Query 034564
Match_columns 91
No_of_seqs 103 out of 1090
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 04:10:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034564hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00737 small nuclear ribonuc 99.9 4.1E-25 8.9E-30 133.5 10.1 70 13-82 3-72 (72)
2 cd01726 LSm6 The eukaryotic Sm 99.9 3.6E-25 7.8E-30 131.9 9.5 67 15-81 1-67 (67)
3 cd01721 Sm_D3 The eukaryotic S 99.9 6.8E-25 1.5E-29 131.9 9.9 70 15-84 1-70 (70)
4 cd01722 Sm_F The eukaryotic Sm 99.9 7.7E-25 1.7E-29 130.9 9.0 68 14-81 1-68 (68)
5 cd01731 archaeal_Sm1 The archa 99.9 1.2E-24 2.6E-29 129.9 9.6 68 15-82 1-68 (68)
6 cd01723 LSm4 The eukaryotic Sm 99.9 3.2E-24 7E-29 130.7 9.5 73 14-86 1-74 (76)
7 cd01719 Sm_G The eukaryotic Sm 99.9 4.1E-24 8.8E-29 129.3 9.2 71 15-85 1-71 (72)
8 cd01732 LSm5 The eukaryotic Sm 99.9 7.1E-24 1.5E-28 129.5 10.0 71 13-83 2-75 (76)
9 cd01724 Sm_D1 The eukaryotic S 99.9 1.6E-23 3.4E-28 131.6 10.4 73 15-87 2-74 (90)
10 cd01733 LSm10 The eukaryotic S 99.9 3.7E-23 8.1E-28 126.8 10.2 73 11-83 6-78 (78)
11 cd01730 LSm3 The eukaryotic Sm 99.9 4.1E-23 9E-28 127.4 9.2 69 14-82 1-82 (82)
12 COG1958 LSM1 Small nuclear rib 99.9 1.9E-22 4.1E-27 123.5 9.9 73 10-82 3-79 (79)
13 cd01729 LSm7 The eukaryotic Sm 99.9 1.9E-22 4.1E-27 124.4 9.6 68 17-84 5-80 (81)
14 cd01725 LSm2 The eukaryotic Sm 99.9 2.5E-22 5.3E-27 123.9 9.6 74 15-88 2-77 (81)
15 PF01423 LSM: LSM domain ; In 99.9 4.3E-22 9.4E-27 117.7 10.0 66 17-82 1-67 (67)
16 smart00651 Sm snRNP Sm protein 99.9 3.4E-22 7.4E-27 118.0 9.3 66 17-82 1-67 (67)
17 cd01720 Sm_D2 The eukaryotic S 99.9 4.4E-22 9.5E-27 124.3 9.4 69 14-82 2-85 (87)
18 cd01718 Sm_E The eukaryotic Sm 99.9 1.5E-21 3.3E-26 120.0 9.3 71 12-82 4-79 (79)
19 KOG3482 Small nuclear ribonucl 99.9 9.5E-22 2.1E-26 118.0 6.6 73 10-82 4-76 (79)
20 cd01727 LSm8 The eukaryotic Sm 99.9 5.2E-21 1.1E-25 116.0 9.7 69 17-85 2-74 (74)
21 cd01717 Sm_B The eukaryotic Sm 99.9 4.2E-21 9E-26 117.6 9.2 66 17-82 3-78 (79)
22 cd01728 LSm1 The eukaryotic Sm 99.8 1.5E-20 3.2E-25 114.3 9.9 68 15-82 3-73 (74)
23 cd00600 Sm_like The eukaryotic 99.8 1.6E-20 3.4E-25 109.5 8.5 63 19-81 1-63 (63)
24 cd06168 LSm9 The eukaryotic Sm 99.8 4.8E-20 1E-24 112.3 9.7 66 17-82 3-74 (75)
25 PTZ00138 small nuclear ribonuc 99.8 2.3E-19 5.1E-24 112.4 10.2 77 7-83 7-88 (89)
26 KOG1780 Small Nuclear ribonucl 99.8 7.2E-19 1.6E-23 105.9 6.2 69 18-86 8-76 (77)
27 KOG1783 Small nuclear ribonucl 99.8 1.2E-19 2.7E-24 108.9 1.5 72 13-84 5-76 (77)
28 KOG3293 Small nuclear ribonucl 99.7 1.5E-17 3.3E-22 108.7 5.8 74 14-87 2-76 (134)
29 KOG3460 Small nuclear ribonucl 99.7 1.2E-17 2.7E-22 102.6 1.8 74 12-85 3-89 (91)
30 KOG1781 Small Nuclear ribonucl 99.7 5.9E-18 1.3E-22 106.9 -0.2 73 16-88 19-99 (108)
31 KOG3172 Small nuclear ribonucl 99.6 7.7E-16 1.7E-20 98.7 7.2 75 11-85 2-76 (119)
32 KOG3448 Predicted snRNP core p 99.6 1.4E-15 3E-20 94.5 7.9 71 16-86 4-76 (96)
33 KOG1775 U6 snRNA-associated Sm 99.6 4.3E-16 9.3E-21 94.5 4.3 75 10-84 3-80 (84)
34 KOG1774 Small nuclear ribonucl 99.5 9.4E-15 2E-19 89.6 5.0 81 1-83 1-86 (88)
35 KOG1782 Small Nuclear ribonucl 99.5 2.5E-15 5.3E-20 98.2 -0.2 72 18-89 13-87 (129)
36 KOG3428 Small nuclear ribonucl 99.4 9.4E-13 2E-17 84.5 8.9 74 15-89 3-76 (109)
37 KOG1784 Small Nuclear ribonucl 99.4 2.1E-13 4.6E-18 85.1 4.1 72 17-88 3-78 (96)
38 KOG3168 U1 snRNP component [Tr 99.4 1.3E-13 2.8E-18 94.4 0.5 69 17-85 7-85 (177)
39 KOG3459 Small nuclear ribonucl 98.7 4.5E-09 9.7E-14 67.8 0.0 69 13-81 23-106 (114)
40 PF14438 SM-ATX: Ataxin 2 SM d 98.2 9E-06 2E-10 49.0 6.2 63 16-78 4-76 (77)
41 cd01739 LSm11_C The eukaryotic 98.2 2.1E-06 4.5E-11 50.9 3.1 35 24-58 8-46 (66)
42 PF12701 LSM14: Scd6-like Sm d 97.6 0.00058 1.3E-08 43.3 7.9 68 20-87 4-81 (96)
43 PF06372 Gemin6: Gemin6 protei 96.9 0.0056 1.2E-07 42.4 7.1 65 13-85 7-72 (166)
44 PF02237 BPL_C: Biotin protein 96.9 0.0096 2.1E-07 32.8 6.4 35 22-57 1-35 (48)
45 cd01716 Hfq Hfq, an abundant, 96.5 0.0085 1.8E-07 35.1 4.6 36 18-53 3-40 (61)
46 PF11095 Gemin7: Gem-associate 96.5 0.023 5E-07 35.0 6.6 63 16-83 16-79 (80)
47 cd01736 LSm14_N LSm14 (also kn 96.4 0.03 6.5E-07 34.0 6.6 59 21-79 3-72 (74)
48 TIGR02383 Hfq RNA chaperone Hf 96.1 0.014 3.1E-07 34.1 4.1 36 17-52 6-43 (61)
49 PRK00395 hfq RNA-binding prote 95.8 0.022 4.8E-07 35.0 4.1 39 17-55 10-50 (79)
50 PF10842 DUF2642: Protein of u 95.7 0.093 2E-06 31.2 6.4 54 16-82 13-66 (66)
51 PRK14638 hypothetical protein; 95.1 0.098 2.1E-06 35.4 6.0 35 18-53 94-128 (150)
52 PRK14639 hypothetical protein; 94.9 0.13 2.8E-06 34.5 6.0 34 18-52 82-115 (140)
53 PRK02001 hypothetical protein; 94.8 0.096 2.1E-06 35.7 5.4 37 14-52 81-117 (152)
54 cd01735 LSm12_N LSm12 belongs 94.7 0.12 2.5E-06 30.3 4.8 33 22-54 4-36 (61)
55 COG1923 Hfq Uncharacterized ho 94.0 0.18 4E-06 30.7 4.8 34 17-50 10-45 (77)
56 cd01734 YlxS_C YxlS is a Bacil 93.0 0.54 1.2E-05 28.5 5.8 38 13-52 15-56 (83)
57 PRK14091 RNA-binding protein H 92.6 0.32 6.9E-06 33.7 4.7 40 16-55 94-135 (165)
58 PRK14640 hypothetical protein; 92.4 0.62 1.3E-05 31.5 5.9 37 14-52 88-128 (152)
59 PRK14644 hypothetical protein; 92.2 0.4 8.6E-06 32.0 4.7 35 18-53 79-117 (136)
60 PRK14633 hypothetical protein; 91.8 0.59 1.3E-05 31.6 5.3 34 18-52 88-125 (150)
61 PRK00092 ribosome maturation p 91.5 0.89 1.9E-05 30.6 5.9 29 18-46 92-124 (154)
62 PRK14091 RNA-binding protein H 91.1 0.42 9.2E-06 33.1 4.0 40 16-55 14-55 (165)
63 PRK14634 hypothetical protein; 91.0 0.73 1.6E-05 31.3 5.1 37 14-52 91-131 (155)
64 PRK14632 hypothetical protein; 90.8 0.76 1.6E-05 31.8 5.2 35 18-53 92-133 (172)
65 PRK14645 hypothetical protein; 90.7 0.76 1.7E-05 31.3 5.0 33 18-52 96-128 (154)
66 PRK14636 hypothetical protein; 90.7 1 2.2E-05 31.3 5.7 37 14-52 89-129 (176)
67 PRK14642 hypothetical protein; 90.6 0.55 1.2E-05 33.3 4.4 34 18-52 94-140 (197)
68 PRK06955 biotin--protein ligas 90.2 2.2 4.9E-05 31.6 7.5 50 22-75 247-296 (300)
69 KOG1073 Uncharacterized mRNA-a 90.0 1 2.3E-05 34.7 5.7 66 20-85 5-81 (361)
70 PRK14643 hypothetical protein; 89.8 1.4 3E-05 30.3 5.7 30 18-47 98-131 (164)
71 PF02576 DUF150: Uncharacteris 89.7 1.1 2.5E-05 29.5 5.1 35 17-52 80-118 (141)
72 PRK14646 hypothetical protein; 89.6 1.1 2.4E-05 30.4 5.1 34 18-52 94-131 (155)
73 COG0779 Uncharacterized protei 89.0 2.2 4.8E-05 29.1 6.2 33 16-48 91-127 (153)
74 PRK14647 hypothetical protein; 88.8 1.4 3E-05 30.0 5.1 29 18-46 93-130 (159)
75 PRK11886 bifunctional biotin-- 88.1 3.4 7.3E-05 30.6 7.2 48 22-74 270-317 (319)
76 PRK14637 hypothetical protein; 87.9 1.8 3.8E-05 29.4 5.1 35 18-53 92-127 (151)
77 PRK13325 bifunctional biotin-- 87.9 3.4 7.3E-05 33.7 7.6 33 22-54 276-308 (592)
78 PRK14641 hypothetical protein; 86.9 1.8 3.8E-05 30.1 4.8 28 18-45 98-129 (173)
79 PRK14631 hypothetical protein; 85.7 1.7 3.6E-05 30.2 4.1 28 18-45 111-142 (174)
80 TIGR00121 birA_ligase birA, bi 82.7 7.9 0.00017 27.5 6.7 31 22-53 191-221 (237)
81 PRK14630 hypothetical protein; 79.3 6.3 0.00014 26.4 5.0 33 18-52 91-123 (143)
82 PRK08330 biotin--protein ligas 77.2 16 0.00035 25.9 6.8 33 22-55 186-219 (236)
83 PRK14635 hypothetical protein; 76.6 8.8 0.00019 26.1 5.1 37 14-52 90-131 (162)
84 PTZ00275 biotin-acetyl-CoA-car 76.2 8.1 0.00018 28.5 5.2 32 23-55 236-267 (285)
85 PF11607 DUF3247: Protein of u 74.7 5.1 0.00011 25.5 3.2 17 25-41 29-45 (101)
86 PF03614 Flag1_repress: Repres 74.1 4.3 9.2E-05 28.0 3.0 23 24-46 120-142 (165)
87 PF03614 Flag1_repress: Repres 72.8 7.7 0.00017 26.7 4.0 35 22-56 27-61 (165)
88 PF14563 DUF4444: Domain of un 71.7 6.6 0.00014 21.3 2.8 21 37-57 10-30 (42)
89 TIGR02038 protease_degS peripl 71.4 20 0.00044 27.0 6.5 32 25-56 102-133 (351)
90 COG0340 BirA Biotin-(acetyl-Co 71.1 31 0.00067 24.9 7.1 34 22-55 188-221 (238)
91 PRK10898 serine endoprotease; 70.8 11 0.00024 28.6 4.9 32 25-56 102-133 (353)
92 PF07073 ROF: Modulator of Rho 70.2 4.6 9.9E-05 24.7 2.2 22 19-40 12-33 (80)
93 PRK09618 flgD flagellar basal 69.1 11 0.00024 25.5 4.1 26 20-45 88-113 (142)
94 TIGR02603 CxxCH_TIGR02603 puta 66.5 13 0.00028 24.2 4.0 30 25-55 58-87 (133)
95 PF14153 Spore_coat_CotO: Spor 65.2 11 0.00024 26.5 3.6 32 16-47 123-157 (185)
96 PRK10942 serine endoprotease; 63.5 17 0.00037 28.7 4.8 31 25-55 136-166 (473)
97 PRK10139 serine endoprotease; 63.4 18 0.00039 28.5 4.9 58 25-83 115-174 (455)
98 KOG3382 NADH:ubiquinone oxidor 60.9 4.9 0.00011 27.1 1.2 27 31-57 39-65 (151)
99 TIGR02037 degP_htrA_DO peripla 58.8 24 0.00051 27.2 4.8 32 25-56 82-113 (428)
100 PRK08477 biotin--protein ligas 57.8 37 0.0008 24.1 5.3 36 21-57 172-207 (211)
101 PF05071 NDUFA12: NADH ubiquin 51.9 9.9 0.00021 24.1 1.5 17 39-55 1-17 (105)
102 PRK11911 flgD flagellar basal 51.7 31 0.00067 23.3 3.9 27 20-46 89-115 (140)
103 PRK11625 Rho-binding antitermi 51.4 31 0.00067 21.3 3.6 26 20-47 19-44 (84)
104 cd04479 RPA3 RPA3: A subfamily 49.7 55 0.0012 20.3 4.6 36 16-53 7-47 (101)
105 TIGR03170 flgA_cterm flagella 46.1 30 0.00066 21.7 3.1 23 21-43 93-116 (122)
106 PF09465 LBR_tudor: Lamin-B re 44.4 59 0.0013 18.5 3.7 27 22-48 7-34 (55)
107 PF01887 SAM_adeno_trans: S-ad 44.1 37 0.00081 24.8 3.6 18 36-53 169-186 (258)
108 PRK06630 hypothetical protein; 43.5 13 0.00029 23.7 1.1 20 37-56 11-30 (99)
109 smart00333 TUDOR Tudor domain. 42.7 54 0.0012 17.5 4.3 25 23-47 5-29 (57)
110 PRK07018 flgA flagellar basal 39.9 36 0.00077 24.3 2.9 23 21-43 204-227 (235)
111 PRK06792 flgD flagellar basal 38.3 59 0.0013 23.1 3.8 26 20-45 114-139 (190)
112 PLN02732 Probable NADH dehydro 37.8 31 0.00067 23.8 2.2 19 38-56 48-66 (159)
113 PF06257 DUF1021: Protein of u 37.1 96 0.0021 18.7 4.5 29 16-44 9-41 (76)
114 PF14485 DUF4431: Domain of un 36.8 39 0.00084 18.5 2.2 15 16-30 11-25 (48)
115 smart00166 UBX Domain present 35.6 39 0.00085 19.8 2.2 21 25-45 5-25 (80)
116 PLN03095 NADH:ubiquinone oxido 35.0 24 0.00052 23.1 1.3 19 38-56 9-27 (115)
117 PTZ00276 biotin/lipoate protei 33.0 79 0.0017 22.7 3.9 24 32-55 209-232 (245)
118 cd01767 UBX UBX (ubiquitin reg 32.4 54 0.0012 19.0 2.5 21 25-45 3-23 (77)
119 PF00789 UBX: UBX domain; Int 31.4 53 0.0012 19.0 2.3 22 25-46 7-28 (82)
120 COG0265 DegQ Trypsin-like seri 31.2 1.1E+02 0.0024 22.7 4.5 32 24-55 95-126 (347)
121 TIGR00567 3mg DNA-3-methyladen 30.9 1.7E+02 0.0037 20.7 5.1 37 13-49 8-44 (192)
122 COG4466 Veg Uncharacterized pr 29.8 60 0.0013 19.9 2.3 29 16-44 11-43 (80)
123 PF10618 Tail_tube: Phage tail 29.6 91 0.002 20.1 3.4 28 13-40 63-90 (119)
124 COG5316 Uncharacterized conser 28.7 1.3E+02 0.0027 24.0 4.5 47 10-57 68-114 (421)
125 COG1363 FrvX Cellulase M and r 28.2 74 0.0016 24.6 3.2 23 20-42 93-115 (355)
126 PRK06005 flgA flagellar basal 27.2 92 0.002 21.1 3.2 23 21-43 128-151 (160)
127 cd01772 SAKS1_UBX SAKS1-like U 26.8 55 0.0012 19.3 1.8 23 23-45 3-25 (79)
128 PF02245 Pur_DNA_glyco: Methyl 26.7 1.4E+02 0.003 20.9 4.0 35 14-49 8-42 (184)
129 PRK08183 NADH dehydrogenase; V 26.7 36 0.00079 22.7 1.1 19 38-56 25-43 (133)
130 PRK12617 flgA flagellar basal 26.5 89 0.0019 22.3 3.1 23 21-43 183-206 (214)
131 PF13437 HlyD_3: HlyD family s 26.4 1.5E+02 0.0032 17.6 4.5 32 15-46 43-78 (105)
132 TIGR00999 8a0102 Membrane Fusi 26.3 1.6E+02 0.0035 20.4 4.4 26 23-48 141-166 (265)
133 COG0048 RpsL Ribosomal protein 26.0 75 0.0016 21.2 2.4 27 21-48 53-79 (129)
134 PRK08515 flgA flagellar basal 25.6 1.1E+02 0.0025 21.7 3.6 23 21-43 193-215 (222)
135 PF12945 YcgR_2: Flagellar pro 25.5 1.4E+02 0.0031 17.0 4.7 33 23-55 3-39 (87)
136 KOG4401 Uncharacterized conser 25.4 1.1E+02 0.0023 21.7 3.3 35 22-56 9-43 (184)
137 COG4568 Rof Transcriptional an 24.4 1.3E+02 0.0027 18.5 3.1 22 19-40 18-39 (84)
138 PF05954 Phage_GPD: Phage late 24.1 1.1E+02 0.0023 21.5 3.2 26 20-45 24-49 (292)
139 KOG3493 Ubiquitin-like protein 24.0 69 0.0015 19.1 1.8 19 18-36 5-23 (73)
140 PF02604 PhdYeFM_antitox: Anti 23.9 47 0.001 18.8 1.1 36 14-50 12-48 (75)
141 PF05037 DUF669: Protein of un 23.4 75 0.0016 20.8 2.2 30 12-41 91-121 (141)
142 PRK10708 hypothetical protein; 23.3 1.1E+02 0.0024 17.7 2.5 25 23-47 3-27 (62)
143 PRK06804 flgA flagellar basal 22.6 1.1E+02 0.0024 22.5 3.1 23 21-43 230-253 (261)
144 COG2451 Ribosomal protein L35A 22.3 1.8E+02 0.0038 18.5 3.5 28 18-45 40-68 (100)
