Query 032889
Match_columns 131
No_of_seqs 167 out of 1035
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 07:11:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032889.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032889hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01729 LSm7 The eukaryotic Sm 99.9 7.3E-24 1.6E-28 143.4 10.4 79 38-116 2-80 (81)
2 KOG1781 Small Nuclear ribonucl 99.9 1.2E-25 2.6E-30 155.6 0.5 101 29-129 8-108 (108)
3 cd01719 Sm_G The eukaryotic Sm 99.9 7.2E-22 1.6E-26 130.9 9.7 70 40-117 2-71 (72)
4 cd01717 Sm_B The eukaryotic Sm 99.9 2.7E-21 5.9E-26 129.9 10.3 73 42-114 4-78 (79)
5 cd01727 LSm8 The eukaryotic Sm 99.9 2.9E-21 6.3E-26 128.3 10.0 72 41-116 2-73 (74)
6 cd01728 LSm1 The eukaryotic Sm 99.9 3E-21 6.5E-26 128.7 10.0 71 39-114 3-73 (74)
7 cd01730 LSm3 The eukaryotic Sm 99.9 2.8E-21 6.1E-26 130.7 9.4 75 40-114 2-82 (82)
8 cd01731 archaeal_Sm1 The archa 99.9 3.4E-21 7.3E-26 125.9 8.8 64 43-114 5-68 (68)
9 cd01732 LSm5 The eukaryotic Sm 99.8 1.2E-20 2.5E-25 126.4 9.7 71 40-115 4-75 (76)
10 PRK00737 small nuclear ribonuc 99.8 1.2E-20 2.6E-25 124.9 8.8 68 39-114 4-72 (72)
11 cd01720 Sm_D2 The eukaryotic S 99.8 3E-20 6.6E-25 127.4 9.4 76 39-114 2-85 (87)
12 cd06168 LSm9 The eukaryotic Sm 99.8 4.8E-20 1E-24 123.2 10.1 71 42-114 4-74 (75)
13 cd01726 LSm6 The eukaryotic Sm 99.8 4E-20 8.7E-25 120.6 8.6 66 40-113 1-67 (67)
14 PF01423 LSM: LSM domain ; In 99.8 2.5E-19 5.3E-24 115.8 8.9 66 42-114 2-67 (67)
15 smart00651 Sm snRNP Sm protein 99.8 3E-19 6.4E-24 115.3 9.2 66 42-114 2-67 (67)
16 cd01722 Sm_F The eukaryotic Sm 99.8 2.2E-19 4.7E-24 117.5 8.0 64 42-113 5-68 (68)
17 KOG1780 Small Nuclear ribonucl 99.8 4E-19 8.6E-24 117.5 6.7 68 42-117 8-75 (77)
18 cd00600 Sm_like The eukaryotic 99.8 2.5E-18 5.3E-23 109.5 9.2 63 43-113 1-63 (63)
19 cd01718 Sm_E The eukaryotic Sm 99.8 1.9E-18 4E-23 116.6 8.8 69 39-114 6-79 (79)
20 COG1958 LSM1 Small nuclear rib 99.8 3.5E-18 7.5E-23 114.6 9.4 71 39-114 7-79 (79)
21 cd01721 Sm_D3 The eukaryotic S 99.8 5E-18 1.1E-22 111.8 9.4 68 41-116 2-70 (70)
22 cd01723 LSm4 The eukaryotic Sm 99.7 1.1E-17 2.3E-22 111.8 8.8 70 40-116 2-72 (76)
23 cd01724 Sm_D1 The eukaryotic S 99.7 3.9E-17 8.4E-22 112.5 9.7 68 43-118 6-73 (90)
24 KOG3460 Small nuclear ribonucl 99.7 3.7E-18 8E-23 115.2 2.1 80 37-116 3-88 (91)
25 cd01733 LSm10 The eukaryotic S 99.7 1.6E-16 3.5E-21 106.8 9.2 65 43-115 14-78 (78)
26 cd01725 LSm2 The eukaryotic Sm 99.7 1.5E-16 3.3E-21 107.5 9.0 70 43-118 6-75 (81)
27 PTZ00138 small nuclear ribonuc 99.7 1.4E-16 3.1E-21 109.6 8.8 71 38-115 13-88 (89)
28 KOG1782 Small Nuclear ribonucl 99.6 2.6E-16 5.7E-21 112.9 0.7 84 38-127 9-92 (129)
29 KOG1783 Small nuclear ribonucl 99.5 1.9E-15 4.1E-20 99.8 0.9 72 37-116 4-76 (77)
30 KOG1784 Small Nuclear ribonucl 99.5 1.2E-14 2.6E-19 99.7 4.6 73 41-117 3-75 (96)
31 KOG3482 Small nuclear ribonucl 99.5 6.2E-14 1.3E-18 92.6 6.4 67 41-115 11-77 (79)
32 KOG3168 U1 snRNP component [Tr 99.5 5.9E-15 1.3E-19 111.1 0.9 77 40-116 6-84 (177)
33 KOG1775 U6 snRNA-associated Sm 99.5 6.9E-14 1.5E-18 93.2 4.5 75 37-116 5-80 (84)
34 KOG1774 Small nuclear ribonucl 99.3 1.3E-12 2.8E-17 88.1 3.4 72 38-116 11-87 (88)
35 KOG3293 Small nuclear ribonucl 99.1 1.6E-10 3.5E-15 83.3 6.1 72 39-117 2-74 (134)
36 KOG3448 Predicted snRNP core p 99.1 6.4E-10 1.4E-14 76.1 7.1 68 44-117 8-75 (96)
37 KOG3172 Small nuclear ribonucl 98.9 3.8E-09 8.3E-14 74.7 7.5 79 40-128 6-85 (119)
38 KOG3459 Small nuclear ribonucl 98.8 7.2E-10 1.6E-14 78.5 0.6 76 38-113 23-106 (114)
39 KOG3428 Small nuclear ribonucl 98.7 1.3E-07 2.9E-12 66.9 8.2 67 42-117 6-72 (109)
40 cd01739 LSm11_C The eukaryotic 98.6 4.7E-08 1E-12 63.5 2.9 38 48-85 8-49 (66)
41 PF14438 SM-ATX: Ataxin 2 SM d 97.8 4.2E-05 9.1E-10 50.6 5.1 67 43-110 7-76 (77)
42 PF12701 LSM14: Scd6-like Sm d 97.2 0.0026 5.7E-08 44.3 7.7 76 44-119 4-81 (96)
43 PF02237 BPL_C: Biotin protein 96.7 0.01 2.3E-07 35.8 6.3 35 46-81 1-35 (48)
44 cd01736 LSm14_N LSm14 (also kn 96.3 0.039 8.5E-07 36.8 7.4 67 45-111 3-72 (74)
45 PF06372 Gemin6: Gemin6 protei 96.2 0.011 2.3E-07 45.1 4.9 65 38-117 7-72 (166)
46 cd01716 Hfq Hfq, an abundant, 95.4 0.032 7E-07 35.9 4.2 33 46-78 9-41 (61)
47 TIGR02383 Hfq RNA chaperone Hf 95.4 0.035 7.7E-07 35.7 4.2 33 46-78 13-45 (61)
48 cd01735 LSm12_N LSm12 belongs 94.7 0.097 2.1E-06 33.7 4.8 36 46-81 4-39 (61)
49 PRK00395 hfq RNA-binding prote 94.7 0.072 1.6E-06 36.0 4.4 35 45-79 16-50 (79)
50 PRK14638 hypothetical protein; 94.3 0.078 1.7E-06 39.5 4.4 36 41-77 93-128 (150)
51 PF11095 Gemin7: Gem-associate 93.7 0.56 1.2E-05 31.7 7.2 59 43-114 19-78 (80)
52 PRK14639 hypothetical protein; 93.3 0.15 3.3E-06 37.5 4.3 36 41-77 81-116 (140)
53 PRK02001 hypothetical protein; 93.3 0.15 3.3E-06 38.2 4.4 36 41-77 83-118 (152)
54 PRK14644 hypothetical protein; 91.3 0.51 1.1E-05 34.7 5.0 35 42-77 79-117 (136)
55 COG1923 Hfq Uncharacterized ho 91.3 0.39 8.4E-06 32.3 3.9 31 45-75 16-46 (77)
56 PF10842 DUF2642: Protein of u 91.0 1.5 3.2E-05 28.6 6.4 52 42-114 15-66 (66)
57 PRK14640 hypothetical protein; 90.9 0.56 1.2E-05 34.9 5.0 36 41-77 90-129 (152)
58 cd01734 YlxS_C YxlS is a Bacil 90.7 0.54 1.2E-05 31.3 4.3 36 40-76 17-56 (83)
59 PRK14091 RNA-binding protein H 90.3 0.69 1.5E-05 35.3 4.9 33 47-79 23-55 (165)
60 PRK14633 hypothetical protein; 89.6 0.63 1.4E-05 34.6 4.3 36 41-77 87-126 (150)
61 PF02576 DUF150: Uncharacteris 89.2 0.73 1.6E-05 33.5 4.3 35 41-76 80-118 (141)
62 PRK14091 RNA-binding protein H 88.6 1.4 3.1E-05 33.6 5.6 33 47-79 103-135 (165)
63 PRK14642 hypothetical protein; 88.5 0.96 2.1E-05 35.4 4.7 35 41-76 93-140 (197)
64 PRK14645 hypothetical protein; 88.3 0.8 1.7E-05 34.3 4.0 34 41-76 95-128 (154)
65 PRK00092 ribosome maturation p 88.2 0.94 2E-05 33.6 4.3 31 40-70 90-124 (154)
66 PRK14636 hypothetical protein; 87.5 0.97 2.1E-05 34.6 4.1 35 41-76 91-129 (176)
67 PRK14632 hypothetical protein; 87.2 1.1 2.3E-05 34.1 4.2 36 41-77 91-133 (172)
68 PRK14634 hypothetical protein; 87.1 1.1 2.4E-05 33.5 4.2 36 41-77 93-132 (155)
69 PRK14643 hypothetical protein; 86.8 1.2 2.5E-05 33.8 4.2 31 41-71 97-131 (164)
70 COG0779 Uncharacterized protei 86.4 1.9 4E-05 32.5 5.1 34 42-76 93-130 (153)
71 PRK14646 hypothetical protein; 86.4 1.3 2.8E-05 33.1 4.2 36 41-77 93-132 (155)
72 KOG1073 Uncharacterized mRNA-a 86.3 3 6.5E-05 35.5 6.8 72 44-116 5-80 (361)
73 PRK06955 biotin--protein ligas 85.6 3.6 7.8E-05 33.6 6.8 33 46-78 247-279 (300)
74 PRK14647 hypothetical protein; 85.4 1.5 3.3E-05 32.8 4.2 35 41-76 92-135 (159)
75 PRK14631 hypothetical protein; 84.5 1.7 3.7E-05 33.2 4.2 35 41-76 110-150 (174)
76 PRK14637 hypothetical protein; 83.2 2.1 4.6E-05 31.9 4.1 36 41-77 91-127 (151)
77 PRK14641 hypothetical protein; 81.6 2.3 5E-05 32.5 3.9 29 41-69 97-129 (173)
78 PRK11886 bifunctional biotin-- 80.8 8 0.00017 31.5 7.0 31 46-77 270-300 (319)
79 PF07073 ROF: Modulator of Rho 80.5 1.5 3.2E-05 29.6 2.2 62 46-127 15-76 (80)
80 PF03614 Flag1_repress: Repres 80.4 3.1 6.7E-05 31.5 4.1 36 45-80 26-61 (165)
81 PRK13325 bifunctional biotin-- 79.1 7.5 0.00016 34.9 6.8 33 46-78 276-308 (592)
82 TIGR00121 birA_ligase birA, bi 77.2 12 0.00027 29.1 6.9 31 46-77 191-221 (237)
83 PF03614 Flag1_repress: Repres 76.8 2.8 6E-05 31.8 2.9 24 47-70 119-142 (165)
84 PRK08330 biotin--protein ligas 75.3 11 0.00024 29.4 6.2 32 46-78 186-218 (236)
85 COG0340 BirA Biotin-(acetyl-Co 71.9 16 0.00034 29.1 6.3 34 46-79 188-221 (238)
86 PRK14630 hypothetical protein; 70.0 7.9 0.00017 28.5 3.9 35 41-77 90-124 (143)
87 PRK10898 serine endoprotease; 70.0 9.5 0.0002 31.8 4.8 32 49-80 102-133 (353)
88 PF11607 DUF3247: Protein of u 68.5 7.5 0.00016 27.2 3.3 18 49-66 29-46 (101)
89 TIGR02038 protease_degS peripl 68.5 10 0.00022 31.5 4.8 32 49-80 102-133 (351)
90 PRK14635 hypothetical protein; 68.0 10 0.00022 28.5 4.2 37 40-77 91-132 (162)
91 PTZ00275 biotin-acetyl-CoA-car 66.9 13 0.00028 30.2 5.0 31 47-78 236-266 (285)
92 PRK10942 serine endoprotease; 64.3 13 0.00029 32.3 4.8 32 48-79 135-166 (473)
93 PF14563 DUF4444: Domain of un 63.1 9.2 0.0002 22.8 2.5 22 61-82 10-31 (42)
94 PRK10139 serine endoprotease; 63.0 15 0.00032 31.8 4.9 33 48-80 114-146 (455)
95 TIGR02037 degP_htrA_DO peripla 55.7 23 0.0005 30.0 4.7 32 49-80 82-113 (428)
96 KOG3382 NADH:ubiquinone oxidor 53.1 7.5 0.00016 28.9 1.2 24 57-80 41-64 (151)
97 PRK09618 flgD flagellar basal 53.1 48 0.001 24.6 5.5 27 43-69 87-113 (142)
98 PRK04337 50S ribosomal protein 53.0 30 0.00066 23.7 4.1 55 16-70 3-62 (87)
99 PF05071 NDUFA12: NADH ubiquin 49.1 7.8 0.00017 27.0 0.7 17 63-79 1-17 (105)
100 PF06257 DUF1021: Protein of u 43.3 51 0.0011 21.9 3.9 33 42-76 11-47 (76)
101 PRK08477 biotin--protein ligas 43.1 78 0.0017 24.7 5.6 34 46-80 173-206 (211)
102 TIGR02603 CxxCH_TIGR02603 puta 42.5 34 0.00074 24.4 3.3 28 50-78 59-86 (133)
103 TIGR03170 flgA_cterm flagella 41.6 35 0.00075 23.6 3.1 23 45-67 93-116 (122)
104 cd05791 S1_CSL4 S1_CSL4: CSL4, 39.1 1E+02 0.0023 20.6 5.1 25 55-79 61-85 (92)
105 PRK11625 Rho-binding antitermi 37.1 1.3E+02 0.0029 20.3 6.1 54 47-116 22-75 (84)
106 PHA02723 hypothetical protein; 36.3 19 0.00041 23.5 1.0 19 10-28 47-65 (77)
107 smart00333 TUDOR Tudor domain. 36.0 92 0.002 18.2 4.2 25 47-71 5-29 (57)
108 PF09465 LBR_tudor: Lamin-B re 34.8 83 0.0018 19.8 3.7 24 47-70 8-32 (55)
109 PRK07018 flgA flagellar basal 34.3 46 0.001 26.1 3.1 23 45-67 204-227 (235)
110 KOG3493 Ubiquitin-like protein 33.3 34 0.00074 22.5 1.8 18 43-60 6-23 (73)
111 PRK11911 flgD flagellar basal 32.1 83 0.0018 23.3 3.9 26 44-69 89-114 (140)
112 PRK06630 hypothetical protein; 31.5 25 0.00055 24.7 1.0 19 61-79 11-29 (99)
113 PRK10708 hypothetical protein; 31.2 57 0.0012 20.8 2.5 26 47-72 3-28 (62)
114 smart00166 UBX Domain present 29.7 53 0.0012 21.1 2.3 21 49-69 5-25 (80)
115 PF01887 SAM_adeno_trans: S-ad 29.3 77 0.0017 25.5 3.6 19 60-78 169-187 (258)
116 COG0265 DegQ Trypsin-like seri 26.8 1.2E+02 0.0026 24.7 4.5 33 48-80 95-127 (347)
117 PRK12617 flgA flagellar basal 26.7 77 0.0017 24.9 3.1 22 46-67 184-206 (214)
118 cd01772 SAKS1_UBX SAKS1-like U 26.6 52 0.0011 21.4 1.9 24 46-69 2-25 (79)
119 PF10781 DSRB: Dextransucrase 26.6 68 0.0015 20.5 2.3 26 47-72 3-28 (62)
120 cd01767 UBX UBX (ubiquitin reg 26.6 72 0.0016 20.3 2.5 21 49-69 3-23 (77)
