Query 041342
Match_columns 87
No_of_seqs 166 out of 1047
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 06:10:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041342.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041342hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01732 LSm5 The eukaryotic Sm 100.0 1.6E-27 3.4E-32 143.7 10.8 75 8-82 2-76 (76)
2 PRK00737 small nuclear ribonuc 99.9 2.2E-26 4.7E-31 137.2 9.6 70 8-80 3-72 (72)
3 cd01731 archaeal_Sm1 The archa 99.9 3.7E-26 8.1E-31 134.6 9.4 68 10-80 1-68 (68)
4 cd01726 LSm6 The eukaryotic Sm 99.9 9.1E-26 2E-30 132.7 9.3 67 10-79 1-67 (67)
5 cd01730 LSm3 The eukaryotic Sm 99.9 2E-25 4.4E-30 135.9 9.4 72 9-80 1-82 (82)
6 cd01719 Sm_G The eukaryotic Sm 99.9 7.9E-25 1.7E-29 130.6 9.4 69 11-82 2-70 (72)
7 cd01722 Sm_F The eukaryotic Sm 99.9 6.1E-25 1.3E-29 129.6 8.4 68 9-79 1-68 (68)
8 cd01720 Sm_D2 The eukaryotic S 99.9 1.4E-24 3E-29 133.8 10.3 74 8-81 1-86 (87)
9 cd01729 LSm7 The eukaryotic Sm 99.9 2.1E-24 4.6E-29 131.3 10.2 73 10-82 3-80 (81)
10 cd01718 Sm_E The eukaryotic Sm 99.9 4.2E-24 9.1E-29 129.5 9.7 74 5-80 2-79 (79)
11 cd01728 LSm1 The eukaryotic Sm 99.9 8E-24 1.7E-28 126.9 10.4 71 10-80 3-73 (74)
12 cd01723 LSm4 The eukaryotic Sm 99.9 1.7E-23 3.7E-28 125.8 9.6 71 9-81 1-71 (76)
13 cd01727 LSm8 The eukaryotic Sm 99.9 3E-23 6.5E-28 124.1 10.2 71 12-82 2-73 (74)
14 COG1958 LSM1 Small nuclear rib 99.9 3.1E-23 6.7E-28 125.2 10.1 74 6-80 4-79 (79)
15 cd01717 Sm_B The eukaryotic Sm 99.9 2.7E-23 5.9E-28 125.6 9.7 69 12-80 3-78 (79)
16 cd01721 Sm_D3 The eukaryotic S 99.9 4.8E-23 1E-27 122.2 9.5 69 10-81 1-69 (70)
17 PF01423 LSM: LSM domain ; In 99.9 1.3E-22 2.8E-27 118.4 10.0 67 12-80 1-67 (67)
18 smart00651 Sm snRNP Sm protein 99.9 1.1E-22 2.5E-27 118.5 9.4 66 13-80 2-67 (67)
19 cd06168 LSm9 The eukaryotic Sm 99.9 6.8E-22 1.5E-26 118.8 10.0 69 12-80 3-74 (75)
20 PTZ00138 small nuclear ribonuc 99.9 1E-21 2.2E-26 121.4 10.1 74 6-81 11-88 (89)
21 cd01724 Sm_D1 The eukaryotic S 99.9 1.8E-21 3.9E-26 120.5 9.9 71 10-83 2-72 (90)
22 cd00600 Sm_like The eukaryotic 99.9 4.1E-21 8.9E-26 110.5 8.5 63 14-79 1-63 (63)
23 cd01725 LSm2 The eukaryotic Sm 99.9 6.3E-21 1.4E-25 116.0 9.2 72 9-82 1-73 (81)
24 cd01733 LSm10 The eukaryotic S 99.8 1E-20 2.2E-25 114.4 9.4 71 7-80 7-77 (78)
25 KOG1775 U6 snRNA-associated Sm 99.8 1.8E-21 3.9E-26 116.2 5.7 84 3-86 1-84 (84)
26 KOG1780 Small Nuclear ribonucl 99.8 5E-21 1.1E-25 113.7 6.4 71 8-83 5-75 (77)
27 KOG3482 Small nuclear ribonucl 99.8 6.1E-20 1.3E-24 108.7 6.9 77 3-82 2-78 (79)
28 KOG3460 Small nuclear ribonucl 99.8 8.9E-20 1.9E-24 110.5 2.4 75 7-81 3-87 (91)
29 KOG1783 Small nuclear ribonucl 99.8 8.7E-20 1.9E-24 108.1 1.3 74 6-82 3-76 (77)
30 KOG1781 Small Nuclear ribonucl 99.7 9E-19 1.9E-23 109.0 0.4 75 9-83 17-96 (108)
31 KOG1774 Small nuclear ribonucl 99.7 1.7E-16 3.6E-21 95.9 5.5 75 6-82 9-87 (88)
32 KOG3293 Small nuclear ribonucl 99.7 3.7E-16 8E-21 100.8 6.5 73 8-82 1-73 (134)
33 KOG3168 U1 snRNP component [Tr 99.6 5.3E-17 1.1E-21 109.4 1.2 76 12-87 7-89 (177)
34 KOG1782 Small Nuclear ribonucl 99.6 1.5E-16 3.4E-21 102.4 1.2 74 12-85 12-85 (129)
35 KOG1784 Small Nuclear ribonucl 99.6 1.6E-15 3.4E-20 93.4 4.2 72 12-83 3-75 (96)
36 KOG3448 Predicted snRNP core p 99.5 5.2E-13 1.1E-17 81.9 7.9 71 11-82 4-74 (96)
37 KOG3172 Small nuclear ribonucl 99.5 3.3E-13 7.1E-18 85.4 7.0 73 6-81 2-74 (119)
38 KOG3428 Small nuclear ribonucl 99.2 1.5E-10 3.2E-15 73.4 8.7 68 11-82 4-71 (109)
39 KOG3459 Small nuclear ribonucl 99.1 5.8E-12 1.3E-16 79.9 -0.3 73 8-80 23-107 (114)
40 cd01739 LSm11_C The eukaryotic 98.5 1.5E-07 3.3E-12 55.0 2.8 36 20-55 9-48 (66)
41 PF14438 SM-ATX: Ataxin 2 SM d 98.2 3.1E-06 6.8E-11 50.4 4.7 65 12-76 5-76 (77)
42 PF12701 LSM14: Scd6-like Sm d 98.0 7.2E-05 1.6E-09 46.8 7.5 69 15-85 4-81 (96)
43 PF02237 BPL_C: Biotin protein 97.4 0.0012 2.5E-08 36.0 6.1 48 17-71 1-48 (48)
44 cd01736 LSm14_N LSm14 (also kn 97.2 0.0028 6.2E-08 37.9 6.4 64 15-78 2-73 (74)
45 cd01716 Hfq Hfq, an abundant, 96.8 0.0031 6.7E-08 36.5 4.4 37 13-49 3-41 (61)
46 TIGR02383 Hfq RNA chaperone Hf 96.8 0.0038 8.3E-08 36.1 4.4 37 13-49 7-45 (61)
47 PRK00395 hfq RNA-binding prote 96.6 0.0068 1.5E-07 36.7 4.9 38 13-50 11-50 (79)
48 PF06372 Gemin6: Gemin6 protei 96.3 0.02 4.3E-07 39.1 6.3 64 9-83 8-72 (166)
49 cd01735 LSm12_N LSm12 belongs 95.8 0.04 8.6E-07 31.8 5.1 36 17-52 4-39 (61)
50 COG1923 Hfq Uncharacterized ho 95.8 0.044 9.6E-07 33.0 5.4 28 19-46 19-46 (77)
51 KOG1073 Uncharacterized mRNA-a 95.7 0.042 9E-07 41.6 6.2 71 15-85 5-83 (361)
52 PRK14638 hypothetical protein; 95.5 0.056 1.2E-06 36.1 5.6 45 3-48 81-128 (150)
53 PF10842 DUF2642: Protein of u 95.4 0.14 3.1E-06 29.9 6.5 54 11-80 13-66 (66)
54 PF11095 Gemin7: Gem-associate 95.2 0.31 6.8E-06 29.5 7.7 62 11-80 16-78 (80)
55 PRK02001 hypothetical protein; 95.1 0.084 1.8E-06 35.4 5.7 45 3-48 71-118 (152)
56 PRK14639 hypothetical protein; 95.0 0.094 2E-06 34.6 5.6 43 4-47 70-115 (140)
57 PRK14091 RNA-binding protein H 95.0 0.057 1.2E-06 36.8 4.5 38 13-50 16-55 (165)
58 PRK14644 hypothetical protein; 95.0 0.093 2E-06 34.6 5.4 45 3-48 67-117 (136)
59 PRK14091 RNA-binding protein H 94.8 0.086 1.9E-06 36.0 4.9 38 13-50 96-135 (165)
60 PF02576 DUF150: Uncharacteris 94.0 0.16 3.5E-06 33.1 4.9 44 3-47 68-118 (141)
61 PRK14640 hypothetical protein; 93.5 0.42 9.1E-06 31.9 6.3 45 3-48 78-129 (152)
62 PRK06955 biotin--protein ligas 93.3 0.53 1.1E-05 34.4 7.1 50 17-73 247-296 (300)
63 cd01734 YlxS_C YxlS is a Bacil 93.1 0.51 1.1E-05 28.2 5.7 36 11-47 17-56 (83)
64 PRK14633 hypothetical protein; 93.0 0.41 8.9E-06 31.9 5.6 45 3-48 75-126 (150)
65 PRK14642 hypothetical protein; 92.9 0.38 8.2E-06 33.7 5.6 44 3-47 81-140 (197)
66 COG0779 Uncharacterized protei 92.8 0.6 1.3E-05 31.5 6.2 43 4-47 81-130 (153)
67 PRK14645 hypothetical protein; 92.6 0.43 9.2E-06 32.1 5.3 43 3-47 83-128 (154)
68 PRK14636 hypothetical protein; 91.9 0.65 1.4E-05 31.8 5.6 43 4-47 80-129 (176)
69 PRK14632 hypothetical protein; 91.4 0.77 1.7E-05 31.3 5.6 45 3-48 79-133 (172)
70 PRK14643 hypothetical protein; 91.3 0.82 1.8E-05 31.0 5.6 40 3-42 85-131 (164)
71 PRK13325 bifunctional biotin-- 91.3 1.1 2.4E-05 35.9 7.1 32 17-48 276-307 (592)
72 PRK00092 ribosome maturation p 91.2 0.85 1.8E-05 30.3 5.5 39 3-41 79-124 (154)
73 PRK14634 hypothetical protein; 91.1 0.88 1.9E-05 30.5 5.5 44 3-47 81-131 (155)
74 PRK14646 hypothetical protein; 90.8 1 2.2E-05 30.2 5.6 45 3-48 81-132 (155)
75 PRK14647 hypothetical protein; 90.5 1.1 2.4E-05 30.0 5.6 44 3-47 80-135 (159)
76 PRK11886 bifunctional biotin-- 90.2 1.9 4.1E-05 31.5 7.0 48 17-72 270-317 (319)
77 PRK14631 hypothetical protein; 89.8 1.2 2.7E-05 30.4 5.4 38 3-40 98-142 (174)
78 PRK14641 hypothetical protein; 89.0 1.4 3E-05 30.2 5.2 38 3-40 85-129 (173)
79 PRK14637 hypothetical protein; 88.6 1.7 3.8E-05 29.0 5.4 44 4-48 80-127 (151)
80 TIGR00121 birA_ligase birA, bi 88.2 3.1 6.7E-05 29.1 6.7 31 17-48 191-221 (237)
81 PRK08330 biotin--protein ligas 87.7 3.4 7.5E-05 28.9 6.7 34 16-50 185-219 (236)
82 PRK10898 serine endoprotease; 81.5 3.7 8E-05 30.7 4.8 31 20-50 102-132 (353)
83 COG0340 BirA Biotin-(acetyl-Co 81.2 10 0.00022 27.0 6.8 36 15-50 186-221 (238)
84 PF11607 DUF3247: Protein of u 80.8 2.8 6.1E-05 26.3 3.3 17 20-36 29-45 (101)
85 PRK14630 hypothetical protein; 80.1 6.7 0.00015 25.9 5.2 43 3-47 78-123 (143)
86 TIGR02038 protease_degS peripl 80.0 4.3 9.4E-05 30.2 4.7 31 20-50 102-132 (351)
87 PF03614 Flag1_repress: Repres 79.8 2.3 5E-05 28.9 2.9 23 19-41 120-142 (165)
88 PTZ00275 biotin-acetyl-CoA-car 79.7 5.1 0.00011 29.2 4.9 32 18-50 236-267 (285)
89 PF03614 Flag1_repress: Repres 79.1 5.1 0.00011 27.2 4.4 34 18-51 28-61 (165)
90 PF14563 DUF4444: Domain of un 78.4 2.9 6.3E-05 22.3 2.4 22 32-53 10-31 (42)
91 PHA00672 hypothetical protein 77.7 18 0.00039 24.1 7.3 48 1-50 29-76 (152)
92 PRK14635 hypothetical protein; 77.1 11 0.00023 25.4 5.6 45 3-48 80-132 (162)
93 PRK10942 serine endoprotease; 77.0 5.7 0.00012 30.9 4.7 31 20-50 136-166 (473)
94 PRK10139 serine endoprotease; 76.8 6 0.00013 30.7 4.8 31 20-50 115-145 (455)
95 PRK09618 flgD flagellar basal 74.4 14 0.00031 24.6 5.5 27 14-40 87-113 (142)
96 TIGR02037 degP_htrA_DO peripla 71.0 9.9 0.00022 28.8 4.7 32 20-51 82-113 (428)
97 PRK08477 biotin--protein ligas 69.8 19 0.00041 25.2 5.6 37 16-53 172-208 (211)
98 KOG3382 NADH:ubiquinone oxidor 68.7 2.8 6E-05 27.9 1.1 25 27-51 40-64 (151)
99 KOG3493 Ubiquitin-like protein 62.7 6.8 0.00015 23.1 1.8 20 13-32 5-24 (73)
100 PF05071 NDUFA12: NADH ubiquin 62.3 4.7 0.0001 25.2 1.2 17 34-50 1-17 (105)
101 PF06257 DUF1021: Protein of u 61.9 25 0.00055 21.0 4.3 28 12-39 10-41 (76)
102 PF07073 ROF: Modulator of Rho 59.2 7.3 0.00016 23.4 1.7 54 18-81 16-69 (80)
103 smart00333 TUDOR Tudor domain. 58.2 27 0.00058 18.5 4.8 25 18-42 5-29 (57)
104 PF11743 DUF3301: Protein of u 58.1 38 0.00082 20.8 4.8 40 42-82 57-96 (97)
105 TIGR02603 CxxCH_TIGR02603 puta 55.7 21 0.00045 22.8 3.5 29 21-50 59-87 (133)
106 COG5316 Uncharacterized conser 55.7 30 0.00065 27.0 4.7 47 8-55 71-117 (421)
107 PRK11911 flgD flagellar basal 52.6 32 0.00069 22.9 4.0 27 15-41 89-115 (140)
108 PF09465 LBR_tudor: Lamin-B re 52.1 36 0.00078 19.2 3.6 24 18-41 8-32 (55)
109 TIGR03170 flgA_cterm flagella 50.5 24 0.00051 21.9 3.0 23 16-38 93-116 (122)
110 PRK06630 hypothetical protein; 49.2 9.1 0.0002 24.1 0.9 19 32-50 11-29 (99)
111 PF14485 DUF4431: Domain of un 47.4 22 0.00049 19.2 2.2 15 11-25 11-25 (48)
112 PF01887 SAM_adeno_trans: S-ad 46.3 33 0.00072 24.7 3.6 19 31-49 169-187 (258)
113 PF10618 Tail_tube: Phage tail 44.6 40 0.00088 21.5 3.5 28 8-35 63-90 (119)
114 COG0265 DegQ Trypsin-like seri 43.2 55 0.0012 24.0 4.5 32 19-50 95-126 (347)
115 PRK07018 flgA flagellar basal 42.8 32 0.00069 24.2 3.0 23 16-38 204-227 (235)
116 PRK10708 hypothetical protein; 42.8 34 0.00073 19.6 2.5 26 18-43 3-28 (62)
117 PTZ00276 biotin/lipoate protei 41.5 49 0.0011 23.4 3.8 24 27-50 209-232 (245)
118 PF05735 TSP_C: Thrombospondin 41.5 1.2E+02 0.0027 21.3 6.0 33 22-54 5-44 (201)
119 PLN03095 NADH:ubiquinone oxido 41.0 16 0.00034 23.6 1.1 19 33-51 9-27 (115)
120 smart00166 UBX Domain present 40.3 30 0.00066 20.0 2.2 22 20-41 5-26 (80)
121 PF14153 Spore_coat_CotO: Spor 40.1 40 0.00087 23.3 3.1 59 11-82 123-184 (185)
122 PRK06792 flgD flagellar basal 39.7 57 0.0012 22.8 3.8 26 15-40 114-139 (190)
123 PF10894 DUF2689: Protein of u 37.4 5.1 0.00011 22.8 -1.4 17 39-55 20-36 (61)
124 PF10781 DSRB: Dextransucrase 36.6 43 0.00093 19.1 2.3 26 18-43 3-28 (62)
125 PLN02732 Probable NADH dehydro 36.1 32 0.00068 23.4 2.0 19 33-51 48-66 (159)
126 PF00789 UBX: UBX domain; Int 36.0 50 0.0011 18.9 2.7 21 21-41 8-28 (82)
127 COG4466 Veg Uncharacterized pr 35.7 49 0.0011 20.0 2.6 27 12-38 12-42 (80)
128 cd01767 UBX UBX (ubiquitin reg 35.6 43 0.00093 19.1 2.4 21 20-40 3-23 (77)
129 KOG4401 Uncharacterized conser 34.6 61 0.0013 22.6 3.3 35 17-51 9-43 (184)
130 cd01737 LSm16_N LSm16 belongs 32.9 90 0.0019 18.0 3.3 37 15-51 2-40 (62)
131 PRK08183 NADH dehydrogenase; V 32.4 24 0.00051 23.3 1.0 19 33-51 25-43 (133)
132 cd01772 SAKS1_UBX SAKS1-like U 32.2 38 0.00083 19.7 1.8 23 18-40 3-25 (79)
133 PF05954 Phage_GPD: Phage late 31.5 70 0.0015 22.2 3.3 26 15-40 24-49 (292)
134 PRK06005 flgA flagellar basal 31.3 69 0.0015 21.4 3.1 22 17-38 129-151 (160)
135 PRK08515 flgA flagellar basal 31.0 84 0.0018 22.0 3.6 23 16-38 193-215 (222)
136 PRK12617 flgA flagellar basal 29.8 72 0.0016 22.4 3.1 22 17-38 184-206 (214)
137 PF03122 Herpes_MCP: Herpes vi 29.2 18 0.00039 32.1 0.0 54 24-78 252-305 (1354)
138 PF13793 Pribosyltran_N: N-ter 28.7 1.3E+02 0.0027 19.0 3.8 41 42-84 19-59 (116)
139 PRK04337 50S ribosomal protein 27.6 1.3E+02 0.0028 18.5 3.5 35 12-46 33-67 (87)
140 PF12945 YcgR_2: Flagellar pro 27.1 1.3E+02 0.0027 17.0 4.6 33 18-50 3-39 (87)
141 PRK11625 Rho-binding antitermi 26.8 1.5E+02 0.0033 17.9 6.6 50 18-79 22-72 (84)
142 PRK06151 N-ethylammeline chlor 26.2 2E+02 0.0042 22.2 5.2 39 43-81 1-39 (488)
143 cd04508 TUDOR Tudor domains ar 25.9 1E+02 0.0022 15.5 4.2 22 20-41 2-24 (48)
144 TIGR03361 VI_Rhs_Vgr type VI s 25.8 1.4E+02 0.0029 23.2 4.3 27 14-40 42-72 (513)
145 COG4568 Rof Transcriptional an 25.5 1E+02 0.0022 18.7 2.8 18 19-36 23-40 (84)
146 PF13144 SAF_2: SAF-like 25.3 1.2E+02 0.0027 20.2 3.6 24 16-39 167-191 (196)
147 PRK12618 flgA flagellar basal 25.1 1.1E+02 0.0023 20.1 3.1 22 17-38 110-132 (141)
148 PF12869 tRNA_anti-like: tRNA_ 24.9 67 0.0014 20.2 2.1 20 31-50 124-143 (144)
149 cd01770 p47_UBX p47-like ubiqu 24.8 80 0.0017 18.5 2.3 21 20-40 5-25 (79)
150 PF08661 Rep_fac-A_3: Replicat 24.6 40 0.00087 20.8 1.0 22 4-25 3-24 (109)
151 PRK06804 flgA flagellar basal 24.6 1E+02 0.0022 22.4 3.1 23 17-39 231-254 (261)
152 PRK07228 N-ethylammeline chlor 24.3 1.8E+02 0.004 21.8 4.6 38 43-82 1-38 (445)
153 COG1363 FrvX Cellulase M and r 24.2 97 0.0021 23.6 3.1 22 16-37 94-115 (355)
154 TIGR00008 infA translation ini 23.0 1.5E+02 0.0032 17.2 3.1 21 19-39 17-37 (68)
155 PF02245 Pur_DNA_glyco: Methyl 22.7 2E+02 0.0043 19.8 4.2 34 10-44 9-42 (184)
156 TIGR00999 8a0102 Membrane Fusi 22.6 2E+02 0.0043 19.7 4.3 26 18-43 141-166 (265)
157 TIGR00567 3mg DNA-3-methyladen 22.6 2.4E+02 0.0053 19.6 4.6 35 9-43 9-43 (192)
158 PF11684 DUF3280: Protein of u 22.4 88 0.0019 20.6 2.3 38 30-74 83-123 (140)
159 COG2451 Ribosomal protein L35A 22.2 1.9E+02 0.0041 18.2 3.6 29 12-40 39-68 (100)
160 COG0048 RpsL Ribosomal protein 22.0 1.1E+02 0.0024 20.1 2.6 23 16-38 53-75 (129)
161 PF06115 DUF956: Domain of unk 21.7 2.4E+02 0.0052 18.3 5.5 35 16-55 3-38 (118)
162 KOG3168 U1 snRNP component [Tr 20.8 1.6E+02 0.0035 20.3 3.3 67 11-77 42-115 (177)
