Query 034752
Match_columns 85
No_of_seqs 117 out of 1033
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:05:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034752.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034752hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01730 LSm3 The eukaryotic Sm 99.9 2.4E-22 5.2E-27 126.6 8.7 74 11-84 1-75 (82)
2 cd01720 Sm_D2 The eukaryotic S 99.9 6.8E-22 1.5E-26 126.6 9.1 75 10-84 1-78 (87)
3 cd01732 LSm5 The eukaryotic Sm 99.9 4.2E-21 9.1E-26 120.1 9.3 66 10-84 2-67 (76)
4 PRK00737 small nuclear ribonuc 99.9 4.9E-21 1.1E-25 118.1 8.5 63 10-84 3-65 (72)
5 cd01731 archaeal_Sm1 The archa 99.8 1.3E-20 2.7E-25 114.7 8.2 61 12-84 1-61 (68)
6 cd01726 LSm6 The eukaryotic Sm 99.8 3.2E-20 6.9E-25 112.9 8.0 61 12-84 1-61 (67)
7 cd01729 LSm7 The eukaryotic Sm 99.8 8.8E-20 1.9E-24 115.0 8.9 68 12-84 4-71 (81)
8 cd01717 Sm_B The eukaryotic Sm 99.8 1.4E-19 3E-24 113.1 8.6 68 15-84 4-71 (79)
9 cd01722 Sm_F The eukaryotic Sm 99.8 9.1E-20 2E-24 111.2 7.5 62 11-84 1-62 (68)
10 cd01719 Sm_G The eukaryotic Sm 99.8 1.9E-19 4.1E-24 111.3 8.0 61 12-84 1-61 (72)
11 cd01728 LSm1 The eukaryotic Sm 99.8 1.4E-18 3E-23 108.2 9.3 64 12-84 3-66 (74)
12 COG1958 LSM1 Small nuclear rib 99.8 1.1E-18 2.5E-23 108.7 8.4 67 8-84 4-72 (79)
13 cd01718 Sm_E The eukaryotic Sm 99.8 1.5E-18 3.4E-23 109.5 8.3 67 7-84 2-72 (79)
14 cd06168 LSm9 The eukaryotic Sm 99.8 2.5E-18 5.4E-23 107.3 8.9 65 14-84 3-67 (75)
15 cd01727 LSm8 The eukaryotic Sm 99.8 3E-18 6.6E-23 106.0 8.3 63 14-84 2-64 (74)
16 PF01423 LSM: LSM domain ; In 99.8 6.9E-18 1.5E-22 101.2 8.6 60 14-84 1-60 (67)
17 smart00651 Sm snRNP Sm protein 99.7 1.3E-17 2.8E-22 99.9 8.1 59 15-84 2-60 (67)
18 cd01723 LSm4 The eukaryotic Sm 99.7 1.7E-17 3.7E-22 103.2 7.9 63 11-84 1-63 (76)
19 cd01721 Sm_D3 The eukaryotic S 99.7 1.7E-17 3.6E-22 101.9 7.7 61 12-84 1-61 (70)
20 PTZ00138 small nuclear ribonuc 99.7 3.1E-17 6.8E-22 105.6 8.6 70 4-84 7-80 (89)
21 KOG1775 U6 snRNA-associated Sm 99.7 6.1E-18 1.3E-22 106.4 3.4 68 8-84 4-71 (84)
22 cd00600 Sm_like The eukaryotic 99.7 9.3E-17 2E-21 94.8 7.5 57 16-84 1-57 (63)
23 KOG3460 Small nuclear ribonucl 99.7 3E-18 6.5E-23 109.3 0.8 77 8-84 2-79 (91)
24 cd01724 Sm_D1 The eukaryotic S 99.7 6.5E-16 1.4E-20 99.2 8.1 62 11-84 1-62 (90)
25 KOG3482 Small nuclear ribonucl 99.6 2.2E-16 4.8E-21 98.5 5.0 62 10-83 7-68 (79)
26 cd01733 LSm10 The eukaryotic S 99.6 1.6E-15 3.5E-20 95.1 8.0 65 8-84 6-70 (78)
27 cd01725 LSm2 The eukaryotic Sm 99.6 1.4E-15 3E-20 95.8 7.7 64 11-84 1-64 (81)
28 KOG1781 Small Nuclear ribonucl 99.6 5.9E-17 1.3E-21 106.1 -0.7 68 13-84 19-86 (108)
29 KOG1780 Small Nuclear ribonucl 99.6 1.5E-15 3.4E-20 94.9 5.1 61 10-84 5-65 (77)
30 KOG1774 Small nuclear ribonucl 99.5 2.2E-14 4.8E-19 91.2 2.5 73 1-84 1-78 (88)
31 KOG1783 Small nuclear ribonucl 99.3 1.7E-13 3.8E-18 85.5 -0.0 65 8-84 3-67 (77)
32 KOG3459 Small nuclear ribonucl 99.3 9.2E-14 2E-18 92.4 -1.5 81 4-84 17-100 (114)
33 KOG3168 U1 snRNP component [Tr 99.2 9.5E-13 2.1E-17 93.1 -0.1 71 11-84 5-75 (177)
34 KOG1784 Small Nuclear ribonucl 99.0 2E-10 4.3E-15 74.4 3.5 63 14-84 3-65 (96)
35 KOG3293 Small nuclear ribonucl 99.0 5.2E-10 1.1E-14 76.0 5.3 48 11-58 2-49 (134)
36 KOG3172 Small nuclear ribonucl 98.8 1.8E-08 3.8E-13 67.2 5.5 64 9-84 3-66 (119)
37 cd01739 LSm11_C The eukaryotic 98.7 1.6E-08 3.5E-13 62.0 2.8 37 22-58 9-49 (66)
38 KOG1782 Small Nuclear ribonucl 98.6 2.2E-09 4.8E-14 72.7 -1.7 60 16-84 14-73 (129)
39 KOG3448 Predicted snRNP core p 98.6 2.2E-07 4.7E-12 60.2 7.1 43 13-55 4-46 (96)
40 KOG3428 Small nuclear ribonucl 97.8 4.9E-05 1.1E-09 50.6 5.3 45 13-57 4-48 (109)
41 PF14438 SM-ATX: Ataxin 2 SM d 97.7 0.00028 6E-09 43.3 6.5 45 13-57 4-51 (77)
42 cd01716 Hfq Hfq, an abundant, 96.9 0.0023 5E-08 38.7 4.6 35 15-49 3-39 (61)
43 TIGR02383 Hfq RNA chaperone Hf 96.8 0.0031 6.6E-08 38.2 4.6 35 15-49 7-43 (61)
44 PRK00395 hfq RNA-binding prote 96.6 0.0051 1.1E-07 39.0 4.6 31 21-51 19-49 (79)
45 COG1923 Hfq Uncharacterized ho 95.7 0.047 1E-06 34.5 5.5 31 20-51 18-48 (77)
46 PRK14091 RNA-binding protein H 95.3 0.037 8E-07 39.4 4.5 38 14-51 15-54 (165)
47 cd01735 LSm12_N LSm12 belongs 95.1 0.071 1.5E-06 32.1 4.8 33 19-51 4-36 (61)
48 PF12701 LSM14: Scd6-like Sm d 95.0 0.078 1.7E-06 34.4 5.0 42 17-58 4-46 (96)
49 PF06372 Gemin6: Gemin6 protei 94.9 0.07 1.5E-06 37.9 5.1 43 10-54 7-50 (166)
50 PF02237 BPL_C: Biotin protein 94.8 0.11 2.4E-06 29.2 4.8 34 20-54 2-35 (48)
51 PRK14091 RNA-binding protein H 94.5 0.084 1.8E-06 37.6 4.6 38 14-51 95-134 (165)
52 PRK14638 hypothetical protein; 94.2 0.11 2.4E-06 35.9 4.6 29 16-44 95-123 (150)
53 PRK02001 hypothetical protein; 93.2 0.2 4.4E-06 34.8 4.6 28 17-44 86-113 (152)
54 PRK14639 hypothetical protein; 93.1 0.22 4.7E-06 34.1 4.6 33 16-49 83-115 (140)
55 cd01736 LSm14_N LSm14 (also kn 92.9 0.43 9.3E-06 29.9 5.2 41 18-58 3-44 (74)
56 PF11095 Gemin7: Gem-associate 91.4 0.85 1.9E-05 28.9 5.4 40 12-51 15-55 (80)
57 PRK14644 hypothetical protein; 91.4 0.54 1.2E-05 32.1 4.8 40 9-49 71-116 (136)
58 PRK14640 hypothetical protein; 89.5 0.9 1.9E-05 31.4 4.7 33 16-49 92-128 (152)
59 cd01734 YlxS_C YxlS is a Bacil 89.5 1.1 2.3E-05 27.8 4.5 28 17-44 21-52 (83)
60 PRK14633 hypothetical protein; 89.2 0.99 2.1E-05 31.1 4.7 33 16-49 89-125 (150)
61 PRK14645 hypothetical protein; 88.9 0.93 2E-05 31.5 4.4 27 17-44 98-124 (154)
62 PRK14642 hypothetical protein; 88.6 1 2.3E-05 32.7 4.6 28 17-44 96-136 (197)
63 PF02576 DUF150: Uncharacteris 88.5 1.1 2.4E-05 30.1 4.4 35 9-43 72-113 (141)
64 PRK14636 hypothetical protein; 87.8 1.2 2.6E-05 31.6 4.5 33 16-49 93-129 (176)
65 PRK14632 hypothetical protein; 87.2 1.4 3.1E-05 31.1 4.5 33 16-49 93-132 (172)
66 PRK14634 hypothetical protein; 87.2 1.5 3.2E-05 30.4 4.6 29 16-44 95-127 (155)
67 PRK14646 hypothetical protein; 87.0 1.5 3.3E-05 30.4 4.5 34 15-49 94-131 (155)
68 PRK14643 hypothetical protein; 86.9 1.5 3.3E-05 30.8 4.5 34 15-48 98-136 (164)
69 PRK00092 ribosome maturation p 86.7 1.7 3.7E-05 29.7 4.7 29 15-43 92-124 (154)
70 COG0779 Uncharacterized protei 85.9 2.4 5.3E-05 29.6 5.1 40 9-49 84-130 (153)
71 PRK14647 hypothetical protein; 84.6 2.4 5.1E-05 29.4 4.5 28 16-43 94-130 (159)
72 PRK14631 hypothetical protein; 83.1 2.8 6.2E-05 29.7 4.5 28 15-42 111-142 (174)
73 PRK14637 hypothetical protein; 81.8 3.2 6.9E-05 28.7 4.3 33 16-49 93-126 (151)
74 PRK14641 hypothetical protein; 81.5 3.1 6.8E-05 29.5 4.2 27 16-42 99-129 (173)
75 PF03614 Flag1_repress: Repres 79.6 4.9 0.00011 28.5 4.6 35 19-53 27-61 (165)
76 PF10842 DUF2642: Protein of u 77.7 13 0.00029 22.6 6.9 37 8-45 6-45 (66)
77 PRK10898 serine endoprotease; 77.2 5.6 0.00012 30.6 4.8 32 22-53 102-133 (353)
78 TIGR02038 protease_degS peripl 76.6 5.9 0.00013 30.3 4.7 32 22-53 102-133 (351)
79 PRK10139 serine endoprotease; 72.5 8.4 0.00018 30.8 4.8 32 22-53 115-146 (455)
80 PRK10942 serine endoprotease; 72.4 8.1 0.00017 31.0 4.7 31 22-52 136-166 (473)
81 PRK06955 biotin--protein ligas 67.1 15 0.00032 27.7 4.9 32 19-50 247-278 (300)
82 TIGR02037 degP_htrA_DO peripla 66.7 13 0.00028 29.0 4.7 32 22-53 82-113 (428)
83 PRK14630 hypothetical protein; 65.9 14 0.0003 25.3 4.2 29 16-45 92-120 (143)
84 PRK14635 hypothetical protein; 65.8 15 0.00032 25.6 4.4 28 17-44 95-127 (162)
85 PRK09618 flgD flagellar basal 62.7 31 0.00067 23.9 5.5 26 17-42 88-113 (142)
86 PF11607 DUF3247: Protein of u 61.5 13 0.00028 24.5 3.2 17 22-38 29-45 (101)
87 PF03614 Flag1_repress: Repres 59.5 11 0.00024 26.8 2.8 30 14-43 111-142 (165)
88 TIGR03170 flgA_cterm flagella 57.9 15 0.00032 23.6 3.0 23 18-40 93-116 (122)
89 PF14153 Spore_coat_CotO: Spor 57.4 17 0.00037 26.1 3.6 32 13-44 123-157 (185)
90 PF14563 DUF4444: Domain of un 56.5 17 0.00037 20.4 2.7 22 34-55 10-31 (42)
91 PRK11886 bifunctional biotin-- 56.0 30 0.00065 25.9 4.8 31 19-50 270-300 (319)
92 PF06257 DUF1021: Protein of u 51.6 43 0.00094 20.8 4.3 29 13-41 9-41 (76)
93 PRK13325 bifunctional biotin-- 49.9 39 0.00085 28.1 5.0 33 19-51 276-308 (592)
94 PRK07018 flgA flagellar basal 48.9 22 0.00047 25.8 3.0 23 18-40 204-227 (235)
95 PTZ00275 biotin-acetyl-CoA-car 48.4 48 0.001 24.8 4.9 31 20-51 236-266 (285)
96 TIGR00121 birA_ligase birA, bi 47.2 52 0.0011 23.6 4.8 31 19-50 191-221 (237)
97 PRK08330 biotin--protein ligas 47.1 59 0.0013 23.3 5.1 32 19-51 186-218 (236)
98 COG0340 BirA Biotin-(acetyl-Co 46.2 53 0.0011 24.2 4.7 34 19-52 188-221 (238)
99 PF07073 ROF: Modulator of Rho 44.9 17 0.00037 22.8 1.7 18 20-37 16-33 (80)
100 TIGR02603 CxxCH_TIGR02603 puta 43.9 34 0.00074 22.5 3.2 27 22-48 58-85 (133)
101 cd04479 RPA3 RPA3: A subfamily 39.9 79 0.0017 20.0 4.3 15 13-27 7-21 (101)
102 COG5316 Uncharacterized conser 39.8 90 0.002 25.4 5.4 48 8-56 69-116 (421)
103 PRK11911 flgD flagellar basal 39.7 59 0.0013 22.5 3.9 25 18-42 90-114 (140)
104 PF09465 LBR_tudor: Lamin-B re 38.0 71 0.0015 18.8 3.5 25 19-43 7-32 (55)
105 PRK06005 flgA flagellar basal 36.8 48 0.001 23.0 3.1 22 19-40 129-151 (160)
106 PF10618 Tail_tube: Phage tail 36.0 57 0.0012 21.5 3.3 29 9-37 62-90 (119)
107 KOG3382 NADH:ubiquinone oxidor 35.5 21 0.00046 24.9 1.1 25 28-52 39-63 (151)
108 PRK08515 flgA flagellar basal 34.8 62 0.0013 23.4 3.6 23 18-40 193-215 (222)
109 COG0265 DegQ Trypsin-like seri 34.8 85 0.0018 23.6 4.4 31 21-51 95-125 (347)
110 PRK12617 flgA flagellar basal 34.2 53 0.0011 23.9 3.1 22 19-40 184-206 (214)
111 KOG1073 Uncharacterized mRNA-a 33.5 79 0.0017 25.2 4.2 43 16-58 4-47 (361)
112 PRK12618 flgA flagellar basal 32.1 65 0.0014 21.9 3.1 22 19-40 110-132 (141)
113 PRK10708 hypothetical protein; 31.4 60 0.0013 19.5 2.5 26 20-45 3-28 (62)
114 PRK08477 biotin--protein ligas 31.4 2E+02 0.0043 20.7 5.7 36 19-55 173-208 (211)
115 PRK06804 flgA flagellar basal 30.5 65 0.0014 24.2 3.1 23 18-40 230-253 (261)
116 COG0048 RpsL Ribosomal protein 30.1 55 0.0012 22.5 2.5 28 17-45 52-79 (129)
117 PF05071 NDUFA12: NADH ubiquin 28.7 35 0.00075 22.0 1.3 17 36-52 1-17 (105)
118 PF14485 DUF4431: Domain of un 28.2 69 0.0015 18.0 2.3 15 13-27 11-25 (48)
119 PRK11625 Rho-binding antitermi 27.5 1.1E+02 0.0025 19.2 3.5 19 20-38 22-40 (84)
120 PF10781 DSRB: Dextransucrase 27.1 71 0.0015 19.2 2.3 26 20-45 3-28 (62)
121 smart00333 TUDOR Tudor domain. 27.1 1.1E+02 0.0025 16.5 4.8 25 20-44 5-29 (57)
122 smart00166 UBX Domain present 26.2 67 0.0015 19.1 2.2 21 22-42 5-25 (80)
123 KOG3493 Ubiquitin-like protein 25.8 59 0.0013 20.2 1.8 18 15-32 5-22 (73)
124 cd00319 Ribosomal_S12_like Rib 25.6 72 0.0016 20.8 2.3 26 17-42 31-56 (95)
125 COG4466 Veg Uncharacterized pr 25.5 63 0.0014 20.5 1.9 44 9-52 7-55 (80)
126 KOG4401 Uncharacterized conser 25.4 85 0.0018 22.8 2.9 35 19-53 9-43 (184)
127 PRK05163 rpsL 30S ribosomal pr 25.4 76 0.0016 21.7 2.5 26 17-42 46-71 (124)
128 PRK06792 flgD flagellar basal 25.3 1.3E+02 0.0028 22.0 3.8 25 18-42 115-139 (190)
129 cd01767 UBX UBX (ubiquitin reg 24.7 1E+02 0.0022 18.1 2.8 21 22-42 3-23 (77)
130 PRK12786 flgA flagellar basal 24.4 94 0.002 24.1 3.1 23 19-41 287-310 (338)
131 PF00789 UBX: UBX domain; Int 24.1 1.2E+02 0.0026 17.8 3.0 21 22-42 7-27 (82)
132 PF13144 SAF_2: SAF-like 24.1 1.3E+02 0.0027 20.7 3.5 23 18-40 167-190 (196)
133 TIGR00981 rpsL_bact ribosomal 23.4 83 0.0018 21.5 2.4 26 17-42 46-71 (124)
134 PF05954 Phage_GPD: Phage late 23.2 1.2E+02 0.0026 21.4 3.4 26 17-42 24-49 (292)
135 CHL00051 rps12 ribosomal prote 22.3 86 0.0019 21.4 2.3 31 17-49 46-76 (123)
136 cd01772 SAKS1_UBX SAKS1-like U 21.6 91 0.002 18.7 2.1 23 20-42 3-25 (79)
137 PF08661 Rep_fac-A_3: Replicat 21.3 1.2E+02 0.0026 19.2 2.7 15 13-27 10-24 (109)
138 cd03367 Ribosomal_S23 S12-like 20.8 1.3E+02 0.0029 20.2 2.9 27 17-44 38-65 (115)
139 PF13437 HlyD_3: HlyD family s 20.1 2.1E+02 0.0047 17.1 4.3 33 11-43 42-78 (105)
No 1
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=2.4e-22 Score=126.59 Aligned_cols=74 Identities=73% Similarity=1.101 Sum_probs=62.8
