Query 006991
Match_columns 622
No_of_seqs 202 out of 507
Neff 6.3
Searched_HMMs 46136
Date Thu Mar 28 17:23:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006991.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006991hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04857 CAF1: CAF1 family rib 100.0 1.7E-63 3.8E-68 512.6 14.5 246 30-429 1-262 (262)
2 KOG0304 mRNA deadenylase subun 100.0 1.9E-31 4E-36 258.8 15.4 119 29-159 2-125 (239)
3 KOG1990 Poly(A)-specific exori 100.0 5.1E-30 1.1E-34 288.0 7.5 481 34-591 1-521 (564)
4 COG5228 POP2 mRNA deadenylase 99.9 9.3E-22 2E-26 191.0 13.6 119 27-158 18-140 (299)
5 PF08675 RNA_bind: RNA binding 99.6 4.1E-15 9E-20 125.2 7.2 75 479-572 1-77 (87)
6 PRK07740 hypothetical protein; 97.2 0.0017 3.8E-08 66.7 9.6 89 324-436 140-228 (244)
7 cd06131 DNA_pol_III_epsilon_Ec 97.1 0.0042 9E-08 59.4 10.2 97 313-431 67-167 (167)
8 PRK06195 DNA polymerase III su 97.0 0.0042 9.1E-08 66.1 10.4 95 314-436 67-166 (309)
9 TIGR01406 dnaQ_proteo DNA poly 97.0 0.0049 1.1E-07 62.6 10.3 98 313-432 68-170 (225)
10 cd02637 R3H_PARN R3H domain of 96.9 0.0023 4.9E-08 52.5 5.8 27 242-268 18-44 (65)
11 PRK05711 DNA polymerase III su 96.9 0.0071 1.5E-07 62.2 10.5 99 312-432 71-174 (240)
12 cd06134 RNaseT DEDDh 3'-5' exo 96.9 0.0062 1.3E-07 60.1 9.8 83 324-432 101-187 (189)
13 PF10309 DUF2414: Protein of u 96.8 0.0022 4.8E-08 52.0 5.2 59 485-545 3-61 (62)
14 PRK07942 DNA polymerase III su 96.8 0.0046 9.9E-08 63.1 8.8 88 323-435 91-181 (232)
15 TIGR00573 dnaq exonuclease, DN 96.8 0.0068 1.5E-07 61.1 9.6 99 313-434 73-177 (217)
16 PRK06063 DNA polymerase III su 96.7 0.0091 2E-07 63.7 10.6 97 313-436 80-181 (313)
17 cd06130 DNA_pol_III_epsilon_li 96.7 0.011 2.4E-07 55.6 9.5 88 313-428 63-155 (156)
18 PRK06807 DNA polymerase III su 96.6 0.013 2.7E-07 62.7 10.4 86 324-436 87-174 (313)
19 PRK09145 DNA polymerase III su 96.6 0.016 3.4E-07 57.7 10.5 91 314-432 98-199 (202)
20 PRK05168 ribonuclease T; Provi 96.5 0.0068 1.5E-07 61.0 7.5 87 324-435 113-202 (211)
21 TIGR01298 RNaseT ribonuclease 96.5 0.0089 1.9E-07 59.6 8.0 86 324-434 104-192 (200)
22 PRK09146 DNA polymerase III su 96.5 0.015 3.3E-07 59.6 9.9 96 314-437 116-230 (239)
23 cd06145 REX1_like DEDDh 3'-5' 96.4 0.013 2.8E-07 55.7 7.9 76 324-428 75-150 (150)
24 cd06137 DEDDh_RNase DEDDh 3'-5 96.3 0.012 2.6E-07 56.5 7.3 75 325-428 84-161 (161)
25 PRK07983 exodeoxyribonuclease 96.2 0.021 4.6E-07 57.8 9.2 94 313-436 63-156 (219)
26 cd06127 DEDDh DEDDh 3'-5' exon 96.0 0.034 7.3E-07 51.3 8.6 79 325-428 79-159 (159)
27 PRK06309 DNA polymerase III su 95.7 0.062 1.4E-06 54.8 9.9 98 313-435 65-167 (232)
28 smart00479 EXOIII exonuclease 95.7 0.078 1.7E-06 50.1 10.0 84 325-434 80-167 (169)
29 PRK07246 bifunctional ATP-depe 95.6 0.049 1.1E-06 65.4 10.1 100 313-438 72-174 (820)
30 PRK07883 hypothetical protein; 95.6 0.081 1.8E-06 60.9 11.3 87 325-436 95-184 (557)
31 cd06144 REX4_like DEDDh 3'-5' 95.4 0.049 1.1E-06 51.7 7.2 75 324-427 76-151 (152)
32 TIGR01405 polC_Gram_pos DNA po 95.4 0.065 1.4E-06 66.5 10.1 105 305-434 248-355 (1213)
33 PRK06722 exonuclease; Provisio 95.3 0.09 1.9E-06 55.3 9.5 98 312-432 75-179 (281)
34 PRK07247 DNA polymerase III su 95.2 0.1 2.2E-06 52.0 9.1 83 324-434 83-169 (195)
35 PRK06310 DNA polymerase III su 95.1 0.12 2.6E-06 53.5 9.6 96 314-434 74-174 (250)
36 PRK05601 DNA polymerase III su 95.0 0.13 2.7E-06 56.0 9.6 206 308-538 106-342 (377)
37 KOG4483 Uncharacterized conser 94.9 0.029 6.2E-07 60.3 4.5 66 486-557 390-458 (528)
38 TIGR01407 dinG_rel DnaQ family 94.9 0.11 2.5E-06 62.6 10.1 100 313-438 66-169 (850)
39 cd06149 ISG20 DEDDh 3'-5' exon 94.9 0.085 1.8E-06 50.5 7.4 76 324-427 76-156 (157)
40 PRK07748 sporulation inhibitor 94.8 0.24 5.3E-06 49.5 10.8 97 312-433 77-179 (207)
41 PRK08074 bifunctional ATP-depe 94.6 0.15 3.2E-06 62.2 10.2 90 324-438 83-173 (928)
42 PRK08517 DNA polymerase III su 94.4 0.19 4.2E-06 52.2 9.2 86 324-435 146-232 (257)
43 PRK00448 polC DNA polymerase I 93.9 0.17 3.7E-06 63.8 8.8 106 305-435 477-585 (1437)
44 PF00929 RNase_T: Exonuclease; 91.9 0.0085 1.8E-07 55.4 -5.1 81 323-427 81-164 (164)
45 cd06133 ERI-1_3'hExo_like DEDD 91.0 1.3 2.8E-05 42.2 9.0 92 317-430 82-175 (176)
46 cd06133 ERI-1_3'hExo_like DEDD 90.5 0.64 1.4E-05 44.4 6.4 50 53-121 1-50 (176)
47 cd06136 TREX1_2 DEDDh 3'-5' ex 90.4 0.62 1.3E-05 45.4 6.2 75 325-429 98-176 (177)
48 cd06138 ExoI_N N-terminal DEDD 89.6 1.5 3.2E-05 42.9 8.2 26 319-344 78-104 (183)
49 COG0847 DnaQ DNA polymerase II 88.7 2.5 5.5E-05 42.9 9.4 83 326-433 96-181 (243)
50 PRK05168 ribonuclease T; Provi 87.4 1.7 3.8E-05 43.6 7.2 57 41-120 7-65 (211)
51 PRK09182 DNA polymerase III su 87.0 3.1 6.7E-05 44.2 9.1 88 319-435 115-202 (294)
52 PRK09145 DNA polymerase III su 86.3 1.4 3.1E-05 43.7 5.8 56 41-120 19-74 (202)
53 PF01612 DNA_pol_A_exo1: 3'-5' 86.2 3.6 7.9E-05 38.8 8.4 95 317-434 68-175 (176)
54 PF00076 RRM_1: RNA recognitio 85.9 1.7 3.7E-05 34.3 5.1 56 490-549 1-62 (70)
55 PTZ00315 2'-phosphotransferase 85.4 4.2 9.1E-05 46.9 9.6 83 326-432 154-253 (582)
56 smart00479 EXOIII exonuclease 84.3 1.9 4.1E-05 40.6 5.4 43 52-120 1-43 (169)
57 PF11608 Limkain-b1: Limkain b 82.6 2.5 5.5E-05 36.6 4.8 63 487-552 2-65 (90)
58 PF08777 RRM_3: RNA binding mo 82.0 3.1 6.8E-05 37.3 5.5 54 489-549 3-60 (105)
59 PRK11779 sbcB exonuclease I; P 82.0 3 6.6E-05 47.2 6.7 101 316-433 84-197 (476)
60 PF00929 RNase_T: Exonuclease; 79.6 2.9 6.4E-05 38.3 4.8 44 54-121 1-44 (164)
61 PF14259 RRM_6: RNA recognitio 79.2 4.8 0.0001 32.2 5.3 54 490-547 1-60 (70)
62 COG2176 PolC DNA polymerase II 78.9 4.9 0.00011 49.4 7.2 105 305-435 479-587 (1444)
63 PRK07942 DNA polymerase III su 77.9 5 0.00011 41.0 6.2 48 48-120 3-50 (232)
64 PRK07247 DNA polymerase III su 77.9 4.4 9.6E-05 40.4 5.6 42 52-120 6-47 (195)
65 TIGR00573 dnaq exonuclease, DN 77.8 3.8 8.3E-05 41.2 5.3 48 47-120 3-50 (217)
66 cd06134 RNaseT DEDDh 3'-5' exo 75.3 5.2 0.00011 39.4 5.3 49 49-120 3-53 (189)
67 TIGR01298 RNaseT ribonuclease 75.1 8.3 0.00018 38.4 6.8 50 48-120 5-56 (200)
68 PRK05601 DNA polymerase III su 73.8 6.6 0.00014 43.0 6.0 50 46-120 41-90 (377)
69 PRK09146 DNA polymerase III su 73.7 6 0.00013 40.7 5.5 51 46-120 42-92 (239)
70 smart00362 RRM_2 RNA recogniti 73.2 9.6 0.00021 29.2 5.5 54 490-547 2-60 (72)
71 cd06146 mut-7_like_exo DEDDy 3 72.4 17 0.00038 35.9 8.3 107 315-431 71-192 (193)
72 PRK06310 DNA polymerase III su 71.5 7.1 0.00015 40.3 5.5 48 47-120 3-50 (250)
73 cd06127 DEDDh DEDDh 3'-5' exon 70.4 3.6 7.8E-05 37.6 2.8 42 54-120 1-42 (159)
74 cd06141 WRN_exo DEDDy 3'-5' ex 70.2 27 0.00059 33.2 8.9 96 321-431 69-169 (170)
75 PRK05359 oligoribonuclease; Pr 69.9 7.1 0.00015 38.3 4.8 47 50-120 2-48 (181)
76 PRK07740 hypothetical protein; 69.7 5.9 0.00013 40.8 4.4 55 42-120 50-104 (244)
77 PRK06807 DNA polymerase III su 68.6 8.6 0.00019 41.2 5.5 44 51-120 8-51 (313)
78 cd02642 R3H_encore_like R3H do 67.4 10 0.00022 30.7 4.5 21 242-262 23-43 (63)
79 PRK05755 DNA polymerase I; Pro 66.8 18 0.00039 44.2 8.3 102 317-436 362-471 (880)
80 PRK06063 DNA polymerase III su 66.6 9.2 0.0002 40.9 5.2 46 50-120 14-59 (313)
81 cd06131 DNA_pol_III_epsilon_Ec 64.5 9.9 0.00021 36.0 4.5 44 53-120 1-44 (167)
82 cd06130 DNA_pol_III_epsilon_li 64.3 12 0.00027 34.7 5.1 40 53-120 1-40 (156)
83 PRK09182 DNA polymerase III su 64.0 13 0.00028 39.6 5.7 47 51-120 37-86 (294)
84 PRK07883 hypothetical protein; 62.4 12 0.00026 43.3 5.5 52 43-120 7-58 (557)
85 PRK07748 sporulation inhibitor 62.0 11 0.00024 37.6 4.5 51 50-120 3-53 (207)
86 PRK05711 DNA polymerase III su 61.3 16 0.00034 37.7 5.6 47 50-120 3-49 (240)
87 cd02325 R3H R3H domain. The na 59.6 14 0.00031 28.1 3.9 23 242-264 19-41 (59)
88 PRK08517 DNA polymerase III su 59.5 20 0.00043 37.4 6.0 51 44-120 61-111 (257)
89 cd01201 Neurobeachin Neurobeac 59.3 14 0.0003 33.5 4.2 49 497-545 56-104 (108)
90 cd06129 RNaseD_like DEDDy 3'-5 59.2 49 0.0011 31.4 8.3 95 321-432 63-161 (161)
91 PF01424 R3H: R3H domain; Int 57.7 51 0.0011 26.2 6.9 28 242-271 22-49 (63)
92 PLN03134 glycine-rich RNA-bind 57.1 44 0.00094 31.6 7.4 59 487-549 34-99 (144)
93 cd06139 DNA_polA_I_Ecoli_like_ 56.5 36 0.00077 32.6 7.0 103 319-436 61-172 (193)
94 KOG0132 RNA polymerase II C-te 56.5 20 0.00043 42.4 5.7 99 490-594 424-529 (894)
95 TIGR01406 dnaQ_proteo DNA poly 56.3 21 0.00045 36.3 5.4 44 53-120 2-45 (225)
96 COG0349 Rnd Ribonuclease D [Tr 55.9 44 0.00095 36.6 8.0 100 314-436 59-168 (361)
97 cd00007 35EXOc 3'-5' exonuclea 55.2 36 0.00079 30.8 6.5 59 319-392 48-106 (155)
98 PF15023 DUF4523: Protein of u 54.9 25 0.00053 33.6 5.1 62 485-548 85-147 (166)
99 cd06136 TREX1_2 DEDDh 3'-5' ex 53.9 23 0.00049 34.5 5.1 46 53-120 1-56 (177)
100 TIGR01659 sex-lethal sex-letha 51.9 30 0.00065 37.7 6.1 59 487-549 193-258 (346)
101 PRK10829 ribonuclease D; Provi 48.3 59 0.0013 35.8 7.7 98 315-435 64-171 (373)
102 COG0349 Rnd Ribonuclease D [Tr 48.1 15 0.00033 40.0 3.0 26 39-64 5-30 (361)
103 cd06135 Orn DEDDh 3'-5' exonuc 47.9 27 0.00058 33.8 4.5 75 324-432 93-170 (173)
104 cd00590 RRM RRM (RNA recogniti 47.4 41 0.00088 25.7 4.8 55 490-548 2-62 (74)
105 smart00361 RRM_1 RNA recogniti 46.3 29 0.00064 28.1 3.9 47 502-548 3-59 (70)
106 PRK11779 sbcB exonuclease I; P 46.0 50 0.0011 37.5 6.9 74 49-158 4-77 (476)
107 cd06398 PB1_Joka2 The PB1 doma 43.5 63 0.0014 28.3 5.7 59 487-545 8-72 (91)
108 PTZ00315 2'-phosphotransferase 43.1 43 0.00093 38.9 5.8 49 51-120 56-104 (582)
109 smart00360 RRM RNA recognition 42.9 40 0.00086 25.4 4.0 50 494-547 3-59 (71)
110 KOG4206 Spliceosomal protein s 42.7 47 0.001 33.8 5.4 61 489-549 11-75 (221)
111 smart00474 35EXOc 3'-5' exonuc 40.1 2.3E+02 0.005 26.0 9.5 98 318-434 68-171 (172)
112 TIGR01407 dinG_rel DnaQ family 39.8 47 0.001 40.5 5.8 43 52-120 1-43 (850)
113 PF15342 FAM212: FAM212 family 38.3 19 0.00041 29.0 1.4 23 324-350 38-60 (62)
114 cd06125 DnaQ_like_exo DnaQ-lik 38.1 31 0.00067 30.0 3.0 28 317-344 35-63 (96)
115 TIGR01659 sex-lethal sex-letha 37.7 70 0.0015 34.8 6.2 59 486-548 106-171 (346)
116 PRK08074 bifunctional ATP-depe 37.1 56 0.0012 40.3 5.9 45 51-120 3-47 (928)
117 cd02646 R3H_G-patch R3H domain 36.3 52 0.0011 26.1 3.7 21 242-262 18-38 (58)
118 TIGR01405 polC_Gram_pos DNA po 34.0 64 0.0014 40.9 5.8 46 49-120 188-233 (1213)
119 PF01612 DNA_pol_A_exo1: 3'-5' 33.9 32 0.00068 32.3 2.5 27 38-64 7-33 (176)
120 smart00393 R3H Putative single 33.5 80 0.0017 26.5 4.7 27 242-270 38-64 (79)
121 KOG1990 Poly(A)-specific exori 33.3 16 0.00035 42.4 0.5 128 25-166 100-236 (564)
122 cd02641 R3H_Smubp-2_like R3H d 32.8 65 0.0014 25.9 3.8 21 242-262 19-40 (60)
123 cd06149 ISG20 DEDDh 3'-5' exon 31.9 20 0.00043 34.2 0.7 11 54-64 1-11 (157)
124 cd02640 R3H_NRF R3H domain of 31.2 63 0.0014 26.1 3.4 21 242-262 19-40 (60)
125 cd02638 R3H_unknown_1 R3H doma 30.6 98 0.0021 25.4 4.3 29 241-270 19-47 (62)
126 PRK05359 oligoribonuclease; Pr 30.1 1.8E+02 0.004 28.4 7.2 21 324-344 97-117 (181)
127 cd06396 PB1_NBR1 The PB1 domai 29.4 1.3E+02 0.0029 25.9 5.3 55 493-549 14-70 (81)
128 PF14605 Nup35_RRM_2: Nup53/35 28.9 1E+02 0.0022 24.1 4.1 49 488-541 2-51 (53)
129 cd06138 ExoI_N N-terminal DEDD 28.3 1.2E+02 0.0027 29.3 5.7 41 55-120 2-42 (183)
130 TIGR01661 ELAV_HUD_SF ELAV/HuD 27.0 1.3E+02 0.0029 31.8 6.2 58 487-548 269-333 (352)
131 PRK06195 DNA polymerase III su 27.0 1.1E+02 0.0024 32.6 5.5 41 52-120 2-42 (309)
132 TIGR01388 rnd ribonuclease D. 26.9 57 0.0012 35.7 3.3 25 39-63 6-30 (367)
133 PF13893 RRM_5: RNA recognitio 26.2 79 0.0017 24.1 3.2 36 514-549 7-44 (56)
134 cd06135 Orn DEDDh 3'-5' exonuc 26.0 3E+02 0.0065 26.4 7.9 44 53-120 1-44 (173)
135 PLN03121 nucleic acid binding 25.7 1.2E+02 0.0026 31.4 5.2 74 488-573 6-83 (243)
136 PRK07246 bifunctional ATP-depe 25.3 1.2E+02 0.0025 37.0 5.8 45 50-121 6-50 (820)
137 cd06142 RNaseD_exo DEDDy 3'-5' 25.2 5.6E+02 0.012 23.9 10.2 100 320-436 59-162 (178)
138 TIGR01649 hnRNP-L_PTB hnRNP-L/ 25.1 1.2E+02 0.0027 34.2 5.7 55 488-546 3-58 (481)
139 PRK07983 exodeoxyribonuclease 24.4 1.4E+02 0.003 30.2 5.4 39 53-120 2-40 (219)
140 cd06137 DEDDh_RNase DEDDh 3'-5 23.6 29 0.00062 33.2 0.2 39 54-120 1-39 (161)
141 cd06407 PB1_NLP A PB1 domain i 23.2 1.9E+02 0.0041 24.8 5.2 56 491-546 12-68 (82)
142 PF13606 Ank_3: Ankyrin repeat 22.8 64 0.0014 21.9 1.8 17 135-151 14-30 (30)
143 TIGR01649 hnRNP-L_PTB hnRNP-L/ 21.6 1.7E+02 0.0038 33.0 6.0 60 487-550 275-337 (481)
144 PRK10829 ribonuclease D; Provi 21.1 83 0.0018 34.6 3.2 26 38-63 9-34 (373)
145 KOG0144 RNA-binding protein CU 20.7 1.5E+02 0.0033 33.1 4.9 58 494-555 41-109 (510)
No 1
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=100.00 E-value=1.7e-63 Score=512.64 Aligned_cols=246 Identities=38% Similarity=0.600 Sum_probs=197.4
Q ss_pred EEcCcccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeee-ecCC---
Q 006991 30 KQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPF-KLQA--- 105 (622)
Q Consensus 30 ~dVt~~NF~~~l~~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f-~~~~--- 105 (622)
||||++||+++||.|+++|++|+|||||+||||+...+.+. ..+|+++||+++|.+|++|+|+|+|||+| +.++
T Consensus 1 m~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~~--~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~ 78 (262)
T PF04857_consen 1 MEVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPRS--RFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIP 78 (262)
T ss_dssp EEE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-SH--CSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEE
T ss_pred CcccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCcc--ccccHHHHHHHHHHhhcccccceeeEEEeecccccCC
Confidence 89999999999999999999999999999999997654322 89999999999999999999999999999 4444
Q ss_pred CceeeEeeEEeecCccccccCCCCCceeechhHHHHHHHcCCCcchhhhcccccCCHHHHHHHHHHhCCCccccccccCC
Q 006991 106 SKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKSS 185 (622)
Q Consensus 106 ~~y~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~YLs~~eE~~~r~~~~~~~~~~~~~~~~ 185 (622)
.+|.+|+|||++||.. +.|+ |++||+||++||||||+|+++||||+++.||+.++
T Consensus 79 ~~~~~~~~nf~~f~~~--------~~~~-~~~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~---------------- 133 (262)
T PF04857_consen 79 SSYNVWPFNFYLFPLD--------RDFS-QASSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKAR---------------- 133 (262)
T ss_dssp CCEEEEEEEBSTTSTT--------TCEE-EHHHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHH----------------
T ss_pred ceeEEEEeeeeccccc--------ccee-cchhHHHHHHcccCHHHHHHhCCCcccccccchhh----------------
Confidence 5789999999999974 4677 99999999999999999999999999988775421
Q ss_pred CCCCCCcccHHHHHHHHHHHHHHHhhccCCCchhhHHHHHHHHHHHhcCcccCCCCCccccccchHHHHHHHHHHHhccC
Q 006991 186 SSPALSVADTVFIERVRSRVKHWKNACTDSDIKTEAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFSD 265 (622)
Q Consensus 186 ~~~~~~~~d~~fi~~v~~~I~eWl~~~~~~~~~~~~~l~~~l~~~~~~~e~~~~~p~l~l~~~~~~q~~Lv~q~l~~~~~ 265 (622)
T Consensus 134 -------------------------------------------------------------------------------- 133 (262)
T PF04857_consen 134 -------------------------------------------------------------------------------- 133 (262)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CcceeeeccCCCCceEEEEEEccChHHHHHHHHHhhHHHHhhhhccccHHHHHHHHHhCCCCEEechhHHHHHHHHHhcc
Q 006991 266 VLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFL 345 (622)
Q Consensus 266 ~l~~~~v~~k~g~~~~vrvi~~~~~eek~~l~~e~~~~e~e~~~~~~GFr~Vi~~L~~skKpIVGHN~llDL~~iy~~F~ 345 (622)
+.+|||.|++++.+++||||||||++||+|||++|+
T Consensus 134 --------------------------------------------~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~ 169 (262)
T PF04857_consen 134 --------------------------------------------ELLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFI 169 (262)
T ss_dssp --------------------------------------------HHHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHT
T ss_pred --------------------------------------------hhHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhc
Confidence 123788889999999999999999999999999999
Q ss_pred CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCceeecCCC----C-------CCCC-c
Q 006991 346 APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQ----A-------NENE-G 413 (622)
Q Consensus 346 gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p~ve~~~~----~-------~~~~-~ 413 (622)
||||++++||++.++++||.|||||||++... ...++|+.+.+.+.... .++.+..+.. . ..+. .
T Consensus 170 ~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~--~~~~~L~~l~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 246 (262)
T PF04857_consen 170 GPLPETLEEFKELLRELFPRIYDTKYLAEECP--GKSTSLQELAEELGIRR-NPSSISSPEGFPSYDEEKNNFPMFGEKA 246 (262)
T ss_dssp TS--SSHHHHHHHHHHHSSSEEEHHHHHTSTT--TS-SSHHHHHHHTTSTT-----EEE-TTS-------------SS-T
T ss_pred CCCCCCHHHHHHHHHHHCcccccHHHHHHhcc--ccccCHHHHHHHhCCCc-cccccccccccccccccccccccCCCCC
Confidence 99999999999999999999999999998765 24567888888775433 2222222210 1 1234 7
Q ss_pred ccchhhHHHHHHHHHH
Q 006991 414 KIHGHNVVKICQLFGK 429 (622)
Q Consensus 414 h~AGyDA~mTg~vF~~ 429 (622)
|+|||||||||+||++
T Consensus 247 HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 247 HEAGYDAYMTGCVFIK 262 (262)
T ss_dssp TSHHHHHHHHHHHHHH
T ss_pred CCcchHHHHHHHHHcC
Confidence 9999999999999986
No 2
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=99.97 E-value=1.9e-31 Score=258.80 Aligned_cols=119 Identities=17% Similarity=0.355 Sum_probs=103.3
Q ss_pred eEEcCcccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCC-CCHHHHHHHHHhhhhcccceeEEeeeeecCCCc
Q 006991 29 IKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTF-DTPETAYLKAKFAAERFQILQFAICPFKLQASK 107 (622)
Q Consensus 29 i~dVt~~NF~~~l~~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~-dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~ 107 (622)
|.+||+.|.++++..|++.|++++||||||||||+... +...+ .+.+.+|+.+|.||+..++||+|+++++.+++.