163 PF01176 eIF-1a: Translation i 20.8 1.5E+02 0.0033 16.5 2.8 20 20-39 16-35 (65)
164 PF02014 Reeler: Reeler domain 20.6 94 0.002 19.5 2.1 19 19-37 33-53 (132)
165 PF10246 MRP-S35: Mitochondria 20.4 71 0.0015 20.3 1.5 34 19-53 64-97 (104)
166 PF09883 DUF2110: Uncharacteri 20.4 86 0.0019 22.5 2.0 32 11-43 56-89 (225)
167 PRK15493 5-methylthioadenosine 20.2 2.3E+02 0.0049 21.5 4.4 38 43-81 1-38 (435)
168 cd08544 Reeler Reeler, the N-t 20.1 1.6E+02 0.0035 18.4 3.1 22 19-40 33-56 (135)
No 1
>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=99.95 E-value=1.6e-27 Score=143.65 Aligned_cols=75 Identities=83% Similarity=1.339 Sum_probs=68.9
Q ss_pred cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
.+|+++|.++++++|+|++++||.+.|+|.|||+|||++|+||+|++..+++.+.+.+|.++|||++|++|+|.+
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~~ 76 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPGG 76 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECCC
Confidence 589999999999999999999999999999999999999999999986555555789999999999999999764
No 2
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.94 E-value=2.2e-26 Score=137.15 Aligned_cols=70 Identities=29% Similarity=0.688 Sum_probs=64.7
Q ss_pred cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342 8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
..|+++|+++++++|.|+|+||+.|+|+|.|||+|||++|+||.|++ +++..+.+|.++|||++|++|++
T Consensus 3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ---DGEVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEc---CCCeEeEcCcEEEeCCEEEEEcC
Confidence 47999999999999999999999999999999999999999999975 44557899999999999999974
No 3
>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=99.94 E-value=3.7e-26 Score=134.58 Aligned_cols=68 Identities=31% Similarity=0.644 Sum_probs=63.0
Q ss_pred cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
|+++|+++++++|+|+|+||+.|+|+|.|||+|||++|+||+|++. +...+.+|.++|||++|++|++
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~---~~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDD---GEPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEec---CCeEeEcCcEEEeCCEEEEEcC
Confidence 8999999999999999999999999999999999999999999863 2346899999999999999975
No 4
>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=99.93 E-value=9.1e-26 Score=132.72 Aligned_cols=67 Identities=30% Similarity=0.535 Sum_probs=62.3
Q ss_pred cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEE
Q 041342 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILV 79 (87)
Q Consensus 10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~ 79 (87)
|+++|+++++++|+|+|+||++|+|+|.|||+|||++|+||+|.. ++...+.+|.++|||++|.+|+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~---~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYV---NGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEe---CCceeeEeCCEEEECCEEEEEC
Confidence 899999999999999999999999999999999999999999864 4555789999999999999985
No 5
>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=99.93 E-value=2e-25 Score=135.88 Aligned_cols=72 Identities=29% Similarity=0.585 Sum_probs=64.3
Q ss_pred CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC-C---------eeeEeeCeEEEcCCcEEEE
Q 041342 9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE-G---------RRITKLDQILLNGNNIAIL 78 (87)
Q Consensus 9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~-g---------~~~~~~g~v~IRG~~I~~I 78 (87)
.|+++|+.+++++|.|+++|||.|.|+|.|||+||||+|+||+|++.... + ...+.+|.+||||++|++|
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 49999999999999999999999999999999999999999999985321 1 2468999999999999999
Q ss_pred Ee
Q 041342 79 VP 80 (87)
Q Consensus 79 ~~ 80 (87)
++
T Consensus 81 ~~ 82 (82)
T cd01730 81 SP 82 (82)
T ss_pred CC
Confidence 74
No 6
>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=99.92 E-value=7.9e-25 Score=130.58 Aligned_cols=69 Identities=25% Similarity=0.561 Sum_probs=62.8
Q ss_pred HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
-..|+++++|+|+|+|++|+.|+|+|.|||+||||+|+||+|+. ++...+.+|.++|||++|++|++.+
T Consensus 2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~---~~~~~~~lg~v~IRG~~I~~i~~~~ 70 (72)
T cd01719 2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVN---SGGEKNNIGMVVIRGNSIVMLEALE 70 (72)
T ss_pred chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEc---cCCceeEeceEEECCCEEEEEEccc
Confidence 45789999999999999999999999999999999999999986 3345789999999999999999874
No 7
>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=99.92 E-value=6.1e-25 Score=129.59 Aligned_cols=68 Identities=28% Similarity=0.489 Sum_probs=62.3
Q ss_pred CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEE
Q 041342 9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILV 79 (87)
Q Consensus 9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~ 79 (87)
.|+.+|+++++++|+|+|+||+.|+|+|.|||+|||++|+||+|+. ++.....+|.++|||++|.+|+
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~---~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI---DGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEe---CCccccCcCcEEEECCEEEEEC
Confidence 4899999999999999999999999999999999999999999874 4444678999999999999984
No 8
>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=99.92 E-value=1.4e-24 Score=133.75 Aligned_cols=74 Identities=24% Similarity=0.490 Sum_probs=65.2
Q ss_pred cCcHHHHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC--C--------eeeEeeCeEEEcCCcE
Q 041342 8 LLPSELIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE--G--------RRITKLDQILLNGNNI 75 (87)
Q Consensus 8 ~~Pl~~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~--g--------~~~~~~g~v~IRG~~I 75 (87)
..|+++|.+++ +++|.|+|++|+.+.|+|.|||+|||++|+||+|.+...+ + ...+.+|.+||||++|
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 37999999998 8999999999999999999999999999999999875421 1 2356899999999999
Q ss_pred EEEEeC
Q 041342 76 AILVPG 81 (87)
Q Consensus 76 ~~I~~~ 81 (87)
++|++.
T Consensus 81 v~Is~~ 86 (87)
T cd01720 81 ILVLRN 86 (87)
T ss_pred EEEecC
Confidence 999875
No 9
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.92 E-value=2.1e-24 Score=131.29 Aligned_cols=73 Identities=26% Similarity=0.528 Sum_probs=63.5
Q ss_pred cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCC-----eeeEeeCeEEEcCCcEEEEEeCC
Q 041342 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEG-----RRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g-----~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
+...|.++++++|.|+++|||.|.|+|.|||+||||+|++|+|+....+. ...+.+|.++|||++|++|++.+
T Consensus 3 ~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 3 SILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred chhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 34459999999999999999999999999999999999999999753221 24688999999999999998765
No 10
>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=99.91 E-value=4.2e-24 Score=129.52 Aligned_cols=74 Identities=31% Similarity=0.552 Sum_probs=65.0
Q ss_pred CCCcCcHHHHhhhcCC--EEEEEEc--CCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342 5 PSQLLPSELIDRCIGS--KIWVIMK--GDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 5 ~~~~~Pl~~L~~~l~k--~V~V~l~--dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
+.+..|++.|.+++++ +|.|+++ +|+.++|+|.|||+|||++|+||+|+.. .+...+.+|.++|||++|++|++
T Consensus 2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~--~~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHL--KTKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEec--CCceEeEcCcEEEeCCEEEEEcC
Confidence 4678999999999999 6777776 9999999999999999999999999863 23456789999999999999984
No 11
>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=99.91 E-value=8e-24 Score=126.92 Aligned_cols=71 Identities=21% Similarity=0.404 Sum_probs=63.1
Q ss_pred cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
++..|.++++++|.|.++|||.|.|+|.|||+|||++|+||.|+....+....+.+|.++|||++|++|+.
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 56789999999999999999999999999999999999999998754322246889999999999999975
No 12
>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=99.90 E-value=1.7e-23 Score=125.81 Aligned_cols=71 Identities=24% Similarity=0.372 Sum_probs=64.5
Q ss_pred CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342 9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG 81 (87)
Q Consensus 9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~ 81 (87)
.|+++|+++.|++|.|+|++|+.++|+|.+||+|||++|+||+++. .+|+....++.+||||++|.+|+..
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~--~~g~~~~~~~~v~IRG~~I~~i~~p 71 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTS--KDGDKFWKMPECYIRGNTIKYLRVP 71 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEEC--CCCcEeeeCCcEEEeCCEEEEEEcC
Confidence 4999999999999999999999999999999999999999999874 3565556789999999999999854
No 13
>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=99.90 E-value=3e-23 Score=124.11 Aligned_cols=71 Identities=30% Similarity=0.470 Sum_probs=63.3
Q ss_pred HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcc-CCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA-EGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~-~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
..|.++++++|+|+++|||.|.|+|.|||+|||++|++|.|+.... ++...+.+|.++|||++|++|++.+
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 4689999999999999999999999999999999999999986532 3445778999999999999999865
No 14
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.90 E-value=3.1e-23 Score=125.23 Aligned_cols=74 Identities=34% Similarity=0.694 Sum_probs=63.7
Q ss_pred CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCee-eEee-CeEEEcCCcEEEEEe
Q 041342 6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRR-ITKL-DQILLNGNNIAILVP 80 (87)
Q Consensus 6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~-~~~~-g~v~IRG~~I~~I~~ 80 (87)
....|+++|+++++++|.|+|+||++|+|+|.|||+|||++|+||+|+.. .++.. .+.+ +.++|||++|++|.+
T Consensus 4 ~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 4 LGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIIS-HDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred ccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEec-cCCccccceeccEEEEECCcEEEEeC
Confidence 34578999999999999999999999999999999999999999999974 23433 3444 499999999999863
No 15
>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=2.7e-23 Score=125.61 Aligned_cols=69 Identities=25% Similarity=0.432 Sum_probs=61.2
Q ss_pred HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC-------CeeeEeeCeEEEcCCcEEEEEe
Q 041342 12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE-------GRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~-------g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
+.|.++++++|.|.++|||.+.|+|.|||+||||+|+||.|++.... +.+.+.+|+++|||++|++|+.
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 46899999999999999999999999999999999999999875321 2356899999999999999974
No 16
>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=99.90 E-value=4.8e-23 Score=122.19 Aligned_cols=69 Identities=26% Similarity=0.422 Sum_probs=63.0
Q ss_pred cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG 81 (87)
Q Consensus 10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~ 81 (87)
|+++|+++.|++|+|+|+||.+|+|+|.++|+|||++|+||.+.. .+|+ ...++.+||||++|.+|...
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~--~~g~-~~~~~~v~IRG~nI~~v~lP 69 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTA--RDGR-VSQLEQVYIRGSKIRFFILP 69 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEEC--CCCc-EeEcCcEEEeCCEEEEEEeC
Confidence 889999999999999999999999999999999999999998864 3554 56789999999999999865
No 17
>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=99.89 E-value=1.3e-22 Score=118.39 Aligned_cols=67 Identities=31% Similarity=0.547 Sum_probs=61.1
Q ss_pred HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342 12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
.+|+++++++|+|+++||+.|+|+|.+||+|||++|++|.|+.. ++.+.+.+|.+||||++|++|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~--~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIK--NGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEET--TESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEEC--CCCcEeECcEEEEECCEEEEEEC
Confidence 47999999999999999999999999999999999999999973 22268899999999999999975
No 18
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.89 E-value=1.1e-22 Score=118.52 Aligned_cols=66 Identities=39% Similarity=0.718 Sum_probs=60.4
Q ss_pred HHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342 13 LIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 13 ~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
+|+++++++|+|+++||+.+.|+|.+||+|||++|+||+|+.. +..+.+.+|.+||||++|++|++
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~--~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVK--DGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEec--CCcEEeEeCCEEEcCCEEEEEeC
Confidence 6899999999999999999999999999999999999999874 22457899999999999999974
No 19
>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=6.8e-22 Score=118.82 Aligned_cols=69 Identities=19% Similarity=0.333 Sum_probs=61.9
Q ss_pred HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccC---CeeeEeeCeEEEcCCcEEEEEe
Q 041342 12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAE---GRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~---g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
+.|+++++++|+|.++|||.|.|+|.|||++|||+|+||.|+....+ ..+.+.+|+++|||++|++|+.
