Query 034299
Match_columns 98
No_of_seqs 103 out of 1021
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 11:57:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034299.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034299hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01732 LSm5 The eukaryotic Sm 99.9 1.3E-23 2.9E-28 131.4 10.2 74 1-75 2-75 (76)
2 cd01727 LSm8 The eukaryotic Sm 99.9 1.5E-23 3.3E-28 130.1 10.1 73 5-77 2-74 (74)
3 KOG1784 Small Nuclear ribonucl 99.9 2.5E-24 5.4E-29 137.4 5.3 93 6-98 4-96 (96)
4 cd01729 LSm7 The eukaryotic Sm 99.9 2.9E-23 6.4E-28 131.1 10.1 73 4-76 4-80 (81)
5 cd01719 Sm_G The eukaryotic Sm 99.9 4.1E-23 8.9E-28 127.8 9.7 71 3-77 1-71 (72)
6 cd01730 LSm3 The eukaryotic Sm 99.9 6.8E-23 1.5E-27 129.5 9.4 72 3-74 2-82 (82)
7 cd01717 Sm_B The eukaryotic Sm 99.9 1.4E-22 3.1E-27 127.1 9.9 70 5-74 3-78 (79)
8 cd01731 archaeal_Sm1 The archa 99.9 1.4E-22 3.1E-27 123.7 9.0 68 3-74 1-68 (68)
9 cd01728 LSm1 The eukaryotic Sm 99.9 2.7E-22 5.9E-27 124.9 10.3 72 2-74 2-73 (74)
10 cd06168 LSm9 The eukaryotic Sm 99.9 4E-22 8.7E-27 124.4 10.2 70 5-74 3-74 (75)
11 PRK00737 small nuclear ribonuc 99.9 2.7E-22 5.9E-27 124.0 9.2 68 3-74 5-72 (72)
12 cd01720 Sm_D2 The eukaryotic S 99.9 2.3E-21 5E-26 124.0 9.9 74 1-74 1-85 (87)
13 cd01726 LSm6 The eukaryotic Sm 99.9 2.4E-21 5.3E-26 118.1 9.0 67 3-73 1-67 (67)
14 cd01722 Sm_F The eukaryotic Sm 99.9 3.6E-21 7.9E-26 117.7 7.8 68 2-73 1-68 (68)
15 PF01423 LSM: LSM domain ; In 99.8 1.3E-20 2.9E-25 113.9 8.9 66 6-74 2-67 (67)
16 smart00651 Sm snRNP Sm protein 99.8 1.8E-20 3.9E-25 113.1 9.2 66 6-74 2-67 (67)
17 COG1958 LSM1 Small nuclear rib 99.8 4E-20 8.7E-25 115.8 9.5 72 2-74 7-79 (79)
18 cd01718 Sm_E The eukaryotic Sm 99.8 8.6E-20 1.9E-24 114.9 9.0 70 2-74 6-79 (79)
19 cd01723 LSm4 The eukaryotic Sm 99.8 1.5E-19 3.2E-24 112.7 9.3 73 3-78 2-74 (76)
20 cd01721 Sm_D3 The eukaryotic S 99.8 1.6E-19 3.4E-24 111.1 9.1 70 3-76 1-70 (70)
21 cd00600 Sm_like The eukaryotic 99.8 4.4E-19 9.5E-24 105.7 8.8 63 7-73 1-63 (63)
22 KOG1781 Small Nuclear ribonucl 99.8 3.7E-20 8E-25 119.8 -0.3 79 5-83 20-104 (108)
23 KOG1780 Small Nuclear ribonucl 99.8 1.1E-18 2.5E-23 107.7 6.2 68 5-76 7-74 (77)
24 cd01724 Sm_D1 The eukaryotic S 99.8 5.3E-18 1.1E-22 109.0 9.4 70 5-78 4-73 (90)
25 cd01725 LSm2 The eukaryotic Sm 99.8 4.9E-18 1.1E-22 107.2 8.9 75 4-80 3-77 (81)
26 cd01733 LSm10 The eukaryotic S 99.7 2.3E-17 4.9E-22 103.6 9.1 68 4-75 11-78 (78)
27 PTZ00138 small nuclear ribonuc 99.7 3.7E-17 8E-22 105.0 9.0 71 2-75 14-88 (89)
28 KOG1782 Small Nuclear ribonucl 99.7 4.9E-19 1.1E-23 118.4 -0.5 87 4-92 11-97 (129)
29 KOG3482 Small nuclear ribonucl 99.7 2E-17 4.3E-22 101.9 5.9 70 3-76 9-78 (79)
30 KOG3460 Small nuclear ribonucl 99.6 1.3E-16 2.8E-21 100.6 2.3 74 3-76 6-88 (91)
31 KOG1775 U6 snRNA-associated Sm 99.6 8.8E-16 1.9E-20 95.4 4.6 75 2-77 7-81 (84)
32 KOG1783 Small nuclear ribonucl 99.6 5E-16 1.1E-20 95.7 1.3 70 2-75 6-75 (77)
33 KOG3168 U1 snRNP component [Tr 99.6 7.6E-16 1.7E-20 108.0 1.0 75 3-77 5-85 (177)
34 KOG3293 Small nuclear ribonucl 99.4 8.4E-13 1.8E-17 88.7 6.2 77 1-80 1-77 (134)
35 KOG3448 Predicted snRNP core p 99.4 2.2E-12 4.8E-17 82.3 7.8 74 5-80 5-78 (96)
36 KOG1774 Small nuclear ribonucl 99.3 3.2E-12 6.9E-17 80.4 3.7 72 2-76 12-87 (88)
37 KOG3172 Small nuclear ribonucl 98.9 5.1E-09 1.1E-13 69.1 6.8 77 3-83 6-82 (119)
38 KOG3428 Small nuclear ribonucl 98.8 4.7E-08 1E-12 64.5 8.4 69 4-77 4-72 (109)
39 KOG3459 Small nuclear ribonucl 98.7 3.5E-09 7.5E-14 70.0 -0.6 62 12-73 36-106 (114)
40 cd01739 LSm11_C The eukaryotic 98.4 2E-07 4.3E-12 56.6 2.9 37 13-49 9-49 (66)
41 PF14438 SM-ATX: Ataxin 2 SM d 98.0 1.4E-05 3E-10 49.4 5.3 65 6-70 6-76 (77)
42 PF12701 LSM14: Scd6-like Sm d 97.3 0.001 2.2E-08 43.2 6.1 72 8-79 4-81 (96)
43 PF06372 Gemin6: Gemin6 protei 97.0 0.003 6.4E-08 44.8 6.4 63 5-78 10-73 (166)
44 PF02237 BPL_C: Biotin protein 96.9 0.0065 1.4E-07 34.3 6.2 35 10-45 1-35 (48)
45 cd01736 LSm14_N LSm14 (also kn 96.1 0.048 1E-06 33.9 6.7 64 8-71 2-72 (74)
46 cd01735 LSm12_N LSm12 belongs 95.7 0.038 8.3E-07 33.1 4.9 33 10-42 4-36 (61)
47 PF11095 Gemin7: Gem-associate 95.6 0.067 1.4E-06 33.7 6.0 60 6-74 18-78 (80)
48 cd01716 Hfq Hfq, an abundant, 95.4 0.034 7.4E-07 33.4 4.0 31 12-42 11-41 (61)
49 TIGR02383 Hfq RNA chaperone Hf 95.4 0.036 7.9E-07 33.3 4.0 31 12-42 15-45 (61)
50 PRK14638 hypothetical protein; 95.2 0.049 1.1E-06 37.8 4.8 36 5-41 93-128 (150)
51 COG1923 Hfq Uncharacterized ho 94.8 0.057 1.2E-06 33.8 3.9 31 12-43 19-49 (77)
52 PRK00395 hfq RNA-binding prote 94.8 0.061 1.3E-06 33.9 4.0 31 12-42 19-49 (79)
53 PRK14639 hypothetical protein; 94.5 0.097 2.1E-06 35.9 4.8 36 5-41 81-116 (140)
54 PRK02001 hypothetical protein; 94.5 0.096 2.1E-06 36.6 4.8 36 5-41 83-118 (152)
55 PF10842 DUF2642: Protein of u 94.1 0.44 9.5E-06 29.0 6.5 52 5-73 14-65 (66)
56 PRK14644 hypothetical protein; 93.3 0.3 6.4E-06 33.4 5.4 36 5-41 78-117 (136)
57 PRK14640 hypothetical protein; 93.0 0.35 7.5E-06 33.5 5.5 36 5-41 90-129 (152)
58 cd01734 YlxS_C YxlS is a Bacil 92.4 0.37 8.1E-06 29.9 4.6 36 5-41 18-57 (83)
59 PF02576 DUF150: Uncharacteris 92.0 0.4 8.7E-06 32.5 4.8 35 5-40 80-118 (141)
60 COG0779 Uncharacterized protei 91.9 0.66 1.4E-05 32.5 5.7 37 4-41 91-131 (153)
61 PRK14633 hypothetical protein; 91.9 0.44 9.6E-06 33.0 4.9 36 5-41 87-126 (150)
62 PRK14642 hypothetical protein; 91.5 0.43 9.3E-06 34.7 4.6 35 5-40 93-140 (197)
63 PRK14645 hypothetical protein; 90.9 0.51 1.1E-05 32.9 4.4 35 5-41 95-129 (154)
64 PRK14636 hypothetical protein; 90.9 0.53 1.2E-05 33.5 4.6 36 5-41 91-130 (176)
65 PRK06955 biotin--protein ligas 90.9 1.5 3.3E-05 33.2 7.4 34 9-42 246-279 (300)
66 PRK00092 ribosome maturation p 90.4 0.71 1.5E-05 31.8 4.7 35 5-40 91-129 (154)
67 PRK14632 hypothetical protein; 90.3 0.66 1.4E-05 32.9 4.6 36 5-41 91-133 (172)
68 PRK14643 hypothetical protein; 89.8 0.96 2.1E-05 31.9 5.0 32 5-36 97-132 (164)
69 PRK14634 hypothetical protein; 89.6 0.82 1.8E-05 31.8 4.5 36 5-41 93-132 (155)
70 PRK14646 hypothetical protein; 89.0 0.97 2.1E-05 31.5 4.5 36 5-41 93-132 (155)
71 PRK14091 RNA-binding protein H 88.9 0.77 1.7E-05 32.6 4.0 32 12-43 104-135 (165)
72 PRK14647 hypothetical protein; 88.4 1.1 2.4E-05 31.2 4.5 35 5-40 92-135 (159)
73 PRK14631 hypothetical protein; 87.9 1.1 2.4E-05 31.8 4.4 36 4-40 109-150 (174)
74 PRK14091 RNA-binding protein H 87.7 1 2.2E-05 32.0 3.9 32 12-43 24-55 (165)
75 PRK13325 bifunctional biotin-- 87.3 3.2 7E-05 34.6 7.3 34 9-42 275-308 (592)
76 PRK14641 hypothetical protein; 85.9 1.6 3.4E-05 31.1 4.2 29 5-33 97-129 (173)
77 PRK14637 hypothetical protein; 85.9 1.9 4.1E-05 29.9 4.5 36 5-41 91-127 (151)
78 PRK11886 bifunctional biotin-- 84.5 5.8 0.00012 30.0 7.0 31 10-41 270-300 (319)
79 PF14563 DUF4444: Domain of un 84.1 2.1 4.6E-05 23.8 3.3 22 25-46 10-31 (42)
80 PF03614 Flag1_repress: Repres 84.1 2.5 5.5E-05 29.8 4.5 35 9-43 26-60 (165)
81 TIGR00121 birA_ligase birA, bi 83.6 7.3 0.00016 28.3 7.0 32 9-41 190-221 (237)
82 PF03614 Flag1_repress: Repres 82.9 1.4 3.1E-05 31.0 2.8 24 11-34 119-142 (165)
83 PRK08330 biotin--protein ligas 82.3 6.9 0.00015 28.4 6.5 34 9-43 185-219 (236)
84 KOG1073 Uncharacterized mRNA-a 79.9 7.3 0.00016 30.9 6.2 70 7-76 4-80 (361)
85 PRK14635 hypothetical protein; 79.0 6.8 0.00015 27.4 5.2 36 5-41 92-132 (162)
86 PTZ00275 biotin-acetyl-CoA-car 78.4 5.5 0.00012 30.1 5.0 32 10-42 235-266 (285)
87 COG0340 BirA Biotin-(acetyl-Co 76.7 15 0.00033 27.2 6.8 36 8-43 186-221 (238)
88 PRK14630 hypothetical protein; 75.9 6.9 0.00015 26.9 4.5 35 5-41 90-124 (143)
89 PF11607 DUF3247: Protein of u 75.7 4.6 0.0001 26.3 3.3 19 12-30 28-46 (101)
90 KOG4401 Uncharacterized conser 67.9 7 0.00015 28.2 3.1 43 1-44 1-43 (184)
91 PRK09618 flgD flagellar basal 66.3 31 0.00067 23.9 6.0 28 6-33 86-113 (142)
92 PF06257 DUF1021: Protein of u 65.6 19 0.00042 22.3 4.4 28 5-32 10-41 (76)
93 TIGR02603 CxxCH_TIGR02603 puta 64.2 16 0.00036 24.2 4.3 29 14-43 59-87 (133)
94 PRK10898 serine endoprotease; 64.2 17 0.00037 28.2 4.9 31 13-43 102-132 (353)
95 TIGR02038 protease_degS peripl 63.0 18 0.0004 27.9 4.9 31 13-43 102-132 (351)
96 KOG3382 NADH:ubiquinone oxidor 60.8 4.9 0.00011 27.8 1.2 24 20-43 40-63 (151)
97 PRK08477 biotin--protein ligas 59.4 32 0.0007 25.0 5.4 36 9-45 172-207 (211)
98 PRK10942 serine endoprotease; 58.6 23 0.00049 28.7 4.9 30 13-42 136-165 (473)
99 PRK10139 serine endoprotease; 56.6 27 0.00058 28.2 4.9 31 13-43 115-145 (455)
100 PF05071 NDUFA12: NADH ubiquin 56.1 7.3 0.00016 25.3 1.4 17 27-43 1-17 (105)
101 PF07202 Tcp10_C: T-complex pr 53.7 16 0.00034 26.2 2.9 34 9-42 141-178 (179)
102 PF07073 ROF: Modulator of Rho 52.9 14 0.00031 23.0 2.3 54 11-76 16-70 (80)
103 TIGR02037 degP_htrA_DO peripla 48.9 41 0.00089 26.5 4.8 31 13-43 82-112 (428)
104 COG5316 Uncharacterized conser 47.1 43 0.00092 27.1 4.6 45 2-47 72-116 (421)
105 PRK11911 flgD flagellar basal 45.5 49 0.0011 22.8 4.2 26 8-33 89-114 (140)
106 TIGR03170 flgA_cterm flagella 45.1 32 0.00068 22.2 3.1 24 8-31 92-116 (122)
107 PF01887 SAM_adeno_trans: S-ad 44.4 35 0.00076 25.6 3.6 22 24-45 169-190 (258)
108 smart00333 TUDOR Tudor domain. 42.8 57 0.0012 17.8 4.2 25 11-35 5-29 (57)
109 cd04479 RPA3 RPA3: A subfamily 42.3 68 0.0015 20.4 4.3 14 5-18 8-21 (101)
110 cd01772 SAKS1_UBX SAKS1-like U 38.5 25 0.00054 21.3 1.7 24 10-33 2-25 (79)
111 COG4466 Veg Uncharacterized pr 37.4 41 0.00089 21.1 2.5 20 5-24 12-31 (80)
112 PRK07018 flgA flagellar basal 37.1 44 0.00094 24.4 3.1 24 8-31 203-227 (235)
113 PRK06630 hypothetical protein; 37.1 21 0.00044 23.4 1.2 19 25-43 11-29 (99)
114 KOG3493 Ubiquitin-like protein 36.6 30 0.00065 21.2 1.8 19 6-24 5-23 (73)
115 smart00166 UBX Domain present 36.3 36 0.00077 20.4 2.2 23 12-34 4-26 (80)
116 PRK11625 Rho-binding antitermi 34.9 76 0.0016 20.0 3.5 52 11-74 22-73 (84)
117 PTZ00276 biotin/lipoate protei 34.5 66 0.0014 23.6 3.7 31 12-42 198-231 (245)
118 PF00789 UBX: UBX domain; Int 34.2 49 0.0011 19.6 2.6 23 12-34 6-28 (82)
119 PRK06792 flgD flagellar basal 33.9 80 0.0017 23.0 3.9 26 8-33 114-139 (190)
120 cd01767 UBX UBX (ubiquitin reg 33.0 49 0.0011 19.6 2.4 22 13-34 3-24 (77)
121 PF05954 Phage_GPD: Phage late 32.4 77 0.0017 22.7 3.8 28 6-33 22-49 (292)
122 PF14485 DUF4431: Domain of un 31.0 50 0.0011 18.5 2.0 13 6-18 13-25 (48)
123 COG2451 Ribosomal protein L35A 30.0 1E+02 0.0023 20.1 3.6 29 5-33 39-68 (100)
124 PLN02732 Probable NADH dehydro 29.8 56 0.0012 23.1 2.5 19 26-44 48-66 (159)
125 PRK12617 flgA flagellar basal 29.7 71 0.0015 23.3 3.2 24 8-31 182-206 (214)
