Query 033530
Match_columns 117
No_of_seqs 130 out of 1102
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 03:21:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033530hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01724 Sm_D1 The eukaryotic S 100.0 2.4E-29 5.2E-34 171.1 11.4 87 2-88 1-87 (90)
2 cd01721 Sm_D3 The eukaryotic S 99.9 1E-25 2.3E-30 146.4 9.8 69 4-72 2-70 (70)
3 cd01733 LSm10 The eukaryotic S 99.9 2.2E-25 4.7E-30 148.0 9.9 70 2-71 9-78 (78)
4 cd01723 LSm4 The eukaryotic Sm 99.9 1.9E-24 4.1E-29 142.4 9.0 72 3-74 2-74 (76)
5 cd01725 LSm2 The eukaryotic Sm 99.9 5.1E-24 1.1E-28 142.1 9.4 73 2-74 1-75 (81)
6 KOG3172 Small nuclear ribonucl 99.9 6.6E-23 1.4E-27 142.9 8.3 97 3-99 6-102 (119)
7 cd01726 LSm6 The eukaryotic Sm 99.9 1.8E-22 3.8E-27 129.9 9.3 66 4-69 2-67 (67)
8 cd01722 Sm_F The eukaryotic Sm 99.9 7.9E-22 1.7E-26 127.3 9.3 66 3-68 2-67 (68)
9 KOG3428 Small nuclear ribonucl 99.9 1.9E-21 4.1E-26 135.5 9.1 89 1-90 1-89 (109)
10 PRK00737 small nuclear ribonuc 99.9 4.7E-21 1E-25 125.0 9.4 68 2-69 4-71 (72)
11 cd01731 archaeal_Sm1 The archa 99.8 6.9E-21 1.5E-25 122.6 9.2 66 4-69 2-67 (68)
12 PF01423 LSM: LSM domain ; In 99.8 1.1E-20 2.4E-25 120.2 8.7 66 5-70 1-67 (67)
13 cd01732 LSm5 The eukaryotic Sm 99.8 1.8E-20 4E-25 123.9 9.9 69 1-69 2-73 (76)
14 smart00651 Sm snRNP Sm protein 99.8 1.5E-20 3.3E-25 119.4 9.2 66 5-70 1-67 (67)
15 KOG3293 Small nuclear ribonucl 99.8 1.2E-20 2.7E-25 134.1 6.4 83 1-84 1-84 (134)
16 KOG3448 Predicted snRNP core p 99.8 3.6E-20 7.8E-25 125.2 7.6 86 1-86 1-88 (96)
17 cd01719 Sm_G The eukaryotic Sm 99.8 1.2E-19 2.6E-24 118.7 9.6 68 5-72 3-70 (72)
18 cd00600 Sm_like The eukaryotic 99.8 1.5E-19 3.2E-24 113.3 8.9 63 7-69 1-63 (63)
19 COG1958 LSM1 Small nuclear rib 99.8 3.5E-19 7.5E-24 117.7 9.5 68 2-69 7-78 (79)
20 cd01729 LSm7 The eukaryotic Sm 99.8 3.9E-18 8.4E-23 113.8 9.5 67 6-72 6-80 (81)
21 cd01730 LSm3 The eukaryotic Sm 99.8 7.5E-18 1.6E-22 112.4 9.0 66 4-69 3-81 (82)
22 KOG3482 Small nuclear ribonucl 99.8 2.5E-18 5.3E-23 112.6 6.3 66 4-69 10-75 (79)
23 cd01720 Sm_D2 The eukaryotic S 99.7 3.1E-17 6.6E-22 111.1 9.2 67 3-69 3-84 (87)
24 cd01717 Sm_B The eukaryotic Sm 99.7 5.5E-17 1.2E-21 107.3 9.0 65 6-70 4-78 (79)
25 cd01718 Sm_E The eukaryotic Sm 99.7 9.5E-17 2.1E-21 107.0 9.0 67 3-69 7-78 (79)
26 cd01728 LSm1 The eukaryotic Sm 99.7 2.2E-16 4.8E-21 103.9 9.8 67 4-70 4-73 (74)
27 cd01727 LSm8 The eukaryotic Sm 99.7 4.5E-16 9.9E-21 101.9 9.3 68 5-72 2-73 (74)
28 KOG1783 Small nuclear ribonucl 99.7 1.1E-17 2.5E-22 109.4 0.8 68 4-71 8-75 (77)
29 cd06168 LSm9 The eukaryotic Sm 99.7 1.2E-15 2.5E-20 100.7 9.3 66 5-70 3-74 (75)
30 PTZ00138 small nuclear ribonuc 99.6 3.7E-15 8E-20 101.4 9.2 66 3-70 19-87 (89)
31 KOG1780 Small Nuclear ribonucl 99.6 3.7E-15 8.1E-20 97.8 6.4 68 5-72 7-74 (77)
32 KOG3460 Small nuclear ribonucl 99.3 1.2E-12 2.5E-17 87.9 2.2 71 3-73 6-89 (91)
33 KOG1775 U6 snRNA-associated Sm 99.3 2.6E-12 5.6E-17 85.0 3.2 69 2-71 7-78 (84)
34 KOG1774 Small nuclear ribonucl 99.2 7.8E-12 1.7E-16 83.6 4.3 66 3-70 17-85 (88)
35 KOG1781 Small Nuclear ribonucl 98.9 2.7E-10 5.9E-15 78.6 -0.0 70 6-75 21-98 (108)
36 KOG1784 Small Nuclear ribonucl 98.6 1E-07 2.3E-12 65.0 4.5 79 5-84 3-85 (96)
37 KOG3168 U1 snRNP component [Tr 98.5 2.5E-08 5.4E-13 74.7 0.9 70 8-77 10-89 (177)
38 KOG1782 Small Nuclear ribonucl 98.4 4.6E-08 9.9E-13 69.9 -0.7 64 7-70 14-80 (129)
39 PF14438 SM-ATX: Ataxin 2 SM d 98.3 2.2E-06 4.7E-11 55.9 6.2 47 2-48 2-51 (77)
40 cd01739 LSm11_C The eukaryotic 97.6 5.4E-05 1.2E-09 48.9 3.0 38 11-48 7-48 (66)
41 PF12701 LSM14: Scd6-like Sm d 97.5 0.00061 1.3E-08 46.9 7.1 66 8-73 4-79 (96)
42 KOG3459 Small nuclear ribonucl 97.3 4.7E-05 1E-09 53.6 -0.6 58 12-69 36-106 (114)
43 PF11095 Gemin7: Gem-associate 96.9 0.013 2.9E-07 39.2 8.2 65 2-71 14-79 (80)
44 cd01736 LSm14_N LSm14 (also kn 96.5 0.016 3.5E-07 38.3 6.7 60 8-67 2-72 (74)
45 PF10842 DUF2642: Protein of u 96.3 0.042 9E-07 35.5 7.4 52 3-68 12-64 (66)
46 cd01716 Hfq Hfq, an abundant, 95.5 0.035 7.5E-07 35.4 4.4 31 11-41 10-40 (61)
47 TIGR02383 Hfq RNA chaperone Hf 95.5 0.035 7.5E-07 35.4 4.4 31 11-41 14-44 (61)
48 PF02237 BPL_C: Biotin protein 95.3 0.092 2E-06 31.2 5.7 31 11-42 2-32 (48)
49 PRK00395 hfq RNA-binding prote 95.0 0.054 1.2E-06 36.2 4.4 54 11-76 18-71 (79)
50 cd01735 LSm12_N LSm12 belongs 94.5 0.24 5.2E-06 31.5 6.3 55 10-66 4-58 (61)
51 PF06372 Gemin6: Gemin6 protei 94.2 0.32 6.8E-06 36.6 7.4 63 6-75 11-74 (166)
52 KOG1073 Uncharacterized mRNA-a 93.7 0.18 3.9E-06 42.1 5.8 66 7-72 4-80 (361)
53 COG1923 Hfq Uncharacterized ho 93.5 0.13 2.8E-06 34.2 3.7 27 10-36 17-43 (77)
54 PRK14638 hypothetical protein; 92.1 0.36 7.9E-06 35.4 4.9 35 5-40 93-127 (150)
55 PRK14642 hypothetical protein; 91.7 1.5 3.3E-05 33.8 8.1 71 5-76 93-184 (197)
56 PRK14639 hypothetical protein; 91.4 0.5 1.1E-05 34.3 4.9 36 4-40 80-115 (140)
57 PRK02001 hypothetical protein; 90.7 0.5 1.1E-05 34.9 4.4 35 5-40 83-117 (152)
58 PRK14091 RNA-binding protein H 89.3 0.74 1.6E-05 34.7 4.4 32 11-42 103-134 (165)
59 cd01734 YlxS_C YxlS is a Bacil 88.5 1.4 3E-05 28.9 4.9 31 5-35 18-52 (83)
60 PRK14091 RNA-binding protein H 88.1 0.99 2.2E-05 34.0 4.4 53 11-75 23-75 (165)
61 PRK14644 hypothetical protein; 88.0 1 2.2E-05 32.6 4.3 35 6-41 79-117 (136)
62 COG0779 Uncharacterized protei 87.5 1.9 4.1E-05 32.0 5.5 33 4-36 91-127 (153)
63 PRK00092 ribosome maturation p 87.1 3.3 7.2E-05 30.1 6.6 31 5-35 91-125 (154)
64 PRK14640 hypothetical protein; 86.5 1.4 3E-05 32.3 4.4 35 5-40 90-128 (152)
65 PRK14633 hypothetical protein; 85.2 1.8 3.8E-05 31.7 4.3 35 5-40 87-125 (150)
66 PRK14632 hypothetical protein; 84.2 2 4.2E-05 32.2 4.3 36 5-41 91-133 (172)
67 PRK14636 hypothetical protein; 83.9 2.1 4.5E-05 32.3 4.4 31 5-35 91-125 (176)
68 PRK14645 hypothetical protein; 83.2 2.8 6E-05 31.0 4.7 30 5-35 95-124 (154)
69 PRK14634 hypothetical protein; 82.7 2.5 5.5E-05 31.1 4.3 35 5-40 93-131 (155)
70 PRK14643 hypothetical protein; 82.3 2.6 5.6E-05 31.4 4.3 36 5-40 97-137 (164)
71 PF02576 DUF150: Uncharacteris 81.6 3.9 8.4E-05 29.2 4.9 30 5-34 80-113 (141)
72 PRK14646 hypothetical protein; 81.2 3.1 6.6E-05 30.7 4.3 35 5-40 93-131 (155)
73 PRK14647 hypothetical protein; 80.5 4.2 9.2E-05 29.9 4.8 31 4-34 91-130 (159)
74 PRK14637 hypothetical protein; 77.7 4.4 9.4E-05 29.8 4.1 35 5-40 91-126 (151)
75 PRK14631 hypothetical protein; 77.6 4.5 9.7E-05 30.5 4.3 29 5-33 110-142 (174)
76 PRK06955 biotin--protein ligas 77.5 12 0.00026 30.0 7.0 33 9-41 246-278 (300)
77 PRK09618 flgD flagellar basal 76.9 8.3 0.00018 28.3 5.4 26 8-33 88-113 (142)
78 PRK11886 bifunctional biotin-- 74.1 14 0.00029 29.6 6.5 48 9-62 269-317 (319)
79 PRK14641 hypothetical protein; 73.0 7.7 0.00017 29.2 4.5 29 5-33 97-129 (173)
80 PF11607 DUF3247: Protein of u 70.5 6.5 0.00014 27.2 3.3 18 13-30 29-46 (101)
81 PRK13325 bifunctional biotin-- 68.5 28 0.00061 30.8 7.7 33 9-41 275-307 (592)
82 PF07073 ROF: Modulator of Rho 68.0 5.1 0.00011 26.6 2.3 22 7-28 12-33 (80)
83 PRK14630 hypothetical protein; 66.0 11 0.00025 27.3 4.0 30 5-35 90-119 (143)
84 TIGR00121 birA_ligase birA, bi 62.7 29 0.00062 26.6 5.9 32 9-41 190-221 (237)
85 PRK14635 hypothetical protein; 62.2 27 0.00058 25.8 5.5 35 5-40 92-131 (162)
86 PRK05163 rpsL 30S ribosomal pr 60.7 35 0.00076 24.6 5.6 69 9-93 47-121 (124)
87 PRK08330 biotin--protein ligas 58.9 33 0.00071 26.3 5.7 33 9-42 185-218 (236)
88 PF03614 Flag1_repress: Repres 57.1 13 0.00028 27.9 3.0 25 11-35 119-143 (165)
89 TIGR00981 rpsL_bact ribosomal 57.0 41 0.00088 24.3 5.4 69 9-93 47-121 (124)
90 PRK11911 flgD flagellar basal 55.2 21 0.00045 26.2 3.7 26 9-34 90-115 (140)
91 PRK11625 Rho-binding antitermi 53.1 34 0.00074 22.9 4.3 23 8-30 19-41 (84)
92 PRK10898 serine endoprotease; 51.2 51 0.0011 27.0 5.9 60 12-73 101-162 (353)
93 smart00333 TUDOR Tudor domain. 50.1 49 0.0011 19.1 4.9 25 11-35 5-29 (57)
94 PRK10139 serine endoprotease; 49.6 36 0.00078 29.0 4.9 63 12-75 114-178 (455)
95 CHL00051 rps12 ribosomal prote 48.4 73 0.0016 23.0 5.6 68 9-92 47-120 (123)
96 PTZ00275 biotin-acetyl-CoA-car 47.0 46 0.001 26.5 4.9 32 10-42 235-266 (285)
97 TIGR02038 protease_degS peripl 44.5 72 0.0016 26.0 5.8 33 12-44 101-133 (351)
98 PRK10942 serine endoprotease; 44.3 47 0.001 28.4 4.8 32 12-43 135-166 (473)
99 cd01737 LSm16_N LSm16 belongs 42.3 90 0.0019 19.9 5.2 55 9-66 3-59 (62)
100 TIGR02603 CxxCH_TIGR02603 puta 41.9 40 0.00086 23.6 3.5 20 14-33 59-78 (133)
101 PF11684 DUF3280: Protein of u 41.3 43 0.00092 24.3 3.6 39 22-64 82-123 (140)
102 PF04452 Methyltrans_RNA: RNA 41.2 1.2E+02 0.0026 23.0 6.2 72 3-84 11-83 (225)
103 TIGR00567 3mg DNA-3-methyladen 41.0 47 0.001 25.5 3.9 33 5-37 12-44 (192)
104 TIGR02037 degP_htrA_DO peripla 40.7 56 0.0012 27.1 4.7 32 13-44 82-113 (428)
105 PRK06792 flgD flagellar basal 40.2 44 0.00096 25.8 3.7 25 9-33 115-139 (190)
106 PRK10708 hypothetical protein; 39.7 35 0.00076 21.6 2.5 26 11-36 3-28 (62)
107 PF11743 DUF3301: Protein of u 39.4 55 0.0012 22.1 3.7 29 44-72 68-96 (97)
108 cd04479 RPA3 RPA3: A subfamily 39.0 68 0.0015 21.6 4.1 23 5-35 8-30 (101)
109 PRK06789 flagellar motor switc 38.0 68 0.0015 21.0 3.8 36 7-42 36-71 (74)
110 PF10781 DSRB: Dextransucrase 35.2 41 0.00089 21.3 2.3 26 11-36 3-28 (62)
111 PF02245 Pur_DNA_glyco: Methyl 35.2 58 0.0013 24.7 3.6 32 5-37 11-42 (184)
112 PRK08477 biotin--protein ligas 34.9 1.3E+02 0.0028 23.1 5.6 37 8-45 171-207 (211)
113 COG0340 BirA Biotin-(acetyl-Co 34.6 1.2E+02 0.0025 23.8 5.3 36 8-43 186-221 (238)
114 PTZ00115 40S ribosomal protein 34.1 1.3E+02 0.0028 24.5 5.6 70 8-93 142-217 (290)
115 PF06257 DUF1021: Protein of u 33.7 1.2E+02 0.0026 20.0 4.5 30 5-34 10-43 (76)
116 PF10618 Tail_tube: Phage tail 33.7 64 0.0014 22.6 3.4 25 4-28 66-90 (119)
117 TIGR00999 8a0102 Membrane Fusi 31.1 96 0.0021 23.3 4.3 27 11-37 141-167 (265)
118 PF14485 DUF4431: Domain of un 30.6 49 0.0011 19.7 2.1 15 4-18 11-25 (48)
119 KOG4401 Uncharacterized conser 30.6 74 0.0016 24.4 3.5 43 10-54 9-51 (184)
120 COG1363 FrvX Cellulase M and r 30.5 59 0.0013 27.2 3.2 23 8-30 93-115 (355)
121 PF09465 LBR_tudor: Lamin-B re 30.4 1E+02 0.0022 19.2 3.5 26 10-35 7-33 (55)
122 PF13437 HlyD_3: HlyD family s 30.4 1.2E+02 0.0026 19.6 4.2 24 11-34 53-78 (105)
123 COG1886 FliN Flagellar motor s 30.0 93 0.002 22.2 3.8 36 7-42 100-135 (136)
124 PF03614 Flag1_repress: Repres 29.5 1.1E+02 0.0024 23.0 4.1 34 11-44 28-61 (165)
125 PRK07018 flgA flagellar basal 27.9 70 0.0015 24.7 3.1 23 9-31 204-227 (235)
126 PF05037 DUF669: Protein of un 27.3 44 0.00096 23.7 1.7 27 3-29 94-121 (141)
127 PF05954 Phage_GPD: Phage late 27.1 89 0.0019 23.6 3.5 26 8-33 24-49 (292)
128 TIGR01080 rplX_A_E ribosomal p 26.6 2.3E+02 0.005 19.9 5.7 57 11-70 44-101 (114)