T Consensus 2 ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~r---p~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~ 78 (239)
T KOG0304|consen 2 IREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVAR---PIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNL 78 (239)
T ss_pred hhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeee---cCccccCChHHHHHHHHhchhhhhhhheeeeeeccCCCC
Confidence 67999999999999999999999999999999999753 34444 578889999999999999999999999998743
Q ss_pred e----eeEeeEEeecCccccccCCCCCceeechhHHHHHHHcCCCcchhhhccccc
Q 006991 108 V----IAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISY 159 (622)
Q Consensus 108 y----~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~Y 159 (622)
- ..|+|||.-|.-. +-+.+..||+||+++|+||.|...+||+-
T Consensus 79 p~~g~~tWqfNF~dF~~~---------~D~~a~~SIElLr~~Gidf~K~~e~GI~~ 125 (239)
T KOG0304|consen 79 PDCGTDTWQFNFSDFNLE---------KDMYAQDSIELLRRSGIDFEKHREEGIDI 125 (239)
T ss_pred CCCCCceeEEecccCCch---------hhccchhhHHHHHHcCcCHHHHHHcCCCH
Confidence 3 3999999866642 22577899999999999999999999864
No 3
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.96 E-value=5.1e-30 Score=288.03 Aligned_cols=481 Identities=19% Similarity=0.167 Sum_probs=289.7
Q ss_pred cccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCC--ceeeE
Q 006991 34 KTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQAS--KVIAY 111 (622)
Q Consensus 34 ~~NF~~~l~~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~--~y~~~ 111 (622)
|.||+. +..+...|..++|++||+|++|+...+|...+.+|+++.+|++.|.++..|.++|+|+|+|.++.+ .+...
T Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 79 (564)
T KOG1990|consen 1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMST 79 (564)
T ss_pred CCcccc-hhHHHhhcCHHHHHHHhhhhccceecccccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccC
Confidence 578999 999999999999999999999999888899999999999999999999999999999999999883 46667
Q ss_pred eeEEeecCccccccCCCCCceeechhHHHHHHHcCCCcchhhhcccccCCHHHHHHHHHHhCCCccccccccCCCCCCCC
Q 006991 112 PYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKSSSSPALS 191 (622)
Q Consensus 112 ~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~YLs~~eE~~~r~~~~~~~~~~~~~~~~~~~~~~ 191 (622)
++||++||+ ......+ .|+||.+.+.|+.++ +|
T Consensus 80 ~~n~~~~~~-g~~~s~~--~~~~~~~~~~~~~~~------------------~~-------------------------- 112 (564)
T KOG1990|consen 80 GGNFVVWSR-GDSISSP--EFLCQRSPVDFVARQ------------------QE-------------------------- 112 (564)
T ss_pred CCceeeeec-CccccCC--ccceeecchhhhhhh------------------ch--------------------------
Confidence 999999998 4444444 899999999999998 11
Q ss_pred cccHHHHHHHHHHHHHHHhhccCCCch--hhHHHHHHHHHHHhcCcccCCCCCccccccchHHHHHHHHHHHhccCCcce
Q 006991 192 VADTVFIERVRSRVKHWKNACTDSDIK--TEAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFSDVLVP 269 (622)
Q Consensus 192 ~~d~~fi~~v~~~I~eWl~~~~~~~~~--~~~~l~~~l~~~~~~~e~~~~~p~l~l~~~~~~q~~Lv~q~l~~~~~~l~~ 269 (622)
..+..+.-+++....+|+.+....... ..+.+... ..++.+.-+..++|...++++.+.+...+-.+...+.....+
T Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p 191 (564)
T KOG1990|consen 113 NQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVD-ADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLP 191 (564)
T ss_pred hhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccch-hhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhccccc
Confidence 001234455666777777764322100 00000000 001111112346788888888777766555554333333222
Q ss_pred eeeccC-CCCceEEEEEEccChHHHHHHHHHhhH---HHHhhhhccccHHHHHHHHHhCCCCEEechhHHHHHHHHHhcc
Q 006991 270 LIIPAK-GGGTQAVRAVLTSSDEDKDLLKRELQT---FEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFL 345 (622)
Q Consensus 270 ~~v~~k-~g~~~~vrvi~~~~~eek~~l~~e~~~---~e~e~~~~~~GFr~Vi~~L~~skKpIVGHN~llDL~~iy~~F~ 345 (622)
..+.-. .+..+.+.+... +--++....+...+ .+......+.+++ .+..++++|||||+++|+||+|++|+
T Consensus 192 ~~~~~~~~~~~~~~~~~~~-~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~----~~~~tg~~lv~hN~~~dv~y~~~~Fl 266 (564)
T KOG1990|consen 192 PHFALGRSRKLQGLAVAMV-SFWEKHEFAKILIKRGVLETRKERMADELQ----ELLLTGKVLVLHNKLLDVMYRYKNFL 266 (564)
T ss_pred ccceehhccccccchhHHH-HHHHHHHHHHHHHHhcchhhhccchHHHHH----HHHhcCCeEEeeccceeeeeehhhcc
Confidence 211111 111121211111 11122211111111 1111222233443 57789999999999999999999999
Q ss_pred CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhc---CCCCceee-cC------C-CCCCCCcc
Q 006991 346 APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNR---FFAPIEME-IP------N-QANENEGK 414 (622)
Q Consensus 346 gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~---~~~~p~ve-~~------~-~~~~~~~h 414 (622)
+|||+++++|+.. .++||.++||+.++. ..+..+ .++...+..+... ...+++.. ++ . .......|
T Consensus 267 ~~lp~~l~~f~~~-~~~fp~~~~~~~~~~-~~~~~~-~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~ 343 (564)
T KOG1990|consen 267 SPLPSTLEEFTDS-SSMFPNIEDTKRLAK-LSEYQK-LNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLT 343 (564)
T ss_pred cccchhHHHhhhh-hhhhhhhHHHHHhhc-cccccc-hhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHH
Confidence 9999999999999 999999999999876 333332 2344444333321 22222221 00 0 11124558
Q ss_pred cchhhHHHHHHHHHHHHHHhccCCCCC----------CCCc-H--HHHhhhhhhhccccCCCCCCCCCCCccccCCCCCC
Q 006991 415 IHGHNVVKICQLFGKLCSILKITPDAI----------ESSD-D--FLASAINRYANIFYSLPGSSQEPTNEEIRGWTNDK 481 (622)
Q Consensus 415 ~AGyDA~mTg~vF~~l~~~l~~~~~~~----------~s~~-~--~~~~~l~~~~N~l~~~~~~~~~~~d~~~~~l~g~~ 481 (622)
+++|+++.+|..++..+......+... ++.. + .....+..+.|...+.+.++-
T Consensus 344 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~-------------- 409 (564)
T KOG1990|consen 344 EAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGV-------------- 409 (564)
T ss_pred HHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCccc--------------
Confidence 899999999999999998774433211 1111 1 122245555665555444421
Q ss_pred CCCCcCCEEEEeccccccchhHHHHhhhhhhhccc---cc-eEEEEecCce-EEEEecCCCchhHHHHHhhh--cccccc
Q 006991 482 RKVSCEDVVFLWGFRERISAGILKNMLQGSHEVFA---EA-FNVRMVDRSC-AIVVFGKPGLSNTFKNVMNS--KAVSGP 554 (622)
Q Consensus 482 ~~~~~~~vv~i~~f~~~~~~~~i~~~l~~~~~~F~---~~-~~V~~id~t~-a~V~~~~~~~~~~~l~~~~~--~~~~~~ 554 (622)
.+.+ |.++...|+..+....++.....=+ ++ ..+.|.+.-. +.+.-...+-+..+-...+. .+.++|
T Consensus 410 ----f~g~--i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P 483 (564)
T KOG1990|consen 410 ----FDGV--IENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRP 483 (564)
T ss_pred ----ccce--eecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCc
Confidence 1122 2344444444433322221111000 00 1333433333 44444444443333333322 226899
Q ss_pred chhhhcCC-ccccchHHHHHhhhcCCchhhHHHHHHHH
Q 006991 555 LREMVSDG-LKAAGYETYQRVCSSGLWESALADALDKT 591 (622)
Q Consensus 555 l~~~~~~g-~~~a~~~~y~~~c~~~~~~~~~a~~~~~~ 591 (622)
.+.|..++ |....++.|+++|...++........-.+
T Consensus 484 ~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~ 521 (564)
T KOG1990|consen 484 RNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQA 521 (564)
T ss_pred hhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhc
Confidence 99999999 89999999999999999887765544333
No 4
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=99.87 E-value=9.3e-22 Score=191.00 Aligned_cols=119 Identities=18% Similarity=0.304 Sum_probs=102.5
Q ss_pred cceEEcCcccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCH-HHHHHHHHhhhhcccceeEEeeeeecCC
Q 006991 27 WPIKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTP-ETAYLKAKFAAERFQILQFAICPFKLQA 105 (622)
Q Consensus 27 ~~i~dVt~~NF~~~l~~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~-eerY~~~k~~a~~f~iiQ~Gl~~f~~~~ 105 (622)
..|+|||++|+..++..|+++|..+.+|+|||||+|++. ++.+.|.+. +-.|+.+|+||+-.+|||+||++-+.++
T Consensus 18 ~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvA---rPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~G 94 (299)
T COG5228 18 LFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVA---RPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENG 94 (299)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceee---cccccccccchHHHHHHhcccchhhhhheeeeeccccC
Confidence 468999999999999999999999999999999999975 345556554 4589999999999999999999999987
Q ss_pred ---CceeeEeeEEeecCccccccCCCCCceeechhHHHHHHHcCCCcchhhhcccc
Q 006991 106 ---SKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGIS 158 (622)
Q Consensus 106 ---~~y~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~ 158 (622)
+.-.+|+|||-.-+.. -+..++||+.|++.|+||.|.-.-||.
T Consensus 95 N~P~~~sTWQFNF~F~l~~----------dmya~ESieLL~ksgIdFkkHe~~GI~ 140 (299)
T COG5228 95 NKPNGPSTWQFNFEFDLKK----------DMYATESIELLRKSGIDFKKHENLGID 140 (299)
T ss_pred CCCCCCceeEEEEEecchh----------hhcchHHHHHHHHcCCChhhHhhcCCC
Confidence 4577899999966653 267899999999999999987766663
No 5
>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN). ; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.
Probab=99.57 E-value=4.1e-15 Score=125.18 Aligned_cols=75 Identities=15% Similarity=0.263 Sum_probs=54.1
Q ss_pred CCCCCCCcCCEEEEeccccccchhHHHHhhhhhhhccccc--eEEEEecCceEEEEecCCCchhHHHHHhhhccccccch
Q 006991 479 NDKRKVSCEDVVFLWGFRERISAGILKNMLQGSHEVFAEA--FNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKAVSGPLR 556 (622)
Q Consensus 479 g~~~~~~~~~vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~--~~V~~id~t~a~V~~~~~~~~~~~l~~~~~~~~~~~l~ 556 (622)
|+|+.|+|+||+| ++||++||..||.+ +|+++ +.|+|||||||||+++++++++.++.+++.++
T Consensus 1 G~d~~P~RdHVFh-ltFPkeWK~~DI~q-------lFspfG~I~VsWi~dTSAfV~l~~r~~~~~v~~~~~~~~------ 66 (87)
T PF08675_consen 1 GPDPQPSRDHVFH-LTFPKEWKTSDIYQ-------LFSPFGQIYVSWINDTSAFVALHNRDQAKVVMNTLKKNS------ 66 (87)
T ss_dssp SS----SGCCEEE-EE--TT--HHHHHH-------HCCCCCCEEEEEECTTEEEEEECCCHHHHHHHHHHTT-S------
T ss_pred CCCCCCCcceEEE-EeCchHhhhhhHHH-------HhccCCcEEEEEEcCCcEEEEeecHHHHHHHHHHhccCC------
Confidence 7899999999999 68999999999653 55555 69999999999999999999999888776543
Q ss_pred hhhcCCccccchHHHH
Q 006991 557 EMVSDGLKAAGYETYQ 572 (622)
Q Consensus 557 ~~~~~g~~~a~~~~y~ 572 (622)
+-+..+|..|+
T Consensus 67 -----~y~i~tY~ey~ 77 (87)
T PF08675_consen 67 -----SYRIQTYAEYQ 77 (87)
T ss_dssp -----SSEEEEHHHHH
T ss_pred -----ceEEEEHHHHH
Confidence 35667777774
No 6
>PRK07740 hypothetical protein; Provisional
Probab=97.19 E-value=0.0017 Score=66.72 Aligned_cols=89 Identities=17% Similarity=0.227 Sum_probs=63.2
Q ss_pred CCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCceee
Q 006991 324 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEME 403 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p~ve 403 (622)
.+.++||||.-.|+-++-+.+...+... +...++||..++....|-.+..+|.++.+++. +
T Consensus 140 ~~~~lVahna~fD~~fL~~~~~~~~~~~----------~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~g--------i- 200 (244)
T PRK07740 140 GAGVLVAHHAGHDKAFLRHALWRTYRQP----------FTHRLIDTMFLTKLLAHERDFPTLDDALAYYG--------I- 200 (244)
T ss_pred CCCEEEEeCHHHHHHHHHHHHHHhcCCC----------cCCCeechHHHHHHHcCCCCCCCHHHHHHHCC--------c-
Confidence 4679999999999999877664332111 12468999988877665444556777776651 1
Q ss_pred cCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 006991 404 IPNQANENEGKIHGHNVVKICQLFGKLCSILKI 436 (622)
Q Consensus 404 ~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~~ 436 (622)
+. ...|.|-+||++|+.||.++...+..
T Consensus 201 -~~----~~~H~Al~Da~ata~l~~~ll~~~~~ 228 (244)
T PRK07740 201 -PI----PRRHHALGDALMTAKLWAILLVEAQQ 228 (244)
T ss_pred -CC----CCCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 11 12599999999999999999887743
No 7
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=97.06 E-value=0.0042 Score=59.41 Aligned_cols=97 Identities=21% Similarity=0.177 Sum_probs=60.4
Q ss_pred cHHHHHHHHHh--CCCCEEechhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCC-CccchhhHHhhhCcccccCchHHH
Q 006991 313 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFP-QVIDVNYLLKDIGPVKKMTNISAT 388 (622)
Q Consensus 313 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~g-pLP~t~~EFk~~i~~lFP-~I~DTKyLa~~~~~~~~~~~L~~~ 388 (622)
.|..|++.+.+ .+.++||||.=+|+-++-+.+-. -++.. ...| ..+||-.++....+.. ..+|..+
T Consensus 67 ~~~~v~~~l~~~l~~~~lv~hn~~fD~~~l~~~~~~~~~~~~---------~~~~~~~idt~~~~~~~~~~~-~~~L~~l 136 (167)
T cd06131 67 KFAEIADEFLDFIRGAELVIHNASFDVGFLNAELSLLGLGKK---------IIDFCRVIDTLALARKKFPGK-PNSLDAL 136 (167)
T ss_pred CHHHHHHHHHHHHCCCeEEEeChHHhHHHHHHHHHHhCCCcc---------cccCCCceEhHHHHHHHcCCC-CCCHHHH
Confidence 44455544432 45689999999999988655421 11110 0123 3789977776654432 3467777
Q ss_pred HHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHH
Q 006991 389 IAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLC 431 (622)
Q Consensus 389 ~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~ 431 (622)
.+++. ++.. ....|.|.+||+.|+.+|.+|+
T Consensus 137 ~~~~~----------i~~~--~~~~H~Al~Da~~~a~l~~~l~ 167 (167)
T cd06131 137 CKRFG----------IDNS--HRTLHGALLDAELLAEVYLELT 167 (167)
T ss_pred HHHCC----------CCCC--CCCCCChHHHHHHHHHHHHHhC
Confidence 76652 1111 1247999999999999999874
No 8
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.98 E-value=0.0042 Score=66.09 Aligned_cols=95 Identities=14% Similarity=0.171 Sum_probs=64.4
Q ss_pred HHHHHHHHHh--CCCCEEechhHHHHHHHHHhcc---CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHH
Q 006991 314 FREVIDLISA--SQKPLVAHNSLNDFTFIHSKFL---APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISAT 388 (622)
Q Consensus 314 Fr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~---gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~ 388 (622)
|..|++.+.+ .+.++||||.-+|+-+|.+.+. .++| ....+||--|+....|-.+..+|..+
T Consensus 67 f~ev~~~~~~fl~~~~lVaHNa~FD~~fL~~~~~r~~~~~~-------------~~~~idT~~lar~l~~~~~~~~L~~L 133 (309)
T PRK06195 67 FDKIWEKIKHYFNNNLVIAHNASFDISVLRKTLELYNIPMP-------------SFEYICTMKLAKNFYSNIDNARLNTV 133 (309)
T ss_pred HHHHHHHHHHHhCCCEEEEECcHHHHHHHHHHHHHhCCCCC-------------CCCEEEHHHHHHHHcCCCCcCCHHHH
Confidence 4444444433 4689999999999999876542 2333 12368997777765443234456666
Q ss_pred HHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 006991 389 IAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKI 436 (622)
Q Consensus 389 ~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~~ 436 (622)
.+.+. + + ...|.|-+||++|+.+|.+|+..++.
T Consensus 134 ~~~~g--------i--~-----~~~H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 134 NNFLG--------Y--E-----FKHHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred HHHcC--------C--C-----CcccCCHHHHHHHHHHHHHHHHHhcc
Confidence 65541 1 1 13699999999999999999998866
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=96.97 E-value=0.0049 Score=62.65 Aligned_cols=98 Identities=20% Similarity=0.269 Sum_probs=62.3
Q ss_pred cHHHHHHHHHh--CCCCEEechhHHHHHHHHHhc--cCC-CCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHH
Q 006991 313 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKF--LAP-LPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISA 387 (622)
Q Consensus 313 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F--~gp-LP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~ 387 (622)
-|..|++.+.+ .+.++||||.-+|+-||-..| +|+ +|. + .-|-.++||--|+....|-. ..+|..
T Consensus 68 ~f~ev~~~f~~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~----~-----~~~~~~iDTl~lar~~~p~~-~~~L~~ 137 (225)
T TIGR01406 68 KFKEIADEFLDFIGGSELVIHNAAFDVGFLNYELERLGPTIKK----I-----GEFCRVIDTLAMARERFPGQ-RNSLDA 137 (225)
T ss_pred CHHHHHHHHHHHhCCCEEEEEecHHHHHHHHHHHHHhCCCCcc----c-----ccCCCEEEHHHHHHHHcCCC-CCCHHH
Confidence 45555554443 467899999999999998765 342 110 0 01224899988887765432 235665
Q ss_pred HHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 006991 388 TIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 432 (622)
Q Consensus 388 ~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~ 432 (622)
+.+.+. ++. .....|.|-+||.+|+.||..|..
T Consensus 138 L~~~~g----------i~~--~~r~~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 138 LCKRFK----------VDN--SHRTLHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred HHHhcC----------CCC--CCCCCcCHHHHHHHHHHHHHHHHc
Confidence 555441 111 112469999999999999999876
No 10
>cd02637 R3H_PARN R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=96.90 E-value=0.0023 Score=52.55 Aligned_cols=27 Identities=19% Similarity=0.311 Sum_probs=24.5
Q ss_pred CccccccchHHHHHHHHHHHhccCCcc
Q 006991 242 SMTIDVCSERQVQLVLKMLEDFSDVLV 268 (622)
Q Consensus 242 ~l~l~~~~~~q~~Lv~q~l~~~~~~l~ 268 (622)
.+.+++||+|||+|+||++++.||+..
T Consensus 18 ~l~le~cngf~RkLiyq~l~~~~~~~I 44 (65)
T cd02637 18 DLELEPCNGFQRKLIYQTLEQKYPKGI 44 (65)
T ss_pred cccccccccHHHHHHHHHHHHHccccc
Confidence 478899999999999999999999864
No 11
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.86 E-value=0.0071 Score=62.16 Aligned_cols=99 Identities=20% Similarity=0.249 Sum_probs=64.9
Q ss_pred ccHHHHHHHHHh--CCCCEEechhHHHHHHHHHhc--cC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchH
Q 006991 312 RGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKF--LA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNIS 386 (622)
Q Consensus 312 ~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F--~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~ 386 (622)
..|..|++.+.+ .+-++||||.=+|+-||-..| +| ++|.. . .+..++||--|+....|-. ..+|.
T Consensus 71 p~f~ev~~~f~~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~-~--------~~~~~iDTl~lar~~~p~~-~~~L~ 140 (240)
T PRK05711 71 PTFAEVADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKT-N--------TFCKVTDTLAMARRMFPGK-RNSLD 140 (240)
T ss_pred CCHHHHHHHHHHHhCCCEEEEEccHHhHHHHHHHHHHhCCCCCcc-c--------ccCceeeHHHHHHHHcCCC-CCCHH
Confidence 355555555544 456899999999999998665 33 34421 1 1345899988887765432 23566
Q ss_pred HHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 006991 387 ATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 432 (622)
Q Consensus 387 ~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~ 432 (622)
.+...+. ++ ......|.|-+||.+|+.||++|..
T Consensus 141 aL~~~~g----------i~--~~~r~~H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 141 ALCKRYG----------ID--NSHRTLHGALLDAEILAEVYLAMTG 174 (240)
T ss_pred HHHHHCC----------CC--CCCCCCCCHHHHHHHHHHHHHHHHC
Confidence 6555441 11 1112369999999999999999875
No 12
>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=96.86 E-value=0.0062 Score=60.11 Aligned_cols=83 Identities=19% Similarity=0.159 Sum_probs=54.5
Q ss_pred CCCCEEechhHHHHHHHHHhc--cCCCCCCHHHHHHHHHccC-C-CccchhhHHhhhCcccccCchHHHHHHHHhcCCCC
Q 006991 324 SQKPLVAHNSLNDFTFIHSKF--LAPLPPNMNEFICSLRLAF-P-QVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAP 399 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F--~gpLP~t~~EFk~~i~~lF-P-~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~ 399 (622)
.+.++||||.-+|+.||.+.+ +|--. ..| | ..+||.-|+....+ ...|..+.+.+ ..+
T Consensus 101 ~~~~lVaHna~FD~~fL~~~~~~~~~~~-----------~~~~~~~~lDt~~la~~~~~---~~~L~~l~~~~----gi~ 162 (189)
T cd06134 101 TRAILVGHNAHFDLGFLNAAVARCKIKR-----------NPFHPFSTFDTATLAGLAYG---QTVLAKACQAA----GIE 162 (189)
T ss_pred CCCeEEEecchhhHHHHHHHHHHhCCCC-----------CCCCCCcEEEHHHHHHHHhC---CCcHHHHHHHC----CCC
Confidence 368999999999999998655 22100 112 2 27999988876543 23455544432 111
Q ss_pred ceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 006991 400 IEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 432 (622)
Q Consensus 400 p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~ 432 (622)
.. ....|.|.+||++|+.+|.+|..
T Consensus 163 ------~~--~~~~H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 163 ------FD--NKEAHSALYDTQKTAELFCKIVN 187 (189)
T ss_pred ------CC--CCCCcChHHHHHHHHHHHHHHHH
Confidence 11 12469999999999999999875
No 13
>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function.
Probab=96.84 E-value=0.0022 Score=52.03 Aligned_cols=59 Identities=15% Similarity=0.202 Sum_probs=46.0
Q ss_pred CcCCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecCceEEEEecCCCchhHHHHH
Q 006991 485 SCEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNV 545 (622)
Q Consensus 485 ~~~~vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~t~a~V~~~~~~~~~~~l~~ 545 (622)
.|++.||+.| -.++++.||+.-+..-+..-++ +.|.||||+|+=|+|.+.+.|...|.+
T Consensus 3 ~rpeavhirG-vd~lsT~dI~~y~~~y~~~~~~-~~IEWIdDtScNvvf~d~~~A~~AL~~ 61 (62)
T PF10309_consen 3 IRPEAVHIRG-VDELSTDDIKAYFSEYFDEEGP-FRIEWIDDTSCNVVFKDEETAARALVA 61 (62)
T ss_pred ceeceEEEEc-CCCCCHHHHHHHHHHhcccCCC-ceEEEecCCcEEEEECCHHHHHHHHHc
Confidence 4788999988 5779999999877642111122 699999999999999999888877664
No 14
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.83 E-value=0.0046 Score=63.12 Aligned_cols=88 Identities=17% Similarity=0.216 Sum_probs=59.1
Q ss_pred hCCCCEEechhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCC-CccchhhHHhhhCccc-ccCchHHHHHHHHhcCCCC
Q 006991 323 ASQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFP-QVIDVNYLLKDIGPVK-KMTNISATIAYLKNRFFAP 399 (622)
Q Consensus 323 ~skKpIVGHN~llDL~~iy~~F~g-pLP~t~~EFk~~i~~lFP-~I~DTKyLa~~~~~~~-~~~~L~~~~~~l~~~~~~~ 399 (622)
..+.||||||.-+|+-+|-+.+.. -+|. +.| .++||-.|+....+.. +...|+.+.+.+.
T Consensus 91 ~~~~~lVahNa~FD~~fL~~~~~r~~~~~-----------~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~g------ 153 (232)
T PRK07942 91 ARGVPVVVFNAPYDLTVLDRELRRHGLPS-----------LVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYG------ 153 (232)
T ss_pred hcCCEEEEeCcHhhHHHHHHHHHHcCCCC-----------ccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcC------
Confidence 467899999999999988766521 1111 022 2679987776654432 2345666665441
Q ss_pred ceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 006991 400 IEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 435 (622)
Q Consensus 400 p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~ 435 (622)
++ ....|.|..||.+|+.||.+|+..++
T Consensus 154 ----i~----~~~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 154 ----VR----LDNAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred ----CC----CCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 11 12379999999999999999998764
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=96.79 E-value=0.0068 Score=61.12 Aligned_cols=99 Identities=20% Similarity=0.236 Sum_probs=61.6
Q ss_pred cHHHHHHHHHh--CCCCEEechhHHHHHHHHHhcc--CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcc-c-ccCchH
Q 006991 313 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFL--APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPV-K-KMTNIS 386 (622)
Q Consensus 313 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~--gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~-~-~~~~L~ 386 (622)
.|..|+..+.+ .+.++||||.-+|+-+|-+.|. +..|. ....++||.-++....|. + ...+|.
