Query 034490
Match_columns 93
No_of_seqs 117 out of 1028
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 03:25:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034490.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034490hhsearch_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 1.3E-27 2.8E-32 149.4 10.7 86 2-89 1-87 (90)
2 cd01725 LSm2 The eukaryotic Sm 99.9 2.5E-27 5.4E-32 145.5 9.9 80 2-81 1-80 (81)
3 cd01723 LSm4 The eukaryotic Sm 99.9 8.7E-27 1.9E-31 141.5 9.6 76 2-78 1-76 (76)
4 cd01721 Sm_D3 The eukaryotic S 99.9 2.1E-26 4.5E-31 137.9 10.2 70 3-74 1-70 (70)
5 cd01733 LSm10 The eukaryotic S 99.9 4.9E-25 1.1E-29 134.5 10.3 69 3-73 10-78 (78)
6 cd01726 LSm6 The eukaryotic Sm 99.9 7.2E-25 1.6E-29 130.1 9.3 67 3-71 1-67 (67)
7 KOG3448 Predicted snRNP core p 99.9 1.5E-24 3.3E-29 133.5 9.6 92 1-92 1-92 (96)
8 cd01722 Sm_F The eukaryotic Sm 99.9 5.6E-24 1.2E-28 126.6 8.9 68 2-71 1-68 (68)
9 PRK00737 small nuclear ribonuc 99.9 1.5E-23 3.2E-28 126.1 9.6 68 2-71 4-71 (72)
10 cd01731 archaeal_Sm1 The archa 99.9 1.9E-23 4.1E-28 124.2 9.4 67 3-71 1-67 (68)
11 cd01732 LSm5 The eukaryotic Sm 99.9 2E-23 4.4E-28 126.8 9.6 69 1-71 2-73 (76)
12 KOG3293 Small nuclear ribonucl 99.9 5.7E-24 1.2E-28 137.9 6.6 85 1-86 1-85 (134)
13 cd01719 Sm_G The eukaryotic Sm 99.9 6.8E-22 1.5E-26 119.0 9.4 70 3-74 1-70 (72)
14 PF01423 LSM: LSM domain ; In 99.9 1.3E-21 2.7E-26 115.3 8.9 67 5-72 1-67 (67)
15 COG1958 LSM1 Small nuclear rib 99.9 1.7E-21 3.6E-26 118.8 9.6 70 2-71 7-78 (79)
16 smart00651 Sm snRNP Sm protein 99.9 1.8E-21 3.8E-26 114.6 8.6 67 5-72 1-67 (67)
17 cd01730 LSm3 The eukaryotic Sm 99.9 3.4E-21 7.4E-26 118.4 9.0 69 3-71 2-81 (82)
18 cd01720 Sm_D2 The eukaryotic S 99.8 1.1E-20 2.3E-25 117.5 9.2 71 2-72 2-85 (87)
19 cd00600 Sm_like The eukaryotic 99.8 2.7E-20 5.8E-25 108.2 8.5 63 7-71 1-63 (63)
20 cd01729 LSm7 The eukaryotic Sm 99.8 4.5E-20 9.7E-25 113.3 9.8 70 5-74 5-80 (81)
21 cd01718 Sm_E The eukaryotic Sm 99.8 1.7E-19 3.7E-24 110.3 9.1 69 2-71 6-78 (79)
22 cd01717 Sm_B The eukaryotic Sm 99.8 2.8E-19 6E-24 109.1 9.3 68 5-72 3-78 (79)
23 KOG3172 Small nuclear ribonucl 99.8 1.3E-19 2.8E-24 115.2 7.5 82 2-85 5-86 (119)
24 cd01728 LSm1 The eukaryotic Sm 99.8 6.7E-19 1.5E-23 106.5 10.0 70 3-72 3-73 (74)
25 KOG3482 Small nuclear ribonucl 99.8 1.3E-19 2.9E-24 108.0 6.5 69 2-72 8-76 (79)
26 KOG3428 Small nuclear ribonucl 99.8 1.1E-18 2.3E-23 111.1 9.7 88 1-91 1-89 (109)
27 KOG1783 Small nuclear ribonucl 99.8 1.8E-20 4E-25 111.7 0.7 71 2-74 6-76 (77)
28 cd06168 LSm9 The eukaryotic Sm 99.8 2.3E-18 5.1E-23 104.3 9.8 69 5-73 3-75 (75)
29 cd01727 LSm8 The eukaryotic Sm 99.8 2.9E-18 6.2E-23 103.5 9.6 69 5-74 2-73 (74)
30 PTZ00138 small nuclear ribonuc 99.7 3.9E-17 8.4E-22 101.8 9.5 71 2-73 14-88 (89)
31 KOG1780 Small Nuclear ribonucl 99.7 2.8E-16 6E-21 94.0 6.1 66 5-72 7-72 (77)
32 KOG3460 Small nuclear ribonucl 99.6 1E-16 2.3E-21 97.8 2.1 73 2-74 5-88 (91)
33 KOG1775 U6 snRNA-associated Sm 99.5 2.3E-14 5E-19 86.3 3.5 69 2-71 7-77 (84)
34 KOG1774 Small nuclear ribonucl 99.4 1.4E-13 3E-18 83.8 4.3 67 4-73 18-86 (88)
35 KOG1784 Small Nuclear ribonucl 99.4 6.2E-13 1.3E-17 82.5 4.6 86 5-90 3-90 (96)
36 KOG1781 Small Nuclear ribonucl 99.3 4.3E-13 9.3E-18 84.2 -0.4 76 7-82 22-105 (108)
37 KOG1782 Small Nuclear ribonucl 99.0 4.1E-11 9E-16 77.9 -0.6 69 6-75 13-83 (129)
38 KOG3168 U1 snRNP component [Tr 99.0 8.5E-11 1.8E-15 80.2 -0.3 69 6-75 8-85 (177)
39 KOG3459 Small nuclear ribonucl 98.4 3.1E-08 6.8E-13 63.4 -0.7 69 3-71 25-106 (114)
40 PF14438 SM-ATX: Ataxin 2 SM d 98.4 1.6E-06 3.4E-11 52.2 6.0 44 5-48 5-51 (77)
41 cd01739 LSm11_C The eukaryotic 97.9 1.1E-05 2.3E-10 47.6 2.8 37 12-48 8-48 (66)
42 PF12701 LSM14: Scd6-like Sm d 97.5 0.00085 1.8E-08 42.4 7.5 68 8-75 4-79 (96)
43 PF11095 Gemin7: Gem-associate 97.3 0.0044 9.6E-08 37.9 8.2 64 3-73 15-79 (80)
44 cd01716 Hfq Hfq, an abundant, 96.9 0.0034 7.3E-08 36.6 4.9 37 6-42 3-41 (61)
45 TIGR02383 Hfq RNA chaperone Hf 96.8 0.0038 8.2E-08 36.4 4.6 31 12-42 15-45 (61)
46 cd01736 LSm14_N LSm14 (also kn 96.6 0.024 5.3E-07 34.2 7.3 62 8-69 2-72 (74)
47 PRK00395 hfq RNA-binding prote 96.6 0.006 1.3E-07 37.3 4.6 32 12-43 19-50 (79)
48 PF02237 BPL_C: Biotin protein 96.1 0.027 5.9E-07 30.8 5.3 34 11-45 2-35 (48)
49 COG1923 Hfq Uncharacterized ho 96.1 0.015 3.3E-07 35.2 4.2 35 5-39 10-46 (77)
50 PF06372 Gemin6: Gemin6 protei 96.0 0.041 8.8E-07 38.0 6.8 62 5-75 10-72 (166)
51 PF10842 DUF2642: Protein of u 95.6 0.034 7.4E-07 32.8 4.3 53 4-71 13-65 (66)
52 cd01735 LSm12_N LSm12 belongs 95.5 0.15 3.2E-06 29.7 6.8 36 10-45 4-39 (61)
53 PRK14638 hypothetical protein; 94.8 0.068 1.5E-06 36.1 4.4 36 5-41 93-128 (150)
54 PRK14639 hypothetical protein; 94.4 0.094 2E-06 35.0 4.4 35 5-40 81-115 (140)
55 PRK14091 RNA-binding protein H 94.2 0.12 2.5E-06 35.7 4.6 32 12-43 104-135 (165)
56 PRK14091 RNA-binding protein H 93.8 0.16 3.4E-06 35.0 4.7 38 6-43 16-55 (165)
57 PRK02001 hypothetical protein; 93.7 0.55 1.2E-05 31.8 7.1 34 6-40 84-117 (152)
58 PRK14644 hypothetical protein; 92.5 0.28 6E-06 32.6 4.3 35 6-41 79-117 (136)
59 COG0779 Uncharacterized protei 92.5 0.44 9.5E-06 32.4 5.3 32 5-36 92-127 (153)
60 cd01734 YlxS_C YxlS is a Bacil 92.4 0.35 7.5E-06 29.2 4.3 35 5-40 18-56 (83)
61 KOG1073 Uncharacterized mRNA-a 92.1 0.57 1.2E-05 36.0 6.1 67 8-74 5-80 (361)
62 PRK14640 hypothetical protein; 91.7 0.4 8.6E-06 32.3 4.4 36 5-41 90-129 (152)
63 PRK14642 hypothetical protein; 91.2 0.46 9.9E-06 33.6 4.3 34 6-40 94-140 (197)
64 PRK14633 hypothetical protein; 90.9 0.53 1.2E-05 31.7 4.3 36 5-41 87-126 (150)
65 PRK14632 hypothetical protein; 90.3 0.61 1.3E-05 32.1 4.3 36 5-41 91-133 (172)
66 PRK14636 hypothetical protein; 90.2 0.59 1.3E-05 32.4 4.2 35 5-40 91-129 (176)
67 PRK14643 hypothetical protein; 90.2 0.62 1.3E-05 31.9 4.2 30 6-35 98-131 (164)
68 PRK14645 hypothetical protein; 90.1 0.63 1.4E-05 31.6 4.2 33 6-40 96-128 (154)
69 PRK00092 ribosome maturation p 89.6 0.79 1.7E-05 30.8 4.3 31 5-35 91-125 (154)
70 PF02576 DUF150: Uncharacteris 89.6 0.55 1.2E-05 30.9 3.5 30 5-34 80-113 (141)
71 PRK14634 hypothetical protein; 89.5 0.79 1.7E-05 31.0 4.3 35 5-40 93-131 (155)
72 PRK14646 hypothetical protein; 89.0 0.9 2E-05 30.8 4.3 35 5-40 93-131 (155)
73 PRK14647 hypothetical protein; 88.3 1.1 2.3E-05 30.5 4.3 30 5-34 92-130 (159)
74 PRK14637 hypothetical protein; 87.4 1.3 2.8E-05 30.0 4.2 36 5-41 91-127 (151)
75 PRK09618 flgD flagellar basal 86.8 1.3 2.7E-05 29.9 3.9 26 8-33 88-113 (142)
76 PRK14631 hypothetical protein; 86.7 1.5 3.3E-05 30.3 4.3 29 5-33 110-142 (174)
77 PRK14641 hypothetical protein; 86.5 1.3 2.9E-05 30.6 4.0 29 5-33 97-129 (173)
78 PRK06955 biotin--protein ligas 84.9 5 0.00011 29.6 6.7 33 9-41 246-278 (300)
79 PRK14630 hypothetical protein; 81.1 3.3 7.2E-05 27.7 4.0 29 6-35 91-119 (143)
80 PRK11886 bifunctional biotin-- 81.1 9.8 0.00021 28.0 6.9 31 10-41 270-300 (319)
81 PF11607 DUF3247: Protein of u 80.7 2.6 5.7E-05 26.6 3.2 19 12-30 28-46 (101)
82 PRK13325 bifunctional biotin-- 79.0 10 0.00022 30.9 6.8 33 9-41 275-307 (592)
83 PRK08330 biotin--protein ligas 78.0 17 0.00037 25.7 7.2 34 9-43 185-219 (236)
84 TIGR00121 birA_ligase birA, bi 77.6 14 0.00031 26.0 6.7 32 9-41 190-221 (237)
85 PF03614 Flag1_repress: Repres 77.3 3 6.5E-05 28.5 2.9 25 11-35 119-143 (165)
86 PF07073 ROF: Modulator of Rho 76.1 2.8 6.1E-05 25.5 2.3 23 6-28 11-33 (80)
87 PRK11911 flgD flagellar basal 75.3 5.7 0.00012 26.7 3.8 26 9-34 90-115 (140)
88 PRK14635 hypothetical protein; 73.6 8 0.00017 26.3 4.3 35 6-41 93-132 (162)
89 PTZ00275 biotin-acetyl-CoA-car 67.7 17 0.00038 26.7 5.3 32 10-42 235-266 (285)
90 PRK11625 Rho-binding antitermi 67.4 16 0.00036 22.4 4.3 55 7-71 18-72 (84)
91 PRK10898 serine endoprotease; 66.1 16 0.00035 27.6 5.0 33 12-44 101-133 (353)
92 PF03614 Flag1_repress: Repres 65.5 12 0.00025 25.7 3.6 33 12-44 29-61 (165)
93 PRK10139 serine endoprotease; 62.8 19 0.00042 28.2 5.0 33 12-44 114-146 (455)
94 TIGR02038 protease_degS peripl 62.2 21 0.00045 26.9 4.9 33 12-44 101-133 (351)
95 PRK06792 flgD flagellar basal 61.7 14 0.00031 26.0 3.7 26 9-34 115-140 (190)
96 cd04479 RPA3 RPA3: A subfamily 61.5 22 0.00048 22.0 4.2 14 5-18 8-21 (101)
97 PF10618 Tail_tube: Phage tail 59.9 16 0.00035 23.6 3.5 27 2-28 64-90 (119)
98 COG0340 BirA Biotin-(acetyl-Co 59.7 31 0.00067 24.8 5.2 36 8-43 186-221 (238)
99 PF14563 DUF4444: Domain of un 59.6 11 0.00023 20.3 2.1 22 25-46 10-31 (42)
100 PRK10942 serine endoprotease; 57.6 26 0.00057 27.6 4.9 32 12-43 135-166 (473)
101 TIGR00567 3mg DNA-3-methyladen 56.7 29 0.00064 24.4 4.6 34 4-37 11-44 (192)
102 PF02245 Pur_DNA_glyco: Methyl 54.1 29 0.00064 24.2 4.2 34 3-37 9-42 (184)
103 PF06257 DUF1021: Protein of u 52.4 43 0.00093 20.2 4.2 29 5-33 10-42 (76)
104 TIGR02037 degP_htrA_DO peripla 52.2 35 0.00075 26.2 4.8 32 13-44 82-113 (428)
105 PF14485 DUF4431: Domain of un 52.2 15 0.00033 20.1 2.1 15 4-18 11-25 (48)
106 PRK08477 biotin--protein ligas 50.9 53 0.0012 23.2 5.2 37 8-45 171-207 (211)
107 TIGR02603 CxxCH_TIGR02603 puta 48.7 31 0.00067 22.3 3.5 20 14-33 59-78 (133)
108 TIGR03170 flgA_cterm flagella 48.4 27 0.00058 21.9 3.1 23 9-31 93-116 (122)
109 smart00333 TUDOR Tudor domain. 48.4 42 0.00091 17.8 5.0 25 11-35 5-29 (57)
110 PF09465 LBR_tudor: Lamin-B re 47.0 50 0.0011 18.7 3.7 27 10-36 7-34 (55)
111 PF13437 HlyD_3: HlyD family s 46.6 59 0.0013 19.4 4.4 32 3-34 43-78 (105)
112 PF05954 Phage_GPD: Phage late 45.4 35 0.00077 24.0 3.6 26 8-33 24-49 (292)
113 PF05037 DUF669: Protein of un 43.1 16 0.00036 23.9 1.5 25 5-29 96-121 (141)
114 PRK07018 flgA flagellar basal 42.0 34 0.00073 24.4 3.1 23 9-31 204-227 (235)
115 PRK06789 flagellar motor switc 40.7 80 0.0017 18.8 4.1 36 7-42 36-71 (74)
116 KOG4401 Uncharacterized conser 39.6 45 0.00097 23.5 3.3 35 10-44 9-43 (184)
117 cd00540 AAG Alkyladenine DNA g 37.4 89 0.0019 21.7 4.5 34 3-37 6-39 (179)
118 COG1363 FrvX Cellulase M and r 36.5 47 0.001 25.6 3.3 23 8-30 93-115 (355)
119 PF13861 FLgD_tudor: FlgD Tudo 36.2 79 0.0017 17.5 3.5 24 9-32 9-34 (61)
120 KOG3493 Ubiquitin-like protein 35.3 33 0.00072 20.3 1.8 20 6-25 5-24 (73)
121 PF11743 DUF3301: Protein of u 33.7 91 0.002 19.2 3.8 27 46-74 70-96 (97)
122 COG4568 Rof Transcriptional an 32.6 78 0.0017 19.3 3.1 26 6-31 17-42 (84)
123 TIGR00999 8a0102 Membrane Fusi 32.4 1E+02 0.0023 21.4 4.3 27 11-37 141-167 (265)
124 PRK06005 flgA flagellar basal 32.0 67 0.0015 21.7 3.2 23 9-31 128-151 (160)
125 PF08661 Rep_fac-A_3: Replicat 31.9 81 0.0017 19.6 3.3 21 5-33 11-31 (109)
126 COG4466 Veg Uncharacterized pr 31.4 51 0.0011 20.1 2.2 40 5-44 12-56 (80)
127 cd01737 LSm16_N LSm16 belongs 30.9 1E+02 0.0022 17.8 3.3 55 9-68 3-59 (62)
128 PRK12617 flgA flagellar basal 30.6 69 0.0015 22.8 3.1 23 9-31 183-206 (214)
129 COG1886 FliN Flagellar motor s 30.3 1.3E+02 0.0028 19.7 4.2 36 7-42 100-135 (136)
130 PF01556 CTDII: DnaJ C termina 29.9 28 0.0006 20.4 0.9 25 2-26 6-30 (81)
131 COG0265 DegQ Trypsin-like seri 29.3 1.3E+02 0.0028 22.3 4.5 33 12-44 95-127 (347)
132 PF05071 NDUFA12: NADH ubiquin 29.0 25 0.00055 22.1 0.6 17 27-43 1-17 (105)
133 PRK06009 flgD flagellar basal 28.7 86 0.0019 21.0 3.2 25 8-35 93-117 (140)
134 PF01887 SAM_adeno_trans: S-ad 28.6 96 0.0021 22.6 3.7 22 23-44 168-189 (258)
135 PF06331 Tbf5: Transcription f 28.5 35 0.00077 20.0 1.2 13 24-36 4-16 (68)
136 PRK10708 hypothetical protein; 28.4 79 0.0017 18.2 2.5 26 11-36 3-28 (62)
137 COG5316 Uncharacterized conser 28.3 1.3E+02 0.0028 23.8 4.4 43 2-45 72-114 (421)
138 KOG3382 NADH:ubiquinone oxidor 27.5 33 0.00071 23.1 1.0 26 20-45 40-65 (151)
139 PRK15493 5-methylthioadenosine 27.4 1.5E+02 0.0032 22.8 4.7 37 36-72 1-37 (435)
140 PRK08515 flgA flagellar basal 27.1 1.1E+02 0.0024 21.7 3.7 23 9-31 193-215 (222)