129 PF07076 DUF1344: Protein of u 25.8 77 0.0017 20.1 2.4 23 24-46 4-27 (61)
130 PRK11713 16S ribosomal RNA met 25.5 1.4E+02 0.0031 22.8 4.4 32 3-34 24-55 (234)
131 COG4568 Rof Transcriptional an 25.0 1E+02 0.0022 20.7 3.0 23 7-29 18-40 (84)
132 cd00540 AAG Alkyladenine DNA g 23.7 1.4E+02 0.0029 22.7 3.9 32 5-37 8-39 (179)
133 PF14563 DUF4444: Domain of un 23.0 1.2E+02 0.0025 17.9 2.6 20 25-44 10-29 (42)
134 PRK06009 flgD flagellar basal 22.0 2.2E+02 0.0047 20.8 4.5 25 8-35 93-117 (140)
135 PF12945 YcgR_2: Flagellar pro 21.0 2.2E+02 0.0047 17.6 4.6 33 11-43 3-39 (87)
136 TIGR00046 RNA methyltransferas 20.3 2E+02 0.0044 22.1 4.3 39 3-41 26-65 (240)
137 COG5316 Uncharacterized conser 20.2 2.7E+02 0.0058 24.1 5.2 41 4-45 74-114 (421)
No 1
>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=99.96 E-value=2.4e-29 Score=171.05 Aligned_cols=87 Identities=84% Similarity=1.217 Sum_probs=82.6
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCCCCcchhhhh
Q 033530 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLV 81 (117)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd~id~~~~l~ 81 (117)
+|+.||+++.|++|+||||||.+|+|+|.++|+|||++|+||+++.++++...++.++|||++|+||++||++|+.++|.
T Consensus 1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~~~~~l~ 80 (90)
T cd01724 1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLNLDTLLV 80 (90)
T ss_pred CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCCcchhhh
Confidence 58899999999999999999999999999999999999999999988888899999999999999999999999999999
Q ss_pred hcCcccC
Q 033530 82 EETPRVK 88 (117)
Q Consensus 82 ~~~~~~~ 88 (117)
+.+++.+
T Consensus 81 ~~~~~~~ 87 (90)
T cd01724 81 DSTPKPK 87 (90)
T ss_pred hcCCccc
Confidence 9975544
No 2
>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=99.93 E-value=1e-25 Score=146.43 Aligned_cols=69 Identities=32% Similarity=0.646 Sum_probs=66.5
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCC
Q 033530 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPD 72 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd 72 (117)
+++|++++|++|+||||||.+|+|+|.++|+|||++|+||+++.++|+..+++.+||||++|+||++||
T Consensus 2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence 579999999999999999999999999999999999999999888888889999999999999999997
No 3
>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=99.93 E-value=2.2e-25 Score=148.01 Aligned_cols=70 Identities=36% Similarity=0.578 Sum_probs=67.4
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcC
Q 033530 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILP 71 (117)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lp 71 (117)
.|++||+++.|++|+||||||.+|+|+|.++|+|||++|+||+++.+++.+.+++.+||||++|+||++|
T Consensus 9 tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 9 TLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred hHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence 3789999999999999999999999999999999999999999998888888999999999999999998
No 4
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.91 E-value=1.9e-24 Score=142.40 Aligned_cols=72 Identities=32% Similarity=0.503 Sum_probs=67.4
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCc-eeeceEEEecCeEEEEEcCCCC
Q 033530 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNP-VNLDHLSVRGNNIRYYILPDSL 74 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~-~~~~~v~IRG~~I~~I~lpd~i 74 (117)
.++||+++.|++|+|+||||++|+|+|.++|+|||++|+||+++..+|+. ..++.+||||++|+||++||++
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence 57899999999999999999999999999999999999999999877764 5689999999999999999876
No 5
>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=99.91 E-value=5.1e-24 Score=142.13 Aligned_cols=73 Identities=29% Similarity=0.456 Sum_probs=66.5
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCC--ceeeceEEEecCeEEEEEcCCCC
Q 033530 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKN--PVNLDHLSVRGNNIRYYILPDSL 74 (117)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~--~~~~~~v~IRG~~I~~I~lpd~i 74 (117)
+++.||++++|++|+||||||.+|+|+|.++|+|||++|+||+++.+++. ..+++.++|||++|+||++||.+
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~ 75 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADE 75 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhH
Confidence 47899999999999999999999999999999999999999998876543 45679999999999999999875
No 6
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.89 E-value=6.6e-23 Score=142.86 Aligned_cols=97 Identities=23% Similarity=0.432 Sum_probs=91.9
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCCCCcchhhhhh
Q 033530 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLVE 82 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd~id~~~~l~~ 82 (117)
.+++|++..|+-|++|+++|..|+|+|.+.|++||++|+|++.+.+++...+++.+||||+.|+|+.+||++..+|+|+.
T Consensus 6 piKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmLKnAPmFkk 85 (119)
T KOG3172|consen 6 PIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDMLKNAPMFKK 85 (119)
T ss_pred ceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHhhcCccccc
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcccCCCCCCCCccee
Q 033530 83 ETPRVKPKKPTAGIDII 99 (117)
Q Consensus 83 ~~~~~~~~~~~~~~~~~ 99 (117)
+..++.+..+.||+.+.
T Consensus 86 ~~~~~~g~~~~RG~~~~ 102 (119)
T KOG3172|consen 86 GKSRSLGGGPGRGRARR 102 (119)
T ss_pred ccCCcCCCCCCcccccc
Confidence 99888887788887766
No 7
>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=99.88 E-value=1.8e-22 Score=129.95 Aligned_cols=66 Identities=24% Similarity=0.357 Sum_probs=62.4
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEE
Q 033530 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~ 69 (117)
+++|++++|++|+|+|+||++|+|+|.++|+|||++|+||+++..++++..++.++|||++|+||.
T Consensus 2 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 2 SEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred HHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence 689999999999999999999999999999999999999999887777889999999999999973
No 8
>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=99.87 E-value=7.9e-22 Score=127.34 Aligned_cols=66 Identities=33% Similarity=0.448 Sum_probs=62.2
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEE
Q 033530 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYY 68 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I 68 (117)
.+++|++++|++|+|+|+||++|+|+|.++|+|||++|+||+++..++++..+|.++|||++|+||
T Consensus 2 p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i 67 (68)
T cd01722 2 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYI 67 (68)
T ss_pred HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEE
Confidence 578999999999999999999999999999999999999999987766678899999999999997
No 9
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=99.86 E-value=1.9e-21 Score=135.47 Aligned_cols=89 Identities=74% Similarity=1.136 Sum_probs=84.2
Q ss_pred CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCCCCcchhhh
Q 033530 1 MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLL 80 (117)
Q Consensus 1 m~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd~id~~~~l 80 (117)
|+|+.||+.+.+.+|+|||+||+...|++.++|.+||..|.++..+.++ ++.+++.++|||++|||+++||.+++++++
T Consensus 1 mklvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~ld~Ll 79 (109)
T KOG3428|consen 1 MKLVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLNLDTLL 79 (109)
T ss_pred ChHHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcCcceee
Confidence 8999999999999999999999999999999999999999999998875 888999999999999999999999999999
Q ss_pred hhcCcccCCC
Q 033530 81 VEETPRVKPK 90 (117)
Q Consensus 81 ~~~~~~~~~~ 90 (117)
.++.++.+.+
T Consensus 80 vd~~~~~~~~ 89 (109)
T KOG3428|consen 80 VDDAPRLHLR 89 (109)
T ss_pred eehhhhhhhh
Confidence 9999776554
No 10
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.85 E-value=4.7e-21 Score=125.04 Aligned_cols=68 Identities=28% Similarity=0.421 Sum_probs=63.0
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEE
Q 033530 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (117)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~ 69 (117)
..+.+|++++|++|+|+|+||+.|+|+|.+||+|||++|+||+++.+++....++.++|||++|.+|.
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEc
Confidence 35789999999999999999999999999999999999999999877666779999999999999974
No 11
>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=6.9e-21 Score=122.64 Aligned_cols=66 Identities=24% Similarity=0.359 Sum_probs=62.4
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEE
Q 033530 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~ 69 (117)
+.+|++++|++|.|+|+||+.|+|+|.+||+|||++|+||+++..++....++.++|||++|.||.
T Consensus 2 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 2 LDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred hHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEc
Confidence 578999999999999999999999999999999999999999987777789999999999999974
No 12
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.84 E-value=1.1e-20 Score=120.23 Aligned_cols=66 Identities=41% Similarity=0.554 Sum_probs=62.5
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCC-CceeeceEEEecCeEEEEEc
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK-NPVNLDHLSVRGNNIRYYIL 70 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~-~~~~~~~v~IRG~~I~~I~l 70 (117)
.+|++++|++|+|+|+||++|+|+|.++|+|||++|+||+++..++ +...++.+||||++|++|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 4799999999999999999999999999999999999999998877 78999999999999999974
No 13
>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=1.8e-20 Score=123.86 Aligned_cols=69 Identities=25% Similarity=0.327 Sum_probs=64.1
Q ss_pred CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEe---CCCCceeeceEEEecCeEEEEE
Q 033530 1 MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTL---KGKNPVNLDHLSVRGNNIRYYI 69 (117)
Q Consensus 1 m~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~---~~~~~~~~~~v~IRG~~I~~I~ 69 (117)
|+.+++|++++|++|.|+|++|++|.|+|.+||+|||++|+||+|.. ++++..+++.++|||++|.+|+
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLV 73 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEE
Confidence 78899999999999999999999999999999999999999999886 4445678999999999999986
No 14
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.84 E-value=1.5e-20 Score=119.44 Aligned_cols=66 Identities=44% Similarity=0.601 Sum_probs=61.9
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCC-CCceeeceEEEecCeEEEEEc
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG-KNPVNLDHLSVRGNNIRYYIL 70 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~-~~~~~~~~v~IRG~~I~~I~l 70 (117)
.+|++++|++|+|+|+||+++.|+|.++|+|||++|+||+++..+ +++..++.+||||++|+||+.