T Consensus 73 ~~~ev~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~-----------~~~~~~dtl~l~~~~~~~~~~~~~~L~ 141 (217)
T TIGR00573 73 DFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVEP-----------KTNDVIDTTDTLQYARPEFPGKRNTLD 141 (217)
T ss_pred CHHHHHHHHHHHhCCCEEEEeccHHHHHHHHHHHHHhcCCCC-----------CccceecHHHHHHHHHHhCCCCCCCHH
Confidence 34444444433 4679999999999999988764 11110 113467886666544332 2 223566
Q ss_pred HHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 006991 387 ATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 434 (622)
Q Consensus 387 ~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l 434 (622)
.+.+.+. ++.. ....|.|..||.+|+.+|.+|+...
T Consensus 142 ~l~~~~g----------l~~~--~~~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 142 ALCKRYE----------ITNS--HRALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred HHHHHcC----------CCCC--CcccCCHHHHHHHHHHHHHHHHhcc
Confidence 6665541 1111 1247999999999999999998854
No 16
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.74 E-value=0.0091 Score=63.69 Aligned_cols=97 Identities=16% Similarity=0.199 Sum_probs=65.2
Q ss_pred cHHHHHHHHHh--CCCCEEechhHHHHHHHHHhcc--C-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHH
Q 006991 313 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFL--A-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISA 387 (622)
Q Consensus 313 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~--g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~ 387 (622)
-|..|++.+.+ .+.++||||.=+|+-+|.+.|- | ++|. ...+||.-|+....+-.+...|..
T Consensus 80 ~f~ev~~~l~~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~-------------~~~ldTl~lar~~~~~~~~~kL~~ 146 (313)
T PRK06063 80 QFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPV-------------DQVMCTVELARRLGLGLPNLRLET 146 (313)
T ss_pred CHHHHHHHHHHHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCC-------------CCEEehHHHHHHhccCCCCCCHHH
Confidence 35555555543 4689999999999999987652 2 2331 236899888876643223345666
Q ss_pred HHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 006991 388 TIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKI 436 (622)
Q Consensus 388 ~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~~ 436 (622)
+.+++. | + ....|.|-+||.+|+.||.++...++.
T Consensus 147 l~~~~g--------i--~----~~~~H~Al~DA~ata~l~~~ll~~~~~ 181 (313)
T PRK06063 147 LAAHWG--------V--P----QQRPHDALDDARVLAGILRPSLERARE 181 (313)
T ss_pred HHHHcC--------C--C----CCCCCCcHHHHHHHHHHHHHHHHHHHh
Confidence 665541 1 1 134799999999999999998887744
No 17
>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=96.66 E-value=0.011 Score=55.57 Aligned_cols=88 Identities=19% Similarity=0.228 Sum_probs=58.8
Q ss_pred cHHHHHHHHHh--CCCCEEechhHHHHHHHHHhcc--C-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHH
Q 006991 313 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFL--A-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISA 387 (622)
Q Consensus 313 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~--g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~ 387 (622)
.|..+++.+.+ .++++||||.=.|+-++-+.+- | +.|. + ..+||.-++....+..+..+|..
T Consensus 63 ~~~~v~~~l~~~l~~~~lv~hn~~fD~~~l~~~~~~~g~~~~~------------~-~~idt~~~~~~~~~~~~~~~L~~ 129 (156)
T cd06130 63 TFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPPP------------Y-QYLCTVRLARRVWPLLPNHKLNT 129 (156)
T ss_pred CHHHHHHHHHHHhCCCEEEEeChHHhHHHHHHHHHHcCCCCCC------------C-CEEEHHHHHHHHhccCCCCCHHH
Confidence 34555544443 4689999999999999876652 2 1221 2 37899777766554334567777
Q ss_pred HHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHH
Q 006991 388 TIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFG 428 (622)
Q Consensus 388 ~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~ 428 (622)
+.+++. + + .. .|.|-+||..|+.+|+
T Consensus 130 l~~~~g--------~--~----~~-~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 130 VAEHLG--------I--E----LN-HHDALEDARACAEILL 155 (156)
T ss_pred HHHHcC--------C--C----cc-CcCchHHHHHHHHHHh
Confidence 777652 1 1 12 7999999999999985
No 18
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.59 E-value=0.013 Score=62.66 Aligned_cols=86 Identities=22% Similarity=0.240 Sum_probs=61.4
Q ss_pred CCCCEEechhHHHHHHHHHhc--cCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCce
Q 006991 324 SQKPLVAHNSLNDFTFIHSKF--LAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIE 401 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F--~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p~ 401 (622)
.+.++||||.-+|+-+|.+.| +|. |. ....++||-.++....+..+..+|..+.+.+.
T Consensus 87 ~~~~lVaHNa~FD~~fL~~~~~~~gl-~~-----------~~~~~iDtl~la~~~~~~~~~~kL~~L~~~lg-------- 146 (313)
T PRK06807 87 HTNVIVAHNASFDMRFLKSNVNMLGL-PE-----------PKNKVIDTVFLAKKYMKHAPNHKLETLKRMLG-------- 146 (313)
T ss_pred cCCeEEEEcHHHHHHHHHHHHHHcCC-CC-----------CCCCEeeHHHHHHHHhCCCCCCCHHHHHHHcC--------
Confidence 367899999999999998876 222 21 11237899887776654333446777666551
Q ss_pred eecCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 006991 402 MEIPNQANENEGKIHGHNVVKICQLFGKLCSILKI 436 (622)
Q Consensus 402 ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~~ 436 (622)
++. ..|.|=+||++|+.||.+++...+.
T Consensus 147 --i~~-----~~H~Al~DA~~ta~l~~~l~~~~~~ 174 (313)
T PRK06807 147 --IRL-----SSHNAFDDCITCAAVYQKCASIEEE 174 (313)
T ss_pred --CCC-----CCcChHHHHHHHHHHHHHHHHhhhh
Confidence 111 4799999999999999999998864
No 19
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.59 E-value=0.016 Score=57.68 Aligned_cols=91 Identities=20% Similarity=0.222 Sum_probs=55.5
Q ss_pred HHHHHHHHHh--CCCCEEechhHHHHHHHHHhcc----CCCCCCHHHHHHHHHccCCCccchhhHHhhh--Cccc---cc
Q 006991 314 FREVIDLISA--SQKPLVAHNSLNDFTFIHSKFL----APLPPNMNEFICSLRLAFPQVIDVNYLLKDI--GPVK---KM 382 (622)
Q Consensus 314 Fr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~----gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~--~~~~---~~ 382 (622)
|..|++.+.+ .+.++||||.=+|+.+|-..|. .++|. ..+||.-++... ..+. +.
T Consensus 98 ~~~vl~~~~~~i~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~--------------~~id~~~l~~~~~~~~~~~~~~~ 163 (202)
T PRK09145 98 EEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPN--------------PLIEVSALYYDKKERHLPDAYID 163 (202)
T ss_pred HHHHHHHHHHHHcCCeEEEeCHHHHHHHHHHHHHHhcCCCCCC--------------CeeeHHHHHHHHhhccCCCcccC
Confidence 3444444433 4789999999999999875542 23332 256776554221 1111 12
Q ss_pred CchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 006991 383 TNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 432 (622)
Q Consensus 383 ~~L~~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~ 432 (622)
.+|..+.+.+. ++. ...|.|-.||++|+.||.+|..
T Consensus 164 ~~L~~l~~~~g----------i~~----~~~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 164 LRFDAILKHLD----------LPV----LGRHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCHHHHHHHcC----------CCC----CCCCCcHHHHHHHHHHHHHHHh
Confidence 35666665541 111 2369999999999999999865
No 20
>PRK05168 ribonuclease T; Provisional
Probab=96.53 E-value=0.0068 Score=60.96 Aligned_cols=87 Identities=18% Similarity=0.112 Sum_probs=57.7
Q ss_pred CCCCEEechhHHHHHHHHHhc--cCCCCCCHHHHHHHHHccCC-CccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 006991 324 SQKPLVAHNSLNDFTFIHSKF--LAPLPPNMNEFICSLRLAFP-QVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 400 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F--~gpLP~t~~EFk~~i~~lFP-~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p 400 (622)
.+.++||||.=+|+-||.+.+ +|-.. ..++| .++||.-|+....+ ...|..+.+.+ ..+
T Consensus 113 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~----------~~~~~~~~iDt~~lar~~~~---~~~L~~l~~~~----gl~- 174 (211)
T PRK05168 113 NRAILVAHNAHFDLSFLMAAAERAGLKR----------NPFHPFSTFDTATLSGLALG---QTVLAKACQAA----GIE- 174 (211)
T ss_pred CCceEEEeccHHhHHHHHHHHHHhCCCC----------CCCCCCcEeeHHHHHHHHcC---CCCHHHHHHHC----CCC-
Confidence 378999999999999998655 22100 01133 38999988876533 22455544432 111
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 006991 401 EMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 435 (622)
Q Consensus 401 ~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~ 435 (622)
. .....|.|-+||+.|+.+|.+|...++
T Consensus 175 -----~--~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 175 -----F--DNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred -----C--CCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 0 012479999999999999999999874
No 21
>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=96.49 E-value=0.0089 Score=59.59 Aligned_cols=86 Identities=15% Similarity=0.125 Sum_probs=56.0
Q ss_pred CCCCEEechhHHHHHHHHHhc--cCCCCCCHHHHHHHHHccCC-CccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 006991 324 SQKPLVAHNSLNDFTFIHSKF--LAPLPPNMNEFICSLRLAFP-QVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 400 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F--~gpLP~t~~EFk~~i~~lFP-~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p 400 (622)
.+.++||||.=+|+.||-+.+ +|..+..+ -| .++||--|+....| ..+|..+.+.+ ..+.
T Consensus 104 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~----------~~~~~lDTl~lar~~~~---~~~L~~l~~~~----gi~~ 166 (200)
T TIGR01298 104 QRAILVGHNANFDLGFLNAAVERTSLKRNPF----------HPFSTFDTATLAGLAYG---QTVLAKACQAA----GXDF 166 (200)
T ss_pred CCCEEEEECchhhHHHHHHHHHHhCCCCCCC----------CCCcEEEHHHHHHHHcC---cccHHHHHHHc----CCCc
Confidence 467899999999999998766 23211100 02 27899777765432 22344444433 1111
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 006991 401 EMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 434 (622)
Q Consensus 401 ~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l 434 (622)
. ....|.|-+||++|+.+|.+|...+
T Consensus 167 ~--------~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 167 D--------STQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred c--------ccchhhhHHhHHHHHHHHHHHHHHH
Confidence 0 1247999999999999999999877
No 22
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.48 E-value=0.015 Score=59.64 Aligned_cols=96 Identities=11% Similarity=0.115 Sum_probs=61.7
Q ss_pred HHHHHHHHHh--CCCCEEechhHHHHHHHHHhc---cC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCccc-------
Q 006991 314 FREVIDLISA--SQKPLVAHNSLNDFTFIHSKF---LA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVK------- 380 (622)
Q Consensus 314 Fr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F---~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~------- 380 (622)
|..|++.+.+ .+.++||||.=+|+-++-+.+ .+ ++| +.++||=.|+....+-.
T Consensus 116 ~~evl~~l~~~~~~~~lVaHna~FD~~fL~~~l~~~~~~~~~--------------~~~iDTl~Lar~l~~~~~~~~~~~ 181 (239)
T PRK09146 116 LERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIE--------------FPVIDTMEIEARIQRKQAGGLWNR 181 (239)
T ss_pred HHHHHHHHHHHhCCCEEEEECHHHHHHHHHHHHHHhcCCCCC--------------CceechHHHHHHHcccccccccch
Confidence 4555555544 468999999999999997654 22 222 23689988877643211
Q ss_pred ------ccCchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhccC
Q 006991 381 ------KMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKIT 437 (622)
Q Consensus 381 ------~~~~L~~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~~~ 437 (622)
+.-.|..+.+.+ . ++ ....|.|-.||++|+.+|..++..++..
T Consensus 182 ~~~~~~~~~~L~~l~~~~----g------l~----~~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 182 LKGKKPESIRLADSRLRY----G------LP----AYSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred hccCCCCCCCHHHHHHHc----C------CC----CCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 112344433332 1 11 1236999999999999999999888554
No 23
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=96.37 E-value=0.013 Score=55.71 Aligned_cols=76 Identities=16% Similarity=0.163 Sum_probs=50.1
Q ss_pred CCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCceee
Q 006991 324 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEME 403 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p~ve 403 (622)
.+.+|||||.-.|+-+|-. .-|.++||-.|+....+..+.-+|+.+...+.. ..+.
T Consensus 75 ~~~vlVgHn~~fD~~fL~~-------------------~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~-----~~i~ 130 (150)
T cd06145 75 PDTILVGHSLENDLKALKL-------------------IHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLG-----RDIQ 130 (150)
T ss_pred CCCEEEEcChHHHHHHhhc-------------------cCCCEEEcHHhccccCCCCCChhHHHHHHHHCC-----ccee
Confidence 3589999999999998732 236789998887664432223356665554421 1111
Q ss_pred cCCCCCCCCcccchhhHHHHHHHHH
Q 006991 404 IPNQANENEGKIHGHNVVKICQLFG 428 (622)
Q Consensus 404 ~~~~~~~~~~h~AGyDA~mTg~vF~ 428 (622)
. ....|.|-.||.+|+.+|.
T Consensus 131 --~---~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 131 --Q---GEGGHDSVEDARAALELVK 150 (150)
T ss_pred --C---CCCCCCcHHHHHHHHHHhC
Confidence 0 0246999999999999883
No 24
>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=96.27 E-value=0.012 Score=56.46 Aligned_cols=75 Identities=15% Similarity=0.149 Sum_probs=51.1
Q ss_pred CCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCccc---ccCchHHHHHHHHhcCCCCce
Q 006991 325 QKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVK---KMTNISATIAYLKNRFFAPIE 401 (622)
Q Consensus 325 kKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~---~~~~L~~~~~~l~~~~~~~p~ 401 (622)
..+|||||.-+|+-+|=. ..|.++||-.|+....+.. +.-+|..+...+-+
T Consensus 84 ~~vlVgHn~~fD~~fL~~-------------------~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~------- 137 (161)
T cd06137 84 DTILVGHSLQNDLDALRM-------------------IHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLG------- 137 (161)
T ss_pred CcEEEeccHHHHHHHHhC-------------------cCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCC-------
Confidence 489999999999987731 1467999998888765532 34566666654311
Q ss_pred eecCCCCCCCCcccchhhHHHHHHHHH
Q 006991 402 MEIPNQANENEGKIHGHNVVKICQLFG 428 (622)
Q Consensus 402 ve~~~~~~~~~~h~AGyDA~mTg~vF~ 428 (622)
+ +.+.+ ...|.|-.||.+|+.+|+
T Consensus 138 ~--~~~~~-~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 138 L--KIQGG-GEGHDSLEDALAAREVVL 161 (161)
T ss_pred c--hhcCC-CCCCCcHHHHHHHHHHhC
Confidence 1 11110 246999999999999884
No 25
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=96.24 E-value=0.021 Score=57.84 Aligned_cols=94 Identities=15% Similarity=-0.018 Sum_probs=60.2
Q ss_pred cHHHHHHHHHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHH
Q 006991 313 GFREVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYL 392 (622)
Q Consensus 313 GFr~Vi~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l 392 (622)
-|..|++.+. ...++||||.-+|.-++- .+ --..+||=-|+....|-.+ .+++.+...+
T Consensus 63 ~~~ev~~~~~-~~~~lVaHNa~FD~~~L~-----~~--------------~~~~idTl~lar~l~p~~~-~~l~~L~~~~ 121 (219)
T PRK07983 63 WIEDVIPHYY-GSEWYVAHNASFDRRVLP-----EM--------------PGEWICTMKLARRLWPGIK-YSNMALYKSR 121 (219)
T ss_pred CHHHHHHHHc-CCCEEEEeCcHhhHHHHh-----Cc--------------CCCcEeHHHHHHHHccCCC-CCHHHHHHHc
Confidence 4555665553 467999999999987762 11 1247999888877655322 3444444433
Q ss_pred HhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 006991 393 KNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKI 436 (622)
Q Consensus 393 ~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~~ 436 (622)
... +..+ .....|.|-+||+.|+.+|.+|....|.
T Consensus 122 ----~l~--~~~~---~~~~aHrAl~Da~ata~ll~~l~~~~~~ 156 (219)
T PRK07983 122 ----KLN--VQTP---PGLHHHRALYDCYITAALLIDIMNTSGW 156 (219)
T ss_pred ----CCC--CCCC---CCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 111 1001 1134799999999999999999987765
No 26
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=95.98 E-value=0.034 Score=51.33 Aligned_cols=79 Identities=15% Similarity=0.105 Sum_probs=50.4
Q ss_pred CCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccC-CCccchhhHHhhhCcccccCchHHHH-HHHHhcCCCCcee
Q 006991 325 QKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAF-PQVIDVNYLLKDIGPVKKMTNISATI-AYLKNRFFAPIEM 402 (622)
Q Consensus 325 kKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lF-P~I~DTKyLa~~~~~~~~~~~L~~~~-~~l~~~~~~~p~v 402 (622)
+.++||||.=.|+-++...|..-- ...+ ...+||+.++....+..+...+..+. ..+ ..
T Consensus 79 ~~~~v~~n~~fD~~~l~~~~~~~~-----------~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~----~~---- 139 (159)
T cd06127 79 GRVLVAHNASFDLRFLNRELRRLG-----------GPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERY----GI---- 139 (159)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHhC-----------CCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHc----CC----
Confidence 379999999999887776553100 1122 34889998887766544444444432 111 00
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHHH
Q 006991 403 EIPNQANENEGKIHGHNVVKICQLFG 428 (622)
Q Consensus 403 e~~~~~~~~~~h~AGyDA~mTg~vF~ 428 (622)
.....|.|-+||.+|+.||.
T Consensus 140 ------~~~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 140 ------PLEGAHRALADALATAELLL 159 (159)
T ss_pred ------CCCCCCCcHHHHHHHHHHhC
Confidence 12357999999999999983
No 27
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=95.72 E-value=0.062 Score=54.78 Aligned_cols=98 Identities=21% Similarity=0.250 Sum_probs=61.3
Q ss_pred cHHHHHHHHH---hCCCCEEechh-HHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHH
Q 006991 313 GFREVIDLIS---ASQKPLVAHNS-LNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISA 387 (622)
Q Consensus 313 GFr~Vi~~L~---~skKpIVGHN~-llDL~~iy~~F~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~ 387 (622)
-|..|++.+. +....+||||. -+|+-++-+.|.. .+|.. .-..+||--++....|-.+..+|..
T Consensus 65 ~f~ev~~~~~~fi~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~-----------~~~~iDt~~l~~~~~~~~~~~~L~~ 133 (232)
T PRK06309 65 KFPEAYQKFIEFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPP-----------TLRTIDSLKWAQKYRPDLPKHNLQY 133 (232)
T ss_pred CHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHcCCCCC-----------CCcEEeHHHHHHHHcCCCCCCCHHH
Confidence 3444444443 34568999994 7999888766521 11110 1237899777776544222345666
Q ss_pred HHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 006991 388 TIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 435 (622)
Q Consensus 388 ~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~ 435 (622)
+..... + + ....|.|-+||+.|+.||.+|...++
T Consensus 134 l~~~~~--------~--~----~~~aH~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 134 LRQVYG--------F--E----ENQAHRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred HHHHcC--------C--C----CCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 555441 1 1 13489999999999999999987664
No 28
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=95.71 E-value=0.078 Score=50.11 Aligned_cols=84 Identities=24% Similarity=0.215 Sum_probs=55.7
Q ss_pred CCCEEechh-HHHHHHHHHhcc---CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 006991 325 QKPLVAHNS-LNDFTFIHSKFL---APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 400 (622)
Q Consensus 325 kKpIVGHN~-llDL~~iy~~F~---gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p 400 (622)
+.++||||. =.|+-++-..+. .+.|. +-.++||.-++....+.. ..+|.++.+.+.-
T Consensus 80 ~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~------------~~~~iD~~~~~~~~~~~~-~~~L~~l~~~~~~------ 140 (169)
T smart00479 80 GKILVAGNALNFDLRFLKLEHPRLGIKDPP------------KNPVIDTLKLARALNPGR-KYSLKKLAERLGL------ 140 (169)
T ss_pred CCEEEEeCCHHHhHHHHHHHHHHhCCCCCc------------CCCeeEHHHHHHHHCCCC-CCCHHHHHHHCCC------
Confidence 468899998 889888776552 22331 112789987776654422 4566776665521
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 006991 401 EMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 434 (622)
Q Consensus 401 ~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l 434 (622)
+. .+..|.|-+||.+|+.||.+|...+
T Consensus 141 ----~~---~~~~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 141 ----EV---IGRAHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred ----CC---CCCCcCcHHHHHHHHHHHHHHHHHh
Confidence 11 1226999999999999999998754
No 29
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.65 E-value=0.049 Score=65.40 Aligned_cols=100 Identities=19% Similarity=0.165 Sum_probs=66.0
Q ss_pred cHHHHHHHHHh--CCCCEEechhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHH
Q 006991 313 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATI 389 (622)
Q Consensus 313 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~ 389 (622)
-|..|+..+.+ .+.++||||.=+|+.++...|.. ..|- ..| .+||-.|+...-|-.+..+|..+.
T Consensus 72 ~~~ev~~~~~~~l~~~~lVaHN~~FD~~fL~~~~~~~g~~~-----------~~~-~iDT~~la~~~~p~~~~~~L~~L~ 139 (820)
T PRK07246 72 DFSQVARHIYDLIEDCIFVAHNVKFDANLLAEALFLEGYEL-----------RTP-RVDTVELAQVFFPTLEKYSLSHLS 139 (820)
T ss_pred CHHHHHHHHHHHhCCCEEEEECcHHHHHHHHHHHHHcCCCC-----------CCC-ceeHHHHHHHHhCCCCCCCHHHHH
Confidence 34444444432 47899999999999999876521 1110 012 479988877665533445677766
Q ss_pred HHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhccCC
Q 006991 390 AYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKITP 438 (622)
Q Consensus 390 ~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~~~~ 438 (622)
+.+. + +. ...|.|-.||.+|+.+|.+|...++.-+
T Consensus 140 ~~lg--------l--~~----~~~H~Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 140 RELN--------I--DL----ADAHTAIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred HHcC--------C--CC----CCCCCHHHHHHHHHHHHHHHHHHHhhcC
Confidence 6551 1 11 2469999999999999999999886533
No 30
>PRK07883 hypothetical protein; Validated
Probab=95.61 E-value=0.081 Score=60.86 Aligned_cols=87 Identities=18% Similarity=0.133 Sum_probs=58.7
Q ss_pred CCCEEechhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCc--ccccCchHHHHHHHHhcCCCCce
Q 006991 325 QKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGP--VKKMTNISATIAYLKNRFFAPIE 401 (622)
Q Consensus 325 kKpIVGHN~llDL~~iy~~F~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~--~~~~~~L~~~~~~l~~~~~~~p~ 401 (622)
+.++||||.=+|+-+|-..|.. -+|. ..+..+||-.++...-+ -.+..+|.++.+++. .+
T Consensus 95 ~~~lVaHNa~FD~~fL~~~~~r~g~~~-----------~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~g----i~-- 157 (557)
T PRK07883 95 GAVLVAHNAPFDIGFLRAAAARCGYPW-----------PGPPVLCTVRLARRVLPRDEAPNVRLSTLARLFG----AT-- 157 (557)
T ss_pred CCEEEEeCcHHHHHHHHHHHHHcCCCC-----------CCCCcEecHHHHHHhcccCCCCCCCHHHHHHHCC----cc--
Confidence 6899999999999998766521 1110 01246899777766443 113345666665441 11
Q ss_pred eecCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 006991 402 MEIPNQANENEGKIHGHNVVKICQLFGKLCSILKI 436 (622)
Q Consensus 402 ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~~ 436 (622)
. ...|.|-.||.+|+.+|.++...++.