121 PLN03095 NADH:ubiquinone oxido 25.7 40 0.00086 24.3 1.2 19 62-80 9-27 (115)
122 PF01247 Ribosomal_L35Ae: Ribo 25.4 1.8E+02 0.0039 20.2 4.4 59 17-75 4-75 (95)
123 PRK06005 flgA flagellar basal 24.9 92 0.002 23.2 3.1 22 46-67 129-151 (160)
124 PF00789 UBX: UBX domain; Int 24.8 87 0.0019 19.9 2.7 22 49-70 7-28 (82)
125 PF05735 TSP_C: Thrombospondin 23.7 3.1E+02 0.0068 21.5 6.0 33 51-83 5-44 (201)
126 PF05954 Phage_GPD: Phage late 23.6 1.2E+02 0.0026 23.4 3.7 28 42-69 22-49 (292)
127 COG4466 Veg Uncharacterized pr 23.3 77 0.0017 21.4 2.2 21 42-62 13-33 (80)
128 PRK12618 flgA flagellar basal 22.9 1.1E+02 0.0024 22.4 3.2 22 46-67 110-132 (141)
129 KOG4401 Uncharacterized conser 22.7 97 0.0021 24.1 2.9 37 44-80 7-43 (184)
130 PLN02732 Probable NADH dehydro 22.6 68 0.0015 24.4 2.0 19 62-80 48-66 (159)
131 PRK06789 flagellar motor switc 22.6 1.9E+02 0.0042 19.0 4.0 42 37-78 30-71 (74)
132 PRK08515 flgA flagellar basal 22.6 1.2E+02 0.0027 23.6 3.6 23 45-67 193-215 (222)
133 PRK06804 flgA flagellar basal 22.0 1.1E+02 0.0023 24.9 3.2 23 45-67 230-253 (261)
134 COG1886 FliN Flagellar motor s 21.6 1.9E+02 0.0041 20.9 4.2 39 38-76 95-133 (136)
135 PF03122 Herpes_MCP: Herpes vi 21.2 32 0.00069 34.1 0.0 54 53-112 252-305 (1354)
136 COG0048 RpsL Ribosomal protein 20.2 1.3E+02 0.0029 22.0 3.1 26 42-67 50-75 (129)
No 1
>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=99.91 E-value=7.3e-24 Score=143.37 Aligned_cols=79 Identities=71% Similarity=1.192 Sum_probs=68.0
Q ss_pred cCcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889 38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD 116 (131)
Q Consensus 38 ~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d 116 (131)
+++++|.++++++|+|+|+|||+|.|+|.|||+||||+|++|+|+...+.+..+.....+.+|.++|||++|++|++.+
T Consensus 2 ~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 2 ESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred cchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 5788999999999999999999999999999999999999999998653322112235788999999999999999775
No 2
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.91 E-value=1.2e-25 Score=155.58 Aligned_cols=101 Identities=61% Similarity=1.070 Sum_probs=93.1
Q ss_pred cccccccCccCcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCc
Q 032889 29 KSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTA 108 (131)
Q Consensus 29 ~~~~m~~~~~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~ 108 (131)
+...+++++++.++|.+|++++|+|++.+||..+|+|+|||+.|||||+|++|+..+++++.+...+.|++|++++||..
T Consensus 8 ~~~~e~~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTa 87 (108)
T KOG1781|consen 8 RKKFEKPKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTA 87 (108)
T ss_pred cccccccchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccE
Confidence 34456678999999999999999999999999999999999999999999999998888877766778999999999999
Q ss_pred EEEEeeCCCCccccCCCCCCC
Q 032889 109 VMLVSPTDGTDEIANPFMQPD 129 (131)
Q Consensus 109 Iv~I~~~d~~~~~~~p~~~~~ 129 (131)
+++|++.|+.++|.|||.+.+
T Consensus 88 lvlisp~dG~e~I~npf~~~e 108 (108)
T KOG1781|consen 88 LVLISPADGSEEIANPFVQQE 108 (108)
T ss_pred EEEEcCCcchhhhccchhcCC
Confidence 999999999999999999864
No 3
>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=99.87 E-value=7.2e-22 Score=130.93 Aligned_cols=70 Identities=36% Similarity=0.737 Sum_probs=63.3
Q ss_pred cccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG 117 (131)
Q Consensus 40 ~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~ 117 (131)
+++|.++++|+|+|+|++||.++|+|.|||+||||+|+||+|+... ...+.+|.++|||++|++|++.|+
T Consensus 2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~--------~~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG--------GEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC--------CceeEeceEEECCCEEEEEEcccc
Confidence 4689999999999999999999999999999999999999998732 247889999999999999998763
No 4
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=2.7e-21 Score=129.85 Aligned_cols=73 Identities=26% Similarity=0.530 Sum_probs=62.5
Q ss_pred cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCC--CccCcceEEeceEEEeCCcEEEEee
Q 032889 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIVCRGTAVMLVSP 114 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~--~~~~~~~r~lg~v~IRG~~Iv~I~~ 114 (131)
.|.+|++++|+|+|+|||.+.|+|.|||+||||+|+||+|++...... .....+++.+|+++|||++|++|+.
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 588999999999999999999999999999999999999987643211 1123467899999999999999974
No 5
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=2.9e-21 Score=128.32 Aligned_cols=72 Identities=36% Similarity=0.587 Sum_probs=63.5
Q ss_pred ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD 116 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d 116 (131)
+.|.++++++|+|+++|||.+.|+|+|||+||||+|++|.|+....+. ....+.+|.+++||++|++|++.|
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~----~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDE----GVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCC----CceeeEeceEEECCCEEEEEEccC
Confidence 478999999999999999999999999999999999999998754322 135778999999999999999876
No 6
>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=99.86 E-value=3e-21 Score=128.72 Aligned_cols=71 Identities=34% Similarity=0.500 Sum_probs=63.0
Q ss_pred CcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP 114 (131)
Q Consensus 39 ~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 114 (131)
+.++|.++++++|.|+++|||+|.|+|.|||+||||+|+||.|+...++ ...++.+|.++|||++|++|+.
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~-----~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD-----KYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC-----ccceeEeeEEEEECCEEEEEEc
Confidence 4567999999999999999999999999999999999999999876432 1346889999999999999975
No 7
>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=99.86 E-value=2.8e-21 Score=130.74 Aligned_cols=75 Identities=36% Similarity=0.569 Sum_probs=62.4
Q ss_pred cccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCC-----ccCcceEEeceEEEeCCcEEEEe
Q 032889 40 VLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIVCRGTAVMLVS 113 (131)
Q Consensus 40 ~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~-----~~~~~~r~lg~v~IRG~~Iv~I~ 113 (131)
|+++ ...++++|.|+|+|||.+.|+|.|||+||||+|+||+|++....++. ......|.+|.++|||++|++|+
T Consensus 2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence 6676 56799999999999999999999999999999999999986532211 11235789999999999999987
Q ss_pred e
Q 032889 114 P 114 (131)
Q Consensus 114 ~ 114 (131)
+
T Consensus 82 ~ 82 (82)
T cd01730 82 P 82 (82)
T ss_pred C
Confidence 3
No 8
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.85 E-value=3.4e-21 Score=125.88 Aligned_cols=64 Identities=45% Similarity=0.742 Sum_probs=58.5
Q ss_pred HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP 114 (131)
Q Consensus 43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 114 (131)
|.++++++|+|+|+||+.|+|+|.|||+||||+|+||+|++.. ..++.+|.++|||++|++|++
T Consensus 5 L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 5 LKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG--------EPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred HHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC--------CeEeEcCcEEEeCCEEEEEcC
Confidence 6789999999999999999999999999999999999998753 247789999999999999974
No 9
>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=99.84 E-value=1.2e-20 Score=126.41 Aligned_cols=71 Identities=23% Similarity=0.505 Sum_probs=61.5
Q ss_pred cccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889 40 VLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT 115 (131)
Q Consensus 40 ~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 115 (131)
|+++ .++++++|+|++++||++.|+|+|||+||||+|+||+|++..++. ...+.+|.++|||++|++|++.
T Consensus 4 P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~-----~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 4 PLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEG-----RKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred hHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCC-----ceeeEcCeEEEeCCeEEEEECC
Confidence 5564 688999999999999999999999999999999999999853221 2467899999999999999863
No 10
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.84 E-value=1.2e-20 Score=124.85 Aligned_cols=68 Identities=46% Similarity=0.724 Sum_probs=59.8
Q ss_pred Cccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889 39 TVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP 114 (131)
Q Consensus 39 ~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 114 (131)
.|++ |.++++++|+|+|+||+.|+|+|.|||+|||++|+||.|...+ ...+.+|.++|||++|++|++
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG--------EVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC--------CeEeEcCcEEEeCCEEEEEcC
Confidence 4555 5789999999999999999999999999999999999997532 246789999999999999963
No 11
>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=99.83 E-value=3e-20 Score=127.38 Aligned_cols=76 Identities=24% Similarity=0.405 Sum_probs=62.4
Q ss_pred CcccH-hhhc--CCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCC-----ccCcceEEeceEEEeCCcEE
Q 032889 39 TVLDL-AKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIVCRGTAVM 110 (131)
Q Consensus 39 ~~l~L-~~~l--~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~-----~~~~~~r~lg~v~IRG~~Iv 110 (131)
+|+++ .+.+ +++|+|+|++||.+.|+|.|||+||||+|+||+|.+....+.. ......+.+|.++|||++|+
T Consensus 2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 57776 4565 8999999999999999999999999999999999986532110 11235778999999999999
Q ss_pred EEee
Q 032889 111 LVSP 114 (131)
Q Consensus 111 ~I~~ 114 (131)
+|+.
T Consensus 82 ~Is~ 85 (87)
T cd01720 82 LVLR 85 (87)
T ss_pred EEec
Confidence 9985
No 12
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.83 E-value=4.8e-20 Score=123.19 Aligned_cols=71 Identities=23% Similarity=0.438 Sum_probs=62.5
Q ss_pred cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP 114 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 114 (131)
.|.++++++|+|+|+|||.|.|+|.|||+||||+|+||.|++..+.+. ...+.|.+|+++|||++|++|+.
