Query psy3154
Match_columns 101
No_of_seqs 114 out of 1061
Neff 6.9
Searched_HMMs 46136
Date Fri Aug 16 17:46:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3154.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3154hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01730 LSm3 The eukaryotic Sm 99.9 2.4E-26 5.2E-31 144.9 9.9 82 13-94 1-82 (82)
2 cd01720 Sm_D2 The eukaryotic S 99.9 3.1E-26 6.7E-31 146.1 10.5 84 12-95 1-86 (87)
3 PRK00737 small nuclear ribonuc 99.9 1E-24 2.2E-29 134.5 9.7 70 12-94 3-72 (72)
4 cd01729 LSm7 The eukaryotic Sm 99.9 2.3E-24 5.1E-29 135.7 10.5 80 12-97 2-81 (81)
5 cd01732 LSm5 The eukaryotic Sm 99.9 2.8E-24 6.1E-29 134.0 10.5 74 12-95 2-75 (76)
6 cd01731 archaeal_Sm1 The archa 99.9 2E-24 4.4E-29 131.6 9.4 68 14-94 1-68 (68)
7 cd01726 LSm6 The eukaryotic Sm 99.9 1.4E-23 3.1E-28 127.6 9.0 67 14-93 1-67 (67)
8 cd01719 Sm_G The eukaryotic Sm 99.9 2.7E-23 5.9E-28 128.3 9.6 71 14-97 1-71 (72)
9 cd01717 Sm_B The eukaryotic Sm 99.9 6.3E-23 1.4E-27 128.4 10.0 76 16-94 3-78 (79)
10 cd01722 Sm_F The eukaryotic Sm 99.9 7.6E-23 1.6E-27 124.8 8.4 68 13-93 1-68 (68)
11 cd01727 LSm8 The eukaryotic Sm 99.9 4.3E-22 9.2E-27 123.3 10.4 73 16-97 2-74 (74)
12 cd01728 LSm1 The eukaryotic Sm 99.9 6.7E-22 1.5E-26 122.7 10.5 71 14-94 3-73 (74)
13 cd01718 Sm_E The eukaryotic Sm 99.9 7.6E-22 1.6E-26 123.8 9.8 74 9-94 2-79 (79)
14 cd06168 LSm9 The eukaryotic Sm 99.9 1E-21 2.2E-26 122.2 10.2 72 16-94 3-74 (75)
15 cd01721 Sm_D3 The eukaryotic S 99.9 1.2E-21 2.7E-26 120.2 9.3 70 14-96 1-70 (70)
16 KOG3460|consensus 99.9 9.3E-23 2E-27 127.6 2.8 87 10-96 2-88 (91)
17 cd01723 LSm4 The eukaryotic Sm 99.9 3.3E-21 7.1E-26 119.9 9.4 73 13-97 1-73 (76)
18 PF01423 LSM: LSM domain ; In 99.9 4.2E-21 9.1E-26 115.9 8.6 67 16-94 1-67 (67)
19 smart00651 Sm snRNP Sm protein 99.9 7E-21 1.5E-25 114.8 9.4 66 17-94 2-67 (67)
20 PTZ00138 small nuclear ribonuc 99.9 1.3E-20 2.7E-25 120.6 10.6 80 4-95 5-88 (89)
21 COG1958 LSM1 Small nuclear rib 99.9 8.8E-21 1.9E-25 118.5 9.5 75 11-94 5-79 (79)
22 cd00600 Sm_like The eukaryotic 99.8 7E-20 1.5E-24 109.0 8.8 63 18-93 1-63 (63)
23 cd01724 Sm_D1 The eukaryotic S 99.8 9.7E-20 2.1E-24 116.7 9.7 71 14-97 2-72 (90)
24 cd01725 LSm2 The eukaryotic Sm 99.8 2.9E-19 6.3E-24 112.5 9.3 74 13-97 1-74 (81)
25 cd01733 LSm10 The eukaryotic S 99.8 8.6E-19 1.9E-23 109.7 9.3 71 12-95 8-78 (78)
26 KOG1780|consensus 99.8 7E-19 1.5E-23 107.9 6.4 71 12-97 5-75 (77)
27 KOG1781|consensus 99.8 9.4E-20 2E-24 117.2 0.6 81 15-100 19-99 (108)
28 KOG3482|consensus 99.7 3.6E-17 7.7E-22 100.1 6.4 72 12-96 7-78 (79)
29 KOG1775|consensus 99.7 1.1E-16 2.5E-21 98.8 4.9 78 10-97 4-81 (84)
30 KOG1783|consensus 99.7 2.3E-17 5E-22 101.0 1.3 73 11-96 4-76 (77)
31 KOG3168|consensus 99.6 4.9E-17 1.1E-21 113.4 0.7 82 11-96 3-84 (177)
32 KOG3459|consensus 99.5 1.7E-15 3.8E-20 99.1 0.1 83 11-93 22-106 (114)
33 KOG1784|consensus 99.5 1.4E-14 3E-19 92.2 4.1 74 16-98 3-76 (96)
34 KOG1774|consensus 99.5 7.5E-14 1.6E-18 87.2 4.6 75 10-96 9-87 (88)
35 KOG1782|consensus 99.5 1.2E-14 2.5E-19 96.9 0.8 74 13-97 10-83 (129)
36 KOG3293|consensus 99.3 2.4E-12 5.2E-17 86.0 5.9 73 13-97 2-74 (134)
37 KOG3448|consensus 99.3 1.1E-11 2.5E-16 78.5 8.4 72 13-95 2-73 (96)
38 KOG3172|consensus 99.2 4.8E-11 1E-15 78.2 7.0 75 9-96 1-75 (119)
39 KOG3428|consensus 99.0 5.6E-09 1.2E-13 68.5 8.3 69 15-97 4-72 (109)
40 cd01739 LSm11_C The eukaryotic 98.8 2.6E-09 5.7E-14 64.4 2.3 41 20-60 3-49 (66)
41 PF14438 SM-ATX: Ataxin 2 SM d 98.0 3.4E-05 7.3E-10 47.5 5.9 69 16-90 5-76 (77)
42 PF12701 LSM14: Scd6-like Sm d 97.4 0.001 2.2E-08 43.1 6.7 76 19-98 4-80 (96)
43 cd01736 LSm14_N LSm14 (also kn 96.7 0.011 2.5E-07 36.5 6.4 69 20-91 3-72 (74)
44 PF02237 BPL_C: Biotin protein 96.6 0.013 2.9E-07 32.9 5.9 33 22-55 2-34 (48)
45 PF06372 Gemin6: Gemin6 protei 96.6 0.0049 1.1E-07 43.6 4.7 66 11-97 6-72 (166)
46 PF11095 Gemin7: Gem-associate 96.5 0.022 4.8E-07 35.8 6.7 65 13-95 14-79 (80)
47 TIGR02383 Hfq RNA chaperone Hf 96.3 0.015 3.2E-07 34.8 5.0 32 22-53 14-45 (61)
48 cd01716 Hfq Hfq, an abundant, 96.2 0.015 3.4E-07 34.7 4.9 32 22-53 10-41 (61)
49 COG1923 Hfq Uncharacterized ho 96.1 0.026 5.6E-07 35.1 5.5 43 9-53 5-48 (77)
50 PRK00395 hfq RNA-binding prote 95.9 0.026 5.6E-07 35.4 4.9 33 22-54 18-50 (79)
51 cd01735 LSm12_N LSm12 belongs 95.8 0.029 6.2E-07 33.5 4.8 36 21-56 4-39 (61)
52 PRK14638 hypothetical protein; 94.2 0.11 2.3E-06 36.1 4.6 33 19-52 96-128 (150)
53 PRK14639 hypothetical protein; 93.3 0.2 4.4E-06 34.3 4.6 33 18-51 83-115 (140)
54 PRK02001 hypothetical protein; 93.1 0.22 4.7E-06 34.7 4.6 31 20-51 87-117 (152)
55 KOG1073|consensus 93.0 0.26 5.7E-06 38.7 5.4 76 18-96 4-80 (361)
56 PF10842 DUF2642: Protein of u 93.0 1 2.2E-05 27.2 6.8 58 11-94 7-66 (66)
57 PRK14091 RNA-binding protein H 91.7 0.48 1E-05 33.5 4.9 33 23-55 104-136 (165)
58 PRK14091 RNA-binding protein H 90.9 0.65 1.4E-05 32.9 4.9 32 23-54 24-55 (165)
59 PRK14644 hypothetical protein; 90.7 0.72 1.6E-05 31.4 4.9 34 18-52 80-117 (136)
60 PF02576 DUF150: Uncharacteris 90.1 0.94 2E-05 30.6 5.1 42 9-51 70-118 (141)
61 PRK14640 hypothetical protein; 89.9 0.82 1.8E-05 31.6 4.7 33 19-52 93-129 (152)
62 cd01734 YlxS_C YxlS is a Bacil 89.6 1.1 2.3E-05 27.8 4.6 32 19-51 21-56 (83)
63 PF03614 Flag1_repress: Repres 89.3 0.99 2.2E-05 31.7 4.7 39 16-55 23-61 (165)
64 PRK14633 hypothetical protein; 89.2 1 2.2E-05 31.1 4.7 33 19-52 90-126 (150)
65 PRK14642 hypothetical protein; 89.1 0.93 2E-05 32.9 4.7 27 20-46 97-136 (197)
66 PRK14636 hypothetical protein; 88.6 1 2.3E-05 31.9 4.6 33 19-52 94-130 (176)
67 PRK14645 hypothetical protein; 87.7 2 4.2E-05 29.9 5.4 32 19-52 98-129 (154)
68 PRK14632 hypothetical protein; 87.6 1.4 2.9E-05 31.2 4.6 33 19-52 94-133 (172)
69 COG0779 Uncharacterized protei 87.4 2 4.4E-05 30.0 5.3 43 9-52 82-131 (153)
70 PRK14643 hypothetical protein; 87.3 1.8 3.9E-05 30.4 5.0 30 18-47 99-132 (164)
71 PRK14634 hypothetical protein; 86.4 1.8 3.9E-05 30.1 4.7 33 19-52 96-132 (155)
72 PRK00092 ribosome maturation p 86.4 1.9 4E-05 29.7 4.7 29 18-46 93-125 (154)
73 PRK14646 hypothetical protein; 85.8 2 4.4E-05 29.8 4.6 34 18-52 95-132 (155)
74 PRK14647 hypothetical protein; 85.1 2.2 4.8E-05 29.6 4.6 28 19-46 95-131 (159)
75 PRK14631 hypothetical protein; 85.1 2.1 4.6E-05 30.3 4.6 27 18-44 112-142 (174)
76 PRK14641 hypothetical protein; 83.0 2.6 5.7E-05 29.9 4.3 26 19-44 100-129 (173)
77 PRK14637 hypothetical protein; 82.5 3 6.4E-05 28.9 4.3 33 19-52 94-127 (151)
78 PRK06955 biotin--protein ligas 82.4 3.2 6.8E-05 31.5 4.8 33 21-53 247-279 (300)
79 PF14563 DUF4444: Domain of un 82.1 2.2 4.7E-05 23.6 2.8 23 36-58 10-32 (42)
80 PF03614 Flag1_repress: Repres 78.9 4.2 9.2E-05 28.6 4.1 40 6-45 101-142 (165)
81 PF11607 DUF3247: Protein of u 74.0 8.6 0.00019 24.9 4.2 17 24-40 29-45 (101)
82 PRK11886 bifunctional biotin-- 73.6 8.4 0.00018 29.2 4.9 31 21-52 270-300 (319)
83 PRK10898 serine endoprotease; 72.5 8.7 0.00019 29.8 4.8 32 24-55 102-133 (353)
84 TIGR02038 protease_degS peripl 72.0 8.9 0.00019 29.6 4.7 32 24-55 102-133 (351)
85 PTZ00275 biotin-acetyl-CoA-car 71.6 10 0.00022 28.6 4.9 31 22-53 236-266 (285)
86 PRK13325 bifunctional biotin-- 71.4 9.1 0.0002 32.0 4.9 33 21-53 276-308 (592)
87 TIGR00121 birA_ligase birA, bi 71.0 11 0.00023 27.4 4.8 30 22-52 192-221 (237)
88 PRK08330 biotin--protein ligas 69.6 14 0.00029 26.9 5.0 32 21-53 186-218 (236)
89 PRK10942 serine endoprotease; 68.4 11 0.00024 30.5 4.7 31 24-54 136-166 (473)
90 PRK10139 serine endoprotease; 68.4 12 0.00025 30.2 4.8 32 24-55 115-146 (455)
91 KOG3382|consensus 66.3 3.4 7.4E-05 28.5 1.2 25 31-55 40-64 (151)
92 PRK14630 hypothetical protein; 64.8 15 0.00033 25.1 4.2 32 19-52 93-124 (143)
93 COG0340 BirA Biotin-(acetyl-Co 64.7 17 0.00036 26.9 4.7 33 22-54 189-221 (238)
94 PRK14635 hypothetical protein; 64.6 16 0.00035 25.4 4.4 32 19-51 95-131 (162)
95 PRK09618 flgD flagellar basal 63.5 15 0.00033 25.3 4.0 26 19-44 88-113 (142)
96 PF07073 ROF: Modulator of Rho 60.6 12 0.00027 23.2 2.9 58 23-100 17-74 (80)
97 TIGR02037 degP_htrA_DO peripla 59.2 21 0.00046 28.1 4.7 32 24-55 82-113 (428)
98 PF05071 NDUFA12: NADH ubiquin 54.9 5.9 0.00013 25.7 0.8 17 38-54 1-17 (105)
99 PRK08477 biotin--protein ligas 49.1 72 0.0016 23.1 5.8 35 21-56 173-207 (211)
100 TIGR03170 flgA_cterm flagella 48.6 24 0.00052 22.7 3.0 22 21-42 94-116 (122)
101 PRK11911 flgD flagellar basal 45.4 43 0.00094 23.0 3.9 26 20-45 90-115 (140)
102 PRK04337 50S ribosomal protein 45.1 47 0.001 21.1 3.7 35 16-50 33-67 (87)
103 TIGR02603 CxxCH_TIGR02603 puta 44.0 38 0.00083 22.4 3.5 41 13-54 38-87 (133)
104 cd01737 LSm16_N LSm16 belongs 43.5 45 0.00097 19.9 3.2 35 20-54 3-39 (62)
105 PF06257 DUF1021: Protein of u 42.8 69 0.0015 19.8 4.2 28 16-43 10-41 (76)
106 PF14485 DUF4431: Domain of un 41.3 32 0.0007 19.2 2.3 22 13-37 9-30 (48)
107 PRK07018 flgA flagellar basal 41.1 32 0.0007 25.1 2.9 22 21-42 205-227 (235)
108 PF01887 SAM_adeno_trans: S-ad 40.5 43 0.00093 25.1 3.6 19 35-53 169-187 (258)
109 KOG4401|consensus 39.5 42 0.0009 24.2 3.2 35 21-55 9-43 (184)
110 KOG3493|consensus 39.1 26 0.00056 21.3 1.8 19 17-35 5-23 (73)
111 PF09465 LBR_tudor: Lamin-B re 39.0 69 0.0015 18.6 3.5 26 21-46 7-33 (55)
112 PRK06630 hypothetical protein; 38.1 19 0.00042 23.4 1.2 19 36-54 11-29 (99)
113 PF14153 Spore_coat_CotO: Spor 37.6 54 0.0012 23.5 3.5 33 14-46 122-157 (185)
114 PRK06005 flgA flagellar basal 32.0 61 0.0013 22.5 3.0 22 21-42 129-151 (160)
115 PLN03095 NADH:ubiquinone oxido 31.7 29 0.00063 23.2 1.3 19 37-55 9-27 (115)
116 COG2451 Ribosomal protein L35A 31.3 98 0.0021 20.1 3.6 29 18-48 41-70 (100)
117 smart00166 UBX Domain present 31.0 48 0.001 19.8 2.1 21 24-44 5-25 (80)
118 PRK12617 flgA flagellar basal 30.8 63 0.0014 23.6 3.0 22 21-42 184-206 (214)
119 PRK06792 flgD flagellar basal 30.6 91 0.002 22.6 3.8 25 20-44 115-139 (190)
120 PRK11625 Rho-binding antitermi 30.4 1.4E+02 0.0031 18.7 6.2 50 23-93 23-72 (84)
121 PF03122 Herpes_MCP: Herpes vi 30.3 17 0.00037 33.4 0.0 56 25-91 249-304 (1354)
122 PTZ00276 biotin/lipoate protei 29.5 92 0.002 22.8 3.8 23 31-53 209-231 (245)
123 COG1976 TIF6 Translation initi 29.3 1.3E+02 0.0029 22.3 4.5 89 7-95 28-117 (222)
124 cd04479 RPA3 RPA3: A subfamily 28.7 1.6E+02 0.0034 18.6 4.4 14 16-29 8-21 (101)
125 PRK08515 flgA flagellar basal 28.2 91 0.002 22.7 3.5 22 21-42 194-215 (222)
126 PF00789 UBX: UBX domain; Int 27.3 68 0.0015 19.0 2.4 21 24-44 7-27 (82)
127 cd01767 UBX UBX (ubiquitin reg 27.2 68 0.0015 18.9 2.3 21 24-44 3-23 (77)
128 PRK06804 flgA flagellar basal 26.0 83 0.0018 23.7 3.0 22 21-42 231-253 (261)
129 COG0265 DegQ Trypsin-like seri 25.2 1.5E+02 0.0033 22.4 4.4 32 24-55 96-127 (347)
130 smart00039 CRF corticotropin-r 24.8 48 0.001 18.0 1.2 17 6-22 2-18 (40)
131 PF05954 Phage_GPD: Phage late 24.6 1E+02 0.0023 22.1 3.3 24 21-44 26-49 (292)
132 PRK12618 flgA flagellar basal 24.4 1E+02 0.0022 20.9 3.0 22 21-42 110-132 (141)
133 cd01772 SAKS1_UBX SAKS1-like U 23.7 78 0.0017 19.0 2.1 22 23-44 4-25 (79)
134 PRK10708 hypothetical protein; 23.5 1E+02 0.0022 18.2 2.5 26 22-47 3-28 (62)
135 PRK08183 NADH dehydrogenase; V 23.4 48 0.001 22.6 1.2 19 37-55 25-43 (133)
136 PF10894 DUF2689: Protein of u 23.1 11 0.00024 22.1 -1.6 19 43-61 20-38 (61)
137 PF01247 Ribosomal_L35Ae: Ribo 22.8 2E+02 0.0042 18.5 3.9 36 17-52 34-77 (95)
138 PF10618 Tail_tube: Phage tail 22.4 1.6E+02 0.0034 19.4 3.5 29 11-39 62-90 (119)
139 PF12869 tRNA_anti-like: tRNA_ 22.2 83 0.0018 20.5 2.2 20 35-54 124-143 (144)
140 COG5316 Uncharacterized conser 22.1 1.9E+02 0.0042 23.4 4.5 45 12-57 71-115 (421)
141 PF11197 DUF2835: Protein of u 21.9 1.9E+02 0.004 17.4 3.5 24 14-37 9-34 (68)
142 COG0048 RpsL Ribosomal protein 21.8 97 0.0021 21.1 2.4 21 21-41 54-74 (129)
143 cd05792 S1_eIF1AD_like S1_eIF1 21.3 59 0.0013 20.1 1.2 18 82-99 7-24 (78)
144 COG4466 Veg Uncharacterized pr 21.2 1E+02 0.0023 19.2 2.3 20 16-35 12-31 (80)
145 KOG4649|consensus 20.6 3.7E+02 0.0081 21.0 5.6 35 18-52 7-48 (354)
146 COG3466 ISA1214 Putative trans 20.5 1.1E+02 0.0023 17.6 2.1 18 15-32 34-51 (52)
147 TIGR00008 infA translation ini 20.4 1.6E+02 0.0035 17.7 3.0 22 23-44 17-38 (68)
148 smart00333 TUDOR Tudor domain. 20.2 1.6E+02 0.0035 15.8 4.2 25 22-46 5-29 (57)
No 1
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.94 E-value=2.4e-26 Score=144.93 Aligned_cols=82 Identities=87% Similarity=1.266 Sum_probs=68.3
