Query 033666
Match_columns 114
No_of_seqs 120 out of 1060
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 04:53:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033666.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033666hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06168 LSm9 The eukaryotic Sm 99.9 1.1E-24 2.3E-29 143.1 11.0 74 26-100 2-75 (75)
2 cd01717 Sm_B The eukaryotic Sm 99.9 9.4E-24 2E-28 139.1 10.3 74 27-100 3-79 (79)
3 cd01729 LSm7 The eukaryotic Sm 99.9 4.8E-22 1E-26 132.0 10.4 75 24-98 2-77 (81)
4 cd01730 LSm3 The eukaryotic Sm 99.9 7.1E-22 1.5E-26 131.1 9.5 74 25-98 2-81 (82)
5 cd01719 Sm_G The eukaryotic Sm 99.9 2.1E-21 4.6E-26 126.4 9.4 68 26-100 2-69 (72)
6 cd01727 LSm8 The eukaryotic Sm 99.9 4.1E-21 8.9E-26 125.2 10.0 70 27-99 2-71 (74)
7 cd01728 LSm1 The eukaryotic Sm 99.9 5.5E-21 1.2E-25 125.2 10.6 71 24-98 2-72 (74)
8 cd01732 LSm5 The eukaryotic Sm 99.9 5.1E-21 1.1E-25 125.9 10.2 72 24-99 3-74 (76)
9 cd01731 archaeal_Sm1 The archa 99.8 7.4E-21 1.6E-25 121.9 8.8 67 25-98 1-67 (68)
10 PRK00737 small nuclear ribonuc 99.8 1.1E-20 2.4E-25 122.7 9.1 69 23-98 3-71 (72)
11 cd01720 Sm_D2 The eukaryotic S 99.8 1.6E-20 3.5E-25 126.5 9.6 74 25-98 3-84 (87)
12 cd01726 LSm6 The eukaryotic Sm 99.8 4.9E-20 1.1E-24 118.0 8.3 67 25-98 1-67 (67)
13 cd01722 Sm_F The eukaryotic Sm 99.8 6.3E-20 1.4E-24 117.9 8.2 67 24-97 1-67 (68)
14 PF01423 LSM: LSM domain ; In 99.8 2.7E-19 5.9E-24 113.3 9.1 67 27-99 1-67 (67)
15 smart00651 Sm snRNP Sm protein 99.8 2.4E-19 5.3E-24 113.3 8.6 65 28-98 2-66 (67)
16 cd01718 Sm_E The eukaryotic Sm 99.8 9E-19 1.9E-23 116.2 8.9 69 24-98 6-78 (79)
17 cd00600 Sm_like The eukaryotic 99.8 2E-18 4.4E-23 107.6 8.3 63 29-98 1-63 (63)
18 COG1958 LSM1 Small nuclear rib 99.8 6E-18 1.3E-22 111.2 9.9 73 22-98 5-78 (79)
19 KOG1780 Small Nuclear ribonucl 99.7 7.3E-18 1.6E-22 110.1 6.2 66 27-99 7-72 (77)
20 KOG3168 U1 snRNP component [Tr 99.7 5.6E-19 1.2E-23 130.7 1.1 78 26-103 6-86 (177)
21 PTZ00138 small nuclear ribonuc 99.7 4.8E-17 1E-21 110.1 8.8 70 23-98 13-86 (89)
22 cd01723 LSm4 The eukaryotic Sm 99.7 9.3E-17 2E-21 105.2 8.4 70 25-100 2-71 (76)
23 cd01721 Sm_D3 The eukaryotic S 99.7 1.4E-16 3.1E-21 102.9 9.0 68 25-99 1-68 (70)
24 KOG1781 Small Nuclear ribonucl 99.7 7.4E-18 1.6E-22 115.4 0.7 85 21-105 14-99 (108)
25 cd01724 Sm_D1 The eukaryotic S 99.7 7.5E-16 1.6E-20 104.2 9.3 72 25-103 2-73 (90)
26 KOG1784 Small Nuclear ribonucl 99.6 2E-16 4.4E-21 106.9 5.0 82 27-111 3-85 (96)
27 cd01733 LSm10 The eukaryotic S 99.6 3.6E-15 7.8E-20 98.4 9.0 70 23-99 8-77 (78)
28 cd01725 LSm2 The eukaryotic Sm 99.6 8.6E-15 1.9E-19 97.1 9.0 71 25-100 2-72 (81)
29 KOG3482 Small nuclear ribonucl 99.6 8.8E-15 1.9E-19 95.5 6.7 68 23-97 7-74 (79)
30 KOG3460 Small nuclear ribonucl 99.6 1.2E-15 2.7E-20 101.7 2.2 77 23-99 4-86 (91)
31 KOG1783 Small nuclear ribonucl 99.5 2.3E-15 5E-20 98.1 1.5 73 22-101 4-76 (77)
32 KOG1782 Small Nuclear ribonucl 99.4 1.1E-14 2.4E-19 103.1 -0.1 76 25-104 10-86 (129)
33 KOG1775 U6 snRNA-associated Sm 99.4 6.1E-13 1.3E-17 87.6 4.7 76 19-98 2-77 (84)
34 KOG1774 Small nuclear ribonucl 99.1 4.8E-11 1E-15 79.5 3.9 70 23-98 11-84 (88)
35 KOG3448 Predicted snRNP core p 98.5 6.8E-07 1.5E-11 60.5 8.3 71 26-101 4-74 (96)
36 KOG3459 Small nuclear ribonucl 98.4 8.3E-08 1.8E-12 67.1 0.2 65 34-98 36-106 (114)
37 KOG3428 Small nuclear ribonucl 98.2 1.9E-05 4E-10 55.2 8.4 67 26-100 4-70 (109)
38 KOG3293 Small nuclear ribonucl 98.1 9.8E-06 2.1E-10 57.9 5.9 71 25-101 3-73 (134)
39 cd01739 LSm11_C The eukaryotic 98.1 3.7E-06 7.9E-11 54.0 2.9 37 35-71 9-49 (66)
40 PF14438 SM-ATX: Ataxin 2 SM d 97.9 1.3E-05 2.9E-10 51.9 4.0 70 26-95 4-76 (77)
41 KOG3172 Small nuclear ribonucl 97.6 0.00025 5.5E-09 49.7 6.4 68 24-98 5-72 (119)
42 PF12701 LSM14: Scd6-like Sm d 97.0 0.0027 5.9E-08 43.5 6.3 75 30-104 4-81 (96)
43 PF06372 Gemin6: Gemin6 protei 96.8 0.0049 1.1E-07 46.1 6.4 63 27-103 10-73 (166)
44 PF02237 BPL_C: Biotin protein 96.7 0.0067 1.5E-07 36.0 5.5 35 32-67 1-35 (48)
45 PF11095 Gemin7: Gem-associate 96.1 0.06 1.3E-06 35.9 7.7 65 25-101 15-80 (80)
46 cd01736 LSm14_N LSm14 (also kn 96.0 0.067 1.4E-06 35.2 7.5 67 30-96 2-72 (74)
47 PRK14638 hypothetical protein; 95.8 0.053 1.1E-06 39.6 6.9 54 8-63 75-128 (150)
48 PRK02001 hypothetical protein; 95.3 0.087 1.9E-06 38.7 6.6 54 8-63 65-118 (152)
49 PRK14639 hypothetical protein; 95.2 0.13 2.7E-06 37.2 7.2 54 8-63 63-116 (140)
50 cd01734 YlxS_C YxlS is a Bacil 95.2 0.15 3.2E-06 33.4 6.9 50 11-62 3-56 (83)
51 cd01735 LSm12_N LSm12 belongs 94.4 0.12 2.5E-06 32.8 4.6 36 32-67 4-39 (61)
52 PF10842 DUF2642: Protein of u 94.1 0.38 8.2E-06 30.9 6.6 53 26-98 13-65 (66)
53 PRK14633 hypothetical protein; 93.5 0.45 9.6E-06 34.7 7.0 55 7-63 68-126 (150)
54 PRK14640 hypothetical protein; 93.1 1.1 2.3E-05 32.8 8.5 54 8-63 72-129 (152)
55 PRK14636 hypothetical protein; 93.1 0.62 1.4E-05 34.9 7.4 53 8-62 73-129 (176)
56 PRK14632 hypothetical protein; 93.1 0.62 1.3E-05 34.8 7.3 81 8-100 73-160 (172)
57 PRK14645 hypothetical protein; 92.9 0.49 1.1E-05 34.8 6.5 53 8-63 77-129 (154)
58 PRK14644 hypothetical protein; 92.8 0.8 1.7E-05 33.0 7.4 52 9-63 62-117 (136)
59 PF02576 DUF150: Uncharacteris 92.7 0.49 1.1E-05 33.7 6.2 52 9-62 63-118 (141)
60 PRK00092 ribosome maturation p 92.2 0.78 1.7E-05 33.3 6.8 49 8-57 73-125 (154)
61 PRK14642 hypothetical protein; 92.1 0.53 1.2E-05 36.1 6.0 47 14-62 81-140 (197)
62 cd01716 Hfq Hfq, an abundant, 92.1 0.38 8.2E-06 30.5 4.3 33 34-66 11-43 (61)
63 TIGR02383 Hfq RNA chaperone Hf 92.0 0.38 8.2E-06 30.5 4.3 32 34-65 15-46 (61)
64 COG0779 Uncharacterized protei 91.7 1.4 3.1E-05 32.5 7.7 47 14-62 80-130 (153)
65 PRK14634 hypothetical protein; 91.5 1.1 2.4E-05 32.9 6.9 54 8-63 75-132 (155)
66 PRK14643 hypothetical protein; 90.6 1.8 3.9E-05 32.1 7.3 44 14-58 85-132 (164)
67 PRK14631 hypothetical protein; 90.5 1.3 2.8E-05 33.2 6.6 52 9-62 93-150 (174)
68 PRK00395 hfq RNA-binding prote 90.5 0.61 1.3E-05 31.0 4.3 34 34-67 19-52 (79)
69 PRK14647 hypothetical protein; 90.3 1.5 3.3E-05 32.2 6.7 52 9-62 75-135 (159)
70 PRK14637 hypothetical protein; 90.2 1.4 3E-05 32.3 6.4 52 10-63 75-127 (151)
71 PRK14646 hypothetical protein; 90.0 3.6 7.7E-05 30.1 8.4 54 8-63 75-132 (155)
72 PRK14641 hypothetical protein; 89.7 1.5 3.3E-05 32.9 6.4 47 8-55 79-129 (173)
73 PRK06955 biotin--protein ligas 87.7 2.3 4.9E-05 33.9 6.6 33 31-63 246-278 (300)
74 PF03614 Flag1_repress: Repres 85.5 1.2 2.6E-05 33.2 3.5 37 30-66 25-61 (165)
75 KOG1073 Uncharacterized mRNA-a 83.8 5.4 0.00012 33.3 7.1 74 30-104 5-83 (361)
76 PRK13325 bifunctional biotin-- 83.0 4.9 0.00011 35.3 6.9 32 32-63 276-307 (592)
77 PF03614 Flag1_repress: Repres 82.9 1.3 2.9E-05 32.9 2.8 43 14-56 98-142 (165)
78 TIGR00121 birA_ligase birA, bi 81.7 9.3 0.0002 29.1 7.3 33 30-63 189-221 (237)
79 COG0340 BirA Biotin-(acetyl-Co 81.2 6.9 0.00015 30.5 6.5 37 29-65 185-221 (238)
80 PRK14630 hypothetical protein; 81.1 7.3 0.00016 28.2 6.2 52 8-62 72-123 (143)
81 PRK11886 bifunctional biotin-- 80.4 7.9 0.00017 30.8 6.7 32 31-63 269-300 (319)
82 PRK14635 hypothetical protein; 80.1 12 0.00027 27.4 7.2 54 8-63 74-132 (162)
83 PRK08330 biotin--protein ligas 79.6 7.8 0.00017 29.6 6.2 34 30-64 184-218 (236)
84 PTZ00275 biotin-acetyl-CoA-car 77.8 5.2 0.00011 31.8 4.9 31 32-63 235-265 (285)
85 PRK14091 RNA-binding protein H 76.7 6.2 0.00013 29.6 4.7 42 27-68 95-138 (165)
86 PF14563 DUF4444: Domain of un 76.4 3.4 7.4E-05 24.3 2.6 23 47-69 10-32 (42)
87 PF07073 ROF: Modulator of Rho 74.4 9.8 0.00021 25.1 4.8 58 28-100 11-69 (80)
88 COG1923 Hfq Uncharacterized ho 73.9 7.4 0.00016 25.8 4.0 31 34-64 19-49 (77)
89 PRK14091 RNA-binding protein H 73.7 8.8 0.00019 28.8 4.9 42 27-68 15-58 (165)
90 PRK10898 serine endoprotease; 71.1 9.1 0.0002 31.2 4.8 31 35-65 102-132 (353)
91 TIGR02038 protease_degS peripl 70.9 9 0.00019 31.1 4.8 31 35-65 102-132 (351)
92 PRK10942 serine endoprotease; 68.3 10 0.00022 32.2 4.8 31 34-64 135-165 (473)
93 TIGR02603 CxxCH_TIGR02603 puta 67.5 12 0.00026 26.2 4.3 30 35-65 58-87 (133)
94 PRK10139 serine endoprotease; 65.5 13 0.00029 31.4 4.9 32 34-65 114-145 (455)
95 PF11607 DUF3247: Protein of u 64.9 9.8 0.00021 26.3 3.2 27 25-51 14-45 (101)
96 PRK09618 flgD flagellar basal 62.3 43 0.00093 24.5 6.4 42 27-68 85-129 (142)
97 PRK08477 biotin--protein ligas 61.8 20 0.00044 27.4 4.9 38 29-67 170-207 (211)
98 KOG3382 NADH:ubiquinone oxidor 61.5 4.5 9.8E-05 29.6 1.2 21 46-66 44-64 (151)
99 KOG3168 U1 snRNP component [Tr 58.6 17 0.00038 27.4 3.9 71 26-96 42-115 (177)
100 PF05071 NDUFA12: NADH ubiquin 57.9 4.7 0.0001 27.6 0.7 17 49-65 1-17 (105)
101 TIGR02037 degP_htrA_DO peripla 57.4 22 0.00048 29.4 4.7 32 35-66 82-113 (428)
102 PF06257 DUF1021: Protein of u 53.9 40 0.00087 22.1 4.6 29 26-54 9-41 (76)
103 PF07202 Tcp10_C: T-complex pr 50.7 22 0.00049 26.7 3.5 34 30-63 140-177 (179)
104 PF14485 DUF4431: Domain of un 45.1 25 0.00055 20.9 2.4 36 23-63 8-43 (48)
105 PF00789 UBX: UBX domain; Int 44.2 23 0.0005 22.2 2.3 23 35-57 7-29 (82)
106 smart00166 UBX Domain present 44.0 22 0.00047 22.5 2.2 23 34-56 4-26 (80)
107 cd01767 UBX UBX (ubiquitin reg 42.0 27 0.00058 21.9 2.4 22 35-56 3-24 (77)
108 PRK04337 50S ribosomal protein 41.5 69 0.0015 21.6 4.3 38 24-61 30-67 (87)
109 COG4466 Veg Uncharacterized pr 41.2 32 0.00069 22.9 2.6 22 26-47 11-32 (80)
110 TIGR03170 flgA_cterm flagella 40.8 35 0.00076 23.1 2.9 23 31-53 93-116 (122)
111 KOG3493 Ubiquitin-like protein 39.9 23 0.0005 23.0 1.8 20 28-47 5-24 (73)
112 COG0265 DegQ Trypsin-like seri 38.4 63 0.0014 25.8 4.5 33 34-66 95-127 (347)
113 PRK06630 hypothetical protein; 36.9 19 0.00042 24.8 1.1 19 47-65 11-29 (99)
114 PF01887 SAM_adeno_trans: S-ad 36.8 51 0.0011 26.0 3.7 19 46-64 169-187 (258)
115 PTZ00276 biotin/lipoate protei 36.3 67 0.0014 24.8 4.2 32 33-64 197-231 (245)
116 cd01772 SAKS1_UBX SAKS1-like U 35.0 27 0.00058 22.3 1.5 25 32-56 2-26 (79)
117 PLN02732 Probable NADH dehydro 34.3 32 0.00069 25.7 2.0 17 49-65 49-65 (159)
118 PRK11911 flgD flagellar basal 33.6 78 0.0017 23.1 3.9 27 29-55 88-114 (140)
119 PLN03095 NADH:ubiquinone oxido 32.1 27 0.00059 24.7 1.3 18 48-65 9-26 (115)
120 PRK07018 flgA flagellar basal 31.7 53 0.0011 25.2 3.0 23 31-53 204-227 (235)
121 PHA00672 hypothetical protein 31.2 2.1E+02 0.0045 21.0 5.7 47 38-92 51-97 (152)
122 PF11743 DUF3301: Protein of u 29.9 1.5E+02 0.0033 19.8 4.7 41 55-100 55-95 (97)
123 PF09465 LBR_tudor: Lamin-B re 29.6 1.1E+02 0.0024 19.0 3.5 26 33-58 8-34 (55)
124 PF03166 MH2: MH2 domain; Int 29.2 84 0.0018 23.2 3.6 35 16-50 47-82 (181)
125 cd04479 RPA3 RPA3: A subfamily 28.2 1.6E+02 0.0034 19.6 4.5 15 26-40 7-21 (101)
126 PF03122 Herpes_MCP: Herpes vi 28.0 20 0.00043 34.8 0.0 54 39-97 252-305 (1354)
127 PRK11625 Rho-binding antitermi 27.0 1.9E+02 0.0042 19.1 6.4 56 28-98 17-72 (84)
128 KOG4401 Uncharacterized conser 26.9 90 0.002 23.9 3.4 34 33-66 10-43 (184)
129 COG2451 Ribosomal protein L35A 26.3 1.6E+02 0.0035 20.3 4.3 33 25-59 37-70 (100)
130 PF06856 DUF1251: Protein of u 25.5 1.2E+02 0.0027 21.5 3.7 27 35-61 22-50 (120)
131 PRK12617 flgA flagellar basal 24.7 87 0.0019 24.1 3.0 22 32-53 184-206 (214)
132 TIGR00008 infA translation ini 24.5 1.1E+02 0.0024 19.6 3.0 24 32-55 15-38 (68)
133 PRK08183 NADH dehydrogenase; V 24.4 42 0.00092 24.2 1.2 18 48-65 25-42 (133)
134 PRK06005 flgA flagellar basal 23.9 97 0.0021 22.6 3.0 23 31-53 128-151 (160)
135 cd01770 p47_UBX p47-like ubiqu 23.8 74 0.0016 20.4 2.1 22 35-56 5-26 (79)
136 PF12945 YcgR_2: Flagellar pro 23.8 1.9E+02 0.004 17.8 4.5 31 33-63 3-37 (87)
137 PRK06792 flgD flagellar basal 23.3 1.3E+02 0.0029 23.0 3.8 28 28-55 112-139 (190)
138 COG5316 Uncharacterized conser 23.0 2.1E+02 0.0045 24.6 5.1 44 25-69 73-116 (421)
139 PF06004 DUF903: Bacterial pro 23.0 73 0.0016 19.2 1.9 11 38-48 3-13 (50)
140 PF01247 Ribosomal_L35Ae: Ribo 22.8 1.7E+02 0.0036 20.0 3.8 37 25-61 31-75 (95)
141 PRK08515 flgA flagellar basal 21.6 1.4E+02 0.003 22.9 3.6 23 31-53 193-215 (222)
142 smart00333 TUDOR Tudor domain. 21.6 1.7E+02 0.0037 16.6 5.0 25 33-57 5-29 (57)
143 PRK10708 hypothetical protein; 21.3 1.1E+02 0.0024 19.2 2.5 25 33-57 3-27 (62)
144 PF05775 AfaD: Enterobacteria 20.9 1.9E+02 0.004 20.4 3.8 28 40-67 7-36 (111)
145 PF12869 tRNA_anti-like: tRNA_ 20.7 90 0.0019 21.4 2.2 21 46-66 124-144 (144)
No 1
>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=99.92 E-value=1.1e-24 Score=143.12 Aligned_cols=74 Identities=41% Similarity=0.681 Sum_probs=66.5
Q ss_pred HHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEc
Q 033666 26 ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVD 100 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~ 100 (114)
++.|++|++++|+|+|+|||.|+|+|.|||++|||||+||.|++..+++ ....+.|.+|+++|||++|++|+++
T Consensus 2 ~~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~-~~~~~~r~lGlv~IrG~~Iv~i~v~ 75 (75)
T cd06168 2 RQKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDS-FSPTEPRVLGLVMIPGHHIVSIEVE 75 (75)
