280)
Q Consensus 41 IAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~~ 120 (280)
|.+|+|.+|+... .-.|||+|...++.+++ ....||.+ +....+ ..
T Consensus 1 v~~D~Ettg~~~~----------------------~~~iiei~~v~~~~~~~----------~~~~~~~~-i~p~~~-~~ 46 (159)
T cd06127 1 VVFDTETTGLDPK----------------------KDRIIEIGAVKVDGGIE----------IVERFETL-VNPGRP-IP 46 (159)
T ss_pred CeEEeeCCCcCCC----------------------CCeEEEEEEEEEECCcC----------hhhhhhee-eCcCCc-CC
Confidence 5799999997421 12399999999998733 23445665 444333 23
Q ss_pred hhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhc
Q 023614 121 LDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFF 200 (280)
Q Consensus 121 ~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~F 200 (280)
+.+.+. +|+.-+.. +.|.+...-.+.+.. .+ .+ -.||++++.+|..+|.+.+...- ...+
T Consensus 47 ~~~~~~---~gi~~~~~-~~~~~~~~~~~~~~~--~l-~~-~~~v~~n~~fD~~~l~~~~~~~~------------~~~~ 106 (159)
T cd06127 47 PEATAI---HGITDEML-ADAPPFEEVLPEFLE--FL-GG-RVLVAHNASFDLRFLNRELRRLG------------GPPL 106 (159)
T ss_pred Hhheec---cCCCHHHH-hcCCCHHHHHHHHHH--HH-CC-CEEEEeCcHhhHHHHHHHHHHhC------------CCCC
Confidence 333332 77766665 477777655444432 22 22 47999999999999988875311 2233
Q ss_pred CCCccchHHHHHhhccc--cchHHHH-HHHcCCCccCCCccchhhhHHHHHHHHH
Q 023614 201 GEKVYDVKHLIRFCTCL--YGGLDRV-CKALGVERVVGKSHQAGSDSLLTLHAFL 252 (280)
Q Consensus 201 p~~iyD~K~la~~~~~l--~~~L~~l-a~~L~v~r~~g~~hqAGsDs~lT~~~F~ 252 (280)
+....|++.+++..-.. ..+|..+ ++.++++. ..+|.|=+|++.|..+|.
T Consensus 107 ~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 107 PNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPL--EGAHRALADALATAELLL 159 (159)
T ss_pred CCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCC--CCCCCcHHHHHHHHHHhC
Confidence 44488999888776433 2467777 78888864 688999999999999873
No 19
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.31 E-value=2.3e-05 Score=73.92 Aligned_cols=163 Identities=17% Similarity=0.148 Sum_probs=106.2
Q ss_pred hCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCc
Q 023614 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (280)
Q Consensus 37 ~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~ 116 (280)
.-+||++|+|-+|+... .=.|||+|...++.+|+.- ..|... .+...
T Consensus 14 ~~~fvvlD~ETTGl~p~----------------------~d~IIeIgav~v~~~g~i~----------~~~~~l-v~P~~ 60 (313)
T PRK06063 14 PRGWAVVDVETSGFRPG----------------------QARIISLAVLGLDADGNVE----------QSVVTL-LNPGV 60 (313)
T ss_pred CCCEEEEEEECCCCCCC----------------------CCEEEEEEEEEEECCceee----------eEEEEE-ECcCC
Confidence 35899999999998321 1149999999998877532 223333 33322
Q ss_pred CCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhh--CCCCCCCHHHHHH
Q 023614 117 HAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVT 194 (280)
Q Consensus 117 d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~--~~~LP~~~~~F~~ 194 (280)
+ +.++. =|||.=+.+... -++....+.|.. .+ . +-.+|+++..+|++||-+.+- +.++|.
T Consensus 61 ~---~~~~~---IhGIt~e~l~~a-p~f~ev~~~l~~--~l-~-~~~lVaHNa~FD~~fL~~~~~r~g~~~~~------- 122 (313)
T PRK06063 61 D---PGPTH---VHGLTAEMLEGQ-PQFADIAGEVAE--LL-R-GRTLVAHNVAFDYSFLAAEAERAGAELPV------- 122 (313)
T ss_pred C---CCCee---cCCCCHHHHhCC-CCHHHHHHHHHH--Hc-C-CCEEEEeCHHHHHHHHHHHHHHcCCCCCC-------
Confidence 2 22222 266665555422 222233233321 11 2 347899999999999987774 334442
Q ss_pred HHhhhcCCCccchHHHHHhhc-cc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 195 RVGVFFGEKVYDVKHLIRFCT-CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 195 ~l~~~Fp~~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
.. .+||..+++... .+ .-.|+.|++.+|++. ...|.|-+|++.|+++|.++.+...
T Consensus 123 ------~~-~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~--~~~H~Al~DA~ata~l~~~ll~~~~ 180 (313)
T PRK06063 123 ------DQ-VMCTVELARRLGLGLPNLRLETLAAHWGVPQ--QRPHDALDDARVLAGILRPSLERAR 180 (313)
T ss_pred ------CC-EEehHHHHHHhccCCCCCCHHHHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 13 678888887652 33 346999999999986 5679999999999999999887764
No 20
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=98.30 E-value=3e-05 Score=69.82 Aligned_cols=167 Identities=20% Similarity=0.207 Sum_probs=107.8
Q ss_pred CeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCC
Q 023614 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (280)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~ 118 (280)
.+|.+|||-||+.... .=.|||+|...... +. + ..-.|+.+ .+..+ .
T Consensus 1 r~vvlD~ETTGl~p~~---------------------~d~IIEIgav~~~~-~~-~--------~~~~f~~~-i~P~~-~ 47 (225)
T TIGR01406 1 RQIILDTETTGLDPKG---------------------GHRIVEIGAVELVN-RM-L--------TGDNFHVY-VNPER-D 47 (225)
T ss_pred CEEEEEeeCCCcCCCC---------------------CCeEEEEEEEEEEC-Cc-E--------ecceEEEE-ECcCC-C
Confidence 4899999999984210 01499999775442 21 1 12346666 45433 3
Q ss_pred CchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhh--CCCCCCCHHHHHHHH
Q 023614 119 HALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVTRV 196 (280)
Q Consensus 119 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~--~~~LP~~~~~F~~~l 196 (280)
..+++.+. |||.-..+... .++....+.+.. .+ . +-.+|.++..+|++||-.-+. |..+|.-
T Consensus 48 i~~~a~~v---hGIt~e~l~~~-p~f~ev~~~f~~--fi-~-~~~lVaHNa~FD~~fL~~el~r~g~~~~~~-------- 111 (225)
T TIGR01406 48 MPAEAAKV---HGITDEFLADK-PKFKEIADEFLD--FI-G-GSELVIHNAAFDVGFLNYELERLGPTIKKI-------- 111 (225)
T ss_pred CCHHHHhc---cCCCHHHHhCC-CCHHHHHHHHHH--Hh-C-CCEEEEEecHHHHHHHHHHHHHhCCCCccc--------
Confidence 45555544 88887777643 444433333332 12 1 236889999999999977663 2111110
Q ss_pred hhhcCCCccchHHHHHhh-ccccchHHHHHHHcCCCccCCC-ccchhhhHHHHHHHHHHHHHh
Q 023614 197 GVFFGEKVYDVKHLIRFC-TCLYGGLDRVCKALGVERVVGK-SHQAGSDSLLTLHAFLKIKDK 257 (280)
Q Consensus 197 ~~~Fp~~iyD~K~la~~~-~~l~~~L~~la~~L~v~r~~g~-~hqAGsDs~lT~~~F~~l~~~ 257 (280)
.-+-. ++||--|++.. ++.+.+|+.+++.+|++. .+. .|-|-.|+.+|+.+|.+|...
T Consensus 112 -~~~~~-~iDTl~lar~~~p~~~~~L~~L~~~~gi~~-~~r~~H~Al~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 112 -GEFCR-VIDTLAMARERFPGQRNSLDALCKRFKVDN-SHRTLHGALLDAHLLAEVYLALTGG 171 (225)
T ss_pred -ccCCC-EEEHHHHHHHHcCCCCCCHHHHHHhcCCCC-CCCCCcCHHHHHHHHHHHHHHHHcC
Confidence 00113 88998888765 345678999999999997 554 799999999999999999775
No 21
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=98.24 E-value=4.9e-05 Score=69.13 Aligned_cols=169 Identities=17% Similarity=0.167 Sum_probs=109.6
Q ss_pred hhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCc
Q 023614 35 IDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDI 114 (280)
Q Consensus 35 i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~ 114 (280)
+.+.+|+++|+|-||+... . =.|||+|...++.+. . .....|... .+.
T Consensus 44 ~~~~~~vviD~ETTGl~p~-------~---------------d~IieIg~v~v~~~~-i--------~~~~~~~~l-i~P 91 (239)
T PRK09146 44 LSEVPFVALDFETTGLDAE-------Q---------------DAIVSIGLVPFTLQR-I--------RCRQARHWV-VKP 91 (239)
T ss_pred cccCCEEEEEeECCCCCCC-------C---------------CcEEEEEEEEEECCe-E--------eecceEEEE-ECC
Confidence 4577999999999998421 0 138999998886532 1 112233333 333
Q ss_pred CcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhC---CCCCCCHHH
Q 023614 115 ARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQ---RVLPEKLSE 191 (280)
Q Consensus 115 ~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~---~~LP~~~~~ 191 (280)
.. ...+++... |||.-+.+. .|-+...-.+.+... + . +-.+|+++..+|.+||-+.+.. .++|.
T Consensus 92 ~~-~i~~~~~~I---hGIt~e~l~-~ap~~~evl~~l~~~--~-~-~~~lVaHna~FD~~fL~~~l~~~~~~~~~~---- 158 (239)
T PRK09146 92 RR-PLEEESVVI---HGITHSELQ-DAPDLERILDELLEA--L-A-GKVVVVHYRRIERDFLDQALRNRIGEGIEF---- 158 (239)
T ss_pred CC-CCChhhhhh---cCCCHHHHh-CCCCHHHHHHHHHHH--h-C-CCEEEEECHHHHHHHHHHHHHHhcCCCCCC----
Confidence 22 345555544 888876654 355554433333321 1 2 2368998999999999887752 23222
Q ss_pred HHHHHhhhcCCCccchHHHHHhhc-c--------c------cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHH
Q 023614 192 FVTRVGVFFGEKVYDVKHLIRFCT-C--------L------YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKD 256 (280)
Q Consensus 192 F~~~l~~~Fp~~iyD~K~la~~~~-~--------l------~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~ 256 (280)
. ++||-.+++..- . + .-.|+.+++.+|++. ..+|.|-+|++.|+.+|.++.+
T Consensus 159 ----------~-~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl~~--~~~H~Al~DA~ata~l~~~~~~ 225 (239)
T PRK09146 159 ----------P-VIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGLPA--YSPHHALTDAIATAELLQAQIA 225 (239)
T ss_pred ----------c-eechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHH
Confidence 2 567777766531 1 1 125999999999986 4569999999999999999998
Q ss_pred hhCCC
Q 023614 257 KHFGN 261 (280)
Q Consensus 257 ~~~~~ 261 (280)
.++..
T Consensus 226 ~~~~~ 230 (239)
T PRK09146 226 HHFSP 230 (239)
T ss_pred HHcCC
Confidence 88643
No 22
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=98.20 E-value=5.9e-05 Score=71.27 Aligned_cols=162 Identities=17% Similarity=0.159 Sum_probs=108.4
Q ss_pred CeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCC
Q 023614 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (280)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~ 118 (280)
+||++|+|.+|+... + -.|||+|...++ +| ....+|+.. ..+...
T Consensus 9 ~~Vv~DlETTGl~p~-------~---------------~eIIEIgaV~v~-~g----------~i~~~f~~l-VkP~~~- 53 (313)
T PRK06807 9 DYVVIDFETTGFNPY-------N---------------DKIIQVAAVKYR-NH----------ELVDQFVSY-VNPERP- 53 (313)
T ss_pred CEEEEEEECCCCCCC-------C---------------CeEEEEEEEEEE-CC----------EEEEEEEEE-ECcCCC-
Confidence 899999999998421 0 159999998886 33 245667766 454433
Q ss_pred CchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhh
Q 023614 119 HALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGV 198 (280)
Q Consensus 119 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~ 198 (280)
..+.+. +-|||.-..+. .+.+.....+.+.. .+ .++ .+|++++.+|+.+|-+.+....+|..
T Consensus 54 I~~~a~---~ihGIT~e~l~-~~~~~~evl~~f~~--fl-~~~-~lVaHNa~FD~~fL~~~~~~~gl~~~---------- 115 (313)
T PRK06807 54 IPDRIT---SLTGITNYRVS-DAPTIEEVLPLFLA--FL-HTN-VIVAHNASFDMRFLKSNVNMLGLPEP---------- 115 (313)
T ss_pred CCHhhh---ccCCCCHHHHh-CCCCHHHHHHHHHH--HH-cCC-eEEEEcHHHHHHHHHHHHHHcCCCCC----------
Confidence 244443 34888866654 45555443333332 12 223 57899999999999888753222211
Q ss_pred hcCCCccchHHHHHhhc-ccc-chHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhh
Q 023614 199 FFGEKVYDVKHLIRFCT-CLY-GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 258 (280)
Q Consensus 199 ~Fp~~iyD~K~la~~~~-~l~-~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~ 258 (280)
... +.||-.+++... .+. .+|+.+++.+|++. .+|.|=.|++.|+.+|.+|...-
T Consensus 116 -~~~-~iDtl~la~~~~~~~~~~kL~~L~~~lgi~~---~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 116 -KNK-VIDTVFLAKKYMKHAPNHKLETLKRMLGIRL---SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred -CCC-EeeHHHHHHHHhCCCCCCCHHHHHHHcCCCC---CCcChHHHHHHHHHHHHHHHHhh
Confidence 113 678877776553 332 37999999999985 68999999999999999987764
No 23
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=98.17 E-value=8.8e-05 Score=65.51 Aligned_cols=179 Identities=18% Similarity=0.236 Sum_probs=113.2
Q ss_pred hhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCC--CCCCCCCCCCCceEEEEeccccC
Q 023614 36 DRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEE--GNLPDLGSGSTYYIWEFNFKDFD 113 (280)
Q Consensus 36 ~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~--g~~p~~~~~~~~~~wqFNF~~F~ 113 (280)
..+.||++|+|-+|+.... + .||++|..-...+ |... ....|+++ +.
T Consensus 6 ~~~~~vv~D~ETTGl~~~~---------d-------------~IieIgav~v~~~~~g~i~--------~~~~f~~~-v~ 54 (200)
T TIGR01298 6 RGYLPVVVDVETGGFNAKT---------D-------------ALLEIAAITLKMDEQGWLF--------PDTTLHFH-VE 54 (200)
T ss_pred cCCeeEEEEeeCCCCCCCC---------C-------------eEEEEEEEEEEEcCCCcEe--------ecceeEEE-Ec
Confidence 3578999999999984321 1 2899998877543 3221 12345555 33
Q ss_pred cC-cCCCchhHHHHHHHcCCCchhhhhcCCChHH-HHHHHHHc-----ccccCCCceEEEeccchhHHHHHHHhhCCCCC
Q 023614 114 IA-RHAHALDSVELLKRQGIDFEKNREFGIDSVR-FAELLMSS-----GLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLP 186 (280)
Q Consensus 114 ~~-~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~-f~e~l~~S-----glv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP 186 (280)
.. .-...+++++. |||.=++..+++.+... +.+.+..- +..+ .+-..|+++-.+|++||-+.+-...++
T Consensus 55 p~p~~~i~~~a~~i---hGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~lVaHNa~FD~~fL~~~~~r~~~~ 130 (200)
T TIGR01298 55 PFEGANIQPEALEF---TGIDLDHPLRGAVSEYEALHEIFKVVRKAMKASGC-QRAILVGHNANFDLGFLNAAVERTSLK 130 (200)
T ss_pred CCCCCCCCHHHHHc---cCCChhhhhhcCcchHHHHHHHHHHHHHHHHhccc-CCCEEEEECchhhHHHHHHHHHHhCCC
Confidence 32 23566777655 99887776777776543 33322210 0111 234688899999999998777421111
Q ss_pred CCHHHHHHHHhhhcCCCccchHHHHHhhccccchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 187 EKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 187 ~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
.. .+-|..+.||--+++..... ..|..+++.+|++...-..|.|-+|++.|+.+|.+|.+.+-
T Consensus 131 ~~---------~~~~~~~lDTl~lar~~~~~-~~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 131 RN---------PFHPFSTFDTATLAGLAYGQ-TVLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred CC---------CCCCCcEEEHHHHHHHHcCc-ccHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 00 00122267888887754322 36999999999985123679999999999999999988763
No 24
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=98.16 E-value=4.6e-05 Score=67.28 Aligned_cols=159 Identities=17% Similarity=0.188 Sum_probs=93.9
Q ss_pred CeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCC
Q 023614 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (280)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~ 118 (280)
.||++|+|.+|+. + . + .|||+|..-++. |. .+..|..+ ..... .