145 PF13144 SAF_2: SAF-like 22.2 1.4E+02 0.0031 20.2 3.5 23 21-43 167-190 (196)
146 PF11743 DUF3301: Protein of u 22.2 1.4E+02 0.0031 18.4 3.1 37 47-84 57-96 (97)
147 PRK09961 exoaminopeptidase; Pr 22.0 1.2E+02 0.0025 23.0 3.2 23 20-42 90-112 (344)
148 PRK12618 flgA flagellar basal 21.7 1.4E+02 0.003 19.8 3.2 23 21-43 109-132 (141)
149 PF08863 YolD: YolD-like prote 21.2 1.9E+02 0.004 16.9 4.3 31 24-54 42-76 (92)
150 PF12869 tRNA_anti-like: tRNA_ 20.8 98 0.0021 19.7 2.3 20 36-55 124-143 (144)
151 PF03122 Herpes_MCP: Herpes vi 20.5 34 0.00073 30.9 0.0 51 29-79 252-304 (1354)
152 cd00319 Ribosomal_S12_like Rib 20.3 1.1E+02 0.0024 19.3 2.4 23 21-43 32-54 (95)
153 PRK05163 rpsL 30S ribosomal pr 20.0 1.3E+02 0.0029 19.9 2.7 25 21-45 47-71 (124)
154 PF05343 Peptidase_M42: M42 gl 20.0 1.2E+02 0.0026 22.5 2.8 24 20-44 49-72 (292)
No 1
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.93 E-value=4.1e-25 Score=133.45 Aligned_cols=70 Identities=37% Similarity=0.687 Sum_probs=65.8
Q ss_pred CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564 13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST 82 (91)
Q Consensus 13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~ 82 (91)
..|+.+|+++++++|+|+|+||+.|.|+|.+||+|||++|+||.|..+++..++++.++|||++|++|++
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 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEcC
Confidence 5799999999999999999999999999999999999999999998777667899999999999999963
No 2
>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=3.6e-25 Score=131.94 Aligned_cols=67 Identities=93% Similarity=1.460 Sum_probs=63.4
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEE
Q 034564 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 81 (91)
Q Consensus 15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~ 81 (91)
|+++|++++|++|+|+|++|++|+|+|.+||+||||+|+||.+..++.....++.++|||++|++|+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence 7899999999999999999999999999999999999999999877767789999999999999984
No 3
>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=99.92 E-value=6.8e-25 Score=131.91 Aligned_cols=70 Identities=23% Similarity=0.405 Sum_probs=64.3
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCC
Q 034564 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK 84 (91)
Q Consensus 15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~ 84 (91)
|+.+|+++.|++|+|+|+||.+|+|+|.++|+|||++|+||.+...+.+..+++.+||||++|+||++||
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence 7899999999999999999999999999999999999999988643334578899999999999999997
No 4
>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=7.7e-25 Score=130.92 Aligned_cols=68 Identities=46% Similarity=0.924 Sum_probs=63.9
Q ss_pred ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEE
Q 034564 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 81 (91)
Q Consensus 14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~ 81 (91)
+|.++|++++|++|+|+|+||++|+|+|.+||+|||++|+||++..++.....+|.++|||++|+||+
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 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence 58999999999999999999999999999999999999999999877766678999999999999984
No 5
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.92 E-value=1.2e-24 Score=129.88 Aligned_cols=68 Identities=46% Similarity=0.736 Sum_probs=63.7
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST 82 (91)
Q Consensus 15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~ 82 (91)
|+.+|+++++++|+|+|++|+.|.|+|.+||+|||++|+||+|...+...+.++.++|||++|++|++
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEcC
Confidence 78999999999999999999999999999999999999999998666567889999999999999974
No 6
>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=99.91 E-value=3.2e-24 Score=130.73 Aligned_cols=73 Identities=29% Similarity=0.528 Sum_probs=66.9
Q ss_pred ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEE-ecCeeeeeeceEEEeCCcEEEEEeCCCc
Q 034564 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEY-VNGQLKNKYGDAFIRGNNVLYISTSKRT 86 (91)
Q Consensus 14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~-~~g~~~~~l~~v~IRG~~I~~i~~~~~~ 86 (91)
.|+.+|+++.|++|.|+|+||++|+|+|.+||+|||++|+||++. .+|++...++.+||||++|+||+.|++.
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence 389999999999999999999999999999999999999999987 4565556789999999999999999864
No 7
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.91 E-value=4.1e-24 Score=129.27 Aligned_cols=71 Identities=30% Similarity=0.464 Sum_probs=65.5
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR 85 (91)
Q Consensus 15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~ 85 (91)
|.++|.++++|+|.|+|++|++|.|+|.+||+||||+|+||.|+.++...+++|.++|||++|++|++.|.
T Consensus 1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEcccc
Confidence 45789999999999999999999999999999999999999998766667899999999999999998764
No 8
>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=99.91 E-value=7.1e-24 Score=129.46 Aligned_cols=71 Identities=23% Similarity=0.484 Sum_probs=65.1
Q ss_pred CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe---cCeeeeeeceEEEeCCcEEEEEeC
Q 034564 13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV---NGQLKNKYGDAFIRGNNVLYISTS 83 (91)
Q Consensus 13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~g~~~~~l~~v~IRG~~I~~i~~~ 83 (91)
..|+.+|+++++++|+|+|++|+++.|+|.|||+|||++|+||.|+. +++..+++|.++|||++|++|++.
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence 46899999999999999999999999999999999999999999975 454567899999999999999853
No 9
>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=99.91 E-value=1.6e-23 Score=131.57 Aligned_cols=73 Identities=22% Similarity=0.326 Sum_probs=68.3
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTL 87 (91)
Q Consensus 15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~~ 87 (91)
+..||+++.|++|+|+|+||.+|+|+|.++|+|||++|+||+++.+++...+++.++|||++|+||++||...
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~ 74 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLN 74 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCC
Confidence 6789999999999999999999999999999999999999999877666778999999999999999998864
No 10
>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=99.90 E-value=3.7e-23 Score=126.81 Aligned_cols=73 Identities=21% Similarity=0.375 Sum_probs=67.0
Q ss_pred cCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeC
Q 034564 11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTS 83 (91)
Q Consensus 11 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~ 83 (91)
....+..||+++.|++|.|+|+||.+|+|+|.++|+|||++|+||++..++....+++.+||||++|+||++|
T Consensus 6 ~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 6 LENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred hhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence 4567899999999999999999999999999999999999999999876565556899999999999999987
No 11
>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=99.90 E-value=4.1e-23 Score=127.42 Aligned_cols=69 Identities=28% Similarity=0.446 Sum_probs=62.2
Q ss_pred ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC-------------eeeeeeceEEEeCCcEEEE
Q 034564 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG-------------QLKNKYGDAFIRGNNVLYI 80 (91)
Q Consensus 14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g-------------~~~~~l~~v~IRG~~I~~i 80 (91)
.|+++|+.+++++|.|.|++||+|.|+|.|||+||||+|+||.|...+ ...+.+|.++|||++|++|
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 389999999999999999999999999999999999999999997432 1467899999999999998
Q ss_pred Ee
Q 034564 81 ST 82 (91)
Q Consensus 81 ~~ 82 (91)
++
T Consensus 81 ~~ 82 (82)
T cd01730 81 SP 82 (82)
T ss_pred CC
Confidence 73
No 12
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.89 E-value=1.9e-22 Score=123.47 Aligned_cols=73 Identities=37% Similarity=0.724 Sum_probs=64.4
Q ss_pred ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe--cCee-eeeec-eEEEeCCcEEEEEe
Q 034564 10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV--NGQL-KNKYG-DAFIRGNNVLYIST 82 (91)
Q Consensus 10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~--~g~~-~~~l~-~v~IRG~~I~~i~~ 82 (91)
+....|..+|+++++++|.|+|++|++|.|+|.+||+||||+|+||.|+. ++.. .+.++ .++|||++|++|.+
T Consensus 3 ~~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 3 MLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred cccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 34567899999999999999999999999999999999999999999986 5654 34454 99999999999863
No 13
>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=99.89 E-value=1.9e-22 Score=124.42 Aligned_cols=68 Identities=26% Similarity=0.413 Sum_probs=61.0
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC--------eeeeeeceEEEeCCcEEEEEeCC
Q 034564 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG--------QLKNKYGDAFIRGNNVLYISTSK 84 (91)
Q Consensus 17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g--------~~~~~l~~v~IRG~~I~~i~~~~ 84 (91)
.-|.++++++|+|.|++|++|.|+|.+||+||||+|+||.|+..+ ...+.+|.++|||++|++|++.+
T Consensus 5 ~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 5 LDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred hhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 448999999999999999999999999999999999999997543 24578999999999999998765
No 14
>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=99.88 E-value=2.5e-22 Score=123.86 Aligned_cols=74 Identities=26% Similarity=0.425 Sum_probs=65.2
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCe--eeeeeceEEEeCCcEEEEEeCCCccc
Q 034564 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ--LKNKYGDAFIRGNNVLYISTSKRTLA 88 (91)
Q Consensus 15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~--~~~~l~~v~IRG~~I~~i~~~~~~~~ 88 (91)
|+.||+++.|++|+|+|++|.+|+|+|.++|+|||++|+||++..++. ....++.++|||++|+||+.||...+
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~ 77 (81)
T cd01725 2 FFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVD 77 (81)
T ss_pred hhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcC
Confidence 689999999999999999999999999999999999999998864321 23467899999999999999987654
No 15
>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=99.88 E-value=4.3e-22 Score=117.70 Aligned_cols=66 Identities=38% Similarity=0.694 Sum_probs=62.0
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCe-eeeeeceEEEeCCcEEEEEe
Q 034564 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ-LKNKYGDAFIRGNNVLYIST 82 (91)
Q Consensus 17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~-~~~~l~~v~IRG~~I~~i~~ 82 (91)
.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||.+...+. +.+.++.+||||++|++|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 3789999999999999999999999999999999999999987766 77899999999999999975
No 16
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.88 E-value=3.4e-22 Score=118.03 Aligned_cols=66 Identities=45% Similarity=0.796 Sum_probs=60.9
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC-eeeeeeceEEEeCCcEEEEEe
Q 034564 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG-QLKNKYGDAFIRGNNVLYIST 82 (91)
Q Consensus 17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g-~~~~~l~~v~IRG~~I~~i~~ 82 (91)
.+|++++|++|+|+|+||+++.|+|.+||+|||++|+||+++..+ ...++++.+||||++|++|++
T Consensus 1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 378999999999999999999999999999999999999998654 567899999999999999974
No 17
>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=99.88 E-value=4.4e-22 Score=124.34 Aligned_cols=69 Identities=17% Similarity=0.319 Sum_probs=61.7
Q ss_pred ChHHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC-------------eeeeeeceEEEeCCcEE
Q 034564 14 TPADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG-------------QLKNKYGDAFIRGNNVL 78 (91)
Q Consensus 14 ~p~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g-------------~~~~~l~~v~IRG~~I~ 78 (91)
+|+++|+.++ +++|.|.|++|+.+.|+|.+||+||||+|+||.|...+ ...+.+|.+||||++|+
T Consensus 2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 6999999997 89999999999999999999999999999999996432 13557899999999999
Q ss_pred EEEe
Q 034564 79 YIST 82 (91)
Q Consensus 79 ~i~~ 82 (91)
+|+.
