Query 034947
Match_columns 78
No_of_seqs 130 out of 1041
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 07:55:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034947.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034947hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00138 small nuclear ribonuc 99.9 1.9E-26 4.1E-31 143.6 10.2 78 1-78 3-80 (89)
2 cd01718 Sm_E The eukaryotic Sm 99.9 2.3E-25 5.1E-30 136.0 9.5 72 7-78 1-72 (79)
3 KOG1774 Small nuclear ribonucl 99.9 6.9E-26 1.5E-30 138.6 5.0 78 1-78 1-78 (88)
4 cd01732 LSm5 The eukaryotic Sm 99.9 8.3E-22 1.8E-26 119.3 8.4 64 11-78 2-67 (76)
5 PRK00737 small nuclear ribonuc 99.9 1.6E-21 3.5E-26 116.5 7.9 63 11-78 3-65 (72)
6 cd01726 LSm6 The eukaryotic Sm 99.9 4.1E-21 8.8E-26 113.2 7.5 61 13-78 1-61 (67)
7 cd01730 LSm3 The eukaryotic Sm 99.8 4.8E-21 1E-25 116.9 7.9 63 12-78 1-75 (82)
8 cd01720 Sm_D2 The eukaryotic S 99.8 7.3E-21 1.6E-25 117.9 8.6 66 11-78 1-78 (87)
9 cd01731 archaeal_Sm1 The archa 99.8 1.1E-20 2.3E-25 111.5 7.7 61 13-78 1-61 (68)
10 cd01722 Sm_F The eukaryotic Sm 99.8 1.3E-20 2.7E-25 111.5 7.3 62 12-78 1-62 (68)
11 cd01719 Sm_G The eukaryotic Sm 99.8 6.4E-20 1.4E-24 109.9 7.4 61 13-78 1-61 (72)
12 COG1958 LSM1 Small nuclear rib 99.8 1.5E-19 3.2E-24 109.3 8.2 67 8-78 3-72 (79)
13 cd01729 LSm7 The eukaryotic Sm 99.8 1.7E-19 3.8E-24 110.1 8.1 61 14-78 4-71 (81)
14 cd01723 LSm4 The eukaryotic Sm 99.8 4.1E-19 8.8E-24 107.1 7.2 63 12-78 1-63 (76)
15 cd01728 LSm1 The eukaryotic Sm 99.8 1.5E-18 3.2E-23 104.7 8.8 63 12-78 2-66 (74)
16 cd01717 Sm_B The eukaryotic Sm 99.8 2E-18 4.3E-23 104.5 7.6 60 15-78 3-71 (79)
17 cd01721 Sm_D3 The eukaryotic S 99.8 3.1E-18 6.8E-23 101.9 7.3 61 13-78 1-61 (70)
18 cd01727 LSm8 The eukaryotic Sm 99.7 7.5E-18 1.6E-22 101.0 7.6 60 15-78 2-64 (74)
19 smart00651 Sm snRNP Sm protein 99.7 8.1E-18 1.8E-22 97.9 7.2 59 16-78 2-60 (67)
20 KOG1780 Small Nuclear ribonucl 99.7 4E-18 8.7E-23 102.7 5.3 58 16-78 8-65 (77)
21 PF01423 LSM: LSM domain ; In 99.7 2.2E-17 4.7E-22 96.2 7.5 60 15-78 1-60 (67)
22 cd06168 LSm9 The eukaryotic Sm 99.7 3.4E-17 7.3E-22 98.9 8.3 60 15-78 3-67 (75)
23 KOG3482 Small nuclear ribonucl 99.7 1.7E-17 3.7E-22 99.8 5.3 62 10-76 6-67 (79)
24 cd01724 Sm_D1 The eukaryotic S 99.7 8.9E-17 1.9E-21 100.0 7.7 61 13-78 2-62 (90)
25 cd00600 Sm_like The eukaryotic 99.7 2.4E-16 5.2E-21 90.4 7.2 57 17-78 1-57 (63)
26 cd01725 LSm2 The eukaryotic Sm 99.7 2.7E-16 5.9E-21 95.9 7.2 63 12-78 1-64 (81)
27 cd01733 LSm10 The eukaryotic S 99.7 4.8E-16 1E-20 94.4 7.4 63 11-78 8-70 (78)
28 KOG1775 U6 snRNA-associated Sm 99.6 1.2E-16 2.6E-21 97.0 3.0 65 10-78 5-71 (84)
29 KOG1781 Small Nuclear ribonucl 99.6 6.5E-17 1.4E-21 102.1 -0.8 65 10-78 15-86 (108)
30 KOG1783 Small nuclear ribonucl 99.6 2.1E-16 4.5E-21 95.1 0.3 63 11-78 5-67 (77)
31 KOG3460 Small nuclear ribonucl 99.4 1E-13 2.2E-18 85.4 0.7 65 10-78 3-79 (91)
32 KOG3293 Small nuclear ribonucl 99.1 8.5E-11 1.9E-15 77.0 5.0 63 12-78 2-64 (134)
33 KOG3168 U1 snRNP component [Tr 99.0 2.5E-11 5.4E-16 82.9 -0.9 57 18-78 10-75 (177)
34 KOG1784 Small Nuclear ribonucl 99.0 7.2E-10 1.6E-14 69.3 3.6 59 16-78 4-65 (96)
35 cd01739 LSm11_C The eukaryotic 98.9 8.8E-10 1.9E-14 65.2 2.3 45 18-62 2-48 (66)
36 KOG3448 Predicted snRNP core p 98.8 3.8E-08 8.3E-13 61.4 6.7 62 13-78 3-65 (96)
37 KOG1782 Small Nuclear ribonucl 98.8 8.5E-10 1.8E-14 72.1 -1.1 58 17-78 14-73 (129)
38 KOG3459 Small nuclear ribonucl 98.7 7.7E-10 1.7E-14 71.1 -1.4 64 12-77 24-99 (114)
39 KOG3172 Small nuclear ribonucl 98.3 2.3E-06 5E-11 55.1 5.1 64 10-78 3-66 (119)
40 KOG3428 Small nuclear ribonucl 97.9 7.3E-05 1.6E-09 48.1 7.1 58 14-77 4-61 (109)
41 cd01716 Hfq Hfq, an abundant, 97.8 9.5E-05 2.1E-09 43.2 5.4 37 15-53 2-38 (61)
42 TIGR02383 Hfq RNA chaperone Hf 97.8 0.00011 2.4E-09 43.0 5.5 37 15-53 6-42 (61)
43 PRK00395 hfq RNA-binding prote 97.6 0.00022 4.8E-09 43.6 5.4 41 14-56 9-49 (79)
44 COG1923 Hfq Uncharacterized ho 97.5 0.00049 1.1E-08 41.9 5.6 39 15-56 10-48 (77)
45 PRK14091 RNA-binding protein H 97.2 0.00095 2.1E-08 45.8 5.4 41 14-56 14-54 (165)
46 PRK14091 RNA-binding protein H 96.8 0.0035 7.6E-08 43.0 5.4 41 14-56 94-134 (165)
47 PF14438 SM-ATX: Ataxin 2 SM d 95.8 0.028 6.1E-07 33.2 4.6 42 16-61 6-50 (77)
48 PF02237 BPL_C: Biotin protein 93.8 0.41 8.8E-06 25.9 5.5 47 21-76 2-48 (48)
49 PF12701 LSM14: Scd6-like Sm d 93.4 0.31 6.8E-06 30.6 5.2 55 19-77 5-68 (96)
50 cd01736 LSm14_N LSm14 (also kn 91.4 1.5 3.3E-05 26.4 6.2 56 19-78 3-68 (74)
51 PRK14633 hypothetical protein; 91.3 0.74 1.6E-05 30.7 5.3 50 2-55 75-126 (150)
52 PRK14634 hypothetical protein; 90.3 1 2.2E-05 30.2 5.3 50 2-55 81-132 (155)
53 cd01734 YlxS_C YxlS is a Bacil 90.0 1.3 2.9E-05 26.4 5.1 50 2-55 6-57 (83)
54 PRK14638 hypothetical protein; 89.4 1.1 2.3E-05 30.0 4.8 48 2-55 81-128 (150)
55 PRK14636 hypothetical protein; 88.2 1.7 3.6E-05 29.9 5.2 50 2-55 79-130 (176)
56 PRK14643 hypothetical protein; 88.2 1.8 3.9E-05 29.4 5.3 49 2-53 85-136 (164)
57 PRK14639 hypothetical protein; 87.8 1.6 3.5E-05 28.8 4.8 47 2-54 69-115 (140)
58 PRK14640 hypothetical protein; 87.8 2 4.4E-05 28.7 5.3 50 2-55 78-129 (152)
59 PRK02001 hypothetical protein; 87.3 1.8 3.9E-05 29.1 4.9 48 2-55 71-118 (152)
60 PRK14632 hypothetical protein; 86.5 2.4 5.3E-05 28.9 5.2 50 2-55 79-133 (172)
61 PRK14645 hypothetical protein; 84.9 2.7 5.8E-05 28.3 4.8 46 2-54 83-128 (154)
62 cd01735 LSm12_N LSm12 belongs 84.5 3.3 7.1E-05 24.0 4.4 31 29-59 9-39 (61)
63 PRK14647 hypothetical protein; 84.0 4 8.6E-05 27.4 5.3 44 2-48 80-130 (159)
64 PRK14644 hypothetical protein; 80.7 4.1 8.9E-05 26.8 4.3 49 2-55 67-117 (136)
65 PRK00092 ribosome maturation p 80.5 6.5 0.00014 26.0 5.3 44 2-48 79-124 (154)
66 PF02576 DUF150: Uncharacteris 79.9 2.6 5.6E-05 27.4 3.1 37 15-54 80-118 (141)
67 PRK14635 hypothetical protein; 79.1 6.8 0.00015 26.4 5.1 49 2-54 80-131 (162)
68 PRK14646 hypothetical protein; 79.0 7.9 0.00017 25.9 5.4 50 2-55 81-132 (155)
69 PRK14631 hypothetical protein; 73.9 12 0.00026 25.6 5.2 43 2-47 98-142 (174)
70 PRK14642 hypothetical protein; 70.3 14 0.0003 26.0 5.0 49 2-54 81-140 (197)
71 COG0779 Uncharacterized protei 65.7 19 0.00042 24.3 4.8 50 2-55 80-131 (153)