T ss_pred HhHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCc-cCCccEEEeeeEEEeCCeEEEEEEC
Confidence 5789999999999999999999999999999999999999999866432 2446789999999999999999875
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=99.91 E-value=9.4e-24 Score=139.11 Aligned_cols=74 Identities=32% Similarity=0.596 Sum_probs=64.7
Q ss_pred HHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCC---CCCCCceEeeeEEEEcCCCEEEEEEc
Q 033666 27 SRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRT---SPSPMEQRCLGIILIPSSCRTSCHVD 100 (114)
Q Consensus 27 ~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~---~~~~~~~r~lG~vlIrG~~Iv~I~v~ 100 (114)
+.|.+|++++|+|+|+|||.|.|+|.|||+||||||+||+|++...+. ......+|.+|+++|||++|++|+++
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v~ 79 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTVE 79 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEEC
Confidence 579999999999999999999999999999999999999998865432 12345679999999999999999864
No 3
>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=99.88 E-value=4.8e-22 Score=131.99 Aligned_cols=75 Identities=21% Similarity=0.311 Sum_probs=63.6
Q ss_pred chHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCC-CCCCceEeeeEEEEcCCCEEEEE
Q 033666 24 NHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTS-PSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 24 ~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~-~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
++...|.+|++++|+|+|+|||.|+|+|.|||+||||+|++|+|+....... ......+.+|+++|||++|++|.
T Consensus 2 ~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~ 77 (81)
T cd01729 2 ESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLIS 77 (81)
T ss_pred cchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEe
Confidence 4567799999999999999999999999999999999999999987543210 11236788999999999999985
No 4
>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=99.87 E-value=7.1e-22 Score=131.14 Aligned_cols=74 Identities=20% Similarity=0.286 Sum_probs=64.0
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCC------CCCceEeeeEEEEcCCCEEEEE
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSP------SPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~------~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
|.+.|+.+++++|.|+|+|||.|.|+|.|||+||||+|+||+|++....+.. .....|.+|+++|||++|++|.
T Consensus 2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence 6788999999999999999999999999999999999999999876543211 2235789999999999999884
No 5
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=2.1e-21 Score=126.37 Aligned_cols=68 Identities=21% Similarity=0.302 Sum_probs=61.5
Q ss_pred HHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEc
Q 033666 26 ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVD 100 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~ 100 (114)
.+.|++|++++|+|+|+|||.|.|+|.|||+||||+|+||.|+.. ....+.+|.++|||++|++|+.-
T Consensus 2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~-------~~~~~~lg~v~IRG~~I~~i~~~ 69 (72)
T cd01719 2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS-------GGEKNNIGMVVIRGNSIVMLEAL 69 (72)
T ss_pred chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEcc-------CCceeEeceEEECCCEEEEEEcc
Confidence 468999999999999999999999999999999999999999762 13578999999999999999754
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=4.1e-21 Score=125.21 Aligned_cols=70 Identities=26% Similarity=0.350 Sum_probs=61.2
Q ss_pred HHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEE
Q 033666 27 SRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHV 99 (114)
Q Consensus 27 ~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v 99 (114)
+.|.+|++++|+|+++|||.|.|+|.|||+||||+|++|.|+..... ....++.+|++++||++|+.|..
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~---~~~~~~~lG~~~iRG~~I~~i~~ 71 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSD---EGVEQVVLGLYIIRGDNIAVVGE 71 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCC---CCceeeEeceEEECCCEEEEEEc
Confidence 57999999999999999999999999999999999999999764321 22357789999999999999863
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=99.86 E-value=5.5e-21 Score=125.23 Aligned_cols=71 Identities=23% Similarity=0.286 Sum_probs=62.5
Q ss_pred chHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 24 NHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 24 ~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
+....|.++++++|.|+++|||.|.|+|.|||+||||+|+||.|+..... ...++.+|.++|||++|+.|.
T Consensus 2 ~~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~----~~~~~~lG~~viRG~~V~~ig 72 (74)
T cd01728 2 PGTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD----KYGDIPRGIFIIRGENVVLLG 72 (74)
T ss_pred CchHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC----ccceeEeeEEEEECCEEEEEE
Confidence 35678999999999999999999999999999999999999999875431 234688999999999999985
No 8
>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=99.86 E-value=5.1e-21 Score=125.92 Aligned_cols=72 Identities=21% Similarity=0.261 Sum_probs=63.7
Q ss_pred chHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEE
Q 033666 24 NHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHV 99 (114)
Q Consensus 24 ~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v 99 (114)
.|.+.|+++++++|+|+++|||.|.|+|.|||+||||+|+||.|++..+ .....+.+|.++|||++|+.|+.
T Consensus 3 ~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~----~~~~~~~lg~v~iRG~nV~~i~p 74 (76)
T cd01732 3 LPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITP----EGRKITKLDQILLNGNNICMLVP 74 (76)
T ss_pred ChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcC----CCceeeEcCeEEEeCCeEEEEEC
Confidence 4788999999999999999999999999999999999999999987432 12356889999999999999863
No 9
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.85 E-value=7.4e-21 Score=121.92 Aligned_cols=67 Identities=22% Similarity=0.305 Sum_probs=61.0
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
|.+.|+++++++|.|.|+|||.|.|+|.|||+||||+|+||.|.... ...+.+|.++|||++|++|.
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-------~~~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG-------EPVRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC-------CeEeEcCcEEEeCCEEEEEc
Confidence 56789999999999999999999999999999999999999997642 25788999999999999884
No 10
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.84 E-value=1.1e-20 Score=122.69 Aligned_cols=69 Identities=25% Similarity=0.320 Sum_probs=62.5
Q ss_pred CchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 23 SNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 23 ~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
..|...|.++++++|.|.|+|||.|.|+|.|||+||||+|+||.|... +...+.+|.++|||++|++|.
T Consensus 3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-------~~~~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-------GEVVRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC-------CCeEeEcCcEEEeCCEEEEEc
Confidence 468899999999999999999999999999999999999999999742 135688999999999999884
No 11
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.84 E-value=1.6e-20 Score=126.47 Aligned_cols=74 Identities=12% Similarity=0.268 Sum_probs=63.6
Q ss_pred hHHHHHHhc--CCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCC------CCCceEeeeEEEEcCCCEEE
Q 033666 25 HISRVRKLL--CRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSP------SPMEQRCLGIILIPSSCRTS 96 (114)
Q Consensus 25 ~~~~L~~~l--~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~------~~~~~r~lG~vlIrG~~Iv~ 96 (114)
|.+.|+..+ +++|+|+|++||.|.|+|.|||+||||+|+||+|++...+++. .....|++|.++|||++|++
T Consensus 3 Pl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~ 82 (87)
T cd01720 3 PLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL 82 (87)
T ss_pred hHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence 678888997 8999999999999999999999999999999999886643211 12357789999999999999
Q ss_pred EE
Q 033666 97 CH 98 (114)
Q Consensus 97 I~ 98 (114)
|.
T Consensus 83 Is 84 (87)
T cd01720 83 VL 84 (87)
T ss_pred Ee
Confidence 85
No 12
>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=99.82 E-value=4.9e-20 Score=117.99 Aligned_cols=67 Identities=19% Similarity=0.267 Sum_probs=60.3
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
|.+.|+++++++|.|.|++||+|.|+|.|||.||||+|+||.|... ...++.+|.++|||++|..|+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~-------~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN-------GQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC-------CceeeEeCCEEEECCEEEEEC
Confidence 5688999999999999999999999999999999999999998642 235778999999999999873
No 13
>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=99.82 E-value=6.3e-20 Score=117.87 Aligned_cols=67 Identities=22% Similarity=0.251 Sum_probs=60.4
Q ss_pred chHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEE
Q 033666 24 NHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSC 97 (114)
Q Consensus 24 ~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I 97 (114)
.|.+.|+++++++|+|.|+|||+|.|+|.|||+||||+|+||.|+... ...+.+|.++|||++|.+|
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~-------~~~~~lg~~~IRG~~I~~i 67 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG-------KSTGNLGEVLIRCNNVLYI 67 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC-------ccccCcCcEEEECCEEEEE
Confidence 367899999999999999999999999999999999999999997421 2467899999999999987
No 14
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.81 E-value=2.7e-19 Score=113.26 Aligned_cols=67 Identities=28% Similarity=0.456 Sum_probs=60.9
Q ss_pred HHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEE
Q 033666 27 SRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHV 99 (114)
Q Consensus 27 ~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v 99 (114)
.+|++++|++|+|.++|||.|.|+|.+||++|||+|+||.|+.... ...+++|.++|||++|.+|.+
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~------~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNG------PEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTE------SEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCC------CcEeECcEEEEECCEEEEEEC
Confidence 3689999999999999999999999999999999999999987542 278999999999999999864
No 15
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.80 E-value=2.4e-19 Score=113.32 Aligned_cols=65 Identities=28% Similarity=0.444 Sum_probs=59.8
Q ss_pred HHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 28 RVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 28 ~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
+|+++++++|+|.|+|||.+.|+|.|||++|||+|+||.|+.... ...+.+|.++|||++|.+|+
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~------~~~~~~~~~~IrG~~I~~i~ 66 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG------EKKRKLGLVFIRGNNIVYII 66 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC------cEEeEeCCEEEcCCEEEEEe
Confidence 689999999999999999999999999999999999999986431 46899999999999999985
No 16
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.79 E-value=9e-19 Score=116.21 Aligned_cols=69 Identities=20% Similarity=0.214 Sum_probs=58.8
Q ss_pred chHHHHHHhcCCe--EEEEEc--CCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 24 NHISRVRKLLCRR--MLVGIK--DGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 24 ~~~~~L~~~l~k~--V~V~L~--dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
.|...+.+|++++ |.|.++ +||.++|+|.|||+||||+|+||+|+... ....+.+|.++|||++|+.|+
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~------~~~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK------TKTRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC------CceEeEcCcEEEeCCEEEEEc
Confidence 5788999999995 444444 99999999999999999999999998642 236788999999999999875
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=99.77 E-value=2e-18 Score=107.61 Aligned_cols=63 Identities=29% Similarity=0.441 Sum_probs=57.6
Q ss_pred HHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 29 VRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 29 L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
|++++|++|+|.++|||.|.|+|.|||++||++|+||.|+... ...+.+|.++|||++|..|+
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 5789999999999999999999999999999999999998653 36899999999999999873
No 18
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.76 E-value=6e-18 Score=111.21 Aligned_cols=73 Identities=30% Similarity=0.387 Sum_probs=61.5
Q ss_pred CCchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCC-ceEeeeEEEEcCCCEEEEE
Q 033666 22 GSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPM-EQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 22 ~~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~-~~r~lG~vlIrG~~Iv~I~ 98 (114)
...|.+.|+++++++|.|.|+|||+|.|+|.|||.||||+|.||.|+.... +.. ..+..|.++|||++|..|.