Q ss_pred ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154 13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV 92 (101)
Q Consensus 13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 92 (101)
.|+++|+.+++++|.|+|++||+|.|+|.|||+||||+|+||.|++....+..+..+.......|.+|.+||||++|++|
T Consensus 1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i 80 (82)
T cd01730 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV 80 (82)
T ss_pred CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence 49999999999999999999999999999999999999999999987543221111122234688999999999999999
Q ss_pred ec
Q psy3154 93 SP 94 (101)
Q Consensus 93 ~~ 94 (101)
++
T Consensus 81 ~~ 82 (82)
T cd01730 81 SP 82 (82)
T ss_pred CC
Confidence 74
No 2
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.94 E-value=3.1e-26 Score=146.07 Aligned_cols=84 Identities=35% Similarity=0.521 Sum_probs=70.3
Q ss_pred CChHHHHHHhc--CCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154 12 KEPLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV 89 (101)
Q Consensus 12 ~~Pl~lL~~~l--~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I 89 (101)
.+|+++|+.++ +++|.|+|++|++|.|+|.|||+||||+|+||.|++...++++...+.......+++|.+||||++|
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~V 80 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSV 80 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEE
Confidence 48999999998 7999999999999999999999999999999999987654332211122245688899999999999
Q ss_pred EEEecC
Q psy3154 90 ILVSPP 95 (101)
Q Consensus 90 v~I~~~ 95 (101)
++|+..
T Consensus 81 v~Is~~ 86 (87)
T cd01720 81 ILVLRN 86 (87)
T ss_pred EEEecC
Confidence 999864
No 3
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.92 E-value=1e-24 Score=134.51 Aligned_cols=70 Identities=37% Similarity=0.696 Sum_probs=63.9
Q ss_pred CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL 91 (101)
Q Consensus 12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 91 (101)
+.|+++|+++++++|.|+|+||++|.|+|.|||+|||++|+||.|++.. ...+++|.+||||++|++
T Consensus 3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------------~~~~~lg~v~iRG~~V~~ 69 (72)
T PRK00737 3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG-------------EVVRKLGKVVIRGDNVVY 69 (72)
T ss_pred cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC-------------CeEeEcCcEEEeCCEEEE
Confidence 6899999999999999999999999999999999999999999997531 246789999999999999
Q ss_pred Eec
Q psy3154 92 VSP 94 (101)
Q Consensus 92 I~~ 94 (101)
|++
T Consensus 70 i~~ 72 (72)
T PRK00737 70 VSP 72 (72)
T ss_pred EcC
Confidence 974
No 4
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.92 E-value=2.3e-24 Score=135.71 Aligned_cols=80 Identities=30% Similarity=0.493 Sum_probs=65.9
Q ss_pred CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL 91 (101)
Q Consensus 12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 91 (101)
+.+++ |.++++++|+|+|+|||+|+|+|.|||+||||+|++|.|+....... .......+.+|.++|||+||++
T Consensus 2 ~~~~~-L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~-----~~~~~~~~~lG~v~iRG~nV~~ 75 (81)
T cd01729 2 ESILD-LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDP-----YKLTDKTRQLGLVVCRGTSVVL 75 (81)
T ss_pred cchhh-HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcc-----cccccceeEccEEEEcCCEEEE
Confidence 34555 78889999999999999999999999999999999999987642110 0012357889999999999999
Q ss_pred EecCCC
Q psy3154 92 VSPPNR 97 (101)
Q Consensus 92 I~~~~~ 97 (101)
|++.||
T Consensus 76 i~~~~~ 81 (81)
T cd01729 76 ISPVDG 81 (81)
T ss_pred EecCCC
Confidence 999886
No 5
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.92 E-value=2.8e-24 Score=133.96 Aligned_cols=74 Identities=26% Similarity=0.490 Sum_probs=65.4
Q ss_pred CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL 91 (101)
Q Consensus 12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 91 (101)
..|+++|+++++++|+|++++||+|.|+|.|||+|||++|+||.|++..+ ++ ...+++|.+||||++|++
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~--~~--------~~~~~lg~v~iRG~nV~~ 71 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITP--EG--------RKITKLDQILLNGNNICM 71 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcC--CC--------ceeeEcCeEEEeCCeEEE
Confidence 36999999999999999999999999999999999999999999998421 11 146789999999999999
Q ss_pred EecC
Q psy3154 92 VSPP 95 (101)
Q Consensus 92 I~~~ 95 (101)
|++.
T Consensus 72 i~p~ 75 (76)
T cd01732 72 LVPG 75 (76)
T ss_pred EECC
Confidence 9964
No 6
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.92 E-value=2e-24 Score=131.63 Aligned_cols=68 Identities=41% Similarity=0.735 Sum_probs=62.6
Q ss_pred hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS 93 (101)
Q Consensus 14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 93 (101)
|+++|+++++++|+|+|++|+.|.|+|.|||+|||++|+||.|++.. ...+.+|.+||||++|++|+
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------------~~~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG-------------EPVRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC-------------CeEeEcCcEEEeCCEEEEEc
Confidence 89999999999999999999999999999999999999999998642 14678999999999999997
Q ss_pred c
Q psy3154 94 P 94 (101)
Q Consensus 94 ~ 94 (101)
+
T Consensus 68 ~ 68 (68)
T cd01731 68 P 68 (68)
T ss_pred C
Confidence 5
No 7
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.90 E-value=1.4e-23 Score=127.63 Aligned_cols=67 Identities=28% Similarity=0.441 Sum_probs=61.0
Q ss_pred hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS 93 (101)
Q Consensus 14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 93 (101)
|+++|+++++++|.|+|++|++|.|+|.|||+|||++|+||.|+... ...+.+|.+||||++|++|+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~-------------~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG-------------QLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC-------------ceeeEeCCEEEECCEEEEEC
Confidence 89999999999999999999999999999999999999999886421 24678999999999999985
No 8
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.90 E-value=2.7e-23 Score=128.26 Aligned_cols=71 Identities=24% Similarity=0.497 Sum_probs=63.3
Q ss_pred hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS 93 (101)
Q Consensus 14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 93 (101)
|-..|+++++|+|+|+|++|++|.|+|.|||+|||++|+||.|++.. ...+.+|.++|||++|++|+
T Consensus 1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~-------------~~~~~lg~v~IRG~~I~~i~ 67 (72)
T cd01719 1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG-------------GEKNNIGMVVIRGNSIVMLE 67 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC-------------CceeEeceEEECCCEEEEEE
Confidence 34678999999999999999999999999999999999999998631 24678999999999999999
Q ss_pred cCCC
Q psy3154 94 PPNR 97 (101)
Q Consensus 94 ~~~~ 97 (101)
+.|.
T Consensus 68 ~~~~ 71 (72)
T cd01719 68 ALER 71 (72)
T ss_pred cccc
Confidence 8874
No 9
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.90 E-value=6.3e-23 Score=128.38 Aligned_cols=76 Identities=22% Similarity=0.469 Sum_probs=62.8
Q ss_pred HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94 (101)
Q Consensus 16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 94 (101)
+-|..+++++|+|+|+|||.|.|+|.|||+||||+|+||.|++...+.+. ........|++|++||||++|++|+.
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~---~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKS---KNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEecccccc---ccccCcceeEeeeEEEcCCEEEEEEE
Confidence 34778899999999999999999999999999999999999987543210 01112467899999999999999985
No 10
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.89 E-value=7.6e-23 Score=124.83 Aligned_cols=68 Identities=19% Similarity=0.331 Sum_probs=61.2
Q ss_pred ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154 13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV 92 (101)
Q Consensus 13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 92 (101)
.|+++|+++++++|+|+|++|++|.|+|.|||+|||++|+||.|+... ...+.+|.+||||++|++|
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~-------------~~~~~lg~~~IRG~~I~~i 67 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG-------------KSTGNLGEVLIRCNNVLYI 67 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC-------------ccccCcCcEEEECCEEEEE
Confidence 489999999999999999999999999999999999999999987421 1356799999999999998
Q ss_pred e
Q psy3154 93 S 93 (101)
Q Consensus 93 ~ 93 (101)
+
T Consensus 68 ~ 68 (68)
T cd01722 68 R 68 (68)
T ss_pred C
Confidence 4
No 11
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=4.3e-22 Score=123.30 Aligned_cols=73 Identities=25% Similarity=0.439 Sum_probs=62.9
Q ss_pred HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecC
Q psy3154 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP 95 (101)
Q Consensus 16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 95 (101)
+.|+++++++|+|+++|||.|.|+|+|||+|||++|++|.|+....+ . ....+.+|.+++||++|++|++.
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~-~--------~~~~~~lG~~~iRG~~I~~i~~~ 72 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSD-E--------GVEQVVLGLYIIRGDNIAVVGEI 72 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCC-C--------CceeeEeceEEECCCEEEEEEcc
Confidence 45788999999999999999999999999999999999999865321 0 12467899999999999999998
Q ss_pred CC
Q psy3154 96 NR 97 (101)
Q Consensus 96 ~~ 97 (101)
|+
T Consensus 73 d~ 74 (74)
T cd01727 73 DE 74 (74)
T ss_pred CC
Confidence 74
No 12
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=6.7e-22 Score=122.68 Aligned_cols=71 Identities=30% Similarity=0.433 Sum_probs=61.9
Q ss_pred hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS 93 (101)
Q Consensus 14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 93 (101)
++..|+++++++|.|+|+|||+|.|+|+|||+|||++|+||.|+..... ....+.+|.++|||++|++|+
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~----------~~~~~~lG~~viRG~~V~~ig 72 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD----------KYGDIPRGIFIIRGENVVLLG 72 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC----------ccceeEeeEEEEECCEEEEEE
Confidence 4567889999999999999999999999999999999999999875321 123578999999999999997
Q ss_pred c
Q psy3154 94 P 94 (101)
Q Consensus 94 ~ 94 (101)
.
T Consensus 73 ~ 73 (74)
T cd01728 73 E 73 (74)
T ss_pred c
Confidence 5
No 13
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=7.6e-22 Score=123.79 Aligned_cols=74 Identities=24% Similarity=0.483 Sum_probs=64.3
Q ss_pred cccCChHHHHHHhcCC--EEEEEEc--CCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEE
Q psy3154 9 ISVKEPLDLIRLSLDE--RVHVKMR--NERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFV 84 (101)
Q Consensus 9 ~~~~~Pl~lL~~~l~k--~V~V~l~--~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~I 84 (101)
..+..|++.+.+++++ +|.|+++ +|++++|+|.|||+|||++|+||.|+... ....+.+|.++|
T Consensus 2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~------------~~~~~~lG~ili 69 (79)
T cd01718 2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK------------TKTRKPLGRILL 69 (79)
T ss_pred ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC------------CceEeEcCcEEE
Confidence 3477899999999997 7888887 89999999999999999999999998641 024678999999
Q ss_pred cCCeEEEEec
Q psy3154 85 RGDGVILVSP 94 (101)
Q Consensus 85 RG~~Iv~I~~ 94 (101)
||+||++|++
T Consensus 70 RGnnV~~I~p 79 (79)
T cd01718 70 KGDNITLIQN 79 (79)
T ss_pred eCCEEEEEcC
Confidence 9999999974
No 14
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=1e-21 Score=122.16 Aligned_cols=72 Identities=19% Similarity=0.343 Sum_probs=62.9
Q ss_pred HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94 (101)
Q Consensus 16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 94 (101)
+-|+++++++|+|+|+|||.|.|+|.|||+|||++|+||.|++..++.. .....|.+|+++|||++|++|+.
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~-------~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSF-------SPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCcc-------CCccEEEeeeEEEeCCeEEEEEE
Confidence 4688999999999999999999999999999999999999998753311 12468999999999999999975
No 15
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=1.2e-21 Score=120.15 Aligned_cols=70 Identities=26% Similarity=0.456 Sum_probs=62.7
Q ss_pred hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS 93 (101)
Q Consensus 14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 93 (101)
|+++|+++.|++|.|+|++|.+|+|+|.++|.|||++|+||.+... ++ +..+++.+||||++|.+|.