T Consensus 4 ~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~--~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 4 KLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSF--SPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred HHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCcc--CCccEEEeeeEEEeCCeEEEEEE
Confidence 578999999999999999999999999999999999999998654321 12468999999999999999974
No 13
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.83 E-value=4e-20 Score=120.62 Aligned_cols=66 Identities=26% Similarity=0.449 Sum_probs=57.9
Q ss_pred ccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEe
Q 032889 40 VLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS 113 (131)
Q Consensus 40 ~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 113 (131)
|++ |.++++++|.|+|++|++|+|+|.|||+||||+|+||+|.... ...+.+|.++|||++|++|+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~--------~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG--------QLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC--------ceeeEeCCEEEECCEEEEEC
Confidence 344 5789999999999999999999999999999999999986532 24778999999999999984
No 14
>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=99.81 E-value=2.5e-19 Score=115.81 Aligned_cols=66 Identities=38% Similarity=0.660 Sum_probs=60.1
Q ss_pred cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP 114 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 114 (131)
.|.+++|++|+|.|+||+.++|+|.+||+|||++|+||.|....+ .+.+++|.++|||++|++|.+
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~-------~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNG-------PEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTE-------SEEEEEEEEEEEGGGEEEEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCC-------CcEeECcEEEEECCEEEEEEC
Confidence 478999999999999999999999999999999999999997542 158899999999999999974
No 15
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.80 E-value=3e-19 Score=115.30 Aligned_cols=66 Identities=41% Similarity=0.731 Sum_probs=59.9
Q ss_pred cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP 114 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 114 (131)
.|.++++++|+|+|+||+.+.|+|.|||+||||+|+||.|+...+ .+.+.+|.++|||++|++|.+
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC-------cEEeEeCCEEEcCCEEEEEeC
Confidence 478999999999999999999999999999999999999987542 358899999999999999863
No 16
>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=99.80 E-value=2.2e-19 Score=117.53 Aligned_cols=64 Identities=31% Similarity=0.433 Sum_probs=56.8
Q ss_pred cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEe
Q 032889 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS 113 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 113 (131)
.|.++++++|+|+|+||++|+|+|.|||+||||+|+||+|+... ...+.+|.++|||++|.+|.
T Consensus 5 ~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~--------~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 5 FLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG--------KSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred HHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC--------ccccCcCcEEEECCEEEEEC
Confidence 36789999999999999999999999999999999999987532 23667999999999999983
No 17
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.78 E-value=4e-19 Score=117.47 Aligned_cols=68 Identities=43% Similarity=0.820 Sum_probs=62.3
Q ss_pred cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG 117 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~ 117 (131)
+|.+|++|++.++|++||.+.|+|.|||.|||+||+++.|...+. .+..+|.++|||++|+.+.+.+.
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~--------~~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDG--------DKNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcC--------CcceeeeEEEeccEEEEEeeccc
Confidence 999999999999999999999999999999999999999986542 36789999999999999988763
No 18
>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=99.77 E-value=2.5e-18 Score=109.50 Aligned_cols=63 Identities=41% Similarity=0.718 Sum_probs=57.7
Q ss_pred HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEe
Q 032889 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS 113 (131)
Q Consensus 43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 113 (131)
|.+++|++|+|+|+||+.|.|+|.|||+|||++|+||.|.... ...+.+|.++|||++|.+|.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~--------~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE--------GKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC--------CcEEECCeEEEECCEEEEEC
Confidence 5688999999999999999999999999999999999998754 25889999999999999874
No 19
>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=99.77 E-value=1.9e-18 Score=116.62 Aligned_cols=69 Identities=28% Similarity=0.531 Sum_probs=57.6
Q ss_pred Cccc-HhhhcCC--eEEEEEc--CCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEe
Q 032889 39 TVLD-LAKFVDK--GVQVKLT--GGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVS 113 (131)
Q Consensus 39 ~~l~-L~~~l~k--~V~V~L~--dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~ 113 (131)
.|++ |.+|+++ +|.|+++ +||.+.|+|.|||+||||+|+||+|+...+ ...+.+|.++|||++|++|+
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~-------~~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKT-------KTRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCC-------ceEeEcCcEEEeCCEEEEEc
Confidence 4555 4689998 5666665 999999999999999999999999997421 24678999999999999987
Q ss_pred e
Q 032889 114 P 114 (131)
Q Consensus 114 ~ 114 (131)
+
T Consensus 79 p 79 (79)
T cd01718 79 N 79 (79)
T ss_pred C
Confidence 4
No 20
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.77 E-value=3.5e-18 Score=114.58 Aligned_cols=71 Identities=42% Similarity=0.703 Sum_probs=57.7
Q ss_pred Cccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEee-cCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889 39 TVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR-DADDPLKTTDQTRQLGLIVCRGTAVMLVSP 114 (131)
Q Consensus 39 ~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~-~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 114 (131)
.|.+ |.++++++|.|+|++|++|.|+|.|||+||||+|+||.|+.. ++. ....+..+.++|||++|++|.+
T Consensus 7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~-----~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGE-----KNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCc-----cccceeccEEEEECCcEEEEeC
Confidence 3444 578999999999999999999999999999999999999974 111 0023344599999999999863
No 21
>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=99.76 E-value=5e-18 Score=111.75 Aligned_cols=68 Identities=24% Similarity=0.294 Sum_probs=59.3
Q ss_pred cc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889 41 LD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD 116 (131)
Q Consensus 41 l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d 116 (131)
++ |.+..|++|.|+|++|.+|+|+|.++|.|||++|+||++...++ +...+|.++|||++|.+|..||
T Consensus 2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g--------~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDG--------RVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCC--------cEeEcCcEEEeCCEEEEEEeCC
Confidence 44 46889999999999999999999999999999999998864332 2567899999999999999875
No 22
>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=99.74 E-value=1.1e-17 Score=111.76 Aligned_cols=70 Identities=23% Similarity=0.329 Sum_probs=60.2
Q ss_pred cccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889 40 VLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD 116 (131)
Q Consensus 40 ~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d 116 (131)
|+++ .++.|++|.|+|++|+.++|+|.+||+|||++|+||+|...++ .....++.++|||++|.+|..++
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g-------~~~~~~~~v~IRG~~I~~i~~p~ 72 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDG-------DKFWKMPECYIRGNTIKYLRVPD 72 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCC-------cEeeeCCcEEEeCCEEEEEEcCH
Confidence 5564 6889999999999999999999999999999999999874332 12456789999999999999876
No 23
>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=99.73 E-value=3.9e-17 Score=112.54 Aligned_cols=68 Identities=25% Similarity=0.364 Sum_probs=61.0
Q ss_pred HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCC
Q 032889 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGT 118 (131)
Q Consensus 43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~ 118 (131)
|.++.|++|.|+|++|..|+|+|.++|.|||++|+||++.... .....+|.++|||++|.+|..||..
T Consensus 6 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~--------~~~~~~~~v~IRG~nI~yi~lPd~l 73 (90)
T cd01724 6 LMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG--------RNPVPLDTLSIRGNNIRYFILPDSL 73 (90)
T ss_pred HHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC--------CceeEcceEEEeCCEEEEEEcCCcC
Confidence 5788999999999999999999999999999999999988543 2366899999999999999999854
No 24
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.70 E-value=3.7e-18 Score=115.22 Aligned_cols=80 Identities=34% Similarity=0.507 Sum_probs=67.7
Q ss_pred ccCcccHhh-hcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCC-----ccCcceEEeceEEEeCCcEE
Q 032889 37 KETVLDLAK-FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIVCRGTAVM 110 (131)
Q Consensus 37 ~~~~l~L~~-~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~-----~~~~~~r~lg~v~IRG~~Iv 110 (131)
...|++|.+ +++.+|.|+++++|.++|+|.|||+|.|++|+|++|....-+..+ .....+|.+..+|+||++|+
T Consensus 3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vi 82 (91)
T KOG3460|consen 3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVI 82 (91)
T ss_pred ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEE
Confidence 467899876 499999999999999999999999999999999999987533221 12356788999999999999
Q ss_pred EEeeCC
Q 032889 111 LVSPTD 116 (131)
Q Consensus 111 ~I~~~d 116 (131)
.|+++-
T Consensus 83 lvspp~ 88 (91)
T KOG3460|consen 83 LVSPPL 88 (91)
T ss_pred EEcCcc
Confidence 999875
No 25
>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=99.69 E-value=1.6e-16 Score=106.78 Aligned_cols=65 Identities=25% Similarity=0.323 Sum_probs=57.1
Q ss_pred HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT 115 (131)
Q Consensus 43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 115 (131)
|..+.|+.|.|+|++|..|+|+|.++|.|||++|+||++...+ .....+|.++|||++|.+|..|
T Consensus 14 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~--------~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 14 LQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN--------GKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred HHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC--------CceeECCcEEEECCEEEEEEcC
Confidence 4678999999999999999999999999999999999877432 1355789999999999999865
No 26
>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=99.69 E-value=1.5e-16 Score=107.52 Aligned_cols=70 Identities=24% Similarity=0.265 Sum_probs=59.2
Q ss_pred HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCC
Q 032889 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGT 118 (131)
Q Consensus 43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~ 118 (131)
|.++.|++|.|+|++|..|+|+|.++|.|||++|+||++...+.. .....++.++|||++|.+|..||..
T Consensus 6 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~------~~~~~~~~v~IRG~~I~~I~lp~~~ 75 (81)
T cd01725 6 FKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKY------PHMLSVKNCFIRGSVVRYVQLPADE 75 (81)
T ss_pred HHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCc------ccccccCeEEEECCEEEEEEeChhH
Confidence 578899999999999999999999999999999999987643211 1234578999999999999999753
No 27
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.69 E-value=1.4e-16 Score=109.64 Aligned_cols=71 Identities=25% Similarity=0.538 Sum_probs=57.0
Q ss_pred cCccc-HhhhcCC--eEEEEEcC--CcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEE
Q 032889 38 ETVLD-LAKFVDK--GVQVKLTG--GRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLV 112 (131)
Q Consensus 38 ~~~l~-L~~~l~k--~V~V~L~d--Gr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 112 (131)
..|.. +.+++.+ +|.|.+.| ++++.|+|.|||+||||+|+||+|++... ...+.+|.++|||++|++|
T Consensus 13 ~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~-------~~~~~lG~ilIRGnnV~~I 85 (89)
T PTZ00138 13 TQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKK-------NTRKDLGRILLKGDNITLI 85 (89)
T ss_pred cCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCC-------ceeeEcCeEEEcCCEEEEE
Confidence 34555 4578775 56677666 58999999999999999999999986432 2477899999999999999
Q ss_pred eeC
Q 032889 113 SPT 115 (131)
Q Consensus 113 ~~~ 115 (131)
++.
T Consensus 86 ~~~ 88 (89)
T PTZ00138 86 MAA 88 (89)
T ss_pred EcC
Confidence 864
No 28
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.58 E-value=2.6e-16 Score=112.91 Aligned_cols=84 Identities=31% Similarity=0.479 Sum_probs=72.3
Q ss_pred cCcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889 38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG 117 (131)
Q Consensus 38 ~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~ 117 (131)
..+.+|.+++++++.|.|+|||.+.|.|.+||||-|++|.+|+|++.-++ .......|..+|||+||++++..|.
T Consensus 9 ~~t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~-----~Y~di~~glfiIRGENVvllGeid~ 83 (129)
T KOG1782|consen 9 PFTTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN-----KYCDIPRGLFIIRGENVVLLGEIDL 83 (129)
T ss_pred CchhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc-----eecccCceEEEEecCcEEEEecCCc
Confidence 34556899999999999999999999999999999999999999987653 3567788999999999999999887
Q ss_pred CccccCCCCC
Q 032889 118 TDEIANPFMQ 127 (131)
Q Consensus 118 ~~~~~~p~~~ 127 (131)
..+ +.|..+
T Consensus 84 dkE-~~~l~~ 92 (129)
T KOG1782|consen 84 DKE-EEPLEQ 92 (129)
T ss_pred chh-hcccee
Confidence 665 566544
No 29
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.53 E-value=1.9e-15 Score=99.79 Aligned_cols=72 Identities=25% Similarity=0.401 Sum_probs=63.0
Q ss_pred ccCccc-HhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889 37 KETVLD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT 115 (131)
Q Consensus 37 ~~~~l~-L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 115 (131)
...|.+ |.+.+|++|.|+|.+|-.|+|+|.|.|.||||.|+.++|+... +.++++|.+||||++|.+|+..
T Consensus 4 ~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ng--------ql~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 4 GSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNG--------QLKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred ccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcC--------cccccccceeeccccEEEEEec
Confidence 344555 6789999999999999999999999999999999999998632 4688999999999999999875
Q ss_pred C
Q 032889 116 D 116 (131)
Q Consensus 116 d 116 (131)
.
T Consensus 76 ~ 76 (77)
T KOG1783|consen 76 K 76 (77)
T ss_pred c
Confidence 3
No 30
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.52 E-value=1.2e-14 Score=99.65 Aligned_cols=73 Identities=32% Similarity=0.532 Sum_probs=65.2
Q ss_pred ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG 117 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~ 117 (131)
..|..|++++|.|...|||.+.|.|+|||+..||+|+++.|+...... ..++..+|..+|||+||..|.++|+
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~----gv~q~~lGlyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETE----GVEQIVLGLYIIRGENVAVIGEIDE 75 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhc----chhheeeEEEEEecCccceeeecch
Confidence 468999999999999999999999999999999999999999765332 3467789999999999999999984
No 31
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.50 E-value=6.2e-14 Score=92.60 Aligned_cols=67 Identities=33% Similarity=0.403 Sum_probs=60.0
Q ss_pred ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT 115 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 115 (131)
+.|..+.+|+|.|+|+.|.+|+|+|++.|.||||.|.+|+|++.. ...-.+|.++||.+||.+|...