T Consensus 6 ~~vvlD~EtTGl~--~-------~-~-------------eIIeIgaV~v~~-g~----------~~~~f~~l-v~P~~-~ 49 (195)
T PRK07247 6 TYIAFDLEFNTVN--G-------V-S-------------HIIQVSAVKYDD-HK----------EVDSFDSY-VYTDV-P 49 (195)
T ss_pred eEEEEEeeCCCCC--C-------C-C-------------eEEEEEEEEEEC-CE----------EEEEEEEE-ECCCC-C
Confidence 7999999999973 1 0 1 499999888874 31 23456655 33322 2
Q ss_pred CchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccc-hhHHHHHHHhhCCCCCCCHHHHHHHHh
Q 023614 119 HALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSA-YDFGYLVKCLTQRVLPEKLSEFVTRVG 197 (280)
Q Consensus 119 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~-yD~gyL~k~l~~~~LP~~~~~F~~~l~ 197 (280)
..+.+.++ +||.=..+. ++.+...-.+.+.. .+ . +..||.++.. +|+++|-+. |.+++..
T Consensus 50 i~~~~~~l---hGIt~~~v~-~ap~~~evl~~f~~--f~-~-~~~lVaHNa~~fD~~fL~~~--g~~~~~~--------- 110 (195)
T PRK07247 50 LQSFINGL---TGITADKIA-DAPKVEEVLAAFKE--FV-G-ELPLIGYNAQKSDLPILAEN--GLDLSDQ--------- 110 (195)
T ss_pred CCccceec---CCCCHHHHh-CCCCHHHHHHHHHH--HH-C-CCeEEEEeCcHhHHHHHHHc--CCCcCCC---------
Confidence 22222222 666655554 34443322222221 12 2 3368888876 899998653 4343321
Q ss_pred hhcCCCccchHHHHHh--hccc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHh
Q 023614 198 VFFGEKVYDVKHLIRF--CTCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 257 (280)
Q Consensus 198 ~~Fp~~iyD~K~la~~--~~~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~ 257 (280)
++.+.||+.+..+. .+++ .-.|+.||+.+|++. ..|.|-+|++.|+.+|.+|.+.
T Consensus 111 --~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~---~~HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 111 --YQVDLYDEAFERRSSDLNGIANLKLQTVADFLGIKG---RGHNSLEDARMTARVYESFLES 168 (195)
T ss_pred --ceeehHHHHHHhhccccCCCCCCCHHHHHHhcCCCC---CCcCCHHHHHHHHHHHHHHHhh
Confidence 11113444332221 1222 247999999999985 3699999999999999999876
No 25
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=98.14 E-value=6.8e-05 Score=64.84 Aligned_cols=169 Identities=20% Similarity=0.205 Sum_probs=103.1
Q ss_pred eeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCC--CCCCceEEEEeccccCcCcC
Q 023614 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLG--SGSTYYIWEFNFKDFDIARH 117 (280)
Q Consensus 40 fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~--~~~~~~~wqFNF~~F~~~~d 117 (280)
||++|+|-||+.. +. . + .|||+|.--.+.++...... +.-...+-.|++. .+..+
T Consensus 1 ~vv~D~ETTGl~~-~~-----~--d-------------~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~l-v~P~~- 57 (177)
T cd06136 1 FVFLDLETTGLPK-HN-----R--P-------------EITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLC-FNPGR- 57 (177)
T ss_pred CeEEeeecCCCCC-CC-----C--C-------------ceEEEEEEEEecccccccccccccccceeeeeeEE-eCCCC-
Confidence 7999999999942 10 1 1 38999999887654321000 0000123456665 55543
Q ss_pred CCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHc-ccccCCCceEEEecc-chhHHHHHHHhh--CCCCCCCHHHHH
Q 023614 118 AHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSS-GLVLNKDVTWVTFHS-AYDFGYLVKCLT--QRVLPEKLSEFV 193 (280)
Q Consensus 118 ~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~S-glv~~~~v~Wvtfhg-~yD~gyL~k~l~--~~~LP~~~~~F~ 193 (280)
...+++... |||.=..+...+-......+.+..- +. ..+....|++++ .+|+.||-+-+. |.++|..
T Consensus 58 ~I~~~a~~I---hGIt~e~l~~~~~~~~~~~~~l~~f~~~-~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~----- 128 (177)
T cd06136 58 AISPGASEI---TGLSNDLLEHKAPFDSDTANLIKLFLRR-QPKPICLVAHNGNRFDFPILRSELERLGTKLPDD----- 128 (177)
T ss_pred cCChhHHHH---hCcCHHHHhcCCCccHHHHHHHHHHHHh-cCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCC-----
Confidence 345566555 8998888888773222222222110 11 123457899998 799999977764 2333311
Q ss_pred HHHhhhcCCCccchHHHHHhhccccchHHHHHHH-cCCCccCCCccchhhhHHHHHHHHHH
Q 023614 194 TRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKA-LGVERVVGKSHQAGSDSLLTLHAFLK 253 (280)
Q Consensus 194 ~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~-L~v~r~~g~~hqAGsDs~lT~~~F~~ 253 (280)
....||-.+++... ..|+.|++. +|++. ..+|.|-+|+..|+++|++
T Consensus 129 --------~~~iDtl~l~r~~~---~~L~~l~~~~~~~~~--~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 129 --------ILCVDSLPAFRELD---QSLGSLYKRLFGQEP--KNSHTAEGDVLALLKCALH 176 (177)
T ss_pred --------CEEEEeHHHHhhhH---hhHHHHHHHHhCCCc--ccccchHHHHHHHHHHHhh
Confidence 11347666665543 289999885 78885 5579999999999999975
No 26
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=98.13 E-value=8.9e-05 Score=69.73 Aligned_cols=160 Identities=18% Similarity=0.202 Sum_probs=106.8
Q ss_pred CeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCC
Q 023614 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (280)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~ 118 (280)
.||++|+|-+|. . . + .|||+|+..++ +|+ .+-+|+.+ .+.....
T Consensus 2 ~~vviD~ETTg~--~-------~--d-------------~IieIgav~v~-~g~----------i~~~f~~l-v~P~~~~ 45 (309)
T PRK06195 2 NFVAIDFETANE--K-------R--N-------------SPCSIGIVVVK-DGE----------IVEKVHYL-IKPKEMR 45 (309)
T ss_pred cEEEEEEeCCCC--C-------C--C-------------ceEEEEEEEEE-CCE----------EEEEEEEE-ECCCCCC
Confidence 699999998863 0 0 1 27999998885 332 23456555 4544334
Q ss_pred CchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhC--CCCCCCHHHHHHHH
Q 023614 119 HALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQ--RVLPEKLSEFVTRV 196 (280)
Q Consensus 119 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~--~~LP~~~~~F~~~l 196 (280)
..+.+++ =|||.=+.....+ ++....+.+.. .+ . +-.+|+++..+|++||-+-+.. .+.|.
T Consensus 46 ~~~~~~~---IhGIT~e~v~~ap-~f~ev~~~~~~--fl-~-~~~lVaHNa~FD~~fL~~~~~r~~~~~~~--------- 108 (309)
T PRK06195 46 FMPINIG---IHGIRPHMVEDEL-EFDKIWEKIKH--YF-N-NNLVIAHNASFDISVLRKTLELYNIPMPS--------- 108 (309)
T ss_pred CChhhee---ccCcCHHHHhCCC-CHHHHHHHHHH--Hh-C-CCEEEEECcHHHHHHHHHHHHHhCCCCCC---------
Confidence 5666654 3888888776643 44332222221 11 1 2378999999999999776642 33332
Q ss_pred hhhcCCCccchHHHHHhh-ccc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 197 GVFFGEKVYDVKHLIRFC-TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 197 ~~~Fp~~iyD~K~la~~~-~~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
.. .+||--+++.. +++ ..+|..|++.+|++- ..|.|-+|++.|+++|.+|.+..-
T Consensus 109 ----~~-~idT~~lar~l~~~~~~~~L~~L~~~~gi~~---~~H~Al~DA~ata~l~~~l~~~~~ 165 (309)
T PRK06195 109 ----FE-YICTMKLAKNFYSNIDNARLNTVNNFLGYEF---KHHDALADAMACSNILLNISKELN 165 (309)
T ss_pred ----CC-EEEHHHHHHHHcCCCCcCCHHHHHHHcCCCC---cccCCHHHHHHHHHHHHHHHHHhc
Confidence 13 67887777654 344 357999999999973 479999999999999999987754
No 27
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=98.05 E-value=0.00023 Score=65.42 Aligned_cols=166 Identities=19% Similarity=0.186 Sum_probs=106.4
Q ss_pred hhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCc
Q 023614 35 IDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDI 114 (280)
Q Consensus 35 i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~ 114 (280)
+.+..||.+|+|-+|..... -.|||+|...++ +|+ ..-+|..+ ...
T Consensus 65 ~~~~~~vv~DiETTG~~~~~----------------------~~IIEIGAv~v~-~g~----------i~~~f~~~-v~p 110 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKK----------------------HQIIEIGAVKVK-NGE----------IIDRFESF-VKA 110 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCC----------------------CeEEEEEEEEEE-CCE----------EEEEEEEE-ECC
Confidence 46789999999999963210 149999998886 332 22234444 222
Q ss_pred CcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHH
Q 023614 115 ARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVT 194 (280)
Q Consensus 115 ~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~ 194 (280)
. ...+.+.+ -+||.=..+. .+.+.....+.+.. . ..+. .||+++..+|+++|-+.+....+|.
T Consensus 111 ~--~ip~~~~~---itGIt~e~l~-~ap~~~evl~~f~~--f-l~~~-v~VaHNa~FD~~fL~~~l~r~g~~~------- 173 (257)
T PRK08517 111 K--EVPEYITE---LTGITYEDLE-NAPSLKEVLEEFRL--F-LGDS-VFVAHNVNFDYNFISRSLEEIGLGP------- 173 (257)
T ss_pred C--CCChhhhh---hcCcCHHHHc-CCCCHHHHHHHHHH--H-HCCC-eEEEECHHHHHHHHHHHHHHcCCCC-------
Confidence 2 23333333 2888777665 35555443333332 1 1223 6999999999999977665322222
Q ss_pred HHhhhcCCCccchHHHHHhh-ccccchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhh
Q 023614 195 RVGVFFGEKVYDVKHLIRFC-TCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 258 (280)
Q Consensus 195 ~l~~~Fp~~iyD~K~la~~~-~~l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~ 258 (280)
+.+. ..||--+++.+ ..-+-+|+.+++.+|++. . .+|.|-+|++.|+.+|.++.+.+
T Consensus 174 ----~~~~-~ldtl~la~~~~~~~~~~L~~L~~~lgi~~-~-~~HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 174 ----LLNR-KLCTIDLAKRTIESPRYGLSFLKELLGIEI-E-VHHRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred ----CCCC-cEehHHHHHHHccCCCCCHHHHHHHcCcCC-C-CCCChHHHHHHHHHHHHHHHHHh
Confidence 1112 45665555543 223458999999999987 3 78999999999999999998765
No 28
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.05 E-value=0.00013 Score=78.04 Aligned_cols=166 Identities=22% Similarity=0.245 Sum_probs=108.4
Q ss_pred CCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcC
Q 023614 38 YPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH 117 (280)
Q Consensus 38 ~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d 117 (280)
-.||++|+|.+|..... . -.|||+|....+ +|+ .+-.|+.+ .+...
T Consensus 3 ~~~vvvD~ETTG~~p~~------~---------------d~IIeigav~v~-~~~----------i~~~f~~~-v~P~~- 48 (928)
T PRK08074 3 KRFVVVDLETTGNSPKK------G---------------DKIIQIAAVVVE-DGE----------ILERFSSF-VNPER- 48 (928)
T ss_pred CCEEEEEEeCCCCCCCC------C---------------CcEEEEEEEEEE-CCE----------EEEEEEEE-ECcCC-
Confidence 46999999999963211 0 149999999985 332 23345555 44432
Q ss_pred CCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHh
Q 023614 118 AHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVG 197 (280)
Q Consensus 118 ~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~ 197 (280)
...+.+.++ +||+=..+. .+.++....+.+.. ++ ++..+|+++..||+.||-+-+...-+|.
T Consensus 49 ~i~~~~~~l---tGIt~~~l~-~ap~f~ev~~~l~~--~l--~~~~~VaHN~~FD~~fL~~~~~~~g~~~---------- 110 (928)
T PRK08074 49 PIPPFITEL---TGISEEMVK-QAPLFEDVAPEIVE--LL--EGAYFVAHNVHFDLNFLNEELERAGYTE---------- 110 (928)
T ss_pred CCCHHHhhc---CCCCHHHHh-cCCCHHHHHHHHHH--Hh--CCCeEEEEChHHHHHHHHHHHHHcCCCC----------
Confidence 244444333 888866654 44555444433332 11 2458999999999999988765322222
Q ss_pred hhcCCCccchHHHHHhh-ccc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 198 VFFGEKVYDVKHLIRFC-TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 198 ~~Fp~~iyD~K~la~~~-~~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
++...+||=.+++.. +.+ .-+|+.|++.++++. ..+|.|-+|++.|+.+|.+|.+...
T Consensus 111 --~~~~~iDt~~la~~~~p~~~~~~L~~l~~~l~i~~--~~~H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 111 --IHCPKLDTVELARILLPTAESYKLRDLSEELGLEH--DQPHRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred --CCCCeeeHHHHHHHhcCCCCCCCHHHHHHhCCCCC--CCCCChHHHHHHHHHHHHHHHHHHH
Confidence 112266776665543 222 247999999999986 5789999999999999999988764
No 29
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.01 E-value=0.00021 Score=75.55 Aligned_cols=162 Identities=21% Similarity=0.259 Sum_probs=107.1
Q ss_pred hCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCc
Q 023614 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (280)
Q Consensus 37 ~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~ 116 (280)
...||++|+|-||+. + . | .|||+|...++ +|+ .+-.|... .+...
T Consensus 6 ~~~~vvvD~ETTGl~--~------~-------------d--~IIeIgaV~v~-~g~----------i~~~f~~l-v~P~~ 50 (820)
T PRK07246 6 LRKYAVVDLEATGAG--P------N-------------A--SIIQVGIVIIE-GGE----------IIDSYTTD-VNPHE 50 (820)
T ss_pred CCCEEEEEEecCCcC--C------C-------------C--eEEEEEEEEEE-CCE----------EEEEEEEE-eCcCC
Confidence 468999999999972 1 0 1 39999998875 332 23345544 33322
Q ss_pred CCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhh--CCCCCCCHHHHHH
Q 023614 117 HAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVT 194 (280)
Q Consensus 117 d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~--~~~LP~~~~~F~~ 194 (280)
...+.+.+. +||.=..+. ++.+.......+.. .+ .+-.+|+++..+|+++|-+.+. |-++|.
T Consensus 51 -~i~~~~~~l---tGIt~e~l~-~ap~~~ev~~~~~~--~l--~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~------- 114 (820)
T PRK07246 51 -PLDEHIKHL---TGITDQQLA-QAPDFSQVARHIYD--LI--EDCIFVAHNVKFDANLLAEALFLEGYELRT------- 114 (820)
T ss_pred -CCCHhHhhc---CCCCHHHHh-cCCCHHHHHHHHHH--Hh--CCCEEEEECcHHHHHHHHHHHHHcCCCCCC-------
Confidence 334444433 787776654 45555544443332 12 2347899999999999988764 333332
Q ss_pred HHhhhcCCCccchHHHHHhh-ccc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 195 RVGVFFGEKVYDVKHLIRFC-TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 195 ~l~~~Fp~~iyD~K~la~~~-~~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
. ..||-.+++.. +.+ +-+|+.+++.+|++. ..+|.|-+|+..|+.+|.+|.+.+.