72 PRK14641 hypothetical protein; 63.6 24 0.00052 24.2 5.0 43 2-47 85-129 (173)
73 PRK06955 biotin--protein ligas 62.4 41 0.00088 24.5 6.3 46 25-77 250-295 (300)
74 PF08863 YolD: YolD-like prote 61.7 30 0.00065 20.2 6.3 39 15-53 33-72 (92)
75 PF14563 DUF4444: Domain of un 61.4 14 0.0003 20.0 2.8 22 39-60 10-31 (42)
76 PRK14630 hypothetical protein; 59.2 22 0.00048 23.5 4.1 47 2-55 78-124 (143)
77 PRK14637 hypothetical protein; 56.0 33 0.00071 22.9 4.5 48 2-55 79-127 (151)
78 PF11095 Gemin7: Gem-associate 56.0 38 0.00082 20.6 4.4 40 13-56 15-55 (80)
79 PRK13325 bifunctional biotin-- 54.5 58 0.0012 26.3 6.4 49 20-77 276-324 (592)
80 PF03614 Flag1_repress: Repres 52.8 27 0.00059 24.0 3.7 36 13-50 109-144 (165)
81 PF14153 Spore_coat_CotO: Spor 52.5 29 0.00062 24.1 3.9 35 14-49 123-157 (185)
82 KOG3382 NADH:ubiquinone oxidor 52.0 8.3 0.00018 26.0 1.1 21 39-59 45-65 (151)
83 PRK10139 serine endoprotease; 50.8 49 0.0011 25.6 5.4 32 24-57 114-145 (455)
84 PF05071 NDUFA12: NADH ubiquin 50.2 7.2 0.00016 24.5 0.6 17 41-57 1-17 (105)
85 PRK10898 serine endoprotease; 48.4 37 0.0008 25.3 4.2 30 26-57 103-132 (353)
86 TIGR02038 protease_degS peripl 45.6 48 0.001 24.6 4.5 30 26-57 103-132 (351)
87 PRK10942 serine endoprotease; 45.5 60 0.0013 25.3 5.1 29 26-56 137-165 (473)
88 PF10842 DUF2642: Protein of u 44.9 59 0.0013 19.0 3.9 39 11-56 8-49 (66)
89 PRK08330 biotin--protein ligas 42.5 1.1E+02 0.0025 21.1 6.0 47 20-76 186-234 (236)
90 TIGR02037 degP_htrA_DO peripla 41.9 67 0.0015 24.3 4.8 30 26-57 83-112 (428)
91 PF11607 DUF3247: Protein of u 41.2 50 0.0011 21.0 3.4 29 14-44 18-46 (101)
92 COG1862 YajC Preprotein transl 40.5 68 0.0015 20.1 3.9 51 4-61 28-79 (97)
93 PF06372 Gemin6: Gemin6 protei 39.5 70 0.0015 21.9 4.2 42 12-59 8-50 (166)
94 PF03614 Flag1_repress: Repres 39.3 58 0.0013 22.4 3.7 32 25-58 30-61 (165)
95 PRK11886 bifunctional biotin-- 38.0 1.5E+02 0.0033 21.4 7.1 45 25-77 273-317 (319)
96 PF03306 AAL_decarboxy: Alpha- 37.1 62 0.0013 22.9 3.8 30 10-46 126-155 (220)
97 TIGR00121 birA_ligase birA, bi 37.1 1.4E+02 0.0031 20.7 7.3 44 25-76 194-237 (237)
98 TIGR00739 yajC preprotein tran 34.2 48 0.001 19.9 2.5 28 16-49 33-60 (84)
99 KOG3865 Arrestin [Signal trans 34.0 82 0.0018 24.3 4.1 41 20-60 207-247 (402)
100 PRK05585 yajC preprotein trans 31.0 55 0.0012 20.6 2.4 28 15-48 47-74 (106)
101 PF12869 tRNA_anti-like: tRNA_ 29.5 47 0.001 20.9 2.0 25 34-58 120-144 (144)
102 COG0340 BirA Biotin-(acetyl-Co 28.9 2.2E+02 0.0047 20.3 6.0 48 21-76 189-236 (238)
103 PRK06630 hypothetical protein; 27.7 34 0.00074 21.7 1.0 19 39-57 11-29 (99)
104 PF10894 DUF2689: Protein of u 26.0 8.2 0.00018 22.3 -1.8 15 47-61 21-35 (61)
105 PTZ00275 biotin-acetyl-CoA-car 23.8 2.9E+02 0.0062 20.0 5.5 29 25-56 238-266 (285)
106 PLN03095 NADH:ubiquinone oxido 23.1 48 0.001 21.5 1.1 20 40-59 9-28 (115)
107 KOG1073 Uncharacterized mRNA-a 23.0 91 0.002 24.0 2.8 57 18-78 5-71 (361)
108 TIGR01252 acetolac_decarb alph 22.4 87 0.0019 22.4 2.4 29 11-46 129-157 (232)
109 KOG0418 Ubiquitin-protein liga 21.7 36 0.00077 24.1 0.3 45 1-46 1-45 (200)
110 PF09340 NuA4: Histone acetylt 21.6 26 0.00057 21.0 -0.3 10 41-50 41-50 (80)
111 COG3620 Predicted transcriptio 21.0 85 0.0018 22.0 2.1 44 1-48 136-179 (187)
112 TIGR03170 flgA_cterm flagella 20.9 1.3E+02 0.0028 18.5 2.8 17 29-45 99-116 (122)
113 PRK08515 flgA flagellar basal 20.6 1.2E+02 0.0027 21.2 2.9 22 20-45 194-215 (222)
114 COG4990 Uncharacterized protei 20.3 2.3E+02 0.005 20.1 4.1 46 12-58 121-167 (195)
115 PRK05886 yajC preprotein trans 20.2 1.2E+02 0.0026 19.3 2.6 36 6-48 25-60 (109)
No 1
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.94 E-value=1.9e-26 Score=143.56 Aligned_cols=78 Identities=63% Similarity=1.019 Sum_probs=73.0
Q ss_pred CCccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 1 ms~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
|+.|+++|.|..|+..+.+++.++.+|.||++++++++++|+|.|||+||||||+||+|+..+++..+.+|.++|||.
T Consensus 3 ~~~~~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGn 80 (89)
T PTZ00138 3 MTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGD 80 (89)
T ss_pred CcccccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCC
Confidence 788889999999999999999999999999999999999999999999999999999999655667889999999995
No 2
>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=99.93 E-value=2.3e-25 Score=136.00 Aligned_cols=72 Identities=75% Similarity=1.175 Sum_probs=66.2
Q ss_pred ceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 7 QRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 7 ~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
+|.|..|++.+.++++++.+|.||+++++|++++|+|.|||+||||||+||+|+...+++.+.+|.++|||.
T Consensus 1 ~~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGn 72 (79)
T cd01718 1 QKVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGD 72 (79)
T ss_pred CccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCC
Confidence 467999999999999999999999998889999999999999999999999999644567788999999995
No 3
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.92 E-value=6.9e-26 Score=138.59 Aligned_cols=78 Identities=68% Similarity=1.077 Sum_probs=74.0
Q ss_pred CCccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 1 ms~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
||++|.||.|++|++++.+|+..+.+|.|||+++-+.+++|.++|||+|||+||+||+|........+.+|.++|.|.
T Consensus 1 ms~~kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGD 78 (88)
T KOG1774|consen 1 MSREKVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGD 78 (88)
T ss_pred CCcccccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCC
Confidence 899999999999999999999999999999999999999999999999999999999999877777779999999983
No 4
>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=99.87 E-value=8.3e-22 Score=119.32 Aligned_cols=64 Identities=30% Similarity=0.480 Sum_probs=55.4
Q ss_pred cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEe--cCCeeeeeeEEEEecC
Q 034947 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI--KKNTRKPLGFFSKETT 78 (78)
Q Consensus 11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~--~~~~~~~lG~ilir~~ 78 (78)
..|+++|.++++++ |.|.+++ |+++.|+|.|||+|||++|+||+|++. ++++.+.+|.++|||.
