Query 034340
Match_columns 97
No_of_seqs 119 out of 1075
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 12:24:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034340hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01720 Sm_D2 The eukaryotic S 99.9 1.7E-26 3.7E-31 145.4 10.6 85 10-94 1-87 (87)
2 cd01730 LSm3 The eukaryotic Sm 99.9 2.7E-26 5.8E-31 142.9 10.0 82 11-92 1-82 (82)
3 PRK00737 small nuclear ribonuc 99.9 5.7E-25 1.2E-29 133.9 9.8 70 10-92 3-72 (72)
4 cd01731 archaeal_Sm1 The archa 99.9 6.5E-25 1.4E-29 132.2 9.6 68 12-92 1-68 (68)
5 cd01732 LSm5 The eukaryotic Sm 99.9 1.9E-24 4.1E-29 133.0 10.5 74 10-93 2-75 (76)
6 cd01726 LSm6 The eukaryotic Sm 99.9 6.2E-24 1.4E-28 127.6 9.1 67 12-91 1-67 (67)
7 cd01719 Sm_G The eukaryotic Sm 99.9 1.2E-23 2.7E-28 128.2 9.5 71 12-95 1-71 (72)
8 cd01729 LSm7 The eukaryotic Sm 99.9 2.1E-23 4.6E-28 129.7 10.3 78 11-94 3-80 (81)
9 cd01722 Sm_F The eukaryotic Sm 99.9 2.5E-23 5.3E-28 125.4 8.6 68 11-91 1-68 (68)
10 cd01717 Sm_B The eukaryotic Sm 99.9 4.7E-23 1E-27 127.4 9.7 75 15-92 4-78 (79)
11 cd01718 Sm_E The eukaryotic Sm 99.9 1.4E-22 3E-27 125.5 9.6 74 7-92 2-79 (79)
12 cd01727 LSm8 The eukaryotic Sm 99.9 3.2E-22 6.8E-27 122.3 9.9 72 14-94 2-73 (74)
13 cd01728 LSm1 The eukaryotic Sm 99.9 5.1E-22 1.1E-26 121.7 10.5 71 12-92 3-73 (74)
14 cd06168 LSm9 The eukaryotic Sm 99.9 6.5E-22 1.4E-26 121.5 10.0 72 14-92 3-74 (75)
15 cd01721 Sm_D3 The eukaryotic S 99.9 7.5E-22 1.6E-26 119.6 9.5 70 12-94 1-70 (70)
16 PF01423 LSM: LSM domain ; In 99.9 7.9E-22 1.7E-26 117.6 8.9 67 14-92 1-67 (67)
17 smart00651 Sm snRNP Sm protein 99.9 2E-21 4.2E-26 115.8 9.4 66 15-92 2-67 (67)
18 COG1958 LSM1 Small nuclear rib 99.9 2.4E-21 5.3E-26 119.6 9.7 75 9-92 5-79 (79)
19 cd01723 LSm4 The eukaryotic Sm 99.9 2.3E-21 5E-26 119.1 9.5 73 11-95 1-73 (76)
20 KOG3460 Small nuclear ribonucl 99.9 1.1E-22 2.4E-27 125.6 2.3 90 8-97 2-91 (91)
21 PTZ00138 small nuclear ribonuc 99.8 1.4E-20 3.1E-25 118.8 10.2 78 4-93 7-88 (89)
22 cd01724 Sm_D1 The eukaryotic S 99.8 4.2E-20 9.1E-25 116.9 9.7 71 12-95 2-72 (90)
23 cd00600 Sm_like The eukaryotic 99.8 3.8E-20 8.2E-25 108.9 8.8 63 16-91 1-63 (63)
24 cd01733 LSm10 The eukaryotic S 99.8 9.8E-20 2.1E-24 112.5 9.6 74 7-93 5-78 (78)
25 cd01725 LSm2 The eukaryotic Sm 99.8 2.1E-19 4.6E-24 111.6 9.4 73 11-94 1-73 (81)
26 KOG1780 Small Nuclear ribonucl 99.8 5E-19 1.1E-23 107.2 5.9 71 10-95 5-75 (77)
27 KOG3482 Small nuclear ribonucl 99.8 1.1E-18 2.5E-23 105.3 6.2 74 8-94 5-78 (79)
28 KOG1781 Small Nuclear ribonucl 99.7 1.1E-18 2.3E-23 110.8 -1.0 84 5-94 12-95 (108)
29 KOG3168 U1 snRNP component [Tr 99.7 7.8E-18 1.7E-22 115.9 -0.2 81 9-93 3-83 (177)
30 KOG1783 Small nuclear ribonucl 99.7 1.8E-17 3.8E-22 100.2 1.0 74 8-94 3-76 (77)
31 KOG1775 U6 snRNA-associated Sm 99.6 2.8E-16 6.1E-21 95.8 3.9 76 8-93 4-79 (84)
32 KOG1774 Small nuclear ribonucl 99.6 3E-15 6.6E-20 92.2 4.5 78 4-93 5-86 (88)
33 KOG1784 Small Nuclear ribonucl 99.5 7.7E-15 1.7E-19 92.1 3.8 72 14-94 3-74 (96)
34 KOG1782 Small Nuclear ribonucl 99.5 2.2E-15 4.8E-20 99.0 -0.5 70 16-95 14-83 (129)
35 KOG3459 Small nuclear ribonucl 99.5 6.7E-15 1.5E-19 95.1 -0.1 89 4-92 17-107 (114)
36 KOG3293 Small nuclear ribonucl 99.4 4.3E-13 9.3E-18 88.4 6.1 72 11-94 2-73 (134)
37 KOG3448 Predicted snRNP core p 99.4 5.3E-12 1.2E-16 79.0 8.0 70 13-93 4-73 (96)
38 KOG3172 Small nuclear ribonucl 99.3 1.5E-11 3.3E-16 79.4 6.8 74 8-94 2-75 (119)
39 cd01739 LSm11_C The eukaryotic 98.9 5.5E-10 1.2E-14 66.5 2.8 37 22-58 9-49 (66)
40 KOG3428 Small nuclear ribonucl 98.8 2.7E-08 5.9E-13 64.4 8.2 68 13-94 4-71 (109)
41 PF14438 SM-ATX: Ataxin 2 SM d 98.2 1E-05 2.2E-10 49.2 6.3 70 13-88 4-76 (77)
42 PF12701 LSM14: Scd6-like Sm d 96.9 0.0075 1.6E-07 38.5 6.9 73 17-93 4-77 (96)
43 PF02237 BPL_C: Biotin protein 96.7 0.0097 2.1E-07 33.0 5.9 34 20-54 2-35 (48)
44 TIGR02383 Hfq RNA chaperone Hf 96.7 0.0071 1.5E-07 35.7 5.2 32 20-51 14-45 (61)
45 cd01716 Hfq Hfq, an abundant, 96.7 0.0075 1.6E-07 35.6 5.2 32 20-51 10-41 (61)
46 PRK00395 hfq RNA-binding prote 96.4 0.012 2.7E-07 36.4 5.2 33 20-52 18-50 (79)
47 PF11095 Gemin7: Gem-associate 96.4 0.024 5.3E-07 35.1 6.5 64 12-93 15-79 (80)
48 cd01735 LSm12_N LSm12 belongs 96.3 0.015 3.2E-07 34.3 4.9 34 19-52 4-37 (61)
49 cd01736 LSm14_N LSm14 (also kn 95.8 0.085 1.8E-06 32.3 6.9 69 18-89 3-72 (74)
50 PF06372 Gemin6: Gemin6 protei 95.4 0.048 1E-06 38.1 5.4 43 10-54 7-50 (166)
51 COG1923 Hfq Uncharacterized ho 95.3 0.056 1.2E-06 33.2 4.6 29 20-48 18-46 (77)
52 PRK14091 RNA-binding protein H 95.1 0.05 1.1E-06 37.9 4.6 33 20-52 103-135 (165)
53 PRK14638 hypothetical protein; 94.5 0.13 2.7E-06 35.2 5.4 37 12-50 92-128 (150)
54 PF10842 DUF2642: Protein of u 93.8 0.56 1.2E-05 28.0 6.5 54 13-92 13-66 (66)
55 PRK02001 hypothetical protein; 93.3 0.28 6E-06 33.7 5.3 37 12-50 82-118 (152)
56 PRK14091 RNA-binding protein H 93.3 0.27 5.8E-06 34.3 5.1 32 21-52 24-55 (165)
57 PRK14639 hypothetical protein; 93.0 0.34 7.3E-06 32.7 5.3 32 17-49 84-115 (140)
58 PRK14644 hypothetical protein; 91.0 0.86 1.9E-05 30.7 5.4 34 16-50 80-117 (136)
59 PF03614 Flag1_repress: Repres 89.9 0.91 2E-05 31.4 4.8 34 20-53 28-61 (165)
60 PRK14640 hypothetical protein; 89.9 1.2 2.6E-05 30.4 5.4 37 12-50 89-129 (152)
61 PRK14642 hypothetical protein; 89.8 1.1 2.4E-05 32.1 5.4 26 19-44 98-136 (197)
62 cd01734 YlxS_C YxlS is a Bacil 89.7 1.5 3.2E-05 26.8 5.3 32 18-50 22-57 (83)
63 PRK14633 hypothetical protein; 89.5 1.3 2.9E-05 30.1 5.4 33 17-50 90-126 (150)
64 PRK14645 hypothetical protein; 89.4 1.2 2.5E-05 30.7 5.1 35 13-50 95-129 (154)
65 PRK14636 hypothetical protein; 88.7 1.4 3E-05 30.9 5.2 37 12-50 90-130 (176)
66 COG0779 Uncharacterized protei 88.4 1.9 4E-05 29.8 5.6 33 16-49 94-130 (153)
67 PF02576 DUF150: Uncharacteris 87.5 1.4 3E-05 29.4 4.5 34 15-49 81-118 (141)
68 PRK14643 hypothetical protein; 87.0 2.2 4.7E-05 29.6 5.3 28 17-44 100-131 (164)
69 PF14563 DUF4444: Domain of un 86.9 1.1 2.4E-05 24.4 2.9 24 34-57 10-33 (42)
70 PRK14632 hypothetical protein; 86.8 2.2 4.8E-05 29.7 5.3 32 18-50 95-133 (172)
71 PRK14634 hypothetical protein; 86.8 2.3 5.1E-05 29.1 5.3 36 12-49 92-131 (155)
72 PRK00092 ribosome maturation p 86.6 2.6 5.6E-05 28.6 5.4 27 17-43 94-124 (154)
73 PRK14646 hypothetical protein; 86.0 2.7 5.8E-05 28.8 5.3 35 13-49 93-131 (155)
74 PRK14647 hypothetical protein; 85.0 3.3 7.2E-05 28.4 5.4 26 18-43 96-130 (159)
75 PRK14631 hypothetical protein; 84.7 3.2 6.9E-05 29.1 5.2 32 17-49 113-150 (174)
76 KOG1073 Uncharacterized mRNA-a 84.6 3.9 8.4E-05 31.9 6.1 75 16-93 4-79 (361)
77 PRK06955 biotin--protein ligas 84.3 2.7 5.8E-05 31.5 5.1 33 19-51 247-279 (300)
78 PRK14637 hypothetical protein; 82.4 4.3 9.4E-05 27.7 5.1 32 18-50 95-127 (151)
79 PRK14641 hypothetical protein; 81.3 4.6 9.9E-05 28.3 4.9 26 17-42 100-129 (173)
80 PRK11886 bifunctional biotin-- 81.1 8.4 0.00018 28.8 6.7 31 19-50 270-300 (319)
81 PRK13325 bifunctional biotin-- 79.3 7.5 0.00016 32.0 6.3 33 19-51 276-308 (592)
82 PF03614 Flag1_repress: Repres 77.4 2.9 6.3E-05 29.0 2.9 33 12-44 109-143 (165)
83 PRK10898 serine endoprotease; 77.0 6.2 0.00013 30.2 4.9 32 22-53 102-133 (353)
84 PF11607 DUF3247: Protein of u 76.9 6.5 0.00014 25.2 4.2 17 22-38 29-45 (101)
85 TIGR02038 protease_degS peripl 75.8 6.8 0.00015 29.9 4.9 32 22-53 102-133 (351)
86 COG0340 BirA Biotin-(acetyl-Co 75.1 17 0.00037 26.5 6.6 33 20-52 189-221 (238)
87 PTZ00275 biotin-acetyl-CoA-car 75.0 8.5 0.00018 28.7 5.1 31 20-51 236-266 (285)
88 TIGR00121 birA_ligase birA, bi 74.9 8.5 0.00018 27.6 5.0 30 20-50 192-221 (237)
89 PRK10942 serine endoprotease; 72.7 8.4 0.00018 30.8 4.8 31 22-52 136-166 (473)
90 PRK08330 biotin--protein ligas 72.6 12 0.00025 26.9 5.2 33 19-52 186-219 (236)
91 PRK10139 serine endoprotease; 71.2 10 0.00022 30.2 4.9 32 22-53 115-146 (455)
92 KOG3382 NADH:ubiquinone oxidor 69.0 2.8 6E-05 28.5 1.2 23 31-53 42-64 (151)
93 PRK14635 hypothetical protein; 66.9 20 0.00043 24.6 5.1 37 11-49 90-131 (162)
94 TIGR02037 degP_htrA_DO peripla 66.0 15 0.00031 28.7 4.8 32 22-53 82-113 (428)
95 PRK14630 hypothetical protein; 62.2 26 0.00057 23.6 5.0 31 17-49 93-123 (143)
96 PRK09618 flgD flagellar basal 59.4 43 0.00094 22.8 5.6 26 17-42 88-113 (142)
97 PF05071 NDUFA12: NADH ubiquin 56.2 7.7 0.00017 24.8 1.5 17 36-52 1-17 (105)
98 PF11743 DUF3301: Protein of u 54.6 12 0.00026 23.6 2.1 22 73-94 75-96 (97)
99 PF14153 Spore_coat_CotO: Spor 52.4 24 0.00051 25.0 3.6 32 13-44 123-157 (185)
100 PRK08477 biotin--protein ligas 48.4 77 0.0017 22.7 5.8 36 18-54 172-207 (211)
101 PF06257 DUF1021: Protein of u 47.6 63 0.0014 19.7 4.5 29 13-41 9-41 (76)
102 PF07073 ROF: Modulator of Rho 47.4 20 0.00043 22.0 2.3 17 21-37 17-33 (80)
103 TIGR02603 CxxCH_TIGR02603 puta 46.9 35 0.00075 22.3 3.5 30 22-52 58-87 (133)
104 KOG4401 Uncharacterized conser 43.8 33 0.00072 24.4 3.2 34 20-53 10-43 (184)
105 COG5316 Uncharacterized conser 42.4 73 0.0016 25.4 5.2 46 10-56 71-116 (421)
106 PRK06630 hypothetical protein; 42.1 15 0.00033 23.6 1.1 19 34-52 11-29 (99)
107 PF14485 DUF4431: Domain of un 40.6 34 0.00074 18.9 2.3 15 13-27 11-25 (48)
108 TIGR03170 flgA_cterm flagella 39.8 41 0.00089 21.3 3.0 22 19-40 94-116 (122)
109 PRK11911 flgD flagellar basal 38.8 67 0.0014 21.8 4.0 26 17-42 89-114 (140)
110 cd04479 RPA3 RPA3: A subfamily 38.4 99 0.0021 19.3 4.6 15 13-27 7-21 (101)
111 PLN03095 NADH:ubiquinone oxido 35.9 23 0.00049 23.4 1.3 19 35-53 9-27 (115)
112 smart00166 UBX Domain present 35.1 39 0.00084 20.0 2.2 22 22-43 5-26 (80)
113 PF01887 SAM_adeno_trans: S-ad 35.0 59 0.0013 24.0 3.5 18 33-50 169-186 (258)
114 PTZ00276 biotin/lipoate protei 33.6 80 0.0017 22.9 4.0 23 29-51 209-231 (245)
115 cd08057 MPN_euk_non_mb Mpr1p, 33.3 84 0.0018 20.9 3.8 28 30-57 21-48 (157)
116 COG0265 DegQ Trypsin-like seri 32.7 98 0.0021 23.2 4.5 32 22-53 96-127 (347)
117 PF11197 DUF2835: Protein of u 32.7 90 0.0019 18.6 3.4 25 11-35 8-34 (68)
118 PRK07018 flgA flagellar basal 32.3 56 0.0012 23.5 3.0 22 19-40 205-227 (235)
119 PRK11625 Rho-binding antitermi 31.1 96 0.0021 19.2 3.5 32 20-57 22-53 (84)
120 PF09465 LBR_tudor: Lamin-B re 30.6 1.1E+02 0.0024 17.5 3.5 26 19-44 7-33 (55)
121 cd01767 UBX UBX (ubiquitin reg 30.6 58 0.0013 19.0 2.4 22 22-43 3-24 (77)
122 cd01772 SAKS1_UBX SAKS1-like U 30.6 41 0.0009 20.0 1.8 23 20-42 3-25 (79)
123 PLN02732 Probable NADH dehydro 30.1 47 0.001 23.1 2.2 19 35-53 48-66 (159)
124 PF03122 Herpes_MCP: Herpes vi 29.6 18 0.00039 32.9 0.0 56 23-89 249-304 (1354)
125 PRK10708 hypothetical protein; 29.3 71 0.0015 18.6 2.5 26 20-45 3-28 (62)
126 PF00789 UBX: UBX domain; Int 28.4 68 0.0015 18.7 2.5 22 22-43 7-28 (82)
127 PF10894 DUF2689: Protein of u 28.1 8.1 0.00018 22.4 -1.6 19 41-59 20-38 (61)
128 PRK08183 NADH dehydrogenase; V 27.6 36 0.00078 22.9 1.2 19 35-53 25-43 (133)
129 PRK06789 flagellar motor switc 26.5 1.4E+02 0.003 18.0 3.6 35 17-51 37-71 (74)
