Query 029428
Match_columns 193
No_of_seqs 240 out of 1085
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 12:45:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029428.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029428hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2249 3'-5' exonuclease [Rep 100.0 2.9E-34 6.3E-39 241.7 11.0 116 78-193 103-219 (280)
2 cd06149 ISG20 DEDDh 3'-5' exon 100.0 6E-29 1.3E-33 197.4 13.7 109 83-191 1-110 (157)
3 cd06144 REX4_like DEDDh 3'-5' 100.0 4.3E-28 9.4E-33 191.1 13.5 110 83-192 1-111 (152)
4 cd06145 REX1_like DEDDh 3'-5' 100.0 1.1E-27 2.5E-32 188.7 12.3 105 83-191 1-107 (150)
5 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 6.6E-27 1.4E-31 186.1 9.0 105 83-191 1-115 (161)
6 cd06143 PAN2_exo DEDDh 3'-5' e 99.9 1.6E-25 3.5E-30 180.4 11.4 110 83-192 1-136 (174)
7 PRK09146 DNA polymerase III su 99.9 7E-24 1.5E-28 179.1 13.2 116 73-188 40-166 (239)
8 PRK05711 DNA polymerase III su 99.9 3.5E-24 7.6E-29 181.1 10.4 110 79-188 3-127 (240)
9 TIGR01406 dnaQ_proteo DNA poly 99.9 5.2E-24 1.1E-28 178.3 10.2 108 81-188 1-123 (225)
10 PRK07247 DNA polymerase III su 99.9 2E-23 4.2E-28 171.6 12.7 95 79-175 4-102 (195)
11 cd06130 DNA_pol_III_epsilon_li 99.9 1.7E-23 3.6E-28 163.3 11.0 106 82-189 1-115 (156)
12 PRK06310 DNA polymerase III su 99.9 1.5E-23 3.2E-28 178.1 11.1 114 76-189 3-128 (250)
13 cd06131 DNA_pol_III_epsilon_Ec 99.9 2.4E-23 5.1E-28 165.0 9.4 107 82-188 1-121 (167)
14 PRK06195 DNA polymerase III su 99.9 6.2E-23 1.3E-27 179.0 12.5 106 81-188 2-117 (309)
15 TIGR00573 dnaq exonuclease, DN 99.9 4.6E-23 1E-27 171.3 10.1 112 77-188 4-125 (217)
16 PRK07740 hypothetical protein; 99.9 1.1E-22 2.4E-27 172.1 11.5 113 75-189 54-179 (244)
17 PRK06807 DNA polymerase III su 99.9 1.6E-22 3.5E-27 176.9 12.5 108 79-188 7-125 (313)
18 PRK09145 DNA polymerase III su 99.9 1.3E-22 2.8E-27 166.7 10.3 110 79-188 28-148 (202)
19 PRK05601 DNA polymerase III su 99.9 1.9E-22 4.1E-27 178.7 12.0 96 76-174 42-141 (377)
20 PRK05168 ribonuclease T; Provi 99.9 2.7E-22 5.9E-27 166.3 10.1 122 68-189 5-155 (211)
21 PRK08517 DNA polymerase III su 99.9 8.9E-22 1.9E-26 168.0 12.9 113 73-188 61-184 (257)
22 PRK07983 exodeoxyribonuclease 99.9 3.5E-22 7.7E-27 166.8 9.9 100 82-189 2-103 (219)
23 PRK06063 DNA polymerase III su 99.9 1.3E-21 2.8E-26 171.2 13.4 108 79-189 14-132 (313)
24 PRK07942 DNA polymerase III su 99.9 6.9E-22 1.5E-26 166.1 10.7 110 78-188 4-131 (232)
25 PRK06309 DNA polymerase III su 99.9 8.9E-22 1.9E-26 165.3 11.2 106 81-189 3-119 (232)
26 TIGR01298 RNaseT ribonuclease 99.9 1.1E-21 2.4E-26 161.4 10.4 113 77-189 5-146 (200)
27 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 6E-22 1.3E-26 159.9 8.4 108 82-189 1-138 (177)
28 COG2176 PolC DNA polymerase II 99.9 2.4E-22 5.2E-27 194.9 5.5 119 69-189 410-539 (1444)
29 smart00479 EXOIII exonuclease 99.9 1.6E-21 3.5E-26 153.1 9.1 109 81-189 1-120 (169)
30 PRK07883 hypothetical protein; 99.9 4.8E-21 1E-25 178.8 12.6 113 74-188 9-132 (557)
31 PRK07246 bifunctional ATP-depe 99.8 5.4E-21 1.2E-25 185.2 12.5 108 79-188 6-122 (820)
32 PRK06722 exonuclease; Provisio 99.8 9.1E-21 2E-25 163.5 11.6 97 79-175 4-107 (281)
33 cd06134 RNaseT DEDDh 3'-5' exo 99.8 3.6E-21 7.7E-26 157.0 8.2 110 80-189 5-143 (189)
34 PRK07748 sporulation inhibitor 99.8 1.5E-20 3.2E-25 155.2 10.2 96 79-174 3-109 (207)
35 KOG2248 3'-5' exonuclease [Rep 99.8 3.4E-20 7.5E-25 165.3 13.1 112 77-192 213-326 (380)
36 PRK05359 oligoribonuclease; Pr 99.8 1.5E-20 3.3E-25 152.6 9.0 109 79-188 2-134 (181)
37 cd06127 DEDDh DEDDh 3'-5' exon 99.8 3E-20 6.4E-25 142.7 9.2 106 83-189 1-117 (159)
38 PRK08074 bifunctional ATP-depe 99.8 4.6E-20 1E-24 180.8 12.2 107 80-188 3-121 (928)
39 TIGR01405 polC_Gram_pos DNA po 99.8 6E-20 1.3E-24 182.9 12.0 116 72-189 181-308 (1213)
40 COG0847 DnaQ DNA polymerase II 99.8 8.9E-20 1.9E-24 152.8 10.3 95 80-174 13-111 (243)
41 TIGR01407 dinG_rel DnaQ family 99.8 9.4E-20 2E-24 177.2 11.7 107 81-189 1-118 (850)
42 cd06138 ExoI_N N-terminal DEDD 99.8 6.4E-20 1.4E-24 148.6 7.6 92 83-175 1-102 (183)
43 PRK09182 DNA polymerase III su 99.8 2.4E-19 5.3E-24 155.7 11.7 99 75-176 32-139 (294)
44 cd06135 Orn DEDDh 3'-5' exonuc 99.8 3.3E-19 7.1E-24 143.5 7.5 106 82-187 1-129 (173)
45 PF00929 RNase_T: Exonuclease; 99.8 4.7E-20 1E-24 141.7 1.4 92 83-174 1-99 (164)
46 cd06133 ERI-1_3'hExo_like DEDD 99.8 1.4E-18 3.1E-23 137.7 9.9 108 82-189 1-131 (176)
47 PTZ00315 2'-phosphotransferase 99.7 2.7E-17 5.8E-22 152.9 12.1 96 79-174 55-170 (582)
48 PRK00448 polC DNA polymerase I 99.7 7.8E-17 1.7E-21 162.7 8.8 113 75-189 414-537 (1437)
49 PRK11779 sbcB exonuclease I; P 99.7 3.3E-16 7.1E-21 143.8 10.7 97 79-176 5-112 (476)
50 KOG3242 Oligoribonuclease (3'- 99.4 9.8E-14 2.1E-18 111.4 3.0 113 79-192 25-161 (208)
51 COG1949 Orn Oligoribonuclease 99.3 2.2E-12 4.9E-17 102.6 3.8 113 79-192 5-141 (184)
52 KOG1275 PAB-dependent poly(A) 98.9 9.3E-10 2E-14 105.8 2.8 122 70-191 898-1047(1118)
53 cd05160 DEDDy_DNA_polB_exo DED 98.9 7.2E-09 1.6E-13 84.3 7.5 85 82-174 1-96 (199)
54 KOG0542 Predicted exonuclease 98.8 3.7E-09 8E-14 89.5 3.4 92 81-173 57-168 (280)
55 cd06125 DnaQ_like_exo DnaQ-lik 98.6 2E-07 4.4E-12 68.1 6.7 37 152-188 35-83 (96)
56 COG5018 KapD Inhibitor of the 98.2 2.2E-07 4.8E-12 74.8 -0.8 93 81-174 5-113 (210)
57 COG2925 SbcB Exonuclease I [DN 98.1 6.7E-06 1.4E-10 73.7 7.0 98 79-177 8-116 (475)
58 cd06139 DNA_polA_I_Ecoli_like_ 97.9 0.00012 2.7E-09 58.2 9.7 90 79-188 4-99 (193)
59 PF01612 DNA_pol_A_exo1: 3'-5' 97.8 0.00011 2.4E-09 57.4 8.2 82 80-185 20-106 (176)
60 cd05780 DNA_polB_Kod1_like_exo 97.4 0.00063 1.4E-08 55.5 7.5 77 80-174 3-89 (195)
61 PF13482 RNase_H_2: RNase_H su 97.3 0.00041 8.8E-09 54.3 5.5 70 83-174 1-74 (164)
62 cd05781 DNA_polB_B3_exo DEDDy 97.2 0.0026 5.6E-08 51.9 8.8 70 79-174 2-81 (188)
63 PRK05755 DNA polymerase I; Pro 97.1 0.0025 5.5E-08 63.1 8.9 83 79-188 314-402 (880)
64 PF04857 CAF1: CAF1 family rib 97.0 0.00069 1.5E-08 57.9 3.7 94 80-173 22-164 (262)
65 cd05785 DNA_polB_like2_exo Unc 97.0 0.0033 7.1E-08 52.1 7.6 33 142-174 55-91 (207)
66 COG3359 Predicted exonuclease 96.8 0.0049 1.1E-07 52.6 7.5 76 76-174 94-173 (278)
67 cd05777 DNA_polB_delta_exo DED 96.4 0.047 1E-06 45.7 10.3 87 78-174 5-104 (230)
68 cd05784 DNA_polB_II_exo DEDDy 96.3 0.014 3.1E-07 47.9 6.9 78 80-174 3-84 (193)
69 cd05783 DNA_polB_B1_exo DEDDy 96.1 0.054 1.2E-06 44.8 9.4 33 142-174 70-104 (204)
70 cd05779 DNA_polB_epsilon_exo D 96.1 0.038 8.3E-07 45.8 8.2 33 142-174 70-106 (204)
71 PF03104 DNA_pol_B_exo1: DNA p 96.0 0.04 8.6E-07 47.4 8.3 87 78-174 155-255 (325)
72 cd06146 mut-7_like_exo DEDDy 3 95.7 0.051 1.1E-06 44.3 7.4 40 149-188 71-120 (193)
73 smart00486 POLBc DNA polymeras 95.6 0.1 2.2E-06 46.8 9.7 31 144-174 68-102 (471)
74 PHA02570 dexA exonuclease; Pro 95.5 0.015 3.3E-07 48.8 3.8 92 83-174 4-124 (220)
75 cd00007 35EXOc 3'-5' exonuclea 95.3 0.22 4.7E-06 37.4 9.4 43 146-188 40-86 (155)
76 PTZ00166 DNA polymerase delta 95.3 0.089 1.9E-06 53.4 9.0 88 78-173 262-362 (1054)
77 cd06148 Egl_like_exo DEDDy 3'- 95.2 0.085 1.8E-06 43.1 7.1 86 77-187 7-96 (197)
78 cd06141 WRN_exo DEDDy 3'-5' ex 94.8 0.062 1.3E-06 42.2 5.1 40 150-189 63-106 (170)
79 cd05778 DNA_polB_zeta_exo inac 94.6 0.27 5.9E-06 41.3 8.8 91 81-173 5-113 (231)
80 PHA02528 43 DNA polymerase; Pr 94.2 0.42 9.1E-06 47.8 10.5 103 72-174 98-211 (881)
81 KOG3657 Mitochondrial DNA poly 93.8 0.041 9E-07 54.0 2.5 32 157-188 240-275 (1075)
82 cd06129 RNaseD_like DEDDy 3'-5 93.2 0.42 9.2E-06 37.5 7.1 39 150-188 57-99 (161)
83 KOG4793 Three prime repair exo 93.0 0.14 3E-06 44.5 4.3 97 78-174 11-137 (318)
84 PRK05762 DNA polymerase II; Re 92.5 0.56 1.2E-05 46.2 8.3 80 78-174 153-236 (786)
85 COG0349 Rnd Ribonuclease D [Tr 92.4 0.18 3.8E-06 45.4 4.3 87 79-192 16-106 (361)
86 PRK10829 ribonuclease D; Provi 92.2 0.41 8.9E-06 43.3 6.4 82 79-189 21-107 (373)
87 PHA02524 43A DNA polymerase su 91.7 0.63 1.4E-05 43.7 7.2 100 74-174 100-213 (498)
88 COG0417 PolB DNA polymerase el 90.5 1.4 3E-05 43.6 8.6 87 76-174 150-244 (792)
89 TIGR01388 rnd ribonuclease D. 89.9 1.3 2.9E-05 39.7 7.4 36 151-187 61-101 (367)
90 cd05776 DNA_polB_alpha_exo ina 88.9 0.51 1.1E-05 39.6 3.8 35 139-173 76-114 (234)
91 cd05782 DNA_polB_like1_exo Unc 87.3 2.2 4.7E-05 35.2 6.5 30 145-174 78-110 (208)
92 PHA02563 DNA polymerase; Provi 82.4 4.6 9.9E-05 39.1 7.1 66 78-174 10-82 (630)
93 PF10108 DNA_pol_B_exo2: Predi 81.7 8.2 0.00018 32.3 7.5 30 145-174 37-69 (209)
94 smart00474 35EXOc 3'-5' exonuc 80.1 18 0.0004 27.2 8.6 39 149-187 64-105 (172)
95 cd06140 DNA_polA_I_Bacillus_li 78.7 18 0.0004 28.0 8.4 80 80-187 3-87 (178)
96 COG0749 PolA DNA polymerase I 78.3 3.7 8E-05 39.4 4.9 40 148-187 66-108 (593)
97 KOG1798 DNA polymerase epsilon 66.2 19 0.00041 38.4 6.9 87 79-174 245-350 (2173)
98 PF13017 Maelstrom: piRNA path 65.6 7.7 0.00017 32.2 3.5 60 98-157 11-79 (213)
99 PHA03036 DNA polymerase; Provi 65.1 65 0.0014 33.1 10.3 99 74-174 154-273 (1004)
100 PF00843 Arena_nucleocap: Aren 63.9 41 0.00088 31.5 7.9 103 76-186 368-474 (533)
101 KOG0969 DNA polymerase delta, 63.2 2.2 4.9E-05 42.1 -0.2 89 78-173 272-370 (1066)
102 PRK05761 DNA polymerase I; Rev 62.1 19 0.00041 35.7 6.0 32 143-174 208-241 (787)
103 KOG0970 DNA polymerase alpha, 59.3 18 0.0004 37.4 5.3 95 77-173 526-639 (1429)
104 TIGR00592 pol2 DNA polymerase 58.0 68 0.0015 33.4 9.3 44 130-173 569-616 (1172)
105 KOG0304 mRNA deadenylase subun 55.5 50 0.0011 28.1 6.5 92 81-173 25-157 (239)
106 TIGR03491 RecB family nuclease 52.5 75 0.0016 29.3 7.9 71 80-174 284-359 (457)
107 cd06142 RNaseD_exo DEDDy 3'-5' 41.3 37 0.00079 26.1 3.6 38 149-186 53-94 (178)
108 cd06147 Rrp6p_like_exo DEDDy 3 39.0 1.9E+02 0.0042 22.8 8.7 24 151-174 68-93 (192)
109 TIGR00593 pola DNA polymerase 38.3 33 0.00071 34.6 3.5 44 144-187 362-409 (887)
110 cd09018 DEDDy_polA_RNaseD_like 28.7 71 0.0015 23.6 3.2 36 152-187 45-84 (150)
111 KOG1615 Phosphoserine phosphat 27.0 8.4 0.00018 32.3 -2.3 26 79-104 15-40 (227)
112 KOG2613 NMD protein affecting 24.5 1.5E+02 0.0032 27.7 4.9 70 70-139 303-384 (502)
113 COG5228 POP2 mRNA deadenylase 24.3 44 0.00095 28.6 1.4 89 80-173 42-173 (299)
114 PF12096 DUF3572: Protein of u 22.9 65 0.0014 23.3 1.9 28 130-157 29-56 (88)
115 PF06821 Ser_hydrolase: Serine 22.2 83 0.0018 24.9 2.6 33 141-173 35-73 (171)
No 1
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2.9e-34 Score=241.72 Aligned_cols=116 Identities=59% Similarity=0.981 Sum_probs=112.0
Q ss_pred CCCcEEEEEEeecCCCC-CcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHh
Q 029428 78 SLTDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (193)
Q Consensus 78 ~~~~~v~lD~EtTGl~~-~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (193)
..+++|||||||+|.++ |+...+|+|+|||..|.++||.||+|..+|++|+|+++||+++++.+|.+|+.|+.+|++||
T Consensus 103 ~~~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL 182 (280)
T KOG2249|consen 103 SLTRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLL 182 (280)
T ss_pred ccceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHHH
Confidence 35579999999999995 78899999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEeChHhhHHHhcccCCCCceeecCCcCcccC
Q 029428 157 EGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLK 193 (193)
Q Consensus 157 ~g~ilVgHn~~fDl~~L~~~~p~~~iiDT~~~~~~~k 193 (193)
.|+|||||.+++||.+|.+.||+..++||+.+.||+|
T Consensus 183 ~gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k 219 (280)
T KOG2249|consen 183 KGRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMK 219 (280)
T ss_pred hCCEEeccccccHHHHHhhhCchhhhcccccCchHHH
Confidence 9999999999999999999999999999999999986
No 2
>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=99.96 E-value=6e-29 Score=197.45 Aligned_cols=109 Identities=47% Similarity=0.797 Sum_probs=102.0
Q ss_pred EEEEEeecCCCC-CcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhCCCEE
Q 029428 83 VAMDCEMVGISQ-GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRIL 161 (193)
Q Consensus 83 v~lD~EtTGl~~-~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~g~il 161 (193)
|||||||||+++ +++.+|++|++++.+|.++|++||+|..+|+++++.+||||+++|++||+|++++.+|.+|++|++|
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~~l~~~vl 80 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHHHHcCCCEE
Confidence 689999999995 4678999999998889999999999999999999999999999999999999999999999999999
Q ss_pred EEeChHhhHHHhcccCCCCceeecCCcCcc
Q 029428 162 VGHALHNDLKALLLTHSKKDLRDTSEYQPF 191 (193)
Q Consensus 162 VgHn~~fDl~~L~~~~p~~~iiDT~~~~~~ 191 (193)
||||+.||+.||++.++...++||..+.++
T Consensus 81 V~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~ 110 (157)
T cd06149 81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLL 110 (157)
T ss_pred EEeCcHHHHHHhcccCCCcCEEECcccccc
Confidence 999999999999999888889999876544
No 3
>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=99.96 E-value=4.3e-28 Score=191.12 Aligned_cols=110 Identities=62% Similarity=0.992 Sum_probs=102.8
Q ss_pred EEEEEeecCCCCC-cEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhCCCEE
Q 029428 83 VAMDCEMVGISQG-NKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRIL 161 (193)
Q Consensus 83 v~lD~EtTGl~~~-~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~g~il 161 (193)
|+|||||||+++. ++++|++|.+++..|.++|++||+|..+++++++.+||||+++|+++|+|.+++.+|.+|+++++|
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~~l~~~vl 80 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCCCCHHHHHHHHHHHhCCCEE
Confidence 6899999999964 689999999999889999999999999999999999999999999999999999999999999999
Q ss_pred EEeChHhhHHHhcccCCCCceeecCCcCccc
Q 029428 162 VGHALHNDLKALLLTHSKKDLRDTSEYQPFL 192 (193)
Q Consensus 162 VgHn~~fDl~~L~~~~p~~~iiDT~~~~~~~ 192 (193)
||||+.||+.||+..+++..++||..+..++
T Consensus 81 VgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~ 111 (152)
T cd06144 81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLR 111 (152)
T ss_pred EEcCcHHHHHHhcCcCCCccEEEeEEeeccc
Confidence 9999999999999998888899998876553
No 4
>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=99.95 E-value=1.1e-27 Score=188.67 Aligned_cols=105 Identities=44% Similarity=0.685 Sum_probs=96.9
Q ss_pred EEEEEeecCCCCCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCC-CHHHHHHHHHHHhC-CCE
Q 029428 83 VAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAK-DFPTVQKKVAELIE-GRI 160 (193)
Q Consensus 83 v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~-~~~ev~~~l~~~l~-g~i 160 (193)
|+|||||||++.+ .+|++|++++.+|+++|++||+|..+|+++++++||||++||+++| +|++++++|.+|++ +++
T Consensus 1 ~~iD~E~~g~~~g--~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl~~~~v 78 (150)
T cd06145 1 FALDCEMCYTTDG--LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTI 78 (150)
T ss_pred CEEeeeeeeecCC--CEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHhCCCCE
Confidence 5899999999966 6889999998889999999999999999999999999999999995 99999999999997 899
Q ss_pred EEEeChHhhHHHhcccCCCCceeecCCcCcc
Q 029428 161 LVGHALHNDLKALLLTHSKKDLRDTSEYQPF 191 (193)
Q Consensus 161 lVgHn~~fDl~~L~~~~p~~~iiDT~~~~~~ 191 (193)
|||||+.||+.||+..+++ ++||+.+++.
T Consensus 79 lVgHn~~fD~~fL~~~~~~--~iDT~~l~r~ 107 (150)
T cd06145 79 LVGHSLENDLKALKLIHPR--VIDTAILFPH 107 (150)
T ss_pred EEEcChHHHHHHhhccCCC--EEEcHHhccc
Confidence 9999999999999987765 8999988653
No 5
>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=99.94 E-value=6.6e-27 Score=186.10 Aligned_cols=105 Identities=39% Similarity=0.693 Sum_probs=94.0
Q ss_pred EEEEEeecCCCC--CcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCC-------HHHHHHHHH
Q 029428 83 VAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKD-------FPTVQKKVA 153 (193)
Q Consensus 83 v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~-------~~ev~~~l~ 153 (193)
|+|||||||+++ ++|++||+|.+.+ |.++|+.||+|..+|+++++++||||++||+++|+ |++++++|.
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~--g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~ 78 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLT--GEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALW 78 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCC--CeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHH
Confidence 689999999994 5788888888754 78889999999999999999999999999999875 458999999
Q ss_pred HHhCC-CEEEEeChHhhHHHhcccCCCCceeecCCcCcc
Q 029428 154 ELIEG-RILVGHALHNDLKALLLTHSKKDLRDTSEYQPF 191 (193)
Q Consensus 154 ~~l~g-~ilVgHn~~fDl~~L~~~~p~~~iiDT~~~~~~ 191 (193)
+|+++ ++|||||+.||+.||+..+++ ++||+.+++.