T Consensus 115 -------~-~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~--~~~H~Al~DA~ata~L~~~l~~~l~ 171 (820)
T PRK07246 115 -------P-RVDTVELAQVFFPTLEKYSLSHLSRELNIDL--ADAHTAIADARATAELFLKLLQKIE 171 (820)
T ss_pred -------C-ceeHHHHHHHHhCCCCCCCHHHHHHHcCCCC--CCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 1 35666666553 223 358999999999986 4679999999999999999988764
No 30
>PRK07883 hypothetical protein; Validated
Probab=97.99 E-value=0.00018 Score=72.98 Aligned_cols=171 Identities=16% Similarity=0.133 Sum_probs=112.3
Q ss_pred HHHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccc
Q 023614 32 RALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKD 111 (280)
Q Consensus 32 ~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~ 111 (280)
..-+.+.+||++|+|.+|+... .-.|||+|.-.++. |+ ...+|+..
T Consensus 9 ~~~~~~~~~Vv~D~ETTGl~p~----------------------~~~IIEIgaV~v~~-g~----------iv~~f~~l- 54 (557)
T PRK07883 9 GTPLRDVTFVVVDLETTGGSPA----------------------GDAITEIGAVKVRG-GE----------VLGEFATL- 54 (557)
T ss_pred CCCCcCCCEEEEEEecCCCCCC----------------------CCeEEEEEEEEEEC-CE----------EEEEEEEE-
Confidence 3456788999999999998321 01399999988863 21 34556665
Q ss_pred cCcCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHH
Q 023614 112 FDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSE 191 (280)
Q Consensus 112 F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~ 191 (280)
.+... ...+.+.+. +||.=..+ +++.+.....+.+.. .+ . +-.+|++++.||+.+|-+.+...-+|.
T Consensus 55 V~P~~-~i~~~~~~i---tGIt~e~l-~~ap~~~evl~~f~~--fl-~-~~~lVaHNa~FD~~fL~~~~~r~g~~~---- 121 (557)
T PRK07883 55 VNPGR-PIPPFITVL---TGITTAMV-AGAPPIEEVLPAFLE--FA-R-GAVLVAHNAPFDIGFLRAAAARCGYPW---- 121 (557)
T ss_pred ECCCC-CCChhHHhh---cCCCHHHH-hCCCCHHHHHHHHHH--Hh-c-CCEEEEeCcHHHHHHHHHHHHHcCCCC----
Confidence 44433 345555433 88765544 445555443333322 11 2 347888888999999988776422221
Q ss_pred HHHHHhhhcCCCccchHHHHHhh-c--cc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 192 FVTRVGVFFGEKVYDVKHLIRFC-T--CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 192 F~~~l~~~Fp~~iyD~K~la~~~-~--~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
.+....||-.+++.. + .. ..+|..+++.+|++. ...|.|-+|++.|+.+|.++.+...
T Consensus 122 --------~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~--~~~H~Al~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 122 --------PGPPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATT--TPTHRALDDARATVDVLHGLIERLG 183 (557)
T ss_pred --------CCCCcEecHHHHHHhcccCCCCCCCHHHHHHHCCccc--CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 111266887777654 2 22 346999999999986 4469999999999999999888775
No 31
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=97.98 E-value=0.00023 Score=77.81 Aligned_cols=168 Identities=21% Similarity=0.270 Sum_probs=116.9
Q ss_pred hhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcC
Q 023614 36 DRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIA 115 (280)
Q Consensus 36 ~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~ 115 (280)
+..+||++|+|-+|+.... + .|||+|....+. |+ ..-.|++. .++.
T Consensus 188 ~~~~~VVfDiETTGL~~~~---------d-------------~IIEIGAVkv~~-g~----------iid~f~~~-V~P~ 233 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQY---------D-------------EIIEFGAVKVKN-GR----------IIDKFQFF-IKPH 233 (1213)
T ss_pred cCCcEEEEEeEecCCCCCC---------C-------------eEEEEEEEEEEC-Ce----------EEEEEEEE-ECCC
Confidence 6789999999999974321 1 499999998874 32 23456665 3433
Q ss_pred cCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHH
Q 023614 116 RHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTR 195 (280)
Q Consensus 116 ~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~ 195 (280)
...++.+.++ +||.-+.+. +|.+.....+.+.. .+ . +-.+|+++..+|++||-+.+...-+|.
T Consensus 234 -~~I~~~~~~l---tGIT~e~L~-~ap~~~evl~~f~~--fl-~-~~iLVaHNa~FD~~fL~~~~~r~g~~~-------- 296 (1213)
T TIGR01405 234 -EPLSAFVTEL---TGITQDMLE-NAPEIEEVLEKFKE--FF-K-DSILVAHNASFDIGFLNTNFEKVGLEP-------- 296 (1213)
T ss_pred -CCCCHHHHHH---hCCCHHHHh-CCCCHHHHHHHHHH--Hh-C-CCeEEEEChHHHHHHHHHHHHHcCCCc--------
Confidence 3455555544 899888764 57766544333332 11 2 347899998999999988765333332
Q ss_pred HhhhcCCCccchHHHHHhhc-cc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhCC
Q 023614 196 VGVFFGEKVYDVKHLIRFCT-CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFG 260 (280)
Q Consensus 196 l~~~Fp~~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~~ 260 (280)
++..+.||--+++... ++ ..+|+.||+.+|++. .+ +|.|-.|+..|+.+|.+|.+...+
T Consensus 297 ----~~~~~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~-~~-~HrAl~DA~aTa~I~~~ll~~l~~ 357 (1213)
T TIGR01405 297 ----LENPVIDTLELARALNPEYKSHRLGNICKKLGVDL-DD-HHRADYDAEATAKVFKVMVEQLKE 357 (1213)
T ss_pred ----cCCCEeEHHHHHHHHhccCCCCCHHHHHHHcCCCC-CC-CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 1223789988887753 34 357999999999997 45 899999999999999999887653
No 32
>PRK06722 exonuclease; Provisional
Probab=97.93 E-value=0.00048 Score=64.27 Aligned_cols=169 Identities=19% Similarity=0.148 Sum_probs=99.5
Q ss_pred hCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCc
Q 023614 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (280)
Q Consensus 37 ~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~ 116 (280)
...||++|+|.+|. |. . . -+.-.|||+|....+.. .. ..+-.|+.+ ..+.
T Consensus 4 ~~~~vViD~ETT~~---p~---~-~------------~~~deIIEIGAVkV~~g-~i--------~Ivd~F~sL-V~P~- 53 (281)
T PRK06722 4 ATHFIVFDIERNFR---PY---K-S------------EDPSEIVDIGAVKIEAS-TM--------KVIGEFSEL-VKPG- 53 (281)
T ss_pred CCEEEEEEeeCCCC---CC---C-C------------CCCCeEEEEEEEEEECC-ce--------eEEeeEEEE-ECCC-
Confidence 35799999999852 21 0 0 01123999998887652 11 134456655 3332
Q ss_pred CCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhh--CCCCCCCHHHHHH
Q 023614 117 HAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLT--QRVLPEKLSEFVT 194 (280)
Q Consensus 117 d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~--~~~LP~~~~~F~~ 194 (280)
...++.+.++ +||.=+.+. .+.+.....+.+.. .+ .+. .+|+.|+.+|.+||-+-+. |.+.|...
T Consensus 54 ~~I~~~i~~L---TGIT~emV~-~AP~f~eVl~ef~~--fi-g~~-~lvahna~FD~~FL~~~l~~~gi~~p~~~----- 120 (281)
T PRK06722 54 ARLTRHTTKL---TGITKKDLI-GVEKFPQIIEKFIQ--FI-GED-SIFVTWGKEDYRFLSHDCTLHSVECPCME----- 120 (281)
T ss_pred CcCCHhHhhh---cCCCHHHHc-CCCCHHHHHHHHHH--HH-CCC-cEEEEEeHHHHHHHHHHHHHcCCCCCccc-----
Confidence 2344555444 676655553 34443332222221 11 222 4667788999999988764 33444311
Q ss_pred HHhhhcCCCccchHHHHHh-hccc---cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHH
Q 023614 195 RVGVFFGEKVYDVKHLIRF-CTCL---YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIK 255 (280)
Q Consensus 195 ~l~~~Fp~~iyD~K~la~~-~~~l---~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~ 255 (280)
+-+ ..|+.-++.. .+.+ .-+|..+++.+|++. .|..|.|-+||..|+.+|.+|.
T Consensus 121 -----~~~-~idl~~la~~~~~~l~~~~~sL~~l~~~lgL~~-~g~~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 121 -----KER-RIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIW-EGKQHRALADAENTANILLKAY 178 (281)
T ss_pred -----ccc-hhHHHHHHHHHhhhhccCCCCHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHHHHHh
Confidence 001 2344333321 1121 136999999999998 7899999999999999999986
No 33
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=97.91 E-value=0.00035 Score=74.09 Aligned_cols=164 Identities=20% Similarity=0.230 Sum_probs=105.0
Q ss_pred CeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCC
Q 023614 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (280)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~ 118 (280)
.||++|+|-+|+... . =.|||+|...++ +|+ ..-+|... .+... .
T Consensus 1 ~~vvvD~ETTG~~~~-------~---------------~~IIeig~v~v~-~~~----------i~~~f~~~-v~P~~-~ 45 (850)
T TIGR01407 1 RYAVVDLETTGTQLS-------F---------------DKIIQIGIVVVE-DGE----------IVDTFHTD-VNPNE-P 45 (850)
T ss_pred CEEEEEEECCCCCCC-------C---------------CeEEEEEEEEEE-CCE----------EEEEEEEE-eCCCC-C
Confidence 489999999997421 1 139999999884 342 22345554 34332 3
Q ss_pred CchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhh
Q 023614 119 HALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGV 198 (280)
Q Consensus 119 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~ 198 (280)
..+.+.+ -+||.-+.+.. +-++....+.+.. ++ . +-.||+++..+|+.+|-+-+...-+|.
T Consensus 46 i~~~~~~---ltGIt~e~l~~-ap~~~ev~~~l~~--~l-~-~~~~VahN~~fD~~fL~~~~~~~g~~~----------- 106 (850)
T TIGR01407 46 IPPFIQE---LTGISDNMLQQ-APYFSQVAQEIYD--LL-E-DGIFVAHNVHFDLNFLAKALKDCGYEP----------- 106 (850)
T ss_pred CChhhhh---hcCcCHHHHhC-CCCHHHHHHHHHH--Hh-C-CCEEEEeCcHHHHHHHHHHHHHcCCCC-----------
Confidence 3444433 38887666553 4444443333332 12 2 336999999999999988775322221
Q ss_pred hcCCCccchHHHHHhhc-cc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 199 FFGEKVYDVKHLIRFCT-CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 199 ~Fp~~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
+|...+||--+++..- .. .-+|..|++.+|++. ..+|.|-+|+..|+.+|.+|.+.+-
T Consensus 107 -~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~--~~~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 107 -LPKPRIDTVELAQIFFPTEESYQLSELSEALGLTH--ENPHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred -CCCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCC--CCCCChHHHHHHHHHHHHHHHHHHH
Confidence 1222667766655442 12 347999999999986 4579999999999999999988764
No 34
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.80 E-value=0.00057 Score=68.08 Aligned_cols=180 Identities=18% Similarity=0.077 Sum_probs=112.9
Q ss_pred hhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcC
Q 023614 36 DRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIA 115 (280)
Q Consensus 36 ~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~ 115 (280)
....||.+|+|-||+.... + .|||+|.--.+.+++. ....|+++ ....
T Consensus 4 ~~~~fvv~D~ETTGLdP~~---------D-------------rIIeiAaVrvd~~~~~---------i~e~~~~~-~~P~ 51 (476)
T PRK11779 4 MQPTFLWHDYETFGANPAL---------D-------------RPAQFAGIRTDADLNI---------IGEPLVFY-CKPA 51 (476)
T ss_pred CCCcEEEEEEECCCCCCCC---------C-------------eeEEEEEEEEeCCCce---------ecceeEEE-EcCC
Confidence 3567999999999985321 1 2899999888776532 22356666 4444
Q ss_pred cC-CCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEecc-chhHHHHHHHhhCCCCCCCHHHHH
Q 023614 116 RH-AHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHS-AYDFGYLVKCLTQRVLPEKLSEFV 193 (280)
Q Consensus 116 ~d-~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg-~yD~gyL~k~l~~~~LP~~~~~F~ 193 (280)
.+ +..++|+ .-|||-=+.+...|++...+.+.+.. .+..++..+|.+|+ .||.+++-+.+.. .+-+++. .
T Consensus 52 ~~~lp~p~a~---~IhGIT~e~l~~~g~~e~e~~~~i~~--~l~~~~~~lVGhNni~FD~eflr~~~~r-~~~d~y~--~ 123 (476)
T PRK11779 52 DDYLPSPEAV---LITGITPQEALEKGLPEAEFAARIHA--EFSQPGTCILGYNNIRFDDEVTRYIFYR-NFYDPYA--R 123 (476)
T ss_pred cCcCCCHHHH---HHhCCCHHHHHhcCCCHHHHHHHHHH--HHhcCCCEEEEeCchhhcHHHHHHHHHh-ccchHHH--H
Confidence 44 3456654 44999999998999987776655442 12223445788876 5999998887752 1111110 0
Q ss_pred HHHhhhcCCCccchHHHHHhh-c----------cc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHh
Q 023614 194 TRVGVFFGEKVYDVKHLIRFC-T----------CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 257 (280)
Q Consensus 194 ~~l~~~Fp~~iyD~K~la~~~-~----------~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~ 257 (280)
+..+...+.++.|+-.+.... + +. .-.|+.|++.+|++. ..+|.|=+|++.|+.++.+|++.
T Consensus 124 ~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~L~~~~gI~~--~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 124 EWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEH--ENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHHHHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHHh
Confidence 000001111133333332221 0 11 246999999999986 67899999999999999999876
No 35
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=97.79 E-value=0.00047 Score=59.77 Aligned_cols=165 Identities=18% Similarity=0.130 Sum_probs=97.1
Q ss_pred EeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcC-CCc
Q 023614 42 SMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH-AHA 120 (280)
Q Consensus 42 AiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d-~~~ 120 (280)
-+|+|-||+.... | .|||+|.-.++.++.. ...|++. ..+... ...
T Consensus 2 ~~D~ETTGl~~~~--------------------d--~Iieig~v~v~~~~~~----------~~~~~~~-v~p~~~~~~~ 48 (183)
T cd06138 2 FYDYETFGLNPSF--------------------D--QILQFAAIRTDENFNE----------IEPFNIF-CRLPPDVLPS 48 (183)
T ss_pred EEEeecCCCCCCC--------------------C--ceEEEEEEEECCCCCC----------ccceeEE-EeCCCCCCCC
Confidence 4799999984210 1 3899999888766532 1345555 333332 345
Q ss_pred hhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEecc-chhHHHHHHHhhC---CCCCCC------HH
Q 023614 121 LDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHS-AYDFGYLVKCLTQ---RVLPEK------LS 190 (280)
Q Consensus 121 ~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg-~yD~gyL~k~l~~---~~LP~~------~~ 190 (280)
++++. -|||.=+.+...|.+.....+.+.. .+..++..+|++|+ .+|.+||-+.+.. .+++.+ .-
T Consensus 49 ~~a~~---ihGIt~e~l~~~~~~~~~~l~~~~~--~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~ 123 (183)
T cd06138 49 PEALI---VTGITPQQLLKEGLSEYEFIAKIHR--LFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRW 123 (183)
T ss_pred HHHHH---HhCCCHHHHHhcCCCHHHHHHHHHH--HHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCcccc
Confidence 55544 4999988887778887665444432 12223446898886 6999999877752 222211 11
Q ss_pred HHHHHHhh---hcCCCccchHHHHHhhccc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHH
Q 023614 191 EFVTRVGV---FFGEKVYDVKHLIRFCTCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 250 (280)
Q Consensus 191 ~F~~~l~~---~Fp~~iyD~K~la~~~~~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~ 250 (280)
..+.+++. ++|. -++.- ..-.++ ...|+.+++.+|++. ..+|.|-+|++.|+.+
T Consensus 124 dtl~l~r~~~~~~~~-~~~~~---~~~~~~~~~~L~~l~~~~gi~~--~~~H~Al~Da~~ta~l 181 (183)
T cd06138 124 DLLDVVRAYYALRPD-GIVWP---KNDDGKPSFKLEDLAQANGIEH--SNAHDALSDVEATIAL 181 (183)
T ss_pred ccHHHHHHHHhhChh-hccCc---cccCCCcchhHHHHHHHCCCCc--cccccHHHHHHHHHHH
Confidence 11222222 2232 11100 000012 246999999999986 6679999999999764
No 36
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=97.77 E-value=3.5e-05 Score=62.90 Aligned_cols=157 Identities=23% Similarity=0.215 Sum_probs=93.8
Q ss_pred eEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCCCc
Q 023614 41 ISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHA 120 (280)
Q Consensus 41 IAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~~ 120 (280)
|.+|+|++|...+ .-.|||+|.-..+.+.. ...-.|+.+..+.......