126 PRK04337 50S ribosomal protein 29.3 1.2E+02 0.0026 19.3 3.8 35 5-39 33-67 (87)
127 PF09465 LBR_tudor: Lamin-B re 28.9 1.3E+02 0.0027 17.6 3.7 27 10-36 7-34 (55)
128 PRK06005 flgA flagellar basal 28.6 81 0.0018 21.9 3.2 23 9-31 128-151 (160)
129 PLN03095 NADH:ubiquinone oxido 27.9 47 0.001 22.2 1.8 18 26-43 9-26 (115)
130 TIGR00008 infA translation ini 27.7 1E+02 0.0023 18.6 3.2 23 10-32 15-37 (68)
131 PF13437 HlyD_3: HlyD family s 27.7 1.5E+02 0.0032 18.0 4.3 32 3-34 43-78 (105)
132 COG0265 DegQ Trypsin-like seri 25.8 1.5E+02 0.0033 22.4 4.5 29 12-40 95-123 (347)
133 PRK08183 NADH dehydrogenase; V 25.1 40 0.00087 23.1 1.1 19 26-44 25-43 (133)
134 PF10618 Tail_tube: Phage tail 24.9 1.2E+02 0.0026 20.0 3.4 26 3-28 65-90 (119)
135 PRK08515 flgA flagellar basal 24.9 1.2E+02 0.0026 22.1 3.6 24 8-31 192-215 (222)
136 PRK12618 flgA flagellar basal 24.6 1.1E+02 0.0024 20.8 3.2 23 9-31 109-132 (141)
137 PRK12442 translation initiatio 22.8 1.5E+02 0.0032 19.0 3.3 24 9-32 16-39 (87)
138 PF12945 YcgR_2: Flagellar pro 22.6 1.7E+02 0.0038 17.0 4.7 33 11-43 3-39 (87)
139 TIGR03361 VI_Rhs_Vgr type VI s 22.6 1.5E+02 0.0032 23.9 4.1 30 5-34 40-73 (513)
140 PRK06804 flgA flagellar basal 22.3 1.2E+02 0.0025 22.9 3.2 24 8-31 229-253 (261)
141 PF12869 tRNA_anti-like: tRNA_ 22.2 86 0.0019 20.5 2.3 20 24-43 124-143 (144)
142 KOG3168 U1 snRNP component [Tr 22.1 1.4E+02 0.003 21.4 3.4 66 5-71 43-115 (177)
143 cd01770 p47_UBX p47-like ubiqu 21.4 95 0.0021 18.9 2.2 23 12-34 4-26 (79)
144 COG3466 ISA1214 Putative trans 21.3 86 0.0019 18.1 1.8 13 8-20 38-50 (52)
145 COG1363 FrvX Cellulase M and r 21.0 1.2E+02 0.0025 24.0 3.1 25 7-31 92-116 (355)
146 PF08661 Rep_fac-A_3: Replicat 20.7 2.4E+02 0.0051 17.9 4.8 21 5-33 11-31 (109)
147 PRK10708 hypothetical protein; 20.6 1.3E+02 0.0029 17.8 2.5 26 11-36 3-28 (62)
148 PF03122 Herpes_MCP: Herpes vi 20.1 35 0.00075 31.6 0.0 57 16-74 251-307 (1354)
No 1
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.91 E-value=1.3e-23 Score=131.35 Aligned_cols=74 Identities=20% Similarity=0.368 Sum_probs=67.0
Q ss_pred CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299 1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV 75 (98)
Q Consensus 1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~ 75 (98)
|.|...|+++++++|+|++++||++.|+|.|||+|||++|+||.|++..++ +...+.+|.++|||++|++|.+.
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 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPE-GRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCC-CceeeEcCeEEEeCCeEEEEECC
Confidence 789999999999999999999999999999999999999999999985443 34567899999999999999863
No 2
>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=99.91 E-value=1.5e-23 Score=130.14 Aligned_cols=73 Identities=71% Similarity=1.122 Sum_probs=66.2
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE 77 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~ 77 (98)
+.|++|++++|+|.++|||.+.|+|+|||+|||++|++|.|+...++++..++.+|.+++||++|++|++.|+
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 4899999999999999999999999999999999999999987655445567889999999999999998864
No 3
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.90 E-value=2.5e-24 Score=137.40 Aligned_cols=93 Identities=67% Similarity=1.133 Sum_probs=89.6
Q ss_pred hHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCccccccCCC
Q 034299 6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSHLDL 85 (98)
Q Consensus 6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e~~~~~ 85 (98)
.|+.|++++|.|...|||.+.|.|+|||+..|++|+++.|++++..++.++..+|+.+|||+||..|+..|+++++.+|+
T Consensus 4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~~ld~ 83 (96)
T KOG1784|consen 4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDSRLDL 83 (96)
T ss_pred hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhhhhhh
Confidence 79999999999999999999999999999999999999999987766778889999999999999999999999999999
Q ss_pred CccccccCCCccC
Q 034299 86 SNLRAHPLKPVIH 98 (98)
Q Consensus 86 ~~~~~~~~~~~~~ 98 (98)
..+|+||++|+.|
T Consensus 84 tkir~epl~~v~h 96 (96)
T KOG1784|consen 84 TKIRAEPLHPVVH 96 (96)
T ss_pred hhcccCCCCCccC
Confidence 9999999999988
No 4
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.90 E-value=2.9e-23 Score=131.07 Aligned_cols=73 Identities=32% Similarity=0.560 Sum_probs=64.2
Q ss_pred hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCC----eeEEEecEEEEcCCcEEEEEecC
Q 034299 4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEG----VQQLVLGLYIIRGDNISIVGEVD 76 (98)
Q Consensus 4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~----~~~r~lg~v~irG~~I~~i~~~d 76 (98)
...|.++++++|+|+|+|||++.|+|.|||+||||+|++|+|+...++++ ...+.+|.++|||++|++|++.+
T Consensus 4 ~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 4 ILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred hhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 35799999999999999999999999999999999999999998653321 35678999999999999998764
No 5
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.90 E-value=4.1e-23 Score=127.83 Aligned_cols=71 Identities=28% Similarity=0.593 Sum_probs=64.0
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE 77 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~ 77 (98)
|.+.|+++++|+|+|+|++|+++.|+|.|||+||||+|+||.|+.. +...+.+|.++|||++|++|++.|.
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 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS----GGEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEcc----CCceeEeceEEECCCEEEEEEcccc
Confidence 4579999999999999999999999999999999999999999862 2346789999999999999998753
No 6
>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=99.89 E-value=6.8e-23 Score=129.47 Aligned_cols=72 Identities=19% Similarity=0.346 Sum_probs=63.6
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCC---------eeEEEecEEEEcCCcEEEEE
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEG---------VQQLVLGLYIIRGDNISIVG 73 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~---------~~~r~lg~v~irG~~I~~i~ 73 (98)
|...|+.+++++|.|+++|||++.|+|.|||+||||+|+||+|++..++++ ...|.+|.++|||++|++|+
T Consensus 2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence 667889999999999999999999999999999999999999998653211 25789999999999999986
Q ss_pred e
Q 034299 74 E 74 (98)
Q Consensus 74 ~ 74 (98)
+
T Consensus 82 ~ 82 (82)
T cd01730 82 P 82 (82)
T ss_pred C
Confidence 3
No 7
>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=99.89 E-value=1.4e-22 Score=127.06 Aligned_cols=70 Identities=30% Similarity=0.500 Sum_probs=62.3
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecC------CCeeEEEecEEEEcCCcEEEEEe
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTK------EGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~------~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
..|.+|++++|+|+++|||++.|+|.|||+||||+|+||.|++..+. .+.+.+.+|+++|||++|++|..
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 57999999999999999999999999999999999999999886432 12467899999999999999974
No 8
>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=99.89 E-value=1.4e-22 Score=123.70 Aligned_cols=68 Identities=25% Similarity=0.385 Sum_probs=61.9
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
|...|+++++++|+|+|++|++|.|+|.|||+|||++|+||+|++.. ..++.+|.++|||++|++|.+
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG----EPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC----CeEeEcCcEEEeCCEEEEEcC
Confidence 56789999999999999999999999999999999999999998642 256789999999999999864
No 9
>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=99.89 E-value=2.7e-22 Score=124.88 Aligned_cols=72 Identities=33% Similarity=0.742 Sum_probs=64.1
Q ss_pred CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299 2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
++.+.|+++++++|.|.++|||++.|+|.|||+|||++|+||.|+....+ ...++.+|.++|||++|++|+.
T Consensus 2 ~~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~-~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 2 PGTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD-KYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred CchHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC-ccceeEeeEEEEECCEEEEEEc
Confidence 45678999999999999999999999999999999999999999876432 2356889999999999999975
No 10
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=4e-22 Score=124.38 Aligned_cols=70 Identities=31% Similarity=0.453 Sum_probs=63.3
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecC--CCeeEEEecEEEEcCCcEEEEEe
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTK--EGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~--~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
..|++|++++|+|+++|||.|.|+|.|||++|||+|+||.|++..+. ...+.|.+|+++|||++|++|..
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 57999999999999999999999999999999999999999986543 23568899999999999999863
No 11
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.88 E-value=2.7e-22 Score=123.95 Aligned_cols=68 Identities=31% Similarity=0.432 Sum_probs=61.1
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
|...|.++++++|+|+|+||++|.|+|.+||+|||++|+||.|.+. +...+.+|.++|||++|++|.+
T Consensus 5 P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~----~~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 5 PLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD----GEVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred hHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC----CCeEeEcCcEEEeCCEEEEEcC
Confidence 5668999999999999999999999999999999999999999752 2356789999999999999863
No 12
>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=99.86 E-value=2.3e-21 Score=124.04 Aligned_cols=74 Identities=20% Similarity=0.347 Sum_probs=64.1
Q ss_pred CCChhhHHhhc--CCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecC-CC--------eeEEEecEEEEcCCcE
Q 034299 1 MSGGPGLESLV--EQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTK-EG--------VQQLVLGLYIIRGDNI 69 (98)
Q Consensus 1 m~~~~~L~~~i--~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~-~~--------~~~r~lg~v~irG~~I 69 (98)
+-|...|.+.+ +++|.|+|++|+++.|+|.|||+||||+|+||.|.+...+ ++ ..++.+|.+||||++|
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~V 80 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSV 80 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEE
Confidence 35778899997 8999999999999999999999999999999999886522 11 2467899999999999
Q ss_pred EEEEe
Q 034299 70 SIVGE 74 (98)
Q Consensus 70 ~~i~~ 74 (98)
++|..