130 KOG3493 Ubiquitin-like protein 26.2 59 0.0013 19.5 1.8 20 15-34 5-24 (73)
131 PRK06792 flgD flagellar basal 26.1 1.3E+02 0.0028 21.6 3.8 26 17-42 114-139 (190)
132 COG1886 FliN Flagellar motor s 26.1 1.2E+02 0.0027 20.1 3.6 32 19-50 103-134 (136)
133 PF10781 DSRB: Dextransucrase 25.3 82 0.0018 18.3 2.3 26 20-45 3-28 (62)
134 PF11620 GABP-alpha: GA-bindin 25.1 8.6 0.00019 24.2 -2.0 41 7-48 9-49 (88)
135 COG0048 RpsL Ribosomal protein 25.0 88 0.0019 21.0 2.7 20 18-37 53-72 (129)
136 COG1363 FrvX Cellulase M and r 24.3 93 0.002 24.3 3.1 21 19-39 95-115 (355)
137 PRK06005 flgA flagellar basal 24.3 1E+02 0.0023 21.0 3.1 22 19-40 129-151 (160)
138 PF05735 TSP_C: Thrombospondin 23.5 2.8E+02 0.0061 20.0 5.2 33 23-55 4-43 (201)
139 PRK12617 flgA flagellar basal 23.4 1.1E+02 0.0023 22.1 3.1 22 19-40 184-206 (214)
140 COG4466 Veg Uncharacterized pr 22.6 95 0.0021 19.2 2.3 22 14-35 12-33 (80)
141 smart00333 TUDOR Tudor domain. 22.6 1.4E+02 0.003 15.9 4.8 25 20-44 5-29 (57)
142 PF05954 Phage_GPD: Phage late 22.4 1.1E+02 0.0024 21.6 3.1 24 19-42 26-49 (292)
143 PF12869 tRNA_anti-like: tRNA_ 21.5 95 0.0021 20.0 2.4 20 33-52 124-143 (144)
144 PRK04337 50S ribosomal protein 20.7 2.3E+02 0.005 17.7 3.8 34 15-48 34-67 (87)
145 PF07202 Tcp10_C: T-complex pr 20.4 2E+02 0.0043 20.2 3.9 32 19-50 142-177 (179)
146 cd01770 p47_UBX p47-like ubiqu 20.3 1.1E+02 0.0023 18.4 2.2 21 22-42 5-25 (79)
147 PRK09961 exoaminopeptidase; Pr 20.2 1.3E+02 0.0028 23.0 3.1 22 18-39 91-112 (344)
No 1
>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=1.7e-26 Score=145.38 Aligned_cols=85 Identities=29% Similarity=0.518 Sum_probs=70.5
Q ss_pred CCcHHHHHHhC--CCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcE
Q 034340 10 KEPLDLIRLSL--DERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGV 87 (97)
Q Consensus 10 ~~P~~lL~~~l--~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I 87 (97)
.+|+++|+.++ +++|.|+|++|+.+.|+|.|||+||||+|+||.|.+...++++++.+.......+++|.+||||++|
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 48999999997 7999999999999999999999999999999999987644332211122235678899999999999
Q ss_pred EEEecCC
Q 034340 88 ILVSPPL 94 (97)
Q Consensus 88 v~I~~~~ 94 (97)
++|+..|
T Consensus 81 v~Is~~~ 87 (87)
T cd01720 81 ILVLRNP 87 (87)
T ss_pred EEEecCC
Confidence 9998754
No 2
>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=2.7e-26 Score=142.89 Aligned_cols=82 Identities=85% Similarity=1.328 Sum_probs=67.6
Q ss_pred CcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEE
Q 034340 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILV 90 (97)
Q Consensus 11 ~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 90 (97)
.|+++|+.+++++|.|+|+|||.|.|+|.|||+||||+|+||.|++.....+++..+.......|.+|.+||||++|++|
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 49999999999999999999999999999999999999999999987543221111111224678999999999999999
Q ss_pred ec
Q 034340 91 SP 92 (97)
Q Consensus 91 ~~ 92 (97)
++
T Consensus 81 ~~ 82 (82)
T cd01730 81 SP 82 (82)
T ss_pred CC
Confidence 74
No 3
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.92 E-value=5.7e-25 Score=133.94 Aligned_cols=70 Identities=37% Similarity=0.740 Sum_probs=63.7
Q ss_pred CCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEE
Q 034340 10 KEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVIL 89 (97)
Q Consensus 10 ~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 89 (97)
..|+++|+++++++|+|+|+||+.|.|+|.|||+||||+|+||.|.+.. ...+.+|.++|||++|++
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 5899999999999999999999999999999999999999999997531 245789999999999999
Q ss_pred Eec
Q 034340 90 VSP 92 (97)
Q Consensus 90 I~~ 92 (97)
|++
T Consensus 70 i~~ 72 (72)
T PRK00737 70 VSP 72 (72)
T ss_pred EcC
Confidence 974
No 4
>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=6.5e-25 Score=132.16 Aligned_cols=68 Identities=41% Similarity=0.786 Sum_probs=62.6
Q ss_pred cHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEe
Q 034340 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVS 91 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 91 (97)
|+++|+.+++++|+|+|++|+.|.|+|.|||+||||+|+||.|++.. ...+.+|.++|||++|++|+
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 24578999999999999997
Q ss_pred c
Q 034340 92 P 92 (97)
Q Consensus 92 ~ 92 (97)
+
T Consensus 68 ~ 68 (68)
T cd01731 68 P 68 (68)
T ss_pred C
Confidence 5
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=1.9e-24 Score=133.02 Aligned_cols=74 Identities=28% Similarity=0.542 Sum_probs=65.4
Q ss_pred CCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEE
Q 034340 10 KEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVIL 89 (97)
Q Consensus 10 ~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 89 (97)
..|+++|+++++++|+|++++||++.|+|.|||+||||+|+||.|++..+ ++ ...+.+|.++|||++|++
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 36999999999999999999999999999999999999999999987421 11 245789999999999999
Q ss_pred EecC
Q 034340 90 VSPP 93 (97)
Q Consensus 90 I~~~ 93 (97)
|++.
T Consensus 72 i~p~ 75 (76)
T cd01732 72 LVPG 75 (76)
T ss_pred EECC
Confidence 9964
No 6
>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=99.91 E-value=6.2e-24 Score=127.64 Aligned_cols=67 Identities=28% Similarity=0.476 Sum_probs=60.9
Q ss_pred cHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEe
Q 034340 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVS 91 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 91 (97)
|+++|+++++++|+|+|++|++|+|+|.|||+||||+|+||+|.... ...+.+|.++|||++|++|+
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 7
>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=99.91 E-value=1.2e-23 Score=128.15 Aligned_cols=71 Identities=21% Similarity=0.495 Sum_probs=63.2
Q ss_pred cHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEe
Q 034340 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVS 91 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 91 (97)
|-..|+++++|+|+|.|++|++|.|+|.|||+||||+|+||.|+... ...+.+|.++|||++|++|+
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 45689999999999999999999999999999999999999998632 24578999999999999999
Q ss_pred cCCC
Q 034340 92 PPLR 95 (97)
Q Consensus 92 ~~~~ 95 (97)
+.++
T Consensus 68 ~~~~ 71 (72)
T cd01719 68 ALER 71 (72)
T ss_pred cccc
Confidence 8754
No 8
>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=99.90 E-value=2.1e-23 Score=129.71 Aligned_cols=78 Identities=32% Similarity=0.500 Sum_probs=63.3
Q ss_pred CcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEE
Q 034340 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILV 90 (97)
Q Consensus 11 ~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 90 (97)
.+++ |.++++++|+|.|+|||.|.|+|.|||+||||+|+||.|+...+..+ .......+.+|.++|||+||++|
T Consensus 3 ~~~~-L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~-----~~~~~~~~~lG~v~iRG~nV~~i 76 (81)
T cd01729 3 SILD-LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDP-----YKLTDKTRQLGLVVCRGTSVVLI 76 (81)
T ss_pred chhh-HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcc-----cccccceeEccEEEEcCCEEEEE
Confidence 3455 78889999999999999999999999999999999999987542100 01123567899999999999999
Q ss_pred ecCC
Q 034340 91 SPPL 94 (97)
Q Consensus 91 ~~~~ 94 (97)
++.+
T Consensus 77 ~~~~ 80 (81)
T cd01729 77 SPVD 80 (81)
T ss_pred ecCC
Confidence 8764
No 9
>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=99.90 E-value=2.5e-23 Score=125.41 Aligned_cols=68 Identities=21% Similarity=0.360 Sum_probs=61.1
Q ss_pred CcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEE
Q 034340 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILV 90 (97)
Q Consensus 11 ~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 90 (97)
.|+++|+++++++|+|+|+||++|.|+|.|||+||||+|+||+|.... .....+|.++|||++|++|
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 2356789999999999998
Q ss_pred e
Q 034340 91 S 91 (97)
Q Consensus 91 ~ 91 (97)
+
T Consensus 68 ~ 68 (68)
T cd01722 68 R 68 (68)
T ss_pred C
Confidence 4
No 10
>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=4.7e-23 Score=127.36 Aligned_cols=75 Identities=24% Similarity=0.500 Sum_probs=62.1
Q ss_pred HHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEec
Q 034340 15 LIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSP 92 (97)
Q Consensus 15 lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 92 (97)
-|..|++++|+|+|+|||.|.|+|.|||+||||+|+||.|++...+.++ ......+.+.+|.+||||++|++|+.
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~---~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKS---KNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEecccccc---ccccCcceeEeeeEEEcCCEEEEEEE
Confidence 4778899999999999999999999999999999999999886543210 01112467899999999999999975
No 11
>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=99.89 E-value=1.4e-22 Score=125.54 Aligned_cols=74 Identities=27% Similarity=0.522 Sum_probs=64.2
Q ss_pred cccCCcHHHHHHhCCC--eEEEEEc--CCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEE
Q 034340 7 SAVKEPLDLIRLSLDE--RIYVKLR--SDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFV 82 (97)
Q Consensus 7 ~~~~~P~~lL~~~l~k--~V~V~l~--~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~I 82 (97)
+.+..|+++|.+++++ +|.|+++ +|+.+.|+|.|||+||||+|+||+|+... ....+.+|.++|
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 4578999999999998 7777776 89999999999999999999999998642 124577999999
Q ss_pred cCCcEEEEec
Q 034340 83 RGDGVILVSP 92 (97)
Q Consensus 83 RG~~Iv~I~~ 92 (97)
||+||++|++
T Consensus 70 RGnnV~~I~p 79 (79)
T cd01718 70 KGDNITLIQN 79 (79)
T ss_pred eCCEEEEEcC
Confidence 9999999984
No 12
>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=3.2e-22 Score=122.35 Aligned_cols=72 Identities=24% Similarity=0.367 Sum_probs=61.8
Q ss_pred HHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEecC
Q 034340 14 DLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSPP 93 (97)
Q Consensus 14 ~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 93 (97)
+.|.++++++|+|+++|||.|.|+|.|||+||||+|++|.|+...+. + ....+.+|.++|||++|++|++.
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 45888899999999999999999999999999999999999864321 1 12467899999999999999976
Q ss_pred C
Q 034340 94 L 94 (97)
Q Consensus 94 ~ 94 (97)
+
T Consensus 73 d 73 (74)
T cd01727 73 D 73 (74)
T ss_pred C
Confidence 4
No 13
>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=5.1e-22 Score=121.68 Aligned_cols=71 Identities=27% Similarity=0.428 Sum_probs=61.7
Q ss_pred cHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEe
Q 034340 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVS 91 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 91 (97)
+...|.++++++|.|.|+|||.|.|+|.|||+||||+|+||.|+..... ...++.+|.++|||++|++|+
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 123578999999999999998
Q ss_pred c
Q 034340 92 P 92 (97)
Q Consensus 92 ~ 92 (97)
.