T Consensus 1 v~~D~Ettg~~~~----------------------~~~iieig~v~~~~~~~---------~~~~~~~~~i~p~~~~~i~ 49 (164)
T PF00929_consen 1 VVFDTETTGLDPR----------------------QDEIIEIGAVKVDDDEN---------EEVESFNSLIRPEEPPKIS 49 (164)
T ss_dssp EEEEEEESSSTTT----------------------TCTEEEEEEEEEETTTT---------EEEEEEEEEBEHSSHCSSE
T ss_pred cEEEeEcCCCCCC----------------------CCeEEEEEEEEeeCCcc---------ccceeeeecccccccccCC
Confidence 6799999998541 12389999988877653 1334566652222222345
Q ss_pred hhHHHHHHHcCCCchhhhhcCCChHH---HHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHh
Q 023614 121 LDSVELLKRQGIDFEKNREFGIDSVR---FAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVG 197 (280)
Q Consensus 121 ~~Si~fL~~~G~DF~k~~~~GI~~~~---f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~ 197 (280)
+.+.+ -+|+.=..+...+-.... |.+.+. +...||..+..+|.+++.+.+. +.++
T Consensus 50 ~~~~~---~~gIt~~~l~~~~~~~~~~~~~~~~~~-------~~~~~v~~n~~fd~~~l~~~~~------------~~~~ 107 (164)
T PF00929_consen 50 PWATK---VHGITQEDLEDAPSFEEALDEFEEFLK-------KNDILVGHNASFDIGFLRREDK------------RFLG 107 (164)
T ss_dssp HHHHH---HHHHCHHHHHCHCEHHHHHHHHHHHHH-------HHTEEEETTCCHEEESSHHHHH------------HHHH
T ss_pred HHHee---ecCCcccccccCCcHHHHHHhhhhhhh-------cccccccccccchhhHHHHhhh------------hccc
Confidence 55443 477777776666543332 222322 1246777777788877655543 1111
Q ss_pred hhcC--CCccchHHHHHh-hcccc-chHHHHHHHcCCCccCCCccchhhhHHHHHHHH
Q 023614 198 VFFG--EKVYDVKHLIRF-CTCLY-GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAF 251 (280)
Q Consensus 198 ~~Fp--~~iyD~K~la~~-~~~l~-~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F 251 (280)
..+| ..+.|+.-+.+. .+... .+|..+++.++++. .+.+|.|-+|++.|+.+|
T Consensus 108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~-~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 108 KPIPKPNPFIDTLELARALFPNRKKYSLDDLAEYFGIPF-DGTAHDALDDARATAELF 164 (164)
T ss_dssp HHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTSSS-TSTTTSHHHHHHHHHHHH
T ss_pred ccccccchhhhhhHHHHHHhhccccCCHHHHHHHcCCCC-CCCCcChHHHHHHHhCcC
Confidence 1111 013343332222 22233 48999999999999 777999999999999987
No 37
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=97.70 E-value=0.0012 Score=59.35 Aligned_cols=149 Identities=13% Similarity=0.081 Sum_probs=96.1
Q ss_pred eeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCCC
Q 023614 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAH 119 (280)
Q Consensus 40 fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~ 119 (280)
++.+|||-+|+. + . |||+|..-+. +|+ .+..|+.. .+... ..
T Consensus 2 ~~vlD~ETTGl~--~---------~--------------IieIg~v~v~-~~~----------i~~~~~~l-v~P~~-~i 43 (219)
T PRK07983 2 LRVIDTETCGLQ--G---------G--------------IVEIASVDVI-DGK----------IVNPMSHL-VRPDR-PI 43 (219)
T ss_pred eEEEEEECCCCC--C---------C--------------CEEEEEEEEE-CCE----------EEEEEEEE-ECcCC-CC
Confidence 789999999972 1 1 8899977654 442 23345444 44433 34
Q ss_pred chhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhh
Q 023614 120 ALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVF 199 (280)
Q Consensus 120 ~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~ 199 (280)
++.+++. |||.=+... |-|. |.+.+-. + .....+|+++-.||.++|-+
T Consensus 44 ~~~~~~i---hgIt~e~v~--~ap~--~~ev~~~--~--~~~~~lVaHNa~FD~~~L~~--------------------- 91 (219)
T PRK07983 44 SPQAMAI---HRITEAMVA--DKPW--IEDVIPH--Y--YGSEWYVAHNASFDRRVLPE--------------------- 91 (219)
T ss_pred CHHHhhc---CCCCHHHHc--CCCC--HHHHHHH--H--cCCCEEEEeCcHhhHHHHhC---------------------
Confidence 4555443 665544432 2222 3333322 1 23447899999999998731
Q ss_pred cCCCccchHHHHHhh-ccccchHHHHHHHcCCCcc---CCCccchhhhHHHHHHHHHHHHHhh
Q 023614 200 FGEKVYDVKHLIRFC-TCLYGGLDRVCKALGVERV---VGKSHQAGSDSLLTLHAFLKIKDKH 258 (280)
Q Consensus 200 Fp~~iyD~K~la~~~-~~l~~~L~~la~~L~v~r~---~g~~hqAGsDs~lT~~~F~~l~~~~ 258 (280)
++...+||-.+++.. +++..+|+.|++.++++.. ...+|.|-+|++.|+.+|.+|.+..
T Consensus 92 ~~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 92 MPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred cCCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHc
Confidence 222378998888764 5567789999999987531 2468999999999999999988653
No 38
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=97.68 E-value=0.0013 Score=63.35 Aligned_cols=180 Identities=14% Similarity=0.190 Sum_probs=109.3
Q ss_pred HhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccC
Q 023614 34 LIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFD 113 (280)
Q Consensus 34 ~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~ 113 (280)
.+++.+||++|+|-||+... +. .||++|.-.+..+|+ .+..|... ++
T Consensus 42 ~~~~~~fVvlDiETTGLdp~-------~d---------------rIIeIgAV~i~~~g~----------ive~f~tL-Vn 88 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPS-------TS---------------RLITIDAVTLTADGE----------EVEHFHAV-LN 88 (377)
T ss_pred CCCCCCEEEEEEECCCCCCC-------CC---------------eEEEEEEEEEEcCCE----------EEEEEEEE-EC
Confidence 46778999999999998421 11 389999988887774 23445554 44
Q ss_pred cCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhC--CCC-----C
Q 023614 114 IARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQ--RVL-----P 186 (280)
Q Consensus 114 ~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~--~~L-----P 186 (280)
...+.. +. .=|||.=+.+.. |.++....+.|.. ++ . +-.||+.+-.+|++||.+-+.- ..+ |
T Consensus 89 P~~~~~---p~---~LHGIT~e~La~-AP~f~eVl~el~~--fL-~-g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~ 157 (377)
T PRK05601 89 PGEDPG---PF---HLHGLSAEEFAQ-GKRFSQILKPLDR--LI-D-GRTLILHNAPRTWGFIVSEAKRAMNAAARANRN 157 (377)
T ss_pred cCCCCC---Cc---cccCCCHHHHhc-CCCHHHHHHHHHH--Hh-C-CCEEEEECcHHHHHHHHHHHHHhhhhhhhcccc
Confidence 443322 11 136666665544 6665554444332 22 2 3479998889999999775521 000 0
Q ss_pred CCHH--------HHHHHHhhhcCCCccchHHHHHhhc-cc-cchHHHHHHHcCCCcc--------CCCccchhh--hHHH
Q 023614 187 EKLS--------EFVTRVGVFFGEKVYDVKHLIRFCT-CL-YGGLDRVCKALGVERV--------VGKSHQAGS--DSLL 246 (280)
Q Consensus 187 ~~~~--------~F~~~l~~~Fp~~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~--------~g~~hqAGs--Ds~l 246 (280)
.... .=...-+..+|..++||=-+++... .+ +-.|..||+.+|++.+ ....|.|=+ |+.+
T Consensus 158 ~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~l 237 (377)
T PRK05601 158 RNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLL 237 (377)
T ss_pred cccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHH
Confidence 0000 0000011234444889977887763 44 3579999999998651 244566654 9999
Q ss_pred HHHHHHHHHHh
Q 023614 247 TLHAFLKIKDK 257 (280)
Q Consensus 247 T~~~F~~l~~~ 257 (280)
+...|.++++.
T Consensus 238 l~~l~~~~~~~ 248 (377)
T PRK05601 238 VARLYFALRAS 248 (377)
T ss_pred HHHHHHHhhcc
Confidence 99999997443
No 39
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.66 E-value=0.0017 Score=58.49 Aligned_cols=161 Identities=17% Similarity=0.196 Sum_probs=99.7
Q ss_pred CeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCC
Q 023614 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHA 118 (280)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~ 118 (280)
.+|.+|||-||+.... + .|||+|. .+ +.. .-.|+-. ++... .
T Consensus 3 ~~vv~D~ETTGl~~~~---------d-------------~IIeig~--v~--~~~----------~~~f~~l-v~P~~-~ 44 (232)
T PRK06309 3 ALIFYDTETTGTQIDK---------D-------------RIIEIAA--YN--GVT----------SESFQTL-VNPEI-P 44 (232)
T ss_pred cEEEEEeeCCCCCCCC---------C-------------EEEEEEE--Ec--Ccc----------ccEEEEE-eCCCC-C
Confidence 4899999999984211 1 3899997 22 211 1124433 44433 3
Q ss_pred CchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEecc-chhHHHHHHHhhCCCCCCCHHHHHHHHh
Q 023614 119 HALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHS-AYDFGYLVKCLTQRVLPEKLSEFVTRVG 197 (280)
Q Consensus 119 ~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg-~yD~gyL~k~l~~~~LP~~~~~F~~~l~ 197 (280)
..+++++. |||.=+...... +.....+.+.. ++ .+.-.+|++++ .||..+|-+.+-...+|..
T Consensus 45 I~~~a~~I---hGIt~e~v~~~p-~f~ev~~~~~~--fi-~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~--------- 108 (232)
T PRK06309 45 IPAEASKI---HGITTDEVADAP-KFPEAYQKFIE--FC-GTDNILVAHNNDAFDFPLLRKECRRHGLEPP--------- 108 (232)
T ss_pred CChhHHhh---cCCCHHHHhCCC-CHHHHHHHHHH--HH-cCCCEEEEeCCHHHHHHHHHHHHHHcCCCCC---------
Confidence 45555443 677666655433 22222222221 11 22346788884 6999999887753222211
Q ss_pred hhcCCCccchHHHHHhh-ccc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhh
Q 023614 198 VFFGEKVYDVKHLIRFC-TCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKH 258 (280)
Q Consensus 198 ~~Fp~~iyD~K~la~~~-~~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~ 258 (280)
+...+||-.+++.. +++ ..+|+.+++.++++. ..+|-|-+|++.|+.+|.+|.+.+
T Consensus 109 ---~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~~~~~--~~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 109 ---TLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEE--NQAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred ---CCcEEeHHHHHHHHcCCCCCCCHHHHHHHcCCCC--CCCCCcHHHHHHHHHHHHHHHHHH
Confidence 12277887777654 333 457999999999875 568999999999999999988765
No 40
>PTZ00315 2'-phosphotransferase; Provisional
Probab=97.65 E-value=0.0022 Score=65.09 Aligned_cols=171 Identities=16% Similarity=0.132 Sum_probs=109.8
Q ss_pred CeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccC-CCCCCCCCCCCCceEEEEeccccCcCc-
Q 023614 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDE-EGNLPDLGSGSTYYIWEFNFKDFDIAR- 116 (280)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~-~g~~p~~~~~~~~~~wqFNF~~F~~~~- 116 (280)
.||++|.|.+|..... . +.-.||++|...++. +|+ .+.+|..+ .....
T Consensus 57 ~~IV~DlETTgl~~~~---~----------------~~dEIIEIGaV~Vd~~ng~----------Ii~~F~~y-VkP~~~ 106 (582)
T PTZ00315 57 AYVVLDFEATCEADRR---I----------------EDAEVIEFPMVLVDARTAT----------PVAEFQRY-VRPVKN 106 (582)
T ss_pred eEEEEEEecCCCCCCC---C----------------CCCceEEEEEEEEEccCCE----------EEEEEEEE-ECCCCC
Confidence 6899999999963211 0 012499999999985 442 45667666 33322
Q ss_pred CCCchhHHHHHHHcCCCchhhhhcCCChHH----HHHHHHHccccc---CCCceEEEeccchhHH-HHHHHhh--C-CCC
Q 023614 117 HAHALDSVELLKRQGIDFEKNREFGIDSVR----FAELLMSSGLVL---NKDVTWVTFHSAYDFG-YLVKCLT--Q-RVL 185 (280)
Q Consensus 117 d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~----f~e~l~~Sglv~---~~~v~Wvtfhg~yD~g-yL~k~l~--~-~~L 185 (280)
...++...++ +||.=+.. ..+.++.. |.+.|..+++.. +.+ ..|...|.+|+. +|-+-+. + ..+
T Consensus 107 p~Ls~fct~L---TGITqe~V-~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~-~~vah~g~fDl~~fL~~e~~~~~~~g~ 181 (582)
T PTZ00315 107 PVLSRFCTEL---TGITQSMV-SRADPFPVVYCEALQFLAEAGLGDAPPLRS-YCVVTCGDWDLKTMLPSQMRVSGQQGT 181 (582)
T ss_pred CCCChhHhhh---cCcCHHHH-hcCCCHHHHHHHHHHHHhccccccccccCc-eEEEeccHHHHHHHHHHHHHHhhhcCC
Confidence 2455655555 77764444 45666553 334444443221 112 345566899995 7765443 1 245
Q ss_pred CCCHHHHHHHHhhhcCCCccchH-HHHHhh-c-----------cc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHH
Q 023614 186 PEKLSEFVTRVGVFFGEKVYDVK-HLIRFC-T-----------CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAF 251 (280)
Q Consensus 186 P~~~~~F~~~l~~~Fp~~iyD~K-~la~~~-~-----------~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F 251 (280)
|. .|.. .+|+| ++++.. + .+ ..+|..+++.+|++- .|..|.|=.|+.-|+.+|
T Consensus 182 p~-----------~f~~-widLk~~lar~l~p~~~~~~~~~~~~~~~~~L~~al~~lgL~~-eGr~HrAlDDA~ntA~L~ 248 (582)
T PTZ00315 182 PL-----------SFQR-WCNLKKYMSQLGFGNGSGCGGGATPPLGPSDMPDMLQMLGLPL-QGRHHSGIDDCRNIAAVL 248 (582)
T ss_pred Cc-----------ccce-EEEhHHHHHHHhCccccccccccccccCCcCHHHHHHHCCCCC-CCCCcCcHHHHHHHHHHH
Confidence 53 2444 66764 666643 2 12 247999999999998 899999999999999999
Q ss_pred HHHHHh
Q 023614 252 LKIKDK 257 (280)
Q Consensus 252 ~~l~~~ 257 (280)
.+|.+.
T Consensus 249 ~~Ll~~ 254 (582)
T PTZ00315 249 CELLRR 254 (582)
T ss_pred HHHHHc
Confidence 999876
No 41
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=97.64 E-value=0.0012 Score=61.98 Aligned_cols=155 Identities=19% Similarity=0.171 Sum_probs=100.4
Q ss_pred CeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccC--CCCCCCCCCCCCceEEEEeccccCcCc
Q 023614 39 PIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDE--EGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (280)
Q Consensus 39 ~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~--~g~~p~~~~~~~~~~wqFNF~~F~~~~ 116 (280)
.+|++|||-||+.... =.|||+|+..++. +|+.- .....|++. .+...