T Consensus 5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~----~~~~~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHD----GEKNVRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccC----CccccceeccEEEEECCcEEEEe
Confidence 356789999999999999999999999999999999999999999987411 111 2344459999999999885
No 19
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.73 E-value=7.3e-18 Score=110.09 Aligned_cols=66 Identities=18% Similarity=0.364 Sum_probs=59.8
Q ss_pred HHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEE
Q 033666 27 SRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHV 99 (114)
Q Consensus 27 ~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v 99 (114)
+.|++|++|++.++|.+||.+.|.|+|||.||||||++|.|... ...+..+|.++|||+.|+.++.
T Consensus 7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~-------~~~~~~ig~~vIrgnsiv~~ea 72 (77)
T KOG1780|consen 7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNG-------DGDKNNIGMVVIRGNSIVMVEA 72 (77)
T ss_pred chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecC-------cCCcceeeeEEEeccEEEEEee
Confidence 38999999999999999999999999999999999999999643 2357889999999999998853
No 20
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.73 E-value=5.6e-19 Score=130.72 Aligned_cols=78 Identities=32% Similarity=0.520 Sum_probs=70.2
Q ss_pred HHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCC---CCCCCceEeeeEEEEcCCCEEEEEEccC
Q 033666 26 ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRT---SPSPMEQRCLGIILIPSSCRTSCHVDCS 102 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~---~~~~~~~r~lG~vlIrG~~Iv~I~v~~~ 102 (114)
...|.+++|.+++|+++|||+|+|.|.+||+||||+|.||+|++..+.+ ....+++|.+|++++||.||++..++..
T Consensus 6 sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegp 85 (177)
T KOG3168|consen 6 SSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGP 85 (177)
T ss_pred hhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCC
Confidence 4578999999999999999999999999999999999999999987653 3567789999999999999999999854
Q ss_pred h
Q 033666 103 I 103 (114)
Q Consensus 103 ~ 103 (114)
+
T Consensus 86 p 86 (177)
T KOG3168|consen 86 P 86 (177)
T ss_pred C
Confidence 3
No 21
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.71 E-value=4.8e-17 Score=110.11 Aligned_cols=70 Identities=23% Similarity=0.255 Sum_probs=59.9
Q ss_pred CchHHHHHHhcCCeEEEEEc--C--CeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 23 SNHISRVRKLLCRRMLVGIK--D--GRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 23 ~~~~~~L~~~l~k~V~V~L~--d--GR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
..|...+..|+..+.+|.+. | +|.|.|+|.|||+||||+|+||+|++.. ....+.+|.++|||++|+.|+
T Consensus 13 ~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~------~~~~~~lG~ilIRGnnV~~I~ 86 (89)
T PTZ00138 13 TQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK------KNTRKDLGRILLKGDNITLIM 86 (89)
T ss_pred cCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC------CceeeEcCeEEEcCCEEEEEE
Confidence 56889999999987766664 5 6999999999999999999999997642 235789999999999999985
No 22
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.70 E-value=9.3e-17 Score=105.19 Aligned_cols=70 Identities=19% Similarity=0.148 Sum_probs=60.7
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEc
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVD 100 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~ 100 (114)
|...|+++.|++|.|.|++|+.+.|+|.+||.|||++|.||.|.... +.....+|.++|||++|.+|.+.
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~------g~~~~~~~~v~IRG~~I~~i~~p 71 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKD------GDKFWKMPECYIRGNTIKYLRVP 71 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCC------CcEeeeCCcEEEeCCEEEEEEcC
Confidence 67889999999999999999999999999999999999999986322 22335679999999999999743
No 23
>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=99.70 E-value=1.4e-16 Score=102.90 Aligned_cols=68 Identities=16% Similarity=0.093 Sum_probs=59.9
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEE
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHV 99 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v 99 (114)
|...|+++.|++|.|.|+||++|.|+|.++|.+||+.|.||.+.... .....+|.++|||++|..|.+
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~-------g~~~~~~~v~IRG~nI~~v~l 68 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARD-------GRVSQLEQVYIRGSKIRFFIL 68 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCC-------CcEeEcCcEEEeCCEEEEEEe
Confidence 45789999999999999999999999999999999999999885322 135678999999999999975
No 24
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.67 E-value=7.4e-18 Score=115.39 Aligned_cols=85 Identities=22% Similarity=0.266 Sum_probs=72.1
Q ss_pred CCCchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCC-CCCCceEeeeEEEEcCCCEEEEEE
Q 033666 21 KGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTS-PSPMEQRCLGIILIPSSCRTSCHV 99 (114)
Q Consensus 21 ~~~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~-~~~~~~r~lG~vlIrG~~Iv~I~v 99 (114)
++.+++-.|.+|++++|+|++.+||...|+|.|||+.|||||.||+||...++.. .-..+.|.+|++++||..++.|..
T Consensus 14 ~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp 93 (108)
T KOG1781|consen 14 PKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISP 93 (108)
T ss_pred cchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcC
Confidence 4567788999999999999999999999999999999999999999997665432 234456999999999999999976
Q ss_pred ccChhh
Q 033666 100 DCSIDE 105 (114)
Q Consensus 100 ~~~~~e 105 (114)
..-.++
T Consensus 94 ~dG~e~ 99 (108)
T KOG1781|consen 94 ADGSEE 99 (108)
T ss_pred Ccchhh
Confidence 555444
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=99.66 E-value=7.5e-16 Score=104.20 Aligned_cols=72 Identities=15% Similarity=0.116 Sum_probs=63.5
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEccCh
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDCSI 103 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~~~~ 103 (114)
...+|+++.|++|.|.|++|+.|.|+|.++|.+||+.|+||.|+... .....+|.++|||++|.+|.+-..+
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~-------~~~~~~~~v~IRG~nI~yi~lPd~l 73 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG-------RNPVPLDTLSIRGNNIRYFILPDSL 73 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC-------CceeEcceEEEeCCEEEEEEcCCcC
Confidence 45689999999999999999999999999999999999999987432 2467899999999999999876554
No 26
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.64 E-value=2e-16 Score=106.93 Aligned_cols=82 Identities=27% Similarity=0.418 Sum_probs=69.1
Q ss_pred HHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEE-EEccChhh
Q 033666 27 SRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSC-HVDCSIDE 105 (114)
Q Consensus 27 ~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I-~v~~~~~e 105 (114)
.-|..|++++|.|.+.|||+++|.|.|||+..||+|++|.|+.... ....+.-.+|+++|||+||..| ++|.+.+.
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~---~~gv~q~~lGlyiirgeNva~ig~iDEe~d~ 79 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSE---TEGVEQIVLGLYIIRGENVAVIGEIDEELDS 79 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhh---hcchhheeeEEEEEecCccceeeecchhhhh
Confidence 4689999999999999999999999999999999999999965432 2456778899999999999999 66666666
Q ss_pred hhcccc
Q 033666 106 QLSLLK 111 (114)
Q Consensus 106 ~~~~l~ 111 (114)
.++|=|
T Consensus 80 ~ld~tk 85 (96)
T KOG1784|consen 80 RLDLTK 85 (96)
T ss_pred hhhhhh
Confidence 665543
No 27
>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=99.62 E-value=3.6e-15 Score=98.45 Aligned_cols=70 Identities=16% Similarity=0.148 Sum_probs=61.0
Q ss_pred CchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEE
Q 033666 23 SNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHV 99 (114)
Q Consensus 23 ~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v 99 (114)
+.....|+.+.|+.|.|.|++|..|.|+|.++|.+||+.|+||.+.... .....+|.++|||++|.+|.+
T Consensus 8 ~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~-------~~~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 8 NTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN-------GKQVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred chHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC-------CceeECCcEEEECCEEEEEEc
Confidence 4456788999999999999999999999999999999999999876422 245579999999999999874
No 28
>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=99.60 E-value=8.6e-15 Score=97.11 Aligned_cols=71 Identities=17% Similarity=0.178 Sum_probs=59.6
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEc
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVD 100 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~ 100 (114)
+..+|+++.|++|.|.|++|..|.|+|.++|.+||++|+||.+..... ......+|.++|||++|..|.+.
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~-----~~~~~~~~~v~IRG~~I~~I~lp 72 (81)
T cd01725 2 FFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEK-----YPHMLSVKNCFIRGSVVRYVQLP 72 (81)
T ss_pred hhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCC-----cccccccCeEEEECCEEEEEEeC
Confidence 356889999999999999999999999999999999999998764221 11234569999999999999754
No 29
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.57 E-value=8.8e-15 Score=95.45 Aligned_cols=68 Identities=26% Similarity=0.287 Sum_probs=63.1
Q ss_pred CchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEE
Q 033666 23 SNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSC 97 (114)
Q Consensus 23 ~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I 97 (114)
-.|.++|+.+.++.|.|+|+.|.+|.|+|.+.|.+|||.|.+|+|++.. ...-.+|-++||++||..|
T Consensus 7 vNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-------~~~g~lGEilIRCNNvlyi 74 (79)
T KOG3482|consen 7 VNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-------VSTGNLGEILIRCNNVLYI 74 (79)
T ss_pred CCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc-------cccccceeEEEEeccEEEE
Confidence 4788999999999999999999999999999999999999999998743 4577899999999999998
No 30
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.56 E-value=1.2e-15 Score=101.75 Aligned_cols=77 Identities=18% Similarity=0.279 Sum_probs=66.3
Q ss_pred CchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCC------CCceEeeeEEEEcCCCEEE
Q 033666 23 SNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPS------PMEQRCLGIILIPSSCRTS 96 (114)
Q Consensus 23 ~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~------~~~~r~lG~vlIrG~~Iv~ 96 (114)
.+|...|+-+++.+|.|+++++|.+.|+|+|||+|.|++|+|++|....-+.+.. ...+|.+.++||||++|+.
T Consensus 4 ~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vil 83 (91)
T KOG3460|consen 4 EEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVIL 83 (91)
T ss_pred cccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEE
Confidence 4678999999999999999999999999999999999999999998765432222 2467899999999999998
Q ss_pred EEE
Q 033666 97 CHV 99 (114)
Q Consensus 97 I~v 99 (114)
|+.
T Consensus 84 vsp 86 (91)
T KOG3460|consen 84 VSP 86 (91)
T ss_pred EcC
Confidence 853
No 31
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.53 E-value=2.3e-15 Score=98.14 Aligned_cols=73 Identities=21% Similarity=0.268 Sum_probs=66.1
Q ss_pred CCchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEcc
Q 033666 22 GSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDC 101 (114)
Q Consensus 22 ~~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~~ 101 (114)
++.+.++|.+++|++|.|+|.+|-.|.|+|.|.|.+|||-|+.++|+... ..++.+|.+||||++|..|+.++
T Consensus 4 ~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ng-------ql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 4 GSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNG-------QLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred ccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcC-------cccccccceeeccccEEEEEecc
Confidence 35678999999999999999999999999999999999999999998743 47889999999999999997653
No 32
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.44 E-value=1.1e-14 Score=103.10 Aligned_cols=76 Identities=20% Similarity=0.318 Sum_probs=64.2
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEE-EEccCh
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSC-HVDCSI 103 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I-~v~~~~ 103 (114)
....|..++++++.|.|.|||.+.|.|++||+|.|++|.+|+|+..-.. .--.+..|+.+|||.||+.+ +++...
T Consensus 10 ~t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~----~Y~di~~glfiIRGENVvllGeid~dk 85 (129)
T KOG1782|consen 10 FTTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN----KYCDIPRGLFIIRGENVVLLGEIDLDK 85 (129)
T ss_pred chhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc----eecccCceEEEEecCcEEEEecCCcch
Confidence 3455999999999999999999999999999999999999999765432 12345679999999999999 666665
Q ss_pred h
Q 033666 104 D 104 (114)
Q Consensus 104 ~ 104 (114)
+
T Consensus 86 E 86 (129)
T KOG1782|consen 86 E 86 (129)
T ss_pred h
Confidence 5
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.38 E-value=6.1e-13 Score=87.61 Aligned_cols=76 Identities=20% Similarity=0.248 Sum_probs=66.9
Q ss_pred CCCCCchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 19 DTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 19 ~~~~~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
+|++.-|...+.+.+|.++.|.++..|+|.|+|.|||.|.|++|.|+.||...++ ......++.+++.|++|...-
T Consensus 2 n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e----gr~~tk~~~iLLnGNni~mLv 77 (84)
T KOG1775|consen 2 NPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE----GRRMTKLDQILLNGNNITMLV 77 (84)
T ss_pred ChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC----cceeeeeeeeeecCCcEEEEe
Confidence 5677888999999999999999999999999999999999999999999976643 335567999999999997653
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.13 E-value=4.8e-11 Score=79.47 Aligned_cols=70 Identities=27% Similarity=0.286 Sum_probs=57.5
Q ss_pred CchHHHHHHhcCCeEEEEE----cCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 23 SNHISRVRKLLCRRMLVGI----KDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 23 ~~~~~~L~~~l~k~V~V~L----~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
-.|+..+-.||..+.+|.+ +=|-.+.|.+.|||++||+||++|+|..... ...+.+|.+++.||||..|.
T Consensus 11 v~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~------~~rk~lGRilLKGDnItli~ 84 (88)
T KOG1774|consen 11 VQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT------KSRKELGRILLKGDNITLIQ 84 (88)
T ss_pred cCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc------cCCCccccEEEcCCcEEEEe
Confidence 3577788888888877776 3488899999999999999999999965322 23458999999999999884
No 35
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.55 E-value=6.8e-07 Score=60.54 Aligned_cols=71 Identities=17% Similarity=0.182 Sum_probs=58.4
Q ss_pred HHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEcc
Q 033666 26 ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDC 101 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~~ 101 (114)
.++.+.++|++|.|.|+++-.+.|+|.++|++.||-|.|..-....+ -..--.+..++|||+.|-.|.+..
T Consensus 4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~k-----yPhm~Sv~ncfIRGSvvrYv~l~k 74 (96)
T KOG3448|consen 4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDK-----YPHMLSVKNCFIRGSVVRYVQLPK 74 (96)
T ss_pred HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCccc-----CCCeeeeeeEEEeccEEEEEEeCh
Confidence 46788999999999999999999999999999999999876543211 123456788999999999997764
No 36
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.36 E-value=8.3e-08 Score=67.10 Aligned_cols=65 Identities=14% Similarity=0.263 Sum_probs=55.2
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCC----C--CCCceEeeeEEEEcCCCEEEEE
Q 033666 34 CRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTS----P--SPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 34 ~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~----~--~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
...|.|.+.|++.+.|+..|||.|+|++|.++.|.+...+++ + .-...|++|.++||||.|+.+.
