Query 023166
Match_columns 286
No_of_seqs 221 out of 1092
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 08:56:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023166.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023166hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3168 U1 snRNP component [Tr 100.0 1.4E-45 3E-50 320.4 9.8 148 1-153 1-148 (177)
2 cd01717 Sm_B The eukaryotic Sm 99.9 4.6E-25 9.9E-30 170.1 10.1 79 5-87 1-79 (79)
3 cd06168 LSm9 The eukaryotic Sm 99.9 1.6E-23 3.5E-28 161.6 10.1 74 6-87 2-75 (75)
4 cd01729 LSm7 The eukaryotic Sm 99.9 7.5E-22 1.6E-26 153.8 10.2 75 6-86 4-78 (81)
5 cd01730 LSm3 The eukaryotic Sm 99.9 1.3E-21 2.8E-26 152.2 9.4 76 9-85 6-81 (82)
6 cd01727 LSm8 The eukaryotic Sm 99.9 2.2E-21 4.9E-26 148.1 9.7 71 7-87 2-72 (74)
7 cd01728 LSm1 The eukaryotic Sm 99.8 6E-21 1.3E-25 147.0 9.6 70 6-86 4-73 (74)
8 cd01719 Sm_G The eukaryotic Sm 99.8 6.5E-21 1.4E-25 145.6 9.4 69 6-88 2-70 (72)
9 cd01720 Sm_D2 The eukaryotic S 99.8 6.8E-21 1.5E-25 151.0 9.5 79 8-87 6-86 (87)
10 PRK00737 small nuclear ribonuc 99.8 1.8E-20 3.9E-25 142.6 9.2 71 1-85 1-71 (72)
11 cd01731 archaeal_Sm1 The archa 99.8 1.8E-20 3.8E-25 140.6 8.8 65 7-85 3-67 (68)
12 cd01732 LSm5 The eukaryotic Sm 99.8 2.2E-20 4.8E-25 144.4 9.5 69 7-86 6-74 (76)
13 PF01423 LSM: LSM domain ; In 99.8 1.1E-19 2.4E-24 134.1 8.8 67 7-86 1-67 (67)
14 smart00651 Sm snRNP Sm protein 99.8 1.6E-19 3.5E-24 133.0 9.0 66 8-86 2-67 (67)
15 cd01726 LSm6 The eukaryotic Sm 99.8 2E-19 4.3E-24 134.9 8.4 64 8-85 4-67 (67)
16 cd01722 Sm_F The eukaryotic Sm 99.8 3E-19 6.5E-24 134.4 7.9 65 7-85 4-68 (68)
17 cd00600 Sm_like The eukaryotic 99.8 1E-18 2.2E-23 126.9 8.7 63 9-85 1-63 (63)
18 cd01718 Sm_E The eukaryotic Sm 99.8 1.8E-18 4E-23 135.2 9.0 67 6-85 8-78 (79)
19 COG1958 LSM1 Small nuclear rib 99.8 2.9E-18 6.4E-23 132.0 9.1 71 6-86 9-79 (79)
20 PTZ00138 small nuclear ribonuc 99.7 7.9E-17 1.7E-21 128.6 9.5 67 7-86 17-87 (89)
21 cd01721 Sm_D3 The eukaryotic S 99.7 3.2E-16 7E-21 118.8 9.0 67 7-87 3-69 (70)
22 KOG1781 Small Nuclear ribonucl 99.7 1.4E-17 3E-22 135.0 0.7 75 7-87 20-94 (108)
23 cd01723 LSm4 The eukaryotic Sm 99.7 3.7E-16 7.9E-21 120.1 8.3 68 8-88 5-72 (76)
24 KOG1780 Small Nuclear ribonucl 99.6 3.1E-16 6.7E-21 121.4 6.3 74 1-88 1-74 (77)
25 cd01724 Sm_D1 The eukaryotic S 99.6 1.9E-15 4E-20 120.3 8.8 73 8-94 5-77 (90)
26 cd01733 LSm10 The eukaryotic S 99.6 2.2E-15 4.7E-20 117.0 8.3 64 9-86 14-77 (78)
27 cd01725 LSm2 The eukaryotic Sm 99.6 6.4E-15 1.4E-19 114.8 8.6 70 7-88 4-73 (81)
28 KOG3460 Small nuclear ribonucl 99.6 3.4E-16 7.3E-21 123.8 1.1 82 3-85 3-85 (91)
29 KOG3482 Small nuclear ribonucl 99.5 3E-14 6.5E-19 110.3 6.0 69 3-85 7-75 (79)
30 KOG1784 Small Nuclear ribonucl 99.4 8.7E-14 1.9E-18 111.6 4.3 71 7-87 3-73 (96)
31 KOG1783 Small nuclear ribonucl 99.4 8.1E-14 1.8E-18 107.8 1.5 69 6-88 8-76 (77)
32 KOG1782 Small Nuclear ribonucl 99.3 1.1E-13 2.3E-18 116.2 -0.3 70 7-87 12-81 (129)
33 KOG1775 U6 snRNA-associated Sm 99.2 1.1E-11 2.4E-16 96.9 3.5 68 10-88 13-80 (84)
34 KOG1774 Small nuclear ribonucl 99.2 1.5E-11 3.2E-16 97.2 3.8 68 7-87 15-86 (88)
35 KOG3459 Small nuclear ribonucl 98.9 3.8E-10 8.3E-15 93.4 0.4 70 15-85 37-106 (114)
36 KOG3172 Small nuclear ribonucl 98.8 1.7E-08 3.6E-13 83.7 7.8 74 1-88 1-75 (119)
37 KOG3293 Small nuclear ribonucl 98.8 8.8E-09 1.9E-13 87.0 6.1 69 8-89 6-74 (134)
38 KOG3448 Predicted snRNP core p 98.8 2.1E-08 4.5E-13 80.6 8.0 70 7-88 5-74 (96)
39 KOG3428 Small nuclear ribonucl 98.6 3E-07 6.4E-12 76.2 9.2 73 7-94 5-77 (109)
40 cd01739 LSm11_C The eukaryotic 98.5 4.8E-08 1E-12 74.5 2.0 41 11-51 3-49 (66)
41 PF14438 SM-ATX: Ataxin 2 SM d 97.7 7.7E-05 1.7E-09 56.9 4.8 67 9-82 7-76 (77)
42 PF12701 LSM14: Scd6-like Sm d 97.6 0.00019 4E-09 58.4 6.2 79 9-92 3-82 (96)
43 KOG1924 RhoA GTPase effector D 97.5 0.00053 1.2E-08 72.8 10.4 20 232-251 565-584 (1102)
44 KOG1924 RhoA GTPase effector D 97.2 0.003 6.6E-08 67.3 11.6 25 234-258 579-605 (1102)
45 PF02237 BPL_C: Biotin protein 96.6 0.0061 1.3E-07 43.0 5.3 35 12-47 1-35 (48)
46 PF11095 Gemin7: Gem-associate 96.5 0.013 2.8E-07 46.6 7.0 62 8-88 18-80 (80)
47 PF06372 Gemin6: Gemin6 protei 96.4 0.0091 2E-07 53.0 6.6 63 6-89 9-72 (166)
48 cd01736 LSm14_N LSm14 (also kn 96.4 0.015 3.2E-07 45.7 6.8 71 10-84 2-73 (74)
49 KOG1073 Uncharacterized mRNA-a 95.7 0.027 5.8E-07 55.5 6.8 79 9-91 4-83 (361)
50 KOG3168 U1 snRNP component [Tr 95.1 0.093 2E-06 47.0 7.6 73 7-84 43-116 (177)
51 PRK02001 hypothetical protein; 94.4 0.14 3.1E-06 44.7 6.9 39 4-43 80-118 (152)
52 cd01735 LSm12_N LSm12 belongs 93.8 0.11 2.4E-06 39.3 4.3 36 12-47 4-39 (61)
53 PRK14638 hypothetical protein; 93.8 0.16 3.4E-06 44.1 5.8 39 4-43 90-128 (150)
54 PF10842 DUF2642: Protein of u 93.4 0.29 6.3E-06 37.6 6.1 51 8-85 15-65 (66)
55 PRK14639 hypothetical protein; 93.2 0.2 4.4E-06 43.0 5.5 39 4-43 78-116 (140)
56 cd01716 Hfq Hfq, an abundant, 93.1 0.17 3.7E-06 38.4 4.3 30 14-43 11-40 (61)
57 TIGR02383 Hfq RNA chaperone Hf 93.1 0.17 3.7E-06 38.4 4.3 29 14-42 15-43 (61)
58 PF03614 Flag1_repress: Repres 92.5 0.12 2.7E-06 45.8 3.3 75 7-82 22-98 (165)
59 PRK14644 hypothetical protein; 92.0 0.34 7.3E-06 41.6 5.4 36 7-43 78-117 (136)
60 PRK14640 hypothetical protein; 91.4 0.55 1.2E-05 40.8 6.1 39 4-43 87-129 (152)
61 cd01734 YlxS_C YxlS is a Bacil 91.4 0.7 1.5E-05 35.9 6.1 37 5-42 16-56 (83)
62 PRK14636 hypothetical protein; 91.0 0.48 1E-05 42.3 5.4 38 4-42 88-129 (176)
63 PRK14642 hypothetical protein; 91.0 0.5 1.1E-05 43.2 5.6 38 4-42 90-140 (197)
64 PRK14633 hypothetical protein; 90.9 0.47 1E-05 41.1 5.2 39 4-43 84-126 (150)
65 PRK00395 hfq RNA-binding prote 90.9 0.51 1.1E-05 37.6 4.9 31 14-44 19-49 (79)
66 PRK14632 hypothetical protein; 90.5 0.56 1.2E-05 41.6 5.4 39 4-43 88-133 (172)
67 PRK14646 hypothetical protein; 89.6 1 2.2E-05 39.3 6.2 38 4-42 90-131 (155)
68 PF07073 ROF: Modulator of Rho 88.9 0.36 7.9E-06 38.2 2.6 60 9-89 12-71 (80)
69 PRK14634 hypothetical protein; 88.6 1.3 2.9E-05 38.6 6.2 38 4-42 90-131 (155)
70 PRK14643 hypothetical protein; 88.4 0.99 2.2E-05 39.9 5.4 34 4-37 94-131 (164)
71 PRK14645 hypothetical protein; 88.2 1.3 2.8E-05 38.8 5.9 38 4-43 92-129 (154)
72 PF02576 DUF150: Uncharacteris 88.1 0.81 1.8E-05 38.6 4.5 37 5-42 78-118 (141)
73 COG0779 Uncharacterized protei 87.9 1.4 2.9E-05 38.9 5.8 38 4-42 89-130 (153)
74 PRK14647 hypothetical protein; 87.1 1.4 3E-05 38.5 5.4 38 4-42 89-135 (159)
75 PRK14637 hypothetical protein; 86.9 1.3 2.9E-05 38.5 5.2 38 5-43 89-127 (151)
76 PRK14631 hypothetical protein; 85.8 1.7 3.7E-05 38.8 5.4 38 4-42 107-150 (174)
77 PRK00092 ribosome maturation p 85.4 1.5 3.3E-05 37.7 4.8 33 5-37 89-125 (154)
78 PRK06955 biotin--protein ligas 85.3 2.1 4.6E-05 40.5 6.1 34 10-43 245-278 (300)
79 PRK14641 hypothetical protein; 83.3 2.5 5.5E-05 37.8 5.3 31 5-35 95-129 (173)
80 COG0340 BirA Biotin-(acetyl-Co 83.2 3 6.6E-05 38.7 6.0 39 8-46 184-222 (238)
81 KOG4849 mRNA cleavage factor I 81.9 35 0.00075 34.6 13.0 15 189-203 255-269 (498)
82 PRK14091 RNA-binding protein H 80.8 2.4 5.3E-05 38.0 4.2 31 15-45 105-135 (165)
83 PRK11886 bifunctional biotin-- 80.2 4.4 9.6E-05 38.2 6.1 32 11-43 269-300 (319)
84 PRK13325 bifunctional biotin-- 79.4 3.8 8.2E-05 42.8 5.8 34 11-44 275-308 (592)
85 PRK11625 Rho-binding antitermi 79.0 8.5 0.00018 30.9 6.4 53 11-85 20-72 (84)
86 COG1923 Hfq Uncharacterized ho 78.4 4.3 9.3E-05 32.3 4.5 27 14-40 19-45 (77)
87 PRK14091 RNA-binding protein H 77.0 3.8 8.2E-05 36.8 4.3 31 15-45 25-55 (165)
88 PRK14630 hypothetical protein; 77.0 6.7 0.00014 33.9 5.7 37 4-42 87-123 (143)
89 PRK08330 biotin--protein ligas 75.9 8.1 0.00018 35.1 6.3 33 11-44 185-218 (236)
90 PRK14635 hypothetical protein; 75.0 6.8 0.00015 34.3 5.3 38 4-42 89-131 (162)
91 PRK09618 flgD flagellar basal 73.8 9.4 0.0002 33.4 5.8 41 9-49 87-130 (142)
92 PF14563 DUF4444: Domain of un 71.1 3.7 7.9E-05 29.3 2.2 25 27-51 10-34 (42)
93 PRK10898 serine endoprotease; 69.7 7.2 0.00016 37.8 4.7 32 15-46 102-133 (353)
94 TIGR02038 protease_degS peripl 69.5 7.2 0.00016 37.7 4.6 32 15-46 102-133 (351)
95 PTZ00275 biotin-acetyl-CoA-car 68.1 8.7 0.00019 36.3 4.8 33 11-44 234-266 (285)
96 COG5316 Uncharacterized conser 66.7 18 0.00039 36.7 6.7 44 6-50 74-117 (421)
97 PF11607 DUF3247: Protein of u 64.6 7.6 0.00017 32.2 3.2 17 15-31 29-45 (101)
98 TIGR02603 CxxCH_TIGR02603 puta 63.9 12 0.00026 31.2 4.4 29 16-44 59-88 (133)
99 PRK10942 serine endoprotease; 63.7 15 0.00032 37.2 5.7 32 15-46 136-167 (473)
100 PRK10139 serine endoprotease; 61.4 12 0.00027 37.6 4.7 32 15-46 115-146 (455)
101 PF03614 Flag1_repress: Repres 59.6 10 0.00023 33.8 3.3 24 14-37 120-143 (165)
102 TIGR02037 degP_htrA_DO peripla 57.2 16 0.00035 35.9 4.6 32 15-46 82-113 (428)
103 KOG0132 RNA polymerase II C-te 55.7 3.3E+02 0.0072 30.3 14.5 11 172-182 631-641 (894)
104 KOG4849 mRNA cleavage factor I 52.9 1.1E+02 0.0023 31.2 9.4 8 27-34 84-91 (498)
105 KOG0132 RNA polymerase II C-te 48.7 1.9E+02 0.0041 32.1 11.0 17 9-25 441-457 (894)
106 PF11743 DUF3301: Protein of u 47.7 17 0.00037 29.4 2.6 42 34-87 54-95 (97)
107 PF14153 Spore_coat_CotO: Spor 45.3 42 0.00092 30.4 5.0 31 7-37 124-157 (185)
108 PRK11911 flgD flagellar basal 44.9 47 0.001 29.1 5.0 26 10-35 89-114 (140)
109 PRK06792 flgD flagellar basal 35.7 1.4E+02 0.003 27.6 6.7 26 10-35 114-139 (190)
110 TIGR02856 spore_yqfC sporulati 35.7 80 0.0017 25.1 4.6 29 15-48 18-46 (85)
111 cd03367 Ribosomal_S23 S12-like 34.2 37 0.00079 29.0 2.6 24 8-31 36-60 (115)
112 PF06115 DUF956: Domain of unk 33.9 1.4E+02 0.0031 25.6 6.1 73 9-88 1-74 (118)
113 PF08863 YolD: YolD-like prote 33.8 97 0.0021 23.5 4.7 35 7-41 33-72 (92)
114 PF10246 MRP-S35: Mitochondria 33.7 31 0.00067 29.0 2.0 37 13-50 63-99 (104)
115 PF06257 DUF1021: Protein of u 33.5 43 0.00093 26.5 2.7 38 6-45 9-50 (76)
116 smart00333 TUDOR Tudor domain. 32.1 1.2E+02 0.0026 20.9 4.6 25 13-37 5-29 (57)
117 COG0094 RplE Ribosomal protein 31.8 14 0.0003 33.7 -0.3 40 6-45 93-133 (180)
118 cd08057 MPN_euk_non_mb Mpr1p, 31.4 26 0.00057 29.8 1.3 29 23-51 21-49 (157)
119 PRK04211 rps12P 30S ribosomal 31.1 41 0.00089 29.7 2.5 33 8-41 62-95 (145)
120 PF08661 Rep_fac-A_3: Replicat 31.0 1.6E+02 0.0036 23.6 5.9 16 6-21 10-25 (109)
121 cd01772 SAKS1_UBX SAKS1-like U 30.8 32 0.00069 26.3 1.6 25 12-36 2-26 (79)
122 PF06856 DUF1251: Protein of u 30.6 71 0.0015 27.4 3.8 28 15-42 22-51 (120)
123 CHL00078 rpl5 ribosomal protei 30.2 9.7 0.00021 34.3 -1.6 66 6-86 94-160 (181)
124 PF04452 Methyltrans_RNA: RNA 30.1 2.1E+02 0.0046 25.7 7.0 26 13-38 19-44 (225)
125 COG0265 DegQ Trypsin-like seri 29.5 79 0.0017 30.0 4.3 33 14-46 95-127 (347)
126 PF01887 SAM_adeno_trans: S-ad 29.4 56 0.0012 30.8 3.3 21 26-46 169-189 (258)
127 PRK00010 rplE 50S ribosomal pr 27.3 12 0.00026 33.7 -1.5 40 6-45 93-133 (179)
128 PF01052 SpoA: Surface present 27.1 75 0.0016 23.6 3.1 35 11-45 39-73 (77)
129 PTZ00067 40S ribosomal S23; Pr 27.0 42 0.0009 29.6 1.8 31 7-37 60-97 (143)
130 smart00166 UBX Domain present 27.0 53 0.0011 24.9 2.2 23 14-36 4-26 (80)
131 PF13365 Trypsin_2: Trypsin-li 26.9 1.5E+02 0.0033 22.3 4.8 34 13-46 29-65 (120)
132 PRK06009 flgD flagellar basal 26.6 1.3E+02 0.0028 26.4 4.7 38 9-49 92-132 (140)
133 PRK11713 16S ribosomal RNA met 26.3 2.2E+02 0.0047 25.9 6.4 25 13-37 32-56 (234)
134 PF10387 DUF2442: Protein of u 26.1 65 0.0014 24.2 2.6 21 14-34 9-29 (79)
135 PF03293 Pox_RNA_pol: Poxvirus 26.0 3.2E+02 0.0069 24.4 7.1 76 8-85 57-141 (160)
136 cd04479 RPA3 RPA3: A subfamily 26.0 1.4E+02 0.003 24.0 4.6 15 6-20 7-21 (101)
137 KOG4649 PQQ (pyrrolo-quinoline 25.6 1.7E+02 0.0036 29.0 5.8 38 6-43 4-48 (354)
138 PF10055 DUF2292: Uncharacteri 25.5 1.1E+02 0.0023 21.3 3.3 22 7-28 7-29 (38)
139 PF00789 UBX: UBX domain; Int 25.4 73 0.0016 23.8 2.7 22 15-36 7-28 (82)
140 smart00739 KOW KOW (Kyprides, 25.3 1.3E+02 0.0027 17.8 3.3 25 13-37 4-28 (28)
141 PF07873 YabP: YabP family; I 25.2 78 0.0017 23.6 2.8 19 68-86 31-49 (66)
142 cd08062 MPN_RPN7_8 Mpr1p, Pad1 25.2 39 0.00085 32.1 1.5 42 9-50 10-51 (280)
143 PF05833 FbpA: Fibronectin-bin 25.1 65 0.0014 31.7 3.0 35 14-48 94-134 (455)
144 KOG4401 Uncharacterized conser 24.9 79 0.0017 29.0 3.3 35 12-46 9-43 (184)
145 COG4939 Major membrane immunog 24.7 18 0.00039 31.7 -0.8 65 16-85 49-113 (147)
146 cd00319 Ribosomal_S12_like Rib 24.7 42 0.00092 27.7 1.4 26 7-32 28-53 (95)
147 PF05606 DUF777: Borrelia burg 24.4 1.6E+02 0.0036 26.8 5.1 27 6-38 21-47 (181)
148 TIGR00982 S23_S12_E_A ribosoma 23.9 75 0.0016 27.9 2.8 33 8-41 56-89 (139)
149 PF14485 DUF4431: Domain of un 23.9 70 0.0015 23.0 2.2 16 5-20 10-25 (48)
150 PF05954 Phage_GPD: Phage late 23.5 88 0.0019 27.9 3.3 29 7-35 21-49 (292)
151 COG4466 Veg Uncharacterized pr 23.3 77 0.0017 25.5 2.5 24 5-28 10-33 (80)
152 COG1976 TIF6 Translation initi 23.1 1.7E+02 0.0036 27.7 5.0 79 7-87 37-117 (222)
153 cd01767 UBX UBX (ubiquitin reg 22.8 76 0.0017 23.7 2.4 22 15-36 3-24 (77)
154 COG2524 Predicted transcriptio 22.1 55 0.0012 31.9 1.8 47 8-54 123-172 (294)
155 PF07317 YcgR: Flagellar regul 22.0 79 0.0017 25.6 2.5 37 9-45 14-52 (108)
156 PRK08655 prephenate dehydrogen 21.9 1.4E+02 0.003 29.9 4.6 45 6-51 292-337 (437)
157 PF10894 DUF2689: Protein of u 21.9 36 0.00077 25.9 0.4 20 34-53 20-39 (61)
158 KOG3382 NADH:ubiquinone oxidor 20.7 55 0.0012 28.9 1.4 28 22-49 40-67 (151)
159 PRK04337 50S ribosomal protein 20.6 1.8E+02 0.0039 23.7 4.2 37 5-41 31-67 (87)
160 PF08458 PH_2: Plant pleckstri 20.3 85 0.0018 26.5 2.4 68 12-88 20-88 (110)
No 1
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=100.00 E-value=1.4e-45 Score=320.35 Aligned_cols=148 Identities=64% Similarity=1.088 Sum_probs=139.4
Q ss_pred CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166 1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE 80 (286)
Q Consensus 1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen 80 (286)
|+++|++||+++|||+++|+|+|||+|+|+|++||+||||||+|||||++++.++.| ..+.||||.||||+|||||
T Consensus 1 M~~a~sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~----~~~~eEkr~lgLvllRgen 76 (177)
T KOG3168|consen 1 MTVAKSSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRK----MTDGEEKRVLGLVLLRGEN 76 (177)
T ss_pred CCccchhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhcccccccc----ccccceeeEEEEEEecCCc
Confidence 899999999999999999999999999999999999999999999999998876653 3578999999999999999
Q ss_pred eEEeeecCCCCChhhhhhhccccCCCCCCccccCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 023166 81 VISMTVEGPPPPEESRAKAVSASAVAGPGIGRAAGRGVPAAPLVQAQPGLAGPVRGVGGPAPGMMQPQISRPP 153 (286)
