Query 008236
Match_columns 573
No_of_seqs 196 out of 432
Neff 5.7
Searched_HMMs 46136
Date Thu Mar 28 21:14:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008236.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008236hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04857 CAF1: CAF1 family rib 100.0 1.4E-35 3.1E-40 301.8 6.4 127 183-323 135-262 (262)
2 KOG0304 mRNA deadenylase subun 99.7 2.5E-18 5.4E-23 167.5 8.2 111 182-327 121-238 (239)
3 KOG1990 Poly(A)-specific exori 99.7 6.7E-17 1.5E-21 180.5 6.5 426 64-537 117-556 (564)
4 PF08675 RNA_bind: RNA binding 99.6 1.1E-15 2.3E-20 129.0 5.6 56 391-450 8-63 (87)
5 COG5228 POP2 mRNA deadenylase 99.3 2E-12 4.2E-17 126.5 7.7 109 183-328 138-253 (299)
6 cd02637 R3H_PARN R3H domain of 98.1 5.3E-06 1.1E-10 67.9 5.9 32 112-143 19-50 (65)
7 PF10309 DUF2414: Protein of u 97.2 0.0015 3.3E-08 53.0 7.1 55 393-448 7-61 (62)
8 PRK05711 DNA polymerase III su 96.8 0.0077 1.7E-07 61.4 10.3 103 180-326 67-174 (240)
9 TIGR00573 dnaq exonuclease, DN 96.8 0.0097 2.1E-07 59.3 10.7 105 181-328 69-177 (217)
10 PRK07942 DNA polymerase III su 96.7 0.01 2.2E-07 60.0 10.0 98 186-329 79-181 (232)
11 cd06134 RNaseT DEDDh 3'-5' exo 96.6 0.0097 2.1E-07 58.2 8.8 84 196-327 101-188 (189)
12 PRK06195 DNA polymerase III su 96.6 0.056 1.2E-06 56.9 15.1 85 196-330 79-166 (309)
13 PRK09145 DNA polymerase III su 96.4 0.017 3.8E-07 56.7 9.6 101 180-326 92-199 (202)
14 TIGR01406 dnaQ_proteo DNA poly 96.4 0.024 5.1E-07 57.1 10.4 101 182-326 65-170 (225)
15 PRK07740 hypothetical protein; 96.4 0.016 3.4E-07 59.1 9.1 101 182-328 124-226 (244)
16 PRK05168 ribonuclease T; Provi 96.4 0.013 2.8E-07 58.4 8.2 87 196-329 113-202 (211)
17 cd06131 DNA_pol_III_epsilon_Ec 96.1 0.037 7.9E-07 52.2 9.8 99 182-324 64-166 (167)
18 PRK06063 DNA polymerase III su 96.0 0.043 9.4E-07 58.0 10.4 96 185-329 80-180 (313)
19 TIGR01298 RNaseT ribonuclease 95.9 0.025 5.4E-07 55.9 7.6 86 196-328 104-192 (200)
20 cd06130 DNA_pol_III_epsilon_li 95.7 0.069 1.5E-06 49.4 9.2 90 183-322 61-155 (156)
21 smart00479 EXOIII exonuclease 95.6 0.13 2.9E-06 47.8 10.8 101 180-328 61-167 (169)
22 PRK06310 DNA polymerase III su 95.3 0.067 1.5E-06 54.7 8.6 100 183-329 71-175 (250)
23 PF00076 RRM_1: RNA recognitio 95.2 0.08 1.7E-06 41.7 6.9 57 394-451 1-61 (70)
24 PRK06807 DNA polymerase III su 95.0 0.13 2.8E-06 54.6 9.6 86 196-329 87-173 (313)
25 PF14259 RRM_6: RNA recognitio 94.9 0.1 2.2E-06 41.8 6.8 54 394-450 1-60 (70)
26 PRK07983 exodeoxyribonuclease 94.8 0.19 4.2E-06 50.5 9.9 99 180-330 58-156 (219)
27 PRK09146 DNA polymerase III su 94.8 0.18 4E-06 51.3 9.9 108 180-330 110-229 (239)
28 PRK07748 sporulation inhibitor 94.6 0.18 3.8E-06 49.9 9.1 23 305-327 157-179 (207)
29 PRK06722 exonuclease; Provisio 94.5 0.25 5.4E-06 51.7 10.3 22 305-326 158-179 (281)
30 KOG4483 Uncharacterized conser 94.5 0.058 1.3E-06 57.9 5.5 59 391-451 391-449 (528)
31 cd06127 DEDDh DEDDh 3'-5' exon 94.3 0.18 4E-06 45.6 7.9 77 198-322 80-159 (159)
32 PRK06309 DNA polymerase III su 94.1 0.34 7.5E-06 48.9 10.0 100 183-329 63-167 (232)
33 cd06144 REX4_like DEDDh 3'-5' 93.8 0.13 2.9E-06 48.2 6.1 16 306-321 136-151 (152)
34 PRK08517 DNA polymerase III su 93.6 0.6 1.3E-05 48.1 10.9 85 196-328 146-231 (257)
35 cd06145 REX1_like DEDDh 3'-5' 93.6 0.21 4.5E-06 47.0 7.0 75 196-321 75-149 (150)
36 smart00362 RRM_2 RNA recogniti 92.9 0.51 1.1E-05 36.1 7.2 54 394-450 2-60 (72)
37 TIGR01405 polC_Gram_pos DNA po 92.9 0.47 1E-05 58.7 10.2 101 181-328 252-355 (1213)
38 PRK08074 bifunctional ATP-depe 92.9 0.44 9.4E-06 57.6 9.8 100 183-329 68-170 (928)
39 PRK07246 bifunctional ATP-depe 92.8 0.49 1.1E-05 56.4 10.0 99 183-329 70-171 (820)
40 cd06137 DEDDh_RNase DEDDh 3'-5 92.6 0.32 6.9E-06 46.2 6.7 79 196-322 83-161 (161)
41 TIGR01407 dinG_rel DnaQ family 92.3 0.6 1.3E-05 55.8 10.0 100 183-329 64-166 (850)
42 PRK07883 hypothetical protein; 91.4 0.98 2.1E-05 51.6 9.9 88 197-329 95-183 (557)
43 PRK00448 polC DNA polymerase I 91.3 0.71 1.5E-05 58.0 9.2 103 180-329 480-585 (1437)
44 PRK07247 DNA polymerase III su 91.0 0.82 1.8E-05 45.2 7.7 22 306-327 147-168 (195)
45 cd00590 RRM RRM (RNA recogniti 90.8 1.2 2.6E-05 34.3 7.1 57 394-451 2-62 (74)
46 PLN03134 glycine-rich RNA-bind 90.8 1.4 3E-05 41.5 8.6 57 392-451 35-98 (144)
47 PF08777 RRM_3: RNA binding mo 89.6 0.87 1.9E-05 40.7 6.0 54 393-452 3-60 (105)
48 cd06136 TREX1_2 DEDDh 3'-5' ex 89.6 1.3 2.7E-05 42.8 7.5 75 197-323 98-176 (177)
49 smart00360 RRM RNA recognition 88.6 1.6 3.6E-05 33.0 6.3 52 397-450 2-59 (71)
50 PF00929 RNase_T: Exonuclease; 88.4 0.23 5E-06 45.0 1.4 16 306-321 149-164 (164)
51 cd06133 ERI-1_3'hExo_like DEDD 88.0 2.2 4.9E-05 40.0 8.0 82 199-324 92-175 (176)
52 TIGR01659 sex-lethal sex-letha 87.0 2.7 5.8E-05 45.3 8.7 68 391-461 107-181 (346)
53 PF01424 R3H: R3H domain; Int 86.9 2.3 5E-05 33.9 6.3 39 112-154 23-61 (63)
54 cd06149 ISG20 DEDDh 3'-5' exon 86.0 1.8 4E-05 41.0 6.1 17 305-321 140-156 (157)
55 cd06396 PB1_NBR1 The PB1 domai 85.9 2.6 5.6E-05 36.2 6.3 57 394-451 11-69 (81)
56 PRK09182 DNA polymerase III su 85.7 2.9 6.3E-05 44.0 8.0 24 306-329 179-202 (294)
57 cd06407 PB1_NLP A PB1 domain i 85.4 3 6.4E-05 35.8 6.5 59 393-451 10-70 (82)
58 COG0847 DnaQ DNA polymerase II 84.6 5 0.00011 40.2 8.9 82 198-327 96-181 (243)
59 cd06138 ExoI_N N-terminal DEDD 83.7 3.7 8E-05 39.7 7.2 24 193-216 80-104 (183)
60 PF01612 DNA_pol_A_exo1: 3'-5' 83.0 3.6 7.8E-05 38.2 6.7 99 191-328 71-175 (176)
61 PTZ00315 2'-phosphotransferase 82.8 6.1 0.00013 45.4 9.4 108 178-326 122-253 (582)
62 cd02325 R3H R3H domain. The na 81.6 6.5 0.00014 29.8 6.6 27 112-140 20-46 (59)
63 PRK11779 sbcB exonuclease I; P 80.8 7.3 0.00016 43.8 9.1 23 305-327 175-197 (476)
64 TIGR01649 hnRNP-L_PTB hnRNP-L/ 80.4 4.2 9E-05 45.5 7.0 55 392-449 3-58 (481)
65 cd02644 R3H_jag R3H domain fou 80.1 8 0.00017 31.9 6.8 40 112-154 26-65 (67)
66 TIGR01659 sex-lethal sex-letha 79.5 5.3 0.00011 43.0 7.2 56 393-451 195-257 (346)
67 cd02642 R3H_encore_like R3H do 78.5 12 0.00025 30.3 7.3 39 112-155 24-62 (63)
68 TIGR01661 ELAV_HUD_SF ELAV/HuD 78.1 6.4 0.00014 41.3 7.3 59 392-453 4-69 (352)
69 PRK05601 DNA polymerase III su 77.8 8.8 0.00019 41.9 8.2 38 179-216 105-144 (377)
70 TIGR01661 ELAV_HUD_SF ELAV/HuD 77.7 7.2 0.00016 41.0 7.6 59 392-453 270-335 (352)
71 COG2176 PolC DNA polymerase II 75.4 7.9 0.00017 47.5 7.6 84 197-328 501-586 (1444)
72 KOG0144 RNA-binding protein CU 74.1 6.4 0.00014 43.3 5.9 77 394-476 37-120 (510)
73 PLN03120 nucleic acid binding 74.0 13 0.00029 38.5 8.0 53 392-447 5-61 (260)
74 cd06146 mut-7_like_exo DEDDy 3 73.5 12 0.00025 36.7 7.3 105 193-325 78-192 (193)
75 cd02638 R3H_unknown_1 R3H doma 73.0 7.6 0.00016 31.7 4.7 29 112-141 21-49 (62)
76 TIGR01622 SF-CC1 splicing fact 72.5 10 0.00022 41.5 7.3 62 392-456 187-255 (457)
77 TIGR01645 half-pint poly-U bin 71.8 10 0.00023 43.9 7.3 67 392-461 205-278 (612)
78 TIGR01622 SF-CC1 splicing fact 71.3 13 0.00027 40.8 7.7 56 391-449 89-151 (457)
79 TIGR01648 hnRNP-R-Q heterogene 70.9 13 0.00027 43.0 7.7 63 392-456 234-296 (578)
80 cd06141 WRN_exo DEDDy 3'-5' ex 70.4 17 0.00037 34.2 7.4 97 192-325 68-169 (170)
81 PLN03121 nucleic acid binding 69.4 16 0.00034 37.6 7.2 57 392-451 6-66 (243)
82 cd06129 RNaseD_like DEDDy 3'-5 68.8 17 0.00037 34.2 7.0 94 192-326 62-161 (161)
83 smart00393 R3H Putative single 68.7 13 0.00028 31.2 5.5 40 111-154 38-77 (79)
84 TIGR01645 half-pint poly-U bin 67.5 14 0.0003 42.9 7.1 69 392-461 108-181 (612)
85 TIGR01649 hnRNP-L_PTB hnRNP-L/ 65.4 19 0.0004 40.4 7.6 59 391-452 275-336 (481)
86 TIGR01628 PABP-1234 polyadenyl 64.6 18 0.0004 40.9 7.4 56 393-451 180-241 (562)
87 cd06408 PB1_NoxR The PB1 domai 64.5 14 0.00031 32.1 5.0 61 394-455 13-73 (86)
88 KOG0145 RNA-binding protein EL 64.4 8.3 0.00018 40.0 4.1 88 349-451 98-191 (360)
89 cd02643 R3H_NF-X1 R3H domain o 64.3 43 0.00093 28.0 7.7 55 63-141 8-62 (74)
90 KOG0148 Apoptosis-promoting RN 63.9 16 0.00035 38.2 6.0 59 393-453 166-224 (321)
91 cd01201 Neurobeachin Neurobeac 63.2 23 0.00049 32.2 6.2 52 396-447 51-103 (108)
92 TIGR01642 U2AF_lg U2 snRNP aux 63.2 25 0.00054 39.0 8.1 61 391-454 295-362 (509)
93 PF11608 Limkain-b1: Limkain b 59.6 48 0.001 29.0 7.2 68 392-463 3-73 (90)
94 TIGR01648 hnRNP-R-Q heterogene 59.5 30 0.00065 40.0 7.9 60 392-454 59-124 (578)
95 PF13893 RRM_5: RNA recognitio 57.7 30 0.00064 26.4 5.3 41 408-451 1-43 (56)
96 cd05992 PB1 The PB1 domain is 57.7 30 0.00066 28.3 5.8 54 397-450 14-69 (81)
97 PRK05755 DNA polymerase I; Pro 56.7 35 0.00077 41.2 8.3 109 189-329 362-470 (880)
98 PF00564 PB1: PB1 domain; Int 56.5 37 0.0008 28.1 6.1 55 397-451 16-71 (84)
99 smart00361 RRM_1 RNA recogniti 55.5 31 0.00067 27.8 5.3 44 406-451 3-59 (70)
100 smart00666 PB1 PB1 domain. Pho 55.4 50 0.0011 27.2 6.7 58 394-451 12-70 (81)
101 cd02640 R3H_NRF R3H domain of 54.3 54 0.0012 26.5 6.4 29 111-141 19-48 (60)
102 PRK10829 ribonuclease D; Provi 53.9 46 0.00099 36.4 7.8 106 188-329 65-171 (373)
103 KOG0132 RNA polymerase II C-te 52.5 30 0.00064 40.9 6.3 64 385-451 409-479 (894)
104 cd06398 PB1_Joka2 The PB1 doma 52.4 55 0.0012 28.6 6.6 59 391-449 8-73 (91)
105 cd02645 R3H_AAA R3H domain of 52.4 36 0.00079 27.5 5.1 38 112-153 21-58 (60)
106 TIGR01628 PABP-1234 polyadenyl 51.4 43 0.00092 38.0 7.5 56 394-452 3-65 (562)
107 KOG0107 Alternative splicing f 50.6 49 0.0011 32.7 6.5 61 392-456 11-74 (195)
108 cd02636 R3H_sperm-antigen R3H 49.9 49 0.0011 27.1 5.4 41 112-155 20-60 (61)
109 cd06404 PB1_aPKC PB1 domain is 47.0 87 0.0019 27.2 6.8 60 392-451 9-70 (83)
110 cd06125 DnaQ_like_exo DnaQ-lik 46.8 22 0.00049 30.7 3.4 28 189-216 35-63 (96)
111 KOG1457 RNA binding protein (c 46.2 54 0.0012 33.5 6.3 59 392-451 35-99 (284)
112 KOG0148 Apoptosis-promoting RN 42.4 61 0.0013 34.0 6.2 59 392-451 63-126 (321)
113 COG0724 RNA-binding proteins ( 40.3 1E+02 0.0022 29.5 7.2 60 391-451 115-179 (306)
114 cd02641 R3H_Smubp-2_like R3H d 39.4 71 0.0015 25.7 5.0 39 111-153 19-58 (60)
115 KOG0122 Translation initiation 38.9 90 0.0019 32.4 6.7 59 390-451 188-253 (270)
116 COG0349 Rnd Ribonuclease D [Tr 38.3 86 0.0019 34.2 6.8 106 187-328 60-166 (361)
117 PF15023 DUF4523: Protein of u 36.9 94 0.002 29.9 6.0 53 391-446 87-142 (166)
118 TIGR01642 U2AF_lg U2 snRNP aux 36.4 72 0.0016 35.4 6.2 56 392-447 176-241 (509)
119 PRK05359 oligoribonuclease; Pr 36.4 61 0.0013 31.5 5.0 21 196-216 97-117 (181)
120 KOG4212 RNA-binding protein hn 36.1 99 0.0021 34.5 6.8 65 393-459 46-116 (608)
121 cd06007 R3H_DEXH_helicase R3H 35.3 79 0.0017 25.5 4.6 39 112-154 19-58 (59)
122 cd06148 Egl_like_exo DEDDy 3'- 33.2 1.7E+02 0.0038 28.5 7.7 111 192-329 60-178 (197)
123 KOG0127 Nucleolar protein fibr 32.8 1.4E+02 0.003 34.4 7.4 62 386-450 287-355 (678)
124 cd06006 R3H_unknown_2 R3H doma 31.5 1.8E+02 0.0039 23.5 6.0 39 112-154 20-58 (59)
125 COG1847 Jag Predicted RNA-bind 31.4 81 0.0017 31.8 4.9 40 111-153 166-205 (208)
126 PF14605 Nup35_RRM_2: Nup53/35 30.8 1.1E+02 0.0024 23.8 4.7 49 393-445 3-52 (53)
127 cd02646 R3H_G-patch R3H domain 30.2 1.5E+02 0.0033 23.4 5.4 28 111-140 18-45 (58)
128 TIGR01388 rnd ribonuclease D. 29.5 2.5E+02 0.0053 30.5 8.7 100 189-329 62-167 (367)
129 KOG4206 Spliceosomal protein s 28.0 1.7E+02 0.0038 29.8 6.6 59 393-451 11-74 (221)
130 cd06139 DNA_polA_I_Ecoli_like_ 27.1 1E+02 0.0022 29.1 4.7 111 191-329 61-171 (193)
131 PF10792 DUF2605: Protein of u 25.9 50 0.0011 29.4 2.1 27 10-36 18-52 (98)
132 cd00007 35EXOc 3'-5' exonuclea 23.4 1.2E+02 0.0025 27.0 4.2 57 192-268 49-105 (155)
133 KOG0117 Heterogeneous nuclear 22.7 1.8E+02 0.0038 32.7 5.9 94 346-461 232-325 (506)
134 cd06135 Orn DEDDh 3'-5' exonuc 21.6 1.4E+02 0.003 28.6 4.5 22 305-326 149-170 (173)
135 KOG4207 Predicted splicing fac 21.5 2.1E+02 0.0045 29.2 5.7 49 402-451 24-77 (256)
136 PF05172 Nup35_RRM: Nup53/35/4 21.3 2.5E+02 0.0053 25.1 5.6 52 391-446 6-71 (100)
137 KOG0144 RNA-binding protein CU 21.3 1.1E+02 0.0024 34.0 4.1 62 394-456 127-192 (510)
138 KOG2416 Acinus (induces apopto 20.6 75 0.0016 36.7 2.7 58 391-451 444-503 (718)
139 KOG0114 Predicted RNA-binding 20.1 3.1E+02 0.0067 25.1 5.9 59 392-451 19-79 (124)
No 1
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=100.00 E-value=1.4e-35 Score=301.81 Aligned_cols=127 Identities=43% Similarity=0.594 Sum_probs=88.0
Q ss_pred hccHHHHHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCCh
Q 008236 183 SIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSL 262 (573)
Q Consensus 183 ~~Gf~~v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL 262 (573)
.+||+.|++.+.+++||||||||++|++|||++|+||||++++||++.++.+||.|||||||++.++ ...++|
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 4688888888999999999999999999999999999999999999999999999999999998765 247889
Q ss_pred HHHHHhhhhhhccCCccccccCCCCceeeeeeccccccC-CCCCcccchhhhHHHHHHHHHH
Q 008236 263 SKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSN-WNSGVKHEAGYDAFMTGCVFAQ 323 (573)
Q Consensus 263 ~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~-~~~~~~HEAGyDAymTG~vF~k 323 (573)
+.+++.+...-..... ..+.... ......... ......|||||||||||+||++
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 9998775432100000 0000000 011000011 1344599999999999999986
No 2
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=99.74 E-value=2.5e-18 Score=167.48 Aligned_cols=111 Identities=25% Similarity=0.366 Sum_probs=93.8
Q ss_pred hhccHHHHHHHHhcCCCe------EEechhhhHHHHHHHHh-cCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHh
Q 008236 182 ASIGFRHVIDLLSSEKKL------IVGHNCFLDIAHIYSKF-FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQR 254 (573)
Q Consensus 182 ~~~Gf~~v~~~l~~s~kp------iVgHN~~~Dl~~l~~~F-~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~ 254 (573)
+-|+...|.++|+.|++. ||.+|+.||++||++.+ .++||++.+||...++.+||.+||+|||+..+..++.