T Consensus 38 ~~vvlD~ETTGLd~~~----------------------d~IIEIg~V~v~~~~~g~i~-------~v~~~~~~l-v~P~~ 87 (294)
T PRK09182 38 LGVILDTETTGLDPRK----------------------DEIIEIGMVAFEYDDDGRIG-------DVLDTFGGL-QQPSR 87 (294)
T ss_pred eEEEEEeeCCCCCCCC----------------------CeEEEEEEEEEEecCCCcee-------eeeeEEEEE-eCCCC
Confidence 6899999999985321 1399999999975 45431 134556665 44433
Q ss_pred CCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhh---CCCCCCCHHHHH
Q 023614 117 HAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLT---QRVLPEKLSEFV 193 (280)
Q Consensus 117 d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~---~~~LP~~~~~F~ 193 (280)
...+++... |||.=+.....+++...+.+.+.. .-..|+++..+|.+||-+.+. +.+..-+...
T Consensus 88 -~I~~~~t~I---hGIt~e~v~~~~~~~~~l~~fl~~-------~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~-- 154 (294)
T PRK09182 88 -PIPPEITRL---TGITDEMVAGQTIDPAAVDALIAP-------ADLIIAHNAGFDRPFLERFSPVFATKPWACSVSE-- 154 (294)
T ss_pred -CCCHHHHHh---cCCCHHHHhcCCCcHHHHHHHhcC-------CCEEEEeCHHHHHHHHHHHHHhccCCcccccHHH--
Confidence 345666544 898888888878776666555422 236688999999999976542 1121111110
Q ss_pred HHHhhhcCCCccchHHHHHhhccc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHH
Q 023614 194 TRVGVFFGEKVYDVKHLIRFCTCL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIK 255 (280)
Q Consensus 194 ~~l~~~Fp~~iyD~K~la~~~~~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~ 255 (280)
.| . ...++ ...|+.|++.+| . ....|.|-+|++.|+.+|.++.
T Consensus 155 -----------i~--~---~~~~~~~~kL~~La~~~g-~--~~~aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 155 -----------ID--W---SARGFEGTKLGYLAGQAG-F--FHEGHRAVDDCQALLELLARPL 198 (294)
T ss_pred -----------Hh--h---ccccCCCCCHHHHHHHcC-C--CCCCcChHHHHHHHHHHHHHHH
Confidence 01 0 00112 346999999999 3 3567999999999999999754
No 42
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=97.55 E-value=0.00075 Score=56.78 Aligned_cols=69 Identities=16% Similarity=0.165 Sum_probs=47.0
Q ss_pred eEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhc---cccchHHHHHHH-cCCCccCCCcc
Q 023614 163 TWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCT---CLYGGLDRVCKA-LGVERVVGKSH 238 (280)
Q Consensus 163 ~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~---~l~~~L~~la~~-L~v~r~~g~~h 238 (280)
.+|.++..+|+++|- .+.|. .. +.|+-.+..... .-.-+|+.||+. ||++. ....|
T Consensus 79 vlVgHn~~fD~~~L~-----~~~~~-------------~~-~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~-~~~~H 138 (152)
T cd06144 79 ILVGHALKNDLKVLK-----LDHPK-------------KL-IRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDI-QEGEH 138 (152)
T ss_pred EEEEcCcHHHHHHhc-----CcCCC-------------cc-EEEeEEeeccccccCCCChhHHHHHHHHcCccc-CCCCc
Confidence 688988899999884 12222 02 455533322221 123589999997 69876 35679
Q ss_pred chhhhHHHHHHHH
Q 023614 239 QAGSDSLLTLHAF 251 (280)
Q Consensus 239 qAGsDs~lT~~~F 251 (280)
.|.+||+.|+++|
T Consensus 139 ~Al~DA~at~~l~ 151 (152)
T cd06144 139 SSVEDARAAMRLY 151 (152)
T ss_pred CcHHHHHHHHHHh
Confidence 9999999999887
No 43
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=97.47 E-value=0.0023 Score=71.15 Aligned_cols=168 Identities=22% Similarity=0.255 Sum_probs=110.7
Q ss_pred hhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCc
Q 023614 35 IDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDI 114 (280)
Q Consensus 35 i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~ 114 (280)
+.+..||++|+|.+|+... + =.|||+|....+ +|. ....|+.+ ++.
T Consensus 416 L~~~~~VVfDLETTGL~~~-------------~---------deIIEIgAV~V~-~G~----------iie~F~~~-V~P 461 (1437)
T PRK00448 416 LKDATYVVFDVETTGLSAV-------------Y---------DEIIEIGAVKIK-NGE----------IIDKFEFF-IKP 461 (1437)
T ss_pred hccCcEEEEEhhhcCCCCc-------------h---------hhhheeeeEEEe-CCe----------EeeeEEEE-ECC
Confidence 4568899999999997321 1 148889887765 332 33456665 444
Q ss_pred CcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHH
Q 023614 115 ARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVT 194 (280)
Q Consensus 115 ~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~ 194 (280)
. ....+.+.++ +||.=..+. .+.+.....+.+..- ..+..+|++++.||+++|-+.+...-+|.
T Consensus 462 ~-~~I~~~~~~L---TGIT~e~L~-~aps~~EaL~~f~~f----igg~vLVAHNa~FD~~fL~~~l~rlgl~~------- 525 (1437)
T PRK00448 462 G-HPLSAFTTEL---TGITDDMVK-DAPSIEEVLPKFKEF----CGDSILVAHNASFDVGFINTNYEKLGLEK------- 525 (1437)
T ss_pred C-CCCCHHHHHH---hCCCHHHHc-CCCCHHHHHHHHHHH----hCCCEEEEeCccccHHHHHHHHHHcCCcc-------
Confidence 3 2344444444 677766665 567666554444431 12457899999999999877664322221
Q ss_pred HHhhhcCCCccchHHHHHhhc-cc-cchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 195 RVGVFFGEKVYDVKHLIRFCT-CL-YGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 195 ~l~~~Fp~~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
+...+.|+--+++... .. ..+|..||+.+|++. .+ .|-|-+|++.|+.+|.+|.+...
T Consensus 526 -----l~~~~IDTLelar~l~p~~k~~kL~~LAk~lGL~~-~~-~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 526 -----IKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVEL-EH-HHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred -----ccccceeHHHHHHHHcCccccccHHHHHHHcCCCC-CC-CcChHHHHHHHHHHHHHHHHHHH
Confidence 1112567766655442 22 457999999999997 44 59999999999999999988765
No 44
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=97.32 E-value=0.0058 Score=54.81 Aligned_cols=165 Identities=19% Similarity=0.237 Sum_probs=105.8
Q ss_pred CCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcC
Q 023614 38 YPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARH 117 (280)
Q Consensus 38 ~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d 117 (280)
..||.+|+|-+|.... .-.||++|...+..+.... -.|..+ .+. ..
T Consensus 13 ~~~vv~D~ETtg~~~~----------------------~~~iieIgav~~~~~~i~~----------~~~~~~-v~P-~~ 58 (243)
T COG0847 13 TRFVVIDLETTGLNPK----------------------KDRIIEIGAVTLEDGRIVE----------RSFHTL-VNP-ER 58 (243)
T ss_pred CcEEEEecccCCCCCC----------------------CCceEEEEeEEEECCeeec----------ceeEEE-ECC-CC
Confidence 6899999999998541 1248899988776653321 113333 233 33
Q ss_pred CCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhC--CCCCCCHHHHHHH
Q 023614 118 AHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQ--RVLPEKLSEFVTR 195 (280)
Q Consensus 118 ~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~--~~LP~~~~~F~~~ 195 (280)
.+.+++... +||....+... .....-.+.+.. ++ ++.-.+|+++-++|.+||-+-+.. .+.|
T Consensus 59 ~i~~~~~~i---~git~e~l~~~-p~~~~v~~~~~~--~i-~~~~~~Vahna~fD~~fl~~~~~~~~~~~~--------- 122 (243)
T COG0847 59 PIPPEIFKI---HGITDEMLADA-PKFAEVLPEFLD--FI-GGLRLLVAHNAAFDVGFLRVESERLGIEIP--------- 122 (243)
T ss_pred CCChhhhhh---cCCCHHHHhcC-CCHHHHHHHHHH--HH-CCCCeEEEEchhhcHHHHHHHHHHcCCCcc---------
Confidence 344555444 67666666665 222222222211 11 222478899999999999666553 3333
Q ss_pred HhhhcCCCccchHHHHHhh-cc-ccchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHh
Q 023614 196 VGVFFGEKVYDVKHLIRFC-TC-LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 257 (280)
Q Consensus 196 l~~~Fp~~iyD~K~la~~~-~~-l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~ 257 (280)
+..++|+--+++.. ++ -+.+|+.+++.+|+++.....|.|-.|++++..+|.++...
T Consensus 123 -----~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 123 -----GDPVLDTLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred -----cCceehHHHHHHHHcCCCccchHHHHHHHcCCCcCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 22266776666654 44 35689999999999984345689999999999999999874
No 45
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=97.15 E-value=0.0047 Score=52.44 Aligned_cols=69 Identities=22% Similarity=0.229 Sum_probs=51.8
Q ss_pred ceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhc-cc----cchHHHHHHH-cCCCccC-
Q 023614 162 VTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCT-CL----YGGLDRVCKA-LGVERVV- 234 (280)
Q Consensus 162 v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~-~l----~~~L~~la~~-L~v~r~~- 234 (280)
-.+|.++-.+|+++|-. ..+. +.||-.|++... .+ +-+|+.|++. +|++-..
T Consensus 85 ~vlVgHn~~fD~~fL~~--------------------~~~~-~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~ 143 (161)
T cd06137 85 TILVGHSLQNDLDALRM--------------------IHTR-VVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGG 143 (161)
T ss_pred cEEEeccHHHHHHHHhC--------------------cCCC-eeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCC
Confidence 46788888899999732 1245 889999988764 33 4689999987 6876422
Q ss_pred CCccchhhhHHHHHHHH
Q 023614 235 GKSHQAGSDSLLTLHAF 251 (280)
Q Consensus 235 g~~hqAGsDs~lT~~~F 251 (280)
...|.|-.|+..|+++|
T Consensus 144 ~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 144 GEGHDSLEDALAAREVV 160 (161)
T ss_pred CCCCCcHHHHHHHHHHh
Confidence 45799999999999877
No 46
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=96.87 E-value=0.011 Score=49.77 Aligned_cols=98 Identities=19% Similarity=0.143 Sum_probs=61.4
Q ss_pred cCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHH
Q 023614 130 QGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKH 209 (280)
Q Consensus 130 ~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~ 209 (280)
+||.=+.+...+.+.....+.+.. ++ .++..+|..+-.+|+++|-. .-+. ++||-.
T Consensus 48 tGIt~~~l~~a~~~~~~v~~~~~~--fl-~~~~vlVgHn~~fD~~fL~~--------------------~~~~-~iDT~~ 103 (150)
T cd06145 48 SGITEEMLENVTTTLEDVQKKLLS--LI-SPDTILVGHSLENDLKALKL--------------------IHPR-VIDTAI 103 (150)
T ss_pred CCCCHHHhccCCCCHHHHHHHHHH--Hh-CCCCEEEEcChHHHHHHhhc--------------------cCCC-EEEcHH
Confidence 565555554444344333222221 12 22447888888999999732 1245 889988
Q ss_pred HHHhhcc-c-cchHHHHHHHc-CCCccC-CCccchhhhHHHHHHHH
Q 023614 210 LIRFCTC-L-YGGLDRVCKAL-GVERVV-GKSHQAGSDSLLTLHAF 251 (280)
Q Consensus 210 la~~~~~-l-~~~L~~la~~L-~v~r~~-g~~hqAGsDs~lT~~~F 251 (280)
+++.... . +-+|+.|++.+ +..-.. +..|.|-+|++.|+..|
T Consensus 104 l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 104 LFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELV 149 (150)
T ss_pred hccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHh
Confidence 8776432 2 35899999886 433212 46799999999999876
No 47
>PRK05359 oligoribonuclease; Provisional
Probab=96.70 E-value=0.042 Score=47.79 Aligned_cols=171 Identities=15% Similarity=0.156 Sum_probs=95.9
Q ss_pred hCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCc
Q 023614 37 RYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIAR 116 (280)
Q Consensus 37 ~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~ 116 (280)
.-+||++|+|-||+.... + .|||+|.-..+.+.+.- .-.|++. .....
T Consensus 2 ~~~~vvlD~ETTGLdp~~---------d-------------~IieIgaV~~~~~~~~~---------~~~~~~~-i~~~~ 49 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPER---------D-------------RIIEIATIVTDADLNIL---------AEGPVIA-IHQSD 49 (181)
T ss_pred CCcEEEEEeecCCCCCCC---------C-------------eEEEEEEEEEcCCceEc---------ccceEEE-ECCCH
Confidence 347999999999984321 1 28999999876554321 1124443 22211
Q ss_pred C---CCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHH--cccccCCCceEEEecc-chhHHHHHHHhhCCCCCCCHH
Q 023614 117 H---AHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMS--SGLVLNKDVTWVTFHS-AYDFGYLVKCLTQRVLPEKLS 190 (280)
Q Consensus 117 d---~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~--Sglv~~~~v~Wvtfhg-~yD~gyL~k~l~~~~LP~~~~ 190 (280)
. ...+.+...-..+|+. +...+.|.+.....+.+.. .+-+...+ .+++.|+ .+|.+||-+.+-
T Consensus 50 ~~l~~~~~~~~~ih~~tGIt-~~~l~~~~~~~e~~~~~l~fl~~~~~~~~-~~l~g~~v~FD~~FL~~~~~--------- 118 (181)
T PRK05359 50 EALAAMDEWNTRTHTRSGLI-DRVRASTVSEAEAEAQTLEFLKQWVPAGK-SPLCGNSIGQDRRFLARYMP--------- 118 (181)
T ss_pred HHhhccChHHHHhcccccCc-HHHHhcCCCHHHHHHHHHHHHHHhcCCCC-CceeecchhhCHHHHHHHHH---------
Confidence 1 1223333322234777 5666778877765444331 12222222 3455555 799999987763
Q ss_pred HHHHHHhhhcCCCccchHHHHHhhccccchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHhhCCC
Q 023614 191 EFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGN 261 (280)
Q Consensus 191 ~F~~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~~~ 261 (280)
.+...+..++.|+-.+.+.+..+...+ ..+++. ...|.|=+|.+-|.+++...++.++..
T Consensus 119 ----~~~~~l~~~~~Dv~tl~~l~r~~~P~~-----~~~~~~--~~~HRal~D~~~s~~~~~~~~~~~~~~ 178 (181)
T PRK05359 119 ----ELEAYFHYRNLDVSTLKELARRWKPEI-----LNGFKK--QGTHRALADIRESIAELKYYREHFFKL 178 (181)
T ss_pred ----HhcccCCCcccchhHHHHHHHHhChhh-----hhCCCC--cCCcccHHHHHHHHHHHHHHHHHhccC
Confidence 123334433556533322222233332 125555 345999999999999999999988753
No 48
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=96.63 E-value=0.017 Score=49.00 Aligned_cols=97 Identities=13% Similarity=0.070 Sum_probs=57.1
Q ss_pred cCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHH
Q 023614 130 QGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKH 209 (280)
Q Consensus 130 ~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~ 209 (280)
|||.-+.+. .+.+...-.+.+.. .+ . +-.+|.++-.+|+++|-.. ..|. . +-||=.