T Consensus 79 ~~i~~~~vlVgHn~~fD~~fL~~~~~~--~iDT~~l~~~ 115 (161)
T cd06137 79 KFIDPDTILVGHSLQNDLDALRMIHTR--VVDTAILTRE 115 (161)
T ss_pred HhcCCCcEEEeccHHHHHHHHhCcCCC--eeEehhhhhh
Confidence 99997 999999999999999987655 8999998764
No 6
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. 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. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with 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.
Probab=99.93 E-value=1.6e-25 Score=180.45 Aligned_cols=110 Identities=35% Similarity=0.551 Sum_probs=99.1
Q ss_pred EEEEEeecCCCC--------CcE-------eEEEEEEEEe----CCCcEEEEEEecCCCccccccccccCCCHHHHccCC
Q 029428 83 VAMDCEMVGISQ--------GNK-------SALGRVSLVN----KWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAK 143 (193)
Q Consensus 83 v~lD~EtTGl~~--------~~i-------~eia~V~vv~----~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~ 143 (193)
||||||++|+++ |.- .++|+|++|| ..|+++||.||+|..+|.+|+|+++|||+++|.++.
T Consensus 1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred CceeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCccc
Confidence 578888888874 333 4899999999 689999999999999999999999999999998875
Q ss_pred ------CHHHHHHHHHHHhC-CCEEEEeChHhhHHHhcccCCCCceeecCCcCccc
Q 029428 144 ------DFPTVQKKVAELIE-GRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFL 192 (193)
Q Consensus 144 ------~~~ev~~~l~~~l~-g~ilVgHn~~fDl~~L~~~~p~~~iiDT~~~~~~~ 192 (193)
++++++.++.+++. ++|||||++++||.+|++.||+..+|||+.+|++.
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~ 136 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLP 136 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccCC
Confidence 69999999999996 99999999999999999999988899999998753
No 7
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=7e-24 Score=179.14 Aligned_cols=116 Identities=21% Similarity=0.231 Sum_probs=99.1
Q ss_pred CCCCCCCCcEEEEEEeecCCCC--CcEeEEEEEEEEeCCC--cEEEEEEecCCCccccccccccCCCHHHHccCCCHHHH
Q 029428 73 INDDFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWG--NLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTV 148 (193)
Q Consensus 73 ~~~~~~~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g--~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev 148 (193)
...++....|++||+||||+++ ++|+|||+|.+.++.. ...|+++|+|..+|+..++.|||||+++|+++|+|.++
T Consensus 40 ~~~~~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~ev 119 (239)
T PRK09146 40 PDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERI 119 (239)
T ss_pred CCCCcccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHH
Confidence 3445567789999999999994 7999999999875221 13488999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCEEEEeChHhhHHHhccc-------CCCCceeecCCc
Q 029428 149 QKKVAELIEGRILVGHALHNDLKALLLT-------HSKKDLRDTSEY 188 (193)
Q Consensus 149 ~~~l~~~l~g~ilVgHn~~fDl~~L~~~-------~p~~~iiDT~~~ 188 (193)
+.+|.++++|+++||||+.||+.||+.. .....++||..+
T Consensus 120 l~~l~~~~~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~L 166 (239)
T PRK09146 120 LDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEI 166 (239)
T ss_pred HHHHHHHhCCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHH
Confidence 9999999999999999999999999632 123568999876
No 8
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.91 E-value=3.5e-24 Score=181.12 Aligned_cols=110 Identities=21% Similarity=0.283 Sum_probs=94.5
Q ss_pred CCcEEEEEEeecCCCC---CcEeEEEEEEEEeCCC-cEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHH
Q 029428 79 LTDVVAMDCEMVGISQ---GNKSALGRVSLVNKWG-NLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~---~~i~eia~V~vv~~~g-~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (193)
..++|+||+||||+++ ++|+|||+|.+.+... ...|+.||+|..+|++.+++|||||+++|+++|+|.+++.+|.+
T Consensus 3 ~~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~ 82 (240)
T PRK05711 3 IMRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLD 82 (240)
T ss_pred CCeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHHHH
Confidence 3579999999999994 5899999999886322 12489999999999999999999999999999999999999999
Q ss_pred HhCCCEEEEeChHhhHHHhccc-------CCC----CceeecCCc
Q 029428 155 LIEGRILVGHALHNDLKALLLT-------HSK----KDLRDTSEY 188 (193)
Q Consensus 155 ~l~g~ilVgHn~~fDl~~L~~~-------~p~----~~iiDT~~~ 188 (193)
|+++.+|||||+.||+.||+.. .|. ..++||..+
T Consensus 83 fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~l 127 (240)
T PRK05711 83 FIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAM 127 (240)
T ss_pred HhCCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHH
Confidence 9999999999999999999632 231 357888754
No 9
>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=99.90 E-value=5.2e-24 Score=178.33 Aligned_cols=108 Identities=21% Similarity=0.257 Sum_probs=93.5
Q ss_pred cEEEEEEeecCCCC---CcEeEEEEEEEEeCCC-cEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHh
Q 029428 81 DVVAMDCEMVGISQ---GNKSALGRVSLVNKWG-NLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (193)
Q Consensus 81 ~~v~lD~EtTGl~~---~~i~eia~V~vv~~~g-~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (193)
++|+||+||||+++ ++|+|||+|.+.+... ...|+.||+|..+|+++++++||||+++|+++|+|.+++.+|.+|+
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~~fi 80 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHHHHh
Confidence 48999999999994 5899999999886321 1349999999999999999999999999999999999999999999
Q ss_pred CCCEEEEeChHhhHHHhccc-------CC----CCceeecCCc
Q 029428 157 EGRILVGHALHNDLKALLLT-------HS----KKDLRDTSEY 188 (193)
Q Consensus 157 ~g~ilVgHn~~fDl~~L~~~-------~p----~~~iiDT~~~ 188 (193)
++.+|||||+.||+.||+.. ++ ...++||..+
T Consensus 81 ~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~l 123 (225)
T TIGR01406 81 GGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAM 123 (225)
T ss_pred CCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHH
Confidence 99999999999999999622 12 1468898765
No 10
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.90 E-value=2e-23 Score=171.59 Aligned_cols=95 Identities=19% Similarity=0.251 Sum_probs=87.7
Q ss_pred CCcEEEEEEeecCCC-CCcEeEEEEEEEEeCCCcE--EEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHH
Q 029428 79 LTDVVAMDCEMVGIS-QGNKSALGRVSLVNKWGNL--IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~-~~~i~eia~V~vv~~~g~~--i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~ 155 (193)
..+||+||+||||++ .++|+|||+|.+.+ |.+ .|++||+|..+++.+++.+||||+++|+++|+|.+++.+|.+|
T Consensus 4 ~~~~vvlD~EtTGl~~~~eIIeIgaV~v~~--g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~~f 81 (195)
T PRK07247 4 LETYIAFDLEFNTVNGVSHIIQVSAVKYDD--HKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEF 81 (195)
T ss_pred CCeEEEEEeeCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHHHH
Confidence 468999999999998 57899999999986 443 4999999999999999999999999999999999999999999
Q ss_pred hCCCEEEEeChH-hhHHHhcc
Q 029428 156 IEGRILVGHALH-NDLKALLL 175 (193)
Q Consensus 156 l~g~ilVgHn~~-fDl~~L~~ 175 (193)
++++++||||+. ||+.||+.
T Consensus 82 ~~~~~lVaHNa~~fD~~fL~~ 102 (195)
T PRK07247 82 VGELPLIGYNAQKSDLPILAE 102 (195)
T ss_pred HCCCeEEEEeCcHhHHHHHHH
Confidence 999999999996 89999974
No 11
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.90 E-value=1.7e-23 Score=163.34 Aligned_cols=106 Identities=25% Similarity=0.443 Sum_probs=94.4
Q ss_pred EEEEEEeecCCCCCcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhCCC
Q 029428 82 VVAMDCEMVGISQGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGR 159 (193)
Q Consensus 82 ~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~g~ 159 (193)
||+|||||||..+++|++||+|.+.+ |.++ |+.||+|..+++++++++||||+++++++++|.+++.+|.+|+++.
T Consensus 1 ~v~~D~Ettg~~~~~ii~ig~v~~~~--~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~~~l~~~ 78 (156)
T cd06130 1 FVAIDFETANADRASACSIGLVKVRD--GQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78 (156)
T ss_pred CEEEEEeCCCCCCCceEEEEEEEEEC--CEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCCCHHHHHHHHHHHhCCC
Confidence 68999999999889999999998874 4443 8899999999999999999999999999999999999999999999
Q ss_pred EEEEeChHhhHHHhc-------ccCCCCceeecCCcC
Q 029428 160 ILVGHALHNDLKALL-------LTHSKKDLRDTSEYQ 189 (193)
Q Consensus 160 ilVgHn~~fDl~~L~-------~~~p~~~iiDT~~~~ 189 (193)
++||||+.||+.+|+ ...+....+||..++
T Consensus 79 ~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~ 115 (156)
T cd06130 79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLA 115 (156)
T ss_pred EEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHH
Confidence 999999999999995 234556788986553
No 12
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.90 E-value=1.5e-23 Score=178.10 Aligned_cols=114 Identities=19% Similarity=0.212 Sum_probs=96.4
Q ss_pred CCCCCcEEEEEEeecCCCC--CcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHH
Q 029428 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (193)
Q Consensus 76 ~~~~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~ 153 (193)
......||+|||||||+++ ++|+|||+|.+........|+.+|+|..+|+..++.+||||+++|+++|+|.+++.+|.
T Consensus 3 ~l~~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~ 82 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIK 82 (250)
T ss_pred cccCCcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHH
Confidence 3445789999999999984 68999999988642222348999999999999999999999999999999999999999
Q ss_pred HHhCC-CEEEEeChHhhHHHhcccC-------C--CCceeecCCcC
Q 029428 154 ELIEG-RILVGHALHNDLKALLLTH-------S--KKDLRDTSEYQ 189 (193)
Q Consensus 154 ~~l~g-~ilVgHn~~fDl~~L~~~~-------p--~~~iiDT~~~~ 189 (193)
+|+++ .+|||||+.||+.||+..+ + ...++||..++
T Consensus 83 ~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~la 128 (250)
T PRK06310 83 GFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLA 128 (250)
T ss_pred HHhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHH
Confidence 99986 9999999999999996322 1 25689997653
No 13
>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=99.89 E-value=2.4e-23 Score=164.96 Aligned_cols=107 Identities=20% Similarity=0.273 Sum_probs=91.5
Q ss_pred EEEEEEeecCCCC---CcEeEEEEEEEEeCCC-cEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhC
Q 029428 82 VVAMDCEMVGISQ---GNKSALGRVSLVNKWG-NLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (193)
Q Consensus 82 ~v~lD~EtTGl~~---~~i~eia~V~vv~~~g-~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (193)
||+||+||||+++ ++|+|||+|.+.++.. ...|+.+|+|..++++.++++||||+++++++++|.+++.+|.+|++
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~l~ 80 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHHHHC
Confidence 6899999999986 5899999998865221 12488999999999999999999999999999999999999999999
Q ss_pred CCEEEEeChHhhHHHhcccC----------CCCceeecCCc
Q 029428 158 GRILVGHALHNDLKALLLTH----------SKKDLRDTSEY 188 (193)
Q Consensus 158 g~ilVgHn~~fDl~~L~~~~----------p~~~iiDT~~~ 188 (193)
+.++||||+.||+.||+..+ ....++||..+
T Consensus 81 ~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~ 121 (167)
T cd06131 81 GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLAL 121 (167)
T ss_pred CCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHH
Confidence 99999999999999996321 12467898754
No 14
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.89 E-value=6.2e-23 Score=179.00 Aligned_cols=106 Identities=20% Similarity=0.377 Sum_probs=93.9
Q ss_pred cEEEEEEeecCCCCCcEeEEEEEEEEeCCCcEE--EEEEecCCC-ccccccccccCCCHHHHccCCCHHHHHHHHHHHhC
Q 029428 81 DVVAMDCEMVGISQGNKSALGRVSLVNKWGNLI--YDEFVRPLE-RVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (193)
Q Consensus 81 ~~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i--~~~lV~P~~-~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (193)
+||+||+||||...++|++||+|.+.+ |.++ |++||+|.. .+++.++.|||||+++|+++|+|.+++.+|.+|++
T Consensus 2 ~~vviD~ETTg~~~d~IieIgav~v~~--g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~~fl~ 79 (309)
T PRK06195 2 NFVAIDFETANEKRNSPCSIGIVVVKD--GEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFN 79 (309)
T ss_pred cEEEEEEeCCCCCCCceEEEEEEEEEC--CEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHHHHHhC
Confidence 699999999998888999999999976 5544 899999985 57888999999999999999999999999999999
Q ss_pred CCEEEEeChHhhHHHhcc-------cCCCCceeecCCc
Q 029428 158 GRILVGHALHNDLKALLL-------THSKKDLRDTSEY 188 (193)
Q Consensus 158 g~ilVgHn~~fDl~~L~~-------~~p~~~iiDT~~~ 188 (193)
+++|||||+.||+.||+. ..|...++||..+
T Consensus 80 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~l 117 (309)
T PRK06195 80 NNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKL 117 (309)
T ss_pred CCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHH
Confidence 999999999999999962 2345678999764
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=99.89 E-value=4.6e-23 Score=171.32 Aligned_cols=112 Identities=22% Similarity=0.322 Sum_probs=94.8
Q ss_pred CCCCcEEEEEEeecCCCC-CcEeEEEEEEEEeCCCc-EEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHH
Q 029428 77 FSLTDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGN-LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (193)
Q Consensus 77 ~~~~~~v~lD~EtTGl~~-~~i~eia~V~vv~~~g~-~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (193)
.....||+||+||||+++ ..|+|||+|.+.+.... ..|+.||+|..+++++++.+||||+++|+++|+|.+++.+|.+
T Consensus 4 l~~~~fvv~D~ETTGl~~~~~IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~~ 83 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFAD 83 (217)
T ss_pred EEecCEEEEEecCCCCCCCCCEEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHHH
Confidence 345689999999999994 24999999998764221 2499999999999999999999999999999999999999999
Q ss_pred HhCCCEEEEeChHhhHHHhcccC--------CCCceeecCCc
Q 029428 155 LIEGRILVGHALHNDLKALLLTH--------SKKDLRDTSEY 188 (193)
Q Consensus 155 ~l~g~ilVgHn~~fDl~~L~~~~--------p~~~iiDT~~~ 188 (193)
|+++.++||||+.||+.||+..+ +...++||..+
T Consensus 84 ~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l 125 (217)
T TIGR00573 84 YIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDT 125 (217)
T ss_pred HhCCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHH
Confidence 99999999999999999997332 23467887553
No 16
>PRK07740 hypothetical protein; Provisional
Probab=99.89 E-value=1.1e-22 Score=172.14 Aligned_cols=113 Identities=21% Similarity=0.285 Sum_probs=96.6
Q ss_pred CCCCCCcEEEEEEeecCCCC---CcEeEEEEEEEEeCCCcE---EEEEEecCCCccccccccccCCCHHHHccCCCHHHH
Q 029428 75 DDFSLTDVVAMDCEMVGISQ---GNKSALGRVSLVNKWGNL---IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTV 148 (193)
Q Consensus 75 ~~~~~~~~v~lD~EtTGl~~---~~i~eia~V~vv~~~g~~---i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev 148 (193)
.++...+||+|||||||+++ ++|+|||+|.+.+ +.+ .|+.+|+|..+++++++++||||+++|+++|+|.++
T Consensus 54 ~~~~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~--~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev 131 (244)
T PRK07740 54 IPLTDLPFVVFDLETTGFSPQQGDEILSIGAVKTKG--GEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEV 131 (244)
T ss_pred CCccCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHH
Confidence 34456679999999999994 5899999999875 333 288899999999999999999999999999999999
Q ss_pred HHHHHHHhCCCEEEEeChHhhHHHhccc------CC-CCceeecCCcC
Q 029428 149 QKKVAELIEGRILVGHALHNDLKALLLT------HS-KKDLRDTSEYQ 189 (193)
Q Consensus 149 ~~~l~~~l~g~ilVgHn~~fDl~~L~~~------~p-~~~iiDT~~~~ 189 (193)
+.+|.+|++++++||||+.||+.||+.. .+ ...++||..++
T Consensus 132 l~~f~~fi~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~ 179 (244)
T PRK07740 132 LHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLT 179 (244)
T ss_pred HHHHHHHhCCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHH
Confidence 9999999999999999999999999632 11 24689987654
No 17
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=1.6e-22 Score=176.88 Aligned_cols=108 Identities=21% Similarity=0.292 Sum_probs=96.2
Q ss_pred CCcEEEEEEeecCCCC--CcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHH
Q 029428 79 LTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (193)
+.+||+||+||||+++ ++|+|||+|.+.+ |.++ |+.+|+|..+++++++++||||+++|+++++|.+|+.+|.+
T Consensus 7 ~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~--g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f~~ 84 (313)
T PRK06807 7 PLDYVVIDFETTGFNPYNDKIIQVAAVKYRN--HELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLA 84 (313)
T ss_pred CCCEEEEEEECCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHHHH
Confidence 4579999999999994 6999999999865 5544 89999999999999999999999999999999999999999
Q ss_pred HhCCCEEEEeChHhhHHHhcc-------cCCCCceeecCCc
Q 029428 155 LIEGRILVGHALHNDLKALLL-------THSKKDLRDTSEY 188 (193)
Q Consensus 155 ~l~g~ilVgHn~~fDl~~L~~-------~~p~~~iiDT~~~ 188 (193)
|+++.+|||||+.||+.||+. ..+...++||..+
T Consensus 85 fl~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~l 125 (313)
T PRK06807 85 FLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFL 125 (313)
T ss_pred HHcCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHH
Confidence 999999999999999999962 2455678998765
No 18
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=1.3e-22 Score=166.66 Aligned_cols=110 Identities=22% Similarity=0.265 Sum_probs=93.5
Q ss_pred CCcEEEEEEeecCCCC--CcEeEEEEEEEEeCCCc--EEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHH
Q 029428 79 LTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGN--LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~--~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (193)
..+||+||+||||+++ ++|+|||+|.+.++... ..|+.||+|..+++++++++||||++++++++++.+++.+|.+
T Consensus 28 ~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~~~~ 107 (202)
T PRK09145 28 PDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLA 107 (202)
T ss_pred CCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHHHHH
Confidence 4579999999999984 79999999988642111 2388999999999999999999999999999999999999999
Q ss_pred HhCCCEEEEeChHhhHHHhccc------CC-CCceeecCCc
Q 029428 155 LIEGRILVGHALHNDLKALLLT------HS-KKDLRDTSEY 188 (193)
Q Consensus 155 ~l~g~ilVgHn~~fDl~~L~~~------~p-~~~iiDT~~~ 188 (193)
|++++++||||+.||+.||... .+ ....+|++.+
T Consensus 108 ~i~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l 148 (202)
T PRK09145 108 FIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSAL 148 (202)
T ss_pred HHcCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHH
Confidence 9999999999999999999622 11 2457888654
No 19
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=1.9e-22 Score=178.69 Aligned_cols=96 Identities=20% Similarity=0.322 Sum_probs=84.0
Q ss_pred CCCCCcEEEEEEeecCCCC--CcEeEEEEEEEEeCCCcE--EEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHH
Q 029428 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNL--IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKK 151 (193)
Q Consensus 76 ~~~~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~--i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~ 151 (193)
++....|||||+||||+++ ++|++||+|.+.. +|.+ .|++||+|...+.. ..|||||+++|+++|+|.+++.+
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~-~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP~f~eVl~e 118 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTA-DGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGKRFSQILKP 118 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCCCeEEEEEEEEEEc-CCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCCCHHHHHHH
Confidence 4445679999999999994 6899999999873 2444 39999999875443 47999999999999999999999
Q ss_pred HHHHhCCCEEEEeChHhhHHHhc
Q 029428 152 VAELIEGRILVGHALHNDLKALL 174 (193)
Q Consensus 152 l~~~l~g~ilVgHn~~fDl~~L~ 174 (193)
|.+|++|++|||||+.||+.||.
T Consensus 119 l~~fL~g~vLVaHNA~FD~~FL~ 141 (377)
T PRK05601 119 LDRLIDGRTLILHNAPRTWGFIV 141 (377)
T ss_pred HHHHhCCCEEEEECcHHHHHHHH
Confidence 99999999999999999999995
No 20
>PRK05168 ribonuclease T; Provisional
Probab=99.87 E-value=2.7e-22 Score=166.28 Aligned_cols=122 Identities=25% Similarity=0.290 Sum_probs=98.9
Q ss_pred CCCCCCCCCCCCCcEEEEEEeecCCC--CCcEeEEEEEEEEeC-CCcE----EEEEEecC--CCccccccccccCCCHHH
Q 029428 68 SPLTPINDDFSLTDVVAMDCEMVGIS--QGNKSALGRVSLVNK-WGNL----IYDEFVRP--LERVVDFRTRISGIRPRD 138 (193)
Q Consensus 68 ~~~~p~~~~~~~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~-~g~~----i~~~lV~P--~~~i~~~~t~ihGIt~e~ 138 (193)
+.+.|....++...+|+||+||||++ .++|+|||+|.+... +|.+ .|++||+| ..+|+.+++.+||||+++
T Consensus 5 ~~~~~~~~~~~~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~ 84 (211)
T PRK05168 5 NDLNPLKDRFRGFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDN 84 (211)
T ss_pred cccchHHHHhcCCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchh
Confidence 34566667777888999999999999 469999999999742 3442 49999999 468999999999999986
Q ss_pred -HccCCCHHHHHHHHHHHhC---------CCEEEEeChHhhHHHhcccC----------CCCceeecCCcC
Q 029428 139 -LRKAKDFPTVQKKVAELIE---------GRILVGHALHNDLKALLLTH----------SKKDLRDTSEYQ 189 (193)
Q Consensus 139 -l~~a~~~~ev~~~l~~~l~---------g~ilVgHn~~fDl~~L~~~~----------p~~~iiDT~~~~ 189 (193)
+++++++.+++.++.+++. +.++||||+.||+.||+... +...++||..+.