T Consensus 73 ~ 73 (74)
T cd01728 73 E 73 (74)
T ss_pred c
Confidence 5
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=99.88 E-value=6.5e-22 Score=121.47 Aligned_cols=72 Identities=19% Similarity=0.331 Sum_probs=62.5
Q ss_pred HHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEec
Q 034340 14 DLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSP 92 (97)
Q Consensus 14 ~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 92 (97)
+-|+++++++|+|+|+|||.|.|+|.|||+||||+|+||.|++..+... .....|.+|+++|||++|++|+.
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 4688899999999999999999999999999999999999998653211 12467899999999999999974
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=99.88 E-value=7.5e-22 Score=119.61 Aligned_cols=70 Identities=21% Similarity=0.361 Sum_probs=62.2
Q ss_pred cHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEe
Q 034340 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVS 91 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 91 (97)
|+++|+.+.|++|+|+|++|.+|+|+|.++|.|||++|+||.+.... + ....+|.+||||+||.+|.
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~----g---------~~~~~~~v~IRG~nI~~v~ 67 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARD----G---------RVSQLEQVYIRGSKIRFFI 67 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCC----C---------cEeEcCcEEEeCCEEEEEE
Confidence 88999999999999999999999999999999999999999875321 1 2356799999999999999
Q ss_pred cCC
Q 034340 92 PPL 94 (97)
Q Consensus 92 ~~~ 94 (97)
.|+
T Consensus 68 lPd 70 (70)
T cd01721 68 LPD 70 (70)
T ss_pred eCC
Confidence 885
No 16
>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=99.87 E-value=7.9e-22 Score=117.64 Aligned_cols=67 Identities=28% Similarity=0.627 Sum_probs=60.7
Q ss_pred HHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEec
Q 034340 14 DLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSP 92 (97)
Q Consensus 14 ~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 92 (97)
++|+++++++|+|.|+||+.|+|+|.+||+||||+|+||.|.+... ...+++|.+||||++|++|++
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 4789999999999999999999999999999999999999987531 157889999999999999975
No 17
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.87 E-value=2e-21 Score=115.83 Aligned_cols=66 Identities=32% Similarity=0.690 Sum_probs=59.7
Q ss_pred HHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEec
Q 034340 15 LIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSP 92 (97)
Q Consensus 15 lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 92 (97)
+|+.+++++|+|.|+||+.+.|+|.+||+||||+|+||.|++... ...+.+|.+||||++|++|++
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 688999999999999999999999999999999999999987531 356889999999999999974
No 18
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.86 E-value=2.4e-21 Score=119.57 Aligned_cols=75 Identities=40% Similarity=0.744 Sum_probs=62.8
Q ss_pred cCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEE
Q 034340 9 VKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVI 88 (97)
Q Consensus 9 ~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv 88 (97)
...|+++|+.+++++|.|+|++|++|.|+|.|||+||||+|+||.|.... +++ ....+..+.++|||++|+
T Consensus 5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~------~~~~~~~~~~~IRG~~I~ 75 (79)
T COG1958 5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH---DGE------KNVRRLGGEVLIRGDNIV 75 (79)
T ss_pred cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc---CCc------cccceeccEEEEECCcEE
Confidence 45689999999999999999999999999999999999999999998741 110 002345559999999999
Q ss_pred EEec
Q 034340 89 LVSP 92 (97)
Q Consensus 89 ~I~~ 92 (97)
+|.+
T Consensus 76 ~I~~ 79 (79)
T COG1958 76 LISP 79 (79)
T ss_pred EEeC
Confidence 9964
No 19
>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=2.3e-21 Score=119.08 Aligned_cols=73 Identities=22% Similarity=0.393 Sum_probs=63.5
Q ss_pred CcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEE
Q 034340 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILV 90 (97)
Q Consensus 11 ~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 90 (97)
.|+++|+.+.|++|.|+|++|+.|+|+|.+||.|||++|+||++... ++ .....++.+||||++|.+|
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 39999999999999999999999999999999999999999998632 11 1235579999999999999
Q ss_pred ecCCC
Q 034340 91 SPPLR 95 (97)
Q Consensus 91 ~~~~~ 95 (97)
..|+.
T Consensus 69 ~~p~~ 73 (76)
T cd01723 69 RVPDE 73 (76)
T ss_pred EcCHH
Confidence 98763
No 20
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.86 E-value=1.1e-22 Score=125.63 Aligned_cols=90 Identities=80% Similarity=1.258 Sum_probs=77.0
Q ss_pred ccCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcE
Q 034340 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGV 87 (97)
Q Consensus 8 ~~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I 87 (97)
.+..|+++|+-+++.+|.|+++++|+++|+|.|||+|.||+|.|+.|.+.....++.+..+.....+|.+..+|+||++|
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 35689999999999999999999999999999999999999999999987655443333333446778899999999999
Q ss_pred EEEecCCCCC
Q 034340 88 ILVSPPLRTA 97 (97)
Q Consensus 88 v~I~~~~~~~ 97 (97)
++|++|.+.+
T Consensus 82 ilvspp~~~~ 91 (91)
T KOG3460|consen 82 ILVSPPLRLD 91 (91)
T ss_pred EEEcCcccCC
Confidence 9999997753
No 21
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.85 E-value=1.4e-20 Score=118.78 Aligned_cols=78 Identities=27% Similarity=0.506 Sum_probs=66.3
Q ss_pred ccccccCCcHHHHHHhCCC--eEEEEEcC--CeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCe
Q 034340 4 EEESAVKEPLDLIRLSLDE--RIYVKLRS--DRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPF 79 (97)
Q Consensus 4 ~~~~~~~~P~~lL~~~l~k--~V~V~l~~--gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~ 79 (97)
+-++-+..|+..+.+++.. +|.|++.+ ++.|.|+|.|||+||||+|+||+|++... ...+.+|.
T Consensus 7 ~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~------------~~~~~lG~ 74 (89)
T PTZ00138 7 KLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKK------------NTRKDLGR 74 (89)
T ss_pred ccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCC------------ceeeEcCe
Confidence 4456778999999999984 88888877 58999999999999999999999976421 24678999
Q ss_pred EEEcCCcEEEEecC
Q 034340 80 LFVRGDGVILVSPP 93 (97)
Q Consensus 80 v~IRG~~Iv~I~~~ 93 (97)
++|||+||++|++.
T Consensus 75 ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 75 ILLKGDNITLIMAA 88 (89)
T ss_pred EEEcCCEEEEEEcC
Confidence 99999999999875
No 22
>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=99.83 E-value=4.2e-20 Score=116.93 Aligned_cols=71 Identities=15% Similarity=0.256 Sum_probs=63.7
Q ss_pred cHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEe
Q 034340 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVS 91 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 91 (97)
|+.+|+++.|++|+|+|++|..|+|+|.++|.|||++|+||++.... .....+|.++|||++|.+|.
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 67899999999999999999999999999999999999999887432 23567899999999999999
Q ss_pred cCCC
Q 034340 92 PPLR 95 (97)
Q Consensus 92 ~~~~ 95 (97)
.|+.
T Consensus 69 lPd~ 72 (90)
T cd01724 69 LPDS 72 (90)
T ss_pred cCCc
Confidence 9864
No 23
>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=99.83 E-value=3.8e-20 Score=108.85 Aligned_cols=63 Identities=33% Similarity=0.624 Sum_probs=57.0
Q ss_pred HHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEe
Q 034340 16 IRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVS 91 (97)
Q Consensus 16 L~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 91 (97)
|+.++|++|+|.|+||+.|.|+|.|||+|||++|+||.+.+.. ...+.+|.+||||++|++|.
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 5678999999999999999999999999999999999998753 24688999999999999984
No 24
>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=99.82 E-value=9.8e-20 Score=112.52 Aligned_cols=74 Identities=19% Similarity=0.273 Sum_probs=63.5
Q ss_pred cccCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCc
Q 034340 7 SAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDG 86 (97)
Q Consensus 7 ~~~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~ 86 (97)
..-..+..+|+.+.|+.|.|+|++|..|+|+|.++|.|||++|+||.+.... .....+|.++|||++
T Consensus 5 ~~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~-------------~~~~~~~~v~IRG~n 71 (78)
T cd01733 5 LLENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN-------------GKQVQVEEIMVTGRN 71 (78)
T ss_pred hhhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC-------------CceeECCcEEEECCE
Confidence 3344678999999999999999999999999999999999999999865321 133478999999999
Q ss_pred EEEEecC
Q 034340 87 VILVSPP 93 (97)
Q Consensus 87 Iv~I~~~ 93 (97)
|.+|..|
T Consensus 72 I~yI~lP 78 (78)
T cd01733 72 IRYVHIP 78 (78)
T ss_pred EEEEEcC
Confidence 9999876
No 25
>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=2.1e-19 Score=111.64 Aligned_cols=73 Identities=26% Similarity=0.359 Sum_probs=62.0
Q ss_pred CcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEE
Q 034340 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILV 90 (97)
Q Consensus 11 ~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 90 (97)
.|+.+|+++.|++|.|+|++|..|+|+|.++|.|||++|+||++..... ......++.++|||++|.+|
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~-----------~~~~~~~~~v~IRG~~I~~I 69 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEK-----------YPHMLSVKNCFIRGSVVRYV 69 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCC-----------cccccccCeEEEECCEEEEE
Confidence 3789999999999999999999999999999999999999997663210 01234568999999999999
Q ss_pred ecCC
Q 034340 91 SPPL 94 (97)
Q Consensus 91 ~~~~ 94 (97)
..|+
T Consensus 70 ~lp~ 73 (81)
T cd01725 70 QLPA 73 (81)
T ss_pred EeCh
Confidence 9885
No 26
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.78 E-value=5e-19 Score=107.19 Aligned_cols=71 Identities=24% Similarity=0.524 Sum_probs=62.3
Q ss_pred CCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEE
Q 034340 10 KEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVIL 89 (97)
Q Consensus 10 ~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 89 (97)
..| -|++|++|++.++|.+||.+.|.|.|||.|||+||+++.|.... ..+..+|.++|||++|+.
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 356 78999999999999999999999999999999999999997432 235678999999999999
Q ss_pred EecCCC
Q 034340 90 VSPPLR 95 (97)
Q Consensus 90 I~~~~~ 95 (97)
+.+-++
T Consensus 70 ~eaL~~ 75 (77)
T KOG1780|consen 70 VEALER 75 (77)
T ss_pred Eeeccc
Confidence 987665
No 27
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.77 E-value=1.1e-18 Score=105.32 Aligned_cols=74 Identities=19% Similarity=0.311 Sum_probs=66.1
Q ss_pred ccCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcE
Q 034340 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGV 87 (97)
Q Consensus 8 ~~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I 87 (97)
...+|..+|+.+.+++|.|+|+.|.+|.|+|++.|.||||.|.+|+|++.. ...-.+|.++||++||
T Consensus 5 ~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-------------~~~g~lGEilIRCNNv 71 (79)
T KOG3482|consen 5 QPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-------------VSTGNLGEILIRCNNV 71 (79)
T ss_pred ccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc-------------cccccceeEEEEeccE
Confidence 345899999999999999999999999999999999999999999998754 2456799999999999
Q ss_pred EEEecCC
Q 034340 88 ILVSPPL 94 (97)
Q Consensus 88 v~I~~~~ 94 (97)
.+|.-.|
T Consensus 72 lyi~gv~ 78 (79)
T KOG3482|consen 72 LYIRGVP 78 (79)
T ss_pred EEEecCC
Confidence 9996543
No 28
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.70 E-value=1.1e-18 Score=110.83 Aligned_cols=84 Identities=32% Similarity=0.507 Sum_probs=67.3
Q ss_pred cccccCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcC
Q 034340 5 EESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRG 84 (97)
Q Consensus 5 ~~~~~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG 84 (97)
|+......++ |.+|++++|+|++.+||..+|+|.|||+.|||||+|+.|+..++. ++ .+...+.|.+|++++||
T Consensus 12 e~~kkEsilD-Lsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpd-d~----~~~~~~tR~LGLvV~RG 85 (108)
T KOG1781|consen 12 EKPKKESILD-LSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPD-DP----YKLTDETRKLGLVVCRG 85 (108)
T ss_pred cccchhHHhh-HHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCC-Cc----cchhhhhheeeeEEEcc
Confidence 4444445555 455699999999999999999999999999999999999876542 11 12234559999999999
Q ss_pred CcEEEEecCC
Q 034340 85 DGVILVSPPL 94 (97)
Q Consensus 85 ~~Iv~I~~~~ 94 (97)
..+++|++.+
T Consensus 86 Talvlisp~d 95 (108)
T KOG1781|consen 86 TALVLISPAD 95 (108)
T ss_pred cEEEEEcCCc
Confidence 9999999874
No 29
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.66 E-value=7.8e-18 Score=115.85 Aligned_cols=81 Identities=21% Similarity=0.471 Sum_probs=68.0
Q ss_pred cCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEE
Q 034340 9 VKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVI 88 (97)
Q Consensus 9 ~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv 88 (97)
+..+..+|++ ++.+++|.++|||.|.|.|.+||+||||+|.||+|+...+.++. +....+++|.+|++++||+||+
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 4566778888 99999999999999999999999999999999999887655432 1112367899999999999999
Q ss_pred EEecC
Q 034340 89 LVSPP 93 (97)
Q Consensus 89 ~I~~~ 93 (97)
+.++.
T Consensus 79 s~tVe 83 (177)
T KOG3168|consen 79 SMTVE 83 (177)
T ss_pred EEecc
Confidence 98765
No 30
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.66 E-value=1.8e-17 Score=100.20 Aligned_cols=74 Identities=26% Similarity=0.394 Sum_probs=66.8
Q ss_pred ccCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcE
Q 034340 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGV 87 (97)
Q Consensus 8 ~~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I 87 (97)
....|-++|...+|++|.|+|.+|-.|+|+|.|.|.|||+.|+.+.|+... +.++++|.+||||++|
T Consensus 3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ng-------------ql~n~ygdaFirGnnV 69 (77)
T KOG1783|consen 3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNG-------------QLKNKYGDAFIRGNNV 69 (77)
T ss_pred cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcC-------------cccccccceeeccccE
Confidence 456799999999999999999999999999999999999999999987632 4678899999999999
Q ss_pred EEEecCC
Q 034340 88 ILVSPPL 94 (97)
Q Consensus 88 v~I~~~~ 94 (97)
.+|+...