T Consensus 2 ~~P~~~L~~~~~~~--V~V~l~~--gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~ 67 (76)
T cd01732 2 LLPLELIDKCIGSR--IWIVMKS--DKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGN 67 (76)
T ss_pred cChHHHHHHhCCCE--EEEEECC--CeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCC
Confidence 47999999999965 7777755 999999999999999999999999963 3446788999999995
No 5
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.86 E-value=1.6e-21 Score=116.53 Aligned_cols=63 Identities=29% Similarity=0.457 Sum_probs=56.9
Q ss_pred cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
..|+++|.++++++ |.|++++ |+++.|+|.|||+|||++|+||+|.+ +++..+.+|.++|||.
T Consensus 3 ~~P~~~L~~~~~k~--V~V~lk~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~ 65 (72)
T PRK00737 3 QRPLDVLNNALNSP--VLVRLKG--GREFRGELQGYDIHMNLVLDNAEEIQ-DGEVVRKLGKVVIRGD 65 (72)
T ss_pred cchHHHHHHhCCCE--EEEEECC--CCEEEEEEEEEcccceeEEeeEEEEc-CCCeEeEcCcEEEeCC
Confidence 47999999999976 8888866 89999999999999999999999984 6677789999999994
No 6
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.85 E-value=4.1e-21 Score=113.24 Aligned_cols=61 Identities=18% Similarity=0.309 Sum_probs=55.5
Q ss_pred hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
|+++|+++++++ |+|.|++ |++++|+|.|||.|||++|+||+|. .+++....+|.++|||.
T Consensus 1 p~~~L~~~~~~~--V~V~Lk~--g~~~~G~L~~~D~~mNlvL~~~~~~-~~~~~~~~~~~v~IRG~ 61 (67)
T cd01726 1 PSEFLKAIIGRP--VVVKLNS--GVDYRGILACLDGYMNIALEQTEEY-VNGQLKNKYGDAFIRGN 61 (67)
T ss_pred CHHHHHhhCCCe--EEEEECC--CCEEEEEEEEEccceeeEEeeEEEE-eCCceeeEeCCEEEECC
Confidence 899999999975 9999976 8999999999999999999999997 46677889999999995
No 7
>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=99.85 E-value=4.8e-21 Score=116.93 Aligned_cols=63 Identities=24% Similarity=0.435 Sum_probs=54.7
Q ss_pred ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC------------CeeeeeeEEEEecC
Q 034947 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK------------NTRKPLGFFSKETT 78 (78)
Q Consensus 12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~------------~~~~~lG~ilir~~ 78 (78)
.|+++|+.+++++ |.|.+++ ||++.|+|.|||+||||+|+||+|++... +..+.+|.++|||+
T Consensus 1 ~pl~~l~~~~~k~--V~V~l~~--gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd 75 (82)
T cd01730 1 EPLDLIRLSLDER--VYVKLRG--DRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGD 75 (82)
T ss_pred CchHHHHHhCCCE--EEEEECC--CCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCC
Confidence 4999999999975 8888865 89999999999999999999999996431 24778999999995
No 8
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.85 E-value=7.3e-21 Score=117.88 Aligned_cols=66 Identities=20% Similarity=0.346 Sum_probs=56.2
Q ss_pred cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC------------CeeeeeeEEEEecC
Q 034947 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK------------NTRKPLGFFSKETT 78 (78)
Q Consensus 11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~------------~~~~~lG~ilir~~ 78 (78)
..|+++|.+++...++|.|+|++ |+++.|+|.|||+||||+|+||+|++... ...+.+|.+||||.
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~--~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd 78 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRN--NKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGD 78 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcC--CCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCC
Confidence 37999999999655679999976 89999999999999999999999987442 13557899999994
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=99.84 E-value=1.1e-20 Score=111.54 Aligned_cols=61 Identities=26% Similarity=0.437 Sum_probs=54.8
Q ss_pred hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
|+++|.++++++ |.|.+++ |+++.|+|.|||+||||+|+||+|.+ .+...+.+|.++|||.
T Consensus 1 p~~~L~~~~~~~--V~V~l~~--g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~iRG~ 61 (68)
T cd01731 1 PLDVLKDSLNKP--VLVKLKG--GKEVRGRLKSYDQHMNLVLEDAEEID-DGEPVRKYGRVVIRGD 61 (68)
T ss_pred ChHHHHHhcCCE--EEEEECC--CCEEEEEEEEECCcceEEEeeEEEEe-cCCeEeEcCcEEEeCC
Confidence 899999999976 8888865 89999999999999999999999996 4456788999999995
No 10
>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=99.84 E-value=1.3e-20 Score=111.51 Aligned_cols=62 Identities=23% Similarity=0.335 Sum_probs=55.9
Q ss_pred ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
.|+++|.+++++. |.|.|++ |+++.|+|.|||+|||++|+||+|+ .++.....+|.++|||+
T Consensus 1 ~p~~~L~~~~g~~--V~V~Lk~--g~~~~G~L~~~D~~mNi~L~~~~e~-~~~~~~~~lg~~~IRG~ 62 (68)
T cd01722 1 NPKPFLNDLTGKP--VIVKLKW--GMEYKGTLVSVDSYMNLQLANTEEY-IDGKSTGNLGEVLIRCN 62 (68)
T ss_pred CHHHHHHHcCCCE--EEEEECC--CcEEEEEEEEECCCEEEEEeeEEEE-eCCccccCcCcEEEECC
Confidence 4999999999975 8888876 8999999999999999999999998 46666788999999995
No 11
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.82 E-value=6.4e-20 Score=109.90 Aligned_cols=61 Identities=28% Similarity=0.493 Sum_probs=53.8
Q ss_pred hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
|...|.++++|+ |.|.+++ |+++.|+|.|||+||||+|+||+|+. ++...+.+|.++|||.
T Consensus 1 ~~~~L~~~i~k~--V~V~L~~--g~~~~G~L~~~D~~mNlvL~~~~E~~-~~~~~~~lg~v~IRG~ 61 (72)
T cd01719 1 HPPELKKYMDKK--LSLKLNG--NRKVSGILRGFDPFMNLVLDDAVEVN-SGGEKNNIGMVVIRGN 61 (72)
T ss_pred CchhhHHhCCCe--EEEEECC--CeEEEEEEEEEcccccEEeccEEEEc-cCCceeEeceEEECCC
Confidence 557899999976 8888865 89999999999999999999999995 6667789999999994
No 12
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.81 E-value=1.5e-19 Score=109.31 Aligned_cols=67 Identities=30% Similarity=0.505 Sum_probs=56.2
Q ss_pred eeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEe-cCCe-eeeee-EEEEecC
Q 034947 8 RIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI-KKNT-RKPLG-FFSKETT 78 (78)
Q Consensus 8 ~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~-~~~~-~~~lG-~ilir~~ 78 (78)
+....|+++|.+++++ +|.|+|++ |+++.|+|.|||+|||++|+||+|+.. +++. ...+| .++|||+
T Consensus 3 ~~~~~~~~~l~~~~~~--~V~V~lk~--g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~ 72 (79)
T COG1958 3 MLGPLPLSFLKKLLNK--RVLVKLKN--GREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGD 72 (79)
T ss_pred cccCCcHHHHHHhhCC--EEEEEECC--CCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECC
Confidence 3456899999999995 49999977 899999999999999999999999963 4444 34555 9999995
No 13
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.81 E-value=1.7e-19 Score=110.11 Aligned_cols=61 Identities=26% Similarity=0.429 Sum_probs=51.6
Q ss_pred HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC-------CeeeeeeEEEEecC
Q 034947 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK-------NTRKPLGFFSKETT 78 (78)
Q Consensus 14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~-------~~~~~lG~ilir~~ 78 (78)
..-|.++++++ |.|.+++ ||++.|+|.|||+||||||+||+|+..+. +..+.+|.++|||.
T Consensus 4 ~~~L~~~i~k~--V~V~l~~--gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~ 71 (81)
T cd01729 4 ILDLSKYVDKK--IRVKFQG--GREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGT 71 (81)
T ss_pred hhhHHHhcCCe--EEEEECC--CcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCC
Confidence 34489999976 8888855 99999999999999999999999996432 35688999999995
No 14
>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=99.79 E-value=4.1e-19 Score=107.08 Aligned_cols=63 Identities=13% Similarity=0.130 Sum_probs=56.4
Q ss_pred ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
.|+++|+++.+++ |.|.||+ |+++.|+|.+||+|||++|+||+|...+++....+|.++|||.
T Consensus 1 ~Pl~~L~~~~g~~--V~VeLkn--g~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~ 63 (76)
T cd01723 1 LPLSLLKTAQNHP--MLVELKN--GETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGN 63 (76)
T ss_pred CchHHHHhcCCCE--EEEEECC--CCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCC
Confidence 4999999999965 9999977 8999999999999999999999998666666677899999995
No 15
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.78 E-value=1.5e-18 Score=104.67 Aligned_cols=63 Identities=24% Similarity=0.329 Sum_probs=53.2
Q ss_pred ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCC--eeeeeeEEEEecC
Q 034947 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKN--TRKPLGFFSKETT 78 (78)
Q Consensus 12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~--~~~~lG~ilir~~ 78 (78)
.++..|.++++++ |.|.+++ |+++.|+|.|||+|||++|+||+|+...++ ..+.+|.+++||.