Q Consensus 81 IVSIsVe~PPp~d~~~~~~~~~~~~~Gpg~~r~aGRG~p~~~~~~~~~gL~gp~~gvggp~~~~m~p~~~~~~ 153 (286)
|||++||++|+.|++.+++. +++..|+|++|.+||||+..++.+++.||+||++|||++++++|+|++++.+
T Consensus 77 Ivs~tVegppp~s~s~~~v~-ag~~~g~G~ar~~Grgip~~~~~~a~~gLtGp~rg~g~~a~~~~qp~g~g~p 148 (177)
T KOG3168|consen 77 IVSMTVEGPPPPSDSFRRVP-AGAARGPGIARVAGRGIPSGPLGQAPEGLTGPVRGVGGPAPQIMQPQGRGYP 148 (177)
T ss_pred EEEEeccCCCCCcccccccc-ccccCCcccccccCCCccCCCcccCCCCCcCCccccCCCCccccCccccCCC
Confidence 99999999999999998887 8899999999999999998889999999999999999999999999987644
No 2
>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=99.92 E-value=4.6e-25 Score=170.14 Aligned_cols=79 Identities=76% Similarity=1.203 Sum_probs=68.7
Q ss_pred hhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166 5 KSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM 84 (286)
Q Consensus 5 k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI 84 (286)
|++||++||+++|+|+|+|||+|+|+|+|||+||||||+||+|++....+..+ ..+.+++|.+|++||||+||++|
T Consensus 1 ~~~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~----~~~~~~~r~lG~v~iRG~~Vv~i 76 (79)
T cd01717 1 KSSKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSK----NSEREEKRTLGLVLLRGENIVSM 76 (79)
T ss_pred CcchhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccc----cccCcceeEeeeEEEcCCEEEEE
Confidence 56899999999999999999999999999999999999999999875432211 12356789999999999999999
Q ss_pred eec
Q 023166 85 TVE 87 (286)
Q Consensus 85 sVe 87 (286)
+||
T Consensus 77 ~v~ 79 (79)
T cd01717 77 TVE 79 (79)
T ss_pred EEC
Confidence 986
No 3
>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=99.90 E-value=1.6e-23 Score=161.55 Aligned_cols=74 Identities=36% Similarity=0.712 Sum_probs=66.3
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
.++|.+||+++|+|+|+|||+|+|+|.|||+||||||+||+|++....+ ....+.|.||+++|||++|++|+
T Consensus 2 ~~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~--------~~~~~~r~lGlv~IrG~~Iv~i~ 73 (75)
T cd06168 2 RQKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDS--------FSPTEPRVLGLVMIPGHHIVSIE 73 (75)
T ss_pred HhHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCc--------cCCccEEEeeeEEEeCCeEEEEE
Confidence 3689999999999999999999999999999999999999999975432 13467899999999999999999
Q ss_pred ec
Q 023166 86 VE 87 (286)
Q Consensus 86 Ve 87 (286)
+|
T Consensus 74 v~ 75 (75)
T cd06168 74 VE 75 (75)
T ss_pred EC
Confidence 86
No 4
>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=99.87 E-value=7.5e-22 Score=153.84 Aligned_cols=75 Identities=29% Similarity=0.563 Sum_probs=63.6
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
..+|.+|||++|+|+|+|||+|+|+|++||+||||||+||+|++..+.+. ....++++.||+++|||+||++|+
T Consensus 4 ~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~------~~~~~~~~~lG~v~iRG~nV~~i~ 77 (81)
T cd01729 4 ILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDP------YKLTDKTRQLGLVVCRGTSVVLIS 77 (81)
T ss_pred hhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcc------cccccceeEccEEEEcCCEEEEEe
Confidence 35799999999999999999999999999999999999999998632211 112457889999999999999995
Q ss_pred e
Q 023166 86 V 86 (286)
Q Consensus 86 V 86 (286)
.
T Consensus 78 ~ 78 (81)
T cd01729 78 P 78 (81)
T ss_pred c
Confidence 3
No 5
>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=1.3e-21 Score=152.25 Aligned_cols=76 Identities=25% Similarity=0.498 Sum_probs=62.2
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
|.++++++|+|+|+|||+|+|+|++||+||||||+||+|++..+.++.+.. +....+.+|.+|++||||+||++|+
T Consensus 6 l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~-~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 6 IRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETY-EEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred HHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeeccccccccc-ccccceeEEEcCeEEEeCCEEEEEC
Confidence 567799999999999999999999999999999999999987543322100 1122457899999999999999986
No 6
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=2.2e-21 Score=148.13 Aligned_cols=71 Identities=30% Similarity=0.501 Sum_probs=62.1
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
++|++|+|++|+|+|+|||+|+|+|++||+||||||+||+|+.... .+..+++.+|+++|||+||++|+.
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~----------~~~~~~~~lG~~~iRG~~I~~i~~ 71 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSS----------DEGVEQVVLGLYIIRGDNIAVVGE 71 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecC----------CCCceeeEeceEEECCCEEEEEEc
Confidence 6899999999999999999999999999999999999999986421 112467889999999999999974
Q ss_pred c
Q 023166 87 E 87 (286)
Q Consensus 87 e 87 (286)
.
T Consensus 72 ~ 72 (74)
T cd01727 72 I 72 (74)
T ss_pred c
Confidence 3
No 7
>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=99.85 E-value=6e-21 Score=146.98 Aligned_cols=70 Identities=27% Similarity=0.496 Sum_probs=61.7
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
..+|++|||++|+|+|+|||+|+|+|++||+||||||+||+|+.... +...++.+|+++|||+||++|.
T Consensus 4 ~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~-----------~~~~~~~lG~~viRG~~V~~ig 72 (74)
T cd01728 4 TASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVG-----------DKYGDIPRGIFIIRGENVVLLG 72 (74)
T ss_pred hHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecC-----------CccceeEeeEEEEECCEEEEEE
Confidence 46799999999999999999999999999999999999999987632 1234688999999999999986
Q ss_pred e
Q 023166 86 V 86 (286)
Q Consensus 86 V 86 (286)
.
T Consensus 73 ~ 73 (74)
T cd01728 73 E 73 (74)
T ss_pred c
Confidence 3
No 8
>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=99.84 E-value=6.5e-21 Score=145.61 Aligned_cols=69 Identities=22% Similarity=0.552 Sum_probs=62.1
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
..+|++||||+|+|+|+|||+|+|+|++||+||||||+||+|+.. .++++.+|+++|||+||++|+
T Consensus 2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~--------------~~~~~~lg~v~IRG~~I~~i~ 67 (72)
T cd01719 2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS--------------GGEKNNIGMVVIRGNSIVMLE 67 (72)
T ss_pred chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEcc--------------CCceeEeceEEECCCEEEEEE
Confidence 468999999999999999999999999999999999999999862 134789999999999999998
Q ss_pred ecC
Q 023166 86 VEG 88 (286)
Q Consensus 86 Ve~ 88 (286)
..+
T Consensus 68 ~~~ 70 (72)
T cd01719 68 ALE 70 (72)
T ss_pred ccc
Confidence 654
No 9
>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=99.84 E-value=6.8e-21 Score=150.96 Aligned_cols=79 Identities=28% Similarity=0.491 Sum_probs=63.1
Q ss_pred HHHHhc--CCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 8 KMLQFI--NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 8 kL~qlI--gkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
-|.+.+ +++|+|+|+|||+|+|+|+|||+||||||+||+|++..+.+++... .....+++|++|+||||||||++|+
T Consensus 6 ~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~-~~~~~~~~r~lg~v~iRGd~Vv~Is 84 (87)
T cd01720 6 LLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGK-KAKPVNKDRFISKMFLRGDSVILVL 84 (87)
T ss_pred HHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccc-cccceeeeeEcccEEEeCCEEEEEe
Confidence 345665 8999999999999999999999999999999999997654332110 0123457889999999999999997
Q ss_pred ec
Q 023166 86 VE 87 (286)
Q Consensus 86 Ve 87 (286)
-.
T Consensus 85 ~~ 86 (87)
T cd01720 85 RN 86 (87)
T ss_pred cC
Confidence 54
No 10
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.83 E-value=1.8e-20 Score=142.63 Aligned_cols=71 Identities=32% Similarity=0.560 Sum_probs=61.2
Q ss_pred CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166 1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE 80 (286)
Q Consensus 1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen 80 (286)
|+..-...|.++++++|+|+|+|||+|+|+|++||+||||||+||+|++. .+.++.+|+++|||+|
T Consensus 1 ~~~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~--------------~~~~~~lg~v~iRG~~ 66 (72)
T PRK00737 1 MAQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD--------------GEVVRKLGKVVIRGDN 66 (72)
T ss_pred CCcchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC--------------CCeEeEcCcEEEeCCE
Confidence 44333456789999999999999999999999999999999999999742 1356889999999999
Q ss_pred eEEee
Q 023166 81 VISMT 85 (286)
Q Consensus 81 IVSIs 85 (286)
|++|+
T Consensus 67 V~~i~ 71 (72)
T PRK00737 67 VVYVS 71 (72)
T ss_pred EEEEc
Confidence 99985
No 11
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.83 E-value=1.8e-20 Score=140.62 Aligned_cols=65 Identities=32% Similarity=0.595 Sum_probs=58.9
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
+.|.+|++++|+|+|+|||+|+|+|++||+||||+|+||+|++.. .+++.+|+++|||+||++|+
T Consensus 3 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------------~~~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 3 DVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG--------------EPVRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred HHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC--------------CeEeEcCcEEEeCCEEEEEc
Confidence 468899999999999999999999999999999999999998641 25688999999999999985
No 12
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.83 E-value=2.2e-20 Score=144.39 Aligned_cols=69 Identities=25% Similarity=0.492 Sum_probs=60.0
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
..|.++++++|+|+|+|||+|+|+|++||+||||||+||+|++..+ +.++++.+|+++|||+||++|+-
T Consensus 6 ~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~-----------~~~~~~~lg~v~iRG~nV~~i~p 74 (76)
T cd01732 6 ELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITP-----------EGRKITKLDQILLNGNNICMLVP 74 (76)
T ss_pred HHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcC-----------CCceeeEcCeEEEeCCeEEEEEC
Confidence 3467899999999999999999999999999999999999997411 12357889999999999999973
No 13
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.81 E-value=1.1e-19 Score=134.11 Aligned_cols=67 Identities=36% Similarity=0.661 Sum_probs=61.0
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
.+|+++++++|+|+|+||++|+|+|.+||+||||+|+||.|++.. ..+++.++++||||++|++|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~-------------~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKN-------------GPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETT-------------ESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECC-------------CCcEeECcEEEEECCEEEEEEC
Confidence 368999999999999999999999999999999999999999752 1278899999999999999974
No 14
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.80 E-value=1.6e-19 Score=133.00 Aligned_cols=66 Identities=38% Similarity=0.652 Sum_probs=60.1
Q ss_pred HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
.|++|++++|+|+|+|||+|+|+|.+||+||||+|+||+|++.. ..+.+.+++++|||++|++|+.
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~-------------~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD-------------GEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecC-------------CcEEeEeCCEEEcCCEEEEEeC
Confidence 68999999999999999999999999999999999999998751 1467899999999999999863
No 15
>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=99.80 E-value=2e-19 Score=134.92 Aligned_cols=64 Identities=22% Similarity=0.390 Sum_probs=57.9
Q ss_pred HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
.|.++++++|+|+|+||++|+|+|.+||.||||+|+||+|+.. ..+++.+++++|||++|++|+
T Consensus 4 ~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~--------------~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 4 FLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN--------------GQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred HHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC--------------CceeeEeCCEEEECCEEEEEC
Confidence 5789999999999999999999999999999999999998752 235778999999999999985
No 16
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.79 E-value=3e-19 Score=134.42 Aligned_cols=65 Identities=25% Similarity=0.378 Sum_probs=57.9
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
..|.++++++|+|+|+|||+|+|+|.+||+||||+|+||+|+.. ..+++.+|+++|||+||++|+
T Consensus 4 ~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~--------------~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 4 PFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID--------------GKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred HHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC--------------CccccCcCcEEEECCEEEEEC
Confidence 46789999999999999999999999999999999999998742 124678999999999999984
No 17
>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=99.78 E-value=1e-18 Score=126.91 Aligned_cols=63 Identities=46% Similarity=0.717 Sum_probs=58.0
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
|.+|++++|+|+|+||++|+|+|.+||+||||+|+||+|+++. .+.+.+++++|||++|++|+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~--------------~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE--------------GKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC--------------CcEEECCeEEEECCEEEEEC
Confidence 5789999999999999999999999999999999999998752 46789999999999999984
No 18
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.77 E-value=1.8e-18 Score=135.16 Aligned_cols=67 Identities=30% Similarity=0.550 Sum_probs=56.7
Q ss_pred hhHHHHhcCCEEEE--EEe--CCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCcee
Q 023166 6 SSKMLQFINYRMRV--TIQ--DGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEV 81 (286)
Q Consensus 6 ~skL~qlIgkRVRV--tLq--DGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenI 81 (286)
...|.+|++++++| .|+ +||+|+|+|++||+||||||+||+|+... .++++.+|++||||+||
T Consensus 8 ~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~-------------~~~~~~lG~iliRGnnV 74 (79)
T cd01718 8 INLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK-------------TKTRKPLGRILLKGDNI 74 (79)
T ss_pred HHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC-------------CceEeEcCcEEEeCCEE
Confidence 45788999995555 444 99999999999999999999999998741 24678899999999999
Q ss_pred EEee
Q 023166 82 ISMT 85 (286)
Q Consensus 82 VSIs 85 (286)
++|+
T Consensus 75 ~~I~ 78 (79)
T cd01718 75 TLIQ 78 (79)
T ss_pred EEEc
Confidence 9986
No 19
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.76 E-value=2.9e-18 Score=131.95 Aligned_cols=71 Identities=35% Similarity=0.575 Sum_probs=59.2
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
.+.|.+++|++|.|+|+|||+|+|+|++||.||||+|+||+|++..+ .+....+..+.++|||+||++|.