Q ss_pred ChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccce-eeeeeeeeeeEEecCC
Q 034752 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEE-IVRVCCNLKILLLNFK 84 (85)
Q Consensus 11 ~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~-~~~~~r~lg~ill~G~ 84 (85)
.|+++|+.+++++|+|+|++||.|.|+|.|||+||||+|+||+|++......++...+ .....|+||+++|||+
T Consensus 1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd 75 (82)
T cd01730 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGD 75 (82)
T ss_pred CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCC
Confidence 4999999999999999999999999999999999999999999999876544322212 2235789999999997
No 2
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=6.8e-22 Score=126.61 Aligned_cols=75 Identities=24% Similarity=0.420 Sum_probs=63.1
Q ss_pred CChHHHHHhhc--CCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCcccc-ceeeeeeeeeeeEEecCC
Q 034752 10 KEPLDLIRLSL--DERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETY-EEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 10 ~~Pl~~L~~~l--~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~-~~~~~~~r~lg~ill~G~ 84 (85)
.+|+++|..++ +++|.|+|++|+.|.|+|.|||+||||+|+||+|++.+.+++..+. .....+.|+||+++|||+
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd 78 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGD 78 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCC
Confidence 47999999997 8999999999999999999999999999999999998754432221 122456888999999997
No 3
>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=99.86 E-value=4.2e-21 Score=120.05 Aligned_cols=66 Identities=38% Similarity=0.546 Sum_probs=59.0
Q ss_pred CChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 10 KEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 10 ~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
..|+++|+++++++|+|++++|++|.|+|.|||+|||++|+||.|++..++. ...+++|++++||+
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~---------~~~~~lg~v~iRG~ 67 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEG---------RKITKLDQILLNGN 67 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCC---------ceeeEcCeEEEeCC
Confidence 4799999999999999999999999999999999999999999999853221 24688999999997
No 4
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.85 E-value=4.9e-21 Score=118.09 Aligned_cols=63 Identities=32% Similarity=0.635 Sum_probs=57.4
Q ss_pred CChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 10 KEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 10 ~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
..|+++|+++++++|+|+|++|+.|+|+|.|||+|||++|+||.|++++ ...+++|.+++||+
T Consensus 3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~------------~~~~~lg~v~iRG~ 65 (72)
T PRK00737 3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG------------EVVRKLGKVVIRGD 65 (72)
T ss_pred cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC------------CeEeEcCcEEEeCC
Confidence 5899999999999999999999999999999999999999999997532 23588999999996
No 5
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.84 E-value=1.3e-20 Score=114.68 Aligned_cols=61 Identities=34% Similarity=0.626 Sum_probs=56.3
Q ss_pred hHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 12 Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
|+++|+++++++|+|+|++|+.|+|+|.|||+|||++|+||.|++.+. ..+++|.+++||+
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~------------~~~~lg~~~iRG~ 61 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGE------------PVRKYGRVVIRGD 61 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCC------------eEeEcCcEEEeCC
Confidence 899999999999999999999999999999999999999999986532 3678999999996
No 6
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.83 E-value=3.2e-20 Score=112.87 Aligned_cols=61 Identities=23% Similarity=0.334 Sum_probs=55.4
Q ss_pred hHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 12 Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
|+++|+++++++|+|+|++|++|+|+|.|||.||||+|+||+|...+ ...+.+|++++||+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~------------~~~~~~~~v~IRG~ 61 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG------------QLKNKYGDAFIRGN 61 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC------------ceeeEeCCEEEECC
Confidence 89999999999999999999999999999999999999999886432 23678999999996
No 7
>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=99.82 E-value=8.8e-20 Score=115.03 Aligned_cols=68 Identities=28% Similarity=0.403 Sum_probs=56.8
Q ss_pred hHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 12 Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
|++ |.++++++|+|+|++||+|+|+|.|||+||||+|++|.|+..+.+... +.....+.||++++||+
T Consensus 4 ~~~-L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~----~~~~~~~~lG~v~iRG~ 71 (81)
T cd01729 4 ILD-LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPY----KLTDKTRQLGLVVCRGT 71 (81)
T ss_pred hhh-HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCccc----ccccceeEccEEEEcCC
Confidence 444 889999999999999999999999999999999999999987643211 11235788999999996
No 8
>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=99.81 E-value=1.4e-19 Score=113.08 Aligned_cols=68 Identities=24% Similarity=0.370 Sum_probs=57.1
Q ss_pred HHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 15 LIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 15 ~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
-|.++++++|+|.|++||.|.|+|.|||+||||+|+||.|++........ .......|+||++++||+
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~--~~~~~~~r~lG~v~iRG~ 71 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSK--NSEREEKRTLGLVLLRGE 71 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccc--cccCcceeEeeeEEEcCC
Confidence 47789999999999999999999999999999999999999876543210 112346899999999997
No 9
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.81 E-value=9.1e-20 Score=111.23 Aligned_cols=62 Identities=24% Similarity=0.360 Sum_probs=56.0
Q ss_pred ChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 11 ~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
.|+++|+++++++|+|+|++|++|+|+|.|||+|||++|+||.|+..+ ...+++|.+++||+
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~------------~~~~~lg~~~IRG~ 62 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG------------KSTGNLGEVLIRCN 62 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC------------ccccCcCcEEEECC
Confidence 599999999999999999999999999999999999999999987432 12578999999996
No 10
>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=99.81 E-value=1.9e-19 Score=111.34 Aligned_cols=61 Identities=21% Similarity=0.400 Sum_probs=55.1
Q ss_pred hHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 12 Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
|.+.|+++++|+|+|+|++|+.|+|+|.|||+||||+|+||.|+..+ ...+.+|.+++||+
T Consensus 1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~------------~~~~~lg~v~IRG~ 61 (72)
T cd01719 1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG------------GEKNNIGMVVIRGN 61 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC------------CceeEeceEEECCC
Confidence 56789999999999999999999999999999999999999998632 12688999999996
No 11
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.79 E-value=1.4e-18 Score=108.24 Aligned_cols=64 Identities=25% Similarity=0.293 Sum_probs=55.8
Q ss_pred hHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 12 Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
+...|.++++++|.|.+++|+.|.|+|.|||+|||++|+||.|+....+. ...+.+|.+++||+
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~---------~~~~~lG~~viRG~ 66 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDK---------YGDIPRGIFIIRGE 66 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCc---------cceeEeeEEEEECC
Confidence 56778999999999999999999999999999999999999998764321 12578999999996
No 12
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.78 E-value=1.1e-18 Score=108.73 Aligned_cols=67 Identities=33% Similarity=0.496 Sum_probs=57.7
Q ss_pred ccCChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEe--ccccCccccceeeeeeeeeeeEEecCC
Q 034752 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVT--TVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 8 ~~~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~--~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
....|+++|+++++++|.|+|++|++|.|+|.|||.|||++|+||.|++. +.. ...+..|.++|||+
T Consensus 4 ~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~----------~~~~~~~~~~IRG~ 72 (79)
T COG1958 4 LGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEK----------NVRRLGGEVLIRGD 72 (79)
T ss_pred ccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCcc----------ccceeccEEEEECC
Confidence 35678999999999999999999999999999999999999999999985 110 13556669999996
No 13
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.78 E-value=1.5e-18 Score=109.49 Aligned_cols=67 Identities=27% Similarity=0.415 Sum_probs=57.7
Q ss_pred cccCChHHHHHhhcCC--EEEEEEc--CCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEec
Q 034752 7 SAVKEPLDLIRLSLDE--RIYVKLR--SDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLN 82 (85)
Q Consensus 7 ~~~~~Pl~~L~~~l~k--~V~V~L~--~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~ 82 (85)
..+..|++.+.+++++ +|.|.++ +|+.|+|+|.|||+|||++|+||+|+.... ...+++|++++|
T Consensus 2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~-----------~~~~~lG~iliR 70 (79)
T cd01718 2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKT-----------KTRKPLGRILLK 70 (79)
T ss_pred ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCC-----------ceEeEcCcEEEe
Confidence 4578899999999998 6777776 899999999999999999999999986521 236789999999
Q ss_pred CC
Q 034752 83 FK 84 (85)
Q Consensus 83 G~ 84 (85)
|+
T Consensus 71 Gn 72 (79)
T cd01718 71 GD 72 (79)
T ss_pred CC
Confidence 97
No 14
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.77 E-value=2.5e-18 Score=107.31 Aligned_cols=65 Identities=18% Similarity=0.218 Sum_probs=57.3
Q ss_pred HHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 14 DLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 14 ~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
+.|.++++++|+|.|+|||.|.|+|.|||+|||++|+||.|++...+.. .....|+||++++||+
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~------~~~~~r~lGlv~IrG~ 67 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSF------SPTEPRVLGLVMIPGH 67 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCcc------CCccEEEeeeEEEeCC
Confidence 4678999999999999999999999999999999999999998776532 1245899999999997
No 15
>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=99.77 E-value=3e-18 Score=105.98 Aligned_cols=63 Identities=22% Similarity=0.249 Sum_probs=54.6
Q ss_pred HHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 14 DLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 14 ~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
+.|.++++++|+|++++|+.|.|+|.|||+|||++|++|.|+....+. ....+.+|.+++||+
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~--------~~~~~~lG~~~iRG~ 64 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDE--------GVEQVVLGLYIIRGD 64 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCC--------CceeeEeceEEECCC
Confidence 468899999999999999999999999999999999999998654321 124778999999996
No 16
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.76 E-value=6.9e-18 Score=101.21 Aligned_cols=60 Identities=25% Similarity=0.490 Sum_probs=55.1
Q ss_pred HHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 14 DLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 14 ~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
.+|+++++++|+|.|++|+.|+|+|.+||+|||++|+||.|++.... ..+++|.+++||+