T Consensus 1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 378999999999999999999999999999999999999999876 678899999999999999863
No 15
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.82 E-value=1.2e-20 Score=134.11 Aligned_cols=83 Identities=28% Similarity=0.432 Sum_probs=73.8
Q ss_pred CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCC-CceeeceEEEecCeEEEEEcCCCCcchhh
Q 033530 1 MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK-NPVNLDHLSVRGNNIRYYILPDSLNLETL 79 (117)
Q Consensus 1 m~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~-~~~~~~~v~IRG~~I~~I~lpd~id~~~~ 79 (117)
|+.+.+|+...|+++.||||||.+|.|.|.++|.+|||+|++|+++.+|+ +...+++++|||++|+|+.+||++ ++.+
T Consensus 1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~i-id~v 79 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEI-IDKV 79 (134)
T ss_pred CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHH-HHHH
Confidence 78899999999999999999999999999999999999999999998866 468899999999999999999987 2333
Q ss_pred hhhcC
Q 033530 80 LVEET 84 (117)
Q Consensus 80 l~~~~ 84 (117)
=++..
T Consensus 80 kee~~ 84 (134)
T KOG3293|consen 80 KEECV 84 (134)
T ss_pred HHHHH
Confidence 33433
No 16
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.82 E-value=3.6e-20 Score=125.22 Aligned_cols=86 Identities=30% Similarity=0.458 Sum_probs=78.8
Q ss_pred CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCc--eeeceEEEecCeEEEEEcCCCCcchh
Q 033530 1 MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNP--VNLDHLSVRGNNIRYYILPDSLNLET 78 (117)
Q Consensus 1 m~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~--~~~~~v~IRG~~I~~I~lpd~id~~~ 78 (117)
|+++.|+++++|+.|+||||||..+.|+|.++|+|+|+.|.|+.++++++-| .....+||||+.|+||++|......+
T Consensus 1 mLFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtq 80 (96)
T KOG3448|consen 1 MLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQ 80 (96)
T ss_pred CchHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHH
Confidence 8999999999999999999999999999999999999999999999886554 67889999999999999999888778
Q ss_pred hhhhcCcc
Q 033530 79 LLVEETPR 86 (117)
Q Consensus 79 ~l~~~~~~ 86 (117)
.+.++.++
T Consensus 81 ll~da~R~ 88 (96)
T KOG3448|consen 81 LLQDAARR 88 (96)
T ss_pred HHHHHHHH
Confidence 88877643
No 17
>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=99.82 E-value=1.2e-19 Score=118.70 Aligned_cols=68 Identities=25% Similarity=0.299 Sum_probs=62.9
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCC
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPD 72 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd 72 (117)
.+|++++||+|.|+|++|++|+|+|.+||+|||++|+||+++..+.+...+|.++|||++|.+|..-|
T Consensus 3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~ 70 (72)
T cd01719 3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALE 70 (72)
T ss_pred hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEccc
Confidence 57899999999999999999999999999999999999999876667789999999999999987544
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=99.81 E-value=1.5e-19 Score=113.34 Aligned_cols=63 Identities=33% Similarity=0.492 Sum_probs=59.8
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEE
Q 033530 7 LMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (117)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~ 69 (117)
|++++|++|+|+|+||+.|.|+|.++|+|||++|+|++++..++++..++.+||||++|++|+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence 578899999999999999999999999999999999999988888899999999999999984
No 19
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.80 E-value=3.5e-19 Score=117.69 Aligned_cols=68 Identities=35% Similarity=0.482 Sum_probs=59.9
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEe--CCCC-ceeec-eEEEecCeEEEEE
Q 033530 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTL--KGKN-PVNLD-HLSVRGNNIRYYI 69 (117)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~--~~~~-~~~~~-~v~IRG~~I~~I~ 69 (117)
..+.+|++++|++|.|+|+||++|+|+|.+||+|||++|+||+++. ++.. ...++ .++|||++|++|.
T Consensus 7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEe
Confidence 4589999999999999999999999999999999999999999987 3333 23445 9999999999985
No 20
>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=99.77 E-value=3.9e-18 Score=113.79 Aligned_cols=67 Identities=21% Similarity=0.294 Sum_probs=59.6
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCC--------CCceeeceEEEecCeEEEEEcCC
Q 033530 6 FLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG--------KNPVNLDHLSVRGNNIRYYILPD 72 (117)
Q Consensus 6 ~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~--------~~~~~~~~v~IRG~~I~~I~lpd 72 (117)
-|.+++|++|.|.|++|++|.|+|.+||+|||++|+||+|...+ .....+|.++|||++|.+|...+
T Consensus 6 ~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 6 DLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred hHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 48889999999999999999999999999999999999998653 24578999999999999986543
No 21
>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=99.75 E-value=7.5e-18 Score=112.36 Aligned_cols=66 Identities=21% Similarity=0.288 Sum_probs=59.2
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCC-------------CceeeceEEEecCeEEEEE
Q 033530 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK-------------NPVNLDHLSVRGNNIRYYI 69 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~-------------~~~~~~~v~IRG~~I~~I~ 69 (117)
+++|+..++++|.|.|++|+.|.|+|.+||.|||++|+||+|...+. ..+.+|.+||||++|.+|.
T Consensus 3 l~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 3 LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred hHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence 57899999999999999999999999999999999999999986421 2468899999999999974
No 22
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.75 E-value=2.5e-18 Score=112.58 Aligned_cols=66 Identities=32% Similarity=0.416 Sum_probs=62.6
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEE
Q 033530 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~ 69 (117)
-.||+.+.|++|.|.||.|.+|+|+|+++|.|||+.|.+++|..++....++|+++||.+||.||.
T Consensus 10 KpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~ 75 (79)
T KOG3482|consen 10 KPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIR 75 (79)
T ss_pred hHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEe
Confidence 479999999999999999999999999999999999999999888777889999999999999984
No 23
>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=99.73 E-value=3.1e-17 Score=111.09 Aligned_cols=67 Identities=19% Similarity=0.260 Sum_probs=58.4
Q ss_pred hhHHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCC-------------CceeeceEEEecCeEEE
Q 033530 3 LVRFLMKLN--NETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK-------------NPVNLDHLSVRGNNIRY 67 (117)
Q Consensus 3 l~~~L~~l~--gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~-------------~~~~~~~v~IRG~~I~~ 67 (117)
.+.+|+..+ |++|.|.|++|+.+.|+|.+||.|||++|+||+|+..+. +...+|.+||||++|.+
T Consensus 3 Pl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~ 82 (87)
T cd01720 3 PLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL 82 (87)
T ss_pred hHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence 467888886 899999999999999999999999999999999976432 13468999999999999
Q ss_pred EE
Q 033530 68 YI 69 (117)
Q Consensus 68 I~ 69 (117)
|.
T Consensus 83 Is 84 (87)
T cd01720 83 VL 84 (87)
T ss_pred Ee
Confidence 74
No 24
>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=99.72 E-value=5.5e-17 Score=107.35 Aligned_cols=65 Identities=23% Similarity=0.277 Sum_probs=57.7
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCC----------CCceeeceEEEecCeEEEEEc
Q 033530 6 FLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG----------KNPVNLDHLSVRGNNIRYYIL 70 (117)
Q Consensus 6 ~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~----------~~~~~~~~v~IRG~~I~~I~l 70 (117)
-|.+++|++|.|.|++|+.+.|+|.++|.|||++|+||+|+... .+...+|.++|||++|.+|.+
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 47789999999999999999999999999999999999997532 234789999999999999864
No 25
>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=99.70 E-value=9.5e-17 Score=107.01 Aligned_cols=67 Identities=22% Similarity=0.295 Sum_probs=58.3
Q ss_pred hhHHHhhcCCC--EEEEEEc--CCcEEEEEEEEeccccceEEccEEEEeC-CCCceeeceEEEecCeEEEEE
Q 033530 3 LVRFLMKLNNE--TVSIELK--NGTIVHGTITGVDISMNTHLKTVKLTLK-GKNPVNLDHLSVRGNNIRYYI 69 (117)
Q Consensus 3 l~~~L~~l~gk--~V~VeLk--ng~~~~G~L~~~D~~MNl~L~da~~~~~-~~~~~~~~~v~IRG~~I~~I~ 69 (117)
.+..|.++.++ +|.|+|+ +|++++|+|.+||+|||++|+||+|... +.+...+|.++|||+||.+|+
T Consensus 7 P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 7 PINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred CHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEc
Confidence 45667777777 8888887 8999999999999999999999999875 445678999999999999985
No 26
>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=99.70 E-value=2.2e-16 Score=103.92 Aligned_cols=67 Identities=16% Similarity=0.158 Sum_probs=58.4
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCC---CceeeceEEEecCeEEEEEc
Q 033530 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK---NPVNLDHLSVRGNNIRYYIL 70 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~---~~~~~~~v~IRG~~I~~I~l 70 (117)
...|.++++++|.|.|++|+.|.|+|.+||+|||++|+||+|...++ ....+|.++|||++|.++..
T Consensus 4 ~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 4 TASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred hHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 35688899999999999999999999999999999999998875432 24678999999999999853
No 27
>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=99.68 E-value=4.5e-16 Score=101.87 Aligned_cols=68 Identities=28% Similarity=0.303 Sum_probs=59.2
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCC---C-CceeeceEEEecCeEEEEEcCC
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG---K-NPVNLDHLSVRGNNIRYYILPD 72 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~---~-~~~~~~~v~IRG~~I~~I~lpd 72 (117)
..|+++++++|.|.|++|+.|.|+|.+||.|||++|++|++...+ + ....+|.++|||++|.++..-|
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 357889999999999999999999999999999999999987431 2 3567999999999999987543
No 28
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.67 E-value=1.1e-17 Score=109.43 Aligned_cols=68 Identities=26% Similarity=0.360 Sum_probs=64.4
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcC
Q 033530 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILP 71 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lp 71 (117)
-.||++.+|++|.|+|.+|..|+|+|...|.||||.|+.+++...++.+++++.+||||++|.||...
T Consensus 8 ~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 8 GEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred HHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEec
Confidence 47999999999999999999999999999999999999999998888889999999999999999764
No 29
>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=99.65 E-value=1.2e-15 Score=100.70 Aligned_cols=66 Identities=20% Similarity=0.215 Sum_probs=60.1
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCC------CCceeeceEEEecCeEEEEEc
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG------KNPVNLDHLSVRGNNIRYYIL 70 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~------~~~~~~~~v~IRG~~I~~I~l 70 (117)
+.|++++|++|.|.|+||+.+.|+|.++|.+||++|+||.|+..+ .+.+.+|.++|||++|..+++
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 468899999999999999999999999999999999999998643 456899999999999999874
No 30
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.62 E-value=3.7e-15 Score=101.38 Aligned_cols=66 Identities=24% Similarity=0.389 Sum_probs=54.4
Q ss_pred hhHHHhhcCCCEEEEEEcC--CcEEEEEEEEeccccceEEccEEEEeCC-CCceeeceEEEecCeEEEEEc
Q 033530 3 LVRFLMKLNNETVSIELKN--GTIVHGTITGVDISMNTHLKTVKLTLKG-KNPVNLDHLSVRGNNIRYYIL 70 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkn--g~~~~G~L~~~D~~MNl~L~da~~~~~~-~~~~~~~~v~IRG~~I~~I~l 70 (117)
++.|++. ..+|.|.+.+ ++.++|+|.+||+|||++|+||+|...+ .+...+|.++|||+||.+|+.
T Consensus 19 ~~~~~~~--~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~ 87 (89)
T PTZ00138 19 IFRFFTE--KTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA 87 (89)
T ss_pred HHHHhcC--CcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence 4455554 3478888877 4899999999999999999999998653 356789999999999999854
No 31
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.59 E-value=3.7e-15 Score=97.81 Aligned_cols=68 Identities=24% Similarity=0.280 Sum_probs=62.8
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCC
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPD 72 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd 72 (117)
+.|+++.+|++.+.|..|+.+.|+|.+||.|||++|++++|...++....++.++|||++|..+..-+
T Consensus 7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~ 74 (77)
T KOG1780|consen 7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALE 74 (77)
T ss_pred chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeecc
Confidence 46899999999999999999999999999999999999999988888899999999999999875433
No 32
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.29 E-value=1.2e-12 Score=87.90 Aligned_cols=71 Identities=23% Similarity=0.289 Sum_probs=61.4
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeC--C-----------CCceeeceEEEecCeEEEEE
Q 033530 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLK--G-----------KNPVNLDHLSVRGNNIRYYI 69 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~--~-----------~~~~~~~~v~IRG~~I~~I~ 69 (117)
.+++|+-.+..+|.|+|+++++++|+|.+||+|.|++|.||+++.. + ...+.++.+||||++|.+|.
T Consensus 6 PldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvs 85 (91)
T KOG3460|consen 6 PLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVS 85 (91)
T ss_pred cHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEc
Confidence 4688999999999999999999999999999999999999987732 1 12467899999999999997
Q ss_pred cCCC
Q 033530 70 LPDS 73 (117)
Q Consensus 70 lpd~ 73 (117)
-|-.
