Query 007029
Match_columns 621
No_of_seqs 192 out of 503
Neff 6.3
Searched_HMMs 46136
Date Thu Mar 28 17:55:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007029.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007029hhsearch_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 1.1E-63 2.4E-68 513.9 14.6 246 30-428 1-262 (262)
2 KOG0304 mRNA deadenylase subun 100.0 1.3E-30 2.8E-35 252.9 16.1 119 29-159 2-125 (239)
3 KOG1990 Poly(A)-specific exori 100.0 2.6E-30 5.6E-35 290.4 7.5 481 34-590 1-521 (564)
4 COG5228 POP2 mRNA deadenylase 99.8 9.2E-21 2E-25 184.1 13.3 120 26-158 17-140 (299)
5 PF08675 RNA_bind: RNA binding 99.6 3.6E-15 7.9E-20 125.5 7.1 75 478-571 1-77 (87)
6 cd02637 R3H_PARN R3H domain of 97.2 0.00095 2.1E-08 54.8 5.9 26 242-267 19-44 (65)
7 PRK07740 hypothetical protein; 97.2 0.0021 4.5E-08 66.2 9.9 89 323-435 140-228 (244)
8 cd06131 DNA_pol_III_epsilon_Ec 97.0 0.0045 9.8E-08 59.1 10.3 97 312-430 67-167 (167)
9 PRK06195 DNA polymerase III su 97.0 0.0045 9.7E-08 65.9 10.5 95 313-435 67-166 (309)
10 TIGR01406 dnaQ_proteo DNA poly 96.9 0.0056 1.2E-07 62.2 10.4 98 312-431 68-170 (225)
11 cd06134 RNaseT DEDDh 3'-5' exo 96.9 0.0064 1.4E-07 60.0 9.9 83 323-431 101-187 (189)
12 PF10309 DUF2414: Protein of u 96.8 0.0022 4.8E-08 52.0 5.2 59 484-544 3-61 (62)
13 PRK05711 DNA polymerase III su 96.8 0.008 1.7E-07 61.8 10.6 99 311-431 71-174 (240)
14 TIGR00573 dnaq exonuclease, DN 96.8 0.0069 1.5E-07 61.1 9.6 88 323-433 86-177 (217)
15 PRK07942 DNA polymerase III su 96.8 0.0055 1.2E-07 62.5 8.9 88 322-434 91-181 (232)
16 PRK06063 DNA polymerase III su 96.7 0.011 2.4E-07 63.1 10.9 97 312-435 80-181 (313)
17 cd06130 DNA_pol_III_epsilon_li 96.6 0.014 3E-07 54.9 9.9 87 313-427 64-155 (156)
18 PRK06807 DNA polymerase III su 96.6 0.014 3E-07 62.3 10.5 86 323-435 87-174 (313)
19 PRK05168 ribonuclease T; Provi 96.6 0.0064 1.4E-07 61.1 7.6 87 323-434 113-202 (211)
20 PRK09145 DNA polymerase III su 96.5 0.02 4.4E-07 56.9 10.8 81 323-431 110-199 (202)
21 TIGR01298 RNaseT ribonuclease 96.5 0.0095 2.1E-07 59.4 8.1 86 323-433 104-192 (200)
22 PRK09146 DNA polymerase III su 96.4 0.018 3.8E-07 59.2 10.0 96 313-436 116-230 (239)
23 cd06145 REX1_like DEDDh 3'-5' 96.4 0.013 2.8E-07 55.7 7.9 76 323-427 75-150 (150)
24 cd06137 DEDDh_RNase DEDDh 3'-5 96.2 0.013 2.7E-07 56.3 7.3 75 324-427 84-161 (161)
25 PRK07983 exodeoxyribonuclease 96.2 0.022 4.7E-07 57.8 9.3 94 312-435 63-156 (219)
26 cd06127 DEDDh DEDDh 3'-5' exon 95.7 0.047 1E-06 50.3 8.4 78 325-427 80-159 (159)
27 PRK06309 DNA polymerase III su 95.7 0.075 1.6E-06 54.2 10.4 87 323-434 79-167 (232)
28 smart00479 EXOIII exonuclease 95.7 0.083 1.8E-06 49.9 10.1 84 324-433 80-167 (169)
29 PRK07883 hypothetical protein; 95.6 0.088 1.9E-06 60.6 11.4 87 324-435 95-184 (557)
30 PRK07246 bifunctional ATP-depe 95.5 0.063 1.4E-06 64.4 10.4 89 323-437 85-174 (820)
31 cd06144 REX4_like DEDDh 3'-5' 95.3 0.052 1.1E-06 51.6 7.2 75 323-426 76-151 (152)
32 PRK06722 exonuclease; Provisio 95.3 0.093 2E-06 55.2 9.6 97 312-431 76-179 (281)
33 TIGR01405 polC_Gram_pos DNA po 95.3 0.074 1.6E-06 66.0 10.2 105 304-433 248-355 (1213)
34 PRK07247 DNA polymerase III su 95.1 0.11 2.4E-06 51.7 9.2 83 323-433 83-169 (195)
35 PRK06310 DNA polymerase III su 95.0 0.14 3E-06 52.9 9.7 86 323-433 87-174 (250)
36 KOG4483 Uncharacterized conser 94.9 0.029 6.3E-07 60.2 4.5 66 485-556 390-458 (528)
37 PRK07748 sporulation inhibitor 94.9 0.25 5.4E-06 49.4 10.9 83 325-432 94-179 (207)
38 cd06149 ISG20 DEDDh 3'-5' exon 94.8 0.094 2E-06 50.2 7.5 76 323-426 76-156 (157)
39 PRK05601 DNA polymerase III su 94.8 0.15 3.3E-06 55.3 9.7 206 307-537 106-342 (377)
40 TIGR01407 dinG_rel DnaQ family 94.8 0.13 2.9E-06 62.0 10.2 100 312-437 66-169 (850)
41 PRK08074 bifunctional ATP-depe 94.5 0.18 3.9E-06 61.5 10.7 90 323-437 83-173 (928)
42 PRK08517 DNA polymerase III su 94.3 0.22 4.9E-06 51.7 9.3 86 323-434 146-232 (257)
43 PRK00448 polC DNA polymerase I 94.0 0.16 3.5E-06 64.1 8.9 106 304-434 477-585 (1437)
44 PF00929 RNase_T: Exonuclease; 91.8 0.0082 1.8E-07 55.5 -5.2 80 323-426 82-164 (164)
45 cd06133 ERI-1_3'hExo_like DEDD 91.0 1.2 2.5E-05 42.5 8.6 92 316-429 82-175 (176)
46 cd06133 ERI-1_3'hExo_like DEDD 90.2 0.69 1.5E-05 44.1 6.3 50 53-121 1-50 (176)
47 cd06136 TREX1_2 DEDDh 3'-5' ex 89.7 0.99 2.1E-05 44.0 7.0 75 324-428 98-176 (177)
48 cd06138 ExoI_N N-terminal DEDD 88.9 2.1 4.6E-05 41.8 8.7 26 318-343 78-104 (183)
49 COG0847 DnaQ DNA polymerase II 88.5 2.7 5.9E-05 42.6 9.5 83 325-432 96-181 (243)
50 PF01612 DNA_pol_A_exo1: 3'-5' 88.0 1.8 3.8E-05 40.9 7.4 95 316-433 68-175 (176)
51 PRK09145 DNA polymerase III su 87.4 1.2 2.5E-05 44.3 5.9 56 41-120 19-74 (202)
52 PRK05168 ribonuclease T; Provi 87.0 1.9 4E-05 43.4 7.1 57 41-120 7-65 (211)
53 PRK09182 DNA polymerase III su 86.7 3.3 7.1E-05 44.0 9.1 87 319-434 116-202 (294)
54 PF00076 RRM_1: RNA recognitio 86.1 1.6 3.6E-05 34.4 5.1 56 489-548 1-62 (70)
55 smart00479 EXOIII exonuclease 85.8 1.5 3.2E-05 41.3 5.4 43 52-120 1-43 (169)
56 PTZ00315 2'-phosphotransferase 84.8 4.8 0.0001 46.5 9.7 83 325-431 154-253 (582)
57 PF11608 Limkain-b1: Limkain b 82.7 2.5 5.3E-05 36.7 4.8 63 486-551 2-65 (90)
58 PF08777 RRM_3: RNA binding mo 82.2 3 6.6E-05 37.4 5.5 54 488-548 3-60 (105)
59 PRK11779 sbcB exonuclease I; P 81.9 3.2 6.8E-05 47.0 6.8 101 315-432 84-197 (476)
60 PF00929 RNase_T: Exonuclease; 80.3 2.7 5.9E-05 38.5 4.8 44 54-121 1-44 (164)
61 TIGR00573 dnaq exonuclease, DN 80.0 3 6.5E-05 42.0 5.3 48 47-120 3-50 (217)
62 PF14259 RRM_6: RNA recognitio 79.5 4.6 0.0001 32.3 5.3 54 489-546 1-60 (70)
63 cd02642 R3H_encore_like R3H do 78.9 3.8 8.3E-05 33.2 4.6 22 240-261 22-43 (63)
64 PRK07942 DNA polymerase III su 78.7 4.9 0.00011 41.0 6.4 48 48-120 3-50 (232)
65 COG2176 PolC DNA polymerase II 78.3 4.4 9.6E-05 49.8 6.6 105 304-434 479-587 (1444)
66 PRK07247 DNA polymerase III su 78.2 4.3 9.3E-05 40.4 5.7 42 52-120 6-47 (195)
67 cd06134 RNaseT DEDDh 3'-5' exo 77.0 4.4 9.6E-05 39.9 5.4 49 49-120 3-53 (189)
68 PRK09146 DNA polymerase III su 76.0 4.9 0.00011 41.3 5.5 51 46-120 42-92 (239)
69 PRK05601 DNA polymerase III su 75.7 5.6 0.00012 43.5 6.0 50 46-120 41-90 (377)
70 cd02325 R3H R3H domain. The na 74.5 4.8 0.0001 30.8 3.9 23 241-263 19-41 (59)
71 PRK06310 DNA polymerase III su 74.4 5.6 0.00012 41.1 5.5 48 47-120 3-50 (250)
72 smart00362 RRM_2 RNA recogniti 73.6 9.3 0.0002 29.3 5.5 54 489-546 2-60 (72)
73 cd06146 mut-7_like_exo DEDDy 3 73.4 16 0.00035 36.0 8.4 107 314-430 71-192 (193)
74 PRK07740 hypothetical protein; 72.7 3.8 8.1E-05 42.2 3.8 55 42-120 50-104 (244)
75 PRK05359 oligoribonuclease; Pr 72.6 5.7 0.00012 39.0 4.8 47 50-120 2-48 (181)
76 TIGR01298 RNaseT ribonuclease 72.4 6.8 0.00015 39.0 5.4 50 48-120 5-56 (200)
77 cd06127 DEDDh DEDDh 3'-5' exon 70.7 3.5 7.7E-05 37.7 2.8 42 54-120 1-42 (159)
78 cd06141 WRN_exo DEDDy 3'-5' ex 69.8 29 0.00062 33.0 9.0 96 320-430 69-169 (170)
79 PRK06807 DNA polymerase III su 69.4 8.5 0.00018 41.2 5.6 44 51-120 8-51 (313)
80 PRK06063 DNA polymerase III su 69.2 7.6 0.00016 41.6 5.2 46 50-120 14-59 (313)
81 PRK05711 DNA polymerase III su 67.7 10 0.00022 39.1 5.6 47 50-120 3-49 (240)
82 PF01424 R3H: R3H domain; Int 67.6 27 0.00058 27.8 7.0 28 241-270 22-49 (63)
83 PRK09182 DNA polymerase III su 66.5 11 0.00023 40.1 5.7 47 51-120 37-86 (294)
84 cd06130 DNA_pol_III_epsilon_li 66.4 11 0.00023 35.1 5.2 40 53-120 1-40 (156)
85 cd06131 DNA_pol_III_epsilon_Ec 66.3 8.8 0.00019 36.4 4.6 44 53-120 1-44 (167)
86 PRK05755 DNA polymerase I; Pro 66.1 19 0.00041 44.0 8.4 102 316-435 362-471 (880)
87 PRK07883 hypothetical protein; 65.5 10 0.00022 43.9 5.6 52 43-120 7-58 (557)
88 PRK07748 sporulation inhibitor 64.3 9.3 0.0002 38.1 4.5 51 50-120 3-53 (207)
89 PRK08517 DNA polymerase III su 63.2 16 0.00034 38.1 6.1 53 42-120 59-111 (257)
90 cd01201 Neurobeachin Neurobeac 59.5 14 0.0003 33.5 4.2 49 496-544 56-104 (108)
91 TIGR01406 dnaQ_proteo DNA poly 58.9 18 0.00039 36.8 5.5 45 52-120 1-45 (225)
92 PLN03134 glycine-rich RNA-bind 57.9 42 0.0009 31.7 7.4 59 486-548 34-99 (144)
93 KOG0132 RNA polymerase II C-te 57.4 19 0.0004 42.6 5.7 99 489-593 424-529 (894)
94 cd06139 DNA_polA_I_Ecoli_like_ 56.9 36 0.00078 32.6 7.1 103 318-435 61-172 (193)
95 cd06136 TREX1_2 DEDDh 3'-5' ex 56.9 19 0.00041 35.0 5.1 46 53-120 1-56 (177)
96 cd06129 RNaseD_like DEDDy 3'-5 55.3 40 0.00086 32.0 6.9 95 320-431 63-161 (161)
97 PF15023 DUF4523: Protein of u 55.3 24 0.00052 33.7 5.1 63 483-547 84-147 (166)
98 cd00007 35EXOc 3'-5' exonuclea 54.1 39 0.00084 30.6 6.5 59 318-391 48-106 (155)
99 TIGR01659 sex-lethal sex-letha 52.6 29 0.00062 37.8 6.1 59 486-548 193-258 (346)
100 cd02640 R3H_NRF R3H domain of 52.4 19 0.00042 29.1 3.5 20 242-261 20-40 (60)
101 cd02641 R3H_Smubp-2_like R3H d 52.2 22 0.00048 28.7 3.9 22 241-262 19-41 (60)
102 COG0349 Rnd Ribonuclease D [Tr 51.2 58 0.0013 35.7 8.0 99 314-435 60-168 (361)
103 cd06135 Orn DEDDh 3'-5' exonuc 50.7 23 0.00049 34.3 4.5 75 323-431 93-170 (173)
104 PRK10829 ribonuclease D; Provi 49.1 58 0.0013 35.9 7.8 98 314-434 64-171 (373)
105 COG0349 Rnd Ribonuclease D [Tr 48.2 15 0.00033 40.1 3.0 26 39-64 5-30 (361)
106 cd00590 RRM RRM (RNA recogniti 47.9 40 0.00086 25.8 4.8 55 489-547 2-62 (74)
107 smart00361 RRM_1 RNA recogniti 46.9 28 0.00061 28.2 3.9 47 501-547 3-59 (70)
108 PRK11779 sbcB exonuclease I; P 46.6 47 0.001 37.8 6.7 74 49-158 4-77 (476)
109 smart00393 R3H Putative single 46.2 85 0.0018 26.3 6.8 28 240-269 37-64 (79)
110 PTZ00315 2'-phosphotransferase 45.9 36 0.00078 39.5 5.7 49 51-120 56-104 (582)
111 cd06398 PB1_Joka2 The PB1 doma 43.6 63 0.0014 28.3 5.7 59 486-544 8-72 (91)
112 smart00360 RRM RNA recognition 43.6 38 0.00083 25.5 4.0 50 493-546 3-59 (71)
113 TIGR01407 dinG_rel DnaQ family 43.0 39 0.00085 41.1 5.8 43 52-120 1-43 (850)
114 KOG4206 Spliceosomal protein s 42.8 47 0.001 33.8 5.4 61 488-548 11-75 (221)
115 cd02646 R3H_G-patch R3H domain 42.1 38 0.00083 26.9 3.8 22 241-262 18-39 (58)
116 smart00474 35EXOc 3'-5' exonuc 41.7 2.2E+02 0.0048 26.1 9.7 98 317-433 68-171 (172)
117 PF15342 FAM212: FAM212 family 39.4 18 0.00039 29.1 1.4 23 323-349 38-60 (62)
118 TIGR01659 sex-lethal sex-letha 38.3 68 0.0015 34.9 6.2 59 485-547 106-171 (346)
119 cd06125 DnaQ_like_exo DnaQ-lik 37.5 33 0.00072 29.8 3.1 28 316-343 35-63 (96)
120 PRK08074 bifunctional ATP-depe 36.3 57 0.0012 40.2 5.9 45 51-120 3-47 (928)
121 cd02638 R3H_unknown_1 R3H doma 35.7 80 0.0017 25.9 4.6 29 240-269 19-47 (62)
122 PF01612 DNA_pol_A_exo1: 3'-5' 34.0 31 0.00068 32.3 2.5 27 38-64 7-33 (176)
123 TIGR01405 polC_Gram_pos DNA po 33.2 65 0.0014 40.9 5.6 46 49-120 188-233 (1213)
124 cd06149 ISG20 DEDDh 3'-5' exon 30.9 21 0.00045 34.0 0.7 11 54-64 1-11 (157)
125 PRK06195 DNA polymerase III su 30.0 93 0.002 33.1 5.5 41 52-120 2-42 (309)
126 cd06396 PB1_NBR1 The PB1 domai 29.5 1.3E+02 0.0029 25.9 5.3 55 492-548 14-70 (81)
127 PF14605 Nup35_RRM_2: Nup53/35 29.3 98 0.0021 24.1 4.1 49 487-540 2-51 (53)
128 PRK05359 oligoribonuclease; Pr 28.7 2E+02 0.0043 28.1 7.2 21 323-343 97-117 (181)
129 TIGR01661 ELAV_HUD_SF ELAV/HuD 27.6 1.3E+02 0.0028 31.9 6.2 58 486-547 269-333 (352)
130 PRK07246 bifunctional ATP-depe 27.4 1E+02 0.0022 37.5 5.9 45 50-121 6-50 (820)
131 TIGR01388 rnd ribonuclease D. 26.8 57 0.0012 35.7 3.3 25 39-63 6-30 (367)
132 PF13893 RRM_5: RNA recognitio 26.7 76 0.0017 24.2 3.2 37 512-548 6-44 (56)
133 PLN03121 nucleic acid binding 26.5 1.2E+02 0.0025 31.5 5.2 74 487-572 6-83 (243)
134 KOG1990 Poly(A)-specific exori 26.4 23 0.00051 41.0 0.3 127 26-166 101-236 (564)
135 cd06006 R3H_unknown_2 R3H doma 25.7 1.1E+02 0.0024 24.7 4.0 22 240-261 18-39 (59)
136 cd06142 RNaseD_exo DEDDy 3'-5' 25.6 5.5E+02 0.012 23.9 10.3 100 319-435 59-162 (178)
137 TIGR01649 hnRNP-L_PTB hnRNP-L/ 25.5 1.2E+02 0.0026 34.3 5.7 55 487-545 3-58 (481)
138 PRK07983 exodeoxyribonuclease 25.1 1.4E+02 0.0029 30.4 5.5 39 53-120 2-40 (219)
139 cd06135 Orn DEDDh 3'-5' exonuc 24.3 3.4E+02 0.0074 26.1 7.9 44 53-120 1-44 (173)
140 cd06407 PB1_NLP A PB1 domain i 23.4 1.9E+02 0.004 24.8 5.2 56 490-545 12-68 (82)
141 cd06137 DEDDh_RNase DEDDh 3'-5 22.9 30 0.00065 33.0 0.2 39 54-120 1-39 (161)
142 cd06138 ExoI_N N-terminal DEDD 22.8 1.1E+02 0.0024 29.7 4.2 41 55-120 2-42 (183)
143 TIGR01649 hnRNP-L_PTB hnRNP-L/ 22.1 1.7E+02 0.0036 33.1 6.0 60 486-549 275-337 (481)
144 PF13606 Ank_3: Ankyrin repeat 22.0 70 0.0015 21.8 1.8 17 135-151 14-30 (30)
145 cd02644 R3H_jag R3H domain fou 21.4 69 0.0015 26.4 2.1 27 241-268 25-51 (67)
146 PRK06722 exonuclease; Provisio 21.4 1.8E+02 0.0038 30.9 5.6 50 50-120 4-53 (281)
147 PRK10829 ribonuclease D; Provi 21.3 84 0.0018 34.6 3.3 26 38-63 9-34 (373)
148 cd06007 R3H_DEXH_helicase R3H 21.3 1.3E+02 0.0028 24.3 3.5 20 242-261 19-39 (59)
149 KOG0144 RNA-binding protein CU 21.2 1.5E+02 0.0032 33.3 4.9 58 493-554 41-109 (510)
150 cd02643 R3H_NF-X1 R3H domain o 20.9 4E+02 0.0087 22.2 6.6 27 240-268 33-59 (74)
151 TIGR01648 hnRNP-R-Q heterogene 20.1 2E+02 0.0044 33.6 6.2 61 483-547 55-121 (578)
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=1.1e-63 Score=513.95 Aligned_cols=246 Identities=38% Similarity=0.600 Sum_probs=197.7
Q ss_pred EEeCcccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeee-ecCC---
Q 007029 30 KQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPF-KLQA--- 105 (621)
Q Consensus 30 ~eVt~~NF~~~lp~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f-~~~~--- 105 (621)
||||++||+++||.|+++|++|+|||||+||||+...+.+. ..+|+++||+++|++|++|+|+|+|||+| +.++
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 CceeeEeEEEeecCccccccCCCCCceeechhHHHHHHHcCCCccchhhcccccCCHHHHHHHHHHhCCCccccccccCC
Q 007029 106 SKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKSS 185 (621)
Q Consensus 106 ~~y~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~YLs~~eE~~~r~~~~~~~~~~~~~~~~ 185 (621)
.+|.+|||||++||.. +.|+ |++||+||++||||||+|+++||||+++.||+.++
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 4789999999999974 4677 99999999999999999999999999998875421
Q ss_pred CCCCCCcccHHHHHHHHHHHHHHHhhcCCCCchhHHHHHHHHHHHhcCcccCCCCCccccccchHHHHHHHHHHHhhcCC
Q 007029 186 SSPALSVADTVFIERVRSRVKHWKNACTDSDIKTEALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFSDV 265 (621)
Q Consensus 186 ~~~~~~~~d~~fi~~v~~~I~~Wl~~~~~~~~~~e~l~~~l~~~~~~~e~~~~~p~l~l~~~~~~q~~Li~q~l~~~~~~ 265 (621)
T Consensus 134 -------------------------------------------------------------------------------- 133 (262)
T PF04857_consen 134 -------------------------------------------------------------------------------- 133 (262)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred cceeeeccCCCCceeEEEEEccChHHHHHHHHHhhHHHHhhhhhcccHHHHHHHHHhCCCCEEeehhHHHHHHHHHhccC
Q 007029 266 LVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFLA 345 (621)
Q Consensus 266 l~~~~~~~k~g~~~~~rvi~~~~~eek~~l~~e~~~~e~e~~~~~~GFr~Vi~~L~~skKpIVGHN~llDL~~iy~~F~g 345 (621)
+.+|||.|++++.+++||||||||++||+|||++|+|
T Consensus 134 -------------------------------------------~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~~ 170 (262)
T PF04857_consen 134 -------------------------------------------ELLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFIG 170 (262)
T ss_dssp -------------------------------------------HHHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHTT
T ss_pred -------------------------------------------hhHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhcC
Confidence 1237888899999999999999999999999999999
Q ss_pred CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCceeecCCC----C-------CCCC-cc
Q 007029 346 PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQ----A-------NENE-GK 413 (621)
Q Consensus 346 pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~vei~~~----~-------~~~~-~h 413 (621)
|||++++||++.++++||.|||||||++... ...++|+.+.+.+.... .++.+..+.. . ..+. .|
T Consensus 171 ~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~--~~~~~L~~l~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~H 247 (262)
T PF04857_consen 171 PLPETLEEFKELLRELFPRIYDTKYLAEECP--GKSTSLQELAEELGIRR-NPSSISSPEGFPSYDEEKNNFPMFGEKAH 247 (262)
T ss_dssp S--SSHHHHHHHHHHHSSSEEEHHHHHTSTT--TS-SSHHHHHHHTTSTT-----EEE-TTS-------------SS-TT
T ss_pred CCCCCHHHHHHHHHHHCcccccHHHHHHhcc--ccccCHHHHHHHhCCCc-cccccccccccccccccccccccCCCCCC
Confidence 9999999999999999999999999998765 24667888888876443 2222222210 1 1233 79
Q ss_pred cchhhHHHHHHHHHH
Q 007029 414 IHGHNVVKICQLFGK 428 (621)
Q Consensus 414 eAGyDA~mTG~vFik 428 (621)
+|||||||||+||++
T Consensus 248 eAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 248 EAGYDAYMTGCVFIK 262 (262)
T ss_dssp SHHHHHHHHHHHHHH
T ss_pred CcchHHHHHHHHHcC
Confidence 999999999999986
No 2
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=99.97 E-value=1.3e-30 Score=252.90 Aligned_cols=119 Identities=17% Similarity=0.360 Sum_probs=103.3
Q ss_pred eEEeCcccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCC-CCHHHHHHHHHhhhccccceeEEeeeeecCCCc
Q 007029 29 IKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTF-DTPETAYLKAKFAAERFQILQFAICPFKLQASK 107 (621)
Q Consensus 29 i~eVt~~NF~~~lp~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~-dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~ 107 (621)
|++||++|.++++..|++.|++++||||||||||+... +...+ .+.+.+|+.+|.||+...+||+||++++.+++.