141 PF02736 Myosin_N: Myosin N-te 26.5 98 0.0021 16.0 2.6 19 8-26 19-37 (42)
142 COG0048 RpsL Ribosomal protein 26.2 75 0.0016 21.1 2.5 23 8-30 52-74 (129)
143 cd01343 PL1_Passenger_AT Perta 26.1 2.5E+02 0.0054 20.1 5.5 53 14-71 74-126 (233)
144 TIGR03361 VI_Rhs_Vgr type VI s 26.1 1.2E+02 0.0025 23.9 4.0 27 7-33 42-72 (513)
145 PRK05163 rpsL 30S ribosomal pr 25.8 2E+02 0.0044 18.9 4.4 26 8-33 46-71 (124)
146 PF07076 DUF1344: Protein of u 25.7 76 0.0017 18.4 2.2 24 24-47 4-28 (61)
147 PF08863 YolD: YolD-like prote 25.3 1.5E+02 0.0032 17.3 4.5 32 11-42 41-76 (92)
148 PRK06804 flgA flagellar basal 25.3 96 0.0021 22.8 3.2 23 9-31 230-253 (261)
149 PRK04211 rps12P 30S ribosomal 25.2 87 0.0019 21.2 2.7 24 8-31 64-88 (145)
150 PRK12618 flgA flagellar basal 24.9 1.1E+02 0.0024 20.2 3.2 23 9-31 109-132 (141)
151 PF05343 Peptidase_M42: M42 gl 24.9 92 0.002 23.0 3.1 24 8-32 49-72 (292)
152 cd00319 Ribosomal_S12_like Rib 24.2 84 0.0018 19.8 2.3 24 8-31 31-54 (95)
153 PRK04337 50S ribosomal protein 24.2 1.6E+02 0.0034 18.2 3.5 32 8-39 36-67 (87)
154 PRK09961 exoaminopeptidase; Pr 23.8 1E+02 0.0022 23.2 3.2 23 8-30 90-112 (344)
155 PF10781 DSRB: Dextransucrase 23.8 96 0.0021 17.8 2.3 26 11-36 3-28 (62)
156 COG0361 InfA Translation initi 22.9 1.2E+02 0.0027 18.1 2.8 32 9-40 16-47 (75)
157 TIGR00981 rpsL_bact ribosomal 22.5 2.4E+02 0.0052 18.6 4.4 26 8-33 46-71 (124)
158 COG3466 ISA1214 Putative trans 22.3 85 0.0018 17.6 1.9 15 7-21 37-51 (52)
159 PF15107 FAM216B: FAM216B prot 22.2 49 0.0011 21.4 1.0 27 65-91 15-41 (113)
160 PF14685 Tricorn_PDZ: Tricorn 22.1 1.2E+02 0.0025 18.6 2.7 22 2-23 59-80 (88)
161 CHL00051 rps12 ribosomal prote 21.9 2.4E+02 0.0052 18.6 4.2 26 8-33 46-71 (123)
162 COG2094 Mpg 3-methyladenine DN 21.7 2.2E+02 0.0049 20.3 4.3 39 4-45 16-54 (200)
163 COG2451 Ribosomal protein L35A 21.4 2.3E+02 0.0049 18.0 3.8 30 6-35 40-70 (100)
164 PRK09864 putative peptidase; P 21.0 1.4E+02 0.003 22.9 3.4 24 8-31 89-112 (356)
165 PF12945 YcgR_2: Flagellar pro 20.8 1.8E+02 0.0039 16.5 4.8 33 11-43 3-39 (87)
166 PRK06630 hypothetical protein; 20.6 54 0.0012 20.8 1.0 19 25-43 11-29 (99)
167 PF13144 SAF_2: SAF-like 20.5 1.7E+02 0.0038 19.7 3.6 23 9-31 167-190 (196)
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=1.3e-27 Score=149.42 Aligned_cols=86 Identities=27% Similarity=0.459 Sum_probs=78.3
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCC-cchh
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDG-VDVD 80 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~-~d~~ 80 (93)
.|+.||+++.|++|+|+|+||.+|+|+|.++|.|||++|+||+++..++. ...++.+||||++|+||++|+++ +|+.
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 47899999999999999999999999999999999999999999877665 36789999999999999999997 8999
Q ss_pred hhhHhhhhh
Q 034490 81 LLHDATRRE 89 (93)
Q Consensus 81 ~~~~~~~~~ 89 (93)
+++++++++
T Consensus 79 l~~~~~~~~ 87 (90)
T cd01724 79 LVDSTPKPK 87 (90)
T ss_pred hhhcCCccc
Confidence 998876644
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=2.5e-27 Score=145.52 Aligned_cols=80 Identities=81% Similarity=1.280 Sum_probs=71.8
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchhh
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDL 81 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~~ 81 (93)
+|+.||+++.|++|+|+|+||.+|+|+|.++|.|||++|+||+++.+++......++.++|||++|+||++|+..+|...
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 68999999999999999999999999999999999999999998876553333567899999999999999999888764
No 3
>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=99.94 E-value=8.7e-27 Score=141.47 Aligned_cols=76 Identities=29% Similarity=0.550 Sum_probs=68.5
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcc
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVD 78 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d 78 (93)
+|++||+++.|++|.|+|+||++|+|+|.+||.|||++|+||+++..++.. ...++.+||||++|+||++|++++|
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 699999999999999999999999999999999999999999998766542 3457899999999999999997654
No 4
>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=99.94 E-value=2.1e-26 Score=137.92 Aligned_cols=70 Identities=30% Similarity=0.492 Sum_probs=65.2
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490 3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP 74 (93)
Q Consensus 3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~ 74 (93)
|+.||+++.|++|+|+|+||.+|+|+|.+||.|||++|+||+++..++. ..+++.+||||++|+||++||
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 8899999999999999999999999999999999999999998876654 357899999999999999996
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=4.9e-25 Score=134.53 Aligned_cols=69 Identities=32% Similarity=0.679 Sum_probs=64.4
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490 3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP 73 (93)
Q Consensus 3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~ 73 (93)
+.+||+++.|++|.|+||||.+|+|+|.++|.+||++|+||+++.+++.. .+++.+||||++|+||++|
T Consensus 10 l~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~--~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 10 LIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQ--VQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred HHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCce--eECCcEEEECCEEEEEEcC
Confidence 67999999999999999999999999999999999999999998876653 4789999999999999998
No 6
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.92 E-value=7.2e-25 Score=130.11 Aligned_cols=67 Identities=33% Similarity=0.546 Sum_probs=61.8
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490 3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
|++||++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++. ...++.++|||++|+||+
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 8999999999999999999999999999999999999999999776543 367899999999999985
No 7
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.92 E-value=1.5e-24 Score=133.46 Aligned_cols=92 Identities=75% Similarity=1.159 Sum_probs=88.8
Q ss_pred CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchh
Q 034490 1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVD 80 (93)
Q Consensus 1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~ 80 (93)
|+.++|+++++|++|.|+|||+..+.|+|.++|+|+|+.|.|......++.|+..+...+||||+.|+||++|...+|.+
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 89999999999999999999999999999999999999999999999999999899999999999999999999999999
Q ss_pred hhhHhhhhhhcC
Q 034490 81 LLHDATRREARG 92 (93)
Q Consensus 81 ~~~~~~~~~~~~ 92 (93)
.++++.|+++..
T Consensus 81 ll~da~R~e~~~ 92 (96)
T KOG3448|consen 81 LLQDAARREAIL 92 (96)
T ss_pred HHHHHHHHHHHh
Confidence 999999988754
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=99.91 E-value=5.6e-24 Score=126.62 Aligned_cols=68 Identities=34% Similarity=0.475 Sum_probs=61.7
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
.|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||++...+.. ...+|.++|||++|+||+
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 48999999999999999999999999999999999999999998865433 257899999999999984
No 9
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.91 E-value=1.5e-23 Score=126.11 Aligned_cols=68 Identities=25% Similarity=0.390 Sum_probs=62.5
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
.|+.+|++++|++|.|+|+||++|+|+|.+||+|||++|+||+++.++.. ...++.++|||++|.+|+
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEV--VRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCe--EeEcCcEEEeCCEEEEEc
Confidence 59999999999999999999999999999999999999999999865532 368899999999999996
No 10
>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=99.90 E-value=1.9e-23 Score=124.21 Aligned_cols=67 Identities=30% Similarity=0.457 Sum_probs=62.3
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490 3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
|+.+|++++||+|.|+|+||++|+|+|.+||+|||++|+||+++..+.. ...++.++|||++|.+|+
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 367899999999999986
No 11
>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=99.90 E-value=2e-23 Score=126.82 Aligned_cols=69 Identities=19% Similarity=0.410 Sum_probs=63.3
Q ss_pred CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc---CCCCCceEeeeeEEEecCeEEEEE
Q 034490 1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD---QDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~---~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
|+|+.+|+++++++|.|+|++|+++.|+|.+||+|||++|+||+|.. ++. ....+|.++|||++|.+|+
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~--~~~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGR--KITKLDQILLNGNNICMLV 73 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCc--eeeEcCeEEEeCCeEEEEE
Confidence 89999999999999999999999999999999999999999999975 222 2367899999999999998
No 12
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.90 E-value=5.7e-24 Score=137.86 Aligned_cols=85 Identities=26% Similarity=0.479 Sum_probs=77.5
Q ss_pred CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchh
Q 034490 1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVD 80 (93)
Q Consensus 1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~ 80 (93)
|+|+++|+.+.|+++.||||||.+|.|.|+.||.+|||+|.+++++.+++.. +-.+++++|||++|+|+.+|++++|..
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 8999999999999999999999999999999999999999999999887642 456899999999999999999998887
Q ss_pred hhhHhh
Q 034490 81 LLHDAT 86 (93)
Q Consensus 81 ~~~~~~ 86 (93)
.-+-..
T Consensus 80 kee~~~ 85 (134)
T KOG3293|consen 80 KEECVS 85 (134)
T ss_pred HHHHHH
Confidence 776443
No 13
>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=99.88 E-value=6.8e-22 Score=118.97 Aligned_cols=70 Identities=16% Similarity=0.322 Sum_probs=62.8
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490 3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP 74 (93)
Q Consensus 3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~ 74 (93)
|-++|+++++|+|.|+|++|++|+|+|.+||+|||++|+||+|+..+.. ...+|.++|||++|.+|..-+
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 5578999999999999999999999999999999999999999874433 368899999999999998654
No 14
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.87 E-value=1.3e-21 Score=115.32 Aligned_cols=67 Identities=39% Similarity=0.628 Sum_probs=60.9
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL 72 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 72 (93)
.+|++++|++|+|+|+||++++|+|.+||+|||++|+||+++..+.. +...++.+||||++|++|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-EEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-cEeECcEEEEECCEEEEEEC
Confidence 37999999999999999999999999999999999999999976642 24788999999999999984
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.87 E-value=1.7e-21 Score=118.82 Aligned_cols=70 Identities=30% Similarity=0.444 Sum_probs=60.5
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc--CCCCCceEeeeeEEEecCeEEEEE
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD--QDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~--~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
.|+++|++++|++|.|+|+||++|+|+|.+||+|||++|+||+++. ++........+.++|||++|++|.
T Consensus 7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEe
Confidence 5899999999999999999999999999999999999999999986 332211233449999999999996
No 16
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.86 E-value=1.8e-21 Score=114.61 Aligned_cols=67 Identities=37% Similarity=0.607 Sum_probs=60.4
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL 72 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 72 (93)
.+|++++|++|+|+|+||+++.|+|.+||+|||++|+||+++..+.. +..+++.+||||++|++|+.