T Consensus 51 ~GIt~~~l~-~a~~~~~v~~~l~~--~l-~-~~vlV~Hn~~~D~~~l~~~----~~~~--------------~-~~Dt~~ 106 (157)
T cd06149 51 SGIRRQHLV-NATPFAVAQKEILK--IL-K-GKVVVGHAIHNDFKALKYF----HPKH--------------M-TRDTST 106 (157)
T ss_pred CCCCHHHHh-cCCCHHHHHHHHHH--Hc-C-CCEEEEeCcHHHHHHhccc----CCCc--------------C-EEECcc
Confidence 666665553 46665544443332 22 2 3467887777999887422 1111 1 334422
Q ss_pred H--HHh---hccc-cchHHHHHHHc---CCCccCCCccchhhhHHHHHHHH
Q 023614 210 L--IRF---CTCL-YGGLDRVCKAL---GVERVVGKSHQAGSDSLLTLHAF 251 (280)
Q Consensus 210 l--a~~---~~~l-~~~L~~la~~L---~v~r~~g~~hqAGsDs~lT~~~F 251 (280)
+ ++. .+.. +-+|..|++.+ +++. .+..|.|-+||..|+..|
T Consensus 107 l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~-~~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 107 IPLLNRKAGFPENCRVSLKVLAKRLLHRDIQV-GRQGHSSVEDARATMELY 156 (157)
T ss_pred cccchhhcCCcccCChhHHHHHHHHcChhhcC-CCCCcCcHHHHHHHHHHh
Confidence 1 111 1112 35899999998 5665 456799999999999887
No 49
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=95.65 E-value=0.29 Score=40.64 Aligned_cols=84 Identities=17% Similarity=0.323 Sum_probs=55.6
Q ss_pred ccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcccc--chHHHHHHH-cC-CCc
Q 023614 157 VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLY--GGLDRVCKA-LG-VER 232 (280)
Q Consensus 157 v~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~--~~L~~la~~-L~-v~r 232 (280)
+.+++++.|.++..+|+-.|.+.+ | ...++ ++|+ .++..+.+.. .||..+++. +| ...
T Consensus 73 l~~~~i~kv~~n~~~D~~~L~~~~-~---------------i~~~~-~~D~-~l~~~~l~~~~~~~L~~L~~~~l~~~~~ 134 (176)
T PF01612_consen 73 LEDPNIIKVGHNAKFDLKWLYRSF-G---------------IDLKN-VFDT-MLAAYLLDPTRSYSLKDLAEEYLGNIDL 134 (176)
T ss_dssp HTTTTSEEEESSHHHHHHHHHHHH-T---------------S--SS-EEEH-HHHHHHTTTSTTSSHHHHHHHHHSEEE-
T ss_pred HhCCCccEEEEEEechHHHHHHHh-c---------------cccCC-ccch-hhhhhcccccccccHHHHHHHHhhhccC
Confidence 347788899988889999988862 1 22224 9999 5555553332 589999875 56 211
Q ss_pred c----CC--C---------ccchhhhHHHHHHHHHHHHHhh
Q 023614 233 V----VG--K---------SHQAGSDSLLTLHAFLKIKDKH 258 (280)
Q Consensus 233 ~----~g--~---------~hqAGsDs~lT~~~F~~l~~~~ 258 (280)
. .+ . ..=|+.|+.+|.+.|-+|....
T Consensus 135 ~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 135 DKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred cHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 0 11 1 1238889999999999998753
No 50
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=95.58 E-value=0.091 Score=50.67 Aligned_cols=90 Identities=23% Similarity=0.363 Sum_probs=57.6
Q ss_pred HHHHHHHHHcccccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhc-cccchHHH
Q 023614 145 VRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCT-CLYGGLDR 223 (280)
Q Consensus 145 ~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~-~l~~~L~~ 223 (280)
..|.++|.. ++|+=|-.++..|+..|.+.+ .-+|. . +||||..++.|. +.+.||.+
T Consensus 60 ~~l~~Ll~d------~~v~KIfHaa~~DL~~l~~~~--g~~p~--------------p-lfdTqiAa~l~g~~~~~gl~~ 116 (361)
T COG0349 60 PPLVALLAD------PNVVKIFHAARFDLEVLLNLF--GLLPT--------------P-LFDTQIAAKLAGFGTSHGLAD 116 (361)
T ss_pred chHHHHhcC------CceeeeeccccccHHHHHHhc--CCCCC--------------c-hhHHHHHHHHhCCcccccHHH
Confidence 345555543 333334334559999888887 23443 4 999999999995 33779999
Q ss_pred HHHH-cCCCccCCCccc----------------hhhhHHHHHHHHHHHHHhhC
Q 023614 224 VCKA-LGVERVVGKSHQ----------------AGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 224 la~~-L~v~r~~g~~hq----------------AGsDs~lT~~~F~~l~~~~~ 259 (280)
+.++ +||+ +.+.|| |-+|...=...+-+|.+..-
T Consensus 117 Lv~~ll~v~--ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~ 167 (361)
T COG0349 117 LVEELLGVE--LDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELA 167 (361)
T ss_pred HHHHHhCCc--ccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8876 5765 233332 56666666666777766654
No 51
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=95.24 E-value=0.49 Score=40.55 Aligned_cols=165 Identities=15% Similarity=0.195 Sum_probs=88.0
Q ss_pred eeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCCC
Q 023614 40 IISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAH 119 (280)
Q Consensus 40 fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~ 119 (280)
+|.+|+|-+|+... . + .|||+|.-.++.++. .....|+.. .+....+-
T Consensus 1 lv~iD~ETTGl~p~-------~--d-------------~IieIgaV~~~~~~~---------~i~~~f~~~-i~p~~~~~ 48 (173)
T cd06135 1 LVWIDLEMTGLDPE-------K--D-------------RILEIACIITDGDLN---------IIAEGPELV-IHQPDEVL 48 (173)
T ss_pred CEEEEEecCCCCCC-------C--C-------------eeEEEEEEEEeCCCc---------eecCceeEE-ECCCHHHh
Confidence 57899999998521 1 1 289999998865432 122345554 33332211
Q ss_pred ---chhHHHHHHHcCCCchhhhhcCCChHHHHHHHHH--cccccCCCceEEEecc-chhHHHHHHHhhCCCCCCCHHHHH
Q 023614 120 ---ALDSVELLKRQGIDFEKNREFGIDSVRFAELLMS--SGLVLNKDVTWVTFHS-AYDFGYLVKCLTQRVLPEKLSEFV 193 (280)
Q Consensus 120 ---~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~--Sglv~~~~v~Wvtfhg-~yD~gyL~k~l~~~~LP~~~~~F~ 193 (280)
.+.+.+.-..+|+. +.....|.+.....+.+.. .+.+ ..+-.++..|+ .+|++||-+.+..
T Consensus 49 ~~~~~~~~~ih~~tgIt-~~~l~~~~~~~~vl~~~~~f~~~~~-~~~~~~lvgh~~~FD~~fL~~~~~~----------- 115 (173)
T cd06135 49 DGMDEWCTEMHTKSGLT-ERVRASTVTLAQAEAELLEFIKKYV-PKGKSPLAGNSVHQDRRFLDKYMPE----------- 115 (173)
T ss_pred hhccHHHHHcccccccH-HHHHhCCCCHHHHHHHHHHHHHHhc-CCCCCceeecchhhCHHHHHHHHHH-----------
Confidence 11222222223654 2233555555543332221 0111 11224566677 8999999877641
Q ss_pred HHHhhhcCCCccchHHHHHhhccccchHHHHHHHcCCCccCCCccchhhhHHHHHHHHHHHHHh
Q 023614 194 TRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDK 257 (280)
Q Consensus 194 ~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~~l~~~ 257 (280)
....+..+..|+..+.+..+.+...+.+ ++++. +..|.|=+|+.-|...+...++.
T Consensus 116 --~~~~~~~~~~D~~~l~~l~~~l~p~~~~----~~~~~--~~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 116 --LEEYLHYRILDVSSIKELARRWYPEIYR----KAPKK--KGTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred --HhccCCcchhhHHHHHHHHHHhCcHhhh----cCCCC--CCCcchHHHHHHHHHHHHHHHHH
Confidence 1122333366774443333333333333 45554 66799999999999988887664
No 52
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=95.06 E-value=0.75 Score=40.23 Aligned_cols=89 Identities=20% Similarity=0.149 Sum_probs=57.9
Q ss_pred ccCCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcc------------ccchHHHH
Q 023614 157 VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC------------LYGGLDRV 224 (280)
Q Consensus 157 v~~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~------------l~~~L~~l 224 (280)
+.++++.=|.+....|+..|.+-+-. ++. . ..-|.+++|+..++..... -..||+.+
T Consensus 78 l~d~~i~KVg~~~~~D~~~L~~~~~~--~~~-~--------~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l 146 (193)
T cd06146 78 FEDPDVLKLGFGFKQDLKALSASYPA--LKC-M--------FERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADL 146 (193)
T ss_pred hCCCCeeEEEechHHHHHHHHHhcCc--ccc-c--------cccCCceEEHHHHHHHHhhccccccccccCcccCCHHHH
Confidence 34667666777777999998876531 110 0 0113459999988886532 23589999
Q ss_pred HHH-cCCCc------------c--CCCccchhhhHHHHHHHHHHHHH
Q 023614 225 CKA-LGVER------------V--VGKSHQAGSDSLLTLHAFLKIKD 256 (280)
Q Consensus 225 a~~-L~v~r------------~--~g~~hqAGsDs~lT~~~F~~l~~ 256 (280)
++. ||++- + ....+-|..|++....+|-+|.+
T Consensus 147 ~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 147 VQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred HHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 876 45421 0 11235699999999999999863
No 53
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=94.52 E-value=1 Score=37.93 Aligned_cols=80 Identities=18% Similarity=0.141 Sum_probs=56.1
Q ss_pred CCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhccc--cchHHHHHHHc-CCCcc--
Q 023614 159 NKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCL--YGGLDRVCKAL-GVERV-- 233 (280)
Q Consensus 159 ~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l--~~~L~~la~~L-~v~r~-- 233 (280)
+++++.|.++...|+-.|.+.. |-. +.+ ++|+..++..+... ..||+.+++.+ +++-.
T Consensus 71 ~~~i~kv~~~~k~D~~~L~~~~-g~~---------------~~~-~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~ 133 (170)
T cd06141 71 DPSILKVGVGIKGDARKLARDF-GIE---------------VRG-VVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKP 133 (170)
T ss_pred CCCeeEEEeeeHHHHHHHHhHc-CCC---------------CCC-eeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCC
Confidence 5677788887788887775543 211 234 89999999888643 35899998874 54210
Q ss_pred --------------CCCccchhhhHHHHHHHHHHHH
Q 023614 234 --------------VGKSHQAGSDSLLTLHAFLKIK 255 (280)
Q Consensus 234 --------------~g~~hqAGsDs~lT~~~F~~l~ 255 (280)
....|-|..|++++..+|.+|+
T Consensus 134 k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 134 KKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 1234679999999999999886
No 54
>PRK05755 DNA polymerase I; Provisional
Probab=94.51 E-value=0.82 Score=49.06 Aligned_cols=84 Identities=20% Similarity=0.195 Sum_probs=59.1
Q ss_pred CCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcc-ccchHHHHHHHc-CCCc----
Q 023614 159 NKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC-LYGGLDRVCKAL-GVER---- 232 (280)
Q Consensus 159 ~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~-l~~~L~~la~~L-~v~r---- 232 (280)
++.+..|+++.-+|+.+|.+. |.++| +. ++||..++..+.. ..-||+.+++.. +++-
T Consensus 368 d~~v~kV~HNakfDl~~L~~~--gi~~~--------------~~-~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~ 430 (880)
T PRK05755 368 DPAIKKVGQNLKYDLHVLARY--GIELR--------------GI-AFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFE 430 (880)
T ss_pred CCCCcEEEeccHhHHHHHHhC--CCCcC--------------CC-cccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchH
Confidence 455667777778999988752 44433 24 8999998887742 236899988774 5441
Q ss_pred -----c--------CCCccchhhhHHHHHHHHHHHHHhhC
Q 023614 233 -----V--------VGKSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 233 -----~--------~g~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
. ....|.|..|+.+|..+|.+|++.+-
T Consensus 431 ~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 431 EVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred HhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0 01236799999999999999998764
No 55
>PRK10829 ribonuclease D; Provisional
Probab=94.38 E-value=1.4 Score=42.90 Aligned_cols=84 Identities=18% Similarity=0.229 Sum_probs=58.0
Q ss_pred CCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhc-cccchHHHHHHH-cCCCcc---
Q 023614 159 NKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCT-CLYGGLDRVCKA-LGVERV--- 233 (280)
Q Consensus 159 ~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~-~l~~~L~~la~~-L~v~r~--- 233 (280)
++++.-|-+.+.+|+..|.+.+ | ..|..++||...+..+. +..-||..|.++ ||+.-+
T Consensus 72 ~~~ivKV~H~~~~Dl~~l~~~~-g----------------~~p~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~ 134 (373)
T PRK10829 72 DPQVTKFLHAGSEDLEVFLNAF-G----------------ELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSE 134 (373)
T ss_pred CCCeEEEEeChHhHHHHHHHHc-C----------------CCcCCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCccc
Confidence 5554445555679999987754 2 12333999999998885 335689998765 777421
Q ss_pred ---------CC--CccchhhhHHHHHHHHHHHHHhhC
Q 023614 234 ---------VG--KSHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 234 ---------~g--~~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
-. ..+=|..|+.....+|-+|++..-
T Consensus 135 ~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 135 SRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11 223489999999999999888764
No 56
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=91.55 E-value=10 Score=36.69 Aligned_cols=84 Identities=20% Similarity=0.326 Sum_probs=55.2
Q ss_pred CCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcc-ccchHHHHHHH-cCCCccCC-
Q 023614 159 NKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC-LYGGLDRVCKA-LGVERVVG- 235 (280)
Q Consensus 159 ~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~-l~~~L~~la~~-L~v~r~~g- 235 (280)
++++++|.++..+|+-.|.+.. ..+|. . +|||...+..+.. ...||..+++. ||++-.-+
T Consensus 68 d~~i~KV~h~~k~Dl~~L~~~~--~~~~~--------------~-~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~ 130 (367)
T TIGR01388 68 DESVVKVLHAASEDLEVFLNLF--GELPQ--------------P-LFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSE 130 (367)
T ss_pred CCCceEEEeecHHHHHHHHHHh--CCCCC--------------C-cccHHHHHHHhCCCCCccHHHHHHHHcCCCCCccc
Confidence 5678899888888888775442 22332 3 8999988887752 34589998876 56642111
Q ss_pred ----------C---ccchhhhHHHHHHHHHHHHHhhC
Q 023614 236 ----------K---SHQAGSDSLLTLHAFLKIKDKHF 259 (280)
Q Consensus 236 ----------~---~hqAGsDs~lT~~~F~~l~~~~~ 259 (280)
. .+-|..|+......+-+|++..-
T Consensus 131 ~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 131 SRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLE 167 (367)
T ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0 11377778777788888877653
No 57
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=91.34 E-value=5.6 Score=33.37 Aligned_cols=81 Identities=14% Similarity=0.107 Sum_probs=54.9
Q ss_pred CCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcc-ccchHHHHHHH-cCCCc----
Q 023614 159 NKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC-LYGGLDRVCKA-LGVER---- 232 (280)
Q Consensus 159 ~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~-l~~~L~~la~~-L~v~r---- 232 (280)
++++..|.+....|+-.|.+.. |-+ +.+ ++||..++..+.. -+.||+.+++. ||++-
T Consensus 65 d~~i~Kvg~~~k~D~~~L~~~~-gi~---------------~~~-~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~ 127 (161)
T cd06129 65 NPSIVKALHGIEGDLWKLLRDF-GEK---------------LQR-LFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSI 127 (161)
T ss_pred CCCEEEEEeccHHHHHHHHHHc-CCC---------------ccc-HhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccc
Confidence 5677778777778877765432 211 223 7899888887643 24589999887 56532
Q ss_pred --------c--CCCccchhhhHHHHHHHHHHHHH
Q 023614 233 --------V--VGKSHQAGSDSLLTLHAFLKIKD 256 (280)
Q Consensus 233 --------~--~g~~hqAGsDs~lT~~~F~~l~~ 256 (280)
+ ....|-|..|++....+|-+|++
T Consensus 128 ~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 128 SCADWSYRPLTEDQKLYAAADVYALLIIYTKLRN 161 (161)
T ss_pred eeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 1 11335699999999999999863
No 58
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=84.04 E-value=4 Score=45.13 Aligned_cols=85 Identities=25% Similarity=0.305 Sum_probs=62.0
Q ss_pred eEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhc-cc-cchHHHHHHHcCCCccCCCccch
Q 023614 163 TWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCT-CL-YGGLDRVCKALGVERVVGKSHQA 240 (280)
Q Consensus 163 ~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~-~l-~~~L~~la~~L~v~r~~g~~hqA 240 (280)
.-|+.+..+|+|||-.-+.--.||+-. . . +.||=-||+.+. .+ +.+|..|+++|+|.- ...|-|
T Consensus 503 IlVAHNasFD~gFl~~~~~k~~~~~~~----------~-p-vIDTL~lar~L~P~~ksh~Lg~l~kk~~v~l--e~hHRA 568 (1444)
T COG2176 503 ILVAHNASFDMGFLNTNYEKYGLEPLT----------N-P-VIDTLELARALNPEFKSHRLGTLCKKLGVEL--ERHHRA 568 (1444)
T ss_pred EEEeccCccchhHHHHHHHHhCCcccc----------C-c-hhhHHHHHHHhChhhhhcchHHHHHHhCccH--HHhhhh
Confidence 567778889999985444311111100 1 2 568877877764 44 468999999999986 678999
Q ss_pred hhhHHHHHHHHHHHHHhhCCC
Q 023614 241 GSDSLLTLHAFLKIKDKHFGN 261 (280)
Q Consensus 241 GsDs~lT~~~F~~l~~~~~~~ 261 (280)
-+||-.|+++|++|.+...+.