T Consensus 36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~ 106 (114)
T KOG3459|consen 36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVL 106 (114)
T ss_pred CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEE
Confidence 567889999999999999999999999999999998776443 1 1234789999999999999875
No 37
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.17 E-value=1.9e-05 Score=55.22 Aligned_cols=67 Identities=21% Similarity=0.230 Sum_probs=57.4
Q ss_pred HHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEc
Q 033666 26 ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVD 100 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~ 100 (114)
..+|+++.+.++.|.|++|++..|++.++|.+||..|.++.=... .++..+-.+.|||++|-++..-
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~--------~~pv~l~~lsirgnniRy~~lp 70 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK--------GEPVRLDTLSIRGNNIRYYILP 70 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC--------CCceeEEEEEeecceEEEEEcc
Confidence 568999999999999999999999999999999999998764321 1456788999999999988654
No 38
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=98.08 E-value=9.8e-06 Score=57.88 Aligned_cols=71 Identities=15% Similarity=0.138 Sum_probs=59.2
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEcc
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDC 101 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~~ 101 (114)
|...|+..-++.+.|.|++|-+|.|.|...|..|||-|.++.++..+.+ .--.+.-+.|||..|.++.+..
T Consensus 3 PLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd------kf~r~pEcYirGttIkylri~d 73 (134)
T KOG3293|consen 3 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGD------KFFRMPECYIRGTTIKYLRIPD 73 (134)
T ss_pred chhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCC------ceeecceeEEecceeEEEeccH
Confidence 5567778889999999999999999999999999999999999865432 2334567999999999997653
No 39
>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=98.06 E-value=3.7e-06 Score=54.03 Aligned_cols=37 Identities=27% Similarity=0.199 Sum_probs=30.2
Q ss_pred CeEEEEEcC----CeEEEEEEEEecCccceEecccEEEeec
Q 033666 35 RRMLVGIKD----GRFFLGSFHCIDKQGNIILQDAVEYRST 71 (114)
Q Consensus 35 k~V~V~L~d----GR~i~G~L~~~D~~~NLvLsda~E~~~~ 71 (114)
.+|+|.+.. +-.++|.|.+||+|+||+|.|+.|.+..
T Consensus 9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 677777753 2278999999999999999999997643
No 40
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.94 E-value=1.3e-05 Score=51.91 Aligned_cols=70 Identities=17% Similarity=0.358 Sum_probs=41.4
Q ss_pred HHHHHHhcCCeEEEEEcCCeEEEEEEEEecC---ccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEE
Q 033666 26 ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDK---QGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRT 95 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~---~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv 95 (114)
...+..++|++|.|+++||..|.|.|.+++. .+.++|.-+........+............++|+++.|+
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 3457889999999999999999999999998 889999877764322110011112344566777777665
No 41
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=97.61 E-value=0.00025 Score=49.68 Aligned_cols=68 Identities=16% Similarity=0.066 Sum_probs=57.6
Q ss_pred chHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 24 NHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 24 ~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
-|+..|+..=+.-|.+.+..|-+|.|.|+-.+..||+.|.|..-.... -....+-.|+|||+.|-.+-
T Consensus 5 vpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d-------g~vs~le~V~IRGS~IRFlv 72 (119)
T KOG3172|consen 5 VPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD-------GRVSQLEQVFIRGSKIRFLV 72 (119)
T ss_pred cceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC-------CcceeeeeEEEecCeEEEEE
Confidence 355667778889999999999999999999999999999998875432 24667899999999998774
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.04 E-value=0.0027 Score=43.47 Aligned_cols=75 Identities=15% Similarity=0.155 Sum_probs=55.6
Q ss_pred HHhcCCeEEEEEcCCeEEEEEEEEecC-ccceEecccEEEeecCCCC--CCCCceEeeeEEEEcCCCEEEEEEccChh
Q 033666 30 RKLLCRRMLVGIKDGRFFLGSFHCIDK-QGNIILQDAVEYRSTRRTS--PSPMEQRCLGIILIPSSCRTSCHVDCSID 104 (114)
Q Consensus 30 ~~~l~k~V~V~L~dGR~i~G~L~~~D~-~~NLvLsda~E~~~~~~~~--~~~~~~r~lG~vlIrG~~Iv~I~v~~~~~ 104 (114)
.+|||++|.+..+++-.|+|+|...|. ...|.|.++.-+-...... .-......+.-++.||..|..+.+...+.
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~ 81 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP 81 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence 469999999999999999999999995 8899999988764322100 11123345789999999999998775543
No 43
>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=96.80 E-value=0.0049 Score=46.11 Aligned_cols=63 Identities=19% Similarity=0.195 Sum_probs=44.4
Q ss_pred HHHHHhcCCeEEEEEcCCeEEEEEEEEec-CccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEccCh
Q 033666 27 SRVRKLLCRRMLVGIKDGRFFLGSFHCID-KQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDCSI 103 (114)
Q Consensus 27 ~~L~~~l~k~V~V~L~dGR~i~G~L~~~D-~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~~~~ 103 (114)
.....|++|.|+|++.| +++.|.+.++| -..||||-+-.| ...+ ..-+|.|..|..|++....
T Consensus 10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e-----------~~~~--sv~~I~ghaVk~vevl~~~ 73 (166)
T PF06372_consen 10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE-----------DGKR--SVKVIMGHAVKSVEVLSEG 73 (166)
T ss_dssp HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T-----------TS-E--EEEEE-GGGEEEEEEEE--
T ss_pred HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc-----------CCce--eEEEEEccceEEEEEccCC
Confidence 46789999999999999 99999999999 567888874433 1222 4588999999999876543
No 44
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.73 E-value=0.0067 Score=36.04 Aligned_cols=35 Identities=17% Similarity=0.192 Sum_probs=30.1
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEecccEE
Q 033666 32 LLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVE 67 (114)
Q Consensus 32 ~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E 67 (114)
.+|++|++.+ ++..+.|++.++|.+..|++.....
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 4799999999 6666799999999999999976554
No 45
>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=96.09 E-value=0.06 Score=35.85 Aligned_cols=65 Identities=12% Similarity=0.126 Sum_probs=45.9
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecC-ccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEcc
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDK-QGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDC 101 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~-~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~~ 101 (114)
....|..+.|+.+.+.|.++..+.|+|.|.|. ..|+..++ -+ ++ -......++|++.|+++..++
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~-L~---TP--------lGv~~eAlLR~~DVi~~~f~~ 80 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSN-LQ---TP--------LGVQPEALLRCSDVISISFDA 80 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEE-EE---TT--------TTEEEEEEEEGGGEEEEEE--
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhh-cC---CC--------cccChhheeecCCEEEEEecC
Confidence 34567888999999999999999999999995 45555442 22 11 122578999999999998764
No 46
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=96.02 E-value=0.067 Score=35.19 Aligned_cols=67 Identities=13% Similarity=0.197 Sum_probs=50.1
Q ss_pred HHhcCCeEEEEEcCCeEEEEEEEEec-CccceEecccEEEeecCCCCC---CCCceEeeeEEEEcCCCEEE
Q 033666 30 RKLLCRRMLVGIKDGRFFLGSFHCID-KQGNIILQDAVEYRSTRRTSP---SPMEQRCLGIILIPSSCRTS 96 (114)
Q Consensus 30 ~~~l~k~V~V~L~dGR~i~G~L~~~D-~~~NLvLsda~E~~~~~~~~~---~~~~~r~lG~vlIrG~~Iv~ 96 (114)
.+|+|+++.+.-+.+-.|+|.|..+| ...-|-|.|+..+-....+.. .......+..++.||+.|..
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 36899999999999999999999999 556677999887644332111 12244567889999998864
No 47
>PRK14638 hypothetical protein; Provisional
Probab=95.75 E-value=0.053 Score=39.62 Aligned_cols=54 Identities=22% Similarity=0.255 Sum_probs=43.4
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs 63 (114)
.+.+.=+|.+-+-+ .........++|++|+|++.+++.|+|+|.++|.. ++.|.
T Consensus 75 ~Y~LEVSSPGldRp-L~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 75 SYTLEVSSPGLDRP-LRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred ceEEEEeCCCCCCC-CCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 45566677777766 56677888999999999999999999999999964 55553
No 48
>PRK02001 hypothetical protein; Validated
Probab=95.28 E-value=0.087 Score=38.74 Aligned_cols=54 Identities=24% Similarity=0.275 Sum_probs=42.0
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs 63 (114)
.+.+.=+|.+-+-+ .........|+|+.|+|++.+++.|.|+|.++|.. ++.|.
T Consensus 65 ~Y~LEVSSPGldRp-L~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 65 DFELEVGSAGLTSP-LKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred CeEEEEeCCCCCCc-CCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence 44555566666655 45566778999999999999999999999999976 55553
No 49
>PRK14639 hypothetical protein; Provisional
Probab=95.21 E-value=0.13 Score=37.23 Aligned_cols=54 Identities=24% Similarity=0.293 Sum_probs=42.3
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs 63 (114)
.+++-=+|.+-+-+ .......+.|+|+.|+|++.+++.|.|+|.++|.. ++.|.
T Consensus 63 ~Y~LEVSSPGl~Rp-L~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 63 EYFLEVSSPGLERK-LSKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred CeEEEEeCCCCCCc-CCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 44555566666665 55567888999999999999999999999999985 55553
No 50
>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=95.16 E-value=0.15 Score=33.43 Aligned_cols=50 Identities=22% Similarity=0.361 Sum_probs=38.8
Q ss_pred eeecccCCCCCCCchHHHHHHhcCCeEEEEEc---CC-eEEEEEEEEecCccceEe
Q 033666 11 LVESSAGSDTKGSNHISRVRKLLCRRMLVGIK---DG-RFFLGSFHCIDKQGNIIL 62 (114)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~---dG-R~i~G~L~~~D~~~NLvL 62 (114)
+--+|++-+.+ .........++|+.|.|++. +| +.|.|.|.++|.. +++|
T Consensus 3 LEVSSPGl~Rp-L~~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 3 LEVSSPGAERP-LKKEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred EEEcCCCCCCc-CCCHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 33456666666 56677888999999999997 55 5999999999985 4544
No 51
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=94.38 E-value=0.12 Score=32.78 Aligned_cols=36 Identities=6% Similarity=0.034 Sum_probs=31.2
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEecccEE
Q 033666 32 LLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVE 67 (114)
Q Consensus 32 ~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E 67 (114)
.+|.+|++++-.|-.|.|.+.|||...++++-.|.+
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 478999999999999999999999888887655554
No 52
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=94.09 E-value=0.38 Score=30.90 Aligned_cols=53 Identities=15% Similarity=0.215 Sum_probs=40.6
Q ss_pred HHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 26 ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
.+.|++++|+++.|.+..|+. .|+|.+.-.. .|+|+.+. ...+||=.+|++|.
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~~------------------~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEENG------------------TPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeCC------------------cEEEEEeeeEEEEc
Confidence 568999999999999988887 9999998766 55554331 34567777777663
No 53
>PRK14633 hypothetical protein; Provisional
Probab=93.53 E-value=0.45 Score=34.71 Aligned_cols=55 Identities=20% Similarity=0.206 Sum_probs=41.5
Q ss_pred eeeeeeecccCCCCCCCchHHHHHHhcCCeEEEEE----cCCeEEEEEEEEecCccceEec
Q 033666 7 TTETLVESSAGSDTKGSNHISRVRKLLCRRMLVGI----KDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L----~dGR~i~G~L~~~D~~~NLvLs 63 (114)
..+.+-=+|++=+-+ .........|+|++|+|++ .+++.|.|+|.+++.. ++.|.
T Consensus 68 ~~Y~LEVSSPGldRp-L~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 68 GKYILEVSSPGMNRQ-IFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred CCeEEEEeCCCCCCC-CCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 344555566666666 5666788899999999999 4778999999999875 55553
No 54
>PRK14640 hypothetical protein; Provisional
Probab=93.14 E-value=1.1 Score=32.77 Aligned_cols=54 Identities=22% Similarity=0.269 Sum_probs=41.1
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEE----cCCeEEEEEEEEecCccceEec
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGI----KDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L----~dGR~i~G~L~~~D~~~NLvLs 63 (114)
.+.+-=+|.+=+-+ ........+++|+.|+|++ .+++.|.|+|.++|.. ++.|.
T Consensus 72 ~Y~LEVSSPGl~Rp-L~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 72 EYYLEVSSPGLDRP-LFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred CeEEEEeCCCCCCc-CCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 34555566666666 5556778899999999999 5779999999999875 55554
No 55
>PRK14636 hypothetical protein; Provisional
Probab=93.10 E-value=0.62 Score=34.93 Aligned_cols=53 Identities=21% Similarity=0.292 Sum_probs=38.9
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEc---CC-eEEEEEEEEecCccceEe
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIK---DG-RFFLGSFHCIDKQGNIIL 62 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~---dG-R~i~G~L~~~D~~~NLvL 62 (114)
.+.+-=+|.+=+-+ .........|+|+.|+|+++ +| +.|+|+|.++|.. ++.|
T Consensus 73 ~Y~LEVSSPGldRp-L~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 73 AYRLEVSSPGIDRP-LTRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred CeEEEEeCCCCCCC-CCCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 34454455555555 44567788999999999997 55 6999999999885 4554
No 56
>PRK14632 hypothetical protein; Provisional
Probab=93.07 E-value=0.62 Score=34.75 Aligned_cols=81 Identities=14% Similarity=0.167 Sum_probs=53.2
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEcC-------CeEEEEEEEEecCccceEecccEEEeecCCCCCCCCc
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKD-------GRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPME 80 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~d-------GR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~ 80 (114)
.+.+.=+|.+=+-+ .........|+|+.|+|++.+ .+.|.|+|.++|.. ++.|.. + ...+ .
T Consensus 73 ~Y~LEVSSPGldRp-L~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~~--~---~~~~-----~ 140 (172)
T PRK14632 73 AYVLEVSSPGLERP-FFRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLRP--E---GAPA-----P 140 (172)
T ss_pred CeEEEEeCCCCCCc-CCCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEEE--c---Cccc-----c
Confidence 34555566666666 566678889999999999975 67999999999864 555541 1 0000 0
Q ss_pred eEeeeEEEEcCCCEEEEEEc
Q 033666 81 QRCLGIILIPSSCRTSCHVD 100 (114)
Q Consensus 81 ~r~lG~vlIrG~~Iv~I~v~ 100 (114)
...-+.+-||-+.|..+.+.
T Consensus 141 ~~~~~~~~i~~~~I~ka~l~ 160 (172)
T PRK14632 141 EAEEAVLRTSWQGVRKANLI 160 (172)
T ss_pred cCCceeEEEEhHHccEEEEE
Confidence 00123566778888777543
No 57
>PRK14645 hypothetical protein; Provisional
Probab=92.92 E-value=0.49 Score=34.77 Aligned_cols=53 Identities=13% Similarity=0.161 Sum_probs=39.9
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs 63 (114)
.+.+-=+|.+=+-+ ........+++|+.|.|++ +++.|.|+|.++|.. ++.|.
T Consensus 77 ~Y~LEVSSPGldRp-L~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l~ 129 (154)
T PRK14645 77 EYRLEVESPGPKRP-LFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTFD 129 (154)
T ss_pred ceEEEEeCCCCCCC-CCCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEEE
Confidence 34455556665555 5566778899999999986 899999999999875 45553
No 58
>PRK14644 hypothetical protein; Provisional
Probab=92.85 E-value=0.8 Score=32.99 Aligned_cols=52 Identities=19% Similarity=0.264 Sum_probs=38.2
Q ss_pred eeeeecccCCCCCCCchHHHHHHhcCCeEEEEEcCC----eEEEEEEEEecCccceEec
Q 033666 9 ETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDG----RFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~dG----R~i~G~L~~~D~~~NLvLs 63 (114)
+.+-=+|.+-+-+ ... ..+..++|+.|+|++.+. +.|.|.|.++|.. ++.|.