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 37999999999999999999999999999999999999999876522 24789999999999999973
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=99.86 E-value=3.4e-21 Score=118.35 Aligned_cols=69 Identities=26% Similarity=0.337 Sum_probs=61.3
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC-----------CCceEeeeeEEEecCeEEEEE
Q 034490 3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK-----------YPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~-----------~~~~~~~~~~~IRG~~I~~I~ 71 (93)
|+.+|+.+++|+|.|.|++|+++.|+|.+||.||||+|+||+|..... ....+.+|.+||||++|.+|+
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 899999999999999999999999999999999999999999975321 112468899999999999986
No 18
>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=99.85 E-value=1.1e-20 Score=117.50 Aligned_cols=71 Identities=21% Similarity=0.254 Sum_probs=61.4
Q ss_pred chhHHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCC-----------CceEeeeeEEEecCeEE
Q 034490 2 LFFSYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKY-----------PHMLSVRNCFIRGSVVR 68 (93)
Q Consensus 2 ~p~~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~-----------~~~~~~~~~~IRG~~I~ 68 (93)
=|+++|+.++ |++|.|.|++|+.+.|+|.+||.|||++|+||+|...... ...+.+|.+||||++|.
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 4999999997 9999999999999999999999999999999999753311 12356899999999999
Q ss_pred EEEc
Q 034490 69 YVQL 72 (93)
Q Consensus 69 ~I~~ 72 (93)
+|+-
T Consensus 82 ~Is~ 85 (87)
T cd01720 82 LVLR 85 (87)
T ss_pred EEec
Confidence 9873
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=99.84 E-value=2.7e-20 Score=108.17 Aligned_cols=63 Identities=35% Similarity=0.549 Sum_probs=57.5
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490 7 FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 7 L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
|++++|++|+|+|+||+.|.|+|.+||.+||++|+||.++..+.. ...++.+||||++|++|+
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 578899999999999999999999999999999999999876533 478999999999999984
No 20
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.84 E-value=4.5e-20 Score=113.28 Aligned_cols=70 Identities=20% Similarity=0.261 Sum_probs=60.1
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCC------CceEeeeeEEEecCeEEEEEcCC
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKY------PHMLSVRNCFIRGSVVRYVQLPP 74 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~------~~~~~~~~~~IRG~~I~~I~~~~ 74 (93)
.-|.++++|+|.|.|++|+++.|+|.+||+||||+|++|+|...+.. ...+.+|.++|||++|.+|...+
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 45899999999999999999999999999999999999999754311 12467899999999999998553
No 21
>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=99.81 E-value=1.7e-19 Score=110.26 Aligned_cols=69 Identities=19% Similarity=0.338 Sum_probs=60.7
Q ss_pred chhHHHhhcCCC--EEEEEEc--CCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490 2 LFFSYFKDLVGR--EVTVELK--NDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 2 ~p~~~L~~~~gk--~V~V~L~--~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
+|+..+.++.++ +|.|+|+ +|+++.|+|.+||+|||++|+||+|...... ....+|.++|||++|.+|+
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~-~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK-TRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc-eEeEcCcEEEeCCEEEEEc
Confidence 699999999999 8888887 8999999999999999999999999864222 2367899999999999987
No 22
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.81 E-value=2.8e-19 Score=109.07 Aligned_cols=68 Identities=16% Similarity=0.257 Sum_probs=58.5
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC--------CCceEeeeeEEEecCeEEEEEc
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK--------YPHMLSVRNCFIRGSVVRYVQL 72 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~--------~~~~~~~~~~~IRG~~I~~I~~ 72 (93)
+-|.+++|++|.|.|+||+.+.|+|.+||.|||++|+||+|..... ..+.+.+|.++|||++|.+|++
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 3478899999999999999999999999999999999999964211 1124689999999999999985
No 23
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.81 E-value=1.3e-19 Score=115.20 Aligned_cols=82 Identities=26% Similarity=0.414 Sum_probs=76.6
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCCcchhh
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDL 81 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~~ 81 (93)
.|+.+|++..|+-|++|+.+|..|+|+|...|++||++|.|++.+..++. ...++.+||||++|+|+.+||.+.++|+
T Consensus 5 vpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~--vs~le~V~IRGS~IRFlvlPdmLKnAPm 82 (119)
T KOG3172|consen 5 VPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR--VSQLEQVFIRGSKIRFLVLPDMLKNAPM 82 (119)
T ss_pred cceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc--ceeeeeEEEecCeEEEEECchHhhcCcc
Confidence 58899999999999999999999999999999999999999999988775 3678999999999999999999999999
Q ss_pred hhHh
Q 034490 82 LHDA 85 (93)
Q Consensus 82 ~~~~ 85 (93)
|..+
T Consensus 83 Fkk~ 86 (119)
T KOG3172|consen 83 FKKG 86 (119)
T ss_pred cccc
Confidence 9744
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=99.80 E-value=6.7e-19 Score=106.49 Aligned_cols=70 Identities=23% Similarity=0.165 Sum_probs=60.1
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC-CCceEeeeeEEEecCeEEEEEc
Q 034490 3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK-YPHMLSVRNCFIRGSVVRYVQL 72 (93)
Q Consensus 3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~-~~~~~~~~~~~IRG~~I~~I~~ 72 (93)
+...|.++++|+|.|.|++|++|.|+|.+||+|||++|+||.|..... ....+.+|.++|||++|.+|..
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 467899999999999999999999999999999999999998864221 1123678999999999999874
No 25
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.80 E-value=1.3e-19 Score=107.96 Aligned_cols=69 Identities=29% Similarity=0.368 Sum_probs=62.3
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL 72 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 72 (93)
-|-+||+.+.||+|.|+||.|.+|.|+|.++|.|||+.|.+|+|..++... -.+|+++||.+||.||.-
T Consensus 8 NPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~--g~lGEilIRCNNvlyi~g 76 (79)
T KOG3482|consen 8 NPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVST--GNLGEILIRCNNVLYIRG 76 (79)
T ss_pred CchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhccccc--ccceeEEEEeccEEEEec
Confidence 367999999999999999999999999999999999999999997665442 578999999999999953
No 26
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=99.79 E-value=1.1e-18 Score=111.13 Aligned_cols=88 Identities=34% Similarity=0.541 Sum_probs=78.9
Q ss_pred CchhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCCC-cch
Q 034490 1 MLFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPDG-VDV 79 (93)
Q Consensus 1 m~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~~-~d~ 79 (93)
|..+.||+.+.+.+|+|||+||++++|+|.++|.+||..|.++..+.++ ++ .++..++|||++|+|+.+||+. +|+
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 7789999999999999999999999999999999999999999998875 43 4678999999999999999996 888
Q ss_pred hhhhHhhhhhhc
Q 034490 80 DLLHDATRREAR 91 (93)
Q Consensus 80 ~~~~~~~~~~~~ 91 (93)
.+++++++-.++
T Consensus 78 Llvd~~~~~~~~ 89 (109)
T KOG3428|consen 78 LLVDDAPRLHLR 89 (109)
T ss_pred eeeehhhhhhhh
Confidence 888888774443
No 27
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.79 E-value=1.8e-20 Score=111.69 Aligned_cols=71 Identities=32% Similarity=0.523 Sum_probs=65.9
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPP 74 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~ 74 (93)
.|.+||++.+||+|.|+|.+|..|+|+|.++|.|||+.|+.+++..+++.+ .+++.+||||++|.||+..+
T Consensus 6 ~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~--n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 6 MPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLK--NKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred CcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCccc--ccccceeeccccEEEEEecc
Confidence 378999999999999999999999999999999999999999999887764 78899999999999998754
No 28
>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=99.78 E-value=2.3e-18 Score=104.34 Aligned_cols=69 Identities=14% Similarity=0.240 Sum_probs=60.5
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC----CCceEeeeeEEEecCeEEEEEcC
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK----YPHMLSVRNCFIRGSVVRYVQLP 73 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~----~~~~~~~~~~~IRG~~I~~I~~~ 73 (93)
+-|++++|++|+|.|+||+.+.|+|.+||.+||++|+||.|..... ....+.+|.++|||++|..|+++
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v~ 75 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEVE 75 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEEC
Confidence 4688999999999999999999999999999999999999986431 12357999999999999999853
No 29
>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=99.78 E-value=2.9e-18 Score=103.47 Aligned_cols=69 Identities=23% Similarity=0.259 Sum_probs=59.9
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcC---CCCCceEeeeeEEEecCeEEEEEcCC
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQ---DKYPHMLSVRNCFIRGSVVRYVQLPP 74 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~---~~~~~~~~~~~~~IRG~~I~~I~~~~ 74 (93)
+.|+++++++|.|.|++|+.+.|+|.+||+|||++|++|.|... .+. ....+|.+++||++|.+|...|
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 46889999999999999999999999999999999999998642 122 2467899999999999998654
No 30
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.73 E-value=3.9e-17 Score=101.84 Aligned_cols=71 Identities=17% Similarity=0.290 Sum_probs=57.4
Q ss_pred chhHHHhhcCC--CEEEEEEcCC--cEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490 2 LFFSYFKDLVG--REVTVELKND--LAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP 73 (93)
Q Consensus 2 ~p~~~L~~~~g--k~V~V~L~~g--~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~ 73 (93)
.|+..+.+++. .+|.|++.++ +++.|+|.+||.|||++|+||+|...+.. ....+|.++|||++|.+|+..
T Consensus 14 ~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~-~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 14 QPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN-TRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred CCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc-eeeEcCeEEEcCCEEEEEEcC
Confidence 47777777764 4677787774 89999999999999999999999864332 236889999999999999753
No 31
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.66 E-value=2.8e-16 Score=94.04 Aligned_cols=66 Identities=21% Similarity=0.365 Sum_probs=59.3
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL 72 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 72 (93)
+.|+++.+|++.++|..|+.+.|+|.+||.|||++|++++|...+.. ...++.++|||++|..+..
T Consensus 7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~--~~~ig~~vIrgnsiv~~ea 72 (77)
T KOG1780|consen 7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD--KNNIGMVVIRGNSIVMVEA 72 (77)
T ss_pred chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC--cceeeeEEEeccEEEEEee
Confidence 38999999999999999999999999999999999999999876553 2578999999999998853
No 32
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.63 E-value=1e-16 Score=97.83 Aligned_cols=73 Identities=29% Similarity=0.378 Sum_probs=62.6
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc------CCC-----CCceEeeeeEEEecCeEEEE
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD------QDK-----YPHMLSVRNCFIRGSVVRYV 70 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~------~~~-----~~~~~~~~~~~IRG~~I~~I 70 (93)
-|+++|+-.++.+|+|+|+++++++|+|.+||+|+|++|+|++++- ++. ....+.++.+|+||++|.+|
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 4999999999999999999999999999999999999999998852 111 01136788999999999999
Q ss_pred EcCC
Q 034490 71 QLPP 74 (93)
Q Consensus 71 ~~~~ 74 (93)
+.|-
T Consensus 85 spp~ 88 (91)
T KOG3460|consen 85 SPPL 88 (91)
T ss_pred cCcc
Confidence 9774
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.49 E-value=2.3e-14 Score=86.30 Aligned_cols=69 Identities=19% Similarity=0.378 Sum_probs=61.7
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc--CCCCCceEeeeeEEEecCeEEEEE
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD--QDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~--~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
+|++++.+++|.++.|.+++++++.|+|.+||.|.|++|+|++|+. +++. ...+++.+++.|++|....
T Consensus 7 lPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr-~~tk~~~iLLnGNni~mLv 77 (84)
T KOG1775|consen 7 LPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGR-RMTKLDQILLNGNNITMLV 77 (84)
T ss_pred ccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcc-eeeeeeeeeecCCcEEEEe
Confidence 7999999999999999999999999999999999999999999864 3332 2568899999999999875
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.44 E-value=1.4e-13 Score=83.85 Aligned_cols=67 Identities=19% Similarity=0.423 Sum_probs=55.4
Q ss_pred hHHHhhcCCCEEEEEEcC--CcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490 4 FSYFKDLVGREVTVELKN--DLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP 73 (93)
Q Consensus 4 ~~~L~~~~gk~V~V~L~~--g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~ 73 (93)
+.||+. ..+|.|+|.. +..+.|.+.+||+|||++|++|++....... -..+|.++++|++|..|.-.
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 577777 4589999997 6889999999999999999999997643322 14789999999999999743
No 35
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.38 E-value=6.2e-13 Score=82.50 Aligned_cols=86 Identities=21% Similarity=0.242 Sum_probs=73.9
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEc--CCCCCceEeeeeEEEecCeEEEEEcCCCCcchhhh
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVD--QDKYPHMLSVRNCFIRGSVVRYVQLPPDGVDVDLL 82 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~--~~~~~~~~~~~~~~IRG~~I~~I~~~~~~~d~~~~ 82 (93)
+-|.++++++|.|...||+.+.|.|.+||+..||.|+++-+.. ...-.....+|...|||+||..|..-++.+|+.+-
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~~ld 82 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDSRLD 82 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhhhhh
Confidence 3578999999999999999999999999999999999998742 11111136789999999999999999999999999
Q ss_pred hHhhhhhh
Q 034490 83 HDATRREA 90 (93)
Q Consensus 83 ~~~~~~~~ 90 (93)
+...|+++
T Consensus 83 ~tkir~ep 90 (96)
T KOG1784|consen 83 LTKIRAEP 90 (96)
T ss_pred hhhcccCC
Confidence 98888775
No 36
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.28 E-value=4.3e-13 Score=84.24 Aligned_cols=76 Identities=16% Similarity=0.260 Sum_probs=62.5
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCC------CCceEeeeeEEEecCeEEEEEcCCCC--cc
Q 034490 7 FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDK------YPHMLSVRNCFIRGSVVRYVQLPPDG--VD 78 (93)
Q Consensus 7 L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~------~~~~~~~~~~~IRG~~I~~I~~~~~~--~d 78 (93)
|..+++|+|+|++..|++.+|+|.+||+.||++|+|++|.-.+. ....+++|.+.+||..+..|+..+.. +.
T Consensus 22 Lsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e~I~ 101 (108)
T KOG1781|consen 22 LSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSEEIA 101 (108)
T ss_pred HHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchhhhc
Confidence 67889999999999999999999999999999999999863221 11248899999999999999977652 44
Q ss_pred hhhh
Q 034490 79 VDLL 82 (93)
Q Consensus 79 ~~~~ 82 (93)
.|+.
T Consensus 102 npf~ 105 (108)
T KOG1781|consen 102 NPFV 105 (108)
T ss_pred cchh
Confidence 4444
No 37
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.00 E-value=4.1e-11 Score=77.94 Aligned_cols=69 Identities=22% Similarity=0.245 Sum_probs=57.6
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEE--cCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490 6 YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVV--DQDKYPHMLSVRNCFIRGSVVRYVQLPPD 75 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~--~~~~~~~~~~~~~~~IRG~~I~~I~~~~~ 75 (93)
=|-+.+.|++.|-|+||+.+.|.|.+||+|-|++|.+|.|. ..+.+. .+..|.+.|||.||..+..-+.
T Consensus 13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~-di~~glfiIRGENVvllGeid~ 83 (129)
T KOG1782|consen 13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYC-DIPRGLFIIRGENVVLLGEIDL 83 (129)
T ss_pred HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceec-ccCceEEEEecCcEEEEecCCc
Confidence 36678899999999999999999999999999999999984 233332 2567999999999999975543
No 38
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=98.97 E-value=8.5e-11 Score=80.16 Aligned_cols=69 Identities=13% Similarity=0.225 Sum_probs=58.8
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcC---------CCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490 6 YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQ---------DKYPHMLSVRNCFIRGSVVRYVQLPPD 75 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~---------~~~~~~~~~~~~~IRG~~I~~I~~~~~ 75 (93)
-+-.+++.++.|.+.||+++.|.+.+||.|||++|.||+|... +++ ..+-++.+++||.+|.+.++.+-
T Consensus 8 kml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~e-Ekr~lgLvllRgenIvs~tVegp 85 (177)
T KOG3168|consen 8 KMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGE-EKRVLGLVLLRGENIVSMTVEGP 85 (177)
T ss_pred HHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccc-eeeEEEEEEecCCcEEEEeccCC
Confidence 3556789999999999999999999999999999999998531 223 25789999999999999998764
No 39
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.42 E-value=3.1e-08 Score=63.45 Aligned_cols=69 Identities=23% Similarity=0.310 Sum_probs=55.2
Q ss_pred hhHHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcC-------CCC----CceEeeeeEEEecCeEEE
Q 034490 3 FFSYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQ-------DKY----PHMLSVRNCFIRGSVVRY 69 (93)
Q Consensus 3 p~~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~-------~~~----~~~~~~~~~~IRG~~I~~ 69 (93)
|++.+.+.. ..+|.|-++|+..+-|...+||.++|++|+++.+... +.. .+.+.++.+||||++|..