T Consensus 81 v~Is~ 85 (87)
T cd01720 81 ILVLR 85 (87)
T ss_pred EEEec
Confidence 99975
No 13
>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=99.86 E-value=2.4e-21 Score=118.09 Aligned_cols=67 Identities=27% Similarity=0.391 Sum_probs=60.1
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEE
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVG 73 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~ 73 (98)
|...|++++|++|+|+|++|++|.|+|.+||+|||++|+||+|... +...+.+|.++|||++|.+|.
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~----~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN----GQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC----CceeeEeCCEEEECCEEEEEC
Confidence 5678999999999999999999999999999999999999988642 235678999999999999984
No 14
>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=99.85 E-value=3.6e-21 Score=117.69 Aligned_cols=68 Identities=25% Similarity=0.289 Sum_probs=60.6
Q ss_pred CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEE
Q 034299 2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVG 73 (98)
Q Consensus 2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~ 73 (98)
.|.+.|++++|++|+|+|++|++|.|+|.+||++||++|+||+|+.. +.....+|.++|||++|.+|.
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 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID----GKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC----CccccCcCcEEEECCEEEEEC
Confidence 36789999999999999999999999999999999999999998742 234567999999999999983
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=99.84 E-value=1.3e-20 Score=113.86 Aligned_cols=66 Identities=32% Similarity=0.511 Sum_probs=60.3
Q ss_pred hHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299 6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
+|++++|++|+|++++|++++|+|.+||++||++|+||.|.+..+ .+.+++|.+||||++|.+|.+
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~---~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNG---PEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTE---SEEEEEEEEEEEGGGEEEEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCC---CcEeECcEEEEECCEEEEEEC
Confidence 689999999999999999999999999999999999999986432 167899999999999999974
No 16
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.84 E-value=1.8e-20 Score=113.14 Aligned_cols=66 Identities=36% Similarity=0.546 Sum_probs=60.1
Q ss_pred hHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299 6 GLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
.|++++|++|+|+++||+++.|+|.+||++||++|+||.|++..+ .+.+.+|.++|||++|++|.+
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~---~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG---EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC---cEEeEeCCEEEcCCEEEEEeC
Confidence 689999999999999999999999999999999999999986531 467899999999999999863
No 17
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.83 E-value=4e-20 Score=115.79 Aligned_cols=72 Identities=31% Similarity=0.445 Sum_probs=60.7
Q ss_pred CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCe-eEEEecEEEEcCCcEEEEEe
Q 034299 2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGV-QQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~-~~r~lg~v~irG~~I~~i~~ 74 (98)
.|...|.++++++|.|+|++|++|.|+|.|||+|||++|+||.|++.. +... ..+..|.++|||++|.+|.+
T Consensus 7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH-DGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc-CCccccceeccEEEEECCcEEEEeC
Confidence 467899999999999999999999999999999999999999998741 1111 23444599999999999863
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=99.82 E-value=8.6e-20 Score=114.91 Aligned_cols=70 Identities=23% Similarity=0.403 Sum_probs=60.2
Q ss_pred CChhhHHhhcCC--eEEEEEC--CCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299 2 SGGPGLESLVEQ--QISVITN--DGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 2 ~~~~~L~~~i~k--~V~V~l~--~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
.|...+.+|+++ +|.|.++ +|+++.|+|.|||+|||++|+||+|+... +...+.+|.++|||+||++|++
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~---~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK---TKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC---CceEeEcCcEEEeCCEEEEEcC
Confidence 478899999999 6666665 89999999999999999999999998642 2356789999999999999864
No 19
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.82 E-value=1.5e-19 Score=112.73 Aligned_cols=73 Identities=23% Similarity=0.178 Sum_probs=63.2
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcc
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEE 78 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~ 78 (98)
|...|+++.|++|.|+|++|+++.|+|.+||+|||++|+||++... ++.....++.+||||++|.+|..++..
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~---~g~~~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSK---DGDKFWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC---CCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence 6778999999999999999999999999999999999999988632 233345679999999999999887643
No 20
>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=99.82 E-value=1.6e-19 Score=111.08 Aligned_cols=70 Identities=20% Similarity=0.134 Sum_probs=61.3
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD 76 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d 76 (98)
|...|.++.|++|.|+|++|.+|+|+|.++|++||++|+||.+... ++ +...+|.+||||++|.++..+|
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 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTAR---DG-RVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECC---CC-cEeEcCcEEEeCCEEEEEEeCC
Confidence 5678999999999999999999999999999999999999987532 12 3456899999999999998875
No 21
>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=99.80 E-value=4.4e-19 Score=105.66 Aligned_cols=63 Identities=41% Similarity=0.682 Sum_probs=57.4
Q ss_pred HHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEE
Q 034299 7 LESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVG 73 (98)
Q Consensus 7 L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~ 73 (98)
|++++|++|+|+++||+.+.|+|.+||++||++|+||.|.+.. ...+.+|.++|||++|.+|.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~----~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE----GKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC----CcEEECCeEEEECCEEEEEC
Confidence 5789999999999999999999999999999999999998653 35688999999999999873
No 22
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.77 E-value=3.7e-20 Score=119.77 Aligned_cols=79 Identities=27% Similarity=0.503 Sum_probs=69.6
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCC----eeEEEecEEEEcCCcEEEEEecCcc--
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEG----VQQLVLGLYIIRGDNISIVGEVDEE-- 78 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~----~~~r~lg~v~irG~~I~~i~~~d~~-- 78 (98)
.+|.+|++++|+|++.+||+.+|+|+|||+.||+||++++|+..+|+++ .+.|++|+++|||..+++|++.|-.
T Consensus 20 lDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e~ 99 (108)
T KOG1781|consen 20 LDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSEE 99 (108)
T ss_pred hhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchhh
Confidence 4799999999999999999999999999999999999999998777654 3569999999999999999998843
Q ss_pred ccccC
Q 034299 79 LDSHL 83 (98)
Q Consensus 79 ~e~~~ 83 (98)
+.+++
T Consensus 100 I~npf 104 (108)
T KOG1781|consen 100 IANPF 104 (108)
T ss_pred hccch
Confidence 34444
No 23
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.77 E-value=1.1e-18 Score=107.66 Aligned_cols=68 Identities=32% Similarity=0.630 Sum_probs=61.3
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD 76 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d 76 (98)
+.|++|++|++.+++..||.+.|.|+|||.|||++|++++|.... ..+..+|.++|||++|+.+.+.+
T Consensus 7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~----~~~~~ig~~vIrgnsiv~~eaL~ 74 (77)
T KOG1780|consen 7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD----GDKNNIGMVVIRGNSIVMVEALE 74 (77)
T ss_pred chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc----CCcceeeeEEEeccEEEEEeecc
Confidence 699999999999999999999999999999999999999997422 24567999999999999998875
No 24
>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=99.76 E-value=5.3e-18 Score=109.04 Aligned_cols=70 Identities=23% Similarity=0.294 Sum_probs=62.3
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcc
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEE 78 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~ 78 (98)
..|+++.|++|+|+|++|.+|.|+|.++|.+||++|+||++... +.....+|.++|||++|.+|..+|+-
T Consensus 4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~----~~~~~~~~~v~IRG~nI~yi~lPd~l 73 (90)
T cd01724 4 RFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLK----GRNPVPLDTLSIRGNNIRYFILPDSL 73 (90)
T ss_pred HHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcC----CCceeEcceEEEeCCEEEEEEcCCcC
Confidence 47899999999999999999999999999999999999988742 22456799999999999999998763
No 25
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.76 E-value=4.9e-18 Score=107.16 Aligned_cols=75 Identities=24% Similarity=0.249 Sum_probs=62.6
Q ss_pred hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcccc
Q 034299 4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELD 80 (98)
Q Consensus 4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e 80 (98)
...|+++.|++|.|+|++|.++.|+|.++|++||++|+||++.. ++.......++.++|||++|.+|..+|..++
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~--~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~ 77 (81)
T cd01725 3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTD--PEKYPHMLSVKNCFIRGSVVRYVQLPADEVD 77 (81)
T ss_pred hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEc--CCCcccccccCeEEEECCEEEEEEeChhHcC
Confidence 35789999999999999999999999999999999999997653 2111223457899999999999999976554
No 26
>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=99.74 E-value=2.3e-17 Score=103.55 Aligned_cols=68 Identities=19% Similarity=0.144 Sum_probs=58.7
Q ss_pred hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299 4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV 75 (98)
Q Consensus 4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~ 75 (98)
...|+++.|++|.|+|++|.+|.|+|.++|++||++|+||.+... +.....+|.++|||++|.+|..+
T Consensus 11 ~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~----~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 11 IILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDR----NGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred HHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcC----CCceeECCcEEEECCEEEEEEcC
Confidence 347899999999999999999999999999999999999986531 12344789999999999999764
No 27
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.73 E-value=3.7e-17 Score=104.99 Aligned_cols=71 Identities=23% Similarity=0.374 Sum_probs=58.0
Q ss_pred CChhhHHhhcCCe--EEEEECC--CcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299 2 SGGPGLESLVEQQ--ISVITND--GRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV 75 (98)
Q Consensus 2 ~~~~~L~~~i~k~--V~V~l~~--Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~ 75 (98)
+|...+.+++.++ |.|.+++ ++++.|+|.|||+|||++|+||+|++.. +...+.+|.++|||+||++|.+.
T Consensus 14 ~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~---~~~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 14 QPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK---KNTRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred CCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC---CceeeEcCeEEEcCCEEEEEEcC
Confidence 4667788888765 4555556 5999999999999999999999998642 23567899999999999999764
No 28
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.72 E-value=4.9e-19 Score=118.43 Aligned_cols=87 Identities=30% Similarity=0.612 Sum_probs=75.2
Q ss_pred hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCccccccC
Q 034299 4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSHL 83 (98)
Q Consensus 4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e~~~ 83 (98)
...|.+++++++.|.|+|||.+.|.|++||||.|++|++|+|+++-.+. +..+..|..+|||+||++++..|.++| ..
T Consensus 11 t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~-Y~di~~glfiIRGENVvllGeid~dkE-~~ 88 (129)
T KOG1782|consen 11 TTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNK-YCDIPRGLFIIRGENVVLLGEIDLDKE-EE 88 (129)
T ss_pred hhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecce-ecccCceEEEEecCcEEEEecCCcchh-hc
Confidence 4568999999999999999999999999999999999999999986543 456678999999999999999999888 45
Q ss_pred CCCcccccc
Q 034299 84 DLSNLRAHP 92 (98)
Q Consensus 84 ~~~~~~~~~ 92 (98)
.+.+++.+.
T Consensus 89 ~l~~i~~~e 97 (129)
T KOG1782|consen 89 PLEQISFEE 97 (129)
T ss_pred cceeCCHHH
Confidence 555555444
No 29
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.71 E-value=2e-17 Score=101.92 Aligned_cols=70 Identities=27% Similarity=0.326 Sum_probs=63.7
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD 76 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d 76 (98)
|.++|+.+.||+|.|+|++|.+|.|+|.+.|+||||.|.+|+|++. +...-.+|.++||-+||.+|...+
T Consensus 9 PKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~id----G~~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 9 PKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYID----GVSTGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred chHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhc----ccccccceeEEEEeccEEEEecCC
Confidence 6789999999999999999999999999999999999999999874 344567999999999999998664
No 30
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.63 E-value=1.3e-16 Score=100.59 Aligned_cols=74 Identities=19% Similarity=0.328 Sum_probs=64.0
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCC---C------eeEEEecEEEEcCCcEEEEE
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKE---G------VQQLVLGLYIIRGDNISIVG 73 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~---~------~~~r~lg~v~irG~~I~~i~ 73 (98)
|...|.-+++.+|.|+++++|++.|+|+|||+|.||+|.|+.|.++.-+. . ..+|.+..+|+||++|.+|+
T Consensus 6 PldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvs 85 (91)
T KOG3460|consen 6 PLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVS 85 (91)
T ss_pred cHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEc
Confidence 66788889999999999999999999999999999999999998864211 1 24678899999999999998
Q ss_pred ecC
Q 034299 74 EVD 76 (98)
Q Consensus 74 ~~d 76 (98)
++-
T Consensus 86 pp~ 88 (91)
T KOG3460|consen 86 PPL 88 (91)
T ss_pred Ccc
Confidence 864
No 31
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.61 E-value=8.8e-16 Score=95.44 Aligned_cols=75 Identities=23% Similarity=0.383 Sum_probs=66.5
Q ss_pred CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299 2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE 77 (98)
Q Consensus 2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~ 77 (98)
.|...+.+++|.+++|.+++.|++.|+|.|||.|.|++|+|++|+...+. +.....++++++.|++|+.+.+..+
T Consensus 7 lPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e-gr~~tk~~~iLLnGNni~mLvPGGe 81 (84)
T KOG1775|consen 7 LPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE-GRRMTKLDQILLNGNNITMLVPGGE 81 (84)
T ss_pred ccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC-cceeeeeeeeeecCCcEEEEecCCC
Confidence 36678899999999999999999999999999999999999999987653 3556689999999999999987653
No 32
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.57 E-value=5e-16 Score=95.71 Aligned_cols=70 Identities=27% Similarity=0.374 Sum_probs=63.6
Q ss_pred CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEec
Q 034299 2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEV 75 (98)
Q Consensus 2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~ 75 (98)
+|...|++.+||+|.|+|.+|-.|+|+|.|.|.|||+-|+.+.|+. ++..++..|-+||||++|.+|...
T Consensus 6 ~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~----ngql~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 6 MPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV----NGQLKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred CcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh----cCcccccccceeeccccEEEEEec
Confidence 3778999999999999999999999999999999999999999985 245678899999999999999764
No 33
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.55 E-value=7.6e-16 Score=107.99 Aligned_cols=75 Identities=27% Similarity=0.469 Sum_probs=65.4
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeec------CCCeeEEEecEEEEcCCcEEEEEecC
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYST------KEGVQQLVLGLYIIRGDNISIVGEVD 76 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~------~~~~~~r~lg~v~irG~~I~~i~~~d 76 (98)
....|.++++.+++|.++|||+|.|+|.+||+|||++|.+|+|++... .+++++|.+|+|++||++|++.+.-+
T Consensus 5 ~sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg 84 (177)
T KOG3168|consen 5 KSSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG 84 (177)
T ss_pred chhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence 345788999999999999999999999999999999999999987432 12368999999999999999998765
Q ss_pred c
Q 034299 77 E 77 (98)
Q Consensus 77 ~ 77 (98)
.