T Consensus 158 ----~----~~~H~Al~DA~ata~l~~~l~~~~~~ 184 (557)
T PRK07883 158 ----T----TPTHRALDDARATVDVLHGLIERLGN 184 (557)
T ss_pred ----c----CCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 1 23699999999999999999998864
No 31
>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=95.36 E-value=0.049 Score=51.71 Aligned_cols=75 Identities=16% Similarity=0.163 Sum_probs=43.7
Q ss_pred CCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcc-cccCchHHHHHHHHhcCCCCcee
Q 006991 324 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPV-KKMTNISATIAYLKNRFFAPIEM 402 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~-~~~~~L~~~~~~l~~~~~~~p~v 402 (622)
.+.++||||.=+|+-++- .+.|. ..++||=.+.....+. .+.-+|..+.+.+-. +
T Consensus 76 ~~~vlVgHn~~fD~~~L~----~~~~~-------------~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lg-------i 131 (152)
T cd06144 76 KGRILVGHALKNDLKVLK----LDHPK-------------KLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLG-------L 131 (152)
T ss_pred CCCEEEEcCcHHHHHHhc----CcCCC-------------ccEEEeEEeeccccccCCCChhHHHHHHHHcC-------c
Confidence 358999999999997774 12221 1367874332221221 123456665554211 1
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHH
Q 006991 403 EIPNQANENEGKIHGHNVVKICQLF 427 (622)
Q Consensus 403 e~~~~~~~~~~h~AGyDA~mTg~vF 427 (622)
++ . ...|.|..||+.|+.+|
T Consensus 132 ~~--~---~~~H~Al~DA~at~~l~ 151 (152)
T cd06144 132 DI--Q---EGEHSSVEDARAAMRLY 151 (152)
T ss_pred cc--C---CCCcCcHHHHHHHHHHh
Confidence 11 1 23699999999999988
No 32
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=95.36 E-value=0.065 Score=66.49 Aligned_cols=105 Identities=20% Similarity=0.252 Sum_probs=72.9
Q ss_pred HhhhhccccHHHHHHHHHh--CCCCEEechhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccc
Q 006991 305 FEQNKRVRGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKK 381 (622)
Q Consensus 305 ~e~~~~~~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~ 381 (622)
++.+.++.-+..|++.+.+ .+.++||||.-+|+-+|-+.|.. -+|. +...++||--++..+.|-.+
T Consensus 248 ~e~L~~ap~~~evl~~f~~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~-----------~~~~~IDTl~lar~l~p~~k 316 (1213)
T TIGR01405 248 QDMLENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEP-----------LENPVIDTLELARALNPEYK 316 (1213)
T ss_pred HHHHhCCCCHHHHHHHHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCc-----------cCCCEeEHHHHHHHHhccCC
Confidence 3445566667777766655 57899999999999999887632 1121 11347899888877655334
Q ss_pred cCchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 006991 382 MTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 434 (622)
Q Consensus 382 ~~~L~~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l 434 (622)
..+|..+.+.+. + +. ...|.|-+||.+|+.||.+|...+
T Consensus 317 ~~kL~~Lak~lg--------i--~~----~~~HrAl~DA~aTa~I~~~ll~~l 355 (1213)
T TIGR01405 317 SHRLGNICKKLG--------V--DL----DDHHRADYDAEATAKVFKVMVEQL 355 (1213)
T ss_pred CCCHHHHHHHcC--------C--CC----CCCcCHHHHHHHHHHHHHHHHHHH
Confidence 556777666551 1 11 126999999999999999999877
No 33
>PRK06722 exonuclease; Provisional
Probab=95.29 E-value=0.09 Score=55.33 Aligned_cols=98 Identities=11% Similarity=0.152 Sum_probs=56.9
Q ss_pred ccHHHHHHHHHh--CCCCEEechhHHHHHHHHHhc--cC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCc-c-cccCc
Q 006991 312 RGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKF--LA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGP-V-KKMTN 384 (622)
Q Consensus 312 ~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F--~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~-~-~~~~~ 384 (622)
..|..|++.+.+ .+.++|+||.-.|+-++-+.+ +| +.|... +-..+||.-++....+ + ....+
T Consensus 75 P~f~eVl~ef~~fig~~~lvahna~FD~~FL~~~l~~~gi~~p~~~----------~~~~idl~~la~~~~~~l~~~~~s 144 (281)
T PRK06722 75 EKFPQIIEKFIQFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPCME----------KERRIDLQKFVFQAYEELFEHTPS 144 (281)
T ss_pred CCHHHHHHHHHHHHCCCcEEEEEeHHHHHHHHHHHHHcCCCCCccc----------ccchhHHHHHHHHHhhhhccCCCC
Confidence 344445544443 346778788888998888754 33 223210 0113566544433211 1 12346
Q ss_pred hHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 006991 385 ISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 432 (622)
Q Consensus 385 L~~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~ 432 (622)
|+.+.+++. ++. .+..|.|-.||.+||.+|++|..
T Consensus 145 L~~l~~~lg----------L~~---~g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 145 LQSAVEQLG----------LIW---EGKQHRALADAENTANILLKAYS 179 (281)
T ss_pred HHHHHHHCC----------CCC---CCCCcCcHHHHHHHHHHHHHHhc
Confidence 777777651 111 23479999999999999999984
No 34
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=95.19 E-value=0.1 Score=52.04 Aligned_cols=83 Identities=12% Similarity=0.224 Sum_probs=48.2
Q ss_pred CCCCEEechh-HHHHHHHHHhccCCCCCCHHHHHHHHHccCCC-ccchhhHHhhhCccc--ccCchHHHHHHHHhcCCCC
Q 006991 324 SQKPLVAHNS-LNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQ-VIDVNYLLKDIGPVK--KMTNISATIAYLKNRFFAP 399 (622)
Q Consensus 324 skKpIVGHN~-llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~-I~DTKyLa~~~~~~~--~~~~L~~~~~~l~~~~~~~ 399 (622)
...++||||. ++|+-++-+..+ +++.. ++. ++|+.+ ......+. +..+|+.+.+++.
T Consensus 83 ~~~~lVaHNa~~fD~~fL~~~g~-~~~~~-----------~~idt~~~~~-~~~~~~~~~~~~~~L~~La~~~g------ 143 (195)
T PRK07247 83 GELPLIGYNAQKSDLPILAENGL-DLSDQ-----------YQVDLYDEAF-ERRSSDLNGIANLKLQTVADFLG------ 143 (195)
T ss_pred CCCeEEEEeCcHhHHHHHHHcCC-CcCCC-----------ceeehHHHHH-HhhccccCCCCCCCHHHHHHhcC------
Confidence 5668999998 589988865432 33321 111 233332 11111111 2345666655541
Q ss_pred ceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 006991 400 IEMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 434 (622)
Q Consensus 400 p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l 434 (622)
++ ...|.|-+||++|+.||.+|...-
T Consensus 144 ----i~-----~~~HrAl~DA~~ta~v~~~ll~~~ 169 (195)
T PRK07247 144 ----IK-----GRGHNSLEDARMTARVYESFLESD 169 (195)
T ss_pred ----CC-----CCCcCCHHHHHHHHHHHHHHHhhc
Confidence 12 136999999999999999987644
No 35
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=95.09 E-value=0.12 Score=53.47 Aligned_cols=96 Identities=18% Similarity=0.162 Sum_probs=61.7
Q ss_pred HHHHHHHHH---hCCCCEEechhHHHHHHHHHhccC-CCCCCHHHHHHHHHccC-CCccchhhHHhhhCcccccCchHHH
Q 006991 314 FREVIDLIS---ASQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAF-PQVIDVNYLLKDIGPVKKMTNISAT 388 (622)
Q Consensus 314 Fr~Vi~~L~---~skKpIVGHN~llDL~~iy~~F~g-pLP~t~~EFk~~i~~lF-P~I~DTKyLa~~~~~~~~~~~L~~~ 388 (622)
|..|++.+. +...++||||.=+|+-+|-+.|.. -+|.. .+ -.++||-.|+....+. ...+|..+
T Consensus 74 ~~ev~~~~~~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~----------~~~~~~iDtl~lar~~~~~-~~~~L~~l 142 (250)
T PRK06310 74 IAEVFPQIKGFFKEGDYIVGHSVGFDLQVLSQESERIGETFL----------SKHYYIIDTLRLAKEYGDS-PNNSLEAL 142 (250)
T ss_pred HHHHHHHHHHHhCCCCEEEEECHHHHHHHHHHHHHHcCCCcc----------ccCCcEEehHHHHHhcccC-CCCCHHHH
Confidence 444444443 234689999999999999876521 11110 01 2489998888765432 23456666
Q ss_pred HHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 006991 389 IAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 434 (622)
Q Consensus 389 ~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l 434 (622)
..... + + ....|.|-.||++|+.||.+|+..+
T Consensus 143 ~~~~g--------~--~----~~~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 143 AVHFN--------V--P----YDGNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred HHHCC--------C--C----CCCCcChHHHHHHHHHHHHHHHHhc
Confidence 65441 1 1 1237999999999999999998755
No 36
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=94.96 E-value=0.13 Score=56.01 Aligned_cols=206 Identities=12% Similarity=0.095 Sum_probs=103.2
Q ss_pred hhccccHHHHHHHHHh--CCCCEEechhHHHHHHHHHhccCCCCCCH----HHHH------------HHHHccCC-Cccc
Q 006991 308 NKRVRGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLAPLPPNM----NEFI------------CSLRLAFP-QVID 368 (622)
Q Consensus 308 ~~~~~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~gpLP~t~----~EFk------------~~i~~lFP-~I~D 368 (622)
+..+..|..|++.|.+ .+.++||||.-+|+-||.+.|-.-+-... ..+. ..-+..+| .++|
T Consensus 106 La~AP~f~eVl~el~~fL~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iD 185 (377)
T PRK05601 106 FAQGKRFSQILKPLDRLIDGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVD 185 (377)
T ss_pred HhcCCCHHHHHHHHHHHhCCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEE
Confidence 4556678888887765 47899999999999999876511100000 0000 00011234 4899
Q ss_pred hhhHHhhhCcccccCchHHHHHHHHhcCCCCceeecCCC-CC---CCCcccch--hhHHHHHHHHHHHHHHhccCCCCCC
Q 006991 369 VNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQ-AN---ENEGKIHG--HNVVKICQLFGKLCSILKITPDAIE 442 (622)
Q Consensus 369 TKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p~ve~~~~-~~---~~~~h~AG--yDA~mTg~vF~~l~~~l~~~~~~~~ 442 (622)
|=-|+....|..+.-.|+.+.+++. |+.|.. .+ ...-|.|= -||.+++.+|.++... | ...
T Consensus 186 TL~LARrl~p~l~~~rL~~La~~lG--------i~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~-~----~l~ 252 (377)
T PRK05601 186 TLATARRQGVALDDIRIRGVAHTLG--------LDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS-G----PLS 252 (377)
T ss_pred hHHHHHHHcCCCCCCCHHHHHHHhC--------CCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc-C----Ccc
Confidence 9777777665434556777777652 111110 11 12224432 3999999999886211 1 101
Q ss_pred CCcHHHHhhhhhhhc-cccCC--CCCCCCCCCcccc-CCCCCCCC--CCcCCEEEEeccccccchhHHHHhhhhhhhccc
Q 006991 443 SSDDFLASAINRYAN-IFYSL--PGSSQEPTNEEIR-GWTNDKRK--VSCEDVVFLWGFRERISAGILKNMLQGSHEVFA 516 (622)
Q Consensus 443 s~~~~~~~~l~~~~N-~l~~~--~~~~~~~~d~~~~-~l~g~~~~--~~~~~vv~i~~f~~~~~~~~i~~~l~~~~~~F~ 516 (622)
+.. + +.+.+ ++-++ ..+. +..-.+|. --+|...+ +....+-+++.=+-.....+|-+.+-.-+-.
T Consensus 253 ~~~----p--~~l~a~~fglq~s~ir~-~a~~~p~~~~nPG~~~~~~~lv~Gm~v~~~~e~~~~~d~li~~~~~agL~-- 323 (377)
T PRK05601 253 SID----P--EDLRADKFGLQRSIIRV-DAQEAPRTLENPGTYEPGKGLVAGMEVVVAPEITMDPDIIIQAIVRAGLA-- 323 (377)
T ss_pred ccC----h--hhhhccccCcccccccc-ccccCCCCCCCCCccCCCCccccCcEEEEeCCccCCHHHHHHHHHHccch--
Confidence 100 0 11111 11110 0110 11223332 11344332 3566776665644466677776665432222
Q ss_pred cceEEEEecCceEEEEecCCCc
Q 006991 517 EAFNVRMVDRSCAIVVFGKPGL 538 (622)
Q Consensus 517 ~~~~V~~id~t~a~V~~~~~~~ 538 (622)
+-.-++....+|+.+....
T Consensus 324 ---y~~~~~r~tslvv~n~~~~ 342 (377)
T PRK05601 324 ---YSEKLTRQTSVVVCNQTRD 342 (377)
T ss_pred ---hhhccccceeEEEeCCCCC
Confidence 3334566667777666654
No 37
>KOG4483 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.92 E-value=0.029 Score=60.28 Aligned_cols=66 Identities=17% Similarity=0.335 Sum_probs=51.3
Q ss_pred cCCEEEEeccccccchhHHHHhhhhhhhccc-cceEEEEecCceEEEEecCCCchhHHHHHhhhcc--ccccchh
Q 006991 486 CEDVVFLWGFRERISAGILKNMLQGSHEVFA-EAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKA--VSGPLRE 557 (622)
Q Consensus 486 ~~~vv~i~~f~~~~~~~~i~~~l~~~~~~F~-~~~~V~~id~t~a~V~~~~~~~~~~~l~~~~~~~--~~~~l~~ 557 (622)
..||+=|++||.++++.|+-..+++ |+ ..|+|+|+|||.||-+|+..-.|.+.|.. +++ ..-||..
T Consensus 390 lpHVlEIydfp~efkteDll~~f~~----yq~kgfdIkWvDdthalaVFss~~~AaeaLt~--kh~~lKiRpLaq 458 (528)
T KOG4483|consen 390 LPHVLEIYDFPDEFKTEDLLKAFET----YQNKGFDIKWVDDTHALAVFSSVNRAAEALTL--KHDWLKIRPLAQ 458 (528)
T ss_pred ccceeEeccCchhhccHHHHHHHHH----hhcCCceeEEeecceeEEeecchHHHHHHhhc--cCceEEeeehhh
Confidence 6899999999999999886554442 22 33799999999999999999999888875 455 4556643
No 38
>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=94.90 E-value=0.11 Score=62.64 Aligned_cols=100 Identities=19% Similarity=0.201 Sum_probs=66.0
Q ss_pred cHHHHHHHHHh--CCCCEEechhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCC-CccchhhHHhhhCcccccCchHHH
Q 006991 313 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFP-QVIDVNYLLKDIGPVKKMTNISAT 388 (622)
Q Consensus 313 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~g-pLP~t~~EFk~~i~~lFP-~I~DTKyLa~~~~~~~~~~~L~~~ 388 (622)
-|..|+..+.+ .+.++||||.=+|+.++.+.|.. -+| .+| ..+||--|+....|-.+..+|..+
T Consensus 66 ~~~ev~~~l~~~l~~~~~VahN~~fD~~fL~~~~~~~g~~------------~~~~~~iDt~~l~~~~~p~~~~~~L~~l 133 (850)
T TIGR01407 66 YFSQVAQEIYDLLEDGIFVAHNVHFDLNFLAKALKDCGYE------------PLPKPRIDTVELAQIFFPTEESYQLSEL 133 (850)
T ss_pred CHHHHHHHHHHHhCCCEEEEeCcHHHHHHHHHHHHHcCCC------------CCCCCeEeHHHHHHHhcCCCCCCCHHHH
Confidence 44444444433 46899999999999999875521 111 012 368997677665553345567776
Q ss_pred HHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhccCC
Q 006991 389 IAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKITP 438 (622)
Q Consensus 389 ~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~~~~ 438 (622)
.+.+. + +. ...|.|-.||..|+.+|.+|...++.-+
T Consensus 134 ~~~~g--------i--~~----~~~H~Al~DA~ata~l~~~l~~~~~~l~ 169 (850)
T TIGR01407 134 SEALG--------L--TH----ENPHRADSDAQATAELLLLLFEKMEKLP 169 (850)
T ss_pred HHHCC--------C--CC----CCCCChHHHHHHHHHHHHHHHHHHHhcC
Confidence 66551 1 11 2469999999999999999999886533
No 39
>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=94.90 E-value=0.085 Score=50.51 Aligned_cols=76 Identities=17% Similarity=0.194 Sum_probs=45.0
Q ss_pred CCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCC-CccchhhH--Hhhh--CcccccCchHHHHHHHHhcCCC
Q 006991 324 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFP-QVIDVNYL--LKDI--GPVKKMTNISATIAYLKNRFFA 398 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP-~I~DTKyL--a~~~--~~~~~~~~L~~~~~~l~~~~~~ 398 (622)
.++++||||.-.|+-++-.. ..| .+.||=.+ +... .|-.+.-+|+.+.+++...
T Consensus 76 ~~~vlV~Hn~~~D~~~l~~~------------------~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~--- 134 (157)
T cd06149 76 KGKVVVGHAIHNDFKALKYF------------------HPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHR--- 134 (157)
T ss_pred CCCEEEEeCcHHHHHHhccc------------------CCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcCh---
Confidence 47899999999999776522 112 26677432 2221 2211234566666655221
Q ss_pred CceeecCCCCCCCCcccchhhHHHHHHHH
Q 006991 399 PIEMEIPNQANENEGKIHGHNVVKICQLF 427 (622)
Q Consensus 399 ~p~ve~~~~~~~~~~h~AGyDA~mTg~vF 427 (622)
.++ . ....|.|-.||..|+.+|
T Consensus 135 --~i~----~-~~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 135 --DIQ----V-GRQGHSSVEDARATMELY 156 (157)
T ss_pred --hhc----C-CCCCcCcHHHHHHHHHHh
Confidence 111 0 124699999999999987
No 40
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=94.84 E-value=0.24 Score=49.46 Aligned_cols=97 Identities=13% Similarity=0.149 Sum_probs=58.2
Q ss_pred ccHHHHHHHHHh---CCCCEEechhHHHHHHHHHhc--cC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCch
Q 006991 312 RGFREVIDLISA---SQKPLVAHNSLNDFTFIHSKF--LA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNI 385 (622)
Q Consensus 312 ~GFr~Vi~~L~~---skKpIVGHN~llDL~~iy~~F--~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L 385 (622)
.-|..|++.+.+ ...++|.||.=+|+-+|-+.+ +| +.| .++..+|+..+.....+..+..+|
T Consensus 77 p~~~evl~~f~~~~~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~------------~~~~~~dl~~~~~~~~~~~~~~~L 144 (207)
T PRK07748 77 ISFEELVEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFP------------FKGQCRDLSLEYKKFFGERNQTGL 144 (207)
T ss_pred CCHHHHHHHHHHHhCcCCeEEEEECHHHHHHHHHHHHHcCCCCc------------ccccceeHHHHHHHHhCcCCCCCH
Confidence 344444444433 224566666778999987665 23 222 113456776555443332334567
Q ss_pred HHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHH
Q 006991 386 SATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSI 433 (622)
Q Consensus 386 ~~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~ 433 (622)
..+.+.+. ++ ..+..|.|-.||++|+.+|.+|..-
T Consensus 145 ~~~~~~~g----------i~---~~~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 145 WKAIEEYG----------KE---GTGKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred HHHHHHcC----------CC---CCCCCcChHHHHHHHHHHHHHHHhC
Confidence 77776551 11 1234699999999999999999875
No 41
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=94.60 E-value=0.15 Score=62.21 Aligned_cols=90 Identities=17% Similarity=0.175 Sum_probs=61.8
Q ss_pred CCCCEEechhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCcee
Q 006991 324 SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEM 402 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p~v 402 (622)
.+.++||||.=+|+-+|-+.|.. -+|. +.-..+||=.|+...-|-.+.-+|..+.+++. +
T Consensus 83 ~~~~~VaHN~~FD~~fL~~~~~~~g~~~-----------~~~~~iDt~~la~~~~p~~~~~~L~~l~~~l~--------i 143 (928)
T PRK08074 83 EGAYFVAHNVHFDLNFLNEELERAGYTE-----------IHCPKLDTVELARILLPTAESYKLRDLSEELG--------L 143 (928)
T ss_pred CCCeEEEEChHHHHHHHHHHHHHcCCCC-----------CCCCeeeHHHHHHHhcCCCCCCCHHHHHHhCC--------C
Confidence 47899999999999988765521 1121 01237899777766555334446777666551 1
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHHHHHHHHhccCC
Q 006991 403 EIPNQANENEGKIHGHNVVKICQLFGKLCSILKITP 438 (622)
Q Consensus 403 e~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~~~~ 438 (622)
+ ....|.|-.||.+|+.+|.+|...++.-+
T Consensus 144 --~----~~~~H~Al~DA~ata~l~~~l~~~~~~l~ 173 (928)
T PRK08074 144 --E----HDQPHRADSDAEVTAELFLQLLNKLERLP 173 (928)
T ss_pred --C----CCCCCChHHHHHHHHHHHHHHHHHHHhcC
Confidence 1 13579999999999999999999886533
No 42
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=94.40 E-value=0.19 Score=52.16 Aligned_cols=86 Identities=19% Similarity=0.107 Sum_probs=55.3
Q ss_pred CCCCEEechhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCcee
Q 006991 324 SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEM 402 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p~v 402 (622)
.+.++||||.=+|..++-+.|.. -+|. +.+..+||--++...-+. ...+|..+.+.+.
T Consensus 146 ~~~v~VaHNa~FD~~fL~~~l~r~g~~~-----------~~~~~ldtl~la~~~~~~-~~~~L~~L~~~lg--------- 204 (257)
T PRK08517 146 GDSVFVAHNVNFDYNFISRSLEEIGLGP-----------LLNRKLCTIDLAKRTIES-PRYGLSFLKELLG--------- 204 (257)
T ss_pred CCCeEEEECHHHHHHHHHHHHHHcCCCC-----------CCCCcEehHHHHHHHccC-CCCCHHHHHHHcC---------
Confidence 45789999999999998765421 1111 123357876666543322 2335666555431
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 006991 403 EIPNQANENEGKIHGHNVVKICQLFGKLCSILK 435 (622)
Q Consensus 403 e~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~ 435 (622)
++ ....|.|-.||.+|+.||.++...+.
T Consensus 205 -i~----~~~~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 205 -IE----IEVHHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred -cC----CCCCCChHHHHHHHHHHHHHHHHHhH
Confidence 11 12579999999999999999998773
No 43
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=93.90 E-value=0.17 Score=63.81 Aligned_cols=106 Identities=21% Similarity=0.150 Sum_probs=69.7
Q ss_pred HhhhhccccHHHHHHHHHh--CCCCEEechhHHHHHHHHHhccCC-CCCCHHHHHHHHHccCCCccchhhHHhhhCcccc
Q 006991 305 FEQNKRVRGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLAP-LPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKK 381 (622)
Q Consensus 305 ~e~~~~~~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~gp-LP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~ 381 (622)
.+.+....-+..+++.+.+ .+.++||||.-+|+-+|-+.+-.- +|. +...++||--++....|-.+
T Consensus 477 ~e~L~~aps~~EaL~~f~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~-----------l~~~~IDTLelar~l~p~~k 545 (1437)
T PRK00448 477 DDMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEK-----------IKNPVIDTLELSRFLYPELK 545 (1437)
T ss_pred HHHHcCCCCHHHHHHHHHHHhCCCEEEEeCccccHHHHHHHHHHcCCcc-----------ccccceeHHHHHHHHcCccc
Confidence 3445566678888888876 688999999999998875543211 111 12347888666655444223
Q ss_pred cCchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 006991 382 MTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 435 (622)
Q Consensus 382 ~~~L~~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~ 435 (622)
..+|..+.+.+. .+ ....|.|-+||++|+.||.+|...+.
T Consensus 546 ~~kL~~LAk~lG----L~----------~~~~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 546 SHRLNTLAKKFG----VE----------LEHHHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred cccHHHHHHHcC----CC----------CCCCcChHHHHHHHHHHHHHHHHHHH
Confidence 445555555431 11 11249999999999999999998874
No 44
>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=91.87 E-value=0.0085 Score=55.45 Aligned_cols=81 Identities=20% Similarity=0.187 Sum_probs=45.6
Q ss_pred hCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHcc---CCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCC
Q 006991 323 ASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLA---FPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAP 399 (622)
Q Consensus 323 ~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~l---FP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~ 399 (622)
+....+||||.-.|+.++-+. +++.+... ++.++||--+.....+.....+|..+.+.+..
T Consensus 81 ~~~~~~v~~n~~fd~~~l~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~----- 144 (164)
T PF00929_consen 81 KKNDILVGHNASFDIGFLRRE-----------DKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAEYFGI----- 144 (164)
T ss_dssp HHHTEEEETTCCHEEESSHHH-----------HHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTS-----
T ss_pred hcccccccccccchhhHHHHh-----------hhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHHHcCC-----
Confidence 345899999977776555432 22222222 23466775544433221122455555554421
Q ss_pred ceeecCCCCCCCCcccchhhHHHHHHHH
Q 006991 400 IEMEIPNQANENEGKIHGHNVVKICQLF 427 (622)
Q Consensus 400 p~ve~~~~~~~~~~h~AGyDA~mTg~vF 427 (622)
+.. +..|.|..||++|..||
T Consensus 145 -----~~~---~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 145 -----PFD---GTAHDALDDARATAELF 164 (164)
T ss_dssp -----SST---STTTSHHHHHHHHHHHH
T ss_pred -----CCC---CCCcChHHHHHHHhCcC
Confidence 111 12799999999999987
No 45
>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=91.01 E-value=1.3 Score=42.22 Aligned_cols=92 Identities=17% Similarity=0.161 Sum_probs=55.7
Q ss_pred HHHHHHhCCCCEEechhHHHHHHHHHhcc--CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHh
Q 006991 317 VIDLISASQKPLVAHNSLNDFTFIHSKFL--APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKN 394 (622)
Q Consensus 317 Vi~~L~~skKpIVGHN~llDL~~iy~~F~--gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~ 394 (622)
+.+.+......+|.||.-.|+-.+.+.+. +-.| .-..+...+||+.++....+..+..+|.++.+++.
T Consensus 82 ~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~---------~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~~g- 151 (176)
T cd06133 82 FLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIIN---------LPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLG- 151 (176)
T ss_pred HHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCC---------CcccccceEEHHHHHHHHhCCCCCCCHHHHHHHCC-
Confidence 33444333235556666777665554321 1110 01235568999988877655445667777776651
Q ss_pred cCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHH
Q 006991 395 RFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKL 430 (622)
Q Consensus 395 ~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l 430 (622)
+ +. .+..|.|=+||..|+.||.+|
T Consensus 152 -------i--~~---~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 152 -------L--EF---EGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred -------C--CC---CCCCcCcHHHHHHHHHHHHHh
Confidence 1 11 146899999999999999887
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=90.53 E-value=0.64 Score=44.35 Aligned_cols=50 Identities=8% Similarity=0.146 Sum_probs=36.1
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCcc
Q 006991 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRD 121 (622)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~~ 121 (622)
||.+|+|+||+... .. .-..-.|+|+|.+.++.+... ....|+.++-|..