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-----------~~~~~~~~~irG~ 60 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-----------EKRSLGLVFIRGS 60 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-----------EEEEEEEEEEEGG
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-----------cEeECcEEEEECC
Confidence 47899999999999999999999999999999999999999877542 5899999999996
No 17
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.74 E-value=1.3e-17 Score=99.87 Aligned_cols=59 Identities=31% Similarity=0.558 Sum_probs=54.1
Q ss_pred HHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 15 LIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 15 ~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
+|.++++++|+|.|+||+.+.|+|.+||+|||++|+||.|++.+. ...+++|.+++||+
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-----------~~~~~~~~~~IrG~ 60 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-----------EKKRKLGLVFIRGN 60 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC-----------cEEeEeCCEEEcCC
Confidence 688999999999999999999999999999999999999987642 34799999999996
No 18
>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=99.73 E-value=1.7e-17 Score=103.17 Aligned_cols=63 Identities=17% Similarity=0.250 Sum_probs=54.6
Q ss_pred ChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 11 ~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
.|+++|+++.+++|+|+|++|+.|+|+|.+||.|||++|+||.|...+ +....+++.+++||+
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~-----------g~~~~~~~~v~IRG~ 63 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKD-----------GDKFWKMPECYIRGN 63 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCC-----------CcEeeeCCcEEEeCC
Confidence 499999999999999999999999999999999999999999985221 123456799999996
No 19
>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=99.73 E-value=1.7e-17 Score=101.88 Aligned_cols=61 Identities=21% Similarity=0.300 Sum_probs=53.4
Q ss_pred hHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 12 Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
|+++|+++.+++|+|+|+||.+|+|+|.+||.|||++|+||.+...+ + +..++|.+++||.
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~-----------g-~~~~~~~v~IRG~ 61 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARD-----------G-RVSQLEQVYIRGS 61 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCC-----------C-cEeEcCcEEEeCC
Confidence 89999999999999999999999999999999999999999874221 0 1357899999996
No 20
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.72 E-value=3.1e-17 Score=105.59 Aligned_cols=70 Identities=26% Similarity=0.393 Sum_probs=59.2
Q ss_pred ccccccCChHHHHHhhcC--CEEEEEEcC--CeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeE
Q 034752 4 EEESAVKEPLDLIRLSLD--ERIYVKLRS--DRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKIL 79 (85)
Q Consensus 4 ~~~~~~~~Pl~~L~~~l~--k~V~V~L~~--g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~i 79 (85)
..+..+..|+.++.+++. .+|+|.+.+ ++.|+|+|.|||+|||++|+||+|++.+. ...+.+|++
T Consensus 7 ~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~-----------~~~~~lG~i 75 (89)
T PTZ00138 7 KLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKK-----------NTRKDLGRI 75 (89)
T ss_pred ccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCC-----------ceeeEcCeE
Confidence 567788999999999997 566677766 58999999999999999999999986531 137789999
Q ss_pred EecCC
Q 034752 80 LLNFK 84 (85)
Q Consensus 80 ll~G~ 84 (85)
++||+
T Consensus 76 lIRGn 80 (89)
T PTZ00138 76 LLKGD 80 (89)
T ss_pred EEcCC
Confidence 99997
No 21
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.71 E-value=6.1e-18 Score=106.44 Aligned_cols=68 Identities=35% Similarity=0.538 Sum_probs=62.8
Q ss_pred ccCChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 8 ~~~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
+...|+.++.++++.+|+|.+++.+++.|+|.|||.|.|++|+|+.||-..++ .++..++++|||||+
T Consensus 4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e---------gr~~tk~~~iLLnGN 71 (84)
T KOG1775|consen 4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE---------GRRMTKLDQILLNGN 71 (84)
T ss_pred hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC---------cceeeeeeeeeecCC
Confidence 45689999999999999999999999999999999999999999999977663 377999999999997
No 22
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.70 E-value=9.3e-17 Score=94.83 Aligned_cols=57 Identities=28% Similarity=0.446 Sum_probs=52.0
Q ss_pred HHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 16 IRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 16 L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
|+++++++|+|.|++|+.|.|+|.+||+|||++|+||.|++.+ ...+++|.+++||+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~------------~~~~~~~~~~irG~ 57 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE------------GKKRVLGLVLIRGD 57 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC------------CcEEECCeEEEECC
Confidence 4678999999999999999999999999999999999998775 23789999999996
No 23
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.69 E-value=3e-18 Score=109.32 Aligned_cols=77 Identities=68% Similarity=1.076 Sum_probs=70.6
Q ss_pred ccCChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeee-eeeeeeEEecCC
Q 034752 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRV-CCNLKILLLNFK 84 (85)
Q Consensus 8 ~~~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~-~r~lg~ill~G~ 84 (85)
.+..|+++|+-+++.+|.|+++++|+++|+|.+||+|+|++|.+|+|.+...+.++.++++..++ .|.+-++|+||+
T Consensus 2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd 79 (91)
T KOG3460|consen 2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGD 79 (91)
T ss_pred cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCC
Confidence 46789999999999999999999999999999999999999999999999998887777766655 788999999997
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=99.65 E-value=6.5e-16 Score=99.24 Aligned_cols=62 Identities=16% Similarity=0.237 Sum_probs=54.8
Q ss_pred ChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 11 ~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
.|+.+|+++.+++|+|+|+||..|+|+|.++|.|||++|+||.++..+ ....++|.++|||.
T Consensus 1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~------------~~~~~~~~v~IRG~ 62 (90)
T cd01724 1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG------------RNPVPLDTLSIRGN 62 (90)
T ss_pred CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC------------CceeEcceEEEeCC
Confidence 368899999999999999999999999999999999999999887432 12568999999996
No 25
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.65 E-value=2.2e-16 Score=98.53 Aligned_cols=62 Identities=26% Similarity=0.378 Sum_probs=56.7
Q ss_pred CChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecC
Q 034752 10 KEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNF 83 (85)
Q Consensus 10 ~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G 83 (85)
.+|..||+.+.+++|.|+|++|.+|+|+|++.|.||||+|.+|+|++++. .+-+||.|++|=
T Consensus 7 vNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~------------~~g~lGEilIRC 68 (79)
T KOG3482|consen 7 VNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGV------------STGNLGEILIRC 68 (79)
T ss_pred CCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhccc------------ccccceeEEEEe
Confidence 38999999999999999999999999999999999999999999998764 366899999873
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=99.63 E-value=1.6e-15 Score=95.09 Aligned_cols=65 Identities=14% Similarity=0.222 Sum_probs=55.7
Q ss_pred ccCChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 8 ~~~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
.-..+..||+.+.|++|+|+|+||..|+|+|.++|.|||++|+||++...+ ....++|.+++||.
T Consensus 6 ~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~------------~~~~~~~~v~IRG~ 70 (78)
T cd01733 6 LENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN------------GKQVQVEEIMVTGR 70 (78)
T ss_pred hhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC------------CceeECCcEEEECC
Confidence 445678999999999999999999999999999999999999999865321 11347999999996
No 27
>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=99.63 E-value=1.4e-15 Score=95.77 Aligned_cols=64 Identities=20% Similarity=0.273 Sum_probs=53.5
Q ss_pred ChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 11 ~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
.|+.||+++.|++|+|+|++|..|+|+|.++|.|||++|+||++...+ . .....+++.+++||.
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~--~--------~~~~~~~~~v~IRG~ 64 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE--K--------YPHMLSVKNCFIRGS 64 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCC--C--------cccccccCeEEEECC
Confidence 378999999999999999999999999999999999999999765321 1 112456789999986
No 28
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.61 E-value=5.9e-17 Score=106.07 Aligned_cols=68 Identities=26% Similarity=0.315 Sum_probs=59.7
Q ss_pred HHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 13 LDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 13 l~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
.-.|.+|++++|+|++.+||..+|+|.|||+.|||||+++.|+..+++...++ ...+|+||.++.||-
T Consensus 19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~----~~~tR~LGLvV~RGT 86 (108)
T KOG1781|consen 19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKL----TDETRKLGLVVCRGT 86 (108)
T ss_pred HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccch----hhhhheeeeEEEccc
Confidence 44567999999999999999999999999999999999999999998875444 334699999999984
No 29
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.60 E-value=1.5e-15 Score=94.86 Aligned_cols=61 Identities=23% Similarity=0.406 Sum_probs=53.6
Q ss_pred CChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 10 KEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 10 ~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
..| -|++|++|++.++|+.||.+.|+|.|||.|||+||++|.|...+- ....||+.++||+
T Consensus 5 g~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~------------~~~~ig~~vIrgn 65 (77)
T KOG1780|consen 5 GHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDG------------DKNNIGMVVIRGN 65 (77)
T ss_pred cCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcC------------CcceeeeEEEecc
Confidence 356 799999999999999999999999999999999999999974432 2568999999996
No 30
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.47 E-value=2.2e-14 Score=91.22 Aligned_cols=73 Identities=25% Similarity=0.411 Sum_probs=58.3
Q ss_pred Ccc-ccccccCChHHHHHhhcCC--EEEEEEc--CCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeee
Q 034752 1 MAS-EEESAVKEPLDLIRLSLDE--RIYVKLR--SDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCN 75 (85)
Q Consensus 1 m~~-~~~~~~~~Pl~~L~~~l~k--~V~V~L~--~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~ 75 (85)
||. --+..+..|+.++.+++.. +|.|.|. -|-.+.|.++|||+|||+||++|+|..... +..+.
T Consensus 1 ms~~kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~-----------~~rk~ 69 (88)
T KOG1774|consen 1 MSREKVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT-----------KSRKE 69 (88)
T ss_pred CCcccccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc-----------cCCCc
Confidence 555 3456789999999999974 5556664 488999999999999999999999974422 22458
Q ss_pred eeeEEecCC
Q 034752 76 LKILLLNFK 84 (85)
Q Consensus 76 lg~ill~G~ 84 (85)
||.|||+|+
T Consensus 70 lGRilLKGD 78 (88)
T KOG1774|consen 70 LGRILLKGD 78 (88)
T ss_pred cccEEEcCC
Confidence 999999997
No 31
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.33 E-value=1.7e-13 Score=85.51 Aligned_cols=65 Identities=22% Similarity=0.243 Sum_probs=58.3
Q ss_pred ccCChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 8 ~~~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
....|-+||+..++++|.|+|.+|..|+|+|.+.|.|||+.|+.++|+.++.. .++-|..||||.