T Consensus 70 lyIs~~~ 76 (77)
T KOG1783|consen 70 LYISTQK 76 (77)
T ss_pred EEEEecc
Confidence 9998753
No 31
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.63 E-value=2.8e-16 Score=95.78 Aligned_cols=76 Identities=28% Similarity=0.534 Sum_probs=66.2
Q ss_pred ccCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcE
Q 034340 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGV 87 (97)
Q Consensus 8 ~~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I 87 (97)
....|+.++.++++.+++|.+++.|++.|+|.|||.|.|++|.|++|+-..+. .....+++++++.|+||
T Consensus 4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e----------gr~~tk~~~iLLnGNni 73 (84)
T KOG1775|consen 4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE----------GRRMTKLDQILLNGNNI 73 (84)
T ss_pred hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC----------cceeeeeeeeeecCCcE
Confidence 34679999999999999999999999999999999999999999999865431 13456789999999999
Q ss_pred EEEecC
Q 034340 88 ILVSPP 93 (97)
Q Consensus 88 v~I~~~ 93 (97)
..+.+.
T Consensus 74 ~mLvPG 79 (84)
T KOG1775|consen 74 TMLVPG 79 (84)
T ss_pred EEEecC
Confidence 988765
No 32
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.57 E-value=3e-15 Score=92.24 Aligned_cols=78 Identities=23% Similarity=0.501 Sum_probs=64.2
Q ss_pred ccccccCCcHHHHHHhCC--CeEEEEEcC--CeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCe
Q 034340 4 EEESAVKEPLDLIRLSLD--ERIYVKLRS--DRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPF 79 (97)
Q Consensus 4 ~~~~~~~~P~~lL~~~l~--k~V~V~l~~--gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~ 79 (97)
+-.+-+..|++++.+++. .+|.|+|.+ |-.+.|.++|||+|||+||+||+|..... ...+.+|.
T Consensus 5 kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~------------~~rk~lGR 72 (88)
T KOG1774|consen 5 KVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT------------KSRKELGR 72 (88)
T ss_pred cccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc------------cCCCcccc
Confidence 445667899999999997 477777765 78999999999999999999999975421 22348999
Q ss_pred EEEcCCcEEEEecC
Q 034340 80 LFVRGDGVILVSPP 93 (97)
Q Consensus 80 v~IRG~~Iv~I~~~ 93 (97)
++++|+||.+|...
T Consensus 73 ilLKGDnItli~~~ 86 (88)
T KOG1774|consen 73 ILLKGDNITLIQSA 86 (88)
T ss_pred EEEcCCcEEEEeec
Confidence 99999999999764
No 33
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.53 E-value=7.7e-15 Score=92.14 Aligned_cols=72 Identities=18% Similarity=0.332 Sum_probs=61.5
Q ss_pred HHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEecC
Q 034340 14 DLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSPP 93 (97)
Q Consensus 14 ~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 93 (97)
+-|..|++++|.|.+.|||.+.|.|.|||+..||+|+++.|+...-. ...+...+|..+|||+||..|++.
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 34788999999999999999999999999999999999999875311 123456789999999999999886
Q ss_pred C
Q 034340 94 L 94 (97)
Q Consensus 94 ~ 94 (97)
.
T Consensus 74 D 74 (96)
T KOG1784|consen 74 D 74 (96)
T ss_pred c
Confidence 3
No 34
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.50 E-value=2.2e-15 Score=99.04 Aligned_cols=70 Identities=27% Similarity=0.406 Sum_probs=61.1
Q ss_pred HHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEecCCC
Q 034340 16 IRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSPPLR 95 (97)
Q Consensus 16 L~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~~~ 95 (97)
|-.++++++.|-|+|||.+.|.|.+||+|.|++|.+|.|++.... ....+..|..+|||+||++++..+.
T Consensus 14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~----------~Y~di~~glfiIRGENVvllGeid~ 83 (129)
T KOG1782|consen 14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN----------KYCDIPRGLFIIRGENVVLLGEIDL 83 (129)
T ss_pred HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc----------eecccCceEEEEecCcEEEEecCCc
Confidence 555699999999999999999999999999999999999876421 2566778999999999999988754
No 35
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.46 E-value=6.7e-15 Score=95.14 Aligned_cols=89 Identities=31% Similarity=0.504 Sum_probs=76.2
Q ss_pred ccccccCCcHHHHHHhCC--CeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEE
Q 034340 4 EEESAVKEPLDLIRLSLD--ERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLF 81 (97)
Q Consensus 4 ~~~~~~~~P~~lL~~~l~--k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~ 81 (97)
||.++..+|++++..++. .+|.|.++|++.+.|...|||.|+|++|.|+.|.|+..+++++..+.+.....|.+|.+|
T Consensus 17 e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~f 96 (114)
T KOG3459|consen 17 EEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMF 96 (114)
T ss_pred cccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheee
Confidence 666777799999999987 599999999999999999999999999999999999877665443333455689999999
Q ss_pred EcCCcEEEEec
Q 034340 82 VRGDGVILVSP 92 (97)
Q Consensus 82 IRG~~Iv~I~~ 92 (97)
|||++|+.+.-
T Consensus 97 lRGdsvI~v~r 107 (114)
T KOG3459|consen 97 LRGDSVILVLR 107 (114)
T ss_pred ecCCeEEEEEe
Confidence 99999998763
No 36
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.42 E-value=4.3e-13 Score=88.40 Aligned_cols=72 Identities=21% Similarity=0.353 Sum_probs=64.4
Q ss_pred CcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEE
Q 034340 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILV 90 (97)
Q Consensus 11 ~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 90 (97)
.|+.||+.+-+.++.|+|++|.+|.|.|+..|.+|||.|.+++++..+ + .....++.++|||++|-|+
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 699999999999999999999999999999999999999999998642 1 2456789999999999999
Q ss_pred ecCC
Q 034340 91 SPPL 94 (97)
Q Consensus 91 ~~~~ 94 (97)
..++
T Consensus 70 ri~d 73 (134)
T KOG3293|consen 70 RIPD 73 (134)
T ss_pred eccH
Confidence 8764
No 37
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.36 E-value=5.3e-12 Score=79.02 Aligned_cols=70 Identities=29% Similarity=0.429 Sum_probs=58.4
Q ss_pred HHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEec
Q 034340 13 LDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSP 92 (97)
Q Consensus 13 ~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 92 (97)
.++.+.++|++|.|.|+++-.+.|+|.++|+|.||-|.|....-..+ . ...-.+..+||||+.|.||.+
T Consensus 4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~k------y-----Phm~Sv~ncfIRGSvvrYv~l 72 (96)
T KOG3448|consen 4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDK------Y-----PHMLSVKNCFIRGSVVRYVQL 72 (96)
T ss_pred HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCccc------C-----CCeeeeeeEEEeccEEEEEEe
Confidence 57889999999999999999999999999999999999987652210 0 123456789999999999988
Q ss_pred C
Q 034340 93 P 93 (97)
Q Consensus 93 ~ 93 (97)
+
T Consensus 73 ~ 73 (96)
T KOG3448|consen 73 P 73 (96)
T ss_pred C
Confidence 6
No 38
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.28 E-value=1.5e-11 Score=79.44 Aligned_cols=74 Identities=20% Similarity=0.349 Sum_probs=64.7
Q ss_pred ccCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcE
Q 034340 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGV 87 (97)
Q Consensus 8 ~~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I 87 (97)
.+.-|+++|+.+-+.-|++++..|..|+|.|.-.|.+||+.|+|++-+..+ + ....+-++||||+.|
T Consensus 2 s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d----g---------~vs~le~V~IRGS~I 68 (119)
T KOG3172|consen 2 SVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD----G---------RVSQLEQVFIRGSKI 68 (119)
T ss_pred ccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC----C---------cceeeeeEEEecCeE
Confidence 456799999999999999999999999999999999999999999877542 1 234577999999999
Q ss_pred EEEecCC
Q 034340 88 ILVSPPL 94 (97)
Q Consensus 88 v~I~~~~ 94 (97)
.++-+|+
T Consensus 69 RFlvlPd 75 (119)
T KOG3172|consen 69 RFLVLPD 75 (119)
T ss_pred EEEECch
Confidence 9998874
No 39
>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=98.95 E-value=5.5e-10 Score=66.49 Aligned_cols=37 Identities=35% Similarity=0.421 Sum_probs=31.8
Q ss_pred CeEEEEEcCC----eEEEEEEEEECCccCeEEeceEEEEee
Q 034340 22 ERIYVKLRSD----RELRGKLHAYDQHLNMILGDVEEVVTT 58 (97)
Q Consensus 22 k~V~V~l~~g----r~i~G~L~~fD~~mNlvL~d~~e~~~~ 58 (97)
.+|+|.++.- -.++|.|+|||+||||+|.|++|.|..
T Consensus 9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 6888888752 378899999999999999999999865
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.85 E-value=2.7e-08 Score=64.44 Aligned_cols=68 Identities=21% Similarity=0.351 Sum_probs=57.4
Q ss_pred HHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEec
Q 034340 13 LDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSP 92 (97)
Q Consensus 13 ~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 92 (97)
+.+|+.+.+.+|.|.|++|+.+.|++.++|.+||..|.++.=.... +...+-.++|||++|.|+-.
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 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG--------------EPVRLDTLSIRGNNIRYYIL 69 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC--------------CceeEEEEEeecceEEEEEc
Confidence 5688999999999999999999999999999999999998644221 12456689999999999988
Q ss_pred CC
Q 034340 93 PL 94 (97)
Q Consensus 93 ~~ 94 (97)
|+
T Consensus 70 pD 71 (109)
T KOG3428|consen 70 PD 71 (109)
T ss_pred cC
Confidence 74
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.16 E-value=1e-05 Score=49.20 Aligned_cols=70 Identities=13% Similarity=0.211 Sum_probs=42.1
Q ss_pred HHHHHHhCCCeEEEEEcCCeEEEEEEEEECC---ccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEE
Q 034340 13 LDLIRLSLDERIYVKLRSDRELRGKLHAYDQ---HLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVI 88 (97)
Q Consensus 13 ~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~---~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv 88 (97)
.-++..++|++|.|+++||..|+|.|.+++. -+.++|.-+........ +............++|+++.|+
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~------~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQ------SNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------------EEEEEEE-GGGEEE-----
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccc------ccCCccCCCCCceEEEeccccC
Confidence 3467788999999999999999999999998 89999988765422110 0011223445668888888775
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=96.89 E-value=0.0075 Score=38.54 Aligned_cols=73 Identities=16% Similarity=0.198 Sum_probs=52.3
Q ss_pred HHhCCCeEEEEEcCCeEEEEEEEEECC-ccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEecC
Q 034340 17 RLSLDERIYVKLRSDRELRGKLHAYDQ-HLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSPP 93 (97)
Q Consensus 17 ~~~l~k~V~V~l~~gr~i~G~L~~fD~-~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 93 (97)
..|+|++|.+..+.+-.|+|+|..+|. ...|.|.|+.-+-+.....+ ..-.........+..||+.|--+...
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~----~~ipp~~~v~~~I~Fr~sDIkdL~v~ 77 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTD----REIPPSDEVYDYIVFRGSDIKDLKVI 77 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-S----S---C-CSSSSEEEEETTTEEEEEEC
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcC----cccCCCCceeeEEEEEccccceEEEE
Confidence 457999999999999999999999996 68999999877644211000 00011233467899999999877543
No 43
>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=96.74 E-value=0.0097 Score=33.03 Aligned_cols=34 Identities=18% Similarity=0.324 Sum_probs=29.5
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEE
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEE 54 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e 54 (97)
++++|++.+ ++..++|+..++|.+..|++.....
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 689999999 6677799999999999999976544
No 44
>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=96.68 E-value=0.0071 Score=35.70 Aligned_cols=32 Identities=16% Similarity=0.254 Sum_probs=27.8
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEec
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d 51 (97)
-..+|.|.|.+|-.+.|.+.|||+|+=|+-.+
T Consensus 14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 45799999999999999999999998776544
No 45
>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=96.66 E-value=0.0075 Score=35.59 Aligned_cols=32 Identities=16% Similarity=0.344 Sum_probs=27.5
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEec
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d 51 (97)
-..+|.|.|.+|-.++|.+.+||+|+=|+-.+
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 35699999999999999999999998666544
No 46
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=96.40 E-value=0.012 Score=36.36 Aligned_cols=33 Identities=12% Similarity=0.269 Sum_probs=28.6
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEece
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGDV 52 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 52 (97)
-..+|.|.|.+|-.+.|.+.|||+|+=|+-.+.
T Consensus 18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred cCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 457999999999999999999999987776554
No 47
>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=96.39 E-value=0.024 Score=35.13 Aligned_cols=64 Identities=16% Similarity=0.187 Sum_probs=46.3
Q ss_pred cHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCc-cCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEE
Q 034340 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQH-LNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILV 90 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~-mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 90 (97)
-+.+|..+.|++|.+.|.++.+..|++.|+|.. .|+..+|-. + | -...+..++|...|+++
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-T----P-------------lGv~~eAlLR~~DVi~~ 76 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-T----P-------------LGVQPEALLRCSDVISI 76 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-T----T-------------TTEEEEEEEEGGGEEEE
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-C----C-------------cccChhheeecCCEEEE
Confidence 356677778999999999999999999999954 677766632 1 0 11246889999999998
Q ss_pred ecC
Q 034340 91 SPP 93 (97)
Q Consensus 91 ~~~ 93 (97)
+..
T Consensus 77 ~f~ 79 (80)
T PF11095_consen 77 SFD 79 (80)
T ss_dssp EE-
T ss_pred Eec
Confidence 753
No 48
>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=96.27 E-value=0.015 Score=34.33 Aligned_cols=34 Identities=18% Similarity=0.346 Sum_probs=29.4
Q ss_pred hCCCeEEEEEcCCeEEEEEEEEECCccCeEEece
Q 034340 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILGDV 52 (97)
Q Consensus 19 ~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 52 (97)
++|..|++++..|.+|+|.+.+||.-.++++-.|
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~ 37 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKC 37 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEEC
Confidence 4789999999999999999999998877765443
No 49
>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=95.83 E-value=0.085 Score=32.25 Aligned_cols=69 Identities=19% Similarity=0.218 Sum_probs=47.7
Q ss_pred HhCCCeEEEEEcCCeEEEEEEEEECCc-cCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEE
Q 034340 18 LSLDERIYVKLRSDRELRGKLHAYDQH-LNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVIL 89 (97)
Q Consensus 18 ~~l~k~V~V~l~~gr~i~G~L~~fD~~-mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 89 (97)
.++|+++.+..+.+-.|+|+|..+|.. --+.|.|+..+-+.....+ ..+. ......+..++.||+.|--
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~--~~~i-pp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTD--GPEI-PPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCC--CCcc-CCCCcceeEEEEcCCcccc
Confidence 579999999999999999999999965 5677999887655321110 0000 0123345678999988753
No 50
>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=95.43 E-value=0.048 Score=38.09 Aligned_cols=43 Identities=23% Similarity=0.440 Sum_probs=31.3
Q ss_pred CCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECC-ccCeEEeceEE
Q 034340 10 KEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQ-HLNMILGDVEE 54 (97)
Q Consensus 10 ~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~-~mNlvL~d~~e 54 (97)
.+|+.+... ++|.|+|.+.| +++.|.|..+|. --|+||-+-.|
T Consensus 7 ~~p~~~~~y-v~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 7 KSPLEWQDY-VGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp S-HHHHHCT-TT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred CCHHHHHHh-hCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 467777666 99999999999 999999999995 47999885443
No 51
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=95.25 E-value=0.056 Score=33.19 Aligned_cols=29 Identities=14% Similarity=0.330 Sum_probs=25.4
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeE
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMI 48 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlv 48 (97)
-..+|.|.|.||-..+|.+.+||+|.=|+
T Consensus 18 ~~i~VtIfLvNG~~L~G~V~sfD~f~VlL 46 (77)
T COG1923 18 EKIPVTIFLVNGFKLQGQVESFDNFVVLL 46 (77)
T ss_pred cCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence 45799999999999999999999997443
No 52
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.12 E-value=0.05 Score=37.93 Aligned_cols=33 Identities=21% Similarity=0.249 Sum_probs=28.3
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEece
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGDV 52 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 52 (97)
-..+|.|.|.+|-.++|.+.+||+|.=|+..+.