T Consensus 1 ~vv~D~Ettg~~~~--~~----------------~~~~~~IieIgav~v~~~~~~-~~~~f~~~i~P~~ 50 (176)
T cd06133 1 YLVIDFEATCWEGN--SK----------------PDYPNEIIEIGAVLVDVKTKE-IIDTFSSYVKPVI 50 (176)
T ss_pred CEEEEeeccccCCC--CC----------------CCCCcceEEEEEEEEEcCCCe-EEeeeeeeECCCc
Confidence 79999999999432 10 112346999999987666532 6789999999863
No 47
>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=90.36 E-value=0.62 Score=45.40 Aligned_cols=75 Identities=19% Similarity=0.257 Sum_probs=48.2
Q ss_pred CCCEEechh-HHHHHHHHHhcc--C-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 006991 325 QKPLVAHNS-LNDFTFIHSKFL--A-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 400 (622)
Q Consensus 325 kKpIVGHN~-llDL~~iy~~F~--g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p 400 (622)
..++||||. -+|+-++-+.|- | ++|.. +..+||-.++..+.+ +|+++.+.+ +.
T Consensus 98 ~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~------------~~~iDtl~l~r~~~~-----~L~~l~~~~----~~-- 154 (177)
T cd06136 98 PICLVAHNGNRFDFPILRSELERLGTKLPDD------------ILCVDSLPAFRELDQ-----SLGSLYKRL----FG-- 154 (177)
T ss_pred CCEEEEcCCcccCHHHHHHHHHHcCCCCCCC------------CEEEEeHHHHhhhHh-----hHHHHHHHH----hC--
Confidence 348999998 799999977662 2 11110 234688666665433 566665533 11
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHHHH
Q 006991 401 EMEIPNQANENEGKIHGHNVVKICQLFGK 429 (622)
Q Consensus 401 ~ve~~~~~~~~~~h~AGyDA~mTg~vF~~ 429 (622)
++ ....|.|-.||..|+.||++
T Consensus 155 ---~~----~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 155 ---QE----PKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred ---CC----cccccchHHHHHHHHHHHhh
Confidence 11 12469999999999999975
No 48
>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=89.65 E-value=1.5 Score=42.91 Aligned_cols=26 Identities=23% Similarity=0.234 Sum_probs=19.1
Q ss_pred HHHHhCCCCEEech-hHHHHHHHHHhc
Q 006991 319 DLISASQKPLVAHN-SLNDFTFIHSKF 344 (622)
Q Consensus 319 ~~L~~skKpIVGHN-~llDL~~iy~~F 344 (622)
+.+.+.+.++|||| .-+|+.|+-+.|
T Consensus 78 ~~~~~~~~~lVahn~~~FD~~fL~~~~ 104 (183)
T cd06138 78 RLFNTPGTCIVGYNNIRFDDEFLRFAF 104 (183)
T ss_pred HHHccCCCcEEeeCchhhHHHHHHHHH
Confidence 33333567899998 679999997766
No 49
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=88.65 E-value=2.5 Score=42.87 Aligned_cols=83 Identities=23% Similarity=0.171 Sum_probs=53.5
Q ss_pred CCEEechhHHHHHHHHHhcc---CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCcee
Q 006991 326 KPLVAHNSLNDFTFIHSKFL---APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEM 402 (622)
Q Consensus 326 KpIVGHN~llDL~~iy~~F~---gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p~v 402 (622)
.++||||-.+|+.++-..+. ++.| --.++||=-++....|-.+..+|..+.+.+ .
T Consensus 96 ~~~Vahna~fD~~fl~~~~~~~~~~~~-------------~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~----g----- 153 (243)
T COG0847 96 RLLVAHNAAFDVGFLRVESERLGIEIP-------------GDPVLDTLALARRHFPGFDRSSLDALAERL----G----- 153 (243)
T ss_pred CeEEEEchhhcHHHHHHHHHHcCCCcc-------------cCceehHHHHHHHHcCCCccchHHHHHHHc----C-----
Confidence 89999999999999875542 2333 234667766666544422334455544422 1
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHHHHHHHH
Q 006991 403 EIPNQANENEGKIHGHNVVKICQLFGKLCSI 433 (622)
Q Consensus 403 e~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~ 433 (622)
++. +....|.|-+||++|+.+|+.+..-
T Consensus 154 -i~~--~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 154 -IDR--NPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred -CCc--CCcCCcchHHHHHHHHHHHHHHHhc
Confidence 111 1223488999999999999999883
No 50
>PRK05168 ribonuclease T; Provisional
Probab=87.41 E-value=1.7 Score=43.61 Aligned_cols=57 Identities=16% Similarity=0.232 Sum_probs=43.0
Q ss_pred HHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCC-Cc-eeeEeeEEeec
Q 006991 41 LSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQA-SK-VIAYPYNFHLF 118 (622)
Q Consensus 41 l~~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~-~~-y~~~~fNF~lf 118 (622)
+.-|...+++..||++|+|-||+.+.. -.|||+|...++.+. +. .....|..++-
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~-----------------------d~IieIgaV~v~~d~~g~i~~~~~f~~lv~ 63 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKT-----------------------DALLEIAAVTLKMDEQGWLYPDETLHFHVE 63 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCC-----------------------CEEEEEeEEEEEecCCCcEeccceEEEEEC
Confidence 345778899999999999999995321 139999998887653 32 34678999998
Q ss_pred Cc
Q 006991 119 PR 120 (622)
Q Consensus 119 p~ 120 (622)
|.
T Consensus 64 P~ 65 (211)
T PRK05168 64 PF 65 (211)
T ss_pred CC
Confidence 84
No 51
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=86.96 E-value=3.1 Score=44.18 Aligned_cols=88 Identities=14% Similarity=0.022 Sum_probs=47.9
Q ss_pred HHHHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCC
Q 006991 319 DLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFA 398 (622)
Q Consensus 319 ~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~ 398 (622)
..+.+...+|||||.=+|+-|+-+.+ .+++.. | ..+|=-.+.-..+-.+..+|..+...+.
T Consensus 115 ~~fl~~~~vlVAHNA~FD~~fL~~~~-~~~~~~------------~-~~ct~~~i~~~~~~~~~~kL~~La~~~g----- 175 (294)
T PRK09182 115 DALIAPADLIIAHNAGFDRPFLERFS-PVFATK------------P-WACSVSEIDWSARGFEGTKLGYLAGQAG----- 175 (294)
T ss_pred HHHhcCCCEEEEeCHHHHHHHHHHHH-HhccCC------------c-ccccHHHHhhccccCCCCCHHHHHHHcC-----
Confidence 33444457999999999998886543 222211 0 0111000000001012344555554331
Q ss_pred CceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 006991 399 PIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 435 (622)
Q Consensus 399 ~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~ 435 (622)
+ ....|.|..||+.|+.||.++....|
T Consensus 176 ~----------~~~aHrAl~Da~Ata~ll~~~l~~~~ 202 (294)
T PRK09182 176 F----------FHEGHRAVDDCQALLELLARPLPETG 202 (294)
T ss_pred C----------CCCCcChHHHHHHHHHHHHHHHhhcC
Confidence 1 12469999999999999997776554
No 52
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=86.29 E-value=1.4 Score=43.71 Aligned_cols=56 Identities=13% Similarity=0.166 Sum_probs=38.4
Q ss_pred HHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 41 LSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 41 l~~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
+..+.+......||+||+|.||+.+. .-.|+|+|...++.+ .-.....|.+++-|.
T Consensus 19 ~~~~~~~~~~~~~vviD~ETTGl~~~-----------------------~d~IieIgaV~~~~~-~~~~~~~f~~~i~p~ 74 (202)
T PRK09145 19 YAFLFEPPPPDEWVALDCETTGLDPR-----------------------RAEIVSIAAVKIRGN-RILTSERLELLVRPP 74 (202)
T ss_pred HHHHhcCCCCCCEEEEEeECCCCCCC-----------------------CCceEEEEEEEEECC-EEeecCceEEEECCC
Confidence 33445555668999999999998321 235999999887632 222335788888885
No 53
>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=86.25 E-value=3.6 Score=38.77 Aligned_cols=95 Identities=16% Similarity=0.257 Sum_probs=57.4
Q ss_pred HHHHHHh-CCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhh-CcccccCchHHHHHHHHh
Q 006991 317 VIDLISA-SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDI-GPVKKMTNISATIAYLKN 394 (622)
Q Consensus 317 Vi~~L~~-skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~-~~~~~~~~L~~~~~~l~~ 394 (622)
.+..+.+ .+...||||+=.|+..|++.+ | -....++|| .++... .+-.. .+|..+...+..
T Consensus 68 ~l~~ll~~~~i~kv~~n~~~D~~~L~~~~-~--------------i~~~~~~D~-~l~~~~l~~~~~-~~L~~L~~~~l~ 130 (176)
T PF01612_consen 68 ALKELLEDPNIIKVGHNAKFDLKWLYRSF-G--------------IDLKNVFDT-MLAAYLLDPTRS-YSLKDLAEEYLG 130 (176)
T ss_dssp HHHHHHTTTTSEEEESSHHHHHHHHHHHH-T--------------S--SSEEEH-HHHHHHTTTSTT-SSHHHHHHHHHS
T ss_pred HHHHHHhCCCccEEEEEEechHHHHHHHh-c--------------cccCCccch-hhhhhccccccc-ccHHHHHHHHhh
Confidence 3334444 456689999999999999872 2 223458999 555543 33222 677777666543
Q ss_pred cCCCCceeecC--CCCCCCC---------cccchhhHHHHHHHHHHHHHHh
Q 006991 395 RFFAPIEMEIP--NQANENE---------GKIHGHNVVKICQLFGKLCSIL 434 (622)
Q Consensus 395 ~~~~~p~ve~~--~~~~~~~---------~h~AGyDA~mTg~vF~~l~~~l 434 (622)
.+..+ ..-+... ..=|+.||+.|-.+|-+|...|
T Consensus 131 ------~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 131 ------NIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp ------EEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred ------hccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 11111 1111111 1228999999999999998876
No 54
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=85.94 E-value=1.7 Score=34.32 Aligned_cols=56 Identities=13% Similarity=0.282 Sum_probs=40.8
Q ss_pred EEEeccccccchhHHHHhhhhhhhccccceEEEEec------CceEEEEecCCCchhHHHHHhhhc
Q 006991 490 VFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVD------RSCAIVVFGKPGLSNTFKNVMNSK 549 (622)
Q Consensus 490 v~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id------~t~a~V~~~~~~~~~~~l~~~~~~ 549 (622)
|+|.++|..++..+|++.+++ ||+...+.... ...|||.|.+.+.|..++..++..
T Consensus 1 l~v~nlp~~~t~~~l~~~f~~----~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~ 62 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFSQ----FGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGK 62 (70)
T ss_dssp EEEESETTTSSHHHHHHHHHT----TSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred cEEcCCCCcCCHHHHHHHHHH----hhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCC
Confidence 577899999999998887664 44432333333 346999999999999888877553
No 55
>PTZ00315 2'-phosphotransferase; Provisional
Probab=85.41 E-value=4.2 Score=46.94 Aligned_cols=83 Identities=12% Similarity=0.115 Sum_probs=55.2
Q ss_pred CCEEechhHHHHH-HHHHhcc----CCCCCCHHHHHHHHHccCCCccchh-hHHhhhCc---------c--cccCchHHH
Q 006991 326 KPLVAHNSLNDFT-FIHSKFL----APLPPNMNEFICSLRLAFPQVIDVN-YLLKDIGP---------V--KKMTNISAT 388 (622)
Q Consensus 326 KpIVGHN~llDL~-~iy~~F~----gpLP~t~~EFk~~i~~lFP~I~DTK-yLa~~~~~---------~--~~~~~L~~~ 388 (622)
+.+|+||+=.|+. ++.+++. ..+|. .|...+|.| +++....| . .+..+|.++
T Consensus 154 ~~~vah~g~fDl~~fL~~e~~~~~~~g~p~-----------~f~~widLk~~lar~l~p~~~~~~~~~~~~~~~~~L~~a 222 (582)
T PTZ00315 154 SYCVVTCGDWDLKTMLPSQMRVSGQQGTPL-----------SFQRWCNLKKYMSQLGFGNGSGCGGGATPPLGPSDMPDM 222 (582)
T ss_pred ceEEEeccHHHHHHHHHHHHHHhhhcCCCc-----------ccceEEEhHHHHHHHhCccccccccccccccCCcCHHHH
Confidence 4699999999995 6655442 35664 355666754 66654322 1 123578888
Q ss_pred HHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 006991 389 IAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 432 (622)
Q Consensus 389 ~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~ 432 (622)
++.+. + + -.+..|.|=.||..||.||.+|..
T Consensus 223 l~~lg--------L--~---~eGr~HrAlDDA~ntA~L~~~Ll~ 253 (582)
T PTZ00315 223 LQMLG--------L--P---LQGRHHSGIDDCRNIAAVLCELLR 253 (582)
T ss_pred HHHCC--------C--C---CCCCCcCcHHHHHHHHHHHHHHHH
Confidence 77652 1 1 134579999999999999999986
No 56
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=84.26 E-value=1.9 Score=40.61 Aligned_cols=43 Identities=14% Similarity=0.234 Sum_probs=32.5
Q ss_pred CeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 52 DFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 52 ~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.||++|+|+||+.+. .-.|+|+|....+.+ . ...+|+.++-|.
T Consensus 1 ~~v~~D~Ettg~~~~-----------------------~~~Iieig~v~~~~~--~-~~~~f~~~v~p~ 43 (169)
T smart00479 1 TLVVIDCETTGLDPG-----------------------KDEIIEIAAVDVDGG--R-IIVVFDTYVKPD 43 (169)
T ss_pred CEEEEEeeCCCCCCC-----------------------CCeEEEEEEEEEECC--E-eEEEEEEEECCC
Confidence 489999999998321 245999998876553 3 678899998883
No 57
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=82.56 E-value=2.5 Score=36.64 Aligned_cols=63 Identities=16% Similarity=0.204 Sum_probs=44.3
Q ss_pred CCEEEEeccccccchhHHHHhhhhhhhccccc-eEEEEecCceEEEEecCCCchhHHHHHhhhcccc
Q 006991 487 EDVVFLWGFRERISAGILKNMLQGSHEVFAEA-FNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKAVS 552 (622)
Q Consensus 487 ~~vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~-~~V~~id~t~a~V~~~~~~~~~~~l~~~~~~~~~ 552 (622)
..++++..-|.......|+..|.+ ++.++ +.|.-|..++|.|-|.+++.|+-.++-|+.|.|.
T Consensus 2 ~s~L~V~NLP~~~d~~~I~~RL~q---LsdNCGGkVl~v~~~tAilrF~~~~~A~RA~KRmegEdVf 65 (90)
T PF11608_consen 2 HSLLYVSNLPTNKDPSSIKNRLRQ---LSDNCGGKVLSVSGGTAILRFPNQEFAERAQKRMEGEDVF 65 (90)
T ss_dssp SEEEEEES--TTS-HHHHHHHHHH---HHHTTT--EEE--TT-EEEEESSHHHHHHHHHHHTT--SS
T ss_pred ccEEEEecCCCCCCHHHHHHHHHH---HhhccCCEEEEEeCCEEEEEeCCHHHHHHHHHhhcccccc
Confidence 346777888887778889998886 55577 5888899999999999999999999989888743
No 58
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=81.99 E-value=3.1 Score=37.32 Aligned_cols=54 Identities=20% Similarity=0.242 Sum_probs=32.8
Q ss_pred EEEEeccccccchhHHHHhhhhhhhccccceEEEEec----CceEEEEecCCCchhHHHHHhhhc
Q 006991 489 VVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVD----RSCAIVVFGKPGLSNTFKNVMNSK 549 (622)
Q Consensus 489 vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id----~t~a~V~~~~~~~~~~~l~~~~~~ 549 (622)
+|++-+.++..+..+|++ +|++++.|.||| ++.++|=|.+++.|..++..+...
T Consensus 3 il~~~g~~~~~~re~iK~-------~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKE-------AFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp EEEEEE--SS--HHHHHH-------HT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred EEEEecCCCCcCHHHHHH-------HHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 456666777777667654 555666888887 778999999999999998877554
No 59
>PRK11779 sbcB exonuclease I; Provisional
Probab=81.96 E-value=3 Score=47.18 Aligned_cols=101 Identities=9% Similarity=-0.033 Sum_probs=53.1
Q ss_pred HHHHHHHhCCCCEEechhH-HHHHHHHHhccCCCCCCHHHHHHHHHccCC--CccchhhHHhhhCc------c----ccc
Q 006991 316 EVIDLISASQKPLVAHNSL-NDFTFIHSKFLAPLPPNMNEFICSLRLAFP--QVIDVNYLLKDIGP------V----KKM 382 (622)
Q Consensus 316 ~Vi~~L~~skKpIVGHN~l-lDL~~iy~~F~gpLP~t~~EFk~~i~~lFP--~I~DTKyLa~~~~~------~----~~~ 382 (622)
.+.+.+...+.++||||.. +|+-++-+.|+..+-+.|. ..+..--+ -++||--++....| . .+.
T Consensus 84 ~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~---~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s 160 (476)
T PRK11779 84 RIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYA---REWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPS 160 (476)
T ss_pred HHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHH---HHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCC
Confidence 3344444456889999975 8998887777544333221 11111001 13444332222211 0 011
Q ss_pred CchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHH
Q 006991 383 TNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSI 433 (622)
Q Consensus 383 ~~L~~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~ 433 (622)
-.|..+.+.. . ++ ....|.|=.||+.|+.++..|...
T Consensus 161 ~rLe~L~~~~----g------I~----~~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 161 FKLEHLTKAN----G------IE----HENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CcHHHHHHHc----C------CC----CCCCCCcHHHHHHHHHHHHHHHHh
Confidence 2334433322 1 11 134799999999999999998864
No 60
>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=79.59 E-value=2.9 Score=38.26 Aligned_cols=44 Identities=11% Similarity=0.164 Sum_probs=33.6
Q ss_pred EEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCcc
Q 006991 54 IAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRD 121 (622)
Q Consensus 54 VAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~~ 121 (622)
|.||+|+||+.+ ..-.|+|+|...+..... .....|+.++.|..
T Consensus 1 v~~D~Ettg~~~-----------------------~~~~iieig~v~~~~~~~-~~~~~~~~~i~p~~ 44 (164)
T PF00929_consen 1 VVFDTETTGLDP-----------------------RQDEIIEIGAVKVDDDEN-EEVESFNSLIRPEE 44 (164)
T ss_dssp EEEEEEESSSTT-----------------------TTCTEEEEEEEEEETTTT-EEEEEEEEEBEHSS
T ss_pred cEEEeEcCCCCC-----------------------CCCeEEEEEEEEeeCCcc-ccceeeeecccccc
Confidence 689999999832 456699999877665443 46788999998863
No 61
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=79.17 E-value=4.8 Score=32.18 Aligned_cols=54 Identities=19% Similarity=0.313 Sum_probs=39.0
Q ss_pred EEEeccccccchhHHHHhhhhhhhccccceEEEEecC------ceEEEEecCCCchhHHHHHhh
Q 006991 490 VFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR------SCAIVVFGKPGLSNTFKNVMN 547 (622)
Q Consensus 490 v~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~------t~a~V~~~~~~~~~~~l~~~~ 547 (622)
|+|.+.|..++..+|++.++. |++-..|..+-+ ..|||.|.+.+.|..++....
T Consensus 1 v~i~nlp~~~~~~~l~~~f~~----~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~ 60 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNFFSR----FGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLN 60 (70)
T ss_dssp EEEESSTTT--HHHHHHHCTT----SSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHT
T ss_pred CEEeCCCCCCCHHHHHHHHHh----cCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCC
Confidence 578899999888888876654 343347777766 459999999998888777543
No 62
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=78.94 E-value=4.9 Score=49.44 Aligned_cols=105 Identities=21% Similarity=0.219 Sum_probs=76.0
Q ss_pred HhhhhccccHHHHHHHHHh--CCCCEEechhHHHHHHHHHhcc--CCCCCCHHHHHHHHHccCCCccchhhHHhhhCccc
Q 006991 305 FEQNKRVRGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFL--APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVK 380 (622)
Q Consensus 305 ~e~~~~~~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~--gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~ 380 (622)
++.++.+.-.-.|+..+.+ -.-.+|.||.=+|+=||=..|- +-.|-+ -.++||=-|+..+.|--
T Consensus 479 deml~~a~~i~~vL~kf~~~~~d~IlVAHNasFD~gFl~~~~~k~~~~~~~------------~pvIDTL~lar~L~P~~ 546 (1444)
T COG2176 479 DEMLENAPEIEEVLEKFREFIGDSILVAHNASFDMGFLNTNYEKYGLEPLT------------NPVIDTLELARALNPEF 546 (1444)
T ss_pred HHHHcCCccHHHHHHHHHHHhcCcEEEeccCccchhHHHHHHHHhCCcccc------------CchhhHHHHHHHhChhh
Confidence 4566666666777777766 4779999999999999988774 323322 13789988898888644
Q ss_pred ccCchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 006991 381 KMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 435 (622)
Q Consensus 381 ~~~~L~~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~~l~ 435 (622)
+.-.|+.+.+.+. |+ ....|-|-|||=.||.+|+.+...++
T Consensus 547 ksh~Lg~l~kk~~--------v~------le~hHRA~yDaeat~~vf~~f~~~~k 587 (1444)
T COG2176 547 KSHRLGTLCKKLG--------VE------LERHHRADYDAEATAKVFFVFLKDLK 587 (1444)
T ss_pred hhcchHHHHHHhC--------cc------HHHhhhhhhhHHHHHHHHHHHHHHHH
Confidence 4455777666552 21 13468899999999999999988873
No 63
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=77.87 E-value=5 Score=40.96 Aligned_cols=48 Identities=17% Similarity=0.180 Sum_probs=34.4
Q ss_pred hcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 48 ISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 48 I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
..+..||++|+|-||+.+ +.-.|+|+|+..++.++. ....|+.++-|.
T Consensus 3 ~~~~~~vv~D~ETTGl~p-----------------------~~d~Iieig~v~v~~~g~--~~~~~~~lv~P~ 50 (232)
T PRK07942 3 WHPGPLAAFDLETTGVDP-----------------------ETARIVTAALVVVDADGE--VVESREWLADPG 50 (232)
T ss_pred cccCcEEEEEeccCCCCC-----------------------CCCeeEEEEEEEEeCCCc--cccceEEEECCC
Confidence 356789999999999842 122599999998875443 235677777774
No 64
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=77.86 E-value=4.4 Score=40.37 Aligned_cols=42 Identities=12% Similarity=0.139 Sum_probs=31.5
Q ss_pred CeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 52 DFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 52 ~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.||++|+|+||+. + . -.|||+|...+.. + -....|..++-|.
T Consensus 6 ~~vvlD~EtTGl~--~-~---------------------~eIIeIgaV~v~~-g--~~~~~f~~lv~P~ 47 (195)
T PRK07247 6 TYIAFDLEFNTVN--G-V---------------------SHIIQVSAVKYDD-H--KEVDSFDSYVYTD 47 (195)
T ss_pred eEEEEEeeCCCCC--C-C---------------------CeEEEEEEEEEEC-C--EEEEEEEEEECCC
Confidence 7999999999982 1 0 1599999888763 2 2356899999885
No 65
>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=77.82 E-value=3.8 Score=41.23 Aligned_cols=48 Identities=8% Similarity=0.155 Sum_probs=35.1
Q ss_pred hhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 47 HISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 47 ~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.+....||++|+|-||+.+. .- |+|+|...+... .-....|..++.|.
T Consensus 3 ~l~~~~fvv~D~ETTGl~~~-----------------------~~-IIeIgav~v~~~--~~~~~~f~~li~P~ 50 (217)
T TIGR00573 3 QLVLDTETTGDNETTGLYAG-----------------------HD-IIEIGAVEIINR--RITGNKFHTYIKPD 50 (217)
T ss_pred eEEecCEEEEEecCCCCCCC-----------------------CC-EEEEEEEEEECC--CEeeeEEEEEECcC
Confidence 46778999999999998421 12 999999875432 22457888888885
No 66
>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=75.35 E-value=5.2 Score=39.41 Aligned_cols=49 Identities=14% Similarity=0.255 Sum_probs=36.8
Q ss_pred cCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCC-Cc-eeeEeeEEeecCc
Q 006991 49 SSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQA-SK-VIAYPYNFHLFPR 120 (622)
Q Consensus 49 ~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~-~~-y~~~~fNF~lfp~ 120 (622)
....+|++|+|-||+.+. .=.|||+|...++.+. +. .....|++++.|.
T Consensus 3 ~~~~~vv~D~ETTGl~~~-----------------------~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~ 53 (189)
T cd06134 3 RGFLPVVVDVETGGFNPQ-----------------------TDALLEIAAVTLEMDEQGNLYPDETFHFHILPF 53 (189)
T ss_pred ccceeEEEEecCCCCCCC-----------------------CCeEEEEEEEEEEECCCCceeccceEEEEEcCC
Confidence 356799999999999532 1239999999887653 23 4568999999984
No 67
>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=75.09 E-value=8.3 Score=38.38 Aligned_cols=50 Identities=16% Similarity=0.176 Sum_probs=36.0
Q ss_pred hcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCC-c-eeeEeeEEeecCc
Q 006991 48 ISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQAS-K-VIAYPYNFHLFPR 120 (622)
Q Consensus 48 I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~-~-y~~~~fNF~lfp~ 120 (622)
-..+.||++|+|.||+.+. +=.||++|...+..+++ . .....|++++.|.