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~----~g---------~~~~~~~v~IRG~nI~~v~ 67 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTAR----DG---------RVSQLEQVYIRGSKIRFFI 67 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECC----CC---------cEeEcCcEEEeCCEEEEEE
Confidence 8899999999999999999999999999999999999999987532 11 2457899999999999999
Q ss_pred cCC
Q psy3154 94 PPN 96 (101)
Q Consensus 94 ~~~ 96 (101)
.||
T Consensus 68 lPd 70 (70)
T cd01721 68 LPD 70 (70)
T ss_pred eCC
Confidence 886
No 16
>KOG3460|consensus
Probab=99.86 E-value=9.3e-23 Score=127.57 Aligned_cols=87 Identities=79% Similarity=1.197 Sum_probs=76.5
Q ss_pred ccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV 89 (101)
Q Consensus 10 ~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I 89 (101)
.+..|+++|+-+++.+|.|+++++|+++|+|.|||+|.|++|.|+.|+++..+.+..+..+..+...|.+..+||||++|
T Consensus 2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~V 81 (91)
T KOG3460|consen 2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGV 81 (91)
T ss_pred cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeE
Confidence 46789999999999999999999999999999999999999999999998776544343444556789999999999999
Q ss_pred EEEecCC
Q psy3154 90 ILVSPPN 96 (101)
Q Consensus 90 v~I~~~~ 96 (101)
++|+++=
T Consensus 82 ilvspp~ 88 (91)
T KOG3460|consen 82 ILVSPPL 88 (91)
T ss_pred EEEcCcc
Confidence 9999874
No 17
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=3.3e-21 Score=119.91 Aligned_cols=73 Identities=23% Similarity=0.434 Sum_probs=63.7
Q ss_pred ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154 13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV 92 (101)
Q Consensus 13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 92 (101)
.|+++|+++.|++|.|.|++|++|.|+|.+||.|||++|+||.|... ++ .....++.+||||++|.+|
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~g--------~~~~~~~~v~IRG~~I~~i 68 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSK----DG--------DKFWKMPECYIRGNTIKYL 68 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC----CC--------cEeeeCCcEEEeCCEEEEE
Confidence 39999999999999999999999999999999999999999988632 11 1245679999999999999
Q ss_pred ecCCC
Q psy3154 93 SPPNR 97 (101)
Q Consensus 93 ~~~~~ 97 (101)
..+|.
T Consensus 69 ~~p~~ 73 (76)
T cd01723 69 RVPDE 73 (76)
T ss_pred EcCHH
Confidence 98864
No 18
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.85 E-value=4.2e-21 Score=115.89 Aligned_cols=67 Identities=36% Similarity=0.674 Sum_probs=60.6
Q ss_pred HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94 (101)
Q Consensus 16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 94 (101)
.+|+++++++|+|.|++|+.|+|+|.+||+|||++|+||.|++... ...+++|.+||||++|++|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~------------~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNG------------PEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTE------------SEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCC------------CcEeECcEEEEECCEEEEEEC
Confidence 3789999999999999999999999999999999999999987521 157899999999999999975
No 19
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.85 E-value=7e-21 Score=114.80 Aligned_cols=66 Identities=36% Similarity=0.684 Sum_probs=59.9
Q ss_pred HHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154 17 LIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94 (101)
Q Consensus 17 lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 94 (101)
+|+++++++|+|.|+||+++.|+|.+||+|||++|+||.|++... ...+++|.+||||++|++|.+
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~------------~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG------------EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC------------cEEeEeCCEEEcCCEEEEEeC
Confidence 688999999999999999999999999999999999999987521 257899999999999999974
No 20
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.85 E-value=1.3e-20 Score=120.58 Aligned_cols=80 Identities=24% Similarity=0.458 Sum_probs=68.5
Q ss_pred ccCCccccCChHHHHHHhcC--CEEEEEEcCC--eEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeee
Q psy3154 4 EQIPTISVKEPLDLIRLSLD--ERVHVKMRNE--RVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSI 79 (101)
Q Consensus 4 ~~~~~~~~~~Pl~lL~~~l~--k~V~V~l~~g--r~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~l 79 (101)
...++..+..|+.++.+++. .+|.|++.++ ++|.|+|.|||+|||++|+||.|++.. + ...+.+
T Consensus 5 ~~~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~----~--------~~~~~l 72 (89)
T PTZ00138 5 KRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK----K--------NTRKDL 72 (89)
T ss_pred ccccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC----C--------ceeeEc
Confidence 34667779999999999998 4899998774 899999999999999999999997642 1 246789
Q ss_pred CeEEEcCCeEEEEecC
Q psy3154 80 PMLFVRGDGVILVSPP 95 (101)
Q Consensus 80 g~v~IRG~~Iv~I~~~ 95 (101)
|.+|||||||++|++.
T Consensus 73 G~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 73 GRILLKGDNITLIMAA 88 (89)
T ss_pred CeEEEcCCEEEEEEcC
Confidence 9999999999999875
No 21
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.85 E-value=8.8e-21 Score=118.55 Aligned_cols=75 Identities=40% Similarity=0.676 Sum_probs=62.5
Q ss_pred cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEE
Q psy3154 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVI 90 (101)
Q Consensus 11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv 90 (101)
...|+++|+++++++|.|+|++|++|.|+|.|||+|||++|+||.|++.. +++. ...+..+.++|||++|+
T Consensus 5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~~------~~~~~~~~~~IRG~~I~ 75 (79)
T COG1958 5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH---DGEK------NVRRLGGEVLIRGDNIV 75 (79)
T ss_pred cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc---CCcc------ccceeccEEEEECCcEE
Confidence 45689999999999999999999999999999999999999999998741 1100 02344459999999999
Q ss_pred EEec
Q psy3154 91 LVSP 94 (101)
Q Consensus 91 ~I~~ 94 (101)
+|.+
T Consensus 76 ~I~~ 79 (79)
T COG1958 76 LISP 79 (79)
T ss_pred EEeC
Confidence 9964
No 22
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.82 E-value=7e-20 Score=109.01 Aligned_cols=63 Identities=40% Similarity=0.686 Sum_probs=57.4
Q ss_pred HHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154 18 IRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS 93 (101)
Q Consensus 18 L~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 93 (101)
|+++++++|+|.|+||+.|.|+|.+||+|||++|+||.|++.. ...+.++.+||||++|++|.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~-------------~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE-------------GKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC-------------CcEEECCeEEEECCEEEEEC
Confidence 4678999999999999999999999999999999999998753 24789999999999999984
No 23
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.82 E-value=9.7e-20 Score=116.75 Aligned_cols=71 Identities=18% Similarity=0.352 Sum_probs=64.2
Q ss_pred hHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS 93 (101)
Q Consensus 14 Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 93 (101)
++.+|+++.|++|.|+|++|..|.|+|.++|.|||++|+||.++... .....++.+||||++|.+|.
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~-------------~~~~~~~~v~IRG~nI~yi~ 68 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG-------------RNPVPLDTLSIRGNNIRYFI 68 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC-------------CceeEcceEEEeCCEEEEEE
Confidence 67899999999999999999999999999999999999999887431 13568999999999999999
Q ss_pred cCCC
Q psy3154 94 PPNR 97 (101)
Q Consensus 94 ~~~~ 97 (101)
.+|.
T Consensus 69 lPd~ 72 (90)
T cd01724 69 LPDS 72 (90)
T ss_pred cCCc
Confidence 9975
No 24
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.81 E-value=2.9e-19 Score=112.46 Aligned_cols=74 Identities=27% Similarity=0.391 Sum_probs=63.2
Q ss_pred ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154 13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV 92 (101)
Q Consensus 13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 92 (101)
.|+++|+++.|++|.|+|++|..|.|+|.++|.|||++|+||.++... + ......++.++|||++|.+|
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~----~-------~~~~~~~~~v~IRG~~I~~I 69 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE----K-------YPHMLSVKNCFIRGSVVRYV 69 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCC----C-------cccccccCeEEEECCEEEEE
Confidence 489999999999999999999999999999999999999999765321 1 01234579999999999999
Q ss_pred ecCCC
Q psy3154 93 SPPNR 97 (101)
Q Consensus 93 ~~~~~ 97 (101)
..+|.
T Consensus 70 ~lp~~ 74 (81)
T cd01725 70 QLPAD 74 (81)
T ss_pred EeChh
Confidence 99874
No 25
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.79 E-value=8.6e-19 Score=109.68 Aligned_cols=71 Identities=21% Similarity=0.324 Sum_probs=61.9
Q ss_pred CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL 91 (101)
Q Consensus 12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 91 (101)
-.+..+|+.+.|++|.|+|++|..|.|+|.++|.|||++|+||.+.... ....++|.+||||++|.+
T Consensus 8 ~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~-------------~~~~~~~~v~IRG~nI~y 74 (78)
T cd01733 8 NTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN-------------GKQVQVEEIMVTGRNIRY 74 (78)
T ss_pred chHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC-------------CceeECCcEEEECCEEEE
Confidence 4568899999999999999999999999999999999999999865321 134579999999999999
Q ss_pred EecC
Q psy3154 92 VSPP 95 (101)
Q Consensus 92 I~~~ 95 (101)
|..|
T Consensus 75 I~lP 78 (78)
T cd01733 75 VHIP 78 (78)
T ss_pred EEcC
Confidence 9865
No 26
>KOG1780|consensus
Probab=99.78 E-value=7e-19 Score=107.94 Aligned_cols=71 Identities=27% Similarity=0.541 Sum_probs=62.8
Q ss_pred CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL 91 (101)
Q Consensus 12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 91 (101)
..| -|++|++|++.++|.+||.+.|+|.|||.|||+||++++|.... ..+..+|.++|||++|+.
T Consensus 5 g~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~-------------~~~~~ig~~vIrgnsiv~ 69 (77)
T KOG1780|consen 5 GHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD-------------GDKNNIGMVVIRGNSIVM 69 (77)
T ss_pred cCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc-------------CCcceeeeEEEeccEEEE
Confidence 357 68899999999999999999999999999999999999997542 235679999999999999
Q ss_pred EecCCC
Q psy3154 92 VSPPNR 97 (101)
Q Consensus 92 I~~~~~ 97 (101)
+++.|.
T Consensus 70 ~eaL~~ 75 (77)
T KOG1780|consen 70 VEALER 75 (77)
T ss_pred Eeeccc
Confidence 998775
No 27
>KOG1781|consensus
Probab=99.76 E-value=9.4e-20 Score=117.17 Aligned_cols=81 Identities=27% Similarity=0.436 Sum_probs=68.3
Q ss_pred HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154 15 LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94 (101)
Q Consensus 15 l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 94 (101)
+=-|.+|++++|+|++.+||+..|+|+|||+.|||||++++|+...++ +.. +....+|++|++++||..+++|++
T Consensus 19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpd----d~~-~~~~~tR~LGLvV~RGTalvlisp 93 (108)
T KOG1781|consen 19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPD----DPY-KLTDETRKLGLVVCRGTALVLISP 93 (108)
T ss_pred HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCC----Ccc-chhhhhheeeeEEEcccEEEEEcC
Confidence 344567799999999999999999999999999999999999987543 111 123346999999999999999999
Q ss_pred CCCCCC
Q psy3154 95 PNRTPA 100 (101)
Q Consensus 95 ~~~~~~ 100 (101)
.||+++
T Consensus 94 ~dG~e~ 99 (108)
T KOG1781|consen 94 ADGSEE 99 (108)
T ss_pred Ccchhh
Confidence 999875
No 28
>KOG3482|consensus
Probab=99.71 E-value=3.6e-17 Score=100.14 Aligned_cols=72 Identities=18% Similarity=0.306 Sum_probs=65.4
Q ss_pred CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL 91 (101)
Q Consensus 12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 91 (101)
.+|-.||+.+.+++|.|+|+.|.+|.|+|.+.|.|||+.|.+|.|++.. ..+..+|.++||++||.+
T Consensus 7 vNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-------------~~~g~lGEilIRCNNvly 73 (79)
T KOG3482|consen 7 VNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-------------VSTGNLGEILIRCNNVLY 73 (79)
T ss_pred CCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc-------------cccccceeEEEEeccEEE
Confidence 4899999999999999999999999999999999999999999998752 246789999999999999
Q ss_pred EecCC
Q psy3154 92 VSPPN 96 (101)
Q Consensus 92 I~~~~ 96 (101)
|.-.+
T Consensus 74 i~gv~ 78 (79)
T KOG3482|consen 74 IRGVP 78 (79)
T ss_pred EecCC
Confidence 97654
No 29
>KOG1775|consensus
Probab=99.66 E-value=1.1e-16 Score=98.76 Aligned_cols=78 Identities=26% Similarity=0.468 Sum_probs=68.1
Q ss_pred ccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154 10 SVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV 89 (101)
Q Consensus 10 ~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I 89 (101)
+.-.|++++.+|+|++++|.+++.|++.|+|.|||.|.|++|+|+.|+-..++- ....+++++++.|++|
T Consensus 4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~eg----------r~~tk~~~iLLnGNni 73 (84)
T KOG1775|consen 4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEG----------RRMTKLDQILLNGNNI 73 (84)
T ss_pred hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCc----------ceeeeeeeeeecCCcE
Confidence 346799999999999999999999999999999999999999999998765431 2467899999999999
Q ss_pred EEEecCCC
Q psy3154 90 ILVSPPNR 97 (101)
Q Consensus 90 v~I~~~~~ 97 (101)
...-+..+
T Consensus 74 ~mLvPGGe 81 (84)
T KOG1775|consen 74 TMLVPGGE 81 (84)
T ss_pred EEEecCCC
Confidence 98877654
No 30
>KOG1783|consensus
Probab=99.66 E-value=2.3e-17 Score=100.98 Aligned_cols=73 Identities=26% Similarity=0.380 Sum_probs=66.1
Q ss_pred cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEE
Q psy3154 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVI 90 (101)
Q Consensus 11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv 90 (101)
.+.|-++|...+|++|.|+|.+|-.|+|+|.|+|.|||+-|+.+.|+... ...+++|.+||||++|.
T Consensus 4 ~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ng-------------ql~n~ygdaFirGnnVl 70 (77)
T KOG1783|consen 4 GSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNG-------------QLKNKYGDAFIRGNNVL 70 (77)
T ss_pred ccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcC-------------cccccccceeeccccEE
Confidence 46789999999999999999999999999999999999999999987642 24688999999999999
Q ss_pred EEecCC
Q psy3154 91 LVSPPN 96 (101)
Q Consensus 91 ~I~~~~ 96 (101)
+|+...
T Consensus 71 yIs~~~ 76 (77)
T KOG1783|consen 71 YISTQK 76 (77)
T ss_pred EEEecc
Confidence 999764
No 31
>KOG3168|consensus
Probab=99.63 E-value=4.9e-17 Score=113.42 Aligned_cols=82 Identities=22% Similarity=0.472 Sum_probs=68.6
Q ss_pred cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEE
Q psy3154 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVI 90 (101)
Q Consensus 11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv 90 (101)
...+..+|+. ++.+++|.++|||.|+|.+++||+|||++|.+|.|+.....++. +.......|-+|+|++||++|+
T Consensus 3 ~a~sskml~~-iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~---~~~~~eEkr~lgLvllRgenIv 78 (177)
T KOG3168|consen 3 VAKSSKMLQH-INYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNR---KMTDGEEKRVLGLVLLRGENIV 78 (177)
T ss_pred ccchhHHHHh-hcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccc---cccccceeeEEEEEEecCCcEE
Confidence 4556677777 99999999999999999999999999999999999887655432 1123457899999999999999
Q ss_pred EEecCC
Q psy3154 91 LVSPPN 96 (101)
Q Consensus 91 ~I~~~~ 96 (101)
+.+..+
T Consensus 79 s~tVeg 84 (177)
T KOG3168|consen 79 SMTVEG 84 (177)
T ss_pred EEeccC
Confidence 998764
No 32
>KOG3459|consensus
Probab=99.52 E-value=1.7e-15 Score=99.14 Aligned_cols=83 Identities=35% Similarity=0.493 Sum_probs=71.0
Q ss_pred cCChHHHHHHhcC--CEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCe
Q psy3154 11 VKEPLDLIRLSLD--ERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDG 88 (101)
Q Consensus 11 ~~~Pl~lL~~~l~--k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~ 88 (101)
..+|++++..++. .+|.|.++|++.+-|++.|||.|+|++|+++.|.|++.++.+...+.+.....|++|.+|||||+
T Consensus 22 ~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGds 101 (114)
T KOG3459|consen 22 NTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDS 101 (114)
T ss_pred CcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCe
Confidence 4499999999887 69999999999999999999999999999999999987655332232334568999999999999
Q ss_pred EEEEe
Q psy3154 89 VILVS 93 (101)
Q Consensus 89 Iv~I~ 93 (101)
|+.+.