T Consensus 85 ~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~la 155 (211)
T PRK05168 85 PLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLS 155 (211)
T ss_pred hhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHH
Confidence 7889999998888888764 78999999999999996321 223589997664
No 21
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.87 E-value=8.9e-22 Score=167.96 Aligned_cols=113 Identities=19% Similarity=0.268 Sum_probs=95.7
Q ss_pred CCCCCCCCcEEEEEEeecCCCC--CcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHH
Q 029428 73 INDDFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTV 148 (193)
Q Consensus 73 ~~~~~~~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev 148 (193)
...++....||+||+||||+++ ++|+|||+|.+.+ |.++ |+.||+|. +++.+++++||||+++++++|++.+|
T Consensus 61 ~~~~~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~--g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap~~~ev 137 (257)
T PRK08517 61 RFTPIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKN--GEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEV 137 (257)
T ss_pred CCCCCCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCCCHHHH
Confidence 3445567889999999999994 5899999999975 5554 89999996 79999999999999999999999999
Q ss_pred HHHHHHHhCCCEEEEeChHhhHHHhcccC-------CCCceeecCCc
Q 029428 149 QKKVAELIEGRILVGHALHNDLKALLLTH-------SKKDLRDTSEY 188 (193)
Q Consensus 149 ~~~l~~~l~g~ilVgHn~~fDl~~L~~~~-------p~~~iiDT~~~ 188 (193)
+.+|.+|++++++||||+.||+.||+..+ .....+||..+
T Consensus 138 l~~f~~fl~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~l 184 (257)
T PRK08517 138 LEEFRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDL 184 (257)
T ss_pred HHHHHHHHCCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHH
Confidence 99999999999999999999999996321 12346777644
No 22
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.87 E-value=3.5e-22 Score=166.80 Aligned_cols=100 Identities=16% Similarity=0.190 Sum_probs=87.4
Q ss_pred EEEEEEeecCCCCCcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhCCC
Q 029428 82 VVAMDCEMVGISQGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGR 159 (193)
Q Consensus 82 ~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~g~ 159 (193)
+++||+||||++. +|+|||+|.+.+ |.++ |++||+|..+|+.+++.+||||+++++++|+|.+++.+ |+++.
T Consensus 2 ~~vlD~ETTGl~~-~IieIg~v~v~~--~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~---~~~~~ 75 (219)
T PRK07983 2 LRVIDTETCGLQG-GIVEIASVDVID--GKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPH---YYGSE 75 (219)
T ss_pred eEEEEEECCCCCC-CCEEEEEEEEEC--CEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHH---HcCCC
Confidence 7899999999984 599999999886 5544 99999999999999999999999999999999999886 57889
Q ss_pred EEEEeChHhhHHHhcccCCCCceeecCCcC
Q 029428 160 ILVGHALHNDLKALLLTHSKKDLRDTSEYQ 189 (193)
Q Consensus 160 ilVgHn~~fDl~~L~~~~p~~~iiDT~~~~ 189 (193)
+|||||+.||+.||.... ...+||..+.
T Consensus 76 ~lVaHNa~FD~~~L~~~~--~~~idTl~la 103 (219)
T PRK07983 76 WYVAHNASFDRRVLPEMP--GEWICTMKLA 103 (219)
T ss_pred EEEEeCcHhhHHHHhCcC--CCcEeHHHHH
Confidence 999999999999997432 3579987753
No 23
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.87 E-value=1.3e-21 Score=171.16 Aligned_cols=108 Identities=23% Similarity=0.247 Sum_probs=91.8
Q ss_pred CCcEEEEEEeecCCCC--CcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHH
Q 029428 79 LTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (193)
+.+||+||+||||+++ ++|+|||+|.+. .+|.++ |++||+|.. ++..+.|||||+++|+++|+|.+++.+|.+
T Consensus 14 ~~~fvvlD~ETTGl~p~~d~IIeIgav~v~-~~g~i~~~~~~lv~P~~--~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~ 90 (313)
T PRK06063 14 PRGWAVVDVETSGFRPGQARIISLAVLGLD-ADGNVEQSVVTLLNPGV--DPGPTHVHGLTAEMLEGQPQFADIAGEVAE 90 (313)
T ss_pred CCCEEEEEEECCCCCCCCCEEEEEEEEEEE-CCceeeeEEEEEECcCC--CCCCeecCCCCHHHHhCCCCHHHHHHHHHH
Confidence 5679999999999994 589999999885 335544 899999975 456789999999999999999999999999
Q ss_pred HhCCCEEEEeChHhhHHHhccc-------CCCCceeecCCcC
Q 029428 155 LIEGRILVGHALHNDLKALLLT-------HSKKDLRDTSEYQ 189 (193)
Q Consensus 155 ~l~g~ilVgHn~~fDl~~L~~~-------~p~~~iiDT~~~~ 189 (193)
|+++++|||||+.||+.||+.. .|...++||..+.
T Consensus 91 ~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~la 132 (313)
T PRK06063 91 LLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELA 132 (313)
T ss_pred HcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHH
Confidence 9999999999999999999632 2334578987653
No 24
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.87 E-value=6.9e-22 Score=166.09 Aligned_cols=110 Identities=16% Similarity=0.154 Sum_probs=90.7
Q ss_pred CCCcEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHcc-CCCHHHHHHHH
Q 029428 78 SLTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRK-AKDFPTVQKKV 152 (193)
Q Consensus 78 ~~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~-a~~~~ev~~~l 152 (193)
...+||+||+||||++ .++|++||+|.+. .+|.++ |++||+|..+|+++++.|||||++++.+ ++++.+++.+|
T Consensus 4 ~~~~~vv~D~ETTGl~p~~d~Iieig~v~v~-~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~ 82 (232)
T PRK07942 4 HPGPLAAFDLETTGVDPETARIVTAALVVVD-ADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEI 82 (232)
T ss_pred ccCcEEEEEeccCCCCCCCCeeEEEEEEEEe-CCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHH
Confidence 4567999999999999 4689999998875 335443 8899999999999999999999999975 78888888888
Q ss_pred HHHh-----CCCEEEEeChHhhHHHhcccC--------CCCceeecCCc
Q 029428 153 AELI-----EGRILVGHALHNDLKALLLTH--------SKKDLRDTSEY 188 (193)
Q Consensus 153 ~~~l-----~g~ilVgHn~~fDl~~L~~~~--------p~~~iiDT~~~ 188 (193)
.+++ ++++|||||+.||+.||+..+ ....++||..+
T Consensus 83 ~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l 131 (232)
T PRK07942 83 ADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVI 131 (232)
T ss_pred HHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHH
Confidence 8776 589999999999999996322 12357887654
No 25
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=8.9e-22 Score=165.29 Aligned_cols=106 Identities=20% Similarity=0.257 Sum_probs=91.2
Q ss_pred cEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhCC
Q 029428 81 DVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG 158 (193)
Q Consensus 81 ~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~g 158 (193)
++|+||+||||++ .++|+|||++ +......|+.+|+|..+|+..++++||||+++|+++|+|.+++++|.+|+++
T Consensus 3 ~~vv~D~ETTGl~~~~d~IIeig~v---~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~~ 79 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRIIEIAAY---NGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGT 79 (232)
T ss_pred cEEEEEeeCCCCCCCCCEEEEEEEE---cCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHcC
Confidence 5999999999999 3689999975 3334567999999999999999999999999999999999999999999984
Q ss_pred -CEEEEeC-hHhhHHHhccc-------CCCCceeecCCcC
Q 029428 159 -RILVGHA-LHNDLKALLLT-------HSKKDLRDTSEYQ 189 (193)
Q Consensus 159 -~ilVgHn-~~fDl~~L~~~-------~p~~~iiDT~~~~ 189 (193)
.++|||| +.||+.||+.. .+.+.++||..++
T Consensus 80 ~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~ 119 (232)
T PRK06309 80 DNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWA 119 (232)
T ss_pred CCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHH
Confidence 7999999 58999999632 2345789987654
No 26
>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=99.86 E-value=1.1e-21 Score=161.41 Aligned_cols=113 Identities=22% Similarity=0.203 Sum_probs=91.8
Q ss_pred CCCCcEEEEEEeecCCC--CCcEeEEEEEEEEeC-CCcE----EEEEEecCC--CccccccccccCCCHH-HHccCCCHH
Q 029428 77 FSLTDVVAMDCEMVGIS--QGNKSALGRVSLVNK-WGNL----IYDEFVRPL--ERVVDFRTRISGIRPR-DLRKAKDFP 146 (193)
Q Consensus 77 ~~~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~-~g~~----i~~~lV~P~--~~i~~~~t~ihGIt~e-~l~~a~~~~ 146 (193)
+....+|+||+||||++ .++|+|||+|.|... .|.+ .|+++|+|. .+|+..++.|||||++ ++++++++.
T Consensus 5 ~~~~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~ 84 (200)
T TIGR01298 5 FRGYLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEY 84 (200)
T ss_pred hcCCeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchH
Confidence 44567999999999999 468999999999743 3444 289999974 6899999999999976 689999998
Q ss_pred HHHHHHHHHh---------CCCEEEEeChHhhHHHhcccC----------CCCceeecCCcC
Q 029428 147 TVQKKVAELI---------EGRILVGHALHNDLKALLLTH----------SKKDLRDTSEYQ 189 (193)
Q Consensus 147 ev~~~l~~~l---------~g~ilVgHn~~fDl~~L~~~~----------p~~~iiDT~~~~ 189 (193)
+++.++.+++ +++++||||+.||+.||+... +...++||..+.
T Consensus 85 ~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~la 146 (200)
T TIGR01298 85 EALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLA 146 (200)
T ss_pred HHHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHH
Confidence 8888888876 688999999999999996321 123479998764
No 27
>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=99.86 E-value=6e-22 Score=159.90 Aligned_cols=108 Identities=16% Similarity=0.126 Sum_probs=85.8
Q ss_pred EEEEEEeecCCC---CCcEeEEEEEEEEeCC---C--------cE--EEEEEecCCCccccccccccCCCHHHHccCCCH
Q 029428 82 VVAMDCEMVGIS---QGNKSALGRVSLVNKW---G--------NL--IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDF 145 (193)
Q Consensus 82 ~v~lD~EtTGl~---~~~i~eia~V~vv~~~---g--------~~--i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~ 145 (193)
||+||+||||++ .++|+|||+|.+.++. + ++ .|++||+|..+|++.++.|||||++++.++++|
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~~~ 80 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAPF 80 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCCCc
Confidence 689999999998 3699999999987532 1 12 389999999999999999999999999999988
Q ss_pred HH-HHHHHHHHhC----CCEEEEeCh-HhhHHHhccc-------CC-CCceeecCCcC
Q 029428 146 PT-VQKKVAELIE----GRILVGHAL-HNDLKALLLT-------HS-KKDLRDTSEYQ 189 (193)
Q Consensus 146 ~e-v~~~l~~~l~----g~ilVgHn~-~fDl~~L~~~-------~p-~~~iiDT~~~~ 189 (193)
.+ +++.+.+|++ +.+|||||+ .||+.||+.. .+ ....+||..++
T Consensus 81 ~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~ 138 (177)
T cd06136 81 DSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAF 138 (177)
T ss_pred cHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHH
Confidence 74 6666666663 469999998 8999999632 12 23468987654
No 28
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.86 E-value=2.4e-22 Score=194.85 Aligned_cols=119 Identities=25% Similarity=0.348 Sum_probs=106.1
Q ss_pred CCCCCCCCCCCCcEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCC
Q 029428 69 PLTPINDDFSLTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKD 144 (193)
Q Consensus 69 ~~~p~~~~~~~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~ 144 (193)
.+.|....+....||+||+|||||+ .+.|+|+|++.+.+ |+++ |+.||+|..+++...+.+||||++||+++++
T Consensus 410 v~N~~d~~l~datyVVfDiETTGLs~~~d~iIE~aAvKikn--g~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~ 487 (1444)
T COG2176 410 VYNPDDQKLDDATYVVFDIETTGLSPVYDEIIEIAAVKIKN--GRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPE 487 (1444)
T ss_pred ecCccccccccccEEEEEeecCCcCcccchhhhheeeeeeC--CcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCcc
Confidence 3566777778889999999999999 47899999999988 6666 9999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhCCCEEEEeChHhhHHHhccc-----CC--CCceeecCCcC
Q 029428 145 FPTVQKKVAELIEGRILVGHALHNDLKALLLT-----HS--KKDLRDTSEYQ 189 (193)
Q Consensus 145 ~~ev~~~l~~~l~g~ilVgHn~~fDl~~L~~~-----~p--~~~iiDT~~~~ 189 (193)
+.+|+.+|.+|++++||||||++||+.||+.. .+ .+.+|||..+.
T Consensus 488 i~~vL~kf~~~~~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~la 539 (1444)
T COG2176 488 IEEVLEKFREFIGDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELA 539 (1444)
T ss_pred HHHHHHHHHHHhcCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHH
Confidence 99999999999999999999999999999732 22 36789997663
No 29
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.86 E-value=1.6e-21 Score=153.13 Aligned_cols=109 Identities=28% Similarity=0.508 Sum_probs=92.8
Q ss_pred cEEEEEEeecCCCC--CcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhCC
Q 029428 81 DVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG 158 (193)
Q Consensus 81 ~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~g 158 (193)
.||+||+||||+++ ++|+|||+|.+.++.-...|+.||+|..+++++++++||||++++.++++|.+++.+|.+|+++
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~~l~~ 80 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLKG 80 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHhcC
Confidence 38999999999994 5899999998765321344999999999999999999999999999999999999999999999
Q ss_pred CEEEEeCh-HhhHHHhcccCCC--------CceeecCCcC
Q 029428 159 RILVGHAL-HNDLKALLLTHSK--------KDLRDTSEYQ 189 (193)
Q Consensus 159 ~ilVgHn~-~fDl~~L~~~~p~--------~~iiDT~~~~ 189 (193)
.++||||. .||+.+|+..+.+ ..++||..++
T Consensus 81 ~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~ 120 (169)
T smart00479 81 KILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLA 120 (169)
T ss_pred CEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHH
Confidence 99999998 9999999743221 3478986654
No 30
>PRK07883 hypothetical protein; Validated
Probab=99.85 E-value=4.8e-21 Score=178.80 Aligned_cols=113 Identities=21% Similarity=0.270 Sum_probs=98.9
Q ss_pred CCCCCCCcEEEEEEeecCCCC--CcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHHH
Q 029428 74 NDDFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQ 149 (193)
Q Consensus 74 ~~~~~~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~ 149 (193)
...+....||+||+||||+++ ++|+|||+|.+.+ |.++ |+.||+|..+++++++.+||||+++|+++++|.+++
T Consensus 9 ~~~~~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~--g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl 86 (557)
T PRK07883 9 GTPLRDVTFVVVDLETTGGSPAGDAITEIGAVKVRG--GEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVL 86 (557)
T ss_pred CCCCcCCCEEEEEEecCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHH
Confidence 345556789999999999994 6999999999865 5555 999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCEEEEeChHhhHHHhcc-------cCCCCceeecCCc
Q 029428 150 KKVAELIEGRILVGHALHNDLKALLL-------THSKKDLRDTSEY 188 (193)
Q Consensus 150 ~~l~~~l~g~ilVgHn~~fDl~~L~~-------~~p~~~iiDT~~~ 188 (193)
.+|.+|++++++||||+.||+.||+. .++....+||..+
T Consensus 87 ~~f~~fl~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~l 132 (557)
T PRK07883 87 PAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRL 132 (557)
T ss_pred HHHHHHhcCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHH
Confidence 99999999999999999999999963 2344567899765
No 31
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.85 E-value=5.4e-21 Score=185.20 Aligned_cols=108 Identities=28% Similarity=0.411 Sum_probs=95.4
Q ss_pred CCcEEEEEEeecCCC-CCcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHH
Q 029428 79 LTDVVAMDCEMVGIS-QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~-~~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~ 155 (193)
..+|||||+||||++ .++|+|||+|.+.+ |.++ |++||+|..+|+++++.+||||+++|+++|+|++++.+|.+|
T Consensus 6 ~~~~vvvD~ETTGl~~~d~IIeIgaV~v~~--g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~ 83 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNASIIQVGIVIIEG--GEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDL 83 (820)
T ss_pred CCCEEEEEEecCCcCCCCeEEEEEEEEEEC--CEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHH
Confidence 567999999999998 57999999999876 5544 999999999999999999999999999999999999999999
Q ss_pred hCCCEEEEeChHhhHHHhccc-----CC-CCceeecCCc
Q 029428 156 IEGRILVGHALHNDLKALLLT-----HS-KKDLRDTSEY 188 (193)
Q Consensus 156 l~g~ilVgHn~~fDl~~L~~~-----~p-~~~iiDT~~~ 188 (193)
++++++||||+.||+.||+.. ++ ....+||..+
T Consensus 84 l~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~l 122 (820)
T PRK07246 84 IEDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVEL 122 (820)
T ss_pred hCCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHH
Confidence 999999999999999999632 21 2457898764
No 32
>PRK06722 exonuclease; Provisional
Probab=99.84 E-value=9.1e-21 Score=163.49 Aligned_cols=97 Identities=22% Similarity=0.310 Sum_probs=86.9
Q ss_pred CCcEEEEEEeecCCC-----CCcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHHHHH
Q 029428 79 LTDVVAMDCEMVGIS-----QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKK 151 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~-----~~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~ 151 (193)
...|||||+||||.. +++|+|||+|.|.++.+.++ |++||+|..+|+++++.+||||++||.+||+|++|+.+
T Consensus 4 ~~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~f~eVl~e 83 (281)
T PRK06722 4 ATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEK 83 (281)
T ss_pred CCEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHHHH
Confidence 357999999999643 26899999999987544555 99999999999999999999999999999999999999
Q ss_pred HHHHhCCCEEEEeChHhhHHHhcc
Q 029428 152 VAELIEGRILVGHALHNDLKALLL 175 (193)
Q Consensus 152 l~~~l~g~ilVgHn~~fDl~~L~~ 175 (193)
|.+|+++.++|+||+.||++||..
T Consensus 84 f~~fig~~~lvahna~FD~~FL~~ 107 (281)
T PRK06722 84 FIQFIGEDSIFVTWGKEDYRFLSH 107 (281)
T ss_pred HHHHHCCCcEEEEEeHHHHHHHHH
Confidence 999999888888889999999974
No 33
>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=99.84 E-value=3.6e-21 Score=156.97 Aligned_cols=110 Identities=26% Similarity=0.246 Sum_probs=85.2
Q ss_pred CcEEEEEEeecCCC--CCcEeEEEEEEEEeC-CCcE----EEEEEecC--CCccccccccccCCCHHH-HccCCCHHHHH
Q 029428 80 TDVVAMDCEMVGIS--QGNKSALGRVSLVNK-WGNL----IYDEFVRP--LERVVDFRTRISGIRPRD-LRKAKDFPTVQ 149 (193)
Q Consensus 80 ~~~v~lD~EtTGl~--~~~i~eia~V~vv~~-~g~~----i~~~lV~P--~~~i~~~~t~ihGIt~e~-l~~a~~~~ev~ 149 (193)
-.+|+||+||||++ .++|+|||+|.+.+. +|.+ .|++||+| ..+|++.+++|||||+++ +++++...+++
T Consensus 5 ~~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~~ 84 (189)
T cd06134 5 FLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEAL 84 (189)
T ss_pred ceeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHHH
Confidence 35799999999999 468999999999853 3432 49999999 468999999999999987 56677666655
Q ss_pred HHHHHHh---------CCCEEEEeChHhhHHHhcccC--------C--CCceeecCCcC
Q 029428 150 KKVAELI---------EGRILVGHALHNDLKALLLTH--------S--KKDLRDTSEYQ 189 (193)
Q Consensus 150 ~~l~~~l---------~g~ilVgHn~~fDl~~L~~~~--------p--~~~iiDT~~~~ 189 (193)
.+|.+++ ++++|||||+.||+.||+..+ + ...++||..+.
T Consensus 85 ~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la 143 (189)
T cd06134 85 KEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLA 143 (189)
T ss_pred HHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHH
Confidence 5555544 378999999999999996321 1 23579997764
No 34
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.83 E-value=1.5e-20 Score=155.15 Aligned_cols=96 Identities=20% Similarity=0.210 Sum_probs=82.3
Q ss_pred CCcEEEEEEeecCCCC--------CcEeEEEEEEEEeCCCcEEEEEEecCCC--ccccccccccCCCHHHHccCCCHHHH
Q 029428 79 LTDVVAMDCEMVGISQ--------GNKSALGRVSLVNKWGNLIYDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTV 148 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~--------~~i~eia~V~vv~~~g~~i~~~lV~P~~--~i~~~~t~ihGIt~e~l~~a~~~~ev 148 (193)
..+||+||+||||++. ++|+|||+|.+.++.-...|++||+|.. +++++++++||||+++|.++|+|.++
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ev 82 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEEL 82 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHHHH
Confidence 3469999999999762 5799999999976322233999999987 68999999999999999999999999
Q ss_pred HHHHHHHhCC-CEEEEeChHhhHHHhc
Q 029428 149 QKKVAELIEG-RILVGHALHNDLKALL 174 (193)
Q Consensus 149 ~~~l~~~l~g-~ilVgHn~~fDl~~L~ 174 (193)
+.+|.+|+++ ..+|+|++.||+.||+
T Consensus 83 l~~f~~~~~~~~~~iv~~~~fD~~fL~ 109 (207)
T PRK07748 83 VEKLAEYDKRCKPTIVTWGNMDMKVLK 109 (207)
T ss_pred HHHHHHHhCcCCeEEEEECHHHHHHHH
Confidence 9999999998 4566666899999996
No 35
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.83 E-value=3.4e-20 Score=165.33 Aligned_cols=112 Identities=44% Similarity=0.639 Sum_probs=104.3
Q ss_pred CCCCcEEEEEEeecCCCCCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccC-CCHHHHHHHHHHH
Q 029428 77 FSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKA-KDFPTVQKKVAEL 155 (193)
Q Consensus 77 ~~~~~~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a-~~~~ev~~~l~~~ 155 (193)
....+++|+||||.....| .|+++|++||.++.++||.||+|..+|.+|+|+++|||.++++++ .++++++.+|..|
T Consensus 213 ~~~~~i~AlDCEm~~te~g--~el~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~~~ 290 (380)
T KOG2248|consen 213 SKSPNIFALDCEMVVTENG--LELTRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELLEL 290 (380)
T ss_pred CCCCCeEEEEeeeeeeccc--eeeEEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHHhh
Confidence 4467899999999999977 699999999999999999999999999999999999999999855 6899999999999
Q ss_pred hC-CCEEEEeChHhhHHHhcccCCCCceeecCCcCccc
Q 029428 156 IE-GRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFL 192 (193)
Q Consensus 156 l~-g~ilVgHn~~fDl~~L~~~~p~~~iiDT~~~~~~~ 192 (193)
+. +.|||||+++.||.+|++.||. ++||+.+|++.
