Query 007386
Match_columns 605
No_of_seqs 199 out of 423
Neff 5.8
Searched_HMMs 46136
Date Thu Mar 28 22:53:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007386.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007386hhsearch_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 3.1E-41 6.6E-46 345.9 8.5 127 215-355 135-262 (262)
2 KOG1990 Poly(A)-specific exori 99.8 1.6E-19 3.5E-24 202.8 12.0 464 5-569 79-556 (564)
3 KOG0304 mRNA deadenylase subun 99.7 1E-17 2.3E-22 163.9 9.6 111 214-359 121-238 (239)
4 PF08675 RNA_bind: RNA binding 99.6 1.9E-15 4E-20 128.1 5.6 56 423-482 8-63 (87)
5 COG5228 POP2 mRNA deadenylase 99.3 8.3E-12 1.8E-16 122.7 7.7 109 215-360 138-253 (299)
6 cd02637 R3H_PARN R3H domain of 98.0 1.1E-05 2.3E-10 66.5 5.9 31 144-174 19-49 (65)
7 PF10309 DUF2414: Protein of u 97.1 0.0019 4.2E-08 52.7 7.1 56 424-480 6-61 (62)
8 TIGR00573 dnaq exonuclease, DN 97.0 0.0057 1.2E-07 61.5 10.6 106 212-360 68-177 (217)
9 PRK07942 DNA polymerase III su 96.9 0.0041 8.8E-08 63.3 9.3 97 219-361 80-181 (232)
10 PRK05711 DNA polymerase III su 96.9 0.006 1.3E-07 62.6 10.4 103 212-358 67-174 (240)
11 PRK09145 DNA polymerase III su 96.7 0.0093 2E-07 59.1 9.6 100 212-358 92-199 (202)
12 PRK07740 hypothetical protein; 96.7 0.008 1.7E-07 61.7 9.4 101 214-360 124-226 (244)
13 cd06134 RNaseT DEDDh 3'-5' exo 96.6 0.0071 1.5E-07 59.6 8.1 84 228-359 101-188 (189)
14 cd06131 DNA_pol_III_epsilon_Ec 96.6 0.016 3.4E-07 55.1 10.2 101 212-356 62-166 (167)
15 PRK06195 DNA polymerase III su 96.5 0.063 1.4E-06 57.0 15.2 96 217-362 66-166 (309)
16 TIGR01406 dnaQ_proteo DNA poly 96.5 0.017 3.8E-07 58.5 10.4 103 212-358 63-170 (225)
17 PRK05168 ribonuclease T; Provi 96.4 0.012 2.6E-07 59.1 8.3 87 228-361 113-202 (211)
18 PRK06063 DNA polymerase III su 96.3 0.023 4.9E-07 60.5 10.0 96 217-361 80-180 (313)
19 TIGR01298 RNaseT ribonuclease 96.0 0.02 4.3E-07 57.0 7.7 86 228-360 104-192 (200)
20 cd06130 DNA_pol_III_epsilon_li 96.0 0.045 9.8E-07 51.1 9.4 90 215-354 61-155 (156)
21 smart00479 EXOIII exonuclease 95.8 0.091 2E-06 49.3 10.7 101 212-360 61-167 (169)
22 PRK06310 DNA polymerase III su 95.7 0.044 9.5E-07 56.5 8.7 100 215-361 71-175 (250)
23 PRK06722 exonuclease; Provisio 95.6 0.074 1.6E-06 55.9 10.0 22 337-358 158-179 (281)
24 PRK09146 DNA polymerase III su 95.4 0.081 1.8E-06 54.3 9.4 106 212-362 110-229 (239)
25 PRK06807 DNA polymerase III su 95.3 0.094 2E-06 55.9 9.9 86 228-361 87-173 (313)
26 PRK07748 sporulation inhibitor 95.3 0.09 2E-06 52.4 9.2 23 337-359 157-179 (207)
27 PF00076 RRM_1: RNA recognitio 95.2 0.078 1.7E-06 42.1 7.0 57 426-483 1-61 (70)
28 PRK07983 exodeoxyribonuclease 95.2 0.11 2.5E-06 52.5 9.7 99 212-362 58-156 (219)
29 cd06127 DEDDh DEDDh 3'-5' exon 94.9 0.13 2.8E-06 47.1 8.3 77 230-354 80-159 (159)
30 PF14259 RRM_6: RNA recognitio 94.8 0.12 2.5E-06 41.7 6.8 54 426-482 1-60 (70)
31 PRK06309 DNA polymerase III su 94.4 0.25 5.5E-06 50.2 10.0 100 214-361 62-167 (232)
32 cd06145 REX1_like DEDDh 3'-5' 94.4 0.12 2.7E-06 48.9 7.1 75 228-353 75-149 (150)
33 PRK07246 bifunctional ATP-depe 94.1 0.26 5.7E-06 59.1 10.6 100 215-362 70-172 (820)
34 cd06144 REX4_like DEDDh 3'-5' 94.0 0.1 2.2E-06 49.4 5.7 16 338-353 136-151 (152)
35 TIGR01407 dinG_rel DnaQ family 93.9 0.28 6E-06 59.1 10.5 101 214-361 63-166 (850)
36 KOG4483 Uncharacterized conser 93.9 0.088 1.9E-06 56.9 5.5 59 423-483 391-449 (528)
37 PRK08517 DNA polymerase III su 93.9 0.48 1E-05 49.2 10.7 85 228-360 146-231 (257)
38 cd06137 DEDDh_RNase DEDDh 3'-5 93.7 0.14 3E-06 49.0 6.1 79 228-354 83-161 (161)
39 PRK08074 bifunctional ATP-depe 93.7 0.28 6.1E-06 59.6 10.0 86 228-361 83-170 (928)
40 TIGR01405 polC_Gram_pos DNA po 93.4 0.35 7.5E-06 60.2 10.2 102 212-360 251-355 (1213)
41 PRK00448 polC DNA polymerase I 92.7 0.4 8.6E-06 60.6 9.4 103 212-361 480-585 (1437)
42 smart00362 RRM_2 RNA recogniti 92.7 0.58 1.3E-05 36.1 7.3 54 426-482 2-60 (72)
43 PRK07247 DNA polymerase III su 92.5 0.5 1.1E-05 47.1 8.0 22 338-359 147-168 (195)
44 PRK07883 hypothetical protein; 91.8 0.87 1.9E-05 52.4 10.1 88 229-361 95-183 (557)
45 PF00929 RNase_T: Exonuclease; 90.7 0.12 2.6E-06 47.3 1.5 15 339-353 150-164 (164)
46 cd00590 RRM RRM (RNA recogniti 90.6 1.3 2.7E-05 34.4 7.1 57 426-483 2-62 (74)
47 PLN03134 glycine-rich RNA-bind 90.3 1.6 3.4E-05 41.4 8.6 57 424-483 35-98 (144)
48 cd06136 TREX1_2 DEDDh 3'-5' ex 90.2 1 2.2E-05 43.8 7.5 75 229-355 98-176 (177)
49 PF08777 RRM_3: RNA binding mo 89.6 0.85 1.9E-05 41.0 6.0 54 425-484 3-60 (105)
50 cd06149 ISG20 DEDDh 3'-5' exon 89.4 0.62 1.4E-05 44.5 5.2 17 337-353 140-156 (157)
51 PRK09182 DNA polymerase III su 89.2 1.5 3.2E-05 46.5 8.3 24 338-361 179-202 (294)
52 cd06133 ERI-1_3'hExo_like DEDD 88.8 1.9 4.2E-05 40.8 8.2 82 231-356 92-175 (176)
53 smart00360 RRM RNA recognition 88.3 1.8 3.9E-05 33.1 6.3 52 429-482 2-59 (71)
54 cd06138 ExoI_N N-terminal DEDD 87.5 1.6 3.5E-05 42.5 6.9 33 216-248 67-104 (183)
55 PRK05601 DNA polymerase III su 86.7 2.6 5.6E-05 46.1 8.4 39 210-248 104-144 (377)
56 PTZ00315 2'-phosphotransferase 86.4 3.3 7.2E-05 47.8 9.4 108 210-358 122-253 (582)
57 COG0847 DnaQ DNA polymerase II 86.1 3.7 8.1E-05 41.4 8.9 82 230-359 96-181 (243)
58 TIGR01659 sex-lethal sex-letha 85.9 3.3 7.2E-05 44.9 8.8 68 423-493 107-181 (346)
59 cd06396 PB1_NBR1 The PB1 domai 85.6 2.7 5.9E-05 36.3 6.3 57 426-483 11-69 (81)
60 PF01424 R3H: R3H domain; Int 85.1 2.9 6.3E-05 33.6 6.0 39 144-186 23-61 (63)
61 cd06407 PB1_NLP A PB1 domain i 84.9 3.7 7.9E-05 35.4 6.8 60 424-483 9-70 (82)
62 PF01612 DNA_pol_A_exo1: 3'-5' 83.3 4.1 8.9E-05 38.2 7.3 104 223-360 71-175 (176)
63 PRK11779 sbcB exonuclease I; P 81.0 7.3 0.00016 44.1 9.2 23 337-359 175-197 (476)
64 TIGR01649 hnRNP-L_PTB hnRNP-L/ 80.2 4.2 9.2E-05 45.8 7.1 56 424-481 3-58 (481)
65 cd02325 R3H R3H domain. The na 80.0 8.2 0.00018 29.4 6.7 27 144-172 20-46 (59)
66 TIGR01659 sex-lethal sex-letha 79.4 5.3 0.00012 43.3 7.3 56 425-483 195-257 (346)
67 TIGR01661 ELAV_HUD_SF ELAV/HuD 77.7 7.1 0.00015 41.3 7.6 58 424-484 270-334 (352)
68 TIGR01661 ELAV_HUD_SF ELAV/HuD 77.7 6.8 0.00015 41.5 7.4 58 424-484 4-68 (352)
69 cd06146 mut-7_like_exo DEDDy 3 77.5 7.6 0.00017 38.3 7.2 106 224-357 77-192 (193)
70 cd02644 R3H_jag R3H domain fou 76.5 6.6 0.00014 32.5 5.4 40 144-186 26-65 (67)
71 cd02642 R3H_encore_like R3H do 76.2 12 0.00026 30.5 6.7 38 144-186 24-61 (63)
72 cd02638 R3H_unknown_1 R3H doma 74.5 7.1 0.00015 32.0 4.9 29 144-173 21-49 (62)
73 PLN03120 nucleic acid binding 73.9 13 0.00029 38.8 8.0 53 424-479 5-61 (260)
74 cd06141 WRN_exo DEDDy 3'-5' ex 73.5 12 0.00027 35.4 7.3 98 223-357 67-169 (170)
75 KOG0144 RNA-binding protein CU 73.0 7.2 0.00016 43.2 6.0 77 426-508 37-120 (510)
76 TIGR01645 half-pint poly-U bin 72.3 10 0.00022 44.3 7.4 66 424-492 205-277 (612)
77 TIGR01622 SF-CC1 splicing fact 72.1 10 0.00023 41.8 7.3 59 424-485 187-252 (457)
78 cd06129 RNaseD_like DEDDy 3'-5 71.4 14 0.0003 35.1 7.1 100 223-358 61-161 (161)
79 cd01201 Neurobeachin Neurobeac 70.8 13 0.00028 33.9 6.2 52 429-480 52-104 (108)
80 TIGR01622 SF-CC1 splicing fact 69.9 14 0.0003 40.8 7.7 56 423-481 89-151 (457)
81 TIGR01648 hnRNP-R-Q heterogene 69.7 14 0.0003 43.0 7.7 60 424-485 234-293 (578)
82 PLN03121 nucleic acid binding 69.2 16 0.00035 37.8 7.3 57 424-483 6-66 (243)
83 PRK10829 ribonuclease D; Provi 67.7 23 0.00049 39.0 8.6 105 221-361 66-171 (373)
84 TIGR01645 half-pint poly-U bin 67.2 14 0.0003 43.2 7.1 61 423-484 107-172 (612)
85 smart00393 R3H Putative single 66.8 21 0.00045 30.1 6.4 40 143-186 38-77 (79)
86 TIGR01649 hnRNP-L_PTB hnRNP-L/ 66.0 18 0.00039 40.8 7.6 59 423-484 275-336 (481)
87 cd06408 PB1_NoxR The PB1 domai 66.0 13 0.00027 32.6 5.0 61 426-487 13-73 (86)
88 COG2176 PolC DNA polymerase II 65.4 15 0.00033 45.5 7.1 84 229-360 501-586 (1444)
89 KOG0132 RNA polymerase II C-te 65.1 20 0.00043 42.5 7.7 63 418-483 410-479 (894)
90 cd02643 R3H_NF-X1 R3H domain o 64.9 35 0.00075 28.8 7.3 28 144-173 35-62 (74)
91 KOG0148 Apoptosis-promoting RN 64.6 15 0.00033 38.5 6.0 58 425-484 166-223 (321)
92 TIGR01628 PABP-1234 polyadenyl 63.9 19 0.00042 41.1 7.5 56 425-483 180-241 (562)
93 KOG0145 RNA-binding protein EL 60.8 11 0.00025 39.2 4.3 89 381-483 98-191 (360)
94 TIGR01648 hnRNP-R-Q heterogene 58.3 32 0.0007 40.0 7.9 59 424-485 59-123 (578)
95 PF11608 Limkain-b1: Limkain b 58.3 52 0.0011 29.0 7.3 68 424-495 3-73 (90)
96 PRK05755 DNA polymerase I; Pro 58.0 31 0.00068 42.0 8.2 109 221-361 362-470 (880)
97 TIGR01642 U2AF_lg U2 snRNP aux 57.8 34 0.00074 38.3 8.0 60 423-485 295-361 (509)
98 cd05992 PB1 The PB1 domain is 57.1 32 0.00069 28.5 5.8 54 429-482 14-69 (81)
99 PF13893 RRM_5: RNA recognitio 56.8 31 0.00067 26.5 5.3 41 440-483 1-43 (56)
100 PF00564 PB1: PB1 domain; Int 56.4 37 0.0008 28.3 6.2 55 429-483 16-71 (84)
101 smart00666 PB1 PB1 domain. Pho 56.0 48 0.001 27.5 6.8 58 426-483 12-70 (81)
102 smart00361 RRM_1 RNA recogniti 54.1 33 0.00072 27.8 5.4 44 438-483 3-59 (70)
103 cd06398 PB1_Joka2 The PB1 doma 53.3 52 0.0011 29.0 6.7 60 422-481 7-73 (91)
104 cd02645 R3H_AAA R3H domain of 53.3 34 0.00073 27.9 5.1 28 144-173 21-48 (60)
105 KOG0107 Alternative splicing f 51.5 46 0.001 33.0 6.6 56 424-483 11-69 (195)
106 TIGR01628 PABP-1234 polyadenyl 50.9 43 0.00092 38.3 7.5 56 426-484 3-65 (562)
107 cd06125 DnaQ_like_exo DnaQ-lik 49.9 19 0.00041 31.4 3.4 28 221-248 35-63 (96)
108 KOG1457 RNA binding protein (c 49.4 45 0.00098 34.3 6.3 59 424-483 35-99 (284)
109 COG0349 Rnd Ribonuclease D [Tr 49.2 50 0.0011 36.2 7.1 107 219-361 60-167 (361)
110 cd02636 R3H_sperm-antigen R3H 47.9 54 0.0012 26.9 5.4 40 144-186 20-59 (61)
111 KOG0148 Apoptosis-promoting RN 46.6 48 0.001 35.0 6.2 60 423-483 62-126 (321)
112 cd06404 PB1_aPKC PB1 domain is 45.1 97 0.0021 27.0 6.9 61 423-483 8-70 (83)
113 COG0724 RNA-binding proteins ( 40.2 1E+02 0.0022 29.8 7.3 60 423-483 115-179 (306)
114 PRK05359 oligoribonuclease; Pr 39.3 54 0.0012 32.1 5.2 21 228-248 97-117 (181)
115 KOG0122 Translation initiation 38.8 91 0.002 32.5 6.7 58 423-483 189-253 (270)
116 PF15023 DUF4523: Protein of u 38.4 86 0.0019 30.2 6.0 56 423-481 87-145 (166)
117 cd02640 R3H_NRF R3H domain of 38.3 74 0.0016 25.9 4.9 27 144-172 20-47 (60)
118 KOG0304 mRNA deadenylase subun 38.1 18 0.00039 36.9 1.6 26 28-53 100-125 (239)
119 cd06148 Egl_like_exo DEDDy 3'- 36.7 1.2E+02 0.0025 30.0 7.1 111 224-361 60-178 (197)
120 cd02641 R3H_Smubp-2_like R3H d 36.7 84 0.0018 25.4 5.0 27 144-172 20-47 (60)
121 KOG0127 Nucleolar protein fibr 34.4 1.2E+02 0.0027 34.9 7.4 60 420-482 289-355 (678)
122 TIGR01642 U2AF_lg U2 snRNP aux 34.2 82 0.0018 35.3 6.3 56 424-479 176-241 (509)
123 KOG4212 RNA-binding protein hn 32.5 1.2E+02 0.0027 34.0 6.8 64 425-490 46-115 (608)
124 TIGR01388 rnd ribonuclease D. 32.1 2.1E+02 0.0046 31.3 8.8 100 221-361 62-167 (367)
125 COG1847 Jag Predicted RNA-bind 30.7 82 0.0018 32.0 4.9 30 143-173 166-195 (208)
126 cd02646 R3H_G-patch R3H domain 28.7 1.6E+02 0.0035 23.4 5.4 26 144-171 19-44 (58)
127 cd06007 R3H_DEXH_helicase R3H 28.6 1.1E+02 0.0025 24.7 4.5 39 144-186 19-58 (59)
128 KOG4207 Predicted splicing fac 28.2 1.3E+02 0.0028 30.7 5.7 50 433-483 23-77 (256)
129 PF14605 Nup35_RRM_2: Nup53/35 25.3 1.6E+02 0.0035 23.0 4.7 49 425-477 3-52 (53)
130 cd00007 35EXOc 3'-5' exonuclea 24.9 1E+02 0.0022 27.7 4.1 59 223-301 48-106 (155)
131 KOG0117 Heterogeneous nuclear 24.5 2E+02 0.0043 32.5 6.8 94 378-493 232-325 (506)
132 cd06135 Orn DEDDh 3'-5' exonuc 24.4 1.2E+02 0.0026 29.3 4.7 21 228-248 93-113 (173)
133 cd06006 R3H_unknown_2 R3H doma 23.4 1.9E+02 0.0041 23.5 4.9 39 144-186 20-58 (59)
134 KOG0144 RNA-binding protein CU 23.2 98 0.0021 34.7 4.1 63 426-489 127-193 (510)
135 KOG0130 RNA-binding protein RB 21.6 2.2E+02 0.0048 27.3 5.6 67 424-493 73-146 (170)
136 KOG4206 Spliceosomal protein s 21.3 2.8E+02 0.0061 28.5 6.7 57 425-484 11-75 (221)
137 cd06142 RNaseD_exo DEDDy 3'-5' 20.5 4.7E+02 0.01 24.3 7.9 104 223-361 58-161 (178)
138 PF11767 SET_assoc: Histone ly 20.4 2E+02 0.0044 23.9 4.6 39 435-478 12-50 (66)
139 cd06139 DNA_polA_I_Ecoli_like_ 20.2 2.4E+02 0.0051 26.7 5.9 111 223-361 61-171 (193)
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=3.1e-41 Score=345.92 Aligned_cols=127 Identities=43% Similarity=0.600 Sum_probs=88.5
Q ss_pred hccHHHHHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCCh
Q 007386 215 SIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSL 294 (605)
Q Consensus 215 ~iGfr~v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL 294 (605)
.+||+.|++.+.+++||||||||++|++|||++|+||||++++||++.++.+||.|||||||++.++ ...++|
T Consensus 135 ~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~-------~~~~~L 207 (262)
T PF04857_consen 135 LLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECP-------GKSTSL 207 (262)
T ss_dssp HHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTT-------TS-SSH
T ss_pred hHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhcc-------ccccCH
Confidence 4788888899999999999999999999999999999999999999999999999999999998765 247899
Q ss_pred HHHHHhhhhhcccCCcccccccCCCceeeeeecccccc-CCCCCcccchhhhHHHHHHHHHH
Q 007386 295 SKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSS-NWNSGVKHEAGYDAFMTGCVFAQ 355 (605)
Q Consensus 295 ~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~-~~~~~~~HEAGyDA~mTG~vF~k 355 (605)
+.+++.+...-..... ..+.... ........ .......|||||||||||+||++
T Consensus 208 ~~l~~~l~~~~~~~~~-----~~~~~~~--~~~~~~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 208 QELAEELGIRRNPSSI-----SSPEGFP--SYDEEKNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp HHHHHHTTSTT----E-----EE-TTS---------------SS-TTSHHHHHHHHHHHHHH
T ss_pred HHHHHHhCCCcccccc-----ccccccc--cccccccccccCCCCCCCcchHHHHHHHHHcC
Confidence 9998776422100000 0000000 00100000 11334599999999999999986
No 2
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.80 E-value=1.6e-19 Score=202.81 Aligned_cols=464 Identities=18% Similarity=0.145 Sum_probs=254.9
Q ss_pred ceeeeeeecCCCCCCCCCCeeEEEecchHHHHHHcCCCccchhhcCCCcCCHHHHHHHHHHhhhhccccccccccccccc
Q 007386 5 GRHNFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHVNSTYEDESLDSWHSLKEI 84 (605)
Q Consensus 5 rpyNFylFPr~~~~~~~~dr~F~cQaSSL~FLa~~gFDFNk~i~~GIpYLsr~eE~~~~~~l~~~~~~~~~~~~~~~~~~ 84 (605)
.++||++||+ ......+ .|+||.+.+.|++++ +| +.
T Consensus 79 ~~~n~~~~~~-g~~~s~~--~~~~~~~~~~~~~~~------------------~~------------~~----------- 114 (564)
T KOG1990|consen 79 TGGNFVVWSR-GDSISSP--EFLCQRSPVDFVARQ------------------QE------------NQ----------- 114 (564)
T ss_pred CCCceeeeec-CccccCC--ccceeecchhhhhhh------------------ch------------hh-----------
Confidence 5899999999 5555555 999999999999999 11 00
Q ss_pred cccCCCCCcchHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCCcchhhhHHHhhccccccccCCCCHHHHHHHHHHHHHh
Q 007386 85 RDTHLFNIPDILFAERMKDRLSEWLGGLLRNRDEGSEVQPSFNDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKH 164 (605)
Q Consensus 85 ~d~~l~~~~D~~F~e~v~~~I~eWl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~l~L~~~~s~qrrLV~q~lr~~ 164 (605)
+..+.-++.....+|++++......-......+.+...-.+++...++|+..++.+...+...+.++...+
T Consensus 115 ---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~ 185 (564)
T KOG1990|consen 115 ---------AGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRR 185 (564)
T ss_pred ---------hhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHH
Confidence 00123334555677777654333221112223444445567778889999999998888887777777777
Q ss_pred CCCeEEEEeccCCCCceeEEEE-EcchhhHHHHHHHHHHHHHHHHHhhhhhhccHHHHHHHHhcCCCeEEechhhhHHHH
Q 007386 165 FKDLAYLRVSGENSCSQNVIVY-IESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAH 243 (605)
Q Consensus 165 fp~lv~v~~~~~~~~~~~~vv~-~~~~ee~~~l~ke~~ee~~~~~e~~l~~~iGfr~v~~~l~~s~kpiVgHN~~~Dl~~ 243 (605)
....+++.........++.+.+ ..+.-++. +.+++..++-.+.+.....+.++. .+..+++++|+||+++|++|
T Consensus 186 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~-~~~k~~~~rg~~~~~~~~~a~~l~----~~~~tg~~lv~hN~~~dv~y 260 (564)
T KOG1990|consen 186 LGYKLPPHFALGRSRKLQGLAVAMVSFWEKH-EFAKILIKRGVLETRKERMADELQ----ELLLTGKVLVLHNKLLDVMY 260 (564)
T ss_pred hcccccccceehhccccccchhHHHHHHHHH-HHHHHHHHhcchhhhccchHHHHH----HHHhcCCeEEeeccceeeee
Confidence 7666655443222122222222 22211121 122222222222223333344444 68899999999999999999
Q ss_pred HHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhcccCCcccccccCCCceee
Q 007386 244 IYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVE 323 (605)
Q Consensus 244 l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~ 323 (605)
+|++|+++||+++++|+.. .+.||.++||+.++...+ ++. .++...+.++...-....+. ...+...-.