T Consensus 85 p 85 (177)
T KOG3168|consen 85 P 85 (177)
T ss_pred C
Confidence 3
No 34
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.39 E-value=8.4e-13 Score=88.66 Aligned_cols=77 Identities=23% Similarity=0.201 Sum_probs=69.3
Q ss_pred CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcccc
Q 034299 1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELD 80 (98)
Q Consensus 1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e 80 (98)
|-|..+|.-..+.++.|+|++|.+|.|.|..+|..|||.|.+++++.. ++.+...+..+.|||++|.++..+|+-++
T Consensus 1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~---Dgdkf~r~pEcYirGttIkylri~d~iid 77 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSE---DGDKFFRMPECYIRGTTIKYLRIPDEIID 77 (134)
T ss_pred CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEecc---CCCceeecceeEEecceeEEEeccHHHHH
Confidence 889999999999999999999999999999999999999999998753 34456778999999999999999987543
No 35
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.39 E-value=2.2e-12 Score=82.27 Aligned_cols=74 Identities=23% Similarity=0.279 Sum_probs=62.8
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcccc
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELD 80 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e 80 (98)
..++.++|++|.|+|+++-.+.|+|.++|+|.|+.|.|..-. ++++..+--.+..+||||+.|.++..+.+..+
T Consensus 5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~--d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vd 78 (96)
T KOG3448|consen 5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVT--DPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVD 78 (96)
T ss_pred HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEee--CcccCCCeeeeeeEEEeccEEEEEEeChhHHH
Confidence 467899999999999999999999999999999999997543 44344466678899999999999998866544
No 36
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.28 E-value=3.2e-12 Score=80.42 Aligned_cols=72 Identities=25% Similarity=0.385 Sum_probs=56.7
Q ss_pred CChhhHHhhcCCeEEEE--E--CCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299 2 SGGPGLESLVEQQISVI--T--NDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD 76 (98)
Q Consensus 2 ~~~~~L~~~i~k~V~V~--l--~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d 76 (98)
+|-..+.+|+..+.+|. + +-|-.++|.+.|||.|||+||++|+|...+. ...+.+|.++++|+||.+|...+
T Consensus 12 ~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~---~~rk~lGRilLKGDnItli~~~~ 87 (88)
T KOG1774|consen 12 QPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT---KSRKELGRILLKGDNITLIQSAG 87 (88)
T ss_pred CcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc---cCCCccccEEEcCCcEEEEeecC
Confidence 35556777887665555 4 3489999999999999999999999975432 23448999999999999997653
No 37
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=98.92 E-value=5.1e-09 Score=69.05 Aligned_cols=77 Identities=18% Similarity=0.093 Sum_probs=65.2
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcccccc
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEELDSH 82 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~~e~~ 82 (98)
|...|.+.-|.-|.++++.|..|.|.|.-.|.+||+.|+|.+-...+ ..-..+..|||||+.|.++..+|.-+.++
T Consensus 6 piKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d----g~vs~le~V~IRGS~IRFlvlPdmLKnAP 81 (119)
T KOG3172|consen 6 PIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD----GRVSQLEQVFIRGSKIRFLVLPDMLKNAP 81 (119)
T ss_pred ceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC----CcceeeeeEEEecCeEEEEECchHhhcCc
Confidence 45678889999999999999999999999999999999998765432 23456889999999999999998766655
Q ss_pred C
Q 034299 83 L 83 (98)
Q Consensus 83 ~ 83 (98)
+
T Consensus 82 m 82 (119)
T KOG3172|consen 82 M 82 (119)
T ss_pred c
Confidence 4
No 38
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.81 E-value=4.7e-08 Score=64.50 Aligned_cols=69 Identities=23% Similarity=0.304 Sum_probs=60.2
Q ss_pred hhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCc
Q 034299 4 GPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDE 77 (98)
Q Consensus 4 ~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~ 77 (98)
...|.++.+.++.|+|++|....|++.++|.+||..|.++.-... + +...+-.+++||++|-|+-.+|.
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~----~-~pv~l~~lsirgnniRy~~lpD~ 72 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK----G-EPVRLDTLSIRGNNIRYYILPDS 72 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC----C-CceeEEEEEeecceEEEEEccCC
Confidence 457899999999999999999999999999999999999866532 2 34578899999999999988874
No 39
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.65 E-value=3.5e-09 Score=69.98 Aligned_cols=62 Identities=23% Similarity=0.427 Sum_probs=53.3
Q ss_pred CCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEee-cCC--C------eeEEEecEEEEcCCcEEEEE
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYS-TKE--G------VQQLVLGLYIIRGDNISIVG 73 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~-~~~--~------~~~r~lg~v~irG~~I~~i~ 73 (98)
...|.|.++|++.+.|+..|||.|+|++|+++.|-|.. ++. + ...|++|.+||||++|+.+.
T Consensus 36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~ 106 (114)
T KOG3459|consen 36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVL 106 (114)
T ss_pred CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEE
Confidence 46889999999999999999999999999999998864 221 1 23789999999999999886
No 40
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=98.42 E-value=2e-07 Score=56.61 Aligned_cols=37 Identities=24% Similarity=0.280 Sum_probs=31.2
Q ss_pred CeEEEEECC--C--cEEEEEEEEEcCCCceEecceEEEEee
Q 034299 13 QQISVITND--G--RNIVGVLKGFDQATNIILDESHERVYS 49 (98)
Q Consensus 13 k~V~V~l~~--G--r~i~G~L~~~D~~~NlvL~~~~e~~~~ 49 (98)
++|+|.++. | -.++|.|.+||+|+||+|.|+.|.+..
T Consensus 9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 677777754 3 489999999999999999999998754
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.04 E-value=1.4e-05 Score=49.36 Aligned_cols=65 Identities=18% Similarity=0.290 Sum_probs=39.8
Q ss_pred hHHhhcCCeEEEEECCCcEEEEEEEEEcC---CCceEecceEEEEeecC--C-CeeEEEecEEEEcCCcEE
Q 034299 6 GLESLVEQQISVITNDGRNIVGVLKGFDQ---ATNIILDESHERVYSTK--E-GVQQLVLGLYIIRGDNIS 70 (98)
Q Consensus 6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~---~~NlvL~~~~e~~~~~~--~-~~~~r~lg~v~irG~~I~ 70 (98)
.+..++|++|.|+++||..|+|.|.+++. .+.++|+.|........ . .........++++++.|+
T Consensus 6 l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 6 LLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 46788999999999999999999999998 89999988866432111 1 112334556677777665
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.32 E-value=0.001 Score=43.24 Aligned_cols=72 Identities=17% Similarity=0.277 Sum_probs=54.3
Q ss_pred HhhcCCeEEEEECCCcEEEEEEEEEcC-CCceEecceEEEEeecC--CC---eeEEEecEEEEcCCcEEEEEecCccc
Q 034299 8 ESLVEQQISVITNDGRNIVGVLKGFDQ-ATNIILDESHERVYSTK--EG---VQQLVLGLYIIRGDNISIVGEVDEEL 79 (98)
Q Consensus 8 ~~~i~k~V~V~l~~Gr~i~G~L~~~D~-~~NlvL~~~~e~~~~~~--~~---~~~r~lg~v~irG~~I~~i~~~d~~~ 79 (98)
.+|+|++|.+..+++-.|+|+|..+|. ...+.|.|+..+-.... .. ........+..||+.|.-+...+...
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 479999999999999999999999994 88899999866532110 00 11224678899999999998876544
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=97.01 E-value=0.003 Score=44.82 Aligned_cols=63 Identities=21% Similarity=0.341 Sum_probs=45.5
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecCcc
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVDEE 78 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d~~ 78 (98)
..+.+|++|+|+|.+.| +++.|.+.++| -..|++|-+-.| ++ + ...-+|.|..|..+...+++
T Consensus 10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e------~~--~--~sv~~I~ghaVk~vevl~~~ 73 (166)
T PF06372_consen 10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE------DG--K--RSVKVIMGHAVKSVEVLSEG 73 (166)
T ss_dssp HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T------TS-----EEEEEE-GGGEEEEEEEE--
T ss_pred HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc------CC--c--eeEEEEEccceEEEEEccCC
Confidence 46789999999999999 99999999999 788999976433 11 2 24578999999999998864
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=96.92 E-value=0.0065 Score=34.29 Aligned_cols=35 Identities=20% Similarity=0.386 Sum_probs=30.3
Q ss_pred hcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEE
Q 034299 10 LVEQQISVITNDGRNIVGVLKGFDQATNIILDESHE 45 (98)
Q Consensus 10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e 45 (98)
.+|++|++.. ++..++|+..++|.+..|+++....
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 4799999999 6777799999999999999977544
No 45
>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=96.08 E-value=0.048 Score=33.93 Aligned_cols=64 Identities=19% Similarity=0.299 Sum_probs=45.0
Q ss_pred HhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecCC--C----eeEEEecEEEEcCCcEEE
Q 034299 8 ESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTKE--G----VQQLVLGLYIIRGDNISI 71 (98)
Q Consensus 8 ~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~~--~----~~~r~lg~v~irG~~I~~ 71 (98)
.+|+|+++.+..+.+-.|+|.|.++| +..-+.|.|+..+=+..-. + ........++.||+.|.-
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 36999999999999999999999999 5555779998655322110 0 122345567777777643
No 46
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=95.67 E-value=0.038 Score=33.13 Aligned_cols=33 Identities=21% Similarity=0.284 Sum_probs=28.4
Q ss_pred hcCCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299 10 LVEQQISVITNDGRNIVGVLKGFDQATNIILDE 42 (98)
Q Consensus 10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~ 42 (98)
.+|..|++++..|.+|+|.+.+||...+++.=.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk 36 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK 36 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence 479999999999999999999999777776433
No 47
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=95.59 E-value=0.067 Score=33.75 Aligned_cols=60 Identities=12% Similarity=0.211 Sum_probs=44.4
Q ss_pred hHHhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299 6 GLESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
.|....|+++.+.|.++.++.|++.++| ...|+..++- ..|- | .....++|.+.|+++..
T Consensus 18 ~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L----~TPl-G----v~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 18 SLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNL----QTPL-G----VQPEALLRCSDVISISF 78 (80)
T ss_dssp HHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEE----ETTT-T----EEEEEEEEGGGEEEEEE
T ss_pred HHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhc----CCCc-c----cChhheeecCCEEEEEe
Confidence 5677789999999999999999999999 6677776653 1221 1 24677999999999875
No 48
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=95.42 E-value=0.034 Score=33.36 Aligned_cols=31 Identities=16% Similarity=0.400 Sum_probs=25.9
Q ss_pred CCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQATNIILDE 42 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~ 42 (98)
..+|.|-|.+|-.+.|.+.+||+|+=++-.+
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 5678888999999999999999999544333
No 49
>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=95.36 E-value=0.036 Score=33.25 Aligned_cols=31 Identities=23% Similarity=0.455 Sum_probs=26.1
Q ss_pred CCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQATNIILDE 42 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~ 42 (98)
..+|.|-|.+|-.+.|.+.+||+|+=++-.+
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 5678888999999999999999999555433
No 50
>PRK14638 hypothetical protein; Provisional
Probab=95.17 E-value=0.049 Score=37.81 Aligned_cols=36 Identities=17% Similarity=0.442 Sum_probs=31.3
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~ 41 (98)
..+.+++|++|.|++++++.++|+|.++|.. ++.|.
T Consensus 93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 5788999999999999999999999999964 45554
No 51
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=94.82 E-value=0.057 Score=33.77 Aligned_cols=31 Identities=16% Similarity=0.468 Sum_probs=26.6
Q ss_pred CCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
..+|.|-|.+|-.+.|.+.+||+|. +.|++.
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~~ 49 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFDNFV-VLLKNT 49 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeeeeEE-EEEEcC
Confidence 5789999999999999999999998 555553
No 52
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.78 E-value=0.061 Score=33.86 Aligned_cols=31 Identities=13% Similarity=0.363 Sum_probs=26.5
Q ss_pred CCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQATNIILDE 42 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~ 42 (98)
..+|.|-|.+|-.+.|.+.+||+|.=++-.+
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 5788999999999999999999999555444
No 53
>PRK14639 hypothetical protein; Provisional
Probab=94.48 E-value=0.097 Score=35.93 Aligned_cols=36 Identities=19% Similarity=0.375 Sum_probs=31.4
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~ 41 (98)
..+.+++|++|.|.+.+++.+.|+|.++|.. ++.|.
T Consensus 81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 5788999999999999999999999999984 45553
No 54
>PRK02001 hypothetical protein; Validated
Probab=94.47 E-value=0.096 Score=36.55 Aligned_cols=36 Identities=28% Similarity=0.530 Sum_probs=31.4
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~ 41 (98)
..+.+++|+.|+|.+.+++.+.|+|.++|.. ++.|.
T Consensus 83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence 4788999999999999999999999999975 45554
No 55
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=94.07 E-value=0.44 Score=28.97 Aligned_cols=52 Identities=31% Similarity=0.385 Sum_probs=39.3
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEE
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVG 73 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~ 73 (98)
..|++++|+++.|.+..|.. .|+|.+.-..- ++|+.. -...+||=..|++|.
T Consensus 14 q~lq~liG~~vvV~T~~g~v-~G~L~~V~pDh-Ivl~~~---------------~~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 14 QTLQSLIGQRVVVQTTRGSV-RGILVDVKPDH-IVLEEN---------------GTPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHhcCCEEEEEEcCCcE-EEEEEeecCCE-EEEEeC---------------CcEEEEEeeeEEEEc
Confidence 46899999999999988776 99999987543 455432 245678888888775
No 56
>PRK14644 hypothetical protein; Provisional
Probab=93.27 E-value=0.3 Score=33.45 Aligned_cols=36 Identities=28% Similarity=0.272 Sum_probs=30.7
Q ss_pred hhHHhhcCCeEEEEECCC----cEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITNDG----RNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~G----r~i~G~L~~~D~~~NlvL~ 41 (98)
.++.+++|+.|.|++++. +.+.|.|.++|.. ++.|.