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 467888999999998875 89999999999999999 9999999999999999999999999999998865321
Q ss_pred hccCCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHH
Q 008236 255 MKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSH 327 (573)
Q Consensus 255 ~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~ 327 (573)
..+|+.+ ++.+ ++. +.|++|+||+||+||+.+|.||...
T Consensus 200 ----~~GL~~l----A~~L-------------------~~~-------RvG~~HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 200 ----KGGLQRL----ADLL-------------------GLK-------RVGIAHQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred ----hcCHHHH----HHHh-------------------CCC-------eeecccccCcHHHHHHHHHHHHHhc
Confidence 3446554 4433 122 6799999999999999999999653
No 3
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.66 E-value=6.7e-17 Score=180.52 Aligned_cols=426 Identities=17% Similarity=0.107 Sum_probs=236.9
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCCCCcCCCCCcchhhhHHHhhccccccccCCCCHHHHHHHHHHHHHhCCCeEEEEecc
Q 008236 64 LFAERMKDRLSEWLGGLLRNRDEGSEVQPSFNDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSG 143 (573)
Q Consensus 64 ~F~e~v~~~I~eWl~~~l~~~~~~~~~~~~~~~~~~~~q~~~~~~~p~l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~~~ 143 (573)
.|.-++....++|++++.....+-......+.+...-.+++...++|+..++.+...+...+..+..++....+++....
T Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~ 196 (564)
T KOG1990|consen 117 KWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFAL 196 (564)
T ss_pred hhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhccccccccee
Confidence 35566677889999987544433223344466666678889999999999999988888888877777777766655543
Q ss_pred CCCCceeEEEEe-cchhhHHHHHHHHHHHHHHHHHhhhhhhccHHHHHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCC
Q 008236 144 ENSCSQNVIVYI-ESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPL 222 (573)
Q Consensus 144 ~~~~~~~ivv~~-~~~eer~~l~~e~~e~~~~~~e~~l~~~~Gf~~v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~ 222 (573)
......+.+.+. .+.-++ .+.+.+..++-...+.....+.++. .+..+++++|+||+++|++|+|++|+++||+
T Consensus 197 ~~~~~~~~~~~~~~~~~~k-~~~~k~~~~rg~~~~~~~~~a~~l~----~~~~tg~~lv~hN~~~dv~y~~~~Fl~~lp~ 271 (564)
T KOG1990|consen 197 GRSRKLQGLAVAMVSFWEK-HEFAKILIKRGVLETRKERMADELQ----ELLLTGKVLVLHNKLLDVMYRYKNFLSPLPS 271 (564)
T ss_pred hhccccccchhHHHHHHHH-HHHHHHHHHhcchhhhccchHHHHH----HHHhcCCeEEeeccceeeeeehhhcccccch
Confidence 222233333332 222121 1122222222222222233344444 6889999999999999999999999999999
Q ss_pred CHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCC
Q 008236 223 TAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNW 302 (573)
Q Consensus 223 ~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~ 302 (573)
++++|+.. ...||.++||+.++...+ ++. .++...+.++...-...... +..+...-....+ ....
T Consensus 272 ~l~~f~~~-~~~fp~~~~~~~~~~~~~-~~~------~~~~~t~~e~~~~~~~~~~~---~~~~~~~~~~~~e---~~~~ 337 (564)
T KOG1990|consen 272 TLEEFTDS-SSMFPNIEDTKRLAKLSE-YQK------LNLKATLLELARAKAKKEKE---IERRSISSRLKLE---FEKA 337 (564)
T ss_pred hHHHhhhh-hhhhhhhHHHHHhhcccc-ccc------hhhhhhHHHHHHHhcccccC---cccccccchhhhh---hhcc
Confidence 99999999 999999999999987333 222 12333333322211100000 0011000000011 1233
Q ss_pred CCCcccchhhhHHHHHHHHHHHHHHhCCCccc-CCch-h-hhh---------hhhhhccccccccccCCCCcccccCCCC
Q 008236 303 NSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQ-QSSS-E-NLA---------HNEKLREHVNLLYLSWTNGEIINLSTGN 370 (573)
Q Consensus 303 ~~~~~HEAGyDAymTG~vF~kL~~~lg~~~~~-~~~~-~-~l~---------~~~~l~~~~N~L~~~~~~~~~idL~~~~ 370 (573)
..+..|++++++|.+|.+++..+......+.. +.+. . ... ....+..+.|...+.+.-+.+..+...
T Consensus 338 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n- 416 (564)
T KOG1990|consen 338 SSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIEN- 416 (564)
T ss_pred chhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeec-
Confidence 56889999999999999999987765322211 1110 0 000 011222333333333332222222110
Q ss_pred CCCccccccccccCCCcccccceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhc
Q 008236 371 RTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKG 450 (573)
Q Consensus 371 ~~~~~~~~~~l~~~~p~~~~~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~ 450 (573)
... | -+.++. ..-++-.|.+|..|+...+.-+-. =|+. +++|.-++..-|++..
T Consensus 417 --~~l-~----wk~~e~--~k~i~~~~~~~~~~~~~a~~le~e--sg~~-~v~~~~~~~~~ai~~y-------------- 470 (564)
T KOG1990|consen 417 --MHL-H----WKSREL--VKVICKEKNLPSQVKQYASALERE--SGGI-LVSIDKNPKGYAIIAY-------------- 470 (564)
T ss_pred --chh-h----hhhccc--ceeeeccccccHHHHHHHHHHHHH--hCCc-eeeeccCCchhhHHHh--------------
Confidence 000 0 001111 122344444555554444432221 1222 1233333322222211
Q ss_pred ccccCCCCcccccchhhhhcCCcccccchHHHHHHHhcccchhhhHHHHhHhcccccccccccccchhhhhhhhhhcc-c
Q 008236 451 SLDRNNDPISVLHPLAKLLEGGNTCAASYETYKEICSSTVSKVLFADQAKAVGIKWKTKLVESSDKTKEHESLRKVKA-V 529 (573)
Q Consensus 451 ~~~~~~~~~~~~~~l~~~~~~g~~~~a~y~ty~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 529 (573)
.-+..+.+.+ +.|.+.+..++.+..+.++.|+++|...++......+..-+........ +.+.+..+++..+++.. -
T Consensus 471 r~k~y~~p~~-l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~~~-~~~~d~~~en~~t~~~~~~ 548 (564)
T KOG1990|consen 471 RGKNYDRPTS-LRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMPAI-NKKDDLEEENSETVEEDQS 548 (564)
T ss_pred hhhhccCCcc-cCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhccccc-ccccchHHHhhhhhhhhhc
Confidence 1112233444 7899999999999999999999999999999999988888877776663 33555444444333333 2
Q ss_pred CCCCCCCc
Q 008236 530 NSDPSCGE 537 (573)
Q Consensus 530 ~~~~~~~~ 537 (573)
.++..|++
T Consensus 549 ~d~~~~~~ 556 (564)
T KOG1990|consen 549 EDDSLAER 556 (564)
T ss_pred cccccccc
Confidence 35566655
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=99.59 E-value=1.1e-15 Score=129.01 Aligned_cols=56 Identities=21% Similarity=0.316 Sum_probs=45.5
Q ss_pred cceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhc
Q 008236 391 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKG 450 (573)
Q Consensus 391 ~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~ 450 (573)
++||||++||++||.+||.++|+ +||++ +|+|||||||||+|+++++|+..+....
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 35699999999999999999996 89985 5699999999999999999998765554
No 5
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=99.34 E-value=2e-12 Score=126.52 Aligned_cols=109 Identities=24% Similarity=0.346 Sum_probs=88.2
Q ss_pred hccHHHHHHHHhcCCCe------EEechhhhHHHHHHHHh-cCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhh
Q 008236 183 SIGFRHVIDLLSSEKKL------IVGHNCFLDIAHIYSKF-FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRM 255 (573)
Q Consensus 183 ~~Gf~~v~~~l~~s~kp------iVgHN~~~Dl~~l~~~F-~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~ 255 (573)
-|.+..|.++|+.||.+ ||.+|..||++||++.. ..|||+..++|...+|.+||..||.|+++...-..
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 46678899999999985 89999999999999999 99999999999999999999999999998653221
Q ss_pred ccCCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 008236 256 KKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 328 (573)
Q Consensus 256 ~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~l 328 (573)
+..|+++ ...+ .+. +.|..|+||.||++|+..|......+
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 3334432 2211 122 67899999999999999999876655
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=98.12 E-value=5.3e-06 Score=67.87 Aligned_cols=32 Identities=13% Similarity=0.112 Sum_probs=29.5
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEecc
Q 008236 112 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSG 143 (573)
Q Consensus 112 l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~~~ 143 (573)
|.|++||+|||+||||+++++||+.+.+++..
T Consensus 19 l~le~cngf~RkLiyq~l~~~~~~~I~ve~~~ 50 (65)
T cd02637 19 LELEPCNGFQRKLIYQTLEQKYPKGIHVETLE 50 (65)
T ss_pred ccccccccHHHHHHHHHHHHHccccceeeeee
Confidence 67999999999999999999999999988753
No 7
>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function.
Probab=97.17 E-value=0.0015 Score=53.00 Aligned_cols=55 Identities=22% Similarity=0.311 Sum_probs=44.0
Q ss_pred eEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHH
Q 008236 393 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDL 448 (573)
Q Consensus 393 ~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~ 448 (573)
-|++.|- .++++.||++.|..-|+......|-|||||||=|+|.+.+.+..-|..
T Consensus 7 avhirGv-d~lsT~dI~~y~~~y~~~~~~~~IEWIdDtScNvvf~d~~~A~~AL~~ 61 (62)
T PF10309_consen 7 AVHIRGV-DELSTDDIKAYFSEYFDEEGPFRIEWIDDTSCNVVFKDEETAARALVA 61 (62)
T ss_pred eEEEEcC-CCCCHHHHHHHHHHhcccCCCceEEEecCCcEEEEECCHHHHHHHHHc
Confidence 4777785 669999999999755444444578999999999999999999877654
No 8
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.82 E-value=0.0077 Score=61.37 Aligned_cols=103 Identities=22% Similarity=0.309 Sum_probs=66.4
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh--cC-CCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHh
Q 008236 180 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF--FG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQR 254 (573)
Q Consensus 180 l~~~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F--~~-~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~ 254 (573)
+..+-.|..|++.+.+ .+-++|+||.-+|+.+|-..| +| ++|.. . .+..++||--|+...
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 4445566666666654 566899999999999998776 44 24431 1 234588998877532
Q ss_pred hccCCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHH
Q 008236 255 MKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACS 326 (573)
Q Consensus 255 ~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~ 326 (573)
......+|..+ |..+ .++. ..-..|.|-+||++|+.||+.|..
T Consensus 132 ~p~~~~~L~aL----~~~~-------------------gi~~------~~r~~H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 132 FPGKRNSLDAL----CKRY-------------------GIDN------SHRTLHGALLDAEILAEVYLAMTG 174 (240)
T ss_pred cCCCCCCHHHH----HHHC-------------------CCCC------CCCCCCCHHHHHHHHHHHHHHHHC
Confidence 11224467665 4332 1221 112579999999999999999964
No 9
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.79 E-value=0.0097 Score=59.33 Aligned_cols=105 Identities=17% Similarity=0.199 Sum_probs=63.8
Q ss_pred hhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhc--CCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhc
Q 008236 181 KASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFF--GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMK 256 (573)
Q Consensus 181 ~~~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~--~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~ 256 (573)
..+-.|..++..+.. .+.++||||.-+|+.+|-+.|. +..|. ....++||.-++.. +.....
T Consensus 69 ~~~p~~~ev~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~-----------~~~~~~dtl~l~~~---~~~~~~ 134 (217)
T TIGR00573 69 KDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVEP-----------KTNDVIDTTDTLQY---ARPEFP 134 (217)
T ss_pred cCCCCHHHHHHHHHHHhCCCEEEEeccHHHHHHHHHHHHHhcCCCC-----------CccceecHHHHHHH---HHHhCC
Confidence 334455555555544 5679999999999999987763 22110 11245677666543 222222
Q ss_pred cCCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 008236 257 KSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 328 (573)
Q Consensus 257 ~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~l 328 (573)
....+|..+.+. + +++. .....|.|..||.+|+.+|..|+...
T Consensus 135 ~~~~~L~~l~~~----~-------------------gl~~------~~~~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 135 GKRNTLDALCKR----Y-------------------EITN------SHRALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred CCCCCHHHHHHH----c-------------------CCCC------CCcccCCHHHHHHHHHHHHHHHHhcc
Confidence 234467766432 1 1110 11268999999999999999997754
No 10
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.69 E-value=0.01 Score=59.98 Aligned_cols=98 Identities=19% Similarity=0.180 Sum_probs=61.0
Q ss_pred HHHHHHHH---hcCCCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCC
Q 008236 186 FRHVIDLL---SSEKKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSST 260 (573)
Q Consensus 186 f~~v~~~l---~~s~kpiVgHN~~~Dl~~l~~~F--~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~t 260 (573)
+..|.+.| ...+.|+|+||.-+|+.+|-+.+ ++ +|.- .-+ .++||-.|+...... ..+..
T Consensus 79 l~e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~-~~~~---------~~~-~~iDt~~l~~~~~~~----~~~~~ 143 (232)
T PRK07942 79 LAEIADALREAWARGVPVVVFNAPYDLTVLDRELRRHG-LPSL---------VPG-PVIDPYVIDKAVDRY----RKGKR 143 (232)
T ss_pred HHHHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcC-CCCc---------cCC-cEeeHHHHHhhhhcc----cCCCC
Confidence 34444444 34688999999999999998776 22 2211 112 256987776432211 11234
Q ss_pred ChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 261 SLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 261 sL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
+|+.+. ..+ +++ ....|.|..||++|+.+|.+|+..++
T Consensus 144 ~L~~l~----~~~-------------------gi~--------~~~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 144 TLTALC----EHY-------------------GVR--------LDNAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred CHHHHH----HHc-------------------CCC--------CCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 576653 222 111 13479999999999999999988764
No 11
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=96.59 E-value=0.0097 Score=58.15 Aligned_cols=84 Identities=26% Similarity=0.382 Sum_probs=54.1
Q ss_pred CCCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHccC-C-CCcchhHHhhhchHHHHhhccCCCChHHHHHhhhh
Q 008236 196 EKKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYF-P-HIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCP 271 (573)
Q Consensus 196 s~kpiVgHN~~~Dl~~l~~~F--~~~LP~~~~eFk~~l~~~F-P-~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~ 271 (573)
.+.++||||.-+|+.+|-+.+ ++--. ..| | .++||.-|+.. + . +...|..+ |.
T Consensus 101 ~~~~lVaHna~FD~~fL~~~~~~~~~~~-----------~~~~~~~~lDt~~la~~---~---~--~~~~L~~l----~~ 157 (189)
T cd06134 101 TRAILVGHNAHFDLGFLNAAVARCKIKR-----------NPFHPFSTFDTATLAGL---A---Y--GQTVLAKA----CQ 157 (189)
T ss_pred CCCeEEEecchhhHHHHHHHHHHhCCCC-----------CCCCCCcEEEHHHHHHH---H---h--CCCcHHHH----HH
Confidence 367999999999999998766 22100 112 2 36899888753 1 1 13456554 33
Q ss_pred hhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHH
Q 008236 272 QIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSH 327 (573)
Q Consensus 272 ~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~ 327 (573)
.+ .. +. .....|.|.+||++|+.+|.+|.+.
T Consensus 158 ~~----------gi-------~~--------~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 158 AA----------GI-------EF--------DNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred HC----------CC-------CC--------CCCCCcChHHHHHHHHHHHHHHHHh
Confidence 22 01 11 1135799999999999999999753
No 12
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.59 E-value=0.056 Score=56.94 Aligned_cols=85 Identities=19% Similarity=0.262 Sum_probs=55.2
Q ss_pred CCCeEEechhhhHHHHHHHHh--cC-CCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhh
Q 008236 196 EKKLIVGHNCFLDIAHIYSKF--FG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQ 272 (573)
Q Consensus 196 s~kpiVgHN~~~Dl~~l~~~F--~~-~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~ 272 (573)
.+.++|+||.-+|+.+|-+.+ ++ ++| ....+||--|+... + .. ..+.+|..+ +..
T Consensus 79 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~~-------------~~~~idT~~lar~l--~-~~--~~~~~L~~L----~~~ 136 (309)
T PRK06195 79 NNNLVIAHNASFDISVLRKTLELYNIPMP-------------SFEYICTMKLAKNF--Y-SN--IDNARLNTV----NNF 136 (309)
T ss_pred CCCEEEEECcHHHHHHHHHHHHHhCCCCC-------------CCCEEEHHHHHHHH--c-CC--CCcCCHHHH----HHH
Confidence 467999999999999997765 22 222 11356886665421 1 11 124456554 222
Q ss_pred hccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhCC
Q 008236 273 IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGI 330 (573)
Q Consensus 273 l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg~ 330 (573)
+ .++ ...|.|-+||++|+.+|..|+..++.
T Consensus 137 ~-------------------gi~---------~~~H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 137 L-------------------GYE---------FKHHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred c-------------------CCC---------CcccCCHHHHHHHHHHHHHHHHHhcc
Confidence 2 111 13699999999999999999998865
No 13
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.43 E-value=0.017 Score=56.74 Aligned_cols=101 Identities=16% Similarity=0.197 Sum_probs=58.9
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhc----CCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHH
Q 008236 180 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFF----GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQ 253 (573)
Q Consensus 180 l~~~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~----~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~ 253 (573)
+.++.-|..+++.+.+ .+.++||||.-+|+.+|-..|. .++|. ..+||.-|..... ...
T Consensus 92 l~~~~~~~~vl~~~~~~i~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~--------------~~id~~~l~~~~~-~~~ 156 (202)
T PRK09145 92 LEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPN--------------PLIEVSALYYDKK-ERH 156 (202)
T ss_pred HhcCCCHHHHHHHHHHHHcCCeEEEeCHHHHHHHHHHHHHHhcCCCCCC--------------CeeeHHHHHHHHh-hcc
Confidence 3445556666666554 5789999999999998876542 23332 2457765532110 000
Q ss_pred hh-ccCCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHH
Q 008236 254 RM-KKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACS 326 (573)
Q Consensus 254 ~~-~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~ 326 (573)
.- ...+-+|..+.+. + .++ ....|.|-.||++|+.+|.+|..
T Consensus 157 ~~~~~~~~~L~~l~~~----~-------------------gi~--------~~~~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 157 LPDAYIDLRFDAILKH----L-------------------DLP--------VLGRHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCCcccCCCHHHHHHH----c-------------------CCC--------CCCCCCcHHHHHHHHHHHHHHHh
Confidence 00 0113455554221 1 111 13469999999999999999854
No 14
>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=96.39 E-value=0.024 Score=57.14 Aligned_cols=101 Identities=22% Similarity=0.343 Sum_probs=62.2
Q ss_pred hhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh--cCC-CCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhc
Q 008236 182 ASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF--FGP-LPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMK 256 (573)
Q Consensus 182 ~~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F--~~~-LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~ 256 (573)
.+.-|..+++.+.+ .+.++|+||.-+|+.+|-..| +|+ +|. + ..|-.++||--|+... ..
T Consensus 65 ~~p~f~ev~~~f~~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~----~-----~~~~~~iDTl~lar~~------~p 129 (225)
T TIGR01406 65 DKPKFKEIADEFLDFIGGSELVIHNAAFDVGFLNYELERLGPTIKK----I-----GEFCRVIDTLAMARER------FP 129 (225)
T ss_pred CCCCHHHHHHHHHHHhCCCEEEEEecHHHHHHHHHHHHHhCCCCcc----c-----ccCCCEEEHHHHHHHH------cC
Confidence 34456555554432 456899999999999998776 442 111 0 0122478998887531 11
Q ss_pred cCCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHH
Q 008236 257 KSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACS 326 (573)
Q Consensus 257 ~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~ 326 (573)
....+|..+ |..+ .++. ..-..|.|-.||.+|+.+|+.|..
T Consensus 130 ~~~~~L~~L----~~~~-------------------gi~~------~~r~~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 130 GQRNSLDAL----CKRF-------------------KVDN------SHRTLHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred CCCCCHHHH----HHhc-------------------CCCC------CCCCCcCHHHHHHHHHHHHHHHHc
Confidence 224566655 3322 1111 113589999999999999999855
No 15
>PRK07740 hypothetical protein; Provisional
Probab=96.36 E-value=0.016 Score=59.09 Aligned_cols=101 Identities=18% Similarity=0.195 Sum_probs=62.9
Q ss_pred hhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCC
Q 008236 182 ASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 259 (573)
Q Consensus 182 ~~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~ 259 (573)
.+.-|..++..+.. .+.++||||.-+|+.++-+.+...+... +...++||..++.... .. .+.