T Consensus 9 ~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~----------~~~~~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 9 LSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHD----------GEKNVRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred HHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccC----------CccccceeccEEEEECCcEEEEe
Confidence 56788999999999999999999999999999999999999987510 01113455559999999999986
Q ss_pred e
Q 023166 86 V 86 (286)
Q Consensus 86 V 86 (286)
.
T Consensus 79 ~ 79 (79)
T COG1958 79 P 79 (79)
T ss_pred C
Confidence 3
No 20
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.70 E-value=7.9e-17 Score=128.58 Aligned_cols=67 Identities=30% Similarity=0.622 Sum_probs=54.7
Q ss_pred hHHHHhcCC--EEEEEEeC--CcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeE
Q 023166 7 SKMLQFINY--RMRVTIQD--GRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVI 82 (286)
Q Consensus 7 skL~qlIgk--RVRVtLqD--GR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIV 82 (286)
.++.+|+.. +|+|.|.| +|+|+|+|++||+||||||+||+|++.. .++++.||++||||+||+
T Consensus 17 ~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~-------------~~~~~~lG~ilIRGnnV~ 83 (89)
T PTZ00138 17 NQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK-------------KNTRKDLGRILLKGDNIT 83 (89)
T ss_pred HHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC-------------CceeeEcCeEEEcCCEEE
Confidence 456778876 45555656 5999999999999999999999998641 235789999999999999
Q ss_pred Eeee
Q 023166 83 SMTV 86 (286)
Q Consensus 83 SIsV 86 (286)
+|+.
T Consensus 84 ~I~~ 87 (89)
T PTZ00138 84 LIMA 87 (89)
T ss_pred EEEc
Confidence 9964
No 21
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.67 E-value=3.2e-16 Score=118.84 Aligned_cols=67 Identities=18% Similarity=0.218 Sum_probs=57.9
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
..|.++++++|.|+|+||++|+|+|.+||.||||+|+||+|.... .+...++.++|||+||++|.+
T Consensus 3 ~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~--------------g~~~~~~~v~IRG~nI~~v~l 68 (70)
T cd01721 3 KLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARD--------------GRVSQLEQVYIRGSKIRFFIL 68 (70)
T ss_pred HHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCC--------------CcEeEcCcEEEeCCEEEEEEe
Confidence 346789999999999999999999999999999999999875421 123567999999999999987
Q ss_pred c
Q 023166 87 E 87 (286)
Q Consensus 87 e 87 (286)
.
T Consensus 69 P 69 (70)
T cd01721 69 P 69 (70)
T ss_pred C
Confidence 5
No 22
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.66 E-value=1.4e-17 Score=135.03 Aligned_cols=75 Identities=27% Similarity=0.531 Sum_probs=65.0
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
-+|.+|+|++|||++..||+++|+|++||+.|||||+||+||.+..++.. ...++.|.||+|+|||..||+|+-
T Consensus 20 lDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~------~~~~~tR~LGLvV~RGTalvlisp 93 (108)
T KOG1781|consen 20 LDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPY------KLTDETRKLGLVVCRGTALVLISP 93 (108)
T ss_pred hhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCcc------chhhhhheeeeEEEcccEEEEEcC
Confidence 46889999999999999999999999999999999999999987544322 234566999999999999999964
Q ss_pred c
Q 023166 87 E 87 (286)
Q Consensus 87 e 87 (286)
.
T Consensus 94 ~ 94 (108)
T KOG1781|consen 94 A 94 (108)
T ss_pred C
Confidence 4
No 23
>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=99.66 E-value=3.7e-16 Score=120.11 Aligned_cols=68 Identities=19% Similarity=0.264 Sum_probs=58.3
Q ss_pred HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166 8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE 87 (286)
Q Consensus 8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe 87 (286)
-|.++++++|.|+|+||++|+|+|.+||.||||+|+||+|... +.+....++.++|||++|++|++.
T Consensus 5 ~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~-------------~g~~~~~~~~v~IRG~~I~~i~~p 71 (76)
T cd01723 5 LLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSK-------------DGDKFWKMPECYIRGNTIKYLRVP 71 (76)
T ss_pred HHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC-------------CCcEeeeCCcEEEeCCEEEEEEcC
Confidence 4678999999999999999999999999999999999998632 122345679999999999999876
Q ss_pred C
Q 023166 88 G 88 (286)
Q Consensus 88 ~ 88 (286)
+
T Consensus 72 ~ 72 (76)
T cd01723 72 D 72 (76)
T ss_pred H
Confidence 4
No 24
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.64 E-value=3.1e-16 Score=121.40 Aligned_cols=74 Identities=23% Similarity=0.519 Sum_probs=63.4
Q ss_pred CCchhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCce
Q 023166 1 MSMSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEE 80 (286)
Q Consensus 1 m~~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGen 80 (286)
|+.+--.+|++|+||+|.|+|+.||.+.|+|++||.||||||+||.|... .+.+..+|.++|||++
T Consensus 1 Msksg~PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~--------------~~~~~~ig~~vIrgns 66 (77)
T KOG1780|consen 1 MSKSGHPELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNG--------------DGDKNNIGMVVIRGNS 66 (77)
T ss_pred CCcccCchHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecC--------------cCCcceeeeEEEeccE
Confidence 44442259999999999999999999999999999999999999999753 2456789999999999
Q ss_pred eEEeeecC
Q 023166 81 VISMTVEG 88 (286)
Q Consensus 81 IVSIsVe~ 88 (286)
|+.++..+
T Consensus 67 iv~~eaL~ 74 (77)
T KOG1780|consen 67 IVMVEALE 74 (77)
T ss_pred EEEEeecc
Confidence 99986543
No 25
>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=99.62 E-value=1.9e-15 Score=120.34 Aligned_cols=73 Identities=15% Similarity=0.256 Sum_probs=62.6
Q ss_pred HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166 8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE 87 (286)
Q Consensus 8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe 87 (286)
.|.++++++|+|+|+||++|+|+|.++|.||||+|+||+|+.. ......++.++|||+||++|++.
T Consensus 5 fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~--------------~~~~~~~~~v~IRG~nI~yi~lP 70 (90)
T cd01724 5 FLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLK--------------GRNPVPLDTLSIRGNNIRYFILP 70 (90)
T ss_pred HHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcC--------------CCceeEcceEEEeCCEEEEEEcC
Confidence 4678999999999999999999999999999999999998753 12456799999999999999998
Q ss_pred CCCCChh
Q 023166 88 GPPPPEE 94 (286)
Q Consensus 88 ~PPp~d~ 94 (286)
+---.|.
T Consensus 71 d~l~~~~ 77 (90)
T cd01724 71 DSLNLDT 77 (90)
T ss_pred CcCCcch
Confidence 7543333
No 26
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.61 E-value=2.2e-15 Score=117.04 Aligned_cols=64 Identities=11% Similarity=0.284 Sum_probs=56.3
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
|.+++|++|.|+|+||.+|+|+|.++|.||||+|+||+|... ...+..++.++|||+||++|++
T Consensus 14 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~--------------~~~~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 14 LQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDR--------------NGKQVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred HHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcC--------------CCceeECCcEEEECCEEEEEEc
Confidence 567899999999999999999999999999999999987642 1234478999999999999986
No 27
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.58 E-value=6.4e-15 Score=114.84 Aligned_cols=70 Identities=13% Similarity=0.186 Sum_probs=58.9
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
+.|.++++++|.|+|+||++|+|+|.++|.||||+|+||+++.... ......++.++|||++|++|++
T Consensus 4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~------------~~~~~~~~~v~IRG~~I~~I~l 71 (81)
T cd01725 4 SFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEK------------YPHMLSVKNCFIRGSVVRYVQL 71 (81)
T ss_pred HHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCC------------cccccccCeEEEECCEEEEEEe
Confidence 3578899999999999999999999999999999999998764210 1124456999999999999987
Q ss_pred cC
Q 023166 87 EG 88 (286)
Q Consensus 87 e~ 88 (286)
.+
T Consensus 72 p~ 73 (81)
T cd01725 72 PA 73 (81)
T ss_pred Ch
Confidence 65
No 28
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.58 E-value=3.4e-16 Score=123.76 Aligned_cols=82 Identities=28% Similarity=0.492 Sum_probs=64.7
Q ss_pred chhhhHHH-HhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCcee
Q 023166 3 MSKSSKML-QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEV 81 (286)
Q Consensus 3 ~~k~skL~-qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenI 81 (286)
|...-+|+ -+++.||.|+|+++|+++|+|.|||+|+|+||+|++|.....+.+..+ .+...++.+|.+-.+||||++|
T Consensus 3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~-~e~~~k~~~r~~emlFvRGd~V 81 (91)
T KOG3460|consen 3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDT-YEEIVKTTKRTVEMLFVRGDGV 81 (91)
T ss_pred ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchh-HHHHHhhhhcceeEEEEeCCeE
Confidence 33444555 479999999999999999999999999999999999998764322110 1122457789999999999999
Q ss_pred EEee
Q 023166 82 ISMT 85 (286)
Q Consensus 82 VSIs 85 (286)
+.|+
T Consensus 82 ilvs 85 (91)
T KOG3460|consen 82 ILVS 85 (91)
T ss_pred EEEc
Confidence 9983
No 29
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.50 E-value=3e-14 Score=110.28 Aligned_cols=69 Identities=22% Similarity=0.364 Sum_probs=61.7
Q ss_pred chhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeE
Q 023166 3 MSKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVI 82 (286)
Q Consensus 3 ~~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIV 82 (286)
++-+..|+.+++|+|+|+|+.|.+|+|+|.+.|.||||.|.+||||+. .+..-.||.|+||++||.
T Consensus 7 vNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~id--------------G~~~g~lGEilIRCNNvl 72 (79)
T KOG3482|consen 7 VNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYID--------------GVSTGNLGEILIRCNNVL 72 (79)
T ss_pred CCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhc--------------ccccccceeEEEEeccEE
Confidence 455678999999999999999999999999999999999999999974 234567999999999999
Q ss_pred Eee
Q 023166 83 SMT 85 (286)
Q Consensus 83 SIs 85 (286)
+|.
T Consensus 73 yi~ 75 (79)
T KOG3482|consen 73 YIR 75 (79)
T ss_pred EEe
Confidence 984
No 30
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.43 E-value=8.7e-14 Score=111.61 Aligned_cols=71 Identities=31% Similarity=0.512 Sum_probs=62.4
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
+.|..|+|+||.|...|||.|+|+|++||+..||+|+||.|.... ..+..+...||+-+||||||.+|-.
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s----------~~~gv~q~~lGlyiirgeNva~ig~ 72 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFS----------ETEGVEQIVLGLYIIRGENVAVIGE 72 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhh----------hhcchhheeeEEEEEecCccceeee
Confidence 579999999999999999999999999999999999999997651 1245677899999999999999854
Q ss_pred c
Q 023166 87 E 87 (286)
Q Consensus 87 e 87 (286)
-
T Consensus 73 i 73 (96)
T KOG1784|consen 73 I 73 (96)
T ss_pred c
Confidence 3
No 31
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.39 E-value=8.1e-14 Score=107.83 Aligned_cols=69 Identities=20% Similarity=0.391 Sum_probs=62.5
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
...|.++|++.|.|+|.||-.|+|+|.|+|-||||.|+.++|+.. ..++++.|.+||||+||.+|+
T Consensus 8 ~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~n--------------gql~n~ygdaFirGnnVlyIs 73 (77)
T KOG1783|consen 8 GEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVN--------------GQLKNKYGDAFIRGNNVLYIS 73 (77)
T ss_pred HHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhc--------------CcccccccceeeccccEEEEE
Confidence 567889999999999999999999999999999999999999863 246788999999999999998
Q ss_pred ecC
Q 023166 86 VEG 88 (286)
Q Consensus 86 Ve~ 88 (286)
.+.
T Consensus 74 ~~~ 76 (77)
T KOG1783|consen 74 TQK 76 (77)
T ss_pred ecc
Confidence 763
No 32
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.35 E-value=1.1e-13 Score=116.19 Aligned_cols=70 Identities=27% Similarity=0.478 Sum_probs=60.4
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
..|.+|+++++.|.|+|||.+.|.|++||+|.||||.+|.|.+.... .--.+-.|+.+|||||||.|-.
T Consensus 12 ~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~-----------~Y~di~~glfiIRGENVvllGe 80 (129)
T KOG1782|consen 12 TSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN-----------KYCDIPRGLFIIRGENVVLLGE 80 (129)
T ss_pred hHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc-----------eecccCceEEEEecCcEEEEec
Confidence 45899999999999999999999999999999999999999887532 2234567999999999999864
Q ss_pred c
Q 023166 87 E 87 (286)
Q Consensus 87 e 87 (286)
.
T Consensus 81 i 81 (129)
T KOG1782|consen 81 I 81 (129)
T ss_pred C
Confidence 3
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.19 E-value=1.1e-11 Score=96.88 Aligned_cols=68 Identities=25% Similarity=0.518 Sum_probs=57.5
Q ss_pred HHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeecC
Q 023166 10 LQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEG 88 (286)
Q Consensus 10 ~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe~ 88 (286)
-+.|+.+|.|.+++.|+|+|||++||.|.|+||+|+.||.... +......+++++|.|+||..+.--+
T Consensus 13 DkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~-----------egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 13 DKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITP-----------EGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred HHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCC-----------CcceeeeeeeeeecCCcEEEEecCC
Confidence 4788999999999999999999999999999999999997632 2234567899999999998775433
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.18 E-value=1.5e-11 Score=97.20 Aligned_cols=68 Identities=35% Similarity=0.659 Sum_probs=53.9
Q ss_pred hHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeE
Q 023166 7 SKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVI 82 (286)
Q Consensus 7 skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIV 82 (286)
..+.+||..+.+|++ +-+-.+.|++.+||+||||||+|++|... + +...+.||.++|+||||.
T Consensus 15 n~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~-k------------~~~rk~lGRilLKGDnIt 81 (88)
T KOG1774|consen 15 NLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHS-K------------TKSRKELGRILLKGDNIT 81 (88)
T ss_pred HHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccc-c------------ccCCCccccEEEcCCcEE
Confidence 456688887666654 45888999999999999999999999764 1 122348999999999999
Q ss_pred Eeeec
Q 023166 83 SMTVE 87 (286)
Q Consensus 83 SIsVe 87 (286)
.|.-.
T Consensus 82 li~~~ 86 (88)
T KOG1774|consen 82 LIQSA 86 (88)
T ss_pred EEeec
Confidence 98643
No 35
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.88 E-value=3.8e-10 Score=93.37 Aligned_cols=70 Identities=29% Similarity=0.510 Sum_probs=57.6
Q ss_pred CEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
..|.|.++|++.+.|.+.|||.|+|++|+|+.|.+....++++... ....+..|++|.+|||||+|+.+.
T Consensus 37 ~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~~~~~~~r~isK~flRGdsvI~v~ 106 (114)
T KOG3459|consen 37 TQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-AKPVNKDRFISKMFLRGDSVILVL 106 (114)
T ss_pred ceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-CCccchhhhhheeeecCCeEEEEE
Confidence 4677888999999999999999999999999999988766544211 122455899999999999998875
No 36
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=98.81 E-value=1.7e-08 Score=83.68 Aligned_cols=74 Identities=22% Similarity=0.293 Sum_probs=60.7
Q ss_pred CCchhhhHHH-HhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCc
Q 023166 1 MSMSKSSKML-QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGE 79 (286)
Q Consensus 1 m~~~k~skL~-qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGe 79 (286)
|+++-.-||+ +.-++.|.|++..|..|.|.|.-.|++||+.|+|..-... + .....|..|||||+
T Consensus 1 ~s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~----d----------g~vs~le~V~IRGS 66 (119)
T KOG3172|consen 1 MSVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTAR----D----------GRVSQLEQVFIRGS 66 (119)
T ss_pred CccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEcc----C----------CcceeeeeEEEecC
Confidence 4566566655 6778899999999999999999999999999999987653 1 23446789999999
Q ss_pred eeEEeeecC
Q 023166 80 EVISMTVEG 88 (286)
Q Consensus 80 nIVSIsVe~ 88 (286)
.|.++.+.+
T Consensus 67 ~IRFlvlPd 75 (119)
T KOG3172|consen 67 KIRFLVLPD 75 (119)
T ss_pred eEEEEECch
Confidence 999998765
No 37
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=98.80 E-value=8.8e-09 Score=86.99 Aligned_cols=69 Identities=17% Similarity=0.239 Sum_probs=59.0
Q ss_pred HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166 8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE 87 (286)
Q Consensus 8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe 87 (286)
-|...-+..|.|+|++|.+|.|.|+..|.+|||.|.|++++.. +......+..+.|||++|.+|.++
T Consensus 6 LL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~-------------Dgdkf~r~pEcYirGttIkylri~ 72 (134)
T KOG3293|consen 6 LLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSE-------------DGDKFFRMPECYIRGTTIKYLRIP 72 (134)
T ss_pred HHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEecc-------------CCCceeecceeEEecceeEEEecc
Confidence 3455678999999999999999999999999999999998753 223456778999999999999988
Q ss_pred CC
Q 023166 88 GP 89 (286)
Q Consensus 88 ~P 89 (286)
+.
T Consensus 73 d~ 74 (134)
T KOG3293|consen 73 DE 74 (134)
T ss_pred HH
Confidence 64
No 38
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.80 E-value=2.1e-08 Score=80.59 Aligned_cols=70 Identities=16% Similarity=0.201 Sum_probs=58.8
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
+....+|+++|.|+|+++-.|.|||.++|+|+||.|.|....... ..-.--.+-.+||||+.|.+|.+
T Consensus 5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~------------kyPhm~Sv~ncfIRGSvvrYv~l 72 (96)
T KOG3448|consen 5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPD------------KYPHMLSVKNCFIRGSVVRYVQL 72 (96)
T ss_pred HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcc------------cCCCeeeeeeEEEeccEEEEEEe
Confidence 456789999999999999999999999999999999998765321 12345567789999999999988
Q ss_pred cC
Q 023166 87 EG 88 (286)
Q Consensus 87 e~ 88 (286)
..