T Consensus 11 pFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG--------~~~g~lGEilIRCNNvlyi~gv 77 (79)
T KOG3482|consen 11 PFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG--------VSTGNLGEILIRCNNVLYIRGV 77 (79)
T ss_pred HHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc--------cccccceeEEEEeccEEEEecC
Confidence 457889999999999999999999999999999999999998753 2466799999999999999754
No 32
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.48 E-value=5.9e-15 Score=111.08 Aligned_cols=77 Identities=25% Similarity=0.506 Sum_probs=65.8
Q ss_pred cccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCC-C-CccCcceEEeceEEEeCCcEEEEeeCC
Q 032889 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADD-P-LKTTDQTRQLGLIVCRGTAVMLVSPTD 116 (131)
Q Consensus 40 ~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~-~-~~~~~~~r~lg~v~IRG~~Iv~I~~~d 116 (131)
+..|.++++.+++|.++|||.+.|.+.+||+||||+|.||+|....... . .....++|-+|++++||++|++.+..+
T Consensus 6 sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg 84 (177)
T KOG3168|consen 6 SSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG 84 (177)
T ss_pred hhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence 3457899999999999999999999999999999999999998764321 1 234568999999999999999998755
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.46 E-value=6.9e-14 Score=93.16 Aligned_cols=75 Identities=21% Similarity=0.468 Sum_probs=64.8
Q ss_pred ccCcccHh-hhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeC
Q 032889 37 KETVLDLA-KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPT 115 (131)
Q Consensus 37 ~~~~l~L~-~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~ 115 (131)
...|++|. +.+|.+++|.+++.|++.|+|+|||.|.|++|+|+.|+...++. ....+++++++.|++|....+.
T Consensus 5 ~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~eg-----r~~tk~~~iLLnGNni~mLvPG 79 (84)
T KOG1775|consen 5 TLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEG-----RRMTKLDQILLNGNNITMLVPG 79 (84)
T ss_pred hcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCc-----ceeeeeeeeeecCCcEEEEecC
Confidence 45678875 78999999999999999999999999999999999999765442 2456899999999999988765
Q ss_pred C
Q 032889 116 D 116 (131)
Q Consensus 116 d 116 (131)
.
T Consensus 80 G 80 (84)
T KOG1775|consen 80 G 80 (84)
T ss_pred C
Confidence 4
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.31 E-value=1.3e-12 Score=88.06 Aligned_cols=72 Identities=29% Similarity=0.568 Sum_probs=56.8
Q ss_pred cCcccH-hhhcCCe--EEEEEcC--CcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEE
Q 032889 38 ETVLDL-AKFVDKG--VQVKLTG--GRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLV 112 (131)
Q Consensus 38 ~~~l~L-~~~l~k~--V~V~L~d--Gr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 112 (131)
-.|..| .+|+..+ |.|.|.+ |-.++|.++|||+|||+||++|+|.....+ ..+.+|.++++||+|..|
T Consensus 11 v~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~-------~rk~lGRilLKGDnItli 83 (88)
T KOG1774|consen 11 VQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK-------SRKELGRILLKGDNITLI 83 (88)
T ss_pred cCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccccc-------CCCccccEEEcCCcEEEE
Confidence 446666 5887764 5566644 889999999999999999999999865432 344899999999999999
Q ss_pred eeCC
Q 032889 113 SPTD 116 (131)
Q Consensus 113 ~~~d 116 (131)
...+
T Consensus 84 ~~~~ 87 (88)
T KOG1774|consen 84 QSAG 87 (88)
T ss_pred eecC
Confidence 7653
No 35
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.11 E-value=1.6e-10 Score=83.27 Aligned_cols=72 Identities=25% Similarity=0.299 Sum_probs=63.4
Q ss_pred CcccHh-hhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889 39 TVLDLA-KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG 117 (131)
Q Consensus 39 ~~l~L~-~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~ 117 (131)
.|+.|. ..-+.++.|+|++|.+|.|.|+.+|.+|||.|.+++++..+++ +...+..+.|||++|.++..+|.
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd-------kf~r~pEcYirGttIkylri~d~ 74 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGD-------KFFRMPECYIRGTTIKYLRIPDE 74 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCC-------ceeecceeEEecceeEEEeccHH
Confidence 367775 4688999999999999999999999999999999999876543 46778899999999999999874
No 36
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.06 E-value=6.4e-10 Score=76.10 Aligned_cols=68 Identities=28% Similarity=0.287 Sum_probs=56.9
Q ss_pred hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889 44 AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG 117 (131)
Q Consensus 44 ~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~ 117 (131)
..++|++|.|.|+++-.+.|+|.|.|+|.|+.|.|..-...+. -..--.+..++|||+.|.+|..+..
T Consensus 8 kslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~k------yPhm~Sv~ncfIRGSvvrYv~l~kd 75 (96)
T KOG3448|consen 8 KSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDK------YPHMLSVKNCFIRGSVVRYVQLPKD 75 (96)
T ss_pred HHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCccc------CCCeeeeeeEEEeccEEEEEEeChh
Confidence 5679999999999999999999999999999999986553221 1245567889999999999998763
No 37
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=98.95 E-value=3.8e-09 Score=74.65 Aligned_cols=79 Identities=20% Similarity=0.262 Sum_probs=67.5
Q ss_pred cccH-hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCC
Q 032889 40 VLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGT 118 (131)
Q Consensus 40 ~l~L-~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~ 118 (131)
|..| .+.-+.-|.+++..|..|+|+|.-.|.+||+.|+|+.-...++ ....+.+++|||+.|.++..||..
T Consensus 6 piKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg--------~vs~le~V~IRGS~IRFlvlPdmL 77 (119)
T KOG3172|consen 6 PIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDG--------RVSQLEQVFIRGSKIRFLVLPDML 77 (119)
T ss_pred ceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCC--------cceeeeeEEEecCeEEEEECchHh
Confidence 4454 4678899999999999999999999999999999998776543 355788999999999999999977
Q ss_pred ccccCCCCCC
Q 032889 119 DEIANPFMQP 128 (131)
Q Consensus 119 ~~~~~p~~~~ 128 (131)
+ ++|+|+-
T Consensus 78 K--nAPmFkk 85 (119)
T KOG3172|consen 78 K--NAPMFKK 85 (119)
T ss_pred h--cCccccc
Confidence 6 8999863
No 38
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.84 E-value=7.2e-10 Score=78.47 Aligned_cols=76 Identities=21% Similarity=0.340 Sum_probs=60.6
Q ss_pred cCcccHh-hh--cCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCC---CC--ccCcceEEeceEEEeCCcE
Q 032889 38 ETVLDLA-KF--VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADD---PL--KTTDQTRQLGLIVCRGTAV 109 (131)
Q Consensus 38 ~~~l~L~-~~--l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~---~~--~~~~~~r~lg~v~IRG~~I 109 (131)
.+|+++. .. -..+|.|.++|++.+.|++.|||.|+|++|+++.|.|..... +. +.....|.+|.++||||+|
T Consensus 23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv 102 (114)
T KOG3459|consen 23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV 102 (114)
T ss_pred cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence 4566653 22 456899999999999999999999999999999999876321 11 1234588999999999999
Q ss_pred EEEe
Q 032889 110 MLVS 113 (131)
Q Consensus 110 v~I~ 113 (131)
+.+.
T Consensus 103 I~v~ 106 (114)
T KOG3459|consen 103 ILVL 106 (114)
T ss_pred EEEE
Confidence 9886
No 39
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.69 E-value=1.3e-07 Score=66.90 Aligned_cols=67 Identities=22% Similarity=0.331 Sum_probs=58.3
Q ss_pred cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCC
Q 032889 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDG 117 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~ 117 (131)
-|.++.+.+|.|.|++|+...|++.+.|.+||..|.++.-.... ++.++..+.|||++|.++..+|.
T Consensus 6 ~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~---------~pv~l~~lsirgnniRy~~lpD~ 72 (109)
T KOG3428|consen 6 FLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG---------EPVRLDTLSIRGNNIRYYILPDS 72 (109)
T ss_pred HHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC---------CceeEEEEEeecceEEEEEccCC
Confidence 36788999999999999999999999999999999998765431 35678899999999999999874
No 40
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=98.57 E-value=4.7e-08 Score=63.54 Aligned_cols=38 Identities=24% Similarity=0.344 Sum_probs=32.5
Q ss_pred CCeEEEEEcC----CcEEEEEEEEEcCccceEecceEEEeec
Q 032889 48 DKGVQVKLTG----GRQVTGTLKGYDQLLNLVLDEAVEFLRD 85 (131)
Q Consensus 48 ~k~V~V~L~d----Gr~i~G~L~~fD~~mNLVL~da~E~~~~ 85 (131)
+.+|+|.++. +..++|.|+|||+||||+|.|+.|.+..
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 3678888865 4578899999999999999999999864
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.83 E-value=4.2e-05 Score=50.56 Aligned_cols=67 Identities=15% Similarity=0.236 Sum_probs=40.0
Q ss_pred HhhhcCCeEEEEEcCCcEEEEEEEEEcC---ccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEE
Q 032889 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQ---LLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVM 110 (131)
Q Consensus 43 L~~~l~k~V~V~L~dGr~i~G~L~~fD~---~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv 110 (131)
+..++|++|.|+++||..|+|.|.+++. -+-++|.-+........+. ...........++|+++.|+
T Consensus 7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~-~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN-SDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-------EEEEEEE-GGGEEE-----
T ss_pred HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc-CCccCCCCCceEEEeccccC
Confidence 3578999999999999999999999998 8999998887654321110 11123345567777777665
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.22 E-value=0.0026 Score=44.32 Aligned_cols=76 Identities=12% Similarity=0.166 Sum_probs=55.9
Q ss_pred hhhcCCeEEEEEcCCcEEEEEEEEEcC-ccceEecceEEEeecCCCC-CccCcceEEeceEEEeCCcEEEEeeCCCCc
Q 032889 44 AKFVDKGVQVKLTGGRQVTGTLKGYDQ-LLNLVLDEAVEFLRDADDP-LKTTDQTRQLGLIVCRGTAVMLVSPTDGTD 119 (131)
Q Consensus 44 ~~~l~k~V~V~L~dGr~i~G~L~~fD~-~mNLVL~da~E~~~~~~~~-~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~~ 119 (131)
..|+|++|.+..+++-.|+|+|..+|. ...|.|.+|.-+-.++... ............+..||+.|.-+...+...
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~ 81 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP 81 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence 468999999999999999999999995 8999999988664432111 111122345788999999999998876433
No 43
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.69 E-value=0.01 Score=35.83 Aligned_cols=35 Identities=20% Similarity=0.300 Sum_probs=30.5
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEE
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E 81 (131)
++|++|+|.+ ++..++|+..++|....|++.....
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 4789999999 6777899999999999999987544
No 44
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=96.26 E-value=0.039 Score=36.83 Aligned_cols=67 Identities=12% Similarity=0.179 Sum_probs=49.5
Q ss_pred hhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCC--CccCcceEEeceEEEeCCcEEE
Q 032889 45 KFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIVCRGTAVML 111 (131)
Q Consensus 45 ~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~--~~~~~~~r~lg~v~IRG~~Iv~ 111 (131)
.|+|+++.+..+.+-.|+|+|.++| +-.-+.|.|+..+-.++... .+......-+..++.||+.|.-
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 5899999999999999999999999 55667799987665443211 1112234567889999998754
No 45
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=96.15 E-value=0.011 Score=45.11 Aligned_cols=65 Identities=26% Similarity=0.280 Sum_probs=46.2
Q ss_pred cCcccHhhhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889 38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD 116 (131)
Q Consensus 38 ~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d 116 (131)
.+|+.+.+|++|.|+|.+.| +++.|.|..+| -.-||||-+-.|- .++ ..-+|-|-+|..|...+
T Consensus 7 ~~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~------------~~~--sv~~I~ghaVk~vevl~ 71 (166)
T PF06372_consen 7 KSPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQED------------GKR--SVKVIMGHAVKSVEVLS 71 (166)
T ss_dssp S-HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TT------------S-E--EEEEE-GGGEEEEEEEE
T ss_pred CCHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccC------------Cce--eEEEEEccceEEEEEcc
Confidence 56788899999999999999 99999999999 5778998864321 122 24788999999999765
Q ss_pred C
Q 032889 117 G 117 (131)
Q Consensus 117 ~ 117 (131)
+
T Consensus 72 ~ 72 (166)
T PF06372_consen 72 E 72 (166)
T ss_dssp -
T ss_pred C
Confidence 4
No 46
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=95.44 E-value=0.032 Score=35.89 Aligned_cols=33 Identities=21% Similarity=0.363 Sum_probs=28.1
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d 78 (131)
--+.+|.|.|.+|-.++|.+.|||+|+=++-.+
T Consensus 9 ~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 9 KEKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred HcCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 345789999999999999999999998766544
No 47
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=95.35 E-value=0.035 Score=35.74 Aligned_cols=33 Identities=24% Similarity=0.336 Sum_probs=28.2
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d 78 (131)
--+.+|.|.|.+|-.+.|.+.|||+|+=|+-.+
T Consensus 13 ~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 13 KERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred HcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 345789999999999999999999998776544
No 48
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=94.67 E-value=0.097 Score=33.66 Aligned_cols=36 Identities=11% Similarity=0.170 Sum_probs=30.2
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEE
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E 81 (131)
.+|..|++++..|.+++|.+.+||.-.++++-.+.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 478999999999999999999999777776555433
No 49
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.66 E-value=0.072 Score=35.98 Aligned_cols=35 Identities=17% Similarity=0.377 Sum_probs=29.6
Q ss_pred hhcCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889 45 KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (131)
Q Consensus 45 ~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da 79 (131)
+--+.+|.|.|.+|-.+.|.+.|||+|+=|+-.+.
T Consensus 16 r~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 16 RKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred HHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 34567899999999999999999999987776553
No 50
>PRK14638 hypothetical protein; Provisional
Probab=94.31 E-value=0.078 Score=39.53 Aligned_cols=36 Identities=14% Similarity=0.354 Sum_probs=30.0
Q ss_pred ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEec
Q 032889 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~ 77 (131)
.+..+++|++|+|++++++.++|+|.++|.- ++.|.