T Consensus 569 ~yDaeat~~vf~~f~~~~ke~ 589 (1444)
T COG2176 569 DYDAEATAKVFFVFLKDLKEK 589 (1444)
T ss_pred hhhHHHHHHHHHHHHHHHHHh
Confidence 999999999999998887643
No 59
>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=83.33 E-value=0.6 Score=38.91 Aligned_cols=73 Identities=25% Similarity=0.311 Sum_probs=39.6
Q ss_pred ceEEEecc-chhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhccccc-hHHHHHHHcCCCccCCCccc
Q 023614 162 VTWVTFHS-AYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYG-GLDRVCKALGVERVVGKSHQ 239 (280)
Q Consensus 162 v~Wvtfhg-~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~~-~L~~la~~L~v~r~~g~~hq 239 (280)
-.+|+||| .||+.+|-+.+..-.+|. +....|+..+++.... .+ +|..||+.||++| . ....
T Consensus 58 ~~iv~yng~~FD~p~L~~~~~~~~~~~-------------~~~~iDl~~~~~~~~~-~~~~Lk~ve~~lg~~~-~-~~~~ 121 (164)
T PF13482_consen 58 DNIVTYNGKNFDIPFLKRRAKRYGLPP-------------PFNHIDLLKIIKKHFL-ESYSLKNVEKFLGIER-R-DDDI 121 (164)
T ss_dssp --EEESSTTTTHHHHHHHHH-HHHH---------------GGGEEEHHHHHT-TTS-CCTT--SHHH-------------
T ss_pred CeEEEEeCcccCHHHHHHHHHHcCCCc-------------ccchhhHHHHHHhccC-CCCCHHHHhhhccccc-c-cCCC
Confidence 37999998 699999999884323443 4347799888865533 44 8999999999998 2 2345
Q ss_pred hhhhHHHHHHH
Q 023614 240 AGSDSLLTLHA 250 (280)
Q Consensus 240 AGsDs~lT~~~ 250 (280)
.|+++...-.-
T Consensus 122 ~G~~~~~~~~~ 132 (164)
T PF13482_consen 122 SGSESVKLYKE 132 (164)
T ss_dssp HHHHHHHHHH-
T ss_pred CHHHHHHHHHH
Confidence 78887766543
No 60
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=81.16 E-value=5.6 Score=35.70 Aligned_cols=93 Identities=20% Similarity=0.252 Sum_probs=56.9
Q ss_pred CceEEEecc-chhHHHH-HHHhh-CCCCCCCHHHHH----HHHhhhcCCCccchHHHHHhh-ccccchHHHHHHHcCCCc
Q 023614 161 DVTWVTFHS-AYDFGYL-VKCLT-QRVLPEKLSEFV----TRVGVFFGEKVYDVKHLIRFC-TCLYGGLDRVCKALGVER 232 (280)
Q Consensus 161 ~v~Wvtfhg-~yD~gyL-~k~l~-~~~LP~~~~~F~----~~l~~~Fp~~iyD~K~la~~~-~~l~~~L~~la~~L~v~r 232 (280)
+-++|+|+| ++|+-|| .++|. |-++|.-.+.=- ...+.|--. -.|+.-+-..- ..-+.+|..||..||+|-
T Consensus 52 ~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~-H~DLmd~l~~~g~~~~~sLd~la~~lgiPg 130 (209)
T PF10108_consen 52 NPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSER-HLDLMDLLSFYGAKARTSLDELAALLGIPG 130 (209)
T ss_pred CCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcc-cccHHHHHhccCccccCCHHHHHHHcCCCC
Confidence 457999997 6999998 56665 467776443211 111111112 34544332222 123568999999999974
Q ss_pred cCCCccc--------------------hhhhHHHHHHHHHHHHHh
Q 023614 233 VVGKSHQ--------------------AGSDSLLTLHAFLKIKDK 257 (280)
Q Consensus 233 ~~g~~hq--------------------AGsDs~lT~~~F~~l~~~ 257 (280)
+..- --.|.+-|..+|.|+...
T Consensus 131 ---K~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~ 172 (209)
T PF10108_consen 131 ---KDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELL 172 (209)
T ss_pred ---CCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 2222 235799999999998765
No 61
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=73.88 E-value=16 Score=30.74 Aligned_cols=85 Identities=19% Similarity=0.171 Sum_probs=56.7
Q ss_pred CCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcc-c-cchHHHHHHHc-CCCc---
Q 023614 159 NKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC-L-YGGLDRVCKAL-GVER--- 232 (280)
Q Consensus 159 ~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~-l-~~~L~~la~~L-~v~r--- 232 (280)
+.++++|+++..+|+.+|.+. |-++ +..++||..++..+.. . +.+|+.+++.+ +.+-
T Consensus 65 ~~~~~~v~hn~k~d~~~l~~~--gi~~---------------~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~ 127 (193)
T cd06139 65 DPSIKKVGQNLKFDLHVLANH--GIEL---------------RGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISF 127 (193)
T ss_pred CCCCcEEeeccHHHHHHHHHC--CCCC---------------CCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccH
Confidence 345678888889999988642 3232 2337899988887743 3 45888888764 4320
Q ss_pred --------------cCC---CccchhhhHHHHHHHHHHHHHhhCC
Q 023614 233 --------------VVG---KSHQAGSDSLLTLHAFLKIKDKHFG 260 (280)
Q Consensus 233 --------------~~g---~~hqAGsDs~lT~~~F~~l~~~~~~ 260 (280)
... ..|.|..|+..+...+-+|.+..-+
T Consensus 128 ~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 128 EDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred HHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 000 1234888899999999999887643
No 62
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=62.99 E-value=7.6 Score=34.40 Aligned_cols=69 Identities=20% Similarity=0.254 Sum_probs=41.9
Q ss_pred eEEEecc-chhHHHHHH-Hhh-CCCCCCCHHHHHHH---HhhhcCCCccchHHHHHhhccc-cchHHHHHHHcCCCc
Q 023614 163 TWVTFHS-AYDFGYLVK-CLT-QRVLPEKLSEFVTR---VGVFFGEKVYDVKHLIRFCTCL-YGGLDRVCKALGVER 232 (280)
Q Consensus 163 ~Wvtfhg-~yD~gyL~k-~l~-~~~LP~~~~~F~~~---l~~~Fp~~iyD~K~la~~~~~l-~~~L~~la~~L~v~r 232 (280)
.+|+|+| ++|+-||.+ .+. |-++|.......+. ...+-.. .+|+-.+.+....+ +.+|..||+.||+++
T Consensus 95 ~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~-h~DL~~~~~~~~~~~~~~L~~va~~lG~~~ 170 (208)
T cd05782 95 RLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSER-HLDLMDLLAFYGARARASLDLLAKLLGIPG 170 (208)
T ss_pred EEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCC-cccHHHHHhccCccCCCCHHHHHHHhCCCC
Confidence 6899998 799999854 333 45556533221110 1111123 66876666554332 457999999999965
No 63
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=60.26 E-value=31 Score=35.66 Aligned_cols=173 Identities=17% Similarity=0.115 Sum_probs=89.8
Q ss_pred CHHHHHHHHH--HHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCCCCCCCC
Q 023614 23 NLISEFERIR--ALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGS 100 (280)
Q Consensus 23 Nl~~e~~~I~--~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p~~~~~~ 100 (280)
+-+.||..+. ++.+...||.+|.|++--...+ + +.+.|+|++.-
T Consensus 396 ~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~------d-------------sk~~IlQif~~--------------- 441 (617)
T KOG2207|consen 396 GNEKELRDLLLESLSEELRYVGIDSEWKPSKKVS------D-------------SKLAILQIFFK--------------- 441 (617)
T ss_pred CCHHHHHHHHHHHhhhcCEEEEEccccCcccCCC------h-------------hHHHHHHHHhc---------------
Confidence 3345555555 7677889999999997641111 1 12457787642
Q ss_pred CceEEEEeccccCcCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHH-HcccccCCCceEEEeccchhHHHHHHH
Q 023614 101 TYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLM-SSGLVLNKDVTWVTFHSAYDFGYLVKC 179 (280)
Q Consensus 101 ~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~-~Sglv~~~~v~Wvtfhg~yD~gyL~k~ 179 (280)
-++|-.+.- +.+..+++-...+.++=|.=....+-|.+...--+.+. +++-. +-.+ =+-+-++.+.++-
T Consensus 442 -~~v~Lidc~----~l~~~~se~w~~~~s~if~s~~i~kvGf~~~eDL~~l~~s~pa~-~~q~----ki~~~~l~~~~~k 511 (617)
T KOG2207|consen 442 -DCVYLIDCV----KLENLASEIWHLLLSQIFESKSILKVGFSMREDLEVLEASSPAL-RFQM----KIEGLQLVSCVLK 511 (617)
T ss_pred -CeEEEeehH----HhhhchHHHHHHHHHHHccCCceeeeecchhhhHHHHHhhhhhh-hhcc----cccchHHHHHHHH
Confidence 377766543 22233334455666666666666677776665555544 33311 1000 0111222222222
Q ss_pred hhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhccccchHHHHHHH-cCCCcc-----------CCCccc---hhhhH
Q 023614 180 LTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKA-LGVERV-----------VGKSHQ---AGSDS 244 (280)
Q Consensus 180 l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~-L~v~r~-----------~g~~hq---AGsDs 244 (280)
|. .+ +.|.---...+..-.+||+.|+.. ||+.-+ .=..|| ||-|+
T Consensus 512 l~-------------------e~-~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa 571 (617)
T KOG2207|consen 512 LA-------------------EN-VIDLPLSIENLNEATKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDA 571 (617)
T ss_pred HH-------------------HH-HhcccchhhhhcchhhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcc
Confidence 21 11 222212222222234677777764 332110 112355 89999
Q ss_pred HHHHHHHHHHHHhhC
Q 023614 245 LLTLHAFLKIKDKHF 259 (280)
Q Consensus 245 ~lT~~~F~~l~~~~~ 259 (280)
.....+|.+++++--
T Consensus 572 ~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 572 VVLVEIFKKVCSVVE 586 (617)
T ss_pred hhhHHHHHHHHhhcc
Confidence 999999999988753
No 64
>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=56.62 E-value=11 Score=31.83 Aligned_cols=30 Identities=23% Similarity=0.195 Sum_probs=27.1
Q ss_pred ecCccCHHHHHHHHHHHhhhCCeeEeeecc
Q 023614 18 EVFEFNLISEFERIRALIDRYPIISMDTEF 47 (280)
Q Consensus 18 eVw~~Nl~~e~~~I~~~i~~~~fIAiDtEF 47 (280)
-|.+-|+++.++.|.+.-++.-.||||.-.
T Consensus 43 PVHA~NL~e~l~~I~~~~~~~~iIAIDAcL 72 (140)
T TIGR02841 43 PVHAKNLEEKLKIIKKKHPNPFIIAIDACL 72 (140)
T ss_pred CcccccHHHHHHHHHHhCCCCeEEEEECcc
Confidence 489999999999999988899999999855
No 65
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=50.48 E-value=28 Score=24.61 Aligned_cols=33 Identities=30% Similarity=0.457 Sum_probs=25.5
Q ss_pred chhHHHHHHHcCCCc---------hhhhhcCCChHHHHHHHH
Q 023614 120 ALDSVELLKRQGIDF---------EKNREFGIDSVRFAELLM 152 (280)
Q Consensus 120 ~~~Si~fL~~~G~DF---------~k~~~~GI~~~~f~e~l~ 152 (280)
.+.+.+.+.++|||| ....+.||++..+.+.|.
T Consensus 12 ~p~~a~vf~~~gIDfCCgG~~~L~eA~~~~~ld~~~vl~~L~ 53 (56)
T PF04405_consen 12 DPRAARVFRKYGIDFCCGGNRSLEEACEEKGLDPEEVLEELN 53 (56)
T ss_pred ChHHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHH
Confidence 467889999999999 455678888887766653
No 66
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=47.46 E-value=22 Score=32.57 Aligned_cols=99 Identities=18% Similarity=0.153 Sum_probs=59.2
Q ss_pred eccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhccccchHHHHHHHcCCCccCCCccchhhhHHH
Q 023614 167 FHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLL 246 (280)
Q Consensus 167 fhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~L~v~r~~g~~hqAGsDs~l 246 (280)
|-.-||+-|++|...+ +-.-+.|+...|...= ...+...-...|-. |+.+..+| ...-...+-.++|
T Consensus 197 fP~fYDik~v~ks~~~--~~KglQei~ndlql~r---------~g~QhQagsdaLlT-a~~ff~~R-~~~F~~sig~~ll 263 (299)
T COG5228 197 FPNFYDIKLVYKSVLN--NSKGLQEIKNDLQLQR---------SGQQHQAGSDALLT-ADEFFLPR-FSIFTTSIGQSLL 263 (299)
T ss_pred CccccchHHHHHhhhh--hhhHHHHhcCcHhhhc---------cchhhhccchhhhh-hHHhcchh-hheecccccHHHH
Confidence 5577999999876643 2222333333322110 00000001123444 88899998 5665666777888
Q ss_pred HHHHHHHHHHhh---CCCccccccccceEecCCCC
Q 023614 247 TLHAFLKIKDKH---FGNEYELQKYANVLHGLELL 278 (280)
Q Consensus 247 T~~~F~~l~~~~---~~~~~~~~~~~g~i~Gl~~~ 278 (280)
....++.+++.- |....+++++.|++||+..+
T Consensus 264 ~~L~g~~~~~~sl~~~~~~t~f~~~~g~~~gi~~~ 298 (299)
T COG5228 264 MLLSGCQLSKLSLHKFPNGTDFAKYQGVIYGIDGD 298 (299)
T ss_pred HHHhccccCCchheeCCCcccHhhcCCcccCCCCC
Confidence 887788877653 34455789999999999653
No 67
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=42.96 E-value=1e+02 Score=24.19 Aligned_cols=53 Identities=17% Similarity=0.179 Sum_probs=33.7
Q ss_pred CCCceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcc-c-cchHHHHHHHc
Q 023614 159 NKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC-L-YGGLDRVCKAL 228 (280)
Q Consensus 159 ~~~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~-l-~~~L~~la~~L 228 (280)
+++++-|.++..+|+..|.+.. .. +|..++||..++..+.. . +.+|+.+++.+
T Consensus 52 ~~~~~~v~~~~k~d~~~L~~~~--~~---------------~~~~~~D~~~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 52 DEDITKVGHDAKFDLVVLARDG--IE---------------LPGNIFDTMLAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred CCCCcEEeccHHHHHHHHHHCC--CC---------------CCCCcccHHHHHHHhCCCCCcCCHHHHHHHH
Confidence 4455667776667776665432 11 22338999888887743 2 35899998874
No 68
>PF06866 DUF1256: Protein of unknown function (DUF1256); InterPro: IPR009665 This family consists of several uncharacterised bacterial proteins, which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown.
Probab=40.66 E-value=25 Score=30.44 Aligned_cols=31 Identities=23% Similarity=0.241 Sum_probs=27.6
Q ss_pred ecCccCHHHHHHHHHHHhhhCCeeEeeeccc
Q 023614 18 EVFEFNLISEFERIRALIDRYPIISMDTEFP 48 (280)
Q Consensus 18 eVw~~Nl~~e~~~I~~~i~~~~fIAiDtEFp 48 (280)
-|.+-|+++-++.|.+.-++.-.||||.-..