T Consensus 102 vI~v~ 106 (114)
T KOG3459|consen 102 VILVL 106 (114)
T ss_pred EEEEE
Confidence 99886
No 33
>KOG1784|consensus
Probab=99.51 E-value=1.4e-14 Score=92.19 Aligned_cols=74 Identities=19% Similarity=0.396 Sum_probs=63.7
Q ss_pred HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecC
Q psy3154 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP 95 (101)
Q Consensus 16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 95 (101)
+-|+.|++++|.|.+.|||.+.|.|+|||+..|++|+++.|++.... .-..+.-+|.-+|||+||..|...
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~---------~gv~q~~lGlyiirgeNva~ig~i 73 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSET---------EGVEQIVLGLYIIRGENVAVIGEI 73 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhh---------cchhheeeEEEEEecCccceeeec
Confidence 35788999999999999999999999999999999999999876321 113467799999999999999998
Q ss_pred CCC
Q psy3154 96 NRT 98 (101)
Q Consensus 96 ~~~ 98 (101)
|+.
T Consensus 74 DEe 76 (96)
T KOG1784|consen 74 DEE 76 (96)
T ss_pred chh
Confidence 763
No 34
>KOG1774|consensus
Probab=99.46 E-value=7.5e-14 Score=87.21 Aligned_cols=75 Identities=23% Similarity=0.500 Sum_probs=61.6
Q ss_pred ccCChHHHHHHhcC--CEEEEEEcC--CeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEc
Q psy3154 10 SVKEPLDLIRLSLD--ERVHVKMRN--ERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVR 85 (101)
Q Consensus 10 ~~~~Pl~lL~~~l~--k~V~V~l~~--gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IR 85 (101)
-+..|+.++-+++. .+|.|+|.+ |-.+.|.+.|||+|||+||++|+|..... ...+.+|.++++
T Consensus 9 vmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~------------~~rk~lGRilLK 76 (88)
T KOG1774|consen 9 VMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT------------KSRKELGRILLK 76 (88)
T ss_pred eecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc------------cCCCccccEEEc
Confidence 35779999998887 589999976 57899999999999999999999865311 123489999999
Q ss_pred CCeEEEEecCC
Q psy3154 86 GDGVILVSPPN 96 (101)
Q Consensus 86 G~~Iv~I~~~~ 96 (101)
||||.+|...+
T Consensus 77 GDnItli~~~~ 87 (88)
T KOG1774|consen 77 GDNITLIQSAG 87 (88)
T ss_pred CCcEEEEeecC
Confidence 99999997653
No 35
>KOG1782|consensus
Probab=99.46 E-value=1.2e-14 Score=96.93 Aligned_cols=74 Identities=27% Similarity=0.382 Sum_probs=62.6
Q ss_pred ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154 13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV 92 (101)
Q Consensus 13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 92 (101)
...+ |-.++++++.|.|+|||.+.|.|.+||+|-|++|.+|+|++.... ....+..|..+|||+||+++
T Consensus 10 ~t~s-l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~----------~Y~di~~glfiIRGENVvll 78 (129)
T KOG1782|consen 10 FTTS-LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN----------KYCDIPRGLFIIRGENVVLL 78 (129)
T ss_pred chhH-HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc----------eecccCceEEEEecCcEEEE
Confidence 3344 445599999999999999999999999999999999999887532 24567789999999999999
Q ss_pred ecCCC
Q psy3154 93 SPPNR 97 (101)
Q Consensus 93 ~~~~~ 97 (101)
...|-
T Consensus 79 Geid~ 83 (129)
T KOG1782|consen 79 GEIDL 83 (129)
T ss_pred ecCCc
Confidence 88753
No 36
>KOG3293|consensus
Probab=99.34 E-value=2.4e-12 Score=86.02 Aligned_cols=73 Identities=22% Similarity=0.390 Sum_probs=65.5
Q ss_pred ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154 13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV 92 (101)
Q Consensus 13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 92 (101)
.|+.||+.+-+.++.|.|++|.+|.|.|+.-|.+|||.|++|.++..+ + .+--.++.+.|||++|-++
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~D----g--------dkf~r~pEcYirGttIkyl 69 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSED----G--------DKFFRMPECYIRGTTIKYL 69 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccC----C--------CceeecceeEEecceeEEE
Confidence 699999999999999999999999999999999999999999988652 2 2456788999999999999
Q ss_pred ecCCC
Q psy3154 93 SPPNR 97 (101)
Q Consensus 93 ~~~~~ 97 (101)
..+|.
T Consensus 70 ri~d~ 74 (134)
T KOG3293|consen 70 RIPDE 74 (134)
T ss_pred eccHH
Confidence 98864
No 37
>KOG3448|consensus
Probab=99.33 E-value=1.1e-11 Score=78.54 Aligned_cols=72 Identities=28% Similarity=0.359 Sum_probs=60.5
Q ss_pred ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEE
Q psy3154 13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV 92 (101)
Q Consensus 13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 92 (101)
..+++.+.++|++|.|.|+++-.+.|+|.++|+|.|+.|.|..-... ++. ..--.+..+||||+.|.||
T Consensus 2 LFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~--~ky---------Phm~Sv~ncfIRGSvvrYv 70 (96)
T KOG3448|consen 2 LFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDP--DKY---------PHMLSVKNCFIRGSVVRYV 70 (96)
T ss_pred chHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCc--ccC---------CCeeeeeeEEEeccEEEEE
Confidence 35789999999999999999999999999999999999999875422 111 2355678899999999999
Q ss_pred ecC
Q psy3154 93 SPP 95 (101)
Q Consensus 93 ~~~ 95 (101)
..+
T Consensus 71 ~l~ 73 (96)
T KOG3448|consen 71 QLP 73 (96)
T ss_pred EeC
Confidence 876
No 38
>KOG3172|consensus
Probab=99.22 E-value=4.8e-11 Score=78.16 Aligned_cols=75 Identities=25% Similarity=0.437 Sum_probs=66.3
Q ss_pred cccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCe
Q psy3154 9 ISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDG 88 (101)
Q Consensus 9 ~~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~ 88 (101)
+++.-|+.+|.++-+.-|.+.+..|..|+|+|.-.+++||+.|+|+.-+... + ....+.++||||+.
T Consensus 1 ~s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d----g---------~vs~le~V~IRGS~ 67 (119)
T KOG3172|consen 1 MSVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD----G---------RVSQLEQVFIRGSK 67 (119)
T ss_pred CccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC----C---------cceeeeeEEEecCe
Confidence 3567899999999999999999999999999999999999999999876541 2 35678899999999
Q ss_pred EEEEecCC
Q psy3154 89 VILVSPPN 96 (101)
Q Consensus 89 Iv~I~~~~ 96 (101)
|.++.++|
T Consensus 68 IRFlvlPd 75 (119)
T KOG3172|consen 68 IRFLVLPD 75 (119)
T ss_pred EEEEECch
Confidence 99998886
No 39
>KOG3428|consensus
Probab=98.97 E-value=5.6e-09 Score=68.51 Aligned_cols=69 Identities=23% Similarity=0.443 Sum_probs=60.0
Q ss_pred HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEec
Q psy3154 15 LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSP 94 (101)
Q Consensus 15 l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 94 (101)
+.+|+.+.+.+|.|.|++|+.+.|++.++|.+||..|.++.-+.. ....++..++|||++|.|+-.
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~--------------~~pv~l~~lsirgnniRy~~l 69 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK--------------GEPVRLDTLSIRGNNIRYYIL 69 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC--------------CCceeEEEEEeecceEEEEEc
Confidence 468899999999999999999999999999999999999874432 124678899999999999999
Q ss_pred CCC
Q psy3154 95 PNR 97 (101)
Q Consensus 95 ~~~ 97 (101)
+|.
T Consensus 70 pD~ 72 (109)
T KOG3428|consen 70 PDS 72 (109)
T ss_pred cCC
Confidence 874
No 40
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=98.81 E-value=2.6e-09 Score=64.41 Aligned_cols=41 Identities=39% Similarity=0.472 Sum_probs=33.6
Q ss_pred HhcC--CEEEEEEcCC----eEEEEEEEEEcCCCceEecceEEEEee
Q psy3154 20 LSLD--ERVHVKMRNE----RVLRGKLHAYDQHLNMVLGDVEETVTT 60 (101)
Q Consensus 20 ~~l~--k~V~V~l~~g----r~i~G~L~~~D~~mNlvL~~~~E~~~~ 60 (101)
+|+. .+|+|.++.- -.++|.|.+||+||||+|.|+.|.|..
T Consensus 3 ~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 3 RCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred hhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 4444 6888888654 368899999999999999999999875
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.96 E-value=3.4e-05 Score=47.49 Aligned_cols=69 Identities=16% Similarity=0.249 Sum_probs=41.3
Q ss_pred HHHHHhcCCEEEEEEcCCeEEEEEEEEEcC---CCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEE
Q psy3154 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQ---HLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVI 90 (101)
Q Consensus 16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~---~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv 90 (101)
-++..++|++|.|+++||..|.|+|.+++. -+.++|+-+........ .............++|+++.|+
T Consensus 5 ~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~------~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 5 YLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQ------SNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------------EEEEEEE-GGGEEE-----
T ss_pred HHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccc------ccCCccCCCCCceEEEeccccC
Confidence 456778999999999999999999999998 89999988876432110 0011233445567777777665
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.39 E-value=0.001 Score=43.06 Aligned_cols=76 Identities=11% Similarity=0.118 Sum_probs=56.0
Q ss_pred HHhcCCEEEEEEcCCeEEEEEEEEEcC-CCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecCCC
Q psy3154 19 RLSLDERVHVKMRNERVLRGKLHAYDQ-HLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNR 97 (101)
Q Consensus 19 ~~~l~k~V~V~l~~gr~i~G~L~~~D~-~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~~~ 97 (101)
..|+|++|.+..+.+-.|.|+|..+|. ...+.|+||..+-++.+... ........-+..+..||+.|--+...+.
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~----~~ipp~~~v~~~I~Fr~sDIkdL~v~e~ 79 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTD----REIPPSDEVYDYIVFRGSDIKDLKVIEP 79 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-S----S---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcC----cccCCCCceeeEEEEEccccceEEEEcC
Confidence 467999999999999999999999995 88899999988765321110 0112234567899999999988877654
Q ss_pred C
Q psy3154 98 T 98 (101)
Q Consensus 98 ~ 98 (101)
.
T Consensus 80 ~ 80 (96)
T PF12701_consen 80 P 80 (96)
T ss_dssp S
T ss_pred C
Confidence 3
No 43
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=96.69 E-value=0.011 Score=36.54 Aligned_cols=69 Identities=10% Similarity=0.114 Sum_probs=50.0
Q ss_pred HhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154 20 LSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL 91 (101)
Q Consensus 20 ~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 91 (101)
.++|+++.+.-+.+-.|.|+|..+| +-.-+.|+||..+-++-.+.. .. .......-+..++.||+.|--
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~--~~-~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTD--GP-EIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCC--CC-ccCCCCcceeEEEEcCCcccc
Confidence 5799999999999999999999999 455577999988766532111 01 112245567789999988753
No 44
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.60 E-value=0.013 Score=32.85 Aligned_cols=33 Identities=15% Similarity=0.291 Sum_probs=29.0
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~ 55 (101)
+|++|++.+ ++..+.|+..++|....|+++...
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~ 34 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTED 34 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC
Confidence 789999999 667779999999999999997643
No 45
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=96.57 E-value=0.0049 Score=43.59 Aligned_cols=66 Identities=24% Similarity=0.366 Sum_probs=44.2
Q ss_pred cCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeE
Q psy3154 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGV 89 (101)
Q Consensus 11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I 89 (101)
..+|+.+... ++|.|+|.+.| +++.|.|.++| -.-|+||-+..| + ..+ ..-+|.|.+|
T Consensus 6 ~~~p~~~~~y-v~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e-------~----------~~~--sv~~I~ghaV 64 (166)
T PF06372_consen 6 KKSPLEWQDY-VGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE-------D----------GKR--SVKVIMGHAV 64 (166)
T ss_dssp HS-HHHHHCT-TT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T-------T----------S-E--EEEEE-GGGE
T ss_pred hCCHHHHHHh-hCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc-------C----------Cce--eEEEEEccce
Confidence 3567777665 99999999999 99999999999 677888876433 1 112 2467889999
Q ss_pred EEEecCCC
Q psy3154 90 ILVSPPNR 97 (101)
Q Consensus 90 v~I~~~~~ 97 (101)
-.|...+.
T Consensus 65 k~vevl~~ 72 (166)
T PF06372_consen 65 KSVEVLSE 72 (166)
T ss_dssp EEEEEEE-
T ss_pred EEEEEccC
Confidence 88877654
No 46
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=96.47 E-value=0.022 Score=35.79 Aligned_cols=65 Identities=17% Similarity=0.215 Sum_probs=48.2
Q ss_pred ChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154 13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL 91 (101)
Q Consensus 13 ~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 91 (101)
..+.+|....|++|.+.|-++.++.|++.|.| ...|+..++-. + + -..++..++|.+.|++
T Consensus 14 rfLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~---T-----P----------lGv~~eAlLR~~DVi~ 75 (80)
T PF11095_consen 14 RFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ---T-----P----------LGVQPEALLRCSDVIS 75 (80)
T ss_dssp HHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE---T-----T----------TTEEEEEEEEGGGEEE
T ss_pred HHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC---C-----C----------cccChhheeecCCEEE
Confidence 45677888889999999999999999999999 66677766532 1 1 1236789999999999
Q ss_pred EecC
Q psy3154 92 VSPP 95 (101)
Q Consensus 92 I~~~ 95 (101)
++..
T Consensus 76 ~~f~ 79 (80)
T PF11095_consen 76 ISFD 79 (80)
T ss_dssp EEE-
T ss_pred EEec
Confidence 8754
No 47
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=96.29 E-value=0.015 Score=34.79 Aligned_cols=32 Identities=19% Similarity=0.238 Sum_probs=27.3
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGD 53 (101)
Q Consensus 22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~ 53 (101)
-+.+|.|-|.+|-.+.|.+.+||+|+=++-.+
T Consensus 14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 45799999999999999999999999555444
No 48
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=96.25 E-value=0.015 Score=34.69 Aligned_cols=32 Identities=19% Similarity=0.329 Sum_probs=27.1
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGD 53 (101)
Q Consensus 22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~ 53 (101)
-..+|.|-|.+|-.+.|.+.+||+|+=++-.+
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 34699999999999999999999999555444
No 49
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.10 E-value=0.026 Score=35.12 Aligned_cols=43 Identities=21% Similarity=0.439 Sum_probs=31.6
Q ss_pred cccCCh-HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154 9 ISVKEP-LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGD 53 (101)
Q Consensus 9 ~~~~~P-l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~ 53 (101)
.+.+.| +.-+++ -+.+|.|-|.||-.+.|.+++||+|. +.|++
T Consensus 5 ~nlQD~fLn~~Rk-~~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~ 48 (77)
T COG1923 5 QNLQDPFLNALRK-EKIPVTIFLVNGFKLQGQVESFDNFV-VLLKN 48 (77)
T ss_pred cccchHHHHHHHh-cCCeEEEEEEcCEEEEEEEEeeeeEE-EEEEc
Confidence 344444 333333 55799999999999999999999998 44444
No 50
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.89 E-value=0.026 Score=35.39 Aligned_cols=33 Identities=15% Similarity=0.257 Sum_probs=28.2
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCCCceEecce
Q psy3154 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDV 54 (101)
Q Consensus 22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~ 54 (101)
-+.+|.|-|.+|-.+.|.+.|||+|+=++-.+.