T Consensus 261 ~~~~Fl~~lp~~l~~f~~~-~~~fp~~~~~~~~~~~~~-~~~------~~~~~t~~e~~~~~~~~~~~---~~~~~~~~~ 329 (564)
T KOG1990|consen 261 RYKNFLSPLPSTLEEFTDS-SSMFPNIEDTKRLAKLSE-YQK------LNLKATLLELARAKAKKEKE---IERRSISSR 329 (564)
T ss_pred ehhhcccccchhHHHhhhh-hhhhhhhHHHHHhhcccc-ccc------hhhhhhHHHHHHHhcccccC---cccccccch
Confidence 9999999999999999999 999999999999987333 222 12333333222111000000 001110000
Q ss_pred eeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhCCCcc---cCCchhhhh-h--------hhhhccccccccccCC
Q 007386 324 VEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFK---QQSSSENLA-H--------NEKLREHVNLLYLSWT 391 (605)
Q Consensus 324 v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg~~~~---~~~~~~~l~-~--------~~~l~~~~N~L~~~~~ 391 (605)
...+ ......+..|+++++++.+|.+++..+......+. ......... . ...+..+.|...+.+.
T Consensus 330 ~~~e---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~r 406 (564)
T KOG1990|consen 330 LKLE---FEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGR 406 (564)
T ss_pred hhhh---hhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCC
Confidence 0001 12335678999999999999999998776532221 111010000 0 0112233333333332
Q ss_pred CccccccCCCCCCCccccccccccCCCcccccceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecch
Q 007386 392 NGEIINLSTGNRTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRA 471 (605)
Q Consensus 392 ~~~~idL~~~~~~~~~~~~~~l~~~~p~~~~~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~ 471 (605)
-+.+..+... ... | -+.+++ ..-++-.|.+|..|+...+.-+-. =|+.. ++|.-++..-|++.
T Consensus 407 rg~f~g~i~n---~~l-~----wk~~e~--~k~i~~~~~~~~~~~~~a~~le~e--sg~~~-v~~~~~~~~~ai~~---- 469 (564)
T KOG1990|consen 407 RGVFDGVIEN---MHL-H----WKSREL--VKVICKEKNLPSQVKQYASALERE--SGGIL-VSIDKNPKGYAIIA---- 469 (564)
T ss_pred cccccceeec---chh-h----hhhccc--ceeeeccccccHHHHHHHHHHHHH--hCCce-eeeccCCchhhHHH----
Confidence 2222222110 000 0 000111 122333444444444444432221 12222 12333322222221
Q ss_pred hhHHHHHHHhcccccCCCCcccccchhhhhcCCcccccchHHHHHHHhcccchhhhHhhhhHhcccccccccccccchhh
Q 007386 472 EMVSKFLDLKGSLDRNNDPISVLHPLAKLLEGGNTCAASYETYKEICSSTVSKVLFADQAKAVGIKWKTKLVESSDKTKE 551 (605)
Q Consensus 472 e~~~~~L~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~a~~~ty~~~c~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~ 551 (605)
...+..+.+.+ +.|.+.+..++.+..+.++.|+++|...++......+..-+........ +.+.+..+
T Consensus 470 ----------yr~k~y~~p~~-l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~~~-~~~~d~~~ 537 (564)
T KOG1990|consen 470 ----------YRGKNYDRPTS-LRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMPAI-NKKDDLEE 537 (564)
T ss_pred ----------hhhhhccCCcc-cCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhccccc-ccccchHH
Confidence 11122234544 7899999999999999999999999999999998888877777776553 22455444
Q ss_pred hhhhhhhcc-cCCCCCCCc
Q 007386 552 HESLRKVKA-VNSDPSCGE 569 (605)
Q Consensus 552 ~~~~~~~~~-~~~~~~~~~ 569 (605)
++..+++.. -.++..|++
T Consensus 538 en~~t~~~~~~~d~~~~~~ 556 (564)
T KOG1990|consen 538 ENSETVEEDQSEDDSLAER 556 (564)
T ss_pred Hhhhhhhhhhccccccccc
Confidence 444333332 235566655
No 3
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=99.73 E-value=1e-17 Score=163.94 Aligned_cols=111 Identities=25% Similarity=0.358 Sum_probs=93.3
Q ss_pred hhccHHHHHHHHhcCCCe------EEechhhhHHHHHHHHh-cCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHh
Q 007386 214 ASIGFRHVIDLLSSEKKL------IVGHNCFLDIAHIYSKF-FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQR 286 (605)
Q Consensus 214 ~~iGfr~v~~~l~~s~kp------iVgHN~~~Dl~~l~~~F-~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~ 286 (605)
+-|+...|.++|+.|++. ||.+++.||++||++.+ .++||++.+||...++.+||.|||+|||+..|..++.
T Consensus 121 ~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~l- 199 (239)
T KOG0304|consen 121 EGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLSL- 199 (239)
T ss_pred cCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhhh-
Confidence 357788999999998875 89999999999999999 9999999999999999999999999999998876321
Q ss_pred hccCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHH
Q 007386 287 MKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSH 359 (605)
Q Consensus 287 ~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~ 359 (605)
..+|+.+- ..+ ++. +.|++|+||+||+||+.+|.||...
T Consensus 200 ----~~GL~~lA----~~L-------------------~~~-------RvG~~HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 200 ----KGGLQRLA----DLL-------------------GLK-------RVGIAHQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred ----hcCHHHHH----HHh-------------------CCC-------eeecccccCcHHHHHHHHHHHHHhc
Confidence 34566653 322 122 6799999999999999999999653
No 4
>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=1.9e-15 Score=128.08 Aligned_cols=56 Identities=21% Similarity=0.316 Sum_probs=45.8
Q ss_pred cceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhc
Q 007386 423 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKG 482 (605)
Q Consensus 423 ~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~ 482 (605)
++||||++||++||.+||.++|+ +||++ +|+|||||||||+|+++++|+..+....
T Consensus 8 RdHVFhltFPkeWK~~DI~qlFs-pfG~I---~VsWi~dTSAfV~l~~r~~~~~v~~~~~ 63 (87)
T PF08675_consen 8 RDHVFHLTFPKEWKTSDIYQLFS-PFGQI---YVSWINDTSAFVALHNRDQAKVVMNTLK 63 (87)
T ss_dssp GCCEEEEE--TT--HHHHHHHCC-CCCCE---EEEEECTTEEEEEECCCHHHHHHHHHHT
T ss_pred cceEEEEeCchHhhhhhHHHHhc-cCCcE---EEEEEcCCcEEEEeecHHHHHHHHHHhc
Confidence 36699999999999999999996 99986 5699999999999999999998766554
No 5
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=99.27 E-value=8.3e-12 Score=122.70 Aligned_cols=109 Identities=24% Similarity=0.346 Sum_probs=87.5
Q ss_pred hccHHHHHHHHhcCCCe------EEechhhhHHHHHHHHh-cCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhh
Q 007386 215 SIGFRHVIDLLSSEKKL------IVGHNCFLDIAHIYSKF-FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRM 287 (605)
Q Consensus 215 ~iGfr~v~~~l~~s~kp------iVgHN~~~Dl~~l~~~F-~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~ 287 (605)
-+....+.++|+.||.+ ||.++..||++||++.. +.|||+..+||...+|.+||..||.|++++..-..
T Consensus 138 GI~v~eF~elLm~SGLvm~e~VtWitfHsaYDfgyLikilt~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~~~---- 213 (299)
T COG5228 138 GIDVFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNN---- 213 (299)
T ss_pred CCCHHHHHHHHhccCceeccceEEEEeecchhHHHHHHHHhcCCCCccHHHHHHHHHHHCccccchHHHHHhhhhh----
Confidence 35567888999999986 89999999999999999 99999999999999999999999999998653221
Q ss_pred ccCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 007386 288 KKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 360 (605)
Q Consensus 288 ~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~l 360 (605)
+..|+++ ...+ ... +.|..|+||.||++|+..|......+
T Consensus 214 ---~KglQei----~ndl-------------------ql~-------r~g~QhQagsdaLlTa~~ff~~R~~~ 253 (299)
T COG5228 214 ---SKGLQEI----KNDL-------------------QLQ-------RSGQQHQAGSDALLTADEFFLPRFSI 253 (299)
T ss_pred ---hhHHHHh----cCcH-------------------hhh-------ccchhhhccchhhhhhHHhcchhhhe
Confidence 3334443 2111 112 56899999999999999998876555
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=98.03 E-value=1.1e-05 Score=66.48 Aligned_cols=31 Identities=13% Similarity=0.125 Sum_probs=28.9
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEec
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVS 174 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~~ 174 (605)
|.|++||+|||+||||+++++||+.+.+++.
T Consensus 19 l~le~cngf~RkLiyq~l~~~~~~~I~ve~~ 49 (65)
T cd02637 19 LELEPCNGFQRKLIYQTLEQKYPKGIHVETL 49 (65)
T ss_pred ccccccccHHHHHHHHHHHHHccccceeeee
Confidence 6789999999999999999999999998875
No 7
>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function.
Probab=97.12 E-value=0.0019 Score=52.71 Aligned_cols=56 Identities=21% Similarity=0.287 Sum_probs=43.9
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHH
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDL 480 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~ 480 (605)
+.|++.|- .++++.||++.|..-|+......|-|||||||=|+|.+.+.+..-|.+
T Consensus 6 eavhirGv-d~lsT~dI~~y~~~y~~~~~~~~IEWIdDtScNvvf~d~~~A~~AL~~ 61 (62)
T PF10309_consen 6 EAVHIRGV-DELSTDDIKAYFSEYFDEEGPFRIEWIDDTSCNVVFKDEETAARALVA 61 (62)
T ss_pred ceEEEEcC-CCCCHHHHHHHHHHhcccCCCceEEEecCCcEEEEECCHHHHHHHHHc
Confidence 34778885 559999999999754443334577999999999999999999877654
No 8
>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=96.96 E-value=0.0057 Score=61.47 Aligned_cols=106 Identities=17% Similarity=0.211 Sum_probs=64.5
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhc--CCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhh
Q 007386 212 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFF--GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRM 287 (605)
Q Consensus 212 l~~~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~--~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~ 287 (605)
+.++-.|..++..+.. .+.++||||.-+|+.+|-+.|. +..|. ....++||.-++... ....
T Consensus 68 l~~~p~~~ev~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~-----------~~~~~~dtl~l~~~~---~~~~ 133 (217)
T TIGR00573 68 LKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVEP-----------KTNDVIDTTDTLQYA---RPEF 133 (217)
T ss_pred HcCCCCHHHHHHHHHHHhCCCEEEEeccHHHHHHHHHHHHHhcCCCC-----------CccceecHHHHHHHH---HHhC
Confidence 3344455555555544 5679999999999999988773 22111 012456776655421 1222
Q ss_pred ccCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 007386 288 KKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 360 (605)
Q Consensus 288 ~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~l 360 (605)
.....+|..+.+.+ +++. .....|.|..||.+|+.+|.+|+...
T Consensus 134 ~~~~~~L~~l~~~~-----------------------gl~~------~~~~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 134 PGKRNTLDALCKRY-----------------------EITN------SHRALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred CCCCCCHHHHHHHc-----------------------CCCC------CCcccCCHHHHHHHHHHHHHHHHhcc
Confidence 22345677764432 0110 11267999999999999999997754
No 9
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.92 E-value=0.0041 Score=63.31 Aligned_cols=97 Identities=20% Similarity=0.169 Sum_probs=61.2
Q ss_pred HHHHHHH---hcCCCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCC
Q 007386 219 RHVIDLL---SSEKKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTS 293 (605)
Q Consensus 219 r~v~~~l---~~s~kpiVgHN~~~Dl~~l~~~F--~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~ts 293 (605)
..|.+.| ...+.|+||||.-+|+.+|-+.+ +| +|.- .-+ .++||-.|+...... ..+..+
T Consensus 80 ~e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~-~~~~---------~~~-~~iDt~~l~~~~~~~----~~~~~~ 144 (232)
T PRK07942 80 AEIADALREAWARGVPVVVFNAPYDLTVLDRELRRHG-LPSL---------VPG-PVIDPYVIDKAVDRY----RKGKRT 144 (232)
T ss_pred HHHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcC-CCCc---------cCC-cEeeHHHHHhhhhcc----cCCCCC
Confidence 3444444 34688999999999999998776 22 2210 112 256987776532211 112456
Q ss_pred hHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 294 LSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 294 L~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
|+.+.+.+ .++ ....|.|..||++|+.+|.+|++.++
T Consensus 145 L~~l~~~~-----------------------gi~--------~~~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 145 LTALCEHY-----------------------GVR--------LDNAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred HHHHHHHc-----------------------CCC--------CCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 77764321 011 12479999999999999999988764
No 10
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.91 E-value=0.006 Score=62.61 Aligned_cols=103 Identities=21% Similarity=0.272 Sum_probs=67.0
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh--cC-CCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHh
Q 007386 212 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF--FG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQR 286 (605)
Q Consensus 212 l~~~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F--~~-pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~ 286 (605)
+.++-.|..|++.+.+ .+-++|+||.-+|+.+|-..| +| ++|.. . .+..++||--|+...
T Consensus 67 l~~~p~f~ev~~~f~~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~-~--------~~~~~iDTl~lar~~------ 131 (240)
T PRK05711 67 LADKPTFAEVADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKT-N--------TFCKVTDTLAMARRM------ 131 (240)
T ss_pred HcCCCCHHHHHHHHHHHhCCCEEEEEccHHhHHHHHHHHHHhCCCCCcc-c--------ccCceeeHHHHHHHH------
Confidence 4455667777666654 566899999999999998776 44 34431 1 134588998777532
Q ss_pred hccCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHH
Q 007386 287 MKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACS 358 (605)
Q Consensus 287 ~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~ 358 (605)
......+|..+.. .+ .++. ..-..|.|-.||++|+.+|+.|..
T Consensus 132 ~p~~~~~L~aL~~----~~-------------------gi~~------~~r~~H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 132 FPGKRNSLDALCK----RY-------------------GIDN------SHRTLHGALLDAEILAEVYLAMTG 174 (240)
T ss_pred cCCCCCCHHHHHH----HC-------------------CCCC------CCCCCCCHHHHHHHHHHHHHHHHC
Confidence 1122456776633 22 1111 112579999999999999999964
No 11
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.69 E-value=0.0093 Score=59.12 Aligned_cols=100 Identities=18% Similarity=0.226 Sum_probs=59.9
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhc----CCCCCCHHHHHHHHHhhCCCCcchhHHhhhc--hhH
Q 007386 212 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFF----GPLPLTAEEFISSVNKYFPHIIDTKILLNSN--SIL 283 (605)
Q Consensus 212 l~~~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~----~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~--~~l 283 (605)
+.++.-|..+++.+.. .+.++||||.-+|+.+|-..|. .++|. ..+||.-|.... ..+
T Consensus 92 l~~~~~~~~vl~~~~~~i~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~--------------~~id~~~l~~~~~~~~~ 157 (202)
T PRK09145 92 LEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPN--------------PLIEVSALYYDKKERHL 157 (202)
T ss_pred HhcCCCHHHHHHHHHHHHcCCeEEEeCHHHHHHHHHHHHHHhcCCCCCC--------------CeeeHHHHHHHHhhccC
Confidence 4445556666666654 5789999999999999876652 23332 246776553211 001
Q ss_pred HHhhccCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHH
Q 007386 284 QQRMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACS 358 (605)
Q Consensus 284 ~~~~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~ 358 (605)
.. ..++-+|..+.+.+ .++ ....|.|-.||++|+.+|.+|..
T Consensus 158 ~~--~~~~~~L~~l~~~~-----------------------gi~--------~~~~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 158 PD--AYIDLRFDAILKHL-----------------------DLP--------VLGRHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CC--cccCCCHHHHHHHc-----------------------CCC--------CCCCCCcHHHHHHHHHHHHHHHh
Confidence 00 01134566653321 111 12459999999999999999854
No 12
>PRK07740 hypothetical protein; Provisional
Probab=96.69 E-value=0.008 Score=61.71 Aligned_cols=101 Identities=18% Similarity=0.186 Sum_probs=63.7
Q ss_pred hhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCC
Q 007386 214 ASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 291 (605)
Q Consensus 214 ~~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~ 291 (605)
.+.-|..++..+.. .+.++||||.-+|+.+|-+.+...+... +...++||..++....+ . .+.
T Consensus 124 ~ap~~~evl~~f~~fi~~~~lVahna~fD~~fL~~~~~~~~~~~----------~~~~~iDt~~l~r~l~~---~--~~~ 188 (244)
T PRK07740 124 FAPPLAEVLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQP----------FTHRLIDTMFLTKLLAH---E--RDF 188 (244)
T ss_pred CCCCHHHHHHHHHHHhCCCEEEEeCHHHHHHHHHHHHHHhcCCC----------cCCCeechHHHHHHHcC---C--CCC
Confidence 34445555555442 4679999999999999877664332111 12368899888653211 1 124
Q ss_pred CChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 007386 292 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 360 (605)
Q Consensus 292 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~l 360 (605)
-+|.++...+ .++ ....|.|-+||++|+.+|.++...+
T Consensus 189 ~sL~~l~~~~-----------------------gi~--------~~~~H~Al~Da~ata~l~~~ll~~~ 226 (244)
T PRK07740 189 PTLDDALAYY-----------------------GIP--------IPRRHHALGDALMTAKLWAILLVEA 226 (244)
T ss_pred CCHHHHHHHC-----------------------CcC--------CCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 5677764332 011 1234999999999999999997766
No 13
>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=96.62 E-value=0.0071 Score=59.55 Aligned_cols=84 Identities=24% Similarity=0.316 Sum_probs=54.2
Q ss_pred CCCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHhhC-C-CCcchhHHhhhchhHHHhhccCCCChHHHHHhhhh
Q 007386 228 EKKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYF-P-HIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCP 303 (605)
Q Consensus 228 s~kpiVgHN~~~Dl~~l~~~F--~~pLP~~~~EFk~~l~~~F-P-~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~ 303 (605)
.+.++||||.-+|+.+|-+.+ +|--. ..| | .++||.-|+... .+...|..+.+.
T Consensus 101 ~~~~lVaHna~FD~~fL~~~~~~~~~~~-----------~~~~~~~~lDt~~la~~~--------~~~~~L~~l~~~--- 158 (189)
T cd06134 101 TRAILVGHNAHFDLGFLNAAVARCKIKR-----------NPFHPFSTFDTATLAGLA--------YGQTVLAKACQA--- 158 (189)
T ss_pred CCCeEEEecchhhHHHHHHHHHHhCCCC-----------CCCCCCcEEEHHHHHHHH--------hCCCcHHHHHHH---
Confidence 467999999999999998776 22100 112 2 368998887531 123456655322
Q ss_pred hcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHH
Q 007386 304 QIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSH 359 (605)
Q Consensus 304 ~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~ 359 (605)
+ ..| . .....|.|.+||++|+.+|.+|.+.
T Consensus 159 -~----------gi~-------~--------~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 159 -A----------GIE-------F--------DNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred -C----------CCC-------C--------CCCCCcChHHHHHHHHHHHHHHHHh
Confidence 1 011 1 1135799999999999999999753
No 14
>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=96.61 E-value=0.016 Score=55.13 Aligned_cols=101 Identities=18% Similarity=0.116 Sum_probs=60.5
Q ss_pred hhhhccHHHHHHHHh--cCCCeEEechhhhHHHHHHHHhcC-CCCCCHHHHHHHHHhhCC-CCcchhHHhhhchhHHHhh
Q 007386 212 IKASIGFRHVIDLLS--SEKKLIVGHNCFLDIAHIYSKFFG-PLPLTAEEFISSVNKYFP-HIIDTKILLNSNSILQQRM 287 (605)
Q Consensus 212 l~~~iGfr~v~~~l~--~s~kpiVgHN~~~Dl~~l~~~F~~-pLP~~~~EFk~~l~~~FP-~IyDTK~L~~~~~~l~~~~ 287 (605)
+.....|..+++.+. -.+-++||||.-+|+.+|-+.+-. -++.. ...| .++||-.++... .
T Consensus 62 l~~~~~~~~v~~~l~~~l~~~~lv~hn~~fD~~~l~~~~~~~~~~~~---------~~~~~~~idt~~~~~~~------~ 126 (167)
T cd06131 62 LADKPKFAEIADEFLDFIRGAELVIHNASFDVGFLNAELSLLGLGKK---------IIDFCRVIDTLALARKK------F 126 (167)
T ss_pred HhcCCCHHHHHHHHHHHHCCCeEEEeChHHhHHHHHHHHHHhCCCcc---------cccCCCceEhHHHHHHH------c
Confidence 334455665555553 234689999999999988766521 11110 0123 468987666421 1
Q ss_pred ccCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHH
Q 007386 288 KKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQA 356 (605)
Q Consensus 288 ~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL 356 (605)
.....+|+.+.+.+. .| . .....|.|.+||+.|+.+|.+|
T Consensus 127 ~~~~~~L~~l~~~~~--------------i~-------~--------~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 127 PGKPNSLDALCKRFG--------------ID-------N--------SHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCCCHHHHHHHCC--------------CC-------C--------CCCCCCChHHHHHHHHHHHHHh
Confidence 113457877754320 00 0 1135799999999999999987
No 15
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.53 E-value=0.063 Score=56.96 Aligned_cols=96 Identities=18% Similarity=0.284 Sum_probs=59.8
Q ss_pred cHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh--cC-CCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCC
Q 007386 217 GFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF--FG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 291 (605)
Q Consensus 217 Gfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F--~~-pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~ 291 (605)
-|..+++.+.+ .+.++||||.-+|+.+|-+.+ ++ ++|. ...+||--|+... + .. ..+
T Consensus 66 ~f~ev~~~~~~fl~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~-------------~~~idT~~lar~l--~-~~--~~~ 127 (309)
T PRK06195 66 EFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTLELYNIPMPS-------------FEYICTMKLAKNF--Y-SN--IDN 127 (309)
T ss_pred CHHHHHHHHHHHhCCCEEEEECcHHHHHHHHHHHHHhCCCCCC-------------CCEEEHHHHHHHH--c-CC--CCc
Confidence 34444444332 467999999999999997765 22 2331 2357886665421 0 00 124
Q ss_pred CChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhCC
Q 007386 292 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGI 362 (605)
Q Consensus 292 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg~ 362 (605)
.+|..+.+. + .++ ...|.|-+||++|+.+|..|+..++.