T Consensus 3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql------------~n~ygdaFirGn 67 (77)
T KOG1783|consen 3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQL------------KNKYGDAFIRGN 67 (77)
T ss_pred cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcc------------cccccceeeccc
Confidence 34679999999999999999999999999999999999999999999986642 567788999985
No 32
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.33 E-value=9.2e-14 Score=92.40 Aligned_cols=81 Identities=26% Similarity=0.386 Sum_probs=70.8
Q ss_pred ccccccCChHHHHHhhcC--CEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCcccc-ceeeeeeeeeeeEE
Q 034752 4 EEESAVKEPLDLIRLSLD--ERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETY-EEIVRVCCNLKILL 80 (85)
Q Consensus 4 ~~~~~~~~Pl~~L~~~l~--k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~-~~~~~~~r~lg~il 80 (85)
+++.+..+|++++..+.. .+|.|.++|++...|.+.|||.|+|++|+|+.|.|++...+++.+ .+.+...|+||+++
T Consensus 17 e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~f 96 (114)
T KOG3459|consen 17 EEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMF 96 (114)
T ss_pred cccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheee
Confidence 556677899999998885 889999999999999999999999999999999999987765553 34567799999999
Q ss_pred ecCC
Q 034752 81 LNFK 84 (85)
Q Consensus 81 l~G~ 84 (85)
|||+
T Consensus 97 lRGd 100 (114)
T KOG3459|consen 97 LRGD 100 (114)
T ss_pred ecCC
Confidence 9996
No 33
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.25 E-value=9.5e-13 Score=93.10 Aligned_cols=71 Identities=23% Similarity=0.343 Sum_probs=58.0
Q ss_pred ChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 11 ~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
.+..+| +.++.+++|.++|||.|.|.+.+||+|||++|.+|+|+..-..... .....++.|-||.++|||+
T Consensus 5 ~sskml-~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~--~~~~~eEkr~lgLvllRge 75 (177)
T KOG3168|consen 5 KSSKML-QHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNR--KMTDGEEKRVLGLVLLRGE 75 (177)
T ss_pred chhHHH-HhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccc--cccccceeeEEEEEEecCC
Confidence 445555 6799999999999999999999999999999999999866533322 1334567899999999997
No 34
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.03 E-value=2e-10 Score=74.43 Aligned_cols=63 Identities=17% Similarity=0.245 Sum_probs=54.0
Q ss_pred HHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 14 DLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 14 ~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
.-|..|++++|.|...|||.+.|.|.|||+..||+++++.|++.... +...+.-||.-++||+
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~--------~gv~q~~lGlyiirge 65 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSET--------EGVEQIVLGLYIIRGE 65 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhh--------cchhheeeEEEEEecC
Confidence 34789999999999999999999999999999999999999866532 3455677888888886
No 35
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.02 E-value=5.2e-10 Score=75.99 Aligned_cols=48 Identities=23% Similarity=0.394 Sum_probs=45.8
Q ss_pred ChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEec
Q 034752 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTT 58 (85)
Q Consensus 11 ~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~ 58 (85)
.|+.+|+.+-+.++.|+|++|.+|.|.|+.+|.+|||.|.+|+++..+
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~D 49 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSED 49 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccC
Confidence 699999999999999999999999999999999999999999998664
No 36
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=98.77 E-value=1.8e-08 Score=67.25 Aligned_cols=64 Identities=19% Similarity=0.289 Sum_probs=54.2
Q ss_pred cCChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 9 VKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 9 ~~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
...|+++|+++-+.-|++++.+|..|+|+|.-.|++|||+|+|+.-...+ .+..+|-++++||.
T Consensus 3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d------------g~vs~le~V~IRGS 66 (119)
T KOG3172|consen 3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD------------GRVSQLEQVFIRGS 66 (119)
T ss_pred cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC------------CcceeeeeEEEecC
Confidence 46799999999999999999999999999999999999999998765433 12456777888874
No 37
>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=98.67 E-value=1.6e-08 Score=61.98 Aligned_cols=37 Identities=35% Similarity=0.459 Sum_probs=32.1
Q ss_pred CEEEEEEcC----CeEEEEEEEEEcCccceEecceEEEEec
Q 034752 22 ERIYVKLRS----DRELRGKLHAYDQHLNMILGDVEEVVTT 58 (85)
Q Consensus 22 k~V~V~L~~----g~~~~G~L~~fD~~mNlvL~n~~E~~~~ 58 (85)
.+|+|.++. +-.++|.|++||+||||+|.||.|.+..
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 677777764 3489999999999999999999999887
No 38
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.64 E-value=2.2e-09 Score=72.73 Aligned_cols=60 Identities=25% Similarity=0.331 Sum_probs=49.7
Q ss_pred HHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccceeeeeeeeeeeEEecCC
Q 034752 16 IRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFK 84 (85)
Q Consensus 16 L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~~~~~~r~lg~ill~G~ 84 (85)
+..++++++.|-|+|||...|.|.+||+|-|++|..|.|++.--+. =-++..|..++||+
T Consensus 14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~---------Y~di~~glfiIRGE 73 (129)
T KOG1782|consen 14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNK---------YCDIPRGLFIIRGE 73 (129)
T ss_pred HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecce---------ecccCceEEEEecC
Confidence 6688999999999999999999999999999999999997543211 11456788888886
No 39
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.62 E-value=2.2e-07 Score=60.16 Aligned_cols=43 Identities=28% Similarity=0.485 Sum_probs=39.9
Q ss_pred HHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEE
Q 034752 13 LDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEV 55 (85)
Q Consensus 13 l~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~ 55 (85)
.+|.+.++|+.|.|.|+++-.+.|+|.|.|+|+|+-|+|....
T Consensus 4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~ 46 (96)
T KOG3448|consen 4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVT 46 (96)
T ss_pred HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEee
Confidence 5788999999999999999999999999999999999997653
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=97.83 E-value=4.9e-05 Score=50.65 Aligned_cols=45 Identities=22% Similarity=0.442 Sum_probs=40.9
Q ss_pred HHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEe
Q 034752 13 LDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVT 57 (85)
Q Consensus 13 l~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~ 57 (85)
..+|+.+.+.+|+|+|++|..+.|++.+.|.+||..|.++.=...
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~ 48 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK 48 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC
Confidence 568899999999999999999999999999999999999875544
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.66 E-value=0.00028 Score=43.25 Aligned_cols=45 Identities=13% Similarity=0.245 Sum_probs=35.8
Q ss_pred HHHHHhhcCCEEEEEEcCCeEEEEEEEEEcC---ccceEecceEEEEe
Q 034752 13 LDLIRLSLDERIYVKLRSDRELRGKLHAYDQ---HLNMILGDVEEVVT 57 (85)
Q Consensus 13 l~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~---~mNlvL~n~~E~~~ 57 (85)
.-++..++|++|.|+++||..|+|.|.+++. -+-++|..|.....
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~ 51 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK 51 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence 3466788999999999999999999999998 89999998887644
No 42
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=96.94 E-value=0.0023 Score=38.69 Aligned_cols=35 Identities=11% Similarity=0.320 Sum_probs=28.1
Q ss_pred HHHhhc--CCEEEEEEcCCeEEEEEEEEEcCccceEe
Q 034752 15 LIRLSL--DERIYVKLRSDRELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 15 ~L~~~l--~k~V~V~L~~g~~~~G~L~~fD~~mNlvL 49 (85)
+|+.+. ..+|+|.|.||-.++|.+.|||+|+=++-
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~ 39 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLE 39 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEE
Confidence 444433 57889999999999999999999994443
No 43
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=96.84 E-value=0.0031 Score=38.19 Aligned_cols=35 Identities=14% Similarity=0.242 Sum_probs=28.2
Q ss_pred HHHhhc--CCEEEEEEcCCeEEEEEEEEEcCccceEe
Q 034752 15 LIRLSL--DERIYVKLRSDRELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 15 ~L~~~l--~k~V~V~L~~g~~~~G~L~~fD~~mNlvL 49 (85)
+|+.+. ..+|+|.|.||-.++|.+.|||+|+=++-
T Consensus 7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~ 43 (61)
T TIGR02383 7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLE 43 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence 444433 57899999999999999999999995443
No 44
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=96.62 E-value=0.0051 Score=38.98 Aligned_cols=31 Identities=13% Similarity=0.352 Sum_probs=26.8
Q ss_pred CCEEEEEEcCCeEEEEEEEEEcCccceEecc
Q 034752 21 DERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (85)
Q Consensus 21 ~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n 51 (85)
..+|+|.|.||-.++|.+.|||+|+=|+-.+
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 5889999999999999999999999555434
No 45
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=95.70 E-value=0.047 Score=34.47 Aligned_cols=31 Identities=16% Similarity=0.374 Sum_probs=26.6
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCccceEecc
Q 034752 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (85)
Q Consensus 20 l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n 51 (85)
-..+|+|.|.||-..+|.+.|||.|. +.|++
T Consensus 18 ~~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~ 48 (77)
T COG1923 18 EKIPVTIFLVNGFKLQGQVESFDNFV-VLLKN 48 (77)
T ss_pred cCCeEEEEEEcCEEEEEEEEeeeeEE-EEEEc
Confidence 45889999999999999999999998 44444
No 46
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.29 E-value=0.037 Score=39.38 Aligned_cols=38 Identities=13% Similarity=0.149 Sum_probs=29.1
Q ss_pred HHHHhhc--CCEEEEEEcCCeEEEEEEEEEcCccceEecc
Q 034752 14 DLIRLSL--DERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (85)
Q Consensus 14 ~~L~~~l--~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n 51 (85)
.+|+.+. ..+|+|.|.+|-.++|.+.+||+|.=|+-.+
T Consensus 15 ~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~ 54 (165)
T PRK14091 15 IFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRD 54 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 3444444 4778999999999999999999998444434
No 47
>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=95.11 E-value=0.071 Score=32.14 Aligned_cols=33 Identities=18% Similarity=0.357 Sum_probs=28.8
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCccceEecc
Q 034752 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (85)
Q Consensus 19 ~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n 51 (85)
++|.+|++++-.|.+++|.+.+||.-.++++-.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk 36 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK 36 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence 478999999999999999999999888776544
No 48
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=94.96 E-value=0.078 Score=34.45 Aligned_cols=42 Identities=21% Similarity=0.235 Sum_probs=36.9
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEEcC-ccceEecceEEEEec
Q 034752 17 RLSLDERIYVKLRSDRELRGKLHAYDQ-HLNMILGDVEEVVTT 58 (85)
Q Consensus 17 ~~~l~k~V~V~L~~g~~~~G~L~~fD~-~mNlvL~n~~E~~~~ 58 (85)
..|+|++|.+..+.+-.|+|+|...|. --.+.|.||..+-.+
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE 46 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTE 46 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTET
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcC
Confidence 368999999999999999999999995 678999999876543
No 49
>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=94.92 E-value=0.07 Score=37.87 Aligned_cols=43 Identities=23% Similarity=0.387 Sum_probs=31.6
Q ss_pred CChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEc-CccceEecceEE
Q 034752 10 KEPLDLIRLSLDERIYVKLRSDRELRGKLHAYD-QHLNMILGDVEE 54 (85)
Q Consensus 10 ~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD-~~mNlvL~n~~E 54 (85)
.+|+.+. .|++|+|.|.+.+ +++.|.|..+| -.-|++|-+..|
T Consensus 7 ~~p~~~~-~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 7 KSPLEWQ-DYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp S-HHHHH-CTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred CCHHHHH-HhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 4677665 8999999999999 99999999999 566888876444
No 50
>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=94.80 E-value=0.11 Score=29.15 Aligned_cols=34 Identities=18% Similarity=0.324 Sum_probs=29.0
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCccceEecceEE
Q 034752 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEE 54 (85)
Q Consensus 20 l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E 54 (85)
++++|+|.+ ++..++|+..++|..=.|+++....