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 68999999999999999999999999999999999753 34445 478889999999999999999999999987743
Q ss_pred ----eeeEeEEEeecCccccccCCCCCceeechhHHHHHHHcCCCccchhhccccc
Q 007029 108 ----VIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISY 159 (621)
Q Consensus 108 ----y~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~Y 159 (621)
-..|+|||.-|.-. +-+.+..||+||+++|+||.|...+||.-
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 33899999977642 23567899999999999999999999964
No 3
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.96 E-value=2.6e-30 Score=290.36 Aligned_cols=481 Identities=18% Similarity=0.166 Sum_probs=290.3
Q ss_pred cccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCC--ceeeE
Q 007029 34 KTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQAS--KVIAY 111 (621)
Q Consensus 34 ~~NF~~~lp~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~--~y~~~ 111 (621)
|.||+. +..++..|..++|+|||+|++|+...+|...+.+|+++.+|++.|.++..|.++|+|+|+|.++.+ .+...
T Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 79 (564)
T KOG1990|consen 1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMST 79 (564)
T ss_pred CCcccc-hhHHHhhcCHHHHHHHhhhhccceecccccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccC
Confidence 579999 999999999999999999999999888999999999999999999999999999999999999874 56667
Q ss_pred eEEEeecCccccccCCCCCceeechhHHHHHHHcCCCccchhhcccccCCHHHHHHHHHHhCCCccccccccCCCCCCCC
Q 007029 112 PYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKSSSSPALS 191 (621)
Q Consensus 112 ~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~YLs~~eE~~~r~~~~~~~~~~~~~~~~~~~~~~ 191 (621)
++||++||+ ......+ .|+||.+.+.|+.++ +|
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 cccHHHHHHHHHHHHHHHhhcCCCCc--hhHHHHHHHHHHHhcCcccCCCCCccccccchHHHHHHHHHHHhhcCCccee
Q 007029 192 VADTVFIERVRSRVKHWKNACTDSDI--KTEALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFSDVLVPL 269 (621)
Q Consensus 192 ~~d~~fi~~v~~~I~~Wl~~~~~~~~--~~e~l~~~l~~~~~~~e~~~~~p~l~l~~~~~~q~~Li~q~l~~~~~~l~~~ 269 (621)
..+..+.-+++....+|+.+...... ............+.+.-+..++|...++++.+.+...+-.+...+.....+.
T Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~ 192 (564)
T KOG1990|consen 113 NQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPP 192 (564)
T ss_pred hhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhcccccc
Confidence 00123444566666777766432110 0000000000111112235567888888888777776555544433333322
Q ss_pred eec-cCCCCceeEEEEEccChHHHHHHHH-HhhH--HHHhhhhhcccHHHHHHHHHhCCCCEEeehhHHHHHHHHHhccC
Q 007029 270 IIP-AKGGGTQAVRAVLTSSDEDKDLLKR-ELQT--FEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFLA 345 (621)
Q Consensus 270 ~~~-~k~g~~~~~rvi~~~~~eek~~l~~-e~~~--~e~e~~~~~~GFr~Vi~~L~~skKpIVGHN~llDL~~iy~~F~g 345 (621)
.+. ...+..+.+.+... +--++....+ .+++ .+......+.+++ .+..++++|||||+++|+||+|++|++
T Consensus 193 ~~~~~~~~~~~~~~~~~~-~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~----~~~~tg~~lv~hN~~~dv~y~~~~Fl~ 267 (564)
T KOG1990|consen 193 HFALGRSRKLQGLAVAMV-SFWEKHEFAKILIKRGVLETRKERMADELQ----ELLLTGKVLVLHNKLLDVMYRYKNFLS 267 (564)
T ss_pred cceehhccccccchhHHH-HHHHHHHHHHHHHHhcchhhhccchHHHHH----HHHhcCCeEEeeccceeeeeehhhccc
Confidence 111 11111121211111 1111111111 1111 1111222233444 677899999999999999999999999
Q ss_pred CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHh---cCCCCceee-cC------C-CCCCCCccc
Q 007029 346 PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKN---RFFAPIEME-IP------N-QANENEGKI 414 (621)
Q Consensus 346 pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~---~~~~~~~ve-i~------~-~~~~~~~he 414 (621)
|||+++++|+.. .++||.++||+.++. ..+..+ .++...+..+.. ....+++.. ++ . .......|+
T Consensus 268 ~lp~~l~~f~~~-~~~fp~~~~~~~~~~-~~~~~~-~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~ 344 (564)
T KOG1990|consen 268 PLPSTLEEFTDS-SSMFPNIEDTKRLAK-LSEYQK-LNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTE 344 (564)
T ss_pred ccchhHHHhhhh-hhhhhhhHHHHHhhc-cccccc-hhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHHH
Confidence 999999999999 999999999998776 344333 234444433332 122222221 00 0 011234578
Q ss_pred chhhHHHHHHHHHHHHHHhccCCCCC----------CCCc-H--HHHhhhhhhhccccCCCCCCCCCCCccccCCCCCCC
Q 007029 415 HGHNVVKICQLFGKLCSILKITPDAI----------ESSD-D--FLASAINRYANIFYSLPGSSQEPTNEEIRGWTNDKR 481 (621)
Q Consensus 415 AGyDA~mTG~vFikL~~~L~~~~~~~----------~s~~-~--~~~~~l~~~~N~l~~~~~~~~~~~d~~~~~l~g~~~ 481 (621)
++|+++.+|.+++..+......+... ++.. + .....+..+.|...+.+.++- .
T Consensus 345 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~-f------------- 410 (564)
T KOG1990|consen 345 AIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGV-F------------- 410 (564)
T ss_pred HHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCccc-c-------------
Confidence 99999999999999998774432211 1111 1 122345555665555444421 1
Q ss_pred CCCcCCEEEEeccccccchhHHHHhhhhhhhccc---cc-eEEEEecCce-EEEEecCCCchhHHHHHhhh--ccccccc
Q 007029 482 KVSCEDVVFLWGFRERISAGILKNMLQGSHEVFA---EA-FNVRMVDRSC-AIVVFGKPGLSNTFKNVMNS--KAVSGPL 554 (621)
Q Consensus 482 ~~~~~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~---~~-~~V~~id~t~-a~V~~~~~~~~~~~l~~~~~--~~~~~~l 554 (621)
+.+ |.++...|+..+....++.....=+ ++ ..+.|.+.-. +.+.-...+-+..+-...+. .+.++|.
T Consensus 411 ----~g~--i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~ 484 (564)
T KOG1990|consen 411 ----DGV--IENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPR 484 (564)
T ss_pred ----cce--eecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCch
Confidence 112 2344444444433322221111000 00 1233333333 44444444443333333322 2268999
Q ss_pred hhhhcCC-ccccchHHHHHhhhcCCchhhHHHHHHHH
Q 007029 555 REMVSDG-LKAAGYETYQRVCSSGLWESALADALDKT 590 (621)
Q Consensus 555 ~~~~~~g-~~~a~~~~y~~~c~~~~~~~~~a~~~~~~ 590 (621)
+.|..++ |....++.|+++|...++........-.+
T Consensus 485 ~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~ 521 (564)
T KOG1990|consen 485 NLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQA 521 (564)
T ss_pred hhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhc
Confidence 9999999 89999999999999999887765544333
No 4
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=99.85 E-value=9.2e-21 Score=184.10 Aligned_cols=120 Identities=18% Similarity=0.295 Sum_probs=103.6
Q ss_pred ccceEEeCcccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCH-HHHHHHHHhhhccccceeEEeeeeecC
Q 007029 26 HWPIKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTP-ETAYLKAKFAAERFQILQFAICPFKLQ 104 (621)
Q Consensus 26 ~~~i~eVt~~NF~~~lp~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~-eerY~~~k~~a~~f~iiQ~Gl~~f~~~ 104 (621)
-..|++||++|+..++..|++.|..+.+|+|||||+|+.. ++.+.|.+. +-.|+.+|+||+-..|||+||++-+.+
T Consensus 17 ~~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvA---rPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~ 93 (299)
T COG5228 17 YLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVA---RPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDEN 93 (299)
T ss_pred hHHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceee---cccccccccchHHHHHHhcccchhhhhheeeeecccc
Confidence 3568999999999999999999999999999999999975 445666654 458999999999999999999999988
Q ss_pred C---CceeeEeEEEeecCccccccCCCCCceeechhHHHHHHHcCCCccchhhcccc
Q 007029 105 A---SKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGIS 158 (621)
Q Consensus 105 ~---~~y~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~ 158 (621)
+ +.-..|+|||-.-+.. -+..+.||+.|++.|+||.|.-.-||.
T Consensus 94 GN~P~~~sTWQFNF~F~l~~----------dmya~ESieLL~ksgIdFkkHe~~GI~ 140 (299)
T COG5228 94 GNKPNGPSTWQFNFEFDLKK----------DMYATESIELLRKSGIDFKKHENLGID 140 (299)
T ss_pred CCCCCCCceeEEEEEecchh----------hhcchHHHHHHHHcCCChhhHhhcCCC
Confidence 7 4577899999877753 257899999999999999987777763
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=99.58 E-value=3.6e-15 Score=125.51 Aligned_cols=75 Identities=15% Similarity=0.263 Sum_probs=54.1
Q ss_pred CCCCCCCcCCEEEEeccccccchhHHHHhhhhhhhccccc--eEEEEecCceEEEEecCCCchhHHHHHhhhccccccch
Q 007029 478 NDKRKVSCEDVVFLWGFRERISAGILKNMLQGSHEVFAEA--FNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKAVSGPLR 555 (621)
Q Consensus 478 g~~~~~~~~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~--~~V~~id~t~a~V~~~~~~~~~~~l~~~~~~~~~~~l~ 555 (621)
|+|+.|+|+||+| ++||++||..||.+ +|+++ +.|+|||||||||+++++++++.++.+++.++
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 007029 556 EMVSDGLKAAGYETYQ 571 (621)
Q Consensus 556 ~~~~~g~~~a~~~~y~ 571 (621)
+-+..+|..|+
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 45667777774
No 6
>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=97.17 E-value=0.00095 Score=54.75 Aligned_cols=26 Identities=19% Similarity=0.317 Sum_probs=24.2
Q ss_pred ccccccchHHHHHHHHHHHhhcCCcc
Q 007029 242 MTIDVCSERQVQLVLKMLEDFSDVLV 267 (621)
Q Consensus 242 l~l~~~~~~q~~Li~q~l~~~~~~l~ 267 (621)
+.+++||+|||+|+||++++.||...
T Consensus 19 l~le~cngf~RkLiyq~l~~~~~~~I 44 (65)
T cd02637 19 LELEPCNGFQRKLIYQTLEQKYPKGI 44 (65)
T ss_pred ccccccccHHHHHHHHHHHHHccccc
Confidence 88999999999999999999999874
No 7
>PRK07740 hypothetical protein; Provisional
Probab=97.17 E-value=0.0021 Score=66.17 Aligned_cols=89 Identities=17% Similarity=0.227 Sum_probs=63.3
Q ss_pred CCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCceee
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEME 402 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~ve 402 (621)
.+.++||||.-.|+-++-+.+...+... +...++||..++....|..+..+|.++.+++. +
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 12468999988877665444556777776551 1
Q ss_pred cCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 007029 403 IPNQANENEGKIHGHNVVKICQLFGKLCSILKI 435 (621)
Q Consensus 403 i~~~~~~~~~heAGyDA~mTG~vFikL~~~L~~ 435 (621)
+. ...|.|-+||++|+.||.++...+..
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 8
>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=97.04 E-value=0.0045 Score=59.14 Aligned_cols=97 Identities=21% Similarity=0.179 Sum_probs=59.8
Q ss_pred cHHHHHHHHHh--CCCCEEeehhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCC-CccchhhHHhhhCcccccCchHHH
Q 007029 312 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFP-QVIDVNYLLKDIGPVKKMTNISAT 387 (621)
Q Consensus 312 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~g-pLP~t~~eFk~~i~~lFP-~I~DTKyLa~~~~~~~~~~~L~~~ 387 (621)
.|..|++.+.+ .+.++||||.=.|+-++-+.+-. -++.. ...| ..+||-.++....|.. ..+|..+
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 34444444432 45689999999999988655422 11110 0123 3789977776654432 3467777
Q ss_pred HHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHH
Q 007029 388 IAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLC 430 (621)
Q Consensus 388 ~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~ 430 (621)
.+++. ++. .....|.|.+||+.|+.+|.+|+
T Consensus 137 ~~~~~----------i~~--~~~~~H~Al~Da~~~a~l~~~l~ 167 (167)
T cd06131 137 CKRFG----------IDN--SHRTLHGALLDAELLAEVYLELT 167 (167)
T ss_pred HHHCC----------CCC--CCCCCCChHHHHHHHHHHHHHhC
Confidence 66652 111 11247999999999999999874
No 9
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.97 E-value=0.0045 Score=65.87 Aligned_cols=95 Identities=14% Similarity=0.171 Sum_probs=63.8
Q ss_pred HHHHHHHHHh--CCCCEEeehhHHHHHHHHHhcc---CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHH
Q 007029 313 FREVIDLISA--SQKPLVAHNSLNDFTFIHSKFL---APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISAT 387 (621)
Q Consensus 313 Fr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~---gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~ 387 (621)
|..|++.+.+ .+.++||||.-+|+-+|.+.+. .++| ....+||--|+....|-.+..+|..+
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 4444444332 4689999999999999876542 2333 12468997777765443234456666
Q ss_pred HHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 007029 388 IAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKI 435 (621)
Q Consensus 388 ~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~~ 435 (621)
.+.+. + + ...|.|-+||++|+.+|.+|+..++.
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 10
>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=96.94 E-value=0.0056 Score=62.24 Aligned_cols=98 Identities=19% Similarity=0.236 Sum_probs=61.6
Q ss_pred cHHHHHHHHHh--CCCCEEeehhHHHHHHHHHhc--cCC-CCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHH
Q 007029 312 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKF--LAP-LPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISA 386 (621)
Q Consensus 312 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F--~gp-LP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~ 386 (621)
-|..|++.+.+ .+.++||||.-+|+-||-..| +|+ +|. + .-|-.++||--|+...-|-. ..+|..
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 34444444433 457899999999999998765 342 110 0 01224899988887665432 235655
Q ss_pred HHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 007029 387 TIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 431 (621)
Q Consensus 387 ~~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~ 431 (621)
+.+.+ .. +. .....|.|-+||.+||.||+.|..