T Consensus 5 ~~~~~~vv~D~ETTGl~~~-----------------------~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~ 56 (200)
T TIGR01298 5 FRGYLPVVVDVETGGFNAK-----------------------TDALLEIAAITLKMDEQGWLFPDTTLHFHVEPF 56 (200)
T ss_pred hcCCeeEEEEeeCCCCCCC-----------------------CCeEEEEEEEEEEEcCCCcEeecceeEEEEcCC
Confidence 3568899999999999431 12499999988876542 2 2246789998884
No 68
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=73.75 E-value=6.6 Score=42.99 Aligned_cols=50 Identities=20% Similarity=0.324 Sum_probs=38.7
Q ss_pred HhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 46 NHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 46 ~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
..+.++.||+||+|.||+.+. .=.||++|...+..++. .+..|..++-|.
T Consensus 41 ~~~~~~~fVvlDiETTGLdp~-----------------------~drIIeIgAV~i~~~g~--ive~f~tLVnP~ 90 (377)
T PRK05601 41 EAIEAAPFVAVSIQTSGIHPS-----------------------TSRLITIDAVTLTADGE--EVEHFHAVLNPG 90 (377)
T ss_pred CCCCCCCEEEEEEECCCCCCC-----------------------CCeEEEEEEEEEEcCCE--EEEEEEEEECcC
Confidence 368889999999999999432 12489999887776652 468888998885
No 69
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=73.71 E-value=6 Score=40.67 Aligned_cols=51 Identities=24% Similarity=0.384 Sum_probs=35.9
Q ss_pred HhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 46 NHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 46 ~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
..+.+.+||+||+|.||+.+. .=.|||+|...++.. .-.....|..++-|.
T Consensus 42 ~~~~~~~~vviD~ETTGl~p~-----------------------~d~IieIg~v~v~~~-~i~~~~~~~~li~P~ 92 (239)
T PRK09146 42 TPLSEVPFVALDFETTGLDAE-----------------------QDAIVSIGLVPFTLQ-RIRCRQARHWVVKPR 92 (239)
T ss_pred CCcccCCEEEEEeECCCCCCC-----------------------CCcEEEEEEEEEECC-eEeecceEEEEECCC
Confidence 357789999999999999421 225999999887542 223346677777764
No 70
>smart00362 RRM_2 RNA recognition motif.
Probab=73.20 E-value=9.6 Score=29.20 Aligned_cols=54 Identities=17% Similarity=0.250 Sum_probs=39.0
Q ss_pred EEEeccccccchhHHHHhhhhhhhccccceEEEEecC-----ceEEEEecCCCchhHHHHHhh
Q 006991 490 VFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-----SCAIVVFGKPGLSNTFKNVMN 547 (622)
Q Consensus 490 v~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-----t~a~V~~~~~~~~~~~l~~~~ 547 (622)
+++.+.|..++..+|++.+.+ ||+...+...-+ ..+||.|.+++.+..++..++
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~----~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~ 60 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSK----FGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALN 60 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHh----cCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhC
Confidence 456788888888888877653 444345555543 579999999999888776544
No 71
>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=72.39 E-value=17 Score=35.86 Aligned_cols=107 Identities=12% Similarity=0.161 Sum_probs=62.2
Q ss_pred HHHHHHHHhC-CCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcc----------cccC
Q 006991 315 REVIDLISAS-QKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPV----------KKMT 383 (622)
Q Consensus 315 r~Vi~~L~~s-kKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~----------~~~~ 383 (622)
...++.|.+. +.+-||||+--|+-.+++.| |-++.- + ...-.++||..++..+... ....
T Consensus 71 ~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~-~~~~~~---~-----~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~ 141 (193)
T cd06146 71 DRLLKRLFEDPDVLKLGFGFKQDLKALSASY-PALKCM---F-----ERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTK 141 (193)
T ss_pred HHHHHHHhCCCCeeEEEechHHHHHHHHHhc-Cccccc---c-----ccCCceEEHHHHHHHHhhccccccccccCcccC
Confidence 3444445445 45569999999999999755 322210 0 0124599999888765422 1345
Q ss_pred chHHHHHHHHhcCCCCceeecCCCCC----CCCcccchhhHHHHHHHHHHHH
Q 006991 384 NISATIAYLKNRFFAPIEMEIPNQAN----ENEGKIHGHNVVKICQLFGKLC 431 (622)
Q Consensus 384 ~L~~~~~~l~~~~~~~p~ve~~~~~~----~~~~h~AGyDA~mTg~vF~~l~ 431 (622)
+|+.+.+.+-....... ....+=.. ...-+-|+-|||..-.+|-+|+
T Consensus 142 sL~~l~~~~lg~~l~K~-~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 142 GLADLVQEVLGKPLDKS-EQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred CHHHHHHHHhCCCcCcc-cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 78887776643221110 11000001 1122459999999999998886
No 72
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=71.54 E-value=7.1 Score=40.34 Aligned_cols=48 Identities=19% Similarity=0.405 Sum_probs=35.8
Q ss_pred hhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 47 HISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 47 ~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.|++..||+||+|.||+.+. +-.|+|+|...+..+. ...+|+.++-|.
T Consensus 3 ~l~~~~~v~~D~ETTGl~~~-----------------------~d~IIEIa~v~v~~~~---~~~~~~~li~P~ 50 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDVK-----------------------KDRIIEFAAIRFTFDE---VIDSVEFLINPE 50 (250)
T ss_pred cccCCcEEEEEEeCCCCCCC-----------------------CCeEEEEEEEEEECCe---EEEEEEEEECcC
Confidence 57788999999999998421 2359999988876432 346788888774
No 73
>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=70.40 E-value=3.6 Score=37.61 Aligned_cols=42 Identities=12% Similarity=0.129 Sum_probs=31.5
Q ss_pred EEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 54 IAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 54 VAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
|.||+|.||+.+ ..-.|+|+|.+.+..+ .-....||.++-|.
T Consensus 1 v~~D~Ettg~~~-----------------------~~~~iiei~~v~~~~~--~~~~~~~~~~i~p~ 42 (159)
T cd06127 1 VVFDTETTGLDP-----------------------KKDRIIEIGAVKVDGG--IEIVERFETLVNPG 42 (159)
T ss_pred CeEEeeCCCcCC-----------------------CCCeEEEEEEEEEECC--cChhhhhheeeCcC
Confidence 579999999832 2456999999998765 33456788888775
No 74
>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=70.18 E-value=27 Score=33.17 Aligned_cols=96 Identities=16% Similarity=0.197 Sum_probs=57.9
Q ss_pred HHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhc-CCCC
Q 006991 321 ISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNR-FFAP 399 (622)
Q Consensus 321 L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~-~~~~ 399 (622)
+...+...||||+=.|+-.+.+.| |-- +..++||..++..+++-....+|..+.+.+-.. ...+
T Consensus 69 l~~~~i~kv~~~~k~D~~~L~~~~-g~~--------------~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~ 133 (170)
T cd06141 69 LEDPSILKVGVGIKGDARKLARDF-GIE--------------VRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKP 133 (170)
T ss_pred hcCCCeeEEEeeeHHHHHHHHhHc-CCC--------------CCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCC
Confidence 444456679999999999987655 221 345799998887777643334777777665322 1111
Q ss_pred ceeecCCCCC----CCCcccchhhHHHHHHHHHHHH
Q 006991 400 IEMEIPNQAN----ENEGKIHGHNVVKICQLFGKLC 431 (622)
Q Consensus 400 p~ve~~~~~~----~~~~h~AGyDA~mTg~vF~~l~ 431 (622)
..+....=.. ...-+-|+-||+..-.++-+|.
T Consensus 134 k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 134 KKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 1111111011 1122559999999999987774
No 75
>PRK05359 oligoribonuclease; Provisional
Probab=69.89 E-value=7.1 Score=38.32 Aligned_cols=47 Identities=15% Similarity=0.135 Sum_probs=31.2
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.-.||++|+|.||+.+.. =.|+|+|.-..+.+. .-....|++++.|.
T Consensus 2 ~~~~vvlD~ETTGLdp~~-----------------------d~IieIgaV~~~~~~-~~~~~~~~~~i~~~ 48 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPER-----------------------DRIIEIATIVTDADL-NILAEGPVIAIHQS 48 (181)
T ss_pred CCcEEEEEeecCCCCCCC-----------------------CeEEEEEEEEEcCCc-eEcccceEEEECCC
Confidence 347999999999995321 138999987653322 22335677877775
No 76
>PRK07740 hypothetical protein; Provisional
Probab=69.66 E-value=5.9 Score=40.77 Aligned_cols=55 Identities=16% Similarity=0.225 Sum_probs=36.4
Q ss_pred HHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 42 SEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 42 ~~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
+.+..-+.+.+||.||+|.||+.+. ..-.|||+|....+ ++.-....|..++-|.
T Consensus 50 ~~~~~~~~~~~~vv~D~ETTGl~p~----------------------~~deIIeIgaV~~~--~~~i~~~~f~~lv~P~ 104 (244)
T PRK07740 50 DVLDIPLTDLPFVVFDLETTGFSPQ----------------------QGDEILSIGAVKTK--GGEVETDTFYSLVKPK 104 (244)
T ss_pred CccCCCccCCCEEEEEEeCCCCCCC----------------------CCCeEEEEEEEEEE--CCEEEEEEEEEEeCcC
Confidence 3334446778999999999998421 01358999987765 3322456777777664
No 77
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=68.56 E-value=8.6 Score=41.20 Aligned_cols=44 Identities=16% Similarity=0.285 Sum_probs=33.0
Q ss_pred CCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 51 SDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 51 a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.+||++|+|+||+.+ ..-.|+|+|...+. ++ -....|+.++-|.
T Consensus 8 ~~~Vv~DlETTGl~p-----------------------~~~eIIEIgaV~v~--~g-~i~~~f~~lVkP~ 51 (313)
T PRK06807 8 LDYVVIDFETTGFNP-----------------------YNDKIIQVAAVKYR--NH-ELVDQFVSYVNPE 51 (313)
T ss_pred CCEEEEEEECCCCCC-----------------------CCCeEEEEEEEEEE--CC-EEEEEEEEEECcC
Confidence 489999999999932 12379999988775 22 2467889888885
No 78
>cd02642 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=67.35 E-value=10 Score=30.73 Aligned_cols=21 Identities=10% Similarity=0.042 Sum_probs=17.6
Q ss_pred CccccccchHHHHHHHHHHHh
Q 006991 242 SMTIDVCSERQVQLVLKMLED 262 (622)
Q Consensus 242 ~l~l~~~~~~q~~Lv~q~l~~ 262 (622)
.+.+++.|++||.|+|++.+.
T Consensus 23 ~~~f~pm~sy~RllvH~la~~ 43 (63)
T cd02642 23 SLELPPMNSYYRLLAHRVAQY 43 (63)
T ss_pred eeEcCCCCcHHHHHHHHHHHH
Confidence 466788999999999998665
No 79
>PRK05755 DNA polymerase I; Provisional
Probab=66.76 E-value=18 Score=44.21 Aligned_cols=102 Identities=12% Similarity=0.056 Sum_probs=62.3
Q ss_pred HHHHHHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcC
Q 006991 317 VIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRF 396 (622)
Q Consensus 317 Vi~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~ 396 (622)
+.+.|.....++||||.=.|+-++++. | +|- -..++||..++.-+.|-.. .+|..+.+......
T Consensus 362 l~~~L~d~~v~kV~HNakfDl~~L~~~--g-i~~------------~~~~~DT~iAa~Ll~~~~~-~~L~~L~~~ylg~~ 425 (880)
T PRK05755 362 LKPLLEDPAIKKVGQNLKYDLHVLARY--G-IEL------------RGIAFDTMLASYLLDPGRR-HGLDSLAERYLGHK 425 (880)
T ss_pred HHHHHhCCCCcEEEeccHhHHHHHHhC--C-CCc------------CCCcccHHHHHHHcCCCCC-CCHHHHHHHHhCCC
Confidence 445566667789999999999999853 2 221 1458999987766655322 56666665542211
Q ss_pred CCCceee-c-CCCCCC------CCcccchhhHHHHHHHHHHHHHHhcc
Q 006991 397 FAPIEME-I-PNQANE------NEGKIHGHNVVKICQLFGKLCSILKI 436 (622)
Q Consensus 397 ~~~p~ve-~-~~~~~~------~~~h~AGyDA~mTg~vF~~l~~~l~~ 436 (622)
.+..+ + ...... ...|-|+.|+..|..+|.+|...|..
T Consensus 426 --~~~~~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~~ 471 (880)
T PRK05755 426 --TISFEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLLE 471 (880)
T ss_pred --ccchHHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 00000 0 000000 12255899999999999999998743
No 80
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=66.58 E-value=9.2 Score=40.95 Aligned_cols=46 Identities=13% Similarity=0.222 Sum_probs=33.6
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.-+||+||+|.||+.+ ..-.|||+|...++.++. ....|..++-|.
T Consensus 14 ~~~fvvlD~ETTGl~p-----------------------~~d~IIeIgav~v~~~g~--i~~~~~~lv~P~ 59 (313)
T PRK06063 14 PRGWAVVDVETSGFRP-----------------------GQARIISLAVLGLDADGN--VEQSVVTLLNPG 59 (313)
T ss_pred CCCEEEEEEECCCCCC-----------------------CCCEEEEEEEEEEECCce--eeeEEEEEECcC
Confidence 3589999999999942 123699999998876553 346677777664
No 81
>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=64.51 E-value=9.9 Score=36.05 Aligned_cols=44 Identities=14% Similarity=0.253 Sum_probs=30.6
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
||++|+|.||+.+. ..-.|+|+|...+... .-....|++++-|.
T Consensus 1 ~v~~D~ETTGl~~~----------------------~~~~iieig~v~v~~~--~~~~~~~~~~v~P~ 44 (167)
T cd06131 1 QIVLDTETTGLDPR----------------------EGHRIIEIGCVELINR--RLTGNTFHVYINPE 44 (167)
T ss_pred CEEEEeeCCCCCCC----------------------CCCeEEEEEEEEEECC--cEeccEEEEEECCC
Confidence 69999999998320 2457999998876542 22345788887664
No 82
>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=64.30 E-value=12 Score=34.73 Aligned_cols=40 Identities=13% Similarity=0.253 Sum_probs=29.4
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
||++|+|.||.. .-.|+|+|...+.. + . ....|+.++-|.
T Consensus 1 ~v~~D~Ettg~~-------------------------~~~ii~ig~v~~~~-~-~-~~~~~~~~i~p~ 40 (156)
T cd06130 1 FVAIDFETANAD-------------------------RASACSIGLVKVRD-G-Q-IVDTFYTLIRPP 40 (156)
T ss_pred CEEEEEeCCCCC-------------------------CCceEEEEEEEEEC-C-E-EEEEEEEEeCcC
Confidence 799999999852 11379999988863 2 2 347789998885
No 83
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=64.04 E-value=13 Score=39.56 Aligned_cols=47 Identities=11% Similarity=0.112 Sum_probs=34.4
Q ss_pred CCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCC--Cce-eeEeeEEeecCc
Q 006991 51 SDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQA--SKV-IAYPYNFHLFPR 120 (622)
Q Consensus 51 a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~--~~y-~~~~fNF~lfp~ 120 (622)
-.+|++|+|.||+.+. .=.|||+|+..|+.+. .-+ ....|++++-|.
T Consensus 37 ~~~vvlD~ETTGLd~~-----------------------~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~ 86 (294)
T PRK09182 37 RLGVILDTETTGLDPR-----------------------KDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPS 86 (294)
T ss_pred CeEEEEEeeCCCCCCC-----------------------CCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCC
Confidence 3689999999999421 2249999999998753 222 457888888774
No 84
>PRK07883 hypothetical protein; Validated
Probab=62.45 E-value=12 Score=43.26 Aligned_cols=52 Identities=13% Similarity=0.261 Sum_probs=38.3
Q ss_pred HHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 43 EIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 43 ~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.+..-|.+..||+||+|.||+.+ ..-.|+|+|...++ ++. ....|+.++-|.
T Consensus 7 ~~~~~~~~~~~Vv~D~ETTGl~p-----------------------~~~~IIEIgaV~v~--~g~-iv~~f~~lV~P~ 58 (557)
T PRK07883 7 DLGTPLRDVTFVVVDLETTGGSP-----------------------AGDAITEIGAVKVR--GGE-VLGEFATLVNPG 58 (557)
T ss_pred hhCCCCcCCCEEEEEEecCCCCC-----------------------CCCeEEEEEEEEEE--CCE-EEEEEEEEECCC
Confidence 34456888999999999999942 12469999998875 222 346788888885
No 85
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=62.01 E-value=11 Score=37.62 Aligned_cols=51 Identities=10% Similarity=0.128 Sum_probs=32.7
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
...||++|+|+||+.....+ ..+ .-.|||+|...++.. . ....|+-++-|.
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~--~~~---------------~~eIIeIGaV~v~~~--~-i~~~f~~lV~P~ 53 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKP--KGF---------------FPEIIEVGLVSVVGC--E-VEDTFSSYVKPK 53 (207)
T ss_pred cceEEEEEeecCCcCCCCCC--CCC---------------CCceEEEeEEEEecC--c-ChhhhcceECCC
Confidence 46899999999998421100 000 014999998877532 2 346788888775
No 86
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=61.28 E-value=16 Score=37.72 Aligned_cols=47 Identities=13% Similarity=0.214 Sum_probs=33.3
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.-.||++|+|-||+.+. ..=.|||+|...+. +...+...|+.|+-|.
T Consensus 3 ~~r~vvlDtETTGldp~----------------------~~drIIEIGaV~v~--~~~~~~~~f~~~i~P~ 49 (240)
T PRK05711 3 IMRQIVLDTETTGLNQR----------------------EGHRIIEIGAVELI--NRRLTGRNFHVYIKPD 49 (240)
T ss_pred CCeEEEEEeeCCCcCCC----------------------CCCeEEEEEEEEEE--CCEEeccEEEEEECcC
Confidence 34799999999999421 13369999986654 3333556789998884
No 87
>cd02325 R3H R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=59.56 E-value=14 Score=28.08 Aligned_cols=23 Identities=13% Similarity=0.268 Sum_probs=19.7
Q ss_pred CccccccchHHHHHHHHHHHhcc
Q 006991 242 SMTIDVCSERQVQLVLKMLEDFS 264 (622)
Q Consensus 242 ~l~l~~~~~~q~~Lv~q~l~~~~ 264 (622)
.+.++++++++|+++|++++.+.
T Consensus 19 ~~~~~p~~~~~R~~vH~la~~~~ 41 (59)
T cd02325 19 SLELPPMNSYERKLIHDLAEYYG 41 (59)
T ss_pred eEEcCCCCHHHHHHHHHHHHHCC
Confidence 46778899999999999987766
No 88
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=59.54 E-value=20 Score=37.35 Aligned_cols=51 Identities=18% Similarity=0.245 Sum_probs=37.0
Q ss_pred HHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 44 IKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 44 i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
...-+.+..||++|+|-||..+. .-.|+|+|...++ ++. ....|..++.|.
T Consensus 61 ~~~~~~~~~~vv~DiETTG~~~~-----------------------~~~IIEIGAv~v~--~g~-i~~~f~~~v~p~ 111 (257)
T PRK08517 61 RFTPIKDQVFCFVDIETNGSKPK-----------------------KHQIIEIGAVKVK--NGE-IIDRFESFVKAK 111 (257)
T ss_pred CCCCCCCCCEEEEEEeCCCCCCC-----------------------CCeEEEEEEEEEE--CCE-EEEEEEEEECCC
Confidence 33446889999999999998421 1369999998886 222 346788888874
No 89
>cd01201 Neurobeachin Neurobeachin Pleckstrin homology-like domain. Neurobeachin Pleckstrin homology-like domain. This domain is found in the large multi-domain eukaryotic protein Nerubeachin, N-terminal to the BEACH domain. This PH-like domain interacts with the BEACH domain in the same manner used by other PH-like domains to bind peptides.
Probab=59.28 E-value=14 Score=33.49 Aligned_cols=49 Identities=6% Similarity=0.099 Sum_probs=35.0
Q ss_pred cccchhHHHHhhhhhhhccccceEEEEecCceEEEEecCCCchhHHHHH
Q 006991 497 ERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNV 545 (622)
Q Consensus 497 ~~~~~~~i~~~l~~~~~~F~~~~~V~~id~t~a~V~~~~~~~~~~~l~~ 545 (622)
.+|+..+|++.-..=.-+-....+|.|.|.++.|+.|.....+..++.+
T Consensus 56 ~~w~ls~Ir~v~~RRylLr~~alEiF~~d~~~~f~~F~~~~~~k~vv~~ 104 (108)
T cd01201 56 GKWPFSEIRAIFSRRYLLQNTALELFLASRTSIFFAFPDQNAVKKVVYA 104 (108)
T ss_pred ceeeHHHHHHHHHHhhhcccceEEEEEeCCceEEEEeCcHHHHHHHHhh
Confidence 3688888776544322222222599999999999999999888876654
No 90
>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=59.22 E-value=49 Score=31.41 Aligned_cols=95 Identities=9% Similarity=0.112 Sum_probs=55.7
Q ss_pred HHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 006991 321 ISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 400 (622)
Q Consensus 321 L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p 400 (622)
|...+...||||+--|+-.+++.| |-. +..++||..++..+++- ...+|..+.+.+..... ..
T Consensus 63 L~d~~i~Kvg~~~k~D~~~L~~~~-gi~--------------~~~~~D~~~aa~ll~~~-~~~~L~~l~~~~lg~~l-~K 125 (161)
T cd06129 63 LENPSIVKALHGIEGDLWKLLRDF-GEK--------------LQRLFDTTIAANLKGLP-ERWSLASLVEHFLGKTL-DK 125 (161)
T ss_pred hCCCCEEEEEeccHHHHHHHHHHc-CCC--------------cccHhHHHHHHHHhCCC-CCchHHHHHHHHhCCCC-Cc
Confidence 334445569999999998887654 322 23468998877666543 22367777665432111 11
Q ss_pred eeecCCCCC----CCCcccchhhHHHHHHHHHHHHH
Q 006991 401 EMEIPNQAN----ENEGKIHGHNVVKICQLFGKLCS 432 (622)
Q Consensus 401 ~ve~~~~~~----~~~~h~AGyDA~mTg~vF~~l~~ 432 (622)
.+...+=.. ....+=|+.||+..-.+|-+|.+
T Consensus 126 ~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 126 SISCADWSYRPLTEDQKLYAAADVYALLIIYTKLRN 161 (161)
T ss_pred cceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 111110001 11224599999999999988864
No 91
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=57.69 E-value=51 Score=26.21 Aligned_cols=28 Identities=14% Similarity=0.050 Sum_probs=19.9
Q ss_pred CccccccchHHHHHHHHHHHhccCCcceee
Q 006991 242 SMTIDVCSERQVQLVLKMLEDFSDVLVPLI 271 (622)
Q Consensus 242 ~l~l~~~~~~q~~Lv~q~l~~~~~~l~~~~ 271 (622)
.+.+++.++++|++||++.+ +.+|.+..
T Consensus 22 ~~~f~pm~~~~R~~iH~~a~--~~gL~s~S 49 (63)
T PF01424_consen 22 SLEFPPMNSFERKLIHELAE--YYGLKSKS 49 (63)
T ss_dssp EEEEEC--SHHHHHHHHHHH--HCTEEEEE
T ss_pred EEEECCCCHHHHHHHHHHHH--HCCCEEEE
Confidence 46778899999999999877 44666544
No 92
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=57.14 E-value=44 Score=31.57 Aligned_cols=59 Identities=15% Similarity=0.309 Sum_probs=42.5
Q ss_pred CCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecC-------ceEEEEecCCCchhHHHHHhhhc
Q 006991 487 EDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-------SCAIVVFGKPGLSNTFKNVMNSK 549 (622)
Q Consensus 487 ~~vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-------t~a~V~~~~~~~~~~~l~~~~~~ 549 (622)
..-|||-+.|...+..+|++.+. -|++..+|..+-+ -.+||.|.+.+.|+..+..++..
T Consensus 34 ~~~lfVgnL~~~~te~~L~~~F~----~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~ 99 (144)
T PLN03134 34 STKLFIGGLSWGTDDASLRDAFA----HFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK 99 (144)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHh----cCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence 44688889999888888777554 3454345555422 35999999999999988877543
No 93
>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=56.51 E-value=36 Score=32.63 Aligned_cols=103 Identities=12% Similarity=0.063 Sum_probs=60.0
Q ss_pred HHHHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCC
Q 006991 319 DLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFA 398 (622)
Q Consensus 319 ~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~ 398 (622)
+.+.+....+||||.=.|+-++.+..+. +| ..++||..++.-+.|-....+|..+.+.+......
T Consensus 61 ~~l~~~~~~~v~hn~k~d~~~l~~~gi~-~~--------------~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~ 125 (193)
T cd06139 61 PLLEDPSIKKVGQNLKFDLHVLANHGIE-LR--------------GPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTI 125 (193)
T ss_pred HHHhCCCCcEEeeccHHHHHHHHHCCCC-CC--------------CCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCc
Confidence 3444556789999999999988765333 22 24799988877667644123677776654321100
Q ss_pred C-ceee-c-CCC---CCC---CCcccchhhHHHHHHHHHHHHHHhcc
Q 006991 399 P-IEME-I-PNQ---ANE---NEGKIHGHNVVKICQLFGKLCSILKI 436 (622)
Q Consensus 399 ~-p~ve-~-~~~---~~~---~~~h~AGyDA~mTg~vF~~l~~~l~~ 436 (622)
. .++- - ... +.. ...|-|+.|+..|..++-.|...+..