T Consensus 124 ~ap~~~evl~~f~~fi~~~~lVahna~fD~~fL~~~~~~~~~~~----------~~~~~iDt~~l~r~l~---~~--~~~ 188 (244)
T PRK07740 124 FAPPLAEVLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQP----------FTHRLIDTMFLTKLLA---HE--RDF 188 (244)
T ss_pred CCCCHHHHHHHHHHHhCCCEEEEeCHHHHHHHHHHHHHHhcCCC----------cCCCeechHHHHHHHc---CC--CCC
Confidence 34445555555432 4679999999999998876653322111 1236889988865321 11 124
Q ss_pred CChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 008236 260 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 328 (573)
Q Consensus 260 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~l 328 (573)
.+|.++... + .++ ....|.|-+||++|+.+|.++...+
T Consensus 189 ~sL~~l~~~----~-------------------gi~--------~~~~H~Al~Da~ata~l~~~ll~~~ 226 (244)
T PRK07740 189 PTLDDALAY----Y-------------------GIP--------IPRRHHALGDALMTAKLWAILLVEA 226 (244)
T ss_pred CCHHHHHHH----C-------------------CcC--------CCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 567766332 1 011 1235999999999999999997766
No 16
>PRK05168 ribonuclease T; Provisional
Probab=96.36 E-value=0.013 Score=58.38 Aligned_cols=87 Identities=23% Similarity=0.323 Sum_probs=56.3
Q ss_pred CCCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHccCC-CCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhh
Q 008236 196 EKKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFP-HIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQ 272 (573)
Q Consensus 196 s~kpiVgHN~~~Dl~~l~~~F--~~~LP~~~~eFk~~l~~~FP-~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~ 272 (573)
.+.++||||.-+|+.+|.+.+ ++-.. ..++| .++||.-|+... . +...|..+. ..
T Consensus 113 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~----------~~~~~~~~iDt~~lar~~------~--~~~~L~~l~----~~ 170 (211)
T PRK05168 113 NRAILVAHNAHFDLSFLMAAAERAGLKR----------NPFHPFSTFDTATLSGLA------L--GQTVLAKAC----QA 170 (211)
T ss_pred CCceEEEeccHHhHHHHHHHHHHhCCCC----------CCCCCCcEeeHHHHHHHH------c--CCCCHHHHH----HH
Confidence 378999999999999998765 22110 01233 478998887521 1 123455542 21
Q ss_pred hccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 273 IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 273 l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
+ ..| . .....|.|-+||+.|+.+|.+|+..+.
T Consensus 171 ~----------gl~-------~--------~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 171 A----------GIE-------F--------DNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred C----------CCC-------C--------CCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 1 011 1 113689999999999999999988773
No 17
>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=96.15 E-value=0.037 Score=52.20 Aligned_cols=99 Identities=19% Similarity=0.161 Sum_probs=58.6
Q ss_pred hhccHHHHHHHHh--cCCCeEEechhhhHHHHHHHHhcC-CCCCCHHHHHHHHHccCC-CCcchhHHhhhchHHHHhhcc
Q 008236 182 ASIGFRHVIDLLS--SEKKLIVGHNCFLDIAHIYSKFFG-PLPLTAEEFISSVNKYFP-HIIDTKILLNSNSILQQRMKK 257 (573)
Q Consensus 182 ~~~Gf~~v~~~l~--~s~kpiVgHN~~~Dl~~l~~~F~~-~LP~~~~eFk~~l~~~FP-~I~DTK~La~~~~~lk~~~~~ 257 (573)
....|..+++.+. -.+-++||||.-+|+.+|-+.+.. .++.. ...| ..+||-.++... ...
T Consensus 64 ~~~~~~~v~~~l~~~l~~~~lv~hn~~fD~~~l~~~~~~~~~~~~---------~~~~~~~idt~~~~~~~------~~~ 128 (167)
T cd06131 64 DKPKFAEIADEFLDFIRGAELVIHNASFDVGFLNAELSLLGLGKK---------IIDFCRVIDTLALARKK------FPG 128 (167)
T ss_pred cCCCHHHHHHHHHHHHCCCeEEEeChHHhHHHHHHHHHHhCCCcc---------cccCCCceEhHHHHHHH------cCC
Confidence 3445555555543 234689999999999988666521 11110 0123 468987666421 111
Q ss_pred CCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHH
Q 008236 258 SSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQA 324 (573)
Q Consensus 258 ~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL 324 (573)
...+|+.+.+. + .++. .....|.|.+||+.|+.+|.+|
T Consensus 129 ~~~~L~~l~~~----~-------------------~i~~------~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 129 KPNSLDALCKR----F-------------------GIDN------SHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCHHHHHHH----C-------------------CCCC------CCCCCCChHHHHHHHHHHHHHh
Confidence 24567776432 2 0110 1135899999999999999987
No 18
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=95.99 E-value=0.043 Score=58.01 Aligned_cols=96 Identities=17% Similarity=0.199 Sum_probs=60.6
Q ss_pred cHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh--cC-CCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCC
Q 008236 185 GFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF--FG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 259 (573)
Q Consensus 185 Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F--~~-~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~ 259 (573)
-|..+++.|.. .+.++|+||.-+|+.+|.+.| ++ ++|. ...+||--|+.... ....+
T Consensus 80 ~f~ev~~~l~~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~-------------~~~ldTl~lar~~~-----~~~~~ 141 (313)
T PRK06063 80 QFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPV-------------DQVMCTVELARRLG-----LGLPN 141 (313)
T ss_pred CHHHHHHHHHHHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCC-------------CCEEehHHHHHHhc-----cCCCC
Confidence 34444444432 467999999999999998776 22 2231 13578887765321 01124
Q ss_pred CChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 260 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 260 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
..|..+. ..+ .+ .....|.|-.||++|+.+|..+...++
T Consensus 142 ~kL~~l~----~~~-------------------gi--------~~~~~H~Al~DA~ata~l~~~ll~~~~ 180 (313)
T PRK06063 142 LRLETLA----AHW-------------------GV--------PQQRPHDALDDARVLAGILRPSLERAR 180 (313)
T ss_pred CCHHHHH----HHc-------------------CC--------CCCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 4566553 222 11 124679999999999999999877663
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=95.90 E-value=0.025 Score=55.87 Aligned_cols=86 Identities=26% Similarity=0.343 Sum_probs=54.7
Q ss_pred CCCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHccCC-CCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhh
Q 008236 196 EKKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFP-HIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQ 272 (573)
Q Consensus 196 s~kpiVgHN~~~Dl~~l~~~F--~~~LP~~~~eFk~~l~~~FP-~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~ 272 (573)
.+.++||||.-+|+.+|-+.+ ++..+..+ -| .++||--|+... . +..+|..+ |..
T Consensus 104 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~----------~~~~~lDTl~lar~~------~--~~~~L~~l----~~~ 161 (200)
T TIGR01298 104 QRAILVGHNANFDLGFLNAAVERTSLKRNPF----------HPFSTFDTATLAGLA------Y--GQTVLAKA----CQA 161 (200)
T ss_pred CCCEEEEECchhhHHHHHHHHHHhCCCCCCC----------CCCcEEEHHHHHHHH------c--CcccHHHH----HHH
Confidence 467899999999999998776 33221100 01 277997776421 1 12345554 322
Q ss_pred hccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 008236 273 IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 328 (573)
Q Consensus 273 l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~l 328 (573)
+ .++. .....|.|-+||++|+.+|..|+..+
T Consensus 162 ~-------------------gi~~------~~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 162 A-------------------GXDF------DSTQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred c-------------------CCCc------cccchhhhHHhHHHHHHHHHHHHHHH
Confidence 2 0110 11368999999999999999998876
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=95.67 E-value=0.069 Score=49.43 Aligned_cols=90 Identities=18% Similarity=0.214 Sum_probs=55.3
Q ss_pred hccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh--cCC-CCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhcc
Q 008236 183 SIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF--FGP-LPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKK 257 (573)
Q Consensus 183 ~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F--~~~-LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~ 257 (573)
+..|..+++.+.+ .+.++||||.-+|+.+|-+.+ +|. .| -+ ..+||.-++... +.. .
T Consensus 61 ~~~~~~v~~~l~~~l~~~~lv~hn~~fD~~~l~~~~~~~g~~~~------------~~-~~idt~~~~~~~--~~~---~ 122 (156)
T cd06130 61 APTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPP------------PY-QYLCTVRLARRV--WPL---L 122 (156)
T ss_pred CCCHHHHHHHHHHHhCCCEEEEeChHHhHHHHHHHHHHcCCCCC------------CC-CEEEHHHHHHHH--hcc---C
Confidence 3345555444432 458999999999999988776 221 22 12 367887665431 111 1
Q ss_pred CCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHH
Q 008236 258 SSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFA 322 (573)
Q Consensus 258 ~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~ 322 (573)
...+|..+.+. + .++ .. .|.|-+||+.|+.+|+
T Consensus 123 ~~~~L~~l~~~----~-------------------g~~--------~~-~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 123 PNHKLNTVAEH----L-------------------GIE--------LN-HHDALEDARACAEILL 155 (156)
T ss_pred CCCCHHHHHHH----c-------------------CCC--------cc-CcCchHHHHHHHHHHh
Confidence 35667766432 1 111 13 8999999999999985
No 21
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=95.56 E-value=0.13 Score=47.83 Aligned_cols=101 Identities=24% Similarity=0.251 Sum_probs=61.3
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechh-hhHHHHHHHHh--cC-CCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHH
Q 008236 180 IKASIGFRHVIDLLSS--EKKLIVGHNC-FLDIAHIYSKF--FG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQ 253 (573)
Q Consensus 180 l~~~~Gf~~v~~~l~~--s~kpiVgHN~-~~Dl~~l~~~F--~~-~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~ 253 (573)
+.++.-|..+++.+.. .+.++|+||+ -+|+-+|-..+ .+ +.| .+-.++||.-++...
T Consensus 61 l~~~~~~~~~~~~~~~~l~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~------------~~~~~iD~~~~~~~~----- 123 (169)
T smart00479 61 LDDAPTFEEVLEELLEFLKGKILVAGNALNFDLRFLKLEHPRLGIKDP------------PKNPVIDTLKLARAL----- 123 (169)
T ss_pred HhCCCCHHHHHHHHHHHhcCCEEEEeCCHHHhHHHHHHHHHHhCCCCC------------cCCCeeEHHHHHHHH-----
Confidence 3344555555554432 3457888988 99999888776 22 223 111267997665421
Q ss_pred hhccCCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 008236 254 RMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 328 (573)
Q Consensus 254 ~~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~l 328 (573)
......+|..+.+. + .++ ..+..|.|-.||.+|+.+|.+|...+
T Consensus 124 -~~~~~~~L~~l~~~----~-------------------~~~-------~~~~~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 124 -NPGRKYSLKKLAER----L-------------------GLE-------VIGRAHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred -CCCCCCCHHHHHHH----C-------------------CCC-------CCCCCcCcHHHHHHHHHHHHHHHHHh
Confidence 11125667766332 2 011 11347999999999999999998765
No 22
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=95.34 E-value=0.067 Score=54.73 Aligned_cols=100 Identities=21% Similarity=0.151 Sum_probs=62.2
Q ss_pred hccHHHHHHHHh---cCCCeEEechhhhHHHHHHHHhc-CCCCCCHHHHHHHHHccC-CCCcchhHHhhhchHHHHhhcc
Q 008236 183 SIGFRHVIDLLS---SEKKLIVGHNCFLDIAHIYSKFF-GPLPLTAEEFISSVNKYF-PHIIDTKILLNSNSILQQRMKK 257 (573)
Q Consensus 183 ~~Gf~~v~~~l~---~s~kpiVgHN~~~Dl~~l~~~F~-~~LP~~~~eFk~~l~~~F-P~I~DTK~La~~~~~lk~~~~~ 257 (573)
+--|..+++.+. ..+.++||||.-+|+.+|-+.|. .-+|.. .+ -.++||-.++...+ ..
T Consensus 71 ~p~~~ev~~~~~~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~----------~~~~~~iDtl~lar~~~------~~ 134 (250)
T PRK06310 71 KPKIAEVFPQIKGFFKEGDYIVGHSVGFDLQVLSQESERIGETFL----------SKHYYIIDTLRLAKEYG------DS 134 (250)
T ss_pred CCCHHHHHHHHHHHhCCCCEEEEECHHHHHHHHHHHHHHcCCCcc----------ccCCcEEehHHHHHhcc------cC
Confidence 334555544443 34478999999999999987762 112210 01 24789988865321 11
Q ss_pred CCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 258 SSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 258 ~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
.+.+|+.+...+ .+ .....|.|-.||++|+.+|..|+..++
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 245677664321 01 112479999999999999999987663
No 23
>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=95.22 E-value=0.08 Score=41.67 Aligned_cols=57 Identities=23% Similarity=0.353 Sum_probs=45.7
Q ss_pred EEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe----cCceEEEEecchhhHHHHHHHhcc
Q 008236 394 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV----DETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 394 v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i----ddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
+|+.++|..++..+|++.|. .||+.....+..= ....|||.|.+.++++..|..++.
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 5998743333331 268999999999999998876654
No 24
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=94.99 E-value=0.13 Score=54.56 Aligned_cols=86 Identities=21% Similarity=0.251 Sum_probs=55.9
Q ss_pred CCCeEEechhhhHHHHHHHHh-cCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhhhc
Q 008236 196 EKKLIVGHNCFLDIAHIYSKF-FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 274 (573)
Q Consensus 196 s~kpiVgHN~~~Dl~~l~~~F-~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~l~ 274 (573)
.+.++||||+-+|+.+|.+.+ .-.+|. ....++||-.++... + .. .+..+|..+. ..+
T Consensus 87 ~~~~lVaHNa~FD~~fL~~~~~~~gl~~-----------~~~~~iDtl~la~~~--~-~~--~~~~kL~~L~----~~l- 145 (313)
T PRK06807 87 HTNVIVAHNASFDMRFLKSNVNMLGLPE-----------PKNKVIDTVFLAKKY--M-KH--APNHKLETLK----RML- 145 (313)
T ss_pred cCCeEEEEcHHHHHHHHHHHHHHcCCCC-----------CCCCEeeHHHHHHHH--h-CC--CCCCCHHHHH----HHc-
Confidence 356899999999999999887 222221 012367887775421 1 11 1234566552 222
Q ss_pred cCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 275 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 275 ~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
+++ . ..|.|=.||++|+.+|.+++...+
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 25
>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=94.94 E-value=0.1 Score=41.80 Aligned_cols=54 Identities=30% Similarity=0.452 Sum_probs=43.6
Q ss_pred EEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecC------ceEEEEecchhhHHHHHHHhc
Q 008236 394 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE------TAVFVQFSRAEMVSKFLDLKG 450 (573)
Q Consensus 394 v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~idd------tsa~V~l~~~e~~~~~L~~~~ 450 (573)
|++.|.|+.++..||.+.|+ .||. |..|..+-+ ..|||.|.+.+.|+.+|....
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 57899999999999999986 5675 467777644 899999999999999988765
No 26
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=94.80 E-value=0.19 Score=50.53 Aligned_cols=99 Identities=17% Similarity=0.100 Sum_probs=59.8
Q ss_pred hhhhccHHHHHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCC
Q 008236 180 IKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 259 (573)
Q Consensus 180 l~~~~Gf~~v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~ 259 (573)
+..+--|..+++.+. ...++||||.-+|..+|- .+ --..+||=-|++.. + ....
T Consensus 58 v~~ap~~~ev~~~~~-~~~~lVaHNa~FD~~~L~-----~~--------------~~~~idTl~lar~l--~----p~~~ 111 (219)
T PRK07983 58 VADKPWIEDVIPHYY-GSEWYVAHNASFDRRVLP-----EM--------------PGEWICTMKLARRL--W----PGIK 111 (219)
T ss_pred HcCCCCHHHHHHHHc-CCCEEEEeCcHhhHHHHh-----Cc--------------CCCcEeHHHHHHHH--c----cCCC
Confidence 333445666776653 467999999999987762 11 12457887776531 1 1112
Q ss_pred CChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhCC
Q 008236 260 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGI 330 (573)
Q Consensus 260 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg~ 330 (573)
.+|+.+ |..+. +++... .....|.|-+||++|+.+|.+|++..|.
T Consensus 112 ~~l~~L----~~~~~---------------l~~~~~-------~~~~aHrAl~Da~ata~ll~~l~~~~~~ 156 (219)
T PRK07983 112 YSNMAL----YKSRK---------------LNVQTP-------PGLHHHRALYDCYITAALLIDIMNTSGW 156 (219)
T ss_pred CCHHHH----HHHcC---------------CCCCCC-------CCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 345444 33220 000000 1146899999999999999999987764
No 27
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=94.79 E-value=0.18 Score=51.29 Aligned_cols=108 Identities=16% Similarity=0.069 Sum_probs=63.4
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhc--CCCCCCHHHHHHHHHccCCCCcchhHHhhhchH-----
Q 008236 180 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFF--GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSI----- 250 (573)
Q Consensus 180 l~~~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~--~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~----- 250 (573)
+..+--|..+++.+.. .+.++||||.-+|+.+|-+.+- +..|. -+.++||=-|+...-+
T Consensus 110 l~~ap~~~evl~~l~~~~~~~~lVaHna~FD~~fL~~~l~~~~~~~~------------~~~~iDTl~Lar~l~~~~~~~ 177 (239)
T PRK09146 110 LQDAPDLERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGI------------EFPVIDTMEIEARIQRKQAGG 177 (239)
T ss_pred HhCCCCHHHHHHHHHHHhCCCEEEEECHHHHHHHHHHHHHHhcCCCC------------CCceechHHHHHHHccccccc
Confidence 4444556666666664 4679999999999999987652 11111 1125688777653210
Q ss_pred -HHHhhcc--CCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHH
Q 008236 251 -LQQRMKK--SSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSH 327 (573)
Q Consensus 251 -lk~~~~~--~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~ 327 (573)
+...... .+-.|..+ +..+ ++ .....|.|-.||++|+.+|..++..
T Consensus 178 ~~~~~~~~~~~~~~L~~l----~~~~-------------------gl--------~~~~~H~Al~DA~ata~l~~~~~~~ 226 (239)
T PRK09146 178 LWNRLKGKKPESIRLADS----RLRY-------------------GL--------PAYSPHHALTDAIATAELLQAQIAH 226 (239)
T ss_pred ccchhccCCCCCCCHHHH----HHHc-------------------CC--------CCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 0000000 12223332 1111 01 1245799999999999999999988
Q ss_pred hCC
Q 008236 328 LGI 330 (573)
Q Consensus 328 lg~ 330 (573)
++.
T Consensus 227 ~~~ 229 (239)
T PRK09146 227 HFS 229 (239)
T ss_pred HcC
Confidence 854
No 28
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=94.62 E-value=0.18 Score=49.92 Aligned_cols=23 Identities=30% Similarity=0.208 Sum_probs=20.9
Q ss_pred CcccchhhhHHHHHHHHHHHHHH
Q 008236 305 GVKHEAGYDAFMTGCVFAQACSH 327 (573)
Q Consensus 305 ~~~HEAGyDAymTG~vF~kL~~~ 327 (573)
+..|.|-.||++|+.+|.+|...
T Consensus 157 ~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 157 GKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred CCCcChHHHHHHHHHHHHHHHhC
Confidence 56899999999999999999875
No 29
>PRK06722 exonuclease; Provisional
Probab=94.54 E-value=0.25 Score=51.68 Aligned_cols=22 Identities=36% Similarity=0.309 Sum_probs=20.2
Q ss_pred CcccchhhhHHHHHHHHHHHHH
Q 008236 305 GVKHEAGYDAFMTGCVFAQACS 326 (573)
Q Consensus 305 ~~~HEAGyDAymTG~vF~kL~~ 326 (573)
|..|.|-.||.+|+.+|++|..
T Consensus 158 g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 158 GKQHRALADAENTANILLKAYS 179 (281)
T ss_pred CCCcCcHHHHHHHHHHHHHHhc
Confidence 6789999999999999999874
No 30
>KOG4483 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.46 E-value=0.058 Score=57.93 Aligned_cols=59 Identities=22% Similarity=0.413 Sum_probs=50.9
Q ss_pred cceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 008236 391 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 391 ~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
.+++=+.+||...++.|+...|+ -|+..+ +.|.|+|||.||-+|++.-.+.+.|..+-.