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 689999999 6777899999999999999866433
No 51
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=94.51 E-value=0.084 Score=37.56 Aligned_cols=38 Identities=18% Similarity=0.240 Sum_probs=29.6
Q ss_pred HHHHhhc--CCEEEEEEcCCeEEEEEEEEEcCccceEecc
Q 034752 14 DLIRLSL--DERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (85)
Q Consensus 14 ~~L~~~l--~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n 51 (85)
.+|+.+. ..+|+|.|.||-.++|.+.+||.|.=|+-.+
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 3444443 4788999999999999999999999555444
No 52
>PRK14638 hypothetical protein; Provisional
Probab=94.16 E-value=0.11 Score=35.88 Aligned_cols=29 Identities=3% Similarity=0.095 Sum_probs=26.1
Q ss_pred HHhhcCCEEEEEEcCCeEEEEEEEEEcCc
Q 034752 16 IRLSLDERIYVKLRSDRELRGKLHAYDQH 44 (85)
Q Consensus 16 L~~~l~k~V~V~L~~g~~~~G~L~~fD~~ 44 (85)
+.+++|+.|.|++.+++.++|+|.++|.-
T Consensus 95 f~r~~G~~v~V~~~~~k~~~G~L~~~~~~ 123 (150)
T PRK14638 95 YVRFTGKLAKIVTKDGKTFIGRIESFVDG 123 (150)
T ss_pred HHHhCCCEEEEEECCCcEEEEEEEEEeCC
Confidence 34789999999999999999999999964
No 53
>PRK02001 hypothetical protein; Validated
Probab=93.21 E-value=0.2 Score=34.84 Aligned_cols=28 Identities=14% Similarity=0.418 Sum_probs=25.8
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEEcCc
Q 034752 17 RLSLDERIYVKLRSDRELRGKLHAYDQH 44 (85)
Q Consensus 17 ~~~l~k~V~V~L~~g~~~~G~L~~fD~~ 44 (85)
.+++|+.|.|++.+++.|+|+|.++|.-
T Consensus 86 ~r~~G~~v~V~l~~~~~~~G~L~~~~~~ 113 (152)
T PRK02001 86 KKNIGRELEVLTKNGKKIEGELKSADEN 113 (152)
T ss_pred HHhCCCEEEEEECCCCEEEEEEEEEeCC
Confidence 4789999999999999999999999964
No 54
>PRK14639 hypothetical protein; Provisional
Probab=93.15 E-value=0.22 Score=34.10 Aligned_cols=33 Identities=21% Similarity=0.395 Sum_probs=28.0
Q ss_pred HHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEe
Q 034752 16 IRLSLDERIYVKLRSDRELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 16 L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL 49 (85)
+.+++|+.|.|++.+++.++|+|.++|.- ++.|
T Consensus 83 f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 83 FAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 34789999999999999999999999974 3444
No 55
>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=92.90 E-value=0.43 Score=29.89 Aligned_cols=41 Identities=20% Similarity=0.202 Sum_probs=35.2
Q ss_pred hhcCCEEEEEEcCCeEEEEEEEEEcCcc-ceEecceEEEEec
Q 034752 18 LSLDERIYVKLRSDRELRGKLHAYDQHL-NMILGDVEEVVTT 58 (85)
Q Consensus 18 ~~l~k~V~V~L~~g~~~~G~L~~fD~~m-NlvL~n~~E~~~~ 58 (85)
.+++++|.+..+.+-.|.|+|..+|..= -+.|.||..+-++
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTE 44 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTE 44 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeeccc
Confidence 5899999999999999999999999443 5789998877655
No 56
>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=91.43 E-value=0.85 Score=28.87 Aligned_cols=40 Identities=13% Similarity=0.185 Sum_probs=31.2
Q ss_pred hHHHHHhhcCCEEEEEEcCCeEEEEEEEEEc-CccceEecc
Q 034752 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYD-QHLNMILGD 51 (85)
Q Consensus 12 Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD-~~mNlvL~n 51 (85)
-+.+|....+++|.+.|-++.++.|++.++| ...|+..+|
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~ 55 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSN 55 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEE
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhh
Confidence 4566777889999999999999999999999 555777665
No 57
>PRK14644 hypothetical protein; Provisional
Probab=91.41 E-value=0.54 Score=32.11 Aligned_cols=40 Identities=18% Similarity=0.247 Sum_probs=30.5
Q ss_pred cCChHH--HHHhhcCCEEEEEEcCC----eEEEEEEEEEcCccceEe
Q 034752 9 VKEPLD--LIRLSLDERIYVKLRSD----RELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 9 ~~~Pl~--~L~~~l~k~V~V~L~~g----~~~~G~L~~fD~~mNlvL 49 (85)
..+|+. -+.+++|+.|.|+|++. +.++|.|.++|.. ++.|
T Consensus 71 ldRpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l 116 (136)
T PRK14644 71 FDMDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITL 116 (136)
T ss_pred CCCCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEE
Confidence 344533 36688999999999876 8999999999974 3444
No 58
>PRK14640 hypothetical protein; Provisional
Probab=89.54 E-value=0.9 Score=31.36 Aligned_cols=33 Identities=18% Similarity=0.365 Sum_probs=26.5
Q ss_pred HHhhcCCEEEEEE----cCCeEEEEEEEEEcCccceEe
Q 034752 16 IRLSLDERIYVKL----RSDRELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 16 L~~~l~k~V~V~L----~~g~~~~G~L~~fD~~mNlvL 49 (85)
+.+++|+.|.|++ .+.+.++|+|.++|+.. +.|
T Consensus 92 f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~-v~l 128 (152)
T PRK14640 92 FEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDM-ITL 128 (152)
T ss_pred HHHhCCCeEEEEEecccCCceEEEEEEEEEeCCE-EEE
Confidence 3478999999999 46799999999999743 444
No 59
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=89.45 E-value=1.1 Score=27.75 Aligned_cols=28 Identities=25% Similarity=0.404 Sum_probs=23.9
Q ss_pred HhhcCCEEEEEEc---CC-eEEEEEEEEEcCc
Q 034752 17 RLSLDERIYVKLR---SD-RELRGKLHAYDQH 44 (85)
Q Consensus 17 ~~~l~k~V~V~L~---~g-~~~~G~L~~fD~~ 44 (85)
.+++|+.|.|+++ +| +.+.|.|.++|.-
T Consensus 21 ~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 21 ERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred HHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 4789999999997 55 6999999999973
No 60
>PRK14633 hypothetical protein; Provisional
Probab=89.22 E-value=0.99 Score=31.13 Aligned_cols=33 Identities=18% Similarity=0.259 Sum_probs=26.3
Q ss_pred HHhhcCCEEEEEE----cCCeEEEEEEEEEcCccceEe
Q 034752 16 IRLSLDERIYVKL----RSDRELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 16 L~~~l~k~V~V~L----~~g~~~~G~L~~fD~~mNlvL 49 (85)
+.+++|+.|.|++ .+.+.|+|+|.++++. ++.|
T Consensus 89 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 89 AQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 3478999999998 3678999999999975 3444
No 61
>PRK14645 hypothetical protein; Provisional
Probab=88.88 E-value=0.93 Score=31.54 Aligned_cols=27 Identities=11% Similarity=0.132 Sum_probs=23.8
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEEcCc
Q 034752 17 RLSLDERIYVKLRSDRELRGKLHAYDQH 44 (85)
Q Consensus 17 ~~~l~k~V~V~L~~g~~~~G~L~~fD~~ 44 (85)
.+++|+.|.|++ +++.++|+|.++|.-
T Consensus 98 ~r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 98 ERFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred HHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 477899999986 789999999999974
No 62
>PRK14642 hypothetical protein; Provisional
Probab=88.55 E-value=1 Score=32.72 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=24.7
Q ss_pred HhhcCCEEEEEEc-------------CCeEEEEEEEEEcCc
Q 034752 17 RLSLDERIYVKLR-------------SDRELRGKLHAYDQH 44 (85)
Q Consensus 17 ~~~l~k~V~V~L~-------------~g~~~~G~L~~fD~~ 44 (85)
.+++|+.|.|+|+ +.+.|+|+|.++|..
T Consensus 96 ~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 96 ERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG 136 (197)
T ss_pred HHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence 4778999999997 679999999999974
No 63
>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=88.49 E-value=1.1 Score=30.10 Aligned_cols=35 Identities=29% Similarity=0.515 Sum_probs=24.6
Q ss_pred cCChH---HHHHhhcCCEEEEEEc----CCeEEEEEEEEEcC
Q 034752 9 VKEPL---DLIRLSLDERIYVKLR----SDRELRGKLHAYDQ 43 (85)
Q Consensus 9 ~~~Pl---~~L~~~l~k~V~V~L~----~g~~~~G~L~~fD~ 43 (85)
..+|+ .-+.+++|+.|.|.++ +.+.+.|+|.++|.
T Consensus 72 ~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 72 IDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp SSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred CCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 45565 4556899999999994 45799999999998
No 64
>PRK14636 hypothetical protein; Provisional
Probab=87.83 E-value=1.2 Score=31.63 Aligned_cols=33 Identities=15% Similarity=0.294 Sum_probs=26.1
Q ss_pred HHhhcCCEEEEEEc---CC-eEEEEEEEEEcCccceEe
Q 034752 16 IRLSLDERIYVKLR---SD-RELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 16 L~~~l~k~V~V~L~---~g-~~~~G~L~~fD~~mNlvL 49 (85)
+.+++|+.|.|+++ +| +.|+|+|.++|.- ++.|
T Consensus 93 f~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 93 FADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred HHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 34789999999997 45 6999999999873 2444
No 65
>PRK14632 hypothetical protein; Provisional
Probab=87.23 E-value=1.4 Score=31.07 Aligned_cols=33 Identities=24% Similarity=0.425 Sum_probs=26.2
Q ss_pred HHhhcCCEEEEEEcC-------CeEEEEEEEEEcCccceEe
Q 034752 16 IRLSLDERIYVKLRS-------DRELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 16 L~~~l~k~V~V~L~~-------g~~~~G~L~~fD~~mNlvL 49 (85)
+.+++|+.|.|++.+ .+.|+|+|.++|.- ++.|
T Consensus 93 f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l 132 (172)
T PRK14632 93 MSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL 132 (172)
T ss_pred HHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence 347899999999975 57999999999963 3444
No 66
>PRK14634 hypothetical protein; Provisional
Probab=87.22 E-value=1.5 Score=30.44 Aligned_cols=29 Identities=17% Similarity=0.195 Sum_probs=24.1
Q ss_pred HHhhcCCEEEEEEcC----CeEEEEEEEEEcCc
Q 034752 16 IRLSLDERIYVKLRS----DRELRGKLHAYDQH 44 (85)
Q Consensus 16 L~~~l~k~V~V~L~~----g~~~~G~L~~fD~~ 44 (85)
+.+++|+.|.|++.. .+.|+|+|.++|.-
T Consensus 95 f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~ 127 (155)
T PRK14634 95 FQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED 127 (155)
T ss_pred HHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC
Confidence 347899999999864 37999999999974
No 67
>PRK14646 hypothetical protein; Provisional
Probab=86.96 E-value=1.5 Score=30.36 Aligned_cols=34 Identities=15% Similarity=0.131 Sum_probs=26.3
Q ss_pred HHHhhcCCEEEEEEcC---C-eEEEEEEEEEcCccceEe
Q 034752 15 LIRLSLDERIYVKLRS---D-RELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 15 ~L~~~l~k~V~V~L~~---g-~~~~G~L~~fD~~mNlvL 49 (85)
-+.+++|+.|.|+|+. | +.++|+|.++|+- ++.|
T Consensus 94 df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 94 DFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 3457899999999964 2 6889999999975 3444
No 68
>PRK14643 hypothetical protein; Provisional
Probab=86.85 E-value=1.5 Score=30.76 Aligned_cols=34 Identities=21% Similarity=0.414 Sum_probs=26.7
Q ss_pred HHHhhcCCEEEEEEcC----CeEEEEEEEEEcCc-cceE
Q 034752 15 LIRLSLDERIYVKLRS----DRELRGKLHAYDQH-LNMI 48 (85)
Q Consensus 15 ~L~~~l~k~V~V~L~~----g~~~~G~L~~fD~~-mNlv 48 (85)
-+.+++|+.|.|+|+. .+.|+|+|.++|.- ..+.
T Consensus 98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~ 136 (164)
T PRK14643 98 ELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFR 136 (164)
T ss_pred HHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEE
Confidence 3458899999999965 58999999999954 3443
No 69
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=86.74 E-value=1.7 Score=29.75 Aligned_cols=29 Identities=28% Similarity=0.355 Sum_probs=24.9
Q ss_pred HHHhhcCCEEEEEE----cCCeEEEEEEEEEcC
Q 034752 15 LIRLSLDERIYVKL----RSDRELRGKLHAYDQ 43 (85)
Q Consensus 15 ~L~~~l~k~V~V~L----~~g~~~~G~L~~fD~ 43 (85)
-+.+++|+.|.|++ .+++.++|.|.++|.
T Consensus 92 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 92 DFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 34588999999997 567899999999997
No 70
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.93 E-value=2.4 Score=29.62 Aligned_cols=40 Identities=28% Similarity=0.483 Sum_probs=31.3
Q ss_pred cCChH---HHHHhhcCCEEEEEE----cCCeEEEEEEEEEcCccceEe
Q 034752 9 VKEPL---DLIRLSLDERIYVKL----RSDRELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 9 ~~~Pl---~~L~~~l~k~V~V~L----~~g~~~~G~L~~fD~~mNlvL 49 (85)
..+|+ .-+.+++|+.|.|.| .+.+.++|+|.++|.-. +++
T Consensus 84 ldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 84 LDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred CCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 34554 344578999999999 77899999999999876 444
No 71
>PRK14647 hypothetical protein; Provisional
Probab=84.61 E-value=2.4 Score=29.43 Aligned_cols=28 Identities=11% Similarity=0.131 Sum_probs=23.8
Q ss_pred HHhhcCCEEEEEEc---------CCeEEEEEEEEEcC
Q 034752 16 IRLSLDERIYVKLR---------SDRELRGKLHAYDQ 43 (85)
Q Consensus 16 L~~~l~k~V~V~L~---------~g~~~~G~L~~fD~ 43 (85)
+.+++|+.|.|+++ +.+.|+|+|.++|.
