Query psy6026
Match_columns 98
No_of_seqs 113 out of 1016
Neff 6.7
Searched_HMMs 46136
Date Sat Aug 17 00:38:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6026.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6026hhsearch_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 6.1E-28 1.3E-32 154.5 9.5 86 5-92 1-87 (90)
2 cd01725 LSm2 The eukaryotic Sm 100.0 1.2E-27 2.6E-32 150.4 9.8 80 5-84 1-80 (81)
3 cd01721 Sm_D3 The eukaryotic S 99.9 4.6E-27 9.9E-32 144.0 10.3 70 6-77 1-70 (70)
4 cd01723 LSm4 The eukaryotic Sm 99.9 4.7E-27 1E-31 145.9 9.7 76 5-81 1-76 (76)
5 cd01733 LSm10 The eukaryotic S 99.9 2E-25 4.3E-30 139.5 10.3 70 5-76 9-78 (78)
6 KOG3448|consensus 99.9 1.6E-24 3.4E-29 136.9 9.9 92 4-95 1-92 (96)
7 cd01726 LSm6 The eukaryotic Sm 99.9 1.7E-24 3.6E-29 131.5 9.2 67 6-74 1-67 (67)
8 cd01722 Sm_F The eukaryotic Sm 99.9 1.6E-23 3.4E-28 127.6 9.2 68 5-74 1-68 (68)
9 PRK00737 small nuclear ribonuc 99.9 2.4E-23 5.2E-28 128.1 9.9 69 4-74 3-71 (72)
10 KOG3293|consensus 99.9 1.6E-23 3.5E-28 139.2 6.9 88 4-92 1-88 (134)
11 cd01731 archaeal_Sm1 The archa 99.9 8.2E-23 1.8E-27 124.2 9.5 67 6-74 1-67 (68)
12 cd01732 LSm5 The eukaryotic Sm 99.9 8.3E-23 1.8E-27 127.1 9.6 71 3-74 1-73 (76)
13 COG1958 LSM1 Small nuclear rib 99.9 3.3E-21 7.3E-26 120.1 9.5 73 3-75 5-79 (79)
14 cd01719 Sm_G The eukaryotic Sm 99.9 3.2E-21 6.9E-26 118.8 9.1 70 6-77 1-70 (72)
15 PF01423 LSM: LSM domain ; In 99.9 3.9E-21 8.4E-26 115.7 8.8 66 9-75 2-67 (67)
16 smart00651 Sm snRNP Sm protein 99.9 3.4E-21 7.4E-26 115.8 8.5 67 8-75 1-67 (67)
17 cd01730 LSm3 The eukaryotic Sm 99.8 1.6E-20 3.4E-25 118.1 8.9 69 6-74 2-81 (82)
18 KOG3172|consensus 99.8 1.4E-20 3.1E-25 122.7 7.0 86 1-88 1-86 (119)
19 cd00600 Sm_like The eukaryotic 99.8 5E-20 1.1E-24 109.3 8.8 63 10-74 1-63 (63)
20 cd01720 Sm_D2 The eukaryotic S 99.8 5E-20 1.1E-24 117.2 9.0 71 5-75 2-85 (87)
21 cd01729 LSm7 The eukaryotic Sm 99.8 1.9E-19 4E-24 113.1 9.2 70 8-77 5-80 (81)
22 cd01718 Sm_E The eukaryotic Sm 99.8 1E-18 2.3E-23 109.4 8.9 70 4-74 5-78 (79)
23 KOG3428|consensus 99.8 1.2E-18 2.6E-23 113.7 9.1 90 4-96 1-91 (109)
24 cd01728 LSm1 The eukaryotic Sm 99.8 2.4E-18 5.3E-23 106.5 9.4 70 6-75 3-73 (74)
25 cd01717 Sm_B The eukaryotic Sm 99.8 2.7E-18 5.8E-23 107.1 8.5 68 8-75 3-78 (79)
26 KOG3482|consensus 99.8 2E-18 4.4E-23 105.6 6.8 72 2-75 5-76 (79)
27 cd01727 LSm8 The eukaryotic Sm 99.8 1.1E-17 2.3E-22 103.3 9.3 69 8-77 2-73 (74)
28 KOG1783|consensus 99.7 1.7E-19 3.8E-24 110.3 0.7 72 4-77 5-76 (77)
29 cd06168 LSm9 The eukaryotic Sm 99.7 2.6E-17 5.6E-22 102.2 9.2 68 8-75 3-74 (75)
30 PTZ00138 small nuclear ribonuc 99.7 1.7E-16 3.6E-21 101.4 9.2 72 4-76 13-88 (89)
31 KOG1780|consensus 99.7 9.8E-17 2.1E-21 98.4 6.2 66 9-76 8-73 (77)
32 KOG3460|consensus 99.6 3.7E-16 8E-21 97.9 2.2 73 5-77 5-88 (91)
33 KOG1775|consensus 99.6 1.7E-15 3.7E-20 93.5 3.5 73 2-75 4-78 (84)
34 KOG1784|consensus 99.4 5.4E-13 1.2E-17 84.9 3.6 88 8-96 3-93 (96)
35 KOG1774|consensus 99.2 1.2E-11 2.7E-16 77.3 4.4 67 7-76 18-86 (88)
36 KOG1781|consensus 99.1 9E-12 2E-16 80.3 -0.4 70 9-78 21-96 (108)
37 KOG1782|consensus 99.1 3.5E-11 7.7E-16 80.2 1.1 70 8-78 12-83 (129)
38 KOG3168|consensus 98.8 8.1E-10 1.8E-14 77.3 0.1 76 1-78 1-85 (177)
39 PF14438 SM-ATX: Ataxin 2 SM d 98.3 3.3E-06 7.2E-11 51.9 5.9 46 7-52 4-52 (77)
40 KOG3459|consensus 98.3 1.5E-07 3.3E-12 61.8 -0.4 69 6-74 25-106 (114)
41 PF12701 LSM14: Scd6-like Sm d 97.9 0.00015 3.2E-09 46.9 7.9 68 11-78 4-79 (96)
42 cd01739 LSm11_C The eukaryotic 97.5 0.00012 2.7E-09 44.1 2.8 37 15-51 8-48 (66)
43 cd01736 LSm14_N LSm14 (also kn 97.4 0.0016 3.4E-08 40.3 7.1 61 12-72 3-72 (74)
44 PF11095 Gemin7: Gem-associate 97.3 0.006 1.3E-07 38.3 8.9 65 5-76 14-79 (80)
45 PF02237 BPL_C: Biotin protein 96.7 0.013 2.8E-07 32.9 6.4 47 14-66 2-48 (48)
46 cd01716 Hfq Hfq, an abundant, 96.7 0.0048 1E-07 36.8 4.7 37 9-45 3-41 (61)
47 TIGR02383 Hfq RNA chaperone Hf 96.6 0.0055 1.2E-07 36.6 4.6 37 9-45 7-45 (61)
48 PRK00395 hfq RNA-binding prote 96.4 0.0084 1.8E-07 37.5 4.6 38 8-45 10-49 (79)
49 PF10842 DUF2642: Protein of u 96.2 0.056 1.2E-06 32.7 7.1 52 7-74 13-65 (66)
50 COG1923 Hfq Uncharacterized ho 96.1 0.011 2.5E-07 36.7 3.9 35 7-41 9-45 (77)
51 KOG1073|consensus 95.8 0.027 5.9E-07 44.1 5.9 68 11-78 5-81 (361)
52 cd01735 LSm12_N LSm12 belongs 95.1 0.21 4.6E-06 29.7 6.8 33 13-45 4-36 (61)
53 PF06372 Gemin6: Gemin6 protei 94.4 0.22 4.8E-06 35.2 6.6 61 9-78 11-72 (166)
54 PRK14638 hypothetical protein; 93.9 0.12 2.7E-06 35.6 4.4 36 8-44 93-128 (150)
55 PRK14091 RNA-binding protein H 93.8 0.15 3.1E-06 36.0 4.6 38 8-45 95-134 (165)
56 PRK14091 RNA-binding protein H 93.1 0.21 4.5E-06 35.3 4.5 38 8-45 15-54 (165)
57 PRK14639 hypothetical protein; 93.1 0.21 4.5E-06 34.1 4.4 35 8-43 81-115 (140)
58 PRK02001 hypothetical protein; 92.9 0.23 5E-06 34.5 4.4 30 9-38 84-113 (152)
59 cd01734 YlxS_C YxlS is a Bacil 90.6 0.66 1.4E-05 28.6 4.3 31 8-38 18-52 (83)
60 PRK14644 hypothetical protein; 90.3 0.62 1.3E-05 31.7 4.3 35 9-44 79-117 (136)
61 PRK14640 hypothetical protein; 89.7 0.75 1.6E-05 31.7 4.4 35 8-43 90-128 (152)
62 COG0779 Uncharacterized protei 89.6 1.1 2.4E-05 31.2 5.2 33 7-39 91-127 (153)
63 PRK14642 hypothetical protein; 89.0 0.82 1.8E-05 33.1 4.3 35 8-43 93-140 (197)
64 PRK14633 hypothetical protein; 88.7 0.96 2.1E-05 31.1 4.3 35 8-43 87-125 (150)
65 PRK14645 hypothetical protein; 87.4 1.1 2.5E-05 31.0 4.1 30 8-38 95-124 (154)
66 PRK14636 hypothetical protein; 87.0 1.3 2.7E-05 31.5 4.2 30 8-37 91-124 (176)
67 PRK14632 hypothetical protein; 86.9 1.4 2.9E-05 31.1 4.3 36 8-44 91-133 (172)
68 PRK14643 hypothetical protein; 86.5 1.4 3.1E-05 30.8 4.2 36 8-43 97-137 (164)
69 PRK00092 ribosome maturation p 86.4 1.6 3.4E-05 30.0 4.3 30 8-37 91-124 (154)
70 PRK14634 hypothetical protein; 86.2 1.6 3.4E-05 30.3 4.3 35 8-43 93-131 (155)
71 PRK14646 hypothetical protein; 85.3 1.8 4E-05 29.9 4.3 35 8-43 93-131 (155)
72 PF02576 DUF150: Uncharacteris 85.3 1.3 2.8E-05 29.8 3.4 30 8-37 80-113 (141)
73 PRK14647 hypothetical protein; 84.8 2 4.3E-05 29.8 4.3 30 8-37 92-130 (159)
74 PRK06955 biotin--protein ligas 84.0 6.4 0.00014 29.7 7.1 51 12-68 246-296 (300)
75 PRK14637 hypothetical protein; 83.3 2.4 5.3E-05 29.3 4.1 35 8-43 91-126 (151)
76 PRK09618 flgD flagellar basal 82.9 2.3 4.9E-05 29.3 3.8 26 11-36 88-113 (142)
77 PRK14631 hypothetical protein; 82.3 3 6.4E-05 29.5 4.3 29 8-36 110-142 (174)
78 PRK14641 hypothetical protein; 81.4 2.8 6.1E-05 29.7 4.0 29 8-36 97-129 (173)
79 PRK08330 biotin--protein ligas 81.3 10 0.00022 27.5 7.0 33 12-45 185-218 (236)
80 PRK11886 bifunctional biotin-- 79.9 11 0.00023 28.5 7.0 48 13-67 270-317 (319)
81 PF03614 Flag1_repress: Repres 79.2 2.3 5E-05 29.8 2.8 24 14-37 119-142 (165)
82 PRK13325 bifunctional biotin-- 76.0 14 0.00031 30.7 7.1 33 13-45 276-308 (592)
83 COG0340 BirA Biotin-(acetyl-Co 75.3 20 0.00042 26.5 7.0 52 11-67 186-237 (238)
84 PF11607 DUF3247: Protein of u 75.0 4.9 0.00011 26.0 3.3 18 16-33 29-46 (101)
85 PF07073 ROF: Modulator of Rho 74.3 3 6.4E-05 26.0 2.1 22 10-31 12-33 (80)
86 PRK14630 hypothetical protein; 73.5 6.9 0.00015 26.7 4.0 29 8-37 90-118 (143)
87 TIGR00121 birA_ligase birA, bi 73.5 16 0.00035 26.4 6.1 32 12-44 190-221 (237)
88 PRK14635 hypothetical protein; 71.0 14 0.0003 25.7 5.1 35 8-43 92-131 (162)
89 PRK11911 flgD flagellar basal 68.9 9.1 0.0002 26.3 3.7 27 11-37 89-115 (140)
90 PTZ00275 biotin-acetyl-CoA-car 63.7 44 0.00096 25.1 6.9 32 13-45 235-266 (285)
91 PRK11625 Rho-binding antitermi 63.5 34 0.00075 21.4 6.1 23 11-33 19-41 (84)
92 PF10618 Tail_tube: Phage tail 63.1 12 0.00027 24.7 3.4 27 5-31 64-90 (119)
93 PRK10898 serine endoprotease; 56.9 28 0.0006 26.9 4.9 32 15-46 101-132 (353)
94 PF03614 Flag1_repress: Repres 56.1 21 0.00045 25.1 3.7 34 14-47 28-61 (165)
95 PRK06792 flgD flagellar basal 54.5 21 0.00046 25.8 3.6 26 11-36 114-139 (190)
96 PRK10139 serine endoprotease; 52.9 34 0.00073 27.5 4.9 32 15-46 114-145 (455)
97 TIGR02038 protease_degS peripl 51.7 37 0.00081 26.1 4.9 32 16-47 102-133 (351)
98 TIGR00567 3mg DNA-3-methyladen 50.1 43 0.00093 24.1 4.6 35 6-40 10-44 (192)
99 TIGR02603 CxxCH_TIGR02603 puta 49.8 28 0.00062 23.0 3.5 20 17-36 59-78 (133)
100 smart00333 TUDOR Tudor domain. 49.5 43 0.00093 18.2 4.2 25 14-38 5-29 (57)
101 TIGR03170 flgA_cterm flagella 48.9 25 0.00053 22.6 3.1 23 12-34 93-116 (122)
102 PRK10942 serine endoprotease; 48.6 42 0.00091 27.1 4.9 32 15-46 135-166 (473)
103 PF02245 Pur_DNA_glyco: Methyl 47.5 41 0.00089 24.0 4.2 34 6-40 9-42 (184)
104 PF13437 HlyD_3: HlyD family s 47.4 55 0.0012 20.0 4.4 34 4-37 41-78 (105)
105 cd04479 RPA3 RPA3: A subfamily 47.4 49 0.0011 20.9 4.2 24 7-38 7-30 (101)
106 PRK06789 flagellar motor switc 46.1 54 0.0012 20.1 4.0 36 10-45 36-71 (74)
107 PRK07018 flgA flagellar basal 42.5 31 0.00067 25.1 3.0 24 12-35 204-228 (235)
108 TIGR02037 degP_htrA_DO peripla 42.1 58 0.0013 25.5 4.7 31 16-46 82-112 (428)
109 PRK08477 biotin--protein ligas 40.9 93 0.002 22.4 5.3 37 10-47 170-206 (211)
110 PF09465 LBR_tudor: Lamin-B re 40.9 65 0.0014 18.7 3.6 26 13-38 7-33 (55)
111 PF05954 Phage_GPD: Phage late 40.3 45 0.00097 23.9 3.6 26 11-36 24-49 (292)
112 PF14485 DUF4431: Domain of un 39.9 30 0.00066 19.3 2.1 15 7-21 11-25 (48)
113 PF06257 DUF1021: Protein of u 37.7 89 0.0019 19.2 4.1 30 7-36 9-42 (76)
114 COG4568 Rof Transcriptional an 37.1 53 0.0011 20.6 3.0 23 10-32 18-40 (84)
115 PF14563 DUF4444: Domain of un 35.7 63 0.0014 17.8 2.8 20 28-47 10-29 (42)
116 PF05037 DUF669: Protein of un 34.2 27 0.00059 23.4 1.5 26 6-31 94-120 (141)
117 COG1886 FliN Flagellar motor s 33.6 97 0.0021 20.8 4.2 35 11-45 101-135 (136)
118 KOG4401|consensus 33.3 45 0.00098 24.0 2.5 35 13-47 9-43 (184)
119 PRK12617 flgA flagellar basal 31.7 60 0.0013 23.6 3.1 23 12-34 183-206 (214)
120 PF07076 DUF1344: Protein of u 31.7 51 0.0011 19.6 2.2 23 27-49 4-27 (61)
121 PRK06005 flgA flagellar basal 31.5 66 0.0014 22.2 3.1 23 12-34 128-151 (160)
122 cd00540 AAG Alkyladenine DNA g 31.3 1.2E+02 0.0027 21.5 4.6 34 6-40 6-39 (179)
123 PRK10708 hypothetical protein; 30.7 65 0.0014 19.0 2.5 26 14-39 3-28 (62)
124 PF11743 DUF3301: Protein of u 30.1 97 0.0021 19.6 3.5 28 48-77 69-96 (97)
125 PRK08515 flgA flagellar basal 30.0 83 0.0018 22.8 3.6 23 12-34 193-215 (222)
126 COG1363 FrvX Cellulase M and r 29.5 68 0.0015 25.2 3.2 23 11-33 93-115 (355)
127 PF14153 Spore_coat_CotO: Spor 29.3 83 0.0018 22.5 3.4 32 7-38 123-157 (185)
128 cd01737 LSm16_N LSm16 belongs 27.6 1.2E+02 0.0026 18.0 3.3 55 12-71 3-59 (62)
129 PRK12618 flgA flagellar basal 27.4 87 0.0019 21.2 3.1 23 12-34 109-132 (141)
130 COG5316 Uncharacterized conser 27.2 1.4E+02 0.0029 24.2 4.5 43 4-47 71-113 (421)
131 PRK06804 flgA flagellar basal 27.0 80 0.0017 23.7 3.1 24 12-35 230-254 (261)
132 PF10781 DSRB: Dextransucrase 27.0 74 0.0016 18.8 2.3 26 14-39 3-28 (62)
133 TIGR00999 8a0102 Membrane Fusi 26.9 1.4E+02 0.003 21.2 4.3 27 14-40 141-167 (265)
134 PRK15493 5-methylthioadenosine 26.3 1.4E+02 0.003 23.4 4.5 37 39-75 1-37 (435)
135 PF13861 FLgD_tudor: FlgD Tudo 24.2 1.5E+02 0.0032 16.8 3.3 10 12-21 9-18 (61)