T Consensus 291 ~~~~TILVGHSLenDL~aLKl~H~~--ViDTa~lf~~~ 326 (380)
T KOG2248|consen 291 ISKNTILVGHSLENDLKALKLDHPS--VIDTAVLFKHP 326 (380)
T ss_pred cCcCcEEEeechhhHHHHHhhhCCc--eeeeeEEEecC
Confidence 97 9999999999999999999998 99999887654
No 36
>PRK05359 oligoribonuclease; Provisional
Probab=99.83 E-value=1.5e-20 Score=152.64 Aligned_cols=109 Identities=15% Similarity=0.151 Sum_probs=88.9
Q ss_pred CCcEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEE---EEEEecCCCc----ccccccccc---CCCHHHHccCCCHH
Q 029428 79 LTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI---YDEFVRPLER----VVDFRTRIS---GIRPRDLRKAKDFP 146 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i---~~~lV~P~~~----i~~~~t~ih---GIt~e~l~~a~~~~ 146 (193)
..+||+||+|||||+ .++|+|||+|.+. ....++ |+.+|+|... ++.+++.+| |||++++++++++.
T Consensus 2 ~~~~vvlD~ETTGLdp~~d~IieIgaV~~~-~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~ 80 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPERDRIIEIATIVTD-ADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEA 80 (181)
T ss_pred CCcEEEEEeecCCCCCCCCeEEEEEEEEEc-CCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHH
Confidence 357999999999999 4799999999664 333333 8889999864 466788887 89999999999999
Q ss_pred HHHHHHHHHhC------CCEEEEeChHhhHHHhcccC------CCCceeecCCc
Q 029428 147 TVQKKVAELIE------GRILVGHALHNDLKALLLTH------SKKDLRDTSEY 188 (193)
Q Consensus 147 ev~~~l~~~l~------g~ilVgHn~~fDl~~L~~~~------p~~~iiDT~~~ 188 (193)
+++.+|.+|++ +.+|||||+.||+.||+... ..++++|++.+
T Consensus 81 e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl 134 (181)
T PRK05359 81 EAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTL 134 (181)
T ss_pred HHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHH
Confidence 99999999995 58899999999999997432 23557886655
No 37
>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=99.82 E-value=3e-20 Score=142.67 Aligned_cols=106 Identities=25% Similarity=0.307 Sum_probs=92.9
Q ss_pred EEEEEeecCCC--CCcEeEEEEEEEEeCCCc--EEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhCC
Q 029428 83 VAMDCEMVGIS--QGNKSALGRVSLVNKWGN--LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG 158 (193)
Q Consensus 83 v~lD~EtTGl~--~~~i~eia~V~vv~~~g~--~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~g 158 (193)
|+||+||||++ .++|+|||+|.+.+. +. ..|+.||+|...++++++.+|||+++++.+++++.+++.+|.+++.+
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~-~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~l~~ 79 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGG-IEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECC-cChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHHHHHCC
Confidence 58999999999 579999999987653 33 34999999999999999999999999999999999999999999999
Q ss_pred CEEEEeChHhhHHHhccc-------CCCCceeecCCcC
Q 029428 159 RILVGHALHNDLKALLLT-------HSKKDLRDTSEYQ 189 (193)
Q Consensus 159 ~ilVgHn~~fDl~~L~~~-------~p~~~iiDT~~~~ 189 (193)
.++||||+.||+.+|+.. ......+||..++
T Consensus 80 ~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~ 117 (159)
T cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLA 117 (159)
T ss_pred CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHH
Confidence 999999999999999733 3356799997654
No 38
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.82 E-value=4.6e-20 Score=180.80 Aligned_cols=107 Identities=28% Similarity=0.410 Sum_probs=94.6
Q ss_pred CcEEEEEEeecCCCC---CcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHH
Q 029428 80 TDVVAMDCEMVGISQ---GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (193)
Q Consensus 80 ~~~v~lD~EtTGl~~---~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (193)
.+||+||+||||+++ ++|++||+|.+.+ |.++ |+.||+|..+|+++++.+||||+++|+++|+|.+++.+|.+
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~--~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~ 80 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVED--GEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVE 80 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEEC--CEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHHH
Confidence 469999999999973 5899999999875 5554 99999999999999999999999999999999999999999
Q ss_pred HhCCCEEEEeChHhhHHHhccc-----C--CCCceeecCCc
Q 029428 155 LIEGRILVGHALHNDLKALLLT-----H--SKKDLRDTSEY 188 (193)
Q Consensus 155 ~l~g~ilVgHn~~fDl~~L~~~-----~--p~~~iiDT~~~ 188 (193)
|++++++||||+.||+.||+.. + +...++||..+
T Consensus 81 ~l~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~l 121 (928)
T PRK08074 81 LLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVEL 121 (928)
T ss_pred HhCCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHH
Confidence 9999999999999999999632 2 23568999765
No 39
>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=99.82 E-value=6e-20 Score=182.89 Aligned_cols=116 Identities=28% Similarity=0.410 Sum_probs=100.3
Q ss_pred CCCCCC-CCCcEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHH
Q 029428 72 PINDDF-SLTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFP 146 (193)
Q Consensus 72 p~~~~~-~~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ 146 (193)
+...++ ....||+||+||||++ .++|+|||+|.+.+ |.++ |+.||+|..+|+++++++||||+++|++++++.
T Consensus 181 ~~~~~l~~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~--g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~ 258 (1213)
T TIGR01405 181 PDDQKLLDDATYVVFDIETTGLSPQYDEIIEFGAVKVKN--GRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIE 258 (1213)
T ss_pred ccccccccCCcEEEEEeEecCCCCCCCeEEEEEEEEEEC--CeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHH
Confidence 344444 6678999999999999 47999999999986 5554 999999999999999999999999999999999
Q ss_pred HHHHHHHHHhCCCEEEEeChHhhHHHhccc-----C--CCCceeecCCcC
Q 029428 147 TVQKKVAELIEGRILVGHALHNDLKALLLT-----H--SKKDLRDTSEYQ 189 (193)
Q Consensus 147 ev~~~l~~~l~g~ilVgHn~~fDl~~L~~~-----~--p~~~iiDT~~~~ 189 (193)
+++.+|.+|+++++|||||+.||+.||+.. . ....++||..+.
T Consensus 259 evl~~f~~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~la 308 (1213)
T TIGR01405 259 EVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELA 308 (1213)
T ss_pred HHHHHHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHH
Confidence 999999999999999999999999999732 1 124689987654
No 40
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.81 E-value=8.9e-20 Score=152.79 Aligned_cols=95 Identities=26% Similarity=0.343 Sum_probs=87.6
Q ss_pred CcEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEE-EEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHh
Q 029428 80 TDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI-YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (193)
Q Consensus 80 ~~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i-~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (193)
.++++||+||||++ .++|+|||+|.+.+..-... |+.||+|..+|+++..++||||.+++.++|.|.++++++.+|+
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~i 92 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDFI 92 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 67999999999998 67999999999998432222 9999999889999999999999999999999999999999999
Q ss_pred CC-CEEEEeChHhhHHHhc
Q 029428 157 EG-RILVGHALHNDLKALL 174 (193)
Q Consensus 157 ~g-~ilVgHn~~fDl~~L~ 174 (193)
++ +++||||+.||+.||+
T Consensus 93 ~~~~~~Vahna~fD~~fl~ 111 (243)
T COG0847 93 GGLRLLVAHNAAFDVGFLR 111 (243)
T ss_pred CCCCeEEEEchhhcHHHHH
Confidence 99 9999999999999996
No 41
>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=99.81 E-value=9.4e-20 Score=177.22 Aligned_cols=107 Identities=27% Similarity=0.389 Sum_probs=94.4
Q ss_pred cEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHh
Q 029428 81 DVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (193)
Q Consensus 81 ~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (193)
+||+||+||||++ .++|++||+|.+.+ |.++ |+++|+|..+|+++++++||||+++++++|+|.+++.+|.+|+
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~--~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~~l 78 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVED--GEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLL 78 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHHHh
Confidence 4899999999999 47999999999865 5554 9999999999999999999999999999999999999999999
Q ss_pred CCCEEEEeChHhhHHHhccc-----C--CCCceeecCCcC
Q 029428 157 EGRILVGHALHNDLKALLLT-----H--SKKDLRDTSEYQ 189 (193)
Q Consensus 157 ~g~ilVgHn~~fDl~~L~~~-----~--p~~~iiDT~~~~ 189 (193)
+++++||||+.||+.||+.. + .....+||..+.
T Consensus 79 ~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~ 118 (850)
T TIGR01407 79 EDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELA 118 (850)
T ss_pred CCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHH
Confidence 99999999999999999632 1 235689987653
No 42
>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=99.80 E-value=6.4e-20 Score=148.61 Aligned_cols=92 Identities=20% Similarity=0.182 Sum_probs=79.3
Q ss_pred EEEEEeecCCC--CCcEeEEEEEEEEeCCCcE--EEEEEecCCC--ccccccccccCCCHHHHcc-CCCHHHHHHHHHHH
Q 029428 83 VAMDCEMVGIS--QGNKSALGRVSLVNKWGNL--IYDEFVRPLE--RVVDFRTRISGIRPRDLRK-AKDFPTVQKKVAEL 155 (193)
Q Consensus 83 v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~--i~~~lV~P~~--~i~~~~t~ihGIt~e~l~~-a~~~~ev~~~l~~~ 155 (193)
++||+||||++ .++|+|||+|.+.+ .+.+ .|+.+|+|.. .++..++.+||||+++|.+ ++++.+++.+|.+|
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~-~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~~ 79 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDE-NFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHRL 79 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECC-CCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHHH
Confidence 58999999999 46899999998754 3333 3899999874 5677899999999999999 89999999999999
Q ss_pred hC--CCEEEEeC-hHhhHHHhcc
Q 029428 156 IE--GRILVGHA-LHNDLKALLL 175 (193)
Q Consensus 156 l~--g~ilVgHn-~~fDl~~L~~ 175 (193)
++ +.++|||| +.||+.||+.
T Consensus 80 ~~~~~~~lVahn~~~FD~~fL~~ 102 (183)
T cd06138 80 FNTPGTCIVGYNNIRFDDEFLRF 102 (183)
T ss_pred HccCCCcEEeeCchhhHHHHHHH
Confidence 95 68999997 8999999963
No 43
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.80 E-value=2.4e-19 Score=155.67 Aligned_cols=99 Identities=19% Similarity=0.213 Sum_probs=81.7
Q ss_pred CCCCCCcEEEEEEeecCCCC--CcEeEEEEEEEEeC-CCcE-----EEEEEecCCCccccccccccCCCHHHHccCCCHH
Q 029428 75 DDFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNK-WGNL-----IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFP 146 (193)
Q Consensus 75 ~~~~~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~-~g~~-----i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ 146 (193)
....+..+|+||+||||+++ ++|+|||+|.+... .|.+ .|+.|++|..+|+..++.|||||++++++++...
T Consensus 32 ~~~~~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~ 111 (294)
T PRK09182 32 RGEFVRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDP 111 (294)
T ss_pred CCCCCCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcH
Confidence 34456679999999999994 78999999998732 3432 3899999999999999999999999999988654
Q ss_pred HHHHHHHHHhC-CCEEEEeChHhhHHHhccc
Q 029428 147 TVQKKVAELIE-GRILVGHALHNDLKALLLT 176 (193)
Q Consensus 147 ev~~~l~~~l~-g~ilVgHn~~fDl~~L~~~ 176 (193)
+ .|.+|++ +.+|||||+.||+.||+..
T Consensus 112 ~---~l~~fl~~~~vlVAHNA~FD~~fL~~~ 139 (294)
T PRK09182 112 A---AVDALIAPADLIIAHNAGFDRPFLERF 139 (294)
T ss_pred H---HHHHHhcCCCEEEEeCHHHHHHHHHHH
Confidence 3 4667776 4699999999999999743
No 44
>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=99.78 E-value=3.3e-19 Score=143.46 Aligned_cols=106 Identities=17% Similarity=0.232 Sum_probs=84.7
Q ss_pred EEEEEEeecCCCC--CcEeEEEEEEEEeCCCcE--EEEEEecCCCccc----ccccccc---CCCHHHHccCCCHHHHHH
Q 029428 82 VVAMDCEMVGISQ--GNKSALGRVSLVNKWGNL--IYDEFVRPLERVV----DFRTRIS---GIRPRDLRKAKDFPTVQK 150 (193)
Q Consensus 82 ~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~--i~~~lV~P~~~i~----~~~t~ih---GIt~e~l~~a~~~~ev~~ 150 (193)
+|+||+||||+++ ++|+|||+|.+.+..+.+ .|+.+|+|..+++ +++..+| ||++++++++|++.+++.
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl~ 80 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEA 80 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHHH
Confidence 5899999999994 789999999765432333 3999999987554 4556665 999999999999999999
Q ss_pred HHHHHhCC------CEEEEeChHhhHHHhcccC-----C-CCceeecCC
Q 029428 151 KVAELIEG------RILVGHALHNDLKALLLTH-----S-KKDLRDTSE 187 (193)
Q Consensus 151 ~l~~~l~g------~ilVgHn~~fDl~~L~~~~-----p-~~~iiDT~~ 187 (193)
+|.+|+++ .+|||||+.||+.||+..+ + .+..+||..
T Consensus 81 ~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~ 129 (173)
T cd06135 81 ELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSS 129 (173)
T ss_pred HHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHH
Confidence 99999974 6999999999999997432 1 244688743
No 45
>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=99.77 E-value=4.7e-20 Score=141.72 Aligned_cols=92 Identities=26% Similarity=0.449 Sum_probs=83.8
Q ss_pred EEEEEeecCCCC--CcEeEEEEEEEEeCCC--cEEEEEEecCCCc--cccccccccCCCHHHHccCCCHHHHHHHHHHHh
Q 029428 83 VAMDCEMVGISQ--GNKSALGRVSLVNKWG--NLIYDEFVRPLER--VVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (193)
Q Consensus 83 v~lD~EtTGl~~--~~i~eia~V~vv~~~g--~~i~~~lV~P~~~--i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (193)
|+|||||||+++ ++|+|||+|.+.+... ...|+.||+|... ++++++.+||||.++|++++++.+++.++.+++
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~~~ 80 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEEFL 80 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhhhh
Confidence 799999999995 7999999999987653 3459999999987 999999999999999999999999999999999
Q ss_pred C-CCEEEEeChHhhHHHhc
Q 029428 157 E-GRILVGHALHNDLKALL 174 (193)
Q Consensus 157 ~-g~ilVgHn~~fDl~~L~ 174 (193)
+ +.++||||+.||..+|.
T Consensus 81 ~~~~~~v~~n~~fd~~~l~ 99 (164)
T PF00929_consen 81 KKNDILVGHNASFDIGFLR 99 (164)
T ss_dssp HHHTEEEETTCCHEEESSH
T ss_pred hcccccccccccchhhHHH
Confidence 8 89999999999987764
No 46
>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=99.77 E-value=1.4e-18 Score=137.74 Aligned_cols=108 Identities=23% Similarity=0.290 Sum_probs=88.9
Q ss_pred EEEEEEeecCCCC-------CcEeEEEEEEEEeCCCcE--EEEEEecCCC--ccccccccccCCCHHHHccCCCHHHHHH
Q 029428 82 VVAMDCEMVGISQ-------GNKSALGRVSLVNKWGNL--IYDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQK 150 (193)
Q Consensus 82 ~v~lD~EtTGl~~-------~~i~eia~V~vv~~~g~~--i~~~lV~P~~--~i~~~~t~ihGIt~e~l~~a~~~~ev~~ 150 (193)
||+||+||||+++ ++|+|||+|.+....+.+ .|+.||+|.. .++++++++||||++++.++++|.+++.
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 6899999999994 689999999886543323 4999999998 8999999999999999999999999999
Q ss_pred HHHHHhCCC--EEEEeChHhhHHHhccc----------CCCCceeecCCcC
Q 029428 151 KVAELIEGR--ILVGHALHNDLKALLLT----------HSKKDLRDTSEYQ 189 (193)
Q Consensus 151 ~l~~~l~g~--ilVgHn~~fDl~~L~~~----------~p~~~iiDT~~~~ 189 (193)
+|.+|+++. .+++|+..||+.+|... ......+|+..++
T Consensus 81 ~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~ 131 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEF 131 (176)
T ss_pred HHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHH
Confidence 999999987 56666679999877421 1135678887654
No 47
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.73 E-value=2.7e-17 Score=152.95 Aligned_cols=96 Identities=21% Similarity=0.296 Sum_probs=84.0
Q ss_pred CCcEEEEEEeecCCCC-----CcEeEEEEEEEEeCCCcEE--EEEEecCCC--ccccccccccCCCHHHHccCCCHHHHH
Q 029428 79 LTDVVAMDCEMVGISQ-----GNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQ 149 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~-----~~i~eia~V~vv~~~g~~i--~~~lV~P~~--~i~~~~t~ihGIt~e~l~~a~~~~ev~ 149 (193)
-..|||||+||||+++ ++|||||+|.|...+|.++ |++||+|.. +++.+++.+||||++||++||+|.+|+
T Consensus 55 ~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eVl 134 (582)
T PTZ00315 55 FDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVY 134 (582)
T ss_pred CCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHHH
Confidence 3679999999999872 6899999998853346555 999999986 799999999999999999999999999
Q ss_pred HHHHHHhCCC----------EEEEeChHhhHH-Hhc
Q 029428 150 KKVAELIEGR----------ILVGHALHNDLK-ALL 174 (193)
Q Consensus 150 ~~l~~~l~g~----------ilVgHn~~fDl~-~L~ 174 (193)
.+|.+|+++. ++|+||..||+. ||.
T Consensus 135 ~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~ 170 (582)
T PTZ00315 135 CEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLP 170 (582)
T ss_pred HHHHHHHhccccccccccCceEEEeccHHHHHHHHH
Confidence 9999999754 699999999995 773
No 48
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.68 E-value=7.8e-17 Score=162.67 Aligned_cols=113 Identities=27% Similarity=0.412 Sum_probs=97.7
Q ss_pred CCCCCCcEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEE--EEEEecCCCccccccccccCCCHHHHccCCCHHHHHH
Q 029428 75 DDFSLTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQK 150 (193)
Q Consensus 75 ~~~~~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i--~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~ 150 (193)
..+....+|++|+||||++ .++|+++|+|.+.+ |.++ |+.||+|..+++++++++||||++++.+++++.+++.
T Consensus 414 ~~L~~~~~VVfDLETTGL~~~~deIIEIgAV~V~~--G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~ 491 (1437)
T PRK00448 414 RDLKDATYVVFDVETTGLSAVYDEIIEIGAVKIKN--GEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLP 491 (1437)
T ss_pred hhhccCcEEEEEhhhcCCCCchhhhheeeeEEEeC--CeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHH
Confidence 3444568999999999999 46899999999876 5544 9999999999999999999999999999999999999
Q ss_pred HHHHHhCCCEEEEeChHhhHHHhc-------ccCCCCceeecCCcC
Q 029428 151 KVAELIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQ 189 (193)
Q Consensus 151 ~l~~~l~g~ilVgHn~~fDl~~L~-------~~~p~~~iiDT~~~~ 189 (193)
.|.+|++|.++||||+.||+.||+ +..+....+||..+.
T Consensus 492 ~f~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLela 537 (1437)
T PRK00448 492 KFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELS 537 (1437)
T ss_pred HHHHHhCCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHH
Confidence 999999999999999999999985 222345688987653
No 49
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.67 E-value=3.3e-16 Score=143.81 Aligned_cols=97 Identities=12% Similarity=0.147 Sum_probs=81.1
Q ss_pred CCcEEEEEEeecCCCC--CcEeEEEEEEEEeCCCcE---EEEEEecCCC--ccccccccccCCCHHHHcc-CCCHHHHHH
Q 029428 79 LTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNL---IYDEFVRPLE--RVVDFRTRISGIRPRDLRK-AKDFPTVQK 150 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~---i~~~lV~P~~--~i~~~~t~ihGIt~e~l~~-a~~~~ev~~ 150 (193)
...||++|+||||+++ ++|+|+|+|.+.+. +.+ .+..||+|.. .+++.++.|||||++++.+ +.+..+++.
T Consensus 5 ~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~-~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~ 83 (476)
T PRK11779 5 QPTFLWHDYETFGANPALDRPAQFAGIRTDAD-LNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAA 83 (476)
T ss_pred CCcEEEEEEECCCCCCCCCeeEEEEEEEEeCC-CceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHH
Confidence 4469999999999994 79999999988652 223 3899999985 3456789999999999965 457999999
Q ss_pred HHHHHhC--CCEEEEeC-hHhhHHHhccc
Q 029428 151 KVAELIE--GRILVGHA-LHNDLKALLLT 176 (193)
Q Consensus 151 ~l~~~l~--g~ilVgHn-~~fDl~~L~~~ 176 (193)
+|.+++. |.++|||| +.||..||+..
T Consensus 84 ~i~~~l~~~~~~lVGhNni~FD~eflr~~ 112 (476)
T PRK11779 84 RIHAEFSQPGTCILGYNNIRFDDEVTRYI 112 (476)
T ss_pred HHHHHHhcCCCEEEEeCchhhcHHHHHHH
Confidence 9999995 89999997 79999999743
No 50
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=99.41 E-value=9.8e-14 Score=111.40 Aligned_cols=113 Identities=19% Similarity=0.237 Sum_probs=91.3
Q ss_pred CCcEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEE---EEEEecCCC----ccccccccc---cCCCHHHHccCCCHH
Q 029428 79 LTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI---YDEFVRPLE----RVVDFRTRI---SGIRPRDLRKAKDFP 146 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i---~~~lV~P~~----~i~~~~t~i---hGIt~e~l~~a~~~~ 146 (193)
..++|++|||||||+ .++|+|||+| |.|++.+.+ ++..|+-+. ...+++..- +|+|...++...++.
T Consensus 25 ~q~lVWiD~EMTGLdvekd~i~EiacI-ITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl~ 103 (208)
T KOG3242|consen 25 KQPLVWIDCEMTGLDVEKDRIIEIACI-ITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITLA 103 (208)
T ss_pred cCceEEEeeeccccccccceeEEEEEE-EecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccHH
Confidence 467999999999999 6899999955 678777666 778887554 345555544 588999999999999
Q ss_pred HHHHHHHHHh------CCCEEEEeChHhhHHHhccc------CCCCceeecCCcCccc
Q 029428 147 TVQKKVAELI------EGRILVGHALHNDLKALLLT------HSKKDLRDTSEYQPFL 192 (193)
Q Consensus 147 ev~~~l~~~l------~g~ilVgHn~~fDl~~L~~~------~p~~~iiDT~~~~~~~ 192 (193)
++-.++++|+ +.++|.|.++..|..||... |-.++++|++.+..++
T Consensus 104 ~aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVStIkeL~ 161 (208)
T KOG3242|consen 104 DAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVSTIKELA 161 (208)
T ss_pred HHHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHHHHHHH
Confidence 9999999999 36899999999999999743 3346799999886654
No 51
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.28 E-value=2.2e-12 Score=102.62 Aligned_cols=113 Identities=12% Similarity=0.210 Sum_probs=88.3
Q ss_pred CCcEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEE---EEEEecCCC----cccccccccc---CCCHHHHccCCCHH
Q 029428 79 LTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI---YDEFVRPLE----RVVDFRTRIS---GIRPRDLRKAKDFP 146 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i---~~~lV~P~~----~i~~~~t~ih---GIt~e~l~~a~~~~ 146 (193)
..++|+||||||||+ .++|+|||.+ |.|.+.+++ +..-|.-.. ...+++++.| |++..-.+...+..