T Consensus 93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 4467889999999999999999999999963 45553
No 51
>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=93.74 E-value=0.56 Score=31.73 Aligned_cols=59 Identities=19% Similarity=0.175 Sum_probs=43.8
Q ss_pred HhhhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889 43 LAKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP 114 (131)
Q Consensus 43 L~~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 114 (131)
|....|++|.+.|-++.++.|++.|+| ...|+..++-. . + -...+..++|.+.|++++.
T Consensus 19 l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-T---P---------lGv~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 19 LLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-T---P---------LGVQPEALLRCSDVISISF 78 (80)
T ss_dssp HHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-T---T---------TTEEEEEEEEGGGEEEEEE
T ss_pred HHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-C---C---------cccChhheeecCCEEEEEe
Confidence 456789999999999999999999999 56677666632 1 1 1125789999999999875
No 52
>PRK14639 hypothetical protein; Provisional
Probab=93.32 E-value=0.15 Score=37.52 Aligned_cols=36 Identities=19% Similarity=0.306 Sum_probs=30.3
Q ss_pred ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEec
Q 032889 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~ 77 (131)
-+..+++|++|+|++.+++.+.|+|.++|. .++.|.
T Consensus 81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~-~~i~l~ 116 (140)
T PRK14639 81 EHFAKSIGELVKITTNEKEKFEGKIVSVDD-ENITLE 116 (140)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeC-CEEEEE
Confidence 346788999999999999999999999997 455553
No 53
>PRK02001 hypothetical protein; Validated
Probab=93.29 E-value=0.15 Score=38.16 Aligned_cols=36 Identities=22% Similarity=0.448 Sum_probs=30.3
Q ss_pred ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEec
Q 032889 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~ 77 (131)
-+..+++|+.|+|++.+++.++|+|.++|.- ++.|.
T Consensus 83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence 4467889999999999999999999999964 45553
No 54
>PRK14644 hypothetical protein; Provisional
Probab=91.33 E-value=0.51 Score=34.66 Aligned_cols=35 Identities=20% Similarity=0.319 Sum_probs=29.4
Q ss_pred cHhhhcCCeEEEEEcCC----cEEEEEEEEEcCccceEec
Q 032889 42 DLAKFVDKGVQVKLTGG----RQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dG----r~i~G~L~~fD~~mNLVL~ 77 (131)
++.+++|+.|.|++++. +.++|+|.++|. -++.|.
T Consensus 79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~-~~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNP-ETITLK 117 (136)
T ss_pred HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeC-CEEEEE
Confidence 56788999999999876 899999999997 356564
No 55
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=91.28 E-value=0.39 Score=32.25 Aligned_cols=31 Identities=19% Similarity=0.394 Sum_probs=26.2
Q ss_pred hhcCCeEEEEEcCCcEEEEEEEEEcCccceE
Q 032889 45 KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLV 75 (131)
Q Consensus 45 ~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLV 75 (131)
+.-+.+|.|.|.||-.+.|.+.|||+|.=|+
T Consensus 16 Rk~~i~VtIfLvNG~~L~G~V~sfD~f~VlL 46 (77)
T COG1923 16 RKEKIPVTIFLVNGFKLQGQVESFDNFVVLL 46 (77)
T ss_pred HhcCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence 3456789999999999999999999997443
No 56
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=91.02 E-value=1.5 Score=28.58 Aligned_cols=52 Identities=25% Similarity=0.314 Sum_probs=38.3
Q ss_pred cHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEee
Q 032889 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSP 114 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~ 114 (131)
.|++++|++|.|.+..|+. +|+|.+... -.++|+.. -...+||=..|++|.+
T Consensus 15 ~lq~liG~~vvV~T~~g~v-~G~L~~V~p-DhIvl~~~-------------------~~~~~IR~~~IV~v~p 66 (66)
T PF10842_consen 15 TLQSLIGQRVVVQTTRGSV-RGILVDVKP-DHIVLEEN-------------------GTPFFIRIAQIVWVMP 66 (66)
T ss_pred HHHHhcCCEEEEEEcCCcE-EEEEEeecC-CEEEEEeC-------------------CcEEEEEeeeEEEEcC
Confidence 4789999999999976665 999999873 23455432 1247889889988753
No 57
>PRK14640 hypothetical protein; Provisional
Probab=90.93 E-value=0.56 Score=34.91 Aligned_cols=36 Identities=22% Similarity=0.375 Sum_probs=29.1
Q ss_pred ccHhhhcCCeEEEEE----cCCcEEEEEEEEEcCccceEec
Q 032889 41 LDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 41 l~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~~mNLVL~ 77 (131)
.+..+++|++|.|++ .+++.++|+|.++|. -++.|.
T Consensus 90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~-~~v~l~ 129 (152)
T PRK14640 90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQG-DMITLT 129 (152)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeC-CEEEEE
Confidence 446788999999999 567999999999996 355554
No 58
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=90.68 E-value=0.54 Score=31.28 Aligned_cols=36 Identities=39% Similarity=0.515 Sum_probs=28.4
Q ss_pred cccHhhhcCCeEEEEEc---CC-cEEEEEEEEEcCccceEe
Q 032889 40 VLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQLLNLVL 76 (131)
Q Consensus 40 ~l~L~~~l~k~V~V~L~---dG-r~i~G~L~~fD~~mNLVL 76 (131)
+.+..+++|+.|.|+++ +| +.+.|+|.++|.- +++|
T Consensus 17 ~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 17 EADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred HHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 34567889999999997 55 5899999999973 4444
No 59
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=90.28 E-value=0.69 Score=35.27 Aligned_cols=33 Identities=18% Similarity=0.310 Sum_probs=27.7
Q ss_pred cCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (131)
Q Consensus 47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da 79 (131)
-..+|.|.|.+|-.++|++.+||+|.=|.-.+.
T Consensus 23 ~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 23 TKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 446789999999999999999999986665553
No 60
>PRK14633 hypothetical protein; Provisional
Probab=89.64 E-value=0.63 Score=34.59 Aligned_cols=36 Identities=17% Similarity=0.276 Sum_probs=28.9
Q ss_pred ccHhhhcCCeEEEEE----cCCcEEEEEEEEEcCccceEec
Q 032889 41 LDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 41 l~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~~mNLVL~ 77 (131)
.+..+++|++|.|++ .+++.++|+|.++|.. ++.|.
T Consensus 87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 446788999999999 4678999999999873 55553
No 61
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=89.16 E-value=0.73 Score=33.48 Aligned_cols=35 Identities=31% Similarity=0.589 Sum_probs=25.9
Q ss_pred ccHhhhcCCeEEEEE----cCCcEEEEEEEEEcCccceEe
Q 032889 41 LDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL 76 (131)
Q Consensus 41 l~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~~mNLVL 76 (131)
.++.+++|++|.|++ .+.+.++|+|.++|. -.++|
T Consensus 80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 356789999999999 456789999999998 45555
No 62
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=88.61 E-value=1.4 Score=33.56 Aligned_cols=33 Identities=18% Similarity=0.325 Sum_probs=28.3
Q ss_pred cCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (131)
Q Consensus 47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da 79 (131)
-..+|.|.|.+|-.+.|.+.|||+|.=|.-.+.
T Consensus 103 ~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 103 SGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 456899999999999999999999987766554
No 63
>PRK14642 hypothetical protein; Provisional
Probab=88.49 E-value=0.96 Score=35.38 Aligned_cols=35 Identities=17% Similarity=0.366 Sum_probs=28.7
Q ss_pred ccHhhhcCCeEEEEEc-------------CCcEEEEEEEEEcCccceEe
Q 032889 41 LDLAKFVDKGVQVKLT-------------GGRQVTGTLKGYDQLLNLVL 76 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~-------------dGr~i~G~L~~fD~~mNLVL 76 (131)
.+..+++|+.|.|+|+ +.+.++|+|.++|.. ++.|
T Consensus 93 ~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 93 QDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred HHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 4466789999999998 679999999999973 4444
No 64
>PRK14645 hypothetical protein; Provisional
Probab=88.26 E-value=0.8 Score=34.31 Aligned_cols=34 Identities=18% Similarity=0.302 Sum_probs=27.5
Q ss_pred ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEe
Q 032889 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL 76 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL 76 (131)
-+..+++|++|.|++ +++.++|+|.++|.- .+.|
T Consensus 95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 345678999999986 899999999999963 4544
No 65
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=88.15 E-value=0.94 Score=33.57 Aligned_cols=31 Identities=32% Similarity=0.594 Sum_probs=26.6
Q ss_pred cccHhhhcCCeEEEEE----cCCcEEEEEEEEEcC
Q 032889 40 VLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQ 70 (131)
Q Consensus 40 ~l~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~ 70 (131)
+-++.+++|+.|+|++ .+++.++|+|.++|.
T Consensus 90 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 90 ARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 3456788999999997 578899999999997
No 66
>PRK14636 hypothetical protein; Provisional
Probab=87.47 E-value=0.97 Score=34.59 Aligned_cols=35 Identities=29% Similarity=0.546 Sum_probs=28.0
Q ss_pred ccHhhhcCCeEEEEEc---CC-cEEEEEEEEEcCccceEe
Q 032889 41 LDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQLLNLVL 76 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~---dG-r~i~G~L~~fD~~mNLVL 76 (131)
-+..+++|++|.|+++ +| +.++|+|.++|. .++.|
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~-~~v~l 129 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDG-DTVTI 129 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeC-CEEEE
Confidence 4467889999999997 45 699999999986 34555
No 67
>PRK14632 hypothetical protein; Provisional
Probab=87.18 E-value=1.1 Score=34.15 Aligned_cols=36 Identities=19% Similarity=0.389 Sum_probs=28.6
Q ss_pred ccHhhhcCCeEEEEEcC-------CcEEEEEEEEEcCccceEec
Q 032889 41 LDLAKFVDKGVQVKLTG-------GRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~d-------Gr~i~G~L~~fD~~mNLVL~ 77 (131)
-+..+++|+.|.|++.+ .+.++|+|.++|. -++.|.
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~-~~i~l~ 133 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEG-DTVVLR 133 (172)
T ss_pred HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeC-CEEEEE
Confidence 34678899999999975 6799999999985 355553
No 68
>PRK14634 hypothetical protein; Provisional
Probab=87.12 E-value=1.1 Score=33.48 Aligned_cols=36 Identities=19% Similarity=0.264 Sum_probs=28.3
Q ss_pred ccHhhhcCCeEEEEEcC----CcEEEEEEEEEcCccceEec
Q 032889 41 LDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~d----Gr~i~G~L~~fD~~mNLVL~ 77 (131)
.+..+++|++|+|++.+ .+.++|+|.++|. .++.|.
T Consensus 93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~-~~v~l~ 132 (155)
T PRK14634 93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNE-DHLQIN 132 (155)
T ss_pred HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeC-CEEEEE
Confidence 45678899999999963 3789999999996 445553
No 69
>PRK14643 hypothetical protein; Provisional
Probab=86.81 E-value=1.2 Score=33.80 Aligned_cols=31 Identities=23% Similarity=0.324 Sum_probs=26.4
Q ss_pred ccHhhhcCCeEEEEEcC----CcEEEEEEEEEcCc
Q 032889 41 LDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQL 71 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~d----Gr~i~G~L~~fD~~ 71 (131)
.+..+++|++|.|++++ .+.++|+|.++|.-
T Consensus 97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 45678899999999965 68999999999964
No 70
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.39 E-value=1.9 Score=32.47 Aligned_cols=34 Identities=29% Similarity=0.546 Sum_probs=29.0
Q ss_pred cHhhhcCCeEEEEE----cCCcEEEEEEEEEcCccceEe
Q 032889 42 DLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL 76 (131)
Q Consensus 42 ~L~~~l~k~V~V~L----~dGr~i~G~L~~fD~~mNLVL 76 (131)
+..+++|+.|.|+| .+++.+.|+|.++|.-. +++
T Consensus 93 ~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 93 HFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred HHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 35678999999999 78999999999999776 444
No 71
>PRK14646 hypothetical protein; Provisional
Probab=86.38 E-value=1.3 Score=33.14 Aligned_cols=36 Identities=22% Similarity=0.231 Sum_probs=28.3
Q ss_pred ccHhhhcCCeEEEEEcC----CcEEEEEEEEEcCccceEec
Q 032889 41 LDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~d----Gr~i~G~L~~fD~~mNLVL~ 77 (131)
-+..+++|++|+|+|++ -+.++|+|.++|.- ++.|.
T Consensus 93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 45678899999999954 36789999999973 56553
No 72
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.33 E-value=3 Score=35.50 Aligned_cols=72 Identities=15% Similarity=0.180 Sum_probs=53.7
Q ss_pred hhhcCCeEEEEEcCCcEEEEEEEEEc-CccceEecceEEEeecCC--CCC-ccCcceEEeceEEEeCCcEEEEeeCC
Q 032889 44 AKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDAD--DPL-KTTDQTRQLGLIVCRGTAVMLVSPTD 116 (131)
Q Consensus 44 ~~~l~k~V~V~L~dGr~i~G~L~~fD-~~mNLVL~da~E~~~~~~--~~~-~~~~~~r~lg~v~IRG~~Iv~I~~~d 116 (131)
..|||++|.++-+..-.|+|+|.-+| +-.=|-|.+|.-+-.++. ++. .....+ ....++.||+.|.-+...+
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~k-Vy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDK-VYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCcc-ceeeEEecCcccceeeecc
Confidence 46899999999999999999999999 888899999754433221 111 112222 6789999999999777654
No 73
>PRK06955 biotin--protein ligase; Provisional
Probab=85.65 E-value=3.6 Score=33.56 Aligned_cols=33 Identities=24% Similarity=0.400 Sum_probs=28.8
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d 78 (131)
++|++|+|...+++.++|++.|+|....|++..