T Consensus 78 ~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 78 DELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 368899999999999886 8999999999974 56664
No 57
>PRK14640 hypothetical protein; Provisional
Probab=92.97 E-value=0.35 Score=33.55 Aligned_cols=36 Identities=31% Similarity=0.418 Sum_probs=30.2
Q ss_pred hhHHhhcCCeEEEEE----CCCcEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVIT----NDGRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l----~~Gr~i~G~L~~~D~~~NlvL~ 41 (98)
..+.+++|++|.|++ .+++.++|+|.++|.. ++.|.
T Consensus 90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 578899999999999 4669999999999874 46664
No 58
>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=92.39 E-value=0.37 Score=29.90 Aligned_cols=36 Identities=28% Similarity=0.489 Sum_probs=29.5
Q ss_pred hhHHhhcCCeEEEEEC---CC-cEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITN---DG-RNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~---~G-r~i~G~L~~~D~~~NlvL~ 41 (98)
..+.+++|+.|.|+++ +| +.+.|.|.++|.. ++.|.
T Consensus 18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l~ 57 (83)
T cd01734 18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTLE 57 (83)
T ss_pred HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEEE
Confidence 4788999999999997 56 6999999999985 35553
No 59
>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=92.04 E-value=0.4 Score=32.45 Aligned_cols=35 Identities=20% Similarity=0.368 Sum_probs=26.9
Q ss_pred hhHHhhcCCeEEEEEC----CCcEEEEEEEEEcCCCceEe
Q 034299 5 PGLESLVEQQISVITN----DGRNIVGVLKGFDQATNIIL 40 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~----~Gr~i~G~L~~~D~~~NlvL 40 (98)
.++.+++|++|.|.++ +.+.+.|+|.++|. ..++|
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 5789999999999994 45799999999998 44555
No 60
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.87 E-value=0.66 Score=32.48 Aligned_cols=37 Identities=14% Similarity=0.323 Sum_probs=32.0
Q ss_pred hhhHHhhcCCeEEEEE----CCCcEEEEEEEEEcCCCceEec
Q 034299 4 GPGLESLVEQQISVIT----NDGRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 4 ~~~L~~~i~k~V~V~l----~~Gr~i~G~L~~~D~~~NlvL~ 41 (98)
...+..++|+.|.|.+ .+++.+.|+|.++|... +++.
T Consensus 91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~~ 131 (153)
T COG0779 91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTLE 131 (153)
T ss_pred HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEEE
Confidence 4578899999999999 78899999999999887 4443
No 61
>PRK14633 hypothetical protein; Provisional
Probab=91.86 E-value=0.44 Score=32.98 Aligned_cols=36 Identities=25% Similarity=0.410 Sum_probs=30.0
Q ss_pred hhHHhhcCCeEEEEE----CCCcEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVIT----NDGRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l----~~Gr~i~G~L~~~D~~~NlvL~ 41 (98)
.++.+++|++|.|++ .+++.++|+|.+++.. ++.|.
T Consensus 87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 578899999999998 3568999999999875 56664
No 62
>PRK14642 hypothetical protein; Provisional
Probab=91.48 E-value=0.43 Score=34.74 Aligned_cols=35 Identities=11% Similarity=0.272 Sum_probs=29.8
Q ss_pred hhHHhhcCCeEEEEEC-------------CCcEEEEEEEEEcCCCceEe
Q 034299 5 PGLESLVEQQISVITN-------------DGRNIVGVLKGFDQATNIIL 40 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~-------------~Gr~i~G~L~~~D~~~NlvL 40 (98)
.++.+++|+.|.|+++ +.+.|.|+|.++|.. ++.|
T Consensus 93 ~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 93 QDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred HHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 5788999999999998 679999999999974 4444
No 63
>PRK14645 hypothetical protein; Provisional
Probab=90.95 E-value=0.51 Score=32.90 Aligned_cols=35 Identities=20% Similarity=0.334 Sum_probs=29.2
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~ 41 (98)
.++.+++|++|.|.+ +++.+.|+|.++|.. .+.|.
T Consensus 95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l~ 129 (154)
T PRK14645 95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTFD 129 (154)
T ss_pred HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEEE
Confidence 478899999999986 789999999999875 35553
No 64
>PRK14636 hypothetical protein; Provisional
Probab=90.95 E-value=0.53 Score=33.52 Aligned_cols=36 Identities=19% Similarity=0.432 Sum_probs=29.7
Q ss_pred hhHHhhcCCeEEEEEC---CC-cEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITN---DG-RNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~---~G-r~i~G~L~~~D~~~NlvL~ 41 (98)
..+.+++|++|.|+++ +| +.++|+|.++|.. ++.|.
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~ 130 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA 130 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence 5788999999999997 55 6999999999874 45553
No 65
>PRK06955 biotin--protein ligase; Provisional
Probab=90.92 E-value=1.5 Score=33.22 Aligned_cols=34 Identities=18% Similarity=0.446 Sum_probs=29.5
Q ss_pred hhcCCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299 9 SLVEQQISVITNDGRNIVGVLKGFDQATNIILDE 42 (98)
Q Consensus 9 ~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~ 42 (98)
-++|++|++...+++.+.|++.++|..+.|+++.
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 3678999997667788999999999999999864
No 66
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=90.37 E-value=0.71 Score=31.84 Aligned_cols=35 Identities=17% Similarity=0.395 Sum_probs=29.1
Q ss_pred hhHHhhcCCeEEEEE----CCCcEEEEEEEEEcCCCceEe
Q 034299 5 PGLESLVEQQISVIT----NDGRNIVGVLKGFDQATNIIL 40 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l----~~Gr~i~G~L~~~D~~~NlvL 40 (98)
..+.+++|+.|.|++ .+++.++|+|.++|... +.|
T Consensus 91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~-i~l 129 (154)
T PRK00092 91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGET-VTL 129 (154)
T ss_pred HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCCE-EEE
Confidence 578899999999997 56789999999999843 444
No 67
>PRK14632 hypothetical protein; Provisional
Probab=90.31 E-value=0.66 Score=32.87 Aligned_cols=36 Identities=22% Similarity=0.346 Sum_probs=29.9
Q ss_pred hhHHhhcCCeEEEEECC-------CcEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITND-------GRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~-------Gr~i~G~L~~~D~~~NlvL~ 41 (98)
..+.+++|+.|.|++++ .+.+.|+|.++|.. ++.|.
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 47889999999999975 57999999999864 46554
No 68
>PRK14643 hypothetical protein; Provisional
Probab=89.78 E-value=0.96 Score=31.85 Aligned_cols=32 Identities=19% Similarity=0.247 Sum_probs=27.7
Q ss_pred hhHHhhcCCeEEEEECC----CcEEEEEEEEEcCCC
Q 034299 5 PGLESLVEQQISVITND----GRNIVGVLKGFDQAT 36 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~----Gr~i~G~L~~~D~~~ 36 (98)
..+..++|++|.|+++. .+.+.|+|.++|...
T Consensus 97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~ 132 (164)
T PRK14643 97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNT 132 (164)
T ss_pred HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCc
Confidence 57889999999999865 589999999999654
No 69
>PRK14634 hypothetical protein; Provisional
Probab=89.57 E-value=0.82 Score=31.83 Aligned_cols=36 Identities=11% Similarity=0.284 Sum_probs=29.4
Q ss_pred hhHHhhcCCeEEEEECC---C-cEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITND---G-RNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~---G-r~i~G~L~~~D~~~NlvL~ 41 (98)
..+.+++|++|.|+++. | +.|.|+|.++|.. ++.|.
T Consensus 93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14634 93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQIN 132 (155)
T ss_pred HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence 57889999999999864 2 7999999999974 46554
No 70
>PRK14646 hypothetical protein; Provisional
Probab=88.97 E-value=0.97 Score=31.47 Aligned_cols=36 Identities=11% Similarity=0.199 Sum_probs=29.5
Q ss_pred hhHHhhcCCeEEEEECC---C-cEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITND---G-RNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~---G-r~i~G~L~~~D~~~NlvL~ 41 (98)
..+.+++|++|.|++++ | +.+.|.|.++|.. ++.|.
T Consensus 93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 57889999999999865 3 6889999999985 46664
No 71
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=88.86 E-value=0.77 Score=32.61 Aligned_cols=32 Identities=13% Similarity=0.300 Sum_probs=26.5
Q ss_pred CCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
..+|.|-|.+|-.+.|.+.+||+|.=+.-.+.
T Consensus 104 k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 104 GEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 46788889999999999999999995554443
No 72
>PRK14647 hypothetical protein; Provisional
Probab=88.44 E-value=1.1 Score=31.24 Aligned_cols=35 Identities=17% Similarity=0.333 Sum_probs=28.6
Q ss_pred hhHHhhcCCeEEEEEC---------CCcEEEEEEEEEcCCCceEe
Q 034299 5 PGLESLVEQQISVITN---------DGRNIVGVLKGFDQATNIIL 40 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~---------~Gr~i~G~L~~~D~~~NlvL 40 (98)
..+.+++|+.|.|+++ +.+.+.|+|.++|.. .+.|
T Consensus 92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~-~v~l 135 (159)
T PRK14647 92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG-VVTI 135 (159)
T ss_pred HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC-EEEE
Confidence 5788999999999995 348999999999963 3444
No 73
>PRK14631 hypothetical protein; Provisional
Probab=87.88 E-value=1.1 Score=31.81 Aligned_cols=36 Identities=19% Similarity=0.233 Sum_probs=29.4
Q ss_pred hhhHHhhcCCeEEEEEC----CCcEEEEEEEEEc--CCCceEe
Q 034299 4 GPGLESLVEQQISVITN----DGRNIVGVLKGFD--QATNIIL 40 (98)
Q Consensus 4 ~~~L~~~i~k~V~V~l~----~Gr~i~G~L~~~D--~~~NlvL 40 (98)
...+.+++|+.|.|+++ +.+.|+|+|.++| . .++.|
T Consensus 109 ~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~-~~v~l 150 (174)
T PRK14631 109 LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLEN-EEIQV 150 (174)
T ss_pred HHHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCC-CEEEE
Confidence 35788999999999995 4599999999998 4 34555
No 74
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=87.67 E-value=1 Score=32.02 Aligned_cols=32 Identities=13% Similarity=0.371 Sum_probs=26.1
Q ss_pred CCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
..+|.|-|.+|-.+.|.+.+||+|.=+.-.+.
T Consensus 24 k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 24 KTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 46778889999999999999999985554443
No 75
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=87.32 E-value=3.2 Score=34.61 Aligned_cols=34 Identities=15% Similarity=0.233 Sum_probs=29.5
Q ss_pred hhcCCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299 9 SLVEQQISVITNDGRNIVGVLKGFDQATNIILDE 42 (98)
Q Consensus 9 ~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~ 42 (98)
-++|++|++...+++++.|+..++|....|+|+.
T Consensus 275 ~~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 275 RDHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred ccCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 3679999987677788999999999999999964
No 76
>PRK14641 hypothetical protein; Provisional
Probab=85.91 E-value=1.6 Score=31.08 Aligned_cols=29 Identities=17% Similarity=0.231 Sum_probs=25.3
Q ss_pred hhHHhhcCCeEEEEECC----CcEEEEEEEEEc
Q 034299 5 PGLESLVEQQISVITND----GRNIVGVLKGFD 33 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~----Gr~i~G~L~~~D 33 (98)
..+.+++|+.|.|++++ .+.+.|+|.++|
T Consensus 97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 46889999999999976 469999999996
No 77
>PRK14637 hypothetical protein; Provisional
Probab=85.89 E-value=1.9 Score=29.93 Aligned_cols=36 Identities=17% Similarity=0.258 Sum_probs=28.2
Q ss_pred hhHHhhcCCeEEEEECCCcEE-EEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITNDGRNI-VGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i-~G~L~~~D~~~NlvL~ 41 (98)
..+.+++|++|.|++.+.+.+ +|+|.++|.. ++.|.
T Consensus 91 ~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 91 AEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 578899999999999444455 7999999875 45554
No 78
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=84.53 E-value=5.8 Score=30.04 Aligned_cols=31 Identities=19% Similarity=0.617 Sum_probs=27.3
Q ss_pred hcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299 10 LVEQQISVITNDGRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~ 41 (98)
++|++|++.. ++..++|++.++|..+.|++.
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 6789999987 456799999999999999996
No 79
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=84.12 E-value=2.1 Score=23.79 Aligned_cols=22 Identities=18% Similarity=0.495 Sum_probs=14.9
Q ss_pred EEEEEEEEcCCCceEecceEEE
Q 034299 25 IVGVLKGFDQATNIILDESHER 46 (98)
Q Consensus 25 i~G~L~~~D~~~NlvL~~~~e~ 46 (98)
.+|++.|+|..+.|.|.+....
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6899999999999999987554
No 80
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=84.07 E-value=2.5 Score=29.78 Aligned_cols=35 Identities=20% Similarity=0.364 Sum_probs=31.6
Q ss_pred hhcCCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299 9 SLVEQQISVITNDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 9 ~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
+.-+-+|+|.+.||.+|.|-+.+|+.--|.+|..+
T Consensus 26 r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~ 60 (165)
T PF03614_consen 26 RFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPD 60 (165)
T ss_pred HhcCCceEEEecCCcEEEEEEeccCcccCEEeccC
Confidence 44578999999999999999999999999999775
No 81
>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=83.57 E-value=7.3 Score=28.29 Aligned_cols=32 Identities=22% Similarity=0.543 Sum_probs=27.4
Q ss_pred hhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299 9 SLVEQQISVITNDGRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 9 ~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~ 41 (98)
.++|++|.+... +..+.|++.++|....|+++
T Consensus 190 ~~~g~~V~v~~~-~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 190 AHIGREVSLTTG-NGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred hccCCeEEEEeC-CcEEEEEEEeECCCceEEEE
Confidence 356999999865 46799999999999999996
No 82
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=82.91 E-value=1.4 Score=31.03 Aligned_cols=24 Identities=33% Similarity=0.495 Sum_probs=21.6
Q ss_pred cCCeEEEEECCCcEEEEEEEEEcC
Q 034299 11 VEQQISVITNDGRNIVGVLKGFDQ 34 (98)
Q Consensus 11 i~k~V~V~l~~Gr~i~G~L~~~D~ 34 (98)
.|+-++|.+.|||+++|.=.|.|.