T Consensus 103 ~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 103 SGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 346999999999999999999999987666554
No 53
>PRK14638 hypothetical protein; Provisional
Probab=94.49 E-value=0.13 Score=35.21 Aligned_cols=37 Identities=8% Similarity=0.269 Sum_probs=28.6
Q ss_pred cHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEe
Q 034340 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~ 50 (97)
|.++. +++|+.|+|++.+++.++|+|.++|.. ++.|.
T Consensus 92 ~~~f~-r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 92 PKDYV-RFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHHH-HhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 33444 348999999999999999999999863 45443
No 54
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=93.79 E-value=0.56 Score=28.00 Aligned_cols=54 Identities=19% Similarity=0.324 Sum_probs=39.5
Q ss_pred HHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEec
Q 034340 13 LDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSP 92 (97)
Q Consensus 13 ~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 92 (97)
...|++++|++|.|.+..|+. +|+|.+.... .++|+.. -...|||=.+|++|.+
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~------------------------~~~~~IR~~~IV~v~p 66 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN------------------------GTPFFIRIAQIVWVMP 66 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC------------------------CcEEEEEeeeEEEEcC
Confidence 678899999999999987765 9999998632 2244322 1267888888888754
No 55
>PRK02001 hypothetical protein; Validated
Probab=93.34 E-value=0.28 Score=33.70 Aligned_cols=37 Identities=16% Similarity=0.439 Sum_probs=28.7
Q ss_pred cHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEe
Q 034340 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~ 50 (97)
|.++-+ ++|+.|+|++.+++.|.|+|.++|.. ++.|.
T Consensus 82 ~~~f~r-~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 82 PRQYKK-NIGRELEVLTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred HHHHHH-hCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence 344443 48999999999999999999999964 44443
No 56
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.26 E-value=0.27 Score=34.35 Aligned_cols=32 Identities=16% Similarity=0.196 Sum_probs=27.1
Q ss_pred CCeEEEEEcCCeEEEEEEEEECCccCeEEece
Q 034340 21 DERIYVKLRSDRELRGKLHAYDQHLNMILGDV 52 (97)
Q Consensus 21 ~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 52 (97)
..+|.|.|.+|-.++|.+.+||+|.=|+-.+.
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 46899999999999999999999986555443
No 57
>PRK14639 hypothetical protein; Provisional
Probab=93.03 E-value=0.34 Score=32.74 Aligned_cols=32 Identities=22% Similarity=0.397 Sum_probs=27.0
Q ss_pred HHhCCCeEEEEEcCCeEEEEEEEEECCccCeEE
Q 034340 17 RLSLDERIYVKLRSDRELRGKLHAYDQHLNMIL 49 (97)
Q Consensus 17 ~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL 49 (97)
..++|+.|.|++.+++.+.|+|.++|.. ++.|
T Consensus 84 ~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 84 AKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 3448999999999999999999999883 5555
No 58
>PRK14644 hypothetical protein; Provisional
Probab=91.01 E-value=0.86 Score=30.69 Aligned_cols=34 Identities=21% Similarity=0.301 Sum_probs=27.8
Q ss_pred HHHhCCCeEEEEEcCC----eEEEEEEEEECCccCeEEe
Q 034340 16 IRLSLDERIYVKLRSD----RELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 16 L~~~l~k~V~V~l~~g----r~i~G~L~~fD~~mNlvL~ 50 (97)
+.+++|+.|.|+|++. +.|.|.|.++|.. ++.|.
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 5566899999999876 9999999999873 45554
No 59
>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=89.89 E-value=0.91 Score=31.43 Aligned_cols=34 Identities=15% Similarity=0.034 Sum_probs=30.5
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEeceE
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~ 53 (97)
-+-+|+|.+.||..|.|.+.+|+.--|.+|..+.
T Consensus 28 ~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 28 NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 4569999999999999999999999999987653
No 60
>PRK14640 hypothetical protein; Provisional
Probab=89.87 E-value=1.2 Score=30.43 Aligned_cols=37 Identities=16% Similarity=0.233 Sum_probs=27.6
Q ss_pred cHHHHHHhCCCeEEEEE----cCCeEEEEEEEEECCccCeEEe
Q 034340 12 PLDLIRLSLDERIYVKL----RSDRELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l----~~gr~i~G~L~~fD~~mNlvL~ 50 (97)
|.++. +++|+.|.|+| .+++.++|+|.++|.. ++.|.
T Consensus 89 ~~~f~-r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 89 VAQFE-KYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred HHHHH-HhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 33444 44899999999 5679999999999874 45453
No 61
>PRK14642 hypothetical protein; Provisional
Probab=89.80 E-value=1.1 Score=32.14 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=23.1
Q ss_pred hCCCeEEEEEc-------------CCeEEEEEEEEECCc
Q 034340 19 SLDERIYVKLR-------------SDRELRGKLHAYDQH 44 (97)
Q Consensus 19 ~l~k~V~V~l~-------------~gr~i~G~L~~fD~~ 44 (97)
++|+.|.|+|+ +++.|+|+|.++|..
T Consensus 98 fiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 98 FAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG 136 (197)
T ss_pred hCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence 38999999998 679999999999874
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=89.74 E-value=1.5 Score=26.78 Aligned_cols=32 Identities=25% Similarity=0.398 Sum_probs=24.9
Q ss_pred HhCCCeEEEEEc---CC-eEEEEEEEEECCccCeEEe
Q 034340 18 LSLDERIYVKLR---SD-RELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 18 ~~l~k~V~V~l~---~g-r~i~G~L~~fD~~mNlvL~ 50 (97)
.++|+.|.|++. +| +.+.|.|.++|.. ++.|.
T Consensus 22 r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l~ 57 (83)
T cd01734 22 RAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTLE 57 (83)
T ss_pred HhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEEE
Confidence 348999999997 55 6999999999884 44443
No 63
>PRK14633 hypothetical protein; Provisional
Probab=89.52 E-value=1.3 Score=30.14 Aligned_cols=33 Identities=18% Similarity=0.271 Sum_probs=25.8
Q ss_pred HHhCCCeEEEEE----cCCeEEEEEEEEECCccCeEEe
Q 034340 17 RLSLDERIYVKL----RSDRELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 17 ~~~l~k~V~V~l----~~gr~i~G~L~~fD~~mNlvL~ 50 (97)
.+++|+.|.|++ .+++.|+|+|.++|.. ++.|.
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 344899999998 4679999999999874 45553
No 64
>PRK14645 hypothetical protein; Provisional
Probab=89.42 E-value=1.2 Score=30.65 Aligned_cols=35 Identities=9% Similarity=0.111 Sum_probs=26.2
Q ss_pred HHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEe
Q 034340 13 LDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 13 ~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~ 50 (97)
.++. +++|+.|.|++ +++.++|+|.++|.. .+.|.
T Consensus 95 ~df~-r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l~ 129 (154)
T PRK14645 95 RHFE-RFAGLKAKVRG-PGENFTGRIKAVSGD-QVTFD 129 (154)
T ss_pred HHHH-HhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEEE
Confidence 3444 34899999986 789999999999874 44443
No 65
>PRK14636 hypothetical protein; Provisional
Probab=88.69 E-value=1.4 Score=30.90 Aligned_cols=37 Identities=19% Similarity=0.366 Sum_probs=27.3
Q ss_pred cHHHHHHhCCCeEEEEEc---CC-eEEEEEEEEECCccCeEEe
Q 034340 12 PLDLIRLSLDERIYVKLR---SD-RELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~---~g-r~i~G~L~~fD~~mNlvL~ 50 (97)
|.++. +++|+.|.|+|+ +| +.|+|+|.++|.. ++.|.
T Consensus 90 ~~df~-r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~ 130 (176)
T PRK14636 90 PKDFA-DWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA 130 (176)
T ss_pred HHHHH-HhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence 34444 448999999997 45 7999999999873 45553
No 66
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.42 E-value=1.9 Score=29.75 Aligned_cols=33 Identities=27% Similarity=0.432 Sum_probs=27.6
Q ss_pred HHHhCCCeEEEEE----cCCeEEEEEEEEECCccCeEE
Q 034340 16 IRLSLDERIYVKL----RSDRELRGKLHAYDQHLNMIL 49 (97)
Q Consensus 16 L~~~l~k~V~V~l----~~gr~i~G~L~~fD~~mNlvL 49 (97)
...++|+.|.|+| .+++.++|.|.++|.-+ +++
T Consensus 94 f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 94 FARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred HHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 3455899999999 78999999999999876 444
No 67
>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=87.50 E-value=1.4 Score=29.36 Aligned_cols=34 Identities=26% Similarity=0.408 Sum_probs=24.1
Q ss_pred HHHHhCCCeEEEEEc----CCeEEEEEEEEECCccCeEE
Q 034340 15 LIRLSLDERIYVKLR----SDRELRGKLHAYDQHLNMIL 49 (97)
Q Consensus 15 lL~~~l~k~V~V~l~----~gr~i~G~L~~fD~~mNlvL 49 (97)
-+..++|+.|.|+++ +.+.+.|+|.++|. -.++|
T Consensus 81 ~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 81 DFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 445569999999994 55799999999998 34444
No 68
>PRK14643 hypothetical protein; Provisional
Probab=86.95 E-value=2.2 Score=29.61 Aligned_cols=28 Identities=25% Similarity=0.541 Sum_probs=23.7
Q ss_pred HHhCCCeEEEEEcC----CeEEEEEEEEECCc
Q 034340 17 RLSLDERIYVKLRS----DRELRGKLHAYDQH 44 (97)
Q Consensus 17 ~~~l~k~V~V~l~~----gr~i~G~L~~fD~~ 44 (97)
..++|+.|.|+|.. .+.|.|+|.++|.-
T Consensus 100 ~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 100 VKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 44599999999865 69999999999865
No 69
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=86.88 E-value=1.1 Score=24.45 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=15.9
Q ss_pred EEEEEEEECCccCeEEeceEEEEe
Q 034340 34 LRGKLHAYDQHLNMILGDVEEVVT 57 (97)
Q Consensus 34 i~G~L~~fD~~mNlvL~d~~e~~~ 57 (97)
.+|++.|+|+...|.|++.....-
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T~L 33 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTTHL 33 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-EEE
T ss_pred cceeEEeeccccceEEEeCCccEE
Confidence 579999999999999998766543
No 70
>PRK14632 hypothetical protein; Provisional
Probab=86.85 E-value=2.2 Score=29.75 Aligned_cols=32 Identities=25% Similarity=0.404 Sum_probs=25.3
Q ss_pred HhCCCeEEEEEcC-------CeEEEEEEEEECCccCeEEe
Q 034340 18 LSLDERIYVKLRS-------DRELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 18 ~~l~k~V~V~l~~-------gr~i~G~L~~fD~~mNlvL~ 50 (97)
.++|+.|.|+|.+ .+.|.|+|.++|.. ++.|.
T Consensus 95 r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 95 PYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 4489999999975 68999999999863 45553
No 71
>PRK14634 hypothetical protein; Provisional
Probab=86.80 E-value=2.3 Score=29.11 Aligned_cols=36 Identities=17% Similarity=0.207 Sum_probs=26.4
Q ss_pred cHHHHHHhCCCeEEEEEcC----CeEEEEEEEEECCccCeEE
Q 034340 12 PLDLIRLSLDERIYVKLRS----DRELRGKLHAYDQHLNMIL 49 (97)
Q Consensus 12 P~~lL~~~l~k~V~V~l~~----gr~i~G~L~~fD~~mNlvL 49 (97)
|.++-+ ++|+.|.|+|.+ .+.|+|+|.++|.- ++.|
T Consensus 92 ~~~f~r-~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 92 DRDFQT-FRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred HHHHHH-hCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 344444 489999999863 38999999999874 4444
No 72
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=86.61 E-value=2.6 Score=28.64 Aligned_cols=27 Identities=30% Similarity=0.418 Sum_probs=23.3
Q ss_pred HHhCCCeEEEEE----cCCeEEEEEEEEECC
Q 034340 17 RLSLDERIYVKL----RSDRELRGKLHAYDQ 43 (97)
Q Consensus 17 ~~~l~k~V~V~l----~~gr~i~G~L~~fD~ 43 (97)
.+++|+.|.|++ .+++.+.|.|.++|.
T Consensus 94 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 94 RRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 444899999997 568999999999987
No 73
>PRK14646 hypothetical protein; Provisional
Probab=85.96 E-value=2.7 Score=28.81 Aligned_cols=35 Identities=17% Similarity=0.113 Sum_probs=26.1
Q ss_pred HHHHHHhCCCeEEEEEcC----CeEEEEEEEEECCccCeEE
Q 034340 13 LDLIRLSLDERIYVKLRS----DRELRGKLHAYDQHLNMIL 49 (97)
Q Consensus 13 ~~lL~~~l~k~V~V~l~~----gr~i~G~L~~fD~~mNlvL 49 (97)
.++- .++|+.|.|+|.+ .+.|.|+|.++|.- ++.|
T Consensus 93 ~df~-r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 93 RDFK-TFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHH-HhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 3444 4489999999854 37889999999974 5555
No 74
>PRK14647 hypothetical protein; Provisional
Probab=85.05 E-value=3.3 Score=28.39 Aligned_cols=26 Identities=12% Similarity=0.144 Sum_probs=22.2
Q ss_pred HhCCCeEEEEEc---------CCeEEEEEEEEECC
Q 034340 18 LSLDERIYVKLR---------SDRELRGKLHAYDQ 43 (97)
Q Consensus 18 ~~l~k~V~V~l~---------~gr~i~G~L~~fD~ 43 (97)
.++|+.|.|++. +.+.|.|+|.++|.