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 488999997667788999999999999999964
No 74
>PRK14647 hypothetical protein; Provisional
Probab=85.44 E-value=1.5 Score=32.79 Aligned_cols=35 Identities=17% Similarity=0.321 Sum_probs=27.5
Q ss_pred ccHhhhcCCeEEEEEc---------CCcEEEEEEEEEcCccceEe
Q 032889 41 LDLAKFVDKGVQVKLT---------GGRQVTGTLKGYDQLLNLVL 76 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~---------dGr~i~G~L~~fD~~mNLVL 76 (131)
.++.+++|++|.|+++ +.+.++|+|.++|. ..+.|
T Consensus 92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~-~~v~l 135 (159)
T PRK14647 92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD-GVVTI 135 (159)
T ss_pred HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC-CEEEE
Confidence 4567889999999995 35899999999995 34444
No 75
>PRK14631 hypothetical protein; Provisional
Probab=84.54 E-value=1.7 Score=33.21 Aligned_cols=35 Identities=17% Similarity=0.334 Sum_probs=28.0
Q ss_pred ccHhhhcCCeEEEEEc----CCcEEEEEEEEEc--CccceEe
Q 032889 41 LDLAKFVDKGVQVKLT----GGRQVTGTLKGYD--QLLNLVL 76 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~----dGr~i~G~L~~fD--~~mNLVL 76 (131)
.+..+++|+.|.|++. +.+.++|+|.++| . .++.|
T Consensus 110 ~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~-~~v~l 150 (174)
T PRK14631 110 EQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLEN-EEIQV 150 (174)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCC-CEEEE
Confidence 4567889999999995 5699999999998 4 34444
No 76
>PRK14637 hypothetical protein; Provisional
Probab=83.21 E-value=2.1 Score=31.92 Aligned_cols=36 Identities=31% Similarity=0.363 Sum_probs=27.2
Q ss_pred ccHhhhcCCeEEEEEcCCcEE-EEEEEEEcCccceEec
Q 032889 41 LDLAKFVDKGVQVKLTGGRQV-TGTLKGYDQLLNLVLD 77 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~dGr~i-~G~L~~fD~~mNLVL~ 77 (131)
.+..+++|++|.|++.+.+.+ +|+|.++|.- ++.|.
T Consensus 91 ~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 91 AEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 446678999999999544556 7999999964 55554
No 77
>PRK14641 hypothetical protein; Provisional
Probab=81.64 E-value=2.3 Score=32.50 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=24.4
Q ss_pred ccHhhhcCCeEEEEEcC----CcEEEEEEEEEc
Q 032889 41 LDLAKFVDKGVQVKLTG----GRQVTGTLKGYD 69 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~d----Gr~i~G~L~~fD 69 (131)
-+..+++|+.|.|++.+ .+.++|+|.++|
T Consensus 97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 34567899999999965 568999999995
No 78
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=80.77 E-value=8 Score=31.47 Aligned_cols=31 Identities=26% Similarity=0.644 Sum_probs=27.2
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEec
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~ 77 (131)
++|++|.+.. ++..++|++.++|....|++.
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 5889999987 456799999999999999996
No 79
>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=80.51 E-value=1.5 Score=29.55 Aligned_cols=62 Identities=23% Similarity=0.230 Sum_probs=29.5
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCCCCccccCCC
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTDGTDEIANPF 125 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d~~~~~~~p~ 125 (131)
.-+.+|+++|+||..+.|+ +.|-..|- +-.|+..- ...-+...||=++|.++++.. +||-
T Consensus 15 ~~~~~v~L~l~dG~~~~g~--A~dt~~~~---~k~E~L~l----------~~~~~~~~i~Ld~I~~~~al~-----~nPh 74 (80)
T PF07073_consen 15 MYRYPVKLTLKDGEQIEGK--ALDTRTNA---KKEECLVL----------EQDGGEQEIRLDQIASMSALT-----DNPH 74 (80)
T ss_dssp TTTT-EEEE-TTT--EEES--S-EEE------SSS-EEEE----------EETTEEEEESTT--SEEE---------ETT
T ss_pred hcCCeEEEEEeCCCEEEEE--EEEEEEec---CceEEEEE----------ecCCcEEEEEhhheeeeeecC-----CCCe
Confidence 4567999999999999997 44433331 22233221 111245678999999999765 5665
Q ss_pred CC
Q 032889 126 MQ 127 (131)
Q Consensus 126 ~~ 127 (131)
|+
T Consensus 75 F~ 76 (80)
T PF07073_consen 75 FG 76 (80)
T ss_dssp TE
T ss_pred ee
Confidence 43
No 80
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=80.40 E-value=3.1 Score=31.52 Aligned_cols=36 Identities=22% Similarity=0.242 Sum_probs=32.0
Q ss_pred hhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceE
Q 032889 45 KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 45 ~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~ 80 (131)
++-+-+|+|.+.||..+.|.+.+|++--|.+|..+.
T Consensus 26 r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 26 RFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred HhcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 445678999999999999999999999999998754
No 81
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=79.06 E-value=7.5 Score=34.94 Aligned_cols=33 Identities=30% Similarity=0.248 Sum_probs=28.8
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d 78 (131)
++|++|++...+++.++|+..|+|....|+|+.
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 478999987667778999999999999999963
No 82
>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=77.22 E-value=12 Score=29.14 Aligned_cols=31 Identities=19% Similarity=0.384 Sum_probs=27.0
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEec
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~ 77 (131)
++|++|.|... +..+.|++.|+|....|+|+
T Consensus 191 ~~g~~V~v~~~-~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTG-NGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeC-CcEEEEEEEeECCCceEEEE
Confidence 47899999874 46799999999999999996
No 83
>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=76.82 E-value=2.8 Score=31.77 Aligned_cols=24 Identities=25% Similarity=0.554 Sum_probs=22.2
Q ss_pred cCCeEEEEEcCCcEEEEEEEEEcC
Q 032889 47 VDKGVQVKLTGGRQVTGTLKGYDQ 70 (131)
Q Consensus 47 l~k~V~V~L~dGr~i~G~L~~fD~ 70 (131)
-|+-|+|.+.|||+++|+=.|.|.
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccce
Confidence 678999999999999999999984
No 84
>PRK08330 biotin--protein ligase; Provisional
Probab=75.35 E-value=11 Score=29.40 Aligned_cols=32 Identities=22% Similarity=0.320 Sum_probs=26.9
Q ss_pred hcCCeEEEEEcCCcEE-EEEEEEEcCccceEecc
Q 032889 46 FVDKGVQVKLTGGRQV-TGTLKGYDQLLNLVLDE 78 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i-~G~L~~fD~~mNLVL~d 78 (131)
++|++|.+.. +++.+ .|++.++|....|++..
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 5889999875 56665 79999999999999974
No 85
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=71.88 E-value=16 Score=29.15 Aligned_cols=34 Identities=32% Similarity=0.425 Sum_probs=31.2
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da 79 (131)
.+|++|++...++....|+..++|....|+|+..
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 4889999999988899999999999999999876
No 86
>PRK14630 hypothetical protein; Provisional
Probab=69.98 E-value=7.9 Score=28.53 Aligned_cols=35 Identities=11% Similarity=0.180 Sum_probs=26.6
Q ss_pred ccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEec
Q 032889 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (131)
Q Consensus 41 l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~ 77 (131)
.+..+++|++|+|++.+ ...+|+|.++|. -++.|.
T Consensus 90 ~df~r~~G~~v~V~l~~-~~~~G~L~~~~d-~~i~l~ 124 (143)
T PRK14630 90 REFKIFEGKKIKLMLDN-DFEEGFILEAKA-DSFIFK 124 (143)
T ss_pred HHHHHhCCCEEEEEEcC-cceEEEEEEEeC-CEEEEE
Confidence 34667899999999965 445999999996 455553
No 87
>PRK10898 serine endoprotease; Provisional
Probab=69.96 E-value=9.5 Score=31.82 Aligned_cols=32 Identities=28% Similarity=0.352 Sum_probs=28.8
Q ss_pred CeEEEEEcCCcEEEEEEEEEcCccceEecceE
Q 032889 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 49 k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~ 80 (131)
.++.|++.||+.+.++++++|....|-|=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 57999999999999999999999999877654
No 88
>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=68.55 E-value=7.5 Score=27.19 Aligned_cols=18 Identities=28% Similarity=0.554 Sum_probs=14.7
Q ss_pred CeEEEEEcCCcEEEEEEE
Q 032889 49 KGVQVKLTGGRQVTGTLK 66 (131)
Q Consensus 49 k~V~V~L~dGr~i~G~L~ 66 (131)
.+|.+.|+||+.+.|++.
T Consensus 29 ~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 29 ERVELELDDGSMLRGTVA 46 (101)
T ss_dssp -EEEEEETTS-EEEEEEC
T ss_pred ceEEEEEcCCCeeeeeec
Confidence 589999999999999974
No 89
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=68.54 E-value=10 Score=31.49 Aligned_cols=32 Identities=28% Similarity=0.399 Sum_probs=28.7
Q ss_pred CeEEEEEcCCcEEEEEEEEEcCccceEecceE
Q 032889 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 49 k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~ 80 (131)
.++.|.+.||+.+.++++++|...+|.|=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 46899999999999999999999999886654
No 90
>PRK14635 hypothetical protein; Provisional
Probab=68.00 E-value=10 Score=28.48 Aligned_cols=37 Identities=19% Similarity=0.187 Sum_probs=28.1
Q ss_pred cccHhhhcCCeEEEEEc--CCcEEEE---EEEEEcCccceEec
Q 032889 40 VLDLAKFVDKGVQVKLT--GGRQVTG---TLKGYDQLLNLVLD 77 (131)
Q Consensus 40 ~l~L~~~l~k~V~V~L~--dGr~i~G---~L~~fD~~mNLVL~ 77 (131)
+-++.++.|+.|+|++. ++..+.| +|.++|.- ++.|.
T Consensus 91 ~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~ 132 (162)
T PRK14635 91 PEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE 132 (162)
T ss_pred HHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence 34567889999999885 5678888 99999963 45553
No 91
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=66.95 E-value=13 Score=30.17 Aligned_cols=31 Identities=26% Similarity=0.260 Sum_probs=27.2
Q ss_pred cCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (131)
Q Consensus 47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d 78 (131)
+|++|.|.. ++..+.|++.++|....|+|..
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 789998875 6789999999999999999964
No 92
>PRK10942 serine endoprotease; Provisional
Probab=64.32 E-value=13 Score=32.32 Aligned_cols=32 Identities=22% Similarity=0.396 Sum_probs=28.6
Q ss_pred CCeEEEEEcCCcEEEEEEEEEcCccceEecce
Q 032889 48 DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (131)
Q Consensus 48 ~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da 79 (131)
..+++|++.||+++.++++++|...+|-|=..
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 35799999999999999999999999987754
No 93
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=63.08 E-value=9.2 Score=22.80 Aligned_cols=22 Identities=27% Similarity=0.442 Sum_probs=14.9
Q ss_pred EEEEEEEEcCccceEecceEEE
Q 032889 61 VTGTLKGYDQLLNLVLDEAVEF 82 (131)
Q Consensus 61 i~G~L~~fD~~mNLVL~da~E~ 82 (131)
.+|++.|.|+...+.|.+....
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 6899999999999999986644
No 94
>PRK10139 serine endoprotease; Provisional
Probab=62.96 E-value=15 Score=31.81 Aligned_cols=33 Identities=21% Similarity=0.398 Sum_probs=29.2
Q ss_pred CCeEEEEEcCCcEEEEEEEEEcCccceEecceE
Q 032889 48 DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 48 ~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~ 80 (131)
..++.|++.||+.+.++++++|....|-+=.+.
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 368999999999999999999999999886654
No 95
>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=55.74 E-value=23 Score=29.97 Aligned_cols=32 Identities=22% Similarity=0.355 Sum_probs=28.8
Q ss_pred CeEEEEEcCCcEEEEEEEEEcCccceEecceE
Q 032889 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 49 k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~ 80 (131)
.++.|++.||+.+.++++++|...+|.|=...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 57999999999999999999999999887654
No 96
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=53.14 E-value=7.5 Score=28.91 Aligned_cols=24 Identities=25% Similarity=0.270 Sum_probs=18.6
Q ss_pred CCcEEEEEEEEEcCccceEecceE
Q 032889 57 GGRQVTGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 57 dGr~i~G~L~~fD~~mNLVL~da~ 80 (131)
..-.=.|+|+|.|+|.|=--+|-.
T Consensus 41 td~~kiGTLVG~DkfGNkYyen~~ 64 (151)
T KOG3382|consen 41 TDDHKIGTLVGVDKFGNKYYENND 64 (151)
T ss_pred cccccceeeeeecccccchhcccc
Confidence 344456899999999998887753
No 97
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=53.14 E-value=48 Score=24.63 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=24.3
Q ss_pred HhhhcCCeEEEEEcCCcEEEEEEEEEc
Q 032889 43 LAKFVDKGVQVKLTGGRQVTGTLKGYD 69 (131)
Q Consensus 43 L~~~l~k~V~V~L~dGr~i~G~L~~fD 69 (131)
...++||.|.+...+|..++|++.++.
T Consensus 87 a~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 87 YSELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 357899999999999999999999986
No 98
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=52.96 E-value=30 Score=23.70 Aligned_cols=55 Identities=15% Similarity=0.126 Sum_probs=37.5
Q ss_pred eccccccccccccccccccc--CccC---cccHhhhcCCeEEEEEcCCcEEEEEEEEEcC
Q 032889 16 CRSARVSFNLGFLKSLKMSG--RKET---VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQ 70 (131)
Q Consensus 16 ~~~~~~~~~~~~~~~~~m~~--~~~~---~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~ 70 (131)
+.+..++|+-+...+..-.+ +.++ .-+-.-|+||+|--.-+.|+.+-|++.---.