T Consensus 138 L~~~~----gi------~~--~~r~~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 138 LCKRF----KV------DN--SHRTLHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred HHHhc----CC------CC--CCCCCcCHHHHHHHHHHHHHHHHc
Confidence 55544 11 11 112469999999999999999876
No 11
>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=0.0064 Score=60.02 Aligned_cols=83 Identities=19% Similarity=0.159 Sum_probs=54.3
Q ss_pred CCCCEEeehhHHHHHHHHHhc--cCCCCCCHHHHHHHHHccC-C-CccchhhHHhhhCcccccCchHHHHHHHHhcCCCC
Q 007029 323 SQKPLVAHNSLNDFTFIHSKF--LAPLPPNMNEFICSLRLAF-P-QVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAP 398 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F--~gpLP~t~~eFk~~i~~lF-P-~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~ 398 (621)
.+.++||||.-+|+-||.+.+ +|--. ..| | .++||.-|+....+ ...|..+.+.+ ..+
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 367999999999999998665 22100 112 2 27999888876543 22454444432 111
Q ss_pred ceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 007029 399 IEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 431 (621)
Q Consensus 399 ~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~ 431 (621)
.. ....|.|.+||++|+.+|.+|..
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 12
>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=52.04 Aligned_cols=59 Identities=15% Similarity=0.202 Sum_probs=46.0
Q ss_pred CcCCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecCceEEEEecCCCchhHHHHH
Q 007029 484 SCEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNV 544 (621)
Q Consensus 484 ~~~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~t~a~V~~~~~~~~~~~l~~ 544 (621)
.|++.||+.| -.++++.||+.-+..-+..-++ +.|.||||+|+=|+|.+.+.|...|.+
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 13
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.83 E-value=0.008 Score=61.75 Aligned_cols=99 Identities=20% Similarity=0.235 Sum_probs=64.1
Q ss_pred ccHHHHHHHHHh--CCCCEEeehhHHHHHHHHHhc--cC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchH
Q 007029 311 RGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKF--LA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNIS 385 (621)
Q Consensus 311 ~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F--~g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~ 385 (621)
-.|..|++.+.+ .+-++||||.=+|+-||-..| +| ++|.. . .+..++||--|+...-|-. ..+|.
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 345555555543 456799999999999998665 33 34421 1 1355899988887765432 23566
Q ss_pred HHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 007029 386 ATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 431 (621)
Q Consensus 386 ~~~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~ 431 (621)
.+...+ . ++ ......|.|-+||.+|+.||++|..
T Consensus 141 aL~~~~----g------i~--~~~r~~H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 141 ALCKRY----G------ID--NSHRTLHGALLDAEILAEVYLAMTG 174 (240)
T ss_pred HHHHHC----C------CC--CCCCCCCCHHHHHHHHHHHHHHHHC
Confidence 655544 1 11 1112369999999999999999875
No 14
>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=0.0069 Score=61.06 Aligned_cols=88 Identities=19% Similarity=0.199 Sum_probs=57.0
Q ss_pred CCCCEEeehhHHHHHHHHHhcc--CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcc-c-ccCchHHHHHHHHhcCCCC
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFL--APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPV-K-KMTNISATIAYLKNRFFAP 398 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~--gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~-~-~~~~L~~~~~~l~~~~~~~ 398 (621)
.+.++||||.-+|+-+|-+.|. +..|. ....++||.-++....|. + ...+|..+.+.+.
T Consensus 86 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~~-----------~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~g------ 148 (217)
T TIGR00573 86 RGAELVIHNASFDVGFLNYEFSKLYKVEP-----------KTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYE------ 148 (217)
T ss_pred CCCEEEEeccHHHHHHHHHHHHHhcCCCC-----------CccceecHHHHHHHHHHhCCCCCCCHHHHHHHcC------
Confidence 4679999999999999988764 11110 113467886666544332 2 2235666665541
Q ss_pred ceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 007029 399 IEMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 433 (621)
Q Consensus 399 ~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L 433 (621)
+ +.. ....|.|..||.+|+.||.+|+...
T Consensus 149 --l--~~~--~~~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 149 --I--TNS--HRALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred --C--CCC--CcccCCHHHHHHHHHHHHHHHHhcc
Confidence 1 111 1247999999999999999998854
No 15
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.78 E-value=0.0055 Score=62.55 Aligned_cols=88 Identities=17% Similarity=0.205 Sum_probs=59.0
Q ss_pred hCCCCEEeehhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCC-CccchhhHHhhhCccc-ccCchHHHHHHHHhcCCCC
Q 007029 322 ASQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFP-QVIDVNYLLKDIGPVK-KMTNISATIAYLKNRFFAP 398 (621)
Q Consensus 322 ~skKpIVGHN~llDL~~iy~~F~g-pLP~t~~eFk~~i~~lFP-~I~DTKyLa~~~~~~~-~~~~L~~~~~~l~~~~~~~ 398 (621)
..+.||||||.-+|+-+|-+.|.. -+|. +.| .++||-.|+....+.. +...|+.+.+.+. .
T Consensus 91 ~~~~~lVahNa~FD~~fL~~~~~r~~~~~-----------~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~g----i- 154 (232)
T PRK07942 91 ARGVPVVVFNAPYDLTVLDRELRRHGLPS-----------LVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYG----V- 154 (232)
T ss_pred hcCCEEEEeCcHhhHHHHHHHHHHcCCCC-----------ccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcC----C-
Confidence 467899999999999998766521 1111 022 2679987776554432 2345666655441 1
Q ss_pred ceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 007029 399 IEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 434 (621)
Q Consensus 399 ~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~ 434 (621)
+ ....|.|..||.+|+.||.+|+..++
T Consensus 155 -----~----~~~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 155 -----R----LDNAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred -----C----CCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 1 12379999999999999999998764
No 16
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.70 E-value=0.011 Score=63.10 Aligned_cols=97 Identities=16% Similarity=0.199 Sum_probs=64.6
Q ss_pred cHHHHHHHHHh--CCCCEEeehhHHHHHHHHHhcc--C-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHH
Q 007029 312 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFL--A-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISA 386 (621)
Q Consensus 312 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~--g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~ 386 (621)
-|..|++.+.+ ...++||||.=+|+-+|.+.|- | ++|. ...+||.-|+....+-.+...|..
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 34444444432 4689999999999999987662 2 3331 236899888876543223345666
Q ss_pred HHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 007029 387 TIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKI 435 (621)
Q Consensus 387 ~~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~~ 435 (621)
+.+++. | + ....|.|-+||.+|+.||.++...++.
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 134699999999999999998887744
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=96.62 E-value=0.014 Score=54.87 Aligned_cols=87 Identities=20% Similarity=0.215 Sum_probs=58.0
Q ss_pred HHHHHHHHHh--CCCCEEeehhHHHHHHHHHhcc--C-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHH
Q 007029 313 FREVIDLISA--SQKPLVAHNSLNDFTFIHSKFL--A-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISAT 387 (621)
Q Consensus 313 Fr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~--g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~ 387 (621)
|..+++.+.+ .++++||||.=.|+-++-+.+- | +.|. + ..+||.-++....+..+..+|..+
T Consensus 64 ~~~v~~~l~~~l~~~~lv~hn~~fD~~~l~~~~~~~g~~~~~------------~-~~idt~~~~~~~~~~~~~~~L~~l 130 (156)
T cd06130 64 FPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPPP------------Y-QYLCTVRLARRVWPLLPNHKLNTV 130 (156)
T ss_pred HHHHHHHHHHHhCCCEEEEeChHHhHHHHHHHHHHcCCCCCC------------C-CEEEHHHHHHHHhccCCCCCHHHH
Confidence 4444444433 4589999999999999876652 2 1221 2 378997777665443345677777
Q ss_pred HHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHH
Q 007029 388 IAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFG 427 (621)
Q Consensus 388 ~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFi 427 (621)
.+++.- + .. .|.|-+||..|+.+|+
T Consensus 131 ~~~~g~----------~----~~-~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 131 AEHLGI----------E----LN-HHDALEDARACAEILL 155 (156)
T ss_pred HHHcCC----------C----cc-CcCchHHHHHHHHHHh
Confidence 776521 1 12 7999999999999995
No 18
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.57 E-value=0.014 Score=62.35 Aligned_cols=86 Identities=22% Similarity=0.240 Sum_probs=61.3
Q ss_pred CCCCEEeehhHHHHHHHHHhc--cCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCce
Q 007029 323 SQKPLVAHNSLNDFTFIHSKF--LAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIE 400 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F--~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~ 400 (621)
.+.++||||.-.|+-+|.+.| +|. |. ....++||-.++....+..+..+|..+.+.+.
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 367899999999999999876 222 21 11237899877776654333446777666551
Q ss_pred eecCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 007029 401 MEIPNQANENEGKIHGHNVVKICQLFGKLCSILKI 435 (621)
Q Consensus 401 vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~~ 435 (621)
++. ..|.|=+||++|+.||.+++...+.
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
>PRK05168 ribonuclease T; Provisional
Probab=96.56 E-value=0.0064 Score=61.11 Aligned_cols=87 Identities=18% Similarity=0.112 Sum_probs=57.5
Q ss_pred CCCCEEeehhHHHHHHHHHhc--cCCCCCCHHHHHHHHHccCC-CccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 007029 323 SQKPLVAHNSLNDFTFIHSKF--LAPLPPNMNEFICSLRLAFP-QVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 399 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F--~gpLP~t~~eFk~~i~~lFP-~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~ 399 (621)
.+.++||||.=+|+-||...+ +|-.. ...+| .++||.-|+....+ ...|..+.+.+ ..+
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 368999999999999998665 22100 01133 48999888875533 22455444432 111
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 007029 400 EMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 434 (621)
Q Consensus 400 ~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~ 434 (621)
. .....|.|-+||+.|+.+|.+|...++
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 20
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.52 E-value=0.02 Score=56.87 Aligned_cols=81 Identities=20% Similarity=0.230 Sum_probs=51.4
Q ss_pred CCCCEEeehhHHHHHHHHHhcc----CCCCCCHHHHHHHHHccCCCccchhhHHhh--hCccc---ccCchHHHHHHHHh
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFL----APLPPNMNEFICSLRLAFPQVIDVNYLLKD--IGPVK---KMTNISATIAYLKN 393 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~----gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~--~~~~~---~~~~L~~~~~~l~~ 393 (621)
.+.++||||.=.|+.+|-..|. .++|. ..+||.-++.. ...+. +..+|..+.+.+.
T Consensus 110 ~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~--------------~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~g- 174 (202)
T PRK09145 110 GNRPLVGYYLEFDVAMLNRYVRPLLGIPLPN--------------PLIEVSALYYDKKERHLPDAYIDLRFDAILKHLD- 174 (202)
T ss_pred cCCeEEEeCHHHHHHHHHHHHHHhcCCCCCC--------------CeeeHHHHHHHHhhccCCCcccCCCHHHHHHHcC-
Confidence 4689999999999999875542 23432 25677654422 11111 2335666665441
Q ss_pred cCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 007029 394 RFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 431 (621)
Q Consensus 394 ~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~ 431 (621)
+ +. ...|.|-.||++|+.||.+|..
T Consensus 175 -------i--~~----~~~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 175 -------L--PV----LGRHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred -------C--CC----CCCCCcHHHHHHHHHHHHHHHh
Confidence 1 11 2359999999999999999864
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=96.48 E-value=0.0095 Score=59.37 Aligned_cols=86 Identities=15% Similarity=0.125 Sum_probs=55.8
Q ss_pred CCCCEEeehhHHHHHHHHHhc--cCCCCCCHHHHHHHHHccCC-CccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 007029 323 SQKPLVAHNSLNDFTFIHSKF--LAPLPPNMNEFICSLRLAFP-QVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 399 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F--~gpLP~t~~eFk~~i~~lFP-~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~ 399 (621)
.+.++||||.=+|+.||-+.+ +|..+..+ -| .++||--|+....| ..+|..+.+.+ ..+.
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 22344444432 1111
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 007029 400 EMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 433 (621)
Q Consensus 400 ~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L 433 (621)
. ....|.|-+||++|+.+|.+|...+
T Consensus 167 ~--------~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 167 D--------STQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred c--------ccchhhhHHhHHHHHHHHHHHHHHH
Confidence 1 1247999999999999999999877
No 22
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.44 E-value=0.018 Score=59.18 Aligned_cols=96 Identities=11% Similarity=0.101 Sum_probs=61.2
Q ss_pred HHHHHHHHHh--CCCCEEeehhHHHHHHHHHhc---cC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCccc-------
Q 007029 313 FREVIDLISA--SQKPLVAHNSLNDFTFIHSKF---LA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVK------- 379 (621)
Q Consensus 313 Fr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F---~g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~------- 379 (621)
|..|++.+.+ .+.++||||.=+|+-|+-+.+ .+ ++| +.++||-.|+....+-.
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 4445555543 468999999999999997654 22 222 23689988776643211
Q ss_pred ------ccCchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhccC
Q 007029 380 ------KMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKIT 436 (621)
Q Consensus 380 ------~~~~L~~~~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~~~ 436 (621)
+.-.|..+.+.+ .. + ....|.|-.||++|+.+|..++..++..
T Consensus 182 ~~~~~~~~~~L~~l~~~~----gl------~----~~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 182 LKGKKPESIRLADSRLRY----GL------P----AYSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred hccCCCCCCCHHHHHHHc----CC------C----CCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 112344433322 11 1 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=55.68 Aligned_cols=76 Identities=16% Similarity=0.163 Sum_probs=49.8
Q ss_pred CCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCceee
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEME 402 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~ve 402 (621)
...+|||||.-.|+-+|-. .-|.++||-.|+....+..+.-+|..+...+.. ..++
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 3589999999999988732 236789998887654332223356665554421 1111
Q ss_pred cCCCCCCCCcccchhhHHHHHHHHH
Q 007029 403 IPNQANENEGKIHGHNVVKICQLFG 427 (621)
Q Consensus 403 i~~~~~~~~~heAGyDA~mTG~vFi 427 (621)
. ....|.|-.||.+|+.+|.
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=96.25 E-value=0.013 Score=56.33 Aligned_cols=75 Identities=15% Similarity=0.149 Sum_probs=51.0
Q ss_pred CCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCccc---ccCchHHHHHHHHhcCCCCce
Q 007029 324 QKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVK---KMTNISATIAYLKNRFFAPIE 400 (621)
Q Consensus 324 kKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~---~~~~L~~~~~~l~~~~~~~~~ 400 (621)
..+|||||.-.|+-+|=. ..|.++||-.|+....|.. +.-+|..+...+-+
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 489999999999977731 1467999998888765532 34566666554311
Q ss_pred eecCCCCCCCCcccchhhHHHHHHHHH
Q 007029 401 MEIPNQANENEGKIHGHNVVKICQLFG 427 (621)
Q Consensus 401 vei~~~~~~~~~heAGyDA~mTG~vFi 427 (621)
+ +.+.+ ...|.|-.||.+|+.+|+
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 246999999999999984
No 25
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=96.25 E-value=0.022 Score=57.76 Aligned_cols=94 Identities=15% Similarity=-0.018 Sum_probs=59.7
Q ss_pred cHHHHHHHHHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHH
Q 007029 312 GFREVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYL 391 (621)
Q Consensus 312 GFr~Vi~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l 391 (621)
-|..|++.+. ...++||||.-+|.-++- .+ --..+||=-|+....|-.+ .+++.+...+
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 3455555543 467999999999987662 11 1247999888877655322 3444444333
Q ss_pred HhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 007029 392 KNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKI 435 (621)
Q Consensus 392 ~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~~ 435 (621)
... +..+ .....|.|-+||++|+.+|.+|....|.
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=95.71 E-value=0.047 Score=50.31 Aligned_cols=78 Identities=15% Similarity=0.086 Sum_probs=50.0
Q ss_pred CCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHcc-CCCccchhhHHhhhCcccccCchHHHH-HHHHhcCCCCceee
Q 007029 325 KPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLA-FPQVIDVNYLLKDIGPVKKMTNISATI-AYLKNRFFAPIEME 402 (621)
Q Consensus 325 KpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~l-FP~I~DTKyLa~~~~~~~~~~~L~~~~-~~l~~~~~~~~~ve 402 (621)
.++||||.=.|+-++...|..-- ... ....+||+.++....+..+...+..+. ..+ ..
T Consensus 80 ~~~v~~n~~fD~~~l~~~~~~~~-----------~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~----~~----- 139 (159)
T cd06127 80 RVLVAHNASFDLRFLNRELRRLG-----------GPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERY----GI----- 139 (159)
T ss_pred CEEEEeCcHhhHHHHHHHHHHhC-----------CCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHc----CC-----
Confidence 79999999999887776653100 111 234889998887765544444444432 111 00
Q ss_pred cCCCCCCCCcccchhhHHHHHHHHH
Q 007029 403 IPNQANENEGKIHGHNVVKICQLFG 427 (621)
Q Consensus 403 i~~~~~~~~~heAGyDA~mTG~vFi 427 (621)
.....|.|-+||.+|+.||.
T Consensus 140 -----~~~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 140 -----PLEGAHRALADALATAELLL 159 (159)
T ss_pred -----CCCCCCCcHHHHHHHHHHhC
Confidence 11357999999999999983
No 27
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=95.69 E-value=0.075 Score=54.18 Aligned_cols=87 Identities=22% Similarity=0.242 Sum_probs=56.7
Q ss_pred CCCCEEeehh-HHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCce
Q 007029 323 SQKPLVAHNS-LNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIE 400 (621)
Q Consensus 323 skKpIVGHN~-llDL~~iy~~F~g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~ 400 (621)
....+||||. -+|+-++-+.|.. .+|.. .-..+||--++....|-.+..+|..+..... .+
T Consensus 79 ~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~-----------~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~~----~~-- 141 (232)
T PRK06309 79 TDNILVAHNNDAFDFPLLRKECRRHGLEPP-----------TLRTIDSLKWAQKYRPDLPKHNLQYLRQVYG----FE-- 141 (232)
T ss_pred CCCEEEEeCCHHHHHHHHHHHHHHcCCCCC-----------CCcEEeHHHHHHHHcCCCCCCCHHHHHHHcC----CC--
Confidence 4568999994 7999888766521 11110 1237899777776544222345666554441 11
Q ss_pred eecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 007029 401 MEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 434 (621)
Q Consensus 401 vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~ 434 (621)
....|.|-+||+.|+.||.+|...++
T Consensus 142 --------~~~aH~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 142 --------ENQAHRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred --------CCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 13489999999999999999987664
No 28
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=95.69 E-value=0.083 Score=49.92 Aligned_cols=84 Identities=24% Similarity=0.215 Sum_probs=55.7
Q ss_pred CCCEEeehh-HHHHHHHHHhcc---CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 007029 324 QKPLVAHNS-LNDFTFIHSKFL---APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 399 (621)
Q Consensus 324 kKpIVGHN~-llDL~~iy~~F~---gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~ 399 (621)
+.++||||. =.|+-++-..+. .+.|. +-.++||.-++....+.. ..+|.++.+.+.- +
T Consensus 80 ~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~------------~~~~iD~~~~~~~~~~~~-~~~L~~l~~~~~~----~- 141 (169)
T smart00479 80 GKILVAGNALNFDLRFLKLEHPRLGIKDPP------------KNPVIDTLKLARALNPGR-KYSLKKLAERLGL----E- 141 (169)
T ss_pred CCEEEEeCCHHHhHHHHHHHHHHhCCCCCc------------CCCeeEHHHHHHHHCCCC-CCCHHHHHHHCCC----C-
Confidence 468899999 889888776552 22331 122789987776554422 4567776665521 1
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 007029 400 EMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 433 (621)
Q Consensus 400 ~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L 433 (621)
. .+..|.|-+||.+|+.||.+|...+
T Consensus 142 -----~---~~~~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 142 -----V---IGRAHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred -----C---CCCCcCcHHHHHHHHHHHHHHHHHh
Confidence 1 1226999999999999999998754
No 29
>PRK07883 hypothetical protein; Validated
Probab=95.56 E-value=0.088 Score=60.55 Aligned_cols=87 Identities=18% Similarity=0.133 Sum_probs=58.7
Q ss_pred CCCEEeehhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCc--ccccCchHHHHHHHHhcCCCCce
Q 007029 324 QKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGP--VKKMTNISATIAYLKNRFFAPIE 400 (621)
Q Consensus 324 kKpIVGHN~llDL~~iy~~F~g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~--~~~~~~L~~~~~~l~~~~~~~~~ 400 (621)
+.++||||.=+|+-++-..|.. -+|. ..+..+||-.++...-+ -.+..+|.++.+++. .+
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 6899999999999998876532 1110 01246899777766433 113345666665441 11
Q ss_pred eecCCCCCCCCcccchhhHHHHHHHHHHHHHHhcc
Q 007029 401 MEIPNQANENEGKIHGHNVVKICQLFGKLCSILKI 435 (621)
Q Consensus 401 vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~~ 435 (621)
. ...|.|-+||.+|+.||.++...++.