T Consensus 86 pp~~ 89 (91)
T KOG3460|consen 86 PPLR 89 (91)
T ss_pred Cccc
Confidence 7654
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.28 E-value=2.6e-12 Score=85.01 Aligned_cols=69 Identities=25% Similarity=0.289 Sum_probs=60.7
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEe--CCCC-ceeeceEEEecCeEEEEEcC
Q 033530 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTL--KGKN-PVNLDHLSVRGNNIRYYILP 71 (117)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~--~~~~-~~~~~~v~IRG~~I~~I~lp 71 (117)
+.+.++.+.+|+++.|-+|+++++.|+|.+||+|.|++|+||+++. ++++ ..+++.+++.||+|... +|
T Consensus 7 lPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mL-vP 78 (84)
T KOG1775|consen 7 LPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITML-VP 78 (84)
T ss_pred ccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEE-ec
Confidence 4567899999999999999999999999999999999999998763 4443 57899999999999985 44
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.25 E-value=7.8e-12 Score=83.61 Aligned_cols=66 Identities=27% Similarity=0.355 Sum_probs=56.4
Q ss_pred hhHHHhhcCCCEEEEEEcC--CcEEEEEEEEeccccceEEccEEEEeCCCC-ceeeceEEEecCeEEEEEc
Q 033530 3 LVRFLMKLNNETVSIELKN--GTIVHGTITGVDISMNTHLKTVKLTLKGKN-PVNLDHLSVRGNNIRYYIL 70 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkn--g~~~~G~L~~~D~~MNl~L~da~~~~~~~~-~~~~~~v~IRG~~I~~I~l 70 (117)
.+.|||+- .+|.|+|.+ |..++|.+++||+|||++|++|++.....+ ...+|.++++|+||..|+-
T Consensus 17 Ifr~Lq~~--t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~ 85 (88)
T KOG1774|consen 17 IFRFLQNR--TRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQS 85 (88)
T ss_pred HHHHHhcC--CceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEee
Confidence 56788864 489999987 799999999999999999999998875433 3589999999999999864
No 35
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.89 E-value=2.7e-10 Score=78.61 Aligned_cols=70 Identities=19% Similarity=0.256 Sum_probs=61.1
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCC--------CCceeeceEEEecCeEEEEEcCCCCc
Q 033530 6 FLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG--------KNPVNLDHLSVRGNNIRYYILPDSLN 75 (117)
Q Consensus 6 ~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~--------~~~~~~~~v~IRG~~I~~I~lpd~id 75 (117)
-|.+++.++|.|.+.+|+...|+|.+||+.||++|+|++|+-++ .+.+++|.+.+||..+..|...|..+
T Consensus 21 DLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e 98 (108)
T KOG1781|consen 21 DLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE 98 (108)
T ss_pred hHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence 36788999999999999999999999999999999999887432 13489999999999999987777665
No 36
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.56 E-value=1e-07 Score=65.01 Aligned_cols=79 Identities=22% Similarity=0.279 Sum_probs=64.4
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeC----CCCceeeceEEEecCeEEEEEcCCCCcchhhh
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLK----GKNPVNLDHLSVRGNNIRYYILPDSLNLETLL 80 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~----~~~~~~~~~v~IRG~~I~~I~lpd~id~~~~l 80 (117)
.-|..+++++|.|-+.||+.+.|.|.+||...|+.|+++.+..- +-+...+|...|||.||..|..-|+- ..+.|
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe-~d~~l 81 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEE-LDSRL 81 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchh-hhhhh
Confidence 34788999999999999999999999999999999999976532 33457899999999999998775542 34666
Q ss_pred hhcC
Q 033530 81 VEET 84 (117)
Q Consensus 81 ~~~~ 84 (117)
+..+
T Consensus 82 d~tk 85 (96)
T KOG1784|consen 82 DLTK 85 (96)
T ss_pred hhhh
Confidence 6554
No 37
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=98.52 E-value=2.5e-08 Score=74.67 Aligned_cols=70 Identities=21% Similarity=0.261 Sum_probs=57.6
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeC----------CCCceeeceEEEecCeEEEEEcCCCCcch
Q 033530 8 MKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLK----------GKNPVNLDHLSVRGNNIRYYILPDSLNLE 77 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~----------~~~~~~~~~v~IRG~~I~~I~lpd~id~~ 77 (117)
-+.++.+..|.++||+++.|++..||.|||++|.|+++... ..+..-++.+.+||.+|......+-.-.+
T Consensus 10 l~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp~s 89 (177)
T KOG3168|consen 10 LQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPPPS 89 (177)
T ss_pred HHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCCCc
Confidence 34789999999999999999999999999999999987632 12357899999999999998775444333
No 38
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.38 E-value=4.6e-08 Score=69.92 Aligned_cols=64 Identities=19% Similarity=0.265 Sum_probs=53.9
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeC-CCC--ceeeceEEEecCeEEEEEc
Q 033530 7 LMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLK-GKN--PVNLDHLSVRGNNIRYYIL 70 (117)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~-~~~--~~~~~~v~IRG~~I~~I~l 70 (117)
|-+.+.+++.|-|+||+.+.|.|.+||+|-|++|.++++..- +.. ....|.+.|||.||..+..
T Consensus 14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGe 80 (129)
T KOG1782|consen 14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGE 80 (129)
T ss_pred HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEec
Confidence 556788999999999999999999999999999999986543 221 2456899999999999865
No 39
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.32 E-value=2.2e-06 Score=55.92 Aligned_cols=47 Identities=28% Similarity=0.420 Sum_probs=38.4
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEecc---ccceEEccEEEEeC
Q 033530 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDI---SMNTHLKTVKLTLK 48 (117)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~---~MNl~L~da~~~~~ 48 (117)
+|+-++..++|++|.|.++||..|+|.+.+++. -+.++|+.|.....
T Consensus 2 Rl~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~ 51 (77)
T PF14438_consen 2 RLVYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK 51 (77)
T ss_dssp --HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred hHHHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence 467889999999999999999999999999998 89999999998765
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=97.62 E-value=5.4e-05 Score=48.87 Aligned_cols=38 Identities=21% Similarity=0.326 Sum_probs=31.7
Q ss_pred CCCEEEEEEcC--C--cEEEEEEEEeccccceEEccEEEEeC
Q 033530 11 NNETVSIELKN--G--TIVHGTITGVDISMNTHLKTVKLTLK 48 (117)
Q Consensus 11 ~gk~V~VeLkn--g--~~~~G~L~~~D~~MNl~L~da~~~~~ 48 (117)
.+.+|.|.++. | -.++|.|++||.|||+.|.||.|+..
T Consensus 7 er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~ 48 (66)
T cd01739 7 ERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR 48 (66)
T ss_pred CCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence 46778777765 3 57889999999999999999998865
No 41
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.50 E-value=0.00061 Score=46.93 Aligned_cols=66 Identities=17% Similarity=0.169 Sum_probs=54.0
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEccEEEEeCCCC---------ceeeceEEEecCeEEEEEcCCC
Q 033530 8 MKLNNETVSIELKNGTIVHGTITGVDI-SMNTHLKTVKLTLKGKN---------PVNLDHLSVRGNNIRYYILPDS 73 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~-~MNl~L~da~~~~~~~~---------~~~~~~v~IRG~~I~~I~lpd~ 73 (117)
..++|++|.+..+++..|+|+|..+|. .-.|.|.||.-....+. ...++.+..||+-|+-+.+-+.
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~ 79 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEP 79 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcC
Confidence 358999999999999999999999995 68999999986643332 2358899999999999877543
No 42
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=97.27 E-value=4.7e-05 Score=53.62 Aligned_cols=58 Identities=21% Similarity=0.281 Sum_probs=48.8
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeC------CCC-------ceeeceEEEecCeEEEEE
Q 033530 12 NETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLK------GKN-------PVNLDHLSVRGNNIRYYI 69 (117)
Q Consensus 12 gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~------~~~-------~~~~~~v~IRG~~I~~I~ 69 (117)
..+|.|-++|....-|.+.+||-+.|++|+|+.+... +|+ -+.++.+||||++|..+.
T Consensus 36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~ 106 (114)
T KOG3459|consen 36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVL 106 (114)
T ss_pred CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEE
Confidence 5689999999999999999999999999999987642 121 256899999999988764
No 43
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=96.86 E-value=0.013 Score=39.17 Aligned_cols=65 Identities=14% Similarity=0.159 Sum_probs=52.6
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEec-cccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcC
Q 033530 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVD-ISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILP 71 (117)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D-~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lp 71 (117)
+++.+|.++.|++|.+.|.++.+..|+..++| +-.|+..+|-. ++-| ..+...+|.+-|..+.+.
T Consensus 14 rfLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~--TPlG---v~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 14 RFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ--TPLG---VQPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE--TTTT---EEEEEEEEGGGEEEEEE-
T ss_pred HHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC--CCcc---cChhheeecCCEEEEEec
Confidence 46889999999999999999999999999999 55899998876 4444 468999999999887653
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=96.53 E-value=0.016 Score=38.26 Aligned_cols=60 Identities=17% Similarity=0.172 Sum_probs=47.5
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEccEEEEeCCCC----------ceeeceEEEecCeEEE
Q 033530 8 MKLNNETVSIELKNGTIVHGTITGVDI-SMNTHLKTVKLTLKGKN----------PVNLDHLSVRGNNIRY 67 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~-~MNl~L~da~~~~~~~~----------~~~~~~v~IRG~~I~~ 67 (117)
..++|+++.+--+.+..|+|+|.++|. ---+.|+||.....+|. ..-++.+..||+.|+-
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 367999999999999999999999994 46789999986643322 2346778888888764
No 45
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=96.27 E-value=0.042 Score=35.51 Aligned_cols=52 Identities=17% Similarity=0.289 Sum_probs=38.9
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEec-cccceEEccEEEEeCCCCceeeceEEEecCeEEEE
Q 033530 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVD-ISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYY 68 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D-~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I 68 (117)
++..|++++|++|.|++-.|+. +|+|.++- +|. +|+. ++ ...|||=..|.+|
T Consensus 12 vyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~------~~-----~~~~IR~~~IV~v 64 (66)
T PF10842_consen 12 VYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEE------NG-----TPFFIRIAQIVWV 64 (66)
T ss_pred HHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEe------CC-----cEEEEEeeeEEEE
Confidence 4678999999999999977766 99999987 443 2221 11 3577888888776
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=95.47 E-value=0.035 Score=35.37 Aligned_cols=31 Identities=26% Similarity=0.216 Sum_probs=27.1
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISMNTHLK 41 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~ 41 (117)
.+.+|+|-|.||..++|.+.+||.|+=+.-.
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~ 40 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLES 40 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcceEEEEEE
Confidence 4678999999999999999999999865543
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=95.46 E-value=0.035 Score=35.40 Aligned_cols=31 Identities=23% Similarity=0.188 Sum_probs=27.2
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISMNTHLK 41 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~ 41 (117)
.+.+|+|-|.||..++|.+.++|.|+=+.-.
T Consensus 14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~ 44 (61)
T TIGR02383 14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLES 44 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEeeeEEEEEE
Confidence 5779999999999999999999999866543
No 48
>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=95.29 E-value=0.092 Score=31.22 Aligned_cols=31 Identities=19% Similarity=0.260 Sum_probs=27.8
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccceEEcc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKT 42 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~d 42 (117)
+|++|++++ ++..++|+..++|+.-.|.++.
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~ 32 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRT 32 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEE
Confidence 699999999 6777799999999999998865
No 49
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.97 E-value=0.054 Score=36.19 Aligned_cols=54 Identities=24% Similarity=0.200 Sum_probs=39.8
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCCCCcc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNL 76 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd~id~ 76 (117)
.+.+|+|-|.||..++|.+.+||.|+=+.-.+-. .-+|--..|..|..-..+++
T Consensus 18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~gk------------qqLIYKHAISTI~p~~~i~~ 71 (79)
T PRK00395 18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTGK------------SQLVYKHAISTVVPARPVSL 71 (79)
T ss_pred cCCCEEEEEeCCcEEEEEEEEEccEEEEEEECCc------------EEEEEEeeeEEEecCCcccc
Confidence 5789999999999999999999999866544321 23566667777655555544
No 50
>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=94.49 E-value=0.24 Score=31.48 Aligned_cols=55 Identities=15% Similarity=0.102 Sum_probs=36.7
Q ss_pred cCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEE
Q 033530 10 LNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIR 66 (117)
Q Consensus 10 l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~ 66 (117)
.+|..|.+++-.|.+++|.+..||...++..-.+... ++.+..-+..+|+=+.|+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s~--~~~~~~~dv~ivnls~~~ 58 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPSS--SGKPNHADILLVNLSYVS 58 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECccc--cCCCCcceEEEEEhhhEE
Confidence 4799999999999999999999998876654332211 222223344555544444
No 51
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=94.20 E-value=0.32 Score=36.62 Aligned_cols=63 Identities=11% Similarity=0.075 Sum_probs=43.4
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCCCCc
Q 033530 6 FLMKLNNETVSIELKNGTIVHGTITGVDI-SMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLN 75 (117)
Q Consensus 6 ~L~~l~gk~V~VeLkng~~~~G~L~~~D~-~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd~id 75 (117)
.++.++||.|.|.+.| +++.|-|..+|+ .-|++|-+..+ +++ ..--+|-|.+|+.|..-+.-|
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~---~sv~~I~ghaVk~vevl~~~~ 74 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK---RSVKVIMGHAVKSVEVLSEGD 74 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS----EEEEEE-GGGEEEEEEEE---
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc---eeEEEEEccceEEEEEccCCc
Confidence 4678999999999999 999999999994 57888876552 232 235789999999998766543
No 52
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.72 E-value=0.18 Score=42.14 Aligned_cols=66 Identities=17% Similarity=0.188 Sum_probs=52.8
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEEEEec-cccceEEccEEEEeCCCC---------c-eeeceEEEecCeEEEEEcCC
Q 033530 7 LMKLNNETVSIELKNGTIVHGTITGVD-ISMNTHLKTVKLTLKGKN---------P-VNLDHLSVRGNNIRYYILPD 72 (117)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D-~~MNl~L~da~~~~~~~~---------~-~~~~~v~IRG~~I~~I~lpd 72 (117)
...++|+.|.+.=|++..|+|+|..+| +---|-|.+|.-.-.++. . .-++-|+.||+.|+-+.+-+
T Consensus 4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence 456899999999999999999999999 667899999865532221 1 16788999999999777655
No 53
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=93.48 E-value=0.13 Score=34.17 Aligned_cols=27 Identities=26% Similarity=0.300 Sum_probs=24.8
Q ss_pred cCCCEEEEEEcCCcEEEEEEEEecccc
Q 033530 10 LNNETVSIELKNGTIVHGTITGVDISM 36 (117)
Q Consensus 10 l~gk~V~VeLkng~~~~G~L~~~D~~M 36 (117)
..+.+|+|-|.||-..+|.+.+||.|.