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccce
Confidence 378999999999999999999883
No 83
>PRK08330 biotin--protein ligase; Provisional
Probab=82.27 E-value=6.9 Score=28.43 Aligned_cols=34 Identities=21% Similarity=0.453 Sum_probs=27.9
Q ss_pred hhcCCeEEEEECCCcEE-EEEEEEEcCCCceEecce
Q 034299 9 SLVEQQISVITNDGRNI-VGVLKGFDQATNIILDES 43 (98)
Q Consensus 9 ~~i~k~V~V~l~~Gr~i-~G~L~~~D~~~NlvL~~~ 43 (98)
.++|++|.+.. ++..+ .|++.++|....|++...
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence 46799999875 56665 799999999999999753
No 84
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=79.94 E-value=7.3 Score=30.90 Aligned_cols=70 Identities=19% Similarity=0.255 Sum_probs=52.8
Q ss_pred HHhhcCCeEEEEECCCcEEEEEEEEEc-CCCceEecceEEEEeec--CCC----eeEEEecEEEEcCCcEEEEEecC
Q 034299 7 LESLVEQQISVITNDGRNIVGVLKGFD-QATNIILDESHERVYST--KEG----VQQLVLGLYIIRGDNISIVGEVD 76 (98)
Q Consensus 7 L~~~i~k~V~V~l~~Gr~i~G~L~~~D-~~~NlvL~~~~e~~~~~--~~~----~~~r~lg~v~irG~~I~~i~~~d 76 (98)
...|||++|.+.-+....|+|.|.-+| +..=|-|.++.-+=+.. +++ .......-++.||+.|.-+...+
T Consensus 4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence 467999999999999999999999999 77788899973332211 111 11225678999999999887765
No 85
>PRK14635 hypothetical protein; Provisional
Probab=78.96 E-value=6.8 Score=27.36 Aligned_cols=36 Identities=11% Similarity=0.169 Sum_probs=28.7
Q ss_pred hhHHhhcCCeEEEEEC--CCcEEEE---EEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITN--DGRNIVG---VLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~--~Gr~i~G---~L~~~D~~~NlvL~ 41 (98)
..+.+++|+.|.|++. ++..+.| .|.++|.. ++.|.
T Consensus 92 ~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~ 132 (162)
T PRK14635 92 EDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE 132 (162)
T ss_pred HHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence 5788999999999975 4678888 99999875 46554
No 86
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=78.41 E-value=5.5 Score=30.10 Aligned_cols=32 Identities=22% Similarity=0.381 Sum_probs=27.8
Q ss_pred hcCCeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299 10 LVEQQISVITNDGRNIVGVLKGFDQATNIILDE 42 (98)
Q Consensus 10 ~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~ 42 (98)
++|++|.|.. ++..+.|++.++|..+.|++..
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 4799999875 6789999999999999999864
No 87
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=76.73 E-value=15 Score=27.16 Aligned_cols=36 Identities=17% Similarity=0.369 Sum_probs=32.4
Q ss_pred HhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299 8 ESLVEQQISVITNDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 8 ~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
...+|++|++...++..+.|+..++|.+..++|+..
T Consensus 186 ~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 186 SLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred hccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 445899999999999999999999999999999876
No 88
>PRK14630 hypothetical protein; Provisional
Probab=75.93 E-value=6.9 Score=26.85 Aligned_cols=35 Identities=9% Similarity=0.175 Sum_probs=27.8
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEec
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILD 41 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~ 41 (98)
.++.+++|++|.|++.. ....|+|.++|.. ++.|.
T Consensus 90 ~df~r~~G~~v~V~l~~-~~~~G~L~~~~d~-~i~l~ 124 (143)
T PRK14630 90 REFKIFEGKKIKLMLDN-DFEEGFILEAKAD-SFIFK 124 (143)
T ss_pred HHHHHhCCCEEEEEEcC-cceEEEEEEEeCC-EEEEE
Confidence 57889999999999965 4459999999874 45554
No 89
>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=75.75 E-value=4.6 Score=26.32 Aligned_cols=19 Identities=21% Similarity=0.489 Sum_probs=14.9
Q ss_pred CCeEEEEECCCcEEEEEEE
Q 034299 12 EQQISVITNDGRNIVGVLK 30 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~ 30 (98)
..+|.+.|+||+.+.|++-
T Consensus 28 e~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 28 EERVELELDDGSMLRGTVA 46 (101)
T ss_dssp T-EEEEEETTS-EEEEEEC
T ss_pred cceEEEEEcCCCeeeeeec
Confidence 3689999999999999973
No 90
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=67.87 E-value=7 Score=28.24 Aligned_cols=43 Identities=21% Similarity=0.214 Sum_probs=35.7
Q ss_pred CCChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceE
Q 034299 1 MSGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESH 44 (98)
Q Consensus 1 m~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~ 44 (98)
|.| +...-.+|..|.|..-+|....|.+.+||-..++..-++.
T Consensus 1 m~p-~s~~vavg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 1 MKP-ASATVAVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred CCC-CcceeEEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 444 3455567889999999999999999999988888877776
No 91
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=66.34 E-value=31 Score=23.88 Aligned_cols=28 Identities=14% Similarity=0.324 Sum_probs=25.0
Q ss_pred hHHhhcCCeEEEEECCCcEEEEEEEEEc
Q 034299 6 GLESLVEQQISVITNDGRNIVGVLKGFD 33 (98)
Q Consensus 6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D 33 (98)
....++||.|.+...+|..+.|+..++.
T Consensus 86 ~a~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 86 KYSELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 3467999999999999999999999986
No 92
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=65.59 E-value=19 Score=22.32 Aligned_cols=28 Identities=36% Similarity=0.477 Sum_probs=21.4
Q ss_pred hhHHhhcCCeEEEEECCCc----EEEEEEEEE
Q 034299 5 PGLESLVEQQISVITNDGR----NIVGVLKGF 32 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr----~i~G~L~~~ 32 (98)
..|.+++|++|.++.+.|| +-.|.|...
T Consensus 10 ~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 10 KELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 4789999999999999996 678888764
No 93
>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=64.24 E-value=16 Score=24.22 Aligned_cols=29 Identities=21% Similarity=0.344 Sum_probs=21.9
Q ss_pred eEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299 14 QISVITNDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 14 ~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
...|.++||+++.|.+..=| ...+.|.++
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~-~~~~~l~~~ 87 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET-ADGVTVKMP 87 (133)
T ss_pred cEEEEECCCCEEEEEEEecC-CCeEEEEcC
Confidence 47899999999999988844 334555554
No 94
>PRK10898 serine endoprotease; Provisional
Probab=64.21 E-value=17 Score=28.17 Aligned_cols=31 Identities=32% Similarity=0.396 Sum_probs=26.9
Q ss_pred CeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299 13 QQISVITNDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 13 k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
..+.|.+.||+.+.+++.++|...+|-|=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 5789999999999999999999988865444
No 95
>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=62.96 E-value=18 Score=27.92 Aligned_cols=31 Identities=32% Similarity=0.393 Sum_probs=26.9
Q ss_pred CeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299 13 QQISVITNDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 13 k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
..+.|.+.||+.+.+++.++|...++-|=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4689999999999999999999998877443
No 96
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=60.76 E-value=4.9 Score=27.82 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=19.0
Q ss_pred CCCcEEEEEEEEEcCCCceEecce
Q 034299 20 NDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 20 ~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
+..-.=.|+|.|.|+|.|=..+|-
T Consensus 40 rtd~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 40 RTDDHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred hcccccceeeeeecccccchhccc
Confidence 334445799999999999888876
No 97
>PRK08477 biotin--protein ligase; Provisional
Probab=59.45 E-value=32 Score=24.96 Aligned_cols=36 Identities=11% Similarity=0.037 Sum_probs=30.1
Q ss_pred hhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEE
Q 034299 9 SLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHE 45 (98)
Q Consensus 9 ~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e 45 (98)
-.+++.|+|. .+++.++|+..+.|.++-|+++.-.-
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 57899999999999999999877543
No 98
>PRK10942 serine endoprotease; Provisional
Probab=58.59 E-value=23 Score=28.70 Aligned_cols=30 Identities=30% Similarity=0.407 Sum_probs=26.5
Q ss_pred CeEEEEECCCcEEEEEEEEEcCCCceEecc
Q 034299 13 QQISVITNDGRNIVGVLKGFDQATNIILDE 42 (98)
Q Consensus 13 k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~ 42 (98)
..+.|.+.||+++.+++.++|...++-|=.
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlk 165 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQ 165 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEE
Confidence 578999999999999999999998886643
No 99
>PRK10139 serine endoprotease; Provisional
Probab=56.60 E-value=27 Score=28.16 Aligned_cols=31 Identities=39% Similarity=0.493 Sum_probs=26.8
Q ss_pred CeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299 13 QQISVITNDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 13 k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
.++.|.+.||+++.+++.++|....|-+=..
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 5889999999999999999999888766433
No 100
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=56.13 E-value=7.3 Score=25.28 Aligned_cols=17 Identities=29% Similarity=0.419 Sum_probs=15.5
Q ss_pred EEEEEEcCCCceEecce
Q 034299 27 GVLKGFDQATNIILDES 43 (98)
Q Consensus 27 G~L~~~D~~~NlvL~~~ 43 (98)
|+|+|.|.++|...++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999998776
No 101
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=53.69 E-value=16 Score=26.16 Aligned_cols=34 Identities=24% Similarity=0.401 Sum_probs=28.5
Q ss_pred hhcCCeEEEEECCC----cEEEEEEEEEcCCCceEecc
Q 034299 9 SLVEQQISVITNDG----RNIVGVLKGFDQATNIILDE 42 (98)
Q Consensus 9 ~~i~k~V~V~l~~G----r~i~G~L~~~D~~~NlvL~~ 42 (98)
.|.+-.+.+...|| +.-.|+++.-|+..|++|+.
T Consensus 141 eyPDGTvk~vy~dG~qet~y~~gr~r~kd~~g~~~~d~ 178 (179)
T PF07202_consen 141 EYPDGTVKTVYPDGRQETRYASGRVRIKDKDGNVIMDT 178 (179)
T ss_pred EcCCCCEEEEecCCCEEEEeCCCcEEEecCCCCEEecC
Confidence 46778888888898 56679999999999999863
No 102
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=52.93 E-value=14 Score=23.04 Aligned_cols=54 Identities=20% Similarity=0.206 Sum_probs=25.1
Q ss_pred cCCeEEEEECCCcEEEEEEEEEcCCCceEec-ceEEEEeecCCCeeEEEecEEEEcCCcEEEEEecC
Q 034299 11 VEQQISVITNDGRNIVGVLKGFDQATNIILD-ESHERVYSTKEGVQQLVLGLYIIRGDNISIVGEVD 76 (98)
Q Consensus 11 i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~-~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~~d 76 (98)
-+.+|+++|+||..+.|+- .| +..+ +-.|+..-. ..-+...||=+.|..+.+..
T Consensus 16 ~~~~v~L~l~dG~~~~g~A--~d----t~~~~~k~E~L~l~------~~~~~~~i~Ld~I~~~~al~ 70 (80)
T PF07073_consen 16 YRYPVKLTLKDGEQIEGKA--LD----TRTNAKKEECLVLE------QDGGEQEIRLDQIASMSALT 70 (80)
T ss_dssp TTT-EEEE-TTT--EEESS---E----EE---SSS-EEEEE------ETTEEEEESTT--SEEE---
T ss_pred cCCeEEEEEeCCCEEEEEE--EE----EEEecCceEEEEEe------cCCcEEEEEhhheeeeeecC
Confidence 4689999999999999972 22 2222 223333211 11245568888888887653
No 103
>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=48.88 E-value=41 Score=26.48 Aligned_cols=31 Identities=32% Similarity=0.432 Sum_probs=27.0
Q ss_pred CeEEEEECCCcEEEEEEEEEcCCCceEecce
Q 034299 13 QQISVITNDGRNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 13 k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~ 43 (98)
..+.|.+.||+.+.+++.++|...++-|=..
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 5788999999999999999999988876544
No 104
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=47.07 E-value=43 Score=27.14 Aligned_cols=45 Identities=20% Similarity=0.216 Sum_probs=37.1
Q ss_pred CChhhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEE
Q 034299 2 SGGPGLESLVEQQISVITNDGRNIVGVLKGFDQATNIILDESHERV 47 (98)
Q Consensus 2 ~~~~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~ 47 (98)
+|...+++++||.|+- -++|++.+++|.+=|.-.-+-+.+-.|..
T Consensus 72 s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~ 116 (421)
T COG5316 72 SPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVL 116 (421)
T ss_pred CchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEE
Confidence 5667899999999998 89999999999999987766666665544
No 105
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=45.53 E-value=49 Score=22.84 Aligned_cols=26 Identities=15% Similarity=0.353 Sum_probs=23.0
Q ss_pred HhhcCCeEEEEECCCcEEEEEEEEEc
Q 034299 8 ESLVEQQISVITNDGRNIVGVLKGFD 33 (98)
Q Consensus 8 ~~~i~k~V~V~l~~Gr~i~G~L~~~D 33 (98)
..++||.|.....+|..+.|++.++.