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 30
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.51 E-value=0.063 Score=64.43 Aligned_cols=89 Identities=18% Similarity=0.144 Sum_probs=61.5
Q ss_pred CCCCEEeehhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCcee
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEM 401 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~v 401 (621)
.+.++||||.=+|+.++...|.. ..|- ..| .+||-.|+...-|-.+..+|..+.+.+. +
T Consensus 85 ~~~~lVaHN~~FD~~fL~~~~~~~g~~~-----------~~~-~iDT~~la~~~~p~~~~~~L~~L~~~lg--------l 144 (820)
T PRK07246 85 EDCIFVAHNVKFDANLLAEALFLEGYEL-----------RTP-RVDTVELAQVFFPTLEKYSLSHLSRELN--------I 144 (820)
T ss_pred CCCEEEEECcHHHHHHHHHHHHHcCCCC-----------CCC-ceeHHHHHHHHhCCCCCCCHHHHHHHcC--------C
Confidence 46899999999999999876531 1110 012 4799887776555334456777666551 1
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHHHHHHHHhccCC
Q 007029 402 EIPNQANENEGKIHGHNVVKICQLFGKLCSILKITP 437 (621)
Q Consensus 402 ei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~~~~ 437 (621)
+. ...|.|-.||.+|+.+|.+|...++.-+
T Consensus 145 --~~----~~~H~Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 145 --DL----ADAHTAIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred --CC----CCCCCHHHHHHHHHHHHHHHHHHHhhcC
Confidence 11 2469999999999999999999886533
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=95.33 E-value=0.052 Score=51.56 Aligned_cols=75 Identities=16% Similarity=0.163 Sum_probs=43.7
Q ss_pred CCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcc-cccCchHHHHHHHHhcCCCCcee
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPV-KKMTNISATIAYLKNRFFAPIEM 401 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~-~~~~~L~~~~~~l~~~~~~~~~v 401 (621)
.+.++||||.=.|+-++- .+.|. ..++||=.+.....+. .+.-+|..+.+.+.. +
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 1367874322221221 123456665554311 1
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHH
Q 007029 402 EIPNQANENEGKIHGHNVVKICQLF 426 (621)
Q Consensus 402 ei~~~~~~~~~heAGyDA~mTG~vF 426 (621)
++ . ...|.|..||+.|+.+|
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 13699999999999998
No 32
>PRK06722 exonuclease; Provisional
Probab=95.30 E-value=0.093 Score=55.20 Aligned_cols=97 Identities=11% Similarity=0.152 Sum_probs=55.8
Q ss_pred cHHHHHHHHHh--CCCCEEeehhHHHHHHHHHhc--cC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCc-c-cccCch
Q 007029 312 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKF--LA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGP-V-KKMTNI 384 (621)
Q Consensus 312 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F--~g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~-~-~~~~~L 384 (621)
-|..|++.+.+ .+.++|+||.-.|+-|+-+.+ +| +.|... +-..+||.-++....+ + ....+|
T Consensus 76 ~f~eVl~ef~~fig~~~lvahna~FD~~FL~~~l~~~gi~~p~~~----------~~~~idl~~la~~~~~~l~~~~~sL 145 (281)
T PRK06722 76 KFPQIIEKFIQFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPCME----------KERRIDLQKFVFQAYEELFEHTPSL 145 (281)
T ss_pred CHHHHHHHHHHHHCCCcEEEEEeHHHHHHHHHHHHHcCCCCCccc----------ccchhHHHHHHHHHhhhhccCCCCH
Confidence 34444444432 345778777788998888755 33 223210 0113566544433211 1 123467
Q ss_pred HHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 007029 385 SATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 431 (621)
Q Consensus 385 ~~~~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~ 431 (621)
+.+.+++. ++. .+..|.|-.||.|||.+|++|..
T Consensus 146 ~~l~~~lg----------L~~---~g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 146 QSAVEQLG----------LIW---EGKQHRALADAENTANILLKAYS 179 (281)
T ss_pred HHHHHHCC----------CCC---CCCCcCcHHHHHHHHHHHHHHhc
Confidence 77777651 111 23479999999999999999984
No 33
>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=95.29 E-value=0.074 Score=66.03 Aligned_cols=105 Identities=20% Similarity=0.263 Sum_probs=72.7
Q ss_pred HhhhhhcccHHHHHHHHHh--CCCCEEeehhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccc
Q 007029 304 FEQNKRVRGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKK 380 (621)
Q Consensus 304 ~e~~~~~~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~ 380 (621)
++.+.++.-+..|+..+.+ .+.++||||.-.|+-+|-+.|.. -+|. +...++||--++..+.|-.+
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 4445566667667666654 57899999999999999887632 1121 11357899888877655334
Q ss_pred cCchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 007029 381 MTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 433 (621)
Q Consensus 381 ~~~L~~~~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L 433 (621)
..+|..+.+.+. ++ . ...|.|-+||.+|+.||.+|...+
T Consensus 317 ~~kL~~Lak~lg--------i~--~----~~~HrAl~DA~aTa~I~~~ll~~l 355 (1213)
T TIGR01405 317 SHRLGNICKKLG--------VD--L----DDHHRADYDAEATAKVFKVMVEQL 355 (1213)
T ss_pred CCCHHHHHHHcC--------CC--C----CCCcCHHHHHHHHHHHHHHHHHHH
Confidence 556777666551 11 1 126999999999999999999877
No 34
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=95.14 E-value=0.11 Score=51.73 Aligned_cols=83 Identities=12% Similarity=0.224 Sum_probs=48.0
Q ss_pred CCCCEEeehh-HHHHHHHHHhccCCCCCCHHHHHHHHHccCCC-ccchhhHHhhhCccc--ccCchHHHHHHHHhcCCCC
Q 007029 323 SQKPLVAHNS-LNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQ-VIDVNYLLKDIGPVK--KMTNISATIAYLKNRFFAP 398 (621)
Q Consensus 323 skKpIVGHN~-llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~-I~DTKyLa~~~~~~~--~~~~L~~~~~~l~~~~~~~ 398 (621)
...++||||. ++|+-++-...+ +++.. ++. ++|+.+ ......+. +..+|+.+.+++.
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 5668999997 589988865432 33321 111 223332 11111111 2345666655541
Q ss_pred ceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 007029 399 IEMEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 433 (621)
Q Consensus 399 ~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L 433 (621)
++ ...|.|-+||++|+.||.+|...-
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=94.96 E-value=0.14 Score=52.89 Aligned_cols=86 Identities=16% Similarity=0.142 Sum_probs=57.4
Q ss_pred CCCCEEeehhHHHHHHHHHhccC-CCCCCHHHHHHHHHccC-CCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCce
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAF-PQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIE 400 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~g-pLP~t~~eFk~~i~~lF-P~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~ 400 (621)
...++||||.=+|+-+|-..|.. -+|.. .+ -.++||-.++...++. ...+|..+.....
T Consensus 87 ~~~~lvghn~~FD~~~L~~~~~r~g~~~~----------~~~~~~iDtl~lar~~~~~-~~~~L~~l~~~~g-------- 147 (250)
T PRK06310 87 EGDYIVGHSVGFDLQVLSQESERIGETFL----------SKHYYIIDTLRLAKEYGDS-PNNSLEALAVHFN-------- 147 (250)
T ss_pred CCCEEEEECHHHHHHHHHHHHHHcCCCcc----------ccCCcEEehHHHHHhcccC-CCCCHHHHHHHCC--------
Confidence 34689999999999999876631 11110 01 2489998888765432 2345666665441
Q ss_pred eecCCCCCCCCcccchhhHHHHHHHHHHHHHHh
Q 007029 401 MEIPNQANENEGKIHGHNVVKICQLFGKLCSIL 433 (621)
Q Consensus 401 vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L 433 (621)
+ + ....|.|-.||++|+.||.+++..+
T Consensus 148 ~--~----~~~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 148 V--P----YDGNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred C--C----CCCCcChHHHHHHHHHHHHHHHHhc
Confidence 1 1 1237999999999999999998755
No 36
>KOG4483 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.91 E-value=0.029 Score=60.23 Aligned_cols=66 Identities=17% Similarity=0.335 Sum_probs=51.3
Q ss_pred cCCEEEEeccccccchhHHHHhhhhhhhccc-cceEEEEecCceEEEEecCCCchhHHHHHhhhcc--ccccchh
Q 007029 485 CEDVVFLWGFRERISAGILKNMLQGSHEVFA-EAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKA--VSGPLRE 556 (621)
Q Consensus 485 ~~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~-~~~~V~~id~t~a~V~~~~~~~~~~~l~~~~~~~--~~~~l~~ 556 (621)
..||+=|++||.++++.|+-..+++ |+ ..|+|+|+|||.||-+|+..-.|.+.|.. +++ ..-||..
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 37
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=94.86 E-value=0.25 Score=49.38 Aligned_cols=83 Identities=13% Similarity=0.111 Sum_probs=52.2
Q ss_pred CCEEeehhHHHHHHHHHhc--cC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCcee
Q 007029 325 KPLVAHNSLNDFTFIHSKF--LA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEM 401 (621)
Q Consensus 325 KpIVGHN~llDL~~iy~~F--~g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~v 401 (621)
.++|.||.=+|+-+|-+.+ +| +.| .++..+|+..+.....+..+..+|..+.+.+.
T Consensus 94 ~~~iv~~~~fD~~fL~~~~~~~~~~~~------------~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~g--------- 152 (207)
T PRK07748 94 KPTIVTWGNMDMKVLKHNCEKAGVPFP------------FKGQCRDLSLEYKKFFGERNQTGLWKAIEEYG--------- 152 (207)
T ss_pred CeEEEEECHHHHHHHHHHHHHcCCCCc------------ccccceeHHHHHHHHhCcCCCCCHHHHHHHcC---------
Confidence 4556666778999998665 23 222 11345677655444333233456777776551
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHHHHHHHH
Q 007029 402 EIPNQANENEGKIHGHNVVKICQLFGKLCSI 432 (621)
Q Consensus 402 ei~~~~~~~~~heAGyDA~mTG~vFikL~~~ 432 (621)
++ ..+..|.|-.||++|+.+|.+|..-
T Consensus 153 -i~---~~~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 153 -KE---GTGKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred -CC---CCCCCcChHHHHHHHHHHHHHHHhC
Confidence 11 1134689999999999999999875
No 38
>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=94.83 E-value=0.094 Score=50.23 Aligned_cols=76 Identities=17% Similarity=0.194 Sum_probs=44.8
Q ss_pred CCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCC-CccchhhH--Hhhh--CcccccCchHHHHHHHHhcCCC
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFP-QVIDVNYL--LKDI--GPVKKMTNISATIAYLKNRFFA 397 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP-~I~DTKyL--a~~~--~~~~~~~~L~~~~~~l~~~~~~ 397 (621)
.++++||||.-.|+-++-.. ..| .+.||=.+ +... .|-.+.-+|+.+.+++...
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 25677332 2221 2211234566666655211
Q ss_pred CceeecCCCCCCCCcccchhhHHHHHHHH
Q 007029 398 PIEMEIPNQANENEGKIHGHNVVKICQLF 426 (621)
Q Consensus 398 ~~~vei~~~~~~~~~heAGyDA~mTG~vF 426 (621)
.++ . ....|.|-.||.+|+.+|
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 39
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=94.79 E-value=0.15 Score=55.34 Aligned_cols=206 Identities=12% Similarity=0.092 Sum_probs=102.3
Q ss_pred hhhcccHHHHHHHHHh--CCCCEEeehhHHHHHHHHHhccCCCCCCH----HHHH------------HHHHccCC-Cccc
Q 007029 307 NKRVRGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLAPLPPNM----NEFI------------CSLRLAFP-QVID 367 (621)
Q Consensus 307 ~~~~~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~gpLP~t~----~eFk------------~~i~~lFP-~I~D 367 (621)
+..+..|..|++.|.+ .+.++||||.-+|+-||.+.|-.-+-... ..+. ..-+..+| .++|
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 4456678888877765 47899999999999999876511100000 0000 00011234 4899
Q ss_pred hhhHHhhhCcccccCchHHHHHHHHhcCCCCceeecCCC-CC---CCCcccch--hhHHHHHHHHHHHHHHhccCCCCCC
Q 007029 368 VNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQ-AN---ENEGKIHG--HNVVKICQLFGKLCSILKITPDAIE 441 (621)
Q Consensus 368 TKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~vei~~~-~~---~~~~heAG--yDA~mTG~vFikL~~~L~~~~~~~~ 441 (621)
|=-|+....|..+.-.|+.+.+++. |+.|.. .+ ...-|.|= =||.+++.+|.++... | ...
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 9777776665434556777776652 111110 11 11223332 3899999999886211 1 101
Q ss_pred CCcHHHHhhhhhhhcc-ccC--CCCCCCCCCCcccc-CCCCCCCC--CCcCCEEEEeccccccchhHHHHhhhhhhhccc
Q 007029 442 SSDDFLASAINRYANI-FYS--LPGSSQEPTNEEIR-GWTNDKRK--VSCEDVVFLWGFRERISAGILKNMLQGSHEVFA 515 (621)
Q Consensus 442 s~~~~~~~~l~~~~N~-l~~--~~~~~~~~~d~~~~-~l~g~~~~--~~~~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~ 515 (621)
+.. + +.+.+. +-+ +..+. +..-.+|. --+|...+ +....+-+++.=+-.....+|-+.+-.-+-.
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 111111 111 00110 01223332 11344332 3566776665644466677776665432222
Q ss_pred cceEEEEecCceEEEEecCCCc
Q 007029 516 EAFNVRMVDRSCAIVVFGKPGL 537 (621)
Q Consensus 516 ~~~~V~~id~t~a~V~~~~~~~ 537 (621)
+-.-++..+.+|+.+....
T Consensus 324 ---y~~~~~r~tslvv~n~~~~ 342 (377)
T PRK05601 324 ---YSEKLTRQTSVVVCNQTRD 342 (377)
T ss_pred ---hhhccccceeEEEeCCCCC
Confidence 3334566666777666654
No 40
>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=94.76 E-value=0.13 Score=62.02 Aligned_cols=100 Identities=19% Similarity=0.201 Sum_probs=65.5
Q ss_pred cHHHHHHHHHh--CCCCEEeehhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCC-CccchhhHHhhhCcccccCchHHH
Q 007029 312 GFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFP-QVIDVNYLLKDIGPVKKMTNISAT 387 (621)
Q Consensus 312 GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~g-pLP~t~~eFk~~i~~lFP-~I~DTKyLa~~~~~~~~~~~L~~~ 387 (621)
-|..|+..+.+ ...++||||.=+|+.++.+.|.. -+| .+| ..+||--|+....|-.+..+|..+
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 34444443332 46789999999999999876521 111 012 368986666665553345567776
Q ss_pred HHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhccCC
Q 007029 388 IAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKITP 437 (621)
Q Consensus 388 ~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~~~~ 437 (621)
.+.+. + +. ...|.|-.||.+|+.+|.+|...++.-+
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 41
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=94.54 E-value=0.18 Score=61.45 Aligned_cols=90 Identities=17% Similarity=0.175 Sum_probs=61.7
Q ss_pred CCCCEEeehhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCcee
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEM 401 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~v 401 (621)
.+.++||||.=.|+-++-+.|.. -+|. +.-..+||=.|+...-|-.+.-+|..+.+++. +
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 01247899777766554334446777666551 1
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHHHHHHHHhccCC
Q 007029 402 EIPNQANENEGKIHGHNVVKICQLFGKLCSILKITP 437 (621)
Q Consensus 402 ei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~~~~ 437 (621)
+ ....|.|-.||.+|+.+|.+|...++.-+
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=94.27 E-value=0.22 Score=51.69 Aligned_cols=86 Identities=17% Similarity=0.101 Sum_probs=55.2
Q ss_pred CCCCEEeehhHHHHHHHHHhccC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCcee
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEM 401 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~v 401 (621)
.+.++||||.=+|..++-+.|.. -+|. +.+..+||--++...-+. ...+|..+.+.+. +
T Consensus 146 ~~~v~VaHNa~FD~~fL~~~l~r~g~~~-----------~~~~~ldtl~la~~~~~~-~~~~L~~L~~~lg--------i 205 (257)
T PRK08517 146 GDSVFVAHNVNFDYNFISRSLEEIGLGP-----------LLNRKLCTIDLAKRTIES-PRYGLSFLKELLG--------I 205 (257)
T ss_pred CCCeEEEECHHHHHHHHHHHHHHcCCCC-----------CCCCcEehHHHHHHHccC-CCCCHHHHHHHcC--------c
Confidence 35789999999999998765521 1111 123357876566543322 2335666555431 1
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 007029 402 EIPNQANENEGKIHGHNVVKICQLFGKLCSILK 434 (621)
Q Consensus 402 ei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~ 434 (621)
+ ....|.|-+||.+|+.||.++...+.
T Consensus 206 --~----~~~~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 206 --E----IEVHHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred --C----CCCCCChHHHHHHHHHHHHHHHHHhH
Confidence 1 12479999999999999999998773
No 43
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=94.04 E-value=0.16 Score=64.08 Aligned_cols=106 Identities=21% Similarity=0.137 Sum_probs=69.6
Q ss_pred HhhhhhcccHHHHHHHHHh--CCCCEEeehhHHHHHHHHHhccCC-CCCCHHHHHHHHHccCCCccchhhHHhhhCcccc
Q 007029 304 FEQNKRVRGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFLAP-LPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKK 380 (621)
Q Consensus 304 ~e~~~~~~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~gp-LP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~ 380 (621)
.+.+....-+..+++.+.+ .+.++||||.-.|+-+|-+.+-.- +|. +...++||--++....|-.+
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 4455566678888888876 688999999999998885544211 111 12347888665555443223
Q ss_pred cCchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 007029 381 MTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 434 (621)
Q Consensus 381 ~~~L~~~~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~ 434 (621)
..+|..+.+.+ ..+ ....|.|-+||++|+.||.+|...+.
T Consensus 546 ~~kL~~LAk~l----GL~----------~~~~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 546 SHRLNTLAKKF----GVE----------LEHHHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred cccHHHHHHHc----CCC----------CCCCcChHHHHHHHHHHHHHHHHHHH
Confidence 44555555543 111 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=91.83 E-value=0.0082 Score=55.55 Aligned_cols=80 Identities=20% Similarity=0.191 Sum_probs=45.0
Q ss_pred CCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHcc---CCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLA---FPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 399 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~l---FP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~ 399 (621)
....+||||.-.|+.++-+. +++.+... ++.++||--+.....+.....+|..+.+.+.-
T Consensus 82 ~~~~~v~~n~~fd~~~l~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~------ 144 (164)
T PF00929_consen 82 KNDILVGHNASFDIGFLRRE-----------DKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAEYFGI------ 144 (164)
T ss_dssp HHTEEEETTCCHEEESSHHH-----------HHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTS------
T ss_pred cccccccccccchhhHHHHh-----------hhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHHHcCC------
Confidence 45899999977776555432 22222222 23466775444433221122455555554421
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHH
Q 007029 400 EMEIPNQANENEGKIHGHNVVKICQLF 426 (621)
Q Consensus 400 ~vei~~~~~~~~~heAGyDA~mTG~vF 426 (621)
+.. ...|.|..||++|..||
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=90.95 E-value=1.2 Score=42.52 Aligned_cols=92 Identities=17% Similarity=0.161 Sum_probs=55.7
Q ss_pred HHHHHHhCCCCEEeehhHHHHHHHHHhcc--CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHh
Q 007029 316 VIDLISASQKPLVAHNSLNDFTFIHSKFL--APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKN 393 (621)
Q Consensus 316 Vi~~L~~skKpIVGHN~llDL~~iy~~F~--gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~ 393 (621)
+.+.|......+|.||.-.|+-.+.+.+. +-.| .-..+...+||+.++....+..+..+|.++.+++.