T Consensus 82 ~Is~ 85 (87)
T cd01720 82 LVLR 85 (87)
T ss_pred EEec
Confidence 9975
No 18
>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=99.87 E-value=1.5e-21 Score=119.99 Aligned_cols=71 Identities=20% Similarity=0.415 Sum_probs=63.7
Q ss_pred CCChHHHHhhcCCC--eEEEEEc--CCcEEEEEEEEEcCCCceeeeeeEEEec-CeeeeeeceEEEeCCcEEEEEe
Q 034564 12 TKTPADFLKSIRGR--PVVVKLN--SGVDYRGILACLDGYMNIAMEQTEEYVN-GQLKNKYGDAFIRGNNVLYIST 82 (91)
Q Consensus 12 ~~~p~~~L~~~~~k--~V~V~L~--~g~~~~G~L~~~D~~mNlvL~~~~e~~~-g~~~~~l~~v~IRG~~I~~i~~ 82 (91)
+..|+..|.+++++ +|.|+++ +|+++.|+|.|||+||||+|+||+|+.. ++..+++|.++|||++|++|++
T Consensus 4 ~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 4 MVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred ccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence 57899999999998 7788877 8999999999999999999999999864 4566789999999999999973
No 19
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.86 E-value=9.5e-22 Score=118.05 Aligned_cols=73 Identities=41% Similarity=0.800 Sum_probs=69.2
Q ss_pred ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564 10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST 82 (91)
Q Consensus 10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~ 82 (91)
+++.+|.+||+.+.+++|.|.|+.|.+|+|+|++.|.|||+.|.+|+|+.+|....++|+++||.+||.||.-
T Consensus 4 ~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~g 76 (79)
T KOG3482|consen 4 KQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIRG 76 (79)
T ss_pred cccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEec
Confidence 3578999999999999999999999999999999999999999999999999888899999999999999953
No 20
>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=99.86 E-value=5.2e-21 Score=115.98 Aligned_cols=69 Identities=23% Similarity=0.283 Sum_probs=61.4
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec----CeeeeeeceEEEeCCcEEEEEeCCC
Q 034564 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN----GQLKNKYGDAFIRGNNVLYISTSKR 85 (91)
Q Consensus 17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~----g~~~~~l~~v~IRG~~I~~i~~~~~ 85 (91)
+.|.++++++|+|.|++|+.|.|+|.+||+|||++|++|.|+.. +...+.+|.++|||++|++|++.|+
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~ 74 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE 74 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence 46889999999999999999999999999999999999999742 3345689999999999999998763
No 21
>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=99.86 E-value=4.2e-21 Score=117.63 Aligned_cols=66 Identities=21% Similarity=0.395 Sum_probs=58.8
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC----------eeeeeeceEEEeCCcEEEEEe
Q 034564 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG----------QLKNKYGDAFIRGNNVLYIST 82 (91)
Q Consensus 17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g----------~~~~~l~~v~IRG~~I~~i~~ 82 (91)
+-|.++++++|.|.|++||.|.|+|.+||+||||+|+||.|+..+ ...+.+|.++|||++|++|.+
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 357899999999999999999999999999999999999996421 245789999999999999975
No 22
>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=99.85 E-value=1.5e-20 Score=114.33 Aligned_cols=68 Identities=29% Similarity=0.385 Sum_probs=60.4
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe-cCe--eeeeeceEEEeCCcEEEEEe
Q 034564 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-NGQ--LKNKYGDAFIRGNNVLYIST 82 (91)
Q Consensus 15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~g~--~~~~l~~v~IRG~~I~~i~~ 82 (91)
+...|.++++++|.|.|++|++|.|+|.+||+|||++|+||.|.. .+. ..+.+|.++|||++|++|+.
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 467799999999999999999999999999999999999999863 221 35789999999999999975
No 23
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.84 E-value=1.6e-20 Score=109.49 Aligned_cols=63 Identities=35% Similarity=0.611 Sum_probs=58.1
Q ss_pred HhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEE
Q 034564 19 LKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 81 (91)
Q Consensus 19 L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~ 81 (91)
|++++|++|+|+|+||+.|.|+|.+||+|||++|+||.+...+...++++.+||||++|++|.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence 467899999999999999999999999999999999999866556789999999999999984
No 24
>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=99.83 E-value=4.8e-20 Score=112.30 Aligned_cols=66 Identities=24% Similarity=0.436 Sum_probs=60.1
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC------eeeeeeceEEEeCCcEEEEEe
Q 034564 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG------QLKNKYGDAFIRGNNVLYIST 82 (91)
Q Consensus 17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g------~~~~~l~~v~IRG~~I~~i~~ 82 (91)
+.|.++++++|+|.|+|||.|.|+|.+||++||++|+||.|+... ...+.+|.++|||++|+.+..
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 568899999999999999999999999999999999999997532 457899999999999999975
No 25
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.82 E-value=2.3e-19 Score=112.42 Aligned_cols=77 Identities=19% Similarity=0.350 Sum_probs=64.5
Q ss_pred cCCccCCChHHHHhhcCCC--eEEEEEcC--CcEEEEEEEEEcCCCceeeeeeEEEec-CeeeeeeceEEEeCCcEEEEE
Q 034564 7 KGSATTKTPADFLKSIRGR--PVVVKLNS--GVDYRGILACLDGYMNIAMEQTEEYVN-GQLKNKYGDAFIRGNNVLYIS 81 (91)
Q Consensus 7 ~~~~~~~~p~~~L~~~~~k--~V~V~L~~--g~~~~G~L~~~D~~mNlvL~~~~e~~~-g~~~~~l~~v~IRG~~I~~i~ 81 (91)
+....+..|+..+.+++.+ +|.|++.+ ++++.|+|.|||+|||++|+||+|... ++..+.+|.++|||++|++|+
T Consensus 7 ~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~ 86 (89)
T PTZ00138 7 KLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIM 86 (89)
T ss_pred ccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEE
Confidence 3334578999999999985 57777767 599999999999999999999999754 345678999999999999997
Q ss_pred eC
Q 034564 82 TS 83 (91)
Q Consensus 82 ~~ 83 (91)
+.
T Consensus 87 ~~ 88 (89)
T PTZ00138 87 AA 88 (89)
T ss_pred cC
Confidence 64
No 26
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.77 E-value=7.2e-19 Score=105.89 Aligned_cols=69 Identities=35% Similarity=0.503 Sum_probs=62.0
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCc
Q 034564 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRT 86 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~ 86 (91)
.|++|++|++.+.|..||.+.|+|+|||.|||++|++++|.........++.++|||++|+.+...+..
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~~~ 76 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALERV 76 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeecccc
Confidence 789999999999999999999999999999999999999975433457899999999999999877653
No 27
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.76 E-value=1.2e-19 Score=108.93 Aligned_cols=72 Identities=83% Similarity=1.303 Sum_probs=68.5
Q ss_pred CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCC
Q 034564 13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK 84 (91)
Q Consensus 13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~ 84 (91)
..|.+||.+.+|++|.|+|.+|-.|+|+|.+.|.|||+-|+.++|+.+|+..++++..||||++|.||+...
T Consensus 5 ~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 5 SMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEecc
Confidence 568999999999999999999999999999999999999999999999998999999999999999998754
No 28
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.71 E-value=1.5e-17 Score=108.68 Aligned_cols=74 Identities=24% Similarity=0.514 Sum_probs=69.0
Q ss_pred ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe-cCeeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-NGQLKNKYGDAFIRGNNVLYISTSKRTL 87 (91)
Q Consensus 14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~g~~~~~l~~v~IRG~~I~~i~~~~~~~ 87 (91)
.|+.+|....++++.|+|+||.+|.|.|..+|.+|||.|++++++. +|.+...+++++|||++|.|+.+||+..
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~ii 76 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEII 76 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHH
Confidence 5899999999999999999999999999999999999999999974 6777788999999999999999998764
No 29
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.68 E-value=1.2e-17 Score=102.62 Aligned_cols=74 Identities=30% Similarity=0.453 Sum_probs=65.5
Q ss_pred CCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe---cC----------eeeeeeceEEEeCCcEE
Q 034564 12 TKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV---NG----------QLKNKYGDAFIRGNNVL 78 (91)
Q Consensus 12 ~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~g----------~~~~~l~~v~IRG~~I~ 78 (91)
...|+++|+-+++.+|-|+++++|+++|+|.+||+|.|++|.|+.|+. ++ ...+.+..+|+||++|+
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 457999999999999999999999999999999999999999998853 21 13578899999999999
Q ss_pred EEEeCCC
Q 034564 79 YISTSKR 85 (91)
Q Consensus 79 ~i~~~~~ 85 (91)
+|++|-.
T Consensus 83 lvspp~~ 89 (91)
T KOG3460|consen 83 LVSPPLR 89 (91)
T ss_pred EEcCccc
Confidence 9998854
No 30
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.67 E-value=5.9e-18 Score=106.86 Aligned_cols=73 Identities=25% Similarity=0.360 Sum_probs=64.8
Q ss_pred HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEec--------CeeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564 16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVN--------GQLKNKYGDAFIRGNNVLYISTSKRTL 87 (91)
Q Consensus 16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~--------g~~~~~l~~v~IRG~~I~~i~~~~~~~ 87 (91)
+-.|.+|++++|+|++..||+..|+|.|||+.|||+|+|+.|+.. +...|++|.+++||..++.|++.|..+
T Consensus 19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e 98 (108)
T KOG1781|consen 19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE 98 (108)
T ss_pred HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence 556799999999999999999999999999999999999999631 124589999999999999999988765
Q ss_pred c
Q 034564 88 A 88 (91)
Q Consensus 88 ~ 88 (91)
|
T Consensus 99 ~ 99 (108)
T KOG1781|consen 99 E 99 (108)
T ss_pred h
Confidence 4
No 31
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.64 E-value=7.7e-16 Score=98.70 Aligned_cols=75 Identities=21% Similarity=0.367 Sum_probs=68.8
Q ss_pred cCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564 11 TTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR 85 (91)
Q Consensus 11 ~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~ 85 (91)
...-|+.+|.+..|.-|++++.+|..|+|+|+..|++||++|+|++.+..+....+++.|||||+.|+|+.+||-
T Consensus 2 s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdm 76 (119)
T KOG3172|consen 2 SVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDM 76 (119)
T ss_pred ccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchH
Confidence 356789999999999999999999999999999999999999999997655567899999999999999999874
No 32
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.64 E-value=1.4e-15 Score=94.54 Aligned_cols=71 Identities=28% Similarity=0.461 Sum_probs=62.4
Q ss_pred HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCe--eeeeeceEEEeCCcEEEEEeCCCc
Q 034564 16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQ--LKNKYGDAFIRGNNVLYISTSKRT 86 (91)
Q Consensus 16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~--~~~~l~~v~IRG~~I~~i~~~~~~ 86 (91)
.+|++.++|++|.|+|+|+-.+.|+|.++|+|+|+.|.|.....+.+ .-..+..+||||+.|+||.+|...
T Consensus 4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~ 76 (96)
T KOG3448|consen 4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDA 76 (96)
T ss_pred HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhH
Confidence 57899999999999999999999999999999999999999864322 334578999999999999998654
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.62 E-value=4.3e-16 Score=94.46 Aligned_cols=75 Identities=21% Similarity=0.469 Sum_probs=67.4
Q ss_pred ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe---cCeeeeeeceEEEeCCcEEEEEeCC
Q 034564 10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV---NGQLKNKYGDAFIRGNNVLYISTSK 84 (91)
Q Consensus 10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~---~g~~~~~l~~v~IRG~~I~~i~~~~ 84 (91)
+....|+.++.+++|.+|+|.+++.+++.|+|.|||.|.|++|+|++|+. +|....+++++++.|++|..+.+..
T Consensus 3 ~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 3 PSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred hhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence 34578999999999999999999999999999999999999999999973 4556778999999999999887655
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.54 E-value=9.4e-15 Score=89.58 Aligned_cols=81 Identities=23% Similarity=0.413 Sum_probs=64.5
Q ss_pred CCCCCccCCccCCChHHHHhhcCCC--eEEEEEcC--CcEEEEEEEEEcCCCceeeeeeEEEecCeee-eeeceEEEeCC
Q 034564 1 MSTGGEKGSATTKTPADFLKSIRGR--PVVVKLNS--GVDYRGILACLDGYMNIAMEQTEEYVNGQLK-NKYGDAFIRGN 75 (91)
Q Consensus 1 ms~~~~~~~~~~~~p~~~L~~~~~k--~V~V~L~~--g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~-~~l~~v~IRG~ 75 (91)
||. +|.-..+..|+.++.+|+.. +|.|+|.+ |-.++|.++|||.|||++|++|.|....... ..+|.++++|+
T Consensus 1 ms~--~kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGD 78 (88)
T KOG1774|consen 1 MSR--EKVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGD 78 (88)
T ss_pred CCc--ccccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCC
Confidence 566 33233458999999999874 67778876 7899999999999999999999996432223 38999999999
Q ss_pred cEEEEEeC
Q 034564 76 NVLYISTS 83 (91)
Q Consensus 76 ~I~~i~~~ 83 (91)
||.+|...