T Consensus 2 ~~~~~L~~~l~k~--v~V~l~~--gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~ 66 (74)
T cd01728 2 PGTASLVDDLDKK--VVVLLRD--GRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGE 66 (74)
T ss_pred CchHHHHHhcCCE--EEEEEcC--CeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECC
Confidence 3577899999976 7777755 999999999999999999999999864432 4678999999994
No 16
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.77 E-value=2e-18 Score=104.54 Aligned_cols=60 Identities=25% Similarity=0.485 Sum_probs=50.6
Q ss_pred HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC---------CeeeeeeEEEEecC
Q 034947 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK---------NTRKPLGFFSKETT 78 (78)
Q Consensus 15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~---------~~~~~lG~ilir~~ 78 (78)
+-|.++++++ |.|.+++ ||++.|+|.|||+||||||+||+|++... .+.+.+|.++|||.
T Consensus 3 ~~l~~~l~~~--V~V~l~d--gR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~ 71 (79)
T cd01717 3 SKMLQLINYR--LRVTLQD--GRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGE 71 (79)
T ss_pred chhHHHcCCE--EEEEECC--CcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCC
Confidence 3478899976 8888855 99999999999999999999999986422 35688999999995
No 17
>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=99.76 E-value=3.1e-18 Score=101.87 Aligned_cols=61 Identities=18% Similarity=0.165 Sum_probs=53.9
Q ss_pred hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
|+++|.++.++. |+|+||+ |.++.|+|.+||.|||++|+||+|...+++ ...+|+++|||.
T Consensus 1 P~~~L~~~~g~~--V~VeLk~--g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~-~~~~~~v~IRG~ 61 (70)
T cd01721 1 PIKLLHEAEGHI--VTVELKT--GEVYRGKLIEAEDNMNCQLKDVTVTARDGR-VSQLEQVYIRGS 61 (70)
T ss_pred ChHHHhhCCCCE--EEEEECC--CcEEEEEEEEEcCCceeEEEEEEEECCCCc-EeEcCcEEEeCC
Confidence 899999999965 9999987 899999999999999999999998754544 567899999995
No 18
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.75 E-value=7.5e-18 Score=101.01 Aligned_cols=60 Identities=23% Similarity=0.364 Sum_probs=50.1
Q ss_pred HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec---CCeeeeeeEEEEecC
Q 034947 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK---KNTRKPLGFFSKETT 78 (78)
Q Consensus 15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~---~~~~~~lG~ilir~~ 78 (78)
..|.++++++ |.|.+ .+|+.+.|+|.|||+|||++|++|+|+... +...+.+|.++|||.
T Consensus 2 ~~L~~~l~~~--V~V~l--~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~ 64 (74)
T cd01727 2 STLEDYLNKT--VSVIT--VDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGD 64 (74)
T ss_pred hhHHHhcCCE--EEEEE--CCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCC
Confidence 3578899976 76766 559999999999999999999999998542 335778999999995
No 19
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.74 E-value=8.1e-18 Score=97.87 Aligned_cols=59 Identities=25% Similarity=0.486 Sum_probs=52.3
Q ss_pred HHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 16 ~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
+|.++++++ |.|.+++ |+.+.|+|.+||+|||++|+||+|+..+......+|.++|||.
T Consensus 2 ~L~~~~~~~--V~V~l~~--g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~ 60 (67)
T smart00651 2 FLKKLIGKR--VLVELKN--GREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60 (67)
T ss_pred hhHHhCCcE--EEEEECC--CcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCC
Confidence 688999975 8888866 8999999999999999999999999755467889999999995
No 20
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.74 E-value=4e-18 Score=102.69 Aligned_cols=58 Identities=22% Similarity=0.482 Sum_probs=50.8
Q ss_pred HHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 16 ~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
-|++|++|+ +.++| +++|.+.|+|+|||.|||+||+||+|.. ..+.+.++|.++|||.
T Consensus 8 eLkkymdKk--i~lkl--nG~r~v~GiLrGyD~FmNiVlde~vE~~-~~~~~~~ig~~vIrgn 65 (77)
T KOG1780|consen 8 ELKKYMDKK--IVLKL--NGGRKVTGILRGYDPFMNIVLDETVEPN-GDGDKNNIGMVVIRGN 65 (77)
T ss_pred hHHHhhhhe--EEEEe--CCCcEEEEEEeccchHHhhhhhhceeec-CcCCcceeeeEEEecc
Confidence 789999987 55555 8899999999999999999999999995 5556788999999983
No 21
>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=99.73 E-value=2.2e-17 Score=96.18 Aligned_cols=60 Identities=23% Similarity=0.479 Sum_probs=52.3
Q ss_pred HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
++|.++++++ |.|.+++ |+.+.|+|.+||+|||++|+||.|...++.+.+.+|.++|||.
T Consensus 1 ~~L~~~~g~~--V~V~l~~--g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~ 60 (67)
T PF01423_consen 1 NFLQKLIGKR--VRVELKN--GRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGS 60 (67)
T ss_dssp HHHHHTTTSE--EEEEETT--SEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGG
T ss_pred ChhHHhCCcE--EEEEEeC--CEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECC
Confidence 4789999965 8888855 9999999999999999999999999644448899999999994
No 22
>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=99.73 E-value=3.4e-17 Score=98.95 Aligned_cols=60 Identities=17% Similarity=0.241 Sum_probs=51.5
Q ss_pred HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec-----CCeeeeeeEEEEecC
Q 034947 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK-----KNTRKPLGFFSKETT 78 (78)
Q Consensus 15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~-----~~~~~~lG~ilir~~ 78 (78)
+.|.++++++ |.|.+++ ||.+.|+|.+||+||||+|+||.|+..+ ..+.+.+|.++|||.
T Consensus 3 ~~L~~~l~~~--v~V~l~d--gR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~ 67 (75)
T cd06168 3 QKLRSLLGRT--MRIHMTD--GRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGH 67 (75)
T ss_pred hHHHHhcCCe--EEEEEcC--CeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCC
Confidence 4688899976 7777754 9999999999999999999999999743 246889999999995
No 23
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.71 E-value=1.7e-17 Score=99.84 Aligned_cols=62 Identities=24% Similarity=0.297 Sum_probs=58.1
Q ss_pred ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEe
Q 034947 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKE 76 (78)
Q Consensus 10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir 76 (78)
..+|..||+...+| +|.|+||+ |.+|+|+|++.|.||||.|.+|+|+ .++....++|+|+||
T Consensus 6 PvNPKpFL~~l~gk--~V~vkLKw--g~eYkG~LvsvD~YmNlqL~~~eE~-idG~~~g~lGEilIR 67 (79)
T KOG3482|consen 6 PVNPKPFLNGLTGK--PVLVKLKW--GQEYKGTLVSVDNYMNLQLANAEEY-IDGVSTGNLGEILIR 67 (79)
T ss_pred cCCchHHHhhccCC--eEEEEEec--CcEEEEEEEEecchhheehhhhhhh-hcccccccceeEEEE
Confidence 46999999999996 59999988 8999999999999999999999999 699999999999998
No 24
>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=99.70 E-value=8.9e-17 Score=99.97 Aligned_cols=61 Identities=21% Similarity=0.301 Sum_probs=54.7
Q ss_pred hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
|+.||.++.++. |+|+||+ |..|.|+|.++|.|||++|+||+|.. +++....+|.++|||.
T Consensus 2 ~~~fL~~l~g~~--V~VeLKn--g~~~~G~L~~vD~~MNl~L~~a~~~~-~~~~~~~~~~v~IRG~ 62 (90)
T cd01724 2 LVRFLMKLTNET--VTIELKN--GTIVHGTITGVDPSMNTHLKNVKLTL-KGRNPVPLDTLSIRGN 62 (90)
T ss_pred HhHHHHhCCCCE--EEEEECC--CCEEEEEEEEEcCceeEEEEEEEEEc-CCCceeEcceEEEeCC
Confidence 788999999965 9999987 88999999999999999999999984 5666788999999995
No 25
>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=99.68 E-value=2.4e-16 Score=90.42 Aligned_cols=57 Identities=30% Similarity=0.515 Sum_probs=49.3
Q ss_pred HHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 17 L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
|.++++++ |.|.+++ |+.+.|+|.+||+|||++|+||.|...+ .....+|.++|||.