136 COG4466 Veg Uncharacterized pr 24.1 78 0.0017 19.8 2.2 30 7-36 11-44 (80)
137 PF02736 Myosin_N: Myosin N-te 23.3 1.2E+02 0.0026 16.1 2.6 18 11-28 19-36 (42)
138 PF13144 SAF_2: SAF-like 22.4 1.4E+02 0.003 20.6 3.5 23 12-34 167-190 (196)
139 KOG3493|consensus 21.6 78 0.0017 19.2 1.7 20 9-28 5-24 (73)
140 cd01343 PL1_Passenger_AT Perta 21.6 3.1E+02 0.0066 20.0 5.3 51 17-73 74-125 (233)
141 COG0265 DegQ Trypsin-like seri 21.3 2.1E+02 0.0045 21.6 4.5 32 15-46 95-126 (347)
142 PRK06009 flgD flagellar basal 21.2 1.4E+02 0.0029 20.5 3.1 24 11-37 93-116 (140)
143 TIGR03361 VI_Rhs_Vgr type VI s 20.8 1.7E+02 0.0036 23.5 4.0 27 10-36 42-72 (513)
144 PF01556 CTDII: DnaJ C termina 20.6 53 0.0011 19.6 0.9 26 4-29 5-30 (81)
145 PF08661 Rep_fac-A_3: Replicat 20.0 1.7E+02 0.0036 18.5 3.2 22 7-36 10-31 (109)
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=99.95 E-value=6.1e-28 Score=154.45 Aligned_cols=86 Identities=28% Similarity=0.490 Sum_probs=76.4
Q ss_pred chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc-ccccH
Q psy6026 5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD-EVDTQ 83 (98)
Q Consensus 5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~-~~d~~ 83 (98)
.|+.||+++.|++|+|+||||.+|+|+|.++|+|||++|+||+++.+++. ...++.+||||++|+||++||. ..|..
T Consensus 1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~--~~~~~~v~IRG~nI~yi~lPd~l~~~~~ 78 (90)
T cd01724 1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRN--PVPLDTLSIRGNNIRYFILPDSLNLDTL 78 (90)
T ss_pred CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCc--eeEcceEEEeCCEEEEEEcCCcCCcchh
Confidence 37899999999999999999999999999999999999999999988765 4589999999999999999998 47777
Q ss_pred HhHHHHHHH
Q psy6026 84 LLQDATRKE 92 (98)
Q Consensus 84 ~~~~~~r~~ 92 (98)
++++++...
T Consensus 79 l~~~~~~~~ 87 (90)
T cd01724 79 LVDSTPKPK 87 (90)
T ss_pred hhhcCCccc
Confidence 777754433
No 2
>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=99.95 E-value=1.2e-27 Score=150.35 Aligned_cols=80 Identities=88% Similarity=1.344 Sum_probs=72.4
Q ss_pred chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccccHH
Q psy6026 5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQL 84 (98)
Q Consensus 5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~~ 84 (98)
+|+.||+++.|++|+|+||||.+|+|+|.++|.|||++|+||+++.+++......++++||||++|+||++||+.+|.+.
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~~~ 80 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDTEL 80 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcCccc
Confidence 58999999999999999999999999999999999999999999887654334567999999999999999999888764
No 3
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.95 E-value=4.6e-27 Score=144.02 Aligned_cols=70 Identities=30% Similarity=0.468 Sum_probs=66.3
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026 6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG 77 (98)
Q Consensus 6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~ 77 (98)
|+++|+++.|++|+|+||||.+|+|+|.++|+|||++|+||+++.++|+ ...++++||||++|+||++||
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~--~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR--VSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc--EeEcCcEEEeCCEEEEEEeCC
Confidence 8899999999999999999999999999999999999999999888875 357899999999999999996
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=99.95 E-value=4.7e-27 Score=145.92 Aligned_cols=76 Identities=30% Similarity=0.604 Sum_probs=69.5
Q ss_pred chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccc
Q psy6026 5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVD 81 (98)
Q Consensus 5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d 81 (98)
.|++||+++.|++|+|+||||++|+|+|.+||+|||++|+||+++.++|.. ...++.+||||++|+||++|++.+|
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~-~~~~~~v~IRG~~I~~i~~p~~~~~ 76 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDK-FWKMPECYIRGNTIKYLRVPDEIID 76 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcE-eeeCCcEEEeCCEEEEEEcCHHHCC
Confidence 599999999999999999999999999999999999999999999887752 3568999999999999999987543
No 5
>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=2e-25 Score=139.48 Aligned_cols=70 Identities=31% Similarity=0.660 Sum_probs=65.9
Q ss_pred chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026 5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP 76 (98)
Q Consensus 5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p 76 (98)
.+.+||+++.|++|+|+||||.+|+|+|.++|+|||++|+||+++++++.+ ..++.+||||++|+||++|
T Consensus 9 tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~--~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 9 TLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQ--VQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred hHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCce--eECCcEEEECCEEEEEEcC
Confidence 578999999999999999999999999999999999999999999887753 4789999999999999998
No 6
>KOG3448|consensus
Probab=99.92 E-value=1.6e-24 Score=136.85 Aligned_cols=92 Identities=89% Similarity=1.351 Sum_probs=88.1
Q ss_pred cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccccH
Q psy6026 4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQ 83 (98)
Q Consensus 4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~ 83 (98)
|+.++|+++++|+.|.|+||||..+.|+|.++|+|+|+.|+|..+++++..|+......+||||+.|+||++|.+..|.+
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 78899999999999999999999999999999999999999999999998888888999999999999999999999999
Q ss_pred HhHHHHHHHHhh
Q psy6026 84 LLQDATRKEAVN 95 (98)
Q Consensus 84 ~~~~~~r~~~~~ 95 (98)
.++++.|.|.-.
T Consensus 81 ll~da~R~e~~~ 92 (96)
T KOG3448|consen 81 LLQDAARREAIL 92 (96)
T ss_pred HHHHHHHHHHHh
Confidence 999999998753
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=99.92 E-value=1.7e-24 Score=131.49 Aligned_cols=67 Identities=31% Similarity=0.504 Sum_probs=61.9
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026 6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ 74 (98)
Q Consensus 6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 74 (98)
|++||++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++. ...++.+||||++|+||+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~--~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQL--KNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCce--eeEeCCEEEECCEEEEEC
Confidence 8999999999999999999999999999999999999999998776543 458999999999999984
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=99.90 E-value=1.6e-23 Score=127.56 Aligned_cols=68 Identities=32% Similarity=0.424 Sum_probs=61.8
Q ss_pred chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026 5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ 74 (98)
Q Consensus 5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 74 (98)
.|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||++...++. ...+|.+||||++|+||.
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~--~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKS--TGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCcc--ccCcCcEEEECCEEEEEC
Confidence 48999999999999999999999999999999999999999998765433 357999999999999984
No 9
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.90 E-value=2.4e-23 Score=128.08 Aligned_cols=69 Identities=22% Similarity=0.297 Sum_probs=63.5
Q ss_pred cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026 4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ 74 (98)
Q Consensus 4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 74 (98)
..|+.+|++++|++|.|+|+||++|+|+|.+||+|||++|+||+++..++. ...++.+||||++|++|.
T Consensus 3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEV--VRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCe--EeEcCcEEEeCCEEEEEc
Confidence 589999999999999999999999999999999999999999999865532 458999999999999986
No 10
>KOG3293|consensus
Probab=99.89 E-value=1.6e-23 Score=139.22 Aligned_cols=88 Identities=25% Similarity=0.525 Sum_probs=79.4
Q ss_pred cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCcccccH
Q psy6026 4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQ 83 (98)
Q Consensus 4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~ 83 (98)
|+|+++|+...|+++.||||||.+|.|.|.+||.+|||.|.+++++.++|.. +..+++++|||++|+|+.+||+.+|..
T Consensus 1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdk-f~r~pEcYirGttIkylri~d~iid~v 79 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDK-FFRMPECYIRGTTIKYLRIPDEIIDKV 79 (134)
T ss_pred CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCc-eeecceeEEecceeEEEeccHHHHHHH
Confidence 7999999999999999999999999999999999999999999999998864 578999999999999999999988777
Q ss_pred HhHHHHHHH
Q psy6026 84 LLQDATRKE 92 (98)
Q Consensus 84 ~~~~~~r~~ 92 (98)
.-+.....+
T Consensus 80 kee~~~~~~ 88 (134)
T KOG3293|consen 80 KEECVSNNR 88 (134)
T ss_pred HHHHHHhcc
Confidence 655444433
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=99.89 E-value=8.2e-23 Score=124.21 Aligned_cols=67 Identities=28% Similarity=0.377 Sum_probs=62.1
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026 6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ 74 (98)
Q Consensus 6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 74 (98)
|+++|++++|++|.|+|+||+.|.|+|.+||+|||++|+||+++..++. ...++.+||||++|.||.
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~--~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEP--VRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCe--EeEcCcEEEeCCEEEEEc
Confidence 8899999999999999999999999999999999999999999876543 457999999999999986
No 12
>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=99.89 E-value=8.3e-23 Score=127.07 Aligned_cols=71 Identities=21% Similarity=0.454 Sum_probs=63.9
Q ss_pred ccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEEC--CCCCcceeecceEEEEcCeEEEEe
Q psy6026 3 RLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTD--PDKYPHMLSVKNCFIRGSVVRYVQ 74 (98)
Q Consensus 3 ~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~--~~~~~~~~~~~~v~IRG~~I~~I~ 74 (98)
+|+|+++|+++++++|.|+|++|+.|.|+|.+||+|||++|+||++.. +++. ....++.++|||++|.+|+
T Consensus 1 ~~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~-~~~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 1 QLLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGR-KITKLDQILLNGNNICMLV 73 (76)
T ss_pred CcChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCc-eeeEcCeEEEeCCeEEEEE
Confidence 589999999999999999999999999999999999999999999864 3322 2357999999999999998
No 13
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.86 E-value=3.3e-21 Score=120.14 Aligned_cols=73 Identities=33% Similarity=0.384 Sum_probs=62.2
Q ss_pred ccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC-CCCc-ceeecceEEEEcCeEEEEec
Q psy6026 3 RLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP-DKYP-HMLSVKNCFIRGSVVRYVQL 75 (98)
Q Consensus 3 ~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~-~~~~-~~~~~~~v~IRG~~I~~I~~ 75 (98)
.+.|+++|+.++|++|.|+|+||++|.|+|.+||+|||++|+||+++.. ++.. .....+.++|||++|++|..