T Consensus 73 ~k 74 (96)
T KOG3448|consen 73 PK 74 (96)
T ss_pred Ch
Confidence 75
No 39
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.60 E-value=3e-07 Score=76.18 Aligned_cols=73 Identities=16% Similarity=0.251 Sum_probs=61.0
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
..|.++.+.++.|+|+|++++.|++.++|.+||..|.++.-..+ .+-..+-.+.|||+||.++.+
T Consensus 5 r~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~---------------~~pv~l~~lsirgnniRy~~l 69 (109)
T KOG3428|consen 5 RFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK---------------GEPVRLDTLSIRGNNIRYYIL 69 (109)
T ss_pred HHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC---------------CCceeEEEEEeecceEEEEEc
Confidence 35778899999999999999999999999999999999976532 123567789999999999998
Q ss_pred cCCCCChh
Q 023166 87 EGPPPPEE 94 (286)
Q Consensus 87 e~PPp~d~ 94 (286)
.+.-.-|.
T Consensus 70 pD~l~ld~ 77 (109)
T KOG3428|consen 70 PDSLNLDT 77 (109)
T ss_pred cCCcCcce
Confidence 88665554
No 40
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=98.50 E-value=4.8e-08 Score=74.52 Aligned_cols=41 Identities=29% Similarity=0.414 Sum_probs=32.4
Q ss_pred HhcC--CEEEEEEeCC----cEEEEEEEEeccccceEeCceEEeecC
Q 023166 11 QFIN--YRMRVTIQDG----RQLVGKFMAFDRHMNLVLGDCEEFRKL 51 (286)
Q Consensus 11 qlIg--kRVRVtLqDG----R~fvGtLlAFDKhMNLVLsD~eE~r~i 51 (286)
+++. .||+|.++.- -.++|.|+|||||+||+|.|++|.++.
T Consensus 3 ~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 3 RCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred hhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 4445 5777777532 267899999999999999999999874
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.65 E-value=7.7e-05 Score=56.94 Aligned_cols=67 Identities=15% Similarity=0.302 Sum_probs=39.5
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEecc---ccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeE
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFDR---HMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVI 82 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFDK---hMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIV 82 (286)
+..+|+++|.|+++||.+|+|.|.+++. .+.++|+.+.+......+ +...........++|+++.|+
T Consensus 7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~-------~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQS-------NSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-------------EEEEEEE-GGGEEE-----
T ss_pred HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccc-------cCCccCCCCCceEEEeccccC
Confidence 5679999999999999999999999998 889999888765431110 011223334456677777665
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.57 E-value=0.00019 Score=58.42 Aligned_cols=79 Identities=16% Similarity=0.370 Sum_probs=59.8
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEecc-ccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFDR-HMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE 87 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFDK-hMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe 87 (286)
..+||+++|.++.+++-.|+|+|..+|. .-+|.|.|+.-|-...++... ..--.+..+..|++||+.|..|.|.
T Consensus 3 ~~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~-----~ipp~~~v~~~I~Fr~sDIkdL~v~ 77 (96)
T PF12701_consen 3 ADPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDR-----EIPPSDEVYDYIVFRGSDIKDLKVI 77 (96)
T ss_dssp CCCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS--------C-CSSSSEEEEETTTEEEEEEC
T ss_pred cccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCc-----ccCCCCceeeEEEEEccccceEEEE
Confidence 4589999999999999999999999996 689999999888764322111 1122345677999999999999999
Q ss_pred CCCCC
Q 023166 88 GPPPP 92 (286)
Q Consensus 88 ~PPp~ 92 (286)
+.+..
T Consensus 78 e~~~~ 82 (96)
T PF12701_consen 78 EPPPP 82 (96)
T ss_dssp E-S-S
T ss_pred cCCCC
Confidence 87664
No 43
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=97.53 E-value=0.00053 Score=72.81 Aligned_cols=20 Identities=45% Similarity=0.984 Sum_probs=9.3
Q ss_pred CCCCCCCCCCCCCCCCCCCC
Q 023166 232 PMMRGPPSGPPRPGMPNAPP 251 (286)
Q Consensus 232 ~~~~~~p~~p~~~~~~~~~~ 251 (286)
+++.||||||+++|+.||||
T Consensus 565 g~aG~PPpPppppg~~gppP 584 (1102)
T KOG1924|consen 565 GIAGGPPPPPPPPGGGGPPP 584 (1102)
T ss_pred cccCCCCccCCCCCCCCCCC
Confidence 34444444444455554333
No 44
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=97.22 E-value=0.003 Score=67.33 Aligned_cols=25 Identities=52% Similarity=1.060 Sum_probs=11.0
Q ss_pred CCCCCCCCCCCCCCC--CCCCCCCCCC
Q 023166 234 MRGPPSGPPRPGMPN--APPPRPGMPP 258 (286)
Q Consensus 234 ~~~~p~~p~~~~~~~--~~~~~~~~~~ 258 (286)
..||||||+..|-.| ||||.++|.+
T Consensus 579 ~~gppPPPpp~g~~Gg~ppPP~~gm~p 605 (1102)
T KOG1924|consen 579 GGGPPPPPPPGGFLGGPPPPPPPGMFP 605 (1102)
T ss_pred CCCCCCcCCCCCCCCCCCCCCCCCccc
Confidence 334443333344444 4444555555
No 45
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.58 E-value=0.0061 Score=43.05 Aligned_cols=35 Identities=14% Similarity=0.180 Sum_probs=30.7
Q ss_pred hcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEE
Q 023166 12 FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEE 47 (286)
Q Consensus 12 lIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE 47 (286)
+||++|+|++ ++..++|+++++|.+-+|+|.+...
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 5899999999 6777899999999999999976554
No 46
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=96.46 E-value=0.013 Score=46.60 Aligned_cols=62 Identities=19% Similarity=0.325 Sum_probs=43.9
Q ss_pred HHHHhcCCEEEEEEeCCcEEEEEEEEeccc-cceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeee
Q 023166 8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRH-MNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKh-MNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsV 86 (286)
.|+...++.|.++|.++.++.|+|.++|.. .|+..+|-+ .---.....+||...|+++++
T Consensus 18 ~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-------------------TPlGv~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 18 SLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-------------------TPLGVQPEALLRCSDVISISF 78 (80)
T ss_dssp HHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-------------------TTTTEEEEEEEEGGGEEEEEE
T ss_pred HHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-------------------CCcccChhheeecCCEEEEEe
Confidence 366788999999999999999999999954 455544332 112235678999999999998
Q ss_pred cC
Q 023166 87 EG 88 (286)
Q Consensus 87 e~ 88 (286)
+.
T Consensus 79 ~~ 80 (80)
T PF11095_consen 79 DA 80 (80)
T ss_dssp --
T ss_pred cC
Confidence 73
No 47
>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=96.41 E-value=0.0091 Score=53.05 Aligned_cols=63 Identities=21% Similarity=0.352 Sum_probs=44.0
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEEEEEec-cccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFD-RHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM 84 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFD-KhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI 84 (286)
...+.+|++|.|+|++.| +++.|.|..+| ---||||.+-.|- .++. .-+|-|.+|.+|
T Consensus 9 p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~------------------~~~s--v~~I~ghaVk~v 67 (166)
T PF06372_consen 9 PLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQED------------------GKRS--VKVIMGHAVKSV 67 (166)
T ss_dssp HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TT------------------S-EE--EEEE-GGGEEEE
T ss_pred HHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccC------------------Ccee--EEEEEccceEEE
Confidence 356789999999999999 99999999999 4468998854331 1222 467779999999
Q ss_pred eecCC
Q 023166 85 TVEGP 89 (286)
Q Consensus 85 sVe~P 89 (286)
++...
T Consensus 68 evl~~ 72 (166)
T PF06372_consen 68 EVLSE 72 (166)
T ss_dssp EEEE-
T ss_pred EEccC
Confidence 98774
No 48
>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=96.37 E-value=0.015 Score=45.66 Aligned_cols=71 Identities=10% Similarity=0.249 Sum_probs=53.3
Q ss_pred HHhcCCEEEEEEeCCcEEEEEEEEeccc-cceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166 10 LQFINYRMRVTIQDGRQLVGKFMAFDRH-MNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM 84 (286)
Q Consensus 10 ~qlIgkRVRVtLqDGR~fvGtLlAFDKh-MNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI 84 (286)
.+||+++|.+..+.+-.|+|+|..+|.+ --|.|.|+..|-...++... .+.--.......|+.||+.|..+
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~----~~ipp~~~vyd~IvFrgsDIkDL 73 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDG----PEIPPSDEVYDYIVFRGSDIKDL 73 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCC----CccCCCCcceeEEEEcCCccccc
Confidence 4799999999999999999999999966 46779999988775432211 01112345667899999998765
No 49
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.71 E-value=0.027 Score=55.50 Aligned_cols=79 Identities=14% Similarity=0.310 Sum_probs=63.0
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEec-cccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFD-RHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE 87 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFD-KhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe 87 (286)
+..||+++|.++-+....|+|+|.-+| +..=|-|.++.-|-+..+|+. ...+-...| +..-||.||+.|..|.|+
T Consensus 4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~---~pq~p~~~k-Vy~YIlFRGSDIKDL~V~ 79 (361)
T KOG1073|consen 4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTD---GPQVPPDDK-VYDYILFRGSDIKDLIVQ 79 (361)
T ss_pred ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCC---CCcCCCCcc-ceeeEEecCcccceeeec
Confidence 468999999999999999999999999 667899999887776544321 122334455 889999999999999999
Q ss_pred CCCC
Q 023166 88 GPPP 91 (286)
Q Consensus 88 ~PPp 91 (286)
+.|.
T Consensus 80 ~~p~ 83 (361)
T KOG1073|consen 80 ETPA 83 (361)
T ss_pred cCcc
Confidence 8554
No 50
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=95.15 E-value=0.093 Score=47.02 Aligned_cols=73 Identities=15% Similarity=0.078 Sum_probs=54.7
Q ss_pred hHHHHhcCCEEEEE-EeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166 7 SKMLQFINYRMRVT-IQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM 84 (286)
Q Consensus 7 skL~qlIgkRVRVt-LqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI 84 (286)
.++++|.+.+.++. +.|+++.++.++++|+-.|||+..+|++-...++..+ .-..+.+.+|+-.+.|..|++.
T Consensus 43 ~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp~s~s~~~-----v~ag~~~g~G~ar~~Grgip~~ 116 (177)
T KOG3168|consen 43 QDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPPPSDSFRR-----VPAGAARGPGIARVAGRGIPSG 116 (177)
T ss_pred HHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCCCcccccc-----ccccccCCcccccccCCCccCC
Confidence 45667778777775 8999999999999999999999999998653221110 1134567788888888888874
No 51
>PRK02001 hypothetical protein; Validated
Probab=94.40 E-value=0.14 Score=44.69 Aligned_cols=39 Identities=15% Similarity=0.352 Sum_probs=33.1
Q ss_pred hhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166 4 SKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs 43 (286)
.+...+.+|+++.|+|+|.|++.|+|+|.+||.. +++|.
T Consensus 80 ~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 80 KVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred CCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence 3456788999999999999999999999999976 45553
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=93.79 E-value=0.11 Score=39.32 Aligned_cols=36 Identities=17% Similarity=0.312 Sum_probs=30.6
Q ss_pred hcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEE
Q 023166 12 FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEE 47 (286)
Q Consensus 12 lIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE 47 (286)
+|+.+|+|++..|.+|+|.+.|||.-.+++.-.|.+
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 578999999999999999999999887776555544
No 53
>PRK14638 hypothetical protein; Provisional
Probab=93.76 E-value=0.16 Score=44.10 Aligned_cols=39 Identities=13% Similarity=0.417 Sum_probs=33.0
Q ss_pred hhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166 4 SKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs 43 (286)
-+..++.+|++++|+|+|.+++.|+|+|.++|.. +|+|.
T Consensus 90 ~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 90 RGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred CCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 3566788999999999999999999999999964 45553
No 54
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=93.41 E-value=0.29 Score=37.61 Aligned_cols=51 Identities=16% Similarity=0.275 Sum_probs=37.1
Q ss_pred HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
.|+++++++|.|++..|+. .|+|++..-. .|+|+.+. ..++||=.+|++|.
T Consensus 15 ~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~~-------------------------~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 15 TLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEENG-------------------------TPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeCC-------------------------cEEEEEeeeEEEEc
Confidence 4789999999999977665 9999997522 23443331 24678888888874
No 55
>PRK14639 hypothetical protein; Provisional
Probab=93.19 E-value=0.2 Score=42.99 Aligned_cols=39 Identities=23% Similarity=0.384 Sum_probs=33.1
Q ss_pred hhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166 4 SKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs 43 (286)
-+..++.+|+++.|+|+|.+++.|+|+|+++|.. +++|.
T Consensus 78 ~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 78 SKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred CCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 3456788999999999999999999999999985 55553
No 56
>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=93.11 E-value=0.17 Score=38.38 Aligned_cols=30 Identities=23% Similarity=0.397 Sum_probs=24.7
Q ss_pred CCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166 14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 14 gkRVRVtLqDGR~fvGtLlAFDKhMNLVLs 43 (286)
+..|.|-|.||-.++|++++||+|+=|+-+
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~ 40 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFDNFTVLLES 40 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEcceEEEEEE
Confidence 456778889999999999999999855533
No 57
>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=93.06 E-value=0.17 Score=38.38 Aligned_cols=29 Identities=28% Similarity=0.363 Sum_probs=24.1
Q ss_pred CCEEEEEEeCCcEEEEEEEEeccccceEe
Q 023166 14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 14 gkRVRVtLqDGR~fvGtLlAFDKhMNLVL 42 (286)
...|.|-|.+|-.++|++++||+|+=|+-
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~ 43 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLLE 43 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence 34677778999999999999999985543
No 58
>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=92.52 E-value=0.12 Score=45.75 Aligned_cols=75 Identities=17% Similarity=0.145 Sum_probs=48.6
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCC--CCCCcccccceeEeceEEecCceeE
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGK--KNNTNEEREDRRTLGLVLLRGEEVI 82 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~k--k~~~~~e~eekR~LGlVLIRGenIV 82 (286)
-+..++-+.-|||++.||.+|.|++.+||.--|.||+-.. +.+.+.-.-+ ...+-++.......|..+|+.+.+.
T Consensus 22 l~f~r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~-~~~~nRi~~plE~I~t~Ee~~~~d~~g~~ti~~d~~~ 98 (165)
T PF03614_consen 22 LQFWRFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP-FKKENRIRLPLERISTIEELIVSDFKGRLTIHPDYFN 98 (165)
T ss_pred HHHHHhcCCceEEEecCCcEEEEEEeccCcccCEEeccCC-CCCCceEEEEhHHhhhHhhhccccccccEEechhhcc
Confidence 3445677889999999999999999999999999998765 3221110000 0001122333445677777777553
No 59
>PRK14644 hypothetical protein; Provisional
Probab=92.04 E-value=0.34 Score=41.60 Aligned_cols=36 Identities=11% Similarity=0.272 Sum_probs=31.0
Q ss_pred hHHHHhcCCEEEEEEeCC----cEEEEEEEEeccccceEeC
Q 023166 7 SKMLQFINYRMRVTIQDG----RQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDG----R~fvGtLlAFDKhMNLVLs 43 (286)
.++.+|+++.|+|+|++. ++|+|+|.++|.. +++|.
T Consensus 78 ~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 78 DELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 478999999999999877 9999999999975 56554
No 60
>PRK14640 hypothetical protein; Provisional
Probab=91.44 E-value=0.55 Score=40.76 Aligned_cols=39 Identities=18% Similarity=0.311 Sum_probs=32.0
Q ss_pred hhhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEeC
Q 023166 4 SKSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVLs 43 (286)
-+...+.+|++++|+|+| .+.+.|+|+|.++|.. ++.|.
T Consensus 87 ~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 87 FKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred CCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 356678899999999999 5779999999999875 45543
No 61
>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=91.40 E-value=0.7 Score=35.90 Aligned_cols=37 Identities=19% Similarity=0.437 Sum_probs=30.4
Q ss_pred hhhHHHHhcCCEEEEEEe---CC-cEEEEEEEEeccccceEe
Q 023166 5 KSSKMLQFINYRMRVTIQ---DG-RQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 5 k~skL~qlIgkRVRVtLq---DG-R~fvGtLlAFDKhMNLVL 42 (286)
+..++.+|+++.|.|+|+ +| +.|+|+|.++|.. +++|
T Consensus 16 ~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 16 KEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred CHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 456788999999999997 55 6899999999985 4554
No 62
>PRK14636 hypothetical protein; Provisional
Probab=91.01 E-value=0.48 Score=42.30 Aligned_cols=38 Identities=16% Similarity=0.478 Sum_probs=30.8
Q ss_pred hhhhHHHHhcCCEEEEEEe---CC-cEEEEEEEEeccccceEe
Q 023166 4 SKSSKMLQFINYRMRVTIQ---DG-RQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLq---DG-R~fvGtLlAFDKhMNLVL 42 (286)
-+...+.+|+++.|+|+|+ || +.|+|+|.++|.. +++|
T Consensus 88 ~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 88 TRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred CCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 3567789999999999997 55 6999999999874 4544
No 63
>PRK14642 hypothetical protein; Provisional
Probab=90.97 E-value=0.5 Score=43.20 Aligned_cols=38 Identities=8% Similarity=0.238 Sum_probs=31.7
Q ss_pred hhhhHHHHhcCCEEEEEEe-------------CCcEEEEEEEEeccccceEe
Q 023166 4 SKSSKMLQFINYRMRVTIQ-------------DGRQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLq-------------DGR~fvGtLlAFDKhMNLVL 42 (286)
-+..++.+|+++.|.|+|+ +.+.|+|+|.++|.. +|.|
T Consensus 90 k~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 90 RHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred CCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 3567789999999999998 789999999999875 4444
No 64
>PRK14633 hypothetical protein; Provisional
Probab=90.92 E-value=0.47 Score=41.12 Aligned_cols=39 Identities=8% Similarity=0.246 Sum_probs=32.0
Q ss_pred hhhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEeC
Q 023166 4 SKSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVLs 43 (286)
-+..++.+|++++|+|++ .+.+.|+|+|..+|.. +|.|.