T Consensus 17 k~~i~VtIfLvNG~~L~G~V~sfD~f~ 43 (77)
T COG1923 17 KEKIPVTIFLVNGFKLQGQVESFDNFV 43 (77)
T ss_pred hcCCeEEEEEEcCEEEEEEEEeeeeEE
Confidence 357899999999999999999999996
No 54
>PRK14638 hypothetical protein; Provisional
Probab=92.13 E-value=0.36 Score=35.39 Aligned_cols=35 Identities=14% Similarity=0.217 Sum_probs=29.6
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHL 40 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L 40 (117)
.-+..++|+.|.|.+++++.++|+|.++|+. ++.|
T Consensus 93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 4567899999999999999999999999964 3444
No 55
>PRK14642 hypothetical protein; Provisional
Probab=91.69 E-value=1.5 Score=33.81 Aligned_cols=71 Identities=18% Similarity=0.254 Sum_probs=47.1
Q ss_pred HHHhhcCCCEEEEEEc-------------CCcEEEEEEEEeccccceEE--ccEEEEeCC---C---CceeeceEEEecC
Q 033530 5 RFLMKLNNETVSIELK-------------NGTIVHGTITGVDISMNTHL--KTVKLTLKG---K---NPVNLDHLSVRGN 63 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLk-------------ng~~~~G~L~~~D~~MNl~L--~da~~~~~~---~---~~~~~~~v~IRG~ 63 (117)
.-+..++|+.|.|.|+ +.+.++|+|.++|+. ++.| ++.-+-.++ + .+.....+-+-=+
T Consensus 93 ~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l~~~~~~~~k~g~~~~k~~~~~~~~~~~~~~~ 171 (197)
T PRK14642 93 QDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQIVWSDEPPVKPGQRVSKKRVPAPLQALGFTLD 171 (197)
T ss_pred HHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEEEEeecccCCCccccccccccccceeEEeehh
Confidence 4567789999999998 679999999999974 4444 322111111 1 1123345667778
Q ss_pred eEEEEEcCCCCcc
Q 033530 64 NIRYYILPDSLNL 76 (117)
Q Consensus 64 ~I~~I~lpd~id~ 76 (117)
.|+...+-..+|+
T Consensus 172 eik~a~l~p~~~f 184 (197)
T PRK14642 172 ELREARLAPIVDF 184 (197)
T ss_pred heeeEEEEEEEec
Confidence 8888877777764
No 56
>PRK14639 hypothetical protein; Provisional
Probab=91.37 E-value=0.5 Score=34.28 Aligned_cols=36 Identities=28% Similarity=0.309 Sum_probs=30.3
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 033530 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHL 40 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L 40 (117)
..-++.++|+.|.|.|++++.+.|+|.++|+. ++.|
T Consensus 80 ~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 80 IEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 34577899999999999999999999999983 4444
No 57
>PRK02001 hypothetical protein; Validated
Probab=90.69 E-value=0.5 Score=34.89 Aligned_cols=35 Identities=23% Similarity=0.316 Sum_probs=29.6
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHL 40 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L 40 (117)
.-+..++|+.|.|.|.++..+.|+|.++|+. ++.|
T Consensus 83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 4567899999999999999999999999975 3444
No 58
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=89.31 E-value=0.74 Score=34.69 Aligned_cols=32 Identities=25% Similarity=0.384 Sum_probs=27.5
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccceEEcc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKT 42 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~d 42 (117)
...+|+|-|.||-.++|.+.+||.|.=+...+
T Consensus 103 ~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 103 SGEPVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred cCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 46789999999999999999999997665444
No 59
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=88.46 E-value=1.4 Score=28.86 Aligned_cols=31 Identities=26% Similarity=0.345 Sum_probs=26.6
Q ss_pred HHHhhcCCCEEEEEEc---CC-cEEEEEEEEeccc
Q 033530 5 RFLMKLNNETVSIELK---NG-TIVHGTITGVDIS 35 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLk---ng-~~~~G~L~~~D~~ 35 (117)
.-++..+|+.|.|+++ +| +.+.|.|.++|+.
T Consensus 18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 4567899999999998 56 6899999999984
No 60
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=88.12 E-value=0.99 Score=34.00 Aligned_cols=53 Identities=19% Similarity=0.132 Sum_probs=36.5
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCCCCc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLN 75 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd~id 75 (117)
...+|+|-|.||-.++|.+.+||.|.=+.-.+-. .-+|--..|..|...+.++
T Consensus 23 ~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~gk------------qqLIYKHAISTI~p~~~i~ 75 (165)
T PRK14091 23 TKTPVTMFLVKGVKLQGIITWFDNFSILLRRDGQ------------SQLVYKHAISTIMPAHPLD 75 (165)
T ss_pred cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCCc------------eEEEEeeeeeeecccCCcc
Confidence 4678999999999999999999999755543321 2345555566654444443
No 61
>PRK14644 hypothetical protein; Provisional
Probab=88.03 E-value=1 Score=32.61 Aligned_cols=35 Identities=17% Similarity=0.237 Sum_probs=29.1
Q ss_pred HHhhcCCCEEEEEEcCC----cEEEEEEEEeccccceEEc
Q 033530 6 FLMKLNNETVSIELKNG----TIVHGTITGVDISMNTHLK 41 (117)
Q Consensus 6 ~L~~l~gk~V~VeLkng----~~~~G~L~~~D~~MNl~L~ 41 (117)
-++.++|+.|.|.|++. ..+.|.|.++|+. ++.|.
T Consensus 79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 46788999999999887 9999999999973 44443
No 62
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.54 E-value=1.9 Score=32.01 Aligned_cols=33 Identities=21% Similarity=0.335 Sum_probs=29.2
Q ss_pred hHHHhhcCCCEEEEEE----cCCcEEEEEEEEecccc
Q 033530 4 VRFLMKLNNETVSIEL----KNGTIVHGTITGVDISM 36 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeL----kng~~~~G~L~~~D~~M 36 (117)
..-+..++|+.|.|+| .+.+.++|+|.++|+.+
T Consensus 91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 3457789999999999 78899999999999876
No 63
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=87.09 E-value=3.3 Score=30.12 Aligned_cols=31 Identities=19% Similarity=0.280 Sum_probs=26.7
Q ss_pred HHHhhcCCCEEEEEE----cCCcEEEEEEEEeccc
Q 033530 5 RFLMKLNNETVSIEL----KNGTIVHGTITGVDIS 35 (117)
Q Consensus 5 ~~L~~l~gk~V~VeL----kng~~~~G~L~~~D~~ 35 (117)
.-++.++|+.|.|.| .++..+.|+|.++|+.
T Consensus 91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 457789999999998 4678999999999983
No 64
>PRK14640 hypothetical protein; Provisional
Probab=86.49 E-value=1.4 Score=32.28 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=28.4
Q ss_pred HHHhhcCCCEEEEEE----cCCcEEEEEEEEeccccceEE
Q 033530 5 RFLMKLNNETVSIEL----KNGTIVHGTITGVDISMNTHL 40 (117)
Q Consensus 5 ~~L~~l~gk~V~VeL----kng~~~~G~L~~~D~~MNl~L 40 (117)
.-++.++|+.|.|.| .+.+.++|+|.++|+. ++.|
T Consensus 90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 456789999999999 4669999999999974 3444
No 65
>PRK14633 hypothetical protein; Provisional
Probab=85.17 E-value=1.8 Score=31.72 Aligned_cols=35 Identities=20% Similarity=0.059 Sum_probs=28.4
Q ss_pred HHHhhcCCCEEEEEEc----CCcEEEEEEEEeccccceEE
Q 033530 5 RFLMKLNNETVSIELK----NGTIVHGTITGVDISMNTHL 40 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLk----ng~~~~G~L~~~D~~MNl~L 40 (117)
.-++.++|+.|.|.++ +.+.++|+|.++|+. ++.|
T Consensus 87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 4567899999999994 569999999999874 4444
No 66
>PRK14632 hypothetical protein; Provisional
Probab=84.23 E-value=2 Score=32.24 Aligned_cols=36 Identities=11% Similarity=0.192 Sum_probs=28.8
Q ss_pred HHHhhcCCCEEEEEEcC-------CcEEEEEEEEeccccceEEc
Q 033530 5 RFLMKLNNETVSIELKN-------GTIVHGTITGVDISMNTHLK 41 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkn-------g~~~~G~L~~~D~~MNl~L~ 41 (117)
.-++.++|+.|.|.|++ .+.++|+|.++|+. ++.|.
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 45678999999999986 58999999999864 44443
No 67
>PRK14636 hypothetical protein; Provisional
Probab=83.93 E-value=2.1 Score=32.26 Aligned_cols=31 Identities=19% Similarity=0.380 Sum_probs=26.4
Q ss_pred HHHhhcCCCEEEEEEc---CC-cEEEEEEEEeccc
Q 033530 5 RFLMKLNNETVSIELK---NG-TIVHGTITGVDIS 35 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLk---ng-~~~~G~L~~~D~~ 35 (117)
.-++.++|+.|.|+|+ +| +.++|+|.++|+.
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~ 125 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD 125 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC
Confidence 4567899999999998 55 7999999999873
No 68
>PRK14645 hypothetical protein; Provisional
Probab=83.22 E-value=2.8 Score=30.96 Aligned_cols=30 Identities=17% Similarity=0.218 Sum_probs=25.9
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccc
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDIS 35 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~ 35 (117)
.-++..+|+.|.|.+ ++..++|+|.++|+.