T Consensus 128 ~~L~~L~~~----~-------------------gi~---------~~~H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 128 ARLNTVNNF----L-------------------GYE---------FKHHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred CCHHHHHHH----c-------------------CCC---------CcccCCHHHHHHHHHHHHHHHHHhcc
Confidence 556665322 1 111 13699999999999999999998875
No 16
>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=96.52 E-value=0.017 Score=58.54 Aligned_cols=103 Identities=20% Similarity=0.305 Sum_probs=63.5
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh--cCC-CCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHh
Q 007386 212 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF--FGP-LPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQR 286 (605)
Q Consensus 212 l~~~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F--~~p-LP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~ 286 (605)
+..+.-|..+++.+.+ .+.++|+||.-+|+.+|-..| +|+ +|. + ..|-.++||--|+...
T Consensus 63 l~~~p~f~ev~~~f~~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~----~-----~~~~~~iDTl~lar~~------ 127 (225)
T TIGR01406 63 LADKPKFKEIADEFLDFIGGSELVIHNAAFDVGFLNYELERLGPTIKK----I-----GEFCRVIDTLAMARER------ 127 (225)
T ss_pred HhCCCCHHHHHHHHHHHhCCCEEEEEecHHHHHHHHHHHHHhCCCCcc----c-----ccCCCEEEHHHHHHHH------
Confidence 3344556666555442 457899999999999998776 442 111 0 0122478998876531
Q ss_pred hccCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHH
Q 007386 287 MKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACS 358 (605)
Q Consensus 287 ~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~ 358 (605)
......+|..+. ..+ .++. .....|.|-.||.+|+.+|+.|..
T Consensus 128 ~p~~~~~L~~L~----~~~-------------------gi~~------~~r~~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 128 FPGQRNSLDALC----KRF-------------------KVDN------SHRTLHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred cCCCCCCHHHHH----Hhc-------------------CCCC------CCCCCcCHHHHHHHHHHHHHHHHc
Confidence 112245676653 222 1110 112579999999999999999855
No 17
>PRK05168 ribonuclease T; Provisional
Probab=96.40 E-value=0.012 Score=59.05 Aligned_cols=87 Identities=23% Similarity=0.324 Sum_probs=56.8
Q ss_pred CCCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHhhCC-CCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhh
Q 007386 228 EKKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFP-HIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQ 304 (605)
Q Consensus 228 s~kpiVgHN~~~Dl~~l~~~F--~~pLP~~~~EFk~~l~~~FP-~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~ 304 (605)
.+.++||||.-+|+.+|.+.+ +|-.. ..++| .++||.-|+... . +...|..+.+.+
T Consensus 113 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~----------~~~~~~~~iDt~~lar~~------~--~~~~L~~l~~~~--- 171 (211)
T PRK05168 113 NRAILVAHNAHFDLSFLMAAAERAGLKR----------NPFHPFSTFDTATLSGLA------L--GQTVLAKACQAA--- 171 (211)
T ss_pred CCceEEEeccHHhHHHHHHHHHHhCCCC----------CCCCCCcEeeHHHHHHHH------c--CCCCHHHHHHHC---
Confidence 478999999999999998766 33110 01133 489998887521 1 233566553321
Q ss_pred cccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 305 IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 305 l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
..| . .....|.|-+||++|+.+|.+|+..+.
T Consensus 172 -----------gl~-------~--------~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 172 -----------GIE-------F--------DNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred -----------CCC-------C--------CCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 011 0 113579999999999999999988773
No 18
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.26 E-value=0.023 Score=60.53 Aligned_cols=96 Identities=17% Similarity=0.195 Sum_probs=61.3
Q ss_pred cHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh--cC-CCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCC
Q 007386 217 GFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF--FG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 291 (605)
Q Consensus 217 Gfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F--~~-pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~ 291 (605)
-|..+++.|.. .+.++||||.-+|+.+|.+.| ++ ++|. ...+||--|+..... ...+
T Consensus 80 ~f~ev~~~l~~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~-------------~~~ldTl~lar~~~~-----~~~~ 141 (313)
T PRK06063 80 QFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPV-------------DQVMCTVELARRLGL-----GLPN 141 (313)
T ss_pred CHHHHHHHHHHHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCC-------------CCEEehHHHHHHhcc-----CCCC
Confidence 34444444432 468999999999999998777 32 2331 236788877653210 1134
Q ss_pred CChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 292 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 292 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
..|..+.+.+ .+ .....|.|-.||++|+.+|..+...++
T Consensus 142 ~kL~~l~~~~-----------------------gi--------~~~~~H~Al~DA~ata~l~~~ll~~~~ 180 (313)
T PRK06063 142 LRLETLAAHW-----------------------GV--------PQQRPHDALDDARVLAGILRPSLERAR 180 (313)
T ss_pred CCHHHHHHHc-----------------------CC--------CCCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 5576654321 11 113579999999999999999877663
No 19
>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=96.05 E-value=0.02 Score=56.96 Aligned_cols=86 Identities=23% Similarity=0.279 Sum_probs=55.0
Q ss_pred CCCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHhhCC-CCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhh
Q 007386 228 EKKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFP-HIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQ 304 (605)
Q Consensus 228 s~kpiVgHN~~~Dl~~l~~~F--~~pLP~~~~EFk~~l~~~FP-~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~ 304 (605)
.+.++||||.-+|+.+|-+.+ ++..+..+ -| .++||--|+... . +...|..+.+.+
T Consensus 104 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~----------~~~~~lDTl~lar~~------~--~~~~L~~l~~~~--- 162 (200)
T TIGR01298 104 QRAILVGHNANFDLGFLNAAVERTSLKRNPF----------HPFSTFDTATLAGLA------Y--GQTVLAKACQAA--- 162 (200)
T ss_pred CCCEEEEECchhhHHHHHHHHHHhCCCCCCC----------CCCcEEEHHHHHHHH------c--CcccHHHHHHHc---
Confidence 467899999999999998776 33221100 01 278887776421 1 123466553321
Q ss_pred cccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 007386 305 IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 360 (605)
Q Consensus 305 l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~l 360 (605)
..| . .....|.|-+||++|+.+|.+|+..+
T Consensus 163 -----------gi~-------~--------~~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 163 -----------GXD-------F--------DSTQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred -----------CCC-------c--------cccchhhhHHhHHHHHHHHHHHHHHH
Confidence 001 0 11367999999999999999998876
No 20
>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=95.97 E-value=0.045 Score=51.10 Aligned_cols=90 Identities=20% Similarity=0.258 Sum_probs=56.0
Q ss_pred hccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh--cC-CCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhcc
Q 007386 215 SIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF--FG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKK 289 (605)
Q Consensus 215 ~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F--~~-pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~ 289 (605)
+..|..+++.+.+ .+.++||||.-+|+.+|-+.+ +| +.|. + ..+||.-++... +.. .
T Consensus 61 ~~~~~~v~~~l~~~l~~~~lv~hn~~fD~~~l~~~~~~~g~~~~~------------~-~~idt~~~~~~~--~~~---~ 122 (156)
T cd06130 61 APTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPPP------------Y-QYLCTVRLARRV--WPL---L 122 (156)
T ss_pred CCCHHHHHHHHHHHhCCCEEEEeChHHhHHHHHHHHHHcCCCCCC------------C-CEEEHHHHHHHH--hcc---C
Confidence 3445555554433 458999999999999997776 22 1221 2 367887665432 111 1
Q ss_pred CCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHH
Q 007386 290 SSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFA 354 (605)
Q Consensus 290 ~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~ 354 (605)
+..+|..+.+.+ .++ .. .|.|-+||+.|+.+|+
T Consensus 123 ~~~~L~~l~~~~-----------------------g~~--------~~-~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 123 PNHKLNTVAEHL-----------------------GIE--------LN-HHDALEDARACAEILL 155 (156)
T ss_pred CCCCHHHHHHHc-----------------------CCC--------cc-CcCchHHHHHHHHHHh
Confidence 356777764432 111 12 7999999999999985
No 21
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=95.78 E-value=0.091 Score=49.35 Aligned_cols=101 Identities=25% Similarity=0.264 Sum_probs=62.4
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechh-hhHHHHHHHHh--cC-CCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHH
Q 007386 212 IKASIGFRHVIDLLSS--EKKLIVGHNC-FLDIAHIYSKF--FG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQ 285 (605)
Q Consensus 212 l~~~iGfr~v~~~l~~--s~kpiVgHN~-~~Dl~~l~~~F--~~-pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~ 285 (605)
+.++.-|..+++.+.. .+.++|+||. -+|+-+|-..+ .+ +.|. +-.++||.-++....
T Consensus 61 l~~~~~~~~~~~~~~~~l~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~------------~~~~iD~~~~~~~~~---- 124 (169)
T smart00479 61 LDDAPTFEEVLEELLEFLKGKILVAGNALNFDLRFLKLEHPRLGIKDPP------------KNPVIDTLKLARALN---- 124 (169)
T ss_pred HhCCCCHHHHHHHHHHHhcCCEEEEeCCHHHhHHHHHHHHHHhCCCCCc------------CCCeeEHHHHHHHHC----
Confidence 3445555555555432 3457888998 99999888776 22 2331 112678876654211
Q ss_pred hhccCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 007386 286 RMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 360 (605)
Q Consensus 286 ~~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~l 360 (605)
.....+|..+.+.+. ++ ..+..|.|-.||.+|+.+|.+|...+
T Consensus 125 --~~~~~~L~~l~~~~~-----------------------~~-------~~~~~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 125 --PGRKYSLKKLAERLG-----------------------LE-------VIGRAHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred --CCCCCCHHHHHHHCC-----------------------CC-------CCCCCcCcHHHHHHHHHHHHHHHHHh
Confidence 112567777644321 11 11337999999999999999998765
No 22
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=95.68 E-value=0.044 Score=56.50 Aligned_cols=100 Identities=21% Similarity=0.149 Sum_probs=62.7
Q ss_pred hccHHHHHHHHh---cCCCeEEechhhhHHHHHHHHhcC-CCCCCHHHHHHHHHhhC-CCCcchhHHhhhchhHHHhhcc
Q 007386 215 SIGFRHVIDLLS---SEKKLIVGHNCFLDIAHIYSKFFG-PLPLTAEEFISSVNKYF-PHIIDTKILLNSNSILQQRMKK 289 (605)
Q Consensus 215 ~iGfr~v~~~l~---~s~kpiVgHN~~~Dl~~l~~~F~~-pLP~~~~EFk~~l~~~F-P~IyDTK~L~~~~~~l~~~~~~ 289 (605)
+--|..|++.+. ....++||||.-+|+.+|-+.|.. -+|.. .+ -.++||-.++...+. .
T Consensus 71 ~p~~~ev~~~~~~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~----------~~~~~~iDtl~lar~~~~------~ 134 (250)
T PRK06310 71 KPKIAEVFPQIKGFFKEGDYIVGHSVGFDLQVLSQESERIGETFL----------SKHYYIIDTLRLAKEYGD------S 134 (250)
T ss_pred CCCHHHHHHHHHHHhCCCCEEEEECHHHHHHHHHHHHHHcCCCcc----------ccCCcEEehHHHHHhccc------C
Confidence 334555544443 344789999999999999877621 11110 01 247899888653211 1
Q ss_pred CCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 290 SSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 290 ~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
.+.+|+.+...+ .+ .....|.|-.||++|+.+|..|+..++
T Consensus 135 ~~~~L~~l~~~~-----------------------g~--------~~~~aH~Al~Da~at~~vl~~l~~~~~ 175 (250)
T PRK06310 135 PNNSLEALAVHF-----------------------NV--------PYDGNHRAMKDVEINIKVFKHLCKRFR 175 (250)
T ss_pred CCCCHHHHHHHC-----------------------CC--------CCCCCcChHHHHHHHHHHHHHHHHhcc
Confidence 245677765432 00 112479999999999999999987663
No 23
>PRK06722 exonuclease; Provisional
Probab=95.59 E-value=0.074 Score=55.94 Aligned_cols=22 Identities=36% Similarity=0.309 Sum_probs=20.0
Q ss_pred CcccchhhhHHHHHHHHHHHHH
Q 007386 337 GVKHEAGYDAFMTGCVFAQACS 358 (605)
Q Consensus 337 ~~~HEAGyDA~mTG~vF~kL~~ 358 (605)
|..|.|-.||.+|+.+|++|..
T Consensus 158 g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 158 GKQHRALADAENTANILLKAYS 179 (281)
T ss_pred CCCcCcHHHHHHHHHHHHHHhc
Confidence 5689999999999999999874
No 24
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=95.41 E-value=0.081 Score=54.26 Aligned_cols=106 Identities=17% Similarity=0.134 Sum_probs=63.7
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhc---C-CCCCCHHHHHHHHHhhCCCCcchhHHhhhchh---
Q 007386 212 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFF---G-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSI--- 282 (605)
Q Consensus 212 l~~~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~---~-pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~--- 282 (605)
+..+.-|..+++.+.. .+.++||||.-+|+.+|-+.+- + ++|. .++||=-|+...-+
T Consensus 110 l~~ap~~~evl~~l~~~~~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~--------------~~iDTl~Lar~l~~~~~ 175 (239)
T PRK09146 110 LQDAPDLERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEF--------------PVIDTMEIEARIQRKQA 175 (239)
T ss_pred HhCCCCHHHHHHHHHHHhCCCEEEEECHHHHHHHHHHHHHHhcCCCCCC--------------ceechHHHHHHHccccc
Confidence 4444556667776664 4679999999999999987652 2 2221 25788777653210
Q ss_pred ---HHHhhcc--CCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHH
Q 007386 283 ---LQQRMKK--SSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQAC 357 (605)
Q Consensus 283 ---l~~~~~~--~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~ 357 (605)
+...... .+-.|..+.+. + ++ .....|.|-.||++|+.+|..++
T Consensus 176 ~~~~~~~~~~~~~~~~L~~l~~~----~-------------------gl--------~~~~~H~Al~DA~ata~l~~~~~ 224 (239)
T PRK09146 176 GGLWNRLKGKKPESIRLADSRLR----Y-------------------GL--------PAYSPHHALTDAIATAELLQAQI 224 (239)
T ss_pred ccccchhccCCCCCCCHHHHHHH----c-------------------CC--------CCCCCCCcHHHHHHHHHHHHHHH
Confidence 0000000 12234443211 1 01 12356999999999999999999
Q ss_pred HHhCC
Q 007386 358 SHLGI 362 (605)
Q Consensus 358 ~~lg~ 362 (605)
..++.
T Consensus 225 ~~~~~ 229 (239)
T PRK09146 225 AHHFS 229 (239)
T ss_pred HHHcC
Confidence 88854
No 25
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=95.31 E-value=0.094 Score=55.94 Aligned_cols=86 Identities=22% Similarity=0.268 Sum_probs=56.0
Q ss_pred CCCeEEechhhhHHHHHHHHh-cCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhcc
Q 007386 228 EKKLIVGHNCFLDIAHIYSKF-FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 306 (605)
Q Consensus 228 s~kpiVgHN~~~Dl~~l~~~F-~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~ 306 (605)
.+.++||||+-+|+.+|.+.+ .--+|. ....++||-.++... + .. .+..+|..+.+.+
T Consensus 87 ~~~~lVaHNa~FD~~fL~~~~~~~gl~~-----------~~~~~iDtl~la~~~--~-~~--~~~~kL~~L~~~l----- 145 (313)
T PRK06807 87 HTNVIVAHNASFDMRFLKSNVNMLGLPE-----------PKNKVIDTVFLAKKY--M-KH--APNHKLETLKRML----- 145 (313)
T ss_pred cCCeEEEEcHHHHHHHHHHHHHHcCCCC-----------CCCCEeeHHHHHHHH--h-CC--CCCCCHHHHHHHc-----
Confidence 356899999999999999887 212221 012367887775421 1 11 1244566653321
Q ss_pred cCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 307 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 307 ~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
+++ . ..|.|=.||++|+.+|.++++..+
T Consensus 146 ------------------gi~--------~-~~H~Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 146 ------------------GIR--------L-SSHNAFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred ------------------CCC--------C-CCcChHHHHHHHHHHHHHHHHhhh
Confidence 111 1 579999999999999999998875
No 26
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=95.31 E-value=0.09 Score=52.41 Aligned_cols=23 Identities=30% Similarity=0.208 Sum_probs=20.8
Q ss_pred CcccchhhhHHHHHHHHHHHHHH
Q 007386 337 GVKHEAGYDAFMTGCVFAQACSH 359 (605)
Q Consensus 337 ~~~HEAGyDA~mTG~vF~kL~~~ 359 (605)
+..|.|-.||++|+.+|.+|...
T Consensus 157 ~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 157 GKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred CCCcChHHHHHHHHHHHHHHHhC
Confidence 46799999999999999999875
No 27
>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=95.23 E-value=0.078 Score=42.07 Aligned_cols=57 Identities=23% Similarity=0.353 Sum_probs=46.0
Q ss_pred EEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe----cCceEEEEecchhhHHHHHHHhcc
Q 007386 426 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV----DETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 426 v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i----ddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
+|+.++|..++..+|++.|+ .||.+....+..= ....|||.|.+.+++...|..++.
T Consensus 1 l~v~nlp~~~t~~~l~~~f~-~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g 61 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFS-QFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNG 61 (70)
T ss_dssp EEEESETTTSSHHHHHHHHH-TTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred cEEcCCCCcCCHHHHHHHHH-HhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCC
Confidence 57889999999999999997 5998744333331 368999999999999998876655
No 28
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=95.22 E-value=0.11 Score=52.54 Aligned_cols=99 Identities=18% Similarity=0.145 Sum_probs=59.6
Q ss_pred hhhhccHHHHHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCC
Q 007386 212 IKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 291 (605)
Q Consensus 212 l~~~iGfr~v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~ 291 (605)
+..+--|..+++.+. ...++||||.-+|..+|- .++ -..+||=-|+...- ....
T Consensus 58 v~~ap~~~ev~~~~~-~~~~lVaHNa~FD~~~L~-----~~~--------------~~~idTl~lar~l~------p~~~ 111 (219)
T PRK07983 58 VADKPWIEDVIPHYY-GSEWYVAHNASFDRRVLP-----EMP--------------GEWICTMKLARRLW------PGIK 111 (219)
T ss_pred HcCCCCHHHHHHHHc-CCCEEEEeCcHhhHHHHh-----CcC--------------CCcEeHHHHHHHHc------cCCC
Confidence 334445666776654 467999999999987762 111 23578877764311 1112
Q ss_pred CChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhCC
Q 007386 292 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGI 362 (605)
Q Consensus 292 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg~ 362 (605)
.+|+.+.. .+ . +++... .....|.|-+||++|+.+|.+|++..|.
T Consensus 112 ~~l~~L~~----~~----------~-----l~~~~~-------~~~~aHrAl~Da~ata~ll~~l~~~~~~ 156 (219)
T PRK07983 112 YSNMALYK----SR----------K-----LNVQTP-------PGLHHHRALYDCYITAALLIDIMNTSGW 156 (219)
T ss_pred CCHHHHHH----Hc----------C-----CCCCCC-------CCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 44554432 21 0 000000 1135899999999999999999987765
No 29
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=94.88 E-value=0.13 Score=47.08 Aligned_cols=77 Identities=21% Similarity=0.168 Sum_probs=46.3
Q ss_pred CeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHhh-CCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhcc
Q 007386 230 KLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKY-FPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 306 (605)
Q Consensus 230 kpiVgHN~~~Dl~~l~~~F--~~pLP~~~~EFk~~l~~~-FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~ 306 (605)
-++||||.-+|+-+|.+.| ++ ... ....+||..+++...+. .....|..+. +..+
T Consensus 80 ~~~v~~n~~fD~~~l~~~~~~~~-------------~~~~~~~~iDt~~~~~~~~~~-----~~~~~l~~~~---~~~~- 137 (159)
T cd06127 80 RVLVAHNASFDLRFLNRELRRLG-------------GPPLPNPWIDTLRLARRLLPG-----LRSHRLGLLL---AERY- 137 (159)
T ss_pred CEEEEeCcHhhHHHHHHHHHHhC-------------CCCCCCCeeEHHHHHHHHcCC-----CCcCchHHHH---HHHc-
Confidence 7899999999988887776 33 111 23578888776432111 1122333221 0000
Q ss_pred cCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHH
Q 007386 307 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFA 354 (605)
Q Consensus 307 ~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~ 354 (605)
.. .....|.|-+||++|+.+|.
T Consensus 138 ------------------~~--------~~~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 138 ------------------GI--------PLEGAHRALADALATAELLL 159 (159)
T ss_pred ------------------CC--------CCCCCCCcHHHHHHHHHHhC
Confidence 01 23578999999999999983
No 30
>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=94.75 E-value=0.12 Score=41.73 Aligned_cols=54 Identities=30% Similarity=0.452 Sum_probs=43.6
Q ss_pred EEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecC------ceEEEEecchhhHHHHHHHhc
Q 007386 426 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE------TAVFVQFSRAEMVSKFLDLKG 482 (605)
Q Consensus 426 v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~idd------tsa~V~l~~~e~~~~~L~~~~ 482 (605)
|++.|.|+.++..+|.+.|+ .||. |..|..+-+ ..|||.|.+.+.++.+|....
T Consensus 1 v~i~nlp~~~~~~~l~~~f~-~~g~--v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~ 60 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNFFS-RFGP--VEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLN 60 (70)
T ss_dssp EEEESSTTT--HHHHHHHCT-TSSB--EEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHT
T ss_pred CEEeCCCCCCCHHHHHHHHH-hcCC--cceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCC
Confidence 58899999999999999986 5675 456777644 899999999999999988765
No 31
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=94.45 E-value=0.25 Score=50.19 Aligned_cols=100 Identities=17% Similarity=0.192 Sum_probs=60.4
Q ss_pred hhccHHHHHHHHh---cCCCeEEechh-hhHHHHHHHHh--cCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhh
Q 007386 214 ASIGFRHVIDLLS---SEKKLIVGHNC-FLDIAHIYSKF--FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRM 287 (605)
Q Consensus 214 ~~iGfr~v~~~l~---~s~kpiVgHN~-~~Dl~~l~~~F--~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~ 287 (605)
.+--|..+++.+. .....+||||. -+|+-+|-+.| .| +|.. .-..+||--++.. +....