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 45677889999999999999987 677765 699999999999999999999998877444
No 31
>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=94.32 E-value=0.18 Score=45.62 Aligned_cols=77 Identities=21% Similarity=0.172 Sum_probs=46.3
Q ss_pred CeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHccC-CCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhhhc
Q 008236 198 KLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYF-PHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 274 (573)
Q Consensus 198 kpiVgHN~~~Dl~~l~~~F--~~~LP~~~~eFk~~l~~~F-P~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~l~ 274 (573)
-++||||.-+|+-+|.+.| ++ ...+ ...+||..++....+. .....|..+. +..+
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 7899999999988877666 22 1122 3578998776432110 1122232220 0100
Q ss_pred cCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHH
Q 008236 275 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFA 322 (573)
Q Consensus 275 ~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~ 322 (573)
. ......|.|-+||++|+.+|.
T Consensus 138 ------------------~--------~~~~~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 138 ------------------G--------IPLEGAHRALADALATAELLL 159 (159)
T ss_pred ------------------C--------CCCCCCCCcHHHHHHHHHHhC
Confidence 0 123579999999999999983
No 32
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=94.11 E-value=0.34 Score=48.87 Aligned_cols=100 Identities=16% Similarity=0.148 Sum_probs=59.4
Q ss_pred hccHHHHHHHHh---cCCCeEEechh-hhHHHHHHHHhc-CCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhcc
Q 008236 183 SIGFRHVIDLLS---SEKKLIVGHNC-FLDIAHIYSKFF-GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKK 257 (573)
Q Consensus 183 ~~Gf~~v~~~l~---~s~kpiVgHN~-~~Dl~~l~~~F~-~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~ 257 (573)
+--|..+++.+. .....+||||. -+|+-+|-+.|. ..+|.. .-..+||--++.. +....
T Consensus 63 ~p~f~ev~~~~~~fi~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~-----------~~~~iDt~~l~~~---~~~~~-- 126 (232)
T PRK06309 63 APKFPEAYQKFIEFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPP-----------TLRTIDSLKWAQK---YRPDL-- 126 (232)
T ss_pred CCCHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHcCCCCC-----------CCcEEeHHHHHHH---HcCCC--
Confidence 344444444432 34568999995 799999987761 112110 0135788666542 11111
Q ss_pred CCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 258 SSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 258 ~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
...+|+.++.. + .+ .....|.|-.||+.|+.+|.+|+..++
T Consensus 127 ~~~~L~~l~~~----~-------------------~~--------~~~~aH~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 127 PKHNLQYLRQV----Y-------------------GF--------EENQAHRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred CCCCHHHHHHH----c-------------------CC--------CCCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 13456655322 1 01 124689999999999999999987764
No 33
>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=93.85 E-value=0.13 Score=48.24 Aligned_cols=16 Identities=19% Similarity=0.090 Sum_probs=14.7
Q ss_pred cccchhhhHHHHHHHH
Q 008236 306 VKHEAGYDAFMTGCVF 321 (573)
Q Consensus 306 ~~HEAGyDAymTG~vF 321 (573)
..|.|..||+.|+.+|
T Consensus 136 ~~H~Al~DA~at~~l~ 151 (152)
T cd06144 136 GEHSSVEDARAAMRLY 151 (152)
T ss_pred CCcCcHHHHHHHHHHh
Confidence 4699999999999987
No 34
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=93.64 E-value=0.6 Score=48.12 Aligned_cols=85 Identities=20% Similarity=0.137 Sum_probs=52.5
Q ss_pred CCCeEEechhhhHHHHHHHHhc-CCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhhhc
Q 008236 196 EKKLIVGHNCFLDIAHIYSKFF-GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 274 (573)
Q Consensus 196 s~kpiVgHN~~~Dl~~l~~~F~-~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~l~ 274 (573)
.+.++||||.-+|+.++-+.|. ..+|. +.+..+||--++.. .+....-+|+.+. ..+
T Consensus 146 ~~~v~VaHNa~FD~~fL~~~l~r~g~~~-----------~~~~~ldtl~la~~------~~~~~~~~L~~L~----~~l- 203 (257)
T PRK08517 146 GDSVFVAHNVNFDYNFISRSLEEIGLGP-----------LLNRKLCTIDLAKR------TIESPRYGLSFLK----ELL- 203 (257)
T ss_pred CCCeEEEECHHHHHHHHHHHHHHcCCCC-----------CCCCcEehHHHHHH------HccCCCCCHHHHH----HHc-
Confidence 3568999999999999877661 11111 12234566544432 1112234566553 211
Q ss_pred cCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 008236 275 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 328 (573)
Q Consensus 275 ~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~l 328 (573)
+++ ....|.|-.||++|+.+|.++...+
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 2368999999999999999998776
No 35
>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=93.62 E-value=0.21 Score=46.99 Aligned_cols=75 Identities=20% Similarity=0.213 Sum_probs=46.7
Q ss_pred CCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhhhcc
Q 008236 196 EKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIAL 275 (573)
Q Consensus 196 s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~l~~ 275 (573)
.+.++||||.-+|+-+|-. ..|.++||-.|+....+ . ...-+|..+ |..+.
T Consensus 75 ~~~vlVgHn~~fD~~fL~~-------------------~~~~~iDT~~l~r~~~~---~--~~~~~L~~L----~~~~~- 125 (150)
T cd06145 75 PDTILVGHSLENDLKALKL-------------------IHPRVIDTAILFPHPRG---P--PYKPSLKNL----AKKYL- 125 (150)
T ss_pred CCCEEEEcChHHHHHHhhc-------------------cCCCEEEcHHhccccCC---C--CCChhHHHH----HHHHC-
Confidence 4689999999999998631 23678999887653111 0 113456655 33220
Q ss_pred CCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHH
Q 008236 276 GSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVF 321 (573)
Q Consensus 276 ~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF 321 (573)
. + .++ ..+..|.|-.||++|+.+|
T Consensus 126 ---------~----~--~i~-------~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 126 ---------G----R--DIQ-------QGEGGHDSVEDARAALELV 149 (150)
T ss_pred ---------C----c--cee-------CCCCCCCcHHHHHHHHHHh
Confidence 0 0 011 1135699999999999887
No 36
>smart00362 RRM_2 RNA recognition motif.
Probab=92.94 E-value=0.51 Score=36.13 Aligned_cols=54 Identities=28% Similarity=0.401 Sum_probs=43.6
Q ss_pred EEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-cC----ceEEEEecchhhHHHHHHHhc
Q 008236 394 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DE----TAVFVQFSRAEMVSKFLDLKG 450 (573)
Q Consensus 394 v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-dd----tsa~V~l~~~e~~~~~L~~~~ 450 (573)
+++.|.|..+...+|++.|. .||+. ..+... +. ..|||.|.+.+.++..+..++
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 67889999999999999996 78875 345444 44 799999999999999866554
No 37
>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=92.93 E-value=0.47 Score=58.66 Aligned_cols=101 Identities=25% Similarity=0.300 Sum_probs=63.3
Q ss_pred hhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhcC-CCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhcc
Q 008236 181 KASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFFG-PLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKK 257 (573)
Q Consensus 181 ~~~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~~-~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~ 257 (573)
..+.-+..+++.+.+ .+.++|+||.-+|+.+|-+.|.. .+|. +...++||--++... ... .
T Consensus 252 ~~ap~~~evl~~f~~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~-----------~~~~~IDTl~lar~l---~p~--~ 315 (1213)
T TIGR01405 252 ENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEP-----------LENPVIDTLELARAL---NPE--Y 315 (1213)
T ss_pred hCCCCHHHHHHHHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCc-----------cCCCEeEHHHHHHHH---hcc--C
Confidence 344445544444432 46799999999999999887621 1221 113467998776532 111 1
Q ss_pred CCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 008236 258 SSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 328 (573)
Q Consensus 258 ~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~l 328 (573)
+..+|..+... + .+. ....|.|-+||.+|+.+|.+|...+
T Consensus 316 k~~kL~~Lak~----l-------------------gi~--------~~~~HrAl~DA~aTa~I~~~ll~~l 355 (1213)
T TIGR01405 316 KSHRLGNICKK----L-------------------GVD--------LDDHHRADYDAEATAKVFKVMVEQL 355 (1213)
T ss_pred CCCCHHHHHHH----c-------------------CCC--------CCCCcCHHHHHHHHHHHHHHHHHHH
Confidence 35567766322 2 011 1237999999999999999998766
No 38
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=92.90 E-value=0.44 Score=57.57 Aligned_cols=100 Identities=21% Similarity=0.177 Sum_probs=60.0
Q ss_pred hccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh-cCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCC
Q 008236 183 SIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF-FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 259 (573)
Q Consensus 183 ~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F-~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~ 259 (573)
+.-|..++..|.. .+.++||||.-+|+.+|-+.| ..-+|.. ....+||=-++... + .. ..+
T Consensus 68 ap~f~ev~~~l~~~l~~~~~VaHN~~FD~~fL~~~~~~~g~~~~-----------~~~~iDt~~la~~~--~-p~--~~~ 131 (928)
T PRK08074 68 APLFEDVAPEIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEI-----------HCPKLDTVELARIL--L-PT--AES 131 (928)
T ss_pred CCCHHHHHHHHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCCC-----------CCCeeeHHHHHHHh--c-CC--CCC
Confidence 3334444443321 478999999999999987766 1112210 11357875554321 1 00 123
Q ss_pred CChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 260 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 260 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
-+|..+.+. + .+ ..+..|.|-+||++|+.+|.+|...+.
T Consensus 132 ~~L~~l~~~----l-------------------~i--------~~~~~H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 132 YKLRDLSEE----L-------------------GL--------EHDQPHRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred CCHHHHHHh----C-------------------CC--------CCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 456655322 2 11 124789999999999999999988875
No 39
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=92.81 E-value=0.49 Score=56.37 Aligned_cols=99 Identities=23% Similarity=0.226 Sum_probs=60.2
Q ss_pred hccHHHHHHHHh--cCCCeEEechhhhHHHHHHHHhc-CCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCC
Q 008236 183 SIGFRHVIDLLS--SEKKLIVGHNCFLDIAHIYSKFF-GPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 259 (573)
Q Consensus 183 ~~Gf~~v~~~l~--~s~kpiVgHN~~~Dl~~l~~~F~-~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~ 259 (573)
+--|..|+..+. -.+.++||||.-+|+.+|-+.+. ...|. ..| .+||--|+... + .. ..+
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 344444444432 24688999999999999987652 11110 012 36887765421 1 11 124
Q ss_pred CChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 260 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 260 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
.+|..+. ..+ +++ ....|.|-.||++|+.+|.+|...++
T Consensus 133 ~~L~~L~----~~l-------------------gl~--------~~~~H~Al~DA~ata~L~~~l~~~l~ 171 (820)
T PRK07246 133 YSLSHLS----REL-------------------NID--------LADAHTAIADARATAELFLKLLQKIE 171 (820)
T ss_pred CCHHHHH----HHc-------------------CCC--------CCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 5566653 222 111 13579999999999999999988774
No 40
>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=92.63 E-value=0.32 Score=46.20 Aligned_cols=79 Identities=20% Similarity=0.231 Sum_probs=48.0
Q ss_pred CCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhhhcc
Q 008236 196 EKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIAL 275 (573)
Q Consensus 196 s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~l~~ 275 (573)
.+.++||||.-+|+-+|=. ..|.++||-.|+....+. .....+-+|..+...+ +
T Consensus 83 ~~~vlVgHn~~fD~~fL~~-------------------~~~~~iDT~~l~~~~~~~--~~~~~~~~L~~L~~~~---~-- 136 (161)
T cd06137 83 PDTILVGHSLQNDLDALRM-------------------IHTRVVDTAILTREAVKG--PLAKRQWSLRTLCRDF---L-- 136 (161)
T ss_pred CCcEEEeccHHHHHHHHhC-------------------cCCCeeEehhhhhhccCC--CcCCCCccHHHHHHHH---C--
Confidence 3489999999999977631 146789998887642210 0000245666653211 1
Q ss_pred CCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHH
Q 008236 276 GSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFA 322 (573)
Q Consensus 276 ~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~ 322 (573)
.. .++ .....|.|-.||.+|+.+|+
T Consensus 137 --------~~-------~~~-------~~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 137 --------GL-------KIQ-------GGGEGHDSLEDALAAREVVL 161 (161)
T ss_pred --------Cc-------hhc-------CCCCCCCcHHHHHHHHHHhC
Confidence 00 111 11356999999999999874
No 41
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=92.34 E-value=0.6 Score=55.79 Aligned_cols=100 Identities=19% Similarity=0.126 Sum_probs=60.4
Q ss_pred hccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh-cCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCC
Q 008236 183 SIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF-FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSS 259 (573)
Q Consensus 183 ~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F-~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~ 259 (573)
+--|..++..+.+ .+.++||||.-+|+.+|-+.| ..-+|. +-...+||--++...- . ...+
T Consensus 64 ap~~~ev~~~l~~~l~~~~~VahN~~fD~~fL~~~~~~~g~~~-----------~~~~~iDt~~l~~~~~---p--~~~~ 127 (850)
T TIGR01407 64 APYFSQVAQEIYDLLEDGIFVAHNVHFDLNFLAKALKDCGYEP-----------LPKPRIDTVELAQIFF---P--TEES 127 (850)
T ss_pred CCCHHHHHHHHHHHhCCCEEEEeCcHHHHHHHHHHHHHcCCCC-----------CCCCeEeHHHHHHHhc---C--CCCC
Confidence 4445555544332 367899999999999998776 111221 0113578755543210 0 0124
Q ss_pred CChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 260 TSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 260 tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
.+|..+. ..+ .++ ....|.|-.||.+|+.+|.+|...+.
T Consensus 128 ~~L~~l~----~~~-------------------gi~--------~~~~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 128 YQLSELS----EAL-------------------GLT--------HENPHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred CCHHHHH----HHC-------------------CCC--------CCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 5666653 222 111 13579999999999999999988775
No 42
>PRK07883 hypothetical protein; Validated
Probab=91.41 E-value=0.98 Score=51.58 Aligned_cols=88 Identities=24% Similarity=0.185 Sum_probs=55.7
Q ss_pred CCeEEechhhhHHHHHHHHh-cCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhhhcc
Q 008236 197 KKLIVGHNCFLDIAHIYSKF-FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIAL 275 (573)
Q Consensus 197 ~kpiVgHN~~~Dl~~l~~~F-~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~l~~ 275 (573)
+.++||||.-+|+.+|-..| ...+|. ..+..+||--++... + ......+.+|.++.+. +
T Consensus 95 ~~~lVaHNa~FD~~fL~~~~~r~g~~~-----------~~~~~iDTl~lar~l--~-~~~~~~~~~L~~L~~~----~-- 154 (557)
T PRK07883 95 GAVLVAHNAPFDIGFLRAAAARCGYPW-----------PGPPVLCTVRLARRV--L-PRDEAPNVRLSTLARL----F-- 154 (557)
T ss_pred CCEEEEeCcHHHHHHHHHHHHHcCCCC-----------CCCCcEecHHHHHHh--c-ccCCCCCCCHHHHHHH----C--
Confidence 68999999999999998776 222221 012457887665431 1 0001134556665322 1
Q ss_pred CCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 276 GSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 276 ~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
.++ ....|.|-.||.+|+.+|.+++..++
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 43
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=91.31 E-value=0.71 Score=58.00 Aligned_cols=103 Identities=21% Similarity=0.242 Sum_probs=63.5
Q ss_pred hhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHhcCC-CCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhc
Q 008236 180 IKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKFFGP-LPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMK 256 (573)
Q Consensus 180 l~~~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F~~~-LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~ 256 (573)
+..+.-+..+++.+.+ .+.++|+||+-+|+.+|-+.+..- +|. +....+||=-++.... ..
T Consensus 480 L~~aps~~EaL~~f~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~-----------l~~~~IDTLelar~l~---p~-- 543 (1437)
T PRK00448 480 VKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEK-----------IKNPVIDTLELSRFLY---PE-- 543 (1437)
T ss_pred HcCCCCHHHHHHHHHHHhCCCEEEEeCccccHHHHHHHHHHcCCcc-----------ccccceeHHHHHHHHc---Cc--
Confidence 3345667777777765 678999999999999886655211 211 1124568755543211 11
Q ss_pred cCCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 257 KSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 257 ~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
....+|..+ +..+ .+. ....|.|-+||++|+.+|.+|+..+.
T Consensus 544 ~k~~kL~~L----Ak~l-------------------GL~--------~~~~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 544 LKSHRLNTL----AKKF-------------------GVE--------LEHHHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred cccccHHHH----HHHc-------------------CCC--------CCCCcChHHHHHHHHHHHHHHHHHHH
Confidence 124455554 2222 111 12349999999999999999987763
No 44
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=91.04 E-value=0.82 Score=45.22 Aligned_cols=22 Identities=27% Similarity=0.179 Sum_probs=19.4
Q ss_pred cccchhhhHHHHHHHHHHHHHH
Q 008236 306 VKHEAGYDAFMTGCVFAQACSH 327 (573)
Q Consensus 306 ~~HEAGyDAymTG~vF~kL~~~ 327 (573)
..|.|-+||++|+.+|.+|...
T Consensus 147 ~~HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 147 RGHNSLEDARMTARVYESFLES 168 (195)
T ss_pred CCcCCHHHHHHHHHHHHHHHhh
Confidence 3699999999999999998654
No 45
>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=90.83 E-value=1.2 Score=34.26 Aligned_cols=57 Identities=23% Similarity=0.368 Sum_probs=44.0
Q ss_pred EEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEec----CceEEEEecchhhHHHHHHHhcc
Q 008236 394 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVD----ETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 394 v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~id----dtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
+++.|.|..++..+|++.|. .||++.-..+.+-. ...|||.|.+.+.+...++....
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 67889999999999999996 57875333334322 46899999999999998766555
No 46
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=90.77 E-value=1.4 Score=41.49 Aligned_cols=57 Identities=12% Similarity=0.224 Sum_probs=46.2
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-c------CceEEEEecchhhHHHHHHHhcc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-D------ETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-d------dtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
..+|+-+.|...+..+|++.|. .||.+ .++..+ | ...|||.|.+.++|+..|..++.
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 3589999999999999999996 79975 444443 3 35799999999999999877654
No 47
>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=89.60 E-value=0.87 Score=40.68 Aligned_cols=54 Identities=28% Similarity=0.345 Sum_probs=35.8
Q ss_pred eEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe----cCceEEEEecchhhHHHHHHHhccc
Q 008236 393 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV----DETAVFVQFSRAEMVSKFLDLKGSL 452 (573)
Q Consensus 393 ~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i----ddtsa~V~l~~~e~~~~~L~~~~~~ 452 (573)
+|.+-|.++..+..+|++.|+ .|| .|.|| +++.+||=|..++.|+.++......
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 466777899999999998886 477 34666 5999999999999999999888774
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=89.55 E-value=1.3 Score=42.83 Aligned_cols=75 Identities=21% Similarity=0.203 Sum_probs=46.7
Q ss_pred CCeEEechh-hhHHHHHHHHh--cCC-CCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhh
Q 008236 197 KKLIVGHNC-FLDIAHIYSKF--FGP-LPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQ 272 (573)
Q Consensus 197 ~kpiVgHN~-~~Dl~~l~~~F--~~~-LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~ 272 (573)
+.++||||. -+|+-+|-+.| +|. +|.. +..+||=-++.. + . .+|+.++..+
T Consensus 98 ~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~------------~~~iDtl~l~r~---~---~----~~L~~l~~~~--- 152 (177)
T cd06136 98 PICLVAHNGNRFDFPILRSELERLGTKLPDD------------ILCVDSLPAFRE---L---D----QSLGSLYKRL--- 152 (177)
T ss_pred CCEEEEcCCcccCHHHHHHHHHHcCCCCCCC------------CEEEEeHHHHhh---h---H----hhHHHHHHHH---
Confidence 458999998 79999998777 321 1110 123587655542 1 1 1576664321
Q ss_pred hccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHH
Q 008236 273 IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQ 323 (573)
Q Consensus 273 l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~k 323 (573)
+ ++ .....|.|-.||..|+.||++
T Consensus 153 ~-------------------~~--------~~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 153 F-------------------GQ--------EPKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred h-------------------CC--------CcccccchHHHHHHHHHHHhh
Confidence 1 01 123579999999999999975
No 49
>smart00360 RRM RNA recognition motif.
Probab=88.60 E-value=1.6 Score=33.02 Aligned_cols=52 Identities=23% Similarity=0.382 Sum_probs=39.3
Q ss_pred eCCCCcccHHHHHHHHHhhhCCCceeEEEEecC------ceEEEEecchhhHHHHHHHhc
Q 008236 397 WGFPSHLKAWDIRECISKVYGPTSVISVYHVDE------TAVFVQFSRAEMVSKFLDLKG 450 (573)
Q Consensus 397 ~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~idd------tsa~V~l~~~e~~~~~L~~~~ 450 (573)
.|+|..++..+|++.|. .||+..-..|.. +. ..|||.|.+.+.+...+..+.