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 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 46899999999999999999999999999999999999999985422 2357899999999999999974
No 20
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.87 E-value=1e-21 Score=121.43 Aligned_cols=74 Identities=28% Similarity=0.482 Sum_probs=64.0
Q ss_pred CCcCcHHHHhhhcCC--EEEEEEcC--CcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342 6 SQLLPSELIDRCIGS--KIWVIMKG--DKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG 81 (87)
Q Consensus 6 ~~~~Pl~~L~~~l~k--~V~V~l~d--gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~ 81 (87)
.+..|+..+.+++.+ +|.|.+.| ++++.|+|.|||+|||++|+||+|+.. ++...+.+|.++|||++|++|++.
T Consensus 11 ~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~--~~~~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 11 IMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYT--KKNTRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred eecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEec--CCceeeEcCeEEEcCCEEEEEEcC
Confidence 568999999999996 57777766 589999999999999999999999863 234568999999999999999875
No 21
>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=99.87 E-value=1.8e-21 Score=120.50 Aligned_cols=71 Identities=24% Similarity=0.341 Sum_probs=64.1
Q ss_pred cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCC
Q 041342 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGS 83 (87)
Q Consensus 10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~ 83 (87)
++.+|+++.|++|+|+|+||..|+|+|.++|.|||++|+||+++. ++.....++.++|||++|.+|...+.
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~---~~~~~~~~~~v~IRG~nI~yi~lPd~ 72 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTL---KGRNPVPLDTLSIRGNNIRYFILPDS 72 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEc---CCCceeEcceEEEeCCEEEEEEcCCc
Confidence 688999999999999999999999999999999999999999885 33346789999999999999987653
No 22
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=4.1e-21 Score=110.49 Aligned_cols=63 Identities=32% Similarity=0.566 Sum_probs=57.4
Q ss_pred HhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEE
Q 041342 14 IDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILV 79 (87)
Q Consensus 14 L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~ 79 (87)
|++++|++|+|+++||+.|.|+|.+||+|||++|+||.|++. + ...+.++.+||||++|.+|.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~--~-~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIK--E-GKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEec--C-CcEEECCeEEEECCEEEEEC
Confidence 578899999999999999999999999999999999999874 2 35789999999999999874
No 23
>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=99.85 E-value=6.3e-21 Score=115.95 Aligned_cols=72 Identities=19% Similarity=0.339 Sum_probs=62.5
Q ss_pred CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCe-eeEeeCeEEEcCCcEEEEEeCC
Q 041342 9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGR-RITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~-~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
+|+++|+++.|++|.|+|++|..|+|+|.++|+|||++|+||+++.. ++. ....++.++|||++|.+|+..+
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~--~~~~~~~~~~~v~IRG~~I~~I~lp~ 73 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDP--EKYPHMLSVKNCFIRGSVVRYVQLPA 73 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcC--CCcccccccCeEEEECCEEEEEEeCh
Confidence 48899999999999999999999999999999999999999987642 221 2356799999999999998654
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=99.85 E-value=1e-20 Score=114.38 Aligned_cols=71 Identities=20% Similarity=0.375 Sum_probs=62.9
Q ss_pred CcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342 7 QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 7 ~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
...+..+|+++.|+.|.|+|+||..|+|+|.++|+|||++|+||++.. +++ ....+|.++|||++|.+|+.
T Consensus 7 ~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~--~~~-~~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 7 ENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIID--RNG-KQVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred hchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEc--CCC-ceeECCcEEEECCEEEEEEc
Confidence 356788999999999999999999999999999999999999998774 233 35579999999999999975
No 25
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.85 E-value=1.8e-21 Score=116.23 Aligned_cols=84 Identities=79% Similarity=1.237 Sum_probs=78.7
Q ss_pred CCCCCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 3 HNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 3 ~~~~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
++|+..+|++++.++++.++||.+++.|++.|+|.|||.|.|++|+|++|+...++|+...+++++++.|++|.+..+.+
T Consensus 1 ~n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 1 TNPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred CChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence 47889999999999999999999999999999999999999999999999987778877889999999999999999999
Q ss_pred CCCC
Q 041342 83 SPDP 86 (87)
Q Consensus 83 ~p~~ 86 (87)
.|+|
T Consensus 81 e~~E 84 (84)
T KOG1775|consen 81 EGPE 84 (84)
T ss_pred CCCC
Confidence 8764
No 26
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.84 E-value=5e-21 Score=113.66 Aligned_cols=71 Identities=23% Similarity=0.507 Sum_probs=62.9
Q ss_pred cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCC
Q 041342 8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGS 83 (87)
Q Consensus 8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~ 83 (87)
..| .|.+|++|++.+++..||.+.|+|+|||.|||+||++|+|... ++ ....+|.++|||++|+.+.+.+.
T Consensus 5 g~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~--~~-~~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 5 GHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNG--DG-DKNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred cCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecC--cC-CcceeeeEEEeccEEEEEeeccc
Confidence 356 7999999999999999999999999999999999999999853 33 35789999999999999987653
No 27
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.82 E-value=6.1e-20 Score=108.72 Aligned_cols=77 Identities=26% Similarity=0.400 Sum_probs=70.2
Q ss_pred CCCCCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 3 HNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 3 ~~~~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
++.++..|-.+|+.+.+|.|.|+|+.|.+|+|+|.+.|.|||+.|.+|+|+. +|.....+|.++||.+||.+|...+
T Consensus 2 ~a~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~i---dG~~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 2 SAKQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYI---DGVSTGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred CCcccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhh---cccccccceeEEEEeccEEEEecCC
Confidence 4556679999999999999999999999999999999999999999999986 7777889999999999999997543
No 28
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.77 E-value=8.9e-20 Score=110.53 Aligned_cols=75 Identities=29% Similarity=0.507 Sum_probs=66.9
Q ss_pred CcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCC----------eeeEeeCeEEEcCCcEE
Q 041342 7 QLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEG----------RRITKLDQILLNGNNIA 76 (87)
Q Consensus 7 ~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g----------~~~~~~g~v~IRG~~I~ 76 (87)
+..|+++|+-+++.+|.|+++++|.++|+|.|||+|.|++|.||+|+.+.-++ ...+.+..+|+||++|+
T Consensus 3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vi 82 (91)
T KOG3460|consen 3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVI 82 (91)
T ss_pred ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEE
Confidence 56899999999999999999999999999999999999999999999764322 13578899999999999
Q ss_pred EEEeC
Q 041342 77 ILVPG 81 (87)
Q Consensus 77 ~I~~~ 81 (87)
+|++.
T Consensus 83 lvspp 87 (91)
T KOG3460|consen 83 LVSPP 87 (91)
T ss_pred EEcCc
Confidence 99875
No 29
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.77 E-value=8.7e-20 Score=108.07 Aligned_cols=74 Identities=27% Similarity=0.476 Sum_probs=68.7
Q ss_pred CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
....|-++|.+++|++|.|+|.+|-.|+|+|.++|.||||.|+.++|+. +|+.++++|.+||||++|.+|+...
T Consensus 3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~---ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV---NGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh---cCcccccccceeeccccEEEEEecc
Confidence 3456899999999999999999999999999999999999999999985 7888999999999999999998753
No 30
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.72 E-value=9e-19 Score=109.01 Aligned_cols=75 Identities=27% Similarity=0.486 Sum_probs=66.7
Q ss_pred CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCC-----eeeEeeCeEEEcCCcEEEEEeCCC
Q 041342 9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEG-----RRITKLDQILLNGNNIAILVPGGS 83 (87)
Q Consensus 9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g-----~~~~~~g~v~IRG~~I~~I~~~~~ 83 (87)
..+-.|.+|++++|+|++.+||...|+|.|||+.||+||++++|+..+++. .+.|++|++++||..+++|++.+.
T Consensus 17 EsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG 96 (108)
T KOG1781|consen 17 ESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADG 96 (108)
T ss_pred hHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcc
Confidence 346679999999999999999999999999999999999999999876542 246999999999999999998764
No 31
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.66 E-value=1.7e-16 Score=95.91 Aligned_cols=75 Identities=29% Similarity=0.538 Sum_probs=62.4
Q ss_pred CCcCcHHHHhhhcCC--EEEEEEcC--CcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342 6 SQLLPSELIDRCIGS--KIWVIMKG--DKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG 81 (87)
Q Consensus 6 ~~~~Pl~~L~~~l~k--~V~V~l~d--gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~ 81 (87)
.+++|++++.+|+.. +|.|.|.+ |-.++|.+.|||+|||+||++|+|...+.. ..+.+|.++++||||..|...
T Consensus 9 vmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~--~rk~lGRilLKGDnItli~~~ 86 (88)
T KOG1774|consen 9 VMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK--SRKELGRILLKGDNITLIQSA 86 (88)
T ss_pred eecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccccc--CCCccccEEEcCCcEEEEeec
Confidence 468999999999985 46666654 889999999999999999999999864322 234899999999999999876
Q ss_pred C
Q 041342 82 G 82 (87)
Q Consensus 82 ~ 82 (87)
+
T Consensus 87 ~ 87 (88)
T KOG1774|consen 87 G 87 (88)
T ss_pred C
Confidence 4
No 32
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.65 E-value=3.7e-16 Score=100.78 Aligned_cols=73 Identities=21% Similarity=0.363 Sum_probs=67.7
Q ss_pred cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
++||++|...-+..+.|+||+|.+|.|.|..+|.+|||.|.+++++. .||.+...+..++|||++|.++...+
T Consensus 1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts--~Dgdkf~r~pEcYirGttIkylri~d 73 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTS--EDGDKFFRMPECYIRGTTIKYLRIPD 73 (134)
T ss_pred CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEec--cCCCceeecceeEEecceeEEEeccH
Confidence 47999999999999999999999999999999999999999999986 47878889999999999999997643
No 33
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.63 E-value=5.3e-17 Score=109.44 Aligned_cols=76 Identities=28% Similarity=0.530 Sum_probs=67.2
Q ss_pred HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEc-------cCCeeeEeeCeEEEcCCcEEEEEeCCCC
Q 041342 12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEIT-------AEGRRITKLDQILLNGNNIAILVPGGSP 84 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~-------~~g~~~~~~g~v~IRG~~I~~I~~~~~p 84 (87)
+.|.++++.+++|.++|||.|.|.+.+||.|||++|.+|+|.... .++++.|-+|+|++||++|++.+..+.|
T Consensus 7 skml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegpp 86 (177)
T KOG3168|consen 7 SKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPP 86 (177)
T ss_pred hHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCC
Confidence 356778999999999999999999999999999999999997542 2456789999999999999999999999
Q ss_pred CCC
Q 041342 85 DPE 87 (87)
Q Consensus 85 ~~~ 87 (87)
+++
T Consensus 87 p~s 89 (177)
T KOG3168|consen 87 PPS 89 (177)
T ss_pred CCc
Confidence 764
No 34
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.60 E-value=1.5e-16 Score=102.37 Aligned_cols=74 Identities=20% Similarity=0.370 Sum_probs=64.2
Q ss_pred HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342 12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSPD 85 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~p~ 85 (87)
..|.+++++++.|.|+|||.+.|.|++||||.|++|++|.|++...+-...+..|..+|||.||+++...+.-+
T Consensus 12 ~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dk 85 (129)
T KOG1782|consen 12 TSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDK 85 (129)
T ss_pred hHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcch
Confidence 34889999999999999999999999999999999999999987544334577899999999999998766443
No 35
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.58 E-value=1.6e-15 Score=93.37 Aligned_cols=72 Identities=24% Similarity=0.460 Sum_probs=64.5
Q ss_pred HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcc-CCeeeEeeCeEEEcCCcEEEEEeCCC
Q 041342 12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA-EGRRITKLDQILLNGNNIAILVPGGS 83 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~-~g~~~~~~g~v~IRG~~I~~I~~~~~ 83 (87)
+-|..|++++|.|...|||.+.|.|.||||..||+|+++-|+.++. .|.++..+|..+|||+||..|.++..
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDE 75 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecch
Confidence 3589999999999999999999999999999999999999987642 45667899999999999999987653
No 36
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.46 E-value=5.2e-13 Score=81.92 Aligned_cols=71 Identities=18% Similarity=0.338 Sum_probs=59.8
Q ss_pred HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
.++++.++|++|.|+|+++-.+.|+|.+.|||.|+.|+|......++ =..--.+..+||||+.|.+|....
T Consensus 4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~k-yPhm~Sv~ncfIRGSvvrYv~l~k 74 (96)
T KOG3448|consen 4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDK-YPHMLSVKNCFIRGSVVRYVQLPK 74 (96)
T ss_pred HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCccc-CCCeeeeeeEEEeccEEEEEEeCh
Confidence 57899999999999999999999999999999999999998764211 012356779999999999998653
No 37
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.45 E-value=3.3e-13 Score=85.42 Aligned_cols=73 Identities=27% Similarity=0.393 Sum_probs=65.4
Q ss_pred CCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342 6 SQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG 81 (87)
Q Consensus 6 ~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~ 81 (87)
++..|+.+|++.-+.-|+++++.|..|+|.|...|.+||+.|+|.+.+. .+|. ...+.++||||+.|.++...
T Consensus 2 s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~--~dg~-vs~le~V~IRGS~IRFlvlP 74 (119)
T KOG3172|consen 2 SVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTA--RDGR-VSQLEQVFIRGSKIRFLVLP 74 (119)
T ss_pred ccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEc--cCCc-ceeeeeEEEecCeEEEEECc
Confidence 4568999999999999999999999999999999999999999999875 3554 66889999999999998754
No 38
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=99.22 E-value=1.5e-10 Score=73.38 Aligned_cols=68 Identities=22% Similarity=0.384 Sum_probs=61.2
Q ss_pred HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
+.+|+++.+.+|+|+|++|....|++.+.|.+||..|.++.-+. .| ++..+..++|||++|.|+....
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~---~~-~pv~l~~lsirgnniRy~~lpD 71 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTV---KG-EPVRLDTLSIRGNNIRYYILPD 71 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEec---CC-CceeEEEEEeecceEEEEEccC
Confidence 57899999999999999999999999999999999999998764 35 5678999999999999997554
No 39
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.14 E-value=5.8e-12 Score=79.89 Aligned_cols=73 Identities=22% Similarity=0.461 Sum_probs=63.4
Q ss_pred cCcHHHHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcc----CCe------eeEeeCeEEEcCCcE
Q 041342 8 LLPSELIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITA----EGR------RITKLDQILLNGNNI 75 (87)
Q Consensus 8 ~~Pl~~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~----~g~------~~~~~g~v~IRG~~I 75 (87)
.+|++++..... ..|.|.++|++.+-|++.|||.|.|++|+++.|.|+.. +|. ..|.+|.+|||||+|
T Consensus 23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv 102 (114)
T KOG3459|consen 23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV 102 (114)
T ss_pred cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence 479999998887 47899999999999999999999999999999998742 332 268999999999999
Q ss_pred EEEEe
Q 041342 76 AILVP 80 (87)
Q Consensus 76 ~~I~~ 80 (87)
+.+..
T Consensus 103 I~v~r 107 (114)
T KOG3459|consen 103 ILVLR 107 (114)
T ss_pred EEEEe
Confidence 98873
No 40
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=98.46 E-value=1.5e-07 Score=54.98 Aligned_cols=36 Identities=31% Similarity=0.340 Sum_probs=29.8
Q ss_pred CEEEEEEcC----CcEEEEEEEEeccccceEEcceEEEEE
Q 041342 20 SKIWVIMKG----DKELVGTLKGFDVYVNMVLEDVTEYEI 55 (87)
Q Consensus 20 k~V~V~l~d----gr~~~G~L~~~D~~mNlvL~~~~e~~~ 55 (87)
.+|.|.++. +-.++|.|.+||+|+|++|.|+.|.+.