T Consensus 62 ~~p~f~ev~~~~~~fi~~~~~lVaHN~~~FD~~~L~~e~~r~g-~~~~-----------~~~~iDt~~l~~~---~~~~~ 126 (232)
T PRK06309 62 DAPKFPEAYQKFIEFCGTDNILVAHNNDAFDFPLLRKECRRHG-LEPP-----------TLRTIDSLKWAQK---YRPDL 126 (232)
T ss_pred CCCCHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHcC-CCCC-----------CCcEEeHHHHHHH---HcCCC
Confidence 3344444444433 34568999995 79999998776 22 1110 0135788666542 11111
Q ss_pred ccCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 288 KKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 288 ~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
...+|+.+...+ .+ .....|.|-.||+.|+.+|.+|+..++
T Consensus 127 --~~~~L~~l~~~~-----------------------~~--------~~~~aH~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 127 --PKHNLQYLRQVY-----------------------GF--------EENQAHRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred --CCCCHHHHHHHc-----------------------CC--------CCCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 234576654321 00 124589999999999999999987764
No 32
>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=94.39 E-value=0.12 Score=48.91 Aligned_cols=75 Identities=20% Similarity=0.189 Sum_probs=47.0
Q ss_pred CCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhccc
Q 007386 228 EKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIAL 307 (605)
Q Consensus 228 s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~~ 307 (605)
.+.++||||.-+|+-+|-. .-|.++||-.|+....+ . ...-+|..+-..+..
T Consensus 75 ~~~vlVgHn~~fD~~fL~~-------------------~~~~~iDT~~l~r~~~~---~--~~~~~L~~L~~~~~~---- 126 (150)
T cd06145 75 PDTILVGHSLENDLKALKL-------------------IHPRVIDTAILFPHPRG---P--PYKPSLKNLAKKYLG---- 126 (150)
T ss_pred CCCEEEEcChHHHHHHhhc-------------------cCCCEEEcHHhccccCC---C--CCChhHHHHHHHHCC----
Confidence 4689999999999998731 23678999888653111 0 113466665332210
Q ss_pred CCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHH
Q 007386 308 GSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVF 353 (605)
Q Consensus 308 ~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF 353 (605)
+ .++ ..+..|.|-.||++|+.+|
T Consensus 127 --------------~--~i~-------~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 127 --------------R--DIQ-------QGEGGHDSVEDARAALELV 149 (150)
T ss_pred --------------c--cee-------CCCCCCCcHHHHHHHHHHh
Confidence 0 011 0135699999999999987
No 33
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=94.09 E-value=0.26 Score=59.06 Aligned_cols=100 Identities=24% Similarity=0.212 Sum_probs=60.7
Q ss_pred hccHHHHHHHHh--cCCCeEEechhhhHHHHHHHHhc-CCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCC
Q 007386 215 SIGFRHVIDLLS--SEKKLIVGHNCFLDIAHIYSKFF-GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 291 (605)
Q Consensus 215 ~iGfr~v~~~l~--~s~kpiVgHN~~~Dl~~l~~~F~-~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~ 291 (605)
+--|..|+..+. -.+.++||||.-+|+.+|-+.+. ...|. ..| .+||--|+... + .. ..+
T Consensus 70 ap~~~ev~~~~~~~l~~~~lVaHN~~FD~~fL~~~~~~~g~~~-----------~~~-~iDT~~la~~~--~-p~--~~~ 132 (820)
T PRK07246 70 APDFSQVARHIYDLIEDCIFVAHNVKFDANLLAEALFLEGYEL-----------RTP-RVDTVELAQVF--F-PT--LEK 132 (820)
T ss_pred CCCHHHHHHHHHHHhCCCEEEEECcHHHHHHHHHHHHHcCCCC-----------CCC-ceeHHHHHHHH--h-CC--CCC
Confidence 444444444432 23689999999999999987762 11110 012 36877665421 1 00 124
Q ss_pred CChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhCC
Q 007386 292 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGI 362 (605)
Q Consensus 292 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg~ 362 (605)
.+|..+.+.+ .++ ....|.|-.||++|+.+|.+|...++.
T Consensus 133 ~~L~~L~~~l-----------------------gl~--------~~~~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 133 YSLSHLSREL-----------------------NID--------LADAHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred CCHHHHHHHc-----------------------CCC--------CCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 5676653321 111 135699999999999999999887743
No 34
>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=94.05 E-value=0.1 Score=49.42 Aligned_cols=16 Identities=19% Similarity=0.090 Sum_probs=14.6
Q ss_pred cccchhhhHHHHHHHH
Q 007386 338 VKHEAGYDAFMTGCVF 353 (605)
Q Consensus 338 ~~HEAGyDA~mTG~vF 353 (605)
..|.|..||++|+.+|
T Consensus 136 ~~H~Al~DA~at~~l~ 151 (152)
T cd06144 136 GEHSSVEDARAAMRLY 151 (152)
T ss_pred CCcCcHHHHHHHHHHh
Confidence 4699999999999987
No 35
>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=93.95 E-value=0.28 Score=59.08 Aligned_cols=101 Identities=20% Similarity=0.128 Sum_probs=61.0
Q ss_pred hhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhc-CCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccC
Q 007386 214 ASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFF-GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKS 290 (605)
Q Consensus 214 ~~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~-~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~ 290 (605)
.+--|..++..|.+ .+.++||||.-+|+.+|-+.|. .-+|. +-...+||--++...-+ ...
T Consensus 63 ~ap~~~ev~~~l~~~l~~~~~VahN~~fD~~fL~~~~~~~g~~~-----------~~~~~iDt~~l~~~~~p-----~~~ 126 (850)
T TIGR01407 63 QAPYFSQVAQEIYDLLEDGIFVAHNVHFDLNFLAKALKDCGYEP-----------LPKPRIDTVELAQIFFP-----TEE 126 (850)
T ss_pred CCCCHHHHHHHHHHHhCCCEEEEeCcHHHHHHHHHHHHHcCCCC-----------CCCCeEeHHHHHHHhcC-----CCC
Confidence 34455555554432 3678999999999999987761 11120 01135777555432100 012
Q ss_pred CCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 291 STSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 291 ~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
+.+|..+.+.+ .++ ....|.|-.||.+|+.+|.+|...+.
T Consensus 127 ~~~L~~l~~~~-----------------------gi~--------~~~~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 127 SYQLSELSEAL-----------------------GLT--------HENPHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred CCCHHHHHHHC-----------------------CCC--------CCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 45676653321 011 13579999999999999999988775
No 36
>KOG4483 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.93 E-value=0.088 Score=56.91 Aligned_cols=59 Identities=22% Similarity=0.413 Sum_probs=50.7
Q ss_pred cceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 007386 423 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 423 ~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
.+++=+.+||.+.++.|+...|+ .|+... +.|.|+|||.||-+|++.-.+.+.|..+-.
T Consensus 391 pHVlEIydfp~efkteDll~~f~-~yq~kg-fdIkWvDdthalaVFss~~~AaeaLt~kh~ 449 (528)
T KOG4483|consen 391 PHVLEIYDFPDEFKTEDLLKAFE-TYQNKG-FDIKWVDDTHALAVFSSVNRAAEALTLKHD 449 (528)
T ss_pred cceeEeccCchhhccHHHHHHHH-HhhcCC-ceeEEeecceeEEeecchHHHHHHhhccCc
Confidence 46677889999999999999997 677765 589999999999999999999998876443
No 37
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=93.86 E-value=0.48 Score=49.18 Aligned_cols=85 Identities=21% Similarity=0.172 Sum_probs=52.5
Q ss_pred CCCeEEechhhhHHHHHHHHhcC-CCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhcc
Q 007386 228 EKKLIVGHNCFLDIAHIYSKFFG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 306 (605)
Q Consensus 228 s~kpiVgHN~~~Dl~~l~~~F~~-pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~ 306 (605)
.+.++||||.-+|+.+|-+.+.. -+|. +.+..+||--++.. .+....-+|+.+.+.+
T Consensus 146 ~~~v~VaHNa~FD~~fL~~~l~r~g~~~-----------~~~~~ldtl~la~~------~~~~~~~~L~~L~~~l----- 203 (257)
T PRK08517 146 GDSVFVAHNVNFDYNFISRSLEEIGLGP-----------LLNRKLCTIDLAKR------TIESPRYGLSFLKELL----- 203 (257)
T ss_pred CCCeEEEECHHHHHHHHHHHHHHcCCCC-----------CCCCcEehHHHHHH------HccCCCCCHHHHHHHc-----
Confidence 35689999999999999776621 1111 11234566444432 1111244566653321
Q ss_pred cCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 007386 307 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 360 (605)
Q Consensus 307 ~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~l 360 (605)
.++ ....|.|-.||.+|+.+|.++...+
T Consensus 204 ------------------gi~--------~~~~HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 204 ------------------GIE--------IEVHHRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred ------------------CcC--------CCCCCChHHHHHHHHHHHHHHHHHh
Confidence 111 1367999999999999999998776
No 38
>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=93.72 E-value=0.14 Score=49.02 Aligned_cols=79 Identities=20% Similarity=0.225 Sum_probs=48.6
Q ss_pred CCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhccc
Q 007386 228 EKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIAL 307 (605)
Q Consensus 228 s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~~ 307 (605)
.+.++||||.-+|+-+|=. ..|.++||-.|+....+. .....+-+|..+...+..
T Consensus 83 ~~~vlVgHn~~fD~~fL~~-------------------~~~~~iDT~~l~~~~~~~--~~~~~~~~L~~L~~~~~~---- 137 (161)
T cd06137 83 PDTILVGHSLQNDLDALRM-------------------IHTRVVDTAILTREAVKG--PLAKRQWSLRTLCRDFLG---- 137 (161)
T ss_pred CCcEEEeccHHHHHHHHhC-------------------cCCCeeEehhhhhhccCC--CcCCCCccHHHHHHHHCC----
Confidence 3489999999999987731 146789998887642211 000024567765332100
Q ss_pred CCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHH
Q 007386 308 GSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFA 354 (605)
Q Consensus 308 ~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~ 354 (605)
. .++ .....|.|-.||.+|+.+|+
T Consensus 138 ---------~-------~~~-------~~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 138 ---------L-------KIQ-------GGGEGHDSLEDALAAREVVL 161 (161)
T ss_pred ---------c-------hhc-------CCCCCCCcHHHHHHHHHHhC
Confidence 0 111 11346999999999999874
No 39
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=93.71 E-value=0.28 Score=59.60 Aligned_cols=86 Identities=24% Similarity=0.232 Sum_probs=55.2
Q ss_pred CCCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhc
Q 007386 228 EKKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQI 305 (605)
Q Consensus 228 s~kpiVgHN~~~Dl~~l~~~F--~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l 305 (605)
.+.++||||.-+|+.+|-+.| .| +|.. ....+||=-++... + .. ..+-+|+.+.+.+
T Consensus 83 ~~~~~VaHN~~FD~~fL~~~~~~~g-~~~~-----------~~~~iDt~~la~~~--~-p~--~~~~~L~~l~~~l---- 141 (928)
T PRK08074 83 EGAYFVAHNVHFDLNFLNEELERAG-YTEI-----------HCPKLDTVELARIL--L-PT--AESYKLRDLSEEL---- 141 (928)
T ss_pred CCCeEEEEChHHHHHHHHHHHHHcC-CCCC-----------CCCeeeHHHHHHHh--c-CC--CCCCCHHHHHHhC----
Confidence 478999999999999997766 22 2210 01357775554321 0 00 1244566654322
Q ss_pred ccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 306 ALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 306 ~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
.+ ..+..|.|-+||++|+.+|.+|.+.+.
T Consensus 142 -------------------~i--------~~~~~H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 142 -------------------GL--------EHDQPHRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred -------------------CC--------CCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 01 124679999999999999999988875
No 40
>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=93.44 E-value=0.35 Score=60.16 Aligned_cols=102 Identities=25% Similarity=0.310 Sum_probs=64.5
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhcC-CCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhc
Q 007386 212 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFFG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMK 288 (605)
Q Consensus 212 l~~~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~~-pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~ 288 (605)
+.++.-|..+++.+.+ .+.++||||.-+|+.+|-+.|.. -+|. +...++||--++... ...
T Consensus 251 L~~ap~~~evl~~f~~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~-----------~~~~~IDTl~lar~l---~p~-- 314 (1213)
T TIGR01405 251 LENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEP-----------LENPVIDTLELARAL---NPE-- 314 (1213)
T ss_pred HhCCCCHHHHHHHHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCc-----------cCCCEeEHHHHHHHH---hcc--
Confidence 3444445555554433 46799999999999999987721 1221 113478997776532 111
Q ss_pred cCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 007386 289 KSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 360 (605)
Q Consensus 289 ~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~l 360 (605)
.+..+|..+...+ .++ ....|.|-+||.+|+.+|.+|...+
T Consensus 315 ~k~~kL~~Lak~l-----------------------gi~--------~~~~HrAl~DA~aTa~I~~~ll~~l 355 (1213)
T TIGR01405 315 YKSHRLGNICKKL-----------------------GVD--------LDDHHRADYDAEATAKVFKVMVEQL 355 (1213)
T ss_pred CCCCCHHHHHHHc-----------------------CCC--------CCCCcCHHHHHHHHHHHHHHHHHHH
Confidence 1356777764322 011 1237999999999999999998766
No 41
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=92.75 E-value=0.4 Score=60.55 Aligned_cols=103 Identities=21% Similarity=0.226 Sum_probs=64.0
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhcCC-CCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhc
Q 007386 212 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFFGP-LPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMK 288 (605)
Q Consensus 212 l~~~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~~p-LP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~ 288 (605)
+..+.-+..+++.+.+ .+.++|+||.-+|+.+|-+.+..- +|. +...++||=-++... ...
T Consensus 480 L~~aps~~EaL~~f~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~-----------l~~~~IDTLelar~l---~p~-- 543 (1437)
T PRK00448 480 VKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEK-----------IKNPVIDTLELSRFL---YPE-- 543 (1437)
T ss_pred HcCCCCHHHHHHHHHHHhCCCEEEEeCccccHHHHHHHHHHcCCcc-----------ccccceeHHHHHHHH---cCc--
Confidence 4455677777777766 688999999999999886655211 211 112356775544321 110
Q ss_pred cCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 289 KSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 289 ~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
....+|..+... + .+. ....|.|-+||++|+.+|.+|+..+.
T Consensus 544 ~k~~kL~~LAk~----l-------------------GL~--------~~~~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 544 LKSHRLNTLAKK----F-------------------GVE--------LEHHHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred cccccHHHHHHH----c-------------------CCC--------CCCCcChHHHHHHHHHHHHHHHHHHH
Confidence 124456665322 1 011 12349999999999999999987763
No 42
>smart00362 RRM_2 RNA recognition motif.
Probab=92.70 E-value=0.58 Score=36.14 Aligned_cols=54 Identities=28% Similarity=0.401 Sum_probs=43.6
Q ss_pred EEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-cC----ceEEEEecchhhHHHHHHHhc
Q 007386 426 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DE----TAVFVQFSRAEMVSKFLDLKG 482 (605)
Q Consensus 426 v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-dd----tsa~V~l~~~e~~~~~L~~~~ 482 (605)
+++.|.|..++..+|++.|. .||+. ..+... +. ..|||.|.+.+.++..+..++
T Consensus 2 v~i~~l~~~~~~~~l~~~~~-~~g~v--~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~ 60 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFS-KFGPI--ESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALN 60 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHH-hcCCE--EEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhC
Confidence 68889999999999999996 78875 344444 44 799999999999999876554
No 43
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=92.45 E-value=0.5 Score=47.06 Aligned_cols=22 Identities=27% Similarity=0.179 Sum_probs=19.3
Q ss_pred cccchhhhHHHHHHHHHHHHHH
Q 007386 338 VKHEAGYDAFMTGCVFAQACSH 359 (605)
Q Consensus 338 ~~HEAGyDA~mTG~vF~kL~~~ 359 (605)
..|.|-+||++|+.+|.+|...
T Consensus 147 ~~HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 147 RGHNSLEDARMTARVYESFLES 168 (195)
T ss_pred CCcCCHHHHHHHHHHHHHHHhh
Confidence 3599999999999999998654
No 44
>PRK07883 hypothetical protein; Validated
Probab=91.81 E-value=0.87 Score=52.39 Aligned_cols=88 Identities=24% Similarity=0.192 Sum_probs=56.1
Q ss_pred CCeEEechhhhHHHHHHHHhc-CCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhccc
Q 007386 229 KKLIVGHNCFLDIAHIYSKFF-GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIAL 307 (605)
Q Consensus 229 ~kpiVgHN~~~Dl~~l~~~F~-~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~~ 307 (605)
+.++||||.-+|+.+|-..|. .-+|. ..+..+||--++... + ......+.+|..+.+.+
T Consensus 95 ~~~lVaHNa~FD~~fL~~~~~r~g~~~-----------~~~~~iDTl~lar~l--~-~~~~~~~~~L~~L~~~~------ 154 (557)
T PRK07883 95 GAVLVAHNAPFDIGFLRAAAARCGYPW-----------PGPPVLCTVRLARRV--L-PRDEAPNVRLSTLARLF------ 154 (557)
T ss_pred CCEEEEeCcHHHHHHHHHHHHHcCCCC-----------CCCCcEecHHHHHHh--c-ccCCCCCCCHHHHHHHC------
Confidence 689999999999999987772 11221 012457887665431 1 00011345677764321
Q ss_pred CCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 308 GSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 308 ~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
.++ ....|.|-.||.+|+.+|.+++..++
T Consensus 155 -----------------gi~--------~~~~H~Al~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 155 -----------------GAT--------TTPTHRALDDARATVDVLHGLIERLG 183 (557)
T ss_pred -----------------Ccc--------cCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 011 13469999999999999999988875
No 45
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=90.75 E-value=0.12 Score=47.29 Aligned_cols=15 Identities=40% Similarity=0.346 Sum_probs=14.3
Q ss_pred ccchhhhHHHHHHHH
Q 007386 339 KHEAGYDAFMTGCVF 353 (605)
Q Consensus 339 ~HEAGyDA~mTG~vF 353 (605)
.|.|..||++|..+|
T Consensus 150 ~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 150 AHDALDDARATAELF 164 (164)
T ss_dssp TTSHHHHHHHHHHHH
T ss_pred CcChHHHHHHHhCcC
Confidence 899999999999987
No 46
>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=90.63 E-value=1.3 Score=34.40 Aligned_cols=57 Identities=23% Similarity=0.368 Sum_probs=44.4
Q ss_pred EEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEec----CceEEEEecchhhHHHHHHHhcc
Q 007386 426 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVD----ETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 426 v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~id----dtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
+++.|.|..++..+|++.|. .||++.-..+.+-. ...|||.|.+.+.+...++....
T Consensus 2 i~i~~l~~~~~~~~i~~~~~-~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~ 62 (74)
T cd00590 2 LFVGNLPPDVTEEDLRELFS-KFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNG 62 (74)
T ss_pred EEEeCCCCccCHHHHHHHHH-hcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence 67899999999999999996 57876433344322 46899999999999998776555
No 47
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=90.27 E-value=1.6 Score=41.36 Aligned_cols=57 Identities=12% Similarity=0.224 Sum_probs=46.1
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-c------CceEEEEecchhhHHHHHHHhcc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-D------ETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-d------dtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
..+|+-+.|...+..+|++.|. .||.+ .+|..+ | ...|||.|.+.++|+..|..++.
T Consensus 35 ~~lfVgnL~~~~te~~L~~~F~-~~G~I--~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng 98 (144)
T PLN03134 35 TKLFIGGLSWGTDDASLRDAFA-HFGDV--VDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDG 98 (144)
T ss_pred CEEEEeCCCCCCCHHHHHHHHh-cCCCe--EEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCC
Confidence 3489999999999999999996 79975 344443 3 25799999999999999877654
No 48
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=90.23 E-value=1 Score=43.82 Aligned_cols=75 Identities=21% Similarity=0.195 Sum_probs=47.0
Q ss_pred CCeEEechh-hhHHHHHHHHh--cCC-CCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhh
Q 007386 229 KKLIVGHNC-FLDIAHIYSKF--FGP-LPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQ 304 (605)
Q Consensus 229 ~kpiVgHN~-~~Dl~~l~~~F--~~p-LP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~ 304 (605)
+.++||||. -+|+-+|-+.| +|. +|.. +..+||=-++.. + . .+|+.++..+.
T Consensus 98 ~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~------------~~~iDtl~l~r~---~---~----~~L~~l~~~~~-- 153 (177)
T cd06136 98 PICLVAHNGNRFDFPILRSELERLGTKLPDD------------ILCVDSLPAFRE---L---D----QSLGSLYKRLF-- 153 (177)
T ss_pred CCEEEEcCCcccCHHHHHHHHHHcCCCCCCC------------CEEEEeHHHHhh---h---H----hhHHHHHHHHh--
Confidence 458999998 79999998777 331 1210 123587555432 1 1 15777644211
Q ss_pred cccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHH
Q 007386 305 IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQ 355 (605)
Q Consensus 305 l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~k 355 (605)
++ .....|.|-.||..|+.||++
T Consensus 154 --------------------~~--------~~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 154 --------------------GQ--------EPKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred --------------------CC--------CcccccchHHHHHHHHHHHhh
Confidence 01 113569999999999999975
No 49
>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=89.65 E-value=0.85 Score=41.01 Aligned_cols=54 Identities=28% Similarity=0.345 Sum_probs=35.9
Q ss_pred eEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe----cCceEEEEecchhhHHHHHHHhccc
Q 007386 425 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV----DETAVFVQFSRAEMVSKFLDLKGSL 484 (605)
Q Consensus 425 ~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i----ddtsa~V~l~~~e~~~~~L~~~~~~ 484 (605)
+|.+-|.++..+..+|++.|+ .|| .|.|| +++.+||-|..++.|+.++......
T Consensus 3 il~~~g~~~~~~re~iK~~f~-~~g-----~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFS-QFG-----EVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT--SS-------EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred EEEEecCCCCcCHHHHHHHHH-hcC-----CcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 466777899999999999986 577 34566 5999999999999999999888774
No 50
>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=89.42 E-value=0.62 Score=44.48 Aligned_cols=17 Identities=24% Similarity=0.077 Sum_probs=14.9
Q ss_pred CcccchhhhHHHHHHHH
Q 007386 337 GVKHEAGYDAFMTGCVF 353 (605)
Q Consensus 337 ~~~HEAGyDA~mTG~vF 353 (605)
+..|.|-.||.+|+.+|
T Consensus 140 ~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 140 RQGHSSVEDARATMELY 156 (157)
T ss_pred CCCcCcHHHHHHHHHHh
Confidence 35699999999999887
No 51
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=89.17 E-value=1.5 Score=46.54 Aligned_cols=24 Identities=21% Similarity=0.079 Sum_probs=20.6
Q ss_pred cccchhhhHHHHHHHHHHHHHHhC
Q 007386 338 VKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 338 ~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
..|.|..||+.|+.+|.+++...|
T Consensus 179 ~aHrAl~Da~Ata~ll~~~l~~~~ 202 (294)
T PRK09182 179 EGHRAVDDCQALLELLARPLPETG 202 (294)
T ss_pred CCcChHHHHHHHHHHHHHHHhhcC
Confidence 469999999999999998876555
No 52
>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=88.83 E-value=1.9 Score=40.81 Aligned_cols=82 Identities=20% Similarity=0.151 Sum_probs=49.4
Q ss_pred eEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhcccC
Q 007386 231 LIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALG 308 (605)
Q Consensus 231 piVgHN~~~Dl~~l~~~F--~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~~~ 308 (605)
.++.||+-.|...+.+.+ .+-.+ ....+...+||..++...-+ . ....+|..+...+
T Consensus 92 ~~~v~~~~~d~~~l~~~~~~~~~~~---------~~~~~~~~~D~~~~~~~~~~---~--~~~~~L~~l~~~~------- 150 (176)
T cd06133 92 YAFVTWGDWDLKDLLQNQCKYKIIN---------LPPFFRQWIDLKKEFAKFYG---L--KKRTGLSKALEYL------- 150 (176)
T ss_pred eEEEeecHhhHHHHHHHHHHhcCCC---------CcccccceEEHHHHHHHHhC---C--CCCCCHHHHHHHC-------
Confidence 555666678877666543 21111 01234567899888753211 1 1366777764332
Q ss_pred CcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHH
Q 007386 309 SKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQA 356 (605)
Q Consensus 309 ~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL 356 (605)
.++ ..+..|.|=+||..|+.+|.+|
T Consensus 151 ----------------gi~-------~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 151 ----------------GLE-------FEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred ----------------CCC-------CCCCCcCcHHHHHHHHHHHHHh
Confidence 111 1257899999999999999887
No 53
>smart00360 RRM RNA recognition motif.