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 556666655 6789999999999999999999999999999988531 111 124678999999999887
Q ss_pred EE
Q 034490 70 VQ 71 (93)
Q Consensus 70 I~ 71 (93)
+.
T Consensus 105 v~ 106 (114)
T KOG3459|consen 105 VL 106 (114)
T ss_pred EE
Confidence 75
No 40
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.37 E-value=1.6e-06 Score=52.16 Aligned_cols=44 Identities=30% Similarity=0.442 Sum_probs=36.5
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEecc---ccceEEeeEEEEcC
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQ---YLNIKLENTRVVDQ 48 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~---~mNl~L~~~~~~~~ 48 (93)
=++..++|++|.|.++||..|+|++.+++. -+.++|+.+.....
T Consensus 5 ~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~ 51 (77)
T PF14438_consen 5 YLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK 51 (77)
T ss_dssp HHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred HHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence 367889999999999999999999999998 89999999998764
No 41
>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=97.91 E-value=1.1e-05 Score=47.58 Aligned_cols=37 Identities=19% Similarity=0.225 Sum_probs=31.8
Q ss_pred CCEEEEEEcCC----cEEEEEEEEeccccceEEeeEEEEcC
Q 034490 12 GREVTVELKND----LAIRGTLHSVDQYLNIKLENTRVVDQ 48 (93)
Q Consensus 12 gk~V~V~L~~g----~~~~G~L~~~D~~mNl~L~~~~~~~~ 48 (93)
+++|.|.++.- -.++|.|.+||.|+|+.|.|+.|+..
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 67888888863 47889999999999999999999754
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.54 E-value=0.00085 Score=42.36 Aligned_cols=68 Identities=22% Similarity=0.323 Sum_probs=53.8
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCC-------CceEeeeeEEEecCeEEEEEcCCC
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKY-------PHMLSVRNCFIRGSVVRYVQLPPD 75 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~-------~~~~~~~~~~IRG~~I~~I~~~~~ 75 (93)
..++|++|.+..+++..|+|+|..+|. .-.+.|.+|.....+.. +....++.+..||+.|.-+.+-+.
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 468999999999999999999999996 77999999998642110 011246789999999999987654
No 43
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=97.28 E-value=0.0044 Score=37.94 Aligned_cols=64 Identities=17% Similarity=0.254 Sum_probs=49.1
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcC
Q 034490 3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLP 73 (93)
Q Consensus 3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~ 73 (93)
.+.+|.++.||+|.+.|.++.++.|+..++|. ..|+..++-.- += -..++..+|.+-|..++++
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~T--Pl-----Gv~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQT--PL-----GVQPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEET--TT-----TEEEEEEEEGGGEEEEEE-
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCC--Cc-----ccChhheeecCCEEEEEec
Confidence 36788999999999999999999999999995 55887776541 11 1247899999999999875
No 44
>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=96.90 E-value=0.0034 Score=36.60 Aligned_cols=37 Identities=19% Similarity=0.356 Sum_probs=30.2
Q ss_pred HHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEee
Q 034490 6 YFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLEN 42 (93)
Q Consensus 6 ~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~ 42 (93)
||+.+. ..+|+|-|.||-.++|.+.+||.|+=+.-.+
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 344443 6789999999999999999999999776554
No 45
>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=96.80 E-value=0.0038 Score=36.39 Aligned_cols=31 Identities=26% Similarity=0.353 Sum_probs=27.8
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEee
Q 034490 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLEN 42 (93)
Q Consensus 12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~ 42 (93)
+.+|+|-|.||-.++|.+.+||.|+=+.-.+
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 7899999999999999999999998776544
No 46
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=96.61 E-value=0.024 Score=34.20 Aligned_cols=62 Identities=21% Similarity=0.326 Sum_probs=46.5
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCC--------CceEeeeeEEEecCeEEE
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKY--------PHMLSVRNCFIRGSVVRY 69 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~--------~~~~~~~~~~IRG~~I~~ 69 (93)
..++|+++.+.-+.+.-|.|+|.++|. .--+.|+|+...-.++. +...-++.+.-||+.|.-
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 368999999999999999999999995 45788999987632110 112345778888887753
No 47
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=96.58 E-value=0.006 Score=37.25 Aligned_cols=32 Identities=22% Similarity=0.384 Sum_probs=28.6
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEeeE
Q 034490 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENT 43 (93)
Q Consensus 12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~ 43 (93)
+.+|+|-|.||-.++|.+.+||.|+=+.-.+.
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 78999999999999999999999997776554
No 48
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.13 E-value=0.027 Score=30.78 Aligned_cols=34 Identities=26% Similarity=0.335 Sum_probs=29.3
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEE
Q 034490 11 VGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRV 45 (93)
Q Consensus 11 ~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~ 45 (93)
+|++|+|++ ++..++|+..++|+.-.|+++....
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 699999999 6677799999999999999876443
No 49
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.06 E-value=0.015 Score=35.24 Aligned_cols=35 Identities=23% Similarity=0.431 Sum_probs=28.9
Q ss_pred HHHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceE
Q 034490 5 SYFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIK 39 (93)
Q Consensus 5 ~~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~ 39 (93)
.||+++. +.+|.|-|.||-.++|.+.+||.|.=+.
T Consensus 10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~VlL 46 (77)
T COG1923 10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVLL 46 (77)
T ss_pred HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence 3555544 7899999999999999999999997544
No 50
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=96.02 E-value=0.041 Score=37.95 Aligned_cols=62 Identities=27% Similarity=0.348 Sum_probs=43.6
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEecc-ccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEcCCC
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQ-YLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQLPPD 75 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~-~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~~~~ 75 (93)
..+..++||.|.|.+.| +++.|.|..+|+ .-|++|-+-.+ ++. . ..-+|-|.+|..|..-++
T Consensus 10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~---~--sv~~I~ghaVk~vevl~~ 72 (166)
T PF06372_consen 10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK---R--SVKVIMGHAVKSVEVLSE 72 (166)
T ss_dssp HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS----E--EEEEE-GGGEEEEEEEE-
T ss_pred HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc---e--eEEEEEccceEEEEEccC
Confidence 35788999999999999 999999999996 67999885544 222 1 246799999999976654
No 51
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=95.58 E-value=0.034 Score=32.84 Aligned_cols=53 Identities=28% Similarity=0.426 Sum_probs=39.6
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490 4 FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 4 ~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
+..|++++|++|.|++-.|+. +|+|.++-... ++|+.. + ..+|||=.+|.+|.
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDh-Ivl~~~------~-------~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDH-IVLEEN------G-------TPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCE-EEEEeC------C-------cEEEEEeeeEEEEc
Confidence 578999999999999988776 99999987532 233222 1 35688988888875
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=95.53 E-value=0.15 Score=29.67 Aligned_cols=36 Identities=14% Similarity=0.161 Sum_probs=30.8
Q ss_pred cCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEE
Q 034490 10 LVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRV 45 (93)
Q Consensus 10 ~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~ 45 (93)
.+|..|.+++..|.+++|.+.+||...++.+-.+..
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 479999999999999999999999888777555443
No 53
>PRK14638 hypothetical protein; Provisional
Probab=94.75 E-value=0.068 Score=36.08 Aligned_cols=36 Identities=14% Similarity=0.234 Sum_probs=29.9
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEe
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLE 41 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~ 41 (93)
.-+..++|++|.|.+++++.++|+|.++|.. ++.|.
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 3467889999999999999999999999964 34443
No 54
>PRK14639 hypothetical protein; Provisional
Probab=94.39 E-value=0.094 Score=35.00 Aligned_cols=35 Identities=29% Similarity=0.418 Sum_probs=29.8
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKL 40 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L 40 (93)
.-++.++|+.|.|++.+++.+.|+|.++|.. ++.|
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 3467899999999999999999999999983 4444
No 55
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=94.15 E-value=0.12 Score=35.65 Aligned_cols=32 Identities=22% Similarity=0.369 Sum_probs=28.3
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEeeE
Q 034490 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENT 43 (93)
Q Consensus 12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~ 43 (93)
..+|+|-|.||-.++|.+.+||.|.=+...+.
T Consensus 104 k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 104 GEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 67899999999999999999999987766554
No 56
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.82 E-value=0.16 Score=35.01 Aligned_cols=38 Identities=16% Similarity=0.282 Sum_probs=31.0
Q ss_pred HHhhcC--CCEEEEEEcCCcEEEEEEEEeccccceEEeeE
Q 034490 6 YFKDLV--GREVTVELKNDLAIRGTLHSVDQYLNIKLENT 43 (93)
Q Consensus 6 ~L~~~~--gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~ 43 (93)
||+.+. ..+|+|-|.||-.++|.+.+||+|.=+.-.+.
T Consensus 16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 444444 67899999999999999999999987776554
No 57
>PRK02001 hypothetical protein; Validated
Probab=93.67 E-value=0.55 Score=31.84 Aligned_cols=34 Identities=41% Similarity=0.597 Sum_probs=29.2
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490 6 YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKL 40 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L 40 (93)
-+..++|+.|.|.|.++..+.|+|.++|+. ++.|
T Consensus 84 ~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 84 QYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred HHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 467889999999999999999999999975 3444
No 58
>PRK14644 hypothetical protein; Provisional
Probab=92.53 E-value=0.28 Score=32.64 Aligned_cols=35 Identities=23% Similarity=0.348 Sum_probs=29.1
Q ss_pred HHhhcCCCEEEEEEcCC----cEEEEEEEEeccccceEEe
Q 034490 6 YFKDLVGREVTVELKND----LAIRGTLHSVDQYLNIKLE 41 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~g----~~~~G~L~~~D~~mNl~L~ 41 (93)
-+..++|+.|.|.|++. ..++|.|.++|.. ++.|.
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 36788999999999987 9999999999973 45554
No 59
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.50 E-value=0.44 Score=32.43 Aligned_cols=32 Identities=25% Similarity=0.434 Sum_probs=28.9
Q ss_pred HHHhhcCCCEEEEEE----cCCcEEEEEEEEecccc
Q 034490 5 SYFKDLVGREVTVEL----KNDLAIRGTLHSVDQYL 36 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L----~~g~~~~G~L~~~D~~m 36 (93)
.-+..++|+.|.|+| .+.+.++|+|.++|..+
T Consensus 92 ~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 92 EHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred HHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 457788999999999 78899999999999877
No 60
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=92.42 E-value=0.35 Score=29.22 Aligned_cols=35 Identities=34% Similarity=0.493 Sum_probs=27.9
Q ss_pred HHHhhcCCCEEEEEEc---CC-cEEEEEEEEeccccceEE
Q 034490 5 SYFKDLVGREVTVELK---ND-LAIRGTLHSVDQYLNIKL 40 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~---~g-~~~~G~L~~~D~~mNl~L 40 (93)
.-+..++|+.|.|+++ +| +.+.|.|.++|.. ++.|
T Consensus 18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 3467889999999998 55 6899999999984 3444
No 61
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.14 E-value=0.57 Score=35.96 Aligned_cols=67 Identities=21% Similarity=0.327 Sum_probs=51.6
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEec-cccceEEeeEEEEcCCC-------CC-ceEeeeeEEEecCeEEEEEcCC
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVD-QYLNIKLENTRVVDQDK-------YP-HMLSVRNCFIRGSVVRYVQLPP 74 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D-~~mNl~L~~~~~~~~~~-------~~-~~~~~~~~~IRG~~I~~I~~~~ 74 (93)
..++|++|.+.=+++.-|+|+|.-+| +..=|-|.+|..+-.++ .+ ...-++.++-||+.|+-+.+-+
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence 46899999999999999999999999 56689999986642111 01 1114578999999999777655
No 62
>PRK14640 hypothetical protein; Provisional
Probab=91.70 E-value=0.4 Score=32.34 Aligned_cols=36 Identities=31% Similarity=0.501 Sum_probs=28.7
Q ss_pred HHHhhcCCCEEEEEE----cCCcEEEEEEEEeccccceEEe
Q 034490 5 SYFKDLVGREVTVEL----KNDLAIRGTLHSVDQYLNIKLE 41 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L----~~g~~~~G~L~~~D~~mNl~L~ 41 (93)
.-++.++|+.|.|.| .+.+.++|+|.++|.. ++.|.
T Consensus 90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 346788999999999 4679999999999874 44443
No 63
>PRK14642 hypothetical protein; Provisional
Probab=91.15 E-value=0.46 Score=33.62 Aligned_cols=34 Identities=26% Similarity=0.467 Sum_probs=28.2
Q ss_pred HHhhcCCCEEEEEEc-------------CCcEEEEEEEEeccccceEE
Q 034490 6 YFKDLVGREVTVELK-------------NDLAIRGTLHSVDQYLNIKL 40 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~-------------~g~~~~G~L~~~D~~mNl~L 40 (93)
=+..++|+.|.|.|+ +.+.++|+|.++|.. ++.|
T Consensus 94 df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 94 DFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred HHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 356789999999998 679999999999974 4444
No 64
>PRK14633 hypothetical protein; Provisional
Probab=90.88 E-value=0.53 Score=31.69 Aligned_cols=36 Identities=25% Similarity=0.311 Sum_probs=28.6
Q ss_pred HHHhhcCCCEEEEEEc----CCcEEEEEEEEeccccceEEe
Q 034490 5 SYFKDLVGREVTVELK----NDLAIRGTLHSVDQYLNIKLE 41 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~----~g~~~~G~L~~~D~~mNl~L~ 41 (93)
.-++.++|++|.|.++ +.+.++|+|.++++. ++.|.
T Consensus 87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 3467889999999994 569999999999874 44453
No 65
>PRK14632 hypothetical protein; Provisional
Probab=90.28 E-value=0.61 Score=32.12 Aligned_cols=36 Identities=25% Similarity=0.425 Sum_probs=28.8
Q ss_pred HHHhhcCCCEEEEEEcC-------CcEEEEEEEEeccccceEEe
Q 034490 5 SYFKDLVGREVTVELKN-------DLAIRGTLHSVDQYLNIKLE 41 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~-------g~~~~G~L~~~D~~mNl~L~ 41 (93)
.-++.++|+.|.|.|++ .+.++|+|.++|.. ++.|.
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 57999999999864 44553
No 66
>PRK14636 hypothetical protein; Provisional
Probab=90.20 E-value=0.59 Score=32.35 Aligned_cols=35 Identities=26% Similarity=0.511 Sum_probs=27.9
Q ss_pred HHHhhcCCCEEEEEEc---CC-cEEEEEEEEeccccceEE
Q 034490 5 SYFKDLVGREVTVELK---ND-LAIRGTLHSVDQYLNIKL 40 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~---~g-~~~~G~L~~~D~~mNl~L 40 (93)
.-+..++|++|.|+|+ +| +.++|+|.++|.. ++.|
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 3467889999999998 55 7999999999873 3444
No 67
>PRK14643 hypothetical protein; Provisional
Probab=90.18 E-value=0.62 Score=31.91 Aligned_cols=30 Identities=17% Similarity=0.140 Sum_probs=26.1
Q ss_pred HHhhcCCCEEEEEEcC----CcEEEEEEEEeccc
Q 034490 6 YFKDLVGREVTVELKN----DLAIRGTLHSVDQY 35 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~----g~~~~G~L~~~D~~ 35 (93)
-++.++|++|.|.|+. .+.++|+|.++|..