T Consensus 5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 4568999999999999999999999999999999999999999999863 3321 12244599999999999863
No 14
>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=99.86 E-value=3.2e-21 Score=118.76 Aligned_cols=70 Identities=17% Similarity=0.290 Sum_probs=62.6
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026 6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG 77 (98)
Q Consensus 6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~ 77 (98)
|-++|++++||+|.|+|++|+.|.|+|.+||+|||++|+||+++..+.. ...+|.++|||++|.+|..-|
T Consensus 1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~--~~~lg~v~IRG~~I~~i~~~~ 70 (72)
T cd01719 1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGE--KNNIGMVVIRGNSIVMLEALE 70 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCc--eeEeceEEECCCEEEEEEccc
Confidence 4578999999999999999999999999999999999999998864433 468999999999999998654
No 15
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.86 E-value=3.9e-21 Score=115.71 Aligned_cols=66 Identities=44% Similarity=0.646 Sum_probs=60.5
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL 75 (98)
Q Consensus 9 ~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~ 75 (98)
+|++++|++|+|+|+||++|+|+|.+||+|||++|+||.++..++. ....++.+||||++|++|++
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-EEEEEEEEEEEGGGEEEEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-cEeECcEEEEECCEEEEEEC
Confidence 7999999999999999999999999999999999999999877642 24689999999999999985
No 16
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.86 E-value=3.4e-21 Score=115.84 Aligned_cols=67 Identities=40% Similarity=0.606 Sum_probs=60.4
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL 75 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~ 75 (98)
.+|++++|++|+|+|+||+++.|+|.+||+|||++|+||+++..++. +...++.+||||++|+||+.
T Consensus 1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~-~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE-KKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCc-EEeEeCCEEEcCCEEEEEeC
Confidence 37899999999999999999999999999999999999999876521 24689999999999999974
No 17
>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=99.84 E-value=1.6e-20 Score=118.08 Aligned_cols=69 Identities=28% Similarity=0.357 Sum_probs=60.5
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCC-----------CCcceeecceEEEEcCeEEEEe
Q psy6026 6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD-----------KYPHMLSVKNCFIRGSVVRYVQ 74 (98)
Q Consensus 6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~-----------~~~~~~~~~~v~IRG~~I~~I~ 74 (98)
|+++|+..++++|.|.|++|+.|.|+|.+||.|||++|+||.+.... .....+.+|.+||||++|.+|+
T Consensus 2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence 89999999999999999999999999999999999999999986421 1112457899999999999986
No 18
>KOG3172|consensus
Probab=99.83 E-value=1.4e-20 Score=122.69 Aligned_cols=86 Identities=27% Similarity=0.389 Sum_probs=80.7
Q ss_pred CcccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCccc
Q psy6026 1 MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGDEV 80 (98)
Q Consensus 1 ~~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~ 80 (98)
|+.-.|+.+|.+..|+-|++|+++|..|+|+|..+|++||+.|+|++.+.++|. ...++.+||||+.|+|+.+||...
T Consensus 1 ~s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~--vs~le~V~IRGS~IRFlvlPdmLK 78 (119)
T KOG3172|consen 1 MSVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR--VSQLEQVFIRGSKIRFLVLPDMLK 78 (119)
T ss_pred CccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc--ceeeeeEEEecCeEEEEECchHhh
Confidence 567789999999999999999999999999999999999999999999999986 568999999999999999999999
Q ss_pred ccHHhHHH
Q psy6026 81 DTQLLQDA 88 (98)
Q Consensus 81 d~~~~~~~ 88 (98)
++|+++..
T Consensus 79 nAPmFkk~ 86 (119)
T KOG3172|consen 79 NAPMFKKG 86 (119)
T ss_pred cCcccccc
Confidence 99999743
No 19
>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=99.83 E-value=5e-20 Score=109.33 Aligned_cols=63 Identities=38% Similarity=0.514 Sum_probs=57.7
Q ss_pred HhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026 10 FKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ 74 (98)
Q Consensus 10 L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 74 (98)
|++++|++|+|+|+||+.|.|+|.+||+|||++|+||.++.+++. ...++.+||||++|++|+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~--~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGK--KRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCc--EEECCeEEEECCEEEEEC
Confidence 578899999999999999999999999999999999999887643 468999999999999985
No 20
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.83 E-value=5e-20 Score=117.21 Aligned_cols=71 Identities=18% Similarity=0.240 Sum_probs=60.9
Q ss_pred chHHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCC-----------cceeecceEEEEcCeEE
Q psy6026 5 LFYSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKY-----------PHMLSVKNCFIRGSVVR 71 (98)
Q Consensus 5 ~p~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~-----------~~~~~~~~v~IRG~~I~ 71 (98)
-|+++|+.++ |++|.|.|++|+.+.|+|.+||.|||++|+||.++..... .....+|.+||||++|.
T Consensus 2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 4899999997 8999999999999999999999999999999998643210 12346899999999999
Q ss_pred EEec
Q psy6026 72 YVQL 75 (98)
Q Consensus 72 ~I~~ 75 (98)
+|+.
T Consensus 82 ~Is~ 85 (87)
T cd01720 82 LVLR 85 (87)
T ss_pred EEec
Confidence 9874
No 21
>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=99.81 E-value=1.9e-19 Score=113.13 Aligned_cols=70 Identities=21% Similarity=0.219 Sum_probs=59.5
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCC------cceeecceEEEEcCeEEEEecCC
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKY------PHMLSVKNCFIRGSVVRYVQLPG 77 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~------~~~~~~~~v~IRG~~I~~I~~p~ 77 (98)
.-|.+++|++|.|.|++|++|.|+|.+||+|||++|++|++...+.. .....+|.++|||++|.+|...+
T Consensus 5 ~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 5 LDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred hhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 34899999999999999999999999999999999999998643210 12457999999999999998654
No 22
>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=99.79 E-value=1e-18 Score=109.40 Aligned_cols=70 Identities=17% Similarity=0.282 Sum_probs=60.9
Q ss_pred cchHHHHhhcCCC--eEEEEEc--CCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026 4 LLFYSFFKSLVGK--DVVVELK--NDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ 74 (98)
Q Consensus 4 ~~p~~~L~~l~gk--~V~V~Lk--ng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 74 (98)
..|+..+.+++++ +|.|.|+ +|+++.|+|.+||+|||++|+||++....+. ....+|.++|||++|.+|+
T Consensus 5 ~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~-~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 5 VQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK-TRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred cCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc-eEeEcCcEEEeCCEEEEEc
Confidence 5799999999999 7888887 9999999999999999999999998753222 2357999999999999997
No 23
>KOG3428|consensus
Probab=99.78 E-value=1.2e-18 Score=113.71 Aligned_cols=90 Identities=33% Similarity=0.529 Sum_probs=81.6
Q ss_pred cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc-cccc
Q psy6026 4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD-EVDT 82 (98)
Q Consensus 4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~-~~d~ 82 (98)
|..+.||+++.+.+|+|+|+||+...|++.++|.+||..|.++..+.++ ++ ..+..++|||++|||+++||+ .+|.
T Consensus 1 mklvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~p--v~l~~lsirgnniRy~~lpD~l~ld~ 77 (109)
T KOG3428|consen 1 MKLVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EP--VRLDTLSIRGNNIRYYILPDSLNLDT 77 (109)
T ss_pred ChHHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-Cc--eeEEEEEeecceEEEEEccCCcCcce
Confidence 5678999999999999999999999999999999999999999999885 43 578999999999999999998 8888
Q ss_pred HHhHHHHHHHHhhc
Q psy6026 83 QLLQDATRKEAVNA 96 (98)
Q Consensus 83 ~~~~~~~r~~~~~~ 96 (98)
.++.+.++...++.
T Consensus 78 Llvd~~~~~~~~~~ 91 (109)
T KOG3428|consen 78 LLVDDAPRLHLRKN 91 (109)
T ss_pred eeeehhhhhhhhcc
Confidence 88888888777664
No 24
>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=99.78 E-value=2.4e-18 Score=106.51 Aligned_cols=70 Identities=24% Similarity=0.162 Sum_probs=59.4
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCC-CcceeecceEEEEcCeEEEEec
Q psy6026 6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDK-YPHMLSVKNCFIRGSVVRYVQL 75 (98)
Q Consensus 6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~-~~~~~~~~~v~IRG~~I~~I~~ 75 (98)
+...|.++++++|.|.|++|+.|.|+|.+||+|||++|+||.+....+ ......+|.++|||++|.+|..
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 467799999999999999999999999999999999999998753221 1113578999999999999874
No 25
>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=99.77 E-value=2.7e-18 Score=107.14 Aligned_cols=68 Identities=18% Similarity=0.239 Sum_probs=57.9
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCC--------CcceeecceEEEEcCeEEEEec
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDK--------YPHMLSVKNCFIRGSVVRYVQL 75 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~--------~~~~~~~~~v~IRG~~I~~I~~ 75 (98)
+-|.+++|++|.|.|+||+.+.|+|.+||+|||++|+||.++.... ......+|.+||||++|.+|.+
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 3478899999999999999999999999999999999999864211 1123579999999999999975
No 26
>KOG3482|consensus
Probab=99.76 E-value=2e-18 Score=105.59 Aligned_cols=72 Identities=29% Similarity=0.345 Sum_probs=62.9
Q ss_pred cccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026 2 ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL 75 (98)
Q Consensus 2 ~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~ 75 (98)
+-..|-+||+.+.||+|.|+||-|.+|.|+|.++|.|||+.|.+|++.-.+.. .-.+|+++||.+||.||.-
T Consensus 5 ~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~--~g~lGEilIRCNNvlyi~g 76 (79)
T KOG3482|consen 5 QPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVS--TGNLGEILIRCNNVLYIRG 76 (79)
T ss_pred ccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccc--cccceeEEEEeccEEEEec
Confidence 44568999999999999999999999999999999999999999998543321 2479999999999999953
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=99.75 E-value=1.1e-17 Score=103.30 Aligned_cols=69 Identities=25% Similarity=0.218 Sum_probs=59.5
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC---CCCcceeecceEEEEcCeEEEEecCC
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP---DKYPHMLSVKNCFIRGSVVRYVQLPG 77 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~---~~~~~~~~~~~v~IRG~~I~~I~~p~ 77 (98)
+.|+++++++|.|.|++|+.|.|+|.+||+|||++|++|.+... ++. ....+|.++|||++|.+|...|
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~-~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGV-EQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCc-eeeEeceEEECCCEEEEEEccC
Confidence 46889999999999999999999999999999999999997532 232 2357899999999999998654
No 28
>KOG1783|consensus
Probab=99.75 E-value=1.7e-19 Score=110.28 Aligned_cols=72 Identities=31% Similarity=0.461 Sum_probs=65.0
Q ss_pred cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026 4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPG 77 (98)
Q Consensus 4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~ 77 (98)
..|.+||++.+|++|.|+|.+|..|+|+|.++|.|||+.|+.+++...+.. ..+++.+||||++|.||+...
T Consensus 5 ~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql--~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 5 SMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQL--KNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcc--cccccceeeccccEEEEEecc
Confidence 468999999999999999999999999999999999999999998775443 458999999999999998753
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=99.74 E-value=2.6e-17 Score=102.15 Aligned_cols=68 Identities=16% Similarity=0.266 Sum_probs=59.5
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCC----CCcceeecceEEEEcCeEEEEec
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD----KYPHMLSVKNCFIRGSVVRYVQL 75 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~----~~~~~~~~~~v~IRG~~I~~I~~ 75 (98)
+.|++++|++|.|.|+||+.+.|+|.++|.+||++|+||.+.... .....+.+|.++|||++|..|++
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 468899999999999999999999999999999999999987532 11235689999999999999985
No 30
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.70 E-value=1.7e-16 Score=101.40 Aligned_cols=72 Identities=15% Similarity=0.225 Sum_probs=59.2
Q ss_pred cchHHHHhhcCCC--eEEEEEcC--CcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026 4 LLFYSFFKSLVGK--DVVVELKN--DVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP 76 (98)
Q Consensus 4 ~~p~~~L~~l~gk--~V~V~Lkn--g~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p 76 (98)
..|+..+.+++.. +|.|.+.+ ++++.|+|.+||+|||++|+||++...++. ....+|.++|||++|.+|+..
T Consensus 13 ~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~-~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 13 TQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN-TRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred cCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc-eeeEcCeEEEcCCEEEEEEcC
Confidence 4688889888876 57777767 489999999999999999999998754322 245899999999999999753
No 31
>KOG1780|consensus
Probab=99.68 E-value=9.8e-17 Score=98.44 Aligned_cols=66 Identities=23% Similarity=0.352 Sum_probs=60.6
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP 76 (98)
Q Consensus 9 ~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p 76 (98)
.|+++++|++.++|..|+.+.|+|++||.|||++|+++++...++. ....+.++|||++|..+..-
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~--~~~ig~~vIrgnsiv~~eaL 73 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD--KNNIGMVVIRGNSIVMVEAL 73 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC--cceeeeEEEeccEEEEEeec
Confidence 8999999999999999999999999999999999999999887764 35899999999999988644
No 32
>KOG3460|consensus
Probab=99.59 E-value=3.7e-16 Score=97.89 Aligned_cols=73 Identities=30% Similarity=0.393 Sum_probs=62.5
Q ss_pred chHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEE--CC--CCC-------cceeecceEEEEcCeEEEE
Q psy6026 5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVT--DP--DKY-------PHMLSVKNCFIRGSVVRYV 73 (98)
Q Consensus 5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~--~~--~~~-------~~~~~~~~v~IRG~~I~~I 73 (98)
-|+++|+-.++.+|.|+|+++++++|+|.+||+|+|++|+|+.++ .- +.. ...+.++.+||||++|.+|
T Consensus 5 ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilv 84 (91)
T KOG3460|consen 5 EPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILV 84 (91)
T ss_pred ccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEE
Confidence 599999999999999999999999999999999999999999864 11 110 1135789999999999999
Q ss_pred ecCC
Q psy6026 74 QLPG 77 (98)
Q Consensus 74 ~~p~ 77 (98)
+.|-
T Consensus 85 spp~ 88 (91)
T KOG3460|consen 85 SPPL 88 (91)
T ss_pred cCcc
Confidence 9884
No 33
>KOG1775|consensus
Probab=99.57 E-value=1.7e-15 Score=93.52 Aligned_cols=73 Identities=21% Similarity=0.417 Sum_probs=65.0
Q ss_pred cccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEE--CCCCCcceeecceEEEEcCeEEEEec
Q psy6026 2 ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVT--DPDKYPHMLSVKNCFIRGSVVRYVQL 75 (98)
Q Consensus 2 ~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~--~~~~~~~~~~~~~v~IRG~~I~~I~~ 75 (98)
++.+|++++.+++|.++.|.+|+++++.|+|.+||+|.|++|+|++++ .++|+ +..+++.+++.|++|..+..