T Consensus 9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~ 48 (66)
T cd01739 9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR 48 (66)
T ss_pred cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence 567776654 226889999999999999999999875
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.21 E-value=3.1e-06 Score=50.36 Aligned_cols=65 Identities=11% Similarity=0.202 Sum_probs=41.5
Q ss_pred HHHhhhcCCEEEEEEcCCcEEEEEEEEecc---ccceEEcceEEEEEccC--C--eeeEeeCeEEEcCCcEE
Q 041342 12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDV---YVNMVLEDVTEYEITAE--G--RRITKLDQILLNGNNIA 76 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~---~mNlvL~~~~e~~~~~~--g--~~~~~~g~v~IRG~~I~ 76 (87)
-++..++|++|.|.++||..|+|+|.+++. -+.++|+.|........ . .......+++|+++.|+
T Consensus 5 ~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 5 YLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 357789999999999999999999999998 89999999887532110 1 12345567777777665
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.96 E-value=7.2e-05 Score=46.81 Aligned_cols=69 Identities=33% Similarity=0.431 Sum_probs=55.9
Q ss_pred hhhcCCEEEEEEcCCcEEEEEEEEecc-ccceEEcceEEEEEccCCe--------eeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342 15 DRCIGSKIWVIMKGDKELVGTLKGFDV-YVNMVLEDVTEYEITAEGR--------RITKLDQILLNGNNIAILVPGGSPD 85 (87)
Q Consensus 15 ~~~l~k~V~V~l~dgr~~~G~L~~~D~-~mNlvL~~~~e~~~~~~g~--------~~~~~g~v~IRG~~I~~I~~~~~p~ 85 (87)
..|+|++|.+..+++-.|+|+|..+|. ...|.|.++.-+.+ +|. .......+..||..|..+...+.|+
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~Gt--E~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~ 81 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGT--EGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP 81 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTE--TTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCc--CCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence 468999999999999999999999995 89999999986643 221 1346789999999999998877765
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=97.39 E-value=0.0012 Score=36.02 Aligned_cols=48 Identities=21% Similarity=0.302 Sum_probs=35.7
Q ss_pred hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEc
Q 041342 17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLN 71 (87)
Q Consensus 17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IR 71 (87)
.+|++|++.. ++..++|+..++|+...|+++..... ......|.+++|
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g~------~~~i~sGdv~~r 48 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDGS------IRTISSGDVSLR 48 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTEE------EEEESSSEEEEE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCCC------EEEEEEEEEEeC
Confidence 3789999999 56777999999999999999765431 123344666654
No 44
>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=97.16 E-value=0.0028 Score=37.93 Aligned_cols=64 Identities=28% Similarity=0.386 Sum_probs=49.4
Q ss_pred hhhcCCEEEEEEcCCcEEEEEEEEec-cccceEEcceEEEEEcc---CCe----eeEeeCeEEEcCCcEEEE
Q 041342 15 DRCIGSKIWVIMKGDKELVGTLKGFD-VYVNMVLEDVTEYEITA---EGR----RITKLDQILLNGNNIAIL 78 (87)
Q Consensus 15 ~~~l~k~V~V~l~dgr~~~G~L~~~D-~~mNlvL~~~~e~~~~~---~g~----~~~~~g~v~IRG~~I~~I 78 (87)
.+++|+++.+..+.+-.|+|+|..+| +-.-+.|.|+.-+.++. ++. ...-+..++.||+.|..+
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkDL 73 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKDL 73 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccccc
Confidence 36899999999999999999999999 46778899988765421 111 234567899999988654
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=96.84 E-value=0.0031 Score=36.48 Aligned_cols=37 Identities=14% Similarity=0.335 Sum_probs=29.1
Q ss_pred HHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcc
Q 041342 13 LIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLED 49 (87)
Q Consensus 13 ~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~ 49 (87)
+|+.+.. .+|+|.|.||-.++|.+.+||+|+=++-.+
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 3444443 468999999999999999999998666544
No 46
>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=96.76 E-value=0.0038 Score=36.08 Aligned_cols=37 Identities=14% Similarity=0.304 Sum_probs=29.0
Q ss_pred HHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcc
Q 041342 13 LIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLED 49 (87)
Q Consensus 13 ~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~ 49 (87)
+|..+.. .+|+|.|.+|-.++|.+.+||+|+=++-.+
T Consensus 7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 3444443 579999999999999999999998666544
No 47
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=96.61 E-value=0.0068 Score=36.71 Aligned_cols=38 Identities=13% Similarity=0.281 Sum_probs=30.0
Q ss_pred HHhhhc--CCEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 13 LIDRCI--GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 13 ~L~~~l--~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
+|..+. ...|+|.|.+|-.++|.+.|||+|+=++-.+.
T Consensus 11 fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 11 FLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred HHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 444444 35799999999999999999999987765444
No 48
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=96.31 E-value=0.02 Score=39.11 Aligned_cols=64 Identities=19% Similarity=0.277 Sum_probs=44.2
Q ss_pred CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEecc-ccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCC
Q 041342 9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDV-YVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGS 83 (87)
Q Consensus 9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~-~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~ 83 (87)
.|+ .+..|++|.|.|.+.| +++.|.|..+|. .-|+||-+..| ++. . ..-+|-|-+|..|.....
T Consensus 8 ~p~-~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e-----~~~--~--sv~~I~ghaVk~vevl~~ 72 (166)
T PF06372_consen 8 SPL-EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE-----DGK--R--SVKVIMGHAVKSVEVLSE 72 (166)
T ss_dssp -HH-HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T-----TS---E--EEEEE-GGGEEEEEEEE-
T ss_pred CHH-HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc-----CCc--e--eEEEEEccceEEEEEccC
Confidence 455 5678999999999999 999999999996 88999986553 332 2 247888999988876543
No 49
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=95.81 E-value=0.04 Score=31.81 Aligned_cols=36 Identities=19% Similarity=0.286 Sum_probs=30.7
Q ss_pred hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEE
Q 041342 17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTE 52 (87)
Q Consensus 17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e 52 (87)
.+|..|++++..|..++|.+.+||.-.++++-.|.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 478999999999999999999999888877655443
No 50
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=95.80 E-value=0.044 Score=32.96 Aligned_cols=28 Identities=18% Similarity=0.389 Sum_probs=24.5
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceE
Q 041342 19 GSKIWVIMKGDKELVGTLKGFDVYVNMV 46 (87)
Q Consensus 19 ~k~V~V~l~dgr~~~G~L~~~D~~mNlv 46 (87)
+.+|.|.|.||-.++|.+.+||+|.=++
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD~f~VlL 46 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFDNFVVLL 46 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence 4579999999999999999999997443
No 51
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.68 E-value=0.042 Score=41.64 Aligned_cols=71 Identities=27% Similarity=0.361 Sum_probs=57.0
Q ss_pred hhhcCCEEEEEEcCCcEEEEEEEEec-cccceEEcceEEEEEc---cCCe----eeEeeCeEEEcCCcEEEEEeCCCCC
Q 041342 15 DRCIGSKIWVIMKGDKELVGTLKGFD-VYVNMVLEDVTEYEIT---AEGR----RITKLDQILLNGNNIAILVPGGSPD 85 (87)
Q Consensus 15 ~~~l~k~V~V~l~dgr~~~G~L~~~D-~~mNlvL~~~~e~~~~---~~g~----~~~~~g~v~IRG~~I~~I~~~~~p~ 85 (87)
..|||++|.++-+..-.|+|+|.-+| +-.-|-|.++.-+.++ .++. ....+..++.||+.|..+...+.|.
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p~ 83 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETPA 83 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCcc
Confidence 56899999999999999999999999 7888999998655442 1221 1226789999999999998887664
No 52
>PRK14638 hypothetical protein; Provisional
Probab=95.47 E-value=0.056 Score=36.11 Aligned_cols=45 Identities=18% Similarity=0.278 Sum_probs=34.3
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLE 48 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~ 48 (87)
++|=...| ...+.+++|++|.|++++++.++|+|.++|.- ++.|.
T Consensus 81 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 81 SSPGLDRPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred eCCCCCCCCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 34444445 45577889999999999999999999999963 45553
No 53
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=95.41 E-value=0.14 Score=29.93 Aligned_cols=54 Identities=20% Similarity=0.323 Sum_probs=40.6
Q ss_pred HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342 11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
...|++++|++|.|.+..|.. +|+|.+.-.- .++|+.. + ...|||=..|++|.+
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--------G------TPFFIRIAQIVWVMP 66 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC--------C------cEEEEEeeeEEEEcC
Confidence 567999999999999987665 9999998742 2344433 1 368899888888753
No 54
>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=95.18 E-value=0.31 Score=29.55 Aligned_cols=62 Identities=10% Similarity=0.164 Sum_probs=46.9
Q ss_pred HHHHhhhcCCEEEEEEcCCcEEEEEEEEecc-ccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEe
Q 041342 11 SELIDRCIGSKIWVIMKGDKELVGTLKGFDV-YVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVP 80 (87)
Q Consensus 11 l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~-~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~ 80 (87)
|..|....|++|.+.+.++....|++.++|. ..|+..++-. + +=| .....++|..-|++++.
T Consensus 16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-T---PlG----v~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-T---PLG----VQPEALLRCSDVISISF 78 (80)
T ss_dssp HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-T---TTT----EEEEEEEEGGGEEEEEE
T ss_pred HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-C---Ccc----cChhheeecCCEEEEEe
Confidence 4567788899999999999999999999994 6677666653 1 234 35789999999999874
No 55
>PRK02001 hypothetical protein; Validated
Probab=95.13 E-value=0.084 Score=35.45 Aligned_cols=45 Identities=27% Similarity=0.375 Sum_probs=35.1
Q ss_pred CCCCCcCcH---HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 041342 3 HNPSQLLPS---ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLE 48 (87)
Q Consensus 3 ~~~~~~~Pl---~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~ 48 (87)
++|-...|| ..+.+++|+.|.|++.+++.+.|+|.++|.. ++.|.
T Consensus 71 SSPGldRpL~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 71 GSAGLTSPLKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence 455555554 4577889999999999999999999999964 45553
No 56
>PRK14639 hypothetical protein; Provisional
Probab=95.03 E-value=0.094 Score=34.65 Aligned_cols=43 Identities=19% Similarity=0.287 Sum_probs=33.9
Q ss_pred CCCCcCc---HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 041342 4 NPSQLLP---SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVL 47 (87)
Q Consensus 4 ~~~~~~P---l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL 47 (87)
+|=...| ...+.+++|++|.|++.+++.+.|+|.++|. .++.|
T Consensus 70 SPGl~RpL~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~-~~i~l 115 (140)
T PRK14639 70 SPGLERKLSKIEHFAKSIGELVKITTNEKEKFEGKIVSVDD-ENITL 115 (140)
T ss_pred CCCCCCcCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeC-CEEEE
Confidence 4444444 4567789999999999999999999999997 35555
No 57
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=94.99 E-value=0.057 Score=36.83 Aligned_cols=38 Identities=13% Similarity=0.238 Sum_probs=30.1
Q ss_pred HHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 13 LIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 13 ~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
+|..+.. ..|+|.|.+|-.++|++.+||+|.=+.-.+.
T Consensus 16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 4555554 4688999999999999999999986665554
No 58
>PRK14644 hypothetical protein; Provisional
Probab=94.96 E-value=0.093 Score=34.58 Aligned_cols=45 Identities=20% Similarity=0.243 Sum_probs=33.9
Q ss_pred CCCCCcCcHH--HHhhhcCCEEEEEEcCC----cEEEEEEEEeccccceEEc
Q 041342 3 HNPSQLLPSE--LIDRCIGSKIWVIMKGD----KELVGTLKGFDVYVNMVLE 48 (87)
Q Consensus 3 ~~~~~~~Pl~--~L~~~l~k~V~V~l~dg----r~~~G~L~~~D~~mNlvL~ 48 (87)
++|=...||. .+.+++|+.|.|++++. +.+.|+|.++|. -++.|.
T Consensus 67 SSPGldRpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~-~~i~l~ 117 (136)
T PRK14644 67 SSPGFDMDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNP-ETITLK 117 (136)
T ss_pred ECCCCCCCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeC-CEEEEE
Confidence 3444444443 48899999999999887 899999999997 355554
No 59
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=94.77 E-value=0.086 Score=35.98 Aligned_cols=38 Identities=13% Similarity=0.300 Sum_probs=29.8
Q ss_pred HHhhhcC--CEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 13 LIDRCIG--SKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 13 ~L~~~l~--k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
+|..+.. ..|+|.|.+|-.++|.+.+||+|.=+.-.+.
T Consensus 96 fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 96 FLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 4554444 4689999999999999999999986665443
No 60
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=94.02 E-value=0.16 Score=33.15 Aligned_cols=44 Identities=34% Similarity=0.448 Sum_probs=29.0
Q ss_pred CCCCCcCcH---HHHhhhcCCEEEEEEc----CCcEEEEEEEEeccccceEE
Q 041342 3 HNPSQLLPS---ELIDRCIGSKIWVIMK----GDKELVGTLKGFDVYVNMVL 47 (87)
Q Consensus 3 ~~~~~~~Pl---~~L~~~l~k~V~V~l~----dgr~~~G~L~~~D~~mNlvL 47 (87)
++|-...|| ..+.+++|+.|.|+++ +.+.+.|+|.++|. -.++|
T Consensus 68 SSPG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 68 SSPGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp E--SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred eCCCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 345555665 5788999999999994 45689999999998 44444
No 61
>PRK14640 hypothetical protein; Provisional
Probab=93.51 E-value=0.42 Score=31.90 Aligned_cols=45 Identities=16% Similarity=0.307 Sum_probs=33.1
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEE----cCCcEEEEEEEEeccccceEEc
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIM----KGDKELVGTLKGFDVYVNMVLE 48 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l----~dgr~~~G~L~~~D~~mNlvL~ 48 (87)
++|=...| ...+.+++|++|.|++ .+.+.++|+|.++|. -++.|.
T Consensus 78 SSPGl~RpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~-~~v~l~ 129 (152)
T PRK14640 78 SSPGLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQG-DMITLT 129 (152)
T ss_pred eCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeC-CEEEEE
Confidence 34444445 4557788999999999 467899999999987 345553
No 62
>PRK06955 biotin--protein ligase; Provisional
Probab=93.33 E-value=0.53 Score=34.41 Aligned_cols=50 Identities=18% Similarity=0.320 Sum_probs=36.2
Q ss_pred hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCC
Q 041342 17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGN 73 (87)
Q Consensus 17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~ 73 (87)
+++++|+|...+++.++|++.|+|+...|+++.. +|.+....|.+.+|..
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~-------~g~~~~~sGeV~~~~~ 296 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDTP-------AGRQAIAAGDVSLREA 296 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEeC-------CCeEEEEEEEEEEecc
Confidence 5688999976677889999999999999998532 2322334566666543
No 63
>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=93.07 E-value=0.51 Score=28.18 Aligned_cols=36 Identities=31% Similarity=0.436 Sum_probs=28.5
Q ss_pred HHHHhhhcCCEEEEEEc---CC-cEEEEEEEEeccccceEE
Q 041342 11 SELIDRCIGSKIWVIMK---GD-KELVGTLKGFDVYVNMVL 47 (87)
Q Consensus 11 l~~L~~~l~k~V~V~l~---dg-r~~~G~L~~~D~~mNlvL 47 (87)
...+.+++|+.|.|+++ +| +.+.|+|.++|.. ++.|
T Consensus 17 ~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 17 EADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred HHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 45677889999999997 55 5899999999983 4444
No 64
>PRK14633 hypothetical protein; Provisional
Probab=92.99 E-value=0.41 Score=31.91 Aligned_cols=45 Identities=13% Similarity=0.211 Sum_probs=32.8
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEE----cCCcEEEEEEEEeccccceEEc
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIM----KGDKELVGTLKGFDVYVNMVLE 48 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l----~dgr~~~G~L~~~D~~mNlvL~ 48 (87)
++|=...| ...+.+++|++|.|++ .+++.++|+|.++|+. ++.|.
T Consensus 75 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 75 SSPGMNRQIFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred eCCCCCCCCCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 34444445 4567788999999988 3667999999999873 55553
No 65
>PRK14642 hypothetical protein; Provisional
Probab=92.93 E-value=0.38 Score=33.69 Aligned_cols=44 Identities=23% Similarity=0.281 Sum_probs=33.1
Q ss_pred CCCCCcCcH---HHHhhhcCCEEEEEEc-------------CCcEEEEEEEEeccccceEE
Q 041342 3 HNPSQLLPS---ELIDRCIGSKIWVIMK-------------GDKELVGTLKGFDVYVNMVL 47 (87)
Q Consensus 3 ~~~~~~~Pl---~~L~~~l~k~V~V~l~-------------dgr~~~G~L~~~D~~mNlvL 47 (87)
++|=...|| ..+.+++|+.|.|+++ +.+.|+|+|.++|.. ++.|
T Consensus 81 SSPGldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 81 SSPGIDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred eCCCCCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 344444554 4567889999999998 678999999999974 4444
No 66
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.84 E-value=0.6 Score=31.46 Aligned_cols=43 Identities=30% Similarity=0.455 Sum_probs=33.5
Q ss_pred CCCCcCc---HHHHhhhcCCEEEEEE----cCCcEEEEEEEEeccccceEE
Q 041342 4 NPSQLLP---SELIDRCIGSKIWVIM----KGDKELVGTLKGFDVYVNMVL 47 (87)
Q Consensus 4 ~~~~~~P---l~~L~~~l~k~V~V~l----~dgr~~~G~L~~~D~~mNlvL 47 (87)
+|=...| ...+..++|+.|.|.+ .+++.++|+|.++|.-. +++
T Consensus 81 SPGldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 81 SPGLDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred CCCCCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 4433444 4567788999999999 78899999999999876 444
No 67
>PRK14645 hypothetical protein; Provisional
Probab=92.65 E-value=0.43 Score=32.07 Aligned_cols=43 Identities=19% Similarity=0.265 Sum_probs=31.7
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVL 47 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL 47 (87)
++|=...| ...+.+++|++|.|++ +++.++|+|.++|.. .+.|
T Consensus 83 SSPGldRpL~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 83 ESPGPKRPLFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred eCCCCCCCCCCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 34444445 3457788999999986 789999999999973 4444
No 68
>PRK14636 hypothetical protein; Provisional
Probab=91.86 E-value=0.65 Score=31.82 Aligned_cols=43 Identities=21% Similarity=0.349 Sum_probs=31.7
Q ss_pred CCCCcCc---HHHHhhhcCCEEEEEEc---CC-cEEEEEEEEeccccceEE
Q 041342 4 NPSQLLP---SELIDRCIGSKIWVIMK---GD-KELVGTLKGFDVYVNMVL 47 (87)
Q Consensus 4 ~~~~~~P---l~~L~~~l~k~V~V~l~---dg-r~~~G~L~~~D~~mNlvL 47 (87)
+|=...| ...+.+++|++|.|+++ +| +.++|+|.++|.- ++.|
T Consensus 80 SPGldRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 80 SPGIDRPLTRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred CCCCCCCCCCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 4434444 35677899999999997 55 5999999999873 4554
No 69
>PRK14632 hypothetical protein; Provisional
Probab=91.43 E-value=0.77 Score=31.31 Aligned_cols=45 Identities=20% Similarity=0.343 Sum_probs=33.1
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEEcC-------CcEEEEEEEEeccccceEEc
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIMKG-------DKELVGTLKGFDVYVNMVLE 48 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l~d-------gr~~~G~L~~~D~~mNlvL~ 48 (87)
++|=...| ...+.+++|+.|.|++++ .+.+.|+|.++|. -++.|.