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 36799999999999996 789753333333 33 389999999999999866555
No 50
>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=88.35 E-value=0.23 Score=45.00 Aligned_cols=16 Identities=38% Similarity=0.324 Sum_probs=14.7
Q ss_pred cccchhhhHHHHHHHH
Q 008236 306 VKHEAGYDAFMTGCVF 321 (573)
Q Consensus 306 ~~HEAGyDAymTG~vF 321 (573)
..|.|..||++|..+|
T Consensus 149 ~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 149 TAHDALDDARATAELF 164 (164)
T ss_dssp TTTSHHHHHHHHHHHH
T ss_pred CCcChHHHHHHHhCcC
Confidence 3899999999999987
No 51
>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=87.98 E-value=2.2 Score=40.02 Aligned_cols=82 Identities=18% Similarity=0.146 Sum_probs=49.0
Q ss_pred eEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhhhccC
Q 008236 199 LIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALG 276 (573)
Q Consensus 199 piVgHN~~~Dl~~l~~~F--~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~l~~~ 276 (573)
.++.||+-.|...+.+.+ .+-.+ ....+...+||..++...-+ . ....+|..+... +
T Consensus 92 ~~~v~~~~~d~~~l~~~~~~~~~~~---------~~~~~~~~~D~~~~~~~~~~---~--~~~~~L~~l~~~----~--- 150 (176)
T cd06133 92 YAFVTWGDWDLKDLLQNQCKYKIIN---------LPPFFRQWIDLKKEFAKFYG---L--KKRTGLSKALEY----L--- 150 (176)
T ss_pred eEEEeecHhhHHHHHHHHHHhcCCC---------CcccccceEEHHHHHHHHhC---C--CCCCCHHHHHHH----C---
Confidence 455556678877666543 11111 01234567899888754211 1 135677766332 1
Q ss_pred CccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHH
Q 008236 277 SKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQA 324 (573)
Q Consensus 277 ~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL 324 (573)
.++ ..+..|.|=+||..|+.+|.+|
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 2268999999999999999887
No 52
>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=86.99 E-value=2.7 Score=45.26 Aligned_cols=68 Identities=15% Similarity=0.222 Sum_probs=52.2
Q ss_pred cceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecC-------ceEEEEecchhhHHHHHHHhcccccCCCCccc
Q 008236 391 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE-------TAVFVQFSRAEMVSKFLDLKGSLDRNNDPISV 461 (573)
Q Consensus 391 ~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~idd-------tsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~ 461 (573)
...+|+-+.|..++..+|+++|+ .||++ .+|..+-| ..|||.|.+.++|+..+..++..+-.+..+.|
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 45555433 36999999999999998877765544444433
No 53
>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=86.93 E-value=2.3 Score=33.92 Aligned_cols=39 Identities=18% Similarity=0.249 Sum_probs=27.2
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 008236 112 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 154 (573)
Q Consensus 112 l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~~~~~~~~~~ivv~ 154 (573)
+.+++.|+++|++||++.. +.++.+.+. + .+..+.++|+
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 5677789999999999988 678988775 3 3345556654
No 54
>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=85.96 E-value=1.8 Score=40.98 Aligned_cols=17 Identities=24% Similarity=0.077 Sum_probs=15.0
Q ss_pred CcccchhhhHHHHHHHH
Q 008236 305 GVKHEAGYDAFMTGCVF 321 (573)
Q Consensus 305 ~~~HEAGyDAymTG~vF 321 (573)
+..|.|-+||.+|+.+|
T Consensus 140 ~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 140 RQGHSSVEDARATMELY 156 (157)
T ss_pred CCCcCcHHHHHHHHHHh
Confidence 45699999999999887
No 55
>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=85.89 E-value=2.6 Score=36.24 Aligned_cols=57 Identities=12% Similarity=0.038 Sum_probs=47.8
Q ss_pred EEEeCCCC--cccHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 008236 394 VIVWGFPS--HLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 394 v~~~~fp~--~~k~~dI~~~~~~~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
..-..+++ .|.-.++.+-+.+-|+-. .+.|.|+||-.=||.+......++.+++...
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 34445666 899999999999989977 5699999999999999999999988886655
No 56
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=85.66 E-value=2.9 Score=44.03 Aligned_cols=24 Identities=21% Similarity=0.079 Sum_probs=20.7
Q ss_pred cccchhhhHHHHHHHHHHHHHHhC
Q 008236 306 VKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 306 ~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
..|.|..||+.|+.+|.+++...|
T Consensus 179 ~aHrAl~Da~Ata~ll~~~l~~~~ 202 (294)
T PRK09182 179 EGHRAVDDCQALLELLARPLPETG 202 (294)
T ss_pred CCcChHHHHHHHHHHHHHHHhhcC
Confidence 469999999999999998876554
No 57
>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=85.36 E-value=3 Score=35.76 Aligned_cols=59 Identities=15% Similarity=0.228 Sum_probs=50.3
Q ss_pred eEEEeCCCCcccHHHHHHHHHhhhCCC--ceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 008236 393 IVIVWGFPSHLKAWDIRECISKVYGPT--SVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 393 ~v~~~~fp~~~k~~dI~~~~~~~fg~~--~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
-+.-..+|+.|.-.++++.+.+.|+.. +.+.|+|+||---||.+.+..+.++-+++...
T Consensus 10 d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~~~ 70 (82)
T cd06407 10 EKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVYRS 70 (82)
T ss_pred eEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHHHH
Confidence 356677899999999999999988865 46799999999999999999998887776655
No 58
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=84.58 E-value=5 Score=40.16 Aligned_cols=82 Identities=22% Similarity=0.279 Sum_probs=50.8
Q ss_pred CeEEechhhhHHHHHHHHh---cCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhcc-CCCChHHHHHhhhhhh
Q 008236 198 KLIVGHNCFLDIAHIYSKF---FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKK-SSTSLSKAFSVLCPQI 273 (573)
Q Consensus 198 kpiVgHN~~~Dl~~l~~~F---~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~-~~tsL~~l~~~l~~~l 273 (573)
.++|+||-.+|+.++-..+ ..+.| ...++||=-++... ... ...+|..+ |..+
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 22344554444321 111 23445543 3322
Q ss_pred ccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHH
Q 008236 274 ALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSH 327 (573)
Q Consensus 274 ~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~ 327 (573)
+++. .....|.|-+||++|+.+|+.+...
T Consensus 153 -------------------gi~~------~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 153 -------------------GIDR------NPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred -------------------CCCc------CCcCCcchHHHHHHHHHHHHHHHhc
Confidence 1221 1234599999999999999999774
No 59
>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=83.69 E-value=3.7 Score=39.72 Aligned_cols=24 Identities=25% Similarity=0.283 Sum_probs=18.6
Q ss_pred HhcCCCeEEech-hhhHHHHHHHHh
Q 008236 193 LSSEKKLIVGHN-CFLDIAHIYSKF 216 (573)
Q Consensus 193 l~~s~kpiVgHN-~~~Dl~~l~~~F 216 (573)
+.+.+.++|||| .-+|+.+|-..|
T Consensus 80 ~~~~~~~lVahn~~~FD~~fL~~~~ 104 (183)
T cd06138 80 FNTPGTCIVGYNNIRFDDEFLRFAF 104 (183)
T ss_pred HccCCCcEEeeCchhhHHHHHHHHH
Confidence 334567899998 579999998776
No 60
>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=82.96 E-value=3.6 Score=38.23 Aligned_cols=99 Identities=22% Similarity=0.278 Sum_probs=57.9
Q ss_pred HHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhh
Q 008236 191 DLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLC 270 (573)
Q Consensus 191 ~~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~ 270 (573)
+.|...+...||||+-.|+..|++. .....+.++||..++....+ ..+.+|..+...+.
T Consensus 71 ~ll~~~~i~kv~~n~~~D~~~L~~~---------------~~i~~~~~~D~~l~~~~l~~------~~~~~L~~L~~~~l 129 (176)
T PF01612_consen 71 ELLEDPNIIKVGHNAKFDLKWLYRS---------------FGIDLKNVFDTMLAAYLLDP------TRSYSLKDLAEEYL 129 (176)
T ss_dssp HHHTTTTSEEEESSHHHHHHHHHHH---------------HTS--SSEEEHHHHHHHTTT------STTSSHHHHHHHHH
T ss_pred HHHhCCCccEEEEEEechHHHHHHH---------------hccccCCccchhhhhhcccc------cccccHHHHHHHHh
Confidence 3455566679999999999999976 23334568899444322111 11257887755443
Q ss_pred hhhccCCccccccCCCCceeeeeeccccccCC------CCCcccchhhhHHHHHHHHHHHHHHh
Q 008236 271 PQIALGSKSTHLALQPSVKVEVEVDDIRSSNW------NSGVKHEAGYDAFMTGCVFAQACSHL 328 (573)
Q Consensus 271 ~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~------~~~~~HEAGyDAymTG~vF~kL~~~l 328 (573)
..... ..... .+.+ ......-|+.||..|-.+|-+|..+|
T Consensus 130 ~~~~~-----------------~~~~~-~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 130 GNIDL-----------------DKKEQ-MSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp SEEE------------------GHCCT-TSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred hhccC-----------------cHHHh-hccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 31100 00000 0111 11235679999999999999998776
No 61
>PTZ00315 2'-phosphotransferase; Provisional
Probab=82.81 E-value=6.1 Score=45.36 Aligned_cols=108 Identities=14% Similarity=0.046 Sum_probs=63.4
Q ss_pred hhhhhhccHHHHHHH----HhcCC--------CeEEechhhhHHH-HHHHHh--c--CCCCCCHHHHHHHHHccCCCCcc
Q 008236 178 MSIKASIGFRHVIDL----LSSEK--------KLIVGHNCFLDIA-HIYSKF--F--GPLPLTAEEFISSVNKYFPHIID 240 (573)
Q Consensus 178 ~~l~~~~Gf~~v~~~----l~~s~--------kpiVgHN~~~Dl~-~l~~~F--~--~~LP~~~~eFk~~l~~~FP~I~D 240 (573)
+.+.++.-|..|+.. |..+. ..+|+||+=+|+. +|.+.+ + ..+|. .|...+|
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 345566666666644 44432 4699999999996 555544 2 24553 3556667
Q ss_pred hh-HHhhhchH-H-----HHhhccCCCChHHHHHhhhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhh
Q 008236 241 TK-ILLNSNSI-L-----QQRMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYD 313 (573)
Q Consensus 241 TK-~La~~~~~-l-----k~~~~~~~tsL~~l~~~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyD 313 (573)
.| +++...-+ . .........+|..+.+.+ ++. -.|..|.|=.|
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 55432100 0 000011245676664321 111 24789999999
Q ss_pred HHHHHHHHHHHHH
Q 008236 314 AFMTGCVFAQACS 326 (573)
Q Consensus 314 AymTG~vF~kL~~ 326 (573)
|..||.+|.+|..
T Consensus 241 A~ntA~L~~~Ll~ 253 (582)
T PTZ00315 241 CRNIAAVLCELLR 253 (582)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999976
No 62
>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=81.65 E-value=6.5 Score=29.79 Aligned_cols=27 Identities=19% Similarity=0.011 Sum_probs=21.4
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEE
Q 008236 112 ISLNGFTSHQLLLIQLVVRKHFKDLAYLR 140 (573)
Q Consensus 112 l~L~~~~s~QrrLI~q~lr~~fp~lv~v~ 140 (573)
+.++++|+++|++||++++... +.+.+
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 5678889999999999988755 55544
No 63
>PRK11779 sbcB exonuclease I; Provisional
Probab=80.77 E-value=7.3 Score=43.81 Aligned_cols=23 Identities=17% Similarity=0.067 Sum_probs=20.6
Q ss_pred CcccchhhhHHHHHHHHHHHHHH
Q 008236 305 GVKHEAGYDAFMTGCVFAQACSH 327 (573)
Q Consensus 305 ~~~HEAGyDAymTG~vF~kL~~~ 327 (573)
+..|.|=+||+.|+.+|..|...
T Consensus 175 ~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 175 ENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHh
Confidence 46899999999999999998765
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=80.37 E-value=4.2 Score=45.47 Aligned_cols=55 Identities=22% Similarity=0.389 Sum_probs=46.2
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-cCceEEEEecchhhHHHHHHHh
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DETAVFVQFSRAEMVSKFLDLK 449 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-ddtsa~V~l~~~e~~~~~L~~~ 449 (573)
.+||+-+.|..++..+|+++|+ .||++. +|.-+ +...|||.|.+.|+|+..+...
T Consensus 3 ~vv~V~nLp~~~te~~L~~~f~-~fG~V~--~v~i~~~k~~afVef~~~e~A~~Ai~~~ 58 (481)
T TIGR01649 3 PVVHVRNLPQDVVEADLVEALI-PFGPVS--YVMMLPGKRQALVEFEDEESAKACVNFA 58 (481)
T ss_pred cEEEEcCCCCCCCHHHHHHHHH-hcCCee--EEEEECCCCEEEEEeCchHHHHHHHHHh
Confidence 3689999999999999999996 799864 33333 7789999999999999998753
No 65
>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=80.13 E-value=8 Score=31.86 Aligned_cols=40 Identities=15% Similarity=0.188 Sum_probs=29.6
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 008236 112 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 154 (573)
Q Consensus 112 l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~~~~~~~~~~ivv~ 154 (573)
..|++-|+++|++||.++.. |+++.+.+. ++ +..+.+||+
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 56788899999999999875 888988764 33 335556654
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=79.46 E-value=5.3 Score=43.04 Aligned_cols=56 Identities=16% Similarity=0.296 Sum_probs=45.7
Q ss_pred eEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-cC------ceEEEEecchhhHHHHHHHhcc
Q 008236 393 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DE------TAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 393 ~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-dd------tsa~V~l~~~e~~~~~L~~~~~ 451 (573)
.+|+-+.|..++..+|+++|+ .||.+ .++..+ |. ..|||.|.+.++|+..+..++.
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
>cd02642 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=78.54 E-value=12 Score=30.31 Aligned_cols=39 Identities=23% Similarity=0.103 Sum_probs=27.3
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEEe
Q 008236 112 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVYI 155 (573)
Q Consensus 112 l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~~~~~~~~~~ivv~~ 155 (573)
+.+++.|+|||.|||++... -++.+.+. ++ + .+.++|++
T Consensus 24 ~~f~pm~sy~RllvH~la~~--~gL~s~s~-~~-~-~r~vvv~k 62 (63)
T cd02642 24 LELPPMNSYYRLLAHRVAQY--YGLDHNVD-NS-G-GKCVIVNK 62 (63)
T ss_pred eEcCCCCcHHHHHHHHHHHH--hCCeeEee-cC-C-ceEEEEEe
Confidence 56788899999999998665 56776654 22 2 45566653
No 68
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=78.11 E-value=6.4 Score=41.34 Aligned_cols=59 Identities=25% Similarity=0.268 Sum_probs=47.1
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-cC------ceEEEEecchhhHHHHHHHhcccc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DE------TAVFVQFSRAEMVSKFLDLKGSLD 453 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-dd------tsa~V~l~~~e~~~~~L~~~~~~~ 453 (573)
+.+|+-+.|..++..+|+++|+ .||++ .+|.-+ |. ..|||.|.+.++|+..|..++...
T Consensus 4 ~~l~V~nLp~~~~e~~l~~~F~-~~G~i--~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~ 69 (352)
T TIGR01661 4 TNLIVNYLPQTMTQEEIRSLFT-SIGEI--ESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLR 69 (352)
T ss_pred cEEEEeCCCCCCCHHHHHHHHH-ccCCE--EEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEE
Confidence 3589999999999999999997 69986 344544 32 379999999999999887766533
No 69
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=77.75 E-value=8.8 Score=41.85 Aligned_cols=38 Identities=16% Similarity=0.227 Sum_probs=30.8
Q ss_pred hhhhhccHHHHHHHHhc--CCCeEEechhhhHHHHHHHHh
Q 008236 179 SIKASIGFRHVIDLLSS--EKKLIVGHNCFLDIAHIYSKF 216 (573)
Q Consensus 179 ~l~~~~Gf~~v~~~l~~--s~kpiVgHN~~~Dl~~l~~~F 216 (573)
.+..+..|..+++.|.. .+.++|+||.-+|+.||-+.|
T Consensus 105 ~La~AP~f~eVl~el~~fL~g~vLVaHNA~FD~~FL~~e~ 144 (377)
T PRK05601 105 EFAQGKRFSQILKPLDRLIDGRTLILHNAPRTWGFIVSEA 144 (377)
T ss_pred HHhcCCCHHHHHHHHHHHhCCCEEEEECcHHHHHHHHHHH
Confidence 45567788888887753 478999999999999998765
No 70
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=77.74 E-value=7.2 Score=40.96 Aligned_cols=59 Identities=10% Similarity=0.145 Sum_probs=46.7
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-c------CceEEEEecchhhHHHHHHHhcccc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-D------ETAVFVQFSRAEMVSKFLDLKGSLD 453 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-d------dtsa~V~l~~~e~~~~~L~~~~~~~ 453 (573)
..+|+-+.|..|...+|+++|+ .||++ .++.-+ | ...|||.|.+.++|...+..++-.+
T Consensus 270 ~~lfV~NL~~~~~e~~L~~~F~-~fG~v--~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~ 335 (352)
T TIGR01661 270 YCIFVYNLSPDTDETVLWQLFG-PFGAV--QNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYT 335 (352)
T ss_pred cEEEEeCCCCCCCHHHHHHHHH-hCCCe--EEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCE
Confidence 3589999999999999999997 89986 344433 4 3579999999999988777766633
No 71
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=75.44 E-value=7.9 Score=47.55 Aligned_cols=84 Identities=31% Similarity=0.478 Sum_probs=56.8
Q ss_pred CCeEEechhhhHHHHHHHHh--cCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhhhhc
Q 008236 197 KKLIVGHNCFLDIAHIYSKF--FGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 274 (573)
Q Consensus 197 ~kpiVgHN~~~Dl~~l~~~F--~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~~l~ 274 (573)
.-++|.||.-+|+.||=..| ++-.|-+ .| ++||=-|+..-.+ .+ ++-.|+.+ |..+
T Consensus 501 d~IlVAHNasFD~gFl~~~~~k~~~~~~~-----------~p-vIDTL~lar~L~P---~~--ksh~Lg~l----~kk~- 558 (1444)
T COG2176 501 DSILVAHNASFDMGFLNTNYEKYGLEPLT-----------NP-VIDTLELARALNP---EF--KSHRLGTL----CKKL- 558 (1444)
T ss_pred CcEEEeccCccchhHHHHHHHHhCCcccc-----------Cc-hhhHHHHHHHhCh---hh--hhcchHHH----HHHh-
Confidence 44789999999999998777 3322221 23 5699777764322 12 25556655 4433
Q ss_pred cCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 008236 275 LGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 328 (573)
Q Consensus 275 ~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~l 328 (573)
.+. -...|-|-|||=.||.+|+.+...+
T Consensus 559 ------------------~v~--------le~hHRA~yDaeat~~vf~~f~~~~ 586 (1444)
T COG2176 559 ------------------GVE--------LERHHRADYDAEATAKVFFVFLKDL 586 (1444)
T ss_pred ------------------Ccc--------HHHhhhhhhhHHHHHHHHHHHHHHH
Confidence 111 1588999999999999999987766
No 72
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=74.12 E-value=6.4 Score=43.34 Aligned_cols=77 Identities=18% Similarity=0.302 Sum_probs=54.2
Q ss_pred EEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecC-------ceEEEEecchhhHHHHHHHhcccccCCCCcccccchh
Q 008236 394 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE-------TAVFVQFSRAEMVSKFLDLKGSLDRNNDPISVLHPLA 466 (573)
Q Consensus 394 v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~idd-------tsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~~~~l~ 466 (573)
.|+=-.|++|+-.||+.+|. .||. |.+|.-|-| .||||.+..++.+... +++|+....=-.+.||+-
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-KYGN--VYEINLIKDKSTGQSKGCCFVKYYTRKEADEA---INALHNQKTLPGMHHPVQ 110 (510)
T ss_pred heeccCCccccHHHHHHHHH-HhCc--eeEEEeecccccCcccceEEEEeccHHHHHHH---HHHhhcccccCCCCccee
Confidence 45556999999999999996 7886 467887744 7999999998888665 444444332234667776
Q ss_pred hhhcCCcccc
Q 008236 467 KLLEGGNTCA 476 (573)
Q Consensus 467 ~~~~~g~~~~ 476 (573)
.-.++|....