T Consensus 4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr-~~tk~~~iLLnGNni~mLvP 78 (84)
T KOG1775|consen 4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGR-RMTKLDQILLNGNNITMLVP 78 (84)
T ss_pred hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcc-eeeeeeeeeecCCcEEEEec
Confidence 357899999999999999999999999999999999999999999964 55664 35689999999999998753
No 34
>KOG1784|consensus
Probab=99.36 E-value=5.4e-13 Score=84.88 Aligned_cols=88 Identities=20% Similarity=0.271 Sum_probs=75.5
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEE--EC-CCCCcceeecceEEEEcCeEEEEecCCcccccHH
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISV--TD-PDKYPHMLSVKNCFIRGSVVRYVQLPGDEVDTQL 84 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~--~~-~~~~~~~~~~~~v~IRG~~I~~I~~p~~~~d~~~ 84 (98)
.-|..+++++|.|...||+.+.|.|.+||+..|+.|+++-+ +. ..+. ....+|.++|||.||..|..-|+.+|+.+
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 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGV-EQIVLGLYIIRGENVAVIGEIDEELDSRL 81 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcch-hheeeEEEEEecCccceeeecchhhhhhh
Confidence 35788999999999999999999999999999999999984 22 2232 23578999999999999999999999999
Q ss_pred hHHHHHHHHhhc
Q psy6026 85 LQDATRKEAVNA 96 (98)
Q Consensus 85 ~~~~~r~~~~~~ 96 (98)
.+...|+|+-++
T Consensus 82 d~tkir~epl~~ 93 (96)
T KOG1784|consen 82 DLTKIRAEPLHP 93 (96)
T ss_pred hhhhcccCCCCC
Confidence 999999887544
No 35
>KOG1774|consensus
Probab=99.23 E-value=1.2e-11 Score=77.27 Aligned_cols=67 Identities=18% Similarity=0.356 Sum_probs=52.9
Q ss_pred HHHHhhcCCCeEEEEEcC--CcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026 7 YSFFKSLVGKDVVVELKN--DVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP 76 (98)
Q Consensus 7 ~~~L~~l~gk~V~V~Lkn--g~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p 76 (98)
+.||+. -.+|.|.|.. |..+.|.+.+||+|||++|++|++.+..... ...+|.++++|++|..|+-.
T Consensus 18 fr~Lq~--~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~-rk~lGRilLKGDnItli~~~ 86 (88)
T KOG1774|consen 18 FRFLQN--RTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKS-RKELGRILLKGDNITLIQSA 86 (88)
T ss_pred HHHHhc--CCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccC-CCccccEEEcCCcEEEEeec
Confidence 455555 4468888876 7899999999999999999999987653221 23799999999999998754
No 36
>KOG1781|consensus
Probab=99.11 E-value=9e-12 Score=80.31 Aligned_cols=70 Identities=20% Similarity=0.262 Sum_probs=59.6
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC--CC-C---cceeecceEEEEcCeEEEEecCCc
Q psy6026 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP--DK-Y---PHMLSVKNCFIRGSVVRYVQLPGD 78 (98)
Q Consensus 9 ~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~--~~-~---~~~~~~~~v~IRG~~I~~I~~p~~ 78 (98)
-|.++++++|+|++.+|+...|+|.+||+.||++|+|++++-. +. . ...+.+|.+.+||..+..|+..|-
T Consensus 21 DLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG 96 (108)
T KOG1781|consen 21 DLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADG 96 (108)
T ss_pred hHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcc
Confidence 4788999999999999999999999999999999999997532 21 0 124689999999999999997764
No 37
>KOG1782|consensus
Probab=99.07 E-value=3.5e-11 Score=80.25 Aligned_cols=70 Identities=23% Similarity=0.272 Sum_probs=57.7
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEE--ECCCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISV--TDPDKYPHMLSVKNCFIRGSVVRYVQLPGD 78 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~--~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~ 78 (98)
.-|-+.+.+++.|-|+||+.+.|.|.+||+|-|++|.+|++ +..+.. .....|.++|||.||..+..-|.
T Consensus 12 ~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y-~di~~glfiIRGENVvllGeid~ 83 (129)
T KOG1782|consen 12 TSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKY-CDIPRGLFIIRGENVVLLGEIDL 83 (129)
T ss_pred hHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeeccee-cccCceEEEEecCcEEEEecCCc
Confidence 34778889999999999999999999999999999999985 222222 13467999999999999986554
No 38
>KOG3168|consensus
Probab=98.81 E-value=8.1e-10 Score=77.31 Aligned_cols=76 Identities=16% Similarity=0.218 Sum_probs=60.3
Q ss_pred CcccchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC---------CCCcceeecceEEEEcCeEE
Q psy6026 1 MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP---------DKYPHMLSVKNCFIRGSVVR 71 (98)
Q Consensus 1 ~~~~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~---------~~~~~~~~~~~v~IRG~~I~ 71 (98)
|+..-+..+| .+++.++.|.+.||+++.|.+++||.|||++|.||++... ++. ..+-++.+++||.+|.
T Consensus 1 M~~a~sskml-~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~e-Ekr~lgLvllRgenIv 78 (177)
T KOG3168|consen 1 MTVAKSSKML-QHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGE-EKRVLGLVLLRGENIV 78 (177)
T ss_pred CCccchhHHH-HhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccc-eeeEEEEEEecCCcEE
Confidence 4444444444 4679999999999999999999999999999999996421 222 2567999999999999
Q ss_pred EEecCCc
Q psy6026 72 YVQLPGD 78 (98)
Q Consensus 72 ~I~~p~~ 78 (98)
.....+-
T Consensus 79 s~tVegp 85 (177)
T KOG3168|consen 79 SMTVEGP 85 (177)
T ss_pred EEeccCC
Confidence 9987643
No 39
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.27 E-value=3.3e-06 Score=51.91 Aligned_cols=46 Identities=24% Similarity=0.288 Sum_probs=37.2
Q ss_pred HHHHhhcCCCeEEEEEcCCcEEEEEEEEecc---ccceEEeeEEEECCC
Q psy6026 7 YSFFKSLVGKDVVVELKNDVSICGTLHSVDQ---YLNIKLTDISVTDPD 52 (98)
Q Consensus 7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~---~mNi~L~~~~~~~~~ 52 (98)
.-++..++|++|.|.++||..|+|++.+++. -+.++|+-|......
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~ 52 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKS 52 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccc
Confidence 4567899999999999999999999999998 899999999987653
No 40
>KOG3459|consensus
Probab=98.25 E-value=1.5e-07 Score=61.83 Aligned_cols=69 Identities=20% Similarity=0.286 Sum_probs=55.2
Q ss_pred hHHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECC------CCCc-----ceeecceEEEEcCeEEE
Q psy6026 6 FYSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP------DKYP-----HMLSVKNCFIRGSVVRY 72 (98)
Q Consensus 6 p~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~------~~~~-----~~~~~~~v~IRG~~I~~ 72 (98)
|++.+.... ..+|.|-++|+..+-|++.+||.|+|++|+++.+... +|.. ..+..+.+||||++|..
T Consensus 25 pls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~ 104 (114)
T KOG3459|consen 25 PLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVIL 104 (114)
T ss_pred chhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEE
Confidence 667776666 5589999999999999999999999999999986421 1211 13568999999999988
Q ss_pred Ee
Q psy6026 73 VQ 74 (98)
Q Consensus 73 I~ 74 (98)
+.
T Consensus 105 v~ 106 (114)
T KOG3459|consen 105 VL 106 (114)
T ss_pred EE
Confidence 76
No 41
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.87 E-value=0.00015 Score=46.94 Aligned_cols=68 Identities=19% Similarity=0.271 Sum_probs=55.8
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEECCCCCc-------ceeecceEEEEcCeEEEEecCCc
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLHSVDQ-YLNIKLTDISVTDPDKYP-------HMLSVKNCFIRGSVVRYVQLPGD 78 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~~~~-------~~~~~~~v~IRG~~I~~I~~p~~ 78 (98)
..++|++|.+..+++..|+|+|..+|. .-.+.|.++..+..++.+ ...-++.+..||+.|.-+.+-+.
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 368999999999999999999999995 789999999987654421 12358899999999999987654
No 42
>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=97.45 E-value=0.00012 Score=44.15 Aligned_cols=37 Identities=24% Similarity=0.284 Sum_probs=30.2
Q ss_pred CCeEEEEEcCC----cEEEEEEEEeccccceEEeeEEEECC
Q psy6026 15 GKDVVVELKND----VSICGTLHSVDQYLNIKLTDISVTDP 51 (98)
Q Consensus 15 gk~V~V~Lkng----~~~~G~L~~~D~~mNi~L~~~~~~~~ 51 (98)
+.+|.|.++.- -.++|.|.+||.|+|+.|.|+.++-.
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~ 48 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR 48 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence 56777777743 37889999999999999999998654
No 43
>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=97.38 E-value=0.0016 Score=40.31 Aligned_cols=61 Identities=18% Similarity=0.283 Sum_probs=48.8
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEec-cccceEEeeEEEECCCCCc--------ceeecceEEEEcCeEEE
Q psy6026 12 SLVGKDVVVELKNDVSICGTLHSVD-QYLNIKLTDISVTDPDKYP--------HMLSVKNCFIRGSVVRY 72 (98)
Q Consensus 12 ~l~gk~V~V~Lkng~~~~G~L~~~D-~~mNi~L~~~~~~~~~~~~--------~~~~~~~v~IRG~~I~~ 72 (98)
+++|+++.+..+.+..|.|+|.++| +---+.|+|+..+..+|.. ...-++.+..||+.|.-
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 5789999999999999999999999 4668899999987655432 12247788889988753
No 44
>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=97.27 E-value=0.006 Score=38.29 Aligned_cols=65 Identities=18% Similarity=0.308 Sum_probs=51.4
Q ss_pred chHHHHhhcCCCeEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecC
Q psy6026 5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQ-YLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP 76 (98)
Q Consensus 5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p 76 (98)
..+.+|.++.|++|.+.|.++.++.|+..++|. -.|+..++-. .|=| ..+...+|.+-|..+++.
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 357789999999999999999999999999995 5699888844 3333 358999999999999875
No 45
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.73 E-value=0.013 Score=32.89 Aligned_cols=47 Identities=23% Similarity=0.287 Sum_probs=35.1
Q ss_pred CCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEE
Q psy6026 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIR 66 (98)
Q Consensus 14 ~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IR 66 (98)
+|++|++.+ ++..++|+..++|+.-.+.++. ++|..+....+.+++|
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~-----~~g~~~~i~sGdv~~r 48 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRT-----EDGSIRTISSGDVSLR 48 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEE-----TTEEEEEESSSEEEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEE-----CCCCEEEEEEEEEEeC
Confidence 699999999 6677799999999999999976 2332123345666665
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=96.71 E-value=0.0048 Score=36.84 Aligned_cols=37 Identities=24% Similarity=0.367 Sum_probs=29.6
Q ss_pred HHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026 9 FFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 9 ~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~ 45 (98)
||+.+. ..+|+|-|.||..++|.+.+||.|+=+.-.+
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 455544 5579999999999999999999998665443
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=96.64 E-value=0.0055 Score=36.58 Aligned_cols=37 Identities=27% Similarity=0.376 Sum_probs=29.7
Q ss_pred HHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026 9 FFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 9 ~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~ 45 (98)
||+.+. +.+|+|-|.||..+.|.+.+||.|+=+.-.+
T Consensus 7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 455544 5679999999999999999999998665443
No 48
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=96.42 E-value=0.0084 Score=37.53 Aligned_cols=38 Identities=21% Similarity=0.393 Sum_probs=30.6
Q ss_pred HHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026 8 SFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 8 ~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~ 45 (98)
.||+.+. +.+|+|-|.||..+.|.+.+||.|+=+.-.+
T Consensus 10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 3555554 5679999999999999999999998666544
No 49
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=96.16 E-value=0.056 Score=32.70 Aligned_cols=52 Identities=29% Similarity=0.443 Sum_probs=40.2
Q ss_pred HHHHhhcCCCeEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEe
Q psy6026 7 YSFFKSLVGKDVVVELKNDVSICGTLHSVDQ-YLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQ 74 (98)
Q Consensus 7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 74 (98)
...|++++|++|.|++-.|+. +|+|.++-. |. +|+. .+ ..+|||=..|.+|.
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~------~~-------~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEE------NG-------TPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEe------CC-------cEEEEEeeeEEEEc
Confidence 578999999999999988876 999999873 43 3332 12 47889988888874
No 50
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.09 E-value=0.011 Score=36.68 Aligned_cols=35 Identities=23% Similarity=0.382 Sum_probs=29.1
Q ss_pred HHHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccce
Q psy6026 7 YSFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNI 41 (98)
Q Consensus 7 ~~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi 41 (98)
-.||.++. +.+|+|-|.||...+|.+++||.|.=+
T Consensus 9 D~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~Vl 45 (77)
T COG1923 9 DPFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVL 45 (77)
T ss_pred hHHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEE
Confidence 35666654 678999999999999999999999743
No 51
>KOG1073|consensus
Probab=95.83 E-value=0.027 Score=44.07 Aligned_cols=68 Identities=18% Similarity=0.220 Sum_probs=55.2
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEec-cccceEEeeEEEECCCCCc-------c-eeecceEEEEcCeEEEEecCCc
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLHSVD-QYLNIKLTDISVTDPDKYP-------H-MLSVKNCFIRGSVVRYVQLPGD 78 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~~~D-~~mNi~L~~~~~~~~~~~~-------~-~~~~~~v~IRG~~I~~I~~p~~ 78 (98)
..++|+.|.+.-|++..|+|+|.-+| +---|-|.+|..+.+++.. . ..-++.++.||+.|.-+.+-+.