T Consensus 84 ~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 84 FNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred CCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 356678899999999998 4789999999999876 45553
No 65
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=90.88 E-value=0.51 Score=37.57 Aligned_cols=31 Identities=19% Similarity=0.389 Sum_probs=25.2
Q ss_pred CCEEEEEEeCCcEEEEEEEEeccccceEeCc
Q 023166 14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGD 44 (286)
Q Consensus 14 gkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD 44 (286)
...|.|-|.+|-.+.|++++||+|+=|+-+|
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 3467778899999999999999998555444
No 66
>PRK14632 hypothetical protein; Provisional
Probab=90.46 E-value=0.56 Score=41.63 Aligned_cols=39 Identities=21% Similarity=0.487 Sum_probs=31.8
Q ss_pred hhhhHHHHhcCCEEEEEEeC-------CcEEEEEEEEeccccceEeC
Q 023166 4 SKSSKMLQFINYRMRVTIQD-------GRQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLqD-------GR~fvGtLlAFDKhMNLVLs 43 (286)
-+...+.+|+++.|+|+|.+ .+.|+|+|+.+|.. +|+|.
T Consensus 88 ~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 88 FRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred CCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 35667889999999999976 68999999999864 55553
No 67
>PRK14646 hypothetical protein; Provisional
Probab=89.64 E-value=1 Score=39.32 Aligned_cols=38 Identities=13% Similarity=0.267 Sum_probs=30.6
Q ss_pred hhhhHHHHhcCCEEEEEEeC----CcEEEEEEEEeccccceEe
Q 023166 4 SKSSKMLQFINYRMRVTIQD----GRQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLqD----GR~fvGtLlAFDKhMNLVL 42 (286)
-+..++.+|++++|+|+|++ .+.|+|+|++||.. +|.|
T Consensus 90 ~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 90 TSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred CCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 35667899999999999953 37889999999986 4555
No 68
>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=88.86 E-value=0.36 Score=38.18 Aligned_cols=60 Identities=28% Similarity=0.391 Sum_probs=30.0
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeecC
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEG 88 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe~ 88 (286)
|.=.-+|+|+++|+||.++.|+ |.|-..|- +-+|+..+. ..-+...||=++|++|++..
T Consensus 12 iAC~~~~~v~L~l~dG~~~~g~--A~dt~~~~---~k~E~L~l~----------------~~~~~~~i~Ld~I~~~~al~ 70 (80)
T PF07073_consen 12 IACMYRYPVKLTLKDGEQIEGK--ALDTRTNA---KKEECLVLE----------------QDGGEQEIRLDQIASMSALT 70 (80)
T ss_dssp HHHTTTT-EEEE-TTT--EEES--S-EEE------SSS-EEEEE----------------ETTEEEEESTT--SEEE---
T ss_pred HHHhcCCeEEEEEeCCCEEEEE--EEEEEEec---CceEEEEEe----------------cCCcEEEEEhhheeeeeecC
Confidence 4445689999999999999998 44432221 445554431 11245678889999998665
Q ss_pred C
Q 023166 89 P 89 (286)
Q Consensus 89 P 89 (286)
+
T Consensus 71 ~ 71 (80)
T PF07073_consen 71 D 71 (80)
T ss_dssp -
T ss_pred C
Confidence 3
No 69
>PRK14634 hypothetical protein; Provisional
Probab=88.61 E-value=1.3 Score=38.59 Aligned_cols=38 Identities=18% Similarity=0.379 Sum_probs=30.7
Q ss_pred hhhhHHHHhcCCEEEEEEeC----CcEEEEEEEEeccccceEe
Q 023166 4 SKSSKMLQFINYRMRVTIQD----GRQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLqD----GR~fvGtLlAFDKhMNLVL 42 (286)
-+..++.+|+++.|+|+|.+ .+.|+|+|+++|.. +|.|
T Consensus 90 ~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 90 SSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred CCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 35678899999999999863 38999999999875 4555
No 70
>PRK14643 hypothetical protein; Provisional
Probab=88.43 E-value=0.99 Score=39.87 Aligned_cols=34 Identities=9% Similarity=0.284 Sum_probs=29.3
Q ss_pred hhhhHHHHhcCCEEEEEEeC----CcEEEEEEEEeccc
Q 023166 4 SKSSKMLQFINYRMRVTIQD----GRQLVGKFMAFDRH 37 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLqD----GR~fvGtLlAFDKh 37 (286)
-+..++.+|+++.|+|+|++ .+.|+|+|+++|..
T Consensus 94 ~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 94 RSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred CCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 35677899999999999965 69999999999865
No 71
>PRK14645 hypothetical protein; Provisional
Probab=88.24 E-value=1.3 Score=38.79 Aligned_cols=38 Identities=13% Similarity=0.300 Sum_probs=31.2
Q ss_pred hhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166 4 SKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs 43 (286)
-+..++.+|+++.|+|++ +++.|+|+|+++|.. +|+|.
T Consensus 92 ~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l~ 129 (154)
T PRK14645 92 FTARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTFD 129 (154)
T ss_pred CCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEEE
Confidence 356678899999999986 899999999999875 45553
No 72
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=88.14 E-value=0.81 Score=38.64 Aligned_cols=37 Identities=19% Similarity=0.507 Sum_probs=27.9
Q ss_pred hhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEe
Q 023166 5 KSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 5 k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVL 42 (286)
+..++.+|+++.|+|+| .+.+.|+|+|.++|.. +++|
T Consensus 78 ~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~-~i~l 118 (141)
T PF02576_consen 78 SPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDED-EITL 118 (141)
T ss_dssp SHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEETT-EEEE
T ss_pred CHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeCC-EEEE
Confidence 35678999999999999 4667999999999983 4555
No 73
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.88 E-value=1.4 Score=38.87 Aligned_cols=38 Identities=21% Similarity=0.486 Sum_probs=32.8
Q ss_pred hhhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccccceEe
Q 023166 4 SKSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKhMNLVL 42 (286)
-+.....+|+++.|+|+| .+.+.|+|+|.++|... |+|
T Consensus 89 ~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 89 KTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred CCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 356778899999999999 89999999999999886 443
No 74
>PRK14647 hypothetical protein; Provisional
Probab=87.09 E-value=1.4 Score=38.52 Aligned_cols=38 Identities=8% Similarity=0.224 Sum_probs=30.4
Q ss_pred hhhhHHHHhcCCEEEEEEe---------CCcEEEEEEEEeccccceEe
Q 023166 4 SKSSKMLQFINYRMRVTIQ---------DGRQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLq---------DGR~fvGtLlAFDKhMNLVL 42 (286)
-+...+.+|+++.|+|+|+ +.+.|+|+|.++|.. +++|
T Consensus 89 ~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~-~v~l 135 (159)
T PRK14647 89 KKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG-VVTI 135 (159)
T ss_pred CCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC-EEEE
Confidence 3456789999999999995 369999999999864 3443
No 75
>PRK14637 hypothetical protein; Provisional
Probab=86.88 E-value=1.3 Score=38.50 Aligned_cols=38 Identities=24% Similarity=0.303 Sum_probs=29.9
Q ss_pred hhhHHHHhcCCEEEEEEeCCcEE-EEEEEEeccccceEeC
Q 023166 5 KSSKMLQFINYRMRVTIQDGRQL-VGKFMAFDRHMNLVLG 43 (286)
Q Consensus 5 k~skL~qlIgkRVRVtLqDGR~f-vGtLlAFDKhMNLVLs 43 (286)
+...+.+|+++.|+|+|.+.+.+ +|+|.++|.. +++|.
T Consensus 89 ~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 89 NAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred CHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 45678899999999999545566 7999999876 55554
No 76
>PRK14631 hypothetical protein; Provisional
Probab=85.84 E-value=1.7 Score=38.78 Aligned_cols=38 Identities=13% Similarity=0.349 Sum_probs=31.0
Q ss_pred hhhhHHHHhcCCEEEEEEe----CCcEEEEEEEEec--cccceEe
Q 023166 4 SKSSKMLQFINYRMRVTIQ----DGRQLVGKFMAFD--RHMNLVL 42 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLq----DGR~fvGtLlAFD--KhMNLVL 42 (286)
-+...+.+|+++.|+|+|. +.+.|+|+|.++| .. +|.|
T Consensus 107 ~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~-~v~l 150 (174)
T PRK14631 107 FQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLENE-EIQV 150 (174)
T ss_pred CCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCCC-EEEE
Confidence 3567789999999999995 6699999999998 53 4444
No 77
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=85.44 E-value=1.5 Score=37.73 Aligned_cols=33 Identities=21% Similarity=0.473 Sum_probs=28.9
Q ss_pred hhhHHHHhcCCEEEEEE----eCCcEEEEEEEEeccc
Q 023166 5 KSSKMLQFINYRMRVTI----QDGRQLVGKFMAFDRH 37 (286)
Q Consensus 5 k~skL~qlIgkRVRVtL----qDGR~fvGtLlAFDKh 37 (286)
+..++.+|+++.|+|+| .+++.|+|+|..+|..
T Consensus 89 ~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 89 KARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred CHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 45678899999999997 6889999999999874
No 78
>PRK06955 biotin--protein ligase; Provisional
Probab=85.29 E-value=2.1 Score=40.50 Aligned_cols=34 Identities=12% Similarity=0.104 Sum_probs=29.4
Q ss_pred HHhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166 10 LQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 10 ~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs 43 (286)
.-+++++|+|...++++++|+++++|..-.|+|.
T Consensus 245 ~~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 245 HAYAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred hhcCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 3478899999776778899999999999999985
No 79
>PRK14641 hypothetical protein; Provisional
Probab=83.27 E-value=2.5 Score=37.77 Aligned_cols=31 Identities=16% Similarity=0.291 Sum_probs=26.8
Q ss_pred hhhHHHHhcCCEEEEEEeC----CcEEEEEEEEec
Q 023166 5 KSSKMLQFINYRMRVTIQD----GRQLVGKFMAFD 35 (286)
Q Consensus 5 k~skL~qlIgkRVRVtLqD----GR~fvGtLlAFD 35 (286)
+...+.+|+++.|+|+|.+ .+.|+|+|.++|
T Consensus 95 ~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 95 LPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred CHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 4567889999999999975 678999999996
No 80
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=83.22 E-value=3 Score=38.68 Aligned_cols=39 Identities=18% Similarity=0.167 Sum_probs=33.9
Q ss_pred HHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceE
Q 023166 8 KMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCE 46 (286)
Q Consensus 8 kL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~e 46 (286)
+...+++++|+|++.++.++.|+.+++|.+..|+|++.+
T Consensus 184 ~~~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~~ 222 (238)
T COG0340 184 ARSLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETDD 222 (238)
T ss_pred HHhccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeCC
Confidence 345579999999999888999999999999999998763
No 81
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=81.90 E-value=35 Score=34.60 Aligned_cols=15 Identities=47% Similarity=0.853 Sum_probs=10.9
Q ss_pred CCCCCCCCCCCCCCC
Q 023166 189 GPPMARGPPPQGPPQ 203 (286)
Q Consensus 189 ~p~~~~g~ppp~~~~ 203 (286)
+++|-++++|+..+.
T Consensus 255 pppmpp~PpP~~t~~ 269 (498)
T KOG4849|consen 255 PPPMPPAPPPQQTML 269 (498)
T ss_pred CCCCCCCCCCccccC
Confidence 467888888866655
No 82
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=80.78 E-value=2.4 Score=37.97 Aligned_cols=31 Identities=26% Similarity=0.306 Sum_probs=25.4
Q ss_pred CEEEEEEeCCcEEEEEEEEeccccceEeCce
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDC 45 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~ 45 (286)
..|.|-|.+|-.+.|++++||+|+=|+.+|.
T Consensus 105 ~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 105 EPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred CcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 4677778999999999999999986655554
No 83
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=80.16 E-value=4.4 Score=38.21 Aligned_cols=32 Identities=19% Similarity=0.382 Sum_probs=27.6
Q ss_pred HhcCCEEEEEEeCCcEEEEEEEEeccccceEeC
Q 023166 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLG 43 (286)
Q Consensus 11 qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLs 43 (286)
.++|++|+|.. ++..++|+++++|..-+|+|.
T Consensus 269 ~~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 269 LFLGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred cccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 47889999987 456799999999999999985
No 84
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=79.42 E-value=3.8 Score=42.76 Aligned_cols=34 Identities=12% Similarity=-0.007 Sum_probs=29.4
Q ss_pred HhcCCEEEEEEeCCcEEEEEEEEeccccceEeCc
Q 023166 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGD 44 (286)
Q Consensus 11 qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD 44 (286)
-++|++|+|...++++++|+++++|..-+|+|.+
T Consensus 275 ~~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 275 RDHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred ccCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 4788999987667778999999999999999963
No 85
>PRK11625 Rho-binding antiterminator; Provisional
Probab=79.00 E-value=8.5 Score=30.87 Aligned_cols=53 Identities=19% Similarity=0.149 Sum_probs=37.0
Q ss_pred HhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 11 qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
=.-++.|+++|+||.+++|+. .|-+ ..+-+||..+... . +...||=++|++++
T Consensus 20 C~~~~~l~l~l~dGe~~~g~A--~D~~----~~~k~EyL~l~~~-----------g-----~~~~iRLD~I~s~~ 72 (84)
T PRK11625 20 CQHHLMLTLELKDGEVLQAKA--SDLV----SRKNVEYLVVEAA-----------G-----ETRELRLDKIASFS 72 (84)
T ss_pred HhcCCeEEEEECCCCEEEEEE--Eeee----cCCceEEEEEEcC-----------C-----CEEEEEeeeEeecc
Confidence 346789999999999999975 5533 4477788765210 1 24467778888887
No 86
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=78.42 E-value=4.3 Score=32.31 Aligned_cols=27 Identities=22% Similarity=0.433 Sum_probs=23.0
Q ss_pred CCEEEEEEeCCcEEEEEEEEeccccce
Q 023166 14 NYRMRVTIQDGRQLVGKFMAFDRHMNL 40 (286)
Q Consensus 14 gkRVRVtLqDGR~fvGtLlAFDKhMNL 40 (286)
...|.|-|.||-.+.|.+.+||+|.=|
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD~f~Vl 45 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFDNFVVL 45 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeeeeEEEE
Confidence 346778889999999999999999733
No 87
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=77.03 E-value=3.8 Score=36.76 Aligned_cols=31 Identities=23% Similarity=0.246 Sum_probs=24.9
Q ss_pred CEEEEEEeCCcEEEEEEEEeccccceEeCce
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDC 45 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~ 45 (286)
..|.|-|.+|-.++|++++||+|.=|+-+|.
T Consensus 25 ~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 25 TPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred CcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 3566678999999999999999985555554
No 88
>PRK14630 hypothetical protein; Provisional
Probab=76.99 E-value=6.7 Score=33.87 Aligned_cols=37 Identities=5% Similarity=0.204 Sum_probs=29.3
Q ss_pred hhhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEe
Q 023166 4 SKSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVL 42 (286)
-+..++.+|++++|+|+|.+ ..++|+|+++|.. +++|
T Consensus 87 ~~~~df~r~~G~~v~V~l~~-~~~~G~L~~~~d~-~i~l 123 (143)
T PRK14630 87 KSDREFKIFEGKKIKLMLDN-DFEEGFILEAKAD-SFIF 123 (143)
T ss_pred CCHHHHHHhCCCEEEEEEcC-cceEEEEEEEeCC-EEEE
Confidence 35667889999999999965 4569999999875 4444
No 89
>PRK08330 biotin--protein ligase; Provisional
Probab=75.89 E-value=8.1 Score=35.08 Aligned_cols=33 Identities=24% Similarity=0.286 Sum_probs=27.3
Q ss_pred HhcCCEEEEEEeCCcEE-EEEEEEeccccceEeCc
Q 023166 11 QFINYRMRVTIQDGRQL-VGKFMAFDRHMNLVLGD 44 (286)
Q Consensus 11 qlIgkRVRVtLqDGR~f-vGtLlAFDKhMNLVLsD 44 (286)
.+++++|+|.. |++++ +|+++++|..-.|+|.+
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 47889999875 66665 69999999999999864
No 90
>PRK14635 hypothetical protein; Provisional
Probab=75.00 E-value=6.8 Score=34.35 Aligned_cols=38 Identities=11% Similarity=0.235 Sum_probs=30.0
Q ss_pred hhhhHHHHhcCCEEEEEEe--CCcEEEE---EEEEeccccceEe
Q 023166 4 SKSSKMLQFINYRMRVTIQ--DGRQLVG---KFMAFDRHMNLVL 42 (286)
Q Consensus 4 ~k~skL~qlIgkRVRVtLq--DGR~fvG---tLlAFDKhMNLVL 42 (286)
-+...+.+|+++.|+|++. +++.|+| +|.++|.. ++.|
T Consensus 89 ~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 89 RLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred CCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 3456788999999999985 5678887 99999865 4554
No 91
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=73.84 E-value=9.4 Score=33.39 Aligned_cols=41 Identities=17% Similarity=0.215 Sum_probs=30.6
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEecc-c--cceEeCceEEee
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFDR-H--MNLVLGDCEEFR 49 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFDK-h--MNLVLsD~eE~r 49 (286)
...||+|.|.++..||..++|++.++.- . .-+++.|-+|+.