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~ 114 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQ 114 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEE
Confidence 47899999988899999999999776
No 106
>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=45.10 E-value=32 Score=22.15 Aligned_cols=24 Identities=33% Similarity=0.566 Sum_probs=20.4
Q ss_pred HhhcCCeEEEE-ECCCcEEEEEEEE
Q 034299 8 ESLVEQQISVI-TNDGRNIVGVLKG 31 (98)
Q Consensus 8 ~~~i~k~V~V~-l~~Gr~i~G~L~~ 31 (98)
.-.+|..|+|. +.+|+++.|+..+
T Consensus 92 ~g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 92 DGAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred ccCCCCEEEEEECCCCCEEEEEEeC
Confidence 45678999999 7999999998875
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=44.45 E-value=35 Score=25.57 Aligned_cols=22 Identities=32% Similarity=0.327 Sum_probs=18.7
Q ss_pred EEEEEEEEEcCCCceEecceEE
Q 034299 24 NIVGVLKGFDQATNIILDESHE 45 (98)
Q Consensus 24 ~i~G~L~~~D~~~NlvL~~~~e 45 (98)
.+.|.+.-+|.|.|++++=..+
T Consensus 169 ~i~g~Vi~iD~FGNlitnI~~~ 190 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNISRE 190 (258)
T ss_dssp EEEEEEEEEETTSEEEEEEEHH
T ss_pred eEEEEEEEECccCCeeeCCCHH
Confidence 8999999999999999765433
No 108
>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=42.79 E-value=57 Score=17.78 Aligned_cols=25 Identities=16% Similarity=0.157 Sum_probs=21.1
Q ss_pred cCCeEEEEECCCcEEEEEEEEEcCC
Q 034299 11 VEQQISVITNDGRNIVGVLKGFDQA 35 (98)
Q Consensus 11 i~k~V~V~l~~Gr~i~G~L~~~D~~ 35 (98)
.|..+.+...+|..+.|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4677777778999999999999964
No 109
>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=42.31 E-value=68 Score=20.37 Aligned_cols=14 Identities=14% Similarity=0.392 Sum_probs=12.1
Q ss_pred hhHHhhcCCeEEEE
Q 034299 5 PGLESLVEQQISVI 18 (98)
Q Consensus 5 ~~L~~~i~k~V~V~ 18 (98)
+.|.+|+|++|++.
T Consensus 8 ~~L~~f~gk~V~iv 21 (101)
T cd04479 8 AMLSQFVGKTVRIV 21 (101)
T ss_pred HHHHhhCCCEEEEE
Confidence 57999999999865
No 110
>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=38.49 E-value=25 Score=21.31 Aligned_cols=24 Identities=21% Similarity=0.315 Sum_probs=20.0
Q ss_pred hcCCeEEEEECCCcEEEEEEEEEc
Q 034299 10 LVEQQISVITNDGRNIVGVLKGFD 33 (98)
Q Consensus 10 ~i~k~V~V~l~~Gr~i~G~L~~~D 33 (98)
|-..++.|+|-||..+.+++.+-|
T Consensus 2 ~~~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 2 YTETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred CcEEEEEEECCCCCEEEEEeCCCC
Confidence 445789999999999999987654
No 111
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.40 E-value=41 Score=21.14 Aligned_cols=20 Identities=15% Similarity=0.496 Sum_probs=17.3
Q ss_pred hhHHhhcCCeEEEEECCCcE
Q 034299 5 PGLESLVEQQISVITNDGRN 24 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~ 24 (98)
..+...+|++|.++..+||.
T Consensus 12 ~~i~ah~G~~v~lk~ngGRK 31 (80)
T COG4466 12 ESIDAHLGERVTLKANGGRK 31 (80)
T ss_pred HHHHhccCcEEEEEecCCce
Confidence 46778899999999999975
No 112
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=37.10 E-value=44 Score=24.43 Aligned_cols=24 Identities=33% Similarity=0.563 Sum_probs=20.8
Q ss_pred HhhcCCeEEEE-ECCCcEEEEEEEE
Q 034299 8 ESLVEQQISVI-TNDGRNIVGVLKG 31 (98)
Q Consensus 8 ~~~i~k~V~V~-l~~Gr~i~G~L~~ 31 (98)
.-.+|..|+|+ +.+|+++.|+..+
T Consensus 203 ~G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 203 DGAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCCeEEEEECCCCCEEEEEEeC
Confidence 45689999999 9999999999875
No 113
>PRK06630 hypothetical protein; Provisional
Probab=37.10 E-value=21 Score=23.39 Aligned_cols=19 Identities=16% Similarity=0.065 Sum_probs=16.9
Q ss_pred EEEEEEEEcCCCceEecce
Q 034299 25 IVGVLKGFDQATNIILDES 43 (98)
Q Consensus 25 i~G~L~~~D~~~NlvL~~~ 43 (98)
..|+|.|.|+++|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4799999999999998874
No 114
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=36.62 E-value=30 Score=21.19 Aligned_cols=19 Identities=16% Similarity=0.207 Sum_probs=15.0
Q ss_pred hHHhhcCCeEEEEECCCcE
Q 034299 6 GLESLVEQQISVITNDGRN 24 (98)
Q Consensus 6 ~L~~~i~k~V~V~l~~Gr~ 24 (98)
.++..+||+|+|++....+
T Consensus 5 ~~nDrLGKKVRvKCn~dDt 23 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDT 23 (73)
T ss_pred hhhhhcCceEEEEeCCccc
Confidence 5788999999999865443
No 115
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=36.26 E-value=36 Score=20.43 Aligned_cols=23 Identities=17% Similarity=0.300 Sum_probs=19.3
Q ss_pred CCeEEEEECCCcEEEEEEEEEcC
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQ 34 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~ 34 (98)
..+|.|++-||..+.++|..-|.
T Consensus 4 ~~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 4 QCRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred eEEEEEEcCCCCEEEEEeCCCCc
Confidence 46899999999999999986553
No 116
>PRK11625 Rho-binding antiterminator; Provisional
Probab=34.92 E-value=76 Score=19.99 Aligned_cols=52 Identities=15% Similarity=0.124 Sum_probs=32.3
Q ss_pred cCCeEEEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299 11 VEQQISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 11 i~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
-+.++.++++||..+.|+- .|=+ ..+-.|+..-...+ +.-.||=+.|++++.
T Consensus 22 ~~~~l~l~l~dGe~~~g~A--~D~~----~~~k~EyL~l~~~g------~~~~iRLD~I~s~~~ 73 (84)
T PRK11625 22 HHLMLTLELKDGEVLQAKA--SDLV----SRKNVEYLVVEAAG------ETRELRLDKIASFSH 73 (84)
T ss_pred cCCeEEEEECCCCEEEEEE--Eeee----cCCceEEEEEEcCC------CEEEEEeeeEeeccC
Confidence 4688999999999999986 3433 33555655322111 234566666666653
No 117
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=34.55 E-value=66 Score=23.62 Aligned_cols=31 Identities=3% Similarity=0.052 Sum_probs=23.7
Q ss_pred CCeEEEE---ECCCcEEEEEEEEEcCCCceEecc
Q 034299 12 EQQISVI---TNDGRNIVGVLKGFDQATNIILDE 42 (98)
Q Consensus 12 ~k~V~V~---l~~Gr~i~G~L~~~D~~~NlvL~~ 42 (98)
++.+.+. ..++..+.|++.++|..+.|+++.
T Consensus 198 ~~~~~~~~~~~~~~~~~~G~~~gId~~G~Lvv~~ 231 (245)
T PTZ00276 198 DKSLKLHKRTPTGRDPEELTALSLNEWGHLIVRR 231 (245)
T ss_pred hhhhccCeEEEcCCcEEEEEEEEECCCCeEEEEE
Confidence 5554432 246788999999999999999975
No 118
>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=34.23 E-value=49 Score=19.64 Aligned_cols=23 Identities=22% Similarity=0.190 Sum_probs=19.1
Q ss_pred CCeEEEEECCCcEEEEEEEEEcC
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQ 34 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~ 34 (98)
..+|.|++-||..+..++..-|.
T Consensus 6 ~~~I~vRlpdG~~l~~~F~~~~t 28 (82)
T PF00789_consen 6 VVRIQVRLPDGSRLQRRFPKSDT 28 (82)
T ss_dssp EEEEEEEETTSTEEEEEEETTSB
T ss_pred EEEEEEECCCCCEEEEEECCcch
Confidence 35789999999999999986554
No 119
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=33.88 E-value=80 Score=22.96 Aligned_cols=26 Identities=15% Similarity=0.431 Sum_probs=22.9
Q ss_pred HhhcCCeEEEEECCCcEEEEEEEEEc
Q 034299 8 ESLVEQQISVITNDGRNIVGVLKGFD 33 (98)
Q Consensus 8 ~~~i~k~V~V~l~~Gr~i~G~L~~~D 33 (98)
..|+||.|.+.-.+|..+.|++.++.
T Consensus 114 ~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 114 MKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 47899999988889999999998775
No 120
>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=32.96 E-value=49 Score=19.61 Aligned_cols=22 Identities=14% Similarity=0.294 Sum_probs=18.3
Q ss_pred CeEEEEECCCcEEEEEEEEEcC
Q 034299 13 QQISVITNDGRNIVGVLKGFDQ 34 (98)
Q Consensus 13 k~V~V~l~~Gr~i~G~L~~~D~ 34 (98)
.+|.|++-||..+.++|..-|.
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~t 24 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTHK 24 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCCC
Confidence 5789999999999999875543
No 121
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=32.43 E-value=77 Score=22.74 Aligned_cols=28 Identities=18% Similarity=0.362 Sum_probs=23.5
Q ss_pred hHHhhcCCeEEEEECCCcEEEEEEEEEc
Q 034299 6 GLESLVEQQISVITNDGRNIVGVLKGFD 33 (98)
Q Consensus 6 ~L~~~i~k~V~V~l~~Gr~i~G~L~~~D 33 (98)
.+..++|++|.|.+..-+.+.|.+..++
T Consensus 22 ~~~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 22 DLKDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp -CGGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred ChhHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 4567999999999998899999998885
No 122
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=30.96 E-value=50 Score=18.53 Aligned_cols=13 Identities=38% Similarity=0.501 Sum_probs=11.1
Q ss_pred hHHhhcCCeEEEE
Q 034299 6 GLESLVEQQISVI 18 (98)
Q Consensus 6 ~L~~~i~k~V~V~ 18 (98)
.+++++||+|+|.
T Consensus 13 ~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 13 YLKSLLGKRVSVT 25 (48)
T ss_pred HHHHhcCCeEEEE
Confidence 5777999999986
No 123
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=30.04 E-value=1e+02 Score=20.08 Aligned_cols=29 Identities=14% Similarity=0.150 Sum_probs=23.5
Q ss_pred hhHHhhcCCeEEEEECC-CcEEEEEEEEEc
Q 034299 5 PGLESLVEQQISVITND-GRNIVGVLKGFD 33 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~-Gr~i~G~L~~~D 33 (98)
..-+.|+|++|.-+-+. |+.+.|++.-.-
T Consensus 39 ~eA~~y~gk~v~yk~~~~G~Vi~G~V~R~H 68 (100)
T COG2451 39 EEAQFYLGKRVCYKYRSSGRVIKGKVVRTH 68 (100)
T ss_pred HHHHhhhccEEEEEeCCCCcEEEEEEEEec
Confidence 45578999998888877 999999987554
No 124
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=29.77 E-value=56 Score=23.09 Aligned_cols=19 Identities=21% Similarity=0.153 Sum_probs=16.7
Q ss_pred EEEEEEEcCCCceEecceE
Q 034299 26 VGVLKGFDQATNIILDESH 44 (98)
Q Consensus 26 ~G~L~~~D~~~NlvL~~~~ 44 (98)
.|+|+|.|++.|-.-++..
T Consensus 48 ~G~lVG~D~~GNkYYE~~~ 66 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKLG 66 (159)
T ss_pred CcEEEEecCCCCeeeecCC
Confidence 4999999999999988763
No 125
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.75 E-value=71 Score=23.34 Aligned_cols=24 Identities=17% Similarity=0.374 Sum_probs=20.1
Q ss_pred HhhcCCeEEEE-ECCCcEEEEEEEE
Q 034299 8 ESLVEQQISVI-TNDGRNIVGVLKG 31 (98)
Q Consensus 8 ~~~i~k~V~V~-l~~Gr~i~G~L~~ 31 (98)
.-..|..|+|+ +.+|+++.|+..+
T Consensus 182 ~G~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 182 DAGENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCCCEEEEEECCCCCEEEEEEeC
Confidence 34578999999 7999999999764
No 126
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=29.31 E-value=1.2e+02 Score=19.34 Aligned_cols=35 Identities=11% Similarity=0.172 Sum_probs=28.2
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEcCCCceE
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFDQATNII 39 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D~~~Nlv 39 (98)
.+-..|+||++.-..+.|+.+-|.+.---..-..+
T Consensus 33 ~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvV 67 (87)
T PRK04337 33 EEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEV 67 (87)
T ss_pred HHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceE
Confidence 34567999999999999999999988766655555
No 127
>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=28.91 E-value=1.3e+02 Score=17.61 Aligned_cols=27 Identities=11% Similarity=0.126 Sum_probs=18.8
Q ss_pred hcCCeEEEEECCC-cEEEEEEEEEcCCC
Q 034299 10 LVEQQISVITNDG-RNIVGVLKGFDQAT 36 (98)
Q Consensus 10 ~i~k~V~V~l~~G-r~i~G~L~~~D~~~ 36 (98)
-.|..|.+.--+. ..|.|.+.+||.-.
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 4688999998665 56799999999643
No 128
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.62 E-value=81 Score=21.89 Aligned_cols=23 Identities=17% Similarity=0.234 Sum_probs=19.4
Q ss_pred hhcCCeEEEE-ECCCcEEEEEEEE
Q 034299 9 SLVEQQISVI-TNDGRNIVGVLKG 31 (98)
Q Consensus 9 ~~i~k~V~V~-l~~Gr~i~G~L~~ 31 (98)
-..|..|+|+ +.+|+.+.|+..+
T Consensus 128 G~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 128 GAAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4678999999 8999999998764
No 129
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=27.94 E-value=47 Score=22.24 Aligned_cols=18 Identities=28% Similarity=0.329 Sum_probs=16.2
Q ss_pred EEEEEEEcCCCceEecce
Q 034299 26 VGVLKGFDQATNIILDES 43 (98)
Q Consensus 26 ~G~L~~~D~~~NlvL~~~ 43 (98)
.|+|+|.|+++|-.-++.