T Consensus 3 ~kgv~~gykRg~~nQ~~~~aLlkiegv~~~~~a~fylGKrv~yvyk~grviwGKItR~HG 62 (87)
T PRK04337 3 MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIWKDPTGNKYVGKIVRVHG 62 (87)
T ss_pred ceEEEEEeccccCccCCceEEEEEcCcCCHHHHHhhcCceEEEEeCCCCEEEEEEEeeeC
Confidence 45567888877776664332 2222 3344568999999888899999998875433
No 99
>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=49.09 E-value=7.8 Score=27.02 Aligned_cols=17 Identities=35% Similarity=0.483 Sum_probs=15.4
Q ss_pred EEEEEEcCccceEecce
Q 032889 63 GTLKGYDQLLNLVLDEA 79 (131)
Q Consensus 63 G~L~~fD~~mNLVL~da 79 (131)
|+|+|.|.|.|.--+.-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999988775
No 100
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=43.28 E-value=51 Score=21.95 Aligned_cols=33 Identities=27% Similarity=0.433 Sum_probs=22.7
Q ss_pred cHhhhcCCeEEEEEcCCc----EEEEEEEEEcCccceEe
Q 032889 42 DLAKFVDKGVQVKLTGGR----QVTGTLKGYDQLLNLVL 76 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr----~i~G~L~~fD~~mNLVL 76 (131)
+|..++|++|.++.+.|| +-.|+|... |=|+-.
T Consensus 11 ~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t--YPsvFv 47 (76)
T PF06257_consen 11 ELESHVGKRVKLKANKGRKKIIEREGVLEET--YPSVFV 47 (76)
T ss_dssp HHHHTTTSEEEEEE--SSS--S-EEEEEEEE---SSEEE
T ss_pred HHHHcCCCEEEEEEcCCceEEEEEEEEEEee--cCcEEE
Confidence 577899999999999998 467988764 444444
No 101
>PRK08477 biotin--protein ligase; Provisional
Probab=43.15 E-value=78 Score=24.68 Aligned_cols=34 Identities=9% Similarity=-0.007 Sum_probs=29.0
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEcCccceEecceE
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~ 80 (131)
.+++.|+|. .+++.++|+..++|...-|++..-.
T Consensus 173 ~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~ 206 (211)
T PRK08477 173 EKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKK 206 (211)
T ss_pred HcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEE
Confidence 388999986 4789999999999999999887644
No 102
>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=42.49 E-value=34 Score=24.36 Aligned_cols=28 Identities=18% Similarity=0.284 Sum_probs=21.1
Q ss_pred eEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889 50 GVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (131)
Q Consensus 50 ~V~V~L~dGr~i~G~L~~fD~~mNLVL~d 78 (131)
...|.++||+.+.|.+.+=| --.+.|.+
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~-~~~~~l~~ 86 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET-ADGVTVKM 86 (133)
T ss_pred cEEEEECCCCEEEEEEEecC-CCeEEEEc
Confidence 47899999999999998855 33444444
No 103
>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=41.60 E-value=35 Score=23.60 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=19.4
Q ss_pred hhcCCeEEEE-EcCCcEEEEEEEE
Q 032889 45 KFVDKGVQVK-LTGGRQVTGTLKG 67 (131)
Q Consensus 45 ~~l~k~V~V~-L~dGr~i~G~L~~ 67 (131)
-.+|..|+|+ +..|+.+.|+..+
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 3688999999 7899999998875
No 104
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=39.05 E-value=1e+02 Score=20.58 Aligned_cols=25 Identities=16% Similarity=0.173 Sum_probs=20.4
Q ss_pred EcCCcEEEEEEEEEcCccceEecce
Q 032889 55 LTGGRQVTGTLKGYDQLLNLVLDEA 79 (131)
Q Consensus 55 L~dGr~i~G~L~~fD~~mNLVL~da 79 (131)
++-|-.+.+++.+++...++.|+-+
T Consensus 61 f~~GDiV~AkVis~~~~~~~~Lst~ 85 (92)
T cd05791 61 FRPGDIVRAKVISLGDASSYYLSTA 85 (92)
T ss_pred cCCCCEEEEEEEEcCCCCCcEEEec
Confidence 3569999999999998888887643
No 105
>PRK11625 Rho-binding antiterminator; Provisional
Probab=37.09 E-value=1.3e+02 Score=20.31 Aligned_cols=54 Identities=15% Similarity=0.080 Sum_probs=35.5
Q ss_pred cCCeEEEEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEEeeCC
Q 032889 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLVSPTD 116 (131)
Q Consensus 47 l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I~~~d 116 (131)
-+.+|.++++||..+.|+. .|-+ ..+-.|+..-.. .=+.-.||=|+|.+++-++
T Consensus 22 ~~~~l~l~l~dGe~~~g~A--~D~~----~~~k~EyL~l~~----------~g~~~~iRLD~I~s~~~~~ 75 (84)
T PRK11625 22 HHLMLTLELKDGEVLQAKA--SDLV----SRKNVEYLVVEA----------AGETRELRLDKIASFSHPE 75 (84)
T ss_pred cCCeEEEEECCCCEEEEEE--Eeee----cCCceEEEEEEc----------CCCEEEEEeeeEeeccCcc
Confidence 5678999999999999986 4544 234455543211 1134568888888887443
No 106
>PHA02723 hypothetical protein; Provisional
Probab=36.33 E-value=19 Score=23.53 Aligned_cols=19 Identities=37% Similarity=0.574 Sum_probs=13.4
Q ss_pred EEEEEEecccccccccccc
Q 032889 10 VSFFIVCRSARVSFNLGFL 28 (131)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~ 28 (131)
.-=||.||++|.+...-++
T Consensus 47 ivnfimcrsnlnn~~i~~~ 65 (77)
T PHA02723 47 IVNFIMCRSNLNNIFIFFL 65 (77)
T ss_pred ceeeeEecccCCCceeeee
Confidence 4458999999887654443
No 107
>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=36.01 E-value=92 Score=18.19 Aligned_cols=25 Identities=16% Similarity=0.147 Sum_probs=20.9
Q ss_pred cCCeEEEEEcCCcEEEEEEEEEcCc
Q 032889 47 VDKGVQVKLTGGRQVTGTLKGYDQL 71 (131)
Q Consensus 47 l~k~V~V~L~dGr~i~G~L~~fD~~ 71 (131)
.|..+.+...||+-++|++.+++.-
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4667777778999999999999963
No 108
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=34.78 E-value=83 Score=19.77 Aligned_cols=24 Identities=25% Similarity=0.452 Sum_probs=17.9
Q ss_pred cCCeEEEEEcCCcE-EEEEEEEEcC
Q 032889 47 VDKGVQVKLTGGRQ-VTGTLKGYDQ 70 (131)
Q Consensus 47 l~k~V~V~L~dGr~-i~G~L~~fD~ 70 (131)
.|++|.+.--++.. |.|++.+||.
T Consensus 8 ~Ge~V~~rWP~s~lYYe~kV~~~d~ 32 (55)
T PF09465_consen 8 IGEVVMVRWPGSSLYYEGKVLSYDS 32 (55)
T ss_dssp SS-EEEEE-TTTS-EEEEEEEEEET
T ss_pred CCCEEEEECCCCCcEEEEEEEEecc
Confidence 78899999977665 5999999995
No 109
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=34.26 E-value=46 Score=26.11 Aligned_cols=23 Identities=26% Similarity=0.596 Sum_probs=20.0
Q ss_pred hhcCCeEEEE-EcCCcEEEEEEEE
Q 032889 45 KFVDKGVQVK-LTGGRQVTGTLKG 67 (131)
Q Consensus 45 ~~l~k~V~V~-L~dGr~i~G~L~~ 67 (131)
-.+|..|+|+ +..|+.+.|+..+
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeC
Confidence 3688999999 9999999999876
No 110
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=33.33 E-value=34 Score=22.50 Aligned_cols=18 Identities=28% Similarity=0.265 Sum_probs=14.4
Q ss_pred HhhhcCCeEEEEEcCCcE
Q 032889 43 LAKFVDKGVQVKLTGGRQ 60 (131)
Q Consensus 43 L~~~l~k~V~V~L~dGr~ 60 (131)
+.+.+||+|||+......
T Consensus 6 ~nDrLGKKVRvKCn~dDt 23 (73)
T KOG3493|consen 6 LNDRLGKKVRVKCNTDDT 23 (73)
T ss_pred hhhhcCceEEEEeCCccc
Confidence 578899999999976543
No 111
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=32.10 E-value=83 Score=23.32 Aligned_cols=26 Identities=15% Similarity=0.399 Sum_probs=22.8
Q ss_pred hhhcCCeEEEEEcCCcEEEEEEEEEc
Q 032889 44 AKFVDKGVQVKLTGGRQVTGTLKGYD 69 (131)
Q Consensus 44 ~~~l~k~V~V~L~dGr~i~G~L~~fD 69 (131)
..++||.|.....+|..++|++.++.
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~ 114 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQ 114 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEE
Confidence 36899999988889999999999776
No 112
>PRK06630 hypothetical protein; Provisional
Probab=31.54 E-value=25 Score=24.67 Aligned_cols=19 Identities=21% Similarity=0.221 Sum_probs=16.6
Q ss_pred EEEEEEEEcCccceEecce
Q 032889 61 VTGTLKGYDQLLNLVLDEA 79 (131)
Q Consensus 61 i~G~L~~fD~~mNLVL~da 79 (131)
..|+|+|-|+|.|---++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3799999999999988874
No 113
>PRK10708 hypothetical protein; Provisional
Probab=31.15 E-value=57 Score=20.83 Aligned_cols=26 Identities=27% Similarity=0.459 Sum_probs=22.3
Q ss_pred cCCeEEEEEcCCcEEEEEEEEEcCcc
Q 032889 47 VDKGVQVKLTGGRQVTGTLKGYDQLL 72 (131)
Q Consensus 47 l~k~V~V~L~dGr~i~G~L~~fD~~m 72 (131)
++.+|.|++.+|..=.|++.+...|.
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 46789999999999999999988664
No 114
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=29.70 E-value=53 Score=21.11 Aligned_cols=21 Identities=19% Similarity=0.379 Sum_probs=18.5
Q ss_pred CeEEEEEcCCcEEEEEEEEEc
Q 032889 49 KGVQVKLTGGRQVTGTLKGYD 69 (131)
Q Consensus 49 k~V~V~L~dGr~i~G~L~~fD 69 (131)
.+|.|++-||..+.+++.+-|
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~ 25 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSD 25 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 579999999999999988655
No 115
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=29.25 E-value=77 Score=25.50 Aligned_cols=19 Identities=21% Similarity=0.282 Sum_probs=17.6
Q ss_pred EEEEEEEEEcCccceEecc
Q 032889 60 QVTGTLKGYDQLLNLVLDE 78 (131)
Q Consensus 60 ~i~G~L~~fD~~mNLVL~d 78 (131)
.+.|.+.-+|.|.|+++.=
T Consensus 169 ~i~g~Vi~iD~FGNlitnI 187 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNI 187 (258)
T ss_dssp EEEEEEEEEETTSEEEEEE
T ss_pred eEEEEEEEECccCCeeeCC
Confidence 8999999999999999864
No 116
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=26.84 E-value=1.2e+02 Score=24.71 Aligned_cols=33 Identities=27% Similarity=0.426 Sum_probs=27.6
Q ss_pred CCeEEEEEcCCcEEEEEEEEEcCccceEecceE
Q 032889 48 DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 48 ~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~ 80 (131)
..++.|.+.||+.+.+.+.++|...-+.+-...
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki~ 127 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKID 127 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEec
Confidence 468899999999999999999987777665544
No 117
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.66 E-value=77 Score=24.87 Aligned_cols=22 Identities=23% Similarity=0.280 Sum_probs=19.2
Q ss_pred hcCCeEEEE-EcCCcEEEEEEEE
Q 032889 46 FVDKGVQVK-LTGGRQVTGTLKG 67 (131)
Q Consensus 46 ~l~k~V~V~-L~dGr~i~G~L~~ 67 (131)
-.|..|+|+ +..||.+.|+..+
T Consensus 184 ~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 184 GENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 588999999 7999999999865
No 118
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=26.62 E-value=52 Score=21.37 Aligned_cols=24 Identities=21% Similarity=0.524 Sum_probs=19.7
Q ss_pred hcCCeEEEEEcCCcEEEEEEEEEc
Q 032889 46 FVDKGVQVKLTGGRQVTGTLKGYD 69 (131)
Q Consensus 46 ~l~k~V~V~L~dGr~i~G~L~~fD 69 (131)
|-..+|.|+|-||..+.+++.+-|
T Consensus 2 ~~~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 2 YTETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred CcEEEEEEECCCCCEEEEEeCCCC
Confidence 345689999999999999987655
No 119
>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=26.61 E-value=68 Score=20.46 Aligned_cols=26 Identities=27% Similarity=0.433 Sum_probs=22.2
Q ss_pred cCCeEEEEEcCCcEEEEEEEEEcCcc
Q 032889 47 VDKGVQVKLTGGRQVTGTLKGYDQLL 72 (131)
Q Consensus 47 l~k~V~V~L~dGr~i~G~L~~fD~~m 72 (131)
++.+|.|++.+|..=.|++.+...|.