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~ 81 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQET 81 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccC
Confidence 46899999999999999999999999 7889999999877554321 1 1157889999999997776553
No 52
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=95.12 E-value=0.21 Score=29.71 Aligned_cols=33 Identities=15% Similarity=0.148 Sum_probs=28.8
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026 13 LVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 13 l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~ 45 (98)
.+|..|.+++..|..++|.+.+||...++.+=.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk 36 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK 36 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence 479999999999999999999999887766444
No 53
>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=94.42 E-value=0.22 Score=35.15 Aligned_cols=61 Identities=25% Similarity=0.319 Sum_probs=43.0
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEECCCCCcceeecceEEEEcCeEEEEecCCc
Q psy6026 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQ-YLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPGD 78 (98)
Q Consensus 9 ~L~~l~gk~V~V~Lkng~~~~G~L~~~D~-~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~~ 78 (98)
.+..++||.|.|.+.| +++.|.|..+|. .-|++|-+-. .++. ...-+|-|..|..|..-++
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~---e~~~-----~sv~~I~ghaVk~vevl~~ 72 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQ---EDGK-----RSVKVIMGHAVKSVEVLSE 72 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE----TTS------EEEEEE-GGGEEEEEEEE-
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcc---cCCc-----eeEEEEEccceEEEEEccC
Confidence 4678999999999999 999999999995 6688887533 2232 2457899999999986653
No 54
>PRK14638 hypothetical protein; Provisional
Probab=93.92 E-value=0.12 Score=35.63 Aligned_cols=36 Identities=17% Similarity=0.232 Sum_probs=29.6
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEe
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLT 44 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~ 44 (98)
.-+..++|+.|.|.+++++.++|+|.++|+. ++.|+
T Consensus 93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 3467889999999999999999999999963 34443
No 55
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.77 E-value=0.15 Score=36.04 Aligned_cols=38 Identities=24% Similarity=0.373 Sum_probs=30.2
Q ss_pred HHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026 8 SFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 8 ~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~ 45 (98)
.||+.+. ..+|+|-|.||-.++|.+.+||.|+=+.-.+
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 3555555 5579999999999999999999998665444
No 56
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.14 E-value=0.21 Score=35.25 Aligned_cols=38 Identities=24% Similarity=0.287 Sum_probs=30.5
Q ss_pred HHHhhcC--CCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026 8 SFFKSLV--GKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 8 ~~L~~l~--gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~ 45 (98)
.||+.+. ..+|+|-|.||..++|++.+||+|.=+.-.+
T Consensus 15 ~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~ 54 (165)
T PRK14091 15 IFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRD 54 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 4566665 4579999999999999999999998665544
No 57
>PRK14639 hypothetical protein; Provisional
Probab=93.07 E-value=0.21 Score=34.10 Aligned_cols=35 Identities=29% Similarity=0.395 Sum_probs=29.6
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEE
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKL 43 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L 43 (98)
.-++.++|+.|.|.+.+++.+.|+|.++|+. ++.|
T Consensus 81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 4467889999999999999999999999983 4444
No 58
>PRK02001 hypothetical protein; Validated
Probab=92.87 E-value=0.23 Score=34.48 Aligned_cols=30 Identities=33% Similarity=0.468 Sum_probs=27.2
Q ss_pred HHhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy6026 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQY 38 (98)
Q Consensus 9 ~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~ 38 (98)
-+..++|+.|.|.+.++..+.|+|.++|+.
T Consensus 84 ~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~ 113 (152)
T PRK02001 84 QYKKNIGRELEVLTKNGKKIEGELKSADEN 113 (152)
T ss_pred HHHHhCCCEEEEEECCCCEEEEEEEEEeCC
Confidence 456889999999999999999999999974
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=90.59 E-value=0.66 Score=28.61 Aligned_cols=31 Identities=39% Similarity=0.413 Sum_probs=26.1
Q ss_pred HHHhhcCCCeEEEEEc---CC-cEEEEEEEEeccc
Q psy6026 8 SFFKSLVGKDVVVELK---ND-VSICGTLHSVDQY 38 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lk---ng-~~~~G~L~~~D~~ 38 (98)
.-+..++|+.|.|+++ +| +.+.|.|.++|+.
T Consensus 18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 3467889999999998 55 6899999999983
No 60
>PRK14644 hypothetical protein; Provisional
Probab=90.34 E-value=0.62 Score=31.71 Aligned_cols=35 Identities=23% Similarity=0.286 Sum_probs=29.0
Q ss_pred HHhhcCCCeEEEEEcCC----cEEEEEEEEeccccceEEe
Q psy6026 9 FFKSLVGKDVVVELKND----VSICGTLHSVDQYLNIKLT 44 (98)
Q Consensus 9 ~L~~l~gk~V~V~Lkng----~~~~G~L~~~D~~mNi~L~ 44 (98)
-+..++|+.|.|.|++. ..+.|+|.++|+. ++.|+
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 47788999999999987 9999999999973 34443
No 61
>PRK14640 hypothetical protein; Provisional
Probab=89.67 E-value=0.75 Score=31.72 Aligned_cols=35 Identities=29% Similarity=0.445 Sum_probs=28.2
Q ss_pred HHHhhcCCCeEEEEE----cCCcEEEEEEEEeccccceEE
Q psy6026 8 SFFKSLVGKDVVVEL----KNDVSICGTLHSVDQYLNIKL 43 (98)
Q Consensus 8 ~~L~~l~gk~V~V~L----kng~~~~G~L~~~D~~mNi~L 43 (98)
.-+..++|+.|.|.| .+.+.+.|+|.++|+. ++.|
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 346788999999999 5779999999999974 3444
No 62
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.59 E-value=1.1 Score=31.15 Aligned_cols=33 Identities=24% Similarity=0.379 Sum_probs=29.3
Q ss_pred HHHHhhcCCCeEEEEE----cCCcEEEEEEEEecccc
Q psy6026 7 YSFFKSLVGKDVVVEL----KNDVSICGTLHSVDQYL 39 (98)
Q Consensus 7 ~~~L~~l~gk~V~V~L----kng~~~~G~L~~~D~~m 39 (98)
..-+..+.|+.|.|.| .+.+.+.|+|.++|+.+
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 3557788999999999 79999999999999876
No 63
>PRK14642 hypothetical protein; Provisional
Probab=89.03 E-value=0.82 Score=33.10 Aligned_cols=35 Identities=23% Similarity=0.354 Sum_probs=28.4
Q ss_pred HHHhhcCCCeEEEEEc-------------CCcEEEEEEEEeccccceEE
Q psy6026 8 SFFKSLVGKDVVVELK-------------NDVSICGTLHSVDQYLNIKL 43 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lk-------------ng~~~~G~L~~~D~~mNi~L 43 (98)
.-+..++|+.|.|.|+ +.+.++|+|.++|+. ++.|
T Consensus 93 ~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 93 QDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred HHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 3466788999999998 779999999999974 4434
No 64
>PRK14633 hypothetical protein; Provisional
Probab=88.68 E-value=0.96 Score=31.14 Aligned_cols=35 Identities=26% Similarity=0.275 Sum_probs=28.1
Q ss_pred HHHhhcCCCeEEEEEc----CCcEEEEEEEEeccccceEE
Q psy6026 8 SFFKSLVGKDVVVELK----NDVSICGTLHSVDQYLNIKL 43 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lk----ng~~~~G~L~~~D~~mNi~L 43 (98)
.-+..++|+.|.|.++ +++.++|+|.++++. ++.|
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 3467889999999994 669999999999874 4444
No 65
>PRK14645 hypothetical protein; Provisional
Probab=87.44 E-value=1.1 Score=31.03 Aligned_cols=30 Identities=17% Similarity=0.249 Sum_probs=25.5
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQY 38 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~ 38 (98)
.-+..++|+.|.|.+ ++..+.|+|.++|+.
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 345678899999986 889999999999974
No 66
>PRK14636 hypothetical protein; Provisional
Probab=87.02 E-value=1.3 Score=31.45 Aligned_cols=30 Identities=20% Similarity=0.392 Sum_probs=25.8
Q ss_pred HHHhhcCCCeEEEEEc---CC-cEEEEEEEEecc
Q psy6026 8 SFFKSLVGKDVVVELK---ND-VSICGTLHSVDQ 37 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lk---ng-~~~~G~L~~~D~ 37 (98)
.-+..++|+.|.|+|+ +| +.+.|+|.++|+
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~ 124 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDG 124 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeC
Confidence 3467889999999997 55 799999999987
No 67
>PRK14632 hypothetical protein; Provisional
Probab=86.87 E-value=1.4 Score=31.12 Aligned_cols=36 Identities=19% Similarity=0.322 Sum_probs=28.5
Q ss_pred HHHhhcCCCeEEEEEcC-------CcEEEEEEEEeccccceEEe
Q psy6026 8 SFFKSLVGKDVVVELKN-------DVSICGTLHSVDQYLNIKLT 44 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkn-------g~~~~G~L~~~D~~mNi~L~ 44 (98)
.-++.++|+.|.|.|++ .+.+.|+|.++|+. ++.|+
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 34678899999999986 57999999999863 44443
No 68
>PRK14643 hypothetical protein; Provisional
Probab=86.53 E-value=1.4 Score=30.83 Aligned_cols=36 Identities=14% Similarity=0.107 Sum_probs=28.2
Q ss_pred HHHhhcCCCeEEEEEcC----CcEEEEEEEEeccc-cceEE
Q psy6026 8 SFFKSLVGKDVVVELKN----DVSICGTLHSVDQY-LNIKL 43 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkn----g~~~~G~L~~~D~~-mNi~L 43 (98)
.-+..++|+.|.|.|+. .+.+.|+|.++|.. ..+.|
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 34668899999999975 69999999999964 34443
No 69
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=86.41 E-value=1.6 Score=29.99 Aligned_cols=30 Identities=30% Similarity=0.513 Sum_probs=26.2
Q ss_pred HHHhhcCCCeEEEEE----cCCcEEEEEEEEecc
Q psy6026 8 SFFKSLVGKDVVVEL----KNDVSICGTLHSVDQ 37 (98)
Q Consensus 8 ~~L~~l~gk~V~V~L----kng~~~~G~L~~~D~ 37 (98)
.-+..++|+.|.|.+ .++..+.|+|.++|+
T Consensus 91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 456788999999997 577899999999997
No 70
>PRK14634 hypothetical protein; Provisional
Probab=86.23 E-value=1.6 Score=30.27 Aligned_cols=35 Identities=20% Similarity=0.323 Sum_probs=27.3
Q ss_pred HHHhhcCCCeEEEEEcCC----cEEEEEEEEeccccceEE
Q psy6026 8 SFFKSLVGKDVVVELKND----VSICGTLHSVDQYLNIKL 43 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng----~~~~G~L~~~D~~mNi~L 43 (98)
.-+..++|+.|.|+|.+. +.+.|+|.++|+. ++.|
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 346788999999999743 7999999999974 3444
No 71
>PRK14646 hypothetical protein; Provisional
Probab=85.33 E-value=1.8 Score=29.93 Aligned_cols=35 Identities=26% Similarity=0.280 Sum_probs=27.5
Q ss_pred HHHhhcCCCeEEEEEcCC----cEEEEEEEEeccccceEE
Q psy6026 8 SFFKSLVGKDVVVELKND----VSICGTLHSVDQYLNIKL 43 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng----~~~~G~L~~~D~~mNi~L 43 (98)
.-+..++|+.|.|+|++. +.+.|+|.++|+. ++.|
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 346788999999999643 7889999999974 4444
No 72
>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=85.32 E-value=1.3 Score=29.84 Aligned_cols=30 Identities=33% Similarity=0.524 Sum_probs=23.6
Q ss_pred HHHhhcCCCeEEEEEc----CCcEEEEEEEEecc
Q psy6026 8 SFFKSLVGKDVVVELK----NDVSICGTLHSVDQ 37 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lk----ng~~~~G~L~~~D~ 37 (98)
.-+..++|+.|.|.++ +.+.+.|+|.++|+
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 4577889999999994 55799999999998
No 73
>PRK14647 hypothetical protein; Provisional
Probab=84.82 E-value=2 Score=29.78 Aligned_cols=30 Identities=17% Similarity=0.252 Sum_probs=25.6
Q ss_pred HHHhhcCCCeEEEEEc---------CCcEEEEEEEEecc
Q psy6026 8 SFFKSLVGKDVVVELK---------NDVSICGTLHSVDQ 37 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lk---------ng~~~~G~L~~~D~ 37 (98)
.-+..++|+.|.|.|+ +.+.+.|+|.++|+
T Consensus 92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 4467889999999996 35999999999996
No 74
>PRK06955 biotin--protein ligase; Provisional
Probab=84.04 E-value=6.4 Score=29.72 Aligned_cols=51 Identities=18% Similarity=0.297 Sum_probs=36.3
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEcC
Q psy6026 12 SLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68 (98)
Q Consensus 12 ~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~ 68 (98)
...|++|.|...++..+.|+..++|+.-.+.++. .+|. +....|++.+|..