T Consensus 98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 98 ELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 4678899999999976 59999999999964
No 68
>PRK14645 hypothetical protein; Provisional
Probab=90.10 E-value=0.63 Score=31.58 Aligned_cols=33 Identities=15% Similarity=0.272 Sum_probs=26.9
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490 6 YFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKL 40 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L 40 (93)
-+..++|++|.|.+ +++.++|+|.++|.. .+.|
T Consensus 96 df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 96 HFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred HHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 46788999999986 789999999999974 3444
No 69
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=89.58 E-value=0.79 Score=30.77 Aligned_cols=31 Identities=35% Similarity=0.567 Sum_probs=26.5
Q ss_pred HHHhhcCCCEEEEEE----cCCcEEEEEEEEeccc
Q 034490 5 SYFKDLVGREVTVEL----KNDLAIRGTLHSVDQY 35 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L----~~g~~~~G~L~~~D~~ 35 (93)
.-++.++|+.|.|++ .++..++|+|.++|..
T Consensus 91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 456789999999998 5678999999999983
No 70
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=89.56 E-value=0.55 Score=30.95 Aligned_cols=30 Identities=37% Similarity=0.623 Sum_probs=23.7
Q ss_pred HHHhhcCCCEEEEEEc----CCcEEEEEEEEecc
Q 034490 5 SYFKDLVGREVTVELK----NDLAIRGTLHSVDQ 34 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~----~g~~~~G~L~~~D~ 34 (93)
.-+..++|+.|.|+++ +.+.+.|+|.++|.
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 4577899999999994 45799999999998
No 71
>PRK14634 hypothetical protein; Provisional
Probab=89.46 E-value=0.79 Score=31.03 Aligned_cols=35 Identities=20% Similarity=0.373 Sum_probs=27.6
Q ss_pred HHHhhcCCCEEEEEEcCC----cEEEEEEEEeccccceEE
Q 034490 5 SYFKDLVGREVTVELKND----LAIRGTLHSVDQYLNIKL 40 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g----~~~~G~L~~~D~~mNl~L 40 (93)
.-++.++|+.|.|+|.+. +.++|+|.++|.. ++.|
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 72
>PRK14646 hypothetical protein; Provisional
Probab=88.95 E-value=0.9 Score=30.76 Aligned_cols=35 Identities=26% Similarity=0.331 Sum_probs=27.9
Q ss_pred HHHhhcCCCEEEEEEcCC----cEEEEEEEEeccccceEE
Q 034490 5 SYFKDLVGREVTVELKND----LAIRGTLHSVDQYLNIKL 40 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g----~~~~G~L~~~D~~mNl~L 40 (93)
.-++.++|++|.|+|++. +.++|+|.++|+. .+.|
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 346788999999999653 7889999999985 4544
No 73
>PRK14647 hypothetical protein; Provisional
Probab=88.30 E-value=1.1 Score=30.46 Aligned_cols=30 Identities=20% Similarity=0.303 Sum_probs=25.7
Q ss_pred HHHhhcCCCEEEEEEc---------CCcEEEEEEEEecc
Q 034490 5 SYFKDLVGREVTVELK---------NDLAIRGTLHSVDQ 34 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~---------~g~~~~G~L~~~D~ 34 (93)
.-++.++|+.|.|.|+ +.+.++|+|.++|.
T Consensus 92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 3467889999999996 35999999999996
No 74
>PRK14637 hypothetical protein; Provisional
Probab=87.36 E-value=1.3 Score=29.96 Aligned_cols=36 Identities=25% Similarity=0.268 Sum_probs=26.8
Q ss_pred HHHhhcCCCEEEEEEcCCcEE-EEEEEEeccccceEEe
Q 034490 5 SYFKDLVGREVTVELKNDLAI-RGTLHSVDQYLNIKLE 41 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~-~G~L~~~D~~mNl~L~ 41 (93)
.-+..++|+.|.|++.+...+ +|+|.++|+. ++.|.
T Consensus 91 ~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 91 AEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 346788999999999544455 7999999875 44443
No 75
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=86.79 E-value=1.3 Score=29.89 Aligned_cols=26 Identities=35% Similarity=0.542 Sum_probs=23.9
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEec
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVD 33 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D 33 (93)
.+++||.|.+...+|..++|++.++-
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 47899999999999999999999986
No 76
>PRK14631 hypothetical protein; Provisional
Probab=86.66 E-value=1.5 Score=30.30 Aligned_cols=29 Identities=24% Similarity=0.442 Sum_probs=25.3
Q ss_pred HHHhhcCCCEEEEEEc----CCcEEEEEEEEec
Q 034490 5 SYFKDLVGREVTVELK----NDLAIRGTLHSVD 33 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~----~g~~~~G~L~~~D 33 (93)
.-++.++|+.|.|+|. +.+.++|+|.++|
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 3467889999999996 4599999999998
No 77
>PRK14641 hypothetical protein; Provisional
Probab=86.48 E-value=1.3 Score=30.59 Aligned_cols=29 Identities=24% Similarity=0.471 Sum_probs=24.7
Q ss_pred HHHhhcCCCEEEEEEcC----CcEEEEEEEEec
Q 034490 5 SYFKDLVGREVTVELKN----DLAIRGTLHSVD 33 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~----g~~~~G~L~~~D 33 (93)
.-++.++|+.|.|.|.+ .+.++|+|.++|
T Consensus 97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 34678899999999976 468999999996
No 78
>PRK06955 biotin--protein ligase; Provisional
Probab=84.94 E-value=5 Score=29.62 Aligned_cols=33 Identities=27% Similarity=0.384 Sum_probs=28.8
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEEe
Q 034490 9 DLVGREVTVELKNDLAIRGTLHSVDQYLNIKLE 41 (93)
Q Consensus 9 ~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~ 41 (93)
...|++|.|...++..++|+..++|+.-.|.+.
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 367999999766778899999999999999885
No 79
>PRK14630 hypothetical protein; Provisional
Probab=81.11 E-value=3.3 Score=27.66 Aligned_cols=29 Identities=24% Similarity=0.332 Sum_probs=23.8
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEEEEEeccc
Q 034490 6 YFKDLVGREVTVELKNDLAIRGTLHSVDQY 35 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~ 35 (93)
-++.++|++|.|.|... ..+|+|.++|+.
T Consensus 91 df~r~~G~~v~V~l~~~-~~~G~L~~~~d~ 119 (143)
T PRK14630 91 EFKIFEGKKIKLMLDND-FEEGFILEAKAD 119 (143)
T ss_pred HHHHhCCCEEEEEEcCc-ceEEEEEEEeCC
Confidence 46788999999999664 459999999873
No 80
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=81.08 E-value=9.8 Score=28.04 Aligned_cols=31 Identities=32% Similarity=0.502 Sum_probs=27.3
Q ss_pred cCCCEEEEEEcCCcEEEEEEEEeccccceEEe
Q 034490 10 LVGREVTVELKNDLAIRGTLHSVDQYLNIKLE 41 (93)
Q Consensus 10 ~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~ 41 (93)
+.|++|.+... +..++|++.++|+.-.|++.
T Consensus 270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLIIG-DKEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEeC-CcEEEEEEEEECCCceEEEE
Confidence 57999999874 46799999999999999996
No 81
>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=80.68 E-value=2.6 Score=26.60 Aligned_cols=19 Identities=32% Similarity=0.532 Sum_probs=15.4
Q ss_pred CCEEEEEEcCCcEEEEEEE
Q 034490 12 GREVTVELKNDLAIRGTLH 30 (93)
Q Consensus 12 gk~V~V~L~~g~~~~G~L~ 30 (93)
..+|.++|+||+.+.|++.
T Consensus 28 e~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 28 EERVELELDDGSMLRGTVA 46 (101)
T ss_dssp T-EEEEEETTS-EEEEEEC
T ss_pred cceEEEEEcCCCeeeeeec
Confidence 4689999999999999974
No 82
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=78.96 E-value=10 Score=30.92 Aligned_cols=33 Identities=24% Similarity=0.278 Sum_probs=28.9
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEEe
Q 034490 9 DLVGREVTVELKNDLAIRGTLHSVDQYLNIKLE 41 (93)
Q Consensus 9 ~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~ 41 (93)
.+.|++|.+...++..++|+..++|+.-.|.|+
T Consensus 275 ~~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 275 RDHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred ccCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 367999999766777899999999999999996
No 83
>PRK08330 biotin--protein ligase; Provisional
Probab=77.97 E-value=17 Score=25.67 Aligned_cols=34 Identities=15% Similarity=0.300 Sum_probs=27.4
Q ss_pred hcCCCEEEEEEcCCcEE-EEEEEEeccccceEEeeE
Q 034490 9 DLVGREVTVELKNDLAI-RGTLHSVDQYLNIKLENT 43 (93)
Q Consensus 9 ~~~gk~V~V~L~~g~~~-~G~L~~~D~~mNl~L~~~ 43 (93)
...|++|.+.. ++..+ .|+..++|+.-.|.+...
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence 46799999976 55554 799999999999988643
No 84
>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region. The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.
Probab=77.59 E-value=14 Score=26.05 Aligned_cols=32 Identities=31% Similarity=0.415 Sum_probs=27.5
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEEe
Q 034490 9 DLVGREVTVELKNDLAIRGTLHSVDQYLNIKLE 41 (93)
Q Consensus 9 ~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~ 41 (93)
...|++|.|...+ ..+.|+..++|+.-.|.++
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 3569999998754 5689999999999999996
No 85
>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=77.26 E-value=3 Score=28.54 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=22.7
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccc
Q 034490 11 VGREVTVELKNDLAIRGTLHSVDQY 35 (93)
Q Consensus 11 ~gk~V~V~L~~g~~~~G~L~~~D~~ 35 (93)
.|+-++|-+.||++++|+-.++|+.
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 3899999999999999999999863
No 86
>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=76.10 E-value=2.8 Score=25.49 Aligned_cols=23 Identities=22% Similarity=0.232 Sum_probs=16.1
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEE
Q 034490 6 YFKDLVGREVTVELKNDLAIRGT 28 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~g~~~~G~ 28 (93)
.+..+-+-+|.++|+||..+.|+
T Consensus 11 EiAC~~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 11 EIACMYRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp HHHHTTTT-EEEE-TTT--EEES
T ss_pred HHHHhcCCeEEEEEeCCCEEEEE
Confidence 45567788999999999999997
No 87
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=75.26 E-value=5.7 Score=26.70 Aligned_cols=26 Identities=27% Similarity=0.465 Sum_probs=23.1
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEecc
Q 034490 9 DLVGREVTVELKNDLAIRGTLHSVDQ 34 (93)
Q Consensus 9 ~~~gk~V~V~L~~g~~~~G~L~~~D~ 34 (93)
+++||.|.....+|..++|++.++..
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEEE
Confidence 68999999888999999999997764
No 88
>PRK14635 hypothetical protein; Provisional
Probab=73.58 E-value=8 Score=26.27 Aligned_cols=35 Identities=17% Similarity=0.213 Sum_probs=26.8
Q ss_pred HHhhcCCCEEEEEEc--CCcEEEE---EEEEeccccceEEe
Q 034490 6 YFKDLVGREVTVELK--NDLAIRG---TLHSVDQYLNIKLE 41 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~--~g~~~~G---~L~~~D~~mNl~L~ 41 (93)
-+..++|+.|.|.+. ++..+.| +|.++|.. ++.|.
T Consensus 93 ~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~ 132 (162)
T PRK14635 93 DLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE 132 (162)
T ss_pred HHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence 467889999999986 4578887 99999874 44443
No 89
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=67.72 E-value=17 Score=26.67 Aligned_cols=32 Identities=16% Similarity=0.171 Sum_probs=27.4
Q ss_pred cCCCEEEEEEcCCcEEEEEEEEeccccceEEee
Q 034490 10 LVGREVTVELKNDLAIRGTLHSVDQYLNIKLEN 42 (93)
Q Consensus 10 ~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~ 42 (93)
..|++|.|.. ++..+.|++.++|..-.|++..
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 5688999999999999998863
No 90
>PRK11625 Rho-binding antiterminator; Provisional
Probab=67.40 E-value=16 Score=22.37 Aligned_cols=55 Identities=13% Similarity=0.036 Sum_probs=32.9
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490 7 FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 7 L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
+..+.+-+|.++|+||..+.|+.. |-+.+ +.++...-+.. -+...||=++|..++
T Consensus 18 lAC~~~~~l~l~l~dGe~~~g~A~--D~~~~---~k~EyL~l~~~-----g~~~~iRLD~I~s~~ 72 (84)
T PRK11625 18 LACQHHLMLTLELKDGEVLQAKAS--DLVSR---KNVEYLVVEAA-----GETRELRLDKIASFS 72 (84)
T ss_pred HHHhcCCeEEEEECCCCEEEEEEE--eeecC---CceEEEEEEcC-----CCEEEEEeeeEeecc
Confidence 445578899999999999999873 43333 33333211110 123346666666666
No 91
>PRK10898 serine endoprotease; Provisional
Probab=66.12 E-value=16 Score=27.57 Aligned_cols=33 Identities=12% Similarity=0.236 Sum_probs=28.7
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q 034490 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENTR 44 (93)
Q Consensus 12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~ 44 (93)
...+.|.+.||+.+.+++.++|...+|-+=.+.
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 467899999999999999999999999776554
No 92
>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=65.46 E-value=12 Score=25.72 Aligned_cols=33 Identities=15% Similarity=-0.068 Sum_probs=30.1
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q 034490 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENTR 44 (93)
Q Consensus 12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~ 44 (93)
.-+|+|.+.||..+.|.+.+|+.--|.+|.-+.
T Consensus 29 ~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 29 DIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred CCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 568999999999999999999999999987665
No 93
>PRK10139 serine endoprotease; Provisional
Probab=62.81 E-value=19 Score=28.19 Aligned_cols=33 Identities=15% Similarity=0.309 Sum_probs=28.8
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q 034490 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENTR 44 (93)
Q Consensus 12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~ 44 (93)
...+.|.+.||+.+.+++.+.|...+|-+=.+.
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 468999999999999999999999998775553
No 94
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=62.19 E-value=21 Score=26.89 Aligned_cols=33 Identities=12% Similarity=0.246 Sum_probs=28.6
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q 034490 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENTR 44 (93)
Q Consensus 12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~ 44 (93)
...+.|.+.||+.+.+++.++|...++-+=.+.
T Consensus 101 ~~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 101 ADQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 357899999999999999999999999875554
No 95
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=61.68 E-value=14 Score=26.01 Aligned_cols=26 Identities=15% Similarity=0.288 Sum_probs=22.7
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEecc
Q 034490 9 DLVGREVTVELKNDLAIRGTLHSVDQ 34 (93)
Q Consensus 9 ~~~gk~V~V~L~~g~~~~G~L~~~D~ 34 (93)
+++||.|.+.-.+|..+.|++.++.-
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~~ 140 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVRL 140 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEEE
Confidence 67999999888899999999988763
No 96
>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=61.47 E-value=22 Score=22.02 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=12.5
Q ss_pred HHHhhcCCCEEEEE
Q 034490 5 SYFKDLVGREVTVE 18 (93)
Q Consensus 5 ~~L~~~~gk~V~V~ 18 (93)
++|++++||+|++.