T Consensus 18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred cCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 457999999999999999999999996665454
No 51
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=95.85 E-value=0.029 Score=33.52 Aligned_cols=36 Identities=22% Similarity=0.324 Sum_probs=30.6
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEE
Q psy3154 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEE 56 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E 56 (101)
++|..|++++..|.+|.|.+.+||.-.++++-.|.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 478999999999999999999999888877555443
No 52
>PRK14638 hypothetical protein; Provisional
Probab=94.24 E-value=0.11 Score=36.06 Aligned_cols=33 Identities=3% Similarity=0.206 Sum_probs=27.2
Q ss_pred HHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEec
Q psy3154 19 RLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 19 ~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~ 52 (101)
.+++|++|.|++.+++.++|+|.++|.- ++.|.
T Consensus 96 ~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 96 VRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 3458999999999999999999999964 35443
No 53
>PRK14639 hypothetical protein; Provisional
Probab=93.29 E-value=0.2 Score=34.27 Aligned_cols=33 Identities=24% Similarity=0.423 Sum_probs=27.6
Q ss_pred HHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEe
Q psy3154 18 IRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVL 51 (101)
Q Consensus 18 L~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL 51 (101)
.++++|+.|.|++.+++.+.|+|.++|.- ++.|
T Consensus 83 f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 83 FAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 34558999999999999999999999984 4555
No 54
>PRK02001 hypothetical protein; Validated
Probab=93.09 E-value=0.22 Score=34.67 Aligned_cols=31 Identities=19% Similarity=0.462 Sum_probs=26.5
Q ss_pred HhcCCEEEEEEcCCeEEEEEEEEEcCCCceEe
Q psy3154 20 LSLDERVHVKMRNERVLRGKLHAYDQHLNMVL 51 (101)
Q Consensus 20 ~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL 51 (101)
+++|+.|+|++.+++.+.|+|.++|.. ++.|
T Consensus 87 r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 87 KNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred HhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 458999999999999999999999975 3444
No 55
>KOG1073|consensus
Probab=93.03 E-value=0.26 Score=38.75 Aligned_cols=76 Identities=13% Similarity=0.126 Sum_probs=57.2
Q ss_pred HHHhcCCEEEEEEcCCeEEEEEEEEEc-CCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecCC
Q psy3154 18 IRLSLDERVHVKMRNERVLRGKLHAYD-QHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPN 96 (101)
Q Consensus 18 L~~~l~k~V~V~l~~gr~i~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~~ 96 (101)
...+||++|.++=+..-.|+|+|.-+| +-.-|-|.+|..+-++-+++. ........+ -+.-++.||+.|--+...|
T Consensus 4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~--~pq~p~~~k-Vy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTD--GPQVPPDDK-VYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCC--CCcCCCCcc-ceeeEEecCcccceeeecc
Confidence 346799999999999999999999999 788899999987766533221 111111122 6888999999999777766
No 56
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=92.98 E-value=1 Score=27.23 Aligned_cols=58 Identities=24% Similarity=0.375 Sum_probs=41.5
Q ss_pred cCCh--HHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCe
Q psy3154 11 VKEP--LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDG 88 (101)
Q Consensus 11 ~~~P--l~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~ 88 (101)
.-+| .+.|++++|++|.|.+..|+. +|+|.+.-.-. ++|+.. -...|||=..
T Consensus 7 ~vdpyvyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDh-Ivl~~~------------------------~~~~~IR~~~ 60 (66)
T PF10842_consen 7 LVDPYVYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDH-IVLEEN------------------------GTPFFIRIAQ 60 (66)
T ss_pred ccCHHHHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCE-EEEEeC------------------------CcEEEEEeee
Confidence 3455 688999999999999977765 99999876322 233321 2357888888
Q ss_pred EEEEec
Q psy3154 89 VILVSP 94 (101)
Q Consensus 89 Iv~I~~ 94 (101)
|++|.+
T Consensus 61 IV~v~p 66 (66)
T PF10842_consen 61 IVWVMP 66 (66)
T ss_pred EEEEcC
Confidence 888753
No 57
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=91.73 E-value=0.48 Score=33.53 Aligned_cols=33 Identities=24% Similarity=0.297 Sum_probs=27.9
Q ss_pred CCEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154 23 DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 23 ~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~ 55 (101)
..+|.|-|.+|-.+.|.+.+||+|.=|+-.+..
T Consensus 104 k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~gk 136 (165)
T PRK14091 104 GEPVTMFLVNGVMLQGEIAAFDLFCMLLERDGY 136 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceEEEEEeCCc
Confidence 469999999999999999999999966555543
No 58
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=90.90 E-value=0.65 Score=32.86 Aligned_cols=32 Identities=16% Similarity=0.160 Sum_probs=27.0
Q ss_pred CCEEEEEEcCCeEEEEEEEEEcCCCceEecce
Q psy3154 23 DERVHVKMRNERVLRGKLHAYDQHLNMVLGDV 54 (101)
Q Consensus 23 ~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~ 54 (101)
..+|.|-|.+|-.+.|++.+||+|.=|+-.+.
T Consensus 24 k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 24 KTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 36899999999999999999999985555454
No 59
>PRK14644 hypothetical protein; Provisional
Probab=90.71 E-value=0.72 Score=31.45 Aligned_cols=34 Identities=18% Similarity=0.372 Sum_probs=27.9
Q ss_pred HHHhcCCEEEEEEcCC----eEEEEEEEEEcCCCceEec
Q psy3154 18 IRLSLDERVHVKMRNE----RVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 18 L~~~l~k~V~V~l~~g----r~i~G~L~~~D~~mNlvL~ 52 (101)
+.+++|+.|.|+|++. +.+.|+|.++|.. ++.|.
T Consensus 80 f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 80 LENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 5667999999999876 8999999999974 45554
No 60
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=90.12 E-value=0.94 Score=30.59 Aligned_cols=42 Identities=24% Similarity=0.415 Sum_probs=27.1
Q ss_pred cccCChH---HHHHHhcCCEEEEEEc----CCeEEEEEEEEEcCCCceEe
Q psy3154 9 ISVKEPL---DLIRLSLDERVHVKMR----NERVLRGKLHAYDQHLNMVL 51 (101)
Q Consensus 9 ~~~~~Pl---~lL~~~l~k~V~V~l~----~gr~i~G~L~~~D~~mNlvL 51 (101)
+..+.|+ .-+..++|+.|.|+++ +.+.+.|+|.++|. -.++|
T Consensus 70 PG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 70 PGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp -SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred CCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 4455665 4456679999999994 45799999999998 33444
No 61
>PRK14640 hypothetical protein; Provisional
Probab=89.92 E-value=0.82 Score=31.63 Aligned_cols=33 Identities=18% Similarity=0.318 Sum_probs=26.2
Q ss_pred HHhcCCEEEEEE----cCCeEEEEEEEEEcCCCceEec
Q psy3154 19 RLSLDERVHVKM----RNERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 19 ~~~l~k~V~V~l----~~gr~i~G~L~~~D~~mNlvL~ 52 (101)
.+++|+.|.|++ .+++.+.|+|.++|.. ++.|.
T Consensus 93 ~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 93 EKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 355999999999 5669999999999974 35554
No 62
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=89.58 E-value=1.1 Score=27.75 Aligned_cols=32 Identities=25% Similarity=0.444 Sum_probs=25.2
Q ss_pred HHhcCCEEEEEEc---CC-eEEEEEEEEEcCCCceEe
Q psy3154 19 RLSLDERVHVKMR---NE-RVLRGKLHAYDQHLNMVL 51 (101)
Q Consensus 19 ~~~l~k~V~V~l~---~g-r~i~G~L~~~D~~mNlvL 51 (101)
..++|+.|.|+++ +| +.+.|+|.++|.. ++.|
T Consensus 21 ~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 21 ERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred HHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 3458999999997 55 6899999999984 3444
No 63
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=89.30 E-value=0.99 Score=31.66 Aligned_cols=39 Identities=21% Similarity=0.180 Sum_probs=32.5
Q ss_pred HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~ 55 (101)
.+++. -+-+|+|.+.||..|.|.+.+|+..-|.+|..+.
T Consensus 23 ~f~r~-~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 23 QFWRF-NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred HHHHh-cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 34433 4569999999999999999999999999987653
No 64
>PRK14633 hypothetical protein; Provisional
Probab=89.15 E-value=1 Score=31.12 Aligned_cols=33 Identities=15% Similarity=0.253 Sum_probs=26.0
Q ss_pred HHhcCCEEEEEEc----CCeEEEEEEEEEcCCCceEec
Q psy3154 19 RLSLDERVHVKMR----NERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 19 ~~~l~k~V~V~l~----~gr~i~G~L~~~D~~mNlvL~ 52 (101)
.+++|++|.|+++ +++.+.|+|.++|.. ++.|.
T Consensus 90 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 90 QALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 4558999999983 568999999999985 45553
No 65
>PRK14642 hypothetical protein; Provisional
Probab=89.14 E-value=0.93 Score=32.91 Aligned_cols=27 Identities=19% Similarity=0.364 Sum_probs=23.8
Q ss_pred HhcCCEEEEEEc-------------CCeEEEEEEEEEcCC
Q psy3154 20 LSLDERVHVKMR-------------NERVLRGKLHAYDQH 46 (101)
Q Consensus 20 ~~l~k~V~V~l~-------------~gr~i~G~L~~~D~~ 46 (101)
+++|+.|.|+|+ +.+.|.|+|.++|..
T Consensus 97 rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 97 RFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG 136 (197)
T ss_pred HhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence 448999999998 679999999999974
No 66
>PRK14636 hypothetical protein; Provisional
Probab=88.56 E-value=1 Score=31.95 Aligned_cols=33 Identities=12% Similarity=0.292 Sum_probs=25.8
Q ss_pred HHhcCCEEEEEEc---CC-eEEEEEEEEEcCCCceEec
Q psy3154 19 RLSLDERVHVKMR---NE-RVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 19 ~~~l~k~V~V~l~---~g-r~i~G~L~~~D~~mNlvL~ 52 (101)
.+++|++|.|+|+ +| +.++|+|.++|.. ++.|.
T Consensus 94 ~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~ 130 (176)
T PRK14636 94 ADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA 130 (176)
T ss_pred HHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence 3559999999997 55 6999999999874 35543
No 67
>PRK14645 hypothetical protein; Provisional
Probab=87.66 E-value=2 Score=29.92 Aligned_cols=32 Identities=9% Similarity=0.125 Sum_probs=25.3
Q ss_pred HHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEec
Q psy3154 19 RLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 19 ~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~ 52 (101)
.+++|++|.|++ +++.+.|+|.++|... +.|.
T Consensus 98 ~r~~G~~v~v~~-~~k~~~G~L~~~~d~~-i~l~ 129 (154)
T PRK14645 98 ERFAGLKAKVRG-PGENFTGRIKAVSGDQ-VTFD 129 (154)
T ss_pred HHhCCCEEEEEc-CCeEEEEEEEEEeCCE-EEEE
Confidence 345899999986 7899999999999753 5443
No 68
>PRK14632 hypothetical protein; Provisional
Probab=87.59 E-value=1.4 Score=31.20 Aligned_cols=33 Identities=21% Similarity=0.398 Sum_probs=25.9
Q ss_pred HHhcCCEEEEEEcC-------CeEEEEEEEEEcCCCceEec
Q psy3154 19 RLSLDERVHVKMRN-------ERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 19 ~~~l~k~V~V~l~~-------gr~i~G~L~~~D~~mNlvL~ 52 (101)
++++|+.|.|++.+ .+.+.|+|.++|.- ++.|.
T Consensus 94 ~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 94 SPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 45589999999975 57999999999864 45443
No 69
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.40 E-value=2 Score=29.97 Aligned_cols=43 Identities=26% Similarity=0.410 Sum_probs=32.3
Q ss_pred cccCChHH---HHHHhcCCEEEEEE----cCCeEEEEEEEEEcCCCceEec
Q psy3154 9 ISVKEPLD---LIRLSLDERVHVKM----RNERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 9 ~~~~~Pl~---lL~~~l~k~V~V~l----~~gr~i~G~L~~~D~~mNlvL~ 52 (101)
+..+.|+- -...++|+.|.|+| .+++.+.|+|.++|.-+ +++.
T Consensus 82 PGldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~~ 131 (153)
T COG0779 82 PGLDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTLE 131 (153)
T ss_pred CCCCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEEE
Confidence 34455543 34456899999999 78899999999999887 4443
No 70
>PRK14643 hypothetical protein; Provisional
Probab=87.26 E-value=1.8 Score=30.42 Aligned_cols=30 Identities=20% Similarity=0.383 Sum_probs=24.8
Q ss_pred HHHhcCCEEEEEEcC----CeEEEEEEEEEcCCC
Q psy3154 18 IRLSLDERVHVKMRN----ERVLRGKLHAYDQHL 47 (101)
Q Consensus 18 L~~~l~k~V~V~l~~----gr~i~G~L~~~D~~m 47 (101)
+..++|++|.|+|+. .+.+.|+|.++|...
T Consensus 99 f~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~ 132 (164)
T PRK14643 99 LVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNT 132 (164)
T ss_pred HHHhcCCeEEEEEecccCCceEEEEEEEEEeCCc
Confidence 445699999999965 589999999999653
No 71
>PRK14634 hypothetical protein; Provisional
Probab=86.44 E-value=1.8 Score=30.06 Aligned_cols=33 Identities=21% Similarity=0.230 Sum_probs=25.3
Q ss_pred HHhcCCEEEEEEcC----CeEEEEEEEEEcCCCceEec
Q psy3154 19 RLSLDERVHVKMRN----ERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 19 ~~~l~k~V~V~l~~----gr~i~G~L~~~D~~mNlvL~ 52 (101)
.+++|++|.|++.+ .+.|.|+|.++|.-. +.|.
T Consensus 96 ~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~-v~l~ 132 (155)
T PRK14634 96 QTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDH-LQIN 132 (155)
T ss_pred HHhCCCeEEEEEecCCCCeEEEEEEEEEEeCCE-EEEE
Confidence 34589999999963 279999999999743 5443
No 72
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=86.37 E-value=1.9 Score=29.70 Aligned_cols=29 Identities=28% Similarity=0.401 Sum_probs=24.3
Q ss_pred HHHhcCCEEEEEE----cCCeEEEEEEEEEcCC
Q psy3154 18 IRLSLDERVHVKM----RNERVLRGKLHAYDQH 46 (101)
Q Consensus 18 L~~~l~k~V~V~l----~~gr~i~G~L~~~D~~ 46 (101)
+.+++|+.|.|++ .+++.+.|+|..+|..
T Consensus 93 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 93 FRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred HHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 4455999999997 5678999999999973
No 73
>PRK14646 hypothetical protein; Provisional
Probab=85.79 E-value=2 Score=29.81 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=25.9
Q ss_pred HHHhcCCEEEEEEcCC----eEEEEEEEEEcCCCceEec
Q psy3154 18 IRLSLDERVHVKMRNE----RVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 18 L~~~l~k~V~V~l~~g----r~i~G~L~~~D~~mNlvL~ 52 (101)
..+++|++|.|+|++. +.+.|+|.++|.- ++.|.