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~-----~~g~-~~~~sGeV~~~~~ 296 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLDT-----PAGR-QAIAAGDVSLREA 296 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe-----CCCe-EEEEEEEEEEecc
Confidence 3679999997767788999999999999998853 2231 1234566666543
No 75
>PRK14637 hypothetical protein; Provisional
Probab=83.28 E-value=2.4 Score=29.25 Aligned_cols=35 Identities=26% Similarity=0.308 Sum_probs=26.4
Q ss_pred HHHhhcCCCeEEEEEcCCcEE-EEEEEEeccccceEE
Q psy6026 8 SFFKSLVGKDVVVELKNDVSI-CGTLHSVDQYLNIKL 43 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~-~G~L~~~D~~mNi~L 43 (98)
.-+..++|+.|.|.+.+...+ .|+|.++|+. ++.|
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 446788999999999544555 7999999974 3444
No 76
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=82.88 E-value=2.3 Score=29.34 Aligned_cols=26 Identities=35% Similarity=0.484 Sum_probs=24.0
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEec
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLHSVD 36 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~~~D 36 (98)
.+++||.|.+...+|..+.|++.++.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 57899999999999999999999986
No 77
>PRK14631 hypothetical protein; Provisional
Probab=82.25 E-value=3 Score=29.53 Aligned_cols=29 Identities=24% Similarity=0.384 Sum_probs=25.3
Q ss_pred HHHhhcCCCeEEEEEc----CCcEEEEEEEEec
Q psy6026 8 SFFKSLVGKDVVVELK----NDVSICGTLHSVD 36 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lk----ng~~~~G~L~~~D 36 (98)
.-+..++|+.|.|+|+ +.+.++|+|.++|
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 4467889999999996 5599999999998
No 78
>PRK14641 hypothetical protein; Provisional
Probab=81.45 E-value=2.8 Score=29.66 Aligned_cols=29 Identities=21% Similarity=0.402 Sum_probs=24.6
Q ss_pred HHHhhcCCCeEEEEEcC----CcEEEEEEEEec
Q psy6026 8 SFFKSLVGKDVVVELKN----DVSICGTLHSVD 36 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkn----g~~~~G~L~~~D 36 (98)
.-++.++|+.|.|.|++ .+.++|+|.++|
T Consensus 97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 44678899999999976 568999999995
No 79
>PRK08330 biotin--protein ligase; Provisional
Probab=81.26 E-value=10 Score=27.46 Aligned_cols=33 Identities=18% Similarity=0.253 Sum_probs=26.8
Q ss_pred hcCCCeEEEEEcCCcEE-EEEEEEeccccceEEee
Q psy6026 12 SLVGKDVVVELKNDVSI-CGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 12 ~l~gk~V~V~Lkng~~~-~G~L~~~D~~mNi~L~~ 45 (98)
...|++|.+.. ++..+ .|+..++|+.-.+.+..
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 46799999976 55554 79999999999998874
No 80
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=79.88 E-value=11 Score=28.45 Aligned_cols=48 Identities=19% Similarity=0.282 Sum_probs=34.4
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEc
Q psy6026 13 LVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67 (98)
Q Consensus 13 l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG 67 (98)
+.|++|.+... +..+.|++.++|+.-.+.+.+ .++. +....|++.+|+
T Consensus 270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~~-----~g~~-~~~~~gev~~~~ 317 (319)
T PRK11886 270 FLGREVKLIIG-DKEISGIARGIDEQGALLLED-----DGVE-KPFNGGEISLRS 317 (319)
T ss_pred ccCCeEEEEeC-CcEEEEEEEEECCCceEEEEe-----CCcE-EEEEEeEEEEec
Confidence 57999999874 467999999999999999852 2221 123456676654
No 81
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=79.23 E-value=2.3 Score=29.82 Aligned_cols=24 Identities=25% Similarity=0.343 Sum_probs=22.5
Q ss_pred CCCeEEEEEcCCcEEEEEEEEecc
Q psy6026 14 VGKDVVVELKNDVSICGTLHSVDQ 37 (98)
Q Consensus 14 ~gk~V~V~Lkng~~~~G~L~~~D~ 37 (98)
.|+.|+|.+.||++++|+-.++|+
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccce
Confidence 489999999999999999999985
No 82
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=76.03 E-value=14 Score=30.68 Aligned_cols=33 Identities=24% Similarity=0.245 Sum_probs=28.7
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026 13 LVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 13 l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~ 45 (98)
+.|++|.+...++..+.|+..++|+.-.+.|+.
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 679999997667778999999999999998863
No 83
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=75.27 E-value=20 Score=26.47 Aligned_cols=52 Identities=19% Similarity=0.188 Sum_probs=39.0
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEEEECCCCCcceeecceEEEEc
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~~~v~IRG 67 (98)
...+|++|++...++....|+..++|..-.++++.. +|..+...-|.+++|.
T Consensus 186 ~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~-----~g~~~~~~~Gev~~~~ 237 (238)
T COG0340 186 SLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD-----DGEVQTIYSGEVSLRR 237 (238)
T ss_pred hccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC-----CCeEEEEeccEEEeec
Confidence 345799999999999999999999999999998763 2322233456666553
No 84
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=75.05 E-value=4.9 Score=26.05 Aligned_cols=18 Identities=28% Similarity=0.425 Sum_probs=14.8
Q ss_pred CeEEEEEcCCcEEEEEEE
Q psy6026 16 KDVVVELKNDVSICGTLH 33 (98)
Q Consensus 16 k~V~V~Lkng~~~~G~L~ 33 (98)
.+|.++|+||+.+.|++.
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 479999999999999974
No 85
>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=74.27 E-value=3 Score=25.99 Aligned_cols=22 Identities=23% Similarity=0.267 Sum_probs=15.4
Q ss_pred HhhcCCCeEEEEEcCCcEEEEE
Q psy6026 10 FKSLVGKDVVVELKNDVSICGT 31 (98)
Q Consensus 10 L~~l~gk~V~V~Lkng~~~~G~ 31 (98)
+..+.+.+|.++|+||..+.|+
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 4556788999999999999997
No 86
>PRK14630 hypothetical protein; Provisional
Probab=73.54 E-value=6.9 Score=26.71 Aligned_cols=29 Identities=28% Similarity=0.337 Sum_probs=23.7
Q ss_pred HHHhhcCCCeEEEEEcCCcEEEEEEEEecc
Q psy6026 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQ 37 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~ 37 (98)
.-++.++|++|.|.|.... ..|+|.++|+
T Consensus 90 ~df~r~~G~~v~V~l~~~~-~~G~L~~~~d 118 (143)
T PRK14630 90 REFKIFEGKKIKLMLDNDF-EEGFILEAKA 118 (143)
T ss_pred HHHHHhCCCEEEEEEcCcc-eEEEEEEEeC
Confidence 3467889999999996654 5999999987
No 87
>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=73.47 E-value=16 Score=26.39 Aligned_cols=32 Identities=22% Similarity=0.313 Sum_probs=27.2
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEeccccceEEe
Q psy6026 12 SLVGKDVVVELKNDVSICGTLHSVDQYLNIKLT 44 (98)
Q Consensus 12 ~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~ 44 (98)
...|++|.+...+ ..+.|+..++|+.-.+.++
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 3569999998755 5689999999999999986
No 88
>PRK14635 hypothetical protein; Provisional
Probab=70.96 E-value=14 Score=25.69 Aligned_cols=35 Identities=14% Similarity=0.126 Sum_probs=26.4
Q ss_pred HHHhhcCCCeEEEEEc--CCcEEEE---EEEEeccccceEE
Q psy6026 8 SFFKSLVGKDVVVELK--NDVSICG---TLHSVDQYLNIKL 43 (98)
Q Consensus 8 ~~L~~l~gk~V~V~Lk--ng~~~~G---~L~~~D~~mNi~L 43 (98)
.-+..+.|+.|.|.+. ++..+.| +|.++|+. ++.|
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 3466789999999886 4678887 99999864 3444
No 89
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=68.91 E-value=9.1 Score=26.33 Aligned_cols=27 Identities=33% Similarity=0.421 Sum_probs=23.5
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEecc
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLHSVDQ 37 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~~~D~ 37 (98)
.+++||.|.....+|..+.|++.++..
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 368999999888999999999997763
No 90
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=63.73 E-value=44 Score=25.07 Aligned_cols=32 Identities=19% Similarity=0.231 Sum_probs=27.1
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026 13 LVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 13 l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~ 45 (98)
..|+.|.|.. ++..+.|++.++|+.-.+++..
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 4699999975 5688999999999988888864
No 91
>PRK11625 Rho-binding antiterminator; Provisional
Probab=63.46 E-value=34 Score=21.45 Aligned_cols=23 Identities=13% Similarity=0.046 Sum_probs=19.3
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEE
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLH 33 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~ 33 (98)
..+.+-++.++|+||..+.|+..
T Consensus 19 AC~~~~~l~l~l~dGe~~~g~A~ 41 (84)
T PRK11625 19 ACQHHLMLTLELKDGEVLQAKAS 41 (84)
T ss_pred HHhcCCeEEEEECCCCEEEEEEE
Confidence 34568899999999999999873
No 92
>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=63.07 E-value=12 Score=24.70 Aligned_cols=27 Identities=15% Similarity=0.041 Sum_probs=24.0
Q ss_pred chHHHHhhcCCCeEEEEEcCCcEEEEE
Q psy6026 5 LFYSFFKSLVGKDVVVELKNDVSICGT 31 (98)
Q Consensus 5 ~p~~~L~~l~gk~V~V~Lkng~~~~G~ 31 (98)
.|+.-|+...+-+|+.+|.||.+|.+.
T Consensus 64 ~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 64 TDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CCHHHHhCCcccEEEEEecCCcEEEec
Confidence 467888999999999999999999765
No 93
>PRK10898 serine endoprotease; Provisional
Probab=56.94 E-value=28 Score=26.90 Aligned_cols=32 Identities=16% Similarity=0.294 Sum_probs=27.8
Q ss_pred CCeEEEEEcCCcEEEEEEEEeccccceEEeeE
Q psy6026 15 GKDVVVELKNDVSICGTLHSVDQYLNIKLTDI 46 (98)
Q Consensus 15 gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~ 46 (98)
...+.|.+.||+.|.+.+.++|...++-+=.+
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 35789999999999999999999999876554
No 94
>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=56.12 E-value=21 Score=25.11 Aligned_cols=34 Identities=18% Similarity=0.004 Sum_probs=30.1
Q ss_pred CCCeEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q psy6026 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDIS 47 (98)
Q Consensus 14 ~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~ 47 (98)
-.-+|+|.+.||.++.|.+.+|+.-=|.+|..+.
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 3568999999999999999999999999987655
No 95
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=54.53 E-value=21 Score=25.78 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=22.8
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEec
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLHSVD 36 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~~~D 36 (98)
.+++||.|.+.-.+|..+.|++.++.
T Consensus 114 ~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 114 MKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 36899999998889999999998875
No 96
>PRK10139 serine endoprotease; Provisional
Probab=52.86 E-value=34 Score=27.46 Aligned_cols=32 Identities=19% Similarity=0.309 Sum_probs=27.9
Q ss_pred CCeEEEEEcCCcEEEEEEEEeccccceEEeeE
Q psy6026 15 GKDVVVELKNDVSICGTLHSVDQYLNIKLTDI 46 (98)
Q Consensus 15 gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~ 46 (98)
...+.|.+.||+.|.+++.++|...++-+=.+
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 45899999999999999999999998876544
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=51.72 E-value=37 Score=26.10 Aligned_cols=32 Identities=19% Similarity=0.314 Sum_probs=27.7
Q ss_pred CeEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q psy6026 16 KDVVVELKNDVSICGTLHSVDQYLNIKLTDIS 47 (98)
Q Consensus 16 k~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~ 47 (98)
..+.|.+.||+.+.+++.++|...++-+=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 46899999999999999999999998775443
No 98
>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=50.12 E-value=43 Score=24.14 Aligned_cols=35 Identities=17% Similarity=0.362 Sum_probs=30.1
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccc
Q psy6026 6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLN 40 (98)
Q Consensus 6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mN 40 (98)
+..+=+.|+|+.+.-++.+|....|.+....+|+-
T Consensus 10 ~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 10 AVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred HHHHHHHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 45666789999999899889888999999999974
No 99
>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=49.76 E-value=28 Score=22.96 Aligned_cols=20 Identities=25% Similarity=0.265 Sum_probs=17.8
Q ss_pred eEEEEEcCCcEEEEEEEEec
Q psy6026 17 DVVVELKNDVSICGTLHSVD 36 (98)
Q Consensus 17 ~V~V~Lkng~~~~G~L~~~D 36 (98)
...|.++||+++.|.+.+=|
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET 78 (133)
T ss_pred cEEEEECCCCEEEEEEEecC
Confidence 48999999999999998844
No 100
>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=49.46 E-value=43 Score=18.23 Aligned_cols=25 Identities=20% Similarity=0.203 Sum_probs=21.8
Q ss_pred CCCeEEEEEcCCcEEEEEEEEeccc
Q psy6026 14 VGKDVVVELKNDVSICGTLHSVDQY 38 (98)
Q Consensus 14 ~gk~V~V~Lkng~~~~G~L~~~D~~ 38 (98)
.|..+.+...+|.-|+|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5788888888999999999999964
No 101
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=48.92 E-value=25 Score=22.57 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=19.4
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEE
Q psy6026 12 SLVGKDVVVE-LKNDVSICGTLHS 34 (98)
Q Consensus 12 ~l~gk~V~V~-Lkng~~~~G~L~~ 34 (98)
..+|..|.|+ +.+|+.+.|++.+
T Consensus 93 g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 93 GAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred cCCCCEEEEEECCCCCEEEEEEeC
Confidence 4678999999 7899999998875
No 102
>PRK10942 serine endoprotease; Provisional
Probab=48.56 E-value=42 Score=27.08 Aligned_cols=32 Identities=16% Similarity=0.236 Sum_probs=27.5
Q ss_pred CCeEEEEEcCCcEEEEEEEEeccccceEEeeE
Q psy6026 15 GKDVVVELKNDVSICGTLHSVDQYLNIKLTDI 46 (98)
Q Consensus 15 gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~ 46 (98)
...+.|.+.||+.|.+++.+.|...++-|=..
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 45789999999999999999999999876543
No 103
>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=47.46 E-value=41 Score=24.01 Aligned_cols=34 Identities=21% Similarity=0.393 Sum_probs=26.2
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccc
Q psy6026 6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLN 40 (98)
Q Consensus 6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mN 40 (98)
+..+=+.|+|+.+..++.+|. +.|++....+|+-
T Consensus 9 ~~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 9 TVEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp HHHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred HHHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 456678899999999999988 9999999988876
No 104
>PF13437 HlyD_3: HlyD family secretion protein
Probab=47.39 E-value=55 Score=20.00 Aligned_cols=34 Identities=21% Similarity=0.261 Sum_probs=27.7
Q ss_pred cchHHHHhhc--CCCeEEEEEcCC--cEEEEEEEEecc
Q psy6026 4 LLFYSFFKSL--VGKDVVVELKND--VSICGTLHSVDQ 37 (98)
Q Consensus 4 ~~p~~~L~~l--~gk~V~V~Lkng--~~~~G~L~~~D~ 37 (98)
.+|-..+..+ .|..|.+.+.++ ..+.|++..++.