T Consensus 96 r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 96 RYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 448999999995 35999999999986
No 75
>PRK14631 hypothetical protein; Provisional
Probab=84.68 E-value=3.2 Score=29.06 Aligned_cols=32 Identities=19% Similarity=0.327 Sum_probs=25.1
Q ss_pred HHhCCCeEEEEEc----CCeEEEEEEEEEC--CccCeEE
Q 034340 17 RLSLDERIYVKLR----SDRELRGKLHAYD--QHLNMIL 49 (97)
Q Consensus 17 ~~~l~k~V~V~l~----~gr~i~G~L~~fD--~~mNlvL 49 (97)
.+++|+.|.|+|. +.+.|+|+|.++| . .++.|
T Consensus 113 ~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~-~~v~l 150 (174)
T PRK14631 113 QGYIGQQVALRLIAAVENRRKFQAKLLAVDLEN-EEIQV 150 (174)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEeecCC-CEEEE
Confidence 4448999999995 5699999999998 4 34444
No 76
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.57 E-value=3.9 Score=31.92 Aligned_cols=75 Identities=15% Similarity=0.166 Sum_probs=52.7
Q ss_pred HHHhCCCeEEEEEcCCeEEEEEEEEEC-CccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEEEecC
Q 034340 16 IRLSLDERIYVKLRSDRELRGKLHAYD-QHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSPP 93 (97)
Q Consensus 16 L~~~l~k~V~V~l~~gr~i~G~L~~fD-~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 93 (97)
...|+|++|.+.=+....|+|+|.-+| +..=|-|.+|.-+-+...++. ........+ .+.-|+.||+.|--+..-
T Consensus 4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~--~pq~p~~~k-Vy~YIlFRGSDIKDL~V~ 79 (361)
T KOG1073|consen 4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTD--GPQVPPDDK-VYDYILFRGSDIKDLIVQ 79 (361)
T ss_pred ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCC--CCcCCCCcc-ceeeEEecCcccceeeec
Confidence 456799999999999999999999999 667899999765544322111 011111222 567899999999865443
No 77
>PRK06955 biotin--protein ligase; Provisional
Probab=84.34 E-value=2.7 Score=31.48 Aligned_cols=33 Identities=15% Similarity=0.196 Sum_probs=28.4
Q ss_pred hCCCeEEEEEcCCeEEEEEEEEECCccCeEEec
Q 034340 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (97)
Q Consensus 19 ~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d 51 (97)
+++++|++...+++.+.|++.++|....|++..
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 357899997667788999999999999999863
No 78
>PRK14637 hypothetical protein; Provisional
Probab=82.42 E-value=4.3 Score=27.71 Aligned_cols=32 Identities=16% Similarity=0.276 Sum_probs=23.7
Q ss_pred HhCCCeEEEEEcCCeEE-EEEEEEECCccCeEEe
Q 034340 18 LSLDERIYVKLRSDREL-RGKLHAYDQHLNMILG 50 (97)
Q Consensus 18 ~~l~k~V~V~l~~gr~i-~G~L~~fD~~mNlvL~ 50 (97)
.++|+.|.|++.+...+ +|+|.++|.. ++.|.
T Consensus 95 r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 95 IFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 34899999999544556 7999999874 44443
No 79
>PRK14641 hypothetical protein; Provisional
Probab=81.29 E-value=4.6 Score=28.30 Aligned_cols=26 Identities=19% Similarity=0.344 Sum_probs=21.6
Q ss_pred HHhCCCeEEEEEcC----CeEEEEEEEEEC
Q 034340 17 RLSLDERIYVKLRS----DRELRGKLHAYD 42 (97)
Q Consensus 17 ~~~l~k~V~V~l~~----gr~i~G~L~~fD 42 (97)
.+++|+.|.|+|.+ .+.|+|.|.++|
T Consensus 100 ~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 100 GRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 34489999999975 578999999995
No 80
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=81.11 E-value=8.4 Score=28.78 Aligned_cols=31 Identities=19% Similarity=0.363 Sum_probs=26.5
Q ss_pred hCCCeEEEEEcCCeEEEEEEEEECCccCeEEe
Q 034340 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 19 ~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~ 50 (97)
++|++|++... +..++|++.++|....|++.
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 35789999874 45799999999999999996
No 81
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=79.25 E-value=7.5 Score=32.03 Aligned_cols=33 Identities=9% Similarity=0.139 Sum_probs=28.3
Q ss_pred hCCCeEEEEEcCCeEEEEEEEEECCccCeEEec
Q 034340 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (97)
Q Consensus 19 ~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d 51 (97)
++|++|++...+++.+.|+..|+|....|+|..
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 357899987677788999999999999999963
No 82
>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=77.37 E-value=2.9 Score=28.99 Aligned_cols=33 Identities=21% Similarity=0.290 Sum_probs=26.1
Q ss_pred cHHHHHHhC--CCeEEEEEcCCeEEEEEEEEECCc
Q 034340 12 PLDLIRLSL--DERIYVKLRSDRELRGKLHAYDQH 44 (97)
Q Consensus 12 P~~lL~~~l--~k~V~V~l~~gr~i~G~L~~fD~~ 44 (97)
-+++-+++. |+-|+|.+.|||+++|+=.|.|..
T Consensus 109 FF~Icrka~qqg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 109 FFSICRKAHQQGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred HHHHHHHHHHCCCeEEEEEcCCcEEEeeecccceE
Confidence 355555554 689999999999999998888743
No 83
>PRK10898 serine endoprotease; Provisional
Probab=76.95 E-value=6.2 Score=30.20 Aligned_cols=32 Identities=19% Similarity=0.299 Sum_probs=28.6
Q ss_pred CeEEEEEcCCeEEEEEEEEECCccCeEEeceE
Q 034340 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~ 53 (97)
..+.|++.||+.+.+.+.++|...+|-|-.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 58999999999999999999999999876654
No 84
>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=76.91 E-value=6.5 Score=25.15 Aligned_cols=17 Identities=35% Similarity=0.608 Sum_probs=14.1
Q ss_pred CeEEEEEcCCeEEEEEE
Q 034340 22 ERIYVKLRSDRELRGKL 38 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L 38 (97)
.+|.+.|+||+.+.|++
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 59999999999999984
No 85
>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=75.77 E-value=6.8 Score=29.89 Aligned_cols=32 Identities=22% Similarity=0.386 Sum_probs=28.4
Q ss_pred CeEEEEEcCCeEEEEEEEEECCccCeEEeceE
Q 034340 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~ 53 (97)
..+.|.+.||+.+.++++++|...+|-|-.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 47899999999999999999999999886554
No 86
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=75.06 E-value=17 Score=26.54 Aligned_cols=33 Identities=15% Similarity=0.208 Sum_probs=30.5
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEece
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGDV 52 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 52 (97)
++++|++...++..+.|+..++|....|+|...
T Consensus 189 ~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 189 LGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred CCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 689999999999999999999999999999875
No 87
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=75.04 E-value=8.5 Score=28.67 Aligned_cols=31 Identities=13% Similarity=0.237 Sum_probs=26.9
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEec
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d 51 (97)
+|+.|.|.. ++..+.|++.++|....|+|..
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 588998875 5688999999999999999874
No 88
>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=74.90 E-value=8.5 Score=27.58 Aligned_cols=30 Identities=13% Similarity=0.286 Sum_probs=26.1
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEe
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~ 50 (97)
++++|.+...+ ..+.|++.++|....|++.
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 5689999999999999997
No 89
>PRK10942 serine endoprotease; Provisional
Probab=72.72 E-value=8.4 Score=30.75 Aligned_cols=31 Identities=23% Similarity=0.350 Sum_probs=27.9
Q ss_pred CeEEEEEcCCeEEEEEEEEECCccCeEEece
Q 034340 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDV 52 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 52 (97)
..+.|++.||+.|.+.+.++|...+|-|-..
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 5899999999999999999999999987654
No 90
>PRK08330 biotin--protein ligase; Provisional
Probab=72.56 E-value=12 Score=26.87 Aligned_cols=33 Identities=21% Similarity=0.161 Sum_probs=26.6
Q ss_pred hCCCeEEEEEcCCeEE-EEEEEEECCccCeEEece
Q 034340 19 SLDERIYVKLRSDREL-RGKLHAYDQHLNMILGDV 52 (97)
Q Consensus 19 ~l~k~V~V~l~~gr~i-~G~L~~fD~~mNlvL~d~ 52 (97)
+++++|.+.. ++..+ .|++.++|....|++...
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence 4689999875 55564 799999999999999743
No 91
>PRK10139 serine endoprotease; Provisional
Probab=71.21 E-value=10 Score=30.18 Aligned_cols=32 Identities=25% Similarity=0.459 Sum_probs=28.6
Q ss_pred CeEEEEEcCCeEEEEEEEEECCccCeEEeceE
Q 034340 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~ 53 (97)
..+.|++.||+.+.++++++|....|-+-.+.
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 58999999999999999999999999876554
No 92
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=69.03 E-value=2.8 Score=28.52 Aligned_cols=23 Identities=22% Similarity=0.200 Sum_probs=18.4
Q ss_pred CeEEEEEEEEECCccCeEEeceE
Q 034340 31 DRELRGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 31 gr~i~G~L~~fD~~mNlvL~d~~ 53 (97)
.-.=.|+|+|.|+|.|=.-.|-.
T Consensus 42 d~~kiGTLVG~DkfGNkYyen~~ 64 (151)
T KOG3382|consen 42 DDHKIGTLVGVDKFGNKYYENND 64 (151)
T ss_pred ccccceeeeeecccccchhcccc
Confidence 34446899999999998887764
No 93
>PRK14635 hypothetical protein; Provisional
Probab=66.95 E-value=20 Score=24.65 Aligned_cols=37 Identities=22% Similarity=0.216 Sum_probs=25.9
Q ss_pred CcHHHHHHhCCCeEEEEEc--CCeEEEE---EEEEECCccCeEE
Q 034340 11 EPLDLIRLSLDERIYVKLR--SDRELRG---KLHAYDQHLNMIL 49 (97)
Q Consensus 11 ~P~~lL~~~l~k~V~V~l~--~gr~i~G---~L~~fD~~mNlvL 49 (97)
.|.++.+ +.|+.|.|++. ++..+.| .|.++|.. ++.|
T Consensus 90 ~~~~~~r-~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 90 LPEDLDR-FRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred CHHHHHH-hCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 3444444 48999999875 4678887 99999864 4444
No 94
>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=65.96 E-value=15 Score=28.66 Aligned_cols=32 Identities=25% Similarity=0.434 Sum_probs=28.7
Q ss_pred CeEEEEEcCCeEEEEEEEEECCccCeEEeceE
Q 034340 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~ 53 (97)
..+.|.+.||+.+.+.+.++|...+|.|-...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 58899999999999999999999999886654
No 95
>PRK14630 hypothetical protein; Provisional
Probab=62.19 E-value=26 Score=23.62 Aligned_cols=31 Identities=16% Similarity=0.221 Sum_probs=23.0
Q ss_pred HHhCCCeEEEEEcCCeEEEEEEEEECCccCeEE
Q 034340 17 RLSLDERIYVKLRSDRELRGKLHAYDQHLNMIL 49 (97)
Q Consensus 17 ~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL 49 (97)
..++|++|.|++... ...|+|.++|.. ++.|
T Consensus 93 ~r~~G~~v~V~l~~~-~~~G~L~~~~d~-~i~l 123 (143)
T PRK14630 93 KIFEGKKIKLMLDND-FEEGFILEAKAD-SFIF 123 (143)
T ss_pred HHhCCCEEEEEEcCc-ceEEEEEEEeCC-EEEE
Confidence 344899999999654 459999999873 4444
No 96
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=59.39 E-value=43 Score=22.79 Aligned_cols=26 Identities=4% Similarity=0.041 Sum_probs=23.3
Q ss_pred HHhCCCeEEEEEcCCeEEEEEEEEEC
Q 034340 17 RLSLDERIYVKLRSDRELRGKLHAYD 42 (97)
Q Consensus 17 ~~~l~k~V~V~l~~gr~i~G~L~~fD 42 (97)
..++||.|.+...+|..+.|++.++.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 46789999999999999999999885
No 97
>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=56.21 E-value=7.7 Score=24.80 Aligned_cols=17 Identities=24% Similarity=0.208 Sum_probs=15.5
Q ss_pred EEEEEECCccCeEEece
Q 034340 36 GKLHAYDQHLNMILGDV 52 (97)
Q Consensus 36 G~L~~fD~~mNlvL~d~ 52 (97)
|+|+|.|.|.|.--.+-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999998876
No 98
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=54.58 E-value=12 Score=23.61 Aligned_cols=22 Identities=27% Similarity=0.221 Sum_probs=20.4
Q ss_pred eeEecCeEEEcCCcEEEEecCC
Q 034340 73 TRRTVPFLFVRGDGVILVSPPL 94 (97)
Q Consensus 73 ~~r~lg~v~IRG~~Iv~I~~~~ 94 (97)
..|+-|.+.+.|..+..|..||
T Consensus 75 ~~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 75 EDRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred hhcceEEEEEECCeeeEEEcCC
Confidence 5689999999999999999998
No 99
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=52.37 E-value=24 Score=25.03 Aligned_cols=32 Identities=22% Similarity=0.406 Sum_probs=23.0
Q ss_pred HHHHHHhCC--CeEEEEE-cCCeEEEEEEEEECCc
Q 034340 13 LDLIRLSLD--ERIYVKL-RSDRELRGKLHAYDQH 44 (97)
Q Consensus 13 ~~lL~~~l~--k~V~V~l-~~gr~i~G~L~~fD~~ 44 (97)
+++|-++-+ -++.|.+ .++..|+|++.++|.-
T Consensus 123 I~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 566666544 2555554 5689999999999865
No 100
>PRK08477 biotin--protein ligase; Provisional
Probab=48.42 E-value=77 Score=22.65 Aligned_cols=36 Identities=3% Similarity=-0.035 Sum_probs=29.5
Q ss_pred HhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEE
Q 034340 18 LSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEE 54 (97)
Q Consensus 18 ~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e 54 (97)
..+++.|+|. .+++.++|+..++|...-|++.--..
T Consensus 172 ~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~ 207 (211)
T PRK08477 172 FEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKV 207 (211)
T ss_pred HHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEe
Confidence 3468999986 57899999999999999998876443
No 101
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=47.61 E-value=63 Score=19.67 Aligned_cols=29 Identities=21% Similarity=0.272 Sum_probs=20.8
Q ss_pred HHHHHHhCCCeEEEEEcCCe----EEEEEEEEE
Q 034340 13 LDLIRLSLDERIYVKLRSDR----ELRGKLHAY 41 (97)
Q Consensus 13 ~~lL~~~l~k~V~V~l~~gr----~i~G~L~~f 41 (97)
..-|...+|++|.++.+.|| +-.|+|...