T Consensus 111 vk~Ad~E~er 120 (510)
T KOG0144|consen 111 VKYADGERER 120 (510)
T ss_pred ecccchhhhc
Confidence 6665554444
No 73
>PLN03120 nucleic acid binding protein; Provisional
Probab=73.96 E-value=13 Score=38.55 Aligned_cols=53 Identities=21% Similarity=0.150 Sum_probs=43.4
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-c---CceEEEEecchhhHHHHHH
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-D---ETAVFVQFSRAEMVSKFLD 447 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-d---dtsa~V~l~~~e~~~~~L~ 447 (573)
..||+-|.|...+..||++.|+ .||.+ .+|.-+ | ...|||.|.+.+.++..|.
T Consensus 5 rtVfVgNLs~~tTE~dLrefFS-~~G~I--~~V~I~~d~~~~GfAFVtF~d~eaAe~All 61 (260)
T PLN03120 5 RTVKVSNVSLKATERDIKEFFS-FSGDI--EYVEMQSENERSQIAYVTFKDPQGAETALL 61 (260)
T ss_pred CEEEEeCCCCCCCHHHHHHHHH-hcCCe--EEEEEeecCCCCCEEEEEeCcHHHHHHHHH
Confidence 3589999999999999999997 78975 344433 3 3579999999999999985
No 74
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=73.54 E-value=12 Score=36.72 Aligned_cols=105 Identities=14% Similarity=0.174 Sum_probs=61.3
Q ss_pred HhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHH-----hhccCCCChHHHHH
Q 008236 193 LSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQ-----RMKKSSTSLSKAFS 267 (573)
Q Consensus 193 l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~-----~~~~~~tsL~~l~~ 267 (573)
|...+.+-|||++-.|+-.|++.|...... + ...-.++||..++........ .+.....+|+.+-+
T Consensus 78 l~d~~i~KVg~~~~~D~~~L~~~~~~~~~~----~-----~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~ 148 (193)
T cd06146 78 FEDPDVLKLGFGFKQDLKALSASYPALKCM----F-----ERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQ 148 (193)
T ss_pred hCCCCeeEEEechHHHHHHHHHhcCccccc----c-----ccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHH
Confidence 445556679999999999999877432110 0 112478899988764321100 01123567877654
Q ss_pred hhhhhhccCCccccccCCCCceeeeeeccccccCCC-----CCcccchhhhHHHHHHHHHHHH
Q 008236 268 VLCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWN-----SGVKHEAGYDAFMTGCVFAQAC 325 (573)
Q Consensus 268 ~l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~-----~~~~HEAGyDAymTG~vF~kL~ 325 (573)
.+... ...+ ....++|. ..+.+-|+.|||..-.+|-+|+
T Consensus 149 ~~lg~---~l~K----------------~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 149 EVLGK---PLDK----------------SEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHhCC---CcCc----------------ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 33210 0000 01122332 3578899999999999999885
No 75
>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=73.03 E-value=7.6 Score=31.73 Aligned_cols=29 Identities=21% Similarity=0.173 Sum_probs=24.7
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEe
Q 008236 112 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRV 141 (573)
Q Consensus 112 l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~ 141 (573)
+.|++-+++.|++||+.|.. +|++.+.+.
T Consensus 21 v~LePM~~~ERkIIH~~Lq~-~~~v~T~S~ 49 (62)
T cd02638 21 LLFPPLNSRRRYLIHQTVEN-RFLLSTFSV 49 (62)
T ss_pred EecCCCChHHHHHHHHHHhc-CCCceEEEc
Confidence 56888999999999999984 888877764
No 76
>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=72.49 E-value=10 Score=41.55 Aligned_cols=62 Identities=18% Similarity=0.235 Sum_probs=48.3
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-cC------ceEEEEecchhhHHHHHHHhcccccCC
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DE------TAVFVQFSRAEMVSKFLDLKGSLDRNN 456 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-dd------tsa~V~l~~~e~~~~~L~~~~~~~~~~ 456 (573)
..+|+-+.|..++..+|+++|. .||.+ .+|.++ |. ..|||.|.+.+.|...|..++..+-.+
T Consensus 187 ~~l~v~nl~~~~te~~l~~~f~-~~G~i--~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g 255 (457)
T TIGR01622 187 LKLYVGNLHFNITEQELRQIFE-PFGDI--EDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAG 255 (457)
T ss_pred CEEEEcCCCCCCCHHHHHHHHH-hcCCe--EEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECC
Confidence 3589999999999999999996 79975 455554 22 469999999999999887777644333
No 77
>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=71.79 E-value=10 Score=43.87 Aligned_cols=67 Identities=13% Similarity=0.198 Sum_probs=53.1
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-c------CceEEEEecchhhHHHHHHHhcccccCCCCccc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-D------ETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISV 461 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-d------dtsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~ 461 (573)
..+|+.|.|..|+..+|+++|+ .||.+ .++..+ | ...+||.|.+.+++..-+..++.++=.+..+.|
T Consensus 205 ~rLfVgnLp~~vteedLk~lFs-~FG~I--~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV 278 (612)
T TIGR01645 205 NRIYVASVHPDLSETDIKSVFE-AFGEI--VKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278 (612)
T ss_pred ceEEeecCCCCCCHHHHHHHHh-hcCCe--eEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence 3589999999999999999997 79986 445544 2 247999999999999999999987655444433
No 78
>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=71.26 E-value=13 Score=40.83 Aligned_cols=56 Identities=27% Similarity=0.329 Sum_probs=46.6
Q ss_pred cceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEec-------CceEEEEecchhhHHHHHHHh
Q 008236 391 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVD-------ETAVFVQFSRAEMVSKFLDLK 449 (573)
Q Consensus 391 ~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~id-------dtsa~V~l~~~e~~~~~L~~~ 449 (573)
...||+-+.|..++..+|+++|+ .||+ |.+|..+- ...|||.|.+.++|...|.+.
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-KVGK--VRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALT 151 (457)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHH-hcCC--eeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhC
Confidence 34699999999999999999997 6895 46677763 358999999999999998654
No 79
>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=70.91 E-value=13 Score=42.98 Aligned_cols=63 Identities=21% Similarity=0.208 Sum_probs=49.0
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcccccCC
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDRNN 456 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~~~~~~ 456 (573)
..+|+-+.|..++..+|++.|+ .|++..|..|.-+ ...|||.|.+.++|+..|..++..+=.+
T Consensus 234 k~LfVgNL~~~~tee~L~~~F~-~f~~G~I~rV~~~-rgfAFVeF~s~e~A~kAi~~lnG~~i~G 296 (578)
T TIGR01648 234 KILYVRNLMTTTTEEIIEKSFS-EFKPGKVERVKKI-RDYAFVHFEDREDAVKAMDELNGKELEG 296 (578)
T ss_pred cEEEEeCCCCCCCHHHHHHHHH-hcCCCceEEEEee-cCeEEEEeCCHHHHHHHHHHhCCCEECC
Confidence 4689999999999999999997 6833344566544 4599999999999999988777644333
No 80
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=70.43 E-value=17 Score=34.18 Aligned_cols=97 Identities=20% Similarity=0.182 Sum_probs=57.8
Q ss_pred HHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhhh
Q 008236 192 LLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCP 271 (573)
Q Consensus 192 ~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~~ 271 (573)
.|...+...|||++-.|+-.|.+.|.-. +..++||..++....+- ....+|+.+.+.+..
T Consensus 68 ll~~~~i~kv~~~~k~D~~~L~~~~g~~---------------~~~~~Dl~~aa~ll~~~-----~~~~~l~~l~~~~l~ 127 (170)
T cd06141 68 LLEDPSILKVGVGIKGDARKLARDFGIE---------------VRGVVDLSHLAKRVGPR-----RKLVSLARLVEEVLG 127 (170)
T ss_pred HhcCCCeeEEEeeeHHHHHHHHhHcCCC---------------CCCeeeHHHHHHHhCCC-----cCCccHHHHHHHHcC
Confidence 4555566789999999999987666322 33568999887543211 012467766544321
Q ss_pred hhccCCccccccCCCCceeeeeeccccccCC-----CCCcccchhhhHHHHHHHHHHHH
Q 008236 272 QIALGSKSTHLALQPSVKVEVEVDDIRSSNW-----NSGVKHEAGYDAFMTGCVFAQAC 325 (573)
Q Consensus 272 ~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~-----~~~~~HEAGyDAymTG~vF~kL~ 325 (573)
.- ..+ + .....+.| +.++.|-|+.|||.+-.++-+|.
T Consensus 128 ~~---~~k------~--------k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 128 LP---LSK------P--------KKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred cc---cCC------C--------CCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 10 000 0 00011223 24578999999999999998874
No 81
>PLN03121 nucleic acid binding protein; Provisional
Probab=69.39 E-value=16 Score=37.63 Aligned_cols=57 Identities=18% Similarity=0.194 Sum_probs=45.7
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecC----ceEEEEecchhhHHHHHHHhcc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE----TAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~idd----tsa~V~l~~~e~~~~~L~~~~~ 451 (573)
..|++-+.+...+..||+++|+ -||.+ .+|.-+.| .-|||.|.+++.++..|.+-.+
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 68976 45665544 3699999999999998754433
No 82
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=68.77 E-value=17 Score=34.25 Aligned_cols=94 Identities=17% Similarity=0.226 Sum_probs=56.5
Q ss_pred HHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhh-
Q 008236 192 LLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLC- 270 (573)
Q Consensus 192 ~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~- 270 (573)
.|...+...|||++-.|+-.+.+.|.-. +..++||..++....+ ....+|+.+.+.+.
T Consensus 62 lL~d~~i~Kvg~~~k~D~~~L~~~~gi~---------------~~~~~D~~~aa~ll~~------~~~~~L~~l~~~~lg 120 (161)
T cd06129 62 LLENPSIVKALHGIEGDLWKLLRDFGEK---------------LQRLFDTTIAANLKGL------PERWSLASLVEHFLG 120 (161)
T ss_pred HhCCCCEEEEEeccHHHHHHHHHHcCCC---------------cccHhHHHHHHHHhCC------CCCchHHHHHHHHhC
Confidence 3445556679999999988887655211 2245799887653221 11346777654321
Q ss_pred hhhccCCccccccCCCCceeeeeeccccccCC-----CCCcccchhhhHHHHHHHHHHHHH
Q 008236 271 PQIALGSKSTHLALQPSVKVEVEVDDIRSSNW-----NSGVKHEAGYDAFMTGCVFAQACS 326 (573)
Q Consensus 271 ~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~-----~~~~~HEAGyDAymTG~vF~kL~~ 326 (573)
..+ .+. ...+.| +..+.|-|+.||+..-.+|-+|.+
T Consensus 121 ~~l----~K~----------------~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 121 KTL----DKS----------------ISCADWSYRPLTEDQKLYAAADVYALLIIYTKLRN 161 (161)
T ss_pred CCC----Ccc----------------ceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 111 000 011222 245789999999999999998864
No 83
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=68.73 E-value=13 Score=31.20 Aligned_cols=40 Identities=18% Similarity=0.307 Sum_probs=29.3
Q ss_pred ccccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 008236 111 AISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 154 (573)
Q Consensus 111 ~l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~~~~~~~~~~ivv~ 154 (573)
.+.+++.|+++|++||+++.. | ++.+.+. +. |..+.++|+
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 466788999999999999887 5 8887754 32 334556654
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=67.53 E-value=14 Score=42.93 Aligned_cols=69 Identities=22% Similarity=0.280 Sum_probs=50.6
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-----cCceEEEEecchhhHHHHHHHhcccccCCCCccc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-----DETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISV 461 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-----ddtsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~ 461 (573)
..+|+-++|..++..+|+++|. .||++.-+.|.|= ....|||.|.+.++++..+..++...=.+-.+.|
T Consensus 108 ~rLfVGnLp~~~tEe~Lr~lF~-~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV 181 (612)
T TIGR01645 108 CRVYVGSISFELREDTIRRAFD-PFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKV 181 (612)
T ss_pred CEEEEcCCCCCCCHHHHHHHHH-ccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeee
Confidence 4589999999999999999997 6998643333331 3568999999999999988766553333333334
No 85
>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=65.42 E-value=19 Score=40.35 Aligned_cols=59 Identities=12% Similarity=0.216 Sum_probs=48.3
Q ss_pred cceEEEeCCCC-cccHHHHHHHHHhhhCCCceeEEEEe-c-CceEEEEecchhhHHHHHHHhccc
Q 008236 391 ECIVIVWGFPS-HLKAWDIRECISKVYGPTSVISVYHV-D-ETAVFVQFSRAEMVSKFLDLKGSL 452 (573)
Q Consensus 391 ~~~v~~~~fp~-~~k~~dI~~~~~~~fg~~~v~~v~~i-d-dtsa~V~l~~~e~~~~~L~~~~~~ 452 (573)
..++|+-++|. .++..+|+++|+ .||.+ .+|.-+ | ...|||.|.+.++|...|..++..
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 89975 456554 3 479999999999999998877763
No 86
>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=64.56 E-value=18 Score=40.93 Aligned_cols=56 Identities=18% Similarity=0.249 Sum_probs=45.2
Q ss_pred eEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecC------ceEEEEecchhhHHHHHHHhcc
Q 008236 393 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE------TAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 393 ~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~idd------tsa~V~l~~~e~~~~~L~~~~~ 451 (573)
.+|+-++|..++..+|++.|+ .||.+ .++..+.+ ..|||.|.+.+++...+..++.
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 45555533 2699999999999988776654
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=64.54 E-value=14 Score=32.13 Aligned_cols=61 Identities=11% Similarity=0.097 Sum_probs=51.2
Q ss_pred EEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcccccC
Q 008236 394 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDRN 455 (573)
Q Consensus 394 v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~~~~~ 455 (573)
+.....|+...-.++.+.+.+-||-...+.|.|.|+ --+|.+.+.++.+..+..-.+..+.
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 7899999999988888777664443
No 88
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=64.43 E-value=8.3 Score=39.96 Aligned_cols=88 Identities=16% Similarity=0.223 Sum_probs=58.6
Q ss_pred cccccccccCCCCcccccCCCCCCCccccccccccCCCcccccceEEEeCCCCcccHHHHHHHHHhhhCCCceeE-----
Q 008236 349 EHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVIS----- 423 (573)
Q Consensus 349 ~~~N~L~~~~~~~~~idL~~~~~~~~~~~~~~l~~~~p~~~~~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~----- 423 (573)
+-+|.|++-++....|-.+..-+..+ ...+...|+.|.|++++.+++.+.|+ .||.+- ++
T Consensus 98 ~AintlNGLrLQ~KTIKVSyARPSs~-------------~Ik~aNLYvSGlPktMtqkelE~iFs-~fGrII-tSRiL~d 162 (360)
T KOG0145|consen 98 KAINTLNGLRLQNKTIKVSYARPSSD-------------SIKDANLYVSGLPKTMTQKELEQIFS-PFGRII-TSRILVD 162 (360)
T ss_pred HHHhhhcceeeccceEEEEeccCChh-------------hhcccceEEecCCccchHHHHHHHHH-Hhhhhh-hhhhhhh
Confidence 34566666554434455544322222 12355689999999999999999996 899852 22
Q ss_pred -EEEecCceEEEEecchhhHHHHHHHhcc
Q 008236 424 -VYHVDETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 424 -v~~iddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
+--+...-.||-|-+++.++.....++.
T Consensus 163 qvtg~srGVgFiRFDKr~EAe~AIk~lNG 191 (360)
T KOG0145|consen 163 QVTGLSRGVGFIRFDKRIEAEEAIKGLNG 191 (360)
T ss_pred cccceecceeEEEecchhHHHHHHHhccC
Confidence 2334556789999999988887666654
No 89
>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=64.28 E-value=43 Score=28.04 Aligned_cols=55 Identities=7% Similarity=0.118 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHhhhhccCCCCCCCcCCCCCcchhhhHHHhhccccccccCCCCHHHHHHHHHHHHHhCCCeEEEEe
Q 008236 63 ILFAERMKDRLSEWLGGLLRNRDEGSEVQPSFNDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRV 141 (573)
Q Consensus 63 ~~F~e~v~~~I~eWl~~~l~~~~~~~~~~~~~~~~~~~~q~~~~~~~p~l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~ 141 (573)
..|++.|.+.+..-....... . +....+.|++-+++||++||.+ .+++++.+.+.
T Consensus 8 ~~~~~~vE~~l~~la~~~~~~-~---------------------~~~~~~~l~PM~~~eR~iIH~l--a~~~~l~S~S~ 62 (74)
T cd02643 8 PKFVKDVEKDLIELVESVNKG-K---------------------QTSRSHSFPPMNREKRRIVHEL--AEHFGIESVSY 62 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHhc-c---------------------ccCCeeECCCCCHHHHHHHHHH--HhhCCCEEEec
Confidence 457777777777765543221 0 0112356888899999999984 56788887664
No 90
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=63.86 E-value=16 Score=38.16 Aligned_cols=59 Identities=24% Similarity=0.341 Sum_probs=49.2
Q ss_pred eEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcccc
Q 008236 393 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLD 453 (573)
Q Consensus 393 ~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~~~ 453 (573)
.||.=|+++.+.-.+|++.|+ .||++.-+.|+- |..-+||-|..+|++.-....++.-|
T Consensus 166 sVY~G~I~~~lte~~mr~~Fs-~fG~I~EVRvFk-~qGYaFVrF~tkEaAahAIv~mNnte 224 (321)
T KOG0148|consen 166 SVYVGNIASGLTEDLMRQTFS-PFGPIQEVRVFK-DQGYAFVRFETKEAAAHAIVQMNNTE 224 (321)
T ss_pred eEEeCCcCccccHHHHHHhcc-cCCcceEEEEec-ccceEEEEecchhhHHHHHHHhcCce
Confidence 388888999999999999997 999986555544 99999999999999988777776644
No 91
>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=63.22 E-value=23 Score=32.15 Aligned_cols=52 Identities=17% Similarity=0.268 Sum_probs=40.8
Q ss_pred EeCCCCcccHHHHHHHHHhhhCCCce-eEEEEecCceEEEEecchhhHHHHHH
Q 008236 396 VWGFPSHLKAWDIRECISKVYGPTSV-ISVYHVDETAVFVQFSRAEMVSKFLD 447 (573)
Q Consensus 396 ~~~fp~~~k~~dI~~~~~~~fg~~~v-~~v~~iddtsa~V~l~~~e~~~~~L~ 447 (573)
.-+.-..|+.++|++.+..-|.-.++ .+|+|.|.++.|..|.+.+.++.++.
T Consensus 51 ~~~~~~~w~ls~Ir~v~~RRylLr~~alEiF~~d~~~~f~~F~~~~~~k~vv~ 103 (108)
T cd01201 51 CEELHGKWPFSEIRAIFSRRYLLQNTALELFLASRTSIFFAFPDQNAVKKVVY 103 (108)
T ss_pred cccccceeeHHHHHHHHHHhhhcccceEEEEEeCCceEEEEeCcHHHHHHHHh
Confidence 34555579999999887765554332 38999999999999999999988754
No 92
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=63.17 E-value=25 Score=39.01 Aligned_cols=61 Identities=11% Similarity=0.199 Sum_probs=47.8
Q ss_pred cceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-------cCceEEEEecchhhHHHHHHHhccccc
Q 008236 391 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-------DETAVFVQFSRAEMVSKFLDLKGSLDR 454 (573)
Q Consensus 391 ~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-------ddtsa~V~l~~~e~~~~~L~~~~~~~~ 454 (573)
.+.+|+-+.|..++..+|+++|. .||++. .+..+ ....|||.|.+.+.+...+..++...-
T Consensus 295 ~~~l~v~nlp~~~~~~~l~~~f~-~~G~i~--~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~ 362 (509)
T TIGR01642 295 KDRIYIGNLPLYLGEDQIKELLE-SFGDLK--AFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDT 362 (509)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHH-hcCCee--EEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEE
Confidence 34689999999999999999996 799864 34443 235799999999999988777765443
No 93
>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=59.59 E-value=48 Score=29.03 Aligned_cols=68 Identities=18% Similarity=0.243 Sum_probs=44.0
Q ss_pred ceEEEeCCCCcccHHHHHHHHHh---hhCCCceeEEEEecCceEEEEecchhhHHHHHHHhcccccCCCCccccc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISK---VYGPTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISVLH 463 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~---~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~~~ 463 (573)
.++++.+.|..--...|+..+.. .+|.. |--|..++|.|-|.+.|.|+--+.-++.++--+..|+|..