Probab=88.28 E-value=1.8 Score=33.12 Aligned_cols=52 Identities=23% Similarity=0.382 Sum_probs=39.5
Q ss_pred eCCCCcCcHHHHHHHHHhhhCCCceeEEEEecC------ceEEEEecchhhHHHHHHHhc
Q 007386 429 WGFPSHLKAWDIRECISKVYGPTSVISVYHVDE------TAVFVQFSRAEMVSKFLDLKG 482 (605)
Q Consensus 429 ~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~idd------tsa~V~l~~~e~~~~~L~~~~ 482 (605)
.|+|..++..+|++.|. .||++.-..|.. +. ..|||.|.+.+.+...+..+.
T Consensus 2 ~~l~~~~~~~~l~~~f~-~~g~v~~~~i~~-~~~~~~~~~~a~v~f~~~~~a~~a~~~~~ 59 (71)
T smart00360 2 GNLPPDVTEEELRELFS-KFGKIESVRLVR-DKDTGKSKGFAFVEFESEEDAEKALEALN 59 (71)
T ss_pred CCCCcccCHHHHHHHHH-hhCCEeEEEEEe-CCCCCCCCceEEEEeCCHHHHHHHHHHcC
Confidence 36789999999999996 789764333333 33 389999999999999876555
No 54
>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=87.54 E-value=1.6 Score=42.50 Aligned_cols=33 Identities=21% Similarity=0.203 Sum_probs=22.6
Q ss_pred ccHHHHHHH----HhcCCCeEEech-hhhHHHHHHHHh
Q 007386 216 IGFRHVIDL----LSSEKKLIVGHN-CFLDIAHIYSKF 248 (605)
Q Consensus 216 iGfr~v~~~----l~~s~kpiVgHN-~~~Dl~~l~~~F 248 (605)
..+..+++. +.+.+.++|||| .-+|+.+|-+.|
T Consensus 67 ~~~~~~l~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~ 104 (183)
T cd06138 67 LSEYEFIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAF 104 (183)
T ss_pred CCHHHHHHHHHHHHccCCCcEEeeCchhhHHHHHHHHH
Confidence 444444443 333567899998 579999998776
No 55
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=86.73 E-value=2.6 Score=46.09 Aligned_cols=39 Identities=15% Similarity=0.204 Sum_probs=31.6
Q ss_pred hhhhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh
Q 007386 210 MSIKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF 248 (605)
Q Consensus 210 ~~l~~~iGfr~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F 248 (605)
+.+.++..|..+++.|.. .+.++|+||.-+|+.||-+.|
T Consensus 104 e~La~AP~f~eVl~el~~fL~g~vLVaHNA~FD~~FL~~e~ 144 (377)
T PRK05601 104 EEFAQGKRFSQILKPLDRLIDGRTLILHNAPRTWGFIVSEA 144 (377)
T ss_pred HHHhcCCCHHHHHHHHHHHhCCCEEEEECcHHHHHHHHHHH
Confidence 346667888888887753 478999999999999998765
No 56
>PTZ00315 2'-phosphotransferase; Provisional
Probab=86.36 E-value=3.3 Score=47.76 Aligned_cols=108 Identities=13% Similarity=0.045 Sum_probs=64.6
Q ss_pred hhhhhhccHHHHHHHH----hcCC--------CeEEechhhhHHH-HHHHHh--c--CCCCCCHHHHHHHHHhhCCCCcc
Q 007386 210 MSIKASIGFRHVIDLL----SSEK--------KLIVGHNCFLDIA-HIYSKF--F--GPLPLTAEEFISSVNKYFPHIID 272 (605)
Q Consensus 210 ~~l~~~iGfr~v~~~l----~~s~--------kpiVgHN~~~Dl~-~l~~~F--~--~pLP~~~~EFk~~l~~~FP~IyD 272 (605)
+.|.++.-|..|+..+ ..+. ..+|+||+=+|+. +|.+.+ + ..+|. .|...+|
T Consensus 122 e~V~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~-----------~f~~wid 190 (582)
T PTZ00315 122 SMVSRADPFPVVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPL-----------SFQRWCN 190 (582)
T ss_pred HHHhcCCCHHHHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCc-----------ccceEEE
Confidence 4466677777766544 3332 4699999999996 565544 2 25554 3556667
Q ss_pred hh-HHhhhc-hh-----HHHhhccCCCChHHHHHhhhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhh
Q 007386 273 TK-ILLNSN-SI-----LQQRMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYD 345 (605)
Q Consensus 273 TK-~L~~~~-~~-----l~~~~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyD 345 (605)
.| +++... +. ..........+|..+.+.+ ++. -.|..|.|=.|
T Consensus 191 Lk~~lar~l~p~~~~~~~~~~~~~~~~~L~~al~~l-----------------------gL~-------~eGr~HrAlDD 240 (582)
T PTZ00315 191 LKKYMSQLGFGNGSGCGGGATPPLGPSDMPDMLQML-----------------------GLP-------LQGRHHSGIDD 240 (582)
T ss_pred hHHHHHHHhCccccccccccccccCCcCHHHHHHHC-----------------------CCC-------CCCCCcCcHHH
Confidence 54 554321 00 0000011345677765432 111 23678999999
Q ss_pred HHHHHHHHHHHHH
Q 007386 346 AFMTGCVFAQACS 358 (605)
Q Consensus 346 A~mTG~vF~kL~~ 358 (605)
|..|+.+|.+|..
T Consensus 241 A~ntA~L~~~Ll~ 253 (582)
T PTZ00315 241 CRNIAAVLCELLR 253 (582)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999976
No 57
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=86.13 E-value=3.7 Score=41.43 Aligned_cols=82 Identities=22% Similarity=0.279 Sum_probs=50.6
Q ss_pred CeEEechhhhHHHHHHHHh---cCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhcc-CCCChHHHHHhhhhhc
Q 007386 230 KLIVGHNCFLDIAHIYSKF---FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKK-SSTSLSKAFSVLCPQI 305 (605)
Q Consensus 230 kpiVgHN~~~Dl~~l~~~F---~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~-~~tsL~~l~~~l~~~l 305 (605)
.++|+||-.+|+.++-..+ ..+.| --.++||=-++... ... ...+|..+ +..+
T Consensus 96 ~~~Vahna~fD~~fl~~~~~~~~~~~~-------------~~~~~~t~~~~r~~------~~~~~~~~L~~l----~~~~ 152 (243)
T COG0847 96 RLLVAHNAAFDVGFLRVESERLGIEIP-------------GDPVLDTLALARRH------FPGFDRSSLDAL----AERL 152 (243)
T ss_pred CeEEEEchhhcHHHHHHHHHHcCCCcc-------------cCceehHHHHHHHH------cCCCccchHHHH----HHHc
Confidence 8999999999999998776 22233 12344554444321 111 24455554 3322
Q ss_pred ccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHH
Q 007386 306 ALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSH 359 (605)
Q Consensus 306 ~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~ 359 (605)
+++. .....|.|-.||++|+.+|+.+...
T Consensus 153 -------------------gi~~------~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 153 -------------------GIDR------NPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred -------------------CCCc------CCcCCcchHHHHHHHHHHHHHHHhc
Confidence 1111 1134599999999999999999774
No 58
>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=85.92 E-value=3.3 Score=44.88 Aligned_cols=68 Identities=15% Similarity=0.222 Sum_probs=51.6
Q ss_pred cceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecC-------ceEEEEecchhhHHHHHHHhcccccCCCCccc
Q 007386 423 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE-------TAVFVQFSRAEMVSKFLDLKGSLDRNNDPISV 493 (605)
Q Consensus 423 ~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~idd-------tsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~ 493 (605)
...+|+-+.|..++..+|+++|+ .||++ .+|..+-| ..|||.|.+.++|+..+..++..+-.+..+.|
T Consensus 107 ~~~LfVgnLp~~~te~~L~~lF~-~~G~V--~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V 181 (346)
T TIGR01659 107 GTNLIVNYLPQDMTDRELYALFR-TIGPI--NTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV 181 (346)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHH-hcCCE--EEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence 45689999999999999999996 78985 45555432 36999999999999998877665444444333
No 59
>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=85.58 E-value=2.7 Score=36.29 Aligned_cols=57 Identities=12% Similarity=0.038 Sum_probs=47.9
Q ss_pred EEEeCCCC--cCcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 007386 426 VIVWGFPS--HLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 426 v~~~~fp~--~~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
..-..+++ .|+-.++.+-+.+-|+.. .+.|.|+||-.=||.+......++.++....
T Consensus 11 ~~rf~~~~~~~~~~~~L~~ev~~rf~l~-~f~lKYlDde~e~v~lssd~eLeE~~rl~~~ 69 (81)
T cd06396 11 SQSFLVSDSENTTWASVEAMVKVSFGLN-DIQIKYVDEENEEVSVNSQGEYEEALKSAVR 69 (81)
T ss_pred EEEEEecCCCCCCHHHHHHHHHHHhCCC-cceeEEEcCCCCEEEEEchhhHHHHHHHHHh
Confidence 44445666 899999999999999977 5689999999999999999999888876655
No 60
>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=85.06 E-value=2.9 Score=33.56 Aligned_cols=39 Identities=18% Similarity=0.249 Sum_probs=26.0
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~~~~~~~~~~~vv~ 186 (605)
+.+++.|+++|++||++.. +.++.+.+. + .+..+.++|+
T Consensus 23 ~~f~pm~~~~R~~iH~~a~--~~gL~s~S~-g-~~~~R~vvv~ 61 (63)
T PF01424_consen 23 LEFPPMNSFERKLIHELAE--YYGLKSKSE-G-EGPNRRVVVS 61 (63)
T ss_dssp EEEEC--SHHHHHHHHHHH--HCTEEEEEE-S-SSSSSEEEEE
T ss_pred EEECCCCHHHHHHHHHHHH--HCCCEEEEe-c-CCCCeEEEEE
Confidence 4567789999999999987 678887765 3 3334455544
No 61
>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=84.85 E-value=3.7 Score=35.42 Aligned_cols=60 Identities=15% Similarity=0.208 Sum_probs=50.8
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCC--ceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPT--SVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~--~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
.-+.-..+|+.|.-.++++.+.+.|+.. +.+.|+|+||--=||.+.+..+.++-+++...
T Consensus 9 ~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~~~ 70 (82)
T cd06407 9 EEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVYRS 70 (82)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHHHH
Confidence 3356677899999999999999988875 46789999999999999999998887776655
No 62
>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=83.32 E-value=4.1 Score=38.17 Aligned_cols=104 Identities=23% Similarity=0.269 Sum_probs=58.6
Q ss_pred HHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhh
Q 007386 223 DLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLC 302 (605)
Q Consensus 223 ~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~ 302 (605)
+.|...+...||||+=.|+..|++.+ ......++||..++....+ ..+.+|..+...+.
T Consensus 71 ~ll~~~~i~kv~~n~~~D~~~L~~~~---------------~i~~~~~~D~~l~~~~l~~------~~~~~L~~L~~~~l 129 (176)
T PF01612_consen 71 ELLEDPNIIKVGHNAKFDLKWLYRSF---------------GIDLKNVFDTMLAAYLLDP------TRSYSLKDLAEEYL 129 (176)
T ss_dssp HHHTTTTSEEEESSHHHHHHHHHHHH---------------TS--SSEEEHHHHHHHTTT------STTSSHHHHHHHHH
T ss_pred HHHhCCCccEEEEEEechHHHHHHHh---------------ccccCCccchhhhhhcccc------cccccHHHHHHHHh
Confidence 44556667899999999999999872 2223468899444322111 11267888765543
Q ss_pred hhcccCCcccccccCCCceeeeeecccc-ccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 007386 303 PQIALGSKSTHLALQPSVKVEVEVDDIR-SSNWNSGVKHEAGYDAFMTGCVFAQACSHL 360 (605)
Q Consensus 303 ~~l~~~~~~~~~~~~p~v~i~v~~~~~~-~~~~~~~~~HEAGyDA~mTG~vF~kL~~~l 360 (605)
..+... +.. ...... ..........-|+.||..|-.++-+|..+|
T Consensus 130 ~~~~~~-~~~------------~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 130 GNIDLD-KKE------------QMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp SEEE-G-HCC------------TTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred hhccCc-HHH------------hhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 311000 000 000000 000011235679999999999999998776
No 63
>PRK11779 sbcB exonuclease I; Provisional
Probab=80.99 E-value=7.3 Score=44.14 Aligned_cols=23 Identities=17% Similarity=0.067 Sum_probs=20.5
Q ss_pred CcccchhhhHHHHHHHHHHHHHH
Q 007386 337 GVKHEAGYDAFMTGCVFAQACSH 359 (605)
Q Consensus 337 ~~~HEAGyDA~mTG~vF~kL~~~ 359 (605)
+..|.|=+||++|+.++..|...
T Consensus 175 ~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 175 ENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHh
Confidence 46799999999999999998765
No 64
>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=80.24 E-value=4.2 Score=45.76 Aligned_cols=56 Identities=20% Similarity=0.374 Sum_probs=46.3
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHh
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLK 481 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~ 481 (605)
.+||+-+.|..++..+|+++|+ .||++..+.|. -+...|||.|.+.|+|+..+...
T Consensus 3 ~vv~V~nLp~~~te~~L~~~f~-~fG~V~~v~i~-~~k~~afVef~~~e~A~~Ai~~~ 58 (481)
T TIGR01649 3 PVVHVRNLPQDVVEADLVEALI-PFGPVSYVMML-PGKRQALVEFEDEESAKACVNFA 58 (481)
T ss_pred cEEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEE-CCCCEEEEEeCchHHHHHHHHHh
Confidence 3689999999999999999996 89987432222 27789999999999999998753
No 65
>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=80.04 E-value=8.2 Score=29.44 Aligned_cols=27 Identities=19% Similarity=0.011 Sum_probs=20.8
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEE
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYLR 172 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v~ 172 (605)
+.++++|+++|++||+++.... +.+.+
T Consensus 20 ~~~~p~~~~~R~~vH~la~~~~--L~s~s 46 (59)
T cd02325 20 LELPPMNSYERKLIHDLAEYYG--LKSES 46 (59)
T ss_pred EEcCCCCHHHHHHHHHHHHHCC--CEEEE
Confidence 5678889999999999987654 55443
No 66
>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=79.41 E-value=5.3 Score=43.32 Aligned_cols=56 Identities=16% Similarity=0.296 Sum_probs=45.6
Q ss_pred eEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-cC------ceEEEEecchhhHHHHHHHhcc
Q 007386 425 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DE------TAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 425 ~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-dd------tsa~V~l~~~e~~~~~L~~~~~ 483 (605)
.+|+-+.|..++..+|+++|+ .||.+ ..+..+ |. ..|||.|.+.++|+..+..++.
T Consensus 195 ~lfV~nLp~~vtee~L~~~F~-~fG~V--~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng 257 (346)
T TIGR01659 195 NLYVTNLPRTITDDQLDTIFG-KYGQI--VQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNN 257 (346)
T ss_pred eeEEeCCCCcccHHHHHHHHH-hcCCE--EEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence 489999999999999999996 78875 344444 43 4899999999999998877765
No 67
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=77.73 E-value=7.1 Score=41.34 Aligned_cols=58 Identities=10% Similarity=0.160 Sum_probs=46.2
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-c------CceEEEEecchhhHHHHHHHhccc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-D------ETAVFVQFSRAEMVSKFLDLKGSL 484 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-d------dtsa~V~l~~~e~~~~~L~~~~~~ 484 (605)
..+|+-+.|..|...+|+++|+ .||++. ++.-+ | ...+||.|.+.++|...+..++-.
T Consensus 270 ~~lfV~NL~~~~~e~~L~~~F~-~fG~v~--~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~ 334 (352)
T TIGR01661 270 YCIFVYNLSPDTDETVLWQLFG-PFGAVQ--NVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGY 334 (352)
T ss_pred cEEEEeCCCCCCCHHHHHHHHH-hCCCeE--EEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCC
Confidence 3589999999999999999996 899864 33332 4 357999999999998877776664
No 68
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=77.70 E-value=6.8 Score=41.51 Aligned_cols=58 Identities=26% Similarity=0.291 Sum_probs=46.5
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-cC------ceEEEEecchhhHHHHHHHhccc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DE------TAVFVQFSRAEMVSKFLDLKGSL 484 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-dd------tsa~V~l~~~e~~~~~L~~~~~~ 484 (605)
+.+|+-+.|..++..+|+++|+ .||++. +|.-+ |. ..|||.|.+.++|...|..++..
T Consensus 4 ~~l~V~nLp~~~~e~~l~~~F~-~~G~i~--~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~ 68 (352)
T TIGR01661 4 TNLIVNYLPQTMTQEEIRSLFT-SIGEIE--SCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGL 68 (352)
T ss_pred cEEEEeCCCCCCCHHHHHHHHH-ccCCEE--EEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccE
Confidence 4589999999999999999997 799874 44444 22 37999999999999988776653
No 69
>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=77.49 E-value=7.6 Score=38.32 Aligned_cols=106 Identities=15% Similarity=0.186 Sum_probs=62.0
Q ss_pred HHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHH-----hhccCCCChHHHH
Q 007386 224 LLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQ-----RMKKSSTSLSKAF 298 (605)
Q Consensus 224 ~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~-----~~~~~~tsL~~l~ 298 (605)
.|...+.+-|||++-.|+-.|++.|-..... + ...-.++||..++........ .+.....+|+.+-
T Consensus 77 ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~----~-----~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~ 147 (193)
T cd06146 77 LFEDPDVLKLGFGFKQDLKALSASYPALKCM----F-----ERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLV 147 (193)
T ss_pred HhCCCCeeEEEechHHHHHHHHHhcCccccc----c-----ccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHH
Confidence 3445556679999999999999877432110 0 112478999988764321100 0112356788875
Q ss_pred HhhhhhcccCCcccccccCCCceeeeeeccccccCC-----CCCcccchhhhHHHHHHHHHHHH
Q 007386 299 SVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNW-----NSGVKHEAGYDAFMTGCVFAQAC 357 (605)
Q Consensus 299 ~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~-----~~~~~HEAGyDA~mTG~vF~kL~ 357 (605)
+.+... ...++ ...+.| ...+.+-|..|||..-.+|-+|+
T Consensus 148 ~~~lg~---~l~K~----------------~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 148 QEVLGK---PLDKS----------------EQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHHhCC---CcCcc----------------cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 543211 00000 011223 23578899999999999999885
No 70
>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=76.54 E-value=6.6 Score=32.54 Aligned_cols=40 Identities=15% Similarity=0.188 Sum_probs=28.5
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~~~~~~~~~~~vv~ 186 (605)
..|++.|+++|++||.++.. |+++.+.+. ++ |..+.+||+
T Consensus 26 ~~l~PM~~~eRrivH~~~~~-~~~l~T~S~-G~-~~~R~vvI~ 65 (67)
T cd02644 26 VKLEPMNAYERRIIHDALAN-DEDVETESE-GE-GPYRRVVIS 65 (67)
T ss_pred eEeCCCCHHHHHHHHHHHHh-CCCceEEee-cC-CCCeEEEEE
Confidence 45788899999999999864 888887764 32 334555544
No 71
>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=76.20 E-value=12 Score=30.48 Aligned_cols=38 Identities=24% Similarity=0.124 Sum_probs=25.7
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~~~~~~~~~~~vv~ 186 (605)
+.+++.|+|||.|||++... -++.+.+. ++ + .+.++|+
T Consensus 24 ~~f~pm~sy~RllvH~la~~--~gL~s~s~-~~-~-~r~vvv~ 61 (63)
T cd02642 24 LELPPMNSYYRLLAHRVAQY--YGLDHNVD-NS-G-GKCVIVN 61 (63)
T ss_pred eEcCCCCcHHHHHHHHHHHH--hCCeeEee-cC-C-ceEEEEE
Confidence 55778899999999999654 56766554 22 2 3455554
No 72
>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=74.47 E-value=7.1 Score=32.04 Aligned_cols=29 Identities=21% Similarity=0.178 Sum_probs=24.2
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEe
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRV 173 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~ 173 (605)
+.|++.+++.|++||+.|. .+|++.+.+.
T Consensus 21 v~LePM~~~ERkIIH~~Lq-~~~~v~T~S~ 49 (62)
T cd02638 21 LLFPPLNSRRRYLIHQTVE-NRFLLSTFSV 49 (62)
T ss_pred EecCCCChHHHHHHHHHHh-cCCCceEEEc
Confidence 5688889999999999997 5788877664
No 73
>PLN03120 nucleic acid binding protein; Provisional
Probab=73.91 E-value=13 Score=38.76 Aligned_cols=53 Identities=21% Similarity=0.169 Sum_probs=43.4
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-c---CceEEEEecchhhHHHHHH
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-D---ETAVFVQFSRAEMVSKFLD 479 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-d---dtsa~V~l~~~e~~~~~L~ 479 (605)
..||+-|.|...+..||++.|+ .||.+. +|.-+ | ...|||.|.+.+.++..|.
T Consensus 5 rtVfVgNLs~~tTE~dLrefFS-~~G~I~--~V~I~~d~~~~GfAFVtF~d~eaAe~All 61 (260)
T PLN03120 5 RTVKVSNVSLKATERDIKEFFS-FSGDIE--YVEMQSENERSQIAYVTFKDPQGAETALL 61 (260)
T ss_pred CEEEEeCCCCCCCHHHHHHHHH-hcCCeE--EEEEeecCCCCCEEEEEeCcHHHHHHHHH
Confidence 4589999999999999999997 789763 33333 3 3589999999999999985
No 74
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=73.48 E-value=12 Score=35.40 Aligned_cols=98 Identities=18% Similarity=0.152 Sum_probs=59.0
Q ss_pred HHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhh
Q 007386 223 DLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLC 302 (605)
Q Consensus 223 ~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~ 302 (605)
+.|...+...||||+-.|+-.|.+.|.-. +..++||..++....+- ....+|+.+...+.