T Consensus 1 l~~~~g~~--V~V~l~~--g~~~~G~L~~~D~~~Ni~L~~~~~~~~~-~~~~~~~~~~irG~ 57 (63)
T cd00600 1 LKDLVGKT--VRVELKD--GRVLEGVLVAFDKYMNLVLDDVEETIKE-GKKRVLGLVLIRGD 57 (63)
T ss_pred ChHHCCCE--EEEEECC--CcEEEEEEEEECCCCCEEECCEEEEecC-CcEEECCeEEEECC
Confidence 45778865 8888866 8999999999999999999999999643 66788999999995
No 26
>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=99.67 E-value=2.7e-16 Score=95.93 Aligned_cols=63 Identities=16% Similarity=0.213 Sum_probs=53.3
Q ss_pred ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC-CeeeeeeEEEEecC
Q 034947 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK-NTRKPLGFFSKETT 78 (78)
Q Consensus 12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~-~~~~~lG~ilir~~ 78 (78)
.|++||.++.++. |+|.||+ |..+.|+|.++|.|||++|+||++...++ .....+|.++|||.
T Consensus 1 l~~~fL~~l~g~~--V~VeLKn--g~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~ 64 (81)
T cd01725 1 LFFSFFKTLVGKE--VTVELKN--DLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGS 64 (81)
T ss_pred ChhHHHHhCCCCE--EEEEECC--CcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECC
Confidence 4889999999865 9999987 88999999999999999999998874333 23456799999995
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=99.66 E-value=4.8e-16 Score=94.41 Aligned_cols=63 Identities=16% Similarity=0.235 Sum_probs=54.5
Q ss_pred cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
..+..+|..+.++. |+|.||+ |..|.|+|.++|.|||++|+||++.. .++....+|.++|||.
T Consensus 8 ~tl~~~L~~l~g~~--V~VeLKn--g~~~~G~L~~vD~~MNl~L~~~~~~~-~~~~~~~~~~v~IRG~ 70 (78)
T cd01733 8 NTLIILLQGLQGKV--VTVELRN--ETTVTGRIASVDAFMNIRLAKVTIID-RNGKQVQVEEIMVTGR 70 (78)
T ss_pred chHHHHHHHCCCCE--EEEEECC--CCEEEEEEEEEcCCceeEEEEEEEEc-CCCceeECCcEEEECC
Confidence 46788999999865 9999987 78999999999999999999999884 4445568999999995
No 28
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.64 E-value=1.2e-16 Score=97.01 Aligned_cols=65 Identities=29% Similarity=0.554 Sum_probs=56.8
Q ss_pred ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec--CCeeeeeeEEEEecC
Q 034947 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK--KNTRKPLGFFSKETT 78 (78)
Q Consensus 10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~--~~~~~~lG~ilir~~ 78 (78)
...|++++.++++.+ ||+..++++++.|+|.|||.|.|+||+|++||..+ ++...++++++++|.
T Consensus 5 ~llPlEliDkcIgsk----i~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGN 71 (84)
T KOG1775|consen 5 TLLPLELIDKCIGSK----IWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGN 71 (84)
T ss_pred hcccHHHHHHhcCce----EEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCC
Confidence 368999999999987 66666779999999999999999999999999754 457889999999983
No 29
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.60 E-value=6.5e-17 Score=102.13 Aligned_cols=65 Identities=26% Similarity=0.357 Sum_probs=54.5
Q ss_pred ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecC-------CeeeeeeEEEEecC
Q 034947 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK-------NTRKPLGFFSKETT 78 (78)
Q Consensus 10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~-------~~~~~lG~ilir~~ 78 (78)
-...+--|.+|++|+ |++|..+||+..|+|.|||+.|||||+|++|+-.+. ++.+.||.+++|||
T Consensus 15 kkEsilDLsky~Dk~----Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGT 86 (108)
T KOG1781|consen 15 KKESILDLSKYLDKK----IRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGT 86 (108)
T ss_pred chhHHhhHHHhhccc----eEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEccc
Confidence 345567899999988 555558899999999999999999999999995442 35699999999998
No 30
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.58 E-value=2.1e-16 Score=95.09 Aligned_cols=63 Identities=17% Similarity=0.341 Sum_probs=57.9
Q ss_pred cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
..|-+||.+++++. |.|+| ++|..|.|+|...|.|||+.|+.++|+ .+++..+++|++||||+
T Consensus 5 ~~~~~fl~~iiGr~--V~VKl--~sgvdyrG~l~~lDgymNiaLe~tee~-~ngql~n~ygdaFirGn 67 (77)
T KOG1783|consen 5 SMPGEFLKAIIGRT--VVVKL--NSGVDYRGTLVCLDGYMNIALESTEEY-VNGQLKNKYGDAFIRGN 67 (77)
T ss_pred cCcHHHHHHHhCCe--EEEEe--cCCccccceehhhhhHHHHHHHHHHHH-hcCcccccccceeeccc
Confidence 57999999999975 77777 779999999999999999999999999 59999999999999995
No 31
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.37 E-value=1e-13 Score=85.37 Aligned_cols=65 Identities=25% Similarity=0.426 Sum_probs=53.8
Q ss_pred ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec--C----------CeeeeeeEEEEec
Q 034947 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK--K----------NTRKPLGFFSKET 77 (78)
Q Consensus 10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~--~----------~~~~~lG~ilir~ 77 (78)
+..|+++|+-+++++ |-|+++ ++|++.|+|.|||+|+|++|.||+|.... . ..++.+-.+|+||
T Consensus 3 v~ePldllrlsLdEr--VyVKlr--~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRG 78 (91)
T KOG3460|consen 3 VEEPLDLLRLSLDER--VYVKLR--SDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRG 78 (91)
T ss_pred ccccHHHHhhcccce--EEEEec--CChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeC
Confidence 678999999999976 666665 49999999999999999999999998531 1 2457788899998
Q ss_pred C
Q 034947 78 T 78 (78)
Q Consensus 78 ~ 78 (78)
.
T Consensus 79 d 79 (91)
T KOG3460|consen 79 D 79 (91)
T ss_pred C
Confidence 3
No 32
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.13 E-value=8.5e-11 Score=76.95 Aligned_cols=63 Identities=16% Similarity=0.138 Sum_probs=57.4
Q ss_pred ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
.|+.+|..+-+ .|+.|.||+ |-.|.|.|..+|.+|||.|.+++++..|+..--.+-++-||||
T Consensus 2 lPLsLL~~aq~--~pmlvELKN--get~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGt 64 (134)
T KOG3293|consen 2 LPLSLLKTAQN--HPMLVELKN--GETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGT 64 (134)
T ss_pred cchhHHHhcCC--CeEEEEecC--CCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecc
Confidence 69999999988 579999998 6679999999999999999999999888888788889999997
No 33
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.03 E-value=2.5e-11 Score=82.93 Aligned_cols=57 Identities=26% Similarity=0.454 Sum_probs=46.5
Q ss_pred HHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEe---------cCCeeeeeeEEEEecC
Q 034947 18 FRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI---------KKNTRKPLGFFSKETT 78 (78)
Q Consensus 18 ~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~---------~~~~~~~lG~ilir~~ 78 (78)
-+.+|-+ ..|.+ +++|.+.|.+.+||.|||+||.||+|+.. +.++++.+|.+++||.
T Consensus 10 l~~iNyr--~rv~~--qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRge 75 (177)
T KOG3168|consen 10 LQHINYR--MRVRL--QDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGE 75 (177)
T ss_pred HHhhcce--EEEEe--ccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCC
Confidence 3455655 55555 66999999999999999999999999842 3578999999999983
No 34
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.95 E-value=7.2e-10 Score=69.28 Aligned_cols=59 Identities=19% Similarity=0.371 Sum_probs=50.0
Q ss_pred HHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec---CCeeeeeeEEEEecC
Q 034947 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK---KNTRKPLGFFSKETT 78 (78)
Q Consensus 16 ~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~---~~~~~~lG~ilir~~ 78 (78)
-|..|+++. |.+..++||-+.|.|.|||+-.||+|+|+.|+..+ +.+...+|.=+|||.
T Consensus 4 ~L~~y~n~~----V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirge 65 (96)
T KOG1784|consen 4 TLEDYMNQR----VSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGE 65 (96)
T ss_pred hHHHHhhce----EEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecC
Confidence 478899987 55566889999999999999999999999999644 346788999999983
No 35
>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=98.89 E-value=8.8e-10 Score=65.17 Aligned_cols=45 Identities=27% Similarity=0.478 Sum_probs=38.1
Q ss_pred HHhhcCcceEEEEEEecCCe--EEEEEEEEeccccceeEeceEEEEe
Q 034947 18 FRFLQSKARIQIWLFEQKDL--RIEGRIIGFDEYMNLVLDDAEEVHI 62 (78)
Q Consensus 18 ~~~~~k~~~V~V~lk~~~~~--~~~G~L~gfD~~mNlvL~da~E~~~ 62 (78)
.+++..+.+|.|.++..++. .++|.|++||.||||+|.|+.|.+.
T Consensus 2 ~~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~ 48 (66)
T cd01739 2 HRCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR 48 (66)
T ss_pred chhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence 45667778999999876663 5899999999999999999999973
No 36
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.77 E-value=3.8e-08 Score=61.37 Aligned_cols=62 Identities=19% Similarity=0.203 Sum_probs=48.1
Q ss_pred hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCC-eeeeeeEEEEecC
Q 034947 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKN-TRKPLGFFSKETT 78 (78)
Q Consensus 13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~-~~~~lG~ilir~~ 78 (78)
-.+|++..+++. |.|.||+ +..+.|+|.+.|+|+|+-|+|..-...+.- --...-.++|||.