T Consensus 94 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 94 YERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 34789999999995 35899999999996
No 72
>PRK14631 hypothetical protein; Provisional
Probab=83.11 E-value=2.8 Score=29.69 Aligned_cols=28 Identities=21% Similarity=0.374 Sum_probs=23.9
Q ss_pred HHHhhcCCEEEEEEc----CCeEEEEEEEEEc
Q 034752 15 LIRLSLDERIYVKLR----SDRELRGKLHAYD 42 (85)
Q Consensus 15 ~L~~~l~k~V~V~L~----~g~~~~G~L~~fD 42 (85)
-+.+++|+.|.|++. +.+.|+|+|.++|
T Consensus 111 df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 111 QLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 345789999999995 4599999999998
No 73
>PRK14637 hypothetical protein; Provisional
Probab=81.85 E-value=3.2 Score=28.73 Aligned_cols=33 Identities=15% Similarity=0.287 Sum_probs=24.9
Q ss_pred HHhhcCCEEEEEEcCCeEE-EEEEEEEcCccceEe
Q 034752 16 IRLSLDERIYVKLRSDREL-RGKLHAYDQHLNMIL 49 (85)
Q Consensus 16 L~~~l~k~V~V~L~~g~~~-~G~L~~fD~~mNlvL 49 (85)
+.+++|+.|.|++.+.+.+ +|+|.++|.- ++.|
T Consensus 93 f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 93 FSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred HHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 3478999999999544556 7999999975 3444
No 74
>PRK14641 hypothetical protein; Provisional
Probab=81.45 E-value=3.1 Score=29.51 Aligned_cols=27 Identities=19% Similarity=0.322 Sum_probs=22.8
Q ss_pred HHhhcCCEEEEEEcC----CeEEEEEEEEEc
Q 034752 16 IRLSLDERIYVKLRS----DRELRGKLHAYD 42 (85)
Q Consensus 16 L~~~l~k~V~V~L~~----g~~~~G~L~~fD 42 (85)
+.+++|+.|.|++.+ .+.|+|+|.++|
T Consensus 99 f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 99 YGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 347899999999965 468999999995
No 75
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=79.63 E-value=4.9 Score=28.54 Aligned_cols=35 Identities=14% Similarity=0.006 Sum_probs=31.2
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCccceEecceE
Q 034752 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (85)
Q Consensus 19 ~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~ 53 (85)
.-+-+|+|.+.||..|.|.+.+|+.-=|.+|..+.
T Consensus 27 ~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 27 FNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred hcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 35789999999999999999999999999987654
No 76
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=77.68 E-value=13 Score=22.57 Aligned_cols=37 Identities=19% Similarity=0.395 Sum_probs=29.6
Q ss_pred ccCCh--HHHHHhhcCCEEEEEEcCCeEEEEEEEEEc-Ccc
Q 034752 8 AVKEP--LDLIRLSLDERIYVKLRSDRELRGKLHAYD-QHL 45 (85)
Q Consensus 8 ~~~~P--l~~L~~~l~k~V~V~L~~g~~~~G~L~~fD-~~m 45 (85)
+...| ...|++++|++|.|.+-.|.. +|+|.+.- +|+
T Consensus 6 s~vdpyvyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI 45 (66)
T PF10842_consen 6 SLVDPYVYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI 45 (66)
T ss_pred eccCHHHHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE
Confidence 34455 577899999999999976655 99999987 776
No 77
>PRK10898 serine endoprotease; Provisional
Probab=77.22 E-value=5.6 Score=30.57 Aligned_cols=32 Identities=19% Similarity=0.299 Sum_probs=28.2
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCccceEecceE
Q 034752 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (85)
Q Consensus 22 k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~ 53 (85)
..+.|.+.+|+.|.+++.++|...+|.+-.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 67899999999999999999999999776553
No 78
>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=76.56 E-value=5.9 Score=30.35 Aligned_cols=32 Identities=22% Similarity=0.386 Sum_probs=28.0
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCccceEecceE
Q 034752 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (85)
Q Consensus 22 k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~ 53 (85)
..+.|.+.+|+.+.+++.++|...+|.+-.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 46889999999999999999999999885543
No 79
>PRK10139 serine endoprotease; Provisional
Probab=72.51 E-value=8.4 Score=30.77 Aligned_cols=32 Identities=25% Similarity=0.459 Sum_probs=28.2
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCccceEecceE
Q 034752 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (85)
Q Consensus 22 k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~ 53 (85)
..|.|.+.||++|.+++.++|....|.+-.+.
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 67899999999999999999999998875543
No 80
>PRK10942 serine endoprotease; Provisional
Probab=72.42 E-value=8.1 Score=31.01 Aligned_cols=31 Identities=23% Similarity=0.350 Sum_probs=27.6
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCccceEecce
Q 034752 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDV 52 (85)
Q Consensus 22 k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~ 52 (85)
..|.|.+.+|++|.+++.++|...+|.|-..
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 5789999999999999999999999887644
No 81
>PRK06955 biotin--protein ligase; Provisional
Probab=67.07 E-value=15 Score=27.66 Aligned_cols=32 Identities=16% Similarity=0.202 Sum_probs=27.3
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCccceEec
Q 034752 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILG 50 (85)
Q Consensus 19 ~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~ 50 (85)
+++++|+|...+++.++|++.|+|..=.|+++
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 56899999766778899999999998888885
No 82
>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=66.73 E-value=13 Score=28.98 Aligned_cols=32 Identities=25% Similarity=0.434 Sum_probs=28.1
Q ss_pred CEEEEEEcCCeEEEEEEEEEcCccceEecceE
Q 034752 22 ERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (85)
Q Consensus 22 k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~ 53 (85)
..+.|.+.+|+.|.+++.++|...+|.|-.+.
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 57889999999999999999999999876554
No 83
>PRK14630 hypothetical protein; Provisional
Probab=65.94 E-value=14 Score=25.29 Aligned_cols=29 Identities=14% Similarity=0.126 Sum_probs=23.0
Q ss_pred HHhhcCCEEEEEEcCCeEEEEEEEEEcCcc
Q 034752 16 IRLSLDERIYVKLRSDRELRGKLHAYDQHL 45 (85)
Q Consensus 16 L~~~l~k~V~V~L~~g~~~~G~L~~fD~~m 45 (85)
+.+++|++|.|++... ..+|+|.++|.-.
T Consensus 92 f~r~~G~~v~V~l~~~-~~~G~L~~~~d~~ 120 (143)
T PRK14630 92 FKIFEGKKIKLMLDND-FEEGFILEAKADS 120 (143)
T ss_pred HHHhCCCEEEEEEcCc-ceEEEEEEEeCCE
Confidence 3478999999999654 4599999999743
No 84
>PRK14635 hypothetical protein; Provisional
Probab=65.77 E-value=15 Score=25.55 Aligned_cols=28 Identities=11% Similarity=0.075 Sum_probs=22.8
Q ss_pred HhhcCCEEEEEEc--CCeEEEE---EEEEEcCc
Q 034752 17 RLSLDERIYVKLR--SDRELRG---KLHAYDQH 44 (85)
Q Consensus 17 ~~~l~k~V~V~L~--~g~~~~G---~L~~fD~~ 44 (85)
.++.|+.|.|++. ++..++| .|.++|.-
T Consensus 95 ~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~ 127 (162)
T PRK14635 95 DRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD 127 (162)
T ss_pred HHhCCCEEEEEEecCCCcEEEecceEEEEEcCC
Confidence 4789999999875 4678888 99999963
No 85
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=62.72 E-value=31 Score=23.90 Aligned_cols=26 Identities=4% Similarity=0.041 Sum_probs=23.4
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEEc
Q 034752 17 RLSLDERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 17 ~~~l~k~V~V~L~~g~~~~G~L~~fD 42 (85)
..++||.|.+...+|..++|++.+..
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 37899999999999999999998885
No 86
>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=61.55 E-value=13 Score=24.49 Aligned_cols=17 Identities=35% Similarity=0.608 Sum_probs=14.3
Q ss_pred CEEEEEEcCCeEEEEEE
Q 034752 22 ERIYVKLRSDRELRGKL 38 (85)
Q Consensus 22 k~V~V~L~~g~~~~G~L 38 (85)
.+|.+.|+||+.+.|++
T Consensus 29 ~~V~l~L~DGs~l~Gtv 45 (101)
T PF11607_consen 29 ERVELELDDGSMLRGTV 45 (101)
T ss_dssp -EEEEEETTS-EEEEEE
T ss_pred ceEEEEEcCCCeeeeee
Confidence 78999999999999997
No 87
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=59.52 E-value=11 Score=26.75 Aligned_cols=30 Identities=23% Similarity=0.354 Sum_probs=24.0
Q ss_pred HHHHhhc--CCEEEEEEcCCeEEEEEEEEEcC
Q 034752 14 DLIRLSL--DERIYVKLRSDRELRGKLHAYDQ 43 (85)
Q Consensus 14 ~~L~~~l--~k~V~V~L~~g~~~~G~L~~fD~ 43 (85)
+..+++. ++.|+|-+.|||+++|+=.|.|.
T Consensus 111 ~Icrka~qqg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 111 SICRKAHQQGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred HHHHHHHHCCCeEEEEEcCCcEEEeeecccce
Confidence 3334443 68899999999999999999885
No 88
>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=57.90 E-value=15 Score=23.58 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=19.3
Q ss_pred hhcCCEEEEE-EcCCeEEEEEEEE
Q 034752 18 LSLDERIYVK-LRSDRELRGKLHA 40 (85)
Q Consensus 18 ~~l~k~V~V~-L~~g~~~~G~L~~ 40 (85)
-++|..|+|+ +.+|+.+.|++.+
T Consensus 93 g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 93 GAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred cCCCCEEEEEECCCCCEEEEEEeC
Confidence 3578899999 7899999999875
No 89
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=57.40 E-value=17 Score=26.12 Aligned_cols=32 Identities=22% Similarity=0.406 Sum_probs=22.8
Q ss_pred HHHHHhhcC--CEEEEEE-cCCeEEEEEEEEEcCc
Q 034752 13 LDLIRLSLD--ERIYVKL-RSDRELRGKLHAYDQH 44 (85)
Q Consensus 13 l~~L~~~l~--k~V~V~L-~~g~~~~G~L~~fD~~ 44 (85)
++||-++.. -+|.|.+ .++..|+|.+.++|.-
T Consensus 123 I~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 456655544 4566665 5689999999999965
No 90
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=56.50 E-value=17 Score=20.45 Aligned_cols=22 Identities=27% Similarity=0.511 Sum_probs=14.6
Q ss_pred EEEEEEEEcCccceEecceEEE
Q 034752 34 LRGKLHAYDQHLNMILGDVEEV 55 (85)
Q Consensus 34 ~~G~L~~fD~~mNlvL~n~~E~ 55 (85)
.+|+..|.|+.+.|.|.+....
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 6899999999999999876543
No 91
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=55.98 E-value=30 Score=25.86 Aligned_cols=31 Identities=19% Similarity=0.378 Sum_probs=26.1
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCccceEec
Q 034752 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILG 50 (85)
Q Consensus 19 ~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~ 50 (85)
+++++|++.. ++..++|++.|+|..=.|++.
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 4589999986 456799999999999999885
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=51.55 E-value=43 Score=20.84 Aligned_cols=29 Identities=21% Similarity=0.272 Sum_probs=21.4
Q ss_pred HHHHHhhcCCEEEEEEcCCe----EEEEEEEEE
Q 034752 13 LDLIRLSLDERIYVKLRSDR----ELRGKLHAY 41 (85)
Q Consensus 13 l~~L~~~l~k~V~V~L~~g~----~~~G~L~~f 41 (85)
-..|...+|++|.++.+.|| +-.|.|..-
T Consensus 9 k~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 9 KKELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 35677899999999999997 778998754
No 93
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=49.89 E-value=39 Score=28.08 Aligned_cols=33 Identities=9% Similarity=0.139 Sum_probs=27.9
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCccceEecc
Q 034752 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (85)
Q Consensus 19 ~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n 51 (85)
+++++|++...++..++|+..|+|..=.|+|+.
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 568999987667778999999999999999853
No 94
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=48.90 E-value=22 Score=25.84 Aligned_cols=23 Identities=17% Similarity=0.325 Sum_probs=20.0
Q ss_pred hhcCCEEEEE-EcCCeEEEEEEEE
Q 034752 18 LSLDERIYVK-LRSDRELRGKLHA 40 (85)
Q Consensus 18 ~~l~k~V~V~-L~~g~~~~G~L~~ 40 (85)
-.+|..|+|+ +.+|+.+.|++.+
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeC
Confidence 3578999999 9999999999876
No 95
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=48.44 E-value=48 Score=24.82 Aligned_cols=31 Identities=13% Similarity=0.237 Sum_probs=26.0
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCccceEecc
Q 034752 20 LDERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (85)
Q Consensus 20 l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n 51 (85)
++++|+|.. ++..+.|++.|+|..=.|++..