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIEiA~i-VTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t~~ 83 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIEIATI-VTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTEA 83 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEEEEEE-EecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhccHH
Confidence 457999999999999 4789999966 668777777 455555432 4456777665 78888888889999
Q ss_pred HHHHHHHHHhC------CCEEEEeChHhhHHHhcccCCC------CceeecCCcCccc
Q 029428 147 TVQKKVAELIE------GRILVGHALHNDLKALLLTHSK------KDLRDTSEYQPFL 192 (193)
Q Consensus 147 ev~~~l~~~l~------g~ilVgHn~~fDl~~L~~~~p~------~~iiDT~~~~~~~ 192 (193)
++..++++|++ -+++.|.++.-|.+||....|+ ++++|++.+..+.
T Consensus 84 ~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVSTlKELa 141 (184)
T COG1949 84 EAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVSTLKELA 141 (184)
T ss_pred HHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHHHHHHHH
Confidence 99999999983 5799999999999999654442 5689999887654
No 52
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=98.87 E-value=9.3e-10 Score=105.84 Aligned_cols=122 Identities=30% Similarity=0.496 Sum_probs=100.8
Q ss_pred CCCCCCCC--CCCcEEEEEEeecCCCCC---------------cEeEEEEEEEEeCCC----cEEEEEEecCCCcccccc
Q 029428 70 LTPINDDF--SLTDVVAMDCEMVGISQG---------------NKSALGRVSLVNKWG----NLIYDEFVRPLERVVDFR 128 (193)
Q Consensus 70 ~~p~~~~~--~~~~~v~lD~EtTGl~~~---------------~i~eia~V~vv~~~g----~~i~~~lV~P~~~i~~~~ 128 (193)
+.|...+. ....+|+||-|.+-|..+ ...++|+|+++++.| ....|.||--.+.|.||-
T Consensus 898 ~~pLt~dEmPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYL 977 (1118)
T KOG1275|consen 898 LQPLTLDEMPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYL 977 (1118)
T ss_pred eeeccccccCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHH
Confidence 44444333 467899999999998831 124789999999774 344889999999999999
Q ss_pred ccccCCCHHHHccCC------CHHHHHHHHHHHhC-CCEEEEeChHhhHHHhcccCCCCceeecCCcCcc
Q 029428 129 TRISGIRPRDLRKAK------DFPTVQKKVAELIE-GRILVGHALHNDLKALLLTHSKKDLRDTSEYQPF 191 (193)
Q Consensus 129 t~ihGIt~e~l~~a~------~~~ev~~~l~~~l~-g~ilVgHn~~fDl~~L~~~~p~~~iiDT~~~~~~ 191 (193)
|+.+||.+.||.... ++.-++.++.=+++ |++.|||.+..|+++|++..|+.++|||+.+|.+
T Consensus 978 TqySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~ 1047 (1118)
T KOG1275|consen 978 TQYSGIKPGDLDPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRL 1047 (1118)
T ss_pred HHhcCCCccccCCccCcceehhHHHHHHHHHHHHHcCcEEEcccccccceEEEEecChhhheeeeEEEec
Confidence 999999999996432 57888888888887 9999999999999999999999999999998753
No 53
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. 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 domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=98.86 E-value=7.2e-09 Score=84.25 Aligned_cols=85 Identities=18% Similarity=0.182 Sum_probs=63.5
Q ss_pred EEEEEEeecCC----C--CCcEeEEEEEEEEeCCCcEE-EEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHH
Q 029428 82 VVAMDCEMVGI----S--QGNKSALGRVSLVNKWGNLI-YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (193)
Q Consensus 82 ~v~lD~EtTGl----~--~~~i~eia~V~vv~~~g~~i-~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (193)
+++||+||||. + .++|++|+.+...+ |... +.....+...... ||+..++...++..+++..|.+
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~--g~~~~~~~~~~~~~~~~~------~i~~~~v~~~~~E~~lL~~f~~ 72 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFD--GVKVVFLLKTSTVGDDIE------FIDGIEVEYFADEKELLKRFFD 72 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeC--CceeeEEEeecccCCcCC------CCCCceEEEeCCHHHHHHHHHH
Confidence 47899999998 4 46888888765533 4433 3322333221111 8888899999999999999999
Q ss_pred HhCC---CEEEEeCh-HhhHHHhc
Q 029428 155 LIEG---RILVGHAL-HNDLKALL 174 (193)
Q Consensus 155 ~l~g---~ilVgHn~-~fDl~~L~ 174 (193)
++.. .+|||||+ .||+.+|.
T Consensus 73 ~i~~~dpdiivg~N~~~FD~~~L~ 96 (199)
T cd05160 73 IIREYDPDILTGYNIDDFDLPYLL 96 (199)
T ss_pred HHHhcCCCEEEEeccCCCcHHHHH
Confidence 9986 59999999 89999994
No 54
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=98.78 E-value=3.7e-09 Score=89.54 Aligned_cols=92 Identities=26% Similarity=0.391 Sum_probs=73.2
Q ss_pred cEEEEEEeecCCCC------CcEeEEEEEEEEeCCCcEE---EEEEecCCC--ccccccccccCCCHHHHccCCCHHHHH
Q 029428 81 DVVAMDCEMVGISQ------GNKSALGRVSLVNKWGNLI---YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQ 149 (193)
Q Consensus 81 ~~v~lD~EtTGl~~------~~i~eia~V~vv~~~g~~i---~~~lV~P~~--~i~~~~t~ihGIt~e~l~~a~~~~ev~ 149 (193)
-+++||+|+|..+. .+|||+.+|.+.+.+-.++ |+.||+|.. .++++++.+|||..++|..|++|.+|+
T Consensus 57 YLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~vl 136 (280)
T KOG0542|consen 57 YLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQVL 136 (280)
T ss_pred eEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHHHH
Confidence 58899999998872 3788888887766554443 999999985 789999999999999999999999999
Q ss_pred HHHHHHhC--------C-CEEEEeChHhhHHHh
Q 029428 150 KKVAELIE--------G-RILVGHALHNDLKAL 173 (193)
Q Consensus 150 ~~l~~~l~--------g-~ilVgHn~~fDl~~L 173 (193)
.+|..|+. | .-+|.. ...|+...
T Consensus 137 ~~f~~Wlr~~~~~~k~~~~Afvtd-g~wDl~~~ 168 (280)
T KOG0542|consen 137 SEFDSWLRKDSLGDKNGKFAFVTD-GDWDLWVF 168 (280)
T ss_pred HHHHHHHHHhhcccccCceEEEeC-chhhHHHH
Confidence 99999993 2 234444 46777543
No 55
>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=98.57 E-value=2e-07 Score=68.10 Aligned_cols=37 Identities=27% Similarity=0.271 Sum_probs=26.7
Q ss_pred HHHHhCC---CEEEEeChHhhHHHhccc-------CC--CCceeecCCc
Q 029428 152 VAELIEG---RILVGHALHNDLKALLLT-------HS--KKDLRDTSEY 188 (193)
Q Consensus 152 l~~~l~g---~ilVgHn~~fDl~~L~~~-------~p--~~~iiDT~~~ 188 (193)
+.+|+++ +++||||+.||+.||+.. .| ....+||..+
T Consensus 35 f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 35 LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 6667754 689999999999999622 11 3468898653
No 56
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=98.19 E-value=2.2e-07 Score=74.82 Aligned_cols=93 Identities=13% Similarity=0.161 Sum_probs=72.9
Q ss_pred cEEEEEEeecCCCC------CcEeEEEEEEEEeCCCcEE--EEEEecCCC--ccccccccccCCCHHHHccCCCHHHHHH
Q 029428 81 DVVAMDCEMVGISQ------GNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQK 150 (193)
Q Consensus 81 ~~v~lD~EtTGl~~------~~i~eia~V~vv~~~g~~i--~~~lV~P~~--~i~~~~t~ihGIt~e~l~~a~~~~ev~~ 150 (193)
.+++||+|.|.-+. -+|++|.+..+..-+-.++ |++||+|.. .++++|..++||+...|.+||-|..|++
T Consensus 5 ~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v~E 84 (210)
T COG5018 5 SLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMVFE 84 (210)
T ss_pred eEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHHHH
Confidence 47899999998762 2677777544322223344 999999986 6789999999999999999999999999
Q ss_pred HHHHHhC------CCEEEEeChHhhHHHhc
Q 029428 151 KVAELIE------GRILVGHALHNDLKALL 174 (193)
Q Consensus 151 ~l~~~l~------g~ilVgHn~~fDl~~L~ 174 (193)
+|..+|. +..++.+ -.+|++.|+
T Consensus 85 ~f~r~L~~h~Pr~~~~wa~w-G~~Dm~~l~ 113 (210)
T COG5018 85 DFIRKLNEHDPRKNSTWATW-GNMDMKVLK 113 (210)
T ss_pred HHHHHHHhcCcccCCccccc-cchhHHHHH
Confidence 9999994 2345555 489999996
No 57
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.13 E-value=6.7e-06 Score=73.66 Aligned_cols=98 Identities=13% Similarity=0.186 Sum_probs=78.5
Q ss_pred CCcEEEEEEeecCCCC--CcEeEEEEEEEEeCCCcEE---EEEEecCCCcc-c-cccccccCCCHHHH-ccCCCHHHHHH
Q 029428 79 LTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI---YDEFVRPLERV-V-DFRTRISGIRPRDL-RKAKDFPTVQK 150 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~i---~~~lV~P~~~i-~-~~~t~ihGIt~e~l-~~a~~~~ev~~ 150 (193)
...|++.|.||.|.++ ++..++|.|+- |.+.+++ ...|++|.... + +.+.-||||||... +.+.+-.+...
T Consensus 8 ~~tF~~yDYETfG~~Pa~DRPaQFAgiRT-D~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~~ 86 (475)
T COG2925 8 QPTFLFYDYETFGVHPALDRPAQFAGIRT-DIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAA 86 (475)
T ss_pred CCcEEEEehhhcCCCcccccchhhheeec-cccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHHH
Confidence 4469999999999994 68888998875 4445555 77899998743 2 36788999999887 56788889999
Q ss_pred HHHHHhC--CCEEEEeC-hHhhHHHhcccC
Q 029428 151 KVAELIE--GRILVGHA-LHNDLKALLLTH 177 (193)
Q Consensus 151 ~l~~~l~--g~ilVgHn-~~fDl~~L~~~~ 177 (193)
.|...+. +..+||+| +.||=.+-+..+
T Consensus 87 ~I~~~ls~P~Tcv~GYNniRFDDEvtRy~f 116 (475)
T COG2925 87 RIHAELTQPNTCVLGYNNIRFDDEVTRYIF 116 (475)
T ss_pred HHHHHhCCCCeeeecccccccchHHHHHHH
Confidence 9988885 89999999 799988887544
No 58
>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=97.88 E-value=0.00012 Score=58.23 Aligned_cols=90 Identities=20% Similarity=0.129 Sum_probs=57.4
Q ss_pred CCcEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHh
Q 029428 79 LTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (193)
...++++|+|++|++ .++++.++ +....+...+ .-+.+ +.+ .+++++.+++..|.+++
T Consensus 4 ~~~~~a~d~e~~~~~~~~~~i~~l~---~~~~~~~~~~-~~~~~--------~~~--------~~~~~~~~~~~~l~~~l 63 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQAELVGIS---FAVEPGEAYY-IPLGH--------DYG--------GEQLPREEVLAALKPLL 63 (193)
T ss_pred cCCeEEEEeecCCCCcCCCeEEEEE---EEcCCCCEEE-EecCC--------Ccc--------ccCCCHHHHHHHHHHHH
Confidence 356899999999998 45555444 3332232222 11111 001 14567888999999999
Q ss_pred CCC--EEEEeChHhhHHHhcccC--CCCceeecCCc
Q 029428 157 EGR--ILVGHALHNDLKALLLTH--SKKDLRDTSEY 188 (193)
Q Consensus 157 ~g~--ilVgHn~~fDl~~L~~~~--p~~~iiDT~~~ 188 (193)
.+. .+||||+.||+.+|.... ....++||..+
T Consensus 64 ~~~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~ 99 (193)
T cd06139 64 EDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLA 99 (193)
T ss_pred hCCCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHH
Confidence 754 799999999999996322 12346888654
No 59
>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=97.82 E-value=0.00011 Score=57.37 Aligned_cols=82 Identities=27% Similarity=0.398 Sum_probs=52.3
Q ss_pred CcEEEEEEeecCCCC-CcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhC-
Q 029428 80 TDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE- 157 (193)
Q Consensus 80 ~~~v~lD~EtTGl~~-~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~- 157 (193)
.++++||+||+|++. ..-..++.+.+.+. ...| ++.+...-... +...|.+++.
T Consensus 20 ~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~--~~~~--i~~~~~~~~~~--------------------~~~~l~~ll~~ 75 (176)
T PF01612_consen 20 AKVLAFDTETTGLDPYSYNPKIALIQLATG--EGCY--IIDPIDLGDNW--------------------ILDALKELLED 75 (176)
T ss_dssp TSEEEEEEEEETSTSTTSSEEEEEEEEEES--CEEE--EECGTTSTTTT--------------------HHHHHHHHHTT
T ss_pred CCeEEEEEEECCCCccccCCeEEEEEEecC--CCce--eeeeccccccc--------------------hHHHHHHHHhC
Confidence 459999999999995 22345566666553 2221 22221100000 6777888887
Q ss_pred -CCEEEEeChHhhHHHhcc--cCCCCceeec
Q 029428 158 -GRILVGHALHNDLKALLL--THSKKDLRDT 185 (193)
Q Consensus 158 -g~ilVgHn~~fDl~~L~~--~~p~~~iiDT 185 (193)
+.+.||||+.||+.+|.. ...-.+++||
T Consensus 76 ~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~ 106 (176)
T PF01612_consen 76 PNIIKVGHNAKFDLKWLYRSFGIDLKNVFDT 106 (176)
T ss_dssp TTSEEEESSHHHHHHHHHHHHTS--SSEEEH
T ss_pred CCccEEEEEEechHHHHHHHhccccCCccch
Confidence 568999999999999975 3344568998
No 60
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=97.41 E-value=0.00063 Score=55.52 Aligned_cols=77 Identities=13% Similarity=0.165 Sum_probs=49.0
Q ss_pred CcEEEEEEeec---CC-C--CCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHH
Q 029428 80 TDVVAMDCEMV---GI-S--QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (193)
Q Consensus 80 ~~~v~lD~EtT---Gl-~--~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~ 153 (193)
-++++||+||+ |+ + .+.|+.|+.+ ...+..++.. ++.. ...+..-.+-.+++.+|.
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~---~~~~~~~~~~--~~~~-------------~~~v~~~~~E~~lL~~F~ 64 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFA---DEGGNKVITW--KKFD-------------LPFVEVVKTEKEMIKRFI 64 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEe---cCCCceEEEe--cCCC-------------CCeEEEeCCHHHHHHHHH
Confidence 46899999999 44 2 3567666643 2334333211 1111 012333456688889999
Q ss_pred HHhCC---CEEEEeCh-HhhHHHhc
Q 029428 154 ELIEG---RILVGHAL-HNDLKALL 174 (193)
Q Consensus 154 ~~l~g---~ilVgHn~-~fDl~~L~ 174 (193)
+++.. .+|||||. .||+.+|.
T Consensus 65 ~~i~~~dpdiivgyN~~~FD~pyL~ 89 (195)
T cd05780 65 EIVKEKDPDVIYTYNGDNFDFPYLK 89 (195)
T ss_pred HHHHHcCCCEEEecCCCCCcHHHHH
Confidence 98874 79999996 69999994
No 61
>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=97.35 E-value=0.00041 Score=54.32 Aligned_cols=70 Identities=16% Similarity=0.121 Sum_probs=33.6
Q ss_pred EEEEEeecCCCC--CcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHH-HHHHHHHHhCCC
Q 029428 83 VAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPT-VQKKVAELIEGR 159 (193)
Q Consensus 83 v~lD~EtTGl~~--~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~e-v~~~l~~~l~g~ 159 (193)
++||+||||+++ +.+.-+|.+.+ +.+....|..+..... .-++ +++.+..+.+..
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~-~~~~~~~~~~~~~~~~---------------------~ee~~~~~~~~~l~~~~ 58 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADF-DDDEIITFIQWFAEDP---------------------DEEEIILEFFELLDEAD 58 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE--ETTTTE-EEEE-GGGH---------------------HHHHHHHH--HHHHTT-
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEe-CCCceEEeeHhhccCc---------------------HHHHHHHHHHHHHhcCC
Confidence 589999999985 55555554433 3333332433332211 1122 222232344578
Q ss_pred EEEEeC-hHhhHHHhc
Q 029428 160 ILVGHA-LHNDLKALL 174 (193)
Q Consensus 160 ilVgHn-~~fDl~~L~ 174 (193)
.+|+|| ..||+.+|+
T Consensus 59 ~iv~yng~~FD~p~L~ 74 (164)
T PF13482_consen 59 NIVTYNGKNFDIPFLK 74 (164)
T ss_dssp -EEESSTTTTHHHHHH
T ss_pred eEEEEeCcccCHHHHH
Confidence 999999 599999997
No 62
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. 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. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=97.20 E-value=0.0026 Score=51.90 Aligned_cols=70 Identities=16% Similarity=0.191 Sum_probs=47.2
Q ss_pred CCcEEEEEEeec---CC-C--CCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHH
Q 029428 79 LTDVVAMDCEMV---GI-S--QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKV 152 (193)
Q Consensus 79 ~~~~v~lD~EtT---Gl-~--~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l 152 (193)
+-++++||+||+ |+ + .+.|+.|+. ...+|...+-. ....+-.+++..|
T Consensus 2 ~l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~---~~~~g~~~~~~-----------------------~~~~~E~~lL~~F 55 (188)
T cd05781 2 DLKTLAFDIEVYSKYGTPNPRRDPIIVISL---ATSNGDVEFIL-----------------------AEGLDDRKIIREF 55 (188)
T ss_pred CceEEEEEEEecCCCCCCCCCCCCEEEEEE---EeCCCCEEEEE-----------------------ecCCCHHHHHHHH
Confidence 346899999999 43 2 245666664 33334422100 1236678899999
Q ss_pred HHHhC---CCEEEEeCh-HhhHHHhc
Q 029428 153 AELIE---GRILVGHAL-HNDLKALL 174 (193)
Q Consensus 153 ~~~l~---g~ilVgHn~-~fDl~~L~ 174 (193)
.+++. -.+|+|||. .||+.+|.
T Consensus 56 ~~~i~~~dPd~i~gyN~~~FDlpyl~ 81 (188)
T cd05781 56 VKYVKEYDPDIIVGYNSNAFDWPYLV 81 (188)
T ss_pred HHHHHHcCCCEEEecCCCcCcHHHHH
Confidence 99996 369999995 79999994
No 63
>PRK05755 DNA polymerase I; Provisional
Probab=97.07 E-value=0.0025 Score=63.11 Aligned_cols=83 Identities=20% Similarity=0.221 Sum_probs=52.7
Q ss_pred CCcEEEEEEeecCCC--CCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHh
Q 029428 79 LTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~--~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (193)
...+++||+||+|++ .++++.|+ +++ ..|... +|.+ +++. .+++..|.+++
T Consensus 314 ~~~~~a~DtEt~~l~~~~~~i~~i~-ls~--~~g~~~---~ip~-----------~~i~----------~~~l~~l~~~L 366 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQAELVGLS-FAV--EPGEAA---YIPL-----------DQLD----------REVLAALKPLL 366 (880)
T ss_pred ccCeEEEEeccCCCCcccccEEEEE-EEe--CCCcEE---EEec-----------cccc----------HHHHHHHHHHH
Confidence 356999999999998 34555544 232 234322 2211 1221 15778888899
Q ss_pred CCC--EEEEeChHhhHHHhccc-CC-CCceeecCCc
Q 029428 157 EGR--ILVGHALHNDLKALLLT-HS-KKDLRDTSEY 188 (193)
Q Consensus 157 ~g~--ilVgHn~~fDl~~L~~~-~p-~~~iiDT~~~ 188 (193)
++. ++|+||+.||+.+|... .+ ...++||...
T Consensus 367 ~d~~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iA 402 (880)
T PRK05755 367 EDPAIKKVGQNLKYDLHVLARYGIELRGIAFDTMLA 402 (880)
T ss_pred hCCCCcEEEeccHhHHHHHHhCCCCcCCCcccHHHH
Confidence 753 48999999999999732 11 2457888654
No 64
>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=96.99 E-value=0.00069 Score=57.88 Aligned_cols=94 Identities=23% Similarity=0.364 Sum_probs=49.7
Q ss_pred CcEEEEEEeecCCCCC-----------------------cEeEEEEEEEEeCCCcEE-------EEEEecCCCc-cc-cc
Q 029428 80 TDVVAMDCEMVGISQG-----------------------NKSALGRVSLVNKWGNLI-------YDEFVRPLER-VV-DF 127 (193)
Q Consensus 80 ~~~v~lD~EtTGl~~~-----------------------~i~eia~V~vv~~~g~~i-------~~~lV~P~~~-i~-~~ 127 (193)
..||+||+|+||+..+ .++++|.+.+.+.++... |+.++-|... .. ..
T Consensus 22 ~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~~~~ 101 (262)
T PF04857_consen 22 ADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFSQAS 101 (262)
T ss_dssp SSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEEEHH
T ss_pred CCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccceecch
Confidence 4599999999999821 278999555524445432 2323233321 11 11
Q ss_pred cc---cccCCCHHHH-ccCCCHHHHHH-----HHHH---Hh----C-CCEEEEeChHhhHHHh
Q 029428 128 RT---RISGIRPRDL-RKAKDFPTVQK-----KVAE---LI----E-GRILVGHALHNDLKAL 173 (193)
Q Consensus 128 ~t---~ihGIt~e~l-~~a~~~~ev~~-----~l~~---~l----~-g~ilVgHn~~fDl~~L 173 (193)
+. .-||+.-+.+ .++.++....+ +... ++ + ..+|||||.-+|+.+|
T Consensus 102 sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l 164 (262)
T PF04857_consen 102 SLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDLMYL 164 (262)
T ss_dssp HHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHHHHH
T ss_pred hHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHHHHH
Confidence 11 2378876664 56666544442 1111 11 1 4899999999999997
No 65
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=96.99 E-value=0.0033 Score=52.11 Aligned_cols=33 Identities=18% Similarity=0.298 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHhCC---CEEEEeCh-HhhHHHhc
Q 029428 142 AKDFPTVQKKVAELIEG---RILVGHAL-HNDLKALL 174 (193)
Q Consensus 142 a~~~~ev~~~l~~~l~g---~ilVgHn~-~fDl~~L~ 174 (193)
..+-.+++.+|.+++.. .+|||||. .||+.+|.