T Consensus 8 ~~L~~f~gk~V~iv 21 (101)
T cd04479 8 AMLSQFVGKTVRIV 21 (101)
T ss_pred HHHHhhCCCEEEEE
Confidence 68999999999876
No 97
>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=59.95 E-value=16 Score=23.59 Aligned_cols=27 Identities=22% Similarity=0.139 Sum_probs=23.2
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEE
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGT 28 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~ 28 (93)
.|+.-|++..+-+|..+|.||.+|.+.
T Consensus 64 ~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 64 TDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CCHHHHhCCcccEEEEEecCCcEEEec
Confidence 467788999999999999999998754
No 98
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=59.68 E-value=31 Score=24.85 Aligned_cols=36 Identities=22% Similarity=0.322 Sum_probs=32.3
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeE
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENT 43 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~ 43 (93)
...+|++|++...++....|+..++|..-.|.+...
T Consensus 186 ~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 186 SLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred hccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 345799999999999999999999999999998766
No 99
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=59.56 E-value=11 Score=20.31 Aligned_cols=22 Identities=23% Similarity=0.430 Sum_probs=14.8
Q ss_pred EEEEEEEeccccceEEeeEEEE
Q 034490 25 IRGTLHSVDQYLNIKLENTRVV 46 (93)
Q Consensus 25 ~~G~L~~~D~~mNl~L~~~~~~ 46 (93)
.+|+..++|+.+.+.|.+...+
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6899999999999999887654
No 100
>PRK10942 serine endoprotease; Provisional
Probab=57.63 E-value=26 Score=27.62 Aligned_cols=32 Identities=16% Similarity=0.215 Sum_probs=28.0
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEeeE
Q 034490 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENT 43 (93)
Q Consensus 12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~ 43 (93)
...+.|.+.||+.+.+++.+.|...+|-|=..
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 45789999999999999999999999876544
No 101
>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=56.75 E-value=29 Score=24.41 Aligned_cols=34 Identities=18% Similarity=0.418 Sum_probs=29.1
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccc
Q 034490 4 FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLN 37 (93)
Q Consensus 4 ~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mN 37 (93)
..+=+.++||.+..++.+|....|.|++...|+-
T Consensus 11 ~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 11 VTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred HHHHHHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 4556789999999999888888999999999964
No 102
>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=54.09 E-value=29 Score=24.18 Aligned_cols=34 Identities=18% Similarity=0.394 Sum_probs=25.6
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccc
Q 034490 3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLN 37 (93)
Q Consensus 3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mN 37 (93)
+..+=+.++||.+..++.++. +.|.|++...|.-
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 355668899999999999888 9999999988775
No 103
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=52.37 E-value=43 Score=20.16 Aligned_cols=29 Identities=17% Similarity=0.329 Sum_probs=21.2
Q ss_pred HHHhhcCCCEEEEEEcCC----cEEEEEEEEec
Q 034490 5 SYFKDLVGREVTVELKND----LAIRGTLHSVD 33 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g----~~~~G~L~~~D 33 (93)
.-|.+.+|++|.+....| .+-+|+|.+.=
T Consensus 10 ~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~tY 42 (76)
T PF06257_consen 10 KELESHVGKRVKLKANKGRKKIIEREGVLEETY 42 (76)
T ss_dssp HHHHHTTTSEEEEEE--SSS--S-EEEEEEEE-
T ss_pred HHHHHcCCCEEEEEEcCCceEEEEEEEEEEeec
Confidence 457889999999999998 46789998754
No 104
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=52.23 E-value=35 Score=26.21 Aligned_cols=32 Identities=22% Similarity=0.288 Sum_probs=28.0
Q ss_pred CEEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q 034490 13 REVTVELKNDLAIRGTLHSVDQYLNIKLENTR 44 (93)
Q Consensus 13 k~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~ 44 (93)
..+.|.+.||+.+.+++.++|...+|-|=...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 57899999999999999999999998775554
No 105
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=52.17 E-value=15 Score=20.05 Aligned_cols=15 Identities=47% Similarity=0.988 Sum_probs=12.7
Q ss_pred hHHHhhcCCCEEEEE
Q 034490 4 FSYFKDLVGREVTVE 18 (93)
Q Consensus 4 ~~~L~~~~gk~V~V~ 18 (93)
++.++.++||+|.|.
T Consensus 11 ~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVT 25 (48)
T ss_pred hHHHHHhcCCeEEEE
Confidence 467888999999986
No 106
>PRK08477 biotin--protein ligase; Provisional
Probab=50.87 E-value=53 Score=23.18 Aligned_cols=37 Identities=5% Similarity=-0.052 Sum_probs=29.8
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEE
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRV 45 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~ 45 (93)
...+||.|+|. .++..++|+..++|+.--|.+..-..
T Consensus 171 ~~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~ 207 (211)
T PRK08477 171 EFEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKV 207 (211)
T ss_pred HHHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEe
Confidence 44679999997 47899999999999988887765443
No 107
>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=48.73 E-value=31 Score=22.26 Aligned_cols=20 Identities=25% Similarity=0.308 Sum_probs=17.7
Q ss_pred EEEEEEcCCcEEEEEEEEec
Q 034490 14 EVTVELKNDLAIRGTLHSVD 33 (93)
Q Consensus 14 ~V~V~L~~g~~~~G~L~~~D 33 (93)
...|.++||+.+.|.+.+=|
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET 78 (133)
T ss_pred cEEEEECCCCEEEEEEEecC
Confidence 48899999999999998844
No 108
>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=48.45 E-value=27 Score=21.90 Aligned_cols=23 Identities=26% Similarity=0.449 Sum_probs=19.4
Q ss_pred hcCCCEEEEE-EcCCcEEEEEEEE
Q 034490 9 DLVGREVTVE-LKNDLAIRGTLHS 31 (93)
Q Consensus 9 ~~~gk~V~V~-L~~g~~~~G~L~~ 31 (93)
..+|..|+|+ +.++++++|++.+
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 8899999998865
No 109
>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=48.44 E-value=42 Score=17.85 Aligned_cols=25 Identities=24% Similarity=0.284 Sum_probs=21.7
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccc
Q 034490 11 VGREVTVELKNDLAIRGTLHSVDQY 35 (93)
Q Consensus 11 ~gk~V~V~L~~g~~~~G~L~~~D~~ 35 (93)
.|..+.+...+|.-|+|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5778888888999999999999964
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=46.96 E-value=50 Score=18.72 Aligned_cols=27 Identities=22% Similarity=0.224 Sum_probs=19.1
Q ss_pred cCCCEEEEEEcCCcEE-EEEEEEecccc
Q 034490 10 LVGREVTVELKNDLAI-RGTLHSVDQYL 36 (93)
Q Consensus 10 ~~gk~V~V~L~~g~~~-~G~L~~~D~~m 36 (93)
..|..|.++=-++..| .|.+.+||.--
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~~ 34 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSKS 34 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETTT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecccC
Confidence 4589999998887555 99999999743
No 111
>PF13437 HlyD_3: HlyD family secretion protein
Probab=46.57 E-value=59 Score=19.40 Aligned_cols=32 Identities=25% Similarity=0.318 Sum_probs=25.5
Q ss_pred hhHHHhhc--CCCEEEEEEcCC--cEEEEEEEEecc
Q 034490 3 FFSYFKDL--VGREVTVELKND--LAIRGTLHSVDQ 34 (93)
Q Consensus 3 p~~~L~~~--~gk~V~V~L~~g--~~~~G~L~~~D~ 34 (93)
|-..+..+ .|..|.+.+.++ ..+.|++..++.
T Consensus 43 ~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 43 PEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred ChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 44455555 699999999855 699999999998
No 112
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=45.38 E-value=35 Score=23.96 Aligned_cols=26 Identities=38% Similarity=0.650 Sum_probs=22.6
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEec
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVD 33 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D 33 (93)
..++|++|.|.+...+.++|.+.+++
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 55899999999998899999999885
No 113
>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=43.09 E-value=16 Score=23.90 Aligned_cols=25 Identities=20% Similarity=0.462 Sum_probs=20.8
Q ss_pred HHHhhcCCCEEEEEEcCC-cEEEEEE
Q 034490 5 SYFKDLVGREVTVELKND-LAIRGTL 29 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g-~~~~G~L 29 (93)
.++..+.||+|.|.++.. .++.|.-
T Consensus 96 ~~~~~l~gk~l~V~v~~~~~e~nGk~ 121 (141)
T PF05037_consen 96 QFLNQLLGKPLRVTVKWEENEYNGKT 121 (141)
T ss_pred HHHHHHcCCeeEEEecccccCCCCcE
Confidence 578889999999999988 7777743
No 114
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=42.01 E-value=34 Score=24.38 Aligned_cols=23 Identities=17% Similarity=0.458 Sum_probs=20.1
Q ss_pred hcCCCEEEEE-EcCCcEEEEEEEE
Q 034490 9 DLVGREVTVE-LKNDLAIRGTLHS 31 (93)
Q Consensus 9 ~~~gk~V~V~-L~~g~~~~G~L~~ 31 (93)
..+|..|+|+ +.+|+++.|++.+
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeC
Confidence 4679999999 9999999999875
No 115
>PRK06789 flagellar motor switch protein; Validated
Probab=40.66 E-value=80 Score=18.85 Aligned_cols=36 Identities=11% Similarity=0.213 Sum_probs=27.6
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEee
Q 034490 7 FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLEN 42 (93)
Q Consensus 7 L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~ 42 (93)
|....|.+|.|.+++-..-+|-+..+|..+=+.+.+
T Consensus 36 Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 36 LENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred eCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 456678888888888888889998888876665543
No 116
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.59 E-value=45 Score=23.46 Aligned_cols=35 Identities=17% Similarity=0.117 Sum_probs=31.1
Q ss_pred cCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q 034490 10 LVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTR 44 (93)
Q Consensus 10 ~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~ 44 (93)
.+|..|.+...++....|.+.+||-.-+...-++.
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 45889999999999999999999988888777777
No 117
>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=37.41 E-value=89 Score=21.70 Aligned_cols=34 Identities=21% Similarity=0.379 Sum_probs=27.8
Q ss_pred hhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccc
Q 034490 3 FFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLN 37 (93)
Q Consensus 3 p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mN 37 (93)
+..+=+.++||.+.-++. +..+.|.|++...|+-
T Consensus 6 ~~~vA~~LLGk~Lv~~~~-~~~~~grIvEtEAY~G 39 (179)
T cd00540 6 TVEVARDLLGKVLVRRLP-GGILSGRIVETEAYLG 39 (179)
T ss_pred HHHHHHHhCCCEEEEECC-CCEEEEEEEEEeccCC
Confidence 356668899999987775 6689999999999964
No 118
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=36.54 E-value=47 Score=25.55 Aligned_cols=23 Identities=30% Similarity=0.478 Sum_probs=21.0
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEE
Q 034490 8 KDLVGREVTVELKNDLAIRGTLH 30 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~ 30 (93)
+-+.|++|+|...+|..+.|++-
T Consensus 93 ~~~~gq~v~i~t~~g~~i~GvIg 115 (355)
T COG1363 93 QVLEGQRVTIHTDKGKKIRGVIG 115 (355)
T ss_pred hhccCcEEEEEeCCCcEEeeeEc
Confidence 45779999999999999999998
No 119
>PF13861 FLgD_tudor: FlgD Tudor-like domain; PDB: 3OSV_A 3C12_A.
Probab=36.18 E-value=79 Score=17.52 Aligned_cols=24 Identities=33% Similarity=0.573 Sum_probs=14.0
Q ss_pred hcCCCEEEEE--EcCCcEEEEEEEEe
Q 034490 9 DLVGREVTVE--LKNDLAIRGTLHSV 32 (93)
Q Consensus 9 ~~~gk~V~V~--L~~g~~~~G~L~~~ 32 (93)
+++||.|.+. ........|++.++
T Consensus 9 ~lIGk~V~~~~~~~~~~~~~g~V~sV 34 (61)
T PF13861_consen 9 SLIGKEVLVPKSVAATTLVSGRVESV 34 (61)
T ss_dssp CTTTSEEEEEEEEEE-EEEEEEEEEE
T ss_pred HhcCCEEEECCcEeeeeEEEEEEEEE
Confidence 6889999996 22233444444444
No 120
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=35.31 E-value=33 Score=20.32 Aligned_cols=20 Identities=30% Similarity=0.491 Sum_probs=15.4
Q ss_pred HHhhcCCCEEEEEEcCCcEE
Q 034490 6 YFKDLVGREVTVELKNDLAI 25 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~g~~~ 25 (93)
.++..+||+|+|+...+-++
T Consensus 5 ~~nDrLGKKVRvKCn~dDti 24 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDTI 24 (73)
T ss_pred hhhhhcCceEEEEeCCcccc
Confidence 46788999999998766543
No 121
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=33.72 E-value=91 Score=19.25 Aligned_cols=27 Identities=22% Similarity=0.253 Sum_probs=20.8
Q ss_pred EcCCCCCceEeeeeEEEecCeEEEEEcCC
Q 034490 46 VDQDKYPHMLSVRNCFIRGSVVRYVQLPP 74 (93)
Q Consensus 46 ~~~~~~~~~~~~~~~~IRG~~I~~I~~~~ 74 (93)
.+.++.. +.-|.+.+.|..+..|.+|+
T Consensus 70 FS~~G~~--ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 70 FSSDGED--RYQGELVMLGRRLISVELPP 96 (97)
T ss_pred EeCCChh--cceEEEEEECCeeeEEEcCC
Confidence 3444442 56699999999999999986
No 122
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=32.57 E-value=78 Score=19.32 Aligned_cols=26 Identities=19% Similarity=0.183 Sum_probs=20.1
Q ss_pred HHhhcCCCEEEEEEcCCcEEEEEEEE
Q 034490 6 YFKDLVGREVTVELKNDLAIRGTLHS 31 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~g~~~~G~L~~ 31 (93)
.|.-+-.-+++.+|++|..+.|+=..
T Consensus 17 ElACl~hl~l~L~lkdGev~~a~A~d 42 (84)
T COG4568 17 ELACLHHLPLTLELKDGEVLQAKASD 42 (84)
T ss_pred HHHHhhhceEEEEEcCCeEEEEEehh
Confidence 34555667899999999999997543
No 123
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=32.41 E-value=1e+02 Score=21.36 Aligned_cols=27 Identities=22% Similarity=0.291 Sum_probs=23.4
Q ss_pred CCCEEEEEEcCCcEEEEEEEEeccccc
Q 034490 11 VGREVTVELKNDLAIRGTLHSVDQYLN 37 (93)
Q Consensus 11 ~gk~V~V~L~~g~~~~G~L~~~D~~mN 37 (93)
.|.+|.|.+.+|..+.|++..++...+
T Consensus 141 ~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 141 KGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CCCEEEEEECCCCEEEEEEEEEccccC
Confidence 489999999999999999999987543
No 124
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.98 E-value=67 Score=21.68 Aligned_cols=23 Identities=17% Similarity=0.385 Sum_probs=18.9
Q ss_pred hcCCCEEEEE-EcCCcEEEEEEEE
Q 034490 9 DLVGREVTVE-LKNDLAIRGTLHS 31 (93)
Q Consensus 9 ~~~gk~V~V~-L~~g~~~~G~L~~ 31 (93)
...|..|+|+ +..|++++|++.+
T Consensus 128 G~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 128 GAAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4578899999 8899999998764
No 125
>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=31.90 E-value=81 Score=19.58 Aligned_cols=21 Identities=38% Similarity=0.686 Sum_probs=16.1
Q ss_pred HHHhhcCCCEEEEEEcCCcEEEEEEEEec
Q 034490 5 SYFKDLVGREVTVELKNDLAIRGTLHSVD 33 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~~G~L~~~D 33 (93)
+.|++++||+|++. |++.++|
T Consensus 11 ~~L~~~~gk~Vriv--------Gkv~~~~ 31 (109)
T PF08661_consen 11 SMLSQFVGKTVRIV--------GKVESVD 31 (109)
T ss_dssp GGGGGGTTSEEEEE--------EEEEEE-
T ss_pred HHHHhhCCCeEEEE--------EEEeeEc
Confidence 67899999999876 6666666
No 126
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.36 E-value=51 Score=20.09 Aligned_cols=40 Identities=18% Similarity=0.230 Sum_probs=27.0
Q ss_pred HHHhhcCCCEEEEEEcCCcEE----EEEEEEec-cccceEEeeEE
Q 034490 5 SYFKDLVGREVTVELKNDLAI----RGTLHSVD-QYLNIKLENTR 44 (93)
Q Consensus 5 ~~L~~~~gk~V~V~L~~g~~~----~G~L~~~D-~~mNl~L~~~~ 44 (93)
.-+++.+|++|.+.+.+|+.= .|.|...= ..+=+.|++..