T Consensus 87 a~slVGk~V~~~~~~g~~~tG~V~~V~~~~g~~~~~~v~G~~~~ 130 (142)
T PRK09618 87 YSELIGKEVEWEGEDGEIVSGTVTSVKQKDGDYPLVLDNGTWIV 130 (142)
T ss_pred HHHHhCCEEEEEeCCCCEEEEEEEEEEEcCCcEEEEEECCEEEe
Confidence 4579999999999999999999999852 1 124555655553
No 92
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=71.13 E-value=3.7 Score=29.28 Aligned_cols=25 Identities=24% Similarity=0.526 Sum_probs=17.2
Q ss_pred EEEEEEEeccccceEeCceEEeecC
Q 023166 27 LVGKFMAFDRHMNLVLGDCEEFRKL 51 (286)
Q Consensus 27 fvGtLlAFDKhMNLVLsD~eE~r~i 51 (286)
.+|+|+++|+...++|.|.++..-+
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T~LI 34 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTTHLI 34 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-EEEE
T ss_pred cceeEEeeccccceEEEeCCccEEE
Confidence 6899999999999999998876644
No 93
>PRK10898 serine endoprotease; Provisional
Probab=69.74 E-value=7.2 Score=37.82 Aligned_cols=32 Identities=22% Similarity=0.299 Sum_probs=28.6
Q ss_pred CEEEEEEeCCcEEEEEEEEeccccceEeCceE
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCE 46 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~e 46 (286)
.+++|++.||++|.++++++|.+.+|-|-..+
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 57899999999999999999999999776664
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=69.52 E-value=7.2 Score=37.67 Aligned_cols=32 Identities=25% Similarity=0.390 Sum_probs=28.3
Q ss_pred CEEEEEEeCCcEEEEEEEEeccccceEeCceE
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCE 46 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~e 46 (286)
.++.|++.||+++.++++++|.+.+|-|-..+
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 36899999999999999999999999886554
No 95
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=68.08 E-value=8.7 Score=36.31 Aligned_cols=33 Identities=15% Similarity=0.228 Sum_probs=28.0
Q ss_pred HhcCCEEEEEEeCCcEEEEEEEEeccccceEeCc
Q 023166 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGD 44 (286)
Q Consensus 11 qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD 44 (286)
-+++++|+|.. +++.+.|+++++|....|+|.+
T Consensus 234 ~~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 234 LYKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred ccCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 35799999875 6789999999999999998863
No 96
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=66.66 E-value=18 Score=36.72 Aligned_cols=44 Identities=25% Similarity=0.228 Sum_probs=37.1
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeec
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRK 50 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ 50 (286)
...++++++|.||. =+||++.+++|++=|.-.-|-+.|-.|.+.
T Consensus 74 ~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~~ 117 (421)
T COG5316 74 GKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVLG 117 (421)
T ss_pred hhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEEe
Confidence 34466889988888 899999999999999888888888888765
No 97
>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=64.62 E-value=7.6 Score=32.20 Aligned_cols=17 Identities=29% Similarity=0.556 Sum_probs=14.2
Q ss_pred CEEEEEEeCCcEEEEEE
Q 023166 15 YRMRVTIQDGRQLVGKF 31 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtL 31 (286)
.+|+++|+||+.+.||+
T Consensus 29 ~~V~l~L~DGs~l~Gtv 45 (101)
T PF11607_consen 29 ERVELELDDGSMLRGTV 45 (101)
T ss_dssp -EEEEEETTS-EEEEEE
T ss_pred ceEEEEEcCCCeeeeee
Confidence 59999999999999986
No 98
>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=63.91 E-value=12 Score=31.23 Aligned_cols=29 Identities=28% Similarity=0.390 Sum_probs=21.0
Q ss_pred EEEEEEeCCcEEEEEEEEecc-ccceEeCc
Q 023166 16 RMRVTIQDGRQLVGKFMAFDR-HMNLVLGD 44 (286)
Q Consensus 16 RVRVtLqDGR~fvGtLlAFDK-hMNLVLsD 44 (286)
...|+++||++|+|.+..=|. ..+|...+
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~~~~~~l~~~~ 88 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASETADGVTVKMPG 88 (133)
T ss_pred cEEEEECCCCEEEEEEEecCCCeEEEEcCC
Confidence 478999999999999998553 33443333
No 99
>PRK10942 serine endoprotease; Provisional
Probab=63.67 E-value=15 Score=37.22 Aligned_cols=32 Identities=22% Similarity=0.421 Sum_probs=28.3
Q ss_pred CEEEEEEeCCcEEEEEEEEeccccceEeCceE
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCE 46 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~e 46 (286)
.+|+|+|.|+|+|.++++++|.+.+|-|-..+
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki~ 167 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQLQ 167 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 47899999999999999999999998776543
No 100
>PRK10139 serine endoprotease; Provisional
Probab=61.41 E-value=12 Score=37.58 Aligned_cols=32 Identities=19% Similarity=0.449 Sum_probs=28.5
Q ss_pred CEEEEEEeCCcEEEEEEEEeccccceEeCceE
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCE 46 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~e 46 (286)
.+|.|+|.|+++|..+++++|...+|-|-..+
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 48999999999999999999999998876654
No 101
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=59.61 E-value=10 Score=33.85 Aligned_cols=24 Identities=29% Similarity=0.487 Sum_probs=21.6
Q ss_pred CCEEEEEEeCCcEEEEEEEEeccc
Q 023166 14 NYRMRVTIQDGRQLVGKFMAFDRH 37 (286)
Q Consensus 14 gkRVRVtLqDGR~fvGtLlAFDKh 37 (286)
++.|||-+.|||+|+|.-.+.|..
T Consensus 120 g~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 120 GKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCeEEEEEcCCcEEEeeecccceE
Confidence 678999999999999999998854
No 102
>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=57.16 E-value=16 Score=35.89 Aligned_cols=32 Identities=22% Similarity=0.415 Sum_probs=28.7
Q ss_pred CEEEEEEeCCcEEEEEEEEeccccceEeCceE
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCE 46 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~e 46 (286)
.+++|++.|+++|.++++++|.+.+|.|-..+
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 47899999999999999999999999887665
No 103
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=55.74 E-value=3.3e+02 Score=30.34 Aligned_cols=11 Identities=64% Similarity=1.262 Sum_probs=6.0
Q ss_pred CCCCCCCCCCC
Q 023166 172 PVIRPPGQMPP 182 (286)
Q Consensus 172 p~~~ppg~~~~ 182 (286)
+.+.|+|++++
T Consensus 631 p~~pPpg~~pP 641 (894)
T KOG0132|consen 631 PYPPPPGFMPP 641 (894)
T ss_pred CCCCCcccCCC
Confidence 45556666643
No 104
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=52.94 E-value=1.1e+02 Score=31.23 Aligned_cols=8 Identities=25% Similarity=0.712 Sum_probs=4.6
Q ss_pred EEEEEEEe
Q 023166 27 LVGKFMAF 34 (286)
Q Consensus 27 fvGtLlAF 34 (286)
|+|.|+-|
T Consensus 84 YvGNL~W~ 91 (498)
T KOG4849|consen 84 YVGNLLWY 91 (498)
T ss_pred EecceeEE
Confidence 45666555
No 105
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=48.72 E-value=1.9e+02 Score=32.11 Aligned_cols=17 Identities=6% Similarity=0.071 Sum_probs=9.3
Q ss_pred HHHhcCCEEEEEEeCCc
Q 023166 9 MLQFINYRMRVTIQDGR 25 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR 25 (286)
|++-.+.-.+|+|...|
T Consensus 441 ~feefGeiqSi~li~~R 457 (894)
T KOG0132|consen 441 LFEEFGEIQSIILIPPR 457 (894)
T ss_pred HHHhcccceeEeeccCC
Confidence 34444556666665544
No 106
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=47.74 E-value=17 Score=29.38 Aligned_cols=42 Identities=19% Similarity=0.247 Sum_probs=29.9
Q ss_pred eccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166 34 FDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE 87 (286)
Q Consensus 34 FDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe 87 (286)
-|..-.+.+.-+..|.. +...+.|+-|.|+++|..|.+|+++
T Consensus 54 r~~~g~~~~~r~y~FEF------------S~~G~~ry~G~l~m~G~~l~~v~lp 95 (97)
T PF11743_consen 54 RDSRGRLRWRRVYQFEF------------SSDGEDRYQGELVMLGRRLISVELP 95 (97)
T ss_pred cCCCCCeEEEEEEEEEE------------eCCChhcceEEEEEECCeeeEEEcC
Confidence 34455555555555554 1245789999999999999999875
No 107
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=45.29 E-value=42 Score=30.43 Aligned_cols=31 Identities=10% Similarity=0.322 Sum_probs=21.8
Q ss_pred hHHHHhcCC--EEEEEE-eCCcEEEEEEEEeccc
Q 023166 7 SKMLQFINY--RMRVTI-QDGRQLVGKFMAFDRH 37 (286)
Q Consensus 7 skL~qlIgk--RVRVtL-qDGR~fvGtLlAFDKh 37 (286)
..|.++-++ +|+|.+ .++..|+|+++.+|.-
T Consensus 124 ~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 124 DFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 334554444 556655 5899999999999865
No 108
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=44.91 E-value=47 Score=29.06 Aligned_cols=26 Identities=19% Similarity=0.380 Sum_probs=22.9
Q ss_pred HHhcCCEEEEEEeCCcEEEEEEEEec
Q 023166 10 LQFINYRMRVTIQDGRQLVGKFMAFD 35 (286)
Q Consensus 10 ~qlIgkRVRVtLqDGR~fvGtLlAFD 35 (286)
..||+|.|.....||..++|++.++.
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~ 114 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQ 114 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEE
Confidence 36999999988899999999998765
No 109
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=35.73 E-value=1.4e+02 Score=27.60 Aligned_cols=26 Identities=23% Similarity=0.483 Sum_probs=22.8
Q ss_pred HHhcCCEEEEEEeCCcEEEEEEEEec
Q 023166 10 LQFINYRMRVTIQDGRQLVGKFMAFD 35 (286)
Q Consensus 10 ~qlIgkRVRVtLqDGR~fvGtLlAFD 35 (286)
..||+|.|.++-.||+.+.|++.++.
T Consensus 114 ~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 114 MKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 46899999998899999999988765
No 110
>TIGR02856 spore_yqfC sporulation protein YqfC. This small protein, designated YqfC in Bacillus subtilis, is both restricted to and universal in sporulating species of the Firmcutes, such as Bacillus subtilis and Clostridium perfringens. It is part of the sigma(E)-controlled regulon, and its mutation leads to a sporulation defect.
Probab=35.71 E-value=80 Score=25.06 Aligned_cols=29 Identities=24% Similarity=0.289 Sum_probs=16.0
Q ss_pred CEEEEEEeCCcEEEEEEEEeccccceEeCceEEe
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEF 48 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~ 48 (286)
.--+|+|.+.+++. +..|-+|+--|-++.
T Consensus 18 ~~p~itl~gr~~~~-----Ien~k~I~~y~~~~I 46 (85)
T TIGR02856 18 DLPRITLIGNEHIY-----IENHRGLVVFSPEEV 46 (85)
T ss_pred CCCEEEEECCcEEE-----EECccceEEECCCEE
Confidence 34577777776654 445545444444443
No 111
>cd03367 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation. Also members of this subfamily are the archaeal 30S ribosomal S12 proteins. Prokaryotic S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=34.23 E-value=37 Score=29.00 Aligned_cols=24 Identities=17% Similarity=0.294 Sum_probs=18.4
Q ss_pred HHHHhcCCEEEEEE-eCCcEEEEEE
Q 023166 8 KMLQFINYRMRVTI-QDGRQLVGKF 31 (286)
Q Consensus 8 kL~qlIgkRVRVtL-qDGR~fvGtL 31 (286)
+-++.+.|-++|.| ++|++++-.+
T Consensus 36 kPNSA~RK~~rV~L~~ngk~itAyI 60 (115)
T cd03367 36 QPNSAIRKCVRVQLIKNGKKITAFV 60 (115)
T ss_pred CCChhhceEEEEEEccCCeEEEEEe
Confidence 44567889999999 5999887543
No 112
>PF06115 DUF956: Domain of unknown function (DUF956); InterPro: IPR010360 This is a family of bacterial sequences with undetermined function.
Probab=33.90 E-value=1.4e+02 Score=25.59 Aligned_cols=73 Identities=16% Similarity=0.198 Sum_probs=45.7
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCc-eEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeec
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGD-CEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVE 87 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD-~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe 87 (286)
|.+.||.+|..+++ +..|.|. -+|-+|.+.| +.||+..+.. .+-.+-.=.|.+...-.|+.+|..|--..+.
T Consensus 1 MvqSlNtkvdl~~~-ats~~g~----~~yGkimiGDkaFEFyn~~n~--~dyIQIPW~eI~~V~a~V~fkgk~I~RF~I~ 73 (118)
T PF06115_consen 1 MVQSLNTKVDLTTK-ATSYLGL----GKYGKIMIGDKAFEFYNDRNV--EDYIQIPWEEIDYVIASVSFKGKWIPRFAIF 73 (118)
T ss_pred CCcccccEEEEEEe-eEEEecc----cccCeEEEcccceEeecCCCh--hhcEEeChhheeEEEEEEEECCCEEeeEEEE
Confidence 34678888888774 6667763 2888888876 6788753211 1000001135667778888888888766665
Q ss_pred C
Q 023166 88 G 88 (286)
Q Consensus 88 ~ 88 (286)
.
T Consensus 74 T 74 (118)
T PF06115_consen 74 T 74 (118)
T ss_pred E
Confidence 4
No 113
>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=33.75 E-value=97 Score=23.47 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=23.1
Q ss_pred hHHHHhc--CCEEEEEE-eCC--cEEEEEEEEeccccceE
Q 023166 7 SKMLQFI--NYRMRVTI-QDG--RQLVGKFMAFDRHMNLV 41 (286)
Q Consensus 7 skL~qlI--gkRVRVtL-qDG--R~fvGtLlAFDKhMNLV 41 (286)
.+|.+.+ +..|+|+. .+| ..++|++..||...+.+
T Consensus 33 ~~l~~a~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l 72 (92)
T PF08863_consen 33 EKLSEAYQENQPVTITYYEDGYYQSVTGTIHKIDEINRTL 72 (92)
T ss_pred HHHHHHhcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEE
Confidence 3455544 45666665 455 56789999999776544
No 114
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=33.72 E-value=31 Score=28.97 Aligned_cols=37 Identities=19% Similarity=0.339 Sum_probs=30.1
Q ss_pred cCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeec
Q 023166 13 INYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRK 50 (286)
Q Consensus 13 IgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ 50 (286)
.+.||+|.|+| -+++..|++-|+++-|...||+-..-
T Consensus 63 ~G~rV~lrLkd-lELs~~FLG~~~d~TllEAd~~Llgl 99 (104)
T PF10246_consen 63 RGSRVRLRLKD-LELSAHFLGASKDTTLLEADATLLGL 99 (104)
T ss_pred cCCEEEEEECC-HhhhhhhccCCCCcEEEEeeeEEEee
Confidence 46788998875 68899999999999888888876554
No 115
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=33.54 E-value=43 Score=26.49 Aligned_cols=38 Identities=11% Similarity=0.208 Sum_probs=25.2
Q ss_pred hhHHHHhcCCEEEEEEeCCcE----EEEEEEEeccccceEeCce
Q 023166 6 SSKMLQFINYRMRVTIQDGRQ----LVGKFMAFDRHMNLVLGDC 45 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~----fvGtLlAFDKhMNLVLsD~ 45 (286)
+.+|.++++++|+|+.+.||. -.|+|... |=||..-+.
T Consensus 9 k~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t--YPsvFvV~l 50 (76)
T PF06257_consen 9 KKELESHVGKRVKLKANKGRKKIIEREGVLEET--YPSVFVVEL 50 (76)
T ss_dssp HHHHHHTTTSEEEEEE--SSS--S-EEEEEEEE---SSEEEEEE
T ss_pred HHHHHHcCCCEEEEEEcCCceEEEEEEEEEEee--cCcEEEEEE
Confidence 568999999999999998884 46877653 444444333
No 116
>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=32.14 E-value=1.2e+02 Score=20.89 Aligned_cols=25 Identities=12% Similarity=0.291 Sum_probs=20.3
Q ss_pred cCCEEEEEEeCCcEEEEEEEEeccc
Q 023166 13 INYRMRVTIQDGRQLVGKFMAFDRH 37 (286)
Q Consensus 13 IgkRVRVtLqDGR~fvGtLlAFDKh 37 (286)
++..+.+...|++-+.++++.++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4566777768999999999999963
No 117
>COG0094 RplE Ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=31.85 E-value=14 Score=33.68 Aligned_cols=40 Identities=20% Similarity=0.357 Sum_probs=26.6
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEEE-EEeccccceEeCce
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGKF-MAFDRHMNLVLGDC 45 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGtL-lAFDKhMNLVLsD~ 45 (286)
..+|.+||++-+.|.|--=|.|.|.= .+||.|-|..+.=.
T Consensus 93 g~rm~eFL~rl~~i~lPrvrdfrGls~~sFDg~GN~sfGI~ 133 (180)
T COG0094 93 GERMYEFLDRLLNIALPRVRDFRGLSPKSFDGRGNYSFGIK 133 (180)
T ss_pred hHHHHHHHHHHHHhhccccccccCCCccccCCCCceEecch
Confidence 45666777777777665455566544 67888888877654
No 118
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=31.39 E-value=26 Score=29.78 Aligned_cols=29 Identities=7% Similarity=0.124 Sum_probs=24.8
Q ss_pred CCcEEEEEEEEeccccceEeCceEEeecC
Q 023166 23 DGRQLVGKFMAFDRHMNLVLGDCEEFRKL 51 (286)
Q Consensus 23 DGR~fvGtLlAFDKhMNLVLsD~eE~r~i 51 (286)
+...+.|+|++++.--+|.+.||.|.-..