T Consensus 62 Y~LEVSSPGldRp-L~~-~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 62 DSLDISSPGFDMD-YET-DELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred eEEEEECCCCCCC-CCH-HHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 3444445554444 223 489999999999999876 8999999999974 56654
No 59
>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=92.73 E-value=0.49 Score=33.66 Aligned_cols=52 Identities=25% Similarity=0.333 Sum_probs=34.0
Q ss_pred eeeeecccCCCCCCCchHHHHHHhcCCeEEEEE----cCCeEEEEEEEEecCccceEe
Q 033666 9 ETLVESSAGSDTKGSNHISRVRKLLCRRMLVGI----KDGRFFLGSFHCIDKQGNIIL 62 (114)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L----~dGR~i~G~L~~~D~~~NLvL 62 (114)
+.+-=+|.+-+-+ ......+..|+|+.|.|++ .+.+.|.|+|.++|.. +++|
T Consensus 63 y~LEVSSPG~~r~-L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~-~i~l 118 (141)
T PF02576_consen 63 YTLEVSSPGIDRP-LKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDED-EITL 118 (141)
T ss_dssp EEEEEE--SSSS---SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEETT-EEEE
T ss_pred eEEEEeCCCCCCc-CCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeCC-EEEE
Confidence 3444455554444 4556788999999999999 4567999999999993 5665
No 60
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=92.21 E-value=0.78 Score=33.28 Aligned_cols=49 Identities=24% Similarity=0.341 Sum_probs=39.2
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEE----cCCeEEEEEEEEecCc
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGI----KDGRFFLGSFHCIDKQ 57 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L----~dGR~i~G~L~~~D~~ 57 (114)
.+.+-=+|++-+-+ ......+..++|+.|+|++ .+++.|.|+|..+|..
T Consensus 73 ~Y~LEVSSPGi~Rp-L~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 73 AYTLEVSSPGLDRP-LKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred CeEEEEeCCCCCCc-CCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 34555566666666 5666788999999999997 6788999999999984
No 61
>PRK14642 hypothetical protein; Provisional
Probab=92.10 E-value=0.53 Score=36.10 Aligned_cols=47 Identities=17% Similarity=0.256 Sum_probs=36.7
Q ss_pred cccCCCCCCCchHHHHHHhcCCeEEEEEc-------------CCeEEEEEEEEecCccceEe
Q 033666 14 SSAGSDTKGSNHISRVRKLLCRRMLVGIK-------------DGRFFLGSFHCIDKQGNIIL 62 (114)
Q Consensus 14 ~~~~~~~~~~~~~~~L~~~l~k~V~V~L~-------------dGR~i~G~L~~~D~~~NLvL 62 (114)
+|++=|-+ .........|+|+.|.|+|. +++.|.|+|.++|.. ++.|
T Consensus 81 SSPGldRP-Lk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 81 SSPGIDRP-LRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred eCCCCCCC-CCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 44444444 55577889999999999998 679999999999985 4444
No 62
>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=92.08 E-value=0.38 Score=30.46 Aligned_cols=33 Identities=12% Similarity=0.142 Sum_probs=27.5
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEecccE
Q 033666 34 CRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAV 66 (114)
Q Consensus 34 ~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~ 66 (114)
+..|.|-|.+|-.+.|.+.+||+|+=|+-.+..
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~g~ 43 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFDNFTVLLESDGK 43 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEcceEEEEEECCc
Confidence 567888999999999999999999877755443
No 63
>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=92.05 E-value=0.38 Score=30.49 Aligned_cols=32 Identities=13% Similarity=0.109 Sum_probs=27.0
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEeccc
Q 033666 34 CRRMLVGIKDGRFFLGSFHCIDKQGNIILQDA 65 (114)
Q Consensus 34 ~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda 65 (114)
+..|.|-|.+|-.+.|.+.|||+|+=|+-.+.
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~g 46 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQG 46 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEEEECC
Confidence 46788889999999999999999987775544
No 64
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.69 E-value=1.4 Score=32.46 Aligned_cols=47 Identities=19% Similarity=0.343 Sum_probs=36.6
Q ss_pred cccCCCCCCCchHHHHHHhcCCeEEEEE----cCCeEEEEEEEEecCccceEe
Q 033666 14 SSAGSDTKGSNHISRVRKLLCRRMLVGI----KDGRFFLGSFHCIDKQGNIIL 62 (114)
Q Consensus 14 ~~~~~~~~~~~~~~~L~~~l~k~V~V~L----~dGR~i~G~L~~~D~~~NLvL 62 (114)
+|.+=+-+ .........|+|+.|.|+| .+++.+.|+|.++|..+ +++
T Consensus 80 SSPGldRp-L~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 80 SSPGLDRP-LKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred eCCCCCCC-cCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 33333333 4556788999999999999 89999999999999986 444
No 65
>PRK14634 hypothetical protein; Provisional
Probab=91.51 E-value=1.1 Score=32.85 Aligned_cols=54 Identities=13% Similarity=0.075 Sum_probs=39.7
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEcC----CeEEEEEEEEecCccceEec
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKD----GRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~d----GR~i~G~L~~~D~~~NLvLs 63 (114)
.+.+-=+|.+-+-+ .........|+|+.|+|++.+ .+.|.|+|.++|.. ++.|.
T Consensus 75 ~Y~LEVSSPGldRp-L~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14634 75 AYVLEISSPGIGDQ-LSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQIN 132 (155)
T ss_pred CeEEEEeCCCCCCc-CCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence 34555556666655 555677889999999999963 37999999999975 55553
No 66
>PRK14643 hypothetical protein; Provisional
Probab=90.59 E-value=1.8 Score=32.10 Aligned_cols=44 Identities=18% Similarity=0.200 Sum_probs=33.5
Q ss_pred cccCCCCCCCchHHHHHHhcCCeEEEEEcC----CeEEEEEEEEecCcc
Q 033666 14 SSAGSDTKGSNHISRVRKLLCRRMLVGIKD----GRFFLGSFHCIDKQG 58 (114)
Q Consensus 14 ~~~~~~~~~~~~~~~L~~~l~k~V~V~L~d----GR~i~G~L~~~D~~~ 58 (114)
+|.+-+-+ .........|+|+.|+|++.+ .+.|.|+|.++|...
T Consensus 85 SSPGleRp-L~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~ 132 (164)
T PRK14643 85 SSSGIEKQ-IRSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNT 132 (164)
T ss_pred cCCCCCCC-CCCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCc
Confidence 44444444 445667889999999999964 689999999999763
No 67
>PRK14631 hypothetical protein; Provisional
Probab=90.54 E-value=1.3 Score=33.17 Aligned_cols=52 Identities=17% Similarity=0.271 Sum_probs=38.6
Q ss_pred eeeeecccCCCCCCCchHHHHHHhcCCeEEEEEc----CCeEEEEEEEEec--CccceEe
Q 033666 9 ETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIK----DGRFFLGSFHCID--KQGNIIL 62 (114)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~----dGR~i~G~L~~~D--~~~NLvL 62 (114)
+.+-=+|.+=+-+ .........|+|+.|+|++. +.+.|.|+|.++| .. ++.|
T Consensus 93 Y~LEVSSPGldRp-L~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~-~v~l 150 (174)
T PRK14631 93 YALEVSSPGWDRP-FFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLENE-EIQV 150 (174)
T ss_pred eEEEEeCCCCCCc-CCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCCC-EEEE
Confidence 3444455555555 55677889999999999995 5689999999998 53 5554
No 68
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=90.51 E-value=0.61 Score=31.02 Aligned_cols=34 Identities=9% Similarity=0.088 Sum_probs=28.4
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEecccEE
Q 033666 34 CRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVE 67 (114)
Q Consensus 34 ~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E 67 (114)
+..|.|-|.+|-.+.|.+.|||+|+=|+-.+...
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~gkq 52 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNTGKS 52 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEccEEEEEEECCcE
Confidence 5678888999999999999999998777666543
No 69
>PRK14647 hypothetical protein; Provisional
Probab=90.30 E-value=1.5 Score=32.15 Aligned_cols=52 Identities=21% Similarity=0.214 Sum_probs=38.4
Q ss_pred eeeeecccCCCCCCCchHHHHHHhcCCeEEEEEc---------CCeEEEEEEEEecCccceEe
Q 033666 9 ETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIK---------DGRFFLGSFHCIDKQGNIIL 62 (114)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~---------dGR~i~G~L~~~D~~~NLvL 62 (114)
+.+.=+|.+=+-+ ......+..|+|+.|+|++. +.+.|.|+|.++|.. ++.|
T Consensus 75 Y~LEVSSPG~~Rp-L~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~-~v~l 135 (159)
T PRK14647 75 YTLEVSSPGLDRP-LKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG-VVTI 135 (159)
T ss_pred eEEEEcCCCCCCc-CCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC-EEEE
Confidence 4455556665555 45567888999999999995 358999999999964 4444
No 70
>PRK14637 hypothetical protein; Provisional
Probab=90.24 E-value=1.4 Score=32.27 Aligned_cols=52 Identities=15% Similarity=0.169 Sum_probs=37.4
Q ss_pred eeeecccCCCCCCCchHHHHHHhcCCeEEEEEcCCeEE-EEEEEEecCccceEec
Q 033666 10 TLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFF-LGSFHCIDKQGNIILQ 63 (114)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~dGR~i-~G~L~~~D~~~NLvLs 63 (114)
.+-=+|.+-+-+ .........++|+.|+|++.+.+.+ +|+|.++|.. ++.|.
T Consensus 75 ~LEVSSPGldRp-L~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 75 FLEVSSPGIERV-IKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred EEEEeCCCCCCC-CCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 444455555555 5557788999999999999544455 7999999886 55554
No 71
>PRK14646 hypothetical protein; Provisional
Probab=90.02 E-value=3.6 Score=30.14 Aligned_cols=54 Identities=15% Similarity=0.121 Sum_probs=39.0
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEcC----CeEEEEEEEEecCccceEec
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKD----GRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~d----GR~i~G~L~~~D~~~NLvLs 63 (114)
.+.+-=+|.+=+-+ .........|+|+.|+|++.+ .+.|.|+|.++|.. ++.|.
T Consensus 75 ~Y~LEVSSPGldRp-L~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 75 SYVLEISSQGVSDE-LTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred CeEEEEcCCCCCCc-CCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 34454455555555 455678899999999999953 36889999999986 55553
No 72
>PRK14641 hypothetical protein; Provisional
Probab=89.74 E-value=1.5 Score=32.87 Aligned_cols=47 Identities=17% Similarity=0.116 Sum_probs=36.6
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEcC----CeEEEEEEEEec
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKD----GRFFLGSFHCID 55 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~d----GR~i~G~L~~~D 55 (114)
.+.+.=+|.+=+-+ .........|+|+.|+|++.+ .+.|.|+|.++|
T Consensus 79 ~Y~LEVSSPGldRp-L~~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 79 DFDLMVSSPGLGEP-IILPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred CeEEEEeCCCCCCc-CCCHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 45555566665555 555778899999999999975 569999999996
No 73
>PRK06955 biotin--protein ligase; Provisional
Probab=87.73 E-value=2.3 Score=33.94 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=29.3
Q ss_pred HhcCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 033666 31 KLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 31 ~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs 63 (114)
-++|++|+|...+++.+.|++.|+|..+.|++.
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 368899999777788899999999999999985
No 74
>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=85.46 E-value=1.2 Score=33.20 Aligned_cols=37 Identities=16% Similarity=0.060 Sum_probs=32.3
Q ss_pred HHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccE
Q 033666 30 RKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAV 66 (114)
Q Consensus 30 ~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~ 66 (114)
-.+=+-.|+|.+.||.+|.|...||+.--|.||....
T Consensus 25 ~r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 25 WRFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred HHhcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 3455778999999999999999999999999988654
No 75
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=83.84 E-value=5.4 Score=33.33 Aligned_cols=74 Identities=15% Similarity=0.160 Sum_probs=56.8
Q ss_pred HHhcCCeEEEEEcCCeEEEEEEEEec-CccceEecccEEEeecCCCCCC----CCceEeeeEEEEcCCCEEEEEEccChh
Q 033666 30 RKLLCRRMLVGIKDGRFFLGSFHCID-KQGNIILQDAVEYRSTRRTSPS----PMEQRCLGIILIPSSCRTSCHVDCSID 104 (114)
Q Consensus 30 ~~~l~k~V~V~L~dGR~i~G~L~~~D-~~~NLvLsda~E~~~~~~~~~~----~~~~r~lG~vlIrG~~Iv~I~v~~~~~ 104 (114)
..|||++|.++=+..-.|+|+|.-+| +..=|-|.++.-+-+...++.+ ...+ .+--++.||+.|..+.|...+.
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~k-Vy~YIlFRGSDIKDL~V~~~p~ 83 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDK-VYDYILFRGSDIKDLIVQETPA 83 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCcc-ceeeEEecCcccceeeeccCcc
Confidence 46999999999999999999999999 7888999997655443332211 1122 6788999999999888776543
No 76
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=83.01 E-value=4.9 Score=35.28 Aligned_cols=32 Identities=22% Similarity=0.268 Sum_probs=29.1
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 033666 32 LLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 32 ~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs 63 (114)
++|++|++...+++.+.|+..|+|..+.|+|.
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 67999998777888899999999999999996
No 77
>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=82.86 E-value=1.3 Score=32.94 Aligned_cols=43 Identities=19% Similarity=0.193 Sum_probs=31.7
Q ss_pred cccCCCCCCCchHHHHHHh--cCCeEEEEEcCCeEEEEEEEEecC
Q 033666 14 SSAGSDTKGSNHISRVRKL--LCRRMLVGIKDGRFFLGSFHCIDK 56 (114)
Q Consensus 14 ~~~~~~~~~~~~~~~L~~~--l~k~V~V~L~dGR~i~G~L~~~D~ 56 (114)
+.+.-.||++-..+.-++. -++.|+|-+.|||+++|.=.|.|.
T Consensus 98 ~~q~~~psrrDFF~Icrka~qqg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 98 NNQPYKPSRRDFFSICRKAHQQGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred ccccCCCccchHHHHHHHHHHCCCeEEEEEcCCcEEEeeecccce
Confidence 3444456766556555444 378899999999999999888874
No 78
>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region. The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.
Probab=81.65 E-value=9.3 Score=29.14 Aligned_cols=33 Identities=21% Similarity=0.294 Sum_probs=28.1
Q ss_pred HHhcCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 033666 30 RKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 30 ~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs 63 (114)
.-++|++|.|...+ ..+.|++.|+|..+.|++.
T Consensus 189 ~~~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 189 SAHIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred hhccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 34679999998755 5689999999999999996
No 79
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=81.23 E-value=6.9 Score=30.49 Aligned_cols=37 Identities=22% Similarity=0.344 Sum_probs=33.3
Q ss_pred HHHhcCCeEEEEEcCCeEEEEEEEEecCccceEeccc
Q 033666 29 VRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDA 65 (114)
Q Consensus 29 L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda 65 (114)
...++|++|+++..++.++.|+..++|.++.|++...