T Consensus 9 ~g~lVG~D~~GNkYYE~~ 26 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENP 26 (115)
T ss_pred cceEeEEcCCCCeeeEcC
Confidence 699999999999998875
No 130
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=27.71 E-value=1e+02 Score=18.60 Aligned_cols=23 Identities=17% Similarity=0.333 Sum_probs=17.4
Q ss_pred hcCCeEEEEECCCcEEEEEEEEE
Q 034299 10 LVEQQISVITNDGRNIVGVLKGF 32 (98)
Q Consensus 10 ~i~k~V~V~l~~Gr~i~G~L~~~ 32 (98)
+-+...+|.|-||.++.+.+.|=
T Consensus 15 L~~~~f~V~l~ng~~vla~i~GK 37 (68)
T TIGR00008 15 LPNAMFRVELENGHEVLAHISGK 37 (68)
T ss_pred CCCCEEEEEECCCCEEEEEecCc
Confidence 44678888888888888877663
No 131
>PF13437 HlyD_3: HlyD family secretion protein
Probab=27.70 E-value=1.5e+02 Score=18.03 Aligned_cols=32 Identities=16% Similarity=0.317 Sum_probs=24.2
Q ss_pred ChhhHHhh--cCCeEEEEECCC--cEEEEEEEEEcC
Q 034299 3 GGPGLESL--VEQQISVITNDG--RNIVGVLKGFDQ 34 (98)
Q Consensus 3 ~~~~L~~~--i~k~V~V~l~~G--r~i~G~L~~~D~ 34 (98)
|..++... .|.++.+.+.++ ..+.|++..++.
T Consensus 43 ~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 43 PEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred ChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 34455554 688999998755 689999998887
No 132
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.78 E-value=1.5e+02 Score=22.45 Aligned_cols=29 Identities=28% Similarity=0.505 Sum_probs=24.0
Q ss_pred CCeEEEEECCCcEEEEEEEEEcCCCceEe
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQATNIIL 40 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~~~NlvL 40 (98)
..++.+.+.||+++.+.+.++|...-+-+
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlav 123 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAV 123 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEE
Confidence 46788889999999999999997665544
No 133
>PRK08183 NADH dehydrogenase; Validated
Probab=25.07 E-value=40 Score=23.08 Aligned_cols=19 Identities=21% Similarity=0.165 Sum_probs=16.4
Q ss_pred EEEEEEEcCCCceEecceE
Q 034299 26 VGVLKGFDQATNIILDESH 44 (98)
Q Consensus 26 ~G~L~~~D~~~NlvL~~~~ 44 (98)
.|+|+|.|++.|-.-++..
T Consensus 25 ~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cCeEeEecCCCCeeeecCC
Confidence 6999999999999987653
No 134
>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=24.89 E-value=1.2e+02 Score=19.99 Aligned_cols=26 Identities=8% Similarity=0.197 Sum_probs=21.6
Q ss_pred ChhhHHhhcCCeEEEEECCCcEEEEE
Q 034299 3 GGPGLESLVEQQISVITNDGRNIVGV 28 (98)
Q Consensus 3 ~~~~L~~~i~k~V~V~l~~Gr~i~G~ 28 (98)
+...|....+-.|..++.+|++|.+.
T Consensus 65 ~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 65 DVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CHHHHhCCcccEEEEEecCCcEEEec
Confidence 34678888899999999999998764
No 135
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.86 E-value=1.2e+02 Score=22.08 Aligned_cols=24 Identities=4% Similarity=0.063 Sum_probs=20.7
Q ss_pred HhhcCCeEEEEECCCcEEEEEEEE
Q 034299 8 ESLVEQQISVITNDGRNIVGVLKG 31 (98)
Q Consensus 8 ~~~i~k~V~V~l~~Gr~i~G~L~~ 31 (98)
...+|..|+|+-.+|+++.|+..+
T Consensus 192 ~G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 192 DGNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred cCCCCCEEEEEeCCCCEEEEEEec
Confidence 456789999999999999999875
No 136
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.59 E-value=1.1e+02 Score=20.80 Aligned_cols=23 Identities=17% Similarity=0.290 Sum_probs=19.1
Q ss_pred hhcCCeEEEE-ECCCcEEEEEEEE
Q 034299 9 SLVEQQISVI-TNDGRNIVGVLKG 31 (98)
Q Consensus 9 ~~i~k~V~V~-l~~Gr~i~G~L~~ 31 (98)
-..|..|+|+ +.+||++.|+..+
T Consensus 109 G~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 109 GGVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4578899996 7899999998765
No 137
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=22.78 E-value=1.5e+02 Score=18.96 Aligned_cols=24 Identities=17% Similarity=0.252 Sum_probs=18.1
Q ss_pred hhcCCeEEEEECCCcEEEEEEEEE
Q 034299 9 SLVEQQISVITNDGRNIVGVLKGF 32 (98)
Q Consensus 9 ~~i~k~V~V~l~~Gr~i~G~L~~~ 32 (98)
.+-+-..+|+|.||.++.+.+.|=
T Consensus 16 ~Lp~~~frV~LenG~~vla~isGK 39 (87)
T PRK12442 16 VLPDSRFRVTLENGVEVGAYASGR 39 (87)
T ss_pred ECCCCEEEEEeCCCCEEEEEeccc
Confidence 344678888999988888877664
No 138
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=22.56 E-value=1.7e+02 Score=17.03 Aligned_cols=33 Identities=15% Similarity=0.268 Sum_probs=23.3
Q ss_pred cCCeEEEEECCC----cEEEEEEEEEcCCCceEecce
Q 034299 11 VEQQISVITNDG----RNIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 11 i~k~V~V~l~~G----r~i~G~L~~~D~~~NlvL~~~ 43 (98)
+|.++.+++.++ ..+.-++.+++..-.+.++--
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 588999988443 359999999999877777544
No 139
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=22.55 E-value=1.5e+02 Score=23.89 Aligned_cols=30 Identities=30% Similarity=0.513 Sum_probs=24.8
Q ss_pred hhHHhhcCCeEEEEEC--CC--cEEEEEEEEEcC
Q 034299 5 PGLESLVEQQISVITN--DG--RNIVGVLKGFDQ 34 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~--~G--r~i~G~L~~~D~ 34 (98)
..+.+++|+++.|.+. +| |.|.|.+.++..
T Consensus 40 l~~~~llG~~v~l~i~~~~~~~r~f~GiVt~~~~ 73 (513)
T TIGR03361 40 IDLEDLLGQPATLTLGRDGGGPRYFHGIVTRFEQ 73 (513)
T ss_pred CCHHHHcCCeEEEEEEeCCCceEEEEEEEEEEEE
Confidence 4688999999999995 33 789999999863
No 140
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.27 E-value=1.2e+02 Score=22.93 Aligned_cols=24 Identities=21% Similarity=0.332 Sum_probs=20.4
Q ss_pred HhhcCCeEEEE-ECCCcEEEEEEEE
Q 034299 8 ESLVEQQISVI-TNDGRNIVGVLKG 31 (98)
Q Consensus 8 ~~~i~k~V~V~-l~~Gr~i~G~L~~ 31 (98)
.-..|..|+|+ +.+|+++.|+..+
T Consensus 229 ~G~~Gd~IrVrN~~SgkvV~a~V~~ 253 (261)
T PRK06804 229 NGRKGELIKVKNLSSGRVVTATVDG 253 (261)
T ss_pred CCCCCCEEEEEECCCCCEEEEEEec
Confidence 34678999999 8999999999875
No 141
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=22.16 E-value=86 Score=20.46 Aligned_cols=20 Identities=25% Similarity=0.581 Sum_probs=8.8
Q ss_pred EEEEEEEEEcCCCceEecce
Q 034299 24 NIVGVLKGFDQATNIILDES 43 (98)
Q Consensus 24 ~i~G~L~~~D~~~NlvL~~~ 43 (98)
++.|++.+||-..++.|++|
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 56788888876667777776
No 142
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=22.08 E-value=1.4e+02 Score=21.44 Aligned_cols=66 Identities=12% Similarity=0.002 Sum_probs=47.7
Q ss_pred hhHHhhcCCeEEEE-ECCCcEEEEEEEEEcCCCceEecceEEEEeecCCC------eeEEEecEEEEcCCcEEE
Q 034299 5 PGLESLVEQQISVI-TNDGRNIVGVLKGFDQATNIILDESHERVYSTKEG------VQQLVLGLYIIRGDNISI 71 (98)
Q Consensus 5 ~~L~~~i~k~V~V~-l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~------~~~r~lg~v~irG~~I~~ 71 (98)
.+++++...+-... +.++++..+-..+.|.-.||++--+.+.-. ++++ ...+..|...+.|..|..
T Consensus 43 ~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp-~s~s~~~v~ag~~~g~G~ar~~Grgip~ 115 (177)
T KOG3168|consen 43 QDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPP-PSDSFRRVPAGAARGPGIARVAGRGIPS 115 (177)
T ss_pred HHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCC-CccccccccccccCCcccccccCCCccC
Confidence 35566666666666 889999999999999999999887766432 1111 134456777888888776
No 143
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=21.41 E-value=95 Score=18.85 Aligned_cols=23 Identities=17% Similarity=0.342 Sum_probs=18.5
Q ss_pred CCeEEEEECCCcEEEEEEEEEcC
Q 034299 12 EQQISVITNDGRNIVGVLKGFDQ 34 (98)
Q Consensus 12 ~k~V~V~l~~Gr~i~G~L~~~D~ 34 (98)
..+|.|.|-||..+..+|..-|.
T Consensus 4 ~t~iqiRlpdG~r~~~rF~~~~t 26 (79)
T cd01770 4 TTSIQIRLADGKRLVQKFNSSHR 26 (79)
T ss_pred eeEEEEECCCCCEEEEEeCCCCc
Confidence 36899999999999988765543
No 144
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=21.32 E-value=86 Score=18.11 Aligned_cols=13 Identities=15% Similarity=0.291 Sum_probs=10.9
Q ss_pred HhhcCCeEEEEEC
Q 034299 8 ESLVEQQISVITN 20 (98)
Q Consensus 8 ~~~i~k~V~V~l~ 20 (98)
.+|+|+|+.|...
T Consensus 38 K~yiG~rv~viI~ 50 (52)
T COG3466 38 KRYIGKRVYVIIL 50 (52)
T ss_pred hHHcCcEEEEEEe
Confidence 6899999998754
No 145
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=21.02 E-value=1.2e+02 Score=24.04 Aligned_cols=25 Identities=28% Similarity=0.518 Sum_probs=21.7
Q ss_pred HHhhcCCeEEEEECCCcEEEEEEEE
Q 034299 7 LESLVEQQISVITNDGRNIVGVLKG 31 (98)
Q Consensus 7 L~~~i~k~V~V~l~~Gr~i~G~L~~ 31 (98)
-.-+.+++|+|...+|+.+.|++-.
T Consensus 92 ~~~~~gq~v~i~t~~g~~i~GvIg~ 116 (355)
T COG1363 92 PQVLEGQRVTIHTDKGKKIRGVIGS 116 (355)
T ss_pred hhhccCcEEEEEeCCCcEEeeeEcc
Confidence 3457899999999999999999983
No 146
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=20.73 E-value=2.4e+02 Score=17.88 Aligned_cols=21 Identities=19% Similarity=0.471 Sum_probs=15.2
Q ss_pred hhHHhhcCCeEEEEECCCcEEEEEEEEEc
Q 034299 5 PGLESLVEQQISVITNDGRNIVGVLKGFD 33 (98)
Q Consensus 5 ~~L~~~i~k~V~V~l~~Gr~i~G~L~~~D 33 (98)
..|.+|.|+.|++. |++.++|
T Consensus 11 ~~L~~~~gk~Vriv--------Gkv~~~~ 31 (109)
T PF08661_consen 11 SMLSQFVGKTVRIV--------GKVESVD 31 (109)
T ss_dssp GGGGGGTTSEEEEE--------EEEEEE-
T ss_pred HHHHhhCCCeEEEE--------EEEeeEc
Confidence 57899999999864 5555555
No 147
>PRK10708 hypothetical protein; Provisional
Probab=20.61 E-value=1.3e+02 Score=17.82 Aligned_cols=26 Identities=23% Similarity=0.426 Sum_probs=21.8
Q ss_pred cCCeEEEEECCCcEEEEEEEEEcCCC
Q 034299 11 VEQQISVITNDGRNIVGVLKGFDQAT 36 (98)
Q Consensus 11 i~k~V~V~l~~Gr~i~G~L~~~D~~~ 36 (98)
++-+|.|++.+|..=.|++.++..|.
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 46789999999989999999988653
No 148
>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=20.08 E-value=35 Score=31.58 Aligned_cols=57 Identities=21% Similarity=0.289 Sum_probs=0.0
Q ss_pred EEEECCCcEEEEEEEEEcCCCceEecceEEEEeecCCCeeEEEecEEEEcCCcEEEEEe
Q 034299 16 SVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISIVGE 74 (98)
Q Consensus 16 ~V~l~~Gr~i~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~r~lg~v~irG~~I~~i~~ 74 (98)
+=...+|+.+.|.|...|.-++.+|.--.+ +.+. .-......|.++|+|+|.|.--.
T Consensus 251 Tytt~~G~~v~GVlvTT~~V~q~Ll~~l~~-i~~~-~v~~PatYg~~Vi~geNlVTAi~ 307 (1354)
T PF03122_consen 251 TYTTSSGRPVDGVLVTTANVMQKLLNLLGQ-ISDT-SVSVPATYGEFVISGENLVTAIA 307 (1354)
T ss_dssp -----------------------------------------------------------
T ss_pred eeecCCCCEeceEEeccHHHHHHHHHHHhh-hccc-eeecchhheeeeecCccHHHHHH
Confidence 334578999999999999888877765544 2110 11234578999999999875443
Done!