T Consensus 55 ~~~E~~lL~~f~~~i~~~dPdii~g~N~~~FD~pyl~ 91 (207)
T cd05785 55 DAAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLR 91 (207)
T ss_pred CCCHHHHHHHHHHHHHHhCCCEEeccCCcccCHHHHH
Confidence 47788899999999974 79999998 99999994
No 66
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=96.84 E-value=0.0049 Score=52.64 Aligned_cols=76 Identities=17% Similarity=0.219 Sum_probs=45.3
Q ss_pred CCCCCcEEEEEEeecCCCC-C-cEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCC-HHHHHHHH
Q 029428 76 DFSLTDVVAMDCEMVGISQ-G-NKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKD-FPTVQKKV 152 (193)
Q Consensus 76 ~~~~~~~v~lD~EtTGl~~-~-~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~-~~ev~~~l 152 (193)
.....++++||+|||||+. + .|.-+|...+.+ +....-.+.-|. |. -..+++.+
T Consensus 94 g~~~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~--~~~~Vrq~~lp~---------------------p~~E~avle~f 150 (278)
T COG3359 94 GYEAEDVAFFDIETTGLDRAGNTITLVGGARGVD--DTMHVRQHFLPA---------------------PEEEVAVLENF 150 (278)
T ss_pred cccccceEEEeeeccccCCCCCeEEEEEEEEccC--ceEEEEeecCCC---------------------cchhhHHHHHH
Confidence 3446789999999999993 3 333333222222 333333333332 11 12245555
Q ss_pred HHHhCCCEEEEeC-hHhhHHHhc
Q 029428 153 AELIEGRILVGHA-LHNDLKALL 174 (193)
Q Consensus 153 ~~~l~g~ilVgHn-~~fDl~~L~ 174 (193)
....+-..||.+| ..||+.|++
T Consensus 151 l~~~~~~~lvsfNGkaFD~Pfik 173 (278)
T COG3359 151 LHDPDFNMLVSFNGKAFDIPFIK 173 (278)
T ss_pred hcCCCcceEEEecCcccCcHHHH
Confidence 5555567999999 699999997
No 67
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=96.35 E-value=0.047 Score=45.65 Aligned_cols=87 Identities=16% Similarity=0.235 Sum_probs=50.3
Q ss_pred CCCcEEEEEEeecCCC-------CCcEeEEEEEEEEeCCCcEEEEE-E-ecCCCccccccccccCCCHHHHccCCCHHHH
Q 029428 78 SLTDVVAMDCEMVGIS-------QGNKSALGRVSLVNKWGNLIYDE-F-VRPLERVVDFRTRISGIRPRDLRKAKDFPTV 148 (193)
Q Consensus 78 ~~~~~v~lD~EtTGl~-------~~~i~eia~V~vv~~~g~~i~~~-l-V~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev 148 (193)
++-++++||+||.... .+.|+.|+.+.-.++........ + +.+..+++ | ..+..-.+-.+.
T Consensus 5 p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~-------~---~~v~~~~~E~eL 74 (230)
T cd05777 5 APLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIV-------G---AQVFSFETEEEL 74 (230)
T ss_pred CCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCC-------C---CEEEEECCHHHH
Confidence 3557999999998532 24555555432222111111111 1 22222221 1 122334677889
Q ss_pred HHHHHHHhCC---CEEEEeCh-HhhHHHhc
Q 029428 149 QKKVAELIEG---RILVGHAL-HNDLKALL 174 (193)
Q Consensus 149 ~~~l~~~l~g---~ilVgHn~-~fDl~~L~ 174 (193)
+.+|.+++.. .+|+|||. .||+.+|.
T Consensus 75 L~~f~~~i~~~DPDii~GyN~~~FDl~yL~ 104 (230)
T cd05777 75 LLAWRDFVQEVDPDIITGYNICNFDLPYLL 104 (230)
T ss_pred HHHHHHHHHhcCCCEEEEecCCCCCHHHHH
Confidence 9999998864 69999995 78999983
No 68
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. 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 clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=96.32 E-value=0.014 Score=47.86 Aligned_cols=78 Identities=18% Similarity=0.173 Sum_probs=46.8
Q ss_pred CcEEEEEEeecCCCCCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhCC-
Q 029428 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG- 158 (193)
Q Consensus 80 ~~~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~g- 158 (193)
-++++||+||+|.+ .|..|| ..+.....++- +=.+ .... |. .+.--.+-.+++..|.+++..
T Consensus 3 l~~~~fDIE~~~~~--~i~~i~---~~~~~~~~i~~-~~~~-~~~~-------~~---~v~~~~~E~~lL~~f~~~i~~~ 65 (193)
T cd05784 3 LKVVSLDIETSMDG--ELYSIG---LYGEGQERVLM-VGDP-EDDA-------PD---NIEWFADEKSLLLALIAWFAQY 65 (193)
T ss_pred ccEEEEEeecCCCC--CEEEEE---eecCCCCEEEE-ECCC-CCCC-------CC---EEEEECCHHHHHHHHHHHHHhh
Confidence 46899999998755 444444 33322222221 1011 1110 11 122235677888999888863
Q ss_pred --CEEEEeCh-HhhHHHhc
Q 029428 159 --RILVGHAL-HNDLKALL 174 (193)
Q Consensus 159 --~ilVgHn~-~fDl~~L~ 174 (193)
.+|+|||. .||+.+|.
T Consensus 66 dPDvi~g~N~~~FD~~yl~ 84 (193)
T cd05784 66 DPDIIIGWNVINFDLRLLQ 84 (193)
T ss_pred CCCEEEECCCcCcCHHHHH
Confidence 59999995 89999993
No 69
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. 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. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=96.11 E-value=0.054 Score=44.75 Aligned_cols=33 Identities=15% Similarity=0.090 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHHhC-CCEEEEeCh-HhhHHHhc
Q 029428 142 AKDFPTVQKKVAELIE-GRILVGHAL-HNDLKALL 174 (193)
Q Consensus 142 a~~~~ev~~~l~~~l~-g~ilVgHn~-~fDl~~L~ 174 (193)
-.+-.+++.+|.+++. -.+|||||. .||+.+|.
T Consensus 70 ~~~E~~lL~~F~~~i~~~~~iig~N~~~FDlpyl~ 104 (204)
T cd05783 70 FDSEKELIREAFKIISEYPIVLTFNGDNFDLPYLY 104 (204)
T ss_pred cCCHHHHHHHHHHHHhcCCEEEEeCCCCcCHHHHH
Confidence 3577888899999886 569999995 89999994
No 70
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=96.06 E-value=0.038 Score=45.76 Aligned_cols=33 Identities=18% Similarity=0.077 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHHhCC---CEEEEeCh-HhhHHHhc
Q 029428 142 AKDFPTVQKKVAELIEG---RILVGHAL-HNDLKALL 174 (193)
Q Consensus 142 a~~~~ev~~~l~~~l~g---~ilVgHn~-~fDl~~L~ 174 (193)
-.+-.+++.+|.+++.. .+++|||. .||+.+|.
T Consensus 70 ~~~E~~lL~~f~~~i~~~~Pd~i~gyN~~~FD~pyl~ 106 (204)
T cd05779 70 EPDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVE 106 (204)
T ss_pred CCCHHHHHHHHHHHHHHhCCCEEEecCccccCHHHHH
Confidence 35778899999999974 49999995 89999994
No 71
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=95.97 E-value=0.04 Score=47.36 Aligned_cols=87 Identities=13% Similarity=0.095 Sum_probs=51.2
Q ss_pred CCCcEEEEEEeecCCC-------CCcEeEEEEEEEEe---CCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHH
Q 029428 78 SLTDVVAMDCEMVGIS-------QGNKSALGRVSLVN---KWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPT 147 (193)
Q Consensus 78 ~~~~~v~lD~EtTGl~-------~~~i~eia~V~vv~---~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~e 147 (193)
++-++++||+||..-+ .+.|+.|+.+.-.+ ......+..+ .+...+.. ...+.--.+-.+
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~-~~~~~~~~---------~~~v~~~~~E~~ 224 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTL-GSCDSIED---------NVEVIYFDSEKE 224 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEEC-SCSCCTTC---------TTEEEEESSHHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEe-cCCCCCCC---------CcEEEEECCHHH
Confidence 5678999999999765 13455555332211 1122222222 22222221 222333466788
Q ss_pred HHHHHHHHhC---CCEEEEeCh-HhhHHHhc
Q 029428 148 VQKKVAELIE---GRILVGHAL-HNDLKALL 174 (193)
Q Consensus 148 v~~~l~~~l~---g~ilVgHn~-~fDl~~L~ 174 (193)
++..|.+++. =.+|+|||+ .||+.+|.
T Consensus 225 lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~ 255 (325)
T PF03104_consen 225 LLEAFLDIIQEYDPDIITGYNIDGFDLPYLI 255 (325)
T ss_dssp HHHHHHHHHHHHS-SEEEESSTTTTHHHHHH
T ss_pred HHHHHHHHHHhcCCcEEEEecccCCCHHHHH
Confidence 8888888874 579999997 69999993
No 72
>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=95.69 E-value=0.051 Score=44.29 Aligned_cols=40 Identities=23% Similarity=0.365 Sum_probs=28.7
Q ss_pred HHHHHHHhCC--CEEEEeChHhhHHHhcccCC--------CCceeecCCc
Q 029428 149 QKKVAELIEG--RILVGHALHNDLKALLLTHS--------KKDLRDTSEY 188 (193)
Q Consensus 149 ~~~l~~~l~g--~ilVgHn~~fDl~~L~~~~p--------~~~iiDT~~~ 188 (193)
...+.++|.+ -+-|||++.+|+.+|...++ ..+++||..+
T Consensus 71 ~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~ 120 (193)
T cd06146 71 DRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNL 120 (193)
T ss_pred HHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHH
Confidence 3456677764 35599999999999985443 2579998654
No 73
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=95.58 E-value=0.1 Score=46.80 Aligned_cols=31 Identities=26% Similarity=0.418 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHhC---CCEEEEeCh-HhhHHHhc
Q 029428 144 DFPTVQKKVAELIE---GRILVGHAL-HNDLKALL 174 (193)
Q Consensus 144 ~~~ev~~~l~~~l~---g~ilVgHn~-~fDl~~L~ 174 (193)
+..+.+.++.+++. -.+++|||. .||+.+|.
T Consensus 68 ~E~~lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~ 102 (471)
T smart00486 68 NEKELLKAFLEFIKKYDPDIIYGHNISNFDLPYII 102 (471)
T ss_pred CHHHHHHHHHHHHHHhCCCEEEeecCCCCCHHHHH
Confidence 56777788877775 469999997 59999984
No 74
>PHA02570 dexA exonuclease; Provisional
Probab=95.53 E-value=0.015 Score=48.75 Aligned_cols=92 Identities=22% Similarity=0.214 Sum_probs=56.4
Q ss_pred EEEEEeecCCCC-CcEeEEEEEEEEeCCCc-EEEEEEecCCCc------------cccccc--cccCCCHHH---Hc---
Q 029428 83 VAMDCEMVGISQ-GNKSALGRVSLVNKWGN-LIYDEFVRPLER------------VVDFRT--RISGIRPRD---LR--- 140 (193)
Q Consensus 83 v~lD~EtTGl~~-~~i~eia~V~vv~~~g~-~i~~~lV~P~~~------------i~~~~t--~ihGIt~e~---l~--- 140 (193)
+.||+||.|..+ .-|++||+|-+...-|. ..|+.+|..... +.+..| .+-.-++|. |.
T Consensus 4 lMIDlETmG~~p~AaIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~s~ 83 (220)
T PHA02570 4 FIIDFETFGNTPDGAVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKPSD 83 (220)
T ss_pred EEEEeeccCCCCCceEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccCCC
Confidence 689999999995 57999999877542221 124444432111 111111 111222222 11
Q ss_pred cCCCHHHHHHHHHHHhC--C-----CEEEEeChHhhHHHhc
Q 029428 141 KAKDFPTVQKKVAELIE--G-----RILVGHALHNDLKALL 174 (193)
Q Consensus 141 ~a~~~~ev~~~l~~~l~--g-----~ilVgHn~~fDl~~L~ 174 (193)
+..++.+++.+|.+|+. + ..+-|-..+||+..|+
T Consensus 84 ~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 84 EDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred ccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHH
Confidence 23678999999999995 2 3577888999999995
No 75
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=95.33 E-value=0.22 Score=37.40 Aligned_cols=43 Identities=26% Similarity=0.184 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCC--CEEEEeChHhhHHHhcccCC--CCceeecCCc
Q 029428 146 PTVQKKVAELIEG--RILVGHALHNDLKALLLTHS--KKDLRDTSEY 188 (193)
Q Consensus 146 ~ev~~~l~~~l~g--~ilVgHn~~fDl~~L~~~~p--~~~iiDT~~~ 188 (193)
..+...+.+++.+ ..+||||+.+|+.+|..... ...++||...
T Consensus 40 ~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ 86 (155)
T cd00007 40 EEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLA 86 (155)
T ss_pred HHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcccHHHH
Confidence 5567778888874 45999999999999963221 2346887543
No 76
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=95.30 E-value=0.089 Score=53.42 Aligned_cols=88 Identities=15% Similarity=0.119 Sum_probs=53.0
Q ss_pred CCCcEEEEEEeecCCC--------CCcEeEEEEEEEEeCCCc-EEEEEEecCCCccccccccccCCCHHHHccCCCHHHH
Q 029428 78 SLTDVVAMDCEMVGIS--------QGNKSALGRVSLVNKWGN-LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTV 148 (193)
Q Consensus 78 ~~~~~v~lD~EtTGl~--------~~~i~eia~V~vv~~~g~-~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev 148 (193)
.+-++++||+||++.. .|.|++|+.+....+... .....++-+.. +..+.| ..+..-.+-.+.
T Consensus 262 pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~-----c~~i~g---~~V~~f~sE~eL 333 (1054)
T PTZ00166 262 APLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKE-----CASIAG---ANVLSFETEKEL 333 (1054)
T ss_pred CCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCc-----cccCCC---ceEEEeCCHHHH
Confidence 5677999999998642 256777776543332211 11111221211 112222 123334677888
Q ss_pred HHHHHHHhC---CCEEEEeCh-HhhHHHh
Q 029428 149 QKKVAELIE---GRILVGHAL-HNDLKAL 173 (193)
Q Consensus 149 ~~~l~~~l~---g~ilVgHn~-~fDl~~L 173 (193)
+..+.+++. =.||+|||. .||+.+|
T Consensus 334 L~~f~~~I~~~DPDII~GYNi~~FDlpYL 362 (1054)
T PTZ00166 334 LLAWAEFVIAVDPDFLTGYNIINFDLPYL 362 (1054)
T ss_pred HHHHHHHHHhcCCCEEEecCCcCCcHHHH
Confidence 888888885 589999996 7999999
No 77
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=95.16 E-value=0.085 Score=43.05 Aligned_cols=86 Identities=19% Similarity=0.205 Sum_probs=47.4
Q ss_pred CCCCcEEEEEEeecCCCCCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHh
Q 029428 77 FSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (193)
Q Consensus 77 ~~~~~~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (193)
.....+|+||+|+++++....+.+..|... ....-+||.+--+. .. ....+.+++
T Consensus 7 l~~~~~i~~D~E~~~~~~~~~~~LiQia~~-~~~v~l~D~~~~~~---------------------~~---~~~~L~~iL 61 (197)
T cd06148 7 LKKQKVIGLDCEGVNLGRKGKLCLVQIATR-TGQIYLFDILKLGS---------------------IV---FINGLKDIL 61 (197)
T ss_pred hhhCCEEEEEcccccCCCCCCEEEEEEeeC-CCcEEEEEhhhccc---------------------hh---HHHHHHHHh
Confidence 345679999999998884222334333321 01222343321110 01 124455667
Q ss_pred C--CCEEEEeChHhhHHHhcc--cCCCCceeecCC
Q 029428 157 E--GRILVGHALHNDLKALLL--THSKKDLRDTSE 187 (193)
Q Consensus 157 ~--g~ilVgHn~~fDl~~L~~--~~p~~~iiDT~~ 187 (193)
. +.+-|||++.+|+.+|.. ...-..+.||..
T Consensus 62 e~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~i 96 (197)
T cd06148 62 ESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQV 96 (197)
T ss_pred cCCCccEEEEechhHHHHHHHhcCccccceeeHHH
Confidence 5 345699999999999942 222235789864
No 78
>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=94.80 E-value=0.062 Score=42.24 Aligned_cols=40 Identities=20% Similarity=0.311 Sum_probs=27.3
Q ss_pred HHHHHHhCC--CEEEEeChHhhHHHhcccCC--CCceeecCCcC
Q 029428 150 KKVAELIEG--RILVGHALHNDLKALLLTHS--KKDLRDTSEYQ 189 (193)
Q Consensus 150 ~~l~~~l~g--~ilVgHn~~fDl~~L~~~~p--~~~iiDT~~~~ 189 (193)
..|.+++.+ .+.|||++.+|+.+|...++ -..++||....
T Consensus 63 ~~l~~ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa 106 (170)
T cd06141 63 PSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLA 106 (170)
T ss_pred HHHHHHhcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHH
Confidence 356667763 46699999999999963332 24568886543
No 79
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=94.57 E-value=0.27 Score=41.25 Aligned_cols=91 Identities=12% Similarity=0.078 Sum_probs=51.5
Q ss_pred cEEEEEEeecCCC---C----CcEeEEEEEEEEeCCCcEE-E------EEEecCCCccccccccccCCCHHHHccCCCHH
Q 029428 81 DVVAMDCEMVGIS---Q----GNKSALGRVSLVNKWGNLI-Y------DEFVRPLERVVDFRTRISGIRPRDLRKAKDFP 146 (193)
Q Consensus 81 ~~v~lD~EtTGl~---~----~~i~eia~V~vv~~~g~~i-~------~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ 146 (193)
.++.||+|+.+-+ + |.|+.|+.+ +.+ +.... . ..++.+...-........++....+.--.+-.
T Consensus 5 ~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~-~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~ 82 (231)
T cd05778 5 TILSLEVHVNTRGDLLPDPEFDPISAIFYC-IDD-DVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVVESEL 82 (231)
T ss_pred EEEEEEEEECCCCCCCcCCCCCCeeEEEEE-Eec-CCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEeCCHH
Confidence 5789999997543 2 456666644 332 22111 1 12233322110000111223333445556778
Q ss_pred HHHHHHHHHhC---CCEEEEeCh-HhhHHHh
Q 029428 147 TVQKKVAELIE---GRILVGHAL-HNDLKAL 173 (193)
Q Consensus 147 ev~~~l~~~l~---g~ilVgHn~-~fDl~~L 173 (193)
+.+.+|.+++. =.+|+|||+ .||+.+|
T Consensus 83 ~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL 113 (231)
T cd05778 83 ELFEELIDLVRRFDPDILSGYEIQRSSWGYL 113 (231)
T ss_pred HHHHHHHHHHHHhCCCEEEEeccccCcHHHH
Confidence 88888888885 589999997 8999998
No 80
>PHA02528 43 DNA polymerase; Provisional
Probab=94.20 E-value=0.42 Score=47.76 Aligned_cols=103 Identities=12% Similarity=0.058 Sum_probs=54.7
Q ss_pred CCCCCCCCCcEEEEEEeecCCC----CC-cEeEEEEEEEEeCCCcEEEEEEecCCCcccccccccc--CCCHHHHccCCC
Q 029428 72 PINDDFSLTDVVAMDCEMVGIS----QG-NKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRIS--GIRPRDLRKAKD 144 (193)
Q Consensus 72 p~~~~~~~~~~v~lD~EtTGl~----~~-~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ih--GIt~e~l~~a~~ 144 (193)
|.+-+.+.-++++||+||+.-+ +. ..-+|..|++.+..+..++-..+....+....-.... -...-++..-.+
T Consensus 98 ~~~~~~p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~s 177 (881)
T PHA02528 98 EIKYDRSKIRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDT 177 (881)
T ss_pred CCCCCCCCccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCeeEEEcCC
Confidence 3333335678999999997522 11 1124555555655555432222211000000000000 000011112357
Q ss_pred HHHHHHHHHHHhC---CCEEEEeCh-HhhHHHhc
Q 029428 145 FPTVQKKVAELIE---GRILVGHAL-HNDLKALL 174 (193)
Q Consensus 145 ~~ev~~~l~~~l~---g~ilVgHn~-~fDl~~L~ 174 (193)
-.+.+.+|.+++. =.||+|||+ .||+.+|.
T Consensus 178 E~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~ 211 (881)
T PHA02528 178 EREMLLEYINFWEENTPVIFTGWNVELFDVPYII 211 (881)
T ss_pred HHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHH
Confidence 7889999999985 479999995 89999993
No 81
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=93.80 E-value=0.041 Score=53.96 Aligned_cols=32 Identities=25% Similarity=0.296 Sum_probs=25.1
Q ss_pred CCCEEEEeChHhhHHHhccc----CCCCceeecCCc
Q 029428 157 EGRILVGHALHNDLKALLLT----HSKKDLRDTSEY 188 (193)
Q Consensus 157 ~g~ilVgHn~~fDl~~L~~~----~p~~~iiDT~~~ 188 (193)
++.++||||++||..-++-. --+..++||+.|
T Consensus 240 ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSl 275 (1075)
T KOG3657|consen 240 KEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSL 275 (1075)
T ss_pred CCceEEeccccchHHHHHHHHhccccceeeeechhh
Confidence 47899999999999988722 235678899876
No 82
>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=93.24 E-value=0.42 Score=37.46 Aligned_cols=39 Identities=26% Similarity=0.265 Sum_probs=25.9
Q ss_pred HHHHHHhCCC--EEEEeChHhhHHHhcccC--CCCceeecCCc
Q 029428 150 KKVAELIEGR--ILVGHALHNDLKALLLTH--SKKDLRDTSEY 188 (193)
Q Consensus 150 ~~l~~~l~g~--ilVgHn~~fDl~~L~~~~--p~~~iiDT~~~ 188 (193)
..|.+++.+. +.|||++..|+..|...+ .-..++||...