T Consensus 67 ~ll~~~~i~kv~~~~k~D~~~L~~~~g~~---------------~~~~~Dl~~aa~ll~~~-----~~~~~l~~l~~~~l 126 (170)
T cd06141 67 QLLEDPSILKVGVGIKGDARKLARDFGIE---------------VRGVVDLSHLAKRVGPR-----RKLVSLARLVEEVL 126 (170)
T ss_pred HHhcCCCeeEEEeeeHHHHHHHHhHcCCC---------------CCCeeeHHHHHHHhCCC-----cCCccHHHHHHHHc
Confidence 34555666789999999999987666322 33568999887543221 01247777755432
Q ss_pred hhcccCCcccccccCCCceeeeeeccccccCC-----CCCcccchhhhHHHHHHHHHHHH
Q 007386 303 PQIALGSKSTHLALQPSVKVEVEVDDIRSSNW-----NSGVKHEAGYDAFMTGCVFAQAC 357 (605)
Q Consensus 303 ~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~-----~~~~~HEAGyDA~mTG~vF~kL~ 357 (605)
..- ..++ .. ...+.| ..++.|-|+.||+.+-.++-+|.
T Consensus 127 ~~~---~~k~-----k~---------~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 127 GLP---LSKP-----KK---------VRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred Ccc---cCCC-----CC---------cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 110 0000 00 011222 24578999999999999988874
No 75
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=73.02 E-value=7.2 Score=43.19 Aligned_cols=77 Identities=17% Similarity=0.287 Sum_probs=53.7
Q ss_pred EEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecC-------ceEEEEecchhhHHHHHHHhcccccCCCCcccccchh
Q 007386 426 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE-------TAVFVQFSRAEMVSKFLDLKGSLDRNNDPISVLHPLA 498 (605)
Q Consensus 426 v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~idd-------tsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~~~~l~ 498 (605)
.|+=-.|++|+-.||+.+|. .||.+ .+|.-|-| .||||.+..++.+... .++|+....=-.+.||+-
T Consensus 37 lfVgqIprt~sE~dlr~lFe-~yg~V--~einl~kDk~t~~s~gcCFv~~~trk~a~~a---~~Alhn~ktlpG~~~pvq 110 (510)
T KOG0144|consen 37 LFVGQIPRTASEKDLRELFE-KYGNV--YEINLIKDKSTGQSKGCCFVKYYTRKEADEA---INALHNQKTLPGMHHPVQ 110 (510)
T ss_pred heeccCCccccHHHHHHHHH-HhCce--eEEEeecccccCcccceEEEEeccHHHHHHH---HHHhhcccccCCCCccee
Confidence 45556999999999999996 78864 67777743 7999999999888665 444443432224567776
Q ss_pred hhhcCCcccc
Q 007386 499 KLLEGGNTCA 508 (605)
Q Consensus 499 ~~~~~g~~~~ 508 (605)
.-..+|....
T Consensus 111 vk~Ad~E~er 120 (510)
T KOG0144|consen 111 VKYADGERER 120 (510)
T ss_pred ecccchhhhc
Confidence 6565554443
No 76
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=72.29 E-value=10 Score=44.32 Aligned_cols=66 Identities=12% Similarity=0.164 Sum_probs=52.3
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-c------CceEEEEecchhhHHHHHHHhcccccCCCCcc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-D------ETAVFVQFSRAEMVSKFLDLKGSLDRNNDPIS 492 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-d------dtsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~ 492 (605)
..+|+.|.|..|+..+|+++|+ .||.+. ++..+ | ...+||.|.+.+++..-+..++.++=.+..+.
T Consensus 205 ~rLfVgnLp~~vteedLk~lFs-~FG~I~--svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~Lr 277 (612)
T TIGR01645 205 NRIYVASVHPDLSETDIKSVFE-AFGEIV--KCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLR 277 (612)
T ss_pred ceEEeecCCCCCCHHHHHHHHh-hcCCee--EEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence 3589999999999999999996 799863 44443 2 24799999999999999999998764444333
No 77
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=72.10 E-value=10 Score=41.82 Aligned_cols=59 Identities=19% Similarity=0.259 Sum_probs=47.0
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-cC------ceEEEEecchhhHHHHHHHhcccc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DE------TAVFVQFSRAEMVSKFLDLKGSLD 485 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-dd------tsa~V~l~~~e~~~~~L~~~~~~~ 485 (605)
..+|+-+.|..++..+|++.|+ .||.+ .+|.++ |. ..|||.|.+.+.|...|..++..+
T Consensus 187 ~~l~v~nl~~~~te~~l~~~f~-~~G~i--~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~ 252 (457)
T TIGR01622 187 LKLYVGNLHFNITEQELRQIFE-PFGDI--EDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFE 252 (457)
T ss_pred CEEEEcCCCCCCCHHHHHHHHH-hcCCe--EEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcE
Confidence 4589999999999999999996 89976 345554 22 369999999999999887777643
No 78
>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=71.43 E-value=14 Score=35.12 Aligned_cols=100 Identities=15% Similarity=0.135 Sum_probs=57.7
Q ss_pred HHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhh
Q 007386 223 DLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLC 302 (605)
Q Consensus 223 ~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~ 302 (605)
+.|.+.+...|||++-.|+-.+.+.|--. +..++||..++....+ ....+|+.+.+.+.
T Consensus 61 ~lL~d~~i~Kvg~~~k~D~~~L~~~~gi~---------------~~~~~D~~~aa~ll~~------~~~~~L~~l~~~~l 119 (161)
T cd06129 61 MLLENPSIVKALHGIEGDLWKLLRDFGEK---------------LQRLFDTTIAANLKGL------PERWSLASLVEHFL 119 (161)
T ss_pred HHhCCCCEEEEEeccHHHHHHHHHHcCCC---------------cccHhHHHHHHHHhCC------CCCchHHHHHHHHh
Confidence 34555556679999999998887655211 2246799887653221 11347777755432
Q ss_pred h-hcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHH
Q 007386 303 P-QIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACS 358 (605)
Q Consensus 303 ~-~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~ 358 (605)
. .+ .+. . ...+-....-...+.|-|..||+..-.+|-+|.+
T Consensus 120 g~~l----~K~-------~----~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 120 GKTL----DKS-------I----SCADWSYRPLTEDQKLYAAADVYALLIIYTKLRN 161 (161)
T ss_pred CCCC----Ccc-------c----eeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 1 11 000 0 0000000111245789999999999999998854
No 79
>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=70.83 E-value=13 Score=33.89 Aligned_cols=52 Identities=17% Similarity=0.261 Sum_probs=42.0
Q ss_pred eCCCCcCcHHHHHHHHHhhhCCCce-eEEEEecCceEEEEecchhhHHHHHHH
Q 007386 429 WGFPSHLKAWDIRECISKVYGPTSV-ISVYHVDETAVFVQFSRAEMVSKFLDL 480 (605)
Q Consensus 429 ~~fp~~~k~~dI~~~~sk~fg~~~v-~~v~~iddtsa~V~l~~~e~~~~~L~~ 480 (605)
-+.-..|+.++|++.+..-|...++ .+|+|.|.++.|+.|.+.+.++..+..
T Consensus 52 ~~~~~~w~ls~Ir~v~~RRylLr~~alEiF~~d~~~~f~~F~~~~~~k~vv~~ 104 (108)
T cd01201 52 EELHGKWPFSEIRAIFSRRYLLQNTALELFLASRTSIFFAFPDQNAVKKVVYA 104 (108)
T ss_pred ccccceeeHHHHHHHHHHhhhcccceEEEEEeCCceEEEEeCcHHHHHHHHhh
Confidence 3445579999999988877776543 389999999999999999999887543
No 80
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=69.95 E-value=14 Score=40.83 Aligned_cols=56 Identities=25% Similarity=0.309 Sum_probs=46.4
Q ss_pred cceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEec-------CceEEEEecchhhHHHHHHHh
Q 007386 423 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVD-------ETAVFVQFSRAEMVSKFLDLK 481 (605)
Q Consensus 423 ~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~id-------dtsa~V~l~~~e~~~~~L~~~ 481 (605)
...||+-+.|..++..+|+++|+ .||.+ .+|..+- ...|||.|.+.++|...|.+.
T Consensus 89 ~~~l~V~nlp~~~~~~~l~~~F~-~~G~v--~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~ 151 (457)
T TIGR01622 89 DRTVFVLQLALKARERDLYEFFS-KVGKV--RDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALT 151 (457)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHH-hcCCe--eEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhC
Confidence 44699999999999999999996 68954 5667763 358999999999999998643
No 81
>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=69.68 E-value=14 Score=42.96 Aligned_cols=60 Identities=22% Similarity=0.223 Sum_probs=47.6
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcccc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLD 485 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~~~ 485 (605)
..+|+-+.|..++..+|++.|+ .|++..|..|.-+ ...|||.|.+.++|+..+..++..+
T Consensus 234 k~LfVgNL~~~~tee~L~~~F~-~f~~G~I~rV~~~-rgfAFVeF~s~e~A~kAi~~lnG~~ 293 (578)
T TIGR01648 234 KILYVRNLMTTTTEEIIEKSFS-EFKPGKVERVKKI-RDYAFVHFEDREDAVKAMDELNGKE 293 (578)
T ss_pred cEEEEeCCCCCCCHHHHHHHHH-hcCCCceEEEEee-cCeEEEEeCCHHHHHHHHHHhCCCE
Confidence 4689999999999999999996 6833344556544 4599999999999999988776543
No 82
>PLN03121 nucleic acid binding protein; Provisional
Probab=69.23 E-value=16 Score=37.78 Aligned_cols=57 Identities=18% Similarity=0.194 Sum_probs=45.5
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecC----ceEEEEecchhhHHHHHHHhcc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE----TAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~idd----tsa~V~l~~~e~~~~~L~~~~~ 483 (605)
..|++-+.+...+..+|++.|+ -||.+ .+|.-+.| .-|||.|.+.+.++..|.+-.+
T Consensus 6 ~TV~V~NLS~~tTE~dLrefFS-~~G~I--~~V~I~~D~et~gfAfVtF~d~~aaetAllLnGa 66 (243)
T PLN03121 6 YTAEVTNLSPKATEKDVYDFFS-HCGAI--EHVEIIRSGEYACTAYVTFKDAYALETAVLLSGA 66 (243)
T ss_pred eEEEEecCCCCCCHHHHHHHHH-hcCCe--EEEEEecCCCcceEEEEEECCHHHHHHHHhcCCC
Confidence 3589999999999999999997 68986 34555544 3699999999999998754433
No 83
>PRK10829 ribonuclease D; Provisional
Probab=67.70 E-value=23 Score=38.98 Aligned_cols=105 Identities=19% Similarity=0.150 Sum_probs=65.6
Q ss_pred HHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHh
Q 007386 221 VIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSV 300 (605)
Q Consensus 221 v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~ 300 (605)
+.+.|.+.+.+-|+|++-.|+-.+++.| |-.| ..++||...+...+ + ....+|+.+.+.
T Consensus 66 L~~ll~~~~ivKV~H~~~~Dl~~l~~~~-g~~p--------------~~~fDTqiaa~~lg-~-----~~~~gl~~Lv~~ 124 (373)
T PRK10829 66 FKALLRDPQVTKFLHAGSEDLEVFLNAF-GELP--------------QPLIDTQILAAFCG-R-----PLSCGFASMVEE 124 (373)
T ss_pred HHHHHcCCCeEEEEeChHhHHHHHHHHc-CCCc--------------CCeeeHHHHHHHcC-C-----CccccHHHHHHH
Confidence 4456667676679999999999997655 3333 35889988875432 1 124578887766
Q ss_pred hhhh-cccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 301 LCPQ-IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 301 l~~~-l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
++.. +......+++...| -.....+-|.-|+...-.+|-+|...|.
T Consensus 125 ~lgv~ldK~~~~sDW~~RP---------------Ls~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 125 YTGVTLDKSESRTDWLARP---------------LSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred HhCCccCcccccCCCCCCC---------------CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5432 11000001111111 1234678899999999999999988774
No 84
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=67.22 E-value=14 Score=43.16 Aligned_cols=61 Identities=21% Similarity=0.296 Sum_probs=48.1
Q ss_pred cceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-----cCceEEEEecchhhHHHHHHHhccc
Q 007386 423 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-----DETAVFVQFSRAEMVSKFLDLKGSL 484 (605)
Q Consensus 423 ~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-----ddtsa~V~l~~~e~~~~~L~~~~~~ 484 (605)
...+|+-++|..++..+|+++|+ .||++..+.|.|= ....|||.|.+.++++..+..++..
T Consensus 107 ~~rLfVGnLp~~~tEe~Lr~lF~-~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~ 172 (612)
T TIGR01645 107 MCRVYVGSISFELREDTIRRAFD-PFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQ 172 (612)
T ss_pred CCEEEEcCCCCCCCHHHHHHHHH-ccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCe
Confidence 34589999999999999999996 7998743333331 3568999999999999988766553
No 85
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=66.80 E-value=21 Score=30.12 Aligned_cols=40 Identities=18% Similarity=0.307 Sum_probs=28.2
Q ss_pred ccccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 007386 143 AISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186 (605)
Q Consensus 143 ~l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~~~~~~~~~~~vv~ 186 (605)
.+.+++.|+++|++||+++.. | ++-+.+. ++ |..+.++++
T Consensus 38 ~~~~~pm~~~~R~~iH~~a~~-~-~l~s~S~-g~-g~~R~vvv~ 77 (79)
T smart00393 38 SVELPPMNSYERKIVHELAEK-Y-GLESESF-GE-GPKRRVVIS 77 (79)
T ss_pred eEEcCCCCHHHHHHHHHHHHH-c-CCEEEEE-cC-CCCcEEEEE
Confidence 356788999999999999877 5 8877653 32 334455544
No 86
>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=66.03 E-value=18 Score=40.81 Aligned_cols=59 Identities=12% Similarity=0.216 Sum_probs=48.0
Q ss_pred cceEEEeCCCC-cCcHHHHHHHHHhhhCCCceeEEEEe-c-CceEEEEecchhhHHHHHHHhccc
Q 007386 423 ECIVIVWGFPS-HLKAWDIRECISKVYGPTSVISVYHV-D-ETAVFVQFSRAEMVSKFLDLKGSL 484 (605)
Q Consensus 423 ~~~v~~~~fp~-~~k~~dI~~~~sk~fg~~~v~~v~~i-d-dtsa~V~l~~~e~~~~~L~~~~~~ 484 (605)
..++|+-++|. .++..+|+++|+ .||.+ .+|.-+ | ...|||.|.+.++|...|..++..
T Consensus 275 ~~~l~v~nL~~~~vt~~~L~~lF~-~yG~V--~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~ 336 (481)
T TIGR01649 275 GSVLMVSGLHQEKVNCDRLFNLFC-VYGNV--ERVKFMKNKKETALIEMADPYQAQLALTHLNGV 336 (481)
T ss_pred CCEEEEeCCCCCCCCHHHHHHHHH-hcCCe--EEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence 35688889997 699999999997 89976 455554 3 479999999999999998877763
No 87
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play 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 domains, is
Probab=66.00 E-value=13 Score=32.60 Aligned_cols=61 Identities=11% Similarity=0.097 Sum_probs=51.4
Q ss_pred EEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcccccC
Q 007386 426 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDRN 487 (605)
Q Consensus 426 v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~~~~~ 487 (605)
+...-.|+.+.-.++.+.+.+.||-...+.|.|.|+ --+|.+.+.++.+..+..-.+..+.
T Consensus 13 v~~i~v~~~i~f~dL~~kIrdkf~~~~~~~iKykDE-GD~iti~sq~DLd~Ai~~a~~~~~~ 73 (86)
T cd06408 13 TRYIMIGPDTGFADFEDKIRDKFGFKRRLKIKMKDD-GDMITMGDQDDLDMAIDTARSEARK 73 (86)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHhCCCCceEEEEEcC-CCCccccCHHHHHHHHHHHHHHHHh
Confidence 666778999999999999988888877789999999 7899999999988888777764444
No 88
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=65.43 E-value=15 Score=45.49 Aligned_cols=84 Identities=30% Similarity=0.436 Sum_probs=56.9
Q ss_pred CCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhhhhcc
Q 007386 229 KKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 306 (605)
Q Consensus 229 ~kpiVgHN~~~Dl~~l~~~F--~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~~~l~ 306 (605)
.-++|.||.-+|+.||=..| ++-.|.+ . .++||=-|+...-+ .+ ++-.|+.+ |..+
T Consensus 501 d~IlVAHNasFD~gFl~~~~~k~~~~~~~-----------~-pvIDTL~lar~L~P---~~--ksh~Lg~l----~kk~- 558 (1444)
T COG2176 501 DSILVAHNASFDMGFLNTNYEKYGLEPLT-----------N-PVIDTLELARALNP---EF--KSHRLGTL----CKKL- 558 (1444)
T ss_pred CcEEEeccCccchhHHHHHHHHhCCcccc-----------C-chhhHHHHHHHhCh---hh--hhcchHHH----HHHh-
Confidence 44789999999999998888 3333322 1 36688777764321 11 25566665 4332
Q ss_pred cCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 007386 307 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 360 (605)
Q Consensus 307 ~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~l 360 (605)
.+ .-...|-|-|||=.||.+|+.+...+
T Consensus 559 ------------------~v--------~le~hHRA~yDaeat~~vf~~f~~~~ 586 (1444)
T COG2176 559 ------------------GV--------ELERHHRADYDAEATAKVFFVFLKDL 586 (1444)
T ss_pred ------------------Cc--------cHHHhhhhhhhHHHHHHHHHHHHHHH
Confidence 11 11578999999999999999987766
No 89
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=65.09 E-value=20 Score=42.47 Aligned_cols=63 Identities=21% Similarity=0.343 Sum_probs=51.7
Q ss_pred Ccccccce------EEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-cCceEEEEecchhhHHHHHHHhcc
Q 007386 418 PKILFECI------VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 418 p~~~~~~~------v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-ddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
|.|-.+++ .++=+.++.++.+|+.++| +.||.+ .+|.-| ...||||..-++.+|++.|.+++.
T Consensus 410 P~I~pd~isV~SrTLwvG~i~k~v~e~dL~~~f-eefGei--qSi~li~~R~cAfI~M~~RqdA~kalqkl~n 479 (894)
T KOG0132|consen 410 PTIPPDHISVCSRTLWVGGIPKNVTEQDLANLF-EEFGEI--QSIILIPPRGCAFIKMVRRQDAEKALQKLSN 479 (894)
T ss_pred CCCCCcceeEeeeeeeeccccchhhHHHHHHHH-Hhcccc--eeEeeccCCceeEEEEeehhHHHHHHHHHhc
Confidence 66655554 5666799999999999999 489987 456665 789999999999999999888874
No 90
>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=64.92 E-value=35 Score=28.77 Aligned_cols=28 Identities=4% Similarity=0.039 Sum_probs=22.2
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEe
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRV 173 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~ 173 (605)
..+++.++++|++||.+ .+++++.+.+.
T Consensus 35 ~~l~PM~~~eR~iIH~l--a~~~~l~S~S~ 62 (74)
T cd02643 35 HSFPPMNREKRRIVHEL--AEHFGIESVSY 62 (74)
T ss_pred eECCCCCHHHHHHHHHH--HhhCCCEEEec
Confidence 56788899999999984 56788877654
No 91
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=64.62 E-value=15 Score=38.54 Aligned_cols=58 Identities=24% Similarity=0.332 Sum_probs=48.8
Q ss_pred eEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhccc
Q 007386 425 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSL 484 (605)
Q Consensus 425 ~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~~ 484 (605)
.||.=|+++.++-.+|++.|+ .||++.-+.|+- |..-+||-|..+|.+.-....++.-
T Consensus 166 sVY~G~I~~~lte~~mr~~Fs-~fG~I~EVRvFk-~qGYaFVrF~tkEaAahAIv~mNnt 223 (321)
T KOG0148|consen 166 SVYVGNIASGLTEDLMRQTFS-PFGPIQEVRVFK-DQGYAFVRFETKEAAAHAIVQMNNT 223 (321)
T ss_pred eEEeCCcCccccHHHHHHhcc-cCCcceEEEEec-ccceEEEEecchhhHHHHHHHhcCc
Confidence 388888999999999999997 999986555554 9999999999999998877777653
No 92
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=63.92 E-value=19 Score=41.10 Aligned_cols=56 Identities=18% Similarity=0.249 Sum_probs=45.1
Q ss_pred eEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecC------ceEEEEecchhhHHHHHHHhcc
Q 007386 425 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE------TAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 425 ~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~idd------tsa~V~l~~~e~~~~~L~~~~~ 483 (605)
.+|+-++|..++..+|++.|+ .||.+ .++..+.+ ..|||.|.+.+++...+..++.
T Consensus 180 ~l~V~nl~~~~tee~L~~~F~-~fG~i--~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g 241 (562)
T TIGR01628 180 NLYVKNLDPSVNEDKLRELFA-KFGEI--TSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNG 241 (562)
T ss_pred eEEEeCCCCcCCHHHHHHHHH-hcCCE--EEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCC
Confidence 488999999999999999996 79975 44555433 2699999999999988776654
No 93
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=60.78 E-value=11 Score=39.18 Aligned_cols=89 Identities=15% Similarity=0.201 Sum_probs=59.3
Q ss_pred cccccccccCCCccccccCCCCCCCccccccccccCCCcccccceEEEeCCCCcCcHHHHHHHHHhhhCCCce-----eE
Q 007386 381 EHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSV-----IS 455 (605)
Q Consensus 381 ~~~N~L~~~~~~~~~idL~~~~~~~~~~~~~~l~~~~p~~~~~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v-----~~ 455 (605)
+-+|.|++-+.....|-.+..-+..+ ...+...|+.|.|++++.+++.+.|+ .||.+-- ..
T Consensus 98 ~AintlNGLrLQ~KTIKVSyARPSs~-------------~Ik~aNLYvSGlPktMtqkelE~iFs-~fGrIItSRiL~dq 163 (360)
T KOG0145|consen 98 KAINTLNGLRLQNKTIKVSYARPSSD-------------SIKDANLYVSGLPKTMTQKELEQIFS-PFGRIITSRILVDQ 163 (360)
T ss_pred HHHhhhcceeeccceEEEEeccCChh-------------hhcccceEEecCCccchHHHHHHHHH-Hhhhhhhhhhhhhc
Confidence 34566666554444455554322222 12355689999999999999999996 8998621 11
Q ss_pred EEEecCceEEEEecchhhHHHHHHHhcc
Q 007386 456 VYHVDETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 456 v~~iddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
+--+...-.||-|-+++.++.....++.
T Consensus 164 vtg~srGVgFiRFDKr~EAe~AIk~lNG 191 (360)
T KOG0145|consen 164 VTGLSRGVGFIRFDKRIEAEEAIKGLNG 191 (360)
T ss_pred ccceecceeEEEecchhHHHHHHHhccC
Confidence 2345567789999999999887666654
No 94
>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=58.35 E-value=32 Score=40.01 Aligned_cols=59 Identities=22% Similarity=0.315 Sum_probs=48.2
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-c-----CceEEEEecchhhHHHHHHHhcccc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-D-----ETAVFVQFSRAEMVSKFLDLKGSLD 485 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-d-----dtsa~V~l~~~e~~~~~L~~~~~~~ 485 (605)
..+|+-+.|..|+..+|+++|+ .||++ .++..+ | ..-|||.|.+.|+|+..|..++..+
T Consensus 59 ~~lFVgnLp~~~tEd~L~~~F~-~~G~I--~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~ 123 (578)
T TIGR01648 59 CEVFVGKIPRDLYEDELVPLFE-KAGPI--YELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYE 123 (578)
T ss_pred CEEEeCCCCCCCCHHHHHHHHH-hhCCE--EEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCe
Confidence 4589999999999999999997 68976 455554 3 2459999999999999998887644
No 95
>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=58.33 E-value=52 Score=28.95 Aligned_cols=68 Identities=18% Similarity=0.238 Sum_probs=44.3
Q ss_pred ceEEEeCCCCcCcHHHHHHHHH---hhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcccccCCCCccccc
Q 007386 424 CIVIVWGFPSHLKAWDIRECIS---KVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISVLH 495 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~s---k~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~~~ 495 (605)
.++++.+.|..--...|+..+. ..+|.. |--|..++|.|-|.+.|.|+--+.-++..+--+..|+|..