T Consensus 79 SSPGldRpL~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~-~~i~l~ 133 (172)
T PRK14632 79 SSPGLERPFFRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEG-DTVVLR 133 (172)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeC-CEEEEE
Confidence 34544455 355778999999999976 5699999999986 355554
No 70
>PRK14643 hypothetical protein; Provisional
Probab=91.32 E-value=0.82 Score=31.01 Aligned_cols=40 Identities=15% Similarity=0.252 Sum_probs=30.6
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEEcC----CcEEEEEEEEeccc
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIMKG----DKELVGTLKGFDVY 42 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l~d----gr~~~G~L~~~D~~ 42 (87)
++|=...| ...+.+++|++|.|++++ .+.++|+|.++|.-
T Consensus 85 SSPGleRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 85 SSSGIEKQIRSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred cCCCCCCCCCCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 34544445 446778999999999865 57999999999964
No 71
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=91.30 E-value=1.1 Score=35.94 Aligned_cols=32 Identities=28% Similarity=0.394 Sum_probs=28.1
Q ss_pred hcCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 041342 17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLE 48 (87)
Q Consensus 17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~ 48 (87)
++|++|.+...+++.+.|+..|+|+...|+|+
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 56889998766777899999999999999996
No 72
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=91.24 E-value=0.85 Score=30.30 Aligned_cols=39 Identities=28% Similarity=0.407 Sum_probs=30.7
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEE----cCCcEEEEEEEEecc
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIM----KGDKELVGTLKGFDV 41 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l----~dgr~~~G~L~~~D~ 41 (87)
++|-...| ...+.+++|+.|.|++ .+++.+.|+|.++|.
T Consensus 79 SSPGi~RpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 79 SSPGLDRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred eCCCCCCcCCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 34544455 3567889999999997 567899999999997
No 73
>PRK14634 hypothetical protein; Provisional
Probab=91.12 E-value=0.88 Score=30.51 Aligned_cols=44 Identities=14% Similarity=0.088 Sum_probs=31.7
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEEcC----CcEEEEEEEEeccccceEE
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIMKG----DKELVGTLKGFDVYVNMVL 47 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l~d----gr~~~G~L~~~D~~mNlvL 47 (87)
++|=...| ...+.+++|++|.|++.+ .+.|.|+|.++|. .++.|
T Consensus 81 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~-~~v~l 131 (155)
T PRK14634 81 SSPGIGDQLSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNE-DHLQI 131 (155)
T ss_pred eCCCCCCcCCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeC-CEEEE
Confidence 34544445 345778899999999863 2689999999996 34545
No 74
>PRK14646 hypothetical protein; Provisional
Probab=90.80 E-value=1 Score=30.20 Aligned_cols=45 Identities=13% Similarity=0.000 Sum_probs=32.4
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEEcC---C-cEEEEEEEEeccccceEEc
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIMKG---D-KELVGTLKGFDVYVNMVLE 48 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l~d---g-r~~~G~L~~~D~~mNlvL~ 48 (87)
++|=...| ...+.+++|++|.|++++ | +.++|+|.++|.- ++.|.
T Consensus 81 SSPGldRpL~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 81 SSQGVSDELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred cCCCCCCcCCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 34544445 456778999999999864 3 5789999999974 55553
No 75
>PRK14647 hypothetical protein; Provisional
Probab=90.47 E-value=1.1 Score=30.03 Aligned_cols=44 Identities=20% Similarity=0.249 Sum_probs=31.8
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEEc---------CCcEEEEEEEEeccccceEE
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIMK---------GDKELVGTLKGFDVYVNMVL 47 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l~---------dgr~~~G~L~~~D~~mNlvL 47 (87)
++|=...| ...+.+++|++|.|+++ +.+.+.|+|.++|. ..+.|
T Consensus 80 SSPG~~RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~-~~v~l 135 (159)
T PRK14647 80 SSPGLDRPLKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD-GVVTI 135 (159)
T ss_pred cCCCCCCcCCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC-CEEEE
Confidence 34544445 45677899999999995 35799999999996 33444
No 76
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=90.19 E-value=1.9 Score=31.49 Aligned_cols=48 Identities=27% Similarity=0.385 Sum_probs=35.0
Q ss_pred hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcC
Q 041342 17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNG 72 (87)
Q Consensus 17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG 72 (87)
++|++|.+... +..++|++.++|....|++++. .+.+....|.+.+|.
T Consensus 270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~~~-------g~~~~~~~gev~~~~ 317 (319)
T PRK11886 270 FLGREVKLIIG-DKEISGIARGIDEQGALLLEDD-------GVEKPFNGGEISLRS 317 (319)
T ss_pred ccCCeEEEEeC-CcEEEEEEEEECCCceEEEEeC-------CcEEEEEEeEEEEec
Confidence 56889999874 5679999999999999999621 222334557777665
No 77
>PRK14631 hypothetical protein; Provisional
Probab=89.75 E-value=1.2 Score=30.42 Aligned_cols=38 Identities=18% Similarity=0.297 Sum_probs=29.4
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEEc----CCcEEEEEEEEec
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIMK----GDKELVGTLKGFD 40 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l~----dgr~~~G~L~~~D 40 (87)
++|=...| ...+.+++|+.|.|++. +.+.|+|+|.++|
T Consensus 98 SSPGldRpL~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 98 SSPGWDRPFFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred eCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 34444444 45678899999999996 4589999999998
No 78
>PRK14641 hypothetical protein; Provisional
Probab=89.02 E-value=1.4 Score=30.18 Aligned_cols=38 Identities=21% Similarity=0.386 Sum_probs=28.9
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEEcC----CcEEEEEEEEec
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIMKG----DKELVGTLKGFD 40 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l~d----gr~~~G~L~~~D 40 (87)
++|-...| ...+.+++|+.|.|++.+ .+.++|+|.++|
T Consensus 85 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 85 SSPGLGEPIILPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 34444455 355778899999999976 558999999995
No 79
>PRK14637 hypothetical protein; Provisional
Probab=88.62 E-value=1.7 Score=29.01 Aligned_cols=44 Identities=20% Similarity=0.227 Sum_probs=30.7
Q ss_pred CCCCcCc---HHHHhhhcCCEEEEEEcCCcEE-EEEEEEeccccceEEc
Q 041342 4 NPSQLLP---SELIDRCIGSKIWVIMKGDKEL-VGTLKGFDVYVNMVLE 48 (87)
Q Consensus 4 ~~~~~~P---l~~L~~~l~k~V~V~l~dgr~~-~G~L~~~D~~mNlvL~ 48 (87)
+|=...| ...+.+++|++|.|++.+.+.+ +|+|.++|.- ++.|.
T Consensus 80 SPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 80 SPGIERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred CCCCCCCCCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 4444445 4567788999999999444455 7999999874 44443
No 80
>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=88.21 E-value=3.1 Score=29.15 Aligned_cols=31 Identities=26% Similarity=0.402 Sum_probs=26.8
Q ss_pred hcCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 041342 17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLE 48 (87)
Q Consensus 17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~ 48 (87)
.++++|.+...+ ..+.|+..|+|+...|+++
T Consensus 191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 558999998754 5799999999999999996
No 81
>PRK08330 biotin--protein ligase; Provisional
Probab=87.70 E-value=3.4 Score=28.93 Aligned_cols=34 Identities=18% Similarity=0.278 Sum_probs=27.5
Q ss_pred hhcCCEEEEEEcCCcEE-EEEEEEeccccceEEcce
Q 041342 16 RCIGSKIWVIMKGDKEL-VGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 16 ~~l~k~V~V~l~dgr~~-~G~L~~~D~~mNlvL~~~ 50 (87)
.+++++|.+.. ++..+ .|+..++|....|+++..
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence 36789999875 56665 799999999999999744
No 82
>PRK10898 serine endoprotease; Provisional
Probab=81.47 E-value=3.7 Score=30.67 Aligned_cols=31 Identities=16% Similarity=0.312 Sum_probs=27.6
Q ss_pred CEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 20 SKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 20 k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
.++.|.+.||+.+.+++.++|....|-|=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 5789999999999999999999999877554
No 83
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=81.20 E-value=10 Score=27.01 Aligned_cols=36 Identities=22% Similarity=0.333 Sum_probs=32.0
Q ss_pred hhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 15 DRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 15 ~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
...++++|++...++....|+..++|....|+++..
T Consensus 186 ~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 186 SLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred hccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 345789999999998999999999999999999876
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=80.83 E-value=2.8 Score=26.28 Aligned_cols=17 Identities=18% Similarity=0.302 Sum_probs=14.4
Q ss_pred CEEEEEEcCCcEEEEEE
Q 041342 20 SKIWVIMKGDKELVGTL 36 (87)
Q Consensus 20 k~V~V~l~dgr~~~G~L 36 (87)
.+|.+.|+||+.+.|++
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 58999999999999998
No 85
>PRK14630 hypothetical protein; Provisional
Probab=80.09 E-value=6.7 Score=25.90 Aligned_cols=43 Identities=12% Similarity=0.094 Sum_probs=30.5
Q ss_pred CCCCCcCc---HHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 041342 3 HNPSQLLP---SELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVL 47 (87)
Q Consensus 3 ~~~~~~~P---l~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL 47 (87)
++|=...| ...+.+++|++|.|++.. ...+|+|.++|. -++.|
T Consensus 78 SSPGldRpL~~~~df~r~~G~~v~V~l~~-~~~~G~L~~~~d-~~i~l 123 (143)
T PRK14630 78 STPGINRKIKSDREFKIFEGKKIKLMLDN-DFEEGFILEAKA-DSFIF 123 (143)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEEcC-cceEEEEEEEeC-CEEEE
Confidence 34444444 456778899999999965 445999999987 44444
No 86
>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=80.00 E-value=4.3 Score=30.20 Aligned_cols=31 Identities=16% Similarity=0.341 Sum_probs=27.6
Q ss_pred CEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 20 SKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 20 k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
.++.|.+.||+.+.+++.++|...++.|=.+
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4689999999999999999999999988544
No 87
>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=79.83 E-value=2.3 Score=28.87 Aligned_cols=23 Identities=30% Similarity=0.536 Sum_probs=20.9
Q ss_pred CCEEEEEEcCCcEEEEEEEEecc
Q 041342 19 GSKIWVIMKGDKELVGTLKGFDV 41 (87)
Q Consensus 19 ~k~V~V~l~dgr~~~G~L~~~D~ 41 (87)
|+-|+|.+.|||+++|.=.|.|.
T Consensus 120 g~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 120 GKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred CCeEEEEEcCCcEEEeeecccce
Confidence 57899999999999999999884
No 88
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=79.72 E-value=5.1 Score=29.17 Aligned_cols=32 Identities=19% Similarity=0.211 Sum_probs=27.2
Q ss_pred cCCEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 18 IGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 18 l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
+|++|.|.. ++..+.|++.++|+...|+|+..
T Consensus 236 ~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~~ 267 (285)
T PTZ00275 236 KDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLRE 267 (285)
T ss_pred CCCEEEEEe-CCCEEEEEEEEECCCCeEEEEeC
Confidence 688998875 57899999999999999999643
No 89
>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=79.06 E-value=5.1 Score=27.21 Aligned_cols=34 Identities=15% Similarity=0.129 Sum_probs=30.2
Q ss_pred cCCEEEEEEcCCcEEEEEEEEeccccceEEcceE
Q 041342 18 IGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVT 51 (87)
Q Consensus 18 l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~ 51 (87)
-+-.|+|.+.||..+.|.+.+|++--|.+|..+.
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 3457999999999999999999999999987654
No 90
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=78.36 E-value=2.9 Score=22.35 Aligned_cols=22 Identities=36% Similarity=0.463 Sum_probs=15.0
Q ss_pred EEEEEEEeccccceEEcceEEE
Q 041342 32 LVGTLKGFDVYVNMVLEDVTEY 53 (87)
Q Consensus 32 ~~G~L~~~D~~mNlvL~~~~e~ 53 (87)
..|++.|.|+...+.|.+...+
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6899999999999999887654
No 91
>PHA00672 hypothetical protein
Probab=77.75 E-value=18 Score=24.08 Aligned_cols=48 Identities=13% Similarity=0.132 Sum_probs=32.0
Q ss_pred CCCCCCCcCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 1 MAHNPSQLLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 1 ~~~~~~~~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
|+..|++..|..-+...==.-=.+.+..|..+.|.+.-||.+ |.++.-
T Consensus 29 ~a~~pQv~ipv~H~Fs~GvYARei~IPkGt~LtG~~hkf~~~--ii~sG~ 76 (152)
T PHA00672 29 LAELPQVEIPTAHLFHAGVYARTIRIPAGVALTGALIKVSTV--LIFSGH 76 (152)
T ss_pred hhcCCcccchhhhhhccceeEEEEeccCceeeeeeeeEeeEE--EEeccc
Confidence 456677777765443322223356778899999999999988 666543
No 92
>PRK14635 hypothetical protein; Provisional
Probab=77.09 E-value=11 Score=25.36 Aligned_cols=45 Identities=18% Similarity=0.165 Sum_probs=31.6
Q ss_pred CCCCCcCcH---HHHhhhcCCEEEEEEc--CCcEEEE---EEEEeccccceEEc
Q 041342 3 HNPSQLLPS---ELIDRCIGSKIWVIMK--GDKELVG---TLKGFDVYVNMVLE 48 (87)
Q Consensus 3 ~~~~~~~Pl---~~L~~~l~k~V~V~l~--dgr~~~G---~L~~~D~~mNlvL~ 48 (87)
++|=...|| ..+.+++|+.|.|++. ++..+.| +|.++|.- ++.|.
T Consensus 80 SSPGldRpL~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~ 132 (162)
T PRK14635 80 SSAGAERKLRLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE 132 (162)
T ss_pred cCCCCCCcCCCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence 344444453 4577889999999875 4678887 99999864 45553
No 93
>PRK10942 serine endoprotease; Provisional
Probab=77.00 E-value=5.7 Score=30.95 Aligned_cols=31 Identities=19% Similarity=0.278 Sum_probs=27.3
Q ss_pred CEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 20 SKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 20 k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
.+++|.+.||+.|.+++.++|...+|-|=..
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4789999999999999999999999877543
No 94
>PRK10139 serine endoprotease; Provisional
Probab=76.85 E-value=6 Score=30.66 Aligned_cols=31 Identities=23% Similarity=0.323 Sum_probs=27.7
Q ss_pred CEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 20 SKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 20 k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
.++.|.+.||+.+.+++.++|....|-+=..
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 5799999999999999999999999877554
No 95
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=74.42 E-value=14 Score=24.59 Aligned_cols=27 Identities=15% Similarity=0.166 Sum_probs=24.3
Q ss_pred HhhhcCCEEEEEEcCCcEEEEEEEEec
Q 041342 14 IDRCIGSKIWVIMKGDKELVGTLKGFD 40 (87)
Q Consensus 14 L~~~l~k~V~V~l~dgr~~~G~L~~~D 40 (87)
...++||.|.+...+|..+.|++.++.
T Consensus 87 a~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 87 YSELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 357899999999999999999999886
No 96
>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=71.00 E-value=9.9 Score=28.84 Aligned_cols=32 Identities=19% Similarity=0.308 Sum_probs=28.0
Q ss_pred CEEEEEEcCCcEEEEEEEEeccccceEEcceE
Q 041342 20 SKIWVIMKGDKELVGTLKGFDVYVNMVLEDVT 51 (87)
Q Consensus 20 k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~ 51 (87)
.++.|.+.||+.+.+++.++|...+|.|=...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 47899999999999999999999998875553
No 97
>PRK08477 biotin--protein ligase; Provisional
Probab=69.81 E-value=19 Score=25.19 Aligned_cols=37 Identities=5% Similarity=-0.168 Sum_probs=30.2
Q ss_pred hhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEE
Q 041342 16 RCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEY 53 (87)
Q Consensus 16 ~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~ 53 (87)
-.+++.|+|. .+++.++|+..++|+..-|+++.-..+
T Consensus 172 ~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~~ 208 (211)
T PRK08477 172 FEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKVY 208 (211)
T ss_pred HHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEee
Confidence 3568899986 468999999999999999988766543
No 98
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=68.70 E-value=2.8 Score=27.93 Aligned_cols=25 Identities=32% Similarity=0.481 Sum_probs=19.5
Q ss_pred cCCcEEEEEEEEeccccceEEcceE
Q 041342 27 KGDKELVGTLKGFDVYVNMVLEDVT 51 (87)
Q Consensus 27 ~dgr~~~G~L~~~D~~mNlvL~~~~ 51 (87)
+....=.|+|+|.|+|.|=.-+|-.