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 33444433235556666777665554321 1110 01235568999988877655545667777776651
Q ss_pred cCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHH
Q 007029 394 RFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKL 429 (621)
Q Consensus 394 ~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL 429 (621)
+ +. .+..|.|=+||..|+.||.+|
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 145799999999999999876
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=90.16 E-value=0.69 Score=44.11 Aligned_cols=50 Identities=8% Similarity=0.146 Sum_probs=36.2
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCcc
Q 007029 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRD 121 (621)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~~ 121 (621)
||.+|+|+||+.+. .. .-..-.|+|+|.+.++.+... ....|+.++-|..
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 112346999999988665533 7789999999963
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=89.71 E-value=0.99 Score=43.98 Aligned_cols=75 Identities=19% Similarity=0.264 Sum_probs=48.1
Q ss_pred CCCEEeehh-HHHHHHHHHhcc--C-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 007029 324 QKPLVAHNS-LNDFTFIHSKFL--A-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 399 (621)
Q Consensus 324 kKpIVGHN~-llDL~~iy~~F~--g-pLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~ 399 (621)
..++||||. =+|+-++-+.|- | ++|.. +..+||-.++..+.+ +|+++.+.+ +..
T Consensus 98 ~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~------------~~~iDtl~l~r~~~~-----~L~~l~~~~----~~~- 155 (177)
T cd06136 98 PICLVAHNGNRFDFPILRSELERLGTKLPDD------------ILCVDSLPAFRELDQ-----SLGSLYKRL----FGQ- 155 (177)
T ss_pred CCEEEEcCCcccCHHHHHHHHHHcCCCCCCC------------CEEEEeHHHHhhhHh-----hHHHHHHHH----hCC-
Confidence 348999998 799999977662 2 11210 234688666665433 566665533 111
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHHHH
Q 007029 400 EMEIPNQANENEGKIHGHNVVKICQLFGK 428 (621)
Q Consensus 400 ~vei~~~~~~~~~heAGyDA~mTG~vFik 428 (621)
+ ....|.|-.||..|+.||++
T Consensus 156 ----~----~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 156 ----E----PKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred ----C----cccccchHHHHHHHHHHHhh
Confidence 1 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=88.93 E-value=2.1 Score=41.84 Aligned_cols=26 Identities=23% Similarity=0.234 Sum_probs=19.2
Q ss_pred HHHHhCCCCEEeeh-hHHHHHHHHHhc
Q 007029 318 DLISASQKPLVAHN-SLNDFTFIHSKF 343 (621)
Q Consensus 318 ~~L~~skKpIVGHN-~llDL~~iy~~F 343 (621)
+.+.+.+.++|||| .-+|+.|+-..|
T Consensus 78 ~~~~~~~~~lVahn~~~FD~~fL~~~~ 104 (183)
T cd06138 78 RLFNTPGTCIVGYNNIRFDDEFLRFAF 104 (183)
T ss_pred HHHccCCCcEEeeCchhhHHHHHHHHH
Confidence 33333567899998 579999997766
No 49
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=88.45 E-value=2.7 Score=42.59 Aligned_cols=83 Identities=22% Similarity=0.152 Sum_probs=53.3
Q ss_pred CCEEeehhHHHHHHHHHhcc---CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCcee
Q 007029 325 KPLVAHNSLNDFTFIHSKFL---APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEM 401 (621)
Q Consensus 325 KpIVGHN~llDL~~iy~~F~---gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~~v 401 (621)
.++||||-.+|+.++-..+. ++.| --.++||=-++....|-.+..+|..+.+.+ ..
T Consensus 96 ~~~Vahna~fD~~fl~~~~~~~~~~~~-------------~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~----gi---- 154 (243)
T COG0847 96 RLLVAHNAAFDVGFLRVESERLGIEIP-------------GDPVLDTLALARRHFPGFDRSSLDALAERL----GI---- 154 (243)
T ss_pred CeEEEEchhhcHHHHHHHHHHcCCCcc-------------cCceehHHHHHHHHcCCCccchHHHHHHHc----CC----
Confidence 99999999999999975552 2333 234667766665544322344455444422 11
Q ss_pred ecCCCCCCCCcccchhhHHHHHHHHHHHHHH
Q 007029 402 EIPNQANENEGKIHGHNVVKICQLFGKLCSI 432 (621)
Q Consensus 402 ei~~~~~~~~~heAGyDA~mTG~vFikL~~~ 432 (621)
+. +....|.|-+||++|+.+|+.+..-
T Consensus 155 --~~--~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 155 --DR--NPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred --Cc--CCcCCcchHHHHHHHHHHHHHHHhc
Confidence 11 1123488999999999999999883
No 50
>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=88.02 E-value=1.8 Score=40.91 Aligned_cols=95 Identities=16% Similarity=0.234 Sum_probs=57.5
Q ss_pred HHHHHH-hCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhh-CcccccCchHHHHHHHHh
Q 007029 316 VIDLIS-ASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDI-GPVKKMTNISATIAYLKN 393 (621)
Q Consensus 316 Vi~~L~-~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~-~~~~~~~~L~~~~~~l~~ 393 (621)
.+..+. ..+...||||+=.|+..+++.+ |- ....++|| .++... .+-. ..+|..+...+..
T Consensus 68 ~l~~ll~~~~i~kv~~n~~~D~~~L~~~~-~i--------------~~~~~~D~-~l~~~~l~~~~-~~~L~~L~~~~l~ 130 (176)
T PF01612_consen 68 ALKELLEDPNIIKVGHNAKFDLKWLYRSF-GI--------------DLKNVFDT-MLAAYLLDPTR-SYSLKDLAEEYLG 130 (176)
T ss_dssp HHHHHHTTTTSEEEESSHHHHHHHHHHHH-TS----------------SSEEEH-HHHHHHTTTST-TSSHHHHHHHHHS
T ss_pred HHHHHHhCCCccEEEEEEechHHHHHHHh-cc--------------ccCCccch-hhhhhcccccc-cccHHHHHHHHhh
Confidence 333344 4456789999999999999872 21 23458999 555543 3322 2677777666543
Q ss_pred cCCCCceeecC--CCCC--C--CC-----cccchhhHHHHHHHHHHHHHHh
Q 007029 394 RFFAPIEMEIP--NQAN--E--NE-----GKIHGHNVVKICQLFGKLCSIL 433 (621)
Q Consensus 394 ~~~~~~~vei~--~~~~--~--~~-----~heAGyDA~mTG~vFikL~~~L 433 (621)
.+..+ ..-+ . .. ..=|+.||+.|-.++-+|..+|
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 1111 1 11 1227999999999999998876
No 51
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=87.39 E-value=1.2 Score=44.34 Aligned_cols=56 Identities=13% Similarity=0.166 Sum_probs=38.6
Q ss_pred HHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 41 LSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 41 lp~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
+..+.+......||+||+|.||+.+. .-.|+|+|...+..+ .-.....|.+++-|.
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 33455555678999999999998321 235999999888632 222335788888885
No 52
>PRK05168 ribonuclease T; Provisional
Probab=86.98 E-value=1.9 Score=43.39 Aligned_cols=57 Identities=16% Similarity=0.232 Sum_probs=43.2
Q ss_pred HHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCC-Cc-eeeEeEEEeec
Q 007029 41 LSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQA-SK-VIAYPYNFHLF 118 (621)
Q Consensus 41 lp~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~-~~-y~~~~fNF~lf 118 (621)
+.-|...+++..||++|+|-||+.+.. -.|||+|...++.+. +. .....|..++-
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 139999999887653 32 34678999999
Q ss_pred Cc
Q 007029 119 PR 120 (621)
Q Consensus 119 p~ 120 (621)
|.
T Consensus 64 P~ 65 (211)
T PRK05168 64 PF 65 (211)
T ss_pred CC
Confidence 84
No 53
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=86.74 E-value=3.3 Score=43.96 Aligned_cols=87 Identities=13% Similarity=-0.011 Sum_probs=47.4
Q ss_pred HHHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCC
Q 007029 319 LISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAP 398 (621)
Q Consensus 319 ~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~ 398 (621)
.+.+...+|||||.=+|+-|+-..+ .+++.. | ..+|=-.+.-..+-.+..+|..+...+ . +
T Consensus 116 ~fl~~~~vlVAHNA~FD~~fL~~~~-~~~~~~------------~-~~ct~~~i~~~~~~~~~~kL~~La~~~----g-~ 176 (294)
T PRK09182 116 ALIAPADLIIAHNAGFDRPFLERFS-PVFATK------------P-WACSVSEIDWSARGFEGTKLGYLAGQA----G-F 176 (294)
T ss_pred HHhcCCCEEEEeCHHHHHHHHHHHH-HhccCC------------c-ccccHHHHhhccccCCCCCHHHHHHHc----C-C
Confidence 3344457999999999998886543 222211 0 011100000000101234455555433 1 1
Q ss_pred ceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 007029 399 IEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 434 (621)
Q Consensus 399 ~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~ 434 (621)
....|.|..||+.|+.||.++....|
T Consensus 177 ----------~~~aHrAl~Da~Ata~ll~~~l~~~~ 202 (294)
T PRK09182 177 ----------FHEGHRAVDDCQALLELLARPLPETG 202 (294)
T ss_pred ----------CCCCcChHHHHHHHHHHHHHHHhhcC
Confidence 12469999999999999997776554
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=86.12 E-value=1.6 Score=34.40 Aligned_cols=56 Identities=13% Similarity=0.282 Sum_probs=40.8
Q ss_pred EEEeccccccchhHHHHhhhhhhhccccceEEEEec------CceEEEEecCCCchhHHHHHhhhc
Q 007029 489 VFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVD------RSCAIVVFGKPGLSNTFKNVMNSK 548 (621)
Q Consensus 489 v~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id------~t~a~V~~~~~~~~~~~l~~~~~~ 548 (621)
|+|.++|..++..+|++.+++ ||+...+.... ...|||.|.+.+.|..++..++..
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 44433333333 346999999999999888877553
No 55
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=85.77 E-value=1.5 Score=41.33 Aligned_cols=43 Identities=14% Similarity=0.234 Sum_probs=32.8
Q ss_pred CeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 52 DFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 52 ~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.||++|+|+||+.+. .-.|+|+|....+.+ . ...+|+.++-|.
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 678899999883
No 56
>PTZ00315 2'-phosphotransferase; Provisional
Probab=84.80 E-value=4.8 Score=46.47 Aligned_cols=83 Identities=12% Similarity=0.115 Sum_probs=55.0
Q ss_pred CCEEeehhHHHHH-HHHHhcc----CCCCCCHHHHHHHHHccCCCccchh-hHHhhhCc---------c--cccCchHHH
Q 007029 325 KPLVAHNSLNDFT-FIHSKFL----APLPPNMNEFICSLRLAFPQVIDVN-YLLKDIGP---------V--KKMTNISAT 387 (621)
Q Consensus 325 KpIVGHN~llDL~-~iy~~F~----gpLP~t~~eFk~~i~~lFP~I~DTK-yLa~~~~~---------~--~~~~~L~~~ 387 (621)
+.+|+||+=.|+. ++.+++. ..+|. .|...+|.| +++....| . .+..+|.++
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 65554322 1 133578888
Q ss_pred HHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 007029 388 IAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCS 431 (621)
Q Consensus 388 ~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~ 431 (621)
++.+. + + -.+..|.|=.||..||.||.+|..
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 124568899999999999999986
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=82.75 E-value=2.5 Score=36.71 Aligned_cols=63 Identities=16% Similarity=0.204 Sum_probs=44.3
Q ss_pred CCEEEEeccccccchhHHHHhhhhhhhccccc-eEEEEecCceEEEEecCCCchhHHHHHhhhcccc
Q 007029 486 EDVVFLWGFRERISAGILKNMLQGSHEVFAEA-FNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKAVS 551 (621)
Q Consensus 486 ~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~-~~V~~id~t~a~V~~~~~~~~~~~l~~~~~~~~~ 551 (621)
..++++..-|.......|+..|.+ ++.++ +.|.-|..++|.|-|.+++.|+-.++-|+.|.|.
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 356777888887778889998886 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=82.22 E-value=3 Score=37.40 Aligned_cols=54 Identities=20% Similarity=0.242 Sum_probs=32.8
Q ss_pred EEEEeccccccchhHHHHhhhhhhhccccceEEEEec----CceEEEEecCCCchhHHHHHhhhc
Q 007029 488 VVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVD----RSCAIVVFGKPGLSNTFKNVMNSK 548 (621)
Q Consensus 488 vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id----~t~a~V~~~~~~~~~~~l~~~~~~ 548 (621)
+|++-+.++..+..+|++ +|++++.|.||| ++.++|=|..++.|..++..+...
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=81.89 E-value=3.2 Score=47.03 Aligned_cols=101 Identities=8% Similarity=-0.055 Sum_probs=53.2
Q ss_pred HHHHHHHhCCCCEEeehhH-HHHHHHHHhccCCCCCCHHHHHHHHHc-cCC-CccchhhHHhhhCc------c----ccc
Q 007029 315 EVIDLISASQKPLVAHNSL-NDFTFIHSKFLAPLPPNMNEFICSLRL-AFP-QVIDVNYLLKDIGP------V----KKM 381 (621)
Q Consensus 315 ~Vi~~L~~skKpIVGHN~l-lDL~~iy~~F~gpLP~t~~eFk~~i~~-lFP-~I~DTKyLa~~~~~------~----~~~ 381 (621)
.+.+.+...+.++||||.. +|+-++-..|+..+-+.|. ..+.. ..+ -++||--++....| . .+.
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 3344444456889999976 8998887777644333321 11111 101 13344332222211 0 011
Q ss_pred CchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHH
Q 007029 382 TNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSI 432 (621)
Q Consensus 382 ~~L~~~~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~ 432 (621)
-.|..+.... .. + ...+|.|=.||+.|+.++..|...
T Consensus 161 ~rLe~L~~~~----gI------~----~~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 161 FKLEHLTKAN----GI------E----HENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CcHHHHHHHc----CC------C----CCCCCCcHHHHHHHHHHHHHHHHh
Confidence 2334433322 11 1 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=80.27 E-value=2.7 Score=38.47 Aligned_cols=44 Identities=11% Similarity=0.164 Sum_probs=33.8
Q ss_pred EEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCcc
Q 007029 54 IAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRD 121 (621)
Q Consensus 54 VAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~~ 121 (621)
|.||+|+||+.+ ..-.|+|+|...+..... .....|+.++.|..
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 355699999977665443 46788999999863
No 61
>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=79.99 E-value=3 Score=41.96 Aligned_cols=48 Identities=8% Similarity=0.155 Sum_probs=35.2
Q ss_pred hhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 47 HISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 47 ~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.+....||++|+|-||+.+. .- |+|+|...+... .-....|..++.|.
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 62
>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=79.51 E-value=4.6 Score=32.27 Aligned_cols=54 Identities=19% Similarity=0.313 Sum_probs=39.0
Q ss_pred EEEeccccccchhHHHHhhhhhhhccccceEEEEecC------ceEEEEecCCCchhHHHHHhh
Q 007029 489 VFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR------SCAIVVFGKPGLSNTFKNVMN 546 (621)
Q Consensus 489 v~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~------t~a~V~~~~~~~~~~~l~~~~ 546 (621)
|+|.+.|..++..+|++.++. |++-..|..+-+ ..|||.|.+.+.|..++....
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 469999999998888777543
No 63
>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=78.93 E-value=3.8 Score=33.23 Aligned_cols=22 Identities=9% Similarity=0.037 Sum_probs=18.5
Q ss_pred CCccccccchHHHHHHHHHHHh
Q 007029 240 PSMTIDVCSERQVQLVLKMLED 261 (621)
Q Consensus 240 p~l~l~~~~~~q~~Li~q~l~~ 261 (621)
..+.+++.|++||.|+|++.+.
T Consensus 22 ~~~~f~pm~sy~RllvH~la~~ 43 (63)
T cd02642 22 QSLELPPMNSYYRLLAHRVAQY 43 (63)
T ss_pred CeeEcCCCCcHHHHHHHHHHHH
Confidence 3477888999999999997765
No 64
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=78.73 E-value=4.9 Score=41.01 Aligned_cols=48 Identities=15% Similarity=0.156 Sum_probs=34.6
Q ss_pred hcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 48 ISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 48 I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
..+..||++|+|-||+.+. .-.|+|+|+..++.++. ....|+.++-|.
T Consensus 3 ~~~~~~vv~D~ETTGl~p~-----------------------~d~Iieig~v~v~~~g~--~~~~~~~lv~P~ 50 (232)
T PRK07942 3 WHPGPLAAFDLETTGVDPE-----------------------TARIVTAALVVVDADGE--VVESREWLADPG 50 (232)
T ss_pred cccCcEEEEEeccCCCCCC-----------------------CCeeEEEEEEEEeCCCc--cccceEEEECCC
Confidence 3567899999999999421 22599999998875443 245677777774
No 65
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=78.28 E-value=4.4 Score=49.81 Aligned_cols=105 Identities=21% Similarity=0.219 Sum_probs=75.9
Q ss_pred HhhhhhcccHHHHHHHHHh--CCCCEEeehhHHHHHHHHHhcc--CCCCCCHHHHHHHHHccCCCccchhhHHhhhCccc
Q 007029 304 FEQNKRVRGFREVIDLISA--SQKPLVAHNSLNDFTFIHSKFL--APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVK 379 (621)
Q Consensus 304 ~e~~~~~~GFr~Vi~~L~~--skKpIVGHN~llDL~~iy~~F~--gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~ 379 (621)
++.++.+.-.-.|+..+.+ -.-.+|.||.=+|+=||=..|- +-.|-+ --++||=-|+..+.|--
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 333322 13789988888887644
Q ss_pred ccCchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHHHHHHHHHHHHhc
Q 007029 380 KMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILK 434 (621)
Q Consensus 380 ~~~~L~~~~~~l~~~~~~~~~vei~~~~~~~~~heAGyDA~mTG~vFikL~~~L~ 434 (621)
+.-.|+.+.+.+. |+ ....|-|-|||=.||.+|+.+...++
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 66
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=78.21 E-value=4.3 Score=40.44 Aligned_cols=42 Identities=12% Similarity=0.139 Sum_probs=31.7
Q ss_pred CeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 52 DFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 52 ~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.||++|+|+||+. + . -.|||+|...+.. + -....|..++-|.
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 67
>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=77.00 E-value=4.4 Score=39.89 Aligned_cols=49 Identities=14% Similarity=0.255 Sum_probs=36.9
Q ss_pred cCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCC-Cc-eeeEeEEEeecCc
Q 007029 49 SSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQA-SK-VIAYPYNFHLFPR 120 (621)
Q Consensus 49 ~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~-~~-y~~~~fNF~lfp~ 120 (621)
....+|++|+|-||+.+. +=.|||+|...+..+. +. .....|++++.|.
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 1239999999987653 33 4568999999984
No 68
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=76.00 E-value=4.9 Score=41.30 Aligned_cols=51 Identities=24% Similarity=0.384 Sum_probs=36.1
Q ss_pred HhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 46 NHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 46 ~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
..+.+.+||+||+|.||+.+. .=.|||+|...++.. .-.....|..++-|.
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 357789999999999999431 225999999887542 223346677777774
No 69
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=75.68 E-value=5.6 Score=43.54 Aligned_cols=50 Identities=20% Similarity=0.324 Sum_probs=38.8
Q ss_pred HhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 46 NHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 46 ~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
..+.++.||+||+|.||+.+. .=.||++|...+..++. .+..|..++-|.