T Consensus 3 FysfFkslvg~~--V~VeLKn--d~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGS 65 (96)
T KOG3448|consen 3 FYSFFKSLVGKE--VVVELKN--DLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGS 65 (96)
T ss_pred hHHHHHHhcCCe--EEEEEcC--CcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEecc
Confidence 367899999976 9999998 899999999999999999999876632211 1223456788884
No 37
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.75 E-value=8.5e-10 Score=72.13 Aligned_cols=58 Identities=26% Similarity=0.438 Sum_probs=49.0
Q ss_pred HHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCC--eeeeeeEEEEecC
Q 034947 17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKN--TRKPLGFFSKETT 78 (78)
Q Consensus 17 L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~--~~~~lG~ilir~~ 78 (78)
+..+++++ +.|-|++ ||.+.|.|++||+|-|++|++|+|...-++ -....|..+|||.
T Consensus 14 l~~~~dkK--llVlLRD--GR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGE 73 (129)
T KOG1782|consen 14 LVEYLDKK--LLVLLRD--GRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGE 73 (129)
T ss_pred HHHHhcce--EEEEEec--CcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecC
Confidence 77889987 8899977 999999999999999999999999865332 2456799999983
No 38
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.75 E-value=7.7e-10 Score=71.12 Aligned_cols=64 Identities=16% Similarity=0.320 Sum_probs=56.9
Q ss_pred ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEec------CC------eeeeeeEEEEec
Q 034947 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK------KN------TRKPLGFFSKET 77 (78)
Q Consensus 12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~------~~------~~~~lG~ilir~ 77 (78)
.|++.+...+....+|+|.+++ ++.+.|++.|||.|.|++|+++.|.|.+ +. ..+.+|.++|||
T Consensus 24 Gpls~~~~~~~~~~~vLi~cRn--n~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRG 99 (114)
T KOG3459|consen 24 GPLSVLPASVKNNTQVLINCRN--NVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRG 99 (114)
T ss_pred CchhhhHHHhhcCceeEEEecc--cHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecC
Confidence 8999999999999999999987 7889999999999999999999998742 11 256789999999
No 39
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=98.26 E-value=2.3e-06 Score=55.11 Aligned_cols=64 Identities=16% Similarity=0.121 Sum_probs=52.7
Q ss_pred ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEecC
Q 034947 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKETT 78 (78)
Q Consensus 10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~~ 78 (78)
+.-|+.+|+.+-+. -|++.+.+ |-.|.|+|.-.+.+||++|+|.+-...+ .....+-.|+|||.
T Consensus 3 ~gvpiKlLhEaqGh--IVt~Et~t--Ge~YRGkliEaeDnmNcql~di~vT~~d-g~vs~le~V~IRGS 66 (119)
T KOG3172|consen 3 VGVPIKLLHEAQGH--IVTVETKT--GEVYRGKLIEAEDNMNCQLRDITVTARD-GRVSQLEQVFIRGS 66 (119)
T ss_pred cccceeeeecccCc--EEEEEecC--CceeeeeeEEeccccccEEEEEEEEccC-CcceeeeeEEEecC
Confidence 34689999999884 47777755 7889999999999999999999877544 45677899999984
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=97.93 E-value=7.3e-05 Score=48.08 Aligned_cols=58 Identities=21% Similarity=0.223 Sum_probs=47.3
Q ss_pred HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEec
Q 034947 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKET 77 (78)
Q Consensus 14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~ 77 (78)
..+|.++.++. |+|.|++ +....|++.+.|.+||..|.++.-.. .+ +...+-.+.+||
T Consensus 4 vr~L~kl~~e~--vtIeLkn--gt~v~G~I~~Vd~~Mn~~l~~v~~t~-~~-~pv~l~~lsirg 61 (109)
T KOG3428|consen 4 VRFLKKLLNER--VTIELKN--GTIVHGTIDSVDVQMNTHLKHVKMTV-KG-EPVRLDTLSIRG 61 (109)
T ss_pred HHHHHHhhCCe--EEEEecC--CcEEeeeEEEEEhhheeEEEEEEEec-CC-CceeEEEEEeec
Confidence 46888998865 9999988 78899999999999999999877553 44 445677787777
No 41
>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=97.78 E-value=9.5e-05 Score=43.22 Aligned_cols=37 Identities=22% Similarity=0.493 Sum_probs=32.2
Q ss_pred HHHHHhhcCcceEEEEEEecCCeEEEEEEEEecccccee
Q 034947 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLV 53 (78)
Q Consensus 15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlv 53 (78)
.+|+.+-.++.+|+|.|.+ |.+++|.+.|||+|+=++
T Consensus 2 ~fln~~r~~~~~Vtv~L~N--G~~l~G~I~~fD~ftVll 38 (61)
T cd01716 2 QFLNAARKEKIPVTIYLVN--GVQLKGQIESFDNFTVLL 38 (61)
T ss_pred HHHHHHHHcCCcEEEEEeC--CcEEEEEEEEEcceEEEE
Confidence 3678888888999999988 899999999999999443
No 42
>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=97.76 E-value=0.00011 Score=42.96 Aligned_cols=37 Identities=16% Similarity=0.486 Sum_probs=32.4
Q ss_pred HHHHHhhcCcceEEEEEEecCCeEEEEEEEEecccccee
Q 034947 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLV 53 (78)
Q Consensus 15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlv 53 (78)
.+|+.+-.++.+|+|.|.+ |..++|.+.|||.|+=++
T Consensus 6 ~fln~~r~~~~~Vti~L~n--G~~l~G~I~~fD~ftVll 42 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVN--GVQLKGVIESFDNFTVLL 42 (61)
T ss_pred HHHHHHHHcCCcEEEEEeC--CcEEEEEEEEEeeeEEEE
Confidence 4788888888999999987 899999999999999444
No 43
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=97.61 E-value=0.00022 Score=43.65 Aligned_cols=41 Identities=17% Similarity=0.479 Sum_probs=34.0
Q ss_pred HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (78)
Q Consensus 14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d 56 (78)
-.+|+.+-.++.+|+|.|.+ |.++.|.+.|||.|+=|+-.+
T Consensus 9 d~fLn~lr~~~~~VtifL~N--G~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 9 DPFLNALRKERVPVTIYLVN--GIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred HHHHHHHHHcCCCEEEEEeC--CcEEEEEEEEEccEEEEEEEC
Confidence 35788888888999999988 899999999999999444333
No 44
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=97.47 E-value=0.00049 Score=41.86 Aligned_cols=39 Identities=18% Similarity=0.571 Sum_probs=32.4
Q ss_pred HHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (78)
Q Consensus 15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d 56 (78)
.||+.+-.++.+|.|.|.| |..+.|.+.|||+|. +.|++
T Consensus 10 ~fLn~~Rk~~i~VtIfLvN--G~~L~G~V~sfD~f~-VlL~~ 48 (77)
T COG1923 10 PFLNALRKEKIPVTIFLVN--GFKLQGQVESFDNFV-VLLKN 48 (77)
T ss_pred HHHHHHHhcCCeEEEEEEc--CEEEEEEEEeeeeEE-EEEEc
Confidence 4677777777899999988 899999999999998 44444
No 45
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=97.22 E-value=0.00095 Score=45.77 Aligned_cols=41 Identities=20% Similarity=0.402 Sum_probs=34.2
Q ss_pred HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (78)
Q Consensus 14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d 56 (78)
-.+|+.+-.++.+|+|.|.+ |.+++|.+.|||.|.=|+-.+
T Consensus 14 D~fLn~~Rk~k~~VtvfL~n--G~rl~G~I~~fD~ftVlL~~~ 54 (165)
T PRK14091 14 DIFLNSLRKTKTPVTMFLVK--GVKLQGIITWFDNFSILLRRD 54 (165)
T ss_pred HHHHHHHHhcCCcEEEEEec--CcEEEEEEEEEcceEEEEEeC
Confidence 45888888999999999987 899999999999998444334
No 46
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=96.84 E-value=0.0035 Score=43.00 Aligned_cols=41 Identities=20% Similarity=0.345 Sum_probs=34.5
Q ss_pred HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (78)
Q Consensus 14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d 56 (78)
-.+|+.+-.++.+|+|.|.+ |.+++|.+.|||.|.=|.-.+
T Consensus 94 d~fLn~~rk~k~~VtvfL~N--G~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 94 DVFLSAVRDSGEPVTMFLVN--GVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred HHHHHHHHhcCCcEEEEEec--CcEEEEEEEEEcceEEEEEeC
Confidence 45888888999999999987 899999999999999444334
No 47
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=95.78 E-value=0.028 Score=33.16 Aligned_cols=42 Identities=17% Similarity=0.183 Sum_probs=31.5
Q ss_pred HHHHhhcCcceEEEEEEecCCeEEEEEEEEecc---ccceeEeceEEEE
Q 034947 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDE---YMNLVLDDAEEVH 61 (78)
Q Consensus 16 ~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~---~mNlvL~da~E~~ 61 (78)
++..++++. |.|.+++ |..|+|.+.+++. =+.++|.-|....