T Consensus 95 f~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 95 FKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred HHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 3455999999999542 6889999999985 45553
No 74
>PRK14647 hypothetical protein; Provisional
Probab=85.15 E-value=2.2 Score=29.65 Aligned_cols=28 Identities=14% Similarity=0.184 Sum_probs=23.2
Q ss_pred HHhcCCEEEEEEc---------CCeEEEEEEEEEcCC
Q psy3154 19 RLSLDERVHVKMR---------NERVLRGKLHAYDQH 46 (101)
Q Consensus 19 ~~~l~k~V~V~l~---------~gr~i~G~L~~~D~~ 46 (101)
.+++|+.|.|+++ +.+.+.|+|.++|..
T Consensus 95 ~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~ 131 (159)
T PRK14647 95 ERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG 131 (159)
T ss_pred HHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC
Confidence 3458999999995 358999999999963
No 75
>PRK14631 hypothetical protein; Provisional
Probab=85.08 E-value=2.1 Score=30.34 Aligned_cols=27 Identities=26% Similarity=0.422 Sum_probs=22.9
Q ss_pred HHHhcCCEEEEEEc----CCeEEEEEEEEEc
Q psy3154 18 IRLSLDERVHVKMR----NERVLRGKLHAYD 44 (101)
Q Consensus 18 L~~~l~k~V~V~l~----~gr~i~G~L~~~D 44 (101)
+.+++|+.|.|++. +.+.|+|+|.++|
T Consensus 112 f~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 112 LQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 34559999999995 4589999999998
No 76
>PRK14641 hypothetical protein; Provisional
Probab=83.01 E-value=2.6 Score=29.87 Aligned_cols=26 Identities=19% Similarity=0.322 Sum_probs=21.8
Q ss_pred HHhcCCEEEEEEcC----CeEEEEEEEEEc
Q psy3154 19 RLSLDERVHVKMRN----ERVLRGKLHAYD 44 (101)
Q Consensus 19 ~~~l~k~V~V~l~~----gr~i~G~L~~~D 44 (101)
++++|+.|.|+|.+ .+.+.|+|.++|
T Consensus 100 ~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 100 GRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 34589999999975 468999999995
No 77
>PRK14637 hypothetical protein; Provisional
Probab=82.46 E-value=3 Score=28.89 Aligned_cols=33 Identities=21% Similarity=0.242 Sum_probs=24.6
Q ss_pred HHhcCCEEEEEEcCCeEE-EEEEEEEcCCCceEec
Q psy3154 19 RLSLDERVHVKMRNERVL-RGKLHAYDQHLNMVLG 52 (101)
Q Consensus 19 ~~~l~k~V~V~l~~gr~i-~G~L~~~D~~mNlvL~ 52 (101)
.+++|+.|.|++.+.+.+ .|+|.++|.. ++.|.
T Consensus 94 ~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 94 SIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 345899999999545566 7999999975 35444
No 78
>PRK06955 biotin--protein ligase; Provisional
Probab=82.39 E-value=3.2 Score=31.50 Aligned_cols=33 Identities=18% Similarity=0.237 Sum_probs=28.1
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGD 53 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~ 53 (101)
++|++|+|...+++.+.|++.|+|....|+++.
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 367899997667788999999999999999863
No 79
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=82.12 E-value=2.2 Score=23.60 Aligned_cols=23 Identities=30% Similarity=0.482 Sum_probs=15.4
Q ss_pred EEEEEEEEcCCCceEecceEEEE
Q psy3154 36 LRGKLHAYDQHLNMVLGDVEETV 58 (101)
Q Consensus 36 i~G~L~~~D~~mNlvL~~~~E~~ 58 (101)
..|++.|+|+.+.++|++...+.
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T~ 32 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTTH 32 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-EE
T ss_pred cceeEEeeccccceEEEeCCccE
Confidence 67999999999999999876543
No 80
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=78.89 E-value=4.2 Score=28.55 Aligned_cols=40 Identities=18% Similarity=0.215 Sum_probs=33.1
Q ss_pred CCccccCChHHHHHHhc--CCEEEEEEcCCeEEEEEEEEEcC
Q psy3154 6 IPTISVKEPLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQ 45 (101)
Q Consensus 6 ~~~~~~~~Pl~lL~~~l--~k~V~V~l~~gr~i~G~L~~~D~ 45 (101)
.-+++....++.-+++. |+-++|-+.|||++.|+=.|.|.
T Consensus 101 ~~~psrrDFF~Icrka~qqg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 101 PYKPSRRDFFSICRKAHQQGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred cCCCccchHHHHHHHHHHCCCeEEEEEcCCcEEEeeecccce
Confidence 34466777888888886 47999999999999999999884
No 81
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=73.98 E-value=8.6 Score=24.94 Aligned_cols=17 Identities=35% Similarity=0.737 Sum_probs=14.2
Q ss_pred CEEEEEEcCCeEEEEEE
Q psy3154 24 ERVHVKMRNERVLRGKL 40 (101)
Q Consensus 24 k~V~V~l~~gr~i~G~L 40 (101)
.+|.+.|+||+.+.|++
T Consensus 29 ~~V~l~L~DGs~l~Gtv 45 (101)
T PF11607_consen 29 ERVELELDDGSMLRGTV 45 (101)
T ss_dssp -EEEEEETTS-EEEEEE
T ss_pred ceEEEEEcCCCeeeeee
Confidence 59999999999999994
No 82
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=73.60 E-value=8.4 Score=29.15 Aligned_cols=31 Identities=16% Similarity=0.300 Sum_probs=26.5
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCCCceEec
Q psy3154 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~ 52 (101)
++|++|.+... +..+.|++.++|....|+++
T Consensus 270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLIIG-DKEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEeC-CcEEEEEEEEECCCceEEEE
Confidence 36789999874 45799999999999999996
No 83
>PRK10898 serine endoprotease; Provisional
Probab=72.46 E-value=8.7 Score=29.77 Aligned_cols=32 Identities=16% Similarity=0.335 Sum_probs=28.5
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154 24 ERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 24 k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~ 55 (101)
..+.|++.||+.+.+++.++|....|-+=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 57899999999999999999999999776654
No 84
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=71.99 E-value=8.9 Score=29.64 Aligned_cols=32 Identities=16% Similarity=0.342 Sum_probs=28.3
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154 24 ERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 24 k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~ 55 (101)
..+.|.+.||+.+.+++.++|...++-+=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 47899999999999999999999999876554
No 85
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=71.56 E-value=10 Score=28.61 Aligned_cols=31 Identities=16% Similarity=0.269 Sum_probs=26.8
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGD 53 (101)
Q Consensus 22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~ 53 (101)
+|++|.|.. ++..+.|++.++|....|+++.
T Consensus 236 ~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 236 KDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred CCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 678999875 5688999999999999999864
No 86
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=71.39 E-value=9.1 Score=31.96 Aligned_cols=33 Identities=18% Similarity=0.193 Sum_probs=28.3
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCCCceEecc
Q psy3154 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGD 53 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~ 53 (101)
++|++|.+...+++.+.|+..|+|....|+|+.
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 367899987667778999999999999999963
No 87
>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region. The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.
Probab=71.03 E-value=11 Score=27.41 Aligned_cols=30 Identities=17% Similarity=0.276 Sum_probs=26.1
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCCCceEec
Q psy3154 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~ 52 (101)
++++|.+...+ ..+.|++.|+|....|+++
T Consensus 192 ~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 192 IGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred cCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 57999998754 5689999999999999996
No 88
>PRK08330 biotin--protein ligase; Provisional
Probab=69.58 E-value=14 Score=26.89 Aligned_cols=32 Identities=22% Similarity=0.295 Sum_probs=26.2
Q ss_pred hcCCEEEEEEcCCeEE-EEEEEEEcCCCceEecc
Q psy3154 21 SLDERVHVKMRNERVL-RGKLHAYDQHLNMVLGD 53 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~i-~G~L~~~D~~mNlvL~~ 53 (101)
+++++|.+.. +++.+ .|++.++|....|++..
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 4679999875 56665 69999999999999874
No 89
>PRK10942 serine endoprotease; Provisional
Probab=68.37 E-value=11 Score=30.46 Aligned_cols=31 Identities=16% Similarity=0.343 Sum_probs=27.7
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCCCceEecce
Q psy3154 24 ERVHVKMRNERVLRGKLHAYDQHLNMVLGDV 54 (101)
Q Consensus 24 k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~ 54 (101)
..+.|++.||++|.+++.++|...+|-|=.+
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 5789999999999999999999999877654
No 90
>PRK10139 serine endoprotease; Provisional
Probab=68.37 E-value=12 Score=30.21 Aligned_cols=32 Identities=16% Similarity=0.416 Sum_probs=28.5
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154 24 ERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 24 k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~ 55 (101)
..+.|++.||+++.+++.++|....|-+=.+.
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 58999999999999999999999998876553
No 91
>KOG3382|consensus
Probab=66.27 E-value=3.4 Score=28.46 Aligned_cols=25 Identities=20% Similarity=0.190 Sum_probs=19.6
Q ss_pred cCCeEEEEEEEEEcCCCceEecceE
Q psy3154 31 RNERVLRGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 31 ~~gr~i~G~L~~~D~~mNlvL~~~~ 55 (101)
+.+-.=+|+|+|.|+|.|=.-+|-.
T Consensus 40 rtd~~kiGTLVG~DkfGNkYyen~~ 64 (151)
T KOG3382|consen 40 RTDDHKIGTLVGVDKFGNKYYENND 64 (151)
T ss_pred hcccccceeeeeecccccchhcccc
Confidence 3444557999999999998887763
No 92
>PRK14630 hypothetical protein; Provisional
Probab=64.85 E-value=15 Score=25.11 Aligned_cols=32 Identities=6% Similarity=0.188 Sum_probs=23.8
Q ss_pred HHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEec
Q psy3154 19 RLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 19 ~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~ 52 (101)
++++|++|.|++.. ....|+|.++|... +.|.
T Consensus 93 ~r~~G~~v~V~l~~-~~~~G~L~~~~d~~-i~l~ 124 (143)
T PRK14630 93 KIFEGKKIKLMLDN-DFEEGFILEAKADS-FIFK 124 (143)
T ss_pred HHhCCCEEEEEEcC-cceEEEEEEEeCCE-EEEE
Confidence 45599999999965 44599999999843 4443
No 93
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=64.70 E-value=17 Score=26.91 Aligned_cols=33 Identities=15% Similarity=0.262 Sum_probs=30.4
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCCCceEecce
Q psy3154 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDV 54 (101)
Q Consensus 22 l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~ 54 (101)
+|++|++...++..+.|+..++|....|+++..
T Consensus 189 ~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 189 LGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred CCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 789999999999999999999999999999875
No 94
>PRK14635 hypothetical protein; Provisional
Probab=64.63 E-value=16 Score=25.38 Aligned_cols=32 Identities=16% Similarity=0.110 Sum_probs=23.8
Q ss_pred HHhcCCEEEEEEc--CCeEEEE---EEEEEcCCCceEe
Q psy3154 19 RLSLDERVHVKMR--NERVLRG---KLHAYDQHLNMVL 51 (101)
Q Consensus 19 ~~~l~k~V~V~l~--~gr~i~G---~L~~~D~~mNlvL 51 (101)
.+++|+.|.|++. ++..+.| +|.++|.. ++.|
T Consensus 95 ~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 95 DRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 3458999999885 4578887 99999874 3444
No 95
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=63.53 E-value=15 Score=25.35 Aligned_cols=26 Identities=8% Similarity=0.180 Sum_probs=23.5
Q ss_pred HHhcCCEEEEEEcCCeEEEEEEEEEc
Q psy3154 19 RLSLDERVHVKMRNERVLRGKLHAYD 44 (101)
Q Consensus 19 ~~~l~k~V~V~l~~gr~i~G~L~~~D 44 (101)
..++||.|.+...+|..+.|++.++.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 36799999999999999999999986
No 96
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=60.64 E-value=12 Score=23.24 Aligned_cols=58 Identities=21% Similarity=0.246 Sum_probs=26.3
Q ss_pred CCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEecCCCCCC
Q psy3154 23 DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPPNRTPA 100 (101)
Q Consensus 23 ~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~~~~~~ 100 (101)
+-+|+++|+||..+.|+ +.|-..|- +=.|+... ...-+...||=+.|..+++...+|.
T Consensus 17 ~~~v~L~l~dG~~~~g~--A~dt~~~~---~k~E~L~l---------------~~~~~~~~i~Ld~I~~~~al~~nPh 74 (80)
T PF07073_consen 17 RYPVKLTLKDGEQIEGK--ALDTRTNA---KKEECLVL---------------EQDGGEQEIRLDQIASMSALTDNPH 74 (80)
T ss_dssp TT-EEEE-TTT--EEES--S-EEE------SSS-EEEE---------------EETTEEEEESTT--SEEE----ETT
T ss_pred CCeEEEEEeCCCEEEEE--EEEEEEec---CceEEEEE---------------ecCCcEEEEEhhheeeeeecCCCCe
Confidence 46999999999999998 33322221 22222221 1123456788888888887766653
No 97
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=59.22 E-value=21 Score=28.11 Aligned_cols=32 Identities=16% Similarity=0.390 Sum_probs=28.5
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154 24 ERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 24 k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~ 55 (101)
..+.|++.||+.+.+++.++|...+|.|=.+.
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 48899999999999999999999998877654
No 98
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=54.94 E-value=5.9 Score=25.68 Aligned_cols=17 Identities=24% Similarity=0.200 Sum_probs=15.2
Q ss_pred EEEEEEcCCCceEecce
Q psy3154 38 GKLHAYDQHLNMVLGDV 54 (101)
Q Consensus 38 G~L~~~D~~mNlvL~~~ 54 (101)
|+|+|.|.|.|.--++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999987765
No 99
>PRK08477 biotin--protein ligase; Provisional
Probab=49.11 E-value=72 Score=23.09 Aligned_cols=35 Identities=3% Similarity=-0.006 Sum_probs=29.2
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEE
Q psy3154 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEE 56 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E 56 (101)
.+++.|+|. .+++.+.|+..++|...-|+++.-.-
T Consensus 173 ~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~ 207 (211)
T PRK08477 173 EKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKV 207 (211)
T ss_pred HcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEe
Confidence 467899986 56899999999999999999886543
No 100
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=48.56 E-value=24 Score=22.71 Aligned_cols=22 Identities=9% Similarity=0.525 Sum_probs=17.5
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q psy3154 21 SLDERVHVK-MRNERVLRGKLHA 42 (101)
Q Consensus 21 ~l~k~V~V~-l~~gr~i~G~L~~ 42 (101)
++|..|+|. +..|+.+.|++.+
T Consensus 94 ~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 94 AVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 467888888 7888888888765
No 101
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=45.39 E-value=43 Score=23.04 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=22.6
Q ss_pred HhcCCEEEEEEcCCeEEEEEEEEEcC
Q psy3154 20 LSLDERVHVKMRNERVLRGKLHAYDQ 45 (101)
Q Consensus 20 ~~l~k~V~V~l~~gr~i~G~L~~~D~ 45 (101)
.++||.|.....+|..+.|++.++..