T Consensus 40 rtd~~kiGTLVG~DkfGNkYyen~~ 64 (151)
T KOG3382|consen 40 RTDDHKIGTLVGVDKFGNKYYENND 64 (151)
T ss_pred hcccccceeeeeecccccchhcccc
Confidence 3344557999999999998887763
No 99
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=62.65 E-value=6.8 Score=23.09 Aligned_cols=20 Identities=20% Similarity=0.443 Sum_probs=16.4
Q ss_pred HHhhhcCCEEEEEEcCCcEE
Q 041342 13 LIDRCIGSKIWVIMKGDKEL 32 (87)
Q Consensus 13 ~L~~~l~k~V~V~l~dgr~~ 32 (87)
.+++.+||+|+|++....++
T Consensus 5 ~~nDrLGKKVRvKCn~dDti 24 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDTI 24 (73)
T ss_pred hhhhhcCceEEEEeCCcccc
Confidence 46889999999999876554
No 100
>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=62.32 E-value=4.7 Score=25.23 Aligned_cols=17 Identities=41% Similarity=0.505 Sum_probs=15.6
Q ss_pred EEEEEeccccceEEcce
Q 041342 34 GTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 34 G~L~~~D~~mNlvL~~~ 50 (87)
|+|+|.|.|.|..-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999998877
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=61.89 E-value=25 Score=20.97 Aligned_cols=28 Identities=14% Similarity=0.291 Sum_probs=21.2
Q ss_pred HHHhhhcCCEEEEEEcCCc----EEEEEEEEe
Q 041342 12 ELIDRCIGSKIWVIMKGDK----ELVGTLKGF 39 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr----~~~G~L~~~ 39 (87)
..|.+++|++|.++-+.|| +-.|+|...
T Consensus 10 ~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 10 KELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 4578999999999999998 458999764
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=59.23 E-value=7.3 Score=23.42 Aligned_cols=54 Identities=13% Similarity=0.107 Sum_probs=24.6
Q ss_pred cCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342 18 IGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG 81 (87)
Q Consensus 18 l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~ 81 (87)
-+.+|.++++||..+.|+ +.|-..|- +-.|+..- ...-+...||=+.|..+++.
T Consensus 16 ~~~~v~L~l~dG~~~~g~--A~dt~~~~---~k~E~L~l-----~~~~~~~~i~Ld~I~~~~al 69 (80)
T PF07073_consen 16 YRYPVKLTLKDGEQIEGK--ALDTRTNA---KKEECLVL-----EQDGGEQEIRLDQIASMSAL 69 (80)
T ss_dssp TTT-EEEE-TTT--EEES--S-EEE------SSS-EEEE-----EETTEEEEESTT--SEEE--
T ss_pred cCCeEEEEEeCCCEEEEE--EEEEEEec---CceEEEEE-----ecCCcEEEEEhhheeeeeec
Confidence 357899999999999998 44433332 11122110 11124667788888888754
No 103
>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=58.25 E-value=27 Score=18.48 Aligned_cols=25 Identities=12% Similarity=0.064 Sum_probs=20.9
Q ss_pred cCCEEEEEEcCCcEEEEEEEEeccc
Q 041342 18 IGSKIWVIMKGDKELVGTLKGFDVY 42 (87)
Q Consensus 18 l~k~V~V~l~dgr~~~G~L~~~D~~ 42 (87)
.|..+.+...||..|+|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4667777778999999999999964
No 104
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=58.09 E-value=38 Score=20.79 Aligned_cols=40 Identities=10% Similarity=0.176 Sum_probs=28.3
Q ss_pred ccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 42 YVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 42 ~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
..-+.+.......++.+|. .++-|.+.+.|..+..+...+
T Consensus 57 ~g~~~~~r~y~FEFS~~G~-~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 57 RGRLRWRRVYQFEFSSDGE-DRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred CCCeEEEEEEEEEEeCCCh-hcceEEEEEECCeeeEEEcCC
Confidence 3444555555554545664 789999999999999987643
No 105
>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=55.66 E-value=21 Score=22.84 Aligned_cols=29 Identities=14% Similarity=0.098 Sum_probs=21.4
Q ss_pred EEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 21 KIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 21 ~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
...|.++||+.+.|.+..=| .-.+.|.++
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~-~~~~~l~~~ 87 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET-ADGVTVKMP 87 (133)
T ss_pred cEEEEECCCCEEEEEEEecC-CCeEEEEcC
Confidence 47899999999999998855 334444443
No 106
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=55.66 E-value=30 Score=26.95 Aligned_cols=47 Identities=23% Similarity=0.244 Sum_probs=38.6
Q ss_pred cCcHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEE
Q 041342 8 LLPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEI 55 (87)
Q Consensus 8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~ 55 (87)
..|-.++++++||.|+- =+||++.+++|.+=|.-.=+.+.+-.|...
T Consensus 71 ~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~~ 117 (421)
T COG5316 71 LSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVLG 117 (421)
T ss_pred cCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEEe
Confidence 45778899999999998 899999999999999877666666666543
No 107
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=52.55 E-value=32 Score=22.87 Aligned_cols=27 Identities=15% Similarity=0.197 Sum_probs=23.2
Q ss_pred hhhcCCEEEEEEcCCcEEEEEEEEecc
Q 041342 15 DRCIGSKIWVIMKGDKELVGTLKGFDV 41 (87)
Q Consensus 15 ~~~l~k~V~V~l~dgr~~~G~L~~~D~ 41 (87)
..++||.|.....+|..+.|++.++..
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 478999999888899999999997763
No 108
>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=52.10 E-value=36 Score=19.17 Aligned_cols=24 Identities=25% Similarity=0.401 Sum_probs=18.4
Q ss_pred cCCEEEEEEcCCc-EEEEEEEEecc
Q 041342 18 IGSKIWVIMKGDK-ELVGTLKGFDV 41 (87)
Q Consensus 18 l~k~V~V~l~dgr-~~~G~L~~~D~ 41 (87)
.|.+|.++--++. .|.|.+.+||.
T Consensus 8 ~Ge~V~~rWP~s~lYYe~kV~~~d~ 32 (55)
T PF09465_consen 8 IGEVVMVRWPGSSLYYEGKVLSYDS 32 (55)
T ss_dssp SS-EEEEE-TTTS-EEEEEEEEEET
T ss_pred CCCEEEEECCCCCcEEEEEEEEecc
Confidence 5789999888766 55999999996
No 109
>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=50.46 E-value=24 Score=21.92 Aligned_cols=23 Identities=26% Similarity=0.505 Sum_probs=18.8
Q ss_pred hhcCCEEEEE-EcCCcEEEEEEEE
Q 041342 16 RCIGSKIWVI-MKGDKELVGTLKG 38 (87)
Q Consensus 16 ~~l~k~V~V~-l~dgr~~~G~L~~ 38 (87)
..+|..|+|+ +..|+.+.|+..+
T Consensus 93 g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 93 GAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred cCCCCEEEEEECCCCCEEEEEEeC
Confidence 3567889998 7889999998875
No 110
>PRK06630 hypothetical protein; Provisional
Probab=49.18 E-value=9.1 Score=24.08 Aligned_cols=19 Identities=21% Similarity=0.233 Sum_probs=16.9
Q ss_pred EEEEEEEeccccceEEcce
Q 041342 32 LVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 32 ~~G~L~~~D~~mNlvL~~~ 50 (87)
..|+|+|-|+|.|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3799999999999998875
No 111
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=47.43 E-value=22 Score=19.21 Aligned_cols=15 Identities=13% Similarity=0.328 Sum_probs=12.8
Q ss_pred HHHHhhhcCCEEEEE
Q 041342 11 SELIDRCIGSKIWVI 25 (87)
Q Consensus 11 l~~L~~~l~k~V~V~ 25 (87)
.+.+++++||+|+|.
T Consensus 11 ~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVT 25 (48)
T ss_pred hHHHHHhcCCeEEEE
Confidence 567888999999986
No 112
>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=46.31 E-value=33 Score=24.73 Aligned_cols=19 Identities=16% Similarity=0.233 Sum_probs=17.4
Q ss_pred EEEEEEEEeccccceEEcc
Q 041342 31 ELVGTLKGFDVYVNMVLED 49 (87)
Q Consensus 31 ~~~G~L~~~D~~mNlvL~~ 49 (87)
.++|.+.-+|.|.|+++.=
T Consensus 169 ~i~g~Vi~iD~FGNlitnI 187 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNI 187 (258)
T ss_dssp EEEEEEEEEETTSEEEEEE
T ss_pred eEEEEEEEECccCCeeeCC
Confidence 8999999999999999853
No 113
>PF10618 Tail_tube: Phage tail tube protein; InterPro: IPR019596 This entry is represented by Bacteriophage Mu, GpM tail tube protein. Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube.
Probab=44.61 E-value=40 Score=21.48 Aligned_cols=28 Identities=11% Similarity=0.000 Sum_probs=24.6
Q ss_pred cCcHHHHhhhcCCEEEEEEcCCcEEEEE
Q 041342 8 LLPSELIDRCIGSKIWVIMKGDKELVGT 35 (87)
Q Consensus 8 ~~Pl~~L~~~l~k~V~V~l~dgr~~~G~ 35 (87)
..|+..|...-+-.|..++.+|+.|.+.
T Consensus 63 ~~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 63 DTDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CCCHHHHhCCcccEEEEEecCCcEEEec
Confidence 4678889999999999999999999764
No 114
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=43.16 E-value=55 Score=23.95 Aligned_cols=32 Identities=19% Similarity=0.306 Sum_probs=25.9
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEcce
Q 041342 19 GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 19 ~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
..++.|.+.||+.+.+.+.++|...-+.+-..
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki 126 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKI 126 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEe
Confidence 35788899999999999999998766655433
No 115
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=42.84 E-value=32 Score=24.22 Aligned_cols=23 Identities=26% Similarity=0.488 Sum_probs=19.6
Q ss_pred hhcCCEEEEE-EcCCcEEEEEEEE
Q 041342 16 RCIGSKIWVI-MKGDKELVGTLKG 38 (87)
Q Consensus 16 ~~l~k~V~V~-l~dgr~~~G~L~~ 38 (87)
..+|..|+|+ +..|+.+.|+..+
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeC
Confidence 3568899998 8999999999875
No 116
>PRK10708 hypothetical protein; Provisional
Probab=42.75 E-value=34 Score=19.55 Aligned_cols=26 Identities=12% Similarity=0.281 Sum_probs=22.5
Q ss_pred cCCEEEEEEcCCcEEEEEEEEecccc
Q 041342 18 IGSKIWVIMKGDKELVGTLKGFDVYV 43 (87)
Q Consensus 18 l~k~V~V~l~dgr~~~G~L~~~D~~m 43 (87)
++.+|+|++..|-.=.|++.++..|.
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 56789999999999999999988764
No 117
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=41.55 E-value=49 Score=23.44 Aligned_cols=24 Identities=8% Similarity=0.102 Sum_probs=20.5
Q ss_pred cCCcEEEEEEEEeccccceEEcce
Q 041342 27 KGDKELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 27 ~dgr~~~G~L~~~D~~mNlvL~~~ 50 (87)
.++..+.|+..++|+...|+++..
T Consensus 209 ~~~~~~~G~~~gId~~G~Lvv~~~ 232 (245)
T PTZ00276 209 TGRDPEELTALSLNEWGHLIVRRP 232 (245)
T ss_pred cCCcEEEEEEEEECCCCeEEEEEC
Confidence 466788999999999999999653
No 118
>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=41.50 E-value=1.2e+02 Score=21.29 Aligned_cols=33 Identities=21% Similarity=0.294 Sum_probs=22.4
Q ss_pred EEEEEcCCcEEE-------EEEEEeccccceEEcceEEEE
Q 041342 22 IWVIMKGDKELV-------GTLKGFDVYVNMVLEDVTEYE 54 (87)
Q Consensus 22 V~V~l~dgr~~~-------G~L~~~D~~mNlvL~~~~e~~ 54 (87)
.++...+|+++. |.++|.|+|.++-++-.....
T Consensus 5 ~W~v~~~G~ev~Qt~NsdP~l~ig~~~~~~vdf~GT~~Vn 44 (201)
T PF05735_consen 5 NWVVSNQGAEVVQTLNSDPGLAIGPDNFGGVDFSGTFFVN 44 (201)
T ss_dssp -EEEECCCTEEEE-SS-SSEEEEEEEEESSEEEEEEEEE-
T ss_pred ceEEecCCeEEEEeccCCCeEEEccceecceEEEEEEEEe
Confidence 466666676664 677888888888887775554
No 119
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=40.97 E-value=16 Score=23.57 Aligned_cols=19 Identities=32% Similarity=0.403 Sum_probs=16.8
Q ss_pred EEEEEEeccccceEEcceE
Q 041342 33 VGTLKGFDVYVNMVLEDVT 51 (87)
Q Consensus 33 ~G~L~~~D~~mNlvL~~~~ 51 (87)
.|.|+|.|+|.|-.-++..
T Consensus 9 ~g~lVG~D~~GNkYYE~~~ 27 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPS 27 (115)
T ss_pred cceEeEEcCCCCeeeEcCC
Confidence 6999999999999988754
No 120
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=40.34 E-value=30 Score=19.98 Aligned_cols=22 Identities=14% Similarity=0.250 Sum_probs=18.5
Q ss_pred CEEEEEEcCCcEEEEEEEEecc
Q 041342 20 SKIWVIMKGDKELVGTLKGFDV 41 (87)
Q Consensus 20 k~V~V~l~dgr~~~G~L~~~D~ 41 (87)
.+|.|++-||..+.+++..-|.
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCCc
Confidence 4789999999999999876553
No 121
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=40.12 E-value=40 Score=23.33 Aligned_cols=59 Identities=14% Similarity=0.084 Sum_probs=34.8
Q ss_pred HHHHhhhcCC--EEEEE-EcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 11 SELIDRCIGS--KIWVI-MKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 11 l~~L~~~l~k--~V~V~-l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
+++|..+-+. ++.+. ..++..|+|++.++|.-. |.+... . ....+-|.=+.|.+|++++
T Consensus 123 I~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~~-v~i~~~------~------~~~~~~i~~~~I~sI~~iG 184 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEGE-VSIMPF------N------QGEEIEIPIDDITSIKMIG 184 (185)
T ss_pred HHHHHhCcccCCCCceEEEeCCceEEEEEEeccCCE-EEEecc------C------CCcceEeehhheeeeeecc
Confidence 4555555443 34443 356899999999999641 111111 0 1245666777788887765
No 122
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=39.74 E-value=57 Score=22.84 Aligned_cols=26 Identities=12% Similarity=0.286 Sum_probs=22.7
Q ss_pred hhhcCCEEEEEEcCCcEEEEEEEEec
Q 041342 15 DRCIGSKIWVIMKGDKELVGTLKGFD 40 (87)
Q Consensus 15 ~~~l~k~V~V~l~dgr~~~G~L~~~D 40 (87)
..++||.|.+.-.+|..+.|++.+..
T Consensus 114 ~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 114 MKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 47899999988889999999998765
No 123
>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=37.39 E-value=5.1 Score=22.81 Aligned_cols=17 Identities=24% Similarity=0.335 Sum_probs=14.4
Q ss_pred eccccceEEcceEEEEE
Q 041342 39 FDVYVNMVLEDVTEYEI 55 (87)
Q Consensus 39 ~D~~mNlvL~~~~e~~~ 55 (87)
-|.||+-||+||+-++.
T Consensus 20 sDDFmhaVlSNCtTrIv 36 (61)
T PF10894_consen 20 SDDFMHAVLSNCTTRIV 36 (61)
T ss_pred cHHHHHHHHhcCceeEE
Confidence 38899999999987654
No 124
>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=36.63 E-value=43 Score=19.13 Aligned_cols=26 Identities=12% Similarity=0.279 Sum_probs=22.3
Q ss_pred cCCEEEEEEcCCcEEEEEEEEecccc
Q 041342 18 IGSKIWVIMKGDKELVGTLKGFDVYV 43 (87)
Q Consensus 18 l~k~V~V~l~dgr~~~G~L~~~D~~m 43 (87)
++.+|+|++..|-.=.|++.+...|.
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 46789999999989999999988764
No 125
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=36.15 E-value=32 Score=23.43 Aligned_cols=19 Identities=26% Similarity=0.312 Sum_probs=16.8
Q ss_pred EEEEEEeccccceEEcceE
Q 041342 33 VGTLKGFDVYVNMVLEDVT 51 (87)
Q Consensus 33 ~G~L~~~D~~mNlvL~~~~ 51 (87)
.|+|+|-|+|.|-.-++..