T Consensus 95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 456778999999986 789999999999974
No 69
>PRK14634 hypothetical protein; Provisional
Probab=82.72 E-value=2.5 Score=31.09 Aligned_cols=35 Identities=9% Similarity=0.172 Sum_probs=27.7
Q ss_pred HHHhhcCCCEEEEEEcCC----cEEEEEEEEeccccceEE
Q 033530 5 RFLMKLNNETVSIELKNG----TIVHGTITGVDISMNTHL 40 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng----~~~~G~L~~~D~~MNl~L 40 (117)
.-++.++|+.|.|+|++. +.++|+|.++|+. ++.|
T Consensus 93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 446788999999999743 7999999999974 3444
No 70
>PRK14643 hypothetical protein; Provisional
Probab=82.34 E-value=2.6 Score=31.44 Aligned_cols=36 Identities=22% Similarity=0.239 Sum_probs=28.3
Q ss_pred HHHhhcCCCEEEEEEcC----CcEEEEEEEEeccc-cceEE
Q 033530 5 RFLMKLNNETVSIELKN----GTIVHGTITGVDIS-MNTHL 40 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkn----g~~~~G~L~~~D~~-MNl~L 40 (117)
.-++.++|+.|.|.|++ ...++|+|.++|+. ..+.|
T Consensus 97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 34678899999999976 59999999999964 34433
No 71
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=81.64 E-value=3.9 Score=29.16 Aligned_cols=30 Identities=23% Similarity=0.314 Sum_probs=23.7
Q ss_pred HHHhhcCCCEEEEEEc----CCcEEEEEEEEecc
Q 033530 5 RFLMKLNNETVSIELK----NGTIVHGTITGVDI 34 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLk----ng~~~~G~L~~~D~ 34 (117)
.-+...+|+.|.|.++ +...+.|+|.++|+
T Consensus 80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 4677899999999994 44799999999998
No 72
>PRK14646 hypothetical protein; Provisional
Probab=81.25 E-value=3.1 Score=30.66 Aligned_cols=35 Identities=14% Similarity=0.208 Sum_probs=27.9
Q ss_pred HHHhhcCCCEEEEEEcCC----cEEEEEEEEeccccceEE
Q 033530 5 RFLMKLNNETVSIELKNG----TIVHGTITGVDISMNTHL 40 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng----~~~~G~L~~~D~~MNl~L 40 (117)
.-++.++|+.|.|+|++. +.++|+|.++|+. ++.|
T Consensus 93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 346789999999999653 7889999999974 4444
No 73
>PRK14647 hypothetical protein; Provisional
Probab=80.46 E-value=4.2 Score=29.93 Aligned_cols=31 Identities=10% Similarity=0.070 Sum_probs=26.3
Q ss_pred hHHHhhcCCCEEEEEEc---------CCcEEEEEEEEecc
Q 033530 4 VRFLMKLNNETVSIELK---------NGTIVHGTITGVDI 34 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLk---------ng~~~~G~L~~~D~ 34 (117)
..-++.++|+.|.|.|+ +.+.+.|+|.++|+
T Consensus 91 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 91 EADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 34577899999999996 34999999999996
No 74
>PRK14637 hypothetical protein; Provisional
Probab=77.71 E-value=4.4 Score=29.78 Aligned_cols=35 Identities=23% Similarity=0.104 Sum_probs=26.7
Q ss_pred HHHhhcCCCEEEEEEcCCcEE-EEEEEEeccccceEE
Q 033530 5 RFLMKLNNETVSIELKNGTIV-HGTITGVDISMNTHL 40 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~-~G~L~~~D~~MNl~L 40 (117)
.-+..++|+.|.|.|.+...+ +|+|.++|+. ++.|
T Consensus 91 ~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 91 AEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred HHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 456788999999999544556 7999999975 4444
No 75
>PRK14631 hypothetical protein; Provisional
Probab=77.58 E-value=4.5 Score=30.46 Aligned_cols=29 Identities=21% Similarity=0.244 Sum_probs=25.4
Q ss_pred HHHhhcCCCEEEEEEc----CCcEEEEEEEEec
Q 033530 5 RFLMKLNNETVSIELK----NGTIVHGTITGVD 33 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLk----ng~~~~G~L~~~D 33 (117)
.-++.++|+.|.|+|+ +.+.++|+|.++|
T Consensus 110 ~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 110 EQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 4567899999999996 4599999999998
No 76
>PRK06955 biotin--protein ligase; Provisional
Probab=77.51 E-value=12 Score=29.98 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=28.8
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 033530 9 KLNNETVSIELKNGTIVHGTITGVDISMNTHLK 41 (117)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~ 41 (117)
...|++|++...++.+++|+..++|+.-.|.++
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 468999999766778899999999999999885
No 77
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=76.93 E-value=8.3 Score=28.32 Aligned_cols=26 Identities=38% Similarity=0.509 Sum_probs=24.0
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEec
Q 033530 8 MKLNNETVSIELKNGTIVHGTITGVD 33 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D 33 (117)
.+++||.|.+...+|..+.|++.++.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 47899999999999999999999986
No 78
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=74.07 E-value=14 Score=29.57 Aligned_cols=48 Identities=21% Similarity=0.318 Sum_probs=34.7
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCC-CceeeceEEEec
Q 033530 9 KLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK-NPVNLDHLSVRG 62 (117)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~-~~~~~~~v~IRG 62 (117)
...|+.|.+.. ++..++|+..++|+.-.|.+++ +++ +....+++.+++
T Consensus 269 ~~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~~-----~g~~~~~~~gev~~~~ 317 (319)
T PRK11886 269 LFLGREVKLII-GDKEISGIARGIDEQGALLLED-----DGVEKPFNGGEISLRS 317 (319)
T ss_pred cccCCeEEEEe-CCcEEEEEEEEECCCceEEEEe-----CCcEEEEEEeEEEEec
Confidence 36799999987 4467999999999999999851 222 234456666654
No 79
>PRK14641 hypothetical protein; Provisional
Probab=73.02 E-value=7.7 Score=29.21 Aligned_cols=29 Identities=14% Similarity=0.205 Sum_probs=24.8
Q ss_pred HHHhhcCCCEEEEEEcC----CcEEEEEEEEec
Q 033530 5 RFLMKLNNETVSIELKN----GTIVHGTITGVD 33 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkn----g~~~~G~L~~~D 33 (117)
.-++.++|+.|.|.|++ .+.++|+|.++|
T Consensus 97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 45678999999999976 468999999995
No 80
>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=70.53 E-value=6.5 Score=27.24 Aligned_cols=18 Identities=39% Similarity=0.850 Sum_probs=14.8
Q ss_pred CEEEEEEcCCcEEEEEEE
Q 033530 13 ETVSIELKNGTIVHGTIT 30 (117)
Q Consensus 13 k~V~VeLkng~~~~G~L~ 30 (117)
.+|.++|+||+.+.|++.
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 81
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=68.50 E-value=28 Score=30.78 Aligned_cols=33 Identities=27% Similarity=0.348 Sum_probs=28.8
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 033530 9 KLNNETVSIELKNGTIVHGTITGVDISMNTHLK 41 (117)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~ 41 (117)
...|++|.+...++.+++|+..++|+.-.+.|+
T Consensus 275 ~~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 275 RDHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred ccCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 478999999766777899999999999999886
No 82
>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=68.04 E-value=5.1 Score=26.60 Aligned_cols=22 Identities=23% Similarity=0.437 Sum_probs=15.5
Q ss_pred HhhcCCCEEEEEEcCCcEEEEE
Q 033530 7 LMKLNNETVSIELKNGTIVHGT 28 (117)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~ 28 (117)
+-.+-+.+|.++|+||..++|+
T Consensus 12 iAC~~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 12 IACMYRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp HHHTTTT-EEEE-TTT--EEES
T ss_pred HHHhcCCeEEEEEeCCCEEEEE
Confidence 4567789999999999999997
No 83
>PRK14630 hypothetical protein; Provisional
Probab=66.00 E-value=11 Score=27.29 Aligned_cols=30 Identities=17% Similarity=0.215 Sum_probs=24.5
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccc
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDIS 35 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~ 35 (117)
.-++.++|++|.|.|.+.. .+|+|.++|+.
T Consensus 90 ~df~r~~G~~v~V~l~~~~-~~G~L~~~~d~ 119 (143)
T PRK14630 90 REFKIFEGKKIKLMLDNDF-EEGFILEAKAD 119 (143)
T ss_pred HHHHHhCCCEEEEEEcCcc-eEEEEEEEeCC
Confidence 4567899999999996644 59999999873
No 84
>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=62.65 E-value=29 Score=26.57 Aligned_cols=32 Identities=22% Similarity=0.221 Sum_probs=27.5
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEEc
Q 033530 9 KLNNETVSIELKNGTIVHGTITGVDISMNTHLK 41 (117)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~ 41 (117)
...|++|++...+ ..+.|+..++|+.-.+.++
T Consensus 190 ~~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 190 AHIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred hccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 4679999998755 5689999999999999986
No 85
>PRK14635 hypothetical protein; Provisional
Probab=62.21 E-value=27 Score=25.75 Aligned_cols=35 Identities=11% Similarity=0.118 Sum_probs=27.1
Q ss_pred HHHhhcCCCEEEEEEc--CCcEEEE---EEEEeccccceEE
Q 033530 5 RFLMKLNNETVSIELK--NGTIVHG---TITGVDISMNTHL 40 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLk--ng~~~~G---~L~~~D~~MNl~L 40 (117)
.-++.++|+.|.|.+. ++..+.| +|.++|+. ++.|
T Consensus 92 ~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 92 EDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 4567899999999986 4578887 99999874 4444
No 86
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=60.72 E-value=35 Score=24.61 Aligned_cols=69 Identities=22% Similarity=0.270 Sum_probs=46.3
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCe------EEEEEcCCCCcchhhhhh
Q 033530 9 KLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNN------IRYYILPDSLNLETLLVE 82 (117)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~------I~~I~lpd~id~~~~l~~ 82 (117)
+.+-+-+.|.|+||..+..-+=+-. ....+.+.++|||-. |+|=.+--.+|+..+..+
T Consensus 47 SA~RKvarVrL~ngk~v~AyIPGeG----------------hnlqehs~VLvrGGrv~DlPGVrykvVrG~~D~~gv~~R 110 (124)
T PRK05163 47 SALRKVARVRLTNGFEVTAYIPGEG----------------HNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKDR 110 (124)
T ss_pred chhheEEEEEeCCCCEEEEEcCCCC----------------CCccccCEEEEeCCccCCCCCcEEEEeeeeecccccccc
Confidence 4566788899998888754333222 122345677777765 466666778898888888
Q ss_pred cCcccCCCCCC
Q 033530 83 ETPRVKPKKPT 93 (117)
Q Consensus 83 ~~~~~~~~~~~ 93 (117)
.+.+|++..+.
T Consensus 111 ~~~RSkYG~Kk 121 (124)
T PRK05163 111 KQGRSKYGAKR 121 (124)
T ss_pred cccccccccCC
Confidence 78888886553
No 87
>PRK08330 biotin--protein ligase; Provisional
Probab=58.86 E-value=33 Score=26.28 Aligned_cols=33 Identities=21% Similarity=0.211 Sum_probs=26.9
Q ss_pred hcCCCEEEEEEcCCcEE-EEEEEEeccccceEEcc
Q 033530 9 KLNNETVSIELKNGTIV-HGTITGVDISMNTHLKT 42 (117)
Q Consensus 9 ~l~gk~V~VeLkng~~~-~G~L~~~D~~MNl~L~d 42 (117)
...|++|.+.. ++..+ .|+..++|+.-.+.++.
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 46899999976 55554 79999999999998864
No 88
>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=57.09 E-value=13 Score=27.90 Aligned_cols=25 Identities=20% Similarity=0.505 Sum_probs=22.9
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDIS 35 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~ 35 (117)
.|+.+.|.+.||+.++|+-.++|.-
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 6899999999999999999999853
No 89
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=56.99 E-value=41 Score=24.29 Aligned_cols=69 Identities=22% Similarity=0.273 Sum_probs=46.0
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCe------EEEEEcCCCCcchhhhhh
Q 033530 9 KLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNN------IRYYILPDSLNLETLLVE 82 (117)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~------I~~I~lpd~id~~~~l~~ 82 (117)
+.+-+-+.|.|+||..+..-+=+.- ....+.+.++|||-. |+|=.+--.+|+..+..+
T Consensus 47 SA~RKvarVrL~ngk~v~AyIPG~G----------------hnlqehs~VLvrGGrv~DlPGVkykvVrG~~D~~gv~~R 110 (124)
T TIGR00981 47 SALRKVARVRLTNGFEVTAYIPGEG----------------HNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKNR 110 (124)
T ss_pred chhheeEEEEeCCCCEEEEEcCCCC----------------CCccccCEEEEeCCccCCCCCeEEEEEeEeecccccccc
Confidence 4566778889988887754332221 122345677777764 566666777899888888
Q ss_pred cCcccCCCCCC
Q 033530 83 ETPRVKPKKPT 93 (117)
Q Consensus 83 ~~~~~~~~~~~ 93 (117)
.+.+|++..+.
T Consensus 111 ~~~RSkYG~Kk 121 (124)
T TIGR00981 111 KQGRSKYGAKR 121 (124)
T ss_pred cccccccccCC
Confidence 88888887553
No 90
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=55.16 E-value=21 Score=26.20 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=23.1
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEecc
Q 033530 9 KLNNETVSIELKNGTIVHGTITGVDI 34 (117)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~ 34 (117)
+++||.|.....+|..+.|++.++..
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEEE
Confidence 68999999888999999999998863
No 91
>PRK11625 Rho-binding antiterminator; Provisional
Probab=53.07 E-value=34 Score=22.92 Aligned_cols=23 Identities=17% Similarity=0.391 Sum_probs=19.6
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEE
Q 033530 8 MKLNNETVSIELKNGTIVHGTIT 30 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~ 30 (117)
..+.+.+|.++|+||.+++|+..
T Consensus 19 AC~~~~~l~l~l~dGe~~~g~A~ 41 (84)
T PRK11625 19 ACQHHLMLTLELKDGEVLQAKAS 41 (84)
T ss_pred HHhcCCeEEEEECCCCEEEEEEE
Confidence 34578899999999999999874
No 92
>PRK10898 serine endoprotease; Provisional
Probab=51.17 E-value=51 Score=27.00 Aligned_cols=60 Identities=12% Similarity=0.232 Sum_probs=39.4
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeec--eEEEecCeEEEEEcCCC
Q 033530 12 NETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLD--HLSVRGNNIRYYILPDS 73 (117)
Q Consensus 12 gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~--~v~IRG~~I~~I~lpd~ 73 (117)
...+.|.+.+|+.|.+++.++|...++.+-.+.-. +-....++ .-.-.|..|..+..|-.
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~~~--~l~~~~l~~~~~~~~G~~V~aiG~P~g 162 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKINAT--NLPVIPINPKRVPHIGDVVLAIGNPYN 162 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEcCC--CCCeeeccCcCcCCCCCEEEEEeCCCC
Confidence 35789999999999999999999999977665411 10111111 12235666666666644
No 93
>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=50.10 E-value=49 Score=19.12 Aligned_cols=25 Identities=20% Similarity=0.247 Sum_probs=22.0
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDIS 35 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~ 35 (117)
.|..+.+...+|.-|+|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5888888888899999999999974
No 94
>PRK10139 serine endoprotease; Provisional
Probab=49.62 E-value=36 Score=28.96 Aligned_cols=63 Identities=16% Similarity=0.166 Sum_probs=41.4
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeece--EEEecCeEEEEEcCCCCc
Q 033530 12 NETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDH--LSVRGNNIRYYILPDSLN 75 (117)
Q Consensus 12 gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~--v~IRG~~I~~I~lpd~id 75 (117)
...+.|.+.||++|.+++.+.|...+|.+-.+... .+-....++. -.-.|..|.-|.-|-...