T Consensus 236 ~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 236 KDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred CCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 689998875 5689999999999988888753
No 96
>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=47.23 E-value=52 Score=23.58 Aligned_cols=31 Identities=13% Similarity=0.275 Sum_probs=25.9
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCccceEec
Q 034752 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILG 50 (85)
Q Consensus 19 ~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~ 50 (85)
.++++|+|...+ ..+.|+..|+|..=.|+++
T Consensus 191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 458999998654 5699999999999999885
No 97
>PRK08330 biotin--protein ligase; Provisional
Probab=47.12 E-value=59 Score=23.32 Aligned_cols=32 Identities=22% Similarity=0.196 Sum_probs=25.5
Q ss_pred hcCCEEEEEEcCCeEE-EEEEEEEcCccceEecc
Q 034752 19 SLDERIYVKLRSDREL-RGKLHAYDQHLNMILGD 51 (85)
Q Consensus 19 ~l~k~V~V~L~~g~~~-~G~L~~fD~~mNlvL~n 51 (85)
+++++|++.. ++..+ .|+..|+|..=.|++..
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 5689999875 55554 79999999988888863
No 98
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=46.16 E-value=53 Score=24.17 Aligned_cols=34 Identities=18% Similarity=0.223 Sum_probs=30.5
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCccceEecce
Q 034752 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILGDV 52 (85)
Q Consensus 19 ~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~ 52 (85)
.++++|++...++..+.|+..++|..-.|+++..
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 4689999999999999999999999999998765
No 99
>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=44.86 E-value=17 Score=22.76 Aligned_cols=18 Identities=17% Similarity=0.398 Sum_probs=12.4
Q ss_pred cCCEEEEEEcCCeEEEEE
Q 034752 20 LDERIYVKLRSDRELRGK 37 (85)
Q Consensus 20 l~k~V~V~L~~g~~~~G~ 37 (85)
...+|+++|+||..+.|+
T Consensus 16 ~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 16 YRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp TTT-EEEE-TTT--EEES
T ss_pred cCCeEEEEEeCCCEEEEE
Confidence 357899999999999998
No 100
>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=43.93 E-value=34 Score=22.54 Aligned_cols=27 Identities=22% Similarity=0.277 Sum_probs=20.5
Q ss_pred CEEEEEEcCCeEEEEEEEEEc-CccceE
Q 034752 22 ERIYVKLRSDRELRGKLHAYD-QHLNMI 48 (85)
Q Consensus 22 k~V~V~L~~g~~~~G~L~~fD-~~mNlv 48 (85)
....|.++||+.+.|.+..=| ....+.
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~~~~~~l~ 85 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASETADGVTVK 85 (133)
T ss_pred ccEEEEECCCCEEEEEEEecCCCeEEEE
Confidence 447899999999999998855 343443
No 101
>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=39.87 E-value=79 Score=19.99 Aligned_cols=15 Identities=0% Similarity=0.045 Sum_probs=12.5
Q ss_pred HHHHHhhcCCEEEEE
Q 034752 13 LDLIRLSLDERIYVK 27 (85)
Q Consensus 13 l~~L~~~l~k~V~V~ 27 (85)
-+.|.++.+++|++.
T Consensus 7 ~~~L~~f~gk~V~iv 21 (101)
T cd04479 7 GAMLSQFVGKTVRIV 21 (101)
T ss_pred HHHHHhhCCCEEEEE
Confidence 358899999999876
No 102
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=39.83 E-value=90 Score=25.36 Aligned_cols=48 Identities=25% Similarity=0.264 Sum_probs=39.4
Q ss_pred ccCChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEE
Q 034752 8 AVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVV 56 (85)
Q Consensus 8 ~~~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~ 56 (85)
....|-.++.+++||.|+- =++|++++++|.+=|.-.=+.+.+-.|..
T Consensus 69 ~l~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~ 116 (421)
T COG5316 69 DLLSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVL 116 (421)
T ss_pred cccCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEE
Confidence 3467889999999999988 78999999999999977767766665544
No 103
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=39.72 E-value=59 Score=22.46 Aligned_cols=25 Identities=12% Similarity=0.077 Sum_probs=22.1
Q ss_pred hhcCCEEEEEEcCCeEEEEEEEEEc
Q 034752 18 LSLDERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 18 ~~l~k~V~V~L~~g~~~~G~L~~fD 42 (85)
.++||.|.....+|..++|++.++.
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~ 114 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQ 114 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEE
Confidence 6899999988889999999998765
No 104
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=38.02 E-value=71 Score=18.83 Aligned_cols=25 Identities=24% Similarity=0.466 Sum_probs=17.8
Q ss_pred hcCCEEEEEEcCCe-EEEEEEEEEcC
Q 034752 19 SLDERIYVKLRSDR-ELRGKLHAYDQ 43 (85)
Q Consensus 19 ~l~k~V~V~L~~g~-~~~G~L~~fD~ 43 (85)
..|..|.++--+.. -|.|++.+||.
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~ 32 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDS 32 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEET
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecc
Confidence 35788999887654 55999999995
No 105
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=36.80 E-value=48 Score=22.97 Aligned_cols=22 Identities=23% Similarity=0.282 Sum_probs=18.6
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q 034752 19 SLDERIYVK-LRSDRELRGKLHA 40 (85)
Q Consensus 19 ~l~k~V~V~-L~~g~~~~G~L~~ 40 (85)
..|..|+|+ +..|+.++|++.+
T Consensus 129 ~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 129 AAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 567899999 8899999998864
No 106
>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=35.99 E-value=57 Score=21.55 Aligned_cols=29 Identities=14% Similarity=0.047 Sum_probs=24.9
Q ss_pred cCChHHHHHhhcCCEEEEEEcCCeEEEEE
Q 034752 9 VKEPLDLIRLSLDERIYVKLRSDRELRGK 37 (85)
Q Consensus 9 ~~~Pl~~L~~~l~k~V~V~L~~g~~~~G~ 37 (85)
...|+.-|....+-.|+.++.+|+.|.+.
T Consensus 62 ~~~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 62 KDTDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CCCCHHHHhCCcccEEEEEecCCcEEEec
Confidence 34678888899999999999999999765
No 107
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=35.51 E-value=21 Score=24.94 Aligned_cols=25 Identities=24% Similarity=0.231 Sum_probs=19.5
Q ss_pred EcCCeEEEEEEEEEcCccceEecce
Q 034752 28 LRSDRELRGKLHAYDQHLNMILGDV 52 (85)
Q Consensus 28 L~~g~~~~G~L~~fD~~mNlvL~n~ 52 (85)
+++...=.|+|+|.|+|=|=--+|-
T Consensus 39 yrtd~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 39 YRTDDHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred Hhcccccceeeeeecccccchhccc
Confidence 3445566799999999999887775
No 108
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=34.79 E-value=62 Score=23.44 Aligned_cols=23 Identities=26% Similarity=0.320 Sum_probs=19.7
Q ss_pred hhcCCEEEEEEcCCeEEEEEEEE
Q 034752 18 LSLDERIYVKLRSDRELRGKLHA 40 (85)
Q Consensus 18 ~~l~k~V~V~L~~g~~~~G~L~~ 40 (85)
-.+|..|+|+-.+|+.+.|++.|
T Consensus 193 G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 193 GNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCCEEEEEeCCCCEEEEEEec
Confidence 35789999999889999999876
No 109
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=34.79 E-value=85 Score=23.57 Aligned_cols=31 Identities=29% Similarity=0.312 Sum_probs=25.6
Q ss_pred CCEEEEEEcCCeEEEEEEEEEcCccceEecc
Q 034752 21 DERIYVKLRSDRELRGKLHAYDQHLNMILGD 51 (85)
Q Consensus 21 ~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n 51 (85)
..++.|.+.+|+.+.+.+.|+|...-+.+-.
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlk 125 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLK 125 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEE
Confidence 3678888999999999999999877665543
No 110
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=34.23 E-value=53 Score=23.92 Aligned_cols=22 Identities=32% Similarity=0.436 Sum_probs=19.0
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q 034752 19 SLDERIYVK-LRSDRELRGKLHA 40 (85)
Q Consensus 19 ~l~k~V~V~-L~~g~~~~G~L~~ 40 (85)
..|..|+|+ +..|+.+.|++.+
T Consensus 184 ~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 184 GENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 468999999 7999999999865
No 111
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.52 E-value=79 Score=25.16 Aligned_cols=43 Identities=19% Similarity=0.171 Sum_probs=35.8
Q ss_pred HHhhcCCEEEEEEcCCeEEEEEEEEEc-CccceEecceEEEEec
Q 034752 16 IRLSLDERIYVKLRSDRELRGKLHAYD-QHLNMILGDVEEVVTT 58 (85)
Q Consensus 16 L~~~l~k~V~V~L~~g~~~~G~L~~fD-~~mNlvL~n~~E~~~~ 58 (85)
...|+|+.|.+.-+..-+|+|+|.-.| +--=|-|.+|..+-++
T Consensus 4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTE 47 (361)
T KOG1073|consen 4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTE 47 (361)
T ss_pred ccccccceeEEeecccceeeeEEEeccccccceehhheeecccc
Confidence 346899999999999999999999988 5556888998766554
No 112
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=32.12 E-value=65 Score=21.86 Aligned_cols=22 Identities=27% Similarity=0.460 Sum_probs=18.5
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q 034752 19 SLDERIYVK-LRSDRELRGKLHA 40 (85)
Q Consensus 19 ~l~k~V~V~-L~~g~~~~G~L~~ 40 (85)
..|..|+|+ +.+|+.+.|++.+
T Consensus 110 ~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 110 GVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 567899996 7899999999875
No 113
>PRK10708 hypothetical protein; Provisional
Probab=31.43 E-value=60 Score=19.54 Aligned_cols=26 Identities=19% Similarity=0.294 Sum_probs=22.2
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCcc
Q 034752 20 LDERIYVKLRSDRELRGKLHAYDQHL 45 (85)
Q Consensus 20 l~k~V~V~L~~g~~~~G~L~~fD~~m 45 (85)
++.+|+|++.+|-.-.|++.+...|-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 46789999999999999998888664
No 114
>PRK08477 biotin--protein ligase; Provisional
Probab=31.40 E-value=2e+02 Score=20.75 Aligned_cols=36 Identities=3% Similarity=-0.064 Sum_probs=29.3
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEE
Q 034752 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEV 55 (85)
Q Consensus 19 ~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~ 55 (85)
.+++.|+|. .+++.++|+..+.|+.=-|++..-.-+
T Consensus 173 ~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~~ 208 (211)
T PRK08477 173 EKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKVY 208 (211)
T ss_pred HcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEee
Confidence 468999986 578999999999999988887765433
No 115
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=30.46 E-value=65 Score=24.19 Aligned_cols=23 Identities=30% Similarity=0.250 Sum_probs=19.7
Q ss_pred hhcCCEEEEE-EcCCeEEEEEEEE
Q 034752 18 LSLDERIYVK-LRSDRELRGKLHA 40 (85)
Q Consensus 18 ~~l~k~V~V~-L~~g~~~~G~L~~ 40 (85)
-..|..|+|+ +.+|+.+.|++.+
T Consensus 230 G~~Gd~IrVrN~~SgkvV~a~V~~ 253 (261)
T PRK06804 230 GRKGELIKVKNLSSGRVVTATVDG 253 (261)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 3568999999 8999999999876
No 116
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=30.09 E-value=55 Score=22.48 Aligned_cols=28 Identities=18% Similarity=0.258 Sum_probs=21.0
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEEcCcc
Q 034752 17 RLSLDERIYVKLRSDRELRGKLHAYDQHL 45 (85)
Q Consensus 17 ~~~l~k~V~V~L~~g~~~~G~L~~fD~~m 45 (85)
++++.|-++|.|.||++++..+-| |.|.
T Consensus 52 NSAlRK~~RVrL~NG~~VtAyiPg-~Gh~ 79 (129)
T COG0048 52 NSALRKVARVRLINGKEVTAYIPG-EGHN 79 (129)
T ss_pred ChhhheeEEEEeeCCcEEEEEcCC-CCcc
Confidence 356778899999999999876644 4443
No 117
>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=28.71 E-value=35 Score=22.04 Aligned_cols=17 Identities=24% Similarity=0.208 Sum_probs=15.2
Q ss_pred EEEEEEcCccceEecce
Q 034752 36 GKLHAYDQHLNMILGDV 52 (85)
Q Consensus 36 G~L~~fD~~mNlvL~n~ 52 (85)
|+|+|.|.|=|.--++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999988776
No 118
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=28.24 E-value=69 Score=18.04 Aligned_cols=15 Identities=20% Similarity=0.368 Sum_probs=12.4
Q ss_pred HHHHHhhcCCEEEEE
Q 034752 13 LDLIRLSLDERIYVK 27 (85)
Q Consensus 13 l~~L~~~l~k~V~V~ 27 (85)
.+.+++++||+|+|.