T Consensus 6 l~~~lvG~~--V~V~~~~--G~~yeGif~s~s~~~~~~~vvLk~a~~~~ 50 (77)
T PF14438_consen 6 LLTNLVGQT--VEVTTKN--GSVYEGIFHSASPESNEFDVVLKMARKVP 50 (77)
T ss_dssp HHHTTTTSE--EEEEETT--S-EEEEEEEEE-T---T--EEEEEEEETT
T ss_pred HHHhCcCCE--EEEEECC--CCEEEEEEEeCCCcccceeEEEEeeeecc
Confidence 566778855 8888876 8899999999999 8999999888763
No 48
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=93.77 E-value=0.41 Score=25.94 Aligned_cols=47 Identities=21% Similarity=0.192 Sum_probs=32.7
Q ss_pred hcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEe
Q 034947 21 LQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKE 76 (78)
Q Consensus 21 ~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir 76 (78)
+++. |.+.. + +..+.|+..|+|..=.|+++..... .....-|+|.+|
T Consensus 2 lG~~--V~v~~--~-~~~~~G~~~gId~~G~L~v~~~~g~----~~~i~sGdv~~r 48 (48)
T PF02237_consen 2 LGQE--VRVET--G-DGEIEGIAEGIDDDGALLVRTEDGS----IRTISSGDVSLR 48 (48)
T ss_dssp TTSE--EEEEE--T-SCEEEEEEEEEETTSEEEEEETTEE----EEEESSSEEEEE
T ss_pred CCCE--EEEEE--C-CeEEEEEEEEECCCCEEEEEECCCC----EEEEEEEEEEeC
Confidence 4554 65555 3 5678999999999999998764431 234556777765
No 49
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=93.40 E-value=0.31 Score=30.57 Aligned_cols=55 Identities=18% Similarity=0.323 Sum_probs=40.1
Q ss_pred HhhcCcceEEEEEEecCCeEEEEEEEEecc-ccceeEeceEEEEecCC--------eeeeeeEEEEec
Q 034947 19 RFLQSKARIQIWLFEQKDLRIEGRIIGFDE-YMNLVLDDAEEVHIKKN--------TRKPLGFFSKET 77 (78)
Q Consensus 19 ~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~-~mNlvL~da~E~~~~~~--------~~~~lG~ilir~ 77 (78)
.|++++ |.|..+.+.+|+|+|...|. --.|.|.++.-+-.++. ....+..|+.||
T Consensus 5 ~~IGs~----ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~ 68 (96)
T PF12701_consen 5 PYIGSK----ISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRG 68 (96)
T ss_dssp CCTTCE----EEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEET
T ss_pred cccCCE----EEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEc
Confidence 478877 66666779999999999998 56799999887632221 123567777776
No 50
>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=91.44 E-value=1.5 Score=26.44 Aligned_cols=56 Identities=16% Similarity=0.297 Sum_probs=39.5
Q ss_pred HhhcCcceEEEEEEecCCeEEEEEEEEeccccc-eeEeceEEEEecCC---------eeeeeeEEEEecC
Q 034947 19 RFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMN-LVLDDAEEVHIKKN---------TRKPLGFFSKETT 78 (78)
Q Consensus 19 ~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mN-lvL~da~E~~~~~~---------~~~~lG~ilir~~ 78 (78)
.+++++ |.|..+.+.+|+|+|-.+|..=. +.|.|+..+-.++. ....+..|+.||+
T Consensus 3 ~~IG~~----isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgs 68 (74)
T cd01736 3 PYIGSK----ISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGS 68 (74)
T ss_pred cccCce----EEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCC
Confidence 478877 66666779999999999988764 66888877633221 1234677777774
No 51
>PRK14633 hypothetical protein; Provisional
Probab=91.32 E-value=0.74 Score=30.73 Aligned_cols=50 Identities=12% Similarity=0.213 Sum_probs=34.0
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-+| .+++++. |.|.++. ++.+++.|+|.++|+- ++.|+
T Consensus 75 SSPGldRpL~~~~~f-~r~~G~~--v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 75 SSPGMNRQIFNIIQA-QALVGFN--VKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred eCCCCCCCCCCHHHH-HHhCCCe--EEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 555444555555555 4778876 7777764 4679999999999885 34453
No 52
>PRK14634 hypothetical protein; Provisional
Probab=90.34 E-value=1 Score=30.22 Aligned_cols=50 Identities=14% Similarity=0.263 Sum_probs=34.1
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEec--CCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ--KDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~--~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-+|- +++++. |.|+++.. +.+++.|+|.++|+- ++.|+
T Consensus 81 SSPGldRpL~~~~~f~-r~~G~~--V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14634 81 SSPGIGDQLSSDRDFQ-TFRGFP--VEVSHRDDDGSEQRLEGLLLERNED-HLQIN 132 (155)
T ss_pred eCCCCCCcCCCHHHHH-HhCCCe--EEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence 5654556666666654 677876 88887643 348899999999884 34443
No 53
>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=89.98 E-value=1.3 Score=26.41 Aligned_cols=50 Identities=18% Similarity=0.411 Sum_probs=32.6
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-++ .+++++. |.|+++. ++.+++.|.|.++|+- +++|.
T Consensus 6 SSPGl~RpL~~~~~~-~r~~G~~--v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l~ 57 (83)
T cd01734 6 SSPGAERPLKKEADF-ERAVGKY--VHVKLYQPIDGQKEFEGTLLGVDDD-TVTLE 57 (83)
T ss_pred cCCCCCCcCCCHHHH-HHhCCCE--EEEEEEcccCCeEEEEEEEEeEeCC-EEEEE
Confidence 555445555666555 4677866 7777763 3347899999999883 34443
No 54
>PRK14638 hypothetical protein; Provisional
Probab=89.37 E-value=1.1 Score=29.98 Aligned_cols=48 Identities=21% Similarity=0.303 Sum_probs=32.4
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-+|. +++++. |.|+++ +++++.|+|.++|.- ++.|+
T Consensus 81 SSPGldRpL~~~~~f~-r~~G~~--v~V~~~--~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 81 SSPGLDRPLRGPKDYV-RFTGKL--AKIVTK--DGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred eCCCCCCCCCCHHHHH-HhCCCE--EEEEEC--CCcEEEEEEEEEeCC-EEEEE
Confidence 5554445555665554 678876 777774 479999999999974 34443
No 55
>PRK14636 hypothetical protein; Provisional
Probab=88.20 E-value=1.7 Score=29.89 Aligned_cols=50 Identities=20% Similarity=0.349 Sum_probs=33.6
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-+| .+++++. |.|+++. ++.+++.|+|.++|+- ++.|.
T Consensus 79 SSPGldRpL~~~~df-~r~~G~~--V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~ 130 (176)
T PRK14636 79 SSPGIDRPLTRPKDF-ADWAGHE--ARIALSEPLDGRKQFRGELKGIDGD-TVTIA 130 (176)
T ss_pred eCCCCCCCCCCHHHH-HHhCCCe--EEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence 565455666666554 5788876 7777763 2347999999999873 35543
No 56
>PRK14643 hypothetical protein; Provisional
Probab=88.18 E-value=1.8 Score=29.39 Aligned_cols=49 Identities=14% Similarity=0.223 Sum_probs=32.9
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccc-ccee
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEY-MNLV 53 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~-mNlv 53 (78)
||+-..++...|-+| .+++++. |.|+++. ++.+++.|+|.++|.- ..+.