T Consensus 79 nItli~~~ 86 (88)
T KOG1774|consen 79 NITLIQSA 86 (88)
T ss_pred cEEEEeec
Confidence 99998754
No 35
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.50 E-value=2.5e-15 Score=98.21 Aligned_cols=72 Identities=22% Similarity=0.338 Sum_probs=62.9
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe-cCe--eeeeeceEEEeCCcEEEEEeCCCcccc
Q 034564 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-NGQ--LKNKYGDAFIRGNNVLYISTSKRTLAD 89 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~g~--~~~~l~~v~IRG~~I~~i~~~~~~~~~ 89 (91)
-|.+++++++.|-|+|||.+.|+|.|||+|.|++|.+|.|.. -|+ .....|.++|||.||+.++..|..+|+
T Consensus 13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE~ 87 (129)
T KOG1782|consen 13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKEE 87 (129)
T ss_pred HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchhh
Confidence 378899999999999999999999999999999999999952 232 234679999999999999999888885
No 36
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=99.45 E-value=9.4e-13 Score=84.53 Aligned_cols=74 Identities=26% Similarity=0.357 Sum_probs=67.1
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCCcccc
Q 034564 15 PADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLAD 89 (91)
Q Consensus 15 p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~~~~~ 89 (91)
...||+++.+.+++|+|++|+.+.|++.++|.+||..|.++.-...| ++.++...+|||++|+|+..||+..=|
T Consensus 3 lvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~ld 76 (109)
T KOG3428|consen 3 LVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLNLD 76 (109)
T ss_pred HHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcCcc
Confidence 46799999999999999999999999999999999999999988777 556899999999999999999986533
No 37
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.41 E-value=2.1e-13 Score=85.13 Aligned_cols=72 Identities=26% Similarity=0.312 Sum_probs=63.8
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe----cCeeeeeeceEEEeCCcEEEEEeCCCccc
Q 034564 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV----NGQLKNKYGDAFIRGNNVLYISTSKRTLA 88 (91)
Q Consensus 17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~----~g~~~~~l~~v~IRG~~I~~i~~~~~~~~ 88 (91)
.-|..|++++|.|.+.|||.+.|.|.|||+..||+|+++-|+. .|..+..+|..+|||+||..|+..|++..
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d 78 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELD 78 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhh
Confidence 3478999999999999999999999999999999999999853 34456789999999999999999987654
No 38
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.36 E-value=1.3e-13 Score=94.45 Aligned_cols=69 Identities=22% Similarity=0.407 Sum_probs=60.2
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe----------cCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564 17 DFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV----------NGQLKNKYGDAFIRGNNVLYISTSKR 85 (91)
Q Consensus 17 ~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~----------~g~~~~~l~~v~IRG~~I~~i~~~~~ 85 (91)
+-|-++++.+++|.++|||+|.|.+.+||.||||+|.+|.|.. +++..+-+++|++||++|++..+.+.
T Consensus 7 skml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegp 85 (177)
T KOG3168|consen 7 SKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGP 85 (177)
T ss_pred hHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCC
Confidence 3456789999999999999999999999999999999999852 24567889999999999999987654
No 39
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.66 E-value=4.5e-09 Score=67.76 Aligned_cols=69 Identities=20% Similarity=0.367 Sum_probs=59.1
Q ss_pred CChHHHHhhcCC--CeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEe-------cCe------eeeeeceEEEeCCcE
Q 034564 13 KTPADFLKSIRG--RPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYV-------NGQ------LKNKYGDAFIRGNNV 77 (91)
Q Consensus 13 ~~p~~~L~~~~~--k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~-------~g~------~~~~l~~v~IRG~~I 77 (91)
.+|++.+.+... ..|.|-++|++.+.|.+.+||.|.|++|+|+.|.- +|. +.+.++.+||||++|
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 389999988875 57999999999999999999999999999999841 232 257899999999999
Q ss_pred EEEE
Q 034564 78 LYIS 81 (91)
Q Consensus 78 ~~i~ 81 (91)
+.+.
T Consensus 103 I~v~ 106 (114)
T KOG3459|consen 103 ILVL 106 (114)
T ss_pred EEEE
Confidence 8876
No 40
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.18 E-value=9e-06 Score=49.02 Aligned_cols=63 Identities=16% Similarity=0.289 Sum_probs=41.5
Q ss_pred HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcC---CCceeeeeeEEEecCe-------eeeeeceEEEeCCcEE
Q 034564 16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDG---YMNIAMEQTEEYVNGQ-------LKNKYGDAFIRGNNVL 78 (91)
Q Consensus 16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~---~mNlvL~~~~e~~~g~-------~~~~l~~v~IRG~~I~ 78 (91)
.-++..++|++|.|.++||..|+|+|.+++. -+.++|+-+.....+. .....+.++|+++.|+
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 4467789999999999999999999999998 8999999998753321 1234567777776654
No 41
>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=98.16 E-value=2.1e-06 Score=50.88 Aligned_cols=35 Identities=23% Similarity=0.331 Sum_probs=30.2
Q ss_pred CCeEEEEEcC----CcEEEEEEEEEcCCCceeeeeeEEE
Q 034564 24 GRPVVVKLNS----GVDYRGILACLDGYMNIAMEQTEEY 58 (91)
Q Consensus 24 ~k~V~V~L~~----g~~~~G~L~~~D~~mNlvL~~~~e~ 58 (91)
+.+|+|.++. +-.++|.|++||.|+||+|.|+.|.
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~ 46 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDET 46 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhh
Confidence 4788888885 3478899999999999999999995
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.64 E-value=0.00058 Score=43.31 Aligned_cols=68 Identities=18% Similarity=0.343 Sum_probs=53.7
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEEcC-CCceeeeeeEEE-ecC--------eeeeeeceEEEeCCcEEEEEeCCCcc
Q 034564 20 KSIRGRPVVVKLNSGVDYRGILACLDG-YMNIAMEQTEEY-VNG--------QLKNKYGDAFIRGNNVLYISTSKRTL 87 (91)
Q Consensus 20 ~~~~~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~~~~e~-~~g--------~~~~~l~~v~IRG~~I~~i~~~~~~~ 87 (91)
..|+|++|.+..+.+-.|+|+|..+|. .-.|.|+|+..+ ..| ......+.+..||+.|.-+.+.+...
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~ 81 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP 81 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence 368999999999999999999999995 799999999874 111 01235789999999999888776544
No 43
>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=96.94 E-value=0.0056 Score=42.37 Aligned_cols=65 Identities=23% Similarity=0.417 Sum_probs=45.9
Q ss_pred CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcC-CCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeCCC
Q 034564 13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDG-YMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKR 85 (91)
Q Consensus 13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~~~ 85 (91)
.+|+.+ ..|++|.|.|.+.| +++.|.|..+|+ .-|++|-+..+ +++ ...-+|-|..|..|...++
T Consensus 7 ~~p~~~-~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e--~~~----~sv~~I~ghaVk~vevl~~ 72 (166)
T PF06372_consen 7 KSPLEW-QDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE--DGK----RSVKVIMGHAVKSVEVLSE 72 (166)
T ss_dssp S-HHHH-HCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T--TS-----EEEEEE-GGGEEEEEEEE-
T ss_pred CCHHHH-HHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc--CCc----eeEEEEEccceEEEEEccC
Confidence 356666 79999999999999 999999999994 68999987765 332 2357899999999877654
No 44
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.85 E-value=0.0096 Score=32.79 Aligned_cols=35 Identities=17% Similarity=0.220 Sum_probs=30.0
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEE
Q 034564 22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEE 57 (91)
Q Consensus 22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e 57 (91)
.+|++|++.+ ++..++|+..++|....|+++....
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 3789999999 6777799999999999999876543
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=96.47 E-value=0.0085 Score=35.12 Aligned_cols=36 Identities=28% Similarity=0.541 Sum_probs=29.1
Q ss_pred HHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeee
Q 034564 18 FLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAME 53 (91)
Q Consensus 18 ~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~ 53 (91)
||.++. ..+|+|-|.||-.+.|.+.+||+|+=++-.
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~ 40 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLES 40 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEE
Confidence 455544 468999999999999999999999866643
No 46
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=96.46 E-value=0.023 Score=34.99 Aligned_cols=63 Identities=21% Similarity=0.281 Sum_probs=47.9
Q ss_pred HHHHhhcCCCeEEEEEcCCcEEEEEEEEEc-CCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEeC
Q 034564 16 ADFLKSIRGRPVVVKLNSGVDYRGILACLD-GYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTS 83 (91)
Q Consensus 16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~~ 83 (91)
+.+|..+.|++|.+.|.++.++.|++.++| ...|+..+|-.- .-| ..+.-.+|.+-|+.++..
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~ 79 (80)
T PF11095_consen 16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQT-PLG----VQPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEET-TTT----EEEEEEEEGGGEEEEEE-
T ss_pred HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCC-Ccc----cChhheeecCCEEEEEec
Confidence 567788889999999999999999999999 457887776642 223 357889999999998764
No 47
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=96.35 E-value=0.03 Score=34.01 Aligned_cols=59 Identities=20% Similarity=0.371 Sum_probs=45.3
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEEcC-CCceeeeeeEEEe-cC-----e----eeeeeceEEEeCCcEEE
Q 034564 21 SIRGRPVVVKLNSGVDYRGILACLDG-YMNIAMEQTEEYV-NG-----Q----LKNKYGDAFIRGNNVLY 79 (91)
Q Consensus 21 ~~~~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~~~~e~~-~g-----~----~~~~l~~v~IRG~~I~~ 79 (91)
+++|+++.+..+.+-.|+|+|.++|. -.-+.|+|+..+- .| . ...-++.+..||+.|--
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 58999999999999999999999994 4778899988652 11 1 12245778888887743
No 48
>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=96.07 E-value=0.014 Score=34.14 Aligned_cols=36 Identities=31% Similarity=0.623 Sum_probs=29.3
Q ss_pred HHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564 17 DFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAM 52 (91)
Q Consensus 17 ~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL 52 (91)
.||..+. ..+|+|-|.||-.+.|.+.+||+|+=++-
T Consensus 6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~ 43 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLE 43 (61)
T ss_pred HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence 3555544 46899999999999999999999986664
No 49
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.76 E-value=0.022 Score=35.00 Aligned_cols=39 Identities=23% Similarity=0.531 Sum_probs=31.2
Q ss_pred HHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564 17 DFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 17 ~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~ 55 (91)
.||..+. ..+|+|-|.||-.+.|.+.+||+|.=|+-.+.
T Consensus 10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 4555554 46899999999999999999999987765443
No 50
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=95.66 E-value=0.093 Score=31.17 Aligned_cols=54 Identities=31% Similarity=0.483 Sum_probs=40.1
Q ss_pred HHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCCcEEEEEe
Q 034564 16 ADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYIST 82 (91)
Q Consensus 16 ~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~~I~~i~~ 82 (91)
...|++++|++|.|++..|+. +|+|.++... .++|+.. + ..+|||=..|++|.+
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 567899999999999987766 9999988632 1233222 1 478999999998853
No 51
>PRK14638 hypothetical protein; Provisional
Probab=95.13 E-value=0.098 Score=35.43 Aligned_cols=35 Identities=11% Similarity=0.182 Sum_probs=29.2
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeee
Q 034564 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAME 53 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~ 53 (91)
-+.+++|++|.|++.+++.+.|+|.++|.- ++.|.
T Consensus 94 ~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 94 DYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 347899999999999999999999999863 44443
No 52
>PRK14639 hypothetical protein; Provisional
Probab=94.87 E-value=0.13 Score=34.47 Aligned_cols=34 Identities=21% Similarity=0.347 Sum_probs=29.1
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAM 52 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL 52 (91)
-+++++|+.|.|.+.+++.+.|+|.++|.- ++.|
T Consensus 82 ~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 82 HFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 348899999999999999999999999873 4544
No 53
>PRK02001 hypothetical protein; Validated
Probab=94.84 E-value=0.096 Score=35.68 Aligned_cols=37 Identities=27% Similarity=0.425 Sum_probs=30.1
Q ss_pred ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAM 52 (91)
Q Consensus 14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL 52 (91)
.|..| .+++|+.|.|.+.+++.+.|+|.++|.- ++.|
T Consensus 81 ~~~~f-~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 81 VPRQY-KKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred CHHHH-HHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 33444 7899999999999999999999999864 3444
No 54
>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=94.73 E-value=0.12 Score=30.26 Aligned_cols=33 Identities=12% Similarity=0.086 Sum_probs=28.3
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeee
Q 034564 22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ 54 (91)
Q Consensus 22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~ 54 (91)
.+|..|.+++..|.+++|.+.+||.-.+++.-.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk 36 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK 36 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence 478999999999999999999999776666443
No 55
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=94.04 E-value=0.18 Score=30.73 Aligned_cols=34 Identities=26% Similarity=0.583 Sum_probs=27.5
Q ss_pred HHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCce
Q 034564 17 DFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNI 50 (91)
Q Consensus 17 ~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNl 50 (91)
.||.++. +.+|.|-|.||-.+.|.+.+||+|.=|
T Consensus 10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~Vl 45 (77)
T COG1923 10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVL 45 (77)
T ss_pred HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEE
Confidence 3554443 578999999999999999999999644
No 56
>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=93.01 E-value=0.54 Score=28.46 Aligned_cols=38 Identities=34% Similarity=0.554 Sum_probs=29.0
Q ss_pred CChHHHHhhcCCCeEEEEEc---CC-cEEEEEEEEEcCCCceee
Q 034564 13 KTPADFLKSIRGRPVVVKLN---SG-VDYRGILACLDGYMNIAM 52 (91)
Q Consensus 13 ~~p~~~L~~~~~k~V~V~L~---~g-~~~~G~L~~~D~~mNlvL 52 (91)
..|..| .+++|+.|.|+++ +| +.+.|.|.++|.- ++.|
T Consensus 15 ~~~~~~-~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 15 KKEADF-ERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred CCHHHH-HHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 334444 7899999999997 55 6899999999873 3444
No 57
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=92.59 E-value=0.32 Score=33.69 Aligned_cols=40 Identities=30% Similarity=0.484 Sum_probs=31.5
Q ss_pred HHHHhhcC--CCeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564 16 ADFLKSIR--GRPVVVKLNSGVDYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 16 ~~~L~~~~--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~ 55 (91)
-.||..+. ..+|+|-|.||-.+.|.+.+||+|.=|.-.+.
T Consensus 94 d~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 94 DVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 34666655 45799999999999999999999986665443
No 58
>PRK14640 hypothetical protein; Provisional
Probab=92.38 E-value=0.62 Score=31.51 Aligned_cols=37 Identities=22% Similarity=0.481 Sum_probs=28.9
Q ss_pred ChHHHHhhcCCCeEEEEEc----CCcEEEEEEEEEcCCCceee
Q 034564 14 TPADFLKSIRGRPVVVKLN----SGVDYRGILACLDGYMNIAM 52 (91)
Q Consensus 14 ~p~~~L~~~~~k~V~V~L~----~g~~~~G~L~~~D~~mNlvL 52 (91)
.|..| .+++|+.|.|+|+ +.+.+.|+|.++|.. ++.|
T Consensus 88 ~~~~f-~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 88 KVAQF-EKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred CHHHH-HHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 33444 7899999999994 679999999999873 4444
No 59
>PRK14644 hypothetical protein; Provisional
Probab=92.19 E-value=0.4 Score=32.03 Aligned_cols=35 Identities=23% Similarity=0.118 Sum_probs=29.3
Q ss_pred HHhhcCCCeEEEEEcCC----cEEEEEEEEEcCCCceeee
Q 034564 18 FLKSIRGRPVVVKLNSG----VDYRGILACLDGYMNIAME 53 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL~ 53 (91)
-+.+++|+.|.|.|++. +.+.|.|.++|.. ++.|.