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 12489999887776552 468889999885
No 70
>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=74.51 E-value=4.8 Score=30.80 Aligned_cols=23 Identities=13% Similarity=0.268 Sum_probs=20.0
Q ss_pred CccccccchHHHHHHHHHHHhhc
Q 007029 241 SMTIDVCSERQVQLVLKMLEDFS 263 (621)
Q Consensus 241 ~l~l~~~~~~q~~Li~q~l~~~~ 263 (621)
.+.++++++++|+++|++++.+.
T Consensus 19 ~~~~~p~~~~~R~~vH~la~~~~ 41 (59)
T cd02325 19 SLELPPMNSYERKLIHDLAEYYG 41 (59)
T ss_pred eEEcCCCCHHHHHHHHHHHHHCC
Confidence 47788999999999999888765
No 71
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=74.40 E-value=5.6 Score=41.10 Aligned_cols=48 Identities=19% Similarity=0.392 Sum_probs=36.0
Q ss_pred hhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 47 HISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 47 ~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.|++..||+||+|.||+.+. +-.|+|+|...+..+ -...+|+.++-|.
T Consensus 3 ~l~~~~~v~~D~ETTGl~~~-----------------------~d~IIEIa~v~v~~~---~~~~~~~~li~P~ 50 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDVK-----------------------KDRIIEFAAIRFTFD---EVIDSVEFLINPE 50 (250)
T ss_pred cccCCcEEEEEEeCCCCCCC-----------------------CCeEEEEEEEEEECC---eEEEEEEEEECcC
Confidence 57788999999999998421 235999999887643 2356788888874
No 72
>smart00362 RRM_2 RNA recognition motif.
Probab=73.60 E-value=9.3 Score=29.28 Aligned_cols=54 Identities=17% Similarity=0.250 Sum_probs=39.0
Q ss_pred EEEeccccccchhHHHHhhhhhhhccccceEEEEecC-----ceEEEEecCCCchhHHHHHhh
Q 007029 489 VFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-----SCAIVVFGKPGLSNTFKNVMN 546 (621)
Q Consensus 489 v~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-----t~a~V~~~~~~~~~~~l~~~~ 546 (621)
+++.+.|..++..+|++.+.+ ||+...+...-+ ..+||.|.+++.+..++..++
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 73
>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=73.45 E-value=16 Score=36.03 Aligned_cols=107 Identities=12% Similarity=0.153 Sum_probs=62.2
Q ss_pred HHHHHHHHhC-CCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcc----------cccC
Q 007029 314 REVIDLISAS-QKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPV----------KKMT 382 (621)
Q Consensus 314 r~Vi~~L~~s-kKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~----------~~~~ 382 (621)
...++.|.+. +.+-||||+--|+-.+++.|= -++.- + ...-.++||..++..+... ....
T Consensus 71 ~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~-~~~~~---~-----~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~ 141 (193)
T cd06146 71 DRLLKRLFEDPDVLKLGFGFKQDLKALSASYP-ALKCM---F-----ERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTK 141 (193)
T ss_pred HHHHHHHhCCCCeeEEEechHHHHHHHHHhcC-ccccc---c-----ccCCceEEHHHHHHHHhhccccccccccCcccC
Confidence 3344445444 455699999999999997653 22210 0 0124699999888765422 1345
Q ss_pred chHHHHHHHHhcCCCCceeecCCCCC----CCCcccchhhHHHHHHHHHHHH
Q 007029 383 NISATIAYLKNRFFAPIEMEIPNQAN----ENEGKIHGHNVVKICQLFGKLC 430 (621)
Q Consensus 383 ~L~~~~~~l~~~~~~~~~vei~~~~~----~~~~heAGyDA~mTG~vFikL~ 430 (621)
+|+.+.+.+-....... ....+=.. ...-+-|+-|||..-.+|-+|+
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 78887776644222110 11000001 1122449999999999998886
No 74
>PRK07740 hypothetical protein; Provisional
Probab=72.71 E-value=3.8 Score=42.22 Aligned_cols=55 Identities=16% Similarity=0.225 Sum_probs=36.9
Q ss_pred HHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 42 SEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 42 p~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
+.+..-+.+.+||+||+|.||+.+. ..-.|||+|....+ ++.-....|..++-|.
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 3344456778999999999998421 01358999987765 3322366777777764
No 75
>PRK05359 oligoribonuclease; Provisional
Probab=72.61 E-value=5.7 Score=39.00 Aligned_cols=47 Identities=15% Similarity=0.135 Sum_probs=31.6
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.-.||++|+|.||+.+.. =.|+|+|.-..+... .-....|++++.|.
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 138999988663322 22345678887775
No 76
>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=72.37 E-value=6.8 Score=39.00 Aligned_cols=50 Identities=16% Similarity=0.176 Sum_probs=36.1
Q ss_pred hcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCC-c-eeeEeEEEeecCc
Q 007029 48 ISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQAS-K-VIAYPYNFHLFPR 120 (621)
Q Consensus 48 I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~-~-y~~~~fNF~lfp~ 120 (621)
-..+.||++|+|.||+.+. +=.||++|...+..+++ . .....|++++.|.
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 4568999999999999432 12499999988876532 2 2246689999884
No 77
>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=70.67 E-value=3.5 Score=37.66 Aligned_cols=42 Identities=12% Similarity=0.129 Sum_probs=31.5
Q ss_pred EEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 54 IAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 54 VAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
|.||+|.||+.+ ..-.|+|+|.+.+..+ .-....||.++-|.
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 78
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=69.85 E-value=29 Score=32.99 Aligned_cols=96 Identities=16% Similarity=0.174 Sum_probs=57.9
Q ss_pred HHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcC-CCC
Q 007029 320 ISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRF-FAP 398 (621)
Q Consensus 320 L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~-~~~ 398 (621)
+...+...||||+=.|+-.+.+.| |-- +..++||..++..+++-....+|..+.+.+.... .++
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 444556679999999999987555 221 3457999988877776433347777776653321 111
Q ss_pred ceeecCCCCCC----CCcccchhhHHHHHHHHHHHH
Q 007029 399 IEMEIPNQANE----NEGKIHGHNVVKICQLFGKLC 430 (621)
Q Consensus 399 ~~vei~~~~~~----~~~heAGyDA~mTG~vFikL~ 430 (621)
..+....=... ..-+-|+-|||..-.++-+|.
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 11111110111 122558999999999887774
No 79
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=69.40 E-value=8.5 Score=41.24 Aligned_cols=44 Identities=16% Similarity=0.285 Sum_probs=33.2
Q ss_pred CCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 51 SDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 51 a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.+||++|+|+||+.+ ....|+|+|...+. ++ =....|+.++-|.
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 389999999999832 12379999988775 22 2567889988885
No 80
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=69.20 E-value=7.6 Score=41.55 Aligned_cols=46 Identities=13% Similarity=0.231 Sum_probs=33.8
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.-+||+||+|.||+.+. .-.|||+|...++.++. ....|..++-|.
T Consensus 14 ~~~fvvlD~ETTGl~p~-----------------------~d~IIeIgav~v~~~g~--i~~~~~~lv~P~ 59 (313)
T PRK06063 14 PRGWAVVDVETSGFRPG-----------------------QARIISLAVLGLDADGN--VEQSVVTLLNPG 59 (313)
T ss_pred CCCEEEEEEECCCCCCC-----------------------CCEEEEEEEEEEECCce--eeeEEEEEECcC
Confidence 35899999999999421 23699999999876553 346677777774
No 81
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=67.71 E-value=10 Score=39.07 Aligned_cols=47 Identities=13% Similarity=0.214 Sum_probs=33.4
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.-.||++|+|-||+.+. ..=.|||+|...+. +..-+...|+.|+-|.
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 34799999999999431 13369999986654 3233556889999884
No 82
>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=67.63 E-value=27 Score=27.82 Aligned_cols=28 Identities=14% Similarity=0.050 Sum_probs=19.8
Q ss_pred CccccccchHHHHHHHHHHHhhcCCcceee
Q 007029 241 SMTIDVCSERQVQLVLKMLEDFSDVLVPLI 270 (621)
Q Consensus 241 ~l~l~~~~~~q~~Li~q~l~~~~~~l~~~~ 270 (621)
.+.+++.++++|++||++.+ +.++.+..
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 47788899999999999888 34565543
No 83
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=66.49 E-value=11 Score=40.08 Aligned_cols=47 Identities=11% Similarity=0.116 Sum_probs=34.5
Q ss_pred CCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCC-C-ce-eeEeEEEeecCc
Q 007029 51 SDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQA-S-KV-IAYPYNFHLFPR 120 (621)
Q Consensus 51 a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~-~-~y-~~~~fNF~lfp~ 120 (621)
-.+|++|+|.||+.+. .=.|||+|+..|..+. + -+ ....|++++-|.
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 3689999999999431 2249999999998753 2 22 457888888874
No 84
>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=66.42 E-value=11 Score=35.10 Aligned_cols=40 Identities=13% Similarity=0.253 Sum_probs=29.6
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
||++|+|.||.. .-.|+|+|...+.. + . ....|+.++-|.
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 799999999952 11379999988863 2 2 347889998886
No 85
>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=66.31 E-value=8.8 Score=36.39 Aligned_cols=44 Identities=14% Similarity=0.253 Sum_probs=30.7
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
||++|+|.||+.+. ..-.|+|+|...+... .-....|++++-|.
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 2346999998876542 22345788887774
No 86
>PRK05755 DNA polymerase I; Provisional
Probab=66.08 E-value=19 Score=43.95 Aligned_cols=102 Identities=12% Similarity=0.056 Sum_probs=62.4
Q ss_pred HHHHHHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcC
Q 007029 316 VIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRF 395 (621)
Q Consensus 316 Vi~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~ 395 (621)
+.+.|.....++||||.=.|+-++++. | +|- -..++||..++.-+.|-.. .+|..+.+......
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 56766665542211
Q ss_pred CCCceee-c-CCCCCC------CCcccchhhHHHHHHHHHHHHHHhcc
Q 007029 396 FAPIEME-I-PNQANE------NEGKIHGHNVVKICQLFGKLCSILKI 435 (621)
Q Consensus 396 ~~~~~ve-i-~~~~~~------~~~heAGyDA~mTG~vFikL~~~L~~ 435 (621)
.+..+ + ...... ...|-|+.|+..|..+|.+|...|..
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 87
>PRK07883 hypothetical protein; Validated
Probab=65.54 E-value=10 Score=43.95 Aligned_cols=52 Identities=13% Similarity=0.236 Sum_probs=38.6
Q ss_pred HHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 43 EIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 43 ~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.+..-|.+..||+||+|.||+.+. .-.|+|+|...++. +. ....|+.++-|.
T Consensus 7 ~~~~~~~~~~~Vv~D~ETTGl~p~-----------------------~~~IIEIgaV~v~~--g~-iv~~f~~lV~P~ 58 (557)
T PRK07883 7 DLGTPLRDVTFVVVDLETTGGSPA-----------------------GDAITEIGAVKVRG--GE-VLGEFATLVNPG 58 (557)
T ss_pred hhCCCCcCCCEEEEEEecCCCCCC-----------------------CCeEEEEEEEEEEC--CE-EEEEEEEEECCC
Confidence 344568889999999999999421 24699999988752 22 456788888885
No 88
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=64.34 E-value=9.3 Score=38.11 Aligned_cols=51 Identities=10% Similarity=0.163 Sum_probs=33.0
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
..+||++|+|+||+.... .+..+ .-.|||+|...++.. . ....|+-++-|.
T Consensus 3 ~~~~vvlD~EtTg~~~~~--~~~~~---------------~~eIIeIGaV~v~~~--~-i~~~f~~lV~P~ 53 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKK--KPKGF---------------FPEIIEVGLVSVVGC--E-VEDTFSSYVKPK 53 (207)
T ss_pred cceEEEEEeecCCcCCCC--CCCCC---------------CCceEEEeEEEEecC--c-ChhhhcceECCC
Confidence 568999999999984211 00000 114999998877532 2 346788888885
No 89
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=63.19 E-value=16 Score=38.06 Aligned_cols=53 Identities=17% Similarity=0.236 Sum_probs=38.3
Q ss_pred HHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 42 SEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 42 p~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.....-+.+..||++|+|-||..+. .-.|+|+|...+. ++. ....|..++.|.
T Consensus 59 ~~~~~~~~~~~~vv~DiETTG~~~~-----------------------~~~IIEIGAv~v~--~g~-i~~~f~~~v~p~ 111 (257)
T PRK08517 59 KTRFTPIKDQVFCFVDIETNGSKPK-----------------------KHQIIEIGAVKVK--NGE-IIDRFESFVKAK 111 (257)
T ss_pred ccCCCCCCCCCEEEEEEeCCCCCCC-----------------------CCeEEEEEEEEEE--CCE-EEEEEEEEECCC
Confidence 3444457889999999999998421 1369999999886 222 346788888884
No 90
>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=59.46 E-value=14 Score=33.52 Aligned_cols=49 Identities=6% Similarity=0.099 Sum_probs=35.0
Q ss_pred cccchhHHHHhhhhhhhccccceEEEEecCceEEEEecCCCchhHHHHH
Q 007029 496 ERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNV 544 (621)
Q Consensus 496 ~~~~~~~i~~~l~~~~~~F~~~~~V~~id~t~a~V~~~~~~~~~~~l~~ 544 (621)
.+|+..+|++.-..=.-+-....+|.|.|.++.|+.|.....+..++.+
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 3688888776544322222222599999999999999999888877654
No 91
>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=58.95 E-value=18 Score=36.79 Aligned_cols=45 Identities=11% Similarity=0.132 Sum_probs=30.9
Q ss_pred CeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 52 DFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 52 ~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.||.+|+|.||+.+.. .=.|||+|...+.. ..-+...|..|+-|.
T Consensus 1 r~vvlD~ETTGl~p~~----------------------~d~IIEIgav~~~~--~~~~~~~f~~~i~P~ 45 (225)
T TIGR01406 1 RQIILDTETTGLDPKG----------------------GHRIVEIGAVELVN--RMLTGDNFHVYVNPE 45 (225)
T ss_pred CEEEEEeeCCCcCCCC----------------------CCeEEEEEEEEEEC--CcEecceEEEEECcC
Confidence 3899999999994310 12599999775542 223446788898884
No 92
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=57.91 E-value=42 Score=31.71 Aligned_cols=59 Identities=15% Similarity=0.309 Sum_probs=42.6
Q ss_pred CCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecC-------ceEEEEecCCCchhHHHHHhhhc
Q 007029 486 EDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-------SCAIVVFGKPGLSNTFKNVMNSK 548 (621)
Q Consensus 486 ~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-------t~a~V~~~~~~~~~~~l~~~~~~ 548 (621)
..-|||-+.|...+..+|++.+. -|++..+|..+-+ -.+||.|.+.+.|+..+..++..
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 44688889999888888877554 3454345555422 35999999999999988877543
No 93
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=57.39 E-value=19 Score=42.63 Aligned_cols=99 Identities=17% Similarity=0.290 Sum_probs=62.8
Q ss_pred EEEeccccccchhHHHHhhhhhhhccccceEEEEecC-ceEEEEecCCCchhHHHHHhhhcccccc---chhhhcCCccc
Q 007029 489 VFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-SCAIVVFGKPGLSNTFKNVMNSKAVSGP---LREMVSDGLKA 564 (621)
Q Consensus 489 v~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-t~a~V~~~~~~~~~~~l~~~~~~~~~~~---l~~~~~~g~~~ 564 (621)
+++=+-++.++..||++.+. -||....|..|.. .||||...++..|+.+|.+++...+..- ++=-++-|.|.
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 007029 565 AGYETYQRVCSSGLWE---SALADALDKTLAS 593 (621)
Q Consensus 565 a~~~~y~~~c~~~~~~---~~~a~~~~~~~~~ 593 (621)
-|-.|.| ..+|++. ..|.|++++-|+.
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 7777877 4455543 3455667776653
No 94
>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=56.92 E-value=36 Score=32.60 Aligned_cols=103 Identities=12% Similarity=0.063 Sum_probs=60.3
Q ss_pred HHHHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCC
Q 007029 318 DLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFA 397 (621)
Q Consensus 318 ~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~ 397 (621)
+.+.+....+||||.=.|+-++.+..+. +| ..++||..++.-+.|-....+|..+.+.+......
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 3444556789999999999988765433 22 24799988777677644123777776654321100
Q ss_pred C-ceee-c-CCC---CCC---CCcccchhhHHHHHHHHHHHHHHhcc
Q 007029 398 P-IEME-I-PNQ---ANE---NEGKIHGHNVVKICQLFGKLCSILKI 435 (621)
Q Consensus 398 ~-~~ve-i-~~~---~~~---~~~heAGyDA~mTG~vFikL~~~L~~ 435 (621)
. .++- - ... +.. ...|-|+.|+..|..++-+|...+..
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 95
>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=56.87 E-value=19 Score=34.97 Aligned_cols=46 Identities=15% Similarity=0.270 Sum_probs=32.3
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCC--Cce--------eeEeEEEeecCc
Q 007029 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQA--SKV--------IAYPYNFHLFPR 120 (621)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~--~~y--------~~~~fNF~lfp~ 120 (621)
||++|+|-||+.+. .+=.|+|+|....+.++ ... ....|++++-|.
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 11259999998877543 111 356788888885
No 96
>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=55.34 E-value=40 Score=32.03 Aligned_cols=95 Identities=9% Similarity=0.112 Sum_probs=55.8
Q ss_pred HHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCc
Q 007029 320 ISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPI 399 (621)
Q Consensus 320 L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~~ 399 (621)
|.+.+...||||+--|+-.+++.| |-. +..++||..++..+++- ...+|..+.+.+..... ..
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 334455569999999998887654 322 23468998877666543 22367777665432111 11
Q ss_pred eeecCCCCC----CCCcccchhhHHHHHHHHHHHHH
Q 007029 400 EMEIPNQAN----ENEGKIHGHNVVKICQLFGKLCS 431 (621)
Q Consensus 400 ~vei~~~~~----~~~~heAGyDA~mTG~vFikL~~ 431 (621)
.+...+=.. ...-+=|+.||+..-.+|-+|.+
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 97
>PF15023 DUF4523: Protein of unknown function (DUF4523)
Probab=55.28 E-value=24 Score=33.68 Aligned_cols=63 Identities=22% Similarity=0.318 Sum_probs=48.4
Q ss_pred CCcCCEEEEeccccccch-hHHHHhhhhhhhccccceEEEEecCceEEEEecCCCchhHHHHHhhh
Q 007029 483 VSCEDVVFLWGFRERISA-GILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNS 547 (621)
Q Consensus 483 ~~~~~vv~~~~f~~~~~~-~~i~~~l~~~~~~F~~~~~V~~id~t~a~V~~~~~~~~~~~l~~~~~ 547 (621)
|+-..||.-|. .+.++. .|++++++++ .+||+--.|-....++|.|+|..-.+|=..+.|+-+
T Consensus 84 pPMsTIVVRWl-kknm~~~edl~sV~~~L-s~fGpI~SVT~cGrqsavVvF~d~~SAC~Av~Af~s 147 (166)
T PF15023_consen 84 PPMSTIVVRWL-KKNMQPTEDLKSVIQRL-SVFGPIQSVTLCGRQSAVVVFKDITSACKAVSAFQS 147 (166)
T ss_pred CCceeEEeehh-hhcCChHHHHHHHHHHH-HhcCCcceeeecCCceEEEEehhhHHHHHHHHhhcC
Confidence 33456777788 666655 7889888865 469997799999999999999998887767776644
No 98
>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=54.12 E-value=39 Score=30.64 Aligned_cols=59 Identities=14% Similarity=0.174 Sum_probs=39.6
Q ss_pred HHHHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHH
Q 007029 318 DLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYL 391 (621)
Q Consensus 318 ~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l 391 (621)
+.+...+..+||||.=.|+-++.+.+ +.+| +.++||..++--+.|-....+|..+.+..
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 34445667899999999988887654 2222 35799988777777644123677766654
No 99
>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=52.63 E-value=29 Score=37.79 Aligned_cols=59 Identities=12% Similarity=0.242 Sum_probs=42.7
Q ss_pred CCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecC-------ceEEEEecCCCchhHHHHHhhhc
Q 007029 486 EDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-------SCAIVVFGKPGLSNTFKNVMNSK 548 (621)
Q Consensus 486 ~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-------t~a~V~~~~~~~~~~~l~~~~~~ 548 (621)
+.-|||-+.|..++..+|++.++ -|+....|..+-+ .++||.|.+.+.|...+.+++..