T Consensus 41 ~v~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 41 YVPEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred EEChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 3466667776 699999999865 699999999998
No 105
>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=47.36 E-value=49 Score=20.92 Aligned_cols=24 Identities=29% Similarity=0.447 Sum_probs=17.4
Q ss_pred HHHHhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy6026 7 YSFFKSLVGKDVVVELKNDVSICGTLHSVDQY 38 (98)
Q Consensus 7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~ 38 (98)
.+.|.++.|++|++- |++.++|..
T Consensus 7 ~~~L~~f~gk~V~iv--------GkV~~~~~~ 30 (101)
T cd04479 7 GAMLSQFVGKTVRIV--------GKVEKVDGD 30 (101)
T ss_pred HHHHHhhCCCEEEEE--------EEEEEecCC
Confidence 468999999999875 555555543
No 106
>PRK06789 flagellar motor switch protein; Validated
Probab=46.12 E-value=54 Score=20.09 Aligned_cols=36 Identities=11% Similarity=0.220 Sum_probs=29.8
Q ss_pred HhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026 10 FKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 10 L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~ 45 (98)
|.+..|.+|.|.+++-..-+|-+..+|+.+=+.+.+
T Consensus 36 Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 36 LENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred eCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 456778899999999999999999999877776654
No 107
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=42.50 E-value=31 Score=25.13 Aligned_cols=24 Identities=17% Similarity=0.357 Sum_probs=20.5
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEEe
Q psy6026 12 SLVGKDVVVE-LKNDVSICGTLHSV 35 (98)
Q Consensus 12 ~l~gk~V~V~-Lkng~~~~G~L~~~ 35 (98)
+.+|..|.|+ +.+|+.+.|++.+-
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~~ 228 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTGD 228 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeCC
Confidence 4679999999 99999999998753
No 108
>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=42.11 E-value=58 Score=25.53 Aligned_cols=31 Identities=19% Similarity=0.280 Sum_probs=27.1
Q ss_pred CeEEEEEcCCcEEEEEEEEeccccceEEeeE
Q psy6026 16 KDVVVELKNDVSICGTLHSVDQYLNIKLTDI 46 (98)
Q Consensus 16 k~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~ 46 (98)
..+.|.+.||+.|.+.+.++|...++.|=..
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 4788999999999999999999999877544
No 109
>PRK08477 biotin--protein ligase; Provisional
Probab=40.94 E-value=93 Score=22.45 Aligned_cols=37 Identities=5% Similarity=-0.116 Sum_probs=29.9
Q ss_pred HhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q psy6026 10 FKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDIS 47 (98)
Q Consensus 10 L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~ 47 (98)
..-..|+.|+|. .++..++|+..++|+.--+.+..-.
T Consensus 170 ~~~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~ 206 (211)
T PRK08477 170 LEFEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKK 206 (211)
T ss_pred HHHHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEE
Confidence 344679999987 5789999999999998888776544
No 110
>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=40.89 E-value=65 Score=18.74 Aligned_cols=26 Identities=23% Similarity=0.244 Sum_probs=18.5
Q ss_pred cCCCeEEEEEcCCcEE-EEEEEEeccc
Q psy6026 13 LVGKDVVVELKNDVSI-CGTLHSVDQY 38 (98)
Q Consensus 13 l~gk~V~V~Lkng~~~-~G~L~~~D~~ 38 (98)
..|..|.+.=-++..| .|++.+||.-
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 3588999998888655 9999999963
No 111
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=40.31 E-value=45 Score=23.91 Aligned_cols=26 Identities=35% Similarity=0.561 Sum_probs=22.6
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEec
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLHSVD 36 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~~~D 36 (98)
..++|++|.|.+...+.+.|.+.+++
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 45899999999999999999998885
No 112
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=39.88 E-value=30 Score=19.30 Aligned_cols=15 Identities=60% Similarity=0.966 Sum_probs=12.6
Q ss_pred HHHHhhcCCCeEEEE
Q psy6026 7 YSFFKSLVGKDVVVE 21 (98)
Q Consensus 7 ~~~L~~l~gk~V~V~ 21 (98)
.+.+++++||+|+|.
T Consensus 11 ~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVT 25 (48)
T ss_pred hHHHHHhcCCeEEEE
Confidence 467888999999986
No 113
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=37.67 E-value=89 Score=19.22 Aligned_cols=30 Identities=23% Similarity=0.190 Sum_probs=21.9
Q ss_pred HHHHhhcCCCeEEEEEcCCc----EEEEEEEEec
Q psy6026 7 YSFFKSLVGKDVVVELKNDV----SICGTLHSVD 36 (98)
Q Consensus 7 ~~~L~~l~gk~V~V~Lkng~----~~~G~L~~~D 36 (98)
-.-|.+.+|++|.+....|+ +-.|+|.+.=
T Consensus 9 k~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~tY 42 (76)
T PF06257_consen 9 KKELESHVGKRVKLKANKGRKKIIEREGVLEETY 42 (76)
T ss_dssp HHHHHHTTTSEEEEEE--SSS--S-EEEEEEEE-
T ss_pred HHHHHHcCCCEEEEEEcCCceEEEEEEEEEEeec
Confidence 35688899999999999995 6789998764
No 114
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=37.12 E-value=53 Score=20.57 Aligned_cols=23 Identities=17% Similarity=0.192 Sum_probs=18.5
Q ss_pred HhhcCCCeEEEEEcCCcEEEEEE
Q psy6026 10 FKSLVGKDVVVELKNDVSICGTL 32 (98)
Q Consensus 10 L~~l~gk~V~V~Lkng~~~~G~L 32 (98)
|.-+..-+++.+||+|..+.|.-
T Consensus 18 lACl~hl~l~L~lkdGev~~a~A 40 (84)
T COG4568 18 LACLHHLPLTLELKDGEVLQAKA 40 (84)
T ss_pred HHHhhhceEEEEEcCCeEEEEEe
Confidence 44455678999999999999964
No 115
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=35.69 E-value=63 Score=17.77 Aligned_cols=20 Identities=30% Similarity=0.449 Sum_probs=13.8
Q ss_pred EEEEEEEeccccceEEeeEE
Q psy6026 28 ICGTLHSVDQYLNIKLTDIS 47 (98)
Q Consensus 28 ~~G~L~~~D~~mNi~L~~~~ 47 (98)
..|+..++|+...+.|.+..
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 68999999999999998743
No 116
>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=34.24 E-value=27 Score=23.38 Aligned_cols=26 Identities=27% Similarity=0.434 Sum_probs=21.7
Q ss_pred hHHHHhhcCCCeEEEEEcCC-cEEEEE
Q psy6026 6 FYSFFKSLVGKDVVVELKND-VSICGT 31 (98)
Q Consensus 6 p~~~L~~l~gk~V~V~Lkng-~~~~G~ 31 (98)
.-.++..+.|+++.|.++.. ..+.|.
T Consensus 94 l~~~~~~l~gk~l~V~v~~~~~e~nGk 120 (141)
T PF05037_consen 94 LEQFLNQLLGKPLRVTVKWEENEYNGK 120 (141)
T ss_pred HHHHHHHHcCCeeEEEecccccCCCCc
Confidence 45788899999999999988 777774
No 117
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=33.62 E-value=97 Score=20.80 Aligned_cols=35 Identities=20% Similarity=0.354 Sum_probs=29.2
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEeccccceEEee
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~ 45 (98)
.+..|..|.|-+++-..-+|-+.-+|+.+=+.+.+
T Consensus 101 d~~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrIte 135 (136)
T COG1886 101 DKLAGEPVDILVNGRLIGRGEVVVVDDKFGVRITE 135 (136)
T ss_pred CCcCCCceEEEECCEEEEEEeEEEECCeEEEEEEe
Confidence 46678899999888899999999999887777654
No 118
>KOG4401|consensus
Probab=33.25 E-value=45 Score=24.00 Aligned_cols=35 Identities=14% Similarity=0.114 Sum_probs=30.4
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q psy6026 13 LVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDIS 47 (98)
Q Consensus 13 l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~ 47 (98)
.+|..|.+...+|....|.+.+||-.-+...-++.
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 35888999999999999999999988877776666
No 119
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.69 E-value=60 Score=23.59 Aligned_cols=23 Identities=17% Similarity=0.163 Sum_probs=19.5
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEE
Q psy6026 12 SLVGKDVVVE-LKNDVSICGTLHS 34 (98)
Q Consensus 12 ~l~gk~V~V~-Lkng~~~~G~L~~ 34 (98)
...|..|.|+ +.+|+.+.|+..+
T Consensus 183 G~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 183 AGENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCCEEEEEECCCCCEEEEEEeC
Confidence 4578999999 7999999998865
No 120
>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=31.68 E-value=51 Score=19.55 Aligned_cols=23 Identities=30% Similarity=0.460 Sum_probs=18.8
Q ss_pred EEEEEEEEec-cccceEEeeEEEE
Q psy6026 27 SICGTLHSVD-QYLNIKLTDISVT 49 (98)
Q Consensus 27 ~~~G~L~~~D-~~mNi~L~~~~~~ 49 (98)
..+|++.++| ..+-|.|+|-.-+
T Consensus 4 ~veG~I~~id~~~~titLdDGksy 27 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSY 27 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEE
Confidence 4689999999 5779999987643
No 121
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.47 E-value=66 Score=22.25 Aligned_cols=23 Identities=22% Similarity=0.371 Sum_probs=18.8
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEE
Q psy6026 12 SLVGKDVVVE-LKNDVSICGTLHS 34 (98)
Q Consensus 12 ~l~gk~V~V~-Lkng~~~~G~L~~ 34 (98)
...|..|.|+ +.+|+.++|++.+
T Consensus 128 G~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 128 GAAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4568889998 8899999998764
No 122
>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=31.29 E-value=1.2e+02 Score=21.46 Aligned_cols=34 Identities=24% Similarity=0.370 Sum_probs=28.1
Q ss_pred hHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccc
Q psy6026 6 FYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLN 40 (98)
Q Consensus 6 p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mN 40 (98)
+..+=+.|+|+.+.-++. |..+.|.+....+|+-
T Consensus 6 ~~~vA~~LLGk~Lv~~~~-~~~~~grIvEtEAY~G 39 (179)
T cd00540 6 TVEVARDLLGKVLVRRLP-GGILSGRIVETEAYLG 39 (179)
T ss_pred HHHHHHHhCCCEEEEECC-CCEEEEEEEEEeccCC
Confidence 456778899999887775 6689999999999964
No 123
>PRK10708 hypothetical protein; Provisional
Probab=30.68 E-value=65 Score=19.01 Aligned_cols=26 Identities=19% Similarity=0.291 Sum_probs=22.6
Q ss_pred CCCeEEEEEcCCcEEEEEEEEecccc
Q psy6026 14 VGKDVVVELKNDVSICGTLHSVDQYL 39 (98)
Q Consensus 14 ~gk~V~V~Lkng~~~~G~L~~~D~~m 39 (98)
++-+|+|++..|..-.|++.++..|-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 46789999999999999999988764
No 124
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=30.14 E-value=97 Score=19.59 Aligned_cols=28 Identities=18% Similarity=0.059 Sum_probs=22.1
Q ss_pred EECCCCCcceeecceEEEEcCeEEEEecCC
Q psy6026 48 VTDPDKYPHMLSVKNCFIRGSVVRYVQLPG 77 (98)
Q Consensus 48 ~~~~~~~~~~~~~~~v~IRG~~I~~I~~p~ 77 (98)
+.+.+|. ...-|.+...|..+.-|.+|+
T Consensus 69 EFS~~G~--~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 69 EFSSDGE--DRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred EEeCCCh--hcceEEEEEECCeeeEEEcCC
Confidence 3455554 347799999999999999986
No 125
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.96 E-value=83 Score=22.81 Aligned_cols=23 Identities=13% Similarity=0.117 Sum_probs=19.7
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEE
Q psy6026 12 SLVGKDVVVELKNDVSICGTLHS 34 (98)
Q Consensus 12 ~l~gk~V~V~Lkng~~~~G~L~~ 34 (98)
+.+|..|+|+-.+|+++.|++.+
T Consensus 193 G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 193 GNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCCEEEEEeCCCCEEEEEEec
Confidence 46789999999999999998875
No 126
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=29.48 E-value=68 Score=25.23 Aligned_cols=23 Identities=22% Similarity=0.372 Sum_probs=20.9
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEE
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLH 33 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~ 33 (98)
+.+.|++|+|...+|..|.|++-
T Consensus 93 ~~~~gq~v~i~t~~g~~i~GvIg 115 (355)
T COG1363 93 QVLEGQRVTIHTDKGKKIRGVIG 115 (355)
T ss_pred hhccCcEEEEEeCCCcEEeeeEc
Confidence 45779999999999999999997
No 127
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=29.32 E-value=83 Score=22.50 Aligned_cols=32 Identities=25% Similarity=0.311 Sum_probs=22.2
Q ss_pred HHHHhhcCCC--eEEEEE-cCCcEEEEEEEEeccc
Q psy6026 7 YSFFKSLVGK--DVVVEL-KNDVSICGTLHSVDQY 38 (98)
Q Consensus 7 ~~~L~~l~gk--~V~V~L-kng~~~~G~L~~~D~~ 38 (98)
+.||-.+-+. ++.+.+ .++..|+|+|.++|+-
T Consensus 123 I~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 4566666654 344444 4679999999999964
No 128
>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=27.64 E-value=1.2e+02 Score=18.02 Aligned_cols=55 Identities=20% Similarity=0.138 Sum_probs=36.7
Q ss_pred hcCCCeEEEEEcCC-cEEEEEEEEeccc-cceEEeeEEEECCCCCcceeecceEEEEcCeEE
Q psy6026 12 SLVGKDVVVELKND-VSICGTLHSVDQY-LNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVR 71 (98)
Q Consensus 12 ~l~gk~V~V~Lkng-~~~~G~L~~~D~~-mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~ 71 (98)
..+|+.|.|...+. -+|+|.+..+|+- --++|..+. .+|- .....++-+|..-|+
T Consensus 3 dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~---~ngi--k~~~~EVt~~~~DI~ 59 (62)
T cd01737 3 DWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPF---HNGV--KCLVPEVTFRAGDIR 59 (62)
T ss_pred cccceEEEEecCCceEEEEEEEEEeCccceEEEEeecc---cCCc--cccCceEEEEEcchh
Confidence 35789999999888 7999999999964 345555533 2221 234566776665553
No 129
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.43 E-value=87 Score=21.18 Aligned_cols=23 Identities=22% Similarity=0.445 Sum_probs=18.3
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEE
Q psy6026 12 SLVGKDVVVE-LKNDVSICGTLHS 34 (98)
Q Consensus 12 ~l~gk~V~V~-Lkng~~~~G~L~~ 34 (98)
...|..|.|+ +.+|++++|+..+
T Consensus 109 G~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 109 GGVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4568888885 7889999998764
No 130
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=27.18 E-value=1.4e+02 Score=24.24 Aligned_cols=43 Identities=21% Similarity=0.078 Sum_probs=35.2
Q ss_pred cchHHHHhhcCCCeEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q psy6026 4 LLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDIS 47 (98)
Q Consensus 4 ~~p~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~~ 47 (98)
..|-.++.++.||.|+- =|+|+.++++|.+-|.-.-+.+.+-.