T Consensus 79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 46889999999999976 9999999999873 45554
No 60
>PRK14633 hypothetical protein; Provisional
Probab=91.78 E-value=0.59 Score=31.59 Aligned_cols=34 Identities=21% Similarity=0.369 Sum_probs=27.5
Q ss_pred HHhhcCCCeEEEEEc----CCcEEEEEEEEEcCCCceee
Q 034564 18 FLKSIRGRPVVVKLN----SGVDYRGILACLDGYMNIAM 52 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~----~g~~~~G~L~~~D~~mNlvL 52 (91)
-+.+++|++|.|+++ +++.++|+|.+++.. ++.|
T Consensus 88 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 88 QAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 347899999999984 569999999999874 4444
No 61
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=91.48 E-value=0.89 Score=30.62 Aligned_cols=29 Identities=38% Similarity=0.641 Sum_probs=25.4
Q ss_pred HHhhcCCCeEEEEE----cCCcEEEEEEEEEcC
Q 034564 18 FLKSIRGRPVVVKL----NSGVDYRGILACLDG 46 (91)
Q Consensus 18 ~L~~~~~k~V~V~L----~~g~~~~G~L~~~D~ 46 (91)
-+++++|+.|.|.+ .+++.+.|+|.++|.
T Consensus 92 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 92 DFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 34889999999997 467999999999987
No 62
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=91.10 E-value=0.42 Score=33.08 Aligned_cols=40 Identities=30% Similarity=0.504 Sum_probs=31.4
Q ss_pred HHHHhhcCC--CeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564 16 ADFLKSIRG--RPVVVKLNSGVDYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 16 ~~~L~~~~~--k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~ 55 (91)
-.||..+.. .+|+|-|.+|-.++|.+.+||+|.=|.-.+.
T Consensus 14 D~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 14 DIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 446666654 5788999999999999999999976665443
No 63
>PRK14634 hypothetical protein; Provisional
Probab=91.00 E-value=0.73 Score=31.34 Aligned_cols=37 Identities=24% Similarity=0.408 Sum_probs=28.4
Q ss_pred ChHHHHhhcCCCeEEEEEcC----CcEEEEEEEEEcCCCceee
Q 034564 14 TPADFLKSIRGRPVVVKLNS----GVDYRGILACLDGYMNIAM 52 (91)
Q Consensus 14 ~p~~~L~~~~~k~V~V~L~~----g~~~~G~L~~~D~~mNlvL 52 (91)
.|..| .+++|+.|.|+|.+ .+.|.|+|.++|.- ++.|
T Consensus 91 ~~~~f-~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 91 SDRDF-QTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred CHHHH-HHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 34444 78999999999974 28999999999863 4444
No 64
>PRK14632 hypothetical protein; Provisional
Probab=90.84 E-value=0.76 Score=31.79 Aligned_cols=35 Identities=20% Similarity=0.416 Sum_probs=28.0
Q ss_pred HHhhcCCCeEEEEEcC-------CcEEEEEEEEEcCCCceeee
Q 034564 18 FLKSIRGRPVVVKLNS-------GVDYRGILACLDGYMNIAME 53 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~-------g~~~~G~L~~~D~~mNlvL~ 53 (91)
-+++++|+.|.|+|++ .+.+.|+|.++|.- ++.|.
T Consensus 92 ~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 92 QMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 3478999999999986 58999999999863 44443
No 65
>PRK14645 hypothetical protein; Provisional
Probab=90.69 E-value=0.76 Score=31.28 Aligned_cols=33 Identities=15% Similarity=0.391 Sum_probs=26.6
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAM 52 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL 52 (91)
-+.+++|+.|.|.+ +++.+.|+|.++|.- .+.|
T Consensus 96 df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 96 HFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred HHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 34789999999986 789999999999874 3444
No 66
>PRK14636 hypothetical protein; Provisional
Probab=90.65 E-value=1 Score=31.32 Aligned_cols=37 Identities=30% Similarity=0.617 Sum_probs=28.6
Q ss_pred ChHHHHhhcCCCeEEEEEc---CC-cEEEEEEEEEcCCCceee
Q 034564 14 TPADFLKSIRGRPVVVKLN---SG-VDYRGILACLDGYMNIAM 52 (91)
Q Consensus 14 ~p~~~L~~~~~k~V~V~L~---~g-~~~~G~L~~~D~~mNlvL 52 (91)
.|..| .+++|++|.|+|+ +| +.+.|+|.++|.- ++.|
T Consensus 89 ~~~df-~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 89 RPKDF-ADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred CHHHH-HHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 34444 7899999999997 55 7999999999873 3444
No 67
>PRK14642 hypothetical protein; Provisional
Probab=90.63 E-value=0.55 Score=33.34 Aligned_cols=34 Identities=15% Similarity=0.270 Sum_probs=28.0
Q ss_pred HHhhcCCCeEEEEEc-------------CCcEEEEEEEEEcCCCceee
Q 034564 18 FLKSIRGRPVVVKLN-------------SGVDYRGILACLDGYMNIAM 52 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~-------------~g~~~~G~L~~~D~~mNlvL 52 (91)
-+.+++|+.|.|+|+ +.+.|+|+|.++|.. ++.|
T Consensus 94 df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 94 DFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred HHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 347889999999998 679999999999874 4444
No 68
>PRK06955 biotin--protein ligase; Provisional
Probab=90.22 E-value=2.2 Score=31.56 Aligned_cols=50 Identities=22% Similarity=0.290 Sum_probs=35.6
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeCC
Q 034564 22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGN 75 (91)
Q Consensus 22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG~ 75 (91)
++|++|+|...+++.+.|++.++|....|+++.. +|.+.-..|.|.+|..
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 5689999976677889999999999999998532 2222233456665543
No 69
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.00 E-value=1 Score=34.71 Aligned_cols=66 Identities=15% Similarity=0.323 Sum_probs=52.0
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEEc-CCCceeeeeeEEEe------cCe----eeeeeceEEEeCCcEEEEEeCCC
Q 034564 20 KSIRGRPVVVKLNSGVDYRGILACLD-GYMNIAMEQTEEYV------NGQ----LKNKYGDAFIRGNNVLYISTSKR 85 (91)
Q Consensus 20 ~~~~~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~e~~------~g~----~~~~l~~v~IRG~~I~~i~~~~~ 85 (91)
..|||+.|.+.=+..-.|+|+|.-+| +-.-|-|+++..+- ++. ...-+..|+.||+.|.-+.+.+.
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~ 81 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQET 81 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccC
Confidence 46899999999999999999999999 77889999985531 111 11156889999999998877664
No 70
>PRK14643 hypothetical protein; Provisional
Probab=89.77 E-value=1.4 Score=30.29 Aligned_cols=30 Identities=20% Similarity=0.163 Sum_probs=25.9
Q ss_pred HHhhcCCCeEEEEEcC----CcEEEEEEEEEcCC
Q 034564 18 FLKSIRGRPVVVKLNS----GVDYRGILACLDGY 47 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~----g~~~~G~L~~~D~~ 47 (91)
-+.+++|++|.|.|++ .+.+.|+|.++|.-
T Consensus 98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 98 ELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 4478999999999975 59999999999864
No 71
>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=89.70 E-value=1.1 Score=29.50 Aligned_cols=35 Identities=29% Similarity=0.399 Sum_probs=25.5
Q ss_pred HHHhhcCCCeEEEEEc----CCcEEEEEEEEEcCCCceee
Q 034564 17 DFLKSIRGRPVVVKLN----SGVDYRGILACLDGYMNIAM 52 (91)
Q Consensus 17 ~~L~~~~~k~V~V~L~----~g~~~~G~L~~~D~~mNlvL 52 (91)
.-+.+++|++|.|.++ +.+.+.|+|.++|. -.++|
T Consensus 80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 4558999999999995 45799999999998 34444
No 72
>PRK14646 hypothetical protein; Provisional
Probab=89.59 E-value=1.1 Score=30.42 Aligned_cols=34 Identities=29% Similarity=0.322 Sum_probs=27.3
Q ss_pred HHhhcCCCeEEEEEcCC----cEEEEEEEEEcCCCceee
Q 034564 18 FLKSIRGRPVVVKLNSG----VDYRGILACLDGYMNIAM 52 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL 52 (91)
-+.+++|++|.|+|++. +.+.|+|.++|.- ++.|
T Consensus 94 df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 94 DFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 44889999999999742 7889999999974 5555
No 73
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.02 E-value=2.2 Score=29.11 Aligned_cols=33 Identities=27% Similarity=0.466 Sum_probs=28.6
Q ss_pred HHHHhhcCCCeEEEEE----cCCcEEEEEEEEEcCCC
Q 034564 16 ADFLKSIRGRPVVVKL----NSGVDYRGILACLDGYM 48 (91)
Q Consensus 16 ~~~L~~~~~k~V~V~L----~~g~~~~G~L~~~D~~m 48 (91)
..-+..++|+.|.|+| .+++.+.|+|.++|+-.
T Consensus 91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 3445889999999999 68899999999999876
No 74
>PRK14647 hypothetical protein; Provisional
Probab=88.83 E-value=1.4 Score=30.02 Aligned_cols=29 Identities=24% Similarity=0.204 Sum_probs=24.9
Q ss_pred HHhhcCCCeEEEEEc---------CCcEEEEEEEEEcC
Q 034564 18 FLKSIRGRPVVVKLN---------SGVDYRGILACLDG 46 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~---------~g~~~~G~L~~~D~ 46 (91)
-+.+++|+.|.|+|+ +.+.+.|+|.++|.
T Consensus 93 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 93 DYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 447899999999995 35999999999986
No 75
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=88.13 E-value=3.4 Score=30.57 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=34.3
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeeceEEEeC
Q 034564 22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG 74 (91)
Q Consensus 22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~~v~IRG 74 (91)
++|++|.+.. ++..+.|++.++|....|+++.. .+.+.-..|.+.+|.
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~~~----g~~~~~~~gev~~~~ 317 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLEDD----GVEKPFNGGEISLRS 317 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEEeC----CcEEEEEEeEEEEec
Confidence 5689999987 45679999999999999999621 122233456666654
No 76
>PRK14637 hypothetical protein; Provisional
Probab=87.88 E-value=1.8 Score=29.39 Aligned_cols=35 Identities=17% Similarity=0.178 Sum_probs=26.1
Q ss_pred HHhhcCCCeEEEEEcCCcEE-EEEEEEEcCCCceeee
Q 034564 18 FLKSIRGRPVVVKLNSGVDY-RGILACLDGYMNIAME 53 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~g~~~-~G~L~~~D~~mNlvL~ 53 (91)
-+.+++|+.|.|.+.+.+.+ .|+|.++|.- ++.|.
T Consensus 92 ~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 92 EFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 34889999999999544555 7999999874 44443
No 77
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=87.87 E-value=3.4 Score=33.68 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=28.6
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeee
Q 034564 22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ 54 (91)
Q Consensus 22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~ 54 (91)
++|++|.+...++..+.|+..++|....|+|+.
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 568999987667778999999999999999963
No 78
>PRK14641 hypothetical protein; Provisional
Probab=86.88 E-value=1.8 Score=30.11 Aligned_cols=28 Identities=18% Similarity=0.134 Sum_probs=24.0
Q ss_pred HHhhcCCCeEEEEEcC----CcEEEEEEEEEc
Q 034564 18 FLKSIRGRPVVVKLNS----GVDYRGILACLD 45 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~----g~~~~G~L~~~D 45 (91)
-+++++|+.|.|.|.+ .+.+.|+|.++|
T Consensus 98 ~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 98 QYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 3488999999999975 468999999995
No 79
>PRK14631 hypothetical protein; Provisional
Probab=85.70 E-value=1.7 Score=30.23 Aligned_cols=28 Identities=21% Similarity=0.364 Sum_probs=24.7
Q ss_pred HHhhcCCCeEEEEEc----CCcEEEEEEEEEc
Q 034564 18 FLKSIRGRPVVVKLN----SGVDYRGILACLD 45 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~----~g~~~~G~L~~~D 45 (91)
-+.+++|+.|.|+|. +.+.+.|+|.++|
T Consensus 111 df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 111 QLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 448899999999996 4599999999998
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=82.67 E-value=7.9 Score=27.46 Aligned_cols=31 Identities=23% Similarity=0.262 Sum_probs=26.8
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEEcCCCceeee
Q 034564 22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAME 53 (91)
Q Consensus 22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~ 53 (91)
.+|++|.|...+ ..+.|+..++|....|+++
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 458999998754 5799999999999999996
No 81
>PRK14630 hypothetical protein; Provisional
Probab=79.32 E-value=6.3 Score=26.40 Aligned_cols=33 Identities=12% Similarity=0.148 Sum_probs=25.1
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceee
Q 034564 18 FLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAM 52 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL 52 (91)
-+.+++|++|.|.|.. ....|+|.++|. -++.|
T Consensus 91 df~r~~G~~v~V~l~~-~~~~G~L~~~~d-~~i~l 123 (143)
T PRK14630 91 EFKIFEGKKIKLMLDN-DFEEGFILEAKA-DSFIF 123 (143)
T ss_pred HHHHhCCCEEEEEEcC-cceEEEEEEEeC-CEEEE
Confidence 3478999999999965 445999999987 34444
No 82
>PRK08330 biotin--protein ligase; Provisional
Probab=77.25 E-value=16 Score=25.91 Aligned_cols=33 Identities=21% Similarity=0.285 Sum_probs=27.0
Q ss_pred cCCCeEEEEEcCCcEE-EEEEEEEcCCCceeeeee
Q 034564 22 IRGRPVVVKLNSGVDY-RGILACLDGYMNIAMEQT 55 (91)
Q Consensus 22 ~~~k~V~V~L~~g~~~-~G~L~~~D~~mNlvL~~~ 55 (91)
++|++|.+.. ++..+ .|+..++|....|+++..
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence 5789999875 56665 799999999999998744
No 83
>PRK14635 hypothetical protein; Provisional
Probab=76.62 E-value=8.8 Score=26.14 Aligned_cols=37 Identities=24% Similarity=0.464 Sum_probs=27.5
Q ss_pred ChHHHHhhcCCCeEEEEEc--CCcEEEE---EEEEEcCCCceee
Q 034564 14 TPADFLKSIRGRPVVVKLN--SGVDYRG---ILACLDGYMNIAM 52 (91)
Q Consensus 14 ~p~~~L~~~~~k~V~V~L~--~g~~~~G---~L~~~D~~mNlvL 52 (91)
.|..| .++.|+.|.|.+. ++..+.| +|.++|.- ++.|
T Consensus 90 ~~~~~-~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 90 LPEDL-DRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred CHHHH-HHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 34444 7899999999986 4678888 99999864 4444
No 84
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=76.19 E-value=8.1 Score=28.48 Aligned_cols=32 Identities=13% Similarity=0.089 Sum_probs=27.4
Q ss_pred CCCeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564 23 RGRPVVVKLNSGVDYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 23 ~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~ 55 (91)
+|++|.|.. ++..+.|++.++|....|+|+..