T Consensus 185 ~~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 185 RSLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred HhccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 3456899999999999999999999999999999876
No 80
>PRK14630 hypothetical protein; Provisional
Probab=81.06 E-value=7.3 Score=28.16 Aligned_cols=52 Identities=13% Similarity=0.147 Sum_probs=38.4
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEe
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIIL 62 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvL 62 (114)
.+.+-=+|.+=|-+ .........|+|++|+|++.+. ...|+|.++|.. ++.|
T Consensus 72 ~Y~LEVSSPGldRp-L~~~~df~r~~G~~v~V~l~~~-~~~G~L~~~~d~-~i~l 123 (143)
T PRK14630 72 NFSLEISTPGINRK-IKSDREFKIFEGKKIKLMLDND-FEEGFILEAKAD-SFIF 123 (143)
T ss_pred CeEEEEeCCCCCCc-CCCHHHHHHhCCCEEEEEEcCc-ceEEEEEEEeCC-EEEE
Confidence 44555566666666 5566788899999999999654 469999999885 5554
No 81
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=80.42 E-value=7.9 Score=30.77 Aligned_cols=32 Identities=31% Similarity=0.422 Sum_probs=27.6
Q ss_pred HhcCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 033666 31 KLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 31 ~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs 63 (114)
-++|++|++...+ ..+.|++.|+|..+.|++.
T Consensus 269 ~~~g~~v~~~~~~-~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 269 LFLGREVKLIIGD-KEISGIARGIDEQGALLLE 300 (319)
T ss_pred cccCCeEEEEeCC-cEEEEEEEEECCCceEEEE
Confidence 3689999998754 5799999999999999995
No 82
>PRK14635 hypothetical protein; Provisional
Probab=80.06 E-value=12 Score=27.39 Aligned_cols=54 Identities=17% Similarity=0.134 Sum_probs=38.6
Q ss_pred eeeeeecccCCCCCCCchHHHHHHhcCCeEEEEEc--CCeEEEE---EEEEecCccceEec
Q 033666 8 TETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIK--DGRFFLG---SFHCIDKQGNIILQ 63 (114)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~L~~~l~k~V~V~L~--dGR~i~G---~L~~~D~~~NLvLs 63 (114)
.+.+-=+|.+-+-+ ......+..|+|+.|+|++. ++..+.| +|.++|.. ++.|.
T Consensus 74 ~Y~LEVSSPGldRp-L~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~ 132 (162)
T PRK14635 74 DFTLKVSSAGAERK-LRLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE 132 (162)
T ss_pred CeEEEEcCCCCCCc-CCCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence 34444455555555 55567788999999999985 5678887 99999875 55553
No 83
>PRK08330 biotin--protein ligase; Provisional
Probab=79.57 E-value=7.8 Score=29.59 Aligned_cols=34 Identities=29% Similarity=0.371 Sum_probs=28.1
Q ss_pred HHhcCCeEEEEEcCCeEE-EEEEEEecCccceEecc
Q 033666 30 RKLLCRRMLVGIKDGRFF-LGSFHCIDKQGNIILQD 64 (114)
Q Consensus 30 ~~~l~k~V~V~L~dGR~i-~G~L~~~D~~~NLvLsd 64 (114)
..+++++|++.. +++.+ .|++.|+|..+.|++..
T Consensus 184 ~~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 184 SMILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HHhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 357899999975 66665 69999999999999873
No 84
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=77.81 E-value=5.2 Score=31.79 Aligned_cols=31 Identities=16% Similarity=0.420 Sum_probs=27.3
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 033666 32 LLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 32 ~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs 63 (114)
++|+.|+|.. ++..+.|++.|+|..+.|++.
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~ 265 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLL 265 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEE
Confidence 3799999875 678999999999999999986
No 85
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=76.74 E-value=6.2 Score=29.61 Aligned_cols=42 Identities=10% Similarity=0.071 Sum_probs=31.4
Q ss_pred HHHHHhcC--CeEEEEEcCCeEEEEEEEEecCccceEecccEEE
Q 033666 27 SRVRKLLC--RRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEY 68 (114)
Q Consensus 27 ~~L~~~l~--k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~ 68 (114)
.+|..+-. ..|.|-|.+|-.+.|.+.+||+|+=|+-.+....
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~gkqq 138 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDGYVQ 138 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCCcEE
Confidence 34544443 4577778999999999999999987776665543
No 86
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=76.44 E-value=3.4 Score=24.33 Aligned_cols=23 Identities=22% Similarity=0.406 Sum_probs=15.4
Q ss_pred EEEEEEEecCccceEecccEEEe
Q 033666 47 FLGSFHCIDKQGNIILQDAVEYR 69 (114)
Q Consensus 47 i~G~L~~~D~~~NLvLsda~E~~ 69 (114)
..|+|.|+|+...++|.+..+..
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T~ 32 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTTH 32 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-EE
T ss_pred cceeEEeeccccceEEEeCCccE
Confidence 58999999999999998876643
No 87
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=74.35 E-value=9.8 Score=25.10 Aligned_cols=58 Identities=16% Similarity=0.036 Sum_probs=30.7
Q ss_pred HHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEec-ccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEc
Q 033666 28 RVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ-DAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVD 100 (114)
Q Consensus 28 ~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs-da~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~ 100 (114)
+|..+-+.+|+++|+||..+.|+. .| +... +-.|+... ...-|...||=++|.++++-
T Consensus 11 EiAC~~~~~v~L~l~dG~~~~g~A--~d----t~~~~~k~E~L~l---------~~~~~~~~i~Ld~I~~~~al 69 (80)
T PF07073_consen 11 EIACMYRYPVKLTLKDGEQIEGKA--LD----TRTNAKKEECLVL---------EQDGGEQEIRLDQIASMSAL 69 (80)
T ss_dssp HHHHTTTT-EEEE-TTT--EEESS---E----EE---SSS-EEEE---------EETTEEEEESTT--SEEE--
T ss_pred HHHHhcCCeEEEEEeCCCEEEEEE--EE----EEEecCceEEEEE---------ecCCcEEEEEhhheeeeeec
Confidence 466778899999999999999982 22 2222 33343321 11236678889999988643
No 88
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=73.90 E-value=7.4 Score=25.76 Aligned_cols=31 Identities=10% Similarity=0.066 Sum_probs=25.6
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEecc
Q 033666 34 CRRMLVGIKDGRFFLGSFHCIDKQGNIILQD 64 (114)
Q Consensus 34 ~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsd 64 (114)
+..|.|-|.+|-.+.|...+||+|.=|+=++
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD~f~VlL~~~ 49 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFDNFVVLLKNT 49 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeeeeEEEEEEcC
Confidence 5678888999999999999999996555443
No 89
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=73.70 E-value=8.8 Score=28.80 Aligned_cols=42 Identities=12% Similarity=0.067 Sum_probs=31.4
Q ss_pred HHHHHhcCC--eEEEEEcCCeEEEEEEEEecCccceEecccEEE
Q 033666 27 SRVRKLLCR--RMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEY 68 (114)
Q Consensus 27 ~~L~~~l~k--~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~ 68 (114)
.+|..+-.+ .|.|-|.+|-.+.|.+.+||+|.=|+-.+....
T Consensus 15 ~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~gkqq 58 (165)
T PRK14091 15 IFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDGQSQ 58 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCCceE
Confidence 455555444 566778999999999999999987776666443
No 90
>PRK10898 serine endoprotease; Provisional
Probab=71.06 E-value=9.1 Score=31.22 Aligned_cols=31 Identities=19% Similarity=0.386 Sum_probs=27.2
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEeccc
Q 033666 35 RRMLVGIKDGRFFLGSFHCIDKQGNIILQDA 65 (114)
Q Consensus 35 k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda 65 (114)
..+.|++.||+.+.+.+.++|...+|-+=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 5789999999999999999999999865544
No 91
>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=70.92 E-value=9 Score=31.13 Aligned_cols=31 Identities=19% Similarity=0.356 Sum_probs=27.2
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEeccc
Q 033666 35 RRMLVGIKDGRFFLGSFHCIDKQGNIILQDA 65 (114)
Q Consensus 35 k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda 65 (114)
..+.|++.||+.+.+++.++|...+|-|=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 3689999999999999999999999987543
No 92
>PRK10942 serine endoprotease; Provisional
Probab=68.34 E-value=10 Score=32.25 Aligned_cols=31 Identities=26% Similarity=0.360 Sum_probs=27.2
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEecc
Q 033666 34 CRRMLVGIKDGRFFLGSFHCIDKQGNIILQD 64 (114)
Q Consensus 34 ~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsd 64 (114)
...+.|++.|||.|.+.+.++|...+|-|=.
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlk 165 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQ 165 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEE
Confidence 4578999999999999999999999987653
No 93
>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=67.52 E-value=12 Score=26.23 Aligned_cols=30 Identities=20% Similarity=0.314 Sum_probs=22.3
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEeccc
Q 033666 35 RRMLVGIKDGRFFLGSFHCIDKQGNIILQDA 65 (114)
Q Consensus 35 k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda 65 (114)
....|.++||+++.|.+..=|.. .+.|.++
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~~~-~~~l~~~ 87 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASETAD-GVTVKMP 87 (133)
T ss_pred ccEEEEECCCCEEEEEEEecCCC-eEEEEcC
Confidence 34889999999999998886643 4555443
No 94
>PRK10139 serine endoprotease; Provisional
Probab=65.45 E-value=13 Score=31.43 Aligned_cols=32 Identities=25% Similarity=0.404 Sum_probs=27.9
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEeccc
Q 033666 34 CRRMLVGIKDGRFFLGSFHCIDKQGNIILQDA 65 (114)
Q Consensus 34 ~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda 65 (114)
..++.|++.||+.+.+++.|+|....|-+=..
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 35789999999999999999999999977544
No 95
>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=64.93 E-value=9.8 Score=26.26 Aligned_cols=27 Identities=26% Similarity=0.562 Sum_probs=19.2
Q ss_pred hHHHHHHhc-----CCeEEEEEcCCeEEEEEE
Q 033666 25 HISRVRKLL-----CRRMLVGIKDGRFFLGSF 51 (114)
Q Consensus 25 ~~~~L~~~l-----~k~V~V~L~dGR~i~G~L 51 (114)
.+..|..|+ +.+|.+.|+|||.+.|++
T Consensus 14 qIa~LE~lv~~L~ge~~V~l~L~DGs~l~Gtv 45 (101)
T PF11607_consen 14 QIARLEHLVSELDGEERVELELDDGSMLRGTV 45 (101)
T ss_dssp HHHHHHHHHHCTTTT-EEEEEETTS-EEEEEE
T ss_pred HHHHHHHHHhhcCCcceEEEEEcCCCeeeeee
Confidence 455565554 458999999999999995
No 96
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=62.32 E-value=43 Score=24.46 Aligned_cols=42 Identities=17% Similarity=0.381 Sum_probs=31.7
Q ss_pred HHHHHhcCCeEEEEEcCCeEEEEEEEEec-Cccc--eEecccEEE
Q 033666 27 SRVRKLLCRRMLVGIKDGRFFLGSFHCID-KQGN--IILQDAVEY 68 (114)
Q Consensus 27 ~~L~~~l~k~V~V~L~dGR~i~G~L~~~D-~~~N--LvLsda~E~ 68 (114)
.....|+||.|.+...||..+.|+..++. .... +++.|..++
T Consensus 85 ~~a~slVGk~V~~~~~~g~~~tG~V~~V~~~~g~~~~~~v~G~~~ 129 (142)
T PRK09618 85 TKYSELIGKEVEWEGEDGEIVSGTVTSVKQKDGDYPLVLDNGTWI 129 (142)
T ss_pred HHHHHHhCCEEEEEeCCCCEEEEEEEEEEEcCCcEEEEEECCEEE
Confidence 35578999999999999999999999886 2222 345566654
No 97
>PRK08477 biotin--protein ligase; Provisional
Probab=61.78 E-value=20 Score=27.38 Aligned_cols=38 Identities=11% Similarity=0.080 Sum_probs=31.6
Q ss_pred HHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEE
Q 033666 29 VRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVE 67 (114)
Q Consensus 29 L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E 67 (114)
..-.+++.|+|. .+++.+.|+..+.|.++.|+++.-.-
T Consensus 170 ~~~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~ 207 (211)
T PRK08477 170 LEFEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKV 207 (211)
T ss_pred HHHHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEe
Confidence 345689999986 57899999999999999999886543
No 98
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=61.52 E-value=4.5 Score=29.62 Aligned_cols=21 Identities=24% Similarity=0.354 Sum_probs=17.0
Q ss_pred EEEEEEEEecCccceEecccE
Q 033666 46 FFLGSFHCIDKQGNIILQDAV 66 (114)
Q Consensus 46 ~i~G~L~~~D~~~NLvLsda~ 66 (114)
.=+|+|.|.|+++|=--+|-.
T Consensus 44 ~kiGTLVG~DkfGNkYyen~~ 64 (151)
T KOG3382|consen 44 HKIGTLVGVDKFGNKYYENND 64 (151)
T ss_pred ccceeeeeecccccchhcccc
Confidence 347999999999998777653
No 99
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=58.62 E-value=17 Score=27.44 Aligned_cols=71 Identities=11% Similarity=-0.041 Sum_probs=53.4
Q ss_pred HHHHHHhcCCeEEEE-EcCCeEEEEEEEEecCccceEecccEEEeecCCCC--CCCCceEeeeEEEEcCCCEEE
Q 033666 26 ISRVRKLLCRRMLVG-IKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTS--PSPMEQRCLGIILIPSSCRTS 96 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~-L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~--~~~~~~r~lG~vlIrG~~Iv~ 96 (114)
..++..|.+.+-+.. +.|+++..+-..++|.-.|||+-.+++.-..+++. ......+..|+..+.|..|.+
T Consensus 42 l~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp~s~s~~~v~ag~~~g~G~ar~~Grgip~ 115 (177)
T KOG3168|consen 42 LQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPPPSDSFRRVPAGAARGPGIARVAGRGIPS 115 (177)
T ss_pred HHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCCCccccccccccccCCcccccccCCCccC
Confidence 455667777777666 89999999999999999999999888854333211 113456778999999999886
No 100
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=57.85 E-value=4.7 Score=27.62 Aligned_cols=17 Identities=24% Similarity=0.405 Sum_probs=14.7
Q ss_pred EEEEEecCccceEeccc
Q 033666 49 GSFHCIDKQGNIILQDA 65 (114)
Q Consensus 49 G~L~~~D~~~NLvLsda 65 (114)
|+|+|.|.++|---.+-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 88999999999886655
No 101
>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=57.38 E-value=22 Score=29.40 Aligned_cols=32 Identities=22% Similarity=0.282 Sum_probs=27.6
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEecccE
Q 033666 35 RRMLVGIKDGRFFLGSFHCIDKQGNIILQDAV 66 (114)
Q Consensus 35 k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~ 66 (114)
..+.|++.||+.+.+.+.++|...+|-|=...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 47889999999999999999999998775443
No 102
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=53.91 E-value=40 Score=22.09 Aligned_cols=29 Identities=14% Similarity=0.146 Sum_probs=22.2
Q ss_pred HHHHHHhcCCeEEEEEcCCe----EEEEEEEEe
Q 033666 26 ISRVRKLLCRRMLVGIKDGR----FFLGSFHCI 54 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~L~dGR----~i~G~L~~~ 54 (114)
...|..++|++|.++-+.|| +-.|+|...
T Consensus 9 k~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 9 KKELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 46789999999999999999 457888765
No 103
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=50.68 E-value=22 Score=26.72 Aligned_cols=34 Identities=29% Similarity=0.348 Sum_probs=30.3
Q ss_pred HHhcCCeEEEEEcCCeEE----EEEEEEecCccceEec
Q 033666 30 RKLLCRRMLVGIKDGRFF----LGSFHCIDKQGNIILQ 63 (114)
Q Consensus 30 ~~~l~k~V~V~L~dGR~i----~G~L~~~D~~~NLvLs 63 (114)
+.|.+..+++...|||.- .|+++.-|+.+||||.