T Consensus 12 ~~i~ah~G~~v~lk~ngGRKk~~~r~G~L~EtYpSvFIiel~~d~ 56 (80)
T COG4466 12 ESIDAHLGERVTLKANGGRKKTIERSGILIETYPSVFIIELDQDE 56 (80)
T ss_pred HHHHhccCcEEEEEecCCceeeehhceEEeeecCcEEEEEecccC
Confidence 457889999999999999643 37766543 34445554443
No 127
>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=30.93 E-value=1e+02 Score=17.84 Aligned_cols=55 Identities=22% Similarity=0.206 Sum_probs=34.3
Q ss_pred hcCCCEEEEEEcCC-cEEEEEEEEecccc-ceEEeeEEEEcCCCCCceEeeeeEEEecCeEE
Q 034490 9 DLVGREVTVELKND-LAIRGTLHSVDQYL-NIKLENTRVVDQDKYPHMLSVRNCFIRGSVVR 68 (93)
Q Consensus 9 ~~~gk~V~V~L~~g-~~~~G~L~~~D~~m-Nl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~ 68 (93)
+.+|+-|.|.-.+. -.|+|.+..+|+-- -++|....- ++-. ....++..|..-|.
T Consensus 3 dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~~--ngik---~~~~EVt~~~~DI~ 59 (62)
T cd01737 3 DWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPFH--NGVK---CLVPEVTFRAGDIR 59 (62)
T ss_pred cccceEEEEecCCceEEEEEEEEEeCccceEEEEeeccc--CCcc---ccCceEEEEEcchh
Confidence 56789999988877 78999999999643 445444332 1111 22355666655443
No 128
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=30.58 E-value=69 Score=22.77 Aligned_cols=23 Identities=17% Similarity=0.247 Sum_probs=19.5
Q ss_pred hcCCCEEEEE-EcCCcEEEEEEEE
Q 034490 9 DLVGREVTVE-LKNDLAIRGTLHS 31 (93)
Q Consensus 9 ~~~gk~V~V~-L~~g~~~~G~L~~ 31 (93)
...|..|+|+ +..|++++|+..+
T Consensus 183 G~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 183 AGENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCCEEEEEECCCCCEEEEEEeC
Confidence 4579999999 7999999998764
No 129
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=30.28 E-value=1.3e+02 Score=19.73 Aligned_cols=36 Identities=22% Similarity=0.440 Sum_probs=27.9
Q ss_pred HhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEee
Q 034490 7 FKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLEN 42 (93)
Q Consensus 7 L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~ 42 (93)
|....|.+|.|-.++-..-+|-++.+|+.+=+.+.+
T Consensus 100 Ld~~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrIte 135 (136)
T COG1886 100 LDKLAGEPVDILVNGRLIGRGEVVVVDDKFGVRITE 135 (136)
T ss_pred cCCcCCCceEEEECCEEEEEEeEEEECCeEEEEEEe
Confidence 345668888888888888899999999887666543
No 130
>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=29.87 E-value=28 Score=20.44 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=17.9
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEE
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIR 26 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~ 26 (93)
.++++.+++.|..+.|.+-+|+.++
T Consensus 6 ~~I~l~~al~G~~i~i~~l~g~~~~ 30 (81)
T PF01556_consen 6 IPISLKEALLGGTISIPTLDGKTIK 30 (81)
T ss_dssp EEEEHHHHHH-EEEEEE-TTS-EEE
T ss_pred EEeCHHHHhCCCEEEEECCCCCEEE
Confidence 3567889999999999988886554
No 131
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=29.27 E-value=1.3e+02 Score=22.32 Aligned_cols=33 Identities=18% Similarity=0.262 Sum_probs=27.7
Q ss_pred CCEEEEEEcCCcEEEEEEEEeccccceEEeeEE
Q 034490 12 GREVTVELKNDLAIRGTLHSVDQYLNIKLENTR 44 (93)
Q Consensus 12 gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~ 44 (93)
..++.+.+.||+++.+.+.+.|....+-+-...
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki~ 127 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKID 127 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEec
Confidence 567889999999999999999998877665444
No 132
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=29.02 E-value=25 Score=22.09 Aligned_cols=17 Identities=41% Similarity=0.505 Sum_probs=15.2
Q ss_pred EEEEEeccccceEEeeE
Q 034490 27 GTLHSVDQYLNIKLENT 43 (93)
Q Consensus 27 G~L~~~D~~mNl~L~~~ 43 (93)
|+|+|.|.+-|.--++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999988777
No 133
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=28.67 E-value=86 Score=21.03 Aligned_cols=25 Identities=40% Similarity=0.696 Sum_probs=19.0
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEeccc
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVDQY 35 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D~~ 35 (93)
.+++||.|.+ .+| .+.|++.++.-+
T Consensus 93 ~slIGk~V~~--~~~-~~~G~V~sV~~~ 117 (140)
T PRK06009 93 EGLIGRTVTS--ADG-SITGVVKSVTVY 117 (140)
T ss_pred HHhcCCEEEe--cCC-cEEEEEEEEEEe
Confidence 4689999975 455 689999988743
No 134
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=28.59 E-value=96 Score=22.60 Aligned_cols=22 Identities=27% Similarity=0.419 Sum_probs=18.5
Q ss_pred cEEEEEEEEeccccceEEeeEE
Q 034490 23 LAIRGTLHSVDQYLNIKLENTR 44 (93)
Q Consensus 23 ~~~~G~L~~~D~~mNl~L~~~~ 44 (93)
..+.|.+..+|.|-|+.+.=..
T Consensus 168 ~~i~g~Vi~iD~FGNlitnI~~ 189 (258)
T PF01887_consen 168 NGIRGEVIYIDHFGNLITNISR 189 (258)
T ss_dssp TEEEEEEEEEETTSEEEEEEEH
T ss_pred ceEEEEEEEECccCCeeeCCCH
Confidence 3899999999999999875443
No 135
>PF06331 Tbf5: Transcription factor TFIIH complex subunit Tfb5; InterPro: IPR009400 This entry represents nucleotide excision repair (NER) proteins, such as TTDA subunit of TFIIH basal transcription factor complex (also known as subunit 5 of RNA polymerase II transcription factor B), and Rex1. These proteins have a structural motif consisting of a 2-layer sandwich structure with an alpha/beta plait topology. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair. The TFIIH complex consists of ten subunits: ERCC2, ERCC3, GTF2H1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, MNAT1, CDK7 and CCNH. Defects in GTF2H5 cause the disease trichothiodystrophy (TTD), therefore GTF2H5 (general transcription factor 2H subunit 5) is also known as the TTD group A (TTDA) subunit (and as Tfb5) []. The TTDA subunit is responsible for the DNA repair function of the complex. TTDA is present both bound to TFIIH, and as a free fraction that shuffles between the cytoplasm and nucleus; induction of NER-type DNA lesions shifts the balance towards TTDA's more stable association with TFIIH []. TTDA is also required for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell. REX1 (required for excision 1) is required for DNA repair in the single-celled, photosynthetic algae Chlamydomonas reinhardtii [], and has homologues in other eukaryotes.; GO: 0003677 DNA binding, 0006289 nucleotide-excision repair; PDB: 2JNJ_B 1YDL_A 3DGP_B 3DOM_B.
Probab=28.49 E-value=35 Score=20.03 Aligned_cols=13 Identities=38% Similarity=0.590 Sum_probs=9.9
Q ss_pred EEEEEEEEecccc
Q 034490 24 AIRGTLHSVDQYL 36 (93)
Q Consensus 24 ~~~G~L~~~D~~m 36 (93)
.++|+|..||..|
T Consensus 4 a~kGvLv~CDpa~ 16 (68)
T PF06331_consen 4 AIKGVLVECDPAI 16 (68)
T ss_dssp EEEEEEEES-HHH
T ss_pred eeeeEEEEcCHHH
Confidence 5789999999765
No 136
>PRK10708 hypothetical protein; Provisional
Probab=28.37 E-value=79 Score=18.18 Aligned_cols=26 Identities=23% Similarity=0.339 Sum_probs=22.6
Q ss_pred CCCEEEEEEcCCcEEEEEEEEecccc
Q 034490 11 VGREVTVELKNDLAIRGTLHSVDQYL 36 (93)
Q Consensus 11 ~gk~V~V~L~~g~~~~G~L~~~D~~m 36 (93)
++-+|+|++..+..-.|++.++..|-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 46789999999999999999998775
No 137
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=28.33 E-value=1.3e+02 Score=23.82 Aligned_cols=43 Identities=14% Similarity=0.028 Sum_probs=34.0
Q ss_pred chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEE
Q 034490 2 LFFSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRV 45 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~ 45 (93)
.|-.++..++||.|+- =++|++++++|.+=|.-.=+.+.+-.+
T Consensus 72 s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~ 114 (421)
T COG5316 72 SPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVE 114 (421)
T ss_pred CchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEE
Confidence 3667889999999999 799999999999988765555555444
No 138
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=27.54 E-value=33 Score=23.11 Aligned_cols=26 Identities=35% Similarity=0.341 Sum_probs=19.5
Q ss_pred cCCcEEEEEEEEeccccceEEeeEEE
Q 034490 20 KNDLAIRGTLHSVDQYLNIKLENTRV 45 (93)
Q Consensus 20 ~~g~~~~G~L~~~D~~mNl~L~~~~~ 45 (93)
+++..=.|+|+++|.|-|=--+|-..
T Consensus 40 rtd~~kiGTLVG~DkfGNkYyen~~~ 65 (151)
T KOG3382|consen 40 RTDDHKIGTLVGVDKFGNKYYENNDY 65 (151)
T ss_pred hcccccceeeeeecccccchhcccce
Confidence 44555679999999999977666543
No 139
>PRK15493 5-methylthioadenosine/S-adenosylhomocysteine deaminase; Provisional
Probab=27.37 E-value=1.5e+02 Score=22.83 Aligned_cols=37 Identities=8% Similarity=0.135 Sum_probs=23.7
Q ss_pred cceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEEc
Q 034490 36 LNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQL 72 (93)
Q Consensus 36 mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 72 (93)
||+.+.++.....+.......-+.+.|.|+.|..|.-
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 6777788776543322112334688899999988853
No 140
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.09 E-value=1.1e+02 Score=21.70 Aligned_cols=23 Identities=13% Similarity=0.226 Sum_probs=19.6
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEE
Q 034490 9 DLVGREVTVELKNDLAIRGTLHS 31 (93)
Q Consensus 9 ~~~gk~V~V~L~~g~~~~G~L~~ 31 (93)
..+|..|+|+-.+|+++.|++.+
T Consensus 193 G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 193 GNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCCEEEEEeCCCCEEEEEEec
Confidence 46789999999889999998875
No 141
>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=26.53 E-value=98 Score=15.99 Aligned_cols=19 Identities=21% Similarity=0.298 Sum_probs=14.5
Q ss_pred hhcCCCEEEEEEcCCcEEE
Q 034490 8 KDLVGREVTVELKNDLAIR 26 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~ 26 (93)
.+..|..|+|++.+|.+.+
T Consensus 19 ~~~~g~~vtV~~~~G~~~t 37 (42)
T PF02736_consen 19 IEEEGDKVTVKTEDGKEVT 37 (42)
T ss_dssp EEEESSEEEEEETTTEEEE
T ss_pred EEEcCCEEEEEECCCCEEE
Confidence 3556889999999987653
No 142
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=26.19 E-value=75 Score=21.07 Aligned_cols=23 Identities=13% Similarity=0.180 Sum_probs=18.0
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEE
Q 034490 8 KDLVGREVTVELKNDLAIRGTLH 30 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~ 30 (93)
++++-|-++|.|.||.+++.-+=
T Consensus 52 NSAlRK~~RVrL~NG~~VtAyiP 74 (129)
T COG0048 52 NSALRKVARVRLINGKEVTAYIP 74 (129)
T ss_pred ChhhheeEEEEeeCCcEEEEEcC
Confidence 45667899999999999876543
No 143
>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=26.13 E-value=2.5e+02 Score=20.07 Aligned_cols=53 Identities=17% Similarity=0.217 Sum_probs=34.7
Q ss_pred EEEEEEcCCcEEEEEEEEeccccceEEeeEEEEcCCCCCceEeeeeEEEecCeEEEEE
Q 034490 14 EVTVELKNDLAIRGTLHSVDQYLNIKLENTRVVDQDKYPHMLSVRNCFIRGSVVRYVQ 71 (93)
Q Consensus 14 ~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 71 (93)
.+.+.|.++..++|.+.+.+ -++.|.+-..+.-.+. ..++.+-+.|..|.|-.
T Consensus 74 ~~~~~l~~~s~l~G~i~~~~--~~v~l~~~s~W~~tg~---S~v~~L~l~~g~v~f~~ 126 (233)
T cd01343 74 LAELLLGGNAAWTGAIQGLN--ATVSLNLNSVWTLTGD---SNVNNLTLNGGTVDFNG 126 (233)
T ss_pred eEEEEEcCCCEEEeEEeccc--ceEEEcCCCEEEEeCC---cccceeEecCCEEEecc
Confidence 58889999999999999987 5566663333321111 23466777777776643
No 144
>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=26.09 E-value=1.2e+02 Score=23.87 Aligned_cols=27 Identities=22% Similarity=0.449 Sum_probs=22.3
Q ss_pred HhhcCCCEEEEEEc--CC--cEEEEEEEEec
Q 034490 7 FKDLVGREVTVELK--ND--LAIRGTLHSVD 33 (93)
Q Consensus 7 L~~~~gk~V~V~L~--~g--~~~~G~L~~~D 33 (93)
+.+++|++|.|.+. +| +.+.|.+.++.
T Consensus 42 ~~~llG~~v~l~i~~~~~~~r~f~GiVt~~~ 72 (513)
T TIGR03361 42 LEDLLGQPATLTLGRDGGGPRYFHGIVTRFE 72 (513)
T ss_pred HHHHcCCeEEEEEEeCCCceEEEEEEEEEEE
Confidence 56789999999996 33 67899999886
No 145
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=25.81 E-value=2e+02 Score=18.94 Aligned_cols=26 Identities=12% Similarity=0.222 Sum_probs=19.8
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEec
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVD 33 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D 33 (93)
++++-|-+.|.|+||.+++.-+=+-.