T Consensus 126 ~~~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 126 SFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred cHHHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 0 0000 0 000 000 01123788999999999999887743
No 94
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=56.46 E-value=20 Score=42.44 Aligned_cols=99 Identities=17% Similarity=0.290 Sum_probs=62.7
Q ss_pred EEEeccccccchhHHHHhhhhhhhccccceEEEEecC-ceEEEEecCCCchhHHHHHhhhcccccc---chhhhcCCccc
Q 006991 490 VFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-SCAIVVFGKPGLSNTFKNVMNSKAVSGP---LREMVSDGLKA 565 (622)
Q Consensus 490 v~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-t~a~V~~~~~~~~~~~l~~~~~~~~~~~---l~~~~~~g~~~ 565 (622)
+++=+-++.++..||++.+. -||....|..|.. .||||...++..|+.+|.++++..+..- ++=-++-|.|.
T Consensus 424 LwvG~i~k~v~e~dL~~~fe----efGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~ks 499 (894)
T KOG0132|consen 424 LWVGGIPKNVTEQDLANLFE----EFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKS 499 (894)
T ss_pred eeeccccchhhHHHHHHHHH----hcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcch
Confidence 33344577777777665443 4444346666655 4899999999999999999986542111 12245666777
Q ss_pred cchHHHHHhhhcCCch---hhHHHHHHHHhhc
Q 006991 566 AGYETYQRVCSSGLWE---SALADALDKTLAS 594 (622)
Q Consensus 566 a~~~~y~~~c~~~~~~---~~~a~~~~~~~~~ 594 (622)
-|-.|.| ..+|++. ..|.|++++-|+.
T Consensus 500 -e~k~~wD-~~lGVt~IP~~kLt~dl~~~~eg 529 (894)
T KOG0132|consen 500 -EYKDYWD-VELGVTYIPWEKLTDDLEAWCEG 529 (894)
T ss_pred -hhhhhhh-cccCeeEeehHhcCHHHHHhhhh
Confidence 7777777 4455543 3455667776653
No 95
>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=56.31 E-value=21 Score=36.32 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=30.3
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
||.+|+|.||+.+.. .=.|||+|...+.. ..-+...|..|+-|.
T Consensus 2 ~vvlD~ETTGl~p~~----------------------~d~IIEIgav~~~~--~~~~~~~f~~~i~P~ 45 (225)
T TIGR01406 2 QIILDTETTGLDPKG----------------------GHRIVEIGAVELVN--RMLTGDNFHVYVNPE 45 (225)
T ss_pred EEEEEeeCCCcCCCC----------------------CCeEEEEEEEEEEC--CcEecceEEEEECcC
Confidence 899999999994310 12599999775542 223446788888774
No 96
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=55.86 E-value=44 Score=36.58 Aligned_cols=100 Identities=14% Similarity=0.208 Sum_probs=68.2
Q ss_pred HHHHHHHHHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHH
Q 006991 314 FREVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLK 393 (622)
Q Consensus 314 Fr~Vi~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~ 393 (622)
..-+...|......=|-|++-.||-.+++.| |-+| +.|||||..+ .+..+....++..+.+.+.
T Consensus 59 ~~~l~~Ll~d~~v~KIfHaa~~DL~~l~~~~-g~~p--------------~plfdTqiAa-~l~g~~~~~gl~~Lv~~ll 122 (361)
T COG0349 59 LPPLVALLADPNVVKIFHAARFDLEVLLNLF-GLLP--------------TPLFDTQIAA-KLAGFGTSHGLADLVEELL 122 (361)
T ss_pred cchHHHHhcCCceeeeeccccccHHHHHHhc-CCCC--------------CchhHHHHHH-HHhCCcccccHHHHHHHHh
Confidence 3444555555555559999999999999888 8888 4589999855 4444444667888887774
Q ss_pred hcCCCCceeecCCCCC-C--C--Cc-----ccchhhHHHHHHHHHHHHHHhcc
Q 006991 394 NRFFAPIEMEIPNQAN-E--N--EG-----KIHGHNVVKICQLFGKLCSILKI 436 (622)
Q Consensus 394 ~~~~~~p~ve~~~~~~-~--~--~~-----h~AGyDA~mTg~vF~~l~~~l~~ 436 (622)
+ |++..... . . .- --|..|...--.++.+|...|--
T Consensus 123 ~-------v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~ 168 (361)
T COG0349 123 G-------VELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAR 168 (361)
T ss_pred C-------CcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3 44443221 1 1 11 12799999999999999998833
No 97
>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=55.19 E-value=36 Score=30.83 Aligned_cols=59 Identities=14% Similarity=0.174 Sum_probs=39.5
Q ss_pred HHHHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHH
Q 006991 319 DLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYL 392 (622)
Q Consensus 319 ~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l 392 (622)
+.+...+..+||||.=.|+-++.+.+ +.+| +.++||..++--+.|-....+|..+.+..
T Consensus 48 ~~l~~~~~~~v~~~~k~d~~~L~~~~-~~~~--------------~~~~D~~~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 48 ELLEDEDITKVGHDAKFDLVVLARDG-IELP--------------GNIFDTMLAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred HHHcCCCCcEEeccHHHHHHHHHHCC-CCCC--------------CCcccHHHHHHHhCCCCCcCCHHHHHHHH
Confidence 33445667899999999988887654 2222 35799988777777644123677766654
No 98
>PF15023 DUF4523: Protein of unknown function (DUF4523)
Probab=54.85 E-value=25 Score=33.61 Aligned_cols=62 Identities=23% Similarity=0.333 Sum_probs=48.0
Q ss_pred CcCCEEEEeccccccch-hHHHHhhhhhhhccccceEEEEecCceEEEEecCCCchhHHHHHhhh
Q 006991 485 SCEDVVFLWGFRERISA-GILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNS 548 (622)
Q Consensus 485 ~~~~vv~i~~f~~~~~~-~~i~~~l~~~~~~F~~~~~V~~id~t~a~V~~~~~~~~~~~l~~~~~ 548 (622)
+-..||.-|. .+.++. .|++++++++ .+||+--.|-....++|.|+|..-.+|=..+.|+-+
T Consensus 85 PMsTIVVRWl-kknm~~~edl~sV~~~L-s~fGpI~SVT~cGrqsavVvF~d~~SAC~Av~Af~s 147 (166)
T PF15023_consen 85 PMSTIVVRWL-KKNMQPTEDLKSVIQRL-SVFGPIQSVTLCGRQSAVVVFKDITSACKAVSAFQS 147 (166)
T ss_pred CceeEEeehh-hhcCChHHHHHHHHHHH-HhcCCcceeeecCCceEEEEehhhHHHHHHHHhhcC
Confidence 3456777787 666655 7889888865 469997799999999999999998887767776644
No 99
>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=53.86 E-value=23 Score=34.45 Aligned_cols=46 Identities=15% Similarity=0.270 Sum_probs=32.1
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCC--Cce--------eeEeeEEeecCc
Q 006991 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQA--SKV--------IAYPYNFHLFPR 120 (622)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~--~~y--------~~~~fNF~lfp~ 120 (622)
||++|+|-||+.+. .+=.|+|+|....+.++ ... ....|++++-|.
T Consensus 1 ~vv~D~ETTGl~~~----------------------~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~ 56 (177)
T cd06136 1 FVFLDLETTGLPKH----------------------NRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPG 56 (177)
T ss_pred CeEEeeecCCCCCC----------------------CCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCC
Confidence 89999999999411 11259999998877553 111 356788888884
No 100
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=51.89 E-value=30 Score=37.65 Aligned_cols=59 Identities=12% Similarity=0.242 Sum_probs=42.6
Q ss_pred CCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecC-------ceEEEEecCCCchhHHHHHhhhc
Q 006991 487 EDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-------SCAIVVFGKPGLSNTFKNVMNSK 549 (622)
Q Consensus 487 ~~vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-------t~a~V~~~~~~~~~~~l~~~~~~ 549 (622)
+.-|||-+.|..++..+|++.++ -|+....|..+-+ .++||.|.+.+.|...+.+++..
T Consensus 193 ~~~lfV~nLp~~vtee~L~~~F~----~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~ 258 (346)
T TIGR01659 193 DTNLYVTNLPRTITDDQLDTIFG----KYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNV 258 (346)
T ss_pred cceeEEeCCCCcccHHHHHHHHH----hcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence 44578889999998888776544 3343335554433 37999999999999988887654
No 101
>PRK10829 ribonuclease D; Provisional
Probab=48.33 E-value=59 Score=35.82 Aligned_cols=98 Identities=13% Similarity=0.174 Sum_probs=62.5
Q ss_pred HHHHHHHHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHh
Q 006991 315 REVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKN 394 (622)
Q Consensus 315 r~Vi~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~ 394 (622)
..+.+.|.+.+.+-|+|++-.|+-.+++ .+|-.| ..++||...+.-++ .....+++.+.+.+.+
T Consensus 64 ~~L~~ll~~~~ivKV~H~~~~Dl~~l~~-~~g~~p--------------~~~fDTqiaa~~lg-~~~~~gl~~Lv~~~lg 127 (373)
T PRK10829 64 SPFKALLRDPQVTKFLHAGSEDLEVFLN-AFGELP--------------QPLIDTQILAAFCG-RPLSCGFASMVEEYTG 127 (373)
T ss_pred HHHHHHHcCCCeEEEEeChHhHHHHHHH-HcCCCc--------------CCeeeHHHHHHHcC-CCccccHHHHHHHHhC
Confidence 3344445555555589999999999876 445444 34899977555443 3333477887776643
Q ss_pred cCCCCceeecCCCCC-----C-----CCcccchhhHHHHHHHHHHHHHHhc
Q 006991 395 RFFAPIEMEIPNQAN-----E-----NEGKIHGHNVVKICQLFGKLCSILK 435 (622)
Q Consensus 395 ~~~~~p~ve~~~~~~-----~-----~~~h~AGyDA~mTg~vF~~l~~~l~ 435 (622)
|+++.... . ..-+-|.-|+.-.-.+|-+|...|.
T Consensus 128 -------v~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 128 -------VTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred -------CccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22221111 1 1123489999999999999999885
No 102
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=48.08 E-value=15 Score=40.03 Aligned_cols=26 Identities=15% Similarity=0.050 Sum_probs=22.6
Q ss_pred HHHHHHHHhhcCCCeEEEecCCCCcc
Q 006991 39 ESLSEIKNHISSSDFIAVSLQNTGSF 64 (622)
Q Consensus 39 ~~l~~i~~~I~~a~FVAiD~EftGi~ 64 (622)
+.+..+...+..|.+|||||||.|..
T Consensus 5 ~~l~~~~~~~~~~~~iAiDTEf~r~~ 30 (361)
T COG0349 5 DLLAAACALLRGSKAIAIDTEFMRLR 30 (361)
T ss_pred hHHHHHHHHhcCCCceEEeccccccc
Confidence 45677888899999999999999985
No 103
>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=47.94 E-value=27 Score=33.81 Aligned_cols=75 Identities=11% Similarity=0.103 Sum_probs=43.7
Q ss_pred CCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhh---HHhhhCcccccCchHHHHHHHHhcCCCCc
Q 006991 324 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNY---LLKDIGPVKKMTNISATIAYLKNRFFAPI 400 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKy---La~~~~~~~~~~~L~~~~~~l~~~~~~~p 400 (622)
.+.+|||||.=+|+-|+-+.|-. +- ..+...++||-. |+..+.|-. .+
T Consensus 93 ~~~~lvgh~~~FD~~fL~~~~~~--------~~---~~~~~~~~D~~~l~~l~~~l~p~~--~~---------------- 143 (173)
T cd06135 93 GKSPLAGNSVHQDRRFLDKYMPE--------LE---EYLHYRILDVSSIKELARRWYPEI--YR---------------- 143 (173)
T ss_pred CCCceeecchhhCHHHHHHHHHH--------Hh---ccCCcchhhHHHHHHHHHHhCcHh--hh----------------
Confidence 46789999999999998765531 00 112334688743 333322200 00
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 006991 401 EMEIPNQANENEGKIHGHNVVKICQLFGKLCS 432 (622)
Q Consensus 401 ~ve~~~~~~~~~~h~AGyDA~mTg~vF~~l~~ 432 (622)
.. -.....|.|=.||..|+..+..+-.
T Consensus 144 -~~----~~~~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 144 -KA----PKKKGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred -cC----CCCCCCcchHHHHHHHHHHHHHHHH
Confidence 00 0123459999999999998765543
No 104
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=47.38 E-value=41 Score=25.70 Aligned_cols=55 Identities=16% Similarity=0.261 Sum_probs=38.3
Q ss_pred EEEeccccccchhHHHHhhhhhhhccccceEEEEec------CceEEEEecCCCchhHHHHHhhh
Q 006991 490 VFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVD------RSCAIVVFGKPGLSNTFKNVMNS 548 (622)
Q Consensus 490 v~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id------~t~a~V~~~~~~~~~~~l~~~~~ 548 (622)
+++.+.|..++..+|++.++++ ++...+...- ...+||.|.+++.+..++..+..
T Consensus 2 i~i~~l~~~~~~~~i~~~~~~~----g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~ 62 (74)
T cd00590 2 LFVGNLPPDVTEEDLRELFSKF----GKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNG 62 (74)
T ss_pred EEEeCCCCccCHHHHHHHHHhc----CCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence 5678888888888888877653 4333333333 35699999999998877765433
No 105
>smart00361 RRM_1 RNA recognition motif.
Probab=46.29 E-value=29 Score=28.14 Aligned_cols=47 Identities=13% Similarity=0.157 Sum_probs=32.7
Q ss_pred hHHHHhhhhhhhccccceEEE--EecCc--------eEEEEecCCCchhHHHHHhhh
Q 006991 502 GILKNMLQGSHEVFAEAFNVR--MVDRS--------CAIVVFGKPGLSNTFKNVMNS 548 (622)
Q Consensus 502 ~~i~~~l~~~~~~F~~~~~V~--~id~t--------~a~V~~~~~~~~~~~l~~~~~ 548 (622)
.+|++.++.-...||+.+.|. .+|.. .+||.|.+++.|...+..++.
T Consensus 3 ~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g 59 (70)
T smart00361 3 EDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNG 59 (70)
T ss_pred hhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCC
Confidence 356666654445777766664 66642 399999999999988776654
No 106
>PRK11779 sbcB exonuclease I; Provisional
Probab=46.04 E-value=50 Score=37.54 Aligned_cols=74 Identities=16% Similarity=0.188 Sum_probs=47.1
Q ss_pred cCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCccccccCCC
Q 006991 49 SSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDELKMGMP 128 (622)
Q Consensus 49 ~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~~~~~~~~~ 128 (622)
....||.+|+|.||+.+. .=.|+|+|.-.++.+. .-...+|++++-|...
T Consensus 4 ~~~~fvv~D~ETTGLdP~-----------------------~DrIIeiAaVrvd~~~-~~i~e~~~~~~~P~~~------ 53 (476)
T PRK11779 4 MQPTFLWHDYETFGANPA-----------------------LDRPAQFAGIRTDADL-NIIGEPLVFYCKPADD------ 53 (476)
T ss_pred CCCcEEEEEEECCCCCCC-----------------------CCeeEEEEEEEEeCCC-ceecceeEEEEcCCcC------
Confidence 456899999999999532 1149999987665443 2344689999888631
Q ss_pred CCceeechhHHHHHHHcCCCcchhhhcccc
Q 006991 129 SYSFTCQTSYLTAMAKEGFDFNTCIYDGIS 158 (622)
Q Consensus 129 d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~ 158 (622)
....+.| ..=||+-=..+..+|++
T Consensus 54 ---~lp~p~a---~~IhGIT~e~l~~~g~~ 77 (476)
T PRK11779 54 ---YLPSPEA---VLITGITPQEALEKGLP 77 (476)
T ss_pred ---cCCCHHH---HHHhCCCHHHHHhcCCC
Confidence 1122333 34477766666666663
No 107
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=43.45 E-value=63 Score=28.33 Aligned_cols=59 Identities=7% Similarity=0.054 Sum_probs=42.2
Q ss_pred CCEEEEecccc-----ccchhHHHHhhhhhhhccc-cceEEEEecCceEEEEecCCCchhHHHHH
Q 006991 487 EDVVFLWGFRE-----RISAGILKNMLQGSHEVFA-EAFNVRMVDRSCAIVVFGKPGLSNTFKNV 545 (622)
Q Consensus 487 ~~vv~i~~f~~-----~~~~~~i~~~l~~~~~~F~-~~~~V~~id~t~a~V~~~~~~~~~~~l~~ 545 (622)
++.+.-.++|. .|+..++++.|.+.+++=. ..+.++|.|+..-+|.+.+.+.....+..
T Consensus 8 ~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~ 72 (91)
T cd06398 8 GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQY 72 (91)
T ss_pred CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHH
Confidence 34444456664 5888999999988776532 23799999999999999988555544443
No 108
>PTZ00315 2'-phosphotransferase; Provisional
Probab=43.07 E-value=43 Score=38.95 Aligned_cols=49 Identities=8% Similarity=0.236 Sum_probs=35.2
Q ss_pred CCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 51 SDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 51 a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
-.||+||+|.||..+. + . +.-.||+||...++..+.+ ....|..|+-|.
T Consensus 56 d~~IV~DlETTgl~~~--~----~--------------~~dEIIEIGaV~Vd~~ng~-Ii~~F~~yVkP~ 104 (582)
T PTZ00315 56 DAYVVLDFEATCEADR--R----I--------------EDAEVIEFPMVLVDARTAT-PVAEFQRYVRPV 104 (582)
T ss_pred CeEEEEEEecCCCCCC--C----C--------------CCCceEEEEEEEEEccCCE-EEEEEEEEECCC
Confidence 4699999999997321 0 0 1235999999999765543 347899999996
No 109
>smart00360 RRM RNA recognition motif.
Probab=42.87 E-value=40 Score=25.43 Aligned_cols=50 Identities=18% Similarity=0.286 Sum_probs=33.1
Q ss_pred ccccccchhHHHHhhhhhhhccccceEEEEecC-------ceEEEEecCCCchhHHHHHhh
Q 006991 494 GFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-------SCAIVVFGKPGLSNTFKNVMN 547 (622)
Q Consensus 494 ~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-------t~a~V~~~~~~~~~~~l~~~~ 547 (622)
+.|..++..+|++.+++ ||+...+....+ ..+||.|.+++.+..++..++
T Consensus 3 ~l~~~~~~~~l~~~f~~----~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~ 59 (71)
T smart00360 3 NLPPDVTEEELRELFSK----FGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALN 59 (71)
T ss_pred CCCcccCHHHHHHHHHh----hCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcC
Confidence 45777888888876654 443333333332 279999999988887766554
No 110
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=42.70 E-value=47 Score=33.81 Aligned_cols=61 Identities=16% Similarity=0.242 Sum_probs=49.0
Q ss_pred EEEEeccccccchhHHHHhhhhhhhccccceEEEEecC----ceEEEEecCCCchhHHHHHhhhc
Q 006991 489 VVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR----SCAIVVFGKPGLSNTFKNVMNSK 549 (622)
Q Consensus 489 vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~----t~a~V~~~~~~~~~~~l~~~~~~ 549 (622)
-+||-....+++..+++.-|.-+++-||.-.+|.-+.- ..|||.|.+.+.|...+++++.-
T Consensus 11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gf 75 (221)
T KOG4206|consen 11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGF 75 (221)
T ss_pred eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCC
Confidence 67778889999999999988876666666568888754 35999999999999888877653
No 111
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=40.09 E-value=2.3e+02 Score=25.98 Aligned_cols=98 Identities=12% Similarity=0.075 Sum_probs=55.0
Q ss_pred HHHHHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCC
Q 006991 318 IDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFF 397 (622)
Q Consensus 318 i~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~ 397 (622)
.+.+...+.+.||||.=.|+-.+.+ +|--+ +.++||..++--+.|-....+|..+....-....
T Consensus 68 ~~~l~~~~~~kv~~d~k~~~~~L~~--~gi~~--------------~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~ 131 (172)
T smart00474 68 KDLLEDETITKVGHNAKFDLHVLAR--FGIEL--------------ENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVEL 131 (172)
T ss_pred HHHhcCCCceEEEechHHHHHHHHH--CCCcc--------------cchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCC
Confidence 3445566788999999888877763 44211 2259998766555664443477776655422111
Q ss_pred CCceeecCCCC--CCCCcc----cchhhHHHHHHHHHHHHHHh
Q 006991 398 APIEMEIPNQA--NENEGK----IHGHNVVKICQLFGKLCSIL 434 (622)
Q Consensus 398 ~~p~ve~~~~~--~~~~~h----~AGyDA~mTg~vF~~l~~~l 434 (622)
. ++. ...+ ...... -|+.||+.+..++-+|...|
T Consensus 132 ~--~~~-~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 132 D--KEE-QKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred C--ccc-CccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 010 0000 000011 27888888888887777654
No 112
>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=39.80 E-value=47 Score=40.50 Aligned_cols=43 Identities=23% Similarity=0.346 Sum_probs=31.4
Q ss_pred CeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 52 DFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 52 ~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.||++|+|.||+.+. .=.|||+|...+. ++. ....|..++-|.
T Consensus 1 ~~vvvD~ETTG~~~~-----------------------~~~IIeig~v~v~--~~~-i~~~f~~~v~P~ 43 (850)
T TIGR01407 1 RYAVVDLETTGTQLS-----------------------FDKIIQIGIVVVE--DGE-IVDTFHTDVNPN 43 (850)
T ss_pred CEEEEEEECCCCCCC-----------------------CCeEEEEEEEEEE--CCE-EEEEEEEEeCCC
Confidence 499999999998421 1239999998874 222 346788888886
No 113
>PF15342 FAM212: FAM212 family
Probab=38.32 E-value=19 Score=28.97 Aligned_cols=23 Identities=22% Similarity=0.229 Sum_probs=16.0
Q ss_pred CCCCEEechhHHHHHHHHHhccCCCCC
Q 006991 324 SQKPLVAHNSLNDFTFIHSKFLAPLPP 350 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F~gpLP~ 350 (622)
.++.|.|-|+|.||+.=+ =+||+
T Consensus 38 RQPLVLGDN~FADLV~NW----lDLPE 60 (62)
T PF15342_consen 38 RQPLVLGDNVFADLVGNW----LDLPE 60 (62)
T ss_pred CCCeeecccHHHHHHHhh----hcCcc
Confidence 455555999999998644 35554
No 114
>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=38.10 E-value=31 Score=30.04 Aligned_cols=28 Identities=25% Similarity=0.476 Sum_probs=20.5
Q ss_pred HHHHHHhCC-CCEEechhHHHHHHHHHhc
Q 006991 317 VIDLISASQ-KPLVAHNSLNDFTFIHSKF 344 (622)
Q Consensus 317 Vi~~L~~sk-KpIVGHN~llDL~~iy~~F 344 (622)
+.+.|.+.. +.+||||.=.|+.++.+.+
T Consensus 35 f~~~l~~~~~~v~V~hn~~fD~~fL~~~~ 63 (96)
T cd06125 35 LKDILRDKPLAILVGHNGSFDLPFLNNRC 63 (96)
T ss_pred HHHHHhhCCCCEEEEeCcHHhHHHHHHHH
Confidence 334454444 7899999989998888765
No 115
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=37.75 E-value=70 Score=34.82 Aligned_cols=59 Identities=14% Similarity=0.158 Sum_probs=43.4
Q ss_pred cCCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecC-------ceEEEEecCCCchhHHHHHhhh
Q 006991 486 CEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-------SCAIVVFGKPGLSNTFKNVMNS 548 (622)
Q Consensus 486 ~~~vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-------t~a~V~~~~~~~~~~~l~~~~~ 548 (622)
....|||-..|..++..+|++.++ .|++..+|..+-| ..|||.|.+.+.|...+..++.
T Consensus 106 ~~~~LfVgnLp~~~te~~L~~lF~----~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG 171 (346)
T TIGR01659 106 SGTNLIVNYLPQDMTDRELYALFR----TIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNG 171 (346)
T ss_pred CCcEEEEeCCCCCCCHHHHHHHHH----hcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCC
Confidence 456788788999999888777555 4455446665533 2599999999999988877654
No 116
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=37.11 E-value=56 Score=40.26 Aligned_cols=45 Identities=22% Similarity=0.313 Sum_probs=32.9
Q ss_pred CCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 51 SDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 51 a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
-.||++|+|.||+.+.. .-.|||+|.+.+. ++ -....|+.++-|.
T Consensus 3 ~~~vvvD~ETTG~~p~~----------------------~d~IIeigav~v~--~~-~i~~~f~~~v~P~ 47 (928)
T PRK08074 3 KRFVVVDLETTGNSPKK----------------------GDKIIQIAAVVVE--DG-EILERFSSFVNPE 47 (928)
T ss_pred CCEEEEEEeCCCCCCCC----------------------CCcEEEEEEEEEE--CC-EEEEEEEEEECcC
Confidence 46999999999984210 1269999999885 22 2356889999885
No 117
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=36.26 E-value=52 Score=26.14 Aligned_cols=21 Identities=10% Similarity=0.118 Sum_probs=17.4
Q ss_pred CccccccchHHHHHHHHHHHh
Q 006991 242 SMTIDVCSERQVQLVLKMLED 262 (622)
Q Consensus 242 ~l~l~~~~~~q~~Lv~q~l~~ 262 (622)
.+..++.++++|+.||++...
T Consensus 18 ~~~fppm~~~~R~~vH~lA~~ 38 (58)
T cd02646 18 SLSFPPMDKHGRKTIHKLANC 38 (58)
T ss_pred eEecCCCCHHHHHHHHHHHHH
Confidence 456778899999999998766
No 118
>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=34.00 E-value=64 Score=40.93 Aligned_cols=46 Identities=17% Similarity=0.361 Sum_probs=35.2
Q ss_pred cCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 49 SSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 49 ~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
.++.||++|+|.||+.+. .=.|+|+|...+.. + -....|++++-|.