T Consensus 140 reyPDGTvk~vy~dG~qet~y~~gr~r~kd~~g~~~~d 177 (179)
T PF07202_consen 140 REYPDGTVKTVYPDGRQETRYASGRVRIKDKDGNVIMD 177 (179)
T ss_pred EEcCCCCEEEEecCCCEEEEeCCCcEEEecCCCCEEec
Confidence 678899999999999644 7999999999999986
No 104
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=45.11 E-value=25 Score=20.90 Aligned_cols=36 Identities=22% Similarity=0.407 Sum_probs=22.8
Q ss_pred CchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 033666 23 SNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 23 ~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLs 63 (114)
......++.++||+|+|+ |..|-+. .|+ .+..++|+
T Consensus 8 ~~~~~~~~~~~Gk~V~V~---G~l~~a~-t~h-H~Tpvll~ 43 (48)
T PF14485_consen 8 EEDYSYLKSLLGKRVSVT---GKLFHAH-TGH-HHTPVLLD 43 (48)
T ss_pred hhhhHHHHHhcCCeEEEE---EEEeecc-Ccc-cCCceeee
Confidence 345677888999999998 6665443 121 34455554
No 105
>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=44.20 E-value=23 Score=22.24 Aligned_cols=23 Identities=26% Similarity=0.289 Sum_probs=19.4
Q ss_pred CeEEEEEcCCeEEEEEEEEecCc
Q 033666 35 RRMLVGIKDGRFFLGSFHCIDKQ 57 (114)
Q Consensus 35 k~V~V~L~dGR~i~G~L~~~D~~ 57 (114)
.+|+|++.||..++.+|..-|.-
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~tl 29 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSDTL 29 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTSBH
T ss_pred EEEEEECCCCCEEEEEECCcchH
Confidence 47899999999999999866643
No 106
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=43.95 E-value=22 Score=22.54 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=19.7
Q ss_pred CCeEEEEEcCCeEEEEEEEEecC
Q 033666 34 CRRMLVGIKDGRFFLGSFHCIDK 56 (114)
Q Consensus 34 ~k~V~V~L~dGR~i~G~L~~~D~ 56 (114)
..+|.|++-||..++++|..-|.
T Consensus 4 ~~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 4 QCRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred eEEEEEEcCCCCEEEEEeCCCCc
Confidence 35899999999999999887664
No 107
>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=42.04 E-value=27 Score=21.90 Aligned_cols=22 Identities=18% Similarity=0.422 Sum_probs=18.9
Q ss_pred CeEEEEEcCCeEEEEEEEEecC
Q 033666 35 RRMLVGIKDGRFFLGSFHCIDK 56 (114)
Q Consensus 35 k~V~V~L~dGR~i~G~L~~~D~ 56 (114)
.+|+|++-||..++++|..-|.
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~t 24 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTHK 24 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCCC
Confidence 4799999999999999886664
No 108
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=41.51 E-value=69 Score=21.60 Aligned_cols=38 Identities=13% Similarity=0.255 Sum_probs=29.0
Q ss_pred chHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceE
Q 033666 24 NHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNII 61 (114)
Q Consensus 24 ~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLv 61 (114)
.....-.-|+||+|-..-+.||.++|.+.-.-.....+
T Consensus 30 ~~~~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvV 67 (87)
T PRK04337 30 DDREEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEV 67 (87)
T ss_pred CCHHHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceE
Confidence 34556778999999999999999999976554444444
No 109
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.18 E-value=32 Score=22.89 Aligned_cols=22 Identities=18% Similarity=0.173 Sum_probs=19.1
Q ss_pred HHHHHHhcCCeEEEEEcCCeEE
Q 033666 26 ISRVRKLLCRRMLVGIKDGRFF 47 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~L~dGR~i 47 (114)
...+...+|++|.++.++||-=
T Consensus 11 K~~i~ah~G~~v~lk~ngGRKk 32 (80)
T COG4466 11 KESIDAHLGERVTLKANGGRKK 32 (80)
T ss_pred HHHHHhccCcEEEEEecCCcee
Confidence 4578899999999999999953
No 110
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=40.75 E-value=35 Score=23.06 Aligned_cols=23 Identities=13% Similarity=0.242 Sum_probs=19.8
Q ss_pred HhcCCeEEEE-EcCCeEEEEEEEE
Q 033666 31 KLLCRRMLVG-IKDGRFFLGSFHC 53 (114)
Q Consensus 31 ~~l~k~V~V~-L~dGR~i~G~L~~ 53 (114)
..+|..|+|+ +..||++.|+..+
T Consensus 93 g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 93 GAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred cCCCCEEEEEECCCCCEEEEEEeC
Confidence 4589999999 7999999999765
No 111
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=39.93 E-value=23 Score=22.99 Aligned_cols=20 Identities=10% Similarity=0.099 Sum_probs=15.8
Q ss_pred HHHHhcCCeEEEEEcCCeEE
Q 033666 28 RVRKLLCRRMLVGIKDGRFF 47 (114)
Q Consensus 28 ~L~~~l~k~V~V~L~dGR~i 47 (114)
-+++.+||+|||+....-++
T Consensus 5 ~~nDrLGKKVRvKCn~dDti 24 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDTI 24 (73)
T ss_pred hhhhhcCceEEEEeCCcccc
Confidence 36789999999999765543
No 112
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=38.43 E-value=63 Score=25.76 Aligned_cols=33 Identities=15% Similarity=0.178 Sum_probs=26.6
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEecccE
Q 033666 34 CRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAV 66 (114)
Q Consensus 34 ~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~ 66 (114)
..++.|.+.|||.+.+.+.|+|...-+-+-...
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 467888889999999999999987776654333
No 113
>PRK06630 hypothetical protein; Provisional
Probab=36.86 E-value=19 Score=24.85 Aligned_cols=19 Identities=16% Similarity=-0.008 Sum_probs=16.0
Q ss_pred EEEEEEEecCccceEeccc
Q 033666 47 FLGSFHCIDKQGNIILQDA 65 (114)
Q Consensus 47 i~G~L~~~D~~~NLvLsda 65 (114)
..|+|+|.|+++|---.+.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3799999999999887664
No 114
>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=36.80 E-value=51 Score=26.00 Aligned_cols=19 Identities=32% Similarity=0.305 Sum_probs=17.5
Q ss_pred EEEEEEEEecCccceEecc
Q 033666 46 FFLGSFHCIDKQGNIILQD 64 (114)
Q Consensus 46 ~i~G~L~~~D~~~NLvLsd 64 (114)
.+.|...-+|.|+|++++=
T Consensus 169 ~i~g~Vi~iD~FGNlitnI 187 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNI 187 (258)
T ss_dssp EEEEEEEEEETTSEEEEEE
T ss_pred eEEEEEEEECccCCeeeCC
Confidence 8999999999999999873
No 115
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=36.26 E-value=67 Score=24.81 Aligned_cols=32 Identities=6% Similarity=0.038 Sum_probs=24.1
Q ss_pred cCCeEEE---EEcCCeEEEEEEEEecCccceEecc
Q 033666 33 LCRRMLV---GIKDGRFFLGSFHCIDKQGNIILQD 64 (114)
Q Consensus 33 l~k~V~V---~L~dGR~i~G~L~~~D~~~NLvLsd 64 (114)
+++.+.+ ...++..+.|++.|+|..+.|++..
T Consensus 197 ~~~~~~~~~~~~~~~~~~~G~~~gId~~G~Lvv~~ 231 (245)
T PTZ00276 197 MDKSLKLHKRTPTGRDPEELTALSLNEWGHLIVRR 231 (245)
T ss_pred HhhhhccCeEEEcCCcEEEEEEEEECCCCeEEEEE
Confidence 3555543 2246778899999999999999863
No 116
>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=34.97 E-value=27 Score=22.31 Aligned_cols=25 Identities=16% Similarity=0.309 Sum_probs=20.5
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecC
Q 033666 32 LLCRRMLVGIKDGRFFLGSFHCIDK 56 (114)
Q Consensus 32 ~l~k~V~V~L~dGR~i~G~L~~~D~ 56 (114)
|-..+|.|++-||..+.++|..-|.
T Consensus 2 ~~~~~i~iRlp~G~~~~~~F~~~~t 26 (79)
T cd01772 2 YTETRIQIRLLDGTTLKQTFKAREQ 26 (79)
T ss_pred CcEEEEEEECCCCCEEEEEeCCCCh
Confidence 3456899999999999999887654
No 117
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=34.30 E-value=32 Score=25.66 Aligned_cols=17 Identities=29% Similarity=0.354 Sum_probs=15.0
Q ss_pred EEEEEecCccceEeccc
Q 033666 49 GSFHCIDKQGNIILQDA 65 (114)
Q Consensus 49 G~L~~~D~~~NLvLsda 65 (114)
|+|+|-|+++|---++.
T Consensus 49 G~lVG~D~~GNkYYE~~ 65 (159)
T PLN02732 49 ATLVGVDKFGNKYYQKL 65 (159)
T ss_pred cEEEEecCCCCeeeecC
Confidence 99999999999877665
No 118
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=33.62 E-value=78 Score=23.05 Aligned_cols=27 Identities=7% Similarity=0.169 Sum_probs=23.4
Q ss_pred HHHhcCCeEEEEEcCCeEEEEEEEEec
Q 033666 29 VRKLLCRRMLVGIKDGRFFLGSFHCID 55 (114)
Q Consensus 29 L~~~l~k~V~V~L~dGR~i~G~L~~~D 55 (114)
-..|+||.|.....+|..+.|+..++.
T Consensus 88 a~~lIGk~V~~~~~~g~~~tG~V~sV~ 114 (140)
T PRK11911 88 AVNFIGKDIKGVSLNGEVISGKVESVQ 114 (140)
T ss_pred HHHhhCceeEEEecCCCEEEEEEEEEE
Confidence 357999999988899999999988765
No 119
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=32.13 E-value=27 Score=24.67 Aligned_cols=18 Identities=22% Similarity=0.291 Sum_probs=15.4
Q ss_pred EEEEEEecCccceEeccc
Q 033666 48 LGSFHCIDKQGNIILQDA 65 (114)
Q Consensus 48 ~G~L~~~D~~~NLvLsda 65 (114)
.|.|+|.|+++|---.+.
T Consensus 9 ~g~lVG~D~~GNkYYE~~ 26 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENP 26 (115)
T ss_pred cceEeEEcCCCCeeeEcC
Confidence 689999999999876654
No 120
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.72 E-value=53 Score=25.22 Aligned_cols=23 Identities=13% Similarity=0.213 Sum_probs=20.1
Q ss_pred HhcCCeEEEE-EcCCeEEEEEEEE
Q 033666 31 KLLCRRMLVG-IKDGRFFLGSFHC 53 (114)
Q Consensus 31 ~~l~k~V~V~-L~dGR~i~G~L~~ 53 (114)
..+|..|+|+ +..||++.|+..+
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeC
Confidence 4579999999 9999999999765
No 121
>PHA00672 hypothetical protein
Probab=31.23 E-value=2.1e+02 Score=20.97 Aligned_cols=47 Identities=17% Similarity=0.193 Sum_probs=32.9
Q ss_pred EEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCC
Q 033666 38 LVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSS 92 (114)
Q Consensus 38 ~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~ 92 (114)
.+++.-|-.++|.++-||.+ |+++.-.-...+ ++-.|--|..+|+|.
T Consensus 51 ei~IPkGt~LtG~~hkf~~~--ii~sG~itV~td------ge~~rl~g~~~i~~~ 97 (152)
T PHA00672 51 TIRIPAGVALTGALIKVSTV--LIFSGHATVFIG------GEAVELRGYHVIPAS 97 (152)
T ss_pred EEeccCceeeeeeeeEeeEE--EEecccEEEEeC------CcEEEEecceeeecC
Confidence 46778899999999999988 776655444432 245566677777663
No 122
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=29.89 E-value=1.5e+02 Score=19.76 Aligned_cols=41 Identities=15% Similarity=0.240 Sum_probs=27.8
Q ss_pred cCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEc
Q 033666 55 DKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVD 100 (114)
Q Consensus 55 D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~ 100 (114)
|...-+-+.-...+-... ..+.|+-|.+++.|..+..+++.
T Consensus 55 ~~~g~~~~~r~y~FEFS~-----~G~~ry~G~l~m~G~~l~~v~lp 95 (97)
T PF11743_consen 55 DSRGRLRWRRVYQFEFSS-----DGEDRYQGELVMLGRRLISVELP 95 (97)
T ss_pred CCCCCeEEEEEEEEEEeC-----CChhcceEEEEEECCeeeEEEcC
Confidence 334445555555543332 24789999999999999998764
No 123
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=29.63 E-value=1.1e+02 Score=18.95 Aligned_cols=26 Identities=12% Similarity=0.288 Sum_probs=19.3
Q ss_pred cCCeEEEEEcCCe-EEEEEEEEecCcc
Q 033666 33 LCRRMLVGIKDGR-FFLGSFHCIDKQG 58 (114)
Q Consensus 33 l~k~V~V~L~dGR-~i~G~L~~~D~~~ 58 (114)
.|.+|.+.-.++. .|.|.+.+||...
T Consensus 8 ~Ge~V~~rWP~s~lYYe~kV~~~d~~~ 34 (55)
T PF09465_consen 8 IGEVVMVRWPGSSLYYEGKVLSYDSKS 34 (55)
T ss_dssp SS-EEEEE-TTTS-EEEEEEEEEETTT
T ss_pred CCCEEEEECCCCCcEEEEEEEEecccC
Confidence 5888999998766 5599999999643
No 124
>PF03166 MH2: MH2 domain; InterPro: IPR001132 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the SMAD (Mothers against decapentaplegic (MAD) homologue) (also called MH2 for MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C terminus of MH2 [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1MK2_A 1U7F_A 1MJS_A 1KHU_A 1DD1_C 1G88_A 1U7V_B 1MR1_B 1YGS_A 3DIT_B ....
Probab=29.24 E-value=84 Score=23.18 Aligned_cols=35 Identities=14% Similarity=0.328 Sum_probs=24.9
Q ss_pred cCCCCCCCchHHHHHHhcCCeEEEEEc-CCeEEEEE
Q 033666 16 AGSDTKGSNHISRVRKLLCRRMLVGIK-DGRFFLGS 50 (114)
Q Consensus 16 ~~~~~~~~~~~~~L~~~l~k~V~V~L~-dGR~i~G~ 50 (114)
+.+++.+.......++.||+-|++... ||.++.-.
T Consensus 47 ~~~n~~R~~~~~~~R~~IG~Gi~l~~~~~G~V~l~n 82 (181)
T PF03166_consen 47 QLSNVNRDSKTEKIRRHIGKGIKLSYEEDGNVWLYN 82 (181)
T ss_dssp T---TT--HHHHHHHTTCTT-EEEEEETTTEEEEEE
T ss_pred ccCCCCCChHHhhHHheecCcEEEEEecCCeEEEEE
Confidence 456777778899999999999999999 88877554
No 125
>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=28.17 E-value=1.6e+02 Score=19.65 Aligned_cols=15 Identities=0% Similarity=0.036 Sum_probs=12.3
Q ss_pred HHHHHHhcCCeEEEE
Q 033666 26 ISRVRKLLCRRMLVG 40 (114)
Q Consensus 26 ~~~L~~~l~k~V~V~ 40 (114)
.+.|.+|+|++|++.
T Consensus 7 ~~~L~~f~gk~V~iv 21 (101)
T cd04479 7 GAMLSQFVGKTVRIV 21 (101)
T ss_pred HHHHHhhCCCEEEEE
Confidence 458999999999864
No 126
>PF03122 Herpes_MCP: Herpes virus major capsid protein; InterPro: IPR000912 The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces []. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1NO7_B.