T Consensus 67 PVHA~NL~e~l~~I~~~~~~~~IIAIDAcLG 97 (163)
T PF06866_consen 67 PVHALNLEETLNEIKKKHPNPFIIAIDACLG 97 (163)
T ss_pred CcchhhHHHHHHHHHHHCCCCeEEEEECCCC
Confidence 4899999999999999888889999998663
No 69
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=39.92 E-value=58 Score=30.29 Aligned_cols=76 Identities=22% Similarity=0.299 Sum_probs=51.8
Q ss_pred eEEEecc-chhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcc--c-cchHHHHHHHcCCCccCCCcc
Q 023614 163 TWVTFHS-AYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC--L-YGGLDRVCKALGVERVVGKSH 238 (280)
Q Consensus 163 ~Wvtfhg-~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~--l-~~~L~~la~~L~v~r~~g~~h 238 (280)
.||||+| ++|.-|+-++.. ..+|-+ ++.+=||.=|.++..-. | .+||..|-+.||+.|..-.
T Consensus 158 ~lvsfNGkaFD~PfikR~v~-~~~el~-----------l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~R~edt-- 223 (278)
T COG3359 158 MLVSFNGKAFDIPFIKRMVR-DRLELS-----------LEFGHFDLYHPSRRLWKHLLPRCGLKTVERILGIRREEDT-- 223 (278)
T ss_pred eEEEecCcccCcHHHHHHHh-cccccC-----------ccccchhhhhhhhhhhhccCCCCChhhHHHHhCccccccC--
Confidence 8999999 599999987544 334443 23336788888777632 2 5789999999999994222
Q ss_pred chhhhHHHHHHHHHH
Q 023614 239 QAGSDSLLTLHAFLK 253 (280)
Q Consensus 239 qAGsDs~lT~~~F~~ 253 (280)
-|+++-..-.-|.+
T Consensus 224 -dG~~~p~lyr~~~~ 237 (278)
T COG3359 224 -DGYDGPELYRLYRR 237 (278)
T ss_pred -CCcchHHHHHHHHH
Confidence 36666665555543
No 70
>PF13637 Ank_4: Ankyrin repeats (many copies); PDB: 3B95_A 3B7B_A 3F6Q_A 2KBX_A 3IXE_A 2DWZ_C 2DVW_A 3AJI_A 1S70_B 2HE0_A ....
Probab=32.04 E-value=44 Score=22.27 Aligned_cols=29 Identities=31% Similarity=0.492 Sum_probs=21.5
Q ss_pred chhHHHHHHHcCCCchhhhhcCCChHHHH
Q 023614 120 ALDSVELLKRQGIDFEKNREFGIDSVRFA 148 (280)
Q Consensus 120 ~~~Si~fL~~~G~DF~k~~~~GI~~~~f~ 148 (280)
+.+.+++|-++|.|.+..-+.|-.+...|
T Consensus 13 ~~~~~~~Ll~~~~din~~d~~g~t~lh~A 41 (54)
T PF13637_consen 13 NLEIVKLLLEHGADINAQDEDGRTPLHYA 41 (54)
T ss_dssp -HHHHHHHHHTTSGTT-B-TTS--HHHHH
T ss_pred CHHHHHHHHHCCCCCCCCCCCCCCHHHHH
Confidence 56889999999999999999999988765
No 71
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=31.93 E-value=88 Score=23.87 Aligned_cols=20 Identities=15% Similarity=0.310 Sum_probs=16.7
Q ss_pred ceEEEeccchhHHHHHHHhh
Q 023614 162 VTWVTFHSAYDFGYLVKCLT 181 (280)
Q Consensus 162 v~Wvtfhg~yD~gyL~k~l~ 181 (280)
..||++++.+|+.||.+-+.
T Consensus 45 ~v~V~hn~~fD~~fL~~~~~ 64 (96)
T cd06125 45 AILVGHNGSFDLPFLNNRCA 64 (96)
T ss_pred CEEEEeCcHHhHHHHHHHHH
Confidence 47899999999999877664
No 72
>PF12345 DUF3641: Protein of unknown function (DUF3641) ; InterPro: IPR024521 This domain is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. It is found in association with an N-terminal radical_SAM domain (Pfam:PF04055 from PFAM).
Probab=27.97 E-value=59 Score=27.25 Aligned_cols=33 Identities=33% Similarity=0.413 Sum_probs=27.0
Q ss_pred HHHHHcCCCchhhhhc-CCChHHHHHHHHHcccc
Q 023614 125 ELLKRQGIDFEKNREF-GIDSVRFAELLMSSGLV 157 (280)
Q Consensus 125 ~fL~~~G~DF~k~~~~-GI~~~~f~e~l~~Sglv 157 (280)
++..+.||.||.+..- -+|..+|++.|..+|-.
T Consensus 15 ~L~~~~GI~Fn~L~titNmPI~RF~~~L~~~g~~ 48 (134)
T PF12345_consen 15 ELKERFGIVFNNLFTITNMPIGRFGSFLERSGNL 48 (134)
T ss_pred HHHHhcCceecchhhhhcCcHHHHHHHHHHccCH
Confidence 3556889999999874 58899999999988754
No 73
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=27.92 E-value=34 Score=35.19 Aligned_cols=142 Identities=10% Similarity=-0.019 Sum_probs=82.2
Q ss_pred ceEEecCcc--CHHHHHHHHHHHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccC--
Q 023614 14 ILIREVFEF--NLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDE-- 89 (280)
Q Consensus 14 ~~i~eVw~~--Nl~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~-- 89 (280)
+.+..+-+. |....++.....+.+..+.++++|+.++...+. ...-+ +..+++++.-.....++-+|..-.--
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~-dl~~~~i~~~~~p~r~l~~~~~~~l~~~ 178 (564)
T KOG1990|consen 102 SPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDR--LSVDA-DLLPEKIPDYMRPFRTLPVGSPPLLTSI 178 (564)
T ss_pred cchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCC--ccchh-hhchhhhhcccChhccCCCCChhhhhhH
Confidence 444555555 677776666666777899999999999865432 22233 67777777777766666666554321
Q ss_pred -------CCCCCCCCCCCCceEEEEeccccCcCcCCCchhHHHHHHHcCCCchhhhhcCCChHH----HHHH--HHHc-c
Q 023614 90 -------EGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVR----FAEL--LMSS-G 155 (280)
Q Consensus 90 -------~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~----f~e~--l~~S-g 155 (280)
.|.. ..-.|++- ++.......+..+++..++.+++ ....+|+.... ..++ +..+ +
T Consensus 179 ~~~~~r~~~~~---------~p~~~~~~-~~~~~~~~~~~~~~~~~k~~~~k-~~~~rg~~~~~~~~~a~~l~~~~~tg~ 247 (564)
T KOG1990|consen 179 ESTLLRRLGYK---------LPPHFALG-RSRKLQGLAVAMVSFWEKHEFAK-ILIKRGVLETRKERMADELQELLLTGK 247 (564)
T ss_pred HHHHHHHhccc---------ccccceeh-hccccccchhHHHHHHHHHHHHH-HHHHhcchhhhccchHHHHHHHHhcCC
Confidence 1211 01123333 44444556677777777777777 66777776653 2222 3444 4
Q ss_pred cccCCCceEEEecc
Q 023614 156 LVLNKDVTWVTFHS 169 (280)
Q Consensus 156 lv~~~~v~Wvtfhg 169 (280)
++...+.--..+|.
T Consensus 248 ~lv~hN~~~dv~y~ 261 (564)
T KOG1990|consen 248 VLVLHNKLLDVMYR 261 (564)
T ss_pred eEEeeccceeeeee
Confidence 44444444444443
No 74
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=26.06 E-value=1e+02 Score=27.20 Aligned_cols=81 Identities=22% Similarity=0.326 Sum_probs=55.6
Q ss_pred eEEEeccchhHHHHH-HHhhCCCCCCCHHHHHHHHhhhc-CCCccchHHHHHhhcccc--chHHHHHHHcCCCccCCCcc
Q 023614 163 TWVTFHSAYDFGYLV-KCLTQRVLPEKLSEFVTRVGVFF-GEKVYDVKHLIRFCTCLY--GGLDRVCKALGVERVVGKSH 238 (280)
Q Consensus 163 ~Wvtfhg~yD~gyL~-k~l~~~~LP~~~~~F~~~l~~~F-p~~iyD~K~la~~~~~l~--~~L~~la~~L~v~r~~g~~h 238 (280)
+|++ -|.||..-|. +.+.+ .+|.. .| +. .-|+|.--+...+.. .||...++.-|..- .|..|
T Consensus 100 ~wa~-wG~~Dm~~l~q~~~~~-~~~p~----------~~kgp-~vdl~~~yk~v~~~pr~tgln~ale~~G~sf-~G~~H 165 (210)
T COG5018 100 TWAT-WGNMDMKVLKQNCMFN-HIPPF----------PFKGP-MVDLSLEYKNVFGDPRLTGLNKALEEYGDSF-TGTHH 165 (210)
T ss_pred cccc-ccchhHHHHHHHHHhc-CCCCc----------cccCc-cchHHHHHHHHhcCCccccHHHHHHHhcccc-CCchh
Confidence 6776 4889998664 44433 33321 22 12 445555544443332 58999999999999 89999
Q ss_pred chhhhHHHHHHHHHHHHHh
Q 023614 239 QAGSDSLLTLHAFLKIKDK 257 (280)
Q Consensus 239 qAGsDs~lT~~~F~~l~~~ 257 (280)
-|=-|+.-|.+.|.++...
T Consensus 166 raldDArn~~rl~klv~~~ 184 (210)
T COG5018 166 RALDDARNAYRLFKLVEQD 184 (210)
T ss_pred hhHHHHHHHHHHHHHHcch
Confidence 9999999999999887643
No 75
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=22.96 E-value=68 Score=21.18 Aligned_cols=33 Identities=18% Similarity=0.202 Sum_probs=26.1
Q ss_pred CCCHHHHHHHHhhhcCCCccchHHHHHhhccccc
Q 023614 186 PEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYG 219 (280)
Q Consensus 186 P~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~~ 219 (280)
|+.+.+|++.++.|--. ..|.+-+.+.+..|-+
T Consensus 1 p~~Y~~FL~il~~y~~~-~~~~~~v~~~v~~Ll~ 33 (47)
T PF02671_consen 1 PEVYNEFLKILNDYKKG-RISRSEVIEEVSELLR 33 (47)
T ss_dssp HHHHHHHHHHHHHHHCT-CSCHHHHHHHHHHHTT
T ss_pred ChHHHHHHHHHHHHHhc-CCCHHHHHHHHHHHHc
Confidence 67789999999999876 7788888777765533
No 76
>PF13606 Ank_3: Ankyrin repeat
Probab=22.90 E-value=69 Score=19.19 Aligned_cols=18 Identities=22% Similarity=0.394 Sum_probs=14.8
Q ss_pred CchhHHHHHHHcCCCchh
Q 023614 119 HALDSVELLKRQGIDFEK 136 (280)
Q Consensus 119 ~~~~Si~fL~~~G~DF~k 136 (280)
-+.+-+++|.++|.|.|.
T Consensus 13 g~~e~v~~Ll~~gadvn~ 30 (30)
T PF13606_consen 13 GNIEIVKYLLEHGADVNA 30 (30)
T ss_pred CCHHHHHHHHHcCCCCCC
Confidence 367889999999999874
No 77
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=21.80 E-value=46 Score=31.15 Aligned_cols=14 Identities=36% Similarity=0.567 Sum_probs=0.0
Q ss_pred eeEeeecccccccc
Q 023614 40 IISMDTEFPGVVVR 53 (280)
Q Consensus 40 fIAiDtEFpGv~~~ 53 (280)
+||||+|+-|++.+
T Consensus 107 ~vAmDCEMVG~Gp~ 120 (280)
T KOG2249|consen 107 VVAMDCEMVGVGPD 120 (280)
T ss_pred EEEEeeeEeccCCC
No 78
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=21.76 E-value=61 Score=25.48 Aligned_cols=16 Identities=19% Similarity=0.385 Sum_probs=12.4
Q ss_pred HHHHHhhCCCCCCCHH
Q 023614 175 YLVKCLTQRVLPEKLS 190 (280)
Q Consensus 175 yL~k~l~~~~LP~~~~ 190 (280)
-++..+||+|||.+.+
T Consensus 61 AFLHA~TGQPLP~D~D 76 (105)
T PRK05264 61 AFLHAFTGQPLPDDED 76 (105)
T ss_pred HHHHHHcCCCCCChhh
Confidence 3567789999999743
No 79
>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=21.33 E-value=53 Score=27.91 Aligned_cols=16 Identities=50% Similarity=0.982 Sum_probs=12.1
Q ss_pred hCCeeEeeeccccccc
Q 023614 37 RYPIISMDTEFPGVVV 52 (280)
Q Consensus 37 ~~~fIAiDtEFpGv~~ 52 (280)
..+||.+||..||+..
T Consensus 31 ~tpyI~v~t~~pgV~v 46 (155)
T PF04386_consen 31 HTPYITVDTDYPGVQV 46 (155)
T ss_dssp --EEEEEETTSTT-BS
T ss_pred CeEEEEEEeCCCCCCC
Confidence 4499999999999865
No 80
>PF13857 Ank_5: Ankyrin repeats (many copies); PDB: 1SW6_A 3EHR_B 3EHQ_A.
Probab=21.01 E-value=94 Score=21.06 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=17.4
Q ss_pred chhHHHHHHHcCCCchhhhhcCCChHHHH
Q 023614 120 ALDSVELLKRQGIDFEKNREFGIDSVRFA 148 (280)
Q Consensus 120 ~~~Si~fL~~~G~DF~k~~~~GI~~~~f~ 148 (280)
+.+.+++|.+.|.|.+..-.+|-.+...|
T Consensus 28 ~~~~v~~Ll~~g~d~~~~d~~G~Tpl~~A 56 (56)
T PF13857_consen 28 HSEVVRLLLQNGADPNAKDKDGQTPLHYA 56 (56)
T ss_dssp -HHHHHHHHHCT--TT---TTS--HHHH-
T ss_pred cHHHHHHHHHCcCCCCCCcCCCCCHHHhC
Confidence 57889999999999999999998776653
No 81
>TIGR01229 rocF_arginase arginase. This model helps resolve arginases from known and putative agmatinases, formiminoglutamases, and other related proteins of unknown specifity. The pathway from arginine to the polyamine putrescine may procede by hydrolysis to remove urea (arginase) followed by decarboxylation (ornithine decarboxylase), or by decarboxylation first (arginine decarboxylase) followed by removal of urea (agmatinase).
Probab=20.22 E-value=2e+02 Score=26.73 Aligned_cols=68 Identities=10% Similarity=-0.018 Sum_probs=42.0
Q ss_pred ecCccCHHHHHHHHHHHhhhCC---eeEeee------ccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeecc
Q 023614 18 EVFEFNLISEFERIRALIDRYP---IISMDT------EFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSD 88 (280)
Q Consensus 18 eVw~~Nl~~e~~~I~~~i~~~~---fIAiDt------EFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~ 88 (280)
+|++...++.+..+.+.+.... ||++|. ..||+.....+- -+. .|--+.++.-....+++=+.|+=++
T Consensus 196 ~i~~~g~~~v~~~~~~~l~~~~~~vyvS~DiDvlDps~aPgv~tp~pgG--l~~-~e~~~~l~~i~~~~~v~g~DivE~~ 272 (300)
T TIGR01229 196 EIDELGIGKVVEETLEYLKAEDGPIHLSLDVDGLDPSLAPATGTPVVGG--LTF-REGLLIMEMLYETGLLTALDVVEVN 272 (300)
T ss_pred HHhhhhHHHHHHHHHHHHhcCCCeEEEEEeccccCcccCCCCCCCCCCC--CCH-HHHHHHHHHHHhcCCEEEEEEEEEC
Confidence 4556666777777778776544 999996 678875543221 233 6666777776666566545544333
No 82
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=20.11 E-value=69 Score=25.04 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=12.0
Q ss_pred HHHHHhhCCCCCCCH
Q 023614 175 YLVKCLTQRVLPEKL 189 (280)
Q Consensus 175 yL~k~l~~~~LP~~~ 189 (280)
-++..+||+|||.+.
T Consensus 60 AFLHAfTGQPLP~D~ 74 (103)
T cd00490 60 AFLHAFTGQPLPDDA 74 (103)
T ss_pred HHHHHhcCCCCCChh
Confidence 356778999999974
Done!