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~-~~l~~~~lg~s~~~~~G~~V~aiG~P~g~~ 178 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNP-SKLTQIAIADSDKLRVGDFAVAVGNPFGLG 178 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEecCC-CCCceeEecCccccCCCCEEEEEecCCCCC
Confidence 46899999999999999999999999887555311 0101122221 223477777777775543
No 95
>CHL00051 rps12 ribosomal protein S12
Probab=48.40 E-value=73 Score=22.96 Aligned_cols=68 Identities=21% Similarity=0.275 Sum_probs=45.2
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCe------EEEEEcCCCCcchhhhhh
Q 033530 9 KLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNN------IRYYILPDSLNLETLLVE 82 (117)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~------I~~I~lpd~id~~~~l~~ 82 (117)
+.+-+-+.|.|+||.++..-+=+.- + || .+.+.++|||-. |+|=.+--.+|++.+-.+
T Consensus 47 SA~RKvarVrLsngk~v~AyIPGeG-h-nl--------------qehs~VLvrGGrv~DlPGVrykvVRG~~D~~gv~~R 110 (123)
T CHL00051 47 SALRKVARVRLTSGFEITAYIPGIG-H-NL--------------QEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDR 110 (123)
T ss_pred hhheeEEEEEccCCCEEEEEcCCCC-c-cc--------------cccCEEEEeCCccCCCCCeeEEEEeeeecccccccc
Confidence 4566778889998888765443322 2 32 234556666654 466666778888888777
Q ss_pred cCcccCCCCC
Q 033530 83 ETPRVKPKKP 92 (117)
Q Consensus 83 ~~~~~~~~~~ 92 (117)
.+.+|++..+
T Consensus 111 ~~~RSkYG~K 120 (123)
T CHL00051 111 QQGRSKYGVK 120 (123)
T ss_pred cccccccccc
Confidence 7788887654
No 96
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=47.04 E-value=46 Score=26.52 Aligned_cols=32 Identities=16% Similarity=0.243 Sum_probs=27.2
Q ss_pred cCCCEEEEEEcCCcEEEEEEEEeccccceEEcc
Q 033530 10 LNNETVSIELKNGTIVHGTITGVDISMNTHLKT 42 (117)
Q Consensus 10 l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~d 42 (117)
..|+.|.|.. ++..+.|+..++|+.-.+.++.
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 4799999975 5678999999999998888863
No 97
>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=44.53 E-value=72 Score=26.03 Aligned_cols=33 Identities=12% Similarity=0.330 Sum_probs=28.6
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEccEE
Q 033530 12 NETVSIELKNGTIVHGTITGVDISMNTHLKTVK 44 (117)
Q Consensus 12 gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~ 44 (117)
...+.|.+.||+.+.+++.++|...++.+-.+.
T Consensus 101 ~~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 101 ADQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 356899999999999999999999999886554
No 98
>PRK10942 serine endoprotease; Provisional
Probab=44.34 E-value=47 Score=28.43 Aligned_cols=32 Identities=16% Similarity=0.339 Sum_probs=28.1
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEccE
Q 033530 12 NETVSIELKNGTIVHGTITGVDISMNTHLKTV 43 (117)
Q Consensus 12 gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da 43 (117)
...+.|.+.||++|.+++.+.|...++-|-.+
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 45789999999999999999999999877644
No 99
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=42.32 E-value=90 Score=19.89 Aligned_cols=55 Identities=18% Similarity=0.207 Sum_probs=38.9
Q ss_pred hcCCCEEEEEEcCC-cEEEEEEEEeccc-cceEEccEEEEeCCCCceeeceEEEecCeEE
Q 033530 9 KLNNETVSIELKNG-TIVHGTITGVDIS-MNTHLKTVKLTLKGKNPVNLDHLSVRGNNIR 66 (117)
Q Consensus 9 ~l~gk~V~VeLkng-~~~~G~L~~~D~~-MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~ 66 (117)
..+|+-|.|...+. -.|+|.+..+|+- --|+|..+. .+|-.-..+++..|..-|+
T Consensus 3 dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~---~ngik~~~~EVt~~~~DI~ 59 (62)
T cd01737 3 DWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPF---HNGVKCLVPEVTFRAGDIR 59 (62)
T ss_pred cccceEEEEecCCceEEEEEEEEEeCccceEEEEeecc---cCCccccCceEEEEEcchh
Confidence 45799999999887 7999999999965 356666554 3443445566666665554
No 100
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=41.93 E-value=40 Score=23.63 Aligned_cols=20 Identities=25% Similarity=0.532 Sum_probs=17.7
Q ss_pred EEEEEEcCCcEEEEEEEEec
Q 033530 14 TVSIELKNGTIVHGTITGVD 33 (117)
Q Consensus 14 ~V~VeLkng~~~~G~L~~~D 33 (117)
...|.|+||+++.|.+.+=|
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET 78 (133)
T ss_pred cEEEEECCCCEEEEEEEecC
Confidence 47899999999999998855
No 101
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=41.27 E-value=43 Score=24.33 Aligned_cols=39 Identities=23% Similarity=0.418 Sum_probs=30.7
Q ss_pred CcEEEEEEEEec---cccceEEccEEEEeCCCCceeeceEEEecCe
Q 033530 22 GTIVHGTITGVD---ISMNTHLKTVKLTLKGKNPVNLDHLSVRGNN 64 (117)
Q Consensus 22 g~~~~G~L~~~D---~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~ 64 (117)
+..+.|.+..+- -+||+.+.|+. .|+...-+.+-|||++
T Consensus 82 d~~lvG~VqKvS~Lil~~~~~v~Dv~----tg~~v~~~~~diRgnt 123 (140)
T PF11684_consen 82 DYVLVGEVQKVSNLILNMNVYVRDVE----TGKVVRGRSVDIRGNT 123 (140)
T ss_pred CEEEEEEEechhhhheeeeEEEEECC----CCCEEeeeeeeEecCc
Confidence 466778777766 57899999985 6677777889999986
No 102
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=41.18 E-value=1.2e+02 Score=22.98 Aligned_cols=72 Identities=15% Similarity=0.131 Sum_probs=40.9
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEecccc-ceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCCCCcchhhhh
Q 033530 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISM-NTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLV 81 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~M-Nl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd~id~~~~l~ 81 (117)
+...|+.-.|..|.+-..+|..|.+++..++... -+.+..-......... . -..++.+|..-.+.-+++
T Consensus 11 l~~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~~~~~~~~~~~~-~---------i~L~~al~K~~~~d~il~ 80 (225)
T PF04452_consen 11 LVKVLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRILEELEIPPEPPP-E---------ITLAQALPKGDRMDWILQ 80 (225)
T ss_dssp HHTTST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEEEEEE---SSSS-E---------EEEEEE--STTHHHHHHH
T ss_pred HHHhcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEeeeccCCCCCcc-e---------EEEEEEEEcCccHHHHHH
Confidence 3466778899999999999999999999999553 3444433322221111 1 223445566555566666
Q ss_pred hcC
Q 033530 82 EET 84 (117)
Q Consensus 82 ~~~ 84 (117)
+++
T Consensus 81 kat 83 (225)
T PF04452_consen 81 KAT 83 (225)
T ss_dssp HHH
T ss_pred HHH
Confidence 555
No 103
>TIGR00567 3mg DNA-3-methyladenine glycosylase (3mg). This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine.
Probab=41.01 E-value=47 Score=25.46 Aligned_cols=33 Identities=24% Similarity=0.320 Sum_probs=28.2
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccc
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMN 37 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MN 37 (117)
.+=+.|+|+.+.-++.+|....|.+++...|+-
T Consensus 12 ~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 12 TLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred HHHHHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 345689999999999989888999999999964
No 104
>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=40.71 E-value=56 Score=27.14 Aligned_cols=32 Identities=13% Similarity=0.363 Sum_probs=28.2
Q ss_pred CEEEEEEcCCcEEEEEEEEeccccceEEccEE
Q 033530 13 ETVSIELKNGTIVHGTITGVDISMNTHLKTVK 44 (117)
Q Consensus 13 k~V~VeLkng~~~~G~L~~~D~~MNl~L~da~ 44 (117)
..+.|.+.+|+.|.+++...|...++.|=.+.
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 57889999999999999999999998876554
No 105
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=40.21 E-value=44 Score=25.75 Aligned_cols=25 Identities=24% Similarity=0.256 Sum_probs=22.4
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEec
Q 033530 9 KLNNETVSIELKNGTIVHGTITGVD 33 (117)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D 33 (117)
+++||.|.+.-.+|..+.|++.++.
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 6799999988888999999999876
No 106
>PRK10708 hypothetical protein; Provisional
Probab=39.68 E-value=35 Score=21.60 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=23.4
Q ss_pred CCCEEEEEEcCCcEEEEEEEEecccc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISM 36 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~M 36 (117)
++.+|+|++.+|..-.|++..+.+|-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 57899999999999999999998874
No 107
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=39.45 E-value=55 Score=22.10 Aligned_cols=29 Identities=14% Similarity=-0.002 Sum_probs=25.1
Q ss_pred EEEeCCCCceeeceEEEecCeEEEEEcCC
Q 033530 44 KLTLKGKNPVNLDHLSVRGNNIRYYILPD 72 (117)
Q Consensus 44 ~~~~~~~~~~~~~~v~IRG~~I~~I~lpd 72 (117)
-|.+.+|....-|.+.+.|..+.-+.+|+
T Consensus 68 FEFS~~G~~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 68 FEFSSDGEDRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred EEEeCCChhcceEEEEEECCeeeEEEcCC
Confidence 45567788888899999999999999996
No 108
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=39.03 E-value=68 Score=21.58 Aligned_cols=23 Identities=30% Similarity=0.393 Sum_probs=17.0
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccc
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDIS 35 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~ 35 (117)
.+|++++|++|++- |++.++|..
T Consensus 8 ~~L~~f~gk~V~iv--------GkV~~~~~~ 30 (101)
T cd04479 8 AMLSQFVGKTVRIV--------GKVEKVDGD 30 (101)
T ss_pred HHHHhhCCCEEEEE--------EEEEEecCC
Confidence 57899999999876 555555544
No 109
>PRK06789 flagellar motor switch protein; Validated
Probab=38.00 E-value=68 Score=20.98 Aligned_cols=36 Identities=25% Similarity=0.248 Sum_probs=28.6
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEcc
Q 033530 7 LMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKT 42 (117)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~d 42 (117)
|.+..|.+|.|.+++-...+|.++.+|+.+=+.+.+
T Consensus 36 Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 36 LENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred eCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 466778888888888888999999999877666543
No 110
>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=35.23 E-value=41 Score=21.30 Aligned_cols=26 Identities=23% Similarity=0.308 Sum_probs=23.3
Q ss_pred CCCEEEEEEcCCcEEEEEEEEecccc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISM 36 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~M 36 (117)
++.+|+|++.+|..-.|++..+.+|-
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 57799999999999999999998874
No 111
>PF02245 Pur_DNA_glyco: Methylpurine-DNA glycosylase (MPG); InterPro: IPR003180 Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA []. Its action is induced by alkylating chemotherapeutics, as well as deaminated and lipid peroxidation-induced purine adducts []. MPG without an N-terminal extension excises hypoxanthine with one-third of the efficiency of full-length MPG under similar conditions, suggesting that is function may largely be attributable to the N-terminal extension [].; GO: 0003677 DNA binding, 0003905 alkylbase DNA N-glycosylase activity, 0006284 base-excision repair; PDB: 1BNK_A 1F6O_A 3QI5_A 3UBY_B 1F4R_A 1EWN_A.
Probab=35.21 E-value=58 Score=24.74 Aligned_cols=32 Identities=13% Similarity=0.241 Sum_probs=24.3
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccc
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMN 37 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MN 37 (117)
.+=+.|+|+.+..++.+|. +.|.++++..|+-
T Consensus 11 ~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 11 EVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp HHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred HHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 4557899999999999888 9999999988875
No 112
>PRK08477 biotin--protein ligase; Provisional
Probab=34.87 E-value=1.3e+02 Score=23.08 Aligned_cols=37 Identities=11% Similarity=0.010 Sum_probs=30.2
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEE
Q 033530 8 MKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKL 45 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~ 45 (117)
.-..|+.|+|. .++..++|+..++|+.--|.++.-..
T Consensus 171 ~~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~ 207 (211)
T PRK08477 171 EFEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKV 207 (211)
T ss_pred HHHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEe
Confidence 44689999987 57899999999999988887766543
No 113
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=34.62 E-value=1.2e+02 Score=23.78 Aligned_cols=36 Identities=25% Similarity=0.249 Sum_probs=32.1
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccE
Q 033530 8 MKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTV 43 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da 43 (117)
...+|++|++...++....|+-.++|..-.+.++..
T Consensus 186 ~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 186 SLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred hccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 446899999999999999999999999999988764
No 114
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=34.10 E-value=1.3e+02 Score=24.50 Aligned_cols=70 Identities=19% Similarity=0.174 Sum_probs=46.9
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCe------EEEEEcCCCCcchhhhh
Q 033530 8 MKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNN------IRYYILPDSLNLETLLV 81 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~------I~~I~lpd~id~~~~l~ 81 (117)
++++-|-+.|.|.||.++..-+=+... |+. ..+.|+|||-. |+|=.+--.+|+..+-.
T Consensus 142 NSA~RKvarVrLsNGk~VtAyIPGeGH--nLQ--------------EHs~VLVRGGrvkDLPGVrYkvVRG~~D~~gV~~ 205 (290)
T PTZ00115 142 NSGLRKVARVRLSTGRTVTVYIPGIGH--NLN--------------THSVVLVRGGRCKDVPGCNYKAVRGVYDLLPVKN 205 (290)
T ss_pred CccccceEEEEecCCCEEEEEcCCCCc--ccc--------------cCCEEEEeCCCcCCCCCceEEEeeeecccccccc
Confidence 356678889999999888765544332 333 33455556553 45656677788888888
Q ss_pred hcCcccCCCCCC
Q 033530 82 EETPRVKPKKPT 93 (117)
Q Consensus 82 ~~~~~~~~~~~~ 93 (117)
+.+.+++++.+.
T Consensus 206 Rk~~RSKYG~Kk 217 (290)
T PTZ00115 206 RARSRSKYGVKL 217 (290)
T ss_pred ccccccccccCC
Confidence 888888886543
No 115
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=33.68 E-value=1.2e+02 Score=19.95 Aligned_cols=30 Identities=13% Similarity=0.123 Sum_probs=21.9
Q ss_pred HHHhhcCCCEEEEEEcCC----cEEEEEEEEecc
Q 033530 5 RFLMKLNNETVSIELKNG----TIVHGTITGVDI 34 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng----~~~~G~L~~~D~ 34 (117)
.-|.+.+|++|.+.-+.| .+-+|+|.+.=+
T Consensus 10 ~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~tYP 43 (76)
T PF06257_consen 10 KELESHVGKRVKLKANKGRKKIIEREGVLEETYP 43 (76)
T ss_dssp HHHHHTTTSEEEEEE--SSS--S-EEEEEEEE-S
T ss_pred HHHHHcCCCEEEEEEcCCceEEEEEEEEEEeecC
Confidence 467889999999999999 467899987643
No 116
>PF10618 Tail_tube: Phage tail tube protein; InterPro: IPR019596 This entry is represented by Bacteriophage Mu, GpM tail tube protein. Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube.