T Consensus 188 ~~~~~VVfDiETTGL~~~-----------------------~d~IIEIGAVkv~~--g-~iid~f~~~V~P~ 233 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQ-----------------------YDEIIEFGAVKVKN--G-RIIDKFQFFIKPH 233 (1213)
T ss_pred cCCcEEEEEeEecCCCCC-----------------------CCeEEEEEEEEEEC--C-eEEEEEEEEECCC
Confidence 678999999999999421 12699999988763 2 2456799999885
No 119
>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=33.89 E-value=32 Score=32.27 Aligned_cols=27 Identities=22% Similarity=0.319 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhcCCCeEEEecCCCCcc
Q 006991 38 NESLSEIKNHISSSDFIAVSLQNTGSF 64 (622)
Q Consensus 38 ~~~l~~i~~~I~~a~FVAiD~EftGi~ 64 (622)
.+.+..+.+.+.++..||+|+|.+|+.
T Consensus 7 ~~~l~~~~~~l~~~~~~a~D~E~~~~~ 33 (176)
T PF01612_consen 7 EEELEEAIKKLKNAKVLAFDTETTGLD 33 (176)
T ss_dssp HHHHHHHHHHHTTTSEEEEEEEEETST
T ss_pred HHHHHHHHHHHcCCCeEEEEEEECCCC
Confidence 467888889999999999999999984
No 120
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=33.54 E-value=80 Score=26.48 Aligned_cols=27 Identities=15% Similarity=0.203 Sum_probs=22.0
Q ss_pred CccccccchHHHHHHHHHHHhccCCccee
Q 006991 242 SMTIDVCSERQVQLVLKMLEDFSDVLVPL 270 (622)
Q Consensus 242 ~l~l~~~~~~q~~Lv~q~l~~~~~~l~~~ 270 (622)
.+.+++.++++|++||+++..+ ++.+.
T Consensus 38 ~~~~~pm~~~~R~~iH~~a~~~--~l~s~ 64 (79)
T smart00393 38 SVELPPMNSYERKIVHELAEKY--GLESE 64 (79)
T ss_pred eEEcCCCCHHHHHHHHHHHHHc--CCEEE
Confidence 5678889999999999998875 66544
No 121
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=33.33 E-value=16 Score=42.36 Aligned_cols=128 Identities=9% Similarity=-0.066 Sum_probs=88.9
Q ss_pred CccceEEcCcc--cHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeee
Q 006991 25 HHWPIKQITKT--NFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFK 102 (622)
Q Consensus 25 ~~~~i~dVt~~--NF~~~l~~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~ 102 (622)
.+.++..+.++ |+...++.....+.+..+.+++.|++|+.. ..+ .....+..++++......+.++=+|+...-
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~---~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l 175 (564)
T KOG1990|consen 100 QRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGG-SDR---LSVDADLLPEKIPDYMRPFRTLPVGSPPLL 175 (564)
T ss_pred eecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCC-CCC---ccchhhhchhhhhcccChhccCCCCChhhh
Confidence 45566777777 899999999999999999999999999842 222 223345577777777777778777765432
Q ss_pred cCC-------CceeeEeeEEeecCccccccCCCCCceeechhHHHHHHHcCCCcchhhhcccccCCHHHHH
Q 006991 103 LQA-------SKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQES 166 (622)
Q Consensus 103 ~~~-------~~y~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~YLs~~eE~ 166 (622)
-.. ..|.+.+|+--.+.. ......+..++|..+|.|++ -++..|+.+-+.....
T Consensus 176 ~~~~~~~~r~~~~~~p~~~~~~~~~---------~~~~~~~~~~~~~~k~~~~k-~~~~rg~~~~~~~~~a 236 (564)
T KOG1990|consen 176 TSIESTLLRRLGYKLPPHFALGRSR---------KLQGLAVAMVSFWEKHEFAK-ILIKRGVLETRKERMA 236 (564)
T ss_pred hhHHHHHHHHhcccccccceehhcc---------ccccchhHHHHHHHHHHHHH-HHHHhcchhhhccchH
Confidence 221 345555544433332 23345577889999999999 8999999997765544
No 122
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=32.77 E-value=65 Score=25.93 Aligned_cols=21 Identities=19% Similarity=0.237 Sum_probs=17.5
Q ss_pred Cccccc-cchHHHHHHHHHHHh
Q 006991 242 SMTIDV-CSERQVQLVLKMLED 262 (622)
Q Consensus 242 ~l~l~~-~~~~q~~Lv~q~l~~ 262 (622)
.+.+++ .++.||+.||++.+.
T Consensus 19 ~l~F~p~ls~~eR~~vH~lA~~ 40 (60)
T cd02641 19 ELEFPPTLSSHDRLLVHELAEE 40 (60)
T ss_pred cEECCCCCCHHHHHHHHHHHHH
Confidence 466777 889999999998776
No 123
>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=31.92 E-value=20 Score=34.24 Aligned_cols=11 Identities=18% Similarity=0.305 Sum_probs=10.0
Q ss_pred EEEecCCCCcc
Q 006991 54 IAVSLQNTGSF 64 (622)
Q Consensus 54 VAiD~EftGi~ 64 (622)
||||+|+||+.
T Consensus 1 v~~D~EttGl~ 11 (157)
T cd06149 1 VAIDCEMVGTG 11 (157)
T ss_pred CEEEeEecccc
Confidence 69999999995
No 124
>cd02640 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=31.23 E-value=63 Score=26.13 Aligned_cols=21 Identities=14% Similarity=0.275 Sum_probs=17.4
Q ss_pred Cccccc-cchHHHHHHHHHHHh
Q 006991 242 SMTIDV-CSERQVQLVLKMLED 262 (622)
Q Consensus 242 ~l~l~~-~~~~q~~Lv~q~l~~ 262 (622)
.+.+++ +++.+|++||++.+.
T Consensus 19 ~l~f~p~lt~~eR~~vH~~a~~ 40 (60)
T cd02640 19 DMVFSPEFSKEERALIHQIAQK 40 (60)
T ss_pred eEEcCCCCCHHHHHHHHHHHHH
Confidence 356677 889999999998776
No 125
>cd02638 R3H_unknown_1 R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=30.57 E-value=98 Score=25.38 Aligned_cols=29 Identities=14% Similarity=0.152 Sum_probs=22.8
Q ss_pred CCccccccchHHHHHHHHHHHhccCCccee
Q 006991 241 PSMTIDVCSERQVQLVLKMLEDFSDVLVPL 270 (622)
Q Consensus 241 p~l~l~~~~~~q~~Lv~q~l~~~~~~l~~~ 270 (622)
..+.+++.+++.|++||++++.. +++.+.
T Consensus 19 r~v~LePM~~~ERkIIH~~Lq~~-~~v~T~ 47 (62)
T cd02638 19 RVLLFPPLNSRRRYLIHQTVENR-FLLSTF 47 (62)
T ss_pred CeEecCCCChHHHHHHHHHHhcC-CCceEE
Confidence 35778999999999999999864 455544
No 126
>PRK05359 oligoribonuclease; Provisional
Probab=30.12 E-value=1.8e+02 Score=28.38 Aligned_cols=21 Identities=19% Similarity=0.324 Sum_probs=17.9
Q ss_pred CCCCEEechhHHHHHHHHHhc
Q 006991 324 SQKPLVAHNSLNDFTFIHSKF 344 (622)
Q Consensus 324 skKpIVGHN~llDL~~iy~~F 344 (622)
...|+||||.=+|..||-+.+
T Consensus 97 ~~~~l~g~~v~FD~~FL~~~~ 117 (181)
T PRK05359 97 GKSPLCGNSIGQDRRFLARYM 117 (181)
T ss_pred CCCceeecchhhCHHHHHHHH
Confidence 467899999999999998765
No 127
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=29.39 E-value=1.3e+02 Score=25.87 Aligned_cols=55 Identities=11% Similarity=0.121 Sum_probs=41.7
Q ss_pred ecccc--ccchhHHHHhhhhhhhccccceEEEEecCceEEEEecCCCchhHHHHHhhhc
Q 006991 493 WGFRE--RISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSK 549 (622)
Q Consensus 493 ~~f~~--~~~~~~i~~~l~~~~~~F~~~~~V~~id~t~a~V~~~~~~~~~~~l~~~~~~ 549 (622)
..++. .|+-.+++..+...+.+ ..++|+|+|+-.=+|.++.....++.++...+.
T Consensus 14 f~~~~~~~~~~~~L~~ev~~rf~l--~~f~lKYlDde~e~v~lssd~eLeE~~rl~~~~ 70 (81)
T cd06396 14 FLVSDSENTTWASVEAMVKVSFGL--NDIQIKYVDEENEEVSVNSQGEYEEALKSAVRQ 70 (81)
T ss_pred EEecCCCCCCHHHHHHHHHHHhCC--CcceeEEEcCCCCEEEEEchhhHHHHHHHHHhC
Confidence 45665 77878888887754443 248999999999999999988888777765543
No 128
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=28.93 E-value=1e+02 Score=24.08 Aligned_cols=49 Identities=10% Similarity=0.201 Sum_probs=31.7
Q ss_pred CEEEEeccccccchhHHHHhhhhhhhccccceEEEEec-CceEEEEecCCCchhH
Q 006991 488 DVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVD-RSCAIVVFGKPGLSNT 541 (622)
Q Consensus 488 ~vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id-~t~a~V~~~~~~~~~~ 541 (622)
.+|.+.|||.. .+..+|..+.+ ||+-.++.+=+ ...++|.+.++..++.
T Consensus 2 ~wI~V~Gf~~~----~~~~vl~~F~~-fGeI~~~~~~~~~~~~~l~y~~~~~ae~ 51 (53)
T PF14605_consen 2 TWISVSGFPPD----LAEEVLEHFAS-FGEIVDIYVPESTNWMYLKYKSRKDAEK 51 (53)
T ss_pred cEEEEEeECch----HHHHHHHHHHh-cCCEEEEEcCCCCcEEEEEECCHHHHHh
Confidence 57788999864 23444444443 67655655553 4569999999877764
No 129
>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=28.27 E-value=1.2e+02 Score=29.33 Aligned_cols=41 Identities=24% Similarity=0.095 Sum_probs=27.9
Q ss_pred EEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 55 AVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 55 AiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
-+|+|.||+.+. .=.|||+|.-.++.+. . ....|++++-|.
T Consensus 2 ~~D~ETTGl~~~-----------------------~d~Iieig~v~v~~~~-~-~~~~~~~~v~p~ 42 (183)
T cd06138 2 FYDYETFGLNPS-----------------------FDQILQFAAIRTDENF-N-EIEPFNIFCRLP 42 (183)
T ss_pred EEEeecCCCCCC-----------------------CCceEEEEEEEECCCC-C-CccceeEEEeCC
Confidence 589999999421 1148999987665432 2 237888888775
No 130
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=26.98 E-value=1.3e+02 Score=31.78 Aligned_cols=58 Identities=12% Similarity=0.214 Sum_probs=40.2
Q ss_pred CCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecC-------ceEEEEecCCCchhHHHHHhhh
Q 006991 487 EDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-------SCAIVVFGKPGLSNTFKNVMNS 548 (622)
Q Consensus 487 ~~vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-------t~a~V~~~~~~~~~~~l~~~~~ 548 (622)
...+||-.-|..|+-.+|++.++ .||+..+|.-+-| ..+||.|.+.+.|...+.+++.
T Consensus 269 ~~~lfV~NL~~~~~e~~L~~~F~----~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG 333 (352)
T TIGR01661 269 GYCIFVYNLSPDTDETVLWQLFG----PFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNG 333 (352)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHH----hCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCC
Confidence 34688889999888877665433 4555445554422 2599999999999877776654
No 131
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=26.96 E-value=1.1e+02 Score=32.56 Aligned_cols=41 Identities=17% Similarity=0.301 Sum_probs=29.2
Q ss_pred CeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 52 DFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 52 ~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
+||+||+|.||.. .=.|+|+|...+.. + . ....|+.++-|.
T Consensus 2 ~~vviD~ETTg~~-------------------------~d~IieIgav~v~~-g-~-i~~~f~~lv~P~ 42 (309)
T PRK06195 2 NFVAIDFETANEK-------------------------RNSPCSIGIVVVKD-G-E-IVEKVHYLIKPK 42 (309)
T ss_pred cEEEEEEeCCCCC-------------------------CCceEEEEEEEEEC-C-E-EEEEEEEEECCC
Confidence 7999999999741 01379999988752 2 2 346788888875
No 132
>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=26.92 E-value=57 Score=35.73 Aligned_cols=25 Identities=12% Similarity=0.275 Sum_probs=21.8
Q ss_pred HHHHHHHHhhcCCCeEEEecCCCCc
Q 006991 39 ESLSEIKNHISSSDFIAVSLQNTGS 63 (622)
Q Consensus 39 ~~l~~i~~~I~~a~FVAiD~EftGi 63 (622)
+.|..+.+.+..++.|||||||.+.
T Consensus 6 ~~l~~~~~~l~~~~~ia~DtE~~~~ 30 (367)
T TIGR01388 6 DELATVCEAVRTFPFVALDTEFVRE 30 (367)
T ss_pred HHHHHHHHHHhcCCEEEEeccccCC
Confidence 5677888888999999999999876
No 133
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=26.23 E-value=79 Score=24.10 Aligned_cols=36 Identities=17% Similarity=0.286 Sum_probs=24.7
Q ss_pred ccccceEEEEecC--ceEEEEecCCCchhHHHHHhhhc
Q 006991 514 VFAEAFNVRMVDR--SCAIVVFGKPGLSNTFKNVMNSK 549 (622)
Q Consensus 514 ~F~~~~~V~~id~--t~a~V~~~~~~~~~~~l~~~~~~ 549 (622)
-||+-..|....+ ..|||.+.+.++|...+..++..
T Consensus 7 ~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~ 44 (56)
T PF13893_consen 7 KFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGR 44 (56)
T ss_dssp TTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTS
T ss_pred CcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence 4444335555554 56999999999999877766554
No 134
>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=26.02 E-value=3e+02 Score=26.45 Aligned_cols=44 Identities=18% Similarity=0.144 Sum_probs=28.6
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
||.||+|.||+.+. .=.|+|+|...++... .-....|..++-|.
T Consensus 1 lv~iD~ETTGl~p~-----------------------~d~IieIgaV~~~~~~-~~i~~~f~~~i~p~ 44 (173)
T cd06135 1 LVWIDLEMTGLDPE-----------------------KDRILEIACIITDGDL-NIIAEGPELVIHQP 44 (173)
T ss_pred CEEEEEecCCCCCC-----------------------CCeeEEEEEEEEeCCC-ceecCceeEEECCC
Confidence 68999999999431 1249999998775332 12234566665553
No 135
>PLN03121 nucleic acid binding protein; Provisional
Probab=25.73 E-value=1.2e+02 Score=31.43 Aligned_cols=74 Identities=9% Similarity=0.103 Sum_probs=46.5
Q ss_pred CEEEEeccccccchhHHHHhhhhhhhccccceEEEEecCc----eEEEEecCCCchhHHHHHhhhccccccchhhhcCCc
Q 006991 488 DVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRS----CAIVVFGKPGLSNTFKNVMNSKAVSGPLREMVSDGL 563 (622)
Q Consensus 488 ~vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~t----~a~V~~~~~~~~~~~l~~~~~~~~~~~l~~~~~~g~ 563 (622)
..|++-+.+.+.+-.+|++.++ -||+-.+|.-+.+. .+||.|.+++.++..+. ++... |+..-.
T Consensus 6 ~TV~V~NLS~~tTE~dLrefFS----~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~-------l~d~~I 73 (243)
T PLN03121 6 YTAEVTNLSPKATEKDVYDFFS----HCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGAT-------IVDQRV 73 (243)
T ss_pred eEEEEecCCCCCCHHHHHHHHH----hcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCe-------eCCceE
Confidence 3566667777777778776444 33333466666553 49999999999987664 22221 222226
Q ss_pred cccchHHHHH
Q 006991 564 KAAGYETYQR 573 (622)
Q Consensus 564 ~~a~~~~y~~ 573 (622)
+++.|+.|.+
T Consensus 74 ~It~~~~y~~ 83 (243)
T PLN03121 74 CITRWGQYED 83 (243)
T ss_pred EEEeCccccc
Confidence 7788877765
No 136
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=25.27 E-value=1.2e+02 Score=37.05 Aligned_cols=45 Identities=22% Similarity=0.335 Sum_probs=33.0
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCcc
Q 006991 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRD 121 (622)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~~ 121 (622)
...||++|+|.||+.+ .=.|||+|...+. ++ -....|..++-|..
T Consensus 6 ~~~~vvvD~ETTGl~~------------------------~d~IIeIgaV~v~--~g-~i~~~f~~lv~P~~ 50 (820)
T PRK07246 6 LRKYAVVDLEATGAGP------------------------NASIIQVGIVIIE--GG-EIIDSYTTDVNPHE 50 (820)
T ss_pred CCCEEEEEEecCCcCC------------------------CCeEEEEEEEEEE--CC-EEEEEEEEEeCcCC
Confidence 4689999999999821 0149999988774 22 24578888998853
No 137
>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=25.25 E-value=5.6e+02 Score=23.87 Aligned_cols=100 Identities=17% Similarity=0.201 Sum_probs=56.6
Q ss_pred HHHhCCCCEEechhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCC
Q 006991 320 LISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAP 399 (622)
Q Consensus 320 ~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~ 399 (622)
.+...+.+.||||+=.|+-.+.++| |--+ ..++||...+--++|-.. .++..+.+..-.....+
T Consensus 59 ll~~~~i~kv~~d~K~~~~~L~~~~-gi~~--------------~~~~D~~laayLl~p~~~-~~l~~l~~~~l~~~~~~ 122 (178)
T cd06142 59 LLADPNIVKVFHAAREDLELLKRDF-GILP--------------QNLFDTQIAARLLGLGDS-VGLAALVEELLGVELDK 122 (178)
T ss_pred HHcCCCceEEEeccHHHHHHHHHHc-CCCC--------------CCcccHHHHHHHhCCCcc-ccHHHHHHHHhCCCCCc
Confidence 3445678899999988888876554 2112 357999865555566433 36666655432211111
Q ss_pred ceeecCCCCCC----CCcccchhhHHHHHHHHHHHHHHhcc
Q 006991 400 IEMEIPNQANE----NEGKIHGHNVVKICQLFGKLCSILKI 436 (622)
Q Consensus 400 p~ve~~~~~~~----~~~h~AGyDA~mTg~vF~~l~~~l~~ 436 (622)
..+ ...-+.. ...+-|+.||..+..++-+|...|..
T Consensus 123 ~~~-~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e 162 (178)
T cd06142 123 GEQ-RSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEE 162 (178)
T ss_pred ccc-cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 110 0000000 01123788898898888888887743
No 138
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=25.14 E-value=1.2e+02 Score=34.23 Aligned_cols=55 Identities=20% Similarity=0.213 Sum_probs=41.1
Q ss_pred CEEEEeccccccchhHHHHhhhhhhhccccceEEEEe-cCceEEEEecCCCchhHHHHHh
Q 006991 488 DVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMV-DRSCAIVVFGKPGLSNTFKNVM 546 (622)
Q Consensus 488 ~vv~i~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~i-d~t~a~V~~~~~~~~~~~l~~~ 546 (622)
.|||+-+.|..++-.+|++.++ .||+-.+|.-+ +...|||.|.+.++|...+..+
T Consensus 3 ~vv~V~nLp~~~te~~L~~~f~----~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~ 58 (481)
T TIGR01649 3 PVVHVRNLPQDVVEADLVEALI----PFGPVSYVMMLPGKRQALVEFEDEESAKACVNFA 58 (481)
T ss_pred cEEEEcCCCCCCCHHHHHHHHH----hcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHh
Confidence 5788889999998888776544 45554445444 5567999999999999888764
No 139
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=24.44 E-value=1.4e+02 Score=30.25 Aligned_cols=39 Identities=18% Similarity=0.249 Sum_probs=28.3
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
|++||+|-||+. + .|+|+|...+. ++ + ...+|+.++-|.
T Consensus 2 ~~vlD~ETTGl~--~------------------------~IieIg~v~v~-~~-~-i~~~~~~lv~P~ 40 (219)
T PRK07983 2 LRVIDTETCGLQ--G------------------------GIVEIASVDVI-DG-K-IVNPMSHLVRPD 40 (219)
T ss_pred eEEEEEECCCCC--C------------------------CCEEEEEEEEE-CC-E-EEEEEEEEECcC
Confidence 789999999982 1 09999987665 22 2 346788888775
No 140
>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=23.64 E-value=29 Score=33.15 Aligned_cols=39 Identities=10% Similarity=0.157 Sum_probs=25.4
Q ss_pred EEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCCCceeeEeeEEeecCc
Q 006991 54 IAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (622)
Q Consensus 54 VAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (622)
||||+|+||+.+. .=.|+|+|...+. ++ .- .|+-++-|.
T Consensus 1 v~lD~EttGl~~~-----------------------~d~ii~Ig~V~v~-~g-~i---~~~~~v~P~ 39 (161)
T cd06137 1 VALDCEMVGLADG-----------------------DSEVVRISAVDVL-TG-EV---LIDSLVRPS 39 (161)
T ss_pred CEEEeeeeeEcCC-----------------------CCEEEEEEEEEcC-CC-eE---EEeccccCC
Confidence 6999999999431 1248999987662 22 11 266677774
No 141
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=23.20 E-value=1.9e+02 Score=24.78 Aligned_cols=56 Identities=13% Similarity=0.109 Sum_probs=41.3
Q ss_pred EEeccccccchhHHHHhhhhhhhccc-cceEEEEecCceEEEEecCCCchhHHHHHh
Q 006991 491 FLWGFRERISAGILKNMLQGSHEVFA-EAFNVRMVDRSCAIVVFGKPGLSNTFKNVM 546 (622)
Q Consensus 491 ~i~~f~~~~~~~~i~~~l~~~~~~F~-~~~~V~~id~t~a~V~~~~~~~~~~~l~~~ 546 (622)
+....|..|+..+|++.|+...+.=. ..+.++|+|+.-=+|.+.+...-.+.+...
T Consensus 12 ~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~ 68 (82)
T cd06407 12 IRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVY 68 (82)
T ss_pred EEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHH
Confidence 34677889999999998886444311 248999999999999999886655554433
No 142
>PF13606 Ank_3: Ankyrin repeat
Probab=22.80 E-value=64 Score=21.94 Aligned_cols=17 Identities=18% Similarity=0.315 Sum_probs=14.8
Q ss_pred chhHHHHHHHcCCCcch
Q 006991 135 QTSYLTAMAKEGFDFNT 151 (622)
Q Consensus 135 q~sSl~FL~~~gFDFnk 151 (622)
+.+-+++|.++|.|.|+
T Consensus 14 ~~e~v~~Ll~~gadvn~ 30 (30)
T PF13606_consen 14 NIEIVKYLLEHGADVNA 30 (30)
T ss_pred CHHHHHHHHHcCCCCCC
Confidence 46789999999999985
No 143
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=21.57 E-value=1.7e+02 Score=33.02 Aligned_cols=60 Identities=15% Similarity=0.317 Sum_probs=42.7
Q ss_pred CCEEEEecccc-ccchhHHHHhhhhhhhccccceEEEEec--CceEEEEecCCCchhHHHHHhhhcc
Q 006991 487 EDVVFLWGFRE-RISAGILKNMLQGSHEVFAEAFNVRMVD--RSCAIVVFGKPGLSNTFKNVMNSKA 550 (622)
Q Consensus 487 ~~vv~i~~f~~-~~~~~~i~~~l~~~~~~F~~~~~V~~id--~t~a~V~~~~~~~~~~~l~~~~~~~ 550 (622)
..++|+-+.|. .++-.+|++.++ .||....|..+- ...+||.|.+.++|...+..++...
T Consensus 275 ~~~l~v~nL~~~~vt~~~L~~lF~----~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~ 337 (481)
T TIGR01649 275 GSVLMVSGLHQEKVNCDRLFNLFC----VYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVK 337 (481)
T ss_pred CCEEEEeCCCCCCCCHHHHHHHHH----hcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCE
Confidence 46888889986 687777665333 444434555543 3579999999999999998886654
No 144
>PRK10829 ribonuclease D; Provisional
Probab=21.14 E-value=83 Score=34.65 Aligned_cols=26 Identities=12% Similarity=0.162 Sum_probs=21.6
Q ss_pred HHHHHHHHHhhcCCCeEEEecCCCCc
Q 006991 38 NESLSEIKNHISSSDFIAVSLQNTGS 63 (622)
Q Consensus 38 ~~~l~~i~~~I~~a~FVAiD~EftGi 63 (622)
.+.|..+.+.+..+..|||||||.+.
T Consensus 9 ~~~L~~~~~~l~~~~~lalDtEf~~~ 34 (373)
T PRK10829 9 DDALASVCEAARAFPAIALDTEFVRT 34 (373)
T ss_pred HHHHHHHHHHHhcCCeEEEecccccC
Confidence 35677777779999999999999876
No 145
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=20.67 E-value=1.5e+02 Score=33.15 Aligned_cols=58 Identities=14% Similarity=0.370 Sum_probs=41.9
Q ss_pred ccccccchhHHHHhhhhhhhccccceEEEEecCc-------eEEEEecCCCchhHHHHHh-hhcc---ccccc
Q 006991 494 GFRERISAGILKNMLQGSHEVFAEAFNVRMVDRS-------CAIVVFGKPGLSNTFKNVM-NSKA---VSGPL 555 (622)
Q Consensus 494 ~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~t-------~a~V~~~~~~~~~~~l~~~-~~~~---~~~~l 555 (622)
-.|+.|+-.|||..+. -||...+|.-|.|. |+||-+..++.+.....|+ |.-. .-||+
T Consensus 41 qIprt~sE~dlr~lFe----~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv 109 (510)
T KOG0144|consen 41 QIPRTASEKDLRELFE----KYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV 109 (510)
T ss_pred cCCccccHHHHHHHHH----HhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence 3689999888876443 44444688888775 8999999999998887777 3322 45666
Done!