T Consensus 48 ~G~lVG~D~~GNkYYE~~~ 66 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKLG 66 (159)
T ss_pred CcEEEEecCCCCeeeecCC
Confidence 4999999999999988764
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=35.98 E-value=50 Score=18.86 Aligned_cols=21 Identities=19% Similarity=0.183 Sum_probs=17.6
Q ss_pred EEEEEEcCCcEEEEEEEEecc
Q 041342 21 KIWVIMKGDKELVGTLKGFDV 41 (87)
Q Consensus 21 ~V~V~l~dgr~~~G~L~~~D~ 41 (87)
+|.|++.||..+..++..-|.
T Consensus 8 ~I~vRlpdG~~l~~~F~~~~t 28 (82)
T PF00789_consen 8 RIQVRLPDGSRLQRRFPKSDT 28 (82)
T ss_dssp EEEEEETTSTEEEEEEETTSB
T ss_pred EEEEECCCCCEEEEEECCcch
Confidence 688999999999999876553
No 127
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.69 E-value=49 Score=20.01 Aligned_cols=27 Identities=26% Similarity=0.428 Sum_probs=21.0
Q ss_pred HHHhhhcCCEEEEEEcCCcEE----EEEEEE
Q 041342 12 ELIDRCIGSKIWVIMKGDKEL----VGTLKG 38 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr~~----~G~L~~ 38 (87)
..+...+|++|.++.++||.= .|.|..
T Consensus 12 ~~i~ah~G~~v~lk~ngGRKk~~~r~G~L~E 42 (80)
T COG4466 12 ESIDAHLGERVTLKANGGRKKTIERSGILIE 42 (80)
T ss_pred HHHHhccCcEEEEEecCCceeeehhceEEee
Confidence 456788899999999999964 476643
No 128
>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=35.56 E-value=43 Score=19.12 Aligned_cols=21 Identities=19% Similarity=0.240 Sum_probs=17.5
Q ss_pred CEEEEEEcCCcEEEEEEEEec
Q 041342 20 SKIWVIMKGDKELVGTLKGFD 40 (87)
Q Consensus 20 k~V~V~l~dgr~~~G~L~~~D 40 (87)
.+|.|++-||..+.+++..-|
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~ 23 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTH 23 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 368999999999999986554
No 129
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.60 E-value=61 Score=22.58 Aligned_cols=35 Identities=20% Similarity=0.280 Sum_probs=30.6
Q ss_pred hcCCEEEEEEcCCcEEEEEEEEeccccceEEcceE
Q 041342 17 CIGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVT 51 (87)
Q Consensus 17 ~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~ 51 (87)
.++..|.+..-++...+|.+.+||--.+...-++.
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 46778999999999999999999988887777776
No 130
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=32.91 E-value=90 Score=17.96 Aligned_cols=37 Identities=14% Similarity=0.049 Sum_probs=28.4
Q ss_pred hhhcCCEEEEEEcCCc-EEEEEEEEeccc-cceEEcceE
Q 041342 15 DRCIGSKIWVIMKGDK-ELVGTLKGFDVY-VNMVLEDVT 51 (87)
Q Consensus 15 ~~~l~k~V~V~l~dgr-~~~G~L~~~D~~-mNlvL~~~~ 51 (87)
.+++|+-|.|...+.- .|.|.+...|+- .-|+|..+.
T Consensus 2 ~dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~ 40 (62)
T cd01737 2 QDWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPF 40 (62)
T ss_pred CcccceEEEEecCCceEEEEEEEEEeCccceEEEEeecc
Confidence 3678999999887654 899999999963 357776654
No 131
>PRK08183 NADH dehydrogenase; Validated
Probab=32.37 E-value=24 Score=23.29 Aligned_cols=19 Identities=21% Similarity=0.179 Sum_probs=16.5
Q ss_pred EEEEEEeccccceEEcceE
Q 041342 33 VGTLKGFDVYVNMVLEDVT 51 (87)
Q Consensus 33 ~G~L~~~D~~mNlvL~~~~ 51 (87)
.|+|+|-|+|.|-.-++..
T Consensus 25 ~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cCeEeEecCCCCeeeecCC
Confidence 6999999999999887654
No 132
>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=32.16 E-value=38 Score=19.71 Aligned_cols=23 Identities=17% Similarity=0.215 Sum_probs=18.7
Q ss_pred cCCEEEEEEcCCcEEEEEEEEec
Q 041342 18 IGSKIWVIMKGDKELVGTLKGFD 40 (87)
Q Consensus 18 l~k~V~V~l~dgr~~~G~L~~~D 40 (87)
-..+|.|++-||..+.+++..-|
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCC
Confidence 34579999999999999986544
No 133
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=31.55 E-value=70 Score=22.16 Aligned_cols=26 Identities=12% Similarity=0.313 Sum_probs=22.2
Q ss_pred hhhcCCEEEEEEcCCcEEEEEEEEec
Q 041342 15 DRCIGSKIWVIMKGDKELVGTLKGFD 40 (87)
Q Consensus 15 ~~~l~k~V~V~l~dgr~~~G~L~~~D 40 (87)
...+|+.|.|.+...+.+.|.+..++
T Consensus 24 ~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 24 KDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp GGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 44899999999998899999998885
No 134
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.34 E-value=69 Score=21.40 Aligned_cols=22 Identities=23% Similarity=0.250 Sum_probs=17.7
Q ss_pred hcCCEEEEE-EcCCcEEEEEEEE
Q 041342 17 CIGSKIWVI-MKGDKELVGTLKG 38 (87)
Q Consensus 17 ~l~k~V~V~-l~dgr~~~G~L~~ 38 (87)
..|..|+|+ +..|+.++|+..+
T Consensus 129 ~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 129 AAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 467888998 7889999998764
No 135
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=30.97 E-value=84 Score=22.03 Aligned_cols=23 Identities=22% Similarity=0.167 Sum_probs=19.3
Q ss_pred hhcCCEEEEEEcCCcEEEEEEEE
Q 041342 16 RCIGSKIWVIMKGDKELVGTLKG 38 (87)
Q Consensus 16 ~~l~k~V~V~l~dgr~~~G~L~~ 38 (87)
..+|..|+|+-..|+.+.|+..+
T Consensus 193 G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 193 GNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCCEEEEEeCCCCEEEEEEec
Confidence 35688999988889999999876
No 136
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.83 E-value=72 Score=22.44 Aligned_cols=22 Identities=9% Similarity=0.131 Sum_probs=18.3
Q ss_pred hcCCEEEEE-EcCCcEEEEEEEE
Q 041342 17 CIGSKIWVI-MKGDKELVGTLKG 38 (87)
Q Consensus 17 ~l~k~V~V~-l~dgr~~~G~L~~ 38 (87)
..|..|+|+ +..|+.+.|+..+
T Consensus 184 ~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 184 GENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 467889998 7899999998865
No 137
>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=29.22 E-value=18 Score=32.07 Aligned_cols=54 Identities=9% Similarity=0.132 Sum_probs=0.0
Q ss_pred EEEcCCcEEEEEEEEeccccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEE
Q 041342 24 VIMKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAIL 78 (87)
Q Consensus 24 V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I 78 (87)
=...+|+.+.|.|+..|.-|+.+|.--.+.. +..-.-+..+|.++|+|+|.+.-
T Consensus 252 ytt~~G~~v~GVlvTT~~V~q~Ll~~l~~i~-~~~v~~PatYg~~Vi~geNlVTA 305 (1354)
T PF03122_consen 252 YTTSSGRPVDGVLVTTANVMQKLLNLLGQIS-DTSVSVPATYGEFVISGENLVTA 305 (1354)
T ss_dssp -------------------------------------------------------
T ss_pred eecCCCCEeceEEeccHHHHHHHHHHHhhhc-cceeecchhheeeeecCccHHHH
Confidence 3668899999999999998887776555422 11112367899999999998754
No 138
>PF13793 Pribosyltran_N: N-terminal domain of ribose phosphate pyrophosphokinase; PDB: 2JI4_A 1DKU_B 1IBS_B 1DKR_B 3MBI_C 3LRT_B 3LPN_B 3NAG_B 2H07_B 2H06_B ....
Probab=28.70 E-value=1.3e+02 Score=18.97 Aligned_cols=41 Identities=15% Similarity=0.374 Sum_probs=21.7
Q ss_pred ccceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCCCC
Q 041342 42 YVNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGGSP 84 (87)
Q Consensus 42 ~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~~p 84 (87)
.+|+-+..+....+ +||+....+.. -+||..|..|+....|
T Consensus 19 ~L~~~~~~~~~~~F-~dGE~~v~i~~-~v~g~dv~iiqs~~~~ 59 (116)
T PF13793_consen 19 ALGIPLGKVETKRF-PDGETYVRIPE-SVRGKDVFIIQSTSPP 59 (116)
T ss_dssp HTTS-EE-EEEEE--TTS-EEEEESS---TTSEEEEE---SSS
T ss_pred HhCCceeeeEEEEc-CCCCEEEEecc-cccCCceEEEEecCCc
Confidence 45666666655544 57765555555 7889999999877765
No 139
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=27.59 E-value=1.3e+02 Score=18.47 Aligned_cols=35 Identities=20% Similarity=0.138 Sum_probs=26.0
Q ss_pred HHHhhhcCCEEEEEEcCCcEEEEEEEEeccccceE
Q 041342 12 ELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVNMV 46 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlv 46 (87)
+.-.-|+||+|.-.-+.|+.+-|.+.---.....|
T Consensus 33 ~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvV 67 (87)
T PRK04337 33 EEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEV 67 (87)
T ss_pred HHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceE
Confidence 34567899999888888999999887655444443
No 140
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=27.06 E-value=1.3e+02 Score=17.01 Aligned_cols=33 Identities=18% Similarity=0.239 Sum_probs=22.5
Q ss_pred cCCEEEEEEcCC--c--EEEEEEEEeccccceEEcce
Q 041342 18 IGSKIWVIMKGD--K--ELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 18 l~k~V~V~l~dg--r--~~~G~L~~~D~~mNlvL~~~ 50 (87)
+|.+|.|++.++ . .|.-.+.+++..-.+.++--
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~P 39 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISMP 39 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE--
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEcC
Confidence 578899988543 3 59999999998866666544
No 141
>PRK11625 Rho-binding antiterminator; Provisional
Probab=26.81 E-value=1.5e+02 Score=17.88 Aligned_cols=50 Identities=20% Similarity=0.173 Sum_probs=31.6
Q ss_pred cCCEEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEc-cCCeeeEeeCeEEEcCCcEEEEE
Q 041342 18 IGSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEYEIT-AEGRRITKLDQILLNGNNIAILV 79 (87)
Q Consensus 18 l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~-~~g~~~~~~g~v~IRG~~I~~I~ 79 (87)
.+-.+.++++||..+.|+. .|-+.+ +-.|+..- .+| +...||=+.|..|+
T Consensus 22 ~~~~l~l~l~dGe~~~g~A--~D~~~~----~k~EyL~l~~~g------~~~~iRLD~I~s~~ 72 (84)
T PRK11625 22 HHLMLTLELKDGEVLQAKA--SDLVSR----KNVEYLVVEAAG------ETRELRLDKIASFS 72 (84)
T ss_pred cCCeEEEEECCCCEEEEEE--EeeecC----CceEEEEEEcCC------CEEEEEeeeEeecc
Confidence 3568999999999999986 444432 44444321 122 35566777777766
No 142
>PRK06151 N-ethylammeline chlorohydrolase; Provisional
Probab=26.20 E-value=2e+02 Score=22.23 Aligned_cols=39 Identities=8% Similarity=0.199 Sum_probs=23.0
Q ss_pred cceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342 43 VNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG 81 (87)
Q Consensus 43 mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~ 81 (87)
|+++|+++.-...+..+.....-+.+.|+|+.|+.|.+.
T Consensus 1 ~~~li~~~~v~~~d~~~~~~~~~~~VlVe~g~I~~Vg~~ 39 (488)
T PRK06151 1 MRTLIKARWVLGFDDGDHRLLRDGEVVFEGDRILFVGHR 39 (488)
T ss_pred CeEEEEccEEEEEcCCCCeEEeCcEEEEECCEEEEecCC
Confidence 456677766543321121223346788888888888754
No 143
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=25.86 E-value=1e+02 Score=15.49 Aligned_cols=22 Identities=5% Similarity=-0.126 Sum_probs=17.1
Q ss_pred CEEEEEEc-CCcEEEEEEEEecc
Q 041342 20 SKIWVIMK-GDKELVGTLKGFDV 41 (87)
Q Consensus 20 k~V~V~l~-dgr~~~G~L~~~D~ 41 (87)
..+.+... ||+.|+|++.+++.
T Consensus 2 ~~c~a~~~~d~~wyra~V~~~~~ 24 (48)
T cd04508 2 DLCLAKYSDDGKWYRAKITSILS 24 (48)
T ss_pred CEEEEEECCCCeEEEEEEEEECC
Confidence 34556665 49999999999985
No 144
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=25.85 E-value=1.4e+02 Score=23.23 Aligned_cols=27 Identities=15% Similarity=0.428 Sum_probs=22.0
Q ss_pred HhhhcCCEEEEEEc--CC--cEEEEEEEEec
Q 041342 14 IDRCIGSKIWVIMK--GD--KELVGTLKGFD 40 (87)
Q Consensus 14 L~~~l~k~V~V~l~--dg--r~~~G~L~~~D 40 (87)
+.+++|+.+.|.+. +| |.+.|++.++.
T Consensus 42 ~~~llG~~v~l~i~~~~~~~r~f~GiVt~~~ 72 (513)
T TIGR03361 42 LEDLLGQPATLTLGRDGGGPRYFHGIVTRFE 72 (513)
T ss_pred HHHHcCCeEEEEEEeCCCceEEEEEEEEEEE
Confidence 67789999999885 33 67999998886
No 145
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=25.53 E-value=1e+02 Score=18.68 Aligned_cols=18 Identities=11% Similarity=0.034 Sum_probs=15.4
Q ss_pred CCEEEEEEcCCcEEEEEE
Q 041342 19 GSKIWVIMKGDKELVGTL 36 (87)
Q Consensus 19 ~k~V~V~l~dgr~~~G~L 36 (87)
.-.+..+++||..+.|.-
T Consensus 23 hl~l~L~lkdGev~~a~A 40 (84)
T COG4568 23 HLPLTLELKDGEVLQAKA 40 (84)
T ss_pred hceEEEEEcCCeEEEEEe
Confidence 457899999999999963
No 146
>PF13144 SAF_2: SAF-like
Probab=25.32 E-value=1.2e+02 Score=20.22 Aligned_cols=24 Identities=25% Similarity=0.267 Sum_probs=18.8
Q ss_pred hhcCCEEEEEEc-CCcEEEEEEEEe
Q 041342 16 RCIGSKIWVIMK-GDKELVGTLKGF 39 (87)
Q Consensus 16 ~~l~k~V~V~l~-dgr~~~G~L~~~ 39 (87)
..+|..|+|+-. .|+.+.|++.+-
T Consensus 167 G~~G~~I~V~N~~S~k~v~g~V~~~ 191 (196)
T PF13144_consen 167 GALGDTIRVKNLSSGKIVQGRVIGP 191 (196)
T ss_pred CCCCCEEEEEECCCCCEEEEEEecC
Confidence 457889999884 499999998763
No 147
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.07 E-value=1.1e+02 Score=20.05 Aligned_cols=22 Identities=18% Similarity=0.468 Sum_probs=17.6
Q ss_pred hcCCEEEEE-EcCCcEEEEEEEE
Q 041342 17 CIGSKIWVI-MKGDKELVGTLKG 38 (87)
Q Consensus 17 ~l~k~V~V~-l~dgr~~~G~L~~ 38 (87)
.+|..|+|+ +..|+.+.|+..+
T Consensus 110 ~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 110 GVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 467889995 6889999998865
No 148
>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=24.86 E-value=67 Score=20.22 Aligned_cols=20 Identities=20% Similarity=0.476 Sum_probs=7.5
Q ss_pred EEEEEEEEeccccceEEcce
Q 041342 31 ELVGTLKGFDVYVNMVLEDV 50 (87)
Q Consensus 31 ~~~G~L~~~D~~mNlvL~~~ 50 (87)
++.|+..++|-..++.|++|
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 45677777764566666665
No 149
>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=24.79 E-value=80 Score=18.47 Aligned_cols=21 Identities=19% Similarity=0.273 Sum_probs=17.4
Q ss_pred CEEEEEEcCCcEEEEEEEEec
Q 041342 20 SKIWVIMKGDKELVGTLKGFD 40 (87)
Q Consensus 20 k~V~V~l~dgr~~~G~L~~~D 40 (87)
.+|.|++.||..+..++..-|
T Consensus 5 t~iqiRlpdG~r~~~rF~~~~ 25 (79)
T cd01770 5 TSIQIRLADGKRLVQKFNSSH 25 (79)
T ss_pred eEEEEECCCCCEEEEEeCCCC
Confidence 478999999999998876544
No 150
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=24.61 E-value=40 Score=20.78 Aligned_cols=22 Identities=9% Similarity=0.490 Sum_probs=13.9
Q ss_pred CCCCcCcHHHHhhhcCCEEEEE
Q 041342 4 NPSQLLPSELIDRCIGSKIWVI 25 (87)
Q Consensus 4 ~~~~~~Pl~~L~~~l~k~V~V~ 25 (87)
.|.+.---+.|.+|.|+.|++.