Probab=33.65 E-value=64 Score=22.62 Aligned_cols=25 Identities=28% Similarity=0.392 Sum_probs=21.0
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEE
Q 033530 4 VRFLMKLNNETVSIELKNGTIVHGT 28 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~ 28 (117)
+.-|+...+-+|+.||.||.+|.+.
T Consensus 66 ~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 66 VDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred HHHHhCCcccEEEEEecCCcEEEec
Confidence 3457788999999999999999764
No 117
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=31.08 E-value=96 Score=23.28 Aligned_cols=27 Identities=15% Similarity=0.263 Sum_probs=23.8
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISMN 37 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MN 37 (117)
.|.+|.|.+.+|..+.|++..++...+
T Consensus 141 ~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 141 KGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CCCEEEEEECCCCEEEEEEEEEccccC
Confidence 689999999999999999999997643
No 118
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=30.62 E-value=49 Score=19.74 Aligned_cols=15 Identities=27% Similarity=0.390 Sum_probs=12.7
Q ss_pred hHHHhhcCCCEEEEE
Q 033530 4 VRFLMKLNNETVSIE 18 (117)
Q Consensus 4 ~~~L~~l~gk~V~Ve 18 (117)
+..++.++||+|.|.
T Consensus 11 ~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVT 25 (48)
T ss_pred hHHHHHhcCCeEEEE
Confidence 467888999999986
No 119
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.57 E-value=74 Score=24.44 Aligned_cols=43 Identities=12% Similarity=0.176 Sum_probs=33.6
Q ss_pred cCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCcee
Q 033530 10 LNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVN 54 (117)
Q Consensus 10 l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~ 54 (117)
.+|..|.+..-+|...+|.+.+||-.-+...-++. ..++++.+
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~--~s~~~P~~ 51 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP--SSNGKPNH 51 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc--ccCCCCcc
Confidence 46888999999999999999999988777766666 23444443
No 120
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=30.45 E-value=59 Score=27.17 Aligned_cols=23 Identities=26% Similarity=0.453 Sum_probs=21.1
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEE
Q 033530 8 MKLNNETVSIELKNGTIVHGTIT 30 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~ 30 (117)
+.+.|++|+|..++|..|.|++-
T Consensus 93 ~~~~gq~v~i~t~~g~~i~GvIg 115 (355)
T COG1363 93 QVLEGQRVTIHTDKGKKIRGVIG 115 (355)
T ss_pred hhccCcEEEEEeCCCcEEeeeEc
Confidence 45789999999999999999998
No 121
>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=30.44 E-value=1e+02 Score=19.16 Aligned_cols=26 Identities=15% Similarity=0.251 Sum_probs=18.6
Q ss_pred cCCCEEEEEEcCCcE-EEEEEEEeccc
Q 033530 10 LNNETVSIELKNGTI-VHGTITGVDIS 35 (117)
Q Consensus 10 l~gk~V~VeLkng~~-~~G~L~~~D~~ 35 (117)
..|..|.+.=-++.. |.|++.++|.-
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEeccc
Confidence 468999999988755 59999999964
No 122
>PF13437 HlyD_3: HlyD family secretion protein
Probab=30.41 E-value=1.2e+02 Score=19.56 Aligned_cols=24 Identities=17% Similarity=0.495 Sum_probs=21.5
Q ss_pred CCCEEEEEEcCC--cEEEEEEEEecc
Q 033530 11 NNETVSIELKNG--TIVHGTITGVDI 34 (117)
Q Consensus 11 ~gk~V~VeLkng--~~~~G~L~~~D~ 34 (117)
.|..|++.+.++ ..+.|++..++.
T Consensus 53 ~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 53 PGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred CCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 699999999865 699999999998
No 123
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=30.05 E-value=93 Score=22.22 Aligned_cols=36 Identities=28% Similarity=0.327 Sum_probs=28.6
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEcc
Q 033530 7 LMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKT 42 (117)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~d 42 (117)
|.+..|..|.|-+++-..-+|.|+-+|+.+=+.+.+
T Consensus 100 Ld~~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrIte 135 (136)
T COG1886 100 LDKLAGEPVDILVNGRLIGRGEVVVVDDKFGVRITE 135 (136)
T ss_pred cCCcCCCceEEEECCEEEEEEeEEEECCeEEEEEEe
Confidence 446678888888888889999999999887766643
No 124
>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=29.53 E-value=1.1e+02 Score=23.02 Aligned_cols=34 Identities=21% Similarity=0.201 Sum_probs=30.5
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccceEEccEE
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKTVK 44 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~ 44 (117)
..-+|.|.+.||.++.|-+.+++.--|.+|.-+.
T Consensus 28 ~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 28 NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 5678999999999999999999999999987655
No 125
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.94 E-value=70 Score=24.69 Aligned_cols=23 Identities=22% Similarity=0.557 Sum_probs=19.5
Q ss_pred hcCCCEEEEE-EcCCcEEEEEEEE
Q 033530 9 KLNNETVSIE-LKNGTIVHGTITG 31 (117)
Q Consensus 9 ~l~gk~V~Ve-Lkng~~~~G~L~~ 31 (117)
..+|..|.|+ +.+|+.++|++.+
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeC
Confidence 4678999999 9999999998865
No 126
>PF05037 DUF669: Protein of unknown function (DUF669); InterPro: IPR007731 This entry is represented by Streptococcus phage Sfi11, Gp151. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=27.28 E-value=44 Score=23.71 Aligned_cols=27 Identities=22% Similarity=0.320 Sum_probs=22.2
Q ss_pred hhHHHhhcCCCEEEEEEcCC-cEEEEEE
Q 033530 3 LVRFLMKLNNETVSIELKNG-TIVHGTI 29 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng-~~~~G~L 29 (117)
|-.++..+.|+.+.|.++.+ ..+.|.-
T Consensus 94 l~~~~~~l~gk~l~V~v~~~~~e~nGk~ 121 (141)
T PF05037_consen 94 LEQFLNQLLGKPLRVTVKWEENEYNGKT 121 (141)
T ss_pred HHHHHHHHcCCeeEEEecccccCCCCcE
Confidence 45678899999999999988 7777753
No 127
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=27.11 E-value=89 Score=23.62 Aligned_cols=26 Identities=19% Similarity=0.406 Sum_probs=22.5
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEec
Q 033530 8 MKLNNETVSIELKNGTIVHGTITGVD 33 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D 33 (117)
..++|+.|.|.+...+.+.|.+.+++
T Consensus 24 ~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 24 KDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp GGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 45899999999998899999999885
No 128
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=26.61 E-value=2.3e+02 Score=19.90 Aligned_cols=57 Identities=14% Similarity=0.099 Sum_probs=39.9
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccc-eEEccEEEEeCCCCceeeceEEEecCeEEEEEc
Q 033530 11 NNETVSIELKNGTIVHGTITGVDISMN-THLKTVKLTLKGKNPVNLDHLSVRGNNIRYYIL 70 (117)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MN-l~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~l 70 (117)
.|-.|.|.--...-.+|.+..+|..-| +..+.+....++|.. -.+-|.-+||.++.|
T Consensus 44 kGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k~~G~~---~e~pIh~SnV~l~~l 101 (114)
T TIGR01080 44 KGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEKVNGTE---VPVPIHPSNVMITKL 101 (114)
T ss_pred cCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEECCCCeE---EEeeechHHeEEEec
Confidence 467777776666677899999996655 777888766666522 334477777777644
No 129
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=25.77 E-value=77 Score=20.11 Aligned_cols=23 Identities=35% Similarity=0.358 Sum_probs=18.1
Q ss_pred EEEEEEEEecc-ccceEEccEEEE
Q 033530 24 IVHGTITGVDI-SMNTHLKTVKLT 46 (117)
Q Consensus 24 ~~~G~L~~~D~-~MNl~L~da~~~ 46 (117)
..+|++.++|. .|-|.|+|-.-+
T Consensus 4 ~veG~I~~id~~~~titLdDGksy 27 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSY 27 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEE
Confidence 46899999995 478999886543
No 130
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=25.52 E-value=1.4e+02 Score=22.76 Aligned_cols=32 Identities=22% Similarity=0.198 Sum_probs=27.9
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEecc
Q 033530 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDI 34 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~ 34 (117)
+...|+.-.|..|.|-.-+|..|.|++..+|.
T Consensus 24 l~~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~ 55 (234)
T PRK11713 24 LVRVLRLKEGDELRLFDGDGGEYLAEITEIGK 55 (234)
T ss_pred HHhhccCCCCCEEEEEeCCCCEEEEEEEEecC
Confidence 35677888999999988889999999999986
No 131
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=24.99 E-value=1e+02 Score=20.67 Aligned_cols=23 Identities=26% Similarity=0.518 Sum_probs=18.2
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEE
Q 033530 7 LMKLNNETVSIELKNGTIVHGTI 29 (117)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L 29 (117)
|..+-.-+++.+||+|..++|+-
T Consensus 18 lACl~hl~l~L~lkdGev~~a~A 40 (84)
T COG4568 18 LACLHHLPLTLELKDGEVLQAKA 40 (84)
T ss_pred HHHhhhceEEEEEcCCeEEEEEe
Confidence 33445668999999999999964
No 132
>cd00540 AAG Alkyladenine DNA glycosylase (AAG), also known as 3-methyladenine DNA glycosylase, catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site. AAG bends DNA by intercalating between the base pairs, causing the damaged base to flip out of the double helix and into the enzyme active site for cleavage. Although AAG represents one of six DNA glycosylase classes, it lacks the helix-hairpin-helix active site motif associated with the other BER glycosylases and is structurally quite distinct from them.
Probab=23.74 E-value=1.4e+02 Score=22.66 Aligned_cols=32 Identities=19% Similarity=0.281 Sum_probs=26.2
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccc
Q 033530 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMN 37 (117)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MN 37 (117)
.+=+.|+|+.+.-++. |..+.|.+++...|+-
T Consensus 8 ~vA~~LLGk~Lv~~~~-~~~~~grIvEtEAY~G 39 (179)
T cd00540 8 EVARDLLGKVLVRRLP-GGILSGRIVETEAYLG 39 (179)
T ss_pred HHHHHhCCCEEEEECC-CCEEEEEEEEEeccCC
Confidence 4457899999987775 6689999999999964
No 133
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=22.96 E-value=1.2e+02 Score=17.94 Aligned_cols=20 Identities=30% Similarity=0.444 Sum_probs=13.9
Q ss_pred EEEEEEEeccccceEEccEE
Q 033530 25 VHGTITGVDISMNTHLKTVK 44 (117)
Q Consensus 25 ~~G~L~~~D~~MNl~L~da~ 44 (117)
..|+-.++|+...+.|++..
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~ 29 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDD 29 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS
T ss_pred cceeEEeeccccceEEEeCC
Confidence 67999999999999998754
No 134
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=21.99 E-value=2.2e+02 Score=20.82 Aligned_cols=25 Identities=24% Similarity=0.384 Sum_probs=19.2
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEeccc
Q 033530 8 MKLNNETVSIELKNGTIVHGTITGVDIS 35 (117)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~~ 35 (117)
.+++||.|.+ .+| .+.|++.++.-+
T Consensus 93 ~slIGk~V~~--~~~-~~~G~V~sV~~~ 117 (140)
T PRK06009 93 EGLIGRTVTS--ADG-SITGVVKSVTVY 117 (140)
T ss_pred HHhcCCEEEe--cCC-cEEEEEEEEEEe
Confidence 3589999985 455 689999998743
No 135
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=20.98 E-value=2.2e+02 Score=17.56 Aligned_cols=33 Identities=15% Similarity=0.195 Sum_probs=22.1
Q ss_pred CCCEEEEEEcCC----cEEEEEEEEeccccceEEccE
Q 033530 11 NNETVSIELKNG----TIVHGTITGVDISMNTHLKTV 43 (117)
Q Consensus 11 ~gk~V~VeLkng----~~~~G~L~~~D~~MNl~L~da 43 (117)
.|++|.|++.++ ..|.-++.++++.-.+.+.-.
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~P 39 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISMP 39 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE--
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEcC
Confidence 689999999554 259999999997755554433
No 136
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=20.30 E-value=2e+02 Score=22.06 Aligned_cols=39 Identities=23% Similarity=0.286 Sum_probs=30.5
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccc-cceEEc
Q 033530 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDIS-MNTHLK 41 (117)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~-MNl~L~ 41 (117)
+...|+.-.|..|.|-.-+|..|.+++..++.. ..+.+.
T Consensus 26 l~~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i~ 65 (240)
T TIGR00046 26 LVRVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCELL 65 (240)
T ss_pred HHHcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEEE
Confidence 346778889999999888899999999998854 344443
No 137
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=20.16 E-value=2.7e+02 Score=24.06 Aligned_cols=41 Identities=15% Similarity=0.047 Sum_probs=32.8
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEE
Q 033530 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKL 45 (117)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~ 45 (117)
..++.++.||.|+- =|+|++++++|.+-|.-.-+.+.+-++
T Consensus 74 ~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~ 114 (421)
T COG5316 74 GKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVE 114 (421)
T ss_pred hhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEE
Confidence 45788899999999 799999999999998766665555443
Done!