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 45778888888888888865543 56654 3566799999999999999999999988777777776643
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=59.45 E-value=30 Score=39.98 Aligned_cols=60 Identities=22% Similarity=0.297 Sum_probs=48.7
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-c-----CceEEEEecchhhHHHHHHHhccccc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-D-----ETAVFVQFSRAEMVSKFLDLKGSLDR 454 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-d-----dtsa~V~l~~~e~~~~~L~~~~~~~~ 454 (573)
.-+|+-+.|..|...+|+++|+ .||++ .++..+ | ..-|||.|.+.|+|+..|..++..+-
T Consensus 59 ~~lFVgnLp~~~tEd~L~~~F~-~~G~I--~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i 124 (578)
T TIGR01648 59 CEVFVGKIPRDLYEDELVPLFE-KAGPI--YELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEI 124 (578)
T ss_pred CEEEeCCCCCCCCHHHHHHHHH-hhCCE--EEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCee
Confidence 4589999999999999999997 68975 456654 3 24599999999999999988876443
No 95
>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=57.74 E-value=30 Score=26.37 Aligned_cols=41 Identities=17% Similarity=0.271 Sum_probs=28.4
Q ss_pred HHHHHHhhhCCCceeEEEEec-C-ceEEEEecchhhHHHHHHHhcc
Q 008236 408 IRECISKVYGPTSVISVYHVD-E-TAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 408 I~~~~~~~fg~~~v~~v~~id-d-tsa~V~l~~~e~~~~~L~~~~~ 451 (573)
|+++|+ .||.+ ..|.-.. . ..|||.+.+.++|+..+..++.
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 456665 78875 4454443 3 7899999999999998765544
No 96
>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=57.67 E-value=30 Score=28.34 Aligned_cols=54 Identities=17% Similarity=0.185 Sum_probs=43.8
Q ss_pred eCCC-CcccHHHHHHHHHhhhCCC-ceeEEEEecCceEEEEecchhhHHHHHHHhc
Q 008236 397 WGFP-SHLKAWDIRECISKVYGPT-SVISVYHVDETAVFVQFSRAEMVSKFLDLKG 450 (573)
Q Consensus 397 ~~fp-~~~k~~dI~~~~~~~fg~~-~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~ 450 (573)
+..| ...+-.++.+.+.+.|+.. ..+.+.|.|+-.-+|.+.+.++.+..+....
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 3445 8889999999999999876 3468999999999999999988777655543
No 97
>PRK05755 DNA polymerase I; Provisional
Probab=56.75 E-value=35 Score=41.24 Aligned_cols=109 Identities=16% Similarity=-0.065 Sum_probs=61.6
Q ss_pred HHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHh
Q 008236 189 VIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSV 268 (573)
Q Consensus 189 v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~ 268 (573)
+.+.|.....++|+||.-+|+-.|.+. .-++| ..++||..++....+ ....+|..+.+.
T Consensus 362 l~~~L~d~~v~kV~HNakfDl~~L~~~-gi~~~--------------~~~~DT~iAa~Ll~~------~~~~~L~~L~~~ 420 (880)
T PRK05755 362 LKPLLEDPAIKKVGQNLKYDLHVLARY-GIELR--------------GIAFDTMLASYLLDP------GRRHGLDSLAER 420 (880)
T ss_pred HHHHHhCCCCcEEEeccHhHHHHHHhC-CCCcC--------------CCcccHHHHHHHcCC------CCCCCHHHHHHH
Confidence 455666777889999999999998852 11121 457899988754322 012567766544
Q ss_pred hhhhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 269 LCPQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 269 l~~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
....- ..... ..+. ... ..... ......|-|+.|+.+|..+|.+|...|.
T Consensus 421 ylg~~-~~~~~-~~~g-k~~----~~~~~----ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 421 YLGHK-TISFE-EVAG-KQL----TFAQV----DLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred HhCCC-ccchH-HhcC-CCC----Ccccc----CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 32100 00000 0000 000 00000 0113568899999999999999988763
No 98
>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=56.51 E-value=37 Score=28.06 Aligned_cols=55 Identities=20% Similarity=0.236 Sum_probs=46.8
Q ss_pred eCCCCcccHHHHHHHHHhhhCCC-ceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 008236 397 WGFPSHLKAWDIRECISKVYGPT-SVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 397 ~~fp~~~k~~dI~~~~~~~fg~~-~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
+..|...+-.++.+.+.+.||.. ..+.|.|.|+-.-+|.+.+.++.+..+...+.
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 66788889999999999999984 44689999999999999999999888776655
No 99
>smart00361 RRM_1 RNA recognition motif.
Probab=55.53 E-value=31 Score=27.85 Aligned_cols=44 Identities=18% Similarity=0.286 Sum_probs=31.0
Q ss_pred HHHHHHHH---hhhCCCceeEEE--EecC--------ceEEEEecchhhHHHHHHHhcc
Q 008236 406 WDIRECIS---KVYGPTSVISVY--HVDE--------TAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 406 ~dI~~~~~---~~fg~~~v~~v~--~idd--------tsa~V~l~~~e~~~~~L~~~~~ 451 (573)
.||++.|+ ..||.+ .+|. .+|. ..+||.|.+.++|...+..++.
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 268875 4553 5664 3499999999999998776655
No 100
>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=55.38 E-value=50 Score=27.19 Aligned_cols=58 Identities=17% Similarity=0.235 Sum_probs=46.3
Q ss_pred EEEeCCCCcccHHHHHHHHHhhhCCC-ceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 008236 394 VIVWGFPSHLKAWDIRECISKVYGPT-SVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 394 v~~~~fp~~~k~~dI~~~~~~~fg~~-~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
+..+..|+.++-.++.+.+++.|+-. ..+.++|.|+---+|.+.+.++.+..+.....
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 45556788999999999999999864 23589999988889999999988777665543
No 101
>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=54.32 E-value=54 Score=26.48 Aligned_cols=29 Identities=17% Similarity=0.249 Sum_probs=22.5
Q ss_pred ccccCC-CCHHHHHHHHHHHHHhCCCeEEEEe
Q 008236 111 AISLNG-FTSHQLLLIQLVVRKHFKDLAYLRV 141 (573)
Q Consensus 111 ~l~L~~-~~s~QrrLI~q~lr~~fp~lv~v~~ 141 (573)
.+.+++ ++.++|++||++.++ -+|.+.+.
T Consensus 19 ~l~f~p~lt~~eR~~vH~~a~~--~gL~s~S~ 48 (60)
T cd02640 19 DMVFSPEFSKEERALIHQIAQK--YGLKSRSY 48 (60)
T ss_pred eEEcCCCCCHHHHHHHHHHHHH--cCCceeeE
Confidence 356777 899999999999888 56666543
No 102
>PRK10829 ribonuclease D; Provisional
Probab=53.87 E-value=46 Score=36.39 Aligned_cols=106 Identities=17% Similarity=0.097 Sum_probs=64.1
Q ss_pred HHHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHH
Q 008236 188 HVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFS 267 (573)
Q Consensus 188 ~v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~ 267 (573)
.+.+.|...+.+-|+|++-.|+-.+++.| |- ....+|||...+.... + +...+|+.+.+
T Consensus 65 ~L~~ll~~~~ivKV~H~~~~Dl~~l~~~~-g~--------------~p~~~fDTqiaa~~lg-~-----~~~~gl~~Lv~ 123 (373)
T PRK10829 65 PFKALLRDPQVTKFLHAGSEDLEVFLNAF-GE--------------LPQPLIDTQILAAFCG-R-----PLSCGFASMVE 123 (373)
T ss_pred HHHHHHcCCCeEEEEeChHhHHHHHHHHc-CC--------------CcCCeeeHHHHHHHcC-C-----CccccHHHHHH
Confidence 34455666666679999999999987654 21 2235889988775322 1 12457887766
Q ss_pred hhhhh-hccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 268 VLCPQ-IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 268 ~l~~~-l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
.++.. +......+++..-| -.....+-|+-|+...-.+|-+|...+.
T Consensus 124 ~~lgv~ldK~~~~sDW~~RP---------------Ls~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 124 EYTGVTLDKSESRTDWLARP---------------LSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred HHhCCccCcccccCCCCCCC---------------CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 54431 10000000110111 0235678899999999999999988774
No 103
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=52.46 E-value=30 Score=40.91 Aligned_cols=64 Identities=20% Similarity=0.333 Sum_probs=51.6
Q ss_pred CCcccccce------EEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-cCceEEEEecchhhHHHHHHHhcc
Q 008236 385 YPKILFECI------VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 385 ~p~~~~~~~------v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-ddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
-|.+-.+++ .++=+.++.++.+|+.++|. .||.+ .+|.-| ...||||..-++.+|++.|..++.
T Consensus 409 lP~I~pd~isV~SrTLwvG~i~k~v~e~dL~~~fe-efGei--qSi~li~~R~cAfI~M~~RqdA~kalqkl~n 479 (894)
T KOG0132|consen 409 LPTIPPDHISVCSRTLWVGGIPKNVTEQDLANLFE-EFGEI--QSIILIPPRGCAFIKMVRRQDAEKALQKLSN 479 (894)
T ss_pred CCCCCCcceeEeeeeeeeccccchhhHHHHHHHHH-hcccc--eeEeeccCCceeEEEEeehhHHHHHHHHHhc
Confidence 455544444 56667999999999999995 89986 567775 779999999999999998888774
No 104
>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=52.38 E-value=55 Score=28.64 Aligned_cols=59 Identities=15% Similarity=0.224 Sum_probs=44.9
Q ss_pred cceEEEeCCCC-----cccHHHHHHHHHhhhCCC--ceeEEEEecCceEEEEecchhhHHHHHHHh
Q 008236 391 ECIVIVWGFPS-----HLKAWDIRECISKVYGPT--SVISVYHVDETAVFVQFSRAEMVSKFLDLK 449 (573)
Q Consensus 391 ~~~v~~~~fp~-----~~k~~dI~~~~~~~fg~~--~v~~v~~iddtsa~V~l~~~e~~~~~L~~~ 449 (573)
+....-..+|. .|...++++.+.+.|+.. .-+.+.|.|+.--||.+.+.++...-+...
T Consensus 8 ~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~~ 73 (91)
T cd06398 8 GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQYF 73 (91)
T ss_pred CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHHH
Confidence 33344445564 589999999888888765 345799999999999999988887776653
No 105
>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=52.36 E-value=36 Score=27.51 Aligned_cols=38 Identities=13% Similarity=0.133 Sum_probs=26.7
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEE
Q 008236 112 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIV 153 (573)
Q Consensus 112 l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~~~~~~~~~~ivv 153 (573)
..|.+-|+|.|+++|.++.. | ++.+.+. ++ +-.+.+++
T Consensus 21 veL~Pm~~~eRri~H~~v~~-~-~l~s~S~-G~-ep~RrvvI 58 (60)
T cd02645 21 VELLPRSAYIRRLQHDLVER-Y-QLRSESF-GS-EPNRRLRI 58 (60)
T ss_pred EEcCCCCHHHHHHHHHHHHH-C-CCeEEEe-cC-CCCcEEEE
Confidence 45778889999999999994 5 8877654 32 33444544
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=51.38 E-value=43 Score=37.99 Aligned_cols=56 Identities=16% Similarity=0.243 Sum_probs=44.7
Q ss_pred EEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-cCc------eEEEEecchhhHHHHHHHhccc
Q 008236 394 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DET------AVFVQFSRAEMVSKFLDLKGSL 452 (573)
Q Consensus 394 v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-ddt------sa~V~l~~~e~~~~~L~~~~~~ 452 (573)
+|+-+.|..++..+|++.|+ .||++ .+|.-+ |.. .|||.|.+.++|+..|+.++..
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 67788999999999999996 78975 444432 432 6999999999999999877654
No 107
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=50.61 E-value=49 Score=32.68 Aligned_cols=61 Identities=20% Similarity=0.220 Sum_probs=48.4
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecC---ceEEEEecchhhHHHHHHHhcccccCC
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE---TAVFVQFSRAEMVSKFLDLKGSLDRNN 456 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~idd---tsa~V~l~~~e~~~~~L~~~~~~~~~~ 456 (573)
.-||+=+.++..+..||...|. +||+..- .||+- .-|||.|.++.+|+|....+.--+-++
T Consensus 11 ~kVYVGnL~~~a~k~eLE~~F~-~yG~lrs---vWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG 74 (195)
T KOG0107|consen 11 TKVYVGNLGSRATKRELERAFS-KYGPLRS---VWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICG 74 (195)
T ss_pred ceEEeccCCCCcchHHHHHHHH-hcCccee---EEEeecCCCceEEeccCcccHHHHHhhcCCccccC
Confidence 3488888999999999999996 8998765 58865 679999999999988766665544344
No 108
>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=49.94 E-value=49 Score=27.08 Aligned_cols=41 Identities=12% Similarity=0.249 Sum_probs=30.1
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEEe
Q 008236 112 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVYI 155 (573)
Q Consensus 112 l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~~~~~~~~~~ivv~~ 155 (573)
..|++-|.|+|++||-+++. .++.+.+- ++.+-.+.+|||.
T Consensus 20 ~~l~pM~~~eRkivHDv~~~--~Gl~S~S~-Geee~~R~VVv~~ 60 (61)
T cd02636 20 EKFQPMDKVERSIVHDVAEV--AGLTSFSF-GEDEVDRYVMIFK 60 (61)
T ss_pred cccCCCCHHHHHHHHHHHHh--cCceeEec-CCCCCceEEEEec
Confidence 45778889999999998854 88877653 5544567777763
No 109
>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=46.98 E-value=87 Score=27.15 Aligned_cols=60 Identities=7% Similarity=0.040 Sum_probs=45.4
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhC--CCceeEEEEecCceEEEEecchhhHHHHHHHhcc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYG--PTSVISVYHVDETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg--~~~v~~v~~iddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
.-++...++...+-.++.+.+...|+ ....+.+.|+|+--=.|++++.+..+.-+++.+.
T Consensus 9 gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~DEEGDp~tiSS~~EL~EA~rl~~~ 70 (83)
T cd06404 9 GDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDEEGDPCTISSQMELEEAFRLYEL 70 (83)
T ss_pred CcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCceeecCHHHHHHHHHHHHh
Confidence 33666777777787777776666544 4446789999998889999998888887777665
No 110
>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=46.77 E-value=22 Score=30.73 Aligned_cols=28 Identities=25% Similarity=0.551 Sum_probs=21.4
Q ss_pred HHHHHhcCC-CeEEechhhhHHHHHHHHh
Q 008236 189 VIDLLSSEK-KLIVGHNCFLDIAHIYSKF 216 (573)
Q Consensus 189 v~~~l~~s~-kpiVgHN~~~Dl~~l~~~F 216 (573)
+.+.|.... .++||||+-+|+.+|.+.+
T Consensus 35 f~~~l~~~~~~v~V~hn~~fD~~fL~~~~ 63 (96)
T cd06125 35 LKDILRDKPLAILVGHNGSFDLPFLNNRC 63 (96)
T ss_pred HHHHHhhCCCCEEEEeCcHHhHHHHHHHH
Confidence 444455555 7899999999999888776
No 111
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]
Probab=46.20 E-value=54 Score=33.54 Aligned_cols=59 Identities=12% Similarity=0.180 Sum_probs=42.8
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecCc------eEEEEecchhhHHHHHHHhcc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDET------AVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~iddt------sa~V~l~~~e~~~~~L~~~~~ 451 (573)
++.|+.|.|.-+|.++|+.+|. .|-.+--.-+..-+.. =+||.|.+.-.+.+.+.+++.
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 3589999999999999999996 4443321124444443 489999988888887777665
No 112
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=42.42 E-value=61 Score=34.05 Aligned_cols=59 Identities=19% Similarity=0.249 Sum_probs=46.0
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEE-e----cCceEEEEecchhhHHHHHHHhcc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYH-V----DETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~-i----ddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
-|||+--|.++++..+|++.|. +||.++--.|.. . ...-.||.|.+++.+++....++-
T Consensus 63 fhvfvgdls~eI~~e~lr~aF~-pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnG 126 (321)
T KOG0148|consen 63 FHVFVGDLSPEIDNEKLREAFA-PFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNG 126 (321)
T ss_pred eeEEehhcchhcchHHHHHHhc-cccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCC
Confidence 4577777999999999999997 899876322222 1 346799999999999998777764
No 113
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=40.31 E-value=1e+02 Score=29.47 Aligned_cols=60 Identities=20% Similarity=0.345 Sum_probs=47.6
Q ss_pred cceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEE-----ecCceEEEEecchhhHHHHHHHhcc
Q 008236 391 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYH-----VDETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 391 ~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~-----iddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
...+|+-+.|...+-.+|+..|. .||++.-+.|.. .....|||.|.+.+.+...+..++.
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 788863223322 1238899999999999999888874
No 114
>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=39.40 E-value=71 Score=25.68 Aligned_cols=39 Identities=21% Similarity=0.330 Sum_probs=25.9
Q ss_pred ccccCC-CCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEE
Q 008236 111 AISLNG-FTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIV 153 (573)
Q Consensus 111 ~l~L~~-~~s~QrrLI~q~lr~~fp~lv~v~~~~~~~~~~~ivv 153 (573)
.+.+++ .|++||++||++.++ =++.+.+. ++ |..+.++|
T Consensus 19 ~l~F~p~ls~~eR~~vH~lA~~--~gL~s~S~-G~-g~~R~v~v 58 (60)
T cd02641 19 ELEFPPTLSSHDRLLVHELAEE--LGLRHEST-GE-GSDRVITV 58 (60)
T ss_pred cEECCCCCCHHHHHHHHHHHHH--cCCceEee-CC-CCceEEEe
Confidence 356677 899999999999887 44666543 32 33444444
No 115
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=38.93 E-value=90 Score=32.37 Aligned_cols=59 Identities=22% Similarity=0.344 Sum_probs=46.0
Q ss_pred ccceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEE-ecC------ceEEEEecchhhHHHHHHHhcc
Q 008236 390 FECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYH-VDE------TAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 390 ~~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~-idd------tsa~V~l~~~e~~~~~L~~~~~ 451 (573)
-++.|-+.+.+..++-.|+.++| ..||++. .|+- .|. .=|||.|.++|+|...++.++.
T Consensus 188 D~~tvRvtNLsed~~E~dL~eLf-~~fg~i~--rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG 253 (270)
T KOG0122|consen 188 DEATVRVTNLSEDMREDDLEELF-RPFGPIT--RVYLARDKETGLSKGFAFVTFESRDDAARAIADLNG 253 (270)
T ss_pred ccceeEEecCccccChhHHHHHh-hccCccc--eeEEEEccccCcccceEEEEEecHHHHHHHHHHccC
Confidence 35678899999999999999998 5899974 4444 243 5699999999999887665543
No 116
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=38.31 E-value=86 Score=34.19 Aligned_cols=106 Identities=17% Similarity=0.216 Sum_probs=65.1
Q ss_pred HHHHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHH
Q 008236 187 RHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAF 266 (573)
Q Consensus 187 ~~v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~ 266 (573)
.-+..+|......=|.|++-.|+--+++.| |-+|. .||||+..+..+. + +.+.+|..+.
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 334455666666669999999999999887 55553 4789999986543 1 1256677765
Q ss_pred Hhhhhh-hccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHh
Q 008236 267 SVLCPQ-IALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHL 328 (573)
Q Consensus 267 ~~l~~~-l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~l 328 (573)
+.+... +..+...+++..-|- ...+.--|..|...=-.++.+|.+.|
T Consensus 119 ~~ll~v~ldK~~q~SDW~~RPL---------------s~~Ql~YAa~DV~yL~~l~~~L~~~L 166 (361)
T COG0349 119 EELLGVELDKSEQRSDWLARPL---------------SEAQLEYAAADVEYLLPLYDKLTEEL 166 (361)
T ss_pred HHHhCCcccccccccccccCCC---------------CHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 544321 111111111111110 12345568899998888999988877
No 117
>PF15023 DUF4523: Protein of unknown function (DUF4523)
Probab=36.91 E-value=94 Score=29.85 Aligned_cols=53 Identities=25% Similarity=0.439 Sum_probs=37.4
Q ss_pred cceEEEeCCCCccc-HHHHHHHHHh--hhCCCceeEEEEecCceEEEEecchhhHHHHH
Q 008236 391 ECIVIVWGFPSHLK-AWDIRECISK--VYGPTSVISVYHVDETAVFVQFSRAEMVSKFL 446 (573)
Q Consensus 391 ~~~v~~~~fp~~~k-~~dI~~~~~~--~fg~~~v~~v~~iddtsa~V~l~~~e~~~~~L 446 (573)
..+|.-|. ++.++ +.|+++.+.+ +|||+ .+|-.-..++|.|+|.+-.+|=...
T Consensus 87 sTIVVRWl-kknm~~~edl~sV~~~Ls~fGpI--~SVT~cGrqsavVvF~d~~SAC~Av 142 (166)
T PF15023_consen 87 STIVVRWL-KKNMQPTEDLKSVIQRLSVFGPI--QSVTLCGRQSAVVVFKDITSACKAV 142 (166)
T ss_pred eeEEeehh-hhcCChHHHHHHHHHHHHhcCCc--ceeeecCCceEEEEehhhHHHHHHH
Confidence 34566776 55554 4556554433 89997 5788999999999999877775543
No 118
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=36.37 E-value=72 Score=35.40 Aligned_cols=56 Identities=16% Similarity=0.183 Sum_probs=41.6
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCC--------C-ceeEEEE-ecCceEEEEecchhhHHHHHH
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGP--------T-SVISVYH-VDETAVFVQFSRAEMVSKFLD 447 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~--------~-~v~~v~~-iddtsa~V~l~~~e~~~~~L~ 447 (573)
..+|+-+.|..++..+|+++|.+.+.. . .|..+.. -+...|||.|.+.|+|...|.