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEEE
Confidence 57999999888999999999987763
No 102
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=45.06 E-value=47 Score=21.12 Aligned_cols=35 Identities=14% Similarity=0.037 Sum_probs=27.4
Q ss_pred HHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceE
Q psy3154 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMV 50 (101)
Q Consensus 16 ~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlv 50 (101)
+--+.|+||+|...-+.|+.+.|++.---..-..|
T Consensus 33 ~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvV 67 (87)
T PRK04337 33 EEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEV 67 (87)
T ss_pred HHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceE
Confidence 34456799999999999999999987665555554
No 103
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=44.03 E-value=38 Score=22.39 Aligned_cols=41 Identities=20% Similarity=0.255 Sum_probs=27.7
Q ss_pred ChHHHHHHhcC---------CEEEEEEcCCeEEEEEEEEEcCCCceEecce
Q psy3154 13 EPLDLIRLSLD---------ERVHVKMRNERVLRGKLHAYDQHLNMVLGDV 54 (101)
Q Consensus 13 ~Pl~lL~~~l~---------k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~ 54 (101)
.+-.+++..++ ....|.++||+.+.|.+..=|.. .+.|.++
T Consensus 38 ~~~~ll~~I~~P~~~i~~~y~~~~v~~~dG~~~~G~~~~e~~~-~~~l~~~ 87 (133)
T TIGR02603 38 GVEYLLEAILDPSREVAPGFEAYRVTLKDGRILSGIVASETAD-GVTVKMP 87 (133)
T ss_pred CHHHHHHHHhCchhhhCcccccEEEEECCCCEEEEEEEecCCC-eEEEEcC
Confidence 45555555443 36899999999999999885532 3444444
No 104
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=43.46 E-value=45 Score=19.86 Aligned_cols=35 Identities=23% Similarity=0.171 Sum_probs=27.4
Q ss_pred HhcCCEEEEEEcCC-eEEEEEEEEEcCCC-ceEecce
Q psy3154 20 LSLDERVHVKMRNE-RVLRGKLHAYDQHL-NMVLGDV 54 (101)
Q Consensus 20 ~~l~k~V~V~l~~g-r~i~G~L~~~D~~m-NlvL~~~ 54 (101)
.|+|+-|.|...+. -.|+|.++.+|+-- -++|+..
T Consensus 3 dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~ 39 (62)
T cd01737 3 DWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFP 39 (62)
T ss_pred cccceEEEEecCCceEEEEEEEEEeCccceEEEEeec
Confidence 58999999999887 48999999999643 3555543
No 105
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=42.82 E-value=69 Score=19.76 Aligned_cols=28 Identities=21% Similarity=0.280 Sum_probs=20.1
Q ss_pred HHHHHhcCCEEEEEEcCCe----EEEEEEEEE
Q psy3154 16 DLIRLSLDERVHVKMRNER----VLRGKLHAY 43 (101)
Q Consensus 16 ~lL~~~l~k~V~V~l~~gr----~i~G~L~~~ 43 (101)
.-|...+|++|.++.+.|| +-.|+|...
T Consensus 10 ~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 10 KELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 4567889999999999996 466888764
No 106
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=41.29 E-value=32 Score=19.23 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=16.3
Q ss_pred ChHHHHHHhcCCEEEEEEcCCeEEE
Q psy3154 13 EPLDLIRLSLDERVHVKMRNERVLR 37 (101)
Q Consensus 13 ~Pl~lL~~~l~k~V~V~l~~gr~i~ 37 (101)
.-++.+++++||+|+|. |..+-
T Consensus 9 ~~~~~~~~~~Gk~V~V~---G~l~~ 30 (48)
T PF14485_consen 9 EDYSYLKSLLGKRVSVT---GKLFH 30 (48)
T ss_pred hhhHHHHHhcCCeEEEE---EEEee
Confidence 34678888999999987 54443
No 107
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=41.14 E-value=32 Score=25.11 Aligned_cols=22 Identities=18% Similarity=0.498 Sum_probs=18.6
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q psy3154 21 SLDERVHVK-MRNERVLRGKLHA 42 (101)
Q Consensus 21 ~l~k~V~V~-l~~gr~i~G~L~~ 42 (101)
.+|..|+|+ +..|+.+.|++.+
T Consensus 205 ~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 205 AVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCeEEEEECCCCCEEEEEEeC
Confidence 467899998 8999999998765
No 108
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=40.53 E-value=43 Score=25.06 Aligned_cols=19 Identities=21% Similarity=0.267 Sum_probs=17.1
Q ss_pred EEEEEEEEEcCCCceEecc
Q psy3154 35 VLRGKLHAYDQHLNMVLGD 53 (101)
Q Consensus 35 ~i~G~L~~~D~~mNlvL~~ 53 (101)
.+.|.+.-+|.|.|++++=
T Consensus 169 ~i~g~Vi~iD~FGNlitnI 187 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNI 187 (258)
T ss_dssp EEEEEEEEEETTSEEEEEE
T ss_pred eEEEEEEEECccCCeeeCC
Confidence 8999999999999999653
No 109
>KOG4401|consensus
Probab=39.54 E-value=42 Score=24.22 Aligned_cols=35 Identities=14% Similarity=0.242 Sum_probs=31.1
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~ 55 (101)
+++..|.|..-++...+|.+.+||---++..-++.
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 36789999999999999999999988888877776
No 110
>KOG3493|consensus
Probab=39.07 E-value=26 Score=21.33 Aligned_cols=19 Identities=21% Similarity=0.380 Sum_probs=14.9
Q ss_pred HHHHhcCCEEEEEEcCCeE
Q psy3154 17 LIRLSLDERVHVKMRNERV 35 (101)
Q Consensus 17 lL~~~l~k~V~V~l~~gr~ 35 (101)
.+...+||+|+|++....+
T Consensus 5 ~~nDrLGKKVRvKCn~dDt 23 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDT 23 (73)
T ss_pred hhhhhcCceEEEEeCCccc
Confidence 4667799999999976544
No 111
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=38.98 E-value=69 Score=18.63 Aligned_cols=26 Identities=27% Similarity=0.496 Sum_probs=18.5
Q ss_pred hcCCEEEEEEcCCeE-EEEEEEEEcCC
Q psy3154 21 SLDERVHVKMRNERV-LRGKLHAYDQH 46 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~-i~G~L~~~D~~ 46 (101)
..|.+|+++--+... |.|++.+||.-
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEeccc
Confidence 368899999877765 59999999964
No 112
>PRK06630 hypothetical protein; Provisional
Probab=38.14 E-value=19 Score=23.42 Aligned_cols=19 Identities=21% Similarity=0.072 Sum_probs=16.5
Q ss_pred EEEEEEEEcCCCceEecce
Q psy3154 36 LRGKLHAYDQHLNMVLGDV 54 (101)
Q Consensus 36 i~G~L~~~D~~mNlvL~~~ 54 (101)
..|+|+|-|+|.|---++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3699999999999988874
No 113
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=37.65 E-value=54 Score=23.53 Aligned_cols=33 Identities=15% Similarity=0.378 Sum_probs=22.8
Q ss_pred hHHHHHHhcC--CEEEEEE-cCCeEEEEEEEEEcCC
Q psy3154 14 PLDLIRLSLD--ERVHVKM-RNERVLRGKLHAYDQH 46 (101)
Q Consensus 14 Pl~lL~~~l~--k~V~V~l-~~gr~i~G~L~~~D~~ 46 (101)
=++||-++-+ -++.+.+ .++..|+|++.++|.-
T Consensus 122 KI~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 122 KIDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 3566666544 2555544 5679999999999975
No 114
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.96 E-value=61 Score=22.47 Aligned_cols=22 Identities=14% Similarity=0.356 Sum_probs=17.4
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q psy3154 21 SLDERVHVK-MRNERVLRGKLHA 42 (101)
Q Consensus 21 ~l~k~V~V~-l~~gr~i~G~L~~ 42 (101)
.+|..|+|+ +..|+.+.|++.+
T Consensus 129 ~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 129 AAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 467788888 7889999988654
No 115
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=31.72 E-value=29 Score=23.16 Aligned_cols=19 Identities=21% Similarity=0.204 Sum_probs=16.0
Q ss_pred EEEEEEEcCCCceEecceE
Q psy3154 37 RGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 37 ~G~L~~~D~~mNlvL~~~~ 55 (101)
.|+|+|.|++.|---++..
T Consensus 9 ~g~lVG~D~~GNkYYE~~~ 27 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPS 27 (115)
T ss_pred cceEeEEcCCCCeeeEcCC
Confidence 5899999999999877643
No 116
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=31.31 E-value=98 Score=20.09 Aligned_cols=29 Identities=38% Similarity=0.548 Sum_probs=22.4
Q ss_pred HHHhcCCEEEEEEcC-CeEEEEEEEEEcCCCc
Q psy3154 18 IRLSLDERVHVKMRN-ERVLRGKLHAYDQHLN 48 (101)
Q Consensus 18 L~~~l~k~V~V~l~~-gr~i~G~L~~~D~~mN 48 (101)
-+.|++++|.-+-+. |+.+.|++.- -|.|
T Consensus 41 A~~y~gk~v~yk~~~~G~Vi~G~V~R--~HGn 70 (100)
T COG2451 41 AQFYLGKRVCYKYRSSGRVIKGKVVR--THGN 70 (100)
T ss_pred HHhhhccEEEEEeCCCCcEEEEEEEE--ecCC
Confidence 356799999888887 9999999854 4555
No 117
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=31.01 E-value=48 Score=19.80 Aligned_cols=21 Identities=14% Similarity=0.320 Sum_probs=17.8
Q ss_pred CEEEEEEcCCeEEEEEEEEEc
Q psy3154 24 ERVHVKMRNERVLRGKLHAYD 44 (101)
Q Consensus 24 k~V~V~l~~gr~i~G~L~~~D 44 (101)
.+|.|++-||..+.+++..-|
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~ 25 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSD 25 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 489999999999999977654
No 118
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=30.76 E-value=63 Score=23.57 Aligned_cols=22 Identities=36% Similarity=0.548 Sum_probs=18.1
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q psy3154 21 SLDERVHVK-MRNERVLRGKLHA 42 (101)
Q Consensus 21 ~l~k~V~V~-l~~gr~i~G~L~~ 42 (101)
..|..|+|+ +..||.+.|++.+
T Consensus 184 ~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 184 GENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 367899998 7999999998764
No 119
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=30.57 E-value=91 Score=22.61 Aligned_cols=25 Identities=12% Similarity=0.138 Sum_probs=21.9
Q ss_pred HhcCCEEEEEEcCCeEEEEEEEEEc
Q psy3154 20 LSLDERVHVKMRNERVLRGKLHAYD 44 (101)
Q Consensus 20 ~~l~k~V~V~l~~gr~i~G~L~~~D 44 (101)
.++||.|.+.-.+|..+.|++.+..
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 5699999988889999999988775
No 120
>PRK11625 Rho-binding antiterminator; Provisional
Probab=30.45 E-value=1.4e+02 Score=18.67 Aligned_cols=50 Identities=16% Similarity=0.070 Sum_probs=31.7
Q ss_pred CCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEEEe
Q psy3154 23 DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS 93 (101)
Q Consensus 23 ~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 93 (101)
+-+|.+.++||..+.|+. .|-+ .++-.|+.... ..=+...||=|+|+.++
T Consensus 23 ~~~l~l~l~dGe~~~g~A--~D~~----~~~k~EyL~l~---------------~~g~~~~iRLD~I~s~~ 72 (84)
T PRK11625 23 HLMLTLELKDGEVLQAKA--SDLV----SRKNVEYLVVE---------------AAGETRELRLDKIASFS 72 (84)
T ss_pred CCeEEEEECCCCEEEEEE--Eeee----cCCceEEEEEE---------------cCCCEEEEEeeeEeecc
Confidence 459999999999999985 4544 23455555421 11134566667777776
No 121
>PF03122 Herpes_MCP: Herpes virus major capsid protein; InterPro: IPR000912 The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces []. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1NO7_B.
Probab=30.26 E-value=17 Score=33.40 Aligned_cols=56 Identities=13% Similarity=0.182 Sum_probs=0.0
Q ss_pred EEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcchhhhhcceeeeeeCeEEEcCCeEEE
Q psy3154 25 RVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL 91 (101)
Q Consensus 25 ~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 91 (101)
+..=+..+|+.+.|+|+..|.-|+.+|+-.-+.... .......+|.++|+|+|.|.
T Consensus 249 ~~Tytt~~G~~v~GVlvTT~~V~q~Ll~~l~~i~~~-----------~v~~PatYg~~Vi~geNlVT 304 (1354)
T PF03122_consen 249 RSTYTTSSGRPVDGVLVTTANVMQKLLNLLGQISDT-----------SVSVPATYGEFVISGENLVT 304 (1354)
T ss_dssp -------------------------------------------------------------------
T ss_pred cceeecCCCCEeceEEeccHHHHHHHHHHHhhhccc-----------eeecchhheeeeecCccHHH
Confidence 344456889999999999999888887765542210 12346789999999999875
No 122
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=29.48 E-value=92 Score=22.83 Aligned_cols=23 Identities=0% Similarity=-0.054 Sum_probs=20.0
Q ss_pred cCCeEEEEEEEEEcCCCceEecc
Q psy3154 31 RNERVLRGKLHAYDQHLNMVLGD 53 (101)
Q Consensus 31 ~~gr~i~G~L~~~D~~mNlvL~~ 53 (101)
.++..+.|++.++|....|+++.
T Consensus 209 ~~~~~~~G~~~gId~~G~Lvv~~ 231 (245)
T PTZ00276 209 TGRDPEELTALSLNEWGHLIVRR 231 (245)
T ss_pred cCCcEEEEEEEEECCCCeEEEEE
Confidence 46678899999999999999874
No 123
>COG1976 TIF6 Translation initiation factor 6 (eIF-6) [Translation, ribosomal structure and biogenesis]
Probab=29.26 E-value=1.3e+02 Score=22.27 Aligned_cols=89 Identities=21% Similarity=0.087 Sum_probs=58.6
Q ss_pred CccccCChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEEEeecccCcch-hhhhcceeeeeeCeEEEc
Q psy3154 7 PTISVKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEET-YEEIYKTTKRSIPMLFVR 85 (101)
Q Consensus 7 ~~~~~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~-~~~~~~~~~r~lg~v~IR 85 (101)
|+...+.-.+.+++-++-+|.-..-+|..+.|.|.+-.++.=|+-..+.+.-...-++... .-.....+-..+|.+++=
T Consensus 28 ~~~~~e~~~~~i~e~L~v~vv~ttI~gS~lvG~l~~gNsnG~lvP~~~~d~El~~l~~~~~v~V~~l~~k~nAlGN~Il~ 107 (222)
T COG1976 28 PPGLDEKFVDVIREVLGVPVVETTIAGSRLVGALTAGNSNGLLVPYGVRDEELRRLKNALGVEVLILPTKLNALGNLILA 107 (222)
T ss_pred cCCCCHHHHHHHHHHhCCcEEEEEecCceEEeEEEeecCCceEcCCcccHHHHHhhcccCCceEEEeCccccccccEEEe
Confidence 3344555688889989988888888999999999999988866655554311000000000 001123456678999998
Q ss_pred CCeEEEEecC
Q psy3154 86 GDGVILVSPP 95 (101)
Q Consensus 86 G~~Iv~I~~~ 95 (101)
.|...+|++.
T Consensus 108 ND~~Alvhp~ 117 (222)
T COG1976 108 NDKGALVHPD 117 (222)
T ss_pred cCceeEecCc
Confidence 9999888875
No 124
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=28.65 E-value=1.6e+02 Score=18.60 Aligned_cols=14 Identities=7% Similarity=0.216 Sum_probs=11.7
Q ss_pred HHHHHhcCCEEEEE
Q psy3154 16 DLIRLSLDERVHVK 29 (101)
Q Consensus 16 ~lL~~~l~k~V~V~ 29 (101)
++|.++.|++|++.