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 689999875 57899999999999999998643
No 85
>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=74.68 E-value=5.1 Score=25.47 Aligned_cols=17 Identities=29% Similarity=0.507 Sum_probs=14.3
Q ss_pred CeEEEEEcCCcEEEEEE
Q 034564 25 RPVVVKLNSGVDYRGIL 41 (91)
Q Consensus 25 k~V~V~L~~g~~~~G~L 41 (91)
.+|.++|+||+.+.|++
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 58999999999999996
No 86
>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=74.09 E-value=4.3 Score=27.98 Aligned_cols=23 Identities=17% Similarity=0.401 Sum_probs=21.0
Q ss_pred CCeEEEEEcCCcEEEEEEEEEcC
Q 034564 24 GRPVVVKLNSGVDYRGILACLDG 46 (91)
Q Consensus 24 ~k~V~V~L~~g~~~~G~L~~~D~ 46 (91)
|+-|+|.+.|||+++|+-.|+|.
T Consensus 120 g~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 120 GKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred CCeEEEEEcCCcEEEeeecccce
Confidence 68899999999999999988874
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=72.84 E-value=7.7 Score=26.73 Aligned_cols=35 Identities=14% Similarity=0.093 Sum_probs=31.3
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeE
Q 034564 22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTE 56 (91)
Q Consensus 22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~ 56 (91)
+-+-+|+|.+.||..+.|.+.+|++--|.+|.-+.
T Consensus 27 ~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 27 FNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred hcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 34678999999999999999999999999987665
No 88
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=71.75 E-value=6.6 Score=21.28 Aligned_cols=21 Identities=10% Similarity=0.279 Sum_probs=14.3
Q ss_pred EEEEEEEEcCCCceeeeeeEE
Q 034564 37 YRGILACLDGYMNIAMEQTEE 57 (91)
Q Consensus 37 ~~G~L~~~D~~mNlvL~~~~e 57 (91)
..|++.|+|....+.|++...
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~ 30 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDT 30 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-
T ss_pred cceeEEeeccccceEEEeCCc
Confidence 579999999999999988764
No 89
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=71.43 E-value=20 Score=27.02 Aligned_cols=32 Identities=25% Similarity=0.374 Sum_probs=27.9
Q ss_pred CeEEEEEcCCcEEEEEEEEEcCCCceeeeeeE
Q 034564 25 RPVVVKLNSGVDYRGILACLDGYMNIAMEQTE 56 (91)
Q Consensus 25 k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~ 56 (91)
..+.|.+.||+.+.++++++|...+|-|-.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 46899999999999999999999998875554
No 90
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=71.07 E-value=31 Score=24.94 Aligned_cols=34 Identities=26% Similarity=0.377 Sum_probs=31.1
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564 22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~ 55 (91)
.+|++|++...++....|+..++|....|+|+..
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 4789999999999999999999999999998766
No 91
>PRK10898 serine endoprotease; Provisional
Probab=70.78 E-value=11 Score=28.57 Aligned_cols=32 Identities=19% Similarity=0.386 Sum_probs=28.0
Q ss_pred CeEEEEEcCCcEEEEEEEEEcCCCceeeeeeE
Q 034564 25 RPVVVKLNSGVDYRGILACLDGYMNIAMEQTE 56 (91)
Q Consensus 25 k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~ 56 (91)
..+.|.+.||+.|.+.+.++|...+|-|-.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 57899999999999999999999988765553
No 92
>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=70.22 E-value=4.6 Score=24.68 Aligned_cols=22 Identities=23% Similarity=0.406 Sum_probs=15.1
Q ss_pred HhhcCCCeEEEEEcCCcEEEEE
Q 034564 19 LKSIRGRPVVVKLNSGVDYRGI 40 (91)
Q Consensus 19 L~~~~~k~V~V~L~~g~~~~G~ 40 (91)
|.-..+.+|.++|+||..+.|+
T Consensus 12 iAC~~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 12 IACMYRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp HHHTTTT-EEEE-TTT--EEES
T ss_pred HHHhcCCeEEEEEeCCCEEEEE
Confidence 3456678999999999999998
No 93
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=69.08 E-value=11 Score=25.48 Aligned_cols=26 Identities=15% Similarity=0.220 Sum_probs=23.7
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEEc
Q 034564 20 KSIRGRPVVVKLNSGVDYRGILACLD 45 (91)
Q Consensus 20 ~~~~~k~V~V~L~~g~~~~G~L~~~D 45 (91)
..++||.|.+...+|..+.|++.++.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 46899999999999999999998886
No 94
>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=66.48 E-value=13 Score=24.19 Aligned_cols=30 Identities=20% Similarity=0.223 Sum_probs=21.8
Q ss_pred CeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564 25 RPVVVKLNSGVDYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 25 k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~ 55 (91)
....|.++||+.+.|.+.+=| .-.+.|.++
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~-~~~~~l~~~ 87 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASET-ADGVTVKMP 87 (133)
T ss_pred ccEEEEECCCCEEEEEEEecC-CCeEEEEcC
Confidence 348999999999999988844 334444443
No 95
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=65.20 E-value=11 Score=26.47 Aligned_cols=32 Identities=28% Similarity=0.546 Sum_probs=24.3
Q ss_pred HHHHhhcCCC--eEEEEEc-CCcEEEEEEEEEcCC
Q 034564 16 ADFLKSIRGR--PVVVKLN-SGVDYRGILACLDGY 47 (91)
Q Consensus 16 ~~~L~~~~~k--~V~V~L~-~g~~~~G~L~~~D~~ 47 (91)
+.||..+.+. ++.|.+. ++..|+|++.++|.-
T Consensus 123 I~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 6788877763 5555554 689999999999864
No 96
>PRK10942 serine endoprotease; Provisional
Probab=63.49 E-value=17 Score=28.72 Aligned_cols=31 Identities=23% Similarity=0.292 Sum_probs=27.3
Q ss_pred CeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564 25 RPVVVKLNSGVDYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 25 k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~ 55 (91)
..+.|.+.||++|.++++++|...+|-|-..
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 5789999999999999999999998876644
No 97
>PRK10139 serine endoprotease; Provisional
Probab=63.42 E-value=18 Score=28.47 Aligned_cols=58 Identities=17% Similarity=0.255 Sum_probs=37.8
Q ss_pred CeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEEEecCeeeeeec--eEEEeCCcEEEEEeC
Q 034564 25 RPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYG--DAFIRGNNVLYISTS 83 (91)
Q Consensus 25 k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g~~~~~l~--~v~IRG~~I~~i~~~ 83 (91)
..+.|.+.||+.|.++++++|....|-+-.+..- ..-....++ .-+-.|+.|..|+-|
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~-~~l~~~~lg~s~~~~~G~~V~aiG~P 174 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQNP-SKLTQIAIADSDKLRVGDFAVAVGNP 174 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEecCC-CCCceeEecCccccCCCCEEEEEecC
Confidence 5899999999999999999999988877554320 010111221 122347777776665
No 98
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=60.93 E-value=4.9 Score=27.15 Aligned_cols=27 Identities=19% Similarity=0.176 Sum_probs=20.8
Q ss_pred EcCCcEEEEEEEEEcCCCceeeeeeEE
Q 034564 31 LNSGVDYRGILACLDGYMNIAMEQTEE 57 (91)
Q Consensus 31 L~~g~~~~G~L~~~D~~mNlvL~~~~e 57 (91)
+++.-.=.|+|+|.|+|.|=.-+|-..
T Consensus 39 yrtd~~kiGTLVG~DkfGNkYyen~~~ 65 (151)
T KOG3382|consen 39 YRTDDHKIGTLVGVDKFGNKYYENNDY 65 (151)
T ss_pred Hhcccccceeeeeecccccchhcccce
Confidence 345555679999999999988877643
No 99
>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=58.75 E-value=24 Score=27.19 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=27.9
Q ss_pred CeEEEEEcCCcEEEEEEEEEcCCCceeeeeeE
Q 034564 25 RPVVVKLNSGVDYRGILACLDGYMNIAMEQTE 56 (91)
Q Consensus 25 k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~ 56 (91)
..+.|.+.+|+.+.+.+.++|...+|-|-...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 57889999999999999999999998876554
No 100
>PRK08477 biotin--protein ligase; Provisional
Probab=57.78 E-value=37 Score=24.08 Aligned_cols=36 Identities=11% Similarity=-0.135 Sum_probs=30.0
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEE
Q 034564 21 SIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEE 57 (91)
Q Consensus 21 ~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e 57 (91)
-.+++.|.|. .+++.++|+..++|...-|+++.-..
T Consensus 172 ~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~ 207 (211)
T PRK08477 172 FEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKV 207 (211)
T ss_pred HHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEe
Confidence 3568999986 57899999999999999998876544
No 101
>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=51.90 E-value=9.9 Score=24.07 Aligned_cols=17 Identities=29% Similarity=0.315 Sum_probs=15.6
Q ss_pred EEEEEEcCCCceeeeee
Q 034564 39 GILACLDGYMNIAMEQT 55 (91)
Q Consensus 39 G~L~~~D~~mNlvL~~~ 55 (91)
|+|+|.|.|.|..-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999998877
No 102
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=51.70 E-value=31 Score=23.25 Aligned_cols=27 Identities=11% Similarity=0.096 Sum_probs=23.1
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEEcC
Q 034564 20 KSIRGRPVVVKLNSGVDYRGILACLDG 46 (91)
Q Consensus 20 ~~~~~k~V~V~L~~g~~~~G~L~~~D~ 46 (91)
..++||.|.....+|..+.|++.++..
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 368999999888899999999987753
No 103
>PRK11625 Rho-binding antiterminator; Provisional
Probab=51.43 E-value=31 Score=21.26 Aligned_cols=26 Identities=12% Similarity=0.004 Sum_probs=20.4
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEEcCC
Q 034564 20 KSIRGRPVVVKLNSGVDYRGILACLDGY 47 (91)
Q Consensus 20 ~~~~~k~V~V~L~~g~~~~G~L~~~D~~ 47 (91)
.-..+.++.++|+||..+.|+- .|-+
T Consensus 19 AC~~~~~l~l~l~dGe~~~g~A--~D~~ 44 (84)
T PRK11625 19 ACQHHLMLTLELKDGEVLQAKA--SDLV 44 (84)
T ss_pred HHhcCCeEEEEECCCCEEEEEE--Eeee
Confidence 4456789999999999999985 4444
No 104
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=49.68 E-value=55 Score=20.32 Aligned_cols=36 Identities=19% Similarity=0.304 Sum_probs=22.4
Q ss_pred HHHHhhcCCCeEEEEEc----CCcEEEEEEEEEcC-CCceeee
Q 034564 16 ADFLKSIRGRPVVVKLN----SGVDYRGILACLDG-YMNIAME 53 (91)
Q Consensus 16 ~~~L~~~~~k~V~V~L~----~g~~~~G~L~~~D~-~mNlvL~ 53 (91)
...|.+++|++|++.-+ +|. .-++.+.|. ..++.|.
T Consensus 7 ~~~L~~f~gk~V~ivGkV~~~~~~--~~~~~~~Dg~~v~v~l~ 47 (101)
T cd04479 7 GAMLSQFVGKTVRIVGKVEKVDGD--SLTLISSDGVNVTVELN 47 (101)
T ss_pred HHHHHhhCCCEEEEEEEEEEecCC--eEEEEcCCCCEEEEEeC
Confidence 46899999999987644 333 345555554 3444443
No 105
>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=46.10 E-value=30 Score=21.71 Aligned_cols=23 Identities=30% Similarity=0.424 Sum_probs=18.9
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEE
Q 034564 21 SIRGRPVVVK-LNSGVDYRGILAC 43 (91)
Q Consensus 21 ~~~~k~V~V~-L~~g~~~~G~L~~ 43 (91)
..+|..|+|. +..|+.+.|++.+
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 4678889999 7889999998764
No 106
>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=44.38 E-value=59 Score=18.54 Aligned_cols=27 Identities=22% Similarity=0.326 Sum_probs=18.7
Q ss_pred cCCCeEEEEEcCC-cEEEEEEEEEcCCC
Q 034564 22 IRGRPVVVKLNSG-VDYRGILACLDGYM 48 (91)
Q Consensus 22 ~~~k~V~V~L~~g-~~~~G~L~~~D~~m 48 (91)
..|..|.++-.++ ..|.|.+.+||.--
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~~ 34 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSKS 34 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETTT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecccC
Confidence 3688999998876 55599999999643
No 107
>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=44.05 E-value=37 Score=24.83 Aligned_cols=18 Identities=22% Similarity=0.414 Sum_probs=16.7
Q ss_pred EEEEEEEEEcCCCceeee
Q 034564 36 DYRGILACLDGYMNIAME 53 (91)
Q Consensus 36 ~~~G~L~~~D~~mNlvL~ 53 (91)
.+.|.+..+|.|.|+++.
T Consensus 169 ~i~g~Vi~iD~FGNlitn 186 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITN 186 (258)
T ss_dssp EEEEEEEEEETTSEEEEE
T ss_pred eEEEEEEEECccCCeeeC
Confidence 899999999999999864
No 108
>PRK06630 hypothetical protein; Provisional
Probab=43.52 E-value=13 Score=23.66 Aligned_cols=20 Identities=15% Similarity=0.125 Sum_probs=17.1
Q ss_pred EEEEEEEEcCCCceeeeeeE
Q 034564 37 YRGILACLDGYMNIAMEQTE 56 (91)
Q Consensus 37 ~~G~L~~~D~~mNlvL~~~~ 56 (91)
..|+|+|-|.|.|-.-++..
T Consensus 11 r~G~lVG~D~~GNkYYE~~~ 30 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESRN 30 (99)
T ss_pred ccCeEeEEeCCCChhcccCC
Confidence 47999999999999988753
No 109
>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=42.66 E-value=54 Score=17.45 Aligned_cols=25 Identities=28% Similarity=0.407 Sum_probs=20.9
Q ss_pred CCCeEEEEEcCCcEEEEEEEEEcCC
Q 034564 23 RGRPVVVKLNSGVDYRGILACLDGY 47 (91)
Q Consensus 23 ~~k~V~V~L~~g~~~~G~L~~~D~~ 47 (91)
.|..+.+...+|.-|+|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4677777777899999999999864
No 110
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=39.85 E-value=36 Score=24.31 Aligned_cols=23 Identities=26% Similarity=0.426 Sum_probs=19.1
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEE
Q 034564 21 SIRGRPVVVK-LNSGVDYRGILAC 43 (91)
Q Consensus 21 ~~~~k~V~V~-L~~g~~~~G~L~~ 43 (91)
..+|..|+|+ +..|+.+.|++.+
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeC
Confidence 4678899999 8899999998764
No 111
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=38.31 E-value=59 Score=23.06 Aligned_cols=26 Identities=19% Similarity=0.185 Sum_probs=22.5
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEEc
Q 034564 20 KSIRGRPVVVKLNSGVDYRGILACLD 45 (91)
Q Consensus 20 ~~~~~k~V~V~L~~g~~~~G~L~~~D 45 (91)
..++||.|.+.-.+|..+.|++.++.