T Consensus 11 ~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVT 25 (48)
T ss_pred hHHHHHhcCCeEEEE
Confidence 566778999999987
No 119
>PRK11625 Rho-binding antiterminator; Provisional
Probab=27.54 E-value=1.1e+02 Score=19.23 Aligned_cols=19 Identities=16% Similarity=0.207 Sum_probs=16.6
Q ss_pred cCCEEEEEEcCCeEEEEEE
Q 034752 20 LDERIYVKLRSDRELRGKL 38 (85)
Q Consensus 20 l~k~V~V~L~~g~~~~G~L 38 (85)
.+-+|.+++++|..+.|+-
T Consensus 22 ~~~~l~l~l~dGe~~~g~A 40 (84)
T PRK11625 22 HHLMLTLELKDGEVLQAKA 40 (84)
T ss_pred cCCeEEEEECCCCEEEEEE
Confidence 4678999999999999986
No 120
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=27.13 E-value=71 Score=19.20 Aligned_cols=26 Identities=19% Similarity=0.288 Sum_probs=22.0
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCcc
Q 034752 20 LDERIYVKLRSDRELRGKLHAYDQHL 45 (85)
Q Consensus 20 l~k~V~V~L~~g~~~~G~L~~fD~~m 45 (85)
++.+|+|++.+|-.-.|++.+...|-
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 46789999999999999998887664
No 121
>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=27.09 E-value=1.1e+02 Score=16.46 Aligned_cols=25 Identities=8% Similarity=0.249 Sum_probs=20.7
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEcCc
Q 034752 20 LDERIYVKLRSDRELRGKLHAYDQH 44 (85)
Q Consensus 20 l~k~V~V~L~~g~~~~G~L~~fD~~ 44 (85)
.|..+.+...+|.-|+|++.+++.-
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4667777777899999999999963
No 122
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=26.20 E-value=67 Score=19.11 Aligned_cols=21 Identities=19% Similarity=0.335 Sum_probs=17.7
Q ss_pred CEEEEEEcCCeEEEEEEEEEc
Q 034752 22 ERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 22 k~V~V~L~~g~~~~G~L~~fD 42 (85)
.+|.|++-||..+++++..-|
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~ 25 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSD 25 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 578999999999999987644
No 123
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=25.75 E-value=59 Score=20.16 Aligned_cols=18 Identities=22% Similarity=0.396 Sum_probs=14.4
Q ss_pred HHHhhcCCEEEEEEcCCe
Q 034752 15 LIRLSLDERIYVKLRSDR 32 (85)
Q Consensus 15 ~L~~~l~k~V~V~L~~g~ 32 (85)
.++..+||+|+|+.....
T Consensus 5 ~~nDrLGKKVRvKCn~dD 22 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDD 22 (73)
T ss_pred hhhhhcCceEEEEeCCcc
Confidence 567889999999987543
No 124
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=25.63 E-value=72 Score=20.78 Aligned_cols=26 Identities=19% Similarity=0.167 Sum_probs=20.7
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEEc
Q 034752 17 RLSLDERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 17 ~~~l~k~V~V~L~~g~~~~G~L~~fD 42 (85)
++++.|-++|+|.+|+.++..+=|-.
T Consensus 31 NSA~RK~arV~L~ngk~v~ayIPg~G 56 (95)
T cd00319 31 NSALRKVAKVRLTSGYEVTAYIPGEG 56 (95)
T ss_pred ChhhceEEEEEccCCCEEEEECCCCC
Confidence 35677889999999999987776655
No 125
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.49 E-value=63 Score=20.50 Aligned_cols=44 Identities=23% Similarity=0.305 Sum_probs=28.4
Q ss_pred cCChHHHHHhhcCCEEEEEEcCCeEE----EEEE-EEEcCccceEecce
Q 034752 9 VKEPLDLIRLSLDERIYVKLRSDREL----RGKL-HAYDQHLNMILGDV 52 (85)
Q Consensus 9 ~~~Pl~~L~~~l~k~V~V~L~~g~~~----~G~L-~~fD~~mNlvL~n~ 52 (85)
+.....-+...+|++|.++.++||.= .|.| ..|-.++=+-|++.
T Consensus 7 i~~IK~~i~ah~G~~v~lk~ngGRKk~~~r~G~L~EtYpSvFIiel~~d 55 (80)
T COG4466 7 IVDIKESIDAHLGERVTLKANGGRKKTIERSGILIETYPSVFIIELDQD 55 (80)
T ss_pred HHHHHHHHHhccCcEEEEEecCCceeeehhceEEeeecCcEEEEEeccc
Confidence 33445566778899999999999743 4665 34445554545443
No 126
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.40 E-value=85 Score=22.80 Aligned_cols=35 Identities=9% Similarity=0.150 Sum_probs=29.5
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEEcCccceEecceE
Q 034752 19 SLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVE 53 (85)
Q Consensus 19 ~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~ 53 (85)
.++-+|.|..-++...+|.+.+||---+...-.+.
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 35678889999999999999999988887766665
No 127
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=25.37 E-value=76 Score=21.66 Aligned_cols=26 Identities=15% Similarity=0.137 Sum_probs=21.3
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEEc
Q 034752 17 RLSLDERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 17 ~~~l~k~V~V~L~~g~~~~G~L~~fD 42 (85)
++++.|.++|.|.+|++++..+=|-.
T Consensus 46 NSA~RKvarVrL~ngk~v~AyIPGeG 71 (124)
T PRK05163 46 NSALRKVARVRLTNGFEVTAYIPGEG 71 (124)
T ss_pred CchhheEEEEEeCCCCEEEEEcCCCC
Confidence 35667889999999999998887655
No 128
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=25.31 E-value=1.3e+02 Score=21.95 Aligned_cols=25 Identities=8% Similarity=0.125 Sum_probs=21.5
Q ss_pred hhcCCEEEEEEcCCeEEEEEEEEEc
Q 034752 18 LSLDERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 18 ~~l~k~V~V~L~~g~~~~G~L~~fD 42 (85)
.++||.|.+.-.+|..+.|++.+..
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 6799999988888999999997664
No 129
>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=24.69 E-value=1e+02 Score=18.11 Aligned_cols=21 Identities=14% Similarity=0.420 Sum_probs=17.1
Q ss_pred CEEEEEEcCCeEEEEEEEEEc
Q 034752 22 ERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 22 k~V~V~L~~g~~~~G~L~~fD 42 (85)
.+|.|++-||..+++++..-|
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~ 23 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTH 23 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 368999999999999986544
No 130
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.42 E-value=94 Score=24.12 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=19.6
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEEE
Q 034752 19 SLDERIYVK-LRSDRELRGKLHAY 41 (85)
Q Consensus 19 ~l~k~V~V~-L~~g~~~~G~L~~f 41 (85)
.+|..|+|+ +.+|+.+.|++.+=
T Consensus 287 ~~Gd~IrV~N~~S~kiv~g~V~g~ 310 (338)
T PRK12786 287 AEGDVVRVLNLQSKRTVTGTVTGR 310 (338)
T ss_pred CCCCEEEEEECCCCCEEEEEEecC
Confidence 568999996 88999999998764
No 131
>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=24.10 E-value=1.2e+02 Score=17.79 Aligned_cols=21 Identities=29% Similarity=0.407 Sum_probs=17.1
Q ss_pred CEEEEEEcCCeEEEEEEEEEc
Q 034752 22 ERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 22 k~V~V~L~~g~~~~G~L~~fD 42 (85)
-+|.|++-||..++..+..-|
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~ 27 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSD 27 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTS
T ss_pred EEEEEECCCCCEEEEEECCcc
Confidence 468899999999999987544
No 132
>PF13144 SAF_2: SAF-like
Probab=24.06 E-value=1.3e+02 Score=20.73 Aligned_cols=23 Identities=26% Similarity=0.348 Sum_probs=18.7
Q ss_pred hhcCCEEEEEE-cCCeEEEEEEEE
Q 034752 18 LSLDERIYVKL-RSDRELRGKLHA 40 (85)
Q Consensus 18 ~~l~k~V~V~L-~~g~~~~G~L~~ 40 (85)
-++|..|+|+- ..|+.+.|++.+
T Consensus 167 G~~G~~I~V~N~~S~k~v~g~V~~ 190 (196)
T PF13144_consen 167 GALGDTIRVKNLSSGKIVQGRVIG 190 (196)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 35789999997 559999999876
No 133
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=23.42 E-value=83 Score=21.48 Aligned_cols=26 Identities=15% Similarity=0.137 Sum_probs=21.0
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEEc
Q 034752 17 RLSLDERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 17 ~~~l~k~V~V~L~~g~~~~G~L~~fD 42 (85)
++++.|.++|.|.+|+.++..+=|-.
T Consensus 46 NSA~RKvarVrL~ngk~v~AyIPG~G 71 (124)
T TIGR00981 46 NSALRKVARVRLTNGFEVTAYIPGEG 71 (124)
T ss_pred CchhheeEEEEeCCCCEEEEEcCCCC
Confidence 35667889999999999988876655
No 134
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=23.15 E-value=1.2e+02 Score=21.36 Aligned_cols=26 Identities=19% Similarity=0.364 Sum_probs=21.6
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEEc
Q 034752 17 RLSLDERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 17 ~~~l~k~V~V~L~~g~~~~G~L~~fD 42 (85)
...+|++|.|.+...+.+.|.+..++
T Consensus 24 ~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 24 KDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp GGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 34899999999998899999998874
No 135
>CHL00051 rps12 ribosomal protein S12
Probab=22.32 E-value=86 Score=21.37 Aligned_cols=31 Identities=23% Similarity=0.246 Sum_probs=23.7
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEEcCccceEe
Q 034752 17 RLSLDERIYVKLRSDRELRGKLHAYDQHLNMIL 49 (85)
Q Consensus 17 ~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL 49 (85)
++++.|.++|.|.+|++++..+=|.. | ||.=
T Consensus 46 NSA~RKvarVrLsngk~v~AyIPGeG-h-nlqe 76 (123)
T CHL00051 46 NSALRKVARVRLTSGFEITAYIPGIG-H-NLQE 76 (123)
T ss_pred ChhheeEEEEEccCCCEEEEEcCCCC-c-cccc
Confidence 35667889999999999998876654 4 6653
No 136
>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=21.55 E-value=91 Score=18.73 Aligned_cols=23 Identities=22% Similarity=0.405 Sum_probs=18.4
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEc
Q 034752 20 LDERIYVKLRSDRELRGKLHAYD 42 (85)
Q Consensus 20 l~k~V~V~L~~g~~~~G~L~~fD 42 (85)
..-+|.|+|-||..+++++..-|
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCC
Confidence 34678999999999999976544
No 137
>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=21.33 E-value=1.2e+02 Score=19.22 Aligned_cols=15 Identities=0% Similarity=0.062 Sum_probs=11.7
Q ss_pred HHHHHhhcCCEEEEE
Q 034752 13 LDLIRLSLDERIYVK 27 (85)
Q Consensus 13 l~~L~~~l~k~V~V~ 27 (85)
-+.|.++.+++|++.
T Consensus 10 ~~~L~~~~gk~Vriv 24 (109)
T PF08661_consen 10 GSMLSQFVGKTVRIV 24 (109)
T ss_dssp GGGGGGGTTSEEEEE
T ss_pred HHHHHhhCCCeEEEE
Confidence 356788999999876
No 138
>cd03367 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation. Also members of this subfamily are the archaeal 30S ribosomal S12 proteins. Prokaryotic S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=20.82 E-value=1.3e+02 Score=20.22 Aligned_cols=27 Identities=11% Similarity=0.273 Sum_probs=20.5
Q ss_pred HhhcCCEEEEEE-cCCeEEEEEEEEEcCc
Q 034752 17 RLSLDERIYVKL-RSDRELRGKLHAYDQH 44 (85)
Q Consensus 17 ~~~l~k~V~V~L-~~g~~~~G~L~~fD~~ 44 (85)
++++.|-++|+| +||+.++..+=| |.|
T Consensus 38 NSA~RK~~rV~L~~ngk~itAyIPG-~G~ 65 (115)
T cd03367 38 NSAIRKCVRVQLIKNGKKITAFVPG-DGC 65 (115)
T ss_pred ChhhceEEEEEEccCCeEEEEEeCC-CCc
Confidence 356678899999 699999877765 344
No 139
>PF13437 HlyD_3: HlyD family secretion protein
Probab=20.10 E-value=2.1e+02 Score=17.15 Aligned_cols=33 Identities=18% Similarity=0.309 Sum_probs=25.8
Q ss_pred ChHHHHHhh--cCCEEEEEEcCC--eEEEEEEEEEcC
Q 034752 11 EPLDLIRLS--LDERIYVKLRSD--RELRGKLHAYDQ 43 (85)
Q Consensus 11 ~Pl~~L~~~--l~k~V~V~L~~g--~~~~G~L~~fD~ 43 (85)
-|.+.+... .+..|++.+.++ ..+.|++..++.
T Consensus 42 v~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 42 VPEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred EChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 455666665 689999999854 699999999987
Done!