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 46789999999999999999988664
No 120
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=26.61 E-value=72 Score=20.28 Aligned_cols=21 Identities=14% Similarity=0.442 Sum_probs=17.9
Q ss_pred CeEEEEEcCCcEEEEEEEEEc
Q 032889 49 KGVQVKLTGGRQVTGTLKGYD 69 (131)
Q Consensus 49 k~V~V~L~dGr~i~G~L~~fD 69 (131)
.+|+|++-||..+++++..-|
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~ 23 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTH 23 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 478999999999999987555
No 121
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=25.73 E-value=40 Score=24.26 Aligned_cols=19 Identities=26% Similarity=0.365 Sum_probs=16.3
Q ss_pred EEEEEEEcCccceEecceE
Q 032889 62 TGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 62 ~G~L~~fD~~mNLVL~da~ 80 (131)
.|+|+|-|++.|---++..
T Consensus 9 ~g~lVG~D~~GNkYYE~~~ 27 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPS 27 (115)
T ss_pred cceEeEEcCCCCeeeEcCC
Confidence 6999999999999887643
No 122
>PF01247 Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro: IPR001780 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal L35A eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of: Vertebrate L35A. Caenorhabditis elegans L35A (F10E7.7). Saccharomyces cerevisiae L37A/L37B (Rp47). Plant L35A. Pyrococcus woesei L35A homologue []. These proteins have 87 to 110 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_j 2LP6_A 1SQR_A 4A18_H 4A1D_H 4A19_H 4A1B_H 3IZS_j.
Probab=25.38 E-value=1.8e+02 Score=20.18 Aligned_cols=59 Identities=15% Similarity=0.158 Sum_probs=36.7
Q ss_pred ccccccccccccccccccc--C---ccCcccHhhhcCCeEEEEEc--------CCcEEEEEEEEEcCccceE
Q 032889 17 RSARVSFNLGFLKSLKMSG--R---KETVLDLAKFVDKGVQVKLT--------GGRQVTGTLKGYDQLLNLV 75 (131)
Q Consensus 17 ~~~~~~~~~~~~~~~~m~~--~---~~~~l~L~~~l~k~V~V~L~--------dGr~i~G~L~~fD~~mNLV 75 (131)
.+.+++|+-+...+..-.+ + .....+-..|+||+|--.-+ .+|.+-|++..--.--..|
T Consensus 4 kgv~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrv~yvyk~~~~~~~~k~r~iwGkV~r~HGnsGvV 75 (95)
T PF01247_consen 4 KGVFLGYKRGKRNQHPNTALLKIEGVNTKEDAQFYLGKRVAYVYKAKNKKNGSKGRVIWGKVTRPHGNSGVV 75 (95)
T ss_dssp EEEEEEEEEETSTTCEEEEEEEESS-STCHHHHTTTT-EEEEEECE-SSSTTECSEEEEEEEEEESTTTTEE
T ss_pred eEEEEeecccccccCCCeeEEeecCccCHHHHHhhcCcEEEEEEecccccCCCcEeEEEEEEEeEEcCCCEE
Confidence 4567788877776654321 1 23333455689999987766 5899999988764443333
No 123
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.89 E-value=92 Score=23.22 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=18.3
Q ss_pred hcCCeEEEE-EcCCcEEEEEEEE
Q 032889 46 FVDKGVQVK-LTGGRQVTGTLKG 67 (131)
Q Consensus 46 ~l~k~V~V~-L~dGr~i~G~L~~ 67 (131)
..|..|+|+ +..|+.+.|+..+
T Consensus 129 ~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 129 AAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 578889998 7889999998764
No 124
>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=24.76 E-value=87 Score=19.91 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=18.5
Q ss_pred CeEEEEEcCCcEEEEEEEEEcC
Q 032889 49 KGVQVKLTGGRQVTGTLKGYDQ 70 (131)
Q Consensus 49 k~V~V~L~dGr~i~G~L~~fD~ 70 (131)
.+|+|++-||..+..++..-|.
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~t 28 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSDT 28 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTSB
T ss_pred EEEEEECCCCCEEEEEECCcch
Confidence 4789999999999999986553
No 125
>PF05735 TSP_C: Thrombospondin C-terminal region; InterPro: IPR008859 Thrombospondins are multimeric multidomain glycoproteins that function at cell surfaces and in the extracellular matrix milieu. They act as regulators of cell interactions in vertebrates. They are divided into two subfamilies, A and B, according to their overall molecular organisation. The subgroup A proteins TSP-1 and -2 contain an N-terminal domain, a VWFC domain, three TSP1 repeats, three EGF-like domains, TSP3 repeats and a C-terminal domain. They are assembled as trimer. The subgroup B thrombospondins, designated TSP-3, -4, and COMP (cartilage oligomeric matrix protein, also designated TSP-5) are distinct in that they contain unique N-terminal regions, lack the VWFC domain and TSP1 repeats, contain four copies of EGF-like domains, and are assembled as pentamers []. EGF, TSP3 repeats and the C-terminal domain are thus the hallmark of a thrombospondin. The globular C-terminal domain is a beta sandwich of two curved antiparallel beta-sheets []. The fold is an elaboration of the jelly role topology, with strand B3-B7, B11 and B14-B15 forming the eight-stranded jelly roll motif. The function of the C-terminal domain is not yet known.; GO: 0005509 calcium ion binding, 0007155 cell adhesion, 0005576 extracellular region; PDB: 1UX6_A 1YO8_A 2RHP_A 3FBY_C.
Probab=23.71 E-value=3.1e+02 Score=21.53 Aligned_cols=33 Identities=18% Similarity=0.090 Sum_probs=19.9
Q ss_pred EEEEEcCCcEEE-------EEEEEEcCccceEecceEEEe
Q 032889 51 VQVKLTGGRQVT-------GTLKGYDQLLNLVLDEAVEFL 83 (131)
Q Consensus 51 V~V~L~dGr~i~-------G~L~~fD~~mNLVL~da~E~~ 83 (131)
.++...+|+++. |.++|.|++.++-++-.....
T Consensus 5 ~W~v~~~G~ev~Qt~NsdP~l~ig~~~~~~vdf~GT~~Vn 44 (201)
T PF05735_consen 5 NWVVSNQGAEVVQTLNSDPGLAIGPDNFGGVDFSGTFFVN 44 (201)
T ss_dssp -EEEECCCTEEEE-SS-SSEEEEEEEEESSEEEEEEEEE-
T ss_pred ceEEecCCeEEEEeccCCCeEEEccceecceEEEEEEEEe
Confidence 455556666665 667777777777666665443
No 126
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=23.61 E-value=1.2e+02 Score=23.37 Aligned_cols=28 Identities=25% Similarity=0.459 Sum_probs=23.0
Q ss_pred cHhhhcCCeEEEEEcCCcEEEEEEEEEc
Q 032889 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYD 69 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~G~L~~fD 69 (131)
.+..++|++|.|.+...+.+.|.+..++
T Consensus 22 ~~~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 22 DLKDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp -CGGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred ChhHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 4456999999999999999999998885
No 127
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.29 E-value=77 Score=21.40 Aligned_cols=21 Identities=29% Similarity=0.517 Sum_probs=17.6
Q ss_pred cHhhhcCCeEEEEEcCCcEEE
Q 032889 42 DLAKFVDKGVQVKLTGGRQVT 62 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~ 62 (131)
++..++|++|.++.++||.=+
T Consensus 13 ~i~ah~G~~v~lk~ngGRKk~ 33 (80)
T COG4466 13 SIDAHLGERVTLKANGGRKKT 33 (80)
T ss_pred HHHhccCcEEEEEecCCceee
Confidence 566789999999999999644
No 128
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.85 E-value=1.1e+02 Score=22.35 Aligned_cols=22 Identities=23% Similarity=0.357 Sum_probs=18.1
Q ss_pred hcCCeEEEE-EcCCcEEEEEEEE
Q 032889 46 FVDKGVQVK-LTGGRQVTGTLKG 67 (131)
Q Consensus 46 ~l~k~V~V~-L~dGr~i~G~L~~ 67 (131)
.+|..|+|+ +..||++.|+..+
T Consensus 110 ~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 110 GVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 578889996 6889999998775
No 129
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.65 E-value=97 Score=24.09 Aligned_cols=37 Identities=11% Similarity=0.095 Sum_probs=31.6
Q ss_pred hhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecceE
Q 032889 44 AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 44 ~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~da~ 80 (131)
.-.+|.+|+|..-++....|.+.+||--.+...-++.
T Consensus 7 ~vavg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 7 TVAVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred eeEEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 3357889999999999999999999988777777766
No 130
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=22.65 E-value=68 Score=24.35 Aligned_cols=19 Identities=26% Similarity=0.207 Sum_probs=16.5
Q ss_pred EEEEEEEcCccceEecceE
Q 032889 62 TGTLKGYDQLLNLVLDEAV 80 (131)
Q Consensus 62 ~G~L~~fD~~mNLVL~da~ 80 (131)
.|+|+|-|++.|---++..
T Consensus 48 ~G~lVG~D~~GNkYYE~~~ 66 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKLG 66 (159)
T ss_pred CcEEEEecCCCCeeeecCC
Confidence 4999999999999888763
No 131
>PRK06789 flagellar motor switch protein; Validated
Probab=22.59 E-value=1.9e+02 Score=19.05 Aligned_cols=42 Identities=19% Similarity=0.186 Sum_probs=34.0
Q ss_pred ccCcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEecc
Q 032889 37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (131)
Q Consensus 37 ~~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL~d 78 (131)
+.+..+|.+..+.+|.|.+++-..=+|.++..|..+=+-+.+
T Consensus 30 ~Gsvi~Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 30 KGTLYRLENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred CCCEEEeCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 456778889999999999988888899999999866555443
No 132
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.58 E-value=1.2e+02 Score=23.61 Aligned_cols=23 Identities=9% Similarity=0.062 Sum_probs=19.3
Q ss_pred hhcCCeEEEEEcCCcEEEEEEEE
Q 032889 45 KFVDKGVQVKLTGGRQVTGTLKG 67 (131)
Q Consensus 45 ~~l~k~V~V~L~dGr~i~G~L~~ 67 (131)
-.+|..|+|+-..|+++.|+..|
T Consensus 193 G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 193 GNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCCEEEEEeCCCCEEEEEEec
Confidence 35888999999889999998876
No 133
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.98 E-value=1.1e+02 Score=24.87 Aligned_cols=23 Identities=39% Similarity=0.517 Sum_probs=19.6
Q ss_pred hhcCCeEEEE-EcCCcEEEEEEEE
Q 032889 45 KFVDKGVQVK-LTGGRQVTGTLKG 67 (131)
Q Consensus 45 ~~l~k~V~V~-L~dGr~i~G~L~~ 67 (131)
-.+|..|+|+ +..||++.|+..+
T Consensus 230 G~~Gd~IrVrN~~SgkvV~a~V~~ 253 (261)
T PRK06804 230 GRKGELIKVKNLSSGRVVTATVDG 253 (261)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 3588999999 8899999999876
No 134
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=21.61 E-value=1.9e+02 Score=20.93 Aligned_cols=39 Identities=18% Similarity=0.297 Sum_probs=27.4
Q ss_pred cCcccHhhhcCCeEEEEEcCCcEEEEEEEEEcCccceEe
Q 032889 38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL 76 (131)
Q Consensus 38 ~~~l~L~~~l~k~V~V~L~dGr~i~G~L~~fD~~mNLVL 76 (131)
.+..+|.+..+..|.|.+++-..=+|-++.+|..+=+.+
T Consensus 95 Gsvi~Ld~~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrI 133 (136)
T COG1886 95 GSVIELDKLAGEPVDILVNGRLIGRGEVVVVDDKFGVRI 133 (136)
T ss_pred CCEEEcCCcCCCceEEEECCEEEEEEeEEEECCeEEEEE
Confidence 445666677788888888777777788888886654444
No 135
>PF03122 Herpes_MCP: Herpes virus major capsid protein; InterPro: IPR000912 The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces []. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1NO7_B.
Probab=21.23 E-value=32 Score=34.13 Aligned_cols=54 Identities=17% Similarity=0.246 Sum_probs=0.0
Q ss_pred EEEcCCcEEEEEEEEEcCccceEecceEEEeecCCCCCccCcceEEeceEEEeCCcEEEE
Q 032889 53 VKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIVCRGTAVMLV 112 (131)
Q Consensus 53 V~L~dGr~i~G~L~~fD~~mNLVL~da~E~~~~~~~~~~~~~~~r~lg~v~IRG~~Iv~I 112 (131)
=...+|+.+.|+|+.-|.-++.+|.--.+..... ...+-.+|.++|+|+|.|.-
T Consensus 252 ytt~~G~~v~GVlvTT~~V~q~Ll~~l~~i~~~~------v~~PatYg~~Vi~geNlVTA 305 (1354)
T PF03122_consen 252 YTTSSGRPVDGVLVTTANVMQKLLNLLGQISDTS------VSVPATYGEFVISGENLVTA 305 (1354)
T ss_dssp ------------------------------------------------------------
T ss_pred eecCCCCEeceEEeccHHHHHHHHHHHhhhccce------eecchhheeeeecCccHHHH
Confidence 3447899999999999988888876554422111 12466899999999998753
No 136
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=20.18 E-value=1.3e+02 Score=21.99 Aligned_cols=26 Identities=27% Similarity=0.423 Sum_probs=21.2
Q ss_pred cHhhhcCCeEEEEEcCCcEEEEEEEE
Q 032889 42 DLAKFVDKGVQVKLTGGRQVTGTLKG 67 (131)
Q Consensus 42 ~L~~~l~k~V~V~L~dGr~i~G~L~~ 67 (131)
...+.+.|-++|.|.+|++++..+=|
T Consensus 50 kPNSAlRK~~RVrL~NG~~VtAyiPg 75 (129)
T COG0048 50 KPNSALRKVARVRLINGKEVTAYIPG 75 (129)
T ss_pred CCChhhheeEEEEeeCCcEEEEEcCC
Confidence 34677889999999999999976644
Done!