T Consensus 8 ~~L~~f~gk~V~iv 21 (101)
T cd04479 8 AMLSQFVGKTVRIV 21 (101)
T ss_pred HHHHhhCCCEEEEE
Confidence 58899999998864
No 125
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.16 E-value=91 Score=22.67 Aligned_cols=22 Identities=18% Similarity=0.492 Sum_probs=18.4
Q ss_pred hcCCEEEEEEcCCeEEEEEEEE
Q psy3154 21 SLDERVHVKMRNERVLRGKLHA 42 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~i~G~L~~ 42 (101)
.+|..|+|+-.+|+.+.|++.+
T Consensus 194 ~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 194 NLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCEEEEEeCCCCEEEEEEec
Confidence 4678899988889999998765
No 126
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=27.25 E-value=68 Score=18.95 Aligned_cols=21 Identities=19% Similarity=0.395 Sum_probs=17.5
Q ss_pred CEEEEEEcCCeEEEEEEEEEc
Q psy3154 24 ERVHVKMRNERVLRGKLHAYD 44 (101)
Q Consensus 24 k~V~V~l~~gr~i~G~L~~~D 44 (101)
-+|+|++-||..++.++..-|
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~ 27 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSD 27 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTS
T ss_pred EEEEEECCCCCEEEEEECCcc
Confidence 378999999999999977544
No 127
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=27.16 E-value=68 Score=18.93 Aligned_cols=21 Identities=5% Similarity=0.407 Sum_probs=17.2
Q ss_pred CEEEEEEcCCeEEEEEEEEEc
Q psy3154 24 ERVHVKMRNERVLRGKLHAYD 44 (101)
Q Consensus 24 k~V~V~l~~gr~i~G~L~~~D 44 (101)
.+|+|++-||..+++++..-|
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~ 23 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTH 23 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 378999999999999976544
No 128
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.05 E-value=83 Score=23.68 Aligned_cols=22 Identities=23% Similarity=0.383 Sum_probs=18.4
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q psy3154 21 SLDERVHVK-MRNERVLRGKLHA 42 (101)
Q Consensus 21 ~l~k~V~V~-l~~gr~i~G~L~~ 42 (101)
..|..|+|+ +..||.+.|++.+
T Consensus 231 ~~Gd~IrVrN~~SgkvV~a~V~~ 253 (261)
T PRK06804 231 RKGELIKVKNLSSGRVVTATVDG 253 (261)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 467889998 8899999998765
No 129
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.20 E-value=1.5e+02 Score=22.44 Aligned_cols=32 Identities=19% Similarity=0.321 Sum_probs=26.4
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCCCceEecceE
Q psy3154 24 ERVHVKMRNERVLRGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 24 k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~ 55 (101)
.++.+.+.||+++.+.+.++|...-+-+-...
T Consensus 96 ~~i~v~l~dg~~~~a~~vg~d~~~dlavlki~ 127 (347)
T COG0265 96 EEITVTLADGREVPAKLVGKDPISDLAVLKID 127 (347)
T ss_pred ceEEEEeCCCCEEEEEEEecCCccCEEEEEec
Confidence 57888899999999999999987766655444
No 130
>smart00039 CRF corticotropin-releasing factor.
Probab=24.81 E-value=48 Score=18.03 Aligned_cols=17 Identities=35% Similarity=0.606 Sum_probs=13.9
Q ss_pred CCccccCChHHHHHHhc
Q psy3154 6 IPTISVKEPLDLIRLSL 22 (101)
Q Consensus 6 ~~~~~~~~Pl~lL~~~l 22 (101)
-|+.+...|+++|++.+
T Consensus 2 ~PslSIdl~~~vLR~~l 18 (40)
T smart00039 2 GPSLSIDLTFDLLRQRL 18 (40)
T ss_pred CCCcccccHHHHHHHHH
Confidence 47889999999998743
No 131
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=24.64 E-value=1e+02 Score=22.08 Aligned_cols=24 Identities=29% Similarity=0.502 Sum_probs=20.9
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEc
Q psy3154 21 SLDERVHVKMRNERVLRGKLHAYD 44 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~i~G~L~~~D 44 (101)
++|++|.|.+...+.+.|.+..++
T Consensus 26 ~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 26 LLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp TTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hCCCEEEEEEeeeeEeccEEEEEE
Confidence 799999999998899999998885
No 132
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.35 E-value=1e+02 Score=20.88 Aligned_cols=22 Identities=14% Similarity=0.457 Sum_probs=17.2
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q psy3154 21 SLDERVHVK-MRNERVLRGKLHA 42 (101)
Q Consensus 21 ~l~k~V~V~-l~~gr~i~G~L~~ 42 (101)
.+|..|+|+ +..||.+.|++.+
T Consensus 110 ~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 110 GVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 367788884 7889999998765
No 133
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=23.66 E-value=78 Score=19.02 Aligned_cols=22 Identities=14% Similarity=0.469 Sum_probs=17.9
Q ss_pred CCEEEEEEcCCeEEEEEEEEEc
Q psy3154 23 DERVHVKMRNERVLRGKLHAYD 44 (101)
Q Consensus 23 ~k~V~V~l~~gr~i~G~L~~~D 44 (101)
..++.|+|-||..+.+++..-|
T Consensus 4 ~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 4 ETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred EEEEEEECCCCCEEEEEeCCCC
Confidence 4589999999999999976544
No 134
>PRK10708 hypothetical protein; Provisional
Probab=23.52 E-value=1e+02 Score=18.17 Aligned_cols=26 Identities=23% Similarity=0.285 Sum_probs=21.9
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCCC
Q psy3154 22 LDERVHVKMRNERVLRGKLHAYDQHL 47 (101)
Q Consensus 22 l~k~V~V~l~~gr~i~G~L~~~D~~m 47 (101)
++-+|.|++.++-.=.|++.++..|.
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 56799999999988889998888764
No 135
>PRK08183 NADH dehydrogenase; Validated
Probab=23.39 E-value=48 Score=22.63 Aligned_cols=19 Identities=16% Similarity=0.121 Sum_probs=15.7
Q ss_pred EEEEEEEcCCCceEecceE
Q psy3154 37 RGKLHAYDQHLNMVLGDVE 55 (101)
Q Consensus 37 ~G~L~~~D~~mNlvL~~~~ 55 (101)
.|+|+|-|++.|---++-.
T Consensus 25 ~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cCeEeEecCCCCeeeecCC
Confidence 5899999999998876543
No 136
>PF10894 DUF2689: Protein of unknown function (DUF2689); InterPro: IPR024396 Members of this protein family are annotated as conjugal transfer protein TrbD; however, currently no function is known.
Probab=23.06 E-value=11 Score=22.12 Aligned_cols=19 Identities=16% Similarity=0.291 Sum_probs=15.8
Q ss_pred EcCCCceEecceEEEEeec
Q psy3154 43 YDQHLNMVLGDVEETVTTV 61 (101)
Q Consensus 43 ~D~~mNlvL~~~~E~~~~~ 61 (101)
-|.||+-||+||.-.+..+
T Consensus 20 sDDFmhaVlSNCtTrIvLp 38 (61)
T PF10894_consen 20 SDDFMHAVLSNCTTRIVLP 38 (61)
T ss_pred cHHHHHHHHhcCceeEEec
Confidence 4899999999999877653
No 137
>PF01247 Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro: IPR001780 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal L35A eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of: Vertebrate L35A. Caenorhabditis elegans L35A (F10E7.7). Saccharomyces cerevisiae L37A/L37B (Rp47). Plant L35A. Pyrococcus woesei L35A homologue []. These proteins have 87 to 110 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_j 2LP6_A 1SQR_A 4A18_H 4A1D_H 4A19_H 4A1B_H 3IZS_j.
Probab=22.84 E-value=2e+02 Score=18.52 Aligned_cols=36 Identities=22% Similarity=0.263 Sum_probs=25.9
Q ss_pred HHHHhcCCEEEEEEc--------CCeEEEEEEEEEcCCCceEec
Q psy3154 17 LIRLSLDERVHVKMR--------NERVLRGKLHAYDQHLNMVLG 52 (101)
Q Consensus 17 lL~~~l~k~V~V~l~--------~gr~i~G~L~~~D~~mNlvL~ 52 (101)
--+.|+|++|...-+ .+|.+.|++.-.-..-.+|..
T Consensus 34 ~a~fylGKrv~yvyk~~~~~~~~k~r~iwGkV~r~HGnsGvVrA 77 (95)
T PF01247_consen 34 DAQFYLGKRVAYVYKAKNKKNGSKGRVIWGKVTRPHGNSGVVRA 77 (95)
T ss_dssp HHHTTTT-EEEEEECE-SSSTTECSEEEEEEEEEESTTTTEEEE
T ss_pred HHHhhcCcEEEEEEecccccCCCcEeEEEEEEEeEEcCCCEEEE
Confidence 345679999988877 579999999877655555543
No 138
>PF10618 Tail_tube: Phage tail tube protein; InterPro: IPR019596 This entry is represented by Bacteriophage Mu, GpM tail tube protein. Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube.
Probab=22.37 E-value=1.6e+02 Score=19.41 Aligned_cols=29 Identities=21% Similarity=0.139 Sum_probs=24.3
Q ss_pred cCChHHHHHHhcCCEEEEEEcCCeEEEEE
Q psy3154 11 VKEPLDLIRLSLDERVHVKMRNERVLRGK 39 (101)
Q Consensus 11 ~~~Pl~lL~~~l~k~V~V~l~~gr~i~G~ 39 (101)
...|++-|..+-+-.|.+.+.+|+.|.+.
T Consensus 62 ~~~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 62 KDTDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CCCCHHHHhCCcccEEEEEecCCcEEEec
Confidence 45678888888889999999999998765
No 139
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=22.16 E-value=83 Score=20.51 Aligned_cols=20 Identities=20% Similarity=0.326 Sum_probs=8.0
Q ss_pred EEEEEEEEEcCCCceEecce
Q psy3154 35 VLRGKLHAYDQHLNMVLGDV 54 (101)
Q Consensus 35 ~i~G~L~~~D~~mNlvL~~~ 54 (101)
++.|++.+||-..++.|++|
T Consensus 124 ti~G~~~g~~~~~~v~l~~c 143 (144)
T PF12869_consen 124 TIKGICTGYSLMGVVMLDDC 143 (144)
T ss_dssp EEEEE-----SSS-EEEE--
T ss_pred EEEEEEEeeecCCcEEeecc
Confidence 46788888875566666666
No 140
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=22.13 E-value=1.9e+02 Score=23.42 Aligned_cols=45 Identities=27% Similarity=0.241 Sum_probs=35.9
Q ss_pred CChHHHHHHhcCCEEEEEEcCCeEEEEEEEEEcCCCceEecceEEE
Q psy3154 12 KEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEET 57 (101)
Q Consensus 12 ~~Pl~lL~~~l~k~V~V~l~~gr~i~G~L~~~D~~mNlvL~~~~E~ 57 (101)
-.|-.++.+++||.|+- =++|++.+++|.+=|.-.=+-+.+-.|.
T Consensus 71 ~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v 115 (421)
T COG5316 71 LSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEV 115 (421)
T ss_pred cCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEE
Confidence 35677888999999998 8999999999999887666666665554
No 141
>PF11197 DUF2835: Protein of unknown function (DUF2835); InterPro: IPR021363 This is a bacterial family of uncharacterised proteins. One member of this family (A4VM42 from SWISSPROT) is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV).
Probab=21.90 E-value=1.9e+02 Score=17.40 Aligned_cols=24 Identities=13% Similarity=0.209 Sum_probs=19.0
Q ss_pred hHHHHHHhcC--CEEEEEEcCCeEEE
Q psy3154 14 PLDLIRLSLD--ERVHVKMRNERVLR 37 (101)
Q Consensus 14 Pl~lL~~~l~--k~V~V~l~~gr~i~ 37 (101)
+-++|..|-| +.|.|...|||.+.
T Consensus 9 ~~~~l~~Y~G~a~~V~v~s~~Gr~v~ 34 (68)
T PF11197_consen 9 YQEFLAYYQGAASKVVVRSDDGRRVQ 34 (68)
T ss_pred HHHHHHhccccccEEEEEecCCcEEE
Confidence 4567777777 69999999999865
No 142
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=21.83 E-value=97 Score=21.07 Aligned_cols=21 Identities=14% Similarity=0.267 Sum_probs=16.7
Q ss_pred hcCCEEEEEEcCCeEEEEEEE
Q psy3154 21 SLDERVHVKMRNERVLRGKLH 41 (101)
Q Consensus 21 ~l~k~V~V~l~~gr~i~G~L~ 41 (101)
++.|-++|.|.+|++++..+=
T Consensus 54 AlRK~~RVrL~NG~~VtAyiP 74 (129)
T COG0048 54 ALRKVARVRLINGKEVTAYIP 74 (129)
T ss_pred hhheeEEEEeeCCcEEEEEcC
Confidence 466789999999999986543
No 143
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=21.30 E-value=59 Score=20.07 Aligned_cols=18 Identities=28% Similarity=0.394 Sum_probs=14.5
Q ss_pred EEEcCCeEEEEecCCCCC
Q psy3154 82 LFVRGDGVILVSPPNRTP 99 (101)
Q Consensus 82 v~IRG~~Iv~I~~~~~~~ 99 (101)
+=.+|+|++.+.++||..
T Consensus 7 ~~~~G~n~~~V~~~dG~~ 24 (78)
T cd05792 7 LGSKGNNLHEVETPNGSR 24 (78)
T ss_pred EEcCCCcEEEEEcCCCCE
Confidence 346899999999998864
No 144
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.17 E-value=1e+02 Score=19.23 Aligned_cols=20 Identities=35% Similarity=0.428 Sum_probs=16.2
Q ss_pred HHHHHhcCCEEEEEEcCCeE
Q psy3154 16 DLIRLSLDERVHVKMRNERV 35 (101)
Q Consensus 16 ~lL~~~l~k~V~V~l~~gr~ 35 (101)
.-++..+|++|.++..+||.
T Consensus 12 ~~i~ah~G~~v~lk~ngGRK 31 (80)
T COG4466 12 ESIDAHLGERVTLKANGGRK 31 (80)
T ss_pred HHHHhccCcEEEEEecCCce
Confidence 34566689999999999975
No 145
>KOG4649|consensus
Probab=20.60 E-value=3.7e+02 Score=21.03 Aligned_cols=35 Identities=26% Similarity=0.313 Sum_probs=26.7
Q ss_pred HHHhcCCEEEEEEcCCeEEE------EEEEEEc-CCCceEec
Q psy3154 18 IRLSLDERVHVKMRNERVLR------GKLHAYD-QHLNMVLG 52 (101)
Q Consensus 18 L~~~l~k~V~V~l~~gr~i~------G~L~~~D-~~mNlvL~ 52 (101)
+.++++-.-.|.++|-+++. |+++++| +..|+.-+
T Consensus 7 ~~kCVDaspLVV~~dskT~v~igSHs~~~~avd~~sG~~~We 48 (354)
T KOG4649|consen 7 LRKCVDASPLVVCNDSKTLVVIGSHSGIVIAVDPQSGNLIWE 48 (354)
T ss_pred chhhccCCcEEEecCCceEEEEecCCceEEEecCCCCcEEee
Confidence 56788888888888887665 7899999 56676543
No 146
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=20.51 E-value=1.1e+02 Score=17.61 Aligned_cols=18 Identities=22% Similarity=0.311 Sum_probs=13.2
Q ss_pred HHHHHHhcCCEEEEEEcC
Q psy3154 15 LDLIRLSLDERVHVKMRN 32 (101)
Q Consensus 15 l~lL~~~l~k~V~V~l~~ 32 (101)
.+.=++|+|++|.|++.+
T Consensus 34 VdvPK~yiG~rv~viI~k 51 (52)
T COG3466 34 VDVPKRYIGKRVYVIILK 51 (52)
T ss_pred eeCchHHcCcEEEEEEeC
Confidence 445567899999987643
No 147
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=20.40 E-value=1.6e+02 Score=17.70 Aligned_cols=22 Identities=9% Similarity=0.132 Sum_probs=17.1
Q ss_pred CCEEEEEEcCCeEEEEEEEEEc
Q psy3154 23 DERVHVKMRNERVLRGKLHAYD 44 (101)
Q Consensus 23 ~k~V~V~l~~gr~i~G~L~~~D 44 (101)
+...+|.|.||.++.+.+.|==
T Consensus 17 ~~~f~V~l~ng~~vla~i~GKm 38 (68)
T TIGR00008 17 NAMFRVELENGHEVLAHISGKI 38 (68)
T ss_pred CCEEEEEECCCCEEEEEecCcc
Confidence 4688899999988888777643
No 148
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=20.23 E-value=1.6e+02 Score=15.81 Aligned_cols=25 Identities=12% Similarity=0.300 Sum_probs=21.0
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCC
Q psy3154 22 LDERVHVKMRNERVLRGKLHAYDQH 46 (101)
Q Consensus 22 l~k~V~V~l~~gr~i~G~L~~~D~~ 46 (101)
.|..+.+...+|.-|+|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5677777778899999999999964
Done!