T Consensus 21 ~~~~v~G~LlG~~~~~~veV~nsF~lp~~ 49 (157)
T cd08057 21 GIKRVIGVLLGYVDGDKIEVTNSFELPFD 49 (157)
T ss_pred CCCeEEEEEEeEEeCCEEEEEEeEEcccc
Confidence 45678999999998889999999998763
No 119
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=31.13 E-value=41 Score=29.73 Aligned_cols=33 Identities=21% Similarity=0.301 Sum_probs=22.7
Q ss_pred HHHHhcCCEEEEEE-eCCcEEEEEEEEeccccceE
Q 023166 8 KMLQFINYRMRVTI-QDGRQLVGKFMAFDRHMNLV 41 (286)
Q Consensus 8 kL~qlIgkRVRVtL-qDGR~fvGtLlAFDKhMNLV 41 (286)
+-++.+-+-++|.| .+|++++-. .--|.|.|.+
T Consensus 62 KPNSA~RK~arV~L~~Ngk~vtAy-IPg~G~~~~l 95 (145)
T PRK04211 62 QPNSAIRKCVRVQLIKNGKQVTAF-CPGDGAINFI 95 (145)
T ss_pred CCchhhceeEEEEEccCCeEEEEE-eCCCcccccc
Confidence 44567889999999 699988643 3336665443
No 120
>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=31.04 E-value=1.6e+02 Score=23.63 Aligned_cols=16 Identities=25% Similarity=0.370 Sum_probs=12.6
Q ss_pred hhHHHHhcCCEEEEEE
Q 023166 6 SSKMLQFINYRMRVTI 21 (286)
Q Consensus 6 ~skL~qlIgkRVRVtL 21 (286)
.+.|.+|++++|||.-
T Consensus 10 ~~~L~~~~gk~VrivG 25 (109)
T PF08661_consen 10 GSMLSQFVGKTVRIVG 25 (109)
T ss_dssp GGGGGGGTTSEEEEEE
T ss_pred HHHHHhhCCCeEEEEE
Confidence 4568899999998753
No 121
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=30.77 E-value=32 Score=26.35 Aligned_cols=25 Identities=24% Similarity=0.505 Sum_probs=21.0
Q ss_pred hcCCEEEEEEeCCcEEEEEEEEecc
Q 023166 12 FINYRMRVTIQDGRQLVGKFMAFDR 36 (286)
Q Consensus 12 lIgkRVRVtLqDGR~fvGtLlAFDK 36 (286)
|-..+|+|.|-||..++.+|.+-|.
T Consensus 2 ~~~~~i~iRlp~G~~~~~~F~~~~t 26 (79)
T cd01772 2 YTETRIQIRLLDGTTLKQTFKAREQ 26 (79)
T ss_pred CcEEEEEEECCCCCEEEEEeCCCCh
Confidence 4567999999999999999887653
No 122
>PF06856 DUF1251: Protein of unknown function (DUF1251); InterPro: IPR009661 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf17; it is a family of uncharacterised viral proteins.
Probab=30.64 E-value=71 Score=27.38 Aligned_cols=28 Identities=21% Similarity=0.424 Sum_probs=23.7
Q ss_pred CEEEEEEe--CCcEEEEEEEEeccccceEe
Q 023166 15 YRMRVTIQ--DGRQLVGKFMAFDRHMNLVL 42 (286)
Q Consensus 15 kRVRVtLq--DGR~fvGtLlAFDKhMNLVL 42 (286)
.+|+|++. |++.|..||.+-++|+=||=
T Consensus 22 ~kv~V~v~s~~~~~iQatF~~~~~~v~iVN 51 (120)
T PF06856_consen 22 AKVRVRVDSFDNKYIQATFCCGHKHVCIVN 51 (120)
T ss_pred cEEEEEEccCCCceEEEEEEeCCceEEEEe
Confidence 48888884 79999999999999986664
No 123
>CHL00078 rpl5 ribosomal protein L5
Probab=30.15 E-value=9.7 Score=34.29 Aligned_cols=66 Identities=26% Similarity=0.344 Sum_probs=35.7
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEE-EEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGK-FMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM 84 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGt-LlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI 84 (286)
..+|.+||++-+.+.|-.=|.|+|. ..+||.+.|+-+.=.|.... . |.+ +--..-|+|-+|..+
T Consensus 94 g~~my~FL~kli~~vlPrirdf~Gi~~~sfd~~Gn~sfGi~e~~~F-P-----------Ei~---~d~~~~i~G~~Itiv 158 (181)
T CHL00078 94 GDKMYAFLDRLINLALPRIRDFQGLSPKSFDGHGNYNLGLKEQLMF-P-----------EID---YDKIDQIRGMDISIV 158 (181)
T ss_pred cHhHHHHHHHHHHHhcccccccccccccccCCCceEEECcchhccC-C-----------Ccc---cCccCCcCCCeEEEE
Confidence 3456666666555554444455543 56788877776665433221 1 111 111345788888776
Q ss_pred ee
Q 023166 85 TV 86 (286)
Q Consensus 85 sV 86 (286)
+.
T Consensus 159 tt 160 (181)
T CHL00078 159 TT 160 (181)
T ss_pred Ee
Confidence 54
No 124
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=30.12 E-value=2.1e+02 Score=25.70 Aligned_cols=26 Identities=12% Similarity=0.124 Sum_probs=22.0
Q ss_pred cCCEEEEEEeCCcEEEEEEEEecccc
Q 023166 13 INYRMRVTIQDGRQLVGKFMAFDRHM 38 (286)
Q Consensus 13 IgkRVRVtLqDGR~fvGtLlAFDKhM 38 (286)
.+..|+|...+|+.|.+++...|+..
T Consensus 19 ~Gd~i~v~dg~g~~~~a~i~~i~~~~ 44 (225)
T PF04452_consen 19 EGDSIEVFDGDGGEYRAEITEISKKS 44 (225)
T ss_dssp TT-EEEEEESSSEEEEEEEEEEESSE
T ss_pred CCCEEEEEECCCCEEEEEEEECcCcE
Confidence 47788999899999999999999764
No 125
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=29.53 E-value=79 Score=30.03 Aligned_cols=33 Identities=24% Similarity=0.369 Sum_probs=26.3
Q ss_pred CCEEEEEEeCCcEEEEEEEEeccccceEeCceE
Q 023166 14 NYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCE 46 (286)
Q Consensus 14 gkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~e 46 (286)
-.++.|+|.|||++...++++|...-|.+-..+
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 468889999999999999999977655544333
No 126
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=29.39 E-value=56 Score=30.78 Aligned_cols=21 Identities=19% Similarity=0.278 Sum_probs=18.3
Q ss_pred EEEEEEEEeccccceEeCceE
Q 023166 26 QLVGKFMAFDRHMNLVLGDCE 46 (286)
Q Consensus 26 ~fvGtLlAFDKhMNLVLsD~e 46 (286)
.++|.++-+|+|-||++.=..
T Consensus 169 ~i~g~Vi~iD~FGNlitnI~~ 189 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNISR 189 (258)
T ss_dssp EEEEEEEEEETTSEEEEEEEH
T ss_pred eEEEEEEEECccCCeeeCCCH
Confidence 999999999999999976433
No 127
>PRK00010 rplE 50S ribosomal protein L5; Validated
Probab=27.27 E-value=12 Score=33.67 Aligned_cols=40 Identities=23% Similarity=0.371 Sum_probs=25.7
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEE-EEEeccccceEeCce
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGK-FMAFDRHMNLVLGDC 45 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGt-LlAFDKhMNLVLsD~ 45 (286)
..+|.+||++-+.+.|-.-|.|+|. ..+||.+.|+-+.=-
T Consensus 93 g~~my~FL~kli~~vlPrirdf~Gi~~~sfD~~Gn~sfGi~ 133 (179)
T PRK00010 93 GERMYEFLDRLINIALPRVRDFRGLSPKSFDGRGNYTLGIK 133 (179)
T ss_pred cHHHHHHHHHHHHHhcccccccccccccccCCCceEEECcc
Confidence 4566677777666665444555554 568888877776633
No 128
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=27.14 E-value=75 Score=23.64 Aligned_cols=35 Identities=3% Similarity=0.116 Sum_probs=26.5
Q ss_pred HhcCCEEEEEEeCCcEEEEEEEEeccccceEeCce
Q 023166 11 QFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDC 45 (286)
Q Consensus 11 qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~ 45 (286)
...+..|.|.+.+-..|.|++..+|.+.=+-+.+.
T Consensus 39 ~~~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~ 73 (77)
T PF01052_consen 39 KPADEPVELRVNGQPIFRGELGRVNGRLAVRITEL 73 (77)
T ss_dssp CESSTEEEEEETTEEEEEEEEEEETTEEEEEEEEE
T ss_pred CCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEE
Confidence 34567888888888888999998888766655544
No 129
>PTZ00067 40S ribosomal S23; Provisional
Probab=27.04 E-value=42 Score=29.64 Aligned_cols=31 Identities=16% Similarity=0.288 Sum_probs=22.1
Q ss_pred hHHHHhcCCEEEEEEe-CCcEEE------EEEEEeccc
Q 023166 7 SKMLQFINYRMRVTIQ-DGRQLV------GKFMAFDRH 37 (286)
Q Consensus 7 skL~qlIgkRVRVtLq-DGR~fv------GtLlAFDKh 37 (286)
.+-++.+.|-++|.|. +|++++ |.|..+|+|
T Consensus 60 KkPNSA~RK~~rV~L~kngk~vtAyiPg~G~lh~lqEh 97 (143)
T PTZ00067 60 KQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFINEN 97 (143)
T ss_pred CCCChhhceEEEEEEccCCcEEEEEeCCCCcccccccC
Confidence 3456678899999997 999987 344445555
No 130
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=27.03 E-value=53 Score=24.86 Aligned_cols=23 Identities=30% Similarity=0.635 Sum_probs=19.7
Q ss_pred CCEEEEEEeCCcEEEEEEEEecc
Q 023166 14 NYRMRVTIQDGRQLVGKFMAFDR 36 (286)
Q Consensus 14 gkRVRVtLqDGR~fvGtLlAFDK 36 (286)
..+|+|.|-||..++.+|.+-|.
T Consensus 4 ~~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 4 QCRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred eEEEEEEcCCCCEEEEEeCCCCc
Confidence 46899999999999999887663
No 131
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=26.90 E-value=1.5e+02 Score=22.29 Aligned_cols=34 Identities=26% Similarity=0.422 Sum_probs=29.3
Q ss_pred cCCEEEEEEeCCcEEE--EEEEEeccc-cceEeCceE
Q 023166 13 INYRMRVTIQDGRQLV--GKFMAFDRH-MNLVLGDCE 46 (286)
Q Consensus 13 IgkRVRVtLqDGR~fv--GtLlAFDKh-MNLVLsD~e 46 (286)
.+.++.|.+.+++.+. ++++.+|.+ .+|-|-.++
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~All~v~ 65 (120)
T PF13365_consen 29 DNSSVEVVFPDGRRVPPVAEVVYFDPDDYDLALLKVD 65 (120)
T ss_dssp TCSEEEEEETTSCEEETEEEEEEEETT-TTEEEEEES
T ss_pred CCCEEEEEecCCCEEeeeEEEEEECCccccEEEEEEe
Confidence 5788999999999988 999999999 888776655
No 132
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=26.64 E-value=1.3e+02 Score=26.39 Aligned_cols=38 Identities=16% Similarity=0.167 Sum_probs=25.5
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEeccc---cceEeCceEEee
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFDRH---MNLVLGDCEEFR 49 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKh---MNLVLsD~eE~r 49 (286)
-..||+|.|.+ .|+ .+.|++.++.-+ .-++|.|-+|+.
T Consensus 92 a~slIGk~V~~--~~~-~~~G~V~sV~~~~~~~~~~~~dg~~v~ 132 (140)
T PRK06009 92 AEGLIGRTVTS--ADG-SITGVVKSVTVYSDGVIATLEDGKKVL 132 (140)
T ss_pred HHHhcCCEEEe--cCC-cEEEEEEEEEEeCCceEEEEECCEEEE
Confidence 34699999965 566 689999988633 335555655554
No 133
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=26.34 E-value=2.2e+02 Score=25.90 Aligned_cols=25 Identities=12% Similarity=0.240 Sum_probs=20.8
Q ss_pred cCCEEEEEEeCCcEEEEEEEEeccc
Q 023166 13 INYRMRVTIQDGRQLVGKFMAFDRH 37 (286)
Q Consensus 13 IgkRVRVtLqDGR~fvGtLlAFDKh 37 (286)
.+.+|+|...+|..+.+++..+|+.
T Consensus 32 ~Gd~i~v~~g~g~~~~~~i~~i~~~ 56 (234)
T PRK11713 32 EGDELRLFDGDGGEYLAEITEIGKK 56 (234)
T ss_pred CCCEEEEEeCCCCEEEEEEEEecCc
Confidence 4667888888889999999999863
No 134
>PF10387 DUF2442: Protein of unknown function (DUF2442); InterPro: IPR018841 Several proteins in this entry are annotated as being putative molybdopterin-guanine dinucleotide biosynthesis proteins, but this has not been confirmed. The function of these proteins is therefore not known. ; PDB: 2AUW_B 2X8N_A 3K8R_B.
Probab=26.09 E-value=65 Score=24.24 Aligned_cols=21 Identities=33% Similarity=0.637 Sum_probs=14.9
Q ss_pred CCEEEEEEeCCcEEEEEEEEe
Q 023166 14 NYRMRVTIQDGRQLVGKFMAF 34 (286)
Q Consensus 14 gkRVRVtLqDGR~fvGtLlAF 34 (286)
+|+++|++.||++++=-|..|
T Consensus 9 ~~~L~v~f~dG~~~~~dl~~~ 29 (79)
T PF10387_consen 9 DYRLRVTFSDGETRIFDLSPL 29 (79)
T ss_dssp TTEEEEEETTS-EEEEECCCS
T ss_pred CcEEEEEEcCCCEEEEEhHHh
Confidence 569999999999876544443
No 135
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The Poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=26.01 E-value=3.2e+02 Score=24.44 Aligned_cols=76 Identities=18% Similarity=0.195 Sum_probs=42.4
Q ss_pred HHHHhcCCEEEEEE---------eCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecC
Q 023166 8 KMLQFINYRMRVTI---------QDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRG 78 (286)
Q Consensus 8 kL~qlIgkRVRVtL---------qDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRG 78 (286)
-|-+++|..|.|.+ +.|.+++|||.--|+- |+...--+-..++.++.+.-++.+. +-=...-|.+.-.|
T Consensus 57 PLGeivNN~ivv~VPC~vtykyYk~GDvV~GtLnIedES-ni~V~CgDLiCkl~rdsGtVSf~ds-KYCfirNg~vY~ng 134 (160)
T PF03293_consen 57 PLGEIVNNHIVVKVPCNVTYKYYKVGDVVRGTLNIEDES-NITVQCGDLICKLSRDSGTVSFNDS-KYCFIRNGVVYDNG 134 (160)
T ss_pred chHhhcccEEEEEeeeEEEEEEEeeCCEEEEEEEecccC-ceEEEcCcEEEEeeccCCeEEecCc-eEEEEECCEEecCC
Confidence 35677888777764 6899999999877755 5544333333344443332121111 11122346666667
Q ss_pred ceeEEee
Q 023166 79 EEVISMT 85 (286)
Q Consensus 79 enIVSIs 85 (286)
+.|..+-
T Consensus 135 s~Vsv~L 141 (160)
T PF03293_consen 135 SEVSVVL 141 (160)
T ss_pred CEEEEEe
Confidence 7665443
No 136
>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=25.97 E-value=1.4e+02 Score=23.98 Aligned_cols=15 Identities=20% Similarity=0.470 Sum_probs=12.0
Q ss_pred hhHHHHhcCCEEEEE
Q 023166 6 SSKMLQFINYRMRVT 20 (286)
Q Consensus 6 ~skL~qlIgkRVRVt 20 (286)
.+-|.+|++++||+.
T Consensus 7 ~~~L~~f~gk~V~iv 21 (101)
T cd04479 7 GAMLSQFVGKTVRIV 21 (101)
T ss_pred HHHHHhhCCCEEEEE
Confidence 346789999999875
No 137
>KOG4649 consensus PQQ (pyrrolo-quinoline quinone) repeat protein [Secondary metabolites biosynthesis, transport and catabolism]
Probab=25.59 E-value=1.7e+02 Score=29.00 Aligned_cols=38 Identities=24% Similarity=0.343 Sum_probs=30.9
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEE------EEEEEeccc-cceEeC
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLV------GKFMAFDRH-MNLVLG 43 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fv------GtLlAFDKh-MNLVLs 43 (286)
..+|.+.+|-.-.|.++|.++++ |+++|+|-+ -||+-+
T Consensus 4 ~vd~~kCVDaspLVV~~dskT~v~igSHs~~~~avd~~sG~~~We 48 (354)
T KOG4649|consen 4 AVDLRKCVDASPLVVCNDSKTLVVIGSHSGIVIAVDPQSGNLIWE 48 (354)
T ss_pred eccchhhccCCcEEEecCCceEEEEecCCceEEEecCCCCcEEee
Confidence 35788999999999999998885 899999944 677643
No 138
>PF10055 DUF2292: Uncharacterized small protein (DUF2292); InterPro: IPR018743 Members of this family of hypothetical bacterial proteins have no known function.
Probab=25.50 E-value=1.1e+02 Score=21.34 Aligned_cols=22 Identities=36% Similarity=0.582 Sum_probs=15.8
Q ss_pred hHHHHhcCC-EEEEEEeCCcEEE
Q 023166 7 SKMLQFINY-RMRVTIQDGRQLV 28 (286)
Q Consensus 7 skL~qlIgk-RVRVtLqDGR~fv 28 (286)
.++++-|.| .|.|+++||+.+.
T Consensus 7 ~~~l~~i~yGsV~iiiqdG~vvQ 29 (38)
T PF10055_consen 7 LEALKSIRYGSVTIIIQDGRVVQ 29 (38)
T ss_pred HHHHhcCCcceEEEEEECCEEEE
Confidence 444555555 8999999998764
No 139
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=25.36 E-value=73 Score=23.84 Aligned_cols=22 Identities=32% Similarity=0.548 Sum_probs=19.1
Q ss_pred CEEEEEEeCCcEEEEEEEEecc
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDR 36 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDK 36 (286)
.+|+|.|-||..++.+|..-|.
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~t 28 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSDT 28 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTSB
T ss_pred EEEEEECCCCCEEEEEECCcch
Confidence 5889999999999999987664
No 140
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=25.25 E-value=1.3e+02 Score=17.84 Aligned_cols=25 Identities=24% Similarity=0.292 Sum_probs=19.5
Q ss_pred cCCEEEEEEeCCcEEEEEEEEeccc
Q 023166 13 INYRMRVTIQDGRQLVGKFMAFDRH 37 (286)
Q Consensus 13 IgkRVRVtLqDGR~fvGtLlAFDKh 37 (286)
.+.+|+|+-=.-+-++|+++.+|.+
T Consensus 4 ~G~~V~I~~G~~~g~~g~i~~i~~~ 28 (28)
T smart00739 4 VGDTVRVIAGPFKGKVGKVLEVDGE 28 (28)
T ss_pred CCCEEEEeECCCCCcEEEEEEEcCC
Confidence 4678888877777788999988863
No 141
>PF07873 YabP: YabP family; InterPro: IPR022476 Members of this protein family are the YabP and YqfC proteins of the bacterial sporulation program, as found in Bacillus subtilis, Clostridium tetani, and other spore-forming members of the Firmicutes. ; PDB: 2KYI_B 3IPF_B 2KS0_A.