T Consensus 3 ~~~pRVn~~~L~~~~gk~Vriv 24 (109)
T PF08661_consen 3 APTPRVNGSMLSQFVGKTVRIV 24 (109)
T ss_dssp S--EEE-GGGGGGGTTSEEEEE
T ss_pred CCcceECHHHHHhhCCCeEEEE
Confidence 4444444567899999998773
No 151
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.59 E-value=1e+02 Score=22.41 Aligned_cols=23 Identities=22% Similarity=0.253 Sum_probs=19.1
Q ss_pred hcCCEEEEE-EcCCcEEEEEEEEe
Q 041342 17 CIGSKIWVI-MKGDKELVGTLKGF 39 (87)
Q Consensus 17 ~l~k~V~V~-l~dgr~~~G~L~~~ 39 (87)
..|..|+|+ +..|+.+.|+..+-
T Consensus 231 ~~Gd~IrVrN~~SgkvV~a~V~~~ 254 (261)
T PRK06804 231 RKGELIKVKNLSSGRVVTATVDGS 254 (261)
T ss_pred CCCCEEEEEECCCCCEEEEEEecC
Confidence 467889998 78899999998763
No 152
>PRK07228 N-ethylammeline chlorohydrolase; Provisional
Probab=24.30 E-value=1.8e+02 Score=21.82 Aligned_cols=38 Identities=11% Similarity=0.198 Sum_probs=23.7
Q ss_pred cceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeCC
Q 041342 43 VNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPGG 82 (87)
Q Consensus 43 mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~~ 82 (87)
|.+++.++.-... ++.....-|.+.|++..|..|.+..
T Consensus 1 ~~~~i~~~~vi~~--~~~~~~~~g~V~I~dg~I~~vg~~~ 38 (445)
T PRK07228 1 MTILIKNAGIVTM--NAKREIVDGDVLIEDDRIAAVGDRL 38 (445)
T ss_pred CeEEEEccEEEec--CCCcEecccEEEEECCEEEEecCCc
Confidence 5567777765432 2212335578888888888887544
No 153
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=24.18 E-value=97 Score=23.59 Aligned_cols=22 Identities=14% Similarity=0.247 Sum_probs=19.7
Q ss_pred hhcCCEEEEEEcCCcEEEEEEE
Q 041342 16 RCIGSKIWVIMKGDKELVGTLK 37 (87)
Q Consensus 16 ~~l~k~V~V~l~dgr~~~G~L~ 37 (87)
-+.+++|+|...+|+.|.|++-
T Consensus 94 ~~~gq~v~i~t~~g~~i~GvIg 115 (355)
T COG1363 94 VLEGQRVTIHTDKGKKIRGVIG 115 (355)
T ss_pred hccCcEEEEEeCCCcEEeeeEc
Confidence 4568999999999999999997
No 154
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=23.00 E-value=1.5e+02 Score=17.25 Aligned_cols=21 Identities=14% Similarity=0.302 Sum_probs=16.5
Q ss_pred CCEEEEEEcCCcEEEEEEEEe
Q 041342 19 GSKIWVIMKGDKELVGTLKGF 39 (87)
Q Consensus 19 ~k~V~V~l~dgr~~~G~L~~~ 39 (87)
+...+|+|-||..+.+.+.|=
T Consensus 17 ~~~f~V~l~ng~~vla~i~GK 37 (68)
T TIGR00008 17 NAMFRVELENGHEVLAHISGK 37 (68)
T ss_pred CCEEEEEECCCCEEEEEecCc
Confidence 457888999999888877663
No 155
>PF02245 Pur_DNA_glyco: Methylpurine-DNA glycosylase (MPG); InterPro: IPR003180 Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA []. Its action is induced by alkylating chemotherapeutics, as well as deaminated and lipid peroxidation-induced purine adducts []. MPG without an N-terminal extension excises hypoxanthine with one-third of the efficiency of full-length MPG under similar conditions, suggesting that is function may largely be attributable to the N-terminal extension [].; GO: 0003677 DNA binding, 0003905 alkylbase DNA N-glycosylase activity, 0006284 base-excision repair; PDB: 1BNK_A 1F6O_A 3QI5_A 3UBY_B 1F4R_A 1EWN_A.
Probab=22.68 E-value=2e+02 Score=19.85 Aligned_cols=34 Identities=18% Similarity=0.347 Sum_probs=23.6
Q ss_pred cHHHHhhhcCCEEEEEEcCCcEEEEEEEEeccccc
Q 041342 10 PSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYVN 44 (87)
Q Consensus 10 Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~mN 44 (87)
+..+=++++|+.+..++.+|. +.|.++....|.-
T Consensus 9 ~~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 9 TVEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp HHHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred HHHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 456667899999999988877 9999877665544
No 156
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=22.65 E-value=2e+02 Score=19.70 Aligned_cols=26 Identities=23% Similarity=0.238 Sum_probs=21.6
Q ss_pred cCCEEEEEEcCCcEEEEEEEEecccc
Q 041342 18 IGSKIWVIMKGDKELVGTLKGFDVYV 43 (87)
Q Consensus 18 l~k~V~V~l~dgr~~~G~L~~~D~~m 43 (87)
.|.++.|.+.+|+.+.|++..++...
T Consensus 141 ~g~~v~i~~~~~~~~~g~v~~I~~~~ 166 (265)
T TIGR00999 141 KGSKATVLLENGRPLPARVDYVGPEV 166 (265)
T ss_pred CCCEEEEEECCCCEEEEEEEEEcccc
Confidence 35789999988999999999888654
No 157
>TIGR00567 3mg DNA-3-methyladenine glycosylase (3mg). This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine.
Probab=22.56 E-value=2.4e+02 Score=19.59 Aligned_cols=35 Identities=17% Similarity=0.256 Sum_probs=28.8
Q ss_pred CcHHHHhhhcCCEEEEEEcCCcEEEEEEEEecccc
Q 041342 9 LPSELIDRCIGSKIWVIMKGDKELVGTLKGFDVYV 43 (87)
Q Consensus 9 ~Pl~~L~~~l~k~V~V~l~dgr~~~G~L~~~D~~m 43 (87)
.++.+=.+++||.+.-++.+|....|.++....|+
T Consensus 9 ~~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~ 43 (192)
T TIGR00567 9 DAVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYM 43 (192)
T ss_pred CHHHHHHHhCCCEEEEECCCCcEEEEEEEEEeccc
Confidence 45667788999999888888877889999888775
No 158
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=22.37 E-value=88 Score=20.61 Aligned_cols=38 Identities=24% Similarity=0.464 Sum_probs=24.3
Q ss_pred cEEEEEEEEec---cccceEEcceEEEEEccCCeeeEeeCeEEEcCCc
Q 041342 30 KELVGTLKGFD---VYVNMVLEDVTEYEITAEGRRITKLDQILLNGNN 74 (87)
Q Consensus 30 r~~~G~L~~~D---~~mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~ 74 (87)
..+.|.+.=.= .+||+.+.|+. .|+ ...-+.+=||||+
T Consensus 83 ~~lvG~VqKvS~Lil~~~~~v~Dv~------tg~-~v~~~~~diRgnt 123 (140)
T PF11684_consen 83 YVLVGEVQKVSNLILNMNVYVRDVE------TGK-VVRGRSVDIRGNT 123 (140)
T ss_pred EEEEEEEechhhhheeeeEEEEECC------CCC-EEeeeeeeEecCc
Confidence 34555553322 47788888773 343 5667888999986
No 159
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=22.23 E-value=1.9e+02 Score=18.16 Aligned_cols=29 Identities=10% Similarity=0.200 Sum_probs=21.7
Q ss_pred HHHhhhcCCEEEEEEcC-CcEEEEEEEEec
Q 041342 12 ELIDRCIGSKIWVIMKG-DKELVGTLKGFD 40 (87)
Q Consensus 12 ~~L~~~l~k~V~V~l~d-gr~~~G~L~~~D 40 (87)
+.-..|++++|.-+-+. |+.+.|++.-.-
T Consensus 39 ~eA~~y~gk~v~yk~~~~G~Vi~G~V~R~H 68 (100)
T COG2451 39 EEAQFYLGKRVCYKYRSSGRVIKGKVVRTH 68 (100)
T ss_pred HHHHhhhccEEEEEeCCCCcEEEEEEEEec
Confidence 34467889987766666 999999987553
No 160
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=21.96 E-value=1.1e+02 Score=20.15 Aligned_cols=23 Identities=17% Similarity=0.238 Sum_probs=17.8
Q ss_pred hhcCCEEEEEEcCCcEEEEEEEE
Q 041342 16 RCIGSKIWVIMKGDKELVGTLKG 38 (87)
Q Consensus 16 ~~l~k~V~V~l~dgr~~~G~L~~ 38 (87)
+.+-|-++|+|.||++++..+=|
T Consensus 53 SAlRK~~RVrL~NG~~VtAyiPg 75 (129)
T COG0048 53 SALRKVARVRLINGKEVTAYIPG 75 (129)
T ss_pred hhhheeEEEEeeCCcEEEEEcCC
Confidence 45667799999999998866543
No 161
>PF06115 DUF956: Domain of unknown function (DUF956); InterPro: IPR010360 This is a family of bacterial sequences with undetermined function.
Probab=21.69 E-value=2.4e+02 Score=18.28 Aligned_cols=35 Identities=14% Similarity=0.275 Sum_probs=25.0
Q ss_pred hhcCCEEEEEEcCCcEEEEEEEEeccccceEE-cceEEEEE
Q 041342 16 RCIGSKIWVIMKGDKELVGTLKGFDVYVNMVL-EDVTEYEI 55 (87)
Q Consensus 16 ~~l~k~V~V~l~dgr~~~G~L~~~D~~mNlvL-~~~~e~~~ 55 (87)
+.++++|....+ |..|.|.- +|.++.+ +.|.|...
T Consensus 3 qSlNtkvdl~~~-ats~~g~~----~yGkimiGDkaFEFyn 38 (118)
T PF06115_consen 3 QSLNTKVDLTTK-ATSYLGLG----KYGKIMIGDKAFEFYN 38 (118)
T ss_pred cccccEEEEEEe-eEEEeccc----ccCeEEEcccceEeec
Confidence 357888887776 67787733 8899888 45677653
No 162
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=20.79 E-value=1.6e+02 Score=20.33 Aligned_cols=67 Identities=12% Similarity=-0.138 Sum_probs=47.4
Q ss_pred HHHHhhhcCCEEEEE-EcCCcEEEEEEEEeccccceEEcceEEEEEccCC------eeeEeeCeEEEcCCcEEE
Q 041342 11 SELIDRCIGSKIWVI-MKGDKELVGTLKGFDVYVNMVLEDVTEYEITAEG------RRITKLDQILLNGNNIAI 77 (87)
Q Consensus 11 l~~L~~~l~k~V~V~-l~dgr~~~G~L~~~D~~mNlvL~~~~e~~~~~~g------~~~~~~g~v~IRG~~I~~ 77 (87)
+..+.++...+-... ..++++-++.-..+|.-.||++-.|++.-...+. ...+..|.....|..|..
T Consensus 42 l~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp~s~s~~~v~ag~~~g~G~ar~~Grgip~ 115 (177)
T KOG3168|consen 42 LQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPPPSDSFRRVPAGAARGPGIARVAGRGIPS 115 (177)
T ss_pred HHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCCCccccccccccccCCcccccccCCCccC
Confidence 455667777666664 8899999999999999999999888775321111 124556677777776665
No 163
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=20.75 E-value=1.5e+02 Score=16.51 Aligned_cols=20 Identities=15% Similarity=0.117 Sum_probs=15.2
Q ss_pred CEEEEEEcCCcEEEEEEEEe
Q 041342 20 SKIWVIMKGDKELVGTLKGF 39 (87)
Q Consensus 20 k~V~V~l~dgr~~~G~L~~~ 39 (87)
..+.|.+.||.++.+.|.|=
T Consensus 16 ~~~~V~~~dg~~~l~~i~gK 35 (65)
T PF01176_consen 16 NLFEVECEDGEERLARIPGK 35 (65)
T ss_dssp SEEEEEETTSEEEEEEE-HH
T ss_pred CEEEEEeCCCCEEEEEeccc
Confidence 56788888998888887664
No 164
>PF02014 Reeler: Reeler domain Schematic picture including Reeler domain; InterPro: IPR002861 Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment []. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons []. This domain of unknown function is found at the N terminus of reelin and F-spondin.; PDB: 2ZOT_B 2ZOU_B 3COO_A.
Probab=20.62 E-value=94 Score=19.53 Aligned_cols=19 Identities=26% Similarity=0.389 Sum_probs=15.2
Q ss_pred CCEEEEEE--cCCcEEEEEEE
Q 041342 19 GSKIWVIM--KGDKELVGTLK 37 (87)
Q Consensus 19 ~k~V~V~l--~dgr~~~G~L~ 37 (87)
|+.++|.| ..+..|+|.|+
T Consensus 33 g~~~~Vtl~~~~~~~F~GFll 53 (132)
T PF02014_consen 33 GQTYTVTLSSSGSSSFRGFLL 53 (132)
T ss_dssp TBEEEEEEEETTTEEBSEEEE
T ss_pred CCEEEEEEECCCCCceeEEEE
Confidence 56788888 78889998874
No 165
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=20.45 E-value=71 Score=20.26 Aligned_cols=34 Identities=24% Similarity=0.298 Sum_probs=28.0
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEcceEEE
Q 041342 19 GSKIWVIMKGDKELVGTLKGFDVYVNMVLEDVTEY 53 (87)
Q Consensus 19 ~k~V~V~l~dgr~~~G~L~~~D~~mNlvL~~~~e~ 53 (87)
|.+|+++++| -++...+.|-|..+-+.--+|+-.
T Consensus 64 G~rV~lrLkd-lELs~~FLG~~~d~TllEAd~~Ll 97 (104)
T PF10246_consen 64 GSRVRLRLKD-LELSAHFLGASKDTTLLEADATLL 97 (104)
T ss_pred CCEEEEEECC-HhhhhhhccCCCCcEEEEeeeEEE
Confidence 7899999996 778888999998888887777654
No 166
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.44 E-value=86 Score=22.53 Aligned_cols=32 Identities=22% Similarity=0.373 Sum_probs=21.2
Q ss_pred HHHHhhhcCCEEEEEEcC--CcEEEEEEEEecccc
Q 041342 11 SELIDRCIGSKIWVIMKG--DKELVGTLKGFDVYV 43 (87)
Q Consensus 11 l~~L~~~l~k~V~V~l~d--gr~~~G~L~~~D~~m 43 (87)
-++|.+-.|+.+. .+.+ |.+|+|+|.++|+-.
T Consensus 56 ~Nll~eefGei~~-~le~v~Ge~y~G~l~s~~~~G 89 (225)
T PF09883_consen 56 ANLLREEFGEIVY-SLEPVKGETYVGTLISWDEDG 89 (225)
T ss_pred HHHHHHHhCCCCc-hhcccCCceEEEEEEeecccc
Confidence 3456665565432 2333 999999999999643
No 167
>PRK15493 5-methylthioadenosine/S-adenosylhomocysteine deaminase; Provisional
Probab=20.16 E-value=2.3e+02 Score=21.53 Aligned_cols=38 Identities=13% Similarity=0.221 Sum_probs=24.0
Q ss_pred cceEEcceEEEEEccCCeeeEeeCeEEEcCCcEEEEEeC
Q 041342 43 VNMVLEDVTEYEITAEGRRITKLDQILLNGNNIAILVPG 81 (87)
Q Consensus 43 mNlvL~~~~e~~~~~~g~~~~~~g~v~IRG~~I~~I~~~ 81 (87)
||+.+.++.-...+ ++.....-|.+.|.|+.|..|.+.
T Consensus 1 ~~~li~~~~v~t~~-~~~~~~~~g~V~i~~g~I~~vg~~ 38 (435)
T PRK15493 1 MKTTYVNATIVTMN-EQNEVIENGYIIVENDQIIDVNSG 38 (435)
T ss_pred CeEEEEccEEEEeC-CCCcEecCcEEEEECCEEEEEcCc
Confidence 57777777755322 111223347889999999988653
No 168
>cd08544 Reeler Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins. This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, an extracellular glycoprotein involved in the development of the brain cortex, and in a variety of other eukaryotic proteins with different domain architectures, including the animal ferric-chelate reductase 1 or stromal cell-derived receptor 2, a member of the cytochrome B561 family, which reduces ferric iron before its transport from the endosome to the cytoplasm. Also included is the insect putative defense protein 1, which is expressed upon bacterial infection and appears to contain a single reeler domain.
Probab=20.07 E-value=1.6e+02 Score=18.44 Aligned_cols=22 Identities=23% Similarity=0.271 Sum_probs=15.9
Q ss_pred CCEEEEEEcCCc--EEEEEEEEec
Q 041342 19 GSKIWVIMKGDK--ELVGTLKGFD 40 (87)
Q Consensus 19 ~k~V~V~l~dgr--~~~G~L~~~D 40 (87)
|+.+.|.|+... .|+|.|+--.
T Consensus 33 G~~~~Vtl~~~~~~~F~GF~lqAr 56 (135)
T cd08544 33 GETYTVTLSGSSPSPFRGFLLQAR 56 (135)
T ss_pred CCEEEEEEECCCCCceeEEEEEEE
Confidence 567888888776 8888775433
Done!