T Consensus 9 k~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 9 KKELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 34577789999999999997 556888765
No 102
>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=47.43 E-value=20 Score=22.00 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=11.8
Q ss_pred CCeEEEEEcCCeEEEEE
Q 034340 21 DERIYVKLRSDRELRGK 37 (97)
Q Consensus 21 ~k~V~V~l~~gr~i~G~ 37 (97)
+.+|+++|+||..+.|+
T Consensus 17 ~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 17 RYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp TT-EEEE-TTT--EEES
T ss_pred CCeEEEEEeCCCEEEEE
Confidence 46999999999999997
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=46.89 E-value=35 Score=22.33 Aligned_cols=30 Identities=20% Similarity=0.152 Sum_probs=22.0
Q ss_pred CeEEEEEcCCeEEEEEEEEECCccCeEEece
Q 034340 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDV 52 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 52 (97)
....|.++||+.+.|.+..=| .-.+.|.++
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~-~~~~~l~~~ 87 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASET-ADGVTVKMP 87 (133)
T ss_pred ccEEEEECCCCEEEEEEEecC-CCeEEEEcC
Confidence 368999999999999988854 234444444
No 104
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.79 E-value=33 Score=24.41 Aligned_cols=34 Identities=9% Similarity=0.143 Sum_probs=30.4
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEeceE
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~ 53 (97)
++.+|.|..-++...+|.+.+||---++..-++.
T Consensus 10 vg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 10 VGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 5778999999999999999999988888877776
No 105
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=42.44 E-value=73 Score=25.44 Aligned_cols=46 Identities=26% Similarity=0.265 Sum_probs=38.0
Q ss_pred CCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEE
Q 034340 10 KEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVV 56 (97)
Q Consensus 10 ~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~ 56 (97)
..|-.++.+++||.|+- =+||+..+++|.+=|.-.-+-+.|-.|..
T Consensus 71 ~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~ 116 (421)
T COG5316 71 LSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVL 116 (421)
T ss_pred cCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEE
Confidence 36778899999999998 89999999999999987777666666544
No 106
>PRK06630 hypothetical protein; Provisional
Probab=42.14 E-value=15 Score=23.60 Aligned_cols=19 Identities=21% Similarity=0.079 Sum_probs=16.7
Q ss_pred EEEEEEEECCccCeEEece
Q 034340 34 LRGKLHAYDQHLNMILGDV 52 (97)
Q Consensus 34 i~G~L~~fD~~mNlvL~d~ 52 (97)
..|+|+|-|+|.|-.-.+.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3699999999999998874
No 107
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=40.63 E-value=34 Score=18.87 Aligned_cols=15 Identities=20% Similarity=0.368 Sum_probs=12.9
Q ss_pred HHHHHHhCCCeEEEE
Q 034340 13 LDLIRLSLDERIYVK 27 (97)
Q Consensus 13 ~~lL~~~l~k~V~V~ 27 (97)
.+.++.++||+|+|.
T Consensus 11 ~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVT 25 (48)
T ss_pred hHHHHHhcCCeEEEE
Confidence 567888999999987
No 108
>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=39.77 E-value=41 Score=21.30 Aligned_cols=22 Identities=23% Similarity=0.466 Sum_probs=17.4
Q ss_pred hCCCeEEEE-EcCCeEEEEEEEE
Q 034340 19 SLDERIYVK-LRSDRELRGKLHA 40 (97)
Q Consensus 19 ~l~k~V~V~-l~~gr~i~G~L~~ 40 (97)
.+|..|+|. +..|+.+.|+..+
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 7888898888764
No 109
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=38.83 E-value=67 Score=21.84 Aligned_cols=26 Identities=12% Similarity=0.049 Sum_probs=22.3
Q ss_pred HHhCCCeEEEEEcCCeEEEEEEEEEC
Q 034340 17 RLSLDERIYVKLRSDRELRGKLHAYD 42 (97)
Q Consensus 17 ~~~l~k~V~V~l~~gr~i~G~L~~fD 42 (97)
..++||.|.....+|..+.|++.++.
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~ 114 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQ 114 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEE
Confidence 35789999988899999999998775
No 110
>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=38.44 E-value=99 Score=19.30 Aligned_cols=15 Identities=0% Similarity=0.045 Sum_probs=12.5
Q ss_pred HHHHHHhCCCeEEEE
Q 034340 13 LDLIRLSLDERIYVK 27 (97)
Q Consensus 13 ~~lL~~~l~k~V~V~ 27 (97)
-++|..+.|++|++.
T Consensus 7 ~~~L~~f~gk~V~iv 21 (101)
T cd04479 7 GAMLSQFVGKTVRIV 21 (101)
T ss_pred HHHHHhhCCCEEEEE
Confidence 368999999999876
No 111
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=35.88 E-value=23 Score=23.37 Aligned_cols=19 Identities=21% Similarity=0.211 Sum_probs=16.5
Q ss_pred EEEEEEECCccCeEEeceE
Q 034340 35 RGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 35 ~G~L~~fD~~mNlvL~d~~ 53 (97)
.|.|+|.|++.|---.+..
T Consensus 9 ~g~lVG~D~~GNkYYE~~~ 27 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPS 27 (115)
T ss_pred cceEeEEcCCCCeeeEcCC
Confidence 6899999999999988754
No 112
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=35.13 E-value=39 Score=19.96 Aligned_cols=22 Identities=18% Similarity=0.320 Sum_probs=18.7
Q ss_pred CeEEEEEcCCeEEEEEEEEECC
Q 034340 22 ERIYVKLRSDRELRGKLHAYDQ 43 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD~ 43 (97)
.+|.|++-||..+.+++..-|.
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCCc
Confidence 5899999999999999776553
No 113
>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=34.99 E-value=59 Score=24.00 Aligned_cols=18 Identities=28% Similarity=0.414 Sum_probs=16.8
Q ss_pred EEEEEEEEECCccCeEEe
Q 034340 33 ELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 33 ~i~G~L~~fD~~mNlvL~ 50 (97)
.+.|.+.-+|.|.|+++.
T Consensus 169 ~i~g~Vi~iD~FGNlitn 186 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITN 186 (258)
T ss_dssp EEEEEEEEEETTSEEEEE
T ss_pred eEEEEEEEECccCCeeeC
Confidence 899999999999999975
No 114
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=33.63 E-value=80 Score=22.86 Aligned_cols=23 Identities=4% Similarity=-0.032 Sum_probs=20.1
Q ss_pred cCCeEEEEEEEEECCccCeEEec
Q 034340 29 RSDRELRGKLHAYDQHLNMILGD 51 (97)
Q Consensus 29 ~~gr~i~G~L~~fD~~mNlvL~d 51 (97)
.++..+.|++.++|....|++..
T Consensus 209 ~~~~~~~G~~~gId~~G~Lvv~~ 231 (245)
T PTZ00276 209 TGRDPEELTALSLNEWGHLIVRR 231 (245)
T ss_pred cCCcEEEEEEEEECCCCeEEEEE
Confidence 46678899999999999999974
No 115
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=33.33 E-value=84 Score=20.93 Aligned_cols=28 Identities=14% Similarity=0.086 Sum_probs=23.3
Q ss_pred CCeEEEEEEEEECCccCeEEeceEEEEe
Q 034340 30 SDRELRGKLHAYDQHLNMILGDVEEVVT 57 (97)
Q Consensus 30 ~gr~i~G~L~~fD~~mNlvL~d~~e~~~ 57 (97)
....+.|.|.|++.--.+.+.||.+...
T Consensus 21 ~~~~v~G~LlG~~~~~~veV~nsF~lp~ 48 (157)
T cd08057 21 GIKRVIGVLLGYVDGDKIEVTNSFELPF 48 (157)
T ss_pred CCCeEEEEEEeEEeCCEEEEEEeEEccc
Confidence 4467889999999878999999988754
No 116
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=32.70 E-value=98 Score=23.20 Aligned_cols=32 Identities=28% Similarity=0.366 Sum_probs=26.6
Q ss_pred CeEEEEEcCCeEEEEEEEEECCccCeEEeceE
Q 034340 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~ 53 (97)
.++.+.+.||+.+.+.+.++|...-+-+-...
T Consensus 96 ~~i~v~l~dg~~~~a~~vg~d~~~dlavlki~ 127 (347)
T COG0265 96 EEITVTLADGREVPAKLVGKDPISDLAVLKID 127 (347)
T ss_pred ceEEEEeCCCCEEEEEEEecCCccCEEEEEec
Confidence 58889999999999999999988776654443
No 117
>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=32.66 E-value=90 Score=18.55 Aligned_cols=25 Identities=8% Similarity=0.223 Sum_probs=21.0
Q ss_pred CcHHHHHHhCC--CeEEEEEcCCeEEE
Q 034340 11 EPLDLIRLSLD--ERIYVKLRSDRELR 35 (97)
Q Consensus 11 ~P~~lL~~~l~--k~V~V~l~~gr~i~ 35 (97)
++-++|..|-| +.|.|...||+.+.
T Consensus 8 s~~~~l~~Y~G~a~~V~v~s~~Gr~v~ 34 (68)
T PF11197_consen 8 SYQEFLAYYQGAASKVVVRSDDGRRVQ 34 (68)
T ss_pred CHHHHHHhccccccEEEEEecCCcEEE
Confidence 45678888888 69999999999886
No 118
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=32.32 E-value=56 Score=23.53 Aligned_cols=22 Identities=18% Similarity=0.406 Sum_probs=18.3
Q ss_pred hCCCeEEEE-EcCCeEEEEEEEE
Q 034340 19 SLDERIYVK-LRSDRELRGKLHA 40 (97)
Q Consensus 19 ~l~k~V~V~-l~~gr~i~G~L~~ 40 (97)
.+|..|+|+ +..|+.+.|+..+
T Consensus 205 ~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 205 AVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCeEEEEECCCCCEEEEEEeC
Confidence 467899999 8999999998765
No 119
>PRK11625 Rho-binding antiterminator; Provisional
Probab=31.12 E-value=96 Score=19.19 Aligned_cols=32 Identities=16% Similarity=0.091 Sum_probs=22.1
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEe
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVT 57 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~ 57 (97)
.+.+|.++++||..+.|+. .|=+ ..+-.|+..
T Consensus 22 ~~~~l~l~l~dGe~~~g~A--~D~~----~~~k~EyL~ 53 (84)
T PRK11625 22 HHLMLTLELKDGEVLQAKA--SDLV----SRKNVEYLV 53 (84)
T ss_pred cCCeEEEEECCCCEEEEEE--Eeee----cCCceEEEE
Confidence 3579999999999999974 4444 224455543
No 120
>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=30.64 E-value=1.1e+02 Score=17.52 Aligned_cols=26 Identities=23% Similarity=0.431 Sum_probs=17.9
Q ss_pred hCCCeEEEEEcCC-eEEEEEEEEECCc
Q 034340 19 SLDERIYVKLRSD-RELRGKLHAYDQH 44 (97)
Q Consensus 19 ~l~k~V~V~l~~g-r~i~G~L~~fD~~ 44 (97)
..|..|.+.--+. ..|.|.+.+||.-
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 3678999998776 4559999999953
No 121
>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=30.64 E-value=58 Score=18.99 Aligned_cols=22 Identities=14% Similarity=0.424 Sum_probs=18.0
Q ss_pred CeEEEEEcCCeEEEEEEEEECC
Q 034340 22 ERIYVKLRSDRELRGKLHAYDQ 43 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD~ 43 (97)
.+|+|++-||..+++.+..-|.
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~t 24 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTHK 24 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCCC
Confidence 4799999999999998765553
No 122
>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=30.58 E-value=41 Score=20.01 Aligned_cols=23 Identities=22% Similarity=0.405 Sum_probs=18.9
Q ss_pred CCCeEEEEEcCCeEEEEEEEEEC
Q 034340 20 LDERIYVKLRSDRELRGKLHAYD 42 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD 42 (97)
-..+|.|++-||..+++++..-|
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCC
Confidence 34689999999999999877554
No 123
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=30.14 E-value=47 Score=23.09 Aligned_cols=19 Identities=16% Similarity=0.088 Sum_probs=16.7
Q ss_pred EEEEEEECCccCeEEeceE
Q 034340 35 RGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 35 ~G~L~~fD~~mNlvL~d~~ 53 (97)
.|+|+|-|+|.|-.-.+..
T Consensus 48 ~G~lVG~D~~GNkYYE~~~ 66 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKLG 66 (159)
T ss_pred CcEEEEecCCCCeeeecCC
Confidence 4999999999999988763
No 124
>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=29.57 E-value=18 Score=32.87 Aligned_cols=56 Identities=14% Similarity=0.213 Sum_probs=0.0
Q ss_pred eEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcEEE
Q 034340 23 RIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVIL 89 (97)
Q Consensus 23 ~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~ 89 (97)
+.+=...+|+.+.|+|+..|.-|+.+|.--.. ..+.. ....-.+|.++|+|+|.|.
T Consensus 249 ~~Tytt~~G~~v~GVlvTT~~V~q~Ll~~l~~-i~~~~----------v~~PatYg~~Vi~geNlVT 304 (1354)
T PF03122_consen 249 RSTYTTSSGRPVDGVLVTTANVMQKLLNLLGQ-ISDTS----------VSVPATYGEFVISGENLVT 304 (1354)
T ss_dssp -------------------------------------------------------------------
T ss_pred cceeecCCCCEeceEEeccHHHHHHHHHHHhh-hccce----------eecchhheeeeecCccHHH
Confidence 44445678999999999999888777654433 21100 1235678999999999874
No 125
>PRK10708 hypothetical protein; Provisional
Probab=29.25 E-value=71 Score=18.60 Aligned_cols=26 Identities=19% Similarity=0.294 Sum_probs=22.1
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCcc
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHL 45 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~m 45 (97)
++-+|.|++.+|-.=.|++.++..|-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 46789999999988899999988774
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=28.42 E-value=68 Score=18.72 Aligned_cols=22 Identities=27% Similarity=0.389 Sum_probs=18.2
Q ss_pred CeEEEEEcCCeEEEEEEEEECC
Q 034340 22 ERIYVKLRSDRELRGKLHAYDQ 43 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD~ 43 (97)
.+|.|++-||..++..+..-|.