Probab=25.19 E-value=78 Score=23.58 Aligned_cols=19 Identities=16% Similarity=0.345 Sum_probs=12.3
Q ss_pred eeEeceEEecCceeEEeee
Q 023166 68 RRTLGLVLLRGEEVISMTV 86 (286)
Q Consensus 68 kR~LGlVLIRGenIVSIsV 86 (286)
+...|.+.|+|++.+--.+
T Consensus 31 ~t~~g~l~I~G~~L~I~~l 49 (66)
T PF07873_consen 31 NTKKGKLTIKGEGLVIKYL 49 (66)
T ss_dssp EETTEEEEEEEEEEEEEEC
T ss_pred EeCCEEEEEECceEEEeEe
Confidence 4455788888886654443
No 142
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=25.15 E-value=39 Score=32.09 Aligned_cols=42 Identities=14% Similarity=0.141 Sum_probs=30.1
Q ss_pred HHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCceEEeec
Q 023166 9 MLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRK 50 (286)
Q Consensus 9 L~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ 50 (286)
|++.+++--|+.-.....++|+|++.++--.|.+.||.++-.
T Consensus 10 Ll~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~ 51 (280)
T cd08062 10 LLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPF 51 (280)
T ss_pred HHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCc
Confidence 444444333333344678999999999888999999999865
No 143
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=25.12 E-value=65 Score=31.67 Aligned_cols=35 Identities=17% Similarity=0.276 Sum_probs=19.1
Q ss_pred CCEEEEEEeCC------cEEEEEEEEeccccceEeCceEEe
Q 023166 14 NYRMRVTIQDG------RQLVGKFMAFDRHMNLVLGDCEEF 48 (286)
Q Consensus 14 gkRVRVtLqDG------R~fvGtLlAFDKhMNLVLsD~eE~ 48 (286)
|+-|.+++.++ ..++=+|.-|.+|.||||.|-+..
T Consensus 94 dRii~~~~~~~~~~~~~~~~~Li~El~g~~~NiiL~d~~~~ 134 (455)
T PF05833_consen 94 DRIIEIEFESGDELGDDEKYRLIIELMGRHSNIILTDEDGK 134 (455)
T ss_dssp SSEEEEEEEEE-TTS-EEEEEEEEE--GGG-EEEEEETT-B
T ss_pred cEEEEEEeeccCcCCCceeEEEEEEEcCCcccEEEEcCCCe
Confidence 34455555443 334445667899999999975543
No 144
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.94 E-value=79 Score=28.99 Aligned_cols=35 Identities=17% Similarity=0.215 Sum_probs=29.7
Q ss_pred hcCCEEEEEEeCCcEEEEEEEEeccccceEeCceE
Q 023166 12 FINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDCE 46 (286)
Q Consensus 12 lIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~e 46 (286)
.++.+|+|+..|+...+|.+.|||---|...-+|.
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 46789999999999999999999987776666665
No 145
>COG4939 Major membrane immunogen, membrane-anchored lipoprotein [Function unknown]
Probab=24.68 E-value=18 Score=31.70 Aligned_cols=65 Identities=20% Similarity=0.209 Sum_probs=33.4
Q ss_pred EEEEEEeCCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEee
Q 023166 16 RMRVTIQDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMT 85 (286)
Q Consensus 16 RVRVtLqDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIs 85 (286)
-|.|+++||++..-+----|+.-||-=+|++..+..+.+++. ...+..++|..-||.+-+--++.
T Consensus 49 f~~iti~dGKiv~~~ydy~~k~G~~Ks~DAdy~~~mk~~~g~-----gp~~~f~~laD~Lve~q~p~~Vd 113 (147)
T COG4939 49 FVTITIQDGKIVACTYDYRDKKGNIKSDDADYAGEMKYMKGQ-----GPVQGFSTLADKLVEVQDPNEVD 113 (147)
T ss_pred eEEEEEeCCEEEEEEeeeecCCCCccccchhhHHHHHHhccc-----CHHHHHHHHHHHHHhcCCcccee
Confidence 356667777766666555566666666665543332222211 11233455555555555444443
No 146
>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=24.66 E-value=42 Score=27.70 Aligned_cols=26 Identities=12% Similarity=0.112 Sum_probs=19.8
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEE
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFM 32 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLl 32 (286)
.|-++.+.|-++|.|.+|++++..+=
T Consensus 28 KkPNSA~RK~arV~L~ngk~v~ayIP 53 (95)
T cd00319 28 KKPNSALRKVAKVRLTSGYEVTAYIP 53 (95)
T ss_pred cCCChhhceEEEEEccCCCEEEEECC
Confidence 34566788899999999999875443
No 147
>PF05606 DUF777: Borrelia burgdorferi protein of unknown function (DUF777); InterPro: IPR008495 This family consists of several hypothetical proteins of unknown function, found in Borrelia burgdorferi and Borrelia garinii.
Probab=24.35 E-value=1.6e+02 Score=26.83 Aligned_cols=27 Identities=11% Similarity=0.267 Sum_probs=20.4
Q ss_pred hhHHHHhcCCEEEEEEeCCcEEEEEEEEecccc
Q 023166 6 SSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHM 38 (286)
Q Consensus 6 ~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhM 38 (286)
..++++||-..|.|+- +|+++.||...
T Consensus 21 ~ed~K~~iy~NiFI~r------IG~iK~F~~~t 47 (181)
T PF05606_consen 21 QEDIKNWIYSNIFICR------IGTIKSFKFQT 47 (181)
T ss_pred HHHHHHHHhhcEEEEE------Eeeeeeccccc
Confidence 3468888888888763 69999999653
No 148
>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12). This model represents the eukaryotic and archaeal homologs of bacterial ribosomal protein S12. This protein is known typically as S23 in eukaryotes and as either S12 or S23 in the Archaea.
Probab=23.94 E-value=75 Score=27.94 Aligned_cols=33 Identities=18% Similarity=0.233 Sum_probs=22.5
Q ss_pred HHHHhcCCEEEEEE-eCCcEEEEEEEEeccccceE
Q 023166 8 KMLQFINYRMRVTI-QDGRQLVGKFMAFDRHMNLV 41 (286)
Q Consensus 8 kL~qlIgkRVRVtL-qDGR~fvGtLlAFDKhMNLV 41 (286)
+-++.+-|-++|.| .+|++++-.+= -|.|.|.+
T Consensus 56 kPNSA~RK~~rV~L~~ngk~vtAyiP-g~G~~~~l 89 (139)
T TIGR00982 56 QPNSAIRKCVRVQLIKNGKVVTAFCP-GDGAINFI 89 (139)
T ss_pred CCCcccceEEEEEEccCCeEEEEEeC-CCcccccc
Confidence 44567889999999 69988875433 35565433
No 149
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=23.93 E-value=70 Score=22.98 Aligned_cols=16 Identities=25% Similarity=0.308 Sum_probs=12.9
Q ss_pred hhhHHHHhcCCEEEEE
Q 023166 5 KSSKMLQFINYRMRVT 20 (286)
Q Consensus 5 k~skL~qlIgkRVRVt 20 (286)
..+.+++|++|+|+|+
T Consensus 10 ~~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 10 DYSYLKSLLGKRVSVT 25 (48)
T ss_pred hhHHHHHhcCCeEEEE
Confidence 3456777999999998
No 150
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=23.54 E-value=88 Score=27.94 Aligned_cols=29 Identities=14% Similarity=0.250 Sum_probs=24.0
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEec
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFD 35 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFD 35 (286)
..+..++++.|.|.|...|.|+|++..++
T Consensus 21 ~~~~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 21 LDLKDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp S-CGGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred CChhHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 45577999999999999999999998885
No 151
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.33 E-value=77 Score=25.49 Aligned_cols=24 Identities=13% Similarity=0.220 Sum_probs=19.8
Q ss_pred hhhHHHHhcCCEEEEEEeCCcEEE
Q 023166 5 KSSKMLQFINYRMRVTIQDGRQLV 28 (286)
Q Consensus 5 k~skL~qlIgkRVRVtLqDGR~fv 28 (286)
-+.++..+++++|.+++++||.=+
T Consensus 10 IK~~i~ah~G~~v~lk~ngGRKk~ 33 (80)
T COG4466 10 IKESIDAHLGERVTLKANGGRKKT 33 (80)
T ss_pred HHHHHHhccCcEEEEEecCCceee
Confidence 355677899999999999998753
No 152
>COG1976 TIF6 Translation initiation factor 6 (eIF-6) [Translation, ribosomal structure and biogenesis]
Probab=23.09 E-value=1.7e+02 Score=27.69 Aligned_cols=79 Identities=22% Similarity=0.206 Sum_probs=51.2
Q ss_pred hHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceEeCce--EEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEe
Q 023166 7 SKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLVLGDC--EEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISM 84 (286)
Q Consensus 7 skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLVLsD~--eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSI 84 (286)
..+.+-|+-+|.-+..+|..++|+|.+-.++-=|+=..+ +|++.++...+- ......+....||.++|=.|+...+
T Consensus 37 ~~i~e~L~v~vv~ttI~gS~lvG~l~~gNsnG~lvP~~~~d~El~~l~~~~~v--~V~~l~~k~nAlGN~Il~ND~~Alv 114 (222)
T COG1976 37 DVIREVLGVPVVETTIAGSRLVGALTAGNSNGLLVPYGVRDEELRRLKNALGV--EVLILPTKLNALGNLILANDKGALV 114 (222)
T ss_pred HHHHHHhCCcEEEEEecCceEEeEEEeecCCceEcCCcccHHHHHhhcccCCc--eEEEeCccccccccEEEecCceeEe
Confidence 346677887888888899999999999998864443322 234443310010 0112234556889999989999888
Q ss_pred eec
Q 023166 85 TVE 87 (286)
Q Consensus 85 sVe 87 (286)
+-+
T Consensus 115 hp~ 117 (222)
T COG1976 115 HPD 117 (222)
T ss_pred cCc
Confidence 644
No 153
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=22.80 E-value=76 Score=23.74 Aligned_cols=22 Identities=18% Similarity=0.552 Sum_probs=18.7
Q ss_pred CEEEEEEeCCcEEEEEEEEecc
Q 023166 15 YRMRVTIQDGRQLVGKFMAFDR 36 (286)
Q Consensus 15 kRVRVtLqDGR~fvGtLlAFDK 36 (286)
.+|+|.|-||..++.+|..-|.
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~t 24 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTHK 24 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCCC
Confidence 4799999999999999876553
No 154
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=22.09 E-value=55 Score=31.89 Aligned_cols=47 Identities=21% Similarity=0.269 Sum_probs=37.3
Q ss_pred HHHHh-cCCEEEEEE--eCCcEEEEEEEEeccccceEeCceEEeecCCCC
Q 023166 8 KMLQF-INYRMRVTI--QDGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPA 54 (286)
Q Consensus 8 kL~ql-IgkRVRVtL--qDGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k 54 (286)
++.+| ++..|||-= .+.-.+.|++.+-|..-|.+|-|.++...+.++
T Consensus 123 di~~~~~gD~VrVGPtP~~klvv~G~V~g~Dd~~~~ilidi~~m~siPk~ 172 (294)
T COG2524 123 DIRKINIGDSVRVGPTPVNKLVVEGKVIGRDDTANEILIDISKMVSIPKE 172 (294)
T ss_pred ccccCCCCCeEEECCcccceEEEEeEEecccccCCeEEEEEeeeeecCcc
Confidence 45555 788888843 455678899999999999999999999887654
No 155
>PF07317 YcgR: Flagellar regulator YcgR; InterPro: IPR009926 This entry represents the N-terminal domain of YcgR proteins. The function of this domain is not known, but it is known to interact with the C-terminal which has cyclic-di-GMP bound []. YcgR is involved in the flagellar motor function and is a member of the flagellar regulon [, ].; PDB: 2GJG_A 3KYF_A.
Probab=21.97 E-value=79 Score=25.60 Aligned_cols=37 Identities=16% Similarity=0.279 Sum_probs=23.6
Q ss_pred HHHhcCCE--EEEEEeCCcEEEEEEEEeccccceEeCce
Q 023166 9 MLQFINYR--MRVTIQDGRQLVGKFMAFDRHMNLVLGDC 45 (286)
Q Consensus 9 L~qlIgkR--VRVtLqDGR~fvGtLlAFDKhMNLVLsD~ 45 (286)
|.++++++ |+|...+|..|+=+|+++|..-|.++=|+
T Consensus 14 Lr~L~~~~~~l~v~~~~g~~f~T~iL~VD~~~~~l~lD~ 52 (108)
T PF07317_consen 14 LRDLAKQRSPLTVRHPRGQSFITSILAVDPDRGTLVLDE 52 (108)
T ss_dssp HHHHHHTT--EEEETT-SSEEEE-EEEEETTTTEEEEE-
T ss_pred HHHHHhCCCeEEEEeCCCCEEEEEEEEEeCCCCEEEEEc
Confidence 44455554 55555678889999999998876665444
No 156
>PRK08655 prephenate dehydrogenase; Provisional
Probab=21.92 E-value=1.4e+02 Score=29.92 Aligned_cols=45 Identities=20% Similarity=0.202 Sum_probs=33.8
Q ss_pred hhHHHHhcCCEEEEEE-eCCcEEEEEEEEeccccceEeCceEEeecC
Q 023166 6 SSKMLQFINYRMRVTI-QDGRQLVGKFMAFDRHMNLVLGDCEEFRKL 51 (286)
Q Consensus 6 ~skL~qlIgkRVRVtL-qDGR~fvGtLlAFDKhMNLVLsD~eE~r~i 51 (286)
...|++.|++.+-++. -+|++.+|+|+-++.. +++|++-.++.++
T Consensus 292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 337 (437)
T PRK08655 292 FEKLLKSIGKEIGLKHIYSGKIHVGILKKVTPD-YVTLKKNNKEIKL 337 (437)
T ss_pred HHHHHHhhcceeeeEeecCCcEEEEEEEEecCC-eEEEeeCCcEEEE
Confidence 4567888999887765 7899999999999866 5677665544443
No 157
>PF10894 DUF2689: Protein of unknown function (DUF2689); InterPro: IPR024396 Members of this protein family are annotated as conjugal transfer protein TrbD; however, currently no function is known.
Probab=21.91 E-value=36 Score=25.90 Aligned_cols=20 Identities=35% Similarity=0.529 Sum_probs=16.6
Q ss_pred eccccceEeCceEEeecCCC
Q 023166 34 FDRHMNLVLGDCEEFRKLPP 53 (286)
Q Consensus 34 FDKhMNLVLsD~eE~r~ik~ 53 (286)
-|.||+-||+||...+.+..
T Consensus 20 sDDFmhaVlSNCtTrIvLpa 39 (61)
T PF10894_consen 20 SDDFMHAVLSNCTTRIVLPA 39 (61)
T ss_pred cHHHHHHHHhcCceeEEecC
Confidence 48999999999998876643
No 158
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=20.69 E-value=55 Score=28.87 Aligned_cols=28 Identities=14% Similarity=0.282 Sum_probs=22.2
Q ss_pred eCCcEEEEEEEEeccccceEeCceEEee
Q 023166 22 QDGRQLVGKFMAFDRHMNLVLGDCEEFR 49 (286)
Q Consensus 22 qDGR~fvGtLlAFDKhMNLVLsD~eE~r 49 (286)
+..-.=+|||++.|||-|--.+|-.-|.
T Consensus 40 rtd~~kiGTLVG~DkfGNkYyen~~~fy 67 (151)
T KOG3382|consen 40 RTDDHKIGTLVGVDKFGNKYYENNDYFY 67 (151)
T ss_pred hcccccceeeeeecccccchhcccceec
Confidence 3445557999999999999988876654
No 159
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=20.64 E-value=1.8e+02 Score=23.69 Aligned_cols=37 Identities=16% Similarity=0.226 Sum_probs=27.9
Q ss_pred hhhHHHHhcCCEEEEEEeCCcEEEEEEEEeccccceE
Q 023166 5 KSSKMLQFINYRMRVTIQDGRQLVGKFMAFDRHMNLV 41 (286)
Q Consensus 5 k~skL~qlIgkRVRVtLqDGR~fvGtLlAFDKhMNLV 41 (286)
...+-..||+|||...-+.+|.|.|.+.----.-+.|
T Consensus 31 ~~~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvV 67 (87)
T PRK04337 31 DREEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEV 67 (87)
T ss_pred CHHHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceE
Confidence 4456677999999999999999999987654444444
No 160
>PF08458 PH_2: Plant pleckstrin homology-like region; InterPro: IPR013666 This domain describes a pleckstrin homology (PH)-like region found in several plant proteins of unknown function.
Probab=20.32 E-value=85 Score=26.53 Aligned_cols=68 Identities=26% Similarity=0.552 Sum_probs=38.8
Q ss_pred hcCCEEEEEEe-CCcEEEEEEEEeccccceEeCceEEeecCCCCcCCCCCCcccccceeEeceEEecCceeEEeeecC
Q 023166 12 FINYRMRVTIQ-DGRQLVGKFMAFDRHMNLVLGDCEEFRKLPPAKGKKNNTNEEREDRRTLGLVLLRGEEVISMTVEG 88 (286)
Q Consensus 12 lIgkRVRVtLq-DGR~fvGtLlAFDKhMNLVLsD~eE~r~ik~k~~kk~~~~~e~eekR~LGlVLIRGenIVSIsVe~ 88 (286)
|||++-.|.|+ -.+.+.|+|.-..++ +|++=|.|...-. +++ ..++.++.+++|+-..+|- +.+..++
T Consensus 20 yink~~qVilKmKskhv~Gafskkkk~--VV~~V~~~~~awp---gr~--~~e~~~~~~yfgL~T~~G~--vEfec~~ 88 (110)
T PF08458_consen 20 YINKKGQVILKMKSKHVGGAFSKKKKS--VVLDVCSEIPAWP---GRE--LREDGEERRYFGLKTAQGV--VEFECDS 88 (110)
T ss_pred EECCCcEEEEEeecchhhhhhhcCCce--EEEEEccCcccCC---Ccc--cccCCceEEEEEEEecCcE--EEEEeCC
Confidence 66765555443 245577887776654 6766666543221 111 1133468889999888664 5555554
Done!