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 3443335554433 37999999999999988887654
No 100
>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=52.38 E-value=19 Score=29.09 Aligned_cols=20 Identities=15% Similarity=0.280 Sum_probs=17.5
Q ss_pred ccccc-cchHHHHHHHHHHHh
Q 007029 242 MTIDV-CSERQVQLVLKMLED 261 (621)
Q Consensus 242 l~l~~-~~~~q~~Li~q~l~~ 261 (621)
+.+++ +++.+|++||++.+.
T Consensus 20 l~f~p~lt~~eR~~vH~~a~~ 40 (60)
T cd02640 20 MVFSPEFSKEERALIHQIAQK 40 (60)
T ss_pred EEcCCCCCHHHHHHHHHHHHH
Confidence 67777 899999999998876
No 101
>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=52.22 E-value=22 Score=28.66 Aligned_cols=22 Identities=18% Similarity=0.256 Sum_probs=18.4
Q ss_pred Cccccc-cchHHHHHHHHHHHhh
Q 007029 241 SMTIDV-CSERQVQLVLKMLEDF 262 (621)
Q Consensus 241 ~l~l~~-~~~~q~~Li~q~l~~~ 262 (621)
.+.+++ .+++||+.||++.+..
T Consensus 19 ~l~F~p~ls~~eR~~vH~lA~~~ 41 (60)
T cd02641 19 ELEFPPTLSSHDRLLVHELAEEL 41 (60)
T ss_pred cEECCCCCCHHHHHHHHHHHHHc
Confidence 477787 8999999999988763
No 102
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=51.18 E-value=58 Score=35.66 Aligned_cols=99 Identities=14% Similarity=0.203 Sum_probs=67.3
Q ss_pred HHHHHHHHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHh
Q 007029 314 REVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKN 393 (621)
Q Consensus 314 r~Vi~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~ 393 (621)
.-+...|......=|-|++-.||-.+++.| |-+| +.|||||..+ .+..+....++..+.+.+.+
T Consensus 60 ~~l~~Ll~d~~v~KIfHaa~~DL~~l~~~~-g~~p--------------~plfdTqiAa-~l~g~~~~~gl~~Lv~~ll~ 123 (361)
T COG0349 60 PPLVALLADPNVVKIFHAARFDLEVLLNLF-GLLP--------------TPLFDTQIAA-KLAGFGTSHGLADLVEELLG 123 (361)
T ss_pred chHHHHhcCCceeeeeccccccHHHHHHhc-CCCC--------------CchhHHHHHH-HHhCCcccccHHHHHHHHhC
Confidence 344444555544459999999999999888 8888 4589999844 44444446678888877743
Q ss_pred cCCCCceeecCCCCC-C--C--Cc-----ccchhhHHHHHHHHHHHHHHhcc
Q 007029 394 RFFAPIEMEIPNQAN-E--N--EG-----KIHGHNVVKICQLFGKLCSILKI 435 (621)
Q Consensus 394 ~~~~~~~vei~~~~~-~--~--~~-----heAGyDA~mTG~vFikL~~~L~~ 435 (621)
|++..... . . .- --|..|...--.++.+|...|--
T Consensus 124 -------v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~ 168 (361)
T COG0349 124 -------VELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAR 168 (361)
T ss_pred -------CcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44443221 1 1 11 12799999999999999998833
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=50.72 E-value=23 Score=34.28 Aligned_cols=75 Identities=11% Similarity=0.103 Sum_probs=43.6
Q ss_pred CCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhh---HHhhhCcccccCchHHHHHHHHhcCCCCc
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNY---LLKDIGPVKKMTNISATIAYLKNRFFAPI 399 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKy---La~~~~~~~~~~~L~~~~~~l~~~~~~~~ 399 (621)
.+.+|||||.=+|+-|+-+.|-. +- ..+...++||-. |+..+.|-. .
T Consensus 93 ~~~~lvgh~~~FD~~fL~~~~~~--------~~---~~~~~~~~D~~~l~~l~~~l~p~~-----~-------------- 142 (173)
T cd06135 93 GKSPLAGNSVHQDRRFLDKYMPE--------LE---EYLHYRILDVSSIKELARRWYPEI-----Y-------------- 142 (173)
T ss_pred CCCceeecchhhCHHHHHHHHHH--------Hh---ccCCcchhhHHHHHHHHHHhCcHh-----h--------------
Confidence 46788999999999999766531 00 112334688743 333322200 0
Q ss_pred eeecCCCCCCCCcccchhhHHHHHHHHHHHHH
Q 007029 400 EMEIPNQANENEGKIHGHNVVKICQLFGKLCS 431 (621)
Q Consensus 400 ~vei~~~~~~~~~heAGyDA~mTG~vFikL~~ 431 (621)
... -.....|-|=.||..|+..+..+-.
T Consensus 143 ~~~----~~~~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 143 RKA----PKKKGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred hcC----CCCCCCcchHHHHHHHHHHHHHHHH
Confidence 000 0113459999999999998765543
No 104
>PRK10829 ribonuclease D; Provisional
Probab=49.10 E-value=58 Score=35.86 Aligned_cols=98 Identities=13% Similarity=0.174 Sum_probs=62.5
Q ss_pred HHHHHHHHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHh
Q 007029 314 REVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKN 393 (621)
Q Consensus 314 r~Vi~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~ 393 (621)
..+.+.|.+.+.+-|+|++-.|+-.+++ .+|-.| ..++||...+.-++ .....+++.+.+.+.+
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 3344445555555589999999999875 445444 34899977554443 3334578887777643
Q ss_pred cCCCCceeecCCCCC-----C-----CCcccchhhHHHHHHHHHHHHHHhc
Q 007029 394 RFFAPIEMEIPNQAN-----E-----NEGKIHGHNVVKICQLFGKLCSILK 434 (621)
Q Consensus 394 ~~~~~~~vei~~~~~-----~-----~~~heAGyDA~mTG~vFikL~~~L~ 434 (621)
|+++.... . ..-+-|+-|+.-.-.+|-+|...|.
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 105
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=48.21 E-value=15 Score=40.05 Aligned_cols=26 Identities=15% Similarity=0.050 Sum_probs=22.7
Q ss_pred HHHHHHHHhhcCCCeEEEecCCCCcc
Q 007029 39 ESLSEIKNHISSSDFIAVSLQNTGSF 64 (621)
Q Consensus 39 ~~lp~i~~~I~~a~FVAiD~EftGi~ 64 (621)
+.+..+...+..|.+|||||||.|..
T Consensus 5 ~~l~~~~~~~~~~~~iAiDTEf~r~~ 30 (361)
T COG0349 5 DLLAAACALLRGSKAIAIDTEFMRLR 30 (361)
T ss_pred hHHHHHHHHhcCCCceEEeccccccc
Confidence 45677888899999999999999985
No 106
>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=47.87 E-value=40 Score=25.76 Aligned_cols=55 Identities=16% Similarity=0.261 Sum_probs=38.3
Q ss_pred EEEeccccccchhHHHHhhhhhhhccccceEEEEec------CceEEEEecCCCchhHHHHHhhh
Q 007029 489 VFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVD------RSCAIVVFGKPGLSNTFKNVMNS 547 (621)
Q Consensus 489 v~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id------~t~a~V~~~~~~~~~~~l~~~~~ 547 (621)
+++.+.|..++..+|++.++++ ++...+...- ...+||.|.+.+.+..++..+..
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 5678889888888888877653 4333333333 35799999999999887765433
No 107
>smart00361 RRM_1 RNA recognition motif.
Probab=46.94 E-value=28 Score=28.23 Aligned_cols=47 Identities=13% Similarity=0.157 Sum_probs=32.8
Q ss_pred hHHHHhhhhhhhccccceEEE--EecCc--------eEEEEecCCCchhHHHHHhhh
Q 007029 501 GILKNMLQGSHEVFAEAFNVR--MVDRS--------CAIVVFGKPGLSNTFKNVMNS 547 (621)
Q Consensus 501 ~~i~~~l~~~~~~F~~~~~V~--~id~t--------~a~V~~~~~~~~~~~l~~~~~ 547 (621)
.+|++.++.-...||+.+.|. .+|.. .+||.|.+.+.|...+..++.
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 108
>PRK11779 sbcB exonuclease I; Provisional
Probab=46.61 E-value=47 Score=37.80 Aligned_cols=74 Identities=16% Similarity=0.188 Sum_probs=47.3
Q ss_pred cCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCccccccCCC
Q 007029 49 SSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDELKMGMP 128 (621)
Q Consensus 49 ~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~~~~~~~~~ 128 (621)
....||.+|+|.||+.+. .=.|+|+|.-.++.+. .-...+|++++-|..+
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 1149999987765433 2345789999988631
Q ss_pred CCceeechhHHHHHHHcCCCccchhhcccc
Q 007029 129 SYSFTCQTSYLTAMAKEGFDFNTCIYDGIS 158 (621)
Q Consensus 129 d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~ 158 (621)
....+.| ..=||+-=..+..+|++
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 1112333 34477766666666663
No 109
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=46.22 E-value=85 Score=26.32 Aligned_cols=28 Identities=14% Similarity=0.190 Sum_probs=22.6
Q ss_pred CCccccccchHHHHHHHHHHHhhcCCccee
Q 007029 240 PSMTIDVCSERQVQLVLKMLEDFSDVLVPL 269 (621)
Q Consensus 240 p~l~l~~~~~~q~~Li~q~l~~~~~~l~~~ 269 (621)
..+.+++.++++|++||+++..+ ++.+.
T Consensus 37 ~~~~~~pm~~~~R~~iH~~a~~~--~l~s~ 64 (79)
T smart00393 37 ESVELPPMNSYERKIVHELAEKY--GLESE 64 (79)
T ss_pred CeEEcCCCCHHHHHHHHHHHHHc--CCEEE
Confidence 35788899999999999998875 66543
No 110
>PTZ00315 2'-phosphotransferase; Provisional
Probab=45.92 E-value=36 Score=39.52 Aligned_cols=49 Identities=8% Similarity=0.236 Sum_probs=35.4
Q ss_pred CCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 51 SDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 51 a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
-.||+||+|.||..+. + . +.-.||+||...++..+.+ ....|..|+-|.
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 1 0 1235999999999765544 347899999995
No 111
>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=43.59 E-value=63 Score=28.35 Aligned_cols=59 Identities=7% Similarity=0.054 Sum_probs=42.2
Q ss_pred CCEEEEecccc-----ccchhHHHHhhhhhhhccc-cceEEEEecCceEEEEecCCCchhHHHHH
Q 007029 486 EDVVFLWGFRE-----RISAGILKNMLQGSHEVFA-EAFNVRMVDRSCAIVVFGKPGLSNTFKNV 544 (621)
Q Consensus 486 ~~vv~~~~f~~-----~~~~~~i~~~l~~~~~~F~-~~~~V~~id~t~a~V~~~~~~~~~~~l~~ 544 (621)
++.+.-.++|. .|+..++++.|.+.+++=. ..+.++|.|+..-+|.+.+.+.....+..
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 112
>smart00360 RRM RNA recognition motif.
Probab=43.58 E-value=38 Score=25.52 Aligned_cols=50 Identities=18% Similarity=0.286 Sum_probs=33.2
Q ss_pred ccccccchhHHHHhhhhhhhccccceEEEEecC-------ceEEEEecCCCchhHHHHHhh
Q 007029 493 GFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-------SCAIVVFGKPGLSNTFKNVMN 546 (621)
Q Consensus 493 ~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-------t~a~V~~~~~~~~~~~l~~~~ 546 (621)
+.|..++..+|++.+++ ||+...+....+ ..+||.|.+++.|..++..++
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 113
>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=43.01 E-value=39 Score=41.11 Aligned_cols=43 Identities=23% Similarity=0.346 Sum_probs=31.6
Q ss_pred CeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 52 DFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 52 ~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
.||++|+|.||+.+. .=.|||+|...+. +++ ....|..++-|.
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 356888988886
No 114
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=42.76 E-value=47 Score=33.81 Aligned_cols=61 Identities=16% Similarity=0.242 Sum_probs=49.0
Q ss_pred EEEEeccccccchhHHHHhhhhhhhccccceEEEEecC----ceEEEEecCCCchhHHHHHhhhc
Q 007029 488 VVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR----SCAIVVFGKPGLSNTFKNVMNSK 548 (621)
Q Consensus 488 vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~----t~a~V~~~~~~~~~~~l~~~~~~ 548 (621)
-+||-....+++..+++.-|.-+++-||.-.+|.-+.- ..|||.|.+.+.|...+++++.-
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 35999999999999988877653
No 115
>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=42.10 E-value=38 Score=26.89 Aligned_cols=22 Identities=9% Similarity=0.190 Sum_probs=18.4
Q ss_pred CccccccchHHHHHHHHHHHhh
Q 007029 241 SMTIDVCSERQVQLVLKMLEDF 262 (621)
Q Consensus 241 ~l~l~~~~~~q~~Li~q~l~~~ 262 (621)
.+.+|+.++++|+.||++...+
T Consensus 18 ~~~fppm~~~~R~~vH~lA~~~ 39 (58)
T cd02646 18 SLSFPPMDKHGRKTIHKLANCY 39 (58)
T ss_pred eEecCCCCHHHHHHHHHHHHHc
Confidence 4777888999999999987763
No 116
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=41.65 E-value=2.2e+02 Score=26.13 Aligned_cols=98 Identities=12% Similarity=0.075 Sum_probs=55.2
Q ss_pred HHHHHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCC
Q 007029 317 IDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFF 396 (621)
Q Consensus 317 i~~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~ 396 (621)
.+.+...+.+.||||.=.|+-.+.+ +|--+ +.++||...+--+.|-....+|..+.........
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 3445566788999999888877753 44222 2259998765545664443477777655422111
Q ss_pred CCceeecCCCC--CCCCcc----cchhhHHHHHHHHHHHHHHh
Q 007029 397 APIEMEIPNQA--NENEGK----IHGHNVVKICQLFGKLCSIL 433 (621)
Q Consensus 397 ~~~~vei~~~~--~~~~~h----eAGyDA~mTG~vFikL~~~L 433 (621)
. ++. ...+ ...... -|+.||+.+..++-+|...|
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 27888888888888777654
No 117
>PF15342 FAM212: FAM212 family
Probab=39.37 E-value=18 Score=29.12 Aligned_cols=23 Identities=22% Similarity=0.229 Sum_probs=16.2
Q ss_pred CCCCEEeehhHHHHHHHHHhccCCCCC
Q 007029 323 SQKPLVAHNSLNDFTFIHSKFLAPLPP 349 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F~gpLP~ 349 (621)
.++.|.|-|+|.||+.=+ =+||+
T Consensus 38 RQPLVLGDN~FADLV~NW----lDLPE 60 (62)
T PF15342_consen 38 RQPLVLGDNVFADLVGNW----LDLPE 60 (62)
T ss_pred CCCeeecccHHHHHHHhh----hcCcc
Confidence 455555999999998654 35554
No 118
>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=38.28 E-value=68 Score=34.92 Aligned_cols=59 Identities=14% Similarity=0.158 Sum_probs=43.4
Q ss_pred cCCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecC-------ceEEEEecCCCchhHHHHHhhh
Q 007029 485 CEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-------SCAIVVFGKPGLSNTFKNVMNS 547 (621)
Q Consensus 485 ~~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-------t~a~V~~~~~~~~~~~l~~~~~ 547 (621)
....|||-..|..++..+|++.++ .|++..+|..+-| ..|||.|.+.+.|...+..++.
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 456778788999999888777555 4555446665533 2599999999999988877654
No 119
>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=37.47 E-value=33 Score=29.83 Aligned_cols=28 Identities=25% Similarity=0.476 Sum_probs=20.7
Q ss_pred HHHHHHhCC-CCEEeehhHHHHHHHHHhc
Q 007029 316 VIDLISASQ-KPLVAHNSLNDFTFIHSKF 343 (621)
Q Consensus 316 Vi~~L~~sk-KpIVGHN~llDL~~iy~~F 343 (621)
+.+.|.+.. +.+||||.=.|+-++.+.+
T Consensus 35 f~~~l~~~~~~v~V~hn~~fD~~fL~~~~ 63 (96)
T cd06125 35 LKDILRDKPLAILVGHNGSFDLPFLNNRC 63 (96)
T ss_pred HHHHHhhCCCCEEEEeCcHHhHHHHHHHH
Confidence 334454444 7899999989998888766
No 120
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=36.33 E-value=57 Score=40.18 Aligned_cols=45 Identities=22% Similarity=0.285 Sum_probs=33.1
Q ss_pred CCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 51 SDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 51 a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
-.||+||+|.||+.+.. .-.|||+|.+.+.. + -....|+.++-|.
T Consensus 3 ~~~vvvD~ETTG~~p~~----------------------~d~IIeigav~v~~--~-~i~~~f~~~v~P~ 47 (928)
T PRK08074 3 KRFVVVDLETTGNSPKK----------------------GDKIIQIAAVVVED--G-EILERFSSFVNPE 47 (928)
T ss_pred CCEEEEEEeCCCCCCCC----------------------CCcEEEEEEEEEEC--C-EEEEEEEEEECcC
Confidence 46999999999984221 12699999999852 2 2457889999885
No 121
>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=35.72 E-value=80 Score=25.86 Aligned_cols=29 Identities=14% Similarity=0.152 Sum_probs=22.9
Q ss_pred CCccccccchHHHHHHHHHHHhhcCCccee
Q 007029 240 PSMTIDVCSERQVQLVLKMLEDFSDVLVPL 269 (621)
Q Consensus 240 p~l~l~~~~~~q~~Li~q~l~~~~~~l~~~ 269 (621)
..+.+++.+++.|++||++++.. +++.+.
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 45788999999999999999864 455443
No 122
>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=34.05 E-value=31 Score=32.29 Aligned_cols=27 Identities=22% Similarity=0.319 Sum_probs=23.9
Q ss_pred HHHHHHHHHhhcCCCeEEEecCCCCcc
Q 007029 38 NESLSEIKNHISSSDFIAVSLQNTGSF 64 (621)
Q Consensus 38 ~~~lp~i~~~I~~a~FVAiD~EftGi~ 64 (621)
.+.+..+.+.+.++..||+|+|.+|+.
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 123
>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=33.24 E-value=65 Score=40.87 Aligned_cols=46 Identities=17% Similarity=0.361 Sum_probs=35.4
Q ss_pred cCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 49 SSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 49 ~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
+++.||++|+|.||+.+. .=.|+|+|...+.. + -....|++++-|.
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 778999999999998421 22699999988763 2 2457899999885
No 124
>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=30.90 E-value=21 Score=34.04 Aligned_cols=11 Identities=18% Similarity=0.305 Sum_probs=10.0
Q ss_pred EEEecCCCCcc
Q 007029 54 IAVSLQNTGSF 64 (621)
Q Consensus 54 VAiD~EftGi~ 64 (621)
||||+|+||+.
T Consensus 1 v~~D~EttGl~ 11 (157)
T cd06149 1 VAIDCEMVGTG 11 (157)
T ss_pred CEEEeEecccc
Confidence 69999999994
No 125
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=29.96 E-value=93 Score=33.13 Aligned_cols=41 Identities=17% Similarity=0.301 Sum_probs=29.6
Q ss_pred CeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 52 DFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 52 ~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
+||+||+|.||.. .=.|+|+|...+.. +. ....|+.++-|.