T Consensus 3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGk----Vl~v~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~ 73 (90)
T PF11608_consen 3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGK----VLSVSGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF 73 (90)
T ss_dssp EEEEEES--TTS-HHHHHHHHHHHHHTTT------EEE--TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred cEEEEecCCCCCCHHHHHHHHHHHhhccCCE----EEEEeCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence 4578888888888888887554 466653 4566799999999999999999999988777777776653
No 96
>PRK05755 DNA polymerase I; Provisional
Probab=58.04 E-value=31 Score=42.02 Aligned_cols=109 Identities=16% Similarity=-0.069 Sum_probs=62.6
Q ss_pred HHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHh
Q 007386 221 VIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSV 300 (605)
Q Consensus 221 v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~ 300 (605)
+.+.|.....++|+||.-+|+-.|.+. .-++| ..++||..++....+- ...+|..+.+.
T Consensus 362 l~~~L~d~~v~kV~HNakfDl~~L~~~-gi~~~--------------~~~~DT~iAa~Ll~~~------~~~~L~~L~~~ 420 (880)
T PRK05755 362 LKPLLEDPAIKKVGQNLKYDLHVLARY-GIELR--------------GIAFDTMLASYLLDPG------RRHGLDSLAER 420 (880)
T ss_pred HHHHHhCCCCcEEEeccHhHHHHHHhC-CCCcC--------------CCcccHHHHHHHcCCC------CCCCHHHHHHH
Confidence 445677778889999999999998852 22222 4588999887543220 12567776554
Q ss_pred hhhhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 301 LCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 301 l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
+...-. .... .... ... ..... ......|-|..|+.+|..+|.+|...|.
T Consensus 421 ylg~~~-~~~~-~~~g-k~~----~~~~~----ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 421 YLGHKT-ISFE-EVAG-KQL----TFAQV----DLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred HhCCCc-cchH-HhcC-CCC----Ccccc----CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 321100 0000 0000 000 00000 0113568899999999999999988763
No 97
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=57.81 E-value=34 Score=38.30 Aligned_cols=60 Identities=12% Similarity=0.204 Sum_probs=47.3
Q ss_pred cceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-------cCceEEEEecchhhHHHHHHHhcccc
Q 007386 423 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-------DETAVFVQFSRAEMVSKFLDLKGSLD 485 (605)
Q Consensus 423 ~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-------ddtsa~V~l~~~e~~~~~L~~~~~~~ 485 (605)
.+.+|+-+.|..++..+|+++|. .||++. .+..+ ....|||.|.+.+.+...+..++...
T Consensus 295 ~~~l~v~nlp~~~~~~~l~~~f~-~~G~i~--~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~ 361 (509)
T TIGR01642 295 KDRIYIGNLPLYLGEDQIKELLE-SFGDLK--AFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKD 361 (509)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHH-hcCCee--EEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCE
Confidence 35689999999999999999996 799864 33333 23579999999999998877766543
No 98
>cd05992 PB1 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 a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=57.07 E-value=32 Score=28.46 Aligned_cols=54 Identities=17% Similarity=0.185 Sum_probs=43.7
Q ss_pred eCCC-CcCcHHHHHHHHHhhhCCC-ceeEEEEecCceEEEEecchhhHHHHHHHhc
Q 007386 429 WGFP-SHLKAWDIRECISKVYGPT-SVISVYHVDETAVFVQFSRAEMVSKFLDLKG 482 (605)
Q Consensus 429 ~~fp-~~~k~~dI~~~~sk~fg~~-~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~ 482 (605)
+..| ...+-.++.+.+.+.|+.. ..+.+.|.|+-.-+|.+.+.++.+..+....
T Consensus 14 ~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 14 FVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69 (81)
T ss_pred EEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCHHHHHHHHHHHh
Confidence 3345 7889999999999999886 3458999999999999999887777655543
No 99
>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=56.81 E-value=31 Score=26.46 Aligned_cols=41 Identities=17% Similarity=0.271 Sum_probs=28.5
Q ss_pred HHHHHHhhhCCCceeEEEEec-C-ceEEEEecchhhHHHHHHHhcc
Q 007386 440 IRECISKVYGPTSVISVYHVD-E-TAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 440 I~~~~sk~fg~~~v~~v~~id-d-tsa~V~l~~~e~~~~~L~~~~~ 483 (605)
|+++|+ .||.+ ..|.-.. . ..|||.+.+.++|+..+..++.
T Consensus 1 L~~~f~-~fG~V--~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~ 43 (56)
T PF13893_consen 1 LYKLFS-KFGEV--KKIKIFKKKRGFAFVEFASVEDAQKAIEQLNG 43 (56)
T ss_dssp HHHHHT-TTS-E--EEEEEETTSTTEEEEEESSHHHHHHHHHHHTT
T ss_pred ChHHhC-CcccE--EEEEEEeCCCCEEEEEECCHHHHHHHHHHhCC
Confidence 456675 78975 3444433 3 7899999999999998766554
No 100
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=56.37 E-value=37 Score=28.27 Aligned_cols=55 Identities=20% Similarity=0.236 Sum_probs=46.9
Q ss_pred eCCCCcCcHHHHHHHHHhhhCCC-ceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 007386 429 WGFPSHLKAWDIRECISKVYGPT-SVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 429 ~~fp~~~k~~dI~~~~sk~fg~~-~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
+..|...+-.++.+.+.+.||.. ..+.|.|.|+---+|.+.+.++.+..+...+.
T Consensus 16 ~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~~ 71 (84)
T PF00564_consen 16 ISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDEDLQEAIEQAKE 71 (84)
T ss_dssp EEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHHHHHHHHHHHH
T ss_pred EEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHHHHHHHHHHHh
Confidence 67788889999999999999984 44589999999999999999998887776655
No 101
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=56.04 E-value=48 Score=27.50 Aligned_cols=58 Identities=17% Similarity=0.235 Sum_probs=46.4
Q ss_pred EEEeCCCCcCcHHHHHHHHHhhhCCC-ceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 007386 426 VIVWGFPSHLKAWDIRECISKVYGPT-SVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 426 v~~~~fp~~~k~~dI~~~~sk~fg~~-~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
+..+..|+.++-.++.+.+++.|+.. ..+.+.|.|+---+|.+.+.++.+..+.....
T Consensus 12 ~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~~ 70 (81)
T smart00666 12 TRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDEDLEEAIEEYDS 70 (81)
T ss_pred EEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHHHHHHHHHHHHH
Confidence 45556788899999999999999875 24589999988889999999988777665543
No 102
>smart00361 RRM_1 RNA recognition motif.
Probab=54.12 E-value=33 Score=27.84 Aligned_cols=44 Identities=18% Similarity=0.286 Sum_probs=30.8
Q ss_pred HHHHHHHH---hhhCCCceeEEE--EecC--------ceEEEEecchhhHHHHHHHhcc
Q 007386 438 WDIRECIS---KVYGPTSVISVY--HVDE--------TAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 438 ~dI~~~~s---k~fg~~~v~~v~--~idd--------tsa~V~l~~~e~~~~~L~~~~~ 483 (605)
.||++.|+ ..||.+ .+|. .+|. ..+||.|.+.+++...+..++.
T Consensus 3 ~~l~~~~~~~~~~fG~v--~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g 59 (70)
T smart00361 3 EDFEREFSEEEEYFGEV--GKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNG 59 (70)
T ss_pred hhHHHHHHHHHHhcCCe--eEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCC
Confidence 46666663 268876 4443 5554 3499999999999998776655
No 103
>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=53.32 E-value=52 Score=28.97 Aligned_cols=60 Identities=15% Similarity=0.248 Sum_probs=45.5
Q ss_pred ccceEEEeCCCC-----cCcHHHHHHHHHhhhCCC--ceeEEEEecCceEEEEecchhhHHHHHHHh
Q 007386 422 FECIVIVWGFPS-----HLKAWDIRECISKVYGPT--SVISVYHVDETAVFVQFSRAEMVSKFLDLK 481 (605)
Q Consensus 422 ~~~~v~~~~fp~-----~~k~~dI~~~~sk~fg~~--~v~~v~~iddtsa~V~l~~~e~~~~~L~~~ 481 (605)
++....-..+|. .|...++++.+.+.|+.. .-+.+.|.|+.--||.+.+.++...-+...
T Consensus 7 y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~~ 73 (91)
T cd06398 7 YGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQYF 73 (91)
T ss_pred eCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHHH
Confidence 333344445664 599999999998888775 345799999999999999988887766653
No 104
>cd02645 R3H_AAA R3H domain of a group of proteins with unknown function, who also contain a AAA-ATPase (AAA) 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 be binding ssDNA or ssRNA in a sequence-specific manner.
Probab=53.27 E-value=34 Score=27.86 Aligned_cols=28 Identities=14% Similarity=0.071 Sum_probs=22.0
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEe
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRV 173 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~ 173 (605)
..|.+-|++.|+++|.++.. | ++.+.+.
T Consensus 21 veL~Pm~~~eRri~H~~v~~-~-~l~s~S~ 48 (60)
T cd02645 21 VELLPRSAYIRRLQHDLVER-Y-QLRSESF 48 (60)
T ss_pred EEcCCCCHHHHHHHHHHHHH-C-CCeEEEe
Confidence 35677899999999999994 5 7776654
No 105
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=51.52 E-value=46 Score=33.02 Aligned_cols=56 Identities=20% Similarity=0.247 Sum_probs=45.8
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecC---ceEEEEecchhhHHHHHHHhcc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE---TAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~idd---tsa~V~l~~~e~~~~~L~~~~~ 483 (605)
.-||+=+.++..+..||...|. +||++.. .||+- .-|||.|.++.+|+|....+.-
T Consensus 11 ~kVYVGnL~~~a~k~eLE~~F~-~yG~lrs---vWvArnPPGfAFVEFed~RDA~DAvr~LDG 69 (195)
T KOG0107|consen 11 TKVYVGNLGSRATKRELERAFS-KYGPLRS---VWVARNPPGFAFVEFEDPRDAEDAVRYLDG 69 (195)
T ss_pred ceEEeccCCCCcchHHHHHHHH-hcCccee---EEEeecCCCceEEeccCcccHHHHHhhcCC
Confidence 3488888999999999999997 8999765 58865 6799999998888886555544
No 106
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=50.94 E-value=43 Score=38.31 Aligned_cols=56 Identities=16% Similarity=0.243 Sum_probs=44.5
Q ss_pred EEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-cCc------eEEEEecchhhHHHHHHHhccc
Q 007386 426 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DET------AVFVQFSRAEMVSKFLDLKGSL 484 (605)
Q Consensus 426 v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-ddt------sa~V~l~~~e~~~~~L~~~~~~ 484 (605)
+|+-+.|..++..+|++.|+ .||++ .+|.-+ |.. .|||.|.+.++|+..|+.++..
T Consensus 3 l~VgnLp~~vte~~L~~~F~-~~G~v--~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~ 65 (562)
T TIGR01628 3 LYVGDLDPDVTEAKLYDLFK-PFGPV--LSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFK 65 (562)
T ss_pred EEEeCCCCCCCHHHHHHHHH-hcCCE--EEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence 67778899999999999996 78975 344332 432 6999999999999999877653
No 107
>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=49.88 E-value=19 Score=31.43 Aligned_cols=28 Identities=25% Similarity=0.551 Sum_probs=21.6
Q ss_pred HHHHHhcCC-CeEEechhhhHHHHHHHHh
Q 007386 221 VIDLLSSEK-KLIVGHNCFLDIAHIYSKF 248 (605)
Q Consensus 221 v~~~l~~s~-kpiVgHN~~~Dl~~l~~~F 248 (605)
+.+.|.... .++||||+-+|+.+|.+.+
T Consensus 35 f~~~l~~~~~~v~V~hn~~fD~~fL~~~~ 63 (96)
T cd06125 35 LKDILRDKPLAILVGHNGSFDLPFLNNRC 63 (96)
T ss_pred HHHHHhhCCCCEEEEeCcHHhHHHHHHHH
Confidence 444555555 7899999999999988877
No 108
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]
Probab=49.35 E-value=45 Score=34.28 Aligned_cols=59 Identities=12% Similarity=0.180 Sum_probs=42.9
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEecCc------eEEEEecchhhHHHHHHHhcc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDET------AVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~iddt------sa~V~l~~~e~~~~~L~~~~~ 483 (605)
++.|+.|.|..+|.++|+.+|. .|-.+--.-+..-+.. =+||.|.+.-.+.+.+.+++.
T Consensus 35 RTLFVSGLP~DvKpREiynLFR-~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNG 99 (284)
T KOG1457|consen 35 RTLFVSGLPNDVKPREIYNLFR-RFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNG 99 (284)
T ss_pred ceeeeccCCcccCHHHHHHHhc-cCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcC
Confidence 4589999999999999999996 4443322134554444 489999988888777666665
No 109
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=49.19 E-value=50 Score=36.22 Aligned_cols=107 Identities=17% Similarity=0.216 Sum_probs=68.0
Q ss_pred HHHHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHH
Q 007386 219 RHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAF 298 (605)
Q Consensus 219 r~v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~ 298 (605)
.-+..+|......=|.|++-.|+-.+++.| |-+|. .||||+..+..+. + ..+.+|..+.
T Consensus 60 ~~l~~Ll~d~~v~KIfHaa~~DL~~l~~~~-g~~p~--------------plfdTqiAa~l~g-~-----~~~~gl~~Lv 118 (361)
T COG0349 60 PPLVALLADPNVVKIFHAARFDLEVLLNLF-GLLPT--------------PLFDTQIAAKLAG-F-----GTSHGLADLV 118 (361)
T ss_pred chHHHHhcCCceeeeeccccccHHHHHHhc-CCCCC--------------chhHHHHHHHHhC-C-----cccccHHHHH
Confidence 334455666666669999999999999988 77774 6899999987553 1 1266787776
Q ss_pred Hhhhhh-cccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 299 SVLCPQ-IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 299 ~~l~~~-l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
+.+... +..+.-.+++...|- .....--|..|...=-.++.+|.+.|-
T Consensus 119 ~~ll~v~ldK~~q~SDW~~RPL---------------s~~Ql~YAa~DV~yL~~l~~~L~~~L~ 167 (361)
T COG0349 119 EELLGVELDKSEQRSDWLARPL---------------SEAQLEYAAADVEYLLPLYDKLTEELA 167 (361)
T ss_pred HHHhCCcccccccccccccCCC---------------CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 655321 111111111111110 123455688899888889999888773
No 110
>cd02636 R3H_sperm-antigen R3H domain of a group of metazoan proteins that is related to the sperm-associated antigen 7. 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=47.93 E-value=54 Score=26.95 Aligned_cols=40 Identities=13% Similarity=0.272 Sum_probs=28.4
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~~~~~~~~~~~vv~ 186 (605)
..+++.|.+.|++||-+++. .++.+.+- ++.+..+.+||+
T Consensus 20 ~~l~pM~~~eRkivHDv~~~--~Gl~S~S~-Geee~~R~VVv~ 59 (61)
T cd02636 20 EKFQPMDKVERSIVHDVAEV--AGLTSFSF-GEDEVDRYVMIF 59 (61)
T ss_pred cccCCCCHHHHHHHHHHHHh--cCceeEec-CCCCCceEEEEe
Confidence 34677899999999998854 77776653 554445666665
No 111
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=46.55 E-value=48 Score=34.98 Aligned_cols=60 Identities=18% Similarity=0.247 Sum_probs=46.7
Q ss_pred cceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEE-e----cCceEEEEecchhhHHHHHHHhcc
Q 007386 423 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYH-V----DETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 423 ~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~-i----ddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
--|||+--|.++++..+|++.|. +||.++--.|.. . ...-.||.|.+++.+++....|+-
T Consensus 62 hfhvfvgdls~eI~~e~lr~aF~-pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnG 126 (321)
T KOG0148|consen 62 HFHVFVGDLSPEIDNEKLREAFA-PFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNG 126 (321)
T ss_pred ceeEEehhcchhcchHHHHHHhc-cccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCC
Confidence 34577777999999999999997 899886332222 1 346799999999999998877764
No 112
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. 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-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=45.11 E-value=97 Score=27.03 Aligned_cols=61 Identities=7% Similarity=0.029 Sum_probs=46.0
Q ss_pred cceEEEeCCCCcCcHHHHHHHHHhhhCC--CceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 007386 423 ECIVIVWGFPSHLKAWDIRECISKVYGP--TSVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 423 ~~~v~~~~fp~~~k~~dI~~~~sk~fg~--~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
..-++...++...+-.++.+.+...|+. .+.+.+.|+|+--=.|.+++.+..+.-+++.+.
T Consensus 8 ~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~DEEGDp~tiSS~~EL~EA~rl~~~ 70 (83)
T cd06404 8 NGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDEEGDPCTISSQMELEEAFRLYEL 70 (83)
T ss_pred cCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCceeecCHHHHHHHHHHHHh
Confidence 3346677777788888887776665544 446789999998888999988888887777665
No 113
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=40.18 E-value=1e+02 Score=29.75 Aligned_cols=60 Identities=20% Similarity=0.345 Sum_probs=47.8
Q ss_pred cceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEE-----ecCceEEEEecchhhHHHHHHHhcc
Q 007386 423 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYH-----VDETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 423 ~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~-----iddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
...+|+-+.|...+-.+|+..|. .||++.-+.|.. ....-|||.|.+.+.+...+..++.
T Consensus 115 ~~~l~v~nL~~~~~~~~l~~~F~-~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~ 179 (306)
T COG0724 115 NNTLFVGNLPYDVTEEDLRELFK-KFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNG 179 (306)
T ss_pred CceEEEeCCCCCCCHHHHHHHHH-hcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCC
Confidence 46799999999999999999996 788873223322 1238899999999999999888874
No 114
>PRK05359 oligoribonuclease; Provisional
Probab=39.29 E-value=54 Score=32.09 Aligned_cols=21 Identities=14% Similarity=0.086 Sum_probs=18.3
Q ss_pred CCCeEEechhhhHHHHHHHHh
Q 007386 228 EKKLIVGHNCFLDIAHIYSKF 248 (605)
Q Consensus 228 s~kpiVgHN~~~Dl~~l~~~F 248 (605)
...|+||||.-+|..+|-+.+
T Consensus 97 ~~~~l~g~~v~FD~~FL~~~~ 117 (181)
T PRK05359 97 GKSPLCGNSIGQDRRFLARYM 117 (181)
T ss_pred CCCceeecchhhCHHHHHHHH
Confidence 567899999999999998776
No 115
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=38.76 E-value=91 Score=32.51 Aligned_cols=58 Identities=22% Similarity=0.376 Sum_probs=45.5
Q ss_pred cceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEE-ec------CceEEEEecchhhHHHHHHHhcc
Q 007386 423 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYH-VD------ETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 423 ~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~-id------dtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
++.|-+.+.+..++-.|+.++| ..||++. .|+- .| ..=|||.|.++|+|...++.++-
T Consensus 189 ~~tvRvtNLsed~~E~dL~eLf-~~fg~i~--rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG 253 (270)
T KOG0122|consen 189 EATVRVTNLSEDMREDDLEELF-RPFGPIT--RVYLARDKETGLSKGFAFVTFESRDDAARAIADLNG 253 (270)
T ss_pred cceeEEecCccccChhHHHHHh-hccCccc--eeEEEEccccCcccceEEEEEecHHHHHHHHHHccC
Confidence 5678889999999999999999 5899974 3343 23 35699999999999887665544
No 116
>PF15023 DUF4523: Protein of unknown function (DUF4523)
Probab=38.41 E-value=86 Score=30.24 Aligned_cols=56 Identities=23% Similarity=0.392 Sum_probs=38.1
Q ss_pred cceEEEeCCCCcCc-HHHHHHHHHh--hhCCCceeEEEEecCceEEEEecchhhHHHHHHHh
Q 007386 423 ECIVIVWGFPSHLK-AWDIRECISK--VYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLK 481 (605)
Q Consensus 423 ~~~v~~~~fp~~~k-~~dI~~~~sk--~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~ 481 (605)
..+|.-|. ++.++ +.|+++.+.+ +|||+ .+|-.-..++|.|+|.+-..|=....+.