T Consensus 71 ~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~ 113 (421)
T COG5316 71 LSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGV 113 (421)
T ss_pred cCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcE
Confidence 46788899999999999 79999999999999876666555443
No 131
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.01 E-value=80 Score=23.68 Aligned_cols=24 Identities=17% Similarity=0.219 Sum_probs=20.1
Q ss_pred hcCCCeEEEE-EcCCcEEEEEEEEe
Q psy6026 12 SLVGKDVVVE-LKNDVSICGTLHSV 35 (98)
Q Consensus 12 ~l~gk~V~V~-Lkng~~~~G~L~~~ 35 (98)
+..|..|.|+ +.+|+++.|++.+-
T Consensus 230 G~~Gd~IrVrN~~SgkvV~a~V~~~ 254 (261)
T PRK06804 230 GRKGELIKVKNLSSGRVVTATVDGS 254 (261)
T ss_pred CCCCCEEEEEECCCCCEEEEEEecC
Confidence 4578999999 89999999998753
No 132
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=26.97 E-value=74 Score=18.77 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=22.5
Q ss_pred CCCeEEEEEcCCcEEEEEEEEecccc
Q psy6026 14 VGKDVVVELKNDVSICGTLHSVDQYL 39 (98)
Q Consensus 14 ~gk~V~V~Lkng~~~~G~L~~~D~~m 39 (98)
++-+|+|++..|..-.|++.++..|-
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 46789999999999999999988764
No 133
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=26.91 E-value=1.4e+02 Score=21.17 Aligned_cols=27 Identities=19% Similarity=0.231 Sum_probs=23.2
Q ss_pred CCCeEEEEEcCCcEEEEEEEEeccccc
Q psy6026 14 VGKDVVVELKNDVSICGTLHSVDQYLN 40 (98)
Q Consensus 14 ~gk~V~V~Lkng~~~~G~L~~~D~~mN 40 (98)
.|.+|.|.+.+|..+.|++..++...+
T Consensus 141 ~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 141 KGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CCCEEEEEECCCCEEEEEEEEEccccC
Confidence 388999999999999999999986543
No 134
>PRK15493 5-methylthioadenosine/S-adenosylhomocysteine deaminase; Provisional
Probab=26.34 E-value=1.4e+02 Score=23.45 Aligned_cols=37 Identities=3% Similarity=0.097 Sum_probs=24.1
Q ss_pred cceEEeeEEEECCCCCcceeecceEEEEcCeEEEEec
Q psy6026 39 LNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL 75 (98)
Q Consensus 39 mNi~L~~~~~~~~~~~~~~~~~~~v~IRG~~I~~I~~ 75 (98)
||+.+.++.+...+.......-+.+.|.|..|..|..
T Consensus 1 ~~~li~~~~v~t~~~~~~~~~~g~V~i~~g~I~~vg~ 37 (435)
T PRK15493 1 MKTTYVNATIVTMNEQNEVIENGYIIVENDQIIDVNS 37 (435)
T ss_pred CeEEEEccEEEEeCCCCcEecCcEEEEECCEEEEEcC
Confidence 6778888876543321112344688899999998864
No 135
>PF13861 FLgD_tudor: FlgD Tudor-like domain; PDB: 3OSV_A 3C12_A.
Probab=24.18 E-value=1.5e+02 Score=16.77 Aligned_cols=10 Identities=60% Similarity=0.996 Sum_probs=8.7
Q ss_pred hcCCCeEEEE
Q psy6026 12 SLVGKDVVVE 21 (98)
Q Consensus 12 ~l~gk~V~V~ 21 (98)
+++||.|.+.
T Consensus 9 ~lIGk~V~~~ 18 (61)
T PF13861_consen 9 SLIGKEVLVP 18 (61)
T ss_dssp CTTTSEEEEE
T ss_pred HhcCCEEEEC
Confidence 6889999996
No 136
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.14 E-value=78 Score=19.76 Aligned_cols=30 Identities=13% Similarity=0.148 Sum_probs=22.4
Q ss_pred HHHHhhcCCCeEEEEEcCCcEE----EEEEEEec
Q psy6026 7 YSFFKSLVGKDVVVELKNDVSI----CGTLHSVD 36 (98)
Q Consensus 7 ~~~L~~l~gk~V~V~Lkng~~~----~G~L~~~D 36 (98)
-.-+++-+|++|.+.+.+|+.= .|.|...=
T Consensus 11 K~~i~ah~G~~v~lk~ngGRKk~~~r~G~L~EtY 44 (80)
T COG4466 11 KESIDAHLGERVTLKANGGRKKTIERSGILIETY 44 (80)
T ss_pred HHHHHhccCcEEEEEecCCceeeehhceEEeeec
Confidence 3567888999999999999643 46665543
No 137
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=23.34 E-value=1.2e+02 Score=16.06 Aligned_cols=18 Identities=17% Similarity=0.239 Sum_probs=14.1
Q ss_pred hhcCCCeEEEEEcCCcEE
Q psy6026 11 KSLVGKDVVVELKNDVSI 28 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~ 28 (98)
.+.-|..|+|++.+|...
T Consensus 19 ~~~~g~~vtV~~~~G~~~ 36 (42)
T PF02736_consen 19 IEEEGDKVTVKTEDGKEV 36 (42)
T ss_dssp EEEESSEEEEEETTTEEE
T ss_pred EEEcCCEEEEEECCCCEE
Confidence 355688999999998764
No 138
>PF13144 SAF_2: SAF-like
Probab=22.37 E-value=1.4e+02 Score=20.63 Aligned_cols=23 Identities=13% Similarity=0.195 Sum_probs=18.1
Q ss_pred hcCCCeEEEEEcC-CcEEEEEEEE
Q psy6026 12 SLVGKDVVVELKN-DVSICGTLHS 34 (98)
Q Consensus 12 ~l~gk~V~V~Lkn-g~~~~G~L~~ 34 (98)
+.+|..|.|+-.+ |+.+.|++.+
T Consensus 167 G~~G~~I~V~N~~S~k~v~g~V~~ 190 (196)
T PF13144_consen 167 GALGDTIRVKNLSSGKIVQGRVIG 190 (196)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4568888888854 8999998875
No 139
>KOG3493|consensus
Probab=21.59 E-value=78 Score=19.25 Aligned_cols=20 Identities=30% Similarity=0.441 Sum_probs=15.2
Q ss_pred HHhhcCCCeEEEEEcCCcEE
Q psy6026 9 FFKSLVGKDVVVELKNDVSI 28 (98)
Q Consensus 9 ~L~~l~gk~V~V~Lkng~~~ 28 (98)
.++..+||+|+|+...+-++
T Consensus 5 ~~nDrLGKKVRvKCn~dDti 24 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDTI 24 (73)
T ss_pred hhhhhcCceEEEEeCCcccc
Confidence 35667899999998876554
No 140
>cd01343 PL1_Passenger_AT Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases, SPATEs (serine protease autotransporters secreted by Enterobacteriaceae), Bordetella pertacins, and nonprotease autotransporters, TibA and similar AIDA-like proteins.
Probab=21.57 E-value=3.1e+02 Score=20.04 Aligned_cols=51 Identities=16% Similarity=0.204 Sum_probs=34.9
Q ss_pred eEEEEEcCCcEEEEEEEEeccccceEEe-eEEEECCCCCcceeecceEEEEcCeEEEE
Q psy6026 17 DVVVELKNDVSICGTLHSVDQYLNIKLT-DISVTDPDKYPHMLSVKNCFIRGSVVRYV 73 (98)
Q Consensus 17 ~V~V~Lkng~~~~G~L~~~D~~mNi~L~-~~~~~~~~~~~~~~~~~~v~IRG~~I~~I 73 (98)
.+.+.|.++..+.|.+.+.+ -++.|. +..-.-. +. +.++.+-+.|..|.|-
T Consensus 74 ~~~~~l~~~s~l~G~i~~~~--~~v~l~~~s~W~~t-g~---S~v~~L~l~~g~v~f~ 125 (233)
T cd01343 74 LAELLLGGNAAWTGAIQGLN--ATVSLNLNSVWTLT-GD---SNVNNLTLNGGTVDFN 125 (233)
T ss_pred eEEEEEcCCCEEEeEEeccc--ceEEEcCCCEEEEe-CC---cccceeEecCCEEEec
Confidence 58889999999999999987 456666 4443222 22 2457777777777664
No 141
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=21.26 E-value=2.1e+02 Score=21.62 Aligned_cols=32 Identities=16% Similarity=0.288 Sum_probs=26.5
Q ss_pred CCeEEEEEcCCcEEEEEEEEeccccceEEeeE
Q psy6026 15 GKDVVVELKNDVSICGTLHSVDQYLNIKLTDI 46 (98)
Q Consensus 15 gk~V~V~Lkng~~~~G~L~~~D~~mNi~L~~~ 46 (98)
..++.+.+.||+.+.+.+.+.|....+-+-..
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki 126 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKI 126 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEe
Confidence 56788999999999999999998877655433
No 142
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=21.18 E-value=1.4e+02 Score=20.54 Aligned_cols=24 Identities=33% Similarity=0.572 Sum_probs=18.7
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEecc
Q psy6026 11 KSLVGKDVVVELKNDVSICGTLHSVDQ 37 (98)
Q Consensus 11 ~~l~gk~V~V~Lkng~~~~G~L~~~D~ 37 (98)
.+++||.|.+ .+| .+.|++.++.-
T Consensus 93 ~slIGk~V~~--~~~-~~~G~V~sV~~ 116 (140)
T PRK06009 93 EGLIGRTVTS--ADG-SITGVVKSVTV 116 (140)
T ss_pred HHhcCCEEEe--cCC-cEEEEEEEEEE
Confidence 4689999975 455 68999998864
No 143
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=20.76 E-value=1.7e+02 Score=23.50 Aligned_cols=27 Identities=15% Similarity=0.347 Sum_probs=22.2
Q ss_pred HhhcCCCeEEEEEc--CC--cEEEEEEEEec
Q psy6026 10 FKSLVGKDVVVELK--ND--VSICGTLHSVD 36 (98)
Q Consensus 10 L~~l~gk~V~V~Lk--ng--~~~~G~L~~~D 36 (98)
+.+++|++|.|.+. +| +.+.|.+.++.
T Consensus 42 ~~~llG~~v~l~i~~~~~~~r~f~GiVt~~~ 72 (513)
T TIGR03361 42 LEDLLGQPATLTLGRDGGGPRYFHGIVTRFE 72 (513)
T ss_pred HHHHcCCeEEEEEEeCCCceEEEEEEEEEEE
Confidence 67789999999995 33 67899999886
No 144
>PF01556 CTDII: DnaJ C terminal domain; InterPro: IPR002939 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold []. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate. This domain consists of the C-terminal region of the DnaJ protein. The function of this domain is unknown. It is found associated with IPR001623 from INTERPRO and IPR001305 from INTERPRO. ; GO: 0051082 unfolded protein binding, 0006457 protein folding; PDB: 2Q2G_A 2QLD_A 3AGX_A 3AGZ_A 3AGY_A 3I38_J 3LZ8_B 2B26_B 1C3G_A 1XAO_B ....
Probab=20.58 E-value=53 Score=19.64 Aligned_cols=26 Identities=15% Similarity=0.208 Sum_probs=18.6
Q ss_pred cchHHHHhhcCCCeEEEEEcCCcEEE
Q psy6026 4 LLFYSFFKSLVGKDVVVELKNDVSIC 29 (98)
Q Consensus 4 ~~p~~~L~~l~gk~V~V~Lkng~~~~ 29 (98)
..++++..++.|..+.|.+-+|+.+.
T Consensus 5 ~~~I~l~~al~G~~i~i~~l~g~~~~ 30 (81)
T PF01556_consen 5 TIPISLKEALLGGTISIPTLDGKTIK 30 (81)
T ss_dssp EEEEEHHHHHH-EEEEEE-TTS-EEE
T ss_pred EEEeCHHHHhCCCEEEEECCCCCEEE
Confidence 35678899999999999988886554
No 145
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=20.05 E-value=1.7e+02 Score=18.54 Aligned_cols=22 Identities=41% Similarity=0.593 Sum_probs=16.5
Q ss_pred HHHHhhcCCCeEEEEEcCCcEEEEEEEEec
Q psy6026 7 YSFFKSLVGKDVVVELKNDVSICGTLHSVD 36 (98)
Q Consensus 7 ~~~L~~l~gk~V~V~Lkng~~~~G~L~~~D 36 (98)
.+.|.++.|+.|++. |++.++|
T Consensus 10 ~~~L~~~~gk~Vriv--------Gkv~~~~ 31 (109)
T PF08661_consen 10 GSMLSQFVGKTVRIV--------GKVESVD 31 (109)
T ss_dssp GGGGGGGTTSEEEEE--------EEEEEE-
T ss_pred HHHHHhhCCCeEEEE--------EEEeeEc
Confidence 467889999999875 6777776
Done!