T Consensus 46 NSA~RKvarVrL~ngk~v~AyIPGeG 71 (124)
T PRK05163 46 NSALRKVARVRLTNGFEVTAYIPGEG 71 (124)
T ss_pred CchhheEEEEEeCCCCEEEEEcCCCC
Confidence 45667889999999999876665544
No 146
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=25.74 E-value=76 Score=18.35 Aligned_cols=24 Identities=25% Similarity=0.555 Sum_probs=19.7
Q ss_pred EEEEEEEEecc-ccceEEeeEEEEc
Q 034490 24 AIRGTLHSVDQ-YLNIKLENTRVVD 47 (93)
Q Consensus 24 ~~~G~L~~~D~-~mNl~L~~~~~~~ 47 (93)
..+|++.++|. .+-|.|+|-.-..
T Consensus 4 ~veG~I~~id~~~~titLdDGksy~ 28 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSYK 28 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEEE
Confidence 56899999995 6699999987654
No 147
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=25.33 E-value=1.5e+02 Score=17.26 Aligned_cols=32 Identities=28% Similarity=0.505 Sum_probs=24.1
Q ss_pred CCCEEEEEEcCC---cEEEEEEEEeccccce-EEee
Q 034490 11 VGREVTVELKND---LAIRGTLHSVDQYLNI-KLEN 42 (93)
Q Consensus 11 ~gk~V~V~L~~g---~~~~G~L~~~D~~mNl-~L~~ 42 (93)
.+..|+|..-++ ..++|++..+|...+. .+.+
T Consensus 41 ~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~~~ 76 (92)
T PF08863_consen 41 ENQPVTITYYEDGYYQSVTGTIHKIDEINRTLKLKD 76 (92)
T ss_pred CCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEEEe
Confidence 378888887755 7889999999987754 4444
No 148
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.32 E-value=96 Score=22.75 Aligned_cols=23 Identities=17% Similarity=0.287 Sum_probs=19.7
Q ss_pred hcCCCEEEEE-EcCCcEEEEEEEE
Q 034490 9 DLVGREVTVE-LKNDLAIRGTLHS 31 (93)
Q Consensus 9 ~~~gk~V~V~-L~~g~~~~G~L~~ 31 (93)
...|..|+|+ +..|++++|++.+
T Consensus 230 G~~Gd~IrVrN~~SgkvV~a~V~~ 253 (261)
T PRK06804 230 GRKGELIKVKNLSSGRVVTATVDG 253 (261)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4578999999 8999999998875
No 149
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=25.19 E-value=87 Score=21.20 Aligned_cols=24 Identities=21% Similarity=0.252 Sum_probs=17.8
Q ss_pred hhcCCCEEEEEE-cCCcEEEEEEEE
Q 034490 8 KDLVGREVTVEL-KNDLAIRGTLHS 31 (93)
Q Consensus 8 ~~~~gk~V~V~L-~~g~~~~G~L~~ 31 (93)
++++-|.+.|.| +||..++--+=+
T Consensus 64 NSA~RK~arV~L~~Ngk~vtAyIPg 88 (145)
T PRK04211 64 NSAIRKCVRVQLIKNGKQVTAFCPG 88 (145)
T ss_pred chhhceeEEEEEccCCeEEEEEeCC
Confidence 456778999999 799998654433
No 150
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.94 E-value=1.1e+02 Score=20.22 Aligned_cols=23 Identities=26% Similarity=0.432 Sum_probs=18.2
Q ss_pred hcCCCEEEEE-EcCCcEEEEEEEE
Q 034490 9 DLVGREVTVE-LKNDLAIRGTLHS 31 (93)
Q Consensus 9 ~~~gk~V~V~-L~~g~~~~G~L~~ 31 (93)
...|..|.|+ +..+++++|+..+
T Consensus 109 G~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 109 GGVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4568888986 7888999998764
No 151
>PF05343 Peptidase_M42: M42 glutamyl aminopeptidase; InterPro: IPR008007 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M42 (glutamyl aminopeptidase family, clan MH). For members of this family and family M28 the predicted metal ligands occur in the same order in the sequence: H, D, E, D/E, H; and the active site residues occur in the motifs HXD and EE. ; PDB: 2WYR_C 2CF4_A 1VHO_A 3ISX_A 3KL9_G 1YLO_F 3CPX_C 1VHE_A 2GRE_F 1XFO_A ....
Probab=24.90 E-value=92 Score=22.97 Aligned_cols=24 Identities=25% Similarity=0.448 Sum_probs=20.4
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEe
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSV 32 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~ 32 (93)
+.+.|++|+|..++| .+.|++-.-
T Consensus 49 ~~l~gq~v~i~~~~g-~i~Gvig~~ 72 (292)
T PF05343_consen 49 RVLPGQRVRIHTRDG-DIPGVIGSK 72 (292)
T ss_dssp GGTTTEEEEEEETTE-EEEEEEEE-
T ss_pred cccCCCEEEEEcCCc-EEEEEEcCC
Confidence 457899999999999 999999665
No 152
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=24.24 E-value=84 Score=19.77 Aligned_cols=24 Identities=8% Similarity=0.202 Sum_probs=18.3
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEE
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHS 31 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~ 31 (93)
++++-|-+.|.|.||.+++.-+=+
T Consensus 31 NSA~RK~arV~L~ngk~v~ayIPg 54 (95)
T cd00319 31 NSALRKVAKVRLTSGYEVTAYIPG 54 (95)
T ss_pred ChhhceEEEEEccCCCEEEEECCC
Confidence 456678899999999988765544
No 153
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=24.21 E-value=1.6e+02 Score=18.22 Aligned_cols=32 Identities=19% Similarity=0.143 Sum_probs=25.4
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEeccccceE
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVDQYLNIK 39 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~ 39 (93)
+-++||+|.-.-+.|+.+-|++..--..-..+
T Consensus 36 ~fylGKrv~yvyk~grviwGKItR~HGnsGvV 67 (87)
T PRK04337 36 AKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEV 67 (87)
T ss_pred HhhcCceEEEEeCCCCEEEEEEEeeeCCCceE
Confidence 45789999999999999999988766554444
No 154
>PRK09961 exoaminopeptidase; Provisional
Probab=23.79 E-value=1e+02 Score=23.17 Aligned_cols=23 Identities=17% Similarity=0.221 Sum_probs=19.8
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEE
Q 034490 8 KDLVGREVTVELKNDLAIRGTLH 30 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~ 30 (93)
+.+.|++|+|..++|..+.|++.
T Consensus 90 ~~~~~~~v~i~~~~g~~i~Gvi~ 112 (344)
T PRK09961 90 AARQLQPVRITTREECKIPGLLN 112 (344)
T ss_pred cccCCCEEEEEeCCCCEeeEEEC
Confidence 45679999999999988999994
No 155
>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=23.76 E-value=96 Score=17.82 Aligned_cols=26 Identities=23% Similarity=0.332 Sum_probs=22.5
Q ss_pred CCCEEEEEEcCCcEEEEEEEEecccc
Q 034490 11 VGREVTVELKNDLAIRGTLHSVDQYL 36 (93)
Q Consensus 11 ~gk~V~V~L~~g~~~~G~L~~~D~~m 36 (93)
++-+|+|++..+..-.|++.++..|-
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 46789999999999999999998775
No 156
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=22.94 E-value=1.2e+02 Score=18.14 Aligned_cols=32 Identities=19% Similarity=0.140 Sum_probs=25.4
Q ss_pred hcCCCEEEEEEcCCcEEEEEEEEeccccceEE
Q 034490 9 DLVGREVTVELKNDLAIRGTLHSVDQYLNIKL 40 (93)
Q Consensus 9 ~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L 40 (93)
.+=+..+.|+|.||.+..+.|.+=-.-+++-+
T Consensus 16 ~L~~~~f~v~~edg~~~~ahI~GKmr~~~i~I 47 (75)
T COG0361 16 MLPNGRFRVELENGHERLAHISGKMRKNRIRI 47 (75)
T ss_pred ecCCCEEEEEecCCcEEEEEccCcchheeEEe
Confidence 34478899999999999999998776555544
No 157
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=22.53 E-value=2.4e+02 Score=18.61 Aligned_cols=26 Identities=12% Similarity=0.222 Sum_probs=19.4
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEec
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVD 33 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D 33 (93)
++++-|-+.|.|+||.+++.-+=+.-
T Consensus 46 NSA~RKvarVrL~ngk~v~AyIPG~G 71 (124)
T TIGR00981 46 NSALRKVARVRLTNGFEVTAYIPGEG 71 (124)
T ss_pred CchhheeEEEEeCCCCEEEEEcCCCC
Confidence 45667889999999999876554433
No 158
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=22.33 E-value=85 Score=17.55 Aligned_cols=15 Identities=27% Similarity=0.348 Sum_probs=11.4
Q ss_pred HhhcCCCEEEEEEcC
Q 034490 7 FKDLVGREVTVELKN 21 (93)
Q Consensus 7 L~~~~gk~V~V~L~~ 21 (93)
-+.++|++|+|.+.+
T Consensus 37 PK~yiG~rv~viI~k 51 (52)
T COG3466 37 PKRYIGKRVYVIILK 51 (52)
T ss_pred chHHcCcEEEEEEeC
Confidence 367899999987653
No 159
>PF15107 FAM216B: FAM216B protein family
Probab=22.16 E-value=49 Score=21.40 Aligned_cols=27 Identities=22% Similarity=0.416 Sum_probs=22.2
Q ss_pred CeEEEEEcCCCCcchhhhhHhhhhhhc
Q 034490 65 SVVRYVQLPPDGVDVDLLHDATRREAR 91 (93)
Q Consensus 65 ~~I~~I~~~~~~~d~~~~~~~~~~~~~ 91 (93)
-.|-.|++|.+..|+.++.+-+..+.|
T Consensus 15 Pqi~~I~vP~S~~d~s~lkDLT~GQkr 41 (113)
T PF15107_consen 15 PQIPTIHVPKSMTDTSFLKDLTQGQKR 41 (113)
T ss_pred CCCceeecChhhccchhhHhhhhhhhH
Confidence 367789999999999999987776654
No 160
>PF14685 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A.
Probab=22.13 E-value=1.2e+02 Score=18.56 Aligned_cols=22 Identities=9% Similarity=0.234 Sum_probs=17.8
Q ss_pred chhHHHhhcCCCEEEEEEcCCc
Q 034490 2 LFFSYFKDLVGREVTVELKNDL 23 (93)
Q Consensus 2 ~p~~~L~~~~gk~V~V~L~~g~ 23 (93)
-|.++|..--||.|.+++.+..
T Consensus 59 ~~~~lL~~~agk~V~Ltv~~~~ 80 (88)
T PF14685_consen 59 NPYRLLEGKAGKQVLLTVNRKP 80 (88)
T ss_dssp -HHHHHHTTTTSEEEEEEE-ST
T ss_pred CHHHHhcccCCCEEEEEEecCC
Confidence 4788999999999999998764
No 161
>CHL00051 rps12 ribosomal protein S12
Probab=21.88 E-value=2.4e+02 Score=18.57 Aligned_cols=26 Identities=12% Similarity=0.261 Sum_probs=20.1
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEEec
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHSVD 33 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~~D 33 (93)
++++-|-+.|.|+||.+++.-+=+.-
T Consensus 46 NSA~RKvarVrLsngk~v~AyIPGeG 71 (123)
T CHL00051 46 NSALRKVARVRLTSGFEITAYIPGIG 71 (123)
T ss_pred ChhheeEEEEEccCCCEEEEEcCCCC
Confidence 45667889999999999887665544
No 162
>COG2094 Mpg 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=21.65 E-value=2.2e+02 Score=20.26 Aligned_cols=39 Identities=15% Similarity=0.382 Sum_probs=29.6
Q ss_pred hHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEeeEEE
Q 034490 4 FSYFKDLVGREVTVELKNDLAIRGTLHSVDQYLNIKLENTRV 45 (93)
Q Consensus 4 ~~~L~~~~gk~V~V~L~~g~~~~G~L~~~D~~mNl~L~~~~~ 45 (93)
..+=+.++||.+.=+ -+|..+.|.+++...|+- .+|.-.
T Consensus 16 ~~vAr~LLG~~lv~~-~~g~~~~g~IVEtEAY~G--~~D~A~ 54 (200)
T COG2094 16 LVVARELLGKTLVRR-IGGLTTSGRIVETEAYLG--PDDPAC 54 (200)
T ss_pred HHHHHHhcCcEEEEe-cCCcEEEEEEEEEeEecC--CCchhh
Confidence 345578999987755 678999999999999986 334443
No 163
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=21.36 E-value=2.3e+02 Score=17.96 Aligned_cols=30 Identities=13% Similarity=0.214 Sum_probs=23.4
Q ss_pred HHhhcCCCEEEEEEcC-CcEEEEEEEEeccc
Q 034490 6 YFKDLVGREVTVELKN-DLAIRGTLHSVDQY 35 (93)
Q Consensus 6 ~L~~~~gk~V~V~L~~-g~~~~G~L~~~D~~ 35 (93)
.-+.++|+.|.-.-++ |+.+.|++...-..
T Consensus 40 eA~~y~gk~v~yk~~~~G~Vi~G~V~R~HGn 70 (100)
T COG2451 40 EAQFYLGKRVCYKYRSSGRVIKGKVVRTHGN 70 (100)
T ss_pred HHHhhhccEEEEEeCCCCcEEEEEEEEecCC
Confidence 3466889988888887 99999998766544
No 164
>PRK09864 putative peptidase; Provisional
Probab=21.04 E-value=1.4e+02 Score=22.88 Aligned_cols=24 Identities=21% Similarity=0.450 Sum_probs=19.9
Q ss_pred hhcCCCEEEEEEcCCcEEEEEEEE
Q 034490 8 KDLVGREVTVELKNDLAIRGTLHS 31 (93)
Q Consensus 8 ~~~~gk~V~V~L~~g~~~~G~L~~ 31 (93)
+.+.|++|+|..++|..+.|++-.
T Consensus 89 ~~l~~q~V~i~t~~g~~v~GVig~ 112 (356)
T PRK09864 89 QSMLNHRVTIRTHKGVKIPGVIGS 112 (356)
T ss_pred cccCCCEEEEEeCCCCEEEEEEeC
Confidence 457799999999998778899854
No 165
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=20.80 E-value=1.8e+02 Score=16.53 Aligned_cols=33 Identities=12% Similarity=0.328 Sum_probs=22.7
Q ss_pred CCCEEEEEEcCCc----EEEEEEEEeccccceEEeeE
Q 034490 11 VGREVTVELKNDL----AIRGTLHSVDQYLNIKLENT 43 (93)
Q Consensus 11 ~gk~V~V~L~~g~----~~~G~L~~~D~~mNl~L~~~ 43 (93)
+|.+|.|++.++. .|.-.+.+++..-.+.++--
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~P 39 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISMP 39 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE--
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEcC
Confidence 5899999996543 59999999998755655544
No 166
>PRK06630 hypothetical protein; Provisional
Probab=20.59 E-value=54 Score=20.79 Aligned_cols=19 Identities=21% Similarity=0.186 Sum_probs=16.1
Q ss_pred EEEEEEEeccccceEEeeE
Q 034490 25 IRGTLHSVDQYLNIKLENT 43 (93)
Q Consensus 25 ~~G~L~~~D~~mNl~L~~~ 43 (93)
..|+|++.|.+-|---++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3799999999999877764
No 167
>PF13144 SAF_2: SAF-like
Probab=20.51 E-value=1.7e+02 Score=19.69 Aligned_cols=23 Identities=13% Similarity=0.268 Sum_probs=18.2
Q ss_pred hcCCCEEEEEEcC-CcEEEEEEEE
Q 034490 9 DLVGREVTVELKN-DLAIRGTLHS 31 (93)
Q Consensus 9 ~~~gk~V~V~L~~-g~~~~G~L~~ 31 (93)
...|..|.|+-.+ |+.++|++.+
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 4578889998854 8999998865
Done!