T Consensus 2 ~~vviD~ETTg~~-------------------------~d~IieIgav~v~~--g~-i~~~f~~lv~P~ 42 (309)
T PRK06195 2 NFVAIDFETANEK-------------------------RNSPCSIGIVVVKD--GE-IVEKVHYLIKPK 42 (309)
T ss_pred cEEEEEEeCCCCC-------------------------CCceEEEEEEEEEC--CE-EEEEEEEEECCC
Confidence 7999999999751 11379999988752 22 346788888885
No 126
>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=29.47 E-value=1.3e+02 Score=25.88 Aligned_cols=55 Identities=11% Similarity=0.121 Sum_probs=41.7
Q ss_pred ecccc--ccchhHHHHhhhhhhhccccceEEEEecCceEEEEecCCCchhHHHHHhhhc
Q 007029 492 WGFRE--RISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSK 548 (621)
Q Consensus 492 ~~f~~--~~~~~~i~~~l~~~~~~F~~~~~V~~id~t~a~V~~~~~~~~~~~l~~~~~~ 548 (621)
..++. .|+-.+++..+...+.+ ..++|+|+|+-.=+|.++.....++.++...+.
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 248999999999999999988888877765543
No 127
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=29.26 E-value=98 Score=24.12 Aligned_cols=49 Identities=10% Similarity=0.201 Sum_probs=31.7
Q ss_pred CEEEEeccccccchhHHHHhhhhhhhccccceEEEEec-CceEEEEecCCCchhH
Q 007029 487 DVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVD-RSCAIVVFGKPGLSNT 540 (621)
Q Consensus 487 ~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id-~t~a~V~~~~~~~~~~ 540 (621)
.+|.+.|||.. .+..+|..+.+ ||+-.++.+=+ ...++|.+.++..++.
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 128
>PRK05359 oligoribonuclease; Provisional
Probab=28.72 E-value=2e+02 Score=28.11 Aligned_cols=21 Identities=19% Similarity=0.324 Sum_probs=18.0
Q ss_pred CCCCEEeehhHHHHHHHHHhc
Q 007029 323 SQKPLVAHNSLNDFTFIHSKF 343 (621)
Q Consensus 323 skKpIVGHN~llDL~~iy~~F 343 (621)
...|+||||.=+|.-||-+.+
T Consensus 97 ~~~~l~g~~v~FD~~FL~~~~ 117 (181)
T PRK05359 97 GKSPLCGNSIGQDRRFLARYM 117 (181)
T ss_pred CCCceeecchhhCHHHHHHHH
Confidence 467899999999999998765
No 129
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=27.58 E-value=1.3e+02 Score=31.91 Aligned_cols=58 Identities=12% Similarity=0.214 Sum_probs=40.3
Q ss_pred CCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecC-------ceEEEEecCCCchhHHHHHhhh
Q 007029 486 EDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR-------SCAIVVFGKPGLSNTFKNVMNS 547 (621)
Q Consensus 486 ~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~-------t~a~V~~~~~~~~~~~l~~~~~ 547 (621)
...+||-.-|..|+-.+|++.++ .||+..+|.-+-| ..+||.|.+.+.|...+.+++.
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 130
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=27.38 E-value=1e+02 Score=37.51 Aligned_cols=45 Identities=22% Similarity=0.335 Sum_probs=33.2
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCcc
Q 007029 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRD 121 (621)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~~ 121 (621)
...||++|+|.||+.+ .=.|||+|...+. ++ -....|..++-|..
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 0149999988775 22 24578899999853
No 131
>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=26.77 E-value=57 Score=35.69 Aligned_cols=25 Identities=12% Similarity=0.275 Sum_probs=22.0
Q ss_pred HHHHHHHHhhcCCCeEEEecCCCCc
Q 007029 39 ESLSEIKNHISSSDFIAVSLQNTGS 63 (621)
Q Consensus 39 ~~lp~i~~~I~~a~FVAiD~EftGi 63 (621)
+.|..+.+.+..++.|||||||.+.
T Consensus 6 ~~l~~~~~~l~~~~~ia~DtE~~~~ 30 (367)
T TIGR01388 6 DELATVCEAVRTFPFVALDTEFVRE 30 (367)
T ss_pred HHHHHHHHHHhcCCEEEEeccccCC
Confidence 5678888888999999999999876
No 132
>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=26.68 E-value=76 Score=24.17 Aligned_cols=37 Identities=16% Similarity=0.280 Sum_probs=25.1
Q ss_pred hccccceEEEEecC--ceEEEEecCCCchhHHHHHhhhc
Q 007029 512 EVFAEAFNVRMVDR--SCAIVVFGKPGLSNTFKNVMNSK 548 (621)
Q Consensus 512 ~~F~~~~~V~~id~--t~a~V~~~~~~~~~~~l~~~~~~ 548 (621)
+-||+-..|....+ ..|||.+.+.++|...+..++..
T Consensus 6 ~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~ 44 (56)
T PF13893_consen 6 SKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGR 44 (56)
T ss_dssp TTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTS
T ss_pred CCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence 34444335555554 56999999999999877766554
No 133
>PLN03121 nucleic acid binding protein; Provisional
Probab=26.49 E-value=1.2e+02 Score=31.54 Aligned_cols=74 Identities=9% Similarity=0.103 Sum_probs=46.7
Q ss_pred CEEEEeccccccchhHHHHhhhhhhhccccceEEEEecCc----eEEEEecCCCchhHHHHHhhhccccccchhhhcCCc
Q 007029 487 DVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRS----CAIVVFGKPGLSNTFKNVMNSKAVSGPLREMVSDGL 562 (621)
Q Consensus 487 ~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~t----~a~V~~~~~~~~~~~l~~~~~~~~~~~l~~~~~~g~ 562 (621)
..|++-+.+.+.+-.+|++.++ -||+-.+|.-+.+. .+||.|.+++.++..+. ++... |+..-.
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 222236
Q ss_pred cccchHHHHH
Q 007029 563 KAAGYETYQR 572 (621)
Q Consensus 563 ~~a~~~~y~~ 572 (621)
+++.|+.|.+
T Consensus 74 ~It~~~~y~~ 83 (243)
T PLN03121 74 CITRWGQYED 83 (243)
T ss_pred EEEeCccccc
Confidence 7888887765
No 134
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=26.41 E-value=23 Score=41.02 Aligned_cols=127 Identities=9% Similarity=-0.070 Sum_probs=87.7
Q ss_pred ccceEEeCcc--cHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeec
Q 007029 26 HWPIKQITKT--NFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKL 103 (621)
Q Consensus 26 ~~~i~eVt~~--NF~~~lp~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~ 103 (621)
++++..+.++ |+....+.....+.+..+.+++.|++|+.. ..+ ...-.+..++++......+.++=+|+...--
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~---~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~ 176 (564)
T KOG1990|consen 101 RSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGG-SDR---LSVDADLLPEKIPDYMRPFRTLPVGSPPLLT 176 (564)
T ss_pred ecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCC-CCC---ccchhhhchhhhhcccChhccCCCCChhhhh
Confidence 5566777777 899998888899999999999999999842 222 2233455777777777777777777644322
Q ss_pred CC-------CceeeEeEEEeecCccccccCCCCCceeechhHHHHHHHcCCCccchhhcccccCCHHHHH
Q 007029 104 QA-------SKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQES 166 (621)
Q Consensus 104 ~~-------~~y~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~YLs~~eE~ 166 (621)
.. ..|.+.+|+--.+-. ......+..++|..+|.|++ .++..|+.+-+.....
T Consensus 177 ~~~~~~~r~~~~~~p~~~~~~~~~---------~~~~~~~~~~~~~~k~~~~k-~~~~rg~~~~~~~~~a 236 (564)
T KOG1990|consen 177 SIESTLLRRLGYKLPPHFALGRSR---------KLQGLAVAMVSFWEKHEFAK-ILIKRGVLETRKERMA 236 (564)
T ss_pred hHHHHHHHHhcccccccceehhcc---------ccccchhHHHHHHHHHHHHH-HHHHhcchhhhccchH
Confidence 21 345555544433332 12345577889999999999 9999999997766554
No 135
>cd06006 R3H_unknown_2 R3H domain of a group of fungal 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=25.68 E-value=1.1e+02 Score=24.66 Aligned_cols=22 Identities=14% Similarity=0.199 Sum_probs=18.6
Q ss_pred CCccccccchHHHHHHHHHHHh
Q 007029 240 PSMTIDVCSERQVQLVLKMLED 261 (621)
Q Consensus 240 p~l~l~~~~~~q~~Li~q~l~~ 261 (621)
....+++.++.||++||++.+.
T Consensus 18 ~~~~f~pM~~~~R~~vHdla~~ 39 (59)
T cd06006 18 RSLRFPPMRSPQRAFIHELAKD 39 (59)
T ss_pred CceeCCCCCHHHHHHHHHHHHH
Confidence 3467888999999999998876
No 136
>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=25.56 E-value=5.5e+02 Score=23.90 Aligned_cols=100 Identities=17% Similarity=0.201 Sum_probs=56.9
Q ss_pred HHHhCCCCEEeehhHHHHHHHHHhccCCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCC
Q 007029 319 LISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAP 398 (621)
Q Consensus 319 ~L~~skKpIVGHN~llDL~~iy~~F~gpLP~t~~eFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~ 398 (621)
.+...+.+.||||+=-|+-.+.++| |--+ ..++||...+--++|-.. .++..+....-.....+
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 2111 357999865555566433 36666655432211111
Q ss_pred ceeecCCCCCC----CCcccchhhHHHHHHHHHHHHHHhcc
Q 007029 399 IEMEIPNQANE----NEGKIHGHNVVKICQLFGKLCSILKI 435 (621)
Q Consensus 399 ~~vei~~~~~~----~~~heAGyDA~mTG~vFikL~~~L~~ 435 (621)
..+ ...-+.. ...+-|+.||+.+..++-+|...|..
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 01123788999999999888887744
No 137
>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=25.52 E-value=1.2e+02 Score=34.31 Aligned_cols=55 Identities=20% Similarity=0.213 Sum_probs=41.2
Q ss_pred CEEEEeccccccchhHHHHhhhhhhhccccceEEEEe-cCceEEEEecCCCchhHHHHHh
Q 007029 487 DVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMV-DRSCAIVVFGKPGLSNTFKNVM 545 (621)
Q Consensus 487 ~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~i-d~t~a~V~~~~~~~~~~~l~~~ 545 (621)
.|||+-+.|..++-.+|++.++ .||+-.+|.-+ +...|||.|.+.++|...+..+
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 45554455444 5567999999999999888764
No 138
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=25.15 E-value=1.4e+02 Score=30.35 Aligned_cols=39 Identities=18% Similarity=0.249 Sum_probs=28.6
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
|++||+|-||+. + .|+|+|...+. ++ + ...+|+.++-|.
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 09999987765 22 2 356788888885
No 139
>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=24.27 E-value=3.4e+02 Score=26.08 Aligned_cols=44 Identities=18% Similarity=0.144 Sum_probs=28.9
Q ss_pred eEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 53 FIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 53 FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
||.||+|.||+.+. .=.|+|+|...++... .-....|..++-|.
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 1249999999775432 12335566666664
No 140
>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=23.41 E-value=1.9e+02 Score=24.82 Aligned_cols=56 Identities=13% Similarity=0.109 Sum_probs=41.4
Q ss_pred EEeccccccchhHHHHhhhhhhhccc-cceEEEEecCceEEEEecCCCchhHHHHHh
Q 007029 490 FLWGFRERISAGILKNMLQGSHEVFA-EAFNVRMVDRSCAIVVFGKPGLSNTFKNVM 545 (621)
Q Consensus 490 ~~~~f~~~~~~~~i~~~l~~~~~~F~-~~~~V~~id~t~a~V~~~~~~~~~~~l~~~ 545 (621)
+....|..|+..+|++.|+...+.=. ..+.++|+|+.-=+|.+.+...-.+.+...
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 248999999999999999886665554433
No 141
>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=22.87 E-value=30 Score=32.98 Aligned_cols=39 Identities=8% Similarity=0.154 Sum_probs=25.6
Q ss_pred EEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 54 IAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 54 VAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
||||+|+||+.+. .=.|+|+|...+. ++ . . .|+-++-|.
T Consensus 1 v~lD~EttGl~~~-----------------------~d~ii~Ig~V~v~-~g-~-i--~~~~~v~P~ 39 (161)
T cd06137 1 VALDCEMVGLADG-----------------------DSEVVRISAVDVL-TG-E-V--LIDSLVRPS 39 (161)
T ss_pred CEEEeeeeeEcCC-----------------------CCEEEEEEEEEcC-CC-e-E--EEeccccCC
Confidence 6999999999431 1248999987762 22 1 1 266677774
No 142
>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=22.76 E-value=1.1e+02 Score=29.68 Aligned_cols=41 Identities=24% Similarity=0.095 Sum_probs=28.0
Q ss_pred EEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 55 AVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 55 AiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
-+|+|.||+.+. .=.|||+|.-.++.+. . ....|++++-|.
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 237888888885
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=22.09 E-value=1.7e+02 Score=33.14 Aligned_cols=60 Identities=15% Similarity=0.317 Sum_probs=42.7
Q ss_pred CCEEEEecccc-ccchhHHHHhhhhhhhccccceEEEEec--CceEEEEecCCCchhHHHHHhhhcc
Q 007029 486 EDVVFLWGFRE-RISAGILKNMLQGSHEVFAEAFNVRMVD--RSCAIVVFGKPGLSNTFKNVMNSKA 549 (621)
Q Consensus 486 ~~vv~~~~f~~-~~~~~~i~~~l~~~~~~F~~~~~V~~id--~t~a~V~~~~~~~~~~~l~~~~~~~ 549 (621)
..++|+-+.|. .++-.+|++.++ .||....|..+- ...+||.|.+.++|...+..++...
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 687777665433 444434555543 3579999999999999998886654
No 144
>PF13606 Ank_3: Ankyrin repeat
Probab=22.00 E-value=70 Score=21.77 Aligned_cols=17 Identities=18% Similarity=0.315 Sum_probs=14.8
Q ss_pred chhHHHHHHHcCCCccc
Q 007029 135 QTSYLTAMAKEGFDFNT 151 (621)
Q Consensus 135 q~sSl~FL~~~gFDFnk 151 (621)
+.+-+++|.++|.|.|+
T Consensus 14 ~~e~v~~Ll~~gadvn~ 30 (30)
T PF13606_consen 14 NIEIVKYLLEHGADVNA 30 (30)
T ss_pred CHHHHHHHHHcCCCCCC
Confidence 46789999999999985
No 145
>cd02644 R3H_jag R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. 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=21.43 E-value=69 Score=26.36 Aligned_cols=27 Identities=4% Similarity=0.132 Sum_probs=21.4
Q ss_pred CccccccchHHHHHHHHHHHhhcCCcce
Q 007029 241 SMTIDVCSERQVQLVLKMLEDFSDVLVP 268 (621)
Q Consensus 241 ~l~l~~~~~~q~~Li~q~l~~~~~~l~~ 268 (621)
+..+++.++++|++||++++.+ +++.+
T Consensus 25 ~~~l~PM~~~eRrivH~~~~~~-~~l~T 51 (67)
T cd02644 25 PVKLEPMNAYERRIIHDALAND-EDVET 51 (67)
T ss_pred eeEeCCCCHHHHHHHHHHHHhC-CCceE
Confidence 3778889999999999988864 45544
No 146
>PRK06722 exonuclease; Provisional
Probab=21.42 E-value=1.8e+02 Score=30.89 Aligned_cols=50 Identities=8% Similarity=0.163 Sum_probs=33.4
Q ss_pred CCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhccccceeEEeeeeecCCCceeeEeEEEeecCc
Q 007029 50 SSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPR 120 (621)
Q Consensus 50 ~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~~~y~~~~fNF~lfp~ 120 (621)
...||+||+|.||. +. .. .+.-.|||+|...+.... --.+..|+.++-|.
T Consensus 4 ~~~~vViD~ETT~~-p~---~~----------------~~~deIIEIGAVkV~~g~-i~Ivd~F~sLV~P~ 53 (281)
T PRK06722 4 ATHFIVFDIERNFR-PY---KS----------------EDPSEIVDIGAVKIEAST-MKVIGEFSELVKPG 53 (281)
T ss_pred CCEEEEEEeeCCCC-CC---CC----------------CCCCeEEEEEEEEEECCc-eeEEeeEEEEECCC
Confidence 46899999999963 21 00 112359999988775421 13457899999985
No 147
>PRK10829 ribonuclease D; Provisional
Probab=21.35 E-value=84 Score=34.61 Aligned_cols=26 Identities=12% Similarity=0.162 Sum_probs=21.8
Q ss_pred HHHHHHHHHhhcCCCeEEEecCCCCc
Q 007029 38 NESLSEIKNHISSSDFIAVSLQNTGS 63 (621)
Q Consensus 38 ~~~lp~i~~~I~~a~FVAiD~EftGi 63 (621)
.+.|..+.+.+..+..|||||||.+.
T Consensus 9 ~~~L~~~~~~l~~~~~lalDtEf~~~ 34 (373)
T PRK10829 9 DDALASVCEAARAFPAIALDTEFVRT 34 (373)
T ss_pred HHHHHHHHHHHhcCCeEEEecccccC
Confidence 35677777779999999999999876
No 148
>cd06007 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. 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=21.25 E-value=1.3e+02 Score=24.26 Aligned_cols=20 Identities=0% Similarity=0.134 Sum_probs=16.8
Q ss_pred ccccc-cchHHHHHHHHHHHh
Q 007029 242 MTIDV-CSERQVQLVLKMLED 261 (621)
Q Consensus 242 l~l~~-~~~~q~~Li~q~l~~ 261 (621)
+..|+ .++.+|++||++.++
T Consensus 19 l~Fpp~ls~~eR~~vH~~a~~ 39 (59)
T cd06007 19 YEFPSSLTNHERAVIHRLCRK 39 (59)
T ss_pred EEcCCCCCHHHHHHHHHHHHH
Confidence 66675 789999999998876
No 149
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=21.21 E-value=1.5e+02 Score=33.28 Aligned_cols=58 Identities=14% Similarity=0.370 Sum_probs=42.0
Q ss_pred ccccccchhHHHHhhhhhhhccccceEEEEecCc-------eEEEEecCCCchhHHHHHh-hhcc---ccccc
Q 007029 493 GFRERISAGILKNMLQGSHEVFAEAFNVRMVDRS-------CAIVVFGKPGLSNTFKNVM-NSKA---VSGPL 554 (621)
Q Consensus 493 ~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~t-------~a~V~~~~~~~~~~~l~~~-~~~~---~~~~l 554 (621)
-.|+.|+-.|||..+. -||...+|.-|.|. |+||-+..++.+.....|+ |.-. .-||+
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
No 150
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. 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=20.86 E-value=4e+02 Score=22.24 Aligned_cols=27 Identities=7% Similarity=-0.004 Sum_probs=20.0
Q ss_pred CCccccccchHHHHHHHHHHHhhcCCcce
Q 007029 240 PSMTIDVCSERQVQLVLKMLEDFSDVLVP 268 (621)
Q Consensus 240 p~l~l~~~~~~q~~Li~q~l~~~~~~l~~ 268 (621)
....+++-+++||++||++ . ...++.+
T Consensus 33 ~~~~l~PM~~~eR~iIH~l-a-~~~~l~S 59 (74)
T cd02643 33 RSHSFPPMNREKRRIVHEL-A-EHFGIES 59 (74)
T ss_pred CeeECCCCCHHHHHHHHHH-H-hhCCCEE
Confidence 4577889999999999984 3 3455554
No 151
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=20.14 E-value=2e+02 Score=33.57 Aligned_cols=61 Identities=13% Similarity=0.153 Sum_probs=45.1
Q ss_pred CCcCCEEEEeccccccchhHHHHhhhhhhhccccceEEEEecC------ceEEEEecCCCchhHHHHHhhh
Q 007029 483 VSCEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDR------SCAIVVFGKPGLSNTFKNVMNS 547 (621)
Q Consensus 483 ~~~~~vv~~~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~------t~a~V~~~~~~~~~~~l~~~~~ 547 (621)
+....-|||-..|..|+..+|++.+.+ |++..+|+.+-| .-+||.|.+.++|...+..++.
T Consensus 55 p~~~~~lFVgnLp~~~tEd~L~~~F~~----~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng 121 (578)
T TIGR01648 55 PGRGCEVFVGKIPRDLYEDELVPLFEK----AGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNN 121 (578)
T ss_pred CCCCCEEEeCCCCCCCCHHHHHHHHHh----hCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCC
Confidence 345567888899999999998876654 444346665422 2499999999999999988865
Done!