T Consensus 57 ~~L~~lL~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~a 99 (161)
T cd06129 57 QGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIA 99 (161)
T ss_pred HHHHHHhCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHH
Confidence 3455667643 569999999999996422 22456887643
No 83
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=93.03 E-value=0.14 Score=44.47 Aligned_cols=97 Identities=20% Similarity=0.228 Sum_probs=57.8
Q ss_pred CCCcEEEEEEeecCCC--CCcEeEEEEE-----EEEe------CCCc------EE---EEEEecCCCccccccccccCCC
Q 029428 78 SLTDVVAMDCEMVGIS--QGNKSALGRV-----SLVN------KWGN------LI---YDEFVRPLERVVDFRTRISGIR 135 (193)
Q Consensus 78 ~~~~~v~lD~EtTGl~--~~~i~eia~V-----~vv~------~~g~------~i---~~~lV~P~~~i~~~~t~ihGIt 135 (193)
+...++++|+|+||+. ...|.|+-.. .+.. .++. .+ ...++.|.....+.+.+|+|++
T Consensus 11 r~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~v~~p~aeeitgls 90 (318)
T KOG4793|consen 11 RLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVPVTRPIAEEITGLS 90 (318)
T ss_pred ceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcCCcChhhhhhcccc
Confidence 3567999999999998 2233333211 1111 1110 11 3446778777778889999999
Q ss_pred HHHHc--cCCCHH-HHHHHHHHHhC---CC-EEEEeC-hHhhHHHhc
Q 029428 136 PRDLR--KAKDFP-TVQKKVAELIE---GR-ILVGHA-LHNDLKALL 174 (193)
Q Consensus 136 ~e~l~--~a~~~~-ev~~~l~~~l~---g~-ilVgHn-~~fDl~~L~ 174 (193)
..-+. ...-|+ ++.+-|..|+. +- -||+|| -.||+..|.
T Consensus 91 ~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~ 137 (318)
T KOG4793|consen 91 QPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILA 137 (318)
T ss_pred cHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHH
Confidence 86553 223333 34444455553 33 489999 478887774
No 84
>PRK05762 DNA polymerase II; Reviewed
Probab=92.52 E-value=0.56 Score=46.21 Aligned_cols=80 Identities=19% Similarity=0.223 Sum_probs=49.0
Q ss_pred CCCcEEEEEEeecCCCCCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhC
Q 029428 78 SLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (193)
Q Consensus 78 ~~~~~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (193)
+.-++++||+||.+- +.|..|+ +.......++ .+.+..... .+.+..-.+-.+.+..|.+++.
T Consensus 153 p~lrvlsfDIE~~~~--~~i~sI~---~~~~~~~~vi--~ig~~~~~~----------~~~v~~~~sE~~LL~~F~~~i~ 215 (786)
T PRK05762 153 PPLKVVSLDIETSNK--GELYSIG---LEGCGQRPVI--MLGPPNGEA----------LDFLEYVADEKALLEKFNAWFA 215 (786)
T ss_pred CCCeEEEEEEEEcCC--CceEEee---ecCCCCCeEE--EEECCCCCC----------cceEEEcCCHHHHHHHHHHHHH
Confidence 567899999999874 3444444 3221122221 122221110 0114445678889999999996
Q ss_pred C---CEEEEeCh-HhhHHHhc
Q 029428 158 G---RILVGHAL-HNDLKALL 174 (193)
Q Consensus 158 g---~ilVgHn~-~fDl~~L~ 174 (193)
. .+|||||. .||+.+|.
T Consensus 216 ~~DPDIIvGyNi~~FDlpyL~ 236 (786)
T PRK05762 216 EHDPDVIIGWNVVQFDLRLLQ 236 (786)
T ss_pred hcCCCEEEEeCCCCCcHHHHH
Confidence 4 69999995 79999993
No 85
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=92.41 E-value=0.18 Score=45.40 Aligned_cols=87 Identities=20% Similarity=0.241 Sum_probs=52.5
Q ss_pred CCcEEEEEEeecCCCCCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhC-
Q 029428 79 LTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE- 157 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~- 157 (193)
...+|+||+|+.|+.+-. -.++.|-|.++++ ..+|.|-..+. +.++|.. ++.
T Consensus 16 ~~~~iAiDTEf~r~~t~~-p~LcLIQi~~~e~----~~lIdpl~~~~---------------d~~~l~~-------Ll~d 68 (361)
T COG0349 16 GSKAIAIDTEFMRLRTYY-PRLCLIQISDGEG----ASLIDPLAGIL---------------DLPPLVA-------LLAD 68 (361)
T ss_pred CCCceEEecccccccccC-CceEEEEEecCCC----ceEeccccccc---------------ccchHHH-------HhcC
Confidence 456999999999999421 2466666666544 34555543221 1233332 332
Q ss_pred -CCEEEEeChHhhHHHhcccC--CCCceeecCCcCccc
Q 029428 158 -GRILVGHALHNDLKALLLTH--SKKDLRDTSEYQPFL 192 (193)
Q Consensus 158 -g~ilVgHn~~fDl~~L~~~~--p~~~iiDT~~~~~~~ 192 (193)
+-+=|=|+++||+.+|...+ -...++||.....|+
T Consensus 69 ~~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~ 106 (361)
T COG0349 69 PNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLA 106 (361)
T ss_pred CceeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHh
Confidence 33348899999999997432 224688986654443
No 86
>PRK10829 ribonuclease D; Provisional
Probab=92.20 E-value=0.41 Score=43.27 Aligned_cols=82 Identities=24% Similarity=0.337 Sum_probs=47.9
Q ss_pred CCcEEEEEEeecCCCC-CcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhC
Q 029428 79 LTDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~-~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (193)
...+++||+|+.+... .. .++.|.+.+ +..+ .+|.|-. +.+ +..|.+++.
T Consensus 21 ~~~~lalDtEf~~~~ty~~--~l~LiQl~~--~~~~--~LiD~l~-~~d----------------------~~~L~~ll~ 71 (373)
T PRK10829 21 AFPAIALDTEFVRTRTYYP--QLGLIQLYD--GEQL--SLIDPLG-ITD----------------------WSPFKALLR 71 (373)
T ss_pred cCCeEEEecccccCccCCC--ceeEEEEec--CCce--EEEecCC-ccc----------------------hHHHHHHHc
Confidence 4568999999998773 22 244444433 2222 2333421 110 134566776
Q ss_pred C-CE-EEEeChHhhHHHhcc--cCCCCceeecCCcC
Q 029428 158 G-RI-LVGHALHNDLKALLL--THSKKDLRDTSEYQ 189 (193)
Q Consensus 158 g-~i-lVgHn~~fDl~~L~~--~~p~~~iiDT~~~~ 189 (193)
+ .+ -|+|++.+|+.+|.. .+....++||....
T Consensus 72 ~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa 107 (373)
T PRK10829 72 DPQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILA 107 (373)
T ss_pred CCCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHH
Confidence 3 33 389999999999843 23335799996543
No 87
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=91.69 E-value=0.63 Score=43.69 Aligned_cols=100 Identities=13% Similarity=0.078 Sum_probs=55.8
Q ss_pred CCCCCCCcEEEEEEeecCCC-CC---cEeEEEEEEEEeCC--Cc--EEEEEEecCCCccccccccc-cCC-CHHHHccCC
Q 029428 74 NDDFSLTDVVAMDCEMVGIS-QG---NKSALGRVSLVNKW--GN--LIYDEFVRPLERVVDFRTRI-SGI-RPRDLRKAK 143 (193)
Q Consensus 74 ~~~~~~~~~v~lD~EtTGl~-~~---~i~eia~V~vv~~~--g~--~i~~~lV~P~~~i~~~~t~i-hGI-t~e~l~~a~ 143 (193)
.-+.+.-++..||+|+|+-. |+ .-.+|-+|+..+.. .. .+|+.+ .-..+.......+ -++ ..-.+..-.
T Consensus 100 ~~d~~~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~v~v~~f~ 178 (498)
T PHA02524 100 DFDRDDVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNGKKTYYIFDLV-KDVGHWDPKKSVLEKYILDNVVYMPFE 178 (498)
T ss_pred ccchhhceEEEEEEEecCCCCCChhhcCCceEEEEeeecccCCccEEEEecc-ccccCCCcccccccccccCCeEEEEeC
Confidence 34445667999999998765 32 22456666665533 11 223322 1001111000000 011 111122346
Q ss_pred CHHHHHHHHHHHhCC---CEEEEeCh-HhhHHHhc
Q 029428 144 DFPTVQKKVAELIEG---RILVGHAL-HNDLKALL 174 (193)
Q Consensus 144 ~~~ev~~~l~~~l~g---~ilVgHn~-~fDl~~L~ 174 (193)
+-.+++.++.+|+.. .+|+|||. .||+.+|.
T Consensus 179 sE~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~ 213 (498)
T PHA02524 179 DEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYII 213 (498)
T ss_pred CHHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHH
Confidence 778899999999975 89999995 89999983
No 88
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=90.46 E-value=1.4 Score=43.61 Aligned_cols=87 Identities=18% Similarity=0.108 Sum_probs=49.6
Q ss_pred CCCCCcEEEEEEeecCCCC----CcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHH
Q 029428 76 DFSLTDVVAMDCEMVGISQ----GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKK 151 (193)
Q Consensus 76 ~~~~~~~v~lD~EtTGl~~----~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~ 151 (193)
..+..++++||+|+.+... +....+..+......+.... ..+ ..+...|.. +....+-.+++..
T Consensus 150 ~~p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~---~~~------~~~~~~~~~---v~~~~~e~e~l~~ 217 (792)
T COG0417 150 VRPPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI---EVF------IYTSGEGFS---VEVVISEAELLER 217 (792)
T ss_pred cCCCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc---ccc------cccCCCCce---eEEecCHHHHHHH
Confidence 3456789999999998771 12222333333222111111 000 011111111 4445566788888
Q ss_pred HHHHhC---CCEEEEeChH-hhHHHhc
Q 029428 152 VAELIE---GRILVGHALH-NDLKALL 174 (193)
Q Consensus 152 l~~~l~---g~ilVgHn~~-fDl~~L~ 174 (193)
+..++. -.|+||||.. ||+.+|.
T Consensus 218 ~~~~i~~~dPdVIvgyn~~~fd~pyl~ 244 (792)
T COG0417 218 FVELIREYDPDVIVGYNGDNFDWPYLA 244 (792)
T ss_pred HHHHHHhcCCCEEEeccCCcCChHHHH
Confidence 888874 6899999986 9999994
No 89
>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=89.91 E-value=1.3 Score=39.73 Aligned_cols=36 Identities=31% Similarity=0.320 Sum_probs=24.9
Q ss_pred HHHHHhC--CCEEEEeChHhhHHHhccc---CCCCceeecCC
Q 029428 151 KVAELIE--GRILVGHALHNDLKALLLT---HSKKDLRDTSE 187 (193)
Q Consensus 151 ~l~~~l~--g~ilVgHn~~fDl~~L~~~---~p~~~iiDT~~ 187 (193)
.|.+++. +.+.|+|++.+|+.+|... .| ..++||..
T Consensus 61 ~L~~lL~d~~i~KV~h~~k~Dl~~L~~~~~~~~-~~~fDtql 101 (367)
T TIGR01388 61 PLKELLRDESVVKVLHAASEDLEVFLNLFGELP-QPLFDTQI 101 (367)
T ss_pred HHHHHHCCCCceEEEeecHHHHHHHHHHhCCCC-CCcccHHH
Confidence 3445665 3457999999999999632 33 35789854
No 90
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=88.92 E-value=0.51 Score=39.58 Aligned_cols=35 Identities=26% Similarity=0.325 Sum_probs=28.4
Q ss_pred HccCCCHHHHHHHHHHHhC---CCEEEEeCh-HhhHHHh
Q 029428 139 LRKAKDFPTVQKKVAELIE---GRILVGHAL-HNDLKAL 173 (193)
Q Consensus 139 l~~a~~~~ev~~~l~~~l~---g~ilVgHn~-~fDl~~L 173 (193)
+.--.+-.+.+..|.+++. =.+|||||+ .||+.+|
T Consensus 76 v~~~~~E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L 114 (234)
T cd05776 76 VRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVL 114 (234)
T ss_pred EEEeCCHHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHH
Confidence 3344667888888888885 489999998 9999999
No 91
>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=87.35 E-value=2.2 Score=35.22 Aligned_cols=30 Identities=27% Similarity=0.161 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHhC--CCEEEEeCh-HhhHHHhc
Q 029428 145 FPTVQKKVAELIE--GRILVGHAL-HNDLKALL 174 (193)
Q Consensus 145 ~~ev~~~l~~~l~--g~ilVgHn~-~fDl~~L~ 174 (193)
-.+++.+|.+++. ..+|||||. .||+.+|.
T Consensus 78 E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~ 110 (208)
T cd05782 78 EKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLH 110 (208)
T ss_pred HHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHH
Confidence 3677888888886 468999996 99999995
No 92
>PHA02563 DNA polymerase; Provisional
Probab=82.43 E-value=4.6 Score=39.09 Aligned_cols=66 Identities=17% Similarity=0.086 Sum_probs=40.1
Q ss_pred CCCcEEEEEEeecCCCCCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhC
Q 029428 78 SLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (193)
Q Consensus 78 ~~~~~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (193)
.+..+++.|+||++.+.+. ..-+..+.| |... .+|.- .+..+++.+++.
T Consensus 10 ~~~~~~~~DfET~t~~~~~--~~~~~~~~d--~~~~-~s~~~--------------------------~~~~~~f~~~i~ 58 (630)
T PHA02563 10 KPRKILACDFETTTINKDC--RRWFWGEID--VEDF-PSYYG--------------------------GNSFDEFLQWIE 58 (630)
T ss_pred ccceEEEEEEEecccCCcc--eeeeeeEec--ccee-ceeec--------------------------cccHHHHHHHHh
Confidence 3667999999999998542 111123333 3222 11110 111235555555
Q ss_pred -------CCEEEEeChHhhHHHhc
Q 029428 158 -------GRILVGHALHNDLKALL 174 (193)
Q Consensus 158 -------g~ilVgHn~~fDl~~L~ 174 (193)
+.++-.||+.||..||-
T Consensus 59 ~~~~k~~~~~vYfHN~~FD~~Fil 82 (630)
T PHA02563 59 DTTYKETECIIYFHNLKFDGSFIL 82 (630)
T ss_pred hccccccceEEEEecCCccHHHHH
Confidence 78999999999999994
No 93
>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=81.67 E-value=8.2 Score=32.26 Aligned_cols=30 Identities=23% Similarity=0.200 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhC--CCEEEEeC-hHhhHHHhc
Q 029428 145 FPTVQKKVAELIE--GRILVGHA-LHNDLKALL 174 (193)
Q Consensus 145 ~~ev~~~l~~~l~--g~ilVgHn-~~fDl~~L~ 174 (193)
..+++..|.++++ ...||+|| ..||+.+|.
T Consensus 37 E~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~ 69 (209)
T PF10108_consen 37 EKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLC 69 (209)
T ss_pred HHHHHHHHHHHHHhCCCeEEecCCccCCHHHHH
Confidence 6778889999997 45799999 699999994
No 94
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=80.07 E-value=18 Score=27.22 Aligned_cols=39 Identities=26% Similarity=0.246 Sum_probs=25.3
Q ss_pred HHHHHHHhC--CCEEEEeChHhhHHHhcc-cCCCCceeecCC
Q 029428 149 QKKVAELIE--GRILVGHALHNDLKALLL-THSKKDLRDTSE 187 (193)
Q Consensus 149 ~~~l~~~l~--g~ilVgHn~~fDl~~L~~-~~p~~~iiDT~~ 187 (193)
...+.+++. +...||||+.+|+.+|+. ...-..++||..
T Consensus 64 ~~~l~~~l~~~~~~kv~~d~k~~~~~L~~~gi~~~~~~D~~l 105 (172)
T smart00474 64 LEILKDLLEDETITKVGHNAKFDLHVLARFGIELENIFDTML 105 (172)
T ss_pred HHHHHHHhcCCCceEEEechHHHHHHHHHCCCcccchhHHHH
Confidence 345666775 456899999999999963 111122467654
No 95
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=78.68 E-value=18 Score=28.04 Aligned_cols=80 Identities=21% Similarity=0.165 Sum_probs=45.5
Q ss_pred CcEEEEEEeecCCCCCcEeEEEEEEEEeCCCcEEEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhC--
Q 029428 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE-- 157 (193)
Q Consensus 80 ~~~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~-- 157 (193)
.+.+++|+|++|.++.. -.+..+.+... +... ||.+... + .+...+.+++.
T Consensus 3 ~~~~~~~~~~~~~~~~~-~~l~~i~l~~~-~~~~---~i~~~~~----------~------------~~~~~l~~~l~~~ 55 (178)
T cd06140 3 ADEVALYVELLGENYHT-ADIIGLALANG-GGAY---YIPLELA----------L------------LDLAALKEWLEDE 55 (178)
T ss_pred CCceEEEEEEcCCCcce-eeEEEEEEEeC-CcEE---EEeccch----------H------------HHHHHHHHHHhCC
Confidence 45789999999988421 12333444432 2221 3322110 0 13455667776
Q ss_pred CCEEEEeChHhhHHHhcc---cCCCCceeecCC
Q 029428 158 GRILVGHALHNDLKALLL---THSKKDLRDTSE 187 (193)
Q Consensus 158 g~ilVgHn~~fDl~~L~~---~~p~~~iiDT~~ 187 (193)
+...|+||+.+|+.+|.. ..+ ..+.||..
T Consensus 56 ~~~ki~~d~K~~~~~l~~~gi~~~-~~~fDt~l 87 (178)
T cd06140 56 KIPKVGHDAKRAYVALKRHGIELA-GVAFDTML 87 (178)
T ss_pred CCceeccchhHHHHHHHHCCCcCC-CcchhHHH
Confidence 357899999999999952 222 23567643
No 96
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=78.33 E-value=3.7 Score=39.40 Aligned_cols=40 Identities=30% Similarity=0.199 Sum_probs=28.7
Q ss_pred HHHHHHHHhC--CCEEEEeChHhhHHHhcccCC-CCceeecCC
Q 029428 148 VQKKVAELIE--GRILVGHALHNDLKALLLTHS-KKDLRDTSE 187 (193)
Q Consensus 148 v~~~l~~~l~--g~ilVgHn~~fDl~~L~~~~p-~~~iiDT~~ 187 (193)
+...+..|+. +...||||+.||+.+|...-. ...+.||+.
T Consensus 66 ~~~~l~~~l~~~~~~kv~~~~K~d~~~l~~~Gi~~~~~~Dtml 108 (593)
T COG0749 66 VLAALKPLLEDEGIKKVGQNLKYDYKVLANLGIEPGVAFDTML 108 (593)
T ss_pred hHHHHHHHhhCcccchhccccchhHHHHHHcCCcccchHHHHH
Confidence 7788888887 456999999999999964332 123556643
No 97
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=66.20 E-value=19 Score=38.42 Aligned_cols=87 Identities=17% Similarity=0.118 Sum_probs=51.0
Q ss_pred CCcEEEEEEeecCCC---CC-cEeEEEEEE-EEeCCCcEEEEEEe----------cCCCccccccccccCCCHHHHccCC
Q 029428 79 LTDVVAMDCEMVGIS---QG-NKSALGRVS-LVNKWGNLIYDEFV----------RPLERVVDFRTRISGIRPRDLRKAK 143 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~---~~-~i~eia~V~-vv~~~g~~i~~~lV----------~P~~~i~~~~t~ihGIt~e~l~~a~ 143 (193)
...++|||+|||-+. +| +-.+|-.|+ ++|+.|-.+.+.=| -|......+ . .+-+.+
T Consensus 245 dp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~-F--------~v~Ne~ 315 (2173)
T KOG1798|consen 245 DPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGP-F--------CVFNEP 315 (2173)
T ss_pred CceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCccccccc-e--------EEecCC
Confidence 457999999999988 43 334455554 35766654432211 111111100 0 112345
Q ss_pred CHHHHHHHHHHHhC---CCEEEEeCh-HhhHHHhc
Q 029428 144 DFPTVQKKVAELIE---GRILVGHAL-HNDLKALL 174 (193)
Q Consensus 144 ~~~ev~~~l~~~l~---g~ilVgHn~-~fDl~~L~ 174 (193)
.-..++.++.+-+. -.|+|.+|. -||+.|+.
T Consensus 316 dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve 350 (2173)
T KOG1798|consen 316 DEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVE 350 (2173)
T ss_pred cHHHHHHHHHHHHHhcCCcEEEEecCccccchhhH
Confidence 55667777766664 579999995 68999995
No 98
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=65.57 E-value=7.7 Score=32.19 Aligned_cols=60 Identities=10% Similarity=0.226 Sum_probs=40.6
Q ss_pred eEEEEEEEEeCCCcE-EEEEEecCCCccccc-------cccccCCCHHHHccCC-CHHHHHHHHHHHhC
Q 029428 98 SALGRVSLVNKWGNL-IYDEFVRPLERVVDF-------RTRISGIRPRDLRKAK-DFPTVQKKVAELIE 157 (193)
Q Consensus 98 ~eia~V~vv~~~g~~-i~~~lV~P~~~i~~~-------~t~ihGIt~e~l~~a~-~~~ev~~~l~~~l~ 157 (193)
.|||.+..-=.+|.+ .|+.+|+|......+ +..-|+|...-.+.+. .+..++.+|.+||+
T Consensus 11 aEiai~~fSL~~GI~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~ 79 (213)
T PF13017_consen 11 AEIAICKFSLKEGIIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLK 79 (213)
T ss_pred EEEEEEEEecCCccchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhh
Confidence 567766554334533 399999998643332 2345777766555554 79999999999995
No 99
>PHA03036 DNA polymerase; Provisional
Probab=65.06 E-value=65 Score=33.07 Aligned_cols=99 Identities=10% Similarity=-0.100 Sum_probs=55.5
Q ss_pred CCCCCCCcEEEEEEeecCCC--C----CcEeEEEEEEEEeCCCcEEEEEEecCCCcc--ccccccccCCC-HH---HHcc
Q 029428 74 NDDFSLTDVVAMDCEMVGIS--Q----GNKSALGRVSLVNKWGNLIYDEFVRPLERV--VDFRTRISGIR-PR---DLRK 141 (193)
Q Consensus 74 ~~~~~~~~~v~lD~EtTGl~--~----~~i~eia~V~vv~~~g~~i~~~lV~P~~~i--~~~~t~ihGIt-~e---~l~~ 141 (193)
+.-.-+..|++||+|+-.-. | +-|+.|+. ++++..|...--++++..... ......+-|+. -+ ++..
T Consensus 154 ~~~~~~~~~lsfDIEC~~~g~FPs~~~~pvshIs~-~~~~~~~~~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 (1004)
T PHA03036 154 PRFDIPRSYLFLDIECHFDKKFPSVFINPVSHISC-CYIDLSGKEKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDY 232 (1004)
T ss_pred CCccCcceeEEEEEEeccCCCCCCcccCcceEEEE-EEEecCCCeeEEEEeccccccccccccceeeeeeccccccccCC
Confidence 33334667999999998533 2 34667775 566777766655666654311 11122222221 01 1111
Q ss_pred C-----CCHHHHHHHHHHHhC---CCEEEEeCh-HhhHHHhc
Q 029428 142 A-----KDFPTVQKKVAELIE---GRILVGHAL-HNDLKALL 174 (193)
Q Consensus 142 a-----~~~~ev~~~l~~~l~---g~ilVgHn~-~fDl~~L~ 174 (193)
. .+-.+.+ ++.+++. =.+++|+|. .||+..|.