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 348999999999999999999864211 1 1222322 256799999999999999884
No 119
>PRK05359 oligoribonuclease; Provisional
Probab=36.37 E-value=61 Score=31.48 Aligned_cols=21 Identities=14% Similarity=0.086 Sum_probs=18.0
Q ss_pred CCCeEEechhhhHHHHHHHHh
Q 008236 196 EKKLIVGHNCFLDIAHIYSKF 216 (573)
Q Consensus 196 s~kpiVgHN~~~Dl~~l~~~F 216 (573)
...|+||||.-+|..+|-+.+
T Consensus 97 ~~~~l~g~~v~FD~~FL~~~~ 117 (181)
T PRK05359 97 GKSPLCGNSIGQDRRFLARYM 117 (181)
T ss_pred CCCceeecchhhCHHHHHHHH
Confidence 567899999999999998765
No 120
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=36.08 E-value=99 Score=34.54 Aligned_cols=65 Identities=22% Similarity=0.293 Sum_probs=52.4
Q ss_pred eEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-cC-----ceEEEEecchhhHHHHHHHhcccccCCCCc
Q 008236 393 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DE-----TAVFVQFSRAEMVSKFLDLKGSLDRNNDPI 459 (573)
Q Consensus 393 ~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-dd-----tsa~V~l~~~e~~~~~L~~~~~~~~~~~~~ 459 (573)
.||+...|-..|--|+++++.+.-|.+ .+|..+ |+ .||.|.|..+|.++.-|..++..+=+.-++
T Consensus 46 ~vfItNIpyd~rWqdLKdLvrekvGev--~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l 116 (608)
T KOG4212|consen 46 SVFITNIPYDYRWQDLKDLVREKVGEV--EYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGREL 116 (608)
T ss_pred eEEEecCcchhhhHhHHHHHHHhcCce--EeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceE
Confidence 399999999999999999998776754 455554 43 699999999999999998888866554443
No 121
>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=35.26 E-value=79 Score=25.48 Aligned_cols=39 Identities=23% Similarity=0.370 Sum_probs=26.3
Q ss_pred cccCC-CCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 008236 112 ISLNG-FTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 154 (573)
Q Consensus 112 l~L~~-~~s~QrrLI~q~lr~~fp~lv~v~~~~~~~~~~~ivv~ 154 (573)
|.+++ +|.++|++||++.++ -+|.+.+. ++ |..+.++++
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 45554 889999999999888 56666543 33 444555554
No 122
>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=33.19 E-value=1.7e+02 Score=28.51 Aligned_cols=111 Identities=18% Similarity=0.143 Sum_probs=58.7
Q ss_pred HHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHH--hhccCCCChHHHHHhh
Q 008236 192 LLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQ--RMKKSSTSLSKAFSVL 269 (573)
Q Consensus 192 ~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~--~~~~~~tsL~~l~~~l 269 (573)
.|.+.....|||++=.|+-.+++.|.-. |. .++||..++....+-.. .......+|..+.+.+
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 3445566779999999998887766221 11 35799876543222110 0111123666664432
Q ss_pred h-hhhccCCccccccCCCCceeeeeeccccccCC-----CCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 270 C-PQIALGSKSTHLALQPSVKVEVEVDDIRSSNW-----NSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 270 ~-~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~-----~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
. ..+. +.. .+. ..-...+++| .....+-|+.|++.+-.+|-.|...|-
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 1 1110 000 000 0000011122 235677899999999999999988773
No 123
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=32.76 E-value=1.4e+02 Score=34.37 Aligned_cols=62 Identities=18% Similarity=0.251 Sum_probs=48.4
Q ss_pred CcccccceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-------cCceEEEEecchhhHHHHHHHhc
Q 008236 386 PKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-------DETAVFVQFSRAEMVSKFLDLKG 450 (573)
Q Consensus 386 p~~~~~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-------ddtsa~V~l~~~e~~~~~L~~~~ 450 (573)
-.+..+.+||+-+.|-..+-.+|++.|+ .||+.- ++..+ ...+|||.|.....+++-|....
T Consensus 287 en~~~~~tVFvRNL~fD~tEEel~~~fs-kFG~v~--ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~As 355 (678)
T KOG0127|consen 287 ENITEGKTVFVRNLPFDTTEEELKEHFS-KFGEVK--YAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAAS 355 (678)
T ss_pred ccccccceEEEecCCccccHHHHHHHHH-hhccce--eEEEEeccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence 3344456799999999999999999997 899864 33332 45799999999999998766553
No 124
>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=31.53 E-value=1.8e+02 Score=23.54 Aligned_cols=39 Identities=15% Similarity=0.138 Sum_probs=26.2
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEEE
Q 008236 112 ISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 154 (573)
Q Consensus 112 l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~~~~~~~~~~ivv~ 154 (573)
+.+++-+++||++||.+.+. -++.+.+- +... .+.++|+
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 55665443 3333 4445554
No 125
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=31.45 E-value=81 Score=31.83 Aligned_cols=40 Identities=10% Similarity=0.212 Sum_probs=29.9
Q ss_pred ccccCCCCHHHHHHHHHHHHHhCCCeEEEEeccCCCCceeEEE
Q 008236 111 AISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIV 153 (573)
Q Consensus 111 ~l~L~~~~s~QrrLI~q~lr~~fp~lv~v~~~~~~~~~~~ivv 153 (573)
+..|++-++|.||+||..|. .+|++-+.+. + .+-.+.+||
T Consensus 166 ~v~L~pM~~~ERkIVH~~l~-~~~~V~T~Se-G-~ep~R~vVV 205 (208)
T COG1847 166 SVELEPMPPFERKIVHTALS-ANPGVETYSE-G-EEPNRRVVV 205 (208)
T ss_pred eeecCCCCHHHHHHHHHHHH-hcCCcceeec-C-CCCceEEEE
Confidence 45788899999999999998 7999988764 3 233444444
No 126
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=30.76 E-value=1.1e+02 Score=23.75 Aligned_cols=49 Identities=18% Similarity=0.389 Sum_probs=34.0
Q ss_pred eEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEe-cCceEEEEecchhhHHHH
Q 008236 393 IVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHV-DETAVFVQFSRAEMVSKF 445 (573)
Q Consensus 393 ~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~i-ddtsa~V~l~~~e~~~~~ 445 (573)
.|-+.|||.. ...++..-|. .||.+ +.+.+= +-..+||.+.++.+++.-
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 3788999986 4455666665 69986 344442 367788888888888753
No 127
>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=30.22 E-value=1.5e+02 Score=23.40 Aligned_cols=28 Identities=14% Similarity=0.191 Sum_probs=20.9
Q ss_pred ccccCCCCHHHHHHHHHHHHHhCCCeEEEE
Q 008236 111 AISLNGFTSHQLLLIQLVVRKHFKDLAYLR 140 (573)
Q Consensus 111 ~l~L~~~~s~QrrLI~q~lr~~fp~lv~v~ 140 (573)
.+.+++.+.++|++||++... | ++.+.+
T Consensus 18 ~~~fppm~~~~R~~vH~lA~~-~-~L~S~S 45 (58)
T cd02646 18 SLSFPPMDKHGRKTIHKLANC-Y-NLKSKS 45 (58)
T ss_pred eEecCCCCHHHHHHHHHHHHH-c-CCcccc
Confidence 356778899999999999776 3 455543
No 128
>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=29.48 E-value=2.5e+02 Score=30.55 Aligned_cols=100 Identities=20% Similarity=0.244 Sum_probs=57.4
Q ss_pred HHHHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHh
Q 008236 189 VIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSV 268 (573)
Q Consensus 189 v~~~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~ 268 (573)
+.+.|...+...|+|++=.|+-.+.+. ++.+|. .+|||...+...++ ....+|+.+.+.
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 345566677788999999997766543 344443 56899877643221 112366665443
Q ss_pred hhh-hhccCCccccccCCCCceeeeeeccccccCC-----CCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 269 LCP-QIALGSKSTHLALQPSVKVEVEVDDIRSSNW-----NSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 269 l~~-~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~-----~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
+.. .+. ++ ...+.+ .....+-|..|++....++-.|...|.
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 221 110 00 000111 112445589999988888888888774
No 129
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=28.05 E-value=1.7e+02 Score=29.77 Aligned_cols=59 Identities=12% Similarity=0.216 Sum_probs=44.0
Q ss_pred eEEEeCCCCcccHHHHHHHHHhhhCCCc-eeEEEEe----cCceEEEEecchhhHHHHHHHhcc
Q 008236 393 IVIVWGFPSHLKAWDIRECISKVYGPTS-VISVYHV----DETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 393 ~v~~~~fp~~~k~~dI~~~~~~~fg~~~-v~~v~~i----ddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
..|+.......+..+++..+--.|++.+ |.+|.-. =...|||+|.+.+.+...|+.++.
T Consensus 11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~g 74 (221)
T KOG4206|consen 11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQG 74 (221)
T ss_pred eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcC
Confidence 5788889999999999973333344433 4566665 357899999999999998887776
No 130
>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=27.14 E-value=1e+02 Score=29.11 Aligned_cols=111 Identities=15% Similarity=0.043 Sum_probs=56.8
Q ss_pred HHHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHhhh
Q 008236 191 DLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLC 270 (573)
Q Consensus 191 ~~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~l~ 270 (573)
+.+......+|+||.=+|+-.+.+..+. +| ..++||..++....+- ....+|..+.+.+.
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 3444556789999999999887643222 11 2568999887543221 11346776654332
Q ss_pred hhhccCCccccccCCCCceeeeeeccccccCCCCCcccchhhhHHHHHHHHHHHHHHhC
Q 008236 271 PQIALGSKSTHLALQPSVKVEVEVDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329 (573)
Q Consensus 271 ~~l~~~~~~~~~~~~p~v~i~v~~~~~~s~~~~~~~~HEAGyDAymTG~vF~kL~~~lg 329 (573)
..-... . ........-.. ..+.. ......|-|+.|+..|..++-.|...+.
T Consensus 121 ~~~~~~-~-~~~~~k~~~~~--~~~~~----~~~~~~~ya~~d~~~~~~l~~~l~~~l~ 171 (193)
T cd06139 121 GHKTIS-F-EDLVGKGKKQI--TFDQV----PLEKAAEYAAEDADITLRLYELLKPKLK 171 (193)
T ss_pred CCCCcc-H-HHHcCCCcCcC--Ccccc----CHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 110000 0 00000000000 00000 0012345689999999999999988773
No 131
>PF10792 DUF2605: Protein of unknown function (DUF2605); InterPro: IPR019728 This entry represents a protein conserved in Cyanobacteria. The function is not known.
Probab=25.86 E-value=50 Score=29.44 Aligned_cols=27 Identities=30% Similarity=0.538 Sum_probs=21.4
Q ss_pred CchhhhhhC--------CCCCCHHHHHHHHHHhhh
Q 008236 10 DFNACIHEG--------VSYLSREQEDKALKHVNS 36 (573)
Q Consensus 10 DFNk~~~~G--------IpYLsr~eEe~~~~rl~~ 36 (573)
||+-||..| |++||.+|-+.+..|+.+
T Consensus 18 DF~yWF~Rs~~LLe~e~~~fls~~eQ~~Ll~Rv~q 52 (98)
T PF10792_consen 18 DFQYWFSRSRELLETEPISFLSPEEQSDLLERVKQ 52 (98)
T ss_pred HHHHHHHHHHHHHhcCCcccCCHHHHHHHHHHHHH
Confidence 899999776 788998877777777764
No 132
>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=23.44 E-value=1.2e+02 Score=27.04 Aligned_cols=57 Identities=26% Similarity=0.213 Sum_probs=34.5
Q ss_pred HHhcCCCeEEechhhhHHHHHHHHhcCCCCCCHHHHHHHHHccCCCCcchhHHhhhchHHHHhhccCCCChHHHHHh
Q 008236 192 LLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSV 268 (573)
Q Consensus 192 ~l~~s~kpiVgHN~~~Dl~~l~~~F~~~LP~~~~eFk~~l~~~FP~I~DTK~La~~~~~lk~~~~~~~tsL~~l~~~ 268 (573)
.+...+...||||.-.|+-.|.+.+ ..+| +.++||..++....+- ....+|..+.+.
T Consensus 49 ~l~~~~~~~v~~~~k~d~~~L~~~~-~~~~--------------~~~~D~~~~ayll~~~-----~~~~~l~~l~~~ 105 (155)
T cd00007 49 LLEDEDITKVGHDAKFDLVVLARDG-IELP--------------GNIFDTMLAAYLLNPG-----EGSHSLDDLAKE 105 (155)
T ss_pred HHcCCCCcEEeccHHHHHHHHHHCC-CCCC--------------CCcccHHHHHHHhCCC-----CCcCCHHHHHHH
Confidence 3455667799999999988876543 1122 2578998887543221 002467766443
No 133
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=22.71 E-value=1.8e+02 Score=32.73 Aligned_cols=94 Identities=16% Similarity=0.241 Sum_probs=64.9
Q ss_pred hhccccccccccCCCCcccccCCCCCCCccccccccccCCCcccccceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEE
Q 008236 346 KLREHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVY 425 (573)
Q Consensus 346 ~l~~~~N~L~~~~~~~~~idL~~~~~~~~~~~~~~l~~~~p~~~~~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~ 425 (573)
.++-+=|-+.+.|... . ..||.+. .+.--+.|+-+.+.+.+...|+.+|. .||. |..|.
T Consensus 232 ~~klwgn~~tVdWAep-~-------~e~ded~----------ms~VKvLYVRNL~~~tTeE~lk~~F~-~~G~--veRVk 290 (506)
T KOG0117|consen 232 KIKLWGNAITVDWAEP-E-------EEPDEDT----------MSKVKVLYVRNLMESTTEETLKKLFN-EFGK--VERVK 290 (506)
T ss_pred ceeecCCcceeeccCc-c-------cCCChhh----------hhheeeeeeeccchhhhHHHHHHHHH-hccc--eEEee
Confidence 4667888888888632 1 1122210 11123477778999999999999996 6875 35666
Q ss_pred EecCceEEEEecchhhHHHHHHHhcccccCCCCccc
Q 008236 426 HVDETAVFVQFSRAEMVSKFLDLKGSLDRNNDPISV 461 (573)
Q Consensus 426 ~iddtsa~V~l~~~e~~~~~L~~~~~~~~~~~~~~~ 461 (573)
=+-| -|||.|.++++|-..|+.++--|=.+..+.|
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 9999999999998888888776555555555
No 134
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=21.61 E-value=1.4e+02 Score=28.56 Aligned_cols=22 Identities=14% Similarity=-0.189 Sum_probs=18.0
Q ss_pred CcccchhhhHHHHHHHHHHHHH
Q 008236 305 GVKHEAGYDAFMTGCVFAQACS 326 (573)
Q Consensus 305 ~~~HEAGyDAymTG~vF~kL~~ 326 (573)
+..|.|=.||..|+..+..+.+
T Consensus 149 ~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 149 KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred CCCcchHHHHHHHHHHHHHHHH
Confidence 4569999999999998877644
No 135
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=21.51 E-value=2.1e+02 Score=29.20 Aligned_cols=49 Identities=18% Similarity=0.237 Sum_probs=37.3
Q ss_pred cccHHHHHHHHHhhhCCCceeEEEEe-----cCceEEEEecchhhHHHHHHHhcc
Q 008236 402 HLKAWDIRECISKVYGPTSVISVYHV-----DETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 402 ~~k~~dI~~~~~~~fg~~~v~~v~~i-----ddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
..++.+|+..|. .||.+.=++|=|= ...=|||-|+.+.+|++.|+++-.
T Consensus 24 RTspd~LrrvFe-kYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG 77 (256)
T KOG4207|consen 24 RTSPDDLRRVFE-KYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDG 77 (256)
T ss_pred cCCHHHHHHHHH-HhCcccceecccccccccccceeEEEeeecchHHHHHHhhcc
Confidence 458999999996 6888765566662 235699999999999998777654
No 136
>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []. This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.
Probab=21.34 E-value=2.5e+02 Score=25.06 Aligned_cols=52 Identities=17% Similarity=0.392 Sum_probs=30.8
Q ss_pred cceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEE------------Ee--cCceEEEEecchhhHHHHH
Q 008236 391 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVY------------HV--DETAVFVQFSRAEMVSKFL 446 (573)
Q Consensus 391 ~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~------------~i--ddtsa~V~l~~~e~~~~~L 446 (573)
+.-|.+.|||+. .+..|.+.|+ -||.+ .+.. .+ ...-.-|.+.++.+|...|
T Consensus 6 ~~wVtVFGfp~~-~~~~Vl~~F~-~~G~I--le~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL 71 (100)
T PF05172_consen 6 ETWVTVFGFPPS-ASNQVLRHFS-SFGTI--LEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL 71 (100)
T ss_dssp CCEEEEE---GG-GHHHHHHHHH-CCS-E--ECEEGGG----------E-CCTTEEEEEESSHHHHHHHH
T ss_pred CeEEEEEccCHH-HHHHHHHHHH-hcceE--EEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH
Confidence 445999999998 6666667876 68864 3443 23 4444555678888887654
No 137
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=21.30 E-value=1.1e+02 Score=34.04 Aligned_cols=62 Identities=18% Similarity=0.246 Sum_probs=46.2
Q ss_pred EEEeCCCCcccHHHHHHHHHhhhCCCceeEEEE----ecCceEEEEecchhhHHHHHHHhcccccCC
Q 008236 394 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYH----VDETAVFVQFSRAEMVSKFLDLKGSLDRNN 456 (573)
Q Consensus 394 v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~----iddtsa~V~l~~~e~~~~~L~~~~~~~~~~ 456 (573)
.|+--.++..+..+|++.|+ .||.+--.+|-. +...||||.|+.+|.+..-.+.++..+.-.
T Consensus 127 LFvg~lsK~~te~evr~iFs-~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tme 192 (510)
T KOG0144|consen 127 LFVGMLSKQCTENEVREIFS-RFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTME 192 (510)
T ss_pred hhhhhccccccHHHHHHHHH-hhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeec
Confidence 45555788888899999997 688753222222 466899999999999999888888766533
No 138
>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]
Probab=20.56 E-value=75 Score=36.67 Aligned_cols=58 Identities=10% Similarity=0.169 Sum_probs=44.9
Q ss_pred cceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEEecC--ceEEEEecchhhHHHHHHHhcc
Q 008236 391 ECIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDE--TAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 391 ~~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~idd--tsa~V~l~~~e~~~~~L~~~~~ 451 (573)
.|+|++-+|-.-.+...++.+|.+.-|.+ .+. |||. +.|||.++..+.|-+--.++..
T Consensus 444 SnvlhI~nLvRPFTlgQLkelL~rtgg~V--ee~-WmDkIKShCyV~yss~eEA~atr~Alhn 503 (718)
T KOG2416|consen 444 SNVLHIDNLVRPFTLGQLKELLGRTGGNV--EEF-WMDKIKSHCYVSYSSVEEAAATREALHN 503 (718)
T ss_pred cceEeeecccccchHHHHHHHHhhccCch--HHH-HHHHhhcceeEecccHHHHHHHHHHHhc
Confidence 68899999988889999999998776654 333 9995 9999999988877665444433
No 139
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=20.05 E-value=3.1e+02 Score=25.14 Aligned_cols=59 Identities=15% Similarity=0.216 Sum_probs=42.2
Q ss_pred ceEEEeCCCCcccHHHHHHHHHhhhCCCceeEEEE--ecCceEEEEecchhhHHHHHHHhcc
Q 008236 392 CIVIVWGFPSHLKAWDIRECISKVYGPTSVISVYH--VDETAVFVQFSRAEMVSKFLDLKGS 451 (573)
Q Consensus 392 ~~v~~~~fp~~~k~~dI~~~~~~~fg~~~v~~v~~--iddtsa~V~l~~~e~~~~~L~~~~~ 451 (573)
.+.|+-+.|...++.+..++|. .||++.-+.|-- =-..+|||+-.+-.+|+...+-++.
T Consensus 19 riLyirNLp~~ITseemydlFG-kyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg 79 (124)
T KOG0114|consen 19 RILYIRNLPFKITSEEMYDLFG-KYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSG 79 (124)
T ss_pred eeEEEecCCccccHHHHHHHhh-cccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcc
Confidence 3578889999999999999985 688865422211 1346899998887777666555444
Done!