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~t 28 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSDT 28 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTSB
T ss_pred EEEEEECCCCCEEEEEECCcch
Confidence 4899999999999999875553
No 127
>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=28.14 E-value=8.1 Score=22.41 Aligned_cols=19 Identities=11% Similarity=0.254 Sum_probs=16.3
Q ss_pred ECCccCeEEeceEEEEeec
Q 034340 41 YDQHLNMILGDVEEVVTTV 59 (97)
Q Consensus 41 fD~~mNlvL~d~~e~~~~~ 59 (97)
-|.||+-||+||+-++..+
T Consensus 20 sDDFmhaVlSNCtTrIvLp 38 (61)
T PF10894_consen 20 SDDFMHAVLSNCTTRIVLP 38 (61)
T ss_pred cHHHHHHHHhcCceeEEec
Confidence 4899999999999887764
No 128
>PRK08183 NADH dehydrogenase; Validated
Probab=27.59 E-value=36 Score=22.95 Aligned_cols=19 Identities=16% Similarity=0.128 Sum_probs=16.2
Q ss_pred EEEEEEECCccCeEEeceE
Q 034340 35 RGKLHAYDQHLNMILGDVE 53 (97)
Q Consensus 35 ~G~L~~fD~~mNlvL~d~~ 53 (97)
.|.|+|-|++.|-.-.+-.
T Consensus 25 ~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cCeEeEecCCCCeeeecCC
Confidence 5999999999999886644
No 129
>PRK06789 flagellar motor switch protein; Validated
Probab=26.46 E-value=1.4e+02 Score=18.02 Aligned_cols=35 Identities=11% Similarity=0.152 Sum_probs=26.0
Q ss_pred HHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEec
Q 034340 17 RLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (97)
Q Consensus 17 ~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d 51 (97)
.+..+.+|.|.+++--.-+|.++-.|..+=+-+.+
T Consensus 37 dk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 37 ENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred CCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 44566788888888788889988888766665544
No 130
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=26.20 E-value=59 Score=19.52 Aligned_cols=20 Identities=20% Similarity=0.401 Sum_probs=14.8
Q ss_pred HHHHhCCCeEEEEEcCCeEE
Q 034340 15 LIRLSLDERIYVKLRSDREL 34 (97)
Q Consensus 15 lL~~~l~k~V~V~l~~gr~i 34 (97)
.++..+||+|||+....-++
T Consensus 5 ~~nDrLGKKVRvKCn~dDti 24 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDTI 24 (73)
T ss_pred hhhhhcCceEEEEeCCcccc
Confidence 56777999999998665443
No 131
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=26.11 E-value=1.3e+02 Score=21.57 Aligned_cols=26 Identities=8% Similarity=0.098 Sum_probs=22.0
Q ss_pred HHhCCCeEEEEEcCCeEEEEEEEEEC
Q 034340 17 RLSLDERIYVKLRSDRELRGKLHAYD 42 (97)
Q Consensus 17 ~~~l~k~V~V~l~~gr~i~G~L~~fD 42 (97)
..++||.|.+.-.+|..+.|++.+..
T Consensus 114 ~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 114 MKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 35689999988889999999888764
No 132
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=26.05 E-value=1.2e+02 Score=20.05 Aligned_cols=32 Identities=13% Similarity=0.153 Sum_probs=21.8
Q ss_pred hCCCeEEEEEcCCeEEEEEEEEECCccCeEEe
Q 034340 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILG 50 (97)
Q Consensus 19 ~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~ 50 (97)
..+..|.|.+++-..-+|.++-+|..+=+.++
T Consensus 103 ~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrIt 134 (136)
T COG1886 103 LAGEPVDILVNGRLIGRGEVVVVDDKFGVRIT 134 (136)
T ss_pred cCCCceEEEECCEEEEEEeEEEECCeEEEEEE
Confidence 34567777777777777888888776555544
No 133
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=25.34 E-value=82 Score=18.34 Aligned_cols=26 Identities=19% Similarity=0.288 Sum_probs=22.0
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCcc
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQHL 45 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~m 45 (97)
++-+|.|++.+|-.=.|++.++..|-
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 46689999999988899999988774
No 134
>PF11620 GABP-alpha: GA-binding protein alpha chain; InterPro: IPR024668 GA-binding protein alpha is a transcription factor capable of interacting with purine rich repeats (GA repeats). This N-terminal domain found in the transcription factor GABP alpha consists of a five-stranded beta-sheet crossed by a distorted helix and has been termed OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300 [].; PDB: 2JUO_A.
Probab=25.09 E-value=8.6 Score=24.18 Aligned_cols=41 Identities=17% Similarity=0.370 Sum_probs=24.5
Q ss_pred cccCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeE
Q 034340 7 SAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMI 48 (97)
Q Consensus 7 ~~~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlv 48 (97)
+-...|+.-|+++++.|+.+.|.+-..+-=-.. .|.+-||+
T Consensus 9 mDI~epl~~Lk~lLe~Rl~~~L~~~~f~LQD~~-L~~~k~L~ 49 (88)
T PF11620_consen 9 MDIREPLSTLKKLLERRLGISLSDYEFWLQDIQ-LEPHKSLV 49 (88)
T ss_dssp EESSSBGGGHHHHSHHHH-S--SS-EEEETTEE---TTSBTT
T ss_pred EecCCcHHHHHHHHHHhhCCCcCCCeEEeccce-ecCCccHH
Confidence 345689999999999999988877655433223 56666654
No 135
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=25.03 E-value=88 Score=21.02 Aligned_cols=20 Identities=20% Similarity=0.240 Sum_probs=16.1
Q ss_pred HhCCCeEEEEEcCCeEEEEE
Q 034340 18 LSLDERIYVKLRSDRELRGK 37 (97)
Q Consensus 18 ~~l~k~V~V~l~~gr~i~G~ 37 (97)
+++.|-++|.|.+|++++..
T Consensus 53 SAlRK~~RVrL~NG~~VtAy 72 (129)
T COG0048 53 SALRKVARVRLINGKEVTAY 72 (129)
T ss_pred hhhheeEEEEeeCCcEEEEE
Confidence 34567899999999999865
No 136
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=24.29 E-value=93 Score=24.25 Aligned_cols=21 Identities=14% Similarity=0.363 Sum_probs=19.0
Q ss_pred hCCCeEEEEEcCCeEEEEEEE
Q 034340 19 SLDERIYVKLRSDRELRGKLH 39 (97)
Q Consensus 19 ~l~k~V~V~l~~gr~i~G~L~ 39 (97)
+.+++|+|.+.+|..|.|++-
T Consensus 95 ~~gq~v~i~t~~g~~i~GvIg 115 (355)
T COG1363 95 LEGQRVTIHTDKGKKIRGVIG 115 (355)
T ss_pred ccCcEEEEEeCCCcEEeeeEc
Confidence 467999999999999999987
No 137
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.26 E-value=1e+02 Score=21.01 Aligned_cols=22 Identities=23% Similarity=0.282 Sum_probs=16.8
Q ss_pred hCCCeEEEE-EcCCeEEEEEEEE
Q 034340 19 SLDERIYVK-LRSDRELRGKLHA 40 (97)
Q Consensus 19 ~l~k~V~V~-l~~gr~i~G~L~~ 40 (97)
..|..|+|. +..|+.+.|+..+
T Consensus 129 ~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 129 AAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 356788888 7888888887653
No 138
>PF05735 TSP_C: Thrombospondin C-terminal region; InterPro: IPR008859 Thrombospondins are multimeric multidomain glycoproteins that function at cell surfaces and in the extracellular matrix milieu. They act as regulators of cell interactions in vertebrates. They are divided into two subfamilies, A and B, according to their overall molecular organisation. The subgroup A proteins TSP-1 and -2 contain an N-terminal domain, a VWFC domain, three TSP1 repeats, three EGF-like domains, TSP3 repeats and a C-terminal domain. They are assembled as trimer. The subgroup B thrombospondins, designated TSP-3, -4, and COMP (cartilage oligomeric matrix protein, also designated TSP-5) are distinct in that they contain unique N-terminal regions, lack the VWFC domain and TSP1 repeats, contain four copies of EGF-like domains, and are assembled as pentamers []. EGF, TSP3 repeats and the C-terminal domain are thus the hallmark of a thrombospondin. The globular C-terminal domain is a beta sandwich of two curved antiparallel beta-sheets []. The fold is an elaboration of the jelly role topology, with strand B3-B7, B11 and B14-B15 forming the eight-stranded jelly roll motif. The function of the C-terminal domain is not yet known.; GO: 0005509 calcium ion binding, 0007155 cell adhesion, 0005576 extracellular region; PDB: 1UX6_A 1YO8_A 2RHP_A 3FBY_C.
Probab=23.47 E-value=2.8e+02 Score=19.96 Aligned_cols=33 Identities=15% Similarity=-0.007 Sum_probs=24.4
Q ss_pred eEEEEEcCCeEEE-------EEEEEECCccCeEEeceEEE
Q 034340 23 RIYVKLRSDRELR-------GKLHAYDQHLNMILGDVEEV 55 (97)
Q Consensus 23 ~V~V~l~~gr~i~-------G~L~~fD~~mNlvL~d~~e~ 55 (97)
+.++...+|+++. |.++|.|+|.++-++-....
T Consensus 4 P~W~v~~~G~ev~Qt~NsdP~l~ig~~~~~~vdf~GT~~V 43 (201)
T PF05735_consen 4 PNWVVSNQGAEVVQTLNSDPGLAIGPDNFGGVDFSGTFFV 43 (201)
T ss_dssp --EEEECCCTEEEE-SS-SSEEEEEEEEESSEEEEEEEEE
T ss_pred CceEEecCCeEEEEeccCCCeEEEccceecceEEEEEEEE
Confidence 4567778888777 88999999999888766443
No 139
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.40 E-value=1.1e+02 Score=22.06 Aligned_cols=22 Identities=32% Similarity=0.436 Sum_probs=17.5
Q ss_pred hCCCeEEEE-EcCCeEEEEEEEE
Q 034340 19 SLDERIYVK-LRSDRELRGKLHA 40 (97)
Q Consensus 19 ~l~k~V~V~-l~~gr~i~G~L~~ 40 (97)
..|..|+|+ +..|+.+.|+..+
T Consensus 184 ~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 184 GENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 357889999 7889999998654
No 140
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.60 E-value=95 Score=19.15 Aligned_cols=22 Identities=27% Similarity=0.376 Sum_probs=16.9
Q ss_pred HHHHHhCCCeEEEEEcCCeEEE
Q 034340 14 DLIRLSLDERIYVKLRSDRELR 35 (97)
Q Consensus 14 ~lL~~~l~k~V~V~l~~gr~i~ 35 (97)
.-++.-+|++|.++.++||.=+
T Consensus 12 ~~i~ah~G~~v~lk~ngGRKk~ 33 (80)
T COG4466 12 ESIDAHLGERVTLKANGGRKKT 33 (80)
T ss_pred HHHHhccCcEEEEEecCCceee
Confidence 3355568999999999998644
No 141
>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=22.60 E-value=1.4e+02 Score=15.90 Aligned_cols=25 Identities=8% Similarity=0.249 Sum_probs=20.3
Q ss_pred CCCeEEEEEcCCeEEEEEEEEECCc
Q 034340 20 LDERIYVKLRSDRELRGKLHAYDQH 44 (97)
Q Consensus 20 l~k~V~V~l~~gr~i~G~L~~fD~~ 44 (97)
.|..+.+...+|.-|+|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4666667767999999999999864
No 142
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=22.38 E-value=1.1e+02 Score=21.63 Aligned_cols=24 Identities=21% Similarity=0.412 Sum_probs=20.8
Q ss_pred hCCCeEEEEEcCCeEEEEEEEEEC
Q 034340 19 SLDERIYVKLRSDRELRGKLHAYD 42 (97)
Q Consensus 19 ~l~k~V~V~l~~gr~i~G~L~~fD 42 (97)
++|++|.|.+...+.|.|.+..++
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 799999999998899999998874
No 143
>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=21.51 E-value=95 Score=19.98 Aligned_cols=20 Identities=20% Similarity=0.340 Sum_probs=7.1
Q ss_pred EEEEEEEEECCccCeEEece
Q 034340 33 ELRGKLHAYDQHLNMILGDV 52 (97)
Q Consensus 33 ~i~G~L~~fD~~mNlvL~d~ 52 (97)
++.|++.+||-..++.|++|
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 34578778874456666665
No 144
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=20.70 E-value=2.3e+02 Score=17.72 Aligned_cols=34 Identities=9% Similarity=0.057 Sum_probs=24.7
Q ss_pred HHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeE
Q 034340 15 LIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMI 48 (97)
Q Consensus 15 lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlv 48 (97)
--..|+||+|-..-+.|+.|-|.+.---..-..|
T Consensus 34 ~a~fylGKrv~yvyk~grviwGKItR~HGnsGvV 67 (87)
T PRK04337 34 EAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEV 67 (87)
T ss_pred HHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceE
Confidence 4466799999999888999999876554433333
No 145
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=20.44 E-value=2e+02 Score=20.19 Aligned_cols=32 Identities=19% Similarity=0.264 Sum_probs=22.3
Q ss_pred hCCCeEEEEEcCCeEE----EEEEEEECCccCeEEe
Q 034340 19 SLDERIYVKLRSDREL----RGKLHAYDQHLNMILG 50 (97)
Q Consensus 19 ~l~k~V~V~l~~gr~i----~G~L~~fD~~mNlvL~ 50 (97)
|.+..+.+...||+.- .|.+..=|+..||+|+
T Consensus 142 yPDGTvk~vy~dG~qet~y~~gr~r~kd~~g~~~~d 177 (179)
T PF07202_consen 142 YPDGTVKTVYPDGRQETRYASGRVRIKDKDGNVIMD 177 (179)
T ss_pred cCCCCEEEEecCCCEEEEeCCCcEEEecCCCCEEec
Confidence 3556677777777433 3888888888888875
No 146
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. 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=20.33 E-value=1.1e+02 Score=18.36 Aligned_cols=21 Identities=19% Similarity=0.349 Sum_probs=17.4
Q ss_pred CeEEEEEcCCeEEEEEEEEEC
Q 034340 22 ERIYVKLRSDRELRGKLHAYD 42 (97)
Q Consensus 22 k~V~V~l~~gr~i~G~L~~fD 42 (97)
.+|.|.|-||..++..+..-|
T Consensus 5 t~iqiRlpdG~r~~~rF~~~~ 25 (79)
T cd01770 5 TSIQIRLADGKRLVQKFNSSH 25 (79)
T ss_pred eEEEEECCCCCEEEEEeCCCC
Confidence 589999999999998866444
No 147
>PRK09961 exoaminopeptidase; Provisional
Probab=20.15 E-value=1.3e+02 Score=22.95 Aligned_cols=22 Identities=14% Similarity=0.232 Sum_probs=18.5
Q ss_pred HhCCCeEEEEEcCCeEEEEEEE
Q 034340 18 LSLDERIYVKLRSDRELRGKLH 39 (97)
Q Consensus 18 ~~l~k~V~V~l~~gr~i~G~L~ 39 (97)
.+.+++|+|..++|..+.|++.
T Consensus 91 ~~~~~~v~i~~~~g~~i~Gvi~ 112 (344)
T PRK09961 91 ARQLQPVRITTREECKIPGLLN 112 (344)
T ss_pred ccCCCEEEEEeCCCCEeeEEEC
Confidence 3467899999999988999983
Done!