T Consensus 233 ~~~~~~~sE~~ml-~~~~~i~~~d~D~i~~yNg~nFD~~Yi~ 273 (1004)
T PHA03036 233 SKELILCSEIVLL-RIAKKLLELEFDYVVTFNGHNFDLRYIS 273 (1004)
T ss_pred ceeeecCCHHHHH-HHHHHHHhcCCCEEEeccCCCcchHHHH
Confidence 1 2334433 5555553 579999995 89999883
No 100
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=63.91 E-value=41 Score=31.46 Aligned_cols=103 Identities=17% Similarity=0.206 Sum_probs=62.3
Q ss_pred CCCCCcEEEEEEeecCCCCCcEeEEEEEEEEeCCCcEEEEEEecCCC--ccccccccccCCCHHHHccCCCHHHHHHHHH
Q 029428 76 DFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (193)
Q Consensus 76 ~~~~~~~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~i~~~lV~P~~--~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~ 153 (193)
.+.+..-.+||+|-.-.+ -+||| +-.....-..+.|-+|.. .+-+.+..-|||.-.||.++.+ -+...|.
T Consensus 368 ~Ldp~~ttWiDIEG~p~D---PVElA---iyQP~sg~YiHcyR~P~D~K~FK~~SKysHGillkDl~~aqP--GL~S~vi 439 (533)
T PF00843_consen 368 KLDPNATTWIDIEGPPND---PVELA---IYQPSSGNYIHCYREPHDEKQFKNQSKYSHGILLKDLENAQP--GLTSAVI 439 (533)
T ss_dssp CS-TTS-EEEEEESETTS---ESEEE---EEETTTTEEEEEE---S-HHHHHHHHHHTT-B-GGGCTTB-T--THHHHHH
T ss_pred hCCCCCCeeEecCCCCCC---CeEEE---EeccCCCcEEEEecCCcchhhhcccccccccccHHHHhhhcc--chHHHHH
Confidence 445677899999977444 36777 334555566677888875 5556666779999999998866 4566777
Q ss_pred HHhCCCEEEEeChHhhHHHhcccCCC--CceeecC
Q 029428 154 ELIEGRILVGHALHNDLKALLLTHSK--KDLRDTS 186 (193)
Q Consensus 154 ~~l~g~ilVgHn~~fDl~~L~~~~p~--~~iiDT~ 186 (193)
..|....++--.-+=|++-|--.|.| -.+||..
T Consensus 440 ~~LP~~MVlT~QGsDDIrkLld~hGRrDiKlvDV~ 474 (533)
T PF00843_consen 440 ELLPKNMVLTCQGSDDIRKLLDMHGRRDIKLVDVK 474 (533)
T ss_dssp HHS-TT-EEEESSHHHHHHHHHCTT-TTSEEEE--
T ss_pred HhCCcCcEEEeeChHHHHHHHHhcCCCcceEEEee
Confidence 78875555555568888888766765 4567753
No 101
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=63.18 E-value=2.2 Score=42.13 Aligned_cols=89 Identities=13% Similarity=0.180 Sum_probs=51.9
Q ss_pred CCCcEEEEEEeecCCC---C----CcEeEEEEEEEEeCCCcEEE-EEE-ecCCCccccccccccCCCHHHHccCCCHHHH
Q 029428 78 SLTDVVAMDCEMVGIS---Q----GNKSALGRVSLVNKWGNLIY-DEF-VRPLERVVDFRTRISGIRPRDLRKAKDFPTV 148 (193)
Q Consensus 78 ~~~~~v~lD~EtTGl~---~----~~i~eia~V~vv~~~g~~i~-~~l-V~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev 148 (193)
.+-+++.||+|++|-. + +-+++||-+....+.+...+ +.+ ++|-.+|..... +..++. ..+-+.
T Consensus 272 APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~l~~capI~G~~V-~~~~~e------~elL~~ 344 (1066)
T KOG0969|consen 272 APLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFTLKTCAPIVGSNV-HSYETE------KELLES 344 (1066)
T ss_pred ccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhcccCcCCCCCcee-EEeccH------HHHHHH
Confidence 3667999999999876 2 35667776544443333321 122 223233332111 112222 233456
Q ss_pred HHHHHHHhCCCEEEEeCh-HhhHHHh
Q 029428 149 QKKVAELIEGRILVGHAL-HNDLKAL 173 (193)
Q Consensus 149 ~~~l~~~l~g~ilVgHn~-~fDl~~L 173 (193)
|..|..-++-.+|+|+|+ .||+..|
T Consensus 345 W~~firevDPDvI~GYNi~nFDiPYl 370 (1066)
T KOG0969|consen 345 WRKFIREVDPDVIIGYNICNFDIPYL 370 (1066)
T ss_pred HHHHHHhcCCCeEeccccccccccee
Confidence 777777778899999996 8998776
No 102
>PRK05761 DNA polymerase I; Reviewed
Probab=62.09 E-value=19 Score=35.75 Aligned_cols=32 Identities=16% Similarity=0.038 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhC-CCEEEEeCh-HhhHHHhc
Q 029428 143 KDFPTVQKKVAELIE-GRILVGHAL-HNDLKALL 174 (193)
Q Consensus 143 ~~~~ev~~~l~~~l~-g~ilVgHn~-~fDl~~L~ 174 (193)
.+-.+++.++.+++. -.+.|++|. .||+.+|.
T Consensus 208 ~~E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~ 241 (787)
T PRK05761 208 DSEKELLAELFDIILEYPPVVTFNGDNFDLPYLY 241 (787)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEcCCcchHHHHH
Confidence 677889999999996 567778995 79999993
No 103
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=59.32 E-value=18 Score=37.39 Aligned_cols=95 Identities=8% Similarity=0.086 Sum_probs=54.7
Q ss_pred CCCCcEEEEEEeecCCCC---CcEeEEEEEEEEeCC-----Cc----EEEEEEecCCCccccccccccCCCHHH---Hcc
Q 029428 77 FSLTDVVAMDCEMVGISQ---GNKSALGRVSLVNKW-----GN----LIYDEFVRPLERVVDFRTRISGIRPRD---LRK 141 (193)
Q Consensus 77 ~~~~~~v~lD~EtTGl~~---~~i~eia~V~vv~~~-----g~----~i~~~lV~P~~~i~~~~t~ihGIt~e~---l~~ 141 (193)
.++..+.+|.++|+--.. .+|+.|+..+..+.. .. ..+..+++|...+-+...+ -+.... +.-
T Consensus 526 ~Ppl~llsL~i~T~~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~--ela~~k~~~v~~ 603 (1429)
T KOG0970|consen 526 PPPLTLLSLNIRTSMNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLK--ELAKQKLSKVVL 603 (1429)
T ss_pred CCCeeEEEeeeeehhccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHH--HHHHhccCceEE
Confidence 346678999999986552 456666655443322 11 1277788988643332110 000000 222
Q ss_pred CCCHHHHHHHHHHHh---CCCEEEEeC-hHhhHHHh
Q 029428 142 AKDFPTVQKKVAELI---EGRILVGHA-LHNDLKAL 173 (193)
Q Consensus 142 a~~~~ev~~~l~~~l---~g~ilVgHn-~~fDl~~L 173 (193)
.-+-...+..|...+ +-.++|||| ..|++.+|
T Consensus 604 ~~sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VL 639 (1429)
T KOG0970|consen 604 HNSERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVL 639 (1429)
T ss_pred ecCHHHHHHHHHHHhhccCCCEEEEeccccchHHHH
Confidence 234455555565555 368999999 79999999
No 104
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=57.97 E-value=68 Score=33.42 Aligned_cols=44 Identities=23% Similarity=0.332 Sum_probs=34.0
Q ss_pred cccCCCHHHHccCCCHHHHHHHHHHHhC---CCEEEEeCh-HhhHHHh
Q 029428 130 RISGIRPRDLRKAKDFPTVQKKVAELIE---GRILVGHAL-HNDLKAL 173 (193)
Q Consensus 130 ~ihGIt~e~l~~a~~~~ev~~~l~~~l~---g~ilVgHn~-~fDl~~L 173 (193)
..-|+.+..|..-.+-.+.+..+..++. -.+++|||. .||+.+|
T Consensus 569 ~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl 616 (1172)
T TIGR00592 569 EFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVL 616 (1172)
T ss_pred hhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHH
Confidence 4456666666666777788888888774 689999995 8999998
No 105
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=55.48 E-value=50 Score=28.07 Aligned_cols=92 Identities=23% Similarity=0.264 Sum_probs=53.8
Q ss_pred cEEEEEEeecCCC--C-C--------------------cEeEEEEEEEEeCCCcE------EEEEE---ecCCC-ccccc
Q 029428 81 DVVAMDCEMVGIS--Q-G--------------------NKSALGRVSLVNKWGNL------IYDEF---VRPLE-RVVDF 127 (193)
Q Consensus 81 ~~v~lD~EtTGl~--~-~--------------------~i~eia~V~vv~~~g~~------i~~~l---V~P~~-~i~~~ 127 (193)
+||++|+|..|.= + + .+|++| +++.|.+|+. +|..= .++.. ...+.
T Consensus 25 ~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlG-lTlsd~~Gn~p~~g~~tWqfNF~dF~~~~D~~a~~ 103 (239)
T KOG0304|consen 25 PYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLG-LTLSDEKGNLPDCGTDTWQFNFSDFNLEKDMYAQD 103 (239)
T ss_pred CeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhhee-eeeeccCCCCCCCCCceeEEecccCCchhhccchh
Confidence 5899999988864 1 1 367777 6677765543 33322 22222 22222
Q ss_pred c---ccccCCCHHHHc-cCCCHHHHHHHHHH---HhC-CCEEEEeChHhhHHHh
Q 029428 128 R---TRISGIRPRDLR-KAKDFPTVQKKVAE---LIE-GRILVGHALHNDLKAL 173 (193)
Q Consensus 128 ~---t~ihGIt~e~l~-~a~~~~ev~~~l~~---~l~-g~ilVgHn~~fDl~~L 173 (193)
+ .+-+||.-+... .+....+..+.+.. .+. +-.+|-.+..+|+.+|
T Consensus 104 SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYL 157 (239)
T KOG0304|consen 104 SIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYL 157 (239)
T ss_pred hHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHH
Confidence 2 244888877664 45555444333322 223 5678999999999998
No 106
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=52.46 E-value=75 Score=29.27 Aligned_cols=71 Identities=13% Similarity=0.102 Sum_probs=39.7
Q ss_pred CcEEEEEEeecCCCCCcEeEEEEEEEEeCCCcE--EEEEEecCCCccccccccccCCCHHHHccCCCHHHHHHHHHHHhC
Q 029428 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNL--IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (193)
Q Consensus 80 ~~~v~lD~EtTGl~~~~i~eia~V~vv~~~g~~--i~~~lV~P~~~i~~~~t~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (193)
...++||+||+. +.+-.-.+|.+. .+ .|.. .|..|+.... ..-.+++.+|.+|+.
T Consensus 284 ~~~~ffDiEt~P-~~~~~yL~G~~~-~~-~~~~~~~~~~fla~~~--------------------~~E~~~~~~f~~~l~ 340 (457)
T TIGR03491 284 PGELIFDIESDP-DENLDYLHGFLV-VD-KGQENEKYRPFLAEDP--------------------NTEELAWQQFLQLLQ 340 (457)
T ss_pred CccEEEEecCCC-CCCCceEEEEEE-ec-CCCCCcceeeeecCCc--------------------hHHHHHHHHHHHHHH
Confidence 457899999994 223334455433 22 2222 2444443322 112345556666664
Q ss_pred ---CCEEEEeChHhhHHHhc
Q 029428 158 ---GRILVGHALHNDLKALL 174 (193)
Q Consensus 158 ---g~ilVgHn~~fDl~~L~ 174 (193)
+..|+.+| .|...+|+
T Consensus 341 ~~~~~~i~hY~-~~e~~~l~ 359 (457)
T TIGR03491 341 SYPDAPIYHYG-ETEKDSLR 359 (457)
T ss_pred HCCCCeEEeeC-HHHHHHHH
Confidence 55788888 88888886
No 107
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. 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. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=41.31 E-value=37 Score=26.10 Aligned_cols=38 Identities=29% Similarity=0.274 Sum_probs=26.0
Q ss_pred HHHHHHHhC--CCEEEEeChHhhHHHhccc--CCCCceeecC
Q 029428 149 QKKVAELIE--GRILVGHALHNDLKALLLT--HSKKDLRDTS 186 (193)
Q Consensus 149 ~~~l~~~l~--g~ilVgHn~~fDl~~L~~~--~p~~~iiDT~ 186 (193)
...|.+++. +...||||+.+|+.+|... .....+.||.
T Consensus 53 ~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~ 94 (178)
T cd06142 53 LSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQ 94 (178)
T ss_pred HHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCCcccHH
Confidence 344566776 4578999999999999533 2233467875
No 108
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=39.00 E-value=1.9e+02 Score=22.77 Aligned_cols=24 Identities=21% Similarity=0.188 Sum_probs=19.0
Q ss_pred HHHHHhC--CCEEEEeChHhhHHHhc
Q 029428 151 KVAELIE--GRILVGHALHNDLKALL 174 (193)
Q Consensus 151 ~l~~~l~--g~ilVgHn~~fDl~~L~ 174 (193)
.|.+++. +...|||++..|+.+|+
T Consensus 68 ~L~~~L~~~~i~kv~~d~K~~~~~L~ 93 (192)
T cd06147 68 ILNEVFTDPNILKVFHGADSDIIWLQ 93 (192)
T ss_pred HHHHHhcCCCceEEEechHHHHHHHH
Confidence 3556665 46789999999999995
No 109
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.33 E-value=33 Score=34.64 Aligned_cols=44 Identities=16% Similarity=-0.043 Sum_probs=30.0
Q ss_pred CHHHHHHHHHHHhCC--CEEEEeChHhhHHHhcccC--CCCceeecCC
Q 029428 144 DFPTVQKKVAELIEG--RILVGHALHNDLKALLLTH--SKKDLRDTSE 187 (193)
Q Consensus 144 ~~~ev~~~l~~~l~g--~ilVgHn~~fDl~~L~~~~--p~~~iiDT~~ 187 (193)
....+...|..++.+ ...||||+.||+.+|...- ....+.||..
T Consensus 362 ~~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~l 409 (887)
T TIGR00593 362 LTILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTML 409 (887)
T ss_pred hhHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHH
Confidence 345666778888864 4589999999999996211 1224577754
No 110
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy 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. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=28.69 E-value=71 Score=23.56 Aligned_cols=36 Identities=28% Similarity=0.208 Sum_probs=23.8
Q ss_pred HHHHhC--CCEEEEeChHhhHHHhcccC--CCCceeecCC
Q 029428 152 VAELIE--GRILVGHALHNDLKALLLTH--SKKDLRDTSE 187 (193)
Q Consensus 152 l~~~l~--g~ilVgHn~~fDl~~L~~~~--p~~~iiDT~~ 187 (193)
|.+++. +...||||+..|+.+|.... ....+.||..
T Consensus 45 l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~~~~~D~~l 84 (150)
T cd09018 45 LKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFDTML 84 (150)
T ss_pred HHHHhcCCCCceeeecHHHHHHHHHHcCCccCCcchhHHH
Confidence 555664 46689999999999995321 1234577653
No 111
>KOG1615 consensus Phosphoserine phosphatase [Amino acid transport and metabolism]
Probab=26.96 E-value=8.4 Score=32.28 Aligned_cols=26 Identities=19% Similarity=0.236 Sum_probs=18.9
Q ss_pred CCcEEEEEEeecCCCCCcEeEEEEEE
Q 029428 79 LTDVVAMDCEMVGISQGNKSALGRVS 104 (193)
Q Consensus 79 ~~~~v~lD~EtTGl~~~~i~eia~V~ 104 (193)
..+.|+||++.|-....-|.++|+.+
T Consensus 15 ~~~aVcFDvDSTvi~eEgIdelA~~~ 40 (227)
T KOG1615|consen 15 SADAVCFDVDSTVIQEEGIDELAAYC 40 (227)
T ss_pred hcCeEEEecCcchhHHhhHHHHHHHh
Confidence 45799999999987755566666543
No 112
>KOG2613 consensus NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=24.55 E-value=1.5e+02 Score=27.69 Aligned_cols=70 Identities=19% Similarity=0.329 Sum_probs=45.0
Q ss_pred CCCCCCCCCCCcEEEEEEeecCCCCC--cEeEEEEEEEEeCC-C----cEE-----EEEEecCCCccccccccccCCCHH
Q 029428 70 LTPINDDFSLTDVVAMDCEMVGISQG--NKSALGRVSLVNKW-G----NLI-----YDEFVRPLERVVDFRTRISGIRPR 137 (193)
Q Consensus 70 ~~p~~~~~~~~~~v~lD~EtTGl~~~--~i~eia~V~vv~~~-g----~~i-----~~~lV~P~~~i~~~~t~ihGIt~e 137 (193)
|...-+....++|+++|+|-+|-..+ .-..++-|.++... + ... +..+.+|+..+-.|-..-..+.++
T Consensus 303 F~sl~~~kqL~ef~V~dv~~v~~~~~~g~kh~l~dv~v~r~sd~g~nd~~~~~RtHLGhil~~gD~vlgydl~~~N~N~~ 382 (502)
T KOG2613|consen 303 FNSLCDPKQLTEFIVLDVDPVGEAGGKGQKHALADVWVARSSDLGMNDKFHYARTHLGHILKPGDLVLGYDLANANLNDE 382 (502)
T ss_pred chhhcChhhheEEEEEEEecccccCCccceeeeeeEEEEEcCccCcccceeeehhhccccCCCCCeeeeeeeccCccchh
Confidence 33334445578999999999887743 34577777776433 2 122 234678888877777766666655
Q ss_pred HH
Q 029428 138 DL 139 (193)
Q Consensus 138 ~l 139 (193)
.+
T Consensus 383 ~~ 384 (502)
T KOG2613|consen 383 EF 384 (502)
T ss_pred hh
Confidence 44
No 113
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=24.34 E-value=44 Score=28.61 Aligned_cols=89 Identities=25% Similarity=0.263 Sum_probs=51.3
Q ss_pred CcEEEEEEeecCCC--C-C--------------------cEeEEEEEEEEeCCCcEE-------EEEEecCCCccc-ccc
Q 029428 80 TDVVAMDCEMVGIS--Q-G--------------------NKSALGRVSLVNKWGNLI-------YDEFVRPLERVV-DFR 128 (193)
Q Consensus 80 ~~~v~lD~EtTGl~--~-~--------------------~i~eia~V~vv~~~g~~i-------~~~lV~P~~~i~-~~~ 128 (193)
-++|.+|+|..|+- + | .|++|| +++.|.+|+.. |+.-..+...+- .++
T Consensus 42 Yn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlG-lsLSDe~GN~P~~~sTWQFNF~F~l~~dmya~ES 120 (299)
T COG5228 42 YNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLG-LSLSDENGNKPNGPSTWQFNFEFDLKKDMYATES 120 (299)
T ss_pred CCceeeccccCceeecccccccccchHHHHHHhcccchhhhhhee-eeeccccCCCCCCCceeEEEEEecchhhhcchHH
Confidence 46899999999875 1 1 367777 66777777532 455556654321 122
Q ss_pred c---cccCCCHHHHc-cCCCHHHHHHHHHHHh--------CCCEEEEeChHhhHHHh
Q 029428 129 T---RISGIRPRDLR-KAKDFPTVQKKVAELI--------EGRILVGHALHNDLKAL 173 (193)
Q Consensus 129 t---~ihGIt~e~l~-~a~~~~ev~~~l~~~l--------~g~ilVgHn~~fDl~~L 173 (193)
. .-+||.-+.-+ -+... .++.+++ +.-++|.++..+|+.+|
T Consensus 121 ieLL~ksgIdFkkHe~~GI~v----~eF~elLm~SGLvm~e~VtWitfHsaYDfgyL 173 (299)
T COG5228 121 IELLRKSGIDFKKHENLGIDV----FEFSELLMDSGLVMDESVTWITFHSAYDFGYL 173 (299)
T ss_pred HHHHHHcCCChhhHhhcCCCH----HHHHHHHhccCceeccceEEEEeecchhHHHH
Confidence 1 22455433222 12222 2344444 24578899999999998
No 114
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=22.86 E-value=65 Score=23.31 Aligned_cols=28 Identities=29% Similarity=0.520 Sum_probs=23.7
Q ss_pred cccCCCHHHHccCCCHHHHHHHHHHHhC
Q 029428 130 RISGIRPRDLRKAKDFPTVQKKVAELIE 157 (193)
Q Consensus 130 ~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (193)
..||+++++|+.+-.-.+.+..+++|+-
T Consensus 29 a~TG~~p~~LR~~a~dp~FL~~VLdFl~ 56 (88)
T PF12096_consen 29 ALTGLSPDDLRAAAGDPAFLAAVLDFLL 56 (88)
T ss_pred HHhCCCHHHHHHHccChHHHHHHHHHHH
Confidence 4699999999988877888888888883
No 115
>PF06821 Ser_hydrolase: Serine hydrolase; InterPro: IPR010662 This family contains a number of hypothetical bacterial proteins of unknown function, which may be cytosolic. The Crystal Structure Of The Yden Gene Product Swiss:P96671 from B. Subtilis has been solved. The structure shows an alpha-beta hydrolase fold suggesting an enzymatic function for these proteins [].; GO: 0016787 hydrolase activity; PDB: 3BDV_B 2QS9_A 1UXO_A.
Probab=22.18 E-value=83 Score=24.93 Aligned_cols=33 Identities=27% Similarity=0.383 Sum_probs=21.4
Q ss_pred cCCCHHHHHHHHHHHhC----CCEEEEeCh--HhhHHHh
Q 029428 141 KAKDFPTVQKKVAELIE----GRILVGHAL--HNDLKAL 173 (193)
Q Consensus 141 ~a~~~~ev~~~l~~~l~----g~ilVgHn~--~fDl~~L 173 (193)
+.|.+++-...|.+.+. ..+||||++ -.=+.+|
T Consensus 35 ~~P~~~~W~~~l~~~i~~~~~~~ilVaHSLGc~~~l~~l 73 (171)
T PF06821_consen 35 DNPDLDEWVQALDQAIDAIDEPTILVAHSLGCLTALRWL 73 (171)
T ss_dssp TS--HHHHHHHHHHCCHC-TTTEEEEEETHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHhhcCCCeEEEEeCHHHHHHHHHH
Confidence 56778887788877763 469999995 3444444
Done!