T Consensus 114 ~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 114 MKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 36799999988889999999998775
No 112
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=37.85 E-value=31 Score=23.81 Aligned_cols=19 Identities=16% Similarity=0.149 Sum_probs=16.6
Q ss_pred EEEEEEEcCCCceeeeeeE
Q 034564 38 RGILACLDGYMNIAMEQTE 56 (91)
Q Consensus 38 ~G~L~~~D~~mNlvL~~~~ 56 (91)
.|+|+|.|.|.|-.-++..
T Consensus 48 ~G~lVG~D~~GNkYYE~~~ 66 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKLG 66 (159)
T ss_pred CcEEEEecCCCCeeeecCC
Confidence 4999999999999988764
No 113
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=37.08 E-value=96 Score=18.72 Aligned_cols=29 Identities=31% Similarity=0.375 Sum_probs=21.7
Q ss_pred HHHHhhcCCCeEEEEEcCCc----EEEEEEEEE
Q 034564 16 ADFLKSIRGRPVVVKLNSGV----DYRGILACL 44 (91)
Q Consensus 16 ~~~L~~~~~k~V~V~L~~g~----~~~G~L~~~ 44 (91)
...|.+++|++|.+....|| +-+|+|...
T Consensus 9 k~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 9 KKELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 45688999999999999994 567998765
No 114
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=36.76 E-value=39 Score=18.50 Aligned_cols=15 Identities=40% Similarity=0.616 Sum_probs=12.7
Q ss_pred HHHHhhcCCCeEEEE
Q 034564 16 ADFLKSIRGRPVVVK 30 (91)
Q Consensus 16 ~~~L~~~~~k~V~V~ 30 (91)
...+++++||+|+|.
T Consensus 11 ~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVT 25 (48)
T ss_pred hHHHHHhcCCeEEEE
Confidence 567788999999986
No 115
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=35.56 E-value=39 Score=19.76 Aligned_cols=21 Identities=14% Similarity=0.184 Sum_probs=17.8
Q ss_pred CeEEEEEcCCcEEEEEEEEEc
Q 034564 25 RPVVVKLNSGVDYRGILACLD 45 (91)
Q Consensus 25 k~V~V~L~~g~~~~G~L~~~D 45 (91)
.+|.|+|-||..+.+++..-|
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~ 25 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSD 25 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 579999999999999986544
No 116
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=34.96 E-value=24 Score=23.07 Aligned_cols=19 Identities=26% Similarity=0.218 Sum_probs=16.6
Q ss_pred EEEEEEEcCCCceeeeeeE
Q 034564 38 RGILACLDGYMNIAMEQTE 56 (91)
Q Consensus 38 ~G~L~~~D~~mNlvL~~~~ 56 (91)
.|.|+|.|.|.|-.-++..
T Consensus 9 ~g~lVG~D~~GNkYYE~~~ 27 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPS 27 (115)
T ss_pred cceEeEEcCCCCeeeEcCC
Confidence 6899999999999988754
No 117
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=33.04 E-value=79 Score=22.66 Aligned_cols=24 Identities=4% Similarity=-0.004 Sum_probs=20.4
Q ss_pred cCCcEEEEEEEEEcCCCceeeeee
Q 034564 32 NSGVDYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 32 ~~g~~~~G~L~~~D~~mNlvL~~~ 55 (91)
.++..+.|++.++|....|+++..
T Consensus 209 ~~~~~~~G~~~gId~~G~Lvv~~~ 232 (245)
T PTZ00276 209 TGRDPEELTALSLNEWGHLIVRRP 232 (245)
T ss_pred cCCcEEEEEEEEECCCCeEEEEEC
Confidence 366788999999999999998653
No 118
>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=32.37 E-value=54 Score=18.95 Aligned_cols=21 Identities=10% Similarity=0.203 Sum_probs=17.3
Q ss_pred CeEEEEEcCCcEEEEEEEEEc
Q 034564 25 RPVVVKLNSGVDYRGILACLD 45 (91)
Q Consensus 25 k~V~V~L~~g~~~~G~L~~~D 45 (91)
.+|.|.|-||..+.+++..-|
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~ 23 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTH 23 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 478999999999999985444
No 119
>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=31.39 E-value=53 Score=19.02 Aligned_cols=22 Identities=18% Similarity=0.196 Sum_probs=17.8
Q ss_pred CeEEEEEcCCcEEEEEEEEEcC
Q 034564 25 RPVVVKLNSGVDYRGILACLDG 46 (91)
Q Consensus 25 k~V~V~L~~g~~~~G~L~~~D~ 46 (91)
.+|.|+|.||..+...+..-|.
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~t 28 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSDT 28 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTSB
T ss_pred EEEEEECCCCCEEEEEECCcch
Confidence 4789999999999999865443
No 120
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=31.17 E-value=1.1e+02 Score=22.66 Aligned_cols=32 Identities=19% Similarity=0.241 Sum_probs=25.9
Q ss_pred CCeEEEEEcCCcEEEEEEEEEcCCCceeeeee
Q 034564 24 GRPVVVKLNSGVDYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 24 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~ 55 (91)
..++.|.+.||+++.+.++++|...-+-+-..
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 46788999999999999999998766554333
No 121
>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=30.85 E-value=1.7e+02 Score=20.67 Aligned_cols=37 Identities=22% Similarity=0.469 Sum_probs=30.3
Q ss_pred CChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCc
Q 034564 13 KTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMN 49 (91)
Q Consensus 13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mN 49 (91)
..+..+=+.++|+.+...+.+|..+.|.++....|+-
T Consensus 8 ~~~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 8 QDAVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred CCHHHHHHHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 3556666789999999888888888899999988853
No 122
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.79 E-value=60 Score=19.91 Aligned_cols=29 Identities=28% Similarity=0.338 Sum_probs=22.0
Q ss_pred HHHHhhcCCCeEEEEEcCCcEE----EEEEEEE
Q 034564 16 ADFLKSIRGRPVVVKLNSGVDY----RGILACL 44 (91)
Q Consensus 16 ~~~L~~~~~k~V~V~L~~g~~~----~G~L~~~ 44 (91)
..-+++.+|++|.+.+.+||.= .|.|...
T Consensus 11 K~~i~ah~G~~v~lk~ngGRKk~~~r~G~L~Et 43 (80)
T COG4466 11 KESIDAHLGERVTLKANGGRKKTIERSGILIET 43 (80)
T ss_pred HHHHHhccCcEEEEEecCCceeeehhceEEeee
Confidence 4567889999999999999653 3666543
No 123
>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=29.57 E-value=91 Score=20.11 Aligned_cols=28 Identities=25% Similarity=0.281 Sum_probs=24.0
Q ss_pred CChHHHHhhcCCCeEEEEEcCCcEEEEE
Q 034564 13 KTPADFLKSIRGRPVVVKLNSGVDYRGI 40 (91)
Q Consensus 13 ~~p~~~L~~~~~k~V~V~L~~g~~~~G~ 40 (91)
.-|...|...-+-.|..+|.+|++|.+.
T Consensus 63 ~~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 63 DTDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CCCHHHHhCCcccEEEEEecCCcEEEec
Confidence 3457778888999999999999999876
No 124
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=28.70 E-value=1.3e+02 Score=23.95 Aligned_cols=47 Identities=15% Similarity=0.103 Sum_probs=37.7
Q ss_pred ccCCChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeEE
Q 034564 10 ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEE 57 (91)
Q Consensus 10 ~~~~~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~e 57 (91)
.....|-.++.+++||.|+- =++|++.+++|.+-|.-.=+.+.+-.+
T Consensus 68 y~l~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~ 114 (421)
T COG5316 68 YDLLSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVE 114 (421)
T ss_pred ccccCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEE
Confidence 34567888999999988888 789999999999998766666555554
No 125
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=28.25 E-value=74 Score=24.55 Aligned_cols=23 Identities=22% Similarity=0.601 Sum_probs=20.5
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEE
Q 034564 20 KSIRGRPVVVKLNSGVDYRGILA 42 (91)
Q Consensus 20 ~~~~~k~V~V~L~~g~~~~G~L~ 42 (91)
+-+.+++|+|...+|+.|.|++-
T Consensus 93 ~~~~gq~v~i~t~~g~~i~GvIg 115 (355)
T COG1363 93 QVLEGQRVTIHTDKGKKIRGVIG 115 (355)
T ss_pred hhccCcEEEEEeCCCcEEeeeEc
Confidence 34679999999999999999987
No 126
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.23 E-value=92 Score=21.10 Aligned_cols=23 Identities=26% Similarity=0.413 Sum_probs=18.0
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEE
Q 034564 21 SIRGRPVVVK-LNSGVDYRGILAC 43 (91)
Q Consensus 21 ~~~~k~V~V~-L~~g~~~~G~L~~ 43 (91)
...|..|+|. +..|+.+.|++.+
T Consensus 128 G~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 128 GAAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 3568888888 7888999888753
No 127
>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=26.79 E-value=55 Score=19.28 Aligned_cols=23 Identities=9% Similarity=0.250 Sum_probs=18.5
Q ss_pred CCCeEEEEEcCCcEEEEEEEEEc
Q 034564 23 RGRPVVVKLNSGVDYRGILACLD 45 (91)
Q Consensus 23 ~~k~V~V~L~~g~~~~G~L~~~D 45 (91)
-..+|.|+|-||..+.+++-.-|
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCC
Confidence 34689999999999999986544
No 128
>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=26.73 E-value=1.4e+02 Score=20.94 Aligned_cols=35 Identities=14% Similarity=0.409 Sum_probs=24.9
Q ss_pred ChHHHHhhcCCCeEEEEEcCCcEEEEEEEEEcCCCc
Q 034564 14 TPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMN 49 (91)
Q Consensus 14 ~p~~~L~~~~~k~V~V~L~~g~~~~G~L~~~D~~mN 49 (91)
.+..+=+.++|+.+..++.+|. +.|.++....|.-
T Consensus 8 ~~~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 8 DTVEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp BHHHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred CHHHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 4556667899999999999887 9999988776654
No 129
>PRK08183 NADH dehydrogenase; Validated
Probab=26.73 E-value=36 Score=22.74 Aligned_cols=19 Identities=16% Similarity=0.167 Sum_probs=16.4
Q ss_pred EEEEEEEcCCCceeeeeeE
Q 034564 38 RGILACLDGYMNIAMEQTE 56 (91)
Q Consensus 38 ~G~L~~~D~~mNlvL~~~~ 56 (91)
.|.|+|.|.+.|-.-++..
T Consensus 25 ~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cCeEeEecCCCCeeeecCC
Confidence 6999999999999887654
No 130
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.50 E-value=89 Score=22.27 Aligned_cols=23 Identities=22% Similarity=0.180 Sum_probs=18.9
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEE
Q 034564 21 SIRGRPVVVK-LNSGVDYRGILAC 43 (91)
Q Consensus 21 ~~~~k~V~V~-L~~g~~~~G~L~~ 43 (91)
...|..|+|+ +..|+.+.|+..+
T Consensus 183 G~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 183 AGENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCCEEEEEECCCCCEEEEEEeC
Confidence 4578899999 7899999998754
No 131
>PF13437 HlyD_3: HlyD family secretion protein
Probab=26.41 E-value=1.5e+02 Score=17.61 Aligned_cols=32 Identities=25% Similarity=0.483 Sum_probs=24.9
Q ss_pred hHHHHhhc--CCCeEEEEEcCC--cEEEEEEEEEcC
Q 034564 15 PADFLKSI--RGRPVVVKLNSG--VDYRGILACLDG 46 (91)
Q Consensus 15 p~~~L~~~--~~k~V~V~L~~g--~~~~G~L~~~D~ 46 (91)
|...+... .|..+.+.+.++ ..+.|++..++.
T Consensus 43 ~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 43 PEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred ChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 44455554 689999999855 699999999987
No 132
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=26.34 E-value=1.6e+02 Score=20.44 Aligned_cols=26 Identities=15% Similarity=0.220 Sum_probs=22.4
Q ss_pred CCCeEEEEEcCCcEEEEEEEEEcCCC
Q 034564 23 RGRPVVVKLNSGVDYRGILACLDGYM 48 (91)
Q Consensus 23 ~~k~V~V~L~~g~~~~G~L~~~D~~m 48 (91)
.|.++.|.+.+|..+.|++..++...
T Consensus 141 ~g~~v~i~~~~~~~~~g~v~~I~~~~ 166 (265)
T TIGR00999 141 KGSKATVLLENGRPLPARVDYVGPEV 166 (265)
T ss_pred CCCEEEEEECCCCEEEEEEEEEcccc
Confidence 47899999998999999999998654
No 133
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=25.96 E-value=75 Score=21.19 Aligned_cols=27 Identities=19% Similarity=0.146 Sum_probs=19.9
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEEcCCC
Q 034564 21 SIRGRPVVVKLNSGVDYRGILACLDGYM 48 (91)
Q Consensus 21 ~~~~k~V~V~L~~g~~~~G~L~~~D~~m 48 (91)
+++.|.++|.|.||++++..+ --|.|.
T Consensus 53 SAlRK~~RVrL~NG~~VtAyi-Pg~Gh~ 79 (129)
T COG0048 53 SALRKVARVRLINGKEVTAYI-PGEGHN 79 (129)
T ss_pred hhhheeEEEEeeCCcEEEEEc-CCCCcc
Confidence 346788999999999998764 335543
No 134
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.55 E-value=1.1e+02 Score=21.66 Aligned_cols=23 Identities=13% Similarity=0.013 Sum_probs=18.5
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEE
Q 034564 21 SIRGRPVVVKLNSGVDYRGILAC 43 (91)
Q Consensus 21 ~~~~k~V~V~L~~g~~~~G~L~~ 43 (91)
..+|..|+|+-..|+.+.|++.+
T Consensus 193 G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 193 GNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCCEEEEEeCCCCEEEEEEec
Confidence 46788888888888888888765
No 135
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=25.54 E-value=1.4e+02 Score=17.04 Aligned_cols=33 Identities=9% Similarity=0.230 Sum_probs=22.2
Q ss_pred CCCeEEEEEcCC----cEEEEEEEEEcCCCceeeeee
Q 034564 23 RGRPVVVKLNSG----VDYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 23 ~~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL~~~ 55 (91)
+|.+|.+++.++ ..|...+.+++..-.+.+.=-
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 588999998544 359999999987755555433
No 136
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.36 E-value=1.1e+02 Score=21.67 Aligned_cols=35 Identities=14% Similarity=-0.071 Sum_probs=29.8
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEEcCCCceeeeeeE
Q 034564 22 IRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTE 56 (91)
Q Consensus 22 ~~~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~ 56 (91)
.+|.+|.+...+|....|.+.+||---+...-++.