Probab=28.02 E-value=20 Score=34.81 Aligned_cols=54 Identities=15% Similarity=0.054 Sum_probs=0.0
Q ss_pred EEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEE
Q 033666 39 VGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSC 97 (114)
Q Consensus 39 V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I 97 (114)
=+..+||.+-|+|...|.-++.+|+--.+.... .-.-+..+|..+|+|.|.|.-
T Consensus 252 ytt~~G~~v~GVlvTT~~V~q~Ll~~l~~i~~~-----~v~~PatYg~~Vi~geNlVTA 305 (1354)
T PF03122_consen 252 YTTSSGRPVDGVLVTTANVMQKLLNLLGQISDT-----SVSVPATYGEFVISGENLVTA 305 (1354)
T ss_dssp -----------------------------------------------------------
T ss_pred eecCCCCEeceEEeccHHHHHHHHHHHhhhccc-----eeecchhheeeeecCccHHHH
Confidence 345799999999999999998888755543221 123567899999999998753
No 127
>PRK11625 Rho-binding antiterminator; Provisional
Probab=26.98 E-value=1.9e+02 Score=19.14 Aligned_cols=56 Identities=14% Similarity=0.037 Sum_probs=35.9
Q ss_pred HHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEE
Q 033666 28 RVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCH 98 (114)
Q Consensus 28 ~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~ 98 (114)
+|...-+..|++.++||-.+.|+- .|=. ..+-.|+..... .=+.-.||=++|.+++
T Consensus 17 ElAC~~~~~l~l~l~dGe~~~g~A--~D~~----~~~k~EyL~l~~---------~g~~~~iRLD~I~s~~ 72 (84)
T PRK11625 17 ELACQHHLMLTLELKDGEVLQAKA--SDLV----SRKNVEYLVVEA---------AGETRELRLDKIASFS 72 (84)
T ss_pred HHHHhcCCeEEEEECCCCEEEEEE--Eeee----cCCceEEEEEEc---------CCCEEEEEeeeEeecc
Confidence 445567889999999999999985 3332 336666654321 1134466667776664
No 128
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.92 E-value=90 Score=23.85 Aligned_cols=34 Identities=15% Similarity=0.261 Sum_probs=30.6
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecCccceEecccE
Q 033666 33 LCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAV 66 (114)
Q Consensus 33 l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~ 66 (114)
++..|++..-+|...+|.+.+||-..+...-+|.
T Consensus 10 vg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 10 VGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 5778999999999999999999988888877777
No 129
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=26.32 E-value=1.6e+02 Score=20.29 Aligned_cols=33 Identities=21% Similarity=0.329 Sum_probs=25.4
Q ss_pred hHHHHHHhcCCeEEEEEcC-CeEEEEEEEEecCccc
Q 033666 25 HISRVRKLLCRRMLVGIKD-GRFFLGSFHCIDKQGN 59 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~d-GR~i~G~L~~~D~~~N 59 (114)
..++-+.|++++|--+-.. ||++.|++. +-|.|
T Consensus 37 s~~eA~~y~gk~v~yk~~~~G~Vi~G~V~--R~HGn 70 (100)
T COG2451 37 SPEEAQFYLGKRVCYKYRSSGRVIKGKVV--RTHGN 70 (100)
T ss_pred CHHHHHhhhccEEEEEeCCCCcEEEEEEE--EecCC
Confidence 3456678999998888877 999999975 44444
No 130
>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=25.51 E-value=1.2e+02 Score=21.53 Aligned_cols=27 Identities=22% Similarity=0.511 Sum_probs=23.3
Q ss_pred CeEEEEEc--CCeEEEEEEEEecCccceE
Q 033666 35 RRMLVGIK--DGRFFLGSFHCIDKQGNII 61 (114)
Q Consensus 35 k~V~V~L~--dGR~i~G~L~~~D~~~NLv 61 (114)
.+|+|.+. |++.++++|.|=++++=||
T Consensus 22 ~kv~V~v~s~~~~~iQatF~~~~~~v~iV 50 (120)
T PF06856_consen 22 AKVRVRVDSFDNKYIQATFCCGHKHVCIV 50 (120)
T ss_pred cEEEEEEccCCCceEEEEEEeCCceEEEE
Confidence 68888885 6999999999998888777
No 131
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.75 E-value=87 Score=24.09 Aligned_cols=22 Identities=18% Similarity=0.080 Sum_probs=18.9
Q ss_pred hcCCeEEEE-EcCCeEEEEEEEE
Q 033666 32 LLCRRMLVG-IKDGRFFLGSFHC 53 (114)
Q Consensus 32 ~l~k~V~V~-L~dGR~i~G~L~~ 53 (114)
-+|..|+|+ +..||++.|+..+
T Consensus 184 ~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 184 GENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 369999999 7999999999654
No 132
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=24.46 E-value=1.1e+02 Score=19.57 Aligned_cols=24 Identities=17% Similarity=0.091 Sum_probs=19.0
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEec
Q 033666 32 LLCRRMLVGIKDGRFFLGSFHCID 55 (114)
Q Consensus 32 ~l~k~V~V~L~dGR~i~G~L~~~D 55 (114)
+-+...+|.|.||..+.+.+.|==
T Consensus 15 L~~~~f~V~l~ng~~vla~i~GKm 38 (68)
T TIGR00008 15 LPNAMFRVELENGHEVLAHISGKI 38 (68)
T ss_pred CCCCEEEEEECCCCEEEEEecCcc
Confidence 346788999999999988877644
No 133
>PRK08183 NADH dehydrogenase; Validated
Probab=24.36 E-value=42 Score=24.23 Aligned_cols=18 Identities=22% Similarity=0.224 Sum_probs=15.0
Q ss_pred EEEEEEecCccceEeccc
Q 033666 48 LGSFHCIDKQGNIILQDA 65 (114)
Q Consensus 48 ~G~L~~~D~~~NLvLsda 65 (114)
.|.|+|.|+++|---.+-
T Consensus 25 ~g~lVG~D~~GNkYYE~~ 42 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTK 42 (133)
T ss_pred cCeEeEecCCCCeeeecC
Confidence 699999999999876544
No 134
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.95 E-value=97 Score=22.64 Aligned_cols=23 Identities=13% Similarity=0.135 Sum_probs=19.2
Q ss_pred HhcCCeEEEE-EcCCeEEEEEEEE
Q 033666 31 KLLCRRMLVG-IKDGRFFLGSFHC 53 (114)
Q Consensus 31 ~~l~k~V~V~-L~dGR~i~G~L~~ 53 (114)
..+|..|+|+ +..||++.|+..+
T Consensus 128 G~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 128 GAAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4579999999 8899999998653
No 135
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. 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=23.81 E-value=74 Score=20.42 Aligned_cols=22 Identities=14% Similarity=0.430 Sum_probs=18.5
Q ss_pred CeEEEEEcCCeEEEEEEEEecC
Q 033666 35 RRMLVGIKDGRFFLGSFHCIDK 56 (114)
Q Consensus 35 k~V~V~L~dGR~i~G~L~~~D~ 56 (114)
.+|.|.|-||..++.+|...|.
T Consensus 5 t~iqiRlpdG~r~~~rF~~~~t 26 (79)
T cd01770 5 TSIQIRLADGKRLVQKFNSSHR 26 (79)
T ss_pred eEEEEECCCCCEEEEEeCCCCc
Confidence 5789999999999999876554
No 136
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=23.78 E-value=1.9e+02 Score=17.79 Aligned_cols=31 Identities=13% Similarity=0.261 Sum_probs=23.3
Q ss_pred cCCeEEEEEcCC----eEEEEEEEEecCccceEec
Q 033666 33 LCRRMLVGIKDG----RFFLGSFHCIDKQGNIILQ 63 (114)
Q Consensus 33 l~k~V~V~L~dG----R~i~G~L~~~D~~~NLvLs 63 (114)
+|.+|.+.+.++ ..|.-++.|++....|+++
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~ 37 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIIS 37 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEE
Confidence 578899988543 3699999999998777766
No 137
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=23.35 E-value=1.3e+02 Score=23.01 Aligned_cols=28 Identities=18% Similarity=0.165 Sum_probs=23.8
Q ss_pred HHHHhcCCeEEEEEcCCeEEEEEEEEec
Q 033666 28 RVRKLLCRRMLVGIKDGRFFLGSFHCID 55 (114)
Q Consensus 28 ~L~~~l~k~V~V~L~dGR~i~G~L~~~D 55 (114)
.-..||||.|.+.-.||..+.|+..+..
T Consensus 112 qa~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 112 GGMKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHHHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 3458999999998899999999988765
No 138
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=23.00 E-value=2.1e+02 Score=24.60 Aligned_cols=44 Identities=25% Similarity=0.087 Sum_probs=36.6
Q ss_pred hHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEe
Q 033666 25 HISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYR 69 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~ 69 (114)
+-..+.+++||.|+- =+|||..+++|++-|.-.=+-+.+-.|..
T Consensus 73 ~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~ 116 (421)
T COG5316 73 PGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVL 116 (421)
T ss_pred chhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEE
Confidence 445678999999998 89999999999999988777777777754
No 139
>PF06004 DUF903: Bacterial protein of unknown function (DUF903); InterPro: IPR010305 This family consists of several small bacterial proteins several of which are classified as putative lipoproteins. The function of this family is unknown.; PDB: 2RB6_B 3BDU_F 2RA2_F 2RD1_C 3FIF_H 2JN0_A 2K57_A.
Probab=22.97 E-value=73 Score=19.18 Aligned_cols=11 Identities=27% Similarity=0.625 Sum_probs=9.0
Q ss_pred EEEEcCCeEEE
Q 033666 38 LVGIKDGRFFL 48 (114)
Q Consensus 38 ~V~L~dGR~i~ 48 (114)
.|+++|||.|+
T Consensus 3 vi~t~dG~~i~ 13 (50)
T PF06004_consen 3 VITTNDGRTIV 13 (50)
T ss_dssp EEEETTSEEEE
T ss_pred EEEeCCCcEEE
Confidence 57899999884
No 140
>PF01247 Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro: IPR001780 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal L35A eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of: Vertebrate L35A. Caenorhabditis elegans L35A (F10E7.7). Saccharomyces cerevisiae L37A/L37B (Rp47). Plant L35A. Pyrococcus woesei L35A homologue []. These proteins have 87 to 110 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_j 2LP6_A 1SQR_A 4A18_H 4A1D_H 4A19_H 4A1B_H 3IZS_j.
Probab=22.84 E-value=1.7e+02 Score=20.00 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=27.4
Q ss_pred hHHHHHHhcCCeEEEEEc--------CCeEEEEEEEEecCccceE
Q 033666 25 HISRVRKLLCRRMLVGIK--------DGRFFLGSFHCIDKQGNII 61 (114)
Q Consensus 25 ~~~~L~~~l~k~V~V~L~--------dGR~i~G~L~~~D~~~NLv 61 (114)
...+-..|+|++|-..-+ -+|+++|...-.-.....+
T Consensus 31 ~~~~a~fylGKrv~yvyk~~~~~~~~k~r~iwGkV~r~HGnsGvV 75 (95)
T PF01247_consen 31 TKEDAQFYLGKRVAYVYKAKNKKNGSKGRVIWGKVTRPHGNSGVV 75 (95)
T ss_dssp TCHHHHTTTT-EEEEEECE-SSSTTECSEEEEEEEEEESTTTTEE
T ss_pred CHHHHHhhcCcEEEEEEecccccCCCcEeEEEEEEEeEEcCCCEE
Confidence 345667899999998887 6899999987765554444
No 141
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.61 E-value=1.4e+02 Score=22.91 Aligned_cols=23 Identities=9% Similarity=-0.013 Sum_probs=20.0
Q ss_pred HhcCCeEEEEEcCCeEEEEEEEE
Q 033666 31 KLLCRRMLVGIKDGRFFLGSFHC 53 (114)
Q Consensus 31 ~~l~k~V~V~L~dGR~i~G~L~~ 53 (114)
..+|..|+|+-..||++.|+..|
T Consensus 193 G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 193 GNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCCEEEEEeCCCCEEEEEEec
Confidence 35799999999999999999765
No 142
>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=21.59 E-value=1.7e+02 Score=16.60 Aligned_cols=25 Identities=12% Similarity=0.322 Sum_probs=21.2
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecCc
Q 033666 33 LCRRMLVGIKDGRFFLGSFHCIDKQ 57 (114)
Q Consensus 33 l~k~V~V~L~dGR~i~G~L~~~D~~ 57 (114)
.|..+.+...||+.+.|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4667777778999999999999975
No 143
>PRK10708 hypothetical protein; Provisional
Probab=21.27 E-value=1.1e+02 Score=19.24 Aligned_cols=25 Identities=16% Similarity=0.171 Sum_probs=22.0
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecCc
Q 033666 33 LCRRMLVGIKDGRFFLGSFHCIDKQ 57 (114)
Q Consensus 33 l~k~V~V~L~dGR~i~G~L~~~D~~ 57 (114)
++.+|.|++.+|-.=.|++.++..|
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F 27 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEF 27 (62)
T ss_pred cccEEEEecCCCccccceEEEEeec
Confidence 5789999999999999999988865
No 144
>PF05775 AfaD: Enterobacteria AfaD invasin protein; InterPro: IPR008394 This family consists of several AfaD and related proteins from Escherichia coli and Salmonella bacteria. The afa gene clusters encode an afimbrial adhesive sheath produced by E. coli. The adhesive sheath is composed of two proteins, AfaD and AfaE, which are independently exposed at the bacterial cell surface. AfaE is required for bacterial adhesion to HeLa cells and AfaD for the uptake of adherent bacteria into these cells [].; GO: 0009289 pilus; PDB: 3UIZ_F 3UIY_A 2AXW_A 2IXQ_A 2FVN_A.
Probab=20.86 E-value=1.9e+02 Score=20.35 Aligned_cols=28 Identities=18% Similarity=0.368 Sum_probs=18.5
Q ss_pred EEcCCeEE-EEEEEEecCccceEec-ccEE
Q 033666 40 GIKDGRFF-LGSFHCIDKQGNIILQ-DAVE 67 (114)
Q Consensus 40 ~L~dGR~i-~G~L~~~D~~~NLvLs-da~E 67 (114)
.|.||+.+ +|.+.|.+.|.=..+. |+..
T Consensus 7 ~l~DG~~latGrI~~~~~htGF~Vw~na~~ 36 (111)
T PF05775_consen 7 QLRDGMKLATGRIICREAHTGFHVWSNARQ 36 (111)
T ss_dssp EE-TTEEEEEEEEES-SSSSEEEEEESSEE
T ss_pred cccCCCEEEEEEEEeCCCceEEEEEeechh
Confidence 36788855 9999999999855544 4443
No 145
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=20.68 E-value=90 Score=21.39 Aligned_cols=21 Identities=19% Similarity=0.219 Sum_probs=8.7
Q ss_pred EEEEEEEEecCccceEecccE
Q 033666 46 FFLGSFHCIDKQGNIILQDAV 66 (114)
Q Consensus 46 ~i~G~L~~~D~~~NLvLsda~ 66 (114)
++.|++.|||-..++.|.+|.
T Consensus 124 ti~G~~~g~~~~~~v~l~~c~ 144 (144)
T PF12869_consen 124 TIKGICTGYSLMGVVMLDDCQ 144 (144)
T ss_dssp EEEEE-----SSS-EEEE---
T ss_pred EEEEEEEeeecCCcEEeeccC
Confidence 467888888756677777773
Done!