T Consensus 87 sTIVVRWl-kknm~~~edl~sV~~~Ls~fGpI--~SVT~cGrqsavVvF~d~~SAC~Av~Af 145 (166)
T PF15023_consen 87 STIVVRWL-KKNMQPTEDLKSVIQRLSVFGPI--QSVTLCGRQSAVVVFKDITSACKAVSAF 145 (166)
T ss_pred eeEEeehh-hhcCChHHHHHHHHHHHHhcCCc--ceeeecCCceEEEEehhhHHHHHHHHhh
Confidence 45677776 55554 4555544332 89998 4678889999999999887775544333
No 117
>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=38.35 E-value=74 Score=25.88 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=20.6
Q ss_pred cccCC-CCHHHHHHHHHHHHHhCCCeEEEE
Q 007386 144 ISLNG-FTSHQLLLIQLVVRKHFKDLAYLR 172 (605)
Q Consensus 144 l~L~~-~~s~qrrLV~q~lr~~fp~lv~v~ 172 (605)
+.+++ ++.++|++||++.++ -+|.+.+
T Consensus 20 l~f~p~lt~~eR~~vH~~a~~--~gL~s~S 47 (60)
T cd02640 20 MVFSPEFSKEERALIHQIAQK--YGLKSRS 47 (60)
T ss_pred EEcCCCCCHHHHHHHHHHHHH--cCCceee
Confidence 55666 899999999999887 4555554
No 118
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=38.06 E-value=18 Score=36.88 Aligned_cols=26 Identities=23% Similarity=0.448 Sum_probs=23.4
Q ss_pred EecchHHHHHHcCCCccchhhcCCCc
Q 007386 28 CQTTSMDFLAKYQFDFNACIHEGVSY 53 (605)
Q Consensus 28 cQaSSL~FLa~~gFDFNk~i~~GIpY 53 (605)
....||+||+++|.||.|--.+||.-
T Consensus 100 ~a~~SIElLr~~Gidf~K~~e~GI~~ 125 (239)
T KOG0304|consen 100 YAQDSIELLRRSGIDFEKHREEGIDI 125 (239)
T ss_pred cchhhHHHHHHcCcCHHHHHHcCCCH
Confidence 34679999999999999999999985
No 119
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=36.71 E-value=1.2e+02 Score=29.98 Aligned_cols=111 Identities=18% Similarity=0.142 Sum_probs=59.6
Q ss_pred HHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHH--hhccCCCChHHHHHhh
Q 007386 224 LLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQ--RMKKSSTSLSKAFSVL 301 (605)
Q Consensus 224 ~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~--~~~~~~tsL~~l~~~l 301 (605)
.|.+.....|||++=.|+-.|++.|.-. |. .++||..++....+-.. .......+|..+.+.+
T Consensus 60 iLe~~~i~Kv~h~~k~D~~~L~~~~gi~-~~--------------~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~ 124 (197)
T cd06148 60 ILESKKILKVIHDCRRDSDALYHQYGIK-LN--------------NVFDTQVADALLQEQETGGFNPDRVISLVQLLDKY 124 (197)
T ss_pred HhcCCCccEEEEechhHHHHHHHhcCcc-cc--------------ceeeHHHHHHHHHHHhcCCccccccccHHHHHHHh
Confidence 3445566779999999999887766321 22 35899876543322110 0011123677665443
Q ss_pred hh-hcccCCcccccccCCCceeeeeeccccccCC-----CCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 302 CP-QIALGSKSTHLALQPSVKVEVEVDDIRSSNW-----NSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 302 ~~-~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~-----~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
.. .+. +.. .+. ..-....+.| .....+-|+.|++.+-.+|-.|...|-
T Consensus 125 l~~~~~---k~~------~~~---~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~ 178 (197)
T cd06148 125 LYISIS---LKE------DVK---KLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALI 178 (197)
T ss_pred hCCChH---HHH------HHH---HHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhh
Confidence 11 110 000 000 0000001112 235677899999999999999988773
No 120
>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=36.66 E-value=84 Score=25.41 Aligned_cols=27 Identities=19% Similarity=0.274 Sum_probs=20.3
Q ss_pred cccCC-CCHHHHHHHHHHHHHhCCCeEEEE
Q 007386 144 ISLNG-FTSHQLLLIQLVVRKHFKDLAYLR 172 (605)
Q Consensus 144 l~L~~-~~s~qrrLV~q~lr~~fp~lv~v~ 172 (605)
+.+++ .|++||++||++.++ =+|.+.+
T Consensus 20 l~F~p~ls~~eR~~vH~lA~~--~gL~s~S 47 (60)
T cd02641 20 LEFPPTLSSHDRLLVHELAEE--LGLRHES 47 (60)
T ss_pred EECCCCCCHHHHHHHHHHHHH--cCCceEe
Confidence 45666 899999999999877 3455554
No 121
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=34.44 E-value=1.2e+02 Score=34.89 Aligned_cols=60 Identities=18% Similarity=0.262 Sum_probs=47.5
Q ss_pred ccccceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-------cCceEEEEecchhhHHHHHHHhc
Q 007386 420 ILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-------DETAVFVQFSRAEMVSKFLDLKG 482 (605)
Q Consensus 420 ~~~~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-------ddtsa~V~l~~~e~~~~~L~~~~ 482 (605)
+..+.+||+-+.|-..+-.+|++.|+ .||.+-. +..+ ...+|||.|.....+++-|.+..
T Consensus 289 ~~~~~tVFvRNL~fD~tEEel~~~fs-kFG~v~y--a~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~As 355 (678)
T KOG0127|consen 289 ITEGKTVFVRNLPFDTTEEELKEHFS-KFGEVKY--AIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAAS 355 (678)
T ss_pred ccccceEEEecCCccccHHHHHHHHH-hhcccee--EEEEeccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence 34455799999999999999999997 8998743 2222 45799999999999988766553
No 122
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=34.24 E-value=82 Score=35.26 Aligned_cols=56 Identities=16% Similarity=0.185 Sum_probs=41.4
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCC--------Cc-eeEEEE-ecCceEEEEecchhhHHHHHH
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGP--------TS-VISVYH-VDETAVFVQFSRAEMVSKFLD 479 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~--------~~-v~~v~~-iddtsa~V~l~~~e~~~~~L~ 479 (605)
..+|+-+.|..++..+|++.|.+.+.. .. |..+.. -+...|||.|.+.|+|...|.
T Consensus 176 r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~ 241 (509)
T TIGR01642 176 RRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMA 241 (509)
T ss_pred cEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhc
Confidence 348999999999999999999754211 11 222322 256799999999999999884
No 123
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=32.45 E-value=1.2e+02 Score=34.02 Aligned_cols=64 Identities=22% Similarity=0.283 Sum_probs=51.5
Q ss_pred eEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-cC-----ceEEEEecchhhHHHHHHHhcccccCCCC
Q 007386 425 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DE-----TAVFVQFSRAEMVSKFLDLKGSLDRNNDP 490 (605)
Q Consensus 425 ~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-dd-----tsa~V~l~~~e~~~~~L~~~~~~~~~~~~ 490 (605)
.||+...|-..|--|+++++.+.-|.+ .+|..+ |+ .||.|.|..+|.++.-|..++..+=+.-+
T Consensus 46 ~vfItNIpyd~rWqdLKdLvrekvGev--~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~ 115 (608)
T KOG4212|consen 46 SVFITNIPYDYRWQDLKDLVREKVGEV--EYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRE 115 (608)
T ss_pred eEEEecCcchhhhHhHHHHHHHhcCce--EeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCce
Confidence 399999999999999999998776754 455554 43 69999999999999999988886554443
No 124
>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=32.11 E-value=2.1e+02 Score=31.28 Aligned_cols=100 Identities=20% Similarity=0.234 Sum_probs=59.0
Q ss_pred HHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHh
Q 007386 221 VIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSV 300 (605)
Q Consensus 221 v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~ 300 (605)
+.+.|.+.+...|+|++=.|+-.+.+. ++.+|. .+|||...+...++ ....+|+.+.+.
T Consensus 62 L~~lL~d~~i~KV~h~~k~Dl~~L~~~-~~~~~~--------------~~fDtqlAa~lL~~------~~~~~l~~Lv~~ 120 (367)
T TIGR01388 62 LKELLRDESVVKVLHAASEDLEVFLNL-FGELPQ--------------PLFDTQIAAAFCGF------GMSMGYAKLVQE 120 (367)
T ss_pred HHHHHCCCCceEEEeecHHHHHHHHHH-hCCCCC--------------CcccHHHHHHHhCC------CCCccHHHHHHH
Confidence 345566777788999999997776544 444553 57899877643221 113467766544
Q ss_pred hhhh-cccCCcccccccCCCceeeeeeccccccCC-----CCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 301 LCPQ-IALGSKSTHLALQPSVKVEVEVDDIRSSNW-----NSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 301 l~~~-l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~-----~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
+... +. ++ ...+.+ .....+-|..|++....++-.|...|.
T Consensus 121 ~Lg~~l~----K~----------------~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 121 VLGVELD----KS----------------ESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLE 167 (367)
T ss_pred HcCCCCC----cc----------------cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3211 10 00 000111 112345589999988888888888774
No 125
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=30.67 E-value=82 Score=31.96 Aligned_cols=30 Identities=3% Similarity=0.091 Sum_probs=25.4
Q ss_pred ccccCCCCHHHHHHHHHHHHHhCCCeEEEEe
Q 007386 143 AISLNGFTSHQLLLIQLVVRKHFKDLAYLRV 173 (605)
Q Consensus 143 ~l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~ 173 (605)
+..|++.+++.||+||..|. .+|++-+.+.
T Consensus 166 ~v~L~pM~~~ERkIVH~~l~-~~~~V~T~Se 195 (208)
T COG1847 166 SVELEPMPPFERKIVHTALS-ANPGVETYSE 195 (208)
T ss_pred eeecCCCCHHHHHHHHHHHH-hcCCcceeec
Confidence 45688999999999999997 7899987753
No 126
>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=28.71 E-value=1.6e+02 Score=23.41 Aligned_cols=26 Identities=15% Similarity=0.194 Sum_probs=19.5
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEE
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYL 171 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v 171 (605)
+.+++.+.++|++||++... | ++.+.
T Consensus 19 ~~fppm~~~~R~~vH~lA~~-~-~L~S~ 44 (58)
T cd02646 19 LSFPPMDKHGRKTIHKLANC-Y-NLKSK 44 (58)
T ss_pred EecCCCCHHHHHHHHHHHHH-c-CCccc
Confidence 55677899999999999766 3 35444
No 127
>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=28.61 E-value=1.1e+02 Score=24.71 Aligned_cols=39 Identities=23% Similarity=0.370 Sum_probs=24.6
Q ss_pred cccC-CCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 007386 144 ISLN-GFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186 (605)
Q Consensus 144 l~L~-~~~s~qrrLV~q~lr~~fp~lv~v~~~~~~~~~~~~vv~ 186 (605)
|.++ ..|.++|++||++.++ -+|.+.+. ++ |..+.++++
T Consensus 19 l~Fpp~ls~~eR~~vH~~a~~--~gL~s~S~-G~-g~~R~v~v~ 58 (59)
T cd06007 19 YEFPSSLTNHERAVIHRLCRK--LGLKSKSK-GK-GSNRRLSVY 58 (59)
T ss_pred EEcCCCCCHHHHHHHHHHHHH--cCCCceee-cC-CCCeEEEEe
Confidence 4445 3789999999999887 45555443 32 334445544
No 128
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=28.21 E-value=1.3e+02 Score=30.74 Aligned_cols=50 Identities=18% Similarity=0.220 Sum_probs=38.0
Q ss_pred CcCcHHHHHHHHHhhhCCCceeEEEEe-----cCceEEEEecchhhHHHHHHHhcc
Q 007386 433 SHLKAWDIRECISKVYGPTSVISVYHV-----DETAVFVQFSRAEMVSKFLDLKGS 483 (605)
Q Consensus 433 ~~~k~~dI~~~~sk~fg~~~v~~v~~i-----ddtsa~V~l~~~e~~~~~L~~~~~ 483 (605)
-..++.+|+..|. .||.+.=++|=|= ...=|||-|+.+.+|++.|+++--
T Consensus 23 yRTspd~LrrvFe-kYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG 77 (256)
T KOG4207|consen 23 YRTSPDDLRRVFE-KYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDG 77 (256)
T ss_pred ccCCHHHHHHHHH-HhCcccceecccccccccccceeEEEeeecchHHHHHHhhcc
Confidence 3458999999996 6898765566662 235699999999999998877654
No 129
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=25.28 E-value=1.6e+02 Score=23.03 Aligned_cols=49 Identities=18% Similarity=0.389 Sum_probs=34.3
Q ss_pred eEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEEe-cCceEEEEecchhhHHHH
Q 007386 425 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DETAVFVQFSRAEMVSKF 477 (605)
Q Consensus 425 ~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~i-ddtsa~V~l~~~e~~~~~ 477 (605)
.|-+.|||.. ...++..-|. .||.+ +.+.+= +-..+||.+.++.+++.-
T Consensus 3 wI~V~Gf~~~-~~~~vl~~F~-~fGeI--~~~~~~~~~~~~~l~y~~~~~ae~A 52 (53)
T PF14605_consen 3 WISVSGFPPD-LAEEVLEHFA-SFGEI--VDIYVPESTNWMYLKYKSRKDAEKA 52 (53)
T ss_pred EEEEEeECch-HHHHHHHHHH-hcCCE--EEEEcCCCCcEEEEEECCHHHHHhh
Confidence 3778999986 5566666775 69987 333332 367888888888888753
No 130
>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=24.93 E-value=1e+02 Score=27.71 Aligned_cols=59 Identities=25% Similarity=0.222 Sum_probs=36.5
Q ss_pred HHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhh
Q 007386 223 DLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVL 301 (605)
Q Consensus 223 ~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l 301 (605)
+.+...+...||||.-.|+-.|.+.+ ..+| +.++||..++....+- ....+|..+.+.+
T Consensus 48 ~~l~~~~~~~v~~~~k~d~~~L~~~~-~~~~--------------~~~~D~~~~ayll~~~-----~~~~~l~~l~~~~ 106 (155)
T cd00007 48 ELLEDEDITKVGHDAKFDLVVLARDG-IELP--------------GNIFDTMLAAYLLNPG-----EGSHSLDDLAKEY 106 (155)
T ss_pred HHHcCCCCcEEeccHHHHHHHHHHCC-CCCC--------------CCcccHHHHHHHhCCC-----CCcCCHHHHHHHH
Confidence 34555667899999999988876544 2222 2578998887543221 1024777775543
No 131
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=24.49 E-value=2e+02 Score=32.51 Aligned_cols=94 Identities=15% Similarity=0.242 Sum_probs=63.0
Q ss_pred hhccccccccccCCCccccccCCCCCCCccccccccccCCCcccccceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEE
Q 007386 378 KLREHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVY 457 (605)
Q Consensus 378 ~l~~~~N~L~~~~~~~~~idL~~~~~~~~~~~~~~l~~~~p~~~~~~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~ 457 (605)
.++-+=|-+.+.|... ...||.+. ++.--+.|+-+.+.+++...|+.+|. .||.+ ..|.
T Consensus 232 ~~klwgn~~tVdWAep--------~~e~ded~----------ms~VKvLYVRNL~~~tTeE~lk~~F~-~~G~v--eRVk 290 (506)
T KOG0117|consen 232 KIKLWGNAITVDWAEP--------EEEPDEDT----------MSKVKVLYVRNLMESTTEETLKKLFN-EFGKV--ERVK 290 (506)
T ss_pred ceeecCCcceeeccCc--------ccCCChhh----------hhheeeeeeeccchhhhHHHHHHHHH-hccce--EEee
Confidence 4666888888888632 11122210 11123567778999999999999996 78754 4556
Q ss_pred EecCceEEEEecchhhHHHHHHHhcccccCCCCccc
Q 007386 458 HVDETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISV 493 (605)
Q Consensus 458 ~iddtsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~ 493 (605)
=+-| -|||.|.+++++-..|+.++--|=-+..+.|
T Consensus 291 k~rD-YaFVHf~eR~davkAm~~~ngkeldG~~iEv 325 (506)
T KOG0117|consen 291 KPRD-YAFVHFAEREDAVKAMKETNGKELDGSPIEV 325 (506)
T ss_pred cccc-eeEEeecchHHHHHHHHHhcCceecCceEEE
Confidence 6644 9999999999998877777764444444444
No 132
>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=24.45 E-value=1.2e+02 Score=29.25 Aligned_cols=21 Identities=14% Similarity=0.181 Sum_probs=17.8
Q ss_pred CCCeEEechhhhHHHHHHHHh
Q 007386 228 EKKLIVGHNCFLDIAHIYSKF 248 (605)
Q Consensus 228 s~kpiVgHN~~~Dl~~l~~~F 248 (605)
.+.++||||.-+|+.+|-+.|
T Consensus 93 ~~~~lvgh~~~FD~~fL~~~~ 113 (173)
T cd06135 93 GKSPLAGNSVHQDRRFLDKYM 113 (173)
T ss_pred CCCceeecchhhCHHHHHHHH
Confidence 356899999999999998766
No 133
>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=23.43 E-value=1.9e+02 Score=23.52 Aligned_cols=39 Identities=15% Similarity=0.138 Sum_probs=25.0
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 007386 144 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186 (605)
Q Consensus 144 l~L~~~~s~qrrLV~q~lr~~fp~lv~v~~~~~~~~~~~~vv~ 186 (605)
..+++.+++||++||.+.+. -++.+.+- +... .+.++|+
T Consensus 20 ~~f~pM~~~~R~~vHdla~~--~gl~SeS~-d~Ep-~R~V~v~ 58 (59)
T cd06006 20 LRFPPMRSPQRAFIHELAKD--YGLYSESQ-DPEP-KRSVFVK 58 (59)
T ss_pred eeCCCCCHHHHHHHHHHHHH--cCCeeEec-CCCC-CcEEEEe
Confidence 45778899999999999876 45555443 3333 3444443
No 134
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=23.18 E-value=98 Score=34.69 Aligned_cols=63 Identities=17% Similarity=0.243 Sum_probs=46.6
Q ss_pred EEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEE----ecCceEEEEecchhhHHHHHHHhcccccCCC
Q 007386 426 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYH----VDETAVFVQFSRAEMVSKFLDLKGSLDRNND 489 (605)
Q Consensus 426 v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~----iddtsa~V~l~~~e~~~~~L~~~~~~~~~~~ 489 (605)
.|+--.++..+..+|++.|+ .||-+--.+|-. +...||||.|+.+|.+..-.++++..+...+
T Consensus 127 LFvg~lsK~~te~evr~iFs-~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeG 193 (510)
T KOG0144|consen 127 LFVGMLSKQCTENEVREIFS-RFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEG 193 (510)
T ss_pred hhhhhccccccHHHHHHHHH-hhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeecc
Confidence 45555788888899999997 798763222222 4668999999999999998888877655433
No 135
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=21.57 E-value=2.2e+02 Score=27.30 Aligned_cols=67 Identities=18% Similarity=0.247 Sum_probs=50.0
Q ss_pred ceEEEeCCCCcCcHHHHHHHHHhhhCCCceeEEEE-ecCc------eEEEEecchhhHHHHHHHhcccccCCCCccc
Q 007386 424 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYH-VDET------AVFVQFSRAEMVSKFLDLKGSLDRNNDPISV 493 (605)
Q Consensus 424 ~~v~~~~fp~~~k~~dI~~~~sk~fg~~~v~~v~~-iddt------sa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~ 493 (605)
=++|+.|.-++.+-.||...|+ -||++.. |+. +|.- .|+|-....++++...++++..+=.+..++|
T Consensus 73 wIi~VtgvHeEatEedi~d~F~-dyGeiKN--ihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~V 146 (170)
T KOG0130|consen 73 WIIFVTGVHEEATEEDIHDKFA-DYGEIKN--IHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSV 146 (170)
T ss_pred EEEEEeccCcchhHHHHHHHHh-hcccccc--eeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeE
Confidence 3588889889999999999997 7999865 232 4554 4566667888888888888866555666655
No 136
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=21.25 E-value=2.8e+02 Score=28.48 Aligned_cols=57 Identities=16% Similarity=0.276 Sum_probs=44.4
Q ss_pred eEEEeCCCCcCcHHHHHH----HHHhhhCCCceeEEEEe----cCceEEEEecchhhHHHHHHHhccc
Q 007386 425 IVIVWGFPSHLKAWDIRE----CISKVYGPTSVISVYHV----DETAVFVQFSRAEMVSKFLDLKGSL 484 (605)
Q Consensus 425 ~v~~~~fp~~~k~~dI~~----~~sk~fg~~~v~~v~~i----ddtsa~V~l~~~e~~~~~L~~~~~~ 484 (605)
..|+.......+..+++. +|+ -||. |.+|.-. =...|||+|.+.+.+...|++++.+
T Consensus 11 TlYInnLnekI~~~elkrsL~~LFs-qfG~--ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gf 75 (221)
T KOG4206|consen 11 TLYINNLNEKIKKDELKRSLYLLFS-QFGK--ILDISAFKTPKMRGQAFVVFKETEAASAALRALQGF 75 (221)
T ss_pred eEeehhccccccHHHHHHHHHHHHH-hhCC--eEEEEecCCCCccCceEEEecChhHHHHHHHHhcCC
Confidence 578888999999999997 443 5664 3455554 3578999999999999988887774
No 137
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=20.49 E-value=4.7e+02 Score=24.34 Aligned_cols=104 Identities=18% Similarity=0.124 Sum_probs=55.7
Q ss_pred HHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhh
Q 007386 223 DLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLC 302 (605)
Q Consensus 223 ~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~ 302 (605)
+.+.+.+.+.||||.=.|+-.+.+.|.-. + ..++||..++.-.++- ...+|..+...+.
T Consensus 58 ~ll~~~~i~kv~~d~K~~~~~L~~~~gi~-~--------------~~~~D~~laayLl~p~------~~~~l~~l~~~~l 116 (178)
T cd06142 58 ELLADPNIVKVFHAAREDLELLKRDFGIL-P--------------QNLFDTQIAARLLGLG------DSVGLAALVEELL 116 (178)
T ss_pred HHHcCCCceEEEeccHHHHHHHHHHcCCC-C--------------CCcccHHHHHHHhCCC------ccccHHHHHHHHh
Confidence 34556678899999988888876655211 2 2578998665432210 1236766643321
Q ss_pred hhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 303 PQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 303 ~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
.. . ..+. + ....-..........+-|+.||..+..++-.|...+.
T Consensus 117 ~~---~-------~~~~---~-~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~ 161 (178)
T cd06142 117 GV---E-------LDKG---E-QRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELE 161 (178)
T ss_pred CC---C-------CCcc---c-ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 10 0 0000 0 0000000000112344689999999999999888773
No 138
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=20.41 E-value=2e+02 Score=23.87 Aligned_cols=39 Identities=13% Similarity=0.329 Sum_probs=31.0
Q ss_pred CcHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHH
Q 007386 435 LKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFL 478 (605)
Q Consensus 435 ~k~~dI~~~~sk~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L 478 (605)
.+..||+..| +.|+...| -.|.|-.||+|++.+.++.=.
T Consensus 12 ~~v~d~K~~L-r~y~~~~I----~~d~tGfYIvF~~~~Ea~rC~ 50 (66)
T PF11767_consen 12 VTVEDFKKRL-RKYRWDRI----RDDRTGFYIVFNDSKEAERCF 50 (66)
T ss_pred ccHHHHHHHH-hcCCcceE----EecCCEEEEEECChHHHHHHH
Confidence 4788999888 57886654 369999999999999877643
No 139
>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=20.17 E-value=2.4e+02 Score=26.73 Aligned_cols=111 Identities=16% Similarity=0.049 Sum_probs=58.0
Q ss_pred HHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHhhCCCCcchhHHhhhchhHHHhhccCCCChHHHHHhhh
Q 007386 223 DLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLC 302 (605)
Q Consensus 223 ~~l~~s~kpiVgHN~~~Dl~~l~~~F~~pLP~~~~EFk~~l~~~FP~IyDTK~L~~~~~~l~~~~~~~~tsL~~l~~~l~ 302 (605)
+.+......+||||.=+|+-.+.+..+. +| ..++||..++....+- ....+|..+.+.+.
T Consensus 61 ~~l~~~~~~~v~hn~k~d~~~l~~~gi~-~~--------------~~~~Dt~l~a~ll~p~-----~~~~~l~~l~~~~l 120 (193)
T cd06139 61 PLLEDPSIKKVGQNLKFDLHVLANHGIE-LR--------------GPAFDTMLASYLLNPG-----RRRHGLDDLAERYL 120 (193)
T ss_pred HHHhCCCCcEEeeccHHHHHHHHHCCCC-CC--------------CCcccHHHHHHHhCCC-----CCCCCHHHHHHHHh
Confidence 3455556789999999999888654222 21 2578999887643321 11346777655432
Q ss_pred hhcccCCcccccccCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 007386 303 PQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361 (605)
Q Consensus 303 ~~l~~~~~~~~~~~~p~v~i~v~~~~~~~~~~~~~~~HEAGyDA~mTG~vF~kL~~~lg 361 (605)
..-... . ........ .. ...+.. ......|-|+.|+..|..++-.|...+.
T Consensus 121 ~~~~~~-~-~~~~~k~~-~~-~~~~~~----~~~~~~~ya~~d~~~~~~l~~~l~~~l~ 171 (193)
T cd06139 121 GHKTIS-F-EDLVGKGK-KQ-ITFDQV----PLEKAAEYAAEDADITLRLYELLKPKLK 171 (193)
T ss_pred CCCCcc-H-HHHcCCCc-Cc-CCcccc----CHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 110000 0 00000000 00 000000 0011345689999999999999988773
Done!