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 45778999999999999999999987777766666
No 137
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=24.42 E-value=1.3e+02 Score=18.54 Aligned_cols=22 Identities=18% Similarity=0.348 Sum_probs=18.4
Q ss_pred HhhcCCCeEEEEEcCCcEEEEE
Q 034564 19 LKSIRGRPVVVKLNSGVDYRGI 40 (91)
Q Consensus 19 L~~~~~k~V~V~L~~g~~~~G~ 40 (91)
|.-+..-++..+|++|..+.|+
T Consensus 18 lACl~hl~l~L~lkdGev~~a~ 39 (84)
T COG4568 18 LACLHHLPLTLELKDGEVLQAK 39 (84)
T ss_pred HHHhhhceEEEEEcCCeEEEEE
Confidence 4455567999999999999997
No 138
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=24.12 E-value=1.1e+02 Score=21.52 Aligned_cols=26 Identities=27% Similarity=0.618 Sum_probs=22.1
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEEc
Q 034564 20 KSIRGRPVVVKLNSGVDYRGILACLD 45 (91)
Q Consensus 20 ~~~~~k~V~V~L~~g~~~~G~L~~~D 45 (91)
..++|++|.|.+...+.+.|.+.+++
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 44899999999998899999998884
No 139
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=24.04 E-value=69 Score=19.13 Aligned_cols=19 Identities=32% Similarity=0.326 Sum_probs=14.6
Q ss_pred HHhhcCCCeEEEEEcCCcE
Q 034564 18 FLKSIRGRPVVVKLNSGVD 36 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~g~~ 36 (91)
.+...+||+|+|+....-+
T Consensus 5 ~~nDrLGKKVRvKCn~dDt 23 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDT 23 (73)
T ss_pred hhhhhcCceEEEEeCCccc
Confidence 4567899999999876544
No 140
>PF02604 PhdYeFM_antitox: Antitoxin Phd_YefM, type II toxin-antitoxin system; InterPro: IPR006442 This entry is represented by Bacteriophage P1, prevent-host-death protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins is characterised by a region of about 55 amino acids toward the N-terminal end of bacterial proteins which are themselves only 85 amino acids, or thereabouts, in length. The best-characterised member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (IPR006440 from INTERPRO) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. ; PDB: 3DBO_A 2ODK_B 3G5O_D 2A6Q_B 3D55_C 3OEI_E 3CTO_C 3K33_D 3KH2_F 3HS2_C ....
Probab=23.93 E-value=47 Score=18.82 Aligned_cols=36 Identities=14% Similarity=0.315 Sum_probs=23.7
Q ss_pred ChHHHHhhcCCCeE-EEEEcCCcEEEEEEEEEcCCCce
Q 034564 14 TPADFLKSIRGRPV-VVKLNSGVDYRGILACLDGYMNI 50 (91)
Q Consensus 14 ~p~~~L~~~~~k~V-~V~L~~g~~~~G~L~~~D~~mNl 50 (91)
++..++.+.....- .+.+++|+. .++|++++.|-++
T Consensus 12 ~~~~~l~~v~~~~~pv~It~~g~~-~~vli~~~~ye~l 48 (75)
T PF02604_consen 12 NFSELLDEVEEGEEPVIITKNGKP-VAVLISVEDYERL 48 (75)
T ss_dssp THHHHHHHHHHCT-EEEEEETTEE-EEEEEEHHHHHHH
T ss_pred HHHHHHHHHHcCCCeEEEEECCCC-CeecccHHHHHHH
Confidence 45666666654332 466788877 8888888877544
No 141
>PF05037 DUF669: Protein of unknown function (DUF669); InterPro: IPR007731 This entry is represented by Streptococcus phage Sfi11, Gp151. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.35 E-value=75 Score=20.78 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=23.1
Q ss_pred CCChHHHHhhcCCCeEEEEEcCC-cEEEEEE
Q 034564 12 TKTPADFLKSIRGRPVVVKLNSG-VDYRGIL 41 (91)
Q Consensus 12 ~~~p~~~L~~~~~k~V~V~L~~g-~~~~G~L 41 (91)
....-.++..++|+.++|.++.. ..+.|.-
T Consensus 91 ~~sl~~~~~~l~gk~l~V~v~~~~~e~nGk~ 121 (141)
T PF05037_consen 91 FESLEQFLNQLLGKPLRVTVKWEENEYNGKT 121 (141)
T ss_pred cccHHHHHHHHcCCeeEEEecccccCCCCcE
Confidence 34456788889999999999977 6777743
No 142
>PRK10708 hypothetical protein; Provisional
Probab=23.32 E-value=1.1e+02 Score=17.70 Aligned_cols=25 Identities=20% Similarity=0.400 Sum_probs=21.9
Q ss_pred CCCeEEEEEcCCcEEEEEEEEEcCC
Q 034564 23 RGRPVVVKLNSGVDYRGILACLDGY 47 (91)
Q Consensus 23 ~~k~V~V~L~~g~~~~G~L~~~D~~ 47 (91)
++-+|.|++-.|..=.|++.++..|
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F 27 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEF 27 (62)
T ss_pred cccEEEEecCCCccccceEEEEeec
Confidence 4678999999999999999999877
No 143
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.64 E-value=1.1e+02 Score=22.53 Aligned_cols=23 Identities=26% Similarity=0.296 Sum_probs=18.8
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEE
Q 034564 21 SIRGRPVVVK-LNSGVDYRGILAC 43 (91)
Q Consensus 21 ~~~~k~V~V~-L~~g~~~~G~L~~ 43 (91)
...|..|+|+ +..|+.+.|++.+
T Consensus 230 G~~Gd~IrVrN~~SgkvV~a~V~~ 253 (261)
T PRK06804 230 GRKGELIKVKNLSSGRVVTATVDG 253 (261)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4578889999 8889999998764
No 144
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=22.28 E-value=1.8e+02 Score=18.55 Aligned_cols=28 Identities=21% Similarity=0.170 Sum_probs=22.5
Q ss_pred HHhhcCCCeEEEEEcC-CcEEEEEEEEEc
Q 034564 18 FLKSIRGRPVVVKLNS-GVDYRGILACLD 45 (91)
Q Consensus 18 ~L~~~~~k~V~V~L~~-g~~~~G~L~~~D 45 (91)
.-+.|++++|+-.-+. |+.+.|++.-.-
T Consensus 40 eA~~y~gk~v~yk~~~~G~Vi~G~V~R~H 68 (100)
T COG2451 40 EAQFYLGKRVCYKYRSSGRVIKGKVVRTH 68 (100)
T ss_pred HHHhhhccEEEEEeCCCCcEEEEEEEEec
Confidence 3467899998888887 999999986553
No 145
>PF13144 SAF_2: SAF-like
Probab=22.24 E-value=1.4e+02 Score=20.16 Aligned_cols=23 Identities=26% Similarity=0.182 Sum_probs=18.2
Q ss_pred hcCCCeEEEEEcC-CcEEEEEEEE
Q 034564 21 SIRGRPVVVKLNS-GVDYRGILAC 43 (91)
Q Consensus 21 ~~~~k~V~V~L~~-g~~~~G~L~~ 43 (91)
..+|..|+|.-.+ |+.+.|++.+
T Consensus 167 G~~G~~I~V~N~~S~k~v~g~V~~ 190 (196)
T PF13144_consen 167 GALGDTIRVKNLSSGKIVQGRVIG 190 (196)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4678889998754 8999998865
No 146
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=22.18 E-value=1.4e+02 Score=18.44 Aligned_cols=37 Identities=8% Similarity=0.222 Sum_probs=25.6
Q ss_pred CCceeeeeeEE--Ee-cCeeeeeeceEEEeCCcEEEEEeCC
Q 034564 47 YMNIAMEQTEE--YV-NGQLKNKYGDAFIRGNNVLYISTSK 84 (91)
Q Consensus 47 ~mNlvL~~~~e--~~-~g~~~~~l~~v~IRG~~I~~i~~~~ 84 (91)
..-+.+..... .+ +| ..+.-|.+...|..+..+.+|+
T Consensus 57 ~g~~~~~r~y~FEFS~~G-~~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 57 RGRLRWRRVYQFEFSSDG-EDRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred CCCeEEEEEEEEEEeCCC-hhcceEEEEEECCeeeEEEcCC
Confidence 33444444443 23 44 4578899999999999999886
No 147
>PRK09961 exoaminopeptidase; Provisional
Probab=21.99 E-value=1.2e+02 Score=22.98 Aligned_cols=23 Identities=17% Similarity=0.284 Sum_probs=19.6
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEE
Q 034564 20 KSIRGRPVVVKLNSGVDYRGILA 42 (91)
Q Consensus 20 ~~~~~k~V~V~L~~g~~~~G~L~ 42 (91)
+.+.+++|+|..++|+.+.|++.
T Consensus 90 ~~~~~~~v~i~~~~g~~i~Gvi~ 112 (344)
T PRK09961 90 AARQLQPVRITTREECKIPGLLN 112 (344)
T ss_pred cccCCCEEEEEeCCCCEeeEEEC
Confidence 34678999999999988999984
No 148
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.71 E-value=1.4e+02 Score=19.79 Aligned_cols=23 Identities=26% Similarity=0.255 Sum_probs=17.6
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEE
Q 034564 21 SIRGRPVVVK-LNSGVDYRGILAC 43 (91)
Q Consensus 21 ~~~~k~V~V~-L~~g~~~~G~L~~ 43 (91)
...|..|+|+ +..|+.+.|+..+
T Consensus 109 G~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 109 GGVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 3567888886 6788888888754
No 149
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=21.21 E-value=1.9e+02 Score=16.87 Aligned_cols=31 Identities=16% Similarity=0.341 Sum_probs=22.9
Q ss_pred CCeEEEEEcC-C--cEEEEEEEEEcCCCcee-eee
Q 034564 24 GRPVVVKLNS-G--VDYRGILACLDGYMNIA-MEQ 54 (91)
Q Consensus 24 ~k~V~V~L~~-g--~~~~G~L~~~D~~mNlv-L~~ 54 (91)
+..|+|...+ | ..+.|++..+|...+.+ +.+
T Consensus 42 ~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~~~ 76 (92)
T PF08863_consen 42 NQPVTITYYEDGYYQSVTGTIHKIDEINRTLKLKD 76 (92)
T ss_pred CCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEEEe
Confidence 5778888765 4 78899999999776544 344
No 150
>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=20.84 E-value=98 Score=19.70 Aligned_cols=20 Identities=10% Similarity=0.139 Sum_probs=6.9
Q ss_pred EEEEEEEEEcCCCceeeeee
Q 034564 36 DYRGILACLDGYMNIAMEQT 55 (91)
Q Consensus 36 ~~~G~L~~~D~~mNlvL~~~ 55 (91)
++.|+..++|-..++.|++|
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 34577777764456666655
No 151
>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=20.49 E-value=34 Score=30.94 Aligned_cols=51 Identities=20% Similarity=0.328 Sum_probs=0.0
Q ss_pred EEEcCCcEEEEEEEEEcCCCceeeeeeEEEecC--eeeeeeceEEEeCCcEEE
Q 034564 29 VKLNSGVDYRGILACLDGYMNIAMEQTEEYVNG--QLKNKYGDAFIRGNNVLY 79 (91)
Q Consensus 29 V~L~~g~~~~G~L~~~D~~mNlvL~~~~e~~~g--~~~~~l~~v~IRG~~I~~ 79 (91)
=...+|+.+.|+|+..|.-|+..|.--....+. .-+..+|.++|+|+|.|-
T Consensus 252 ytt~~G~~v~GVlvTT~~V~q~Ll~~l~~i~~~~v~~PatYg~~Vi~geNlVT 304 (1354)
T PF03122_consen 252 YTTSSGRPVDGVLVTTANVMQKLLNLLGQISDTSVSVPATYGEFVISGENLVT 304 (1354)
T ss_dssp -----------------------------------------------------
T ss_pred eecCCCCEeceEEeccHHHHHHHHHHHhhhccceeecchhheeeeecCccHHH
Confidence 345689999999999998877666544432111 123568999999999763
No 152
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=20.33 E-value=1.1e+02 Score=19.30 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=17.9
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEE
Q 034564 21 SIRGRPVVVKLNSGVDYRGILAC 43 (91)
Q Consensus 21 ~~~~k~V~V~L~~g~~~~G~L~~ 43 (91)
+.+.|.++|.|.||+++...+=+
T Consensus 32 SA~RK~arV~L~ngk~v~ayIPg 54 (95)
T cd00319 32 SALRKVAKVRLTSGYEVTAYIPG 54 (95)
T ss_pred hhhceEEEEEccCCCEEEEECCC
Confidence 45678899999999998766533
No 153
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=20.04 E-value=1.3e+02 Score=19.91 Aligned_cols=25 Identities=16% Similarity=0.202 Sum_probs=19.2
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEEc
Q 034564 21 SIRGRPVVVKLNSGVDYRGILACLD 45 (91)
Q Consensus 21 ~~~~k~V~V~L~~g~~~~G~L~~~D 45 (91)
+.+.+.++|.|+||+++...+=+..
T Consensus 47 SA~RKvarVrL~ngk~v~AyIPGeG 71 (124)
T PRK05163 47 SALRKVARVRLTNGFEVTAYIPGEG 71 (124)
T ss_pred chhheEEEEEeCCCCEEEEEcCCCC
Confidence 4567889999999999987654433
No 154
>PF05343 Peptidase_M42: M42 glutamyl aminopeptidase; InterPro: IPR008007 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M42 (glutamyl aminopeptidase family, clan MH). For members of this family and family M28 the predicted metal ligands occur in the same order in the sequence: H, D, E, D/E, H; and the active site residues occur in the motifs HXD and EE. ; PDB: 2WYR_C 2CF4_A 1VHO_A 3ISX_A 3KL9_G 1YLO_F 3CPX_C 1VHE_A 2GRE_F 1XFO_A ....
Probab=20.01 E-value=1.2e+02 Score=22.46 Aligned_cols=24 Identities=21% Similarity=0.502 Sum_probs=19.9
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEE
Q 034564 20 KSIRGRPVVVKLNSGVDYRGILACL 44 (91)
Q Consensus 20 ~~~~~k~V~V~L~~g~~~~G~L~~~ 44 (91)
+.+.+++|+|..++| .+.|++-.-
T Consensus 49 ~~l~gq~v~i~~~~g-~i~Gvig~~ 72 (292)
T PF05343_consen 49 RVLPGQRVRIHTRDG-DIPGVIGSK 72 (292)
T ss_dssp GGTTTEEEEEEETTE-EEEEEEEE-
T ss_pred cccCCCEEEEEcCCc-EEEEEEcCC
Confidence 346899999999999 999998554
Done!