T Consensus 85 SSPGleRpL~~~~df-~r~~G~~--V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~ 136 (164)
T PRK14643 85 SSSGIEKQIRSQEEL-VKALNQW--VYVQLNNEIKKVKEFEGYVTKYNVNTNTFR 136 (164)
T ss_pred cCCCCCCCCCCHHHH-HHhcCCe--EEEEEecccCCceEEEEEEEEEeCCcEEEE
Confidence 565445555555555 4677876 7777765 3458899999999864 3443
No 57
>PRK14639 hypothetical protein; Provisional
Probab=87.78 E-value=1.6 Score=28.80 Aligned_cols=47 Identities=19% Similarity=0.347 Sum_probs=32.6
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeE
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL 54 (78)
||+-..++...|-++ .+++++. |.|++. +++++.|+|.++|+- ++.|
T Consensus 69 SSPGl~RpL~~~~~f-~r~~G~~--v~v~l~--~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 69 SSPGLERKLSKIEHF-AKSIGEL--VKITTN--EKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCE--EEEEEC--CCcEEEEEEEEEeCC-EEEE
Confidence 555445555555554 5788876 777774 479999999999883 4555
No 58
>PRK14640 hypothetical protein; Provisional
Probab=87.77 E-value=2 Score=28.66 Aligned_cols=50 Identities=12% Similarity=0.181 Sum_probs=34.0
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-+|. +++++. |.|+++. ++.+++.|+|.++|+- ++.|+
T Consensus 78 SSPGl~RpL~~~~~f~-r~~G~~--v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 78 SSPGLDRPLFKVAQFE-KYVGQE--AAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred eCCCCCCcCCCHHHHH-HhCCCe--EEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 5554456666666554 678866 7777753 3568999999999984 34443
No 59
>PRK02001 hypothetical protein; Validated
Probab=87.31 E-value=1.8 Score=29.14 Aligned_cols=48 Identities=17% Similarity=0.311 Sum_probs=33.0
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-+|- +++++. |.|++. +++++.|+|.++|+- +++|+
T Consensus 71 SSPGldRpL~~~~~f~-r~~G~~--v~V~l~--~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 71 GSAGLTSPLKVPRQYK-KNIGRE--LEVLTK--NGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred eCCCCCCcCCCHHHHH-HhCCCE--EEEEEC--CCCEEEEEEEEEeCC-EEEEE
Confidence 5554455566665554 678866 777774 579999999999875 34443
No 60
>PRK14632 hypothetical protein; Provisional
Probab=86.46 E-value=2.4 Score=28.91 Aligned_cols=50 Identities=14% Similarity=0.322 Sum_probs=33.5
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEec-----CCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ-----KDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~-----~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-+| .+++++. |.|+++.. +.+++.|+|.++|+- +++|+
T Consensus 79 SSPGldRpL~~~~~f-~r~iG~~--V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 79 SSPGLERPFFRAEQM-SPYVGRQ--IELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCE--EEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 555444555555554 4778865 88888762 468999999999873 45554
No 61
>PRK14645 hypothetical protein; Provisional
Probab=84.88 E-value=2.7 Score=28.27 Aligned_cols=46 Identities=17% Similarity=0.198 Sum_probs=30.3
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeE
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL 54 (78)
||+-..++...|-+|. +++++. |.|. . +++++.|+|.++|+- .+.|
T Consensus 83 SSPGldRpL~~~~df~-r~~G~~--v~v~--~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 83 ESPGPKRPLFTARHFE-RFAGLK--AKVR--G-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred eCCCCCCCCCCHHHHH-HhCCCE--EEEE--c-CCeEEEEEEEEEeCC-EEEE
Confidence 5554455556665554 677876 5554 3 478999999999884 2444
No 62
>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=84.50 E-value=3.3 Score=24.02 Aligned_cols=31 Identities=13% Similarity=0.246 Sum_probs=24.3
Q ss_pred EEEEecCCeEEEEEEEEeccccceeEeceEE
Q 034947 29 IWLFEQKDLRIEGRIIGFDEYMNLVLDDAEE 59 (78)
Q Consensus 29 V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E 59 (78)
|++++-.|-+++|.+.+||.-.++++=.|.+
T Consensus 9 V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 9 VSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred EEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 6666677889999999999999877554443
No 63
>PRK14647 hypothetical protein; Provisional
Probab=83.99 E-value=4 Score=27.39 Aligned_cols=44 Identities=18% Similarity=0.339 Sum_probs=30.3
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEec-------CCeEEEEEEEEecc
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ-------KDLRIEGRIIGFDE 48 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~-------~~~~~~G~L~gfD~ 48 (78)
||+-..++...|-+| .+++++. |.|.++.. +.+++.|+|.++|+
T Consensus 80 SSPG~~RpL~~~~~f-~r~~G~~--v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 80 SSPGLDRPLKKEADY-ERYAGRL--VKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred cCCCCCCcCCCHHHH-HHhCCcE--EEEEEeccccccccCCceEEEEEEEeecC
Confidence 555444555555544 5778866 87887642 35899999999987
No 64
>PRK14644 hypothetical protein; Provisional
Probab=80.74 E-value=4.1 Score=26.84 Aligned_cols=49 Identities=14% Similarity=0.117 Sum_probs=32.9
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEec--CCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ--KDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~--~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...+ -+.+++++. |.|+++.. +.+++.|.|.++|+- ++.|+
T Consensus 67 SSPGldRpL~~~--~f~r~~G~~--v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 67 SSPGFDMDYETD--ELENHIGEI--IDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred ECCCCCCCCCHH--HHHHhCCCe--EEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 555444544442 478889976 77887653 238899999999984 35554
No 65
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=80.48 E-value=6.5 Score=26.02 Aligned_cols=44 Identities=18% Similarity=0.440 Sum_probs=30.0
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEecc
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDE 48 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~ 48 (78)
||+-..++...|-+ +.+++++. |.|+++. ++++++.|+|.++|+
T Consensus 79 SSPGi~RpL~~~~~-f~r~~G~~--v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 79 SSPGLDRPLKKARD-FRRFIGRE--VKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred eCCCCCCcCCCHHH-HHHhCCCe--EEEEEEcccCCceEEEEEEEEeeC
Confidence 55544444445544 45788876 7777653 467899999999987
No 66
>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=79.86 E-value=2.6 Score=27.39 Aligned_cols=37 Identities=24% Similarity=0.415 Sum_probs=24.1
Q ss_pred HHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEeccccceeE
Q 034947 15 NLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVL 54 (78)
Q Consensus 15 ~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD~~mNlvL 54 (78)
.-+.+++++. |.|+++. ++.+++.|+|.++|+ =.++|
T Consensus 80 ~~~~~~iG~~--v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 80 RDFERFIGRK--VKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHHH-SEE--EEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHHhcCCe--EEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 4566889965 7788742 334789999999998 33444
No 67
>PRK14635 hypothetical protein; Provisional
Probab=79.14 E-value=6.8 Score=26.36 Aligned_cols=49 Identities=18% Similarity=0.283 Sum_probs=32.9
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEE---EEEEeccccceeE
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEG---RIIGFDEYMNLVL 54 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G---~L~gfD~~mNlvL 54 (78)
||+-..++...|-++. ++.++. |.|.+..+++.++.| .|.++|+- ++.|
T Consensus 80 SSPGldRpL~~~~~~~-r~~G~~--v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 80 SSAGAERKLRLPEDLD-RFRGIP--VRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred cCCCCCCcCCCHHHHH-HhCCCE--EEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 5654556666666654 677865 777776555678888 99999874 3444
No 68
>PRK14646 hypothetical protein; Provisional
Probab=79.01 E-value=7.9 Score=25.92 Aligned_cols=50 Identities=16% Similarity=0.129 Sum_probs=32.6
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEec--CCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ--KDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~--~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-+ +.+++++. |.|+++.. +.+++.|+|.++|+- ++.|+
T Consensus 81 SSPGldRpL~~~~d-f~r~~G~~--v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 81 SSQGVSDELTSERD-FKTFKGFP--VNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred cCCCCCCcCCCHHH-HHHhCCCE--EEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 55544455555544 45677866 77877653 337789999999984 45553
No 69
>PRK14631 hypothetical protein; Provisional
Probab=73.90 E-value=12 Score=25.64 Aligned_cols=43 Identities=12% Similarity=0.255 Sum_probs=28.9
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEec--CCeEEEEEEEEec
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ--KDLRIEGRIIGFD 47 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~--~~~~~~G~L~gfD 47 (78)
||+-..++...|- -+.+++++. |.|+++.. +.++++|+|.++|
T Consensus 98 SSPGldRpL~~~~-df~r~~G~~--V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 98 SSPGWDRPFFQLE-QLQGYIGQQ--VALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred eCCCCCCcCCCHH-HHHHhCCCe--EEEEEecccCCceEEEEEEEEee
Confidence 5554444444544 455678876 77777532 5689999999998
No 70
>PRK14642 hypothetical protein; Provisional
Probab=70.35 E-value=14 Score=26.00 Aligned_cols=49 Identities=16% Similarity=0.203 Sum_probs=31.2
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEec-----------CCeEEEEEEEEeccccceeE
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ-----------KDLRIEGRIIGFDEYMNLVL 54 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~-----------~~~~~~G~L~gfD~~mNlvL 54 (78)
||+-..++...|-+| .+++++. |.|+++.. +.++|+|+|.++|+. ++.|
T Consensus 81 SSPGldRPLk~~~df-~rfiG~~--V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 81 SSPGIDRPLRHEQDF-ERFAGEV--IDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred eCCCCCCCCCCHHHH-HHhCCCe--EEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 444334444454444 5567865 77877621 468999999999884 4545
No 71
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.66 E-value=19 Score=24.29 Aligned_cols=50 Identities=22% Similarity=0.393 Sum_probs=32.2
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEE--ecCCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLF--EQKDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk--~~~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..+++..+ .-+.+++++. |.|+++ -++.+.++|+|.++|+-. ++++
T Consensus 80 SSPGldRpL~~~-~~f~r~~G~~--Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~~ 131 (153)
T COG0779 80 SSPGLDRPLKTA-EHFARFIGEK--VKVKLRLPIEGRKKFEGKIVAVDGET-VTLE 131 (153)
T ss_pred eCCCCCCCcCCH-HHHHHhcCcE--EEEEEecccCCceEEEEEEEEEcCCe-EEEE
Confidence 444323333333 4566788977 666663 245788999999999987 4443
No 72
>PRK14641 hypothetical protein; Provisional
Probab=63.64 E-value=24 Score=24.21 Aligned_cols=43 Identities=9% Similarity=0.131 Sum_probs=27.7
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEe--cCCeEEEEEEEEec
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFD 47 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~--~~~~~~~G~L~gfD 47 (78)
||+-..++...|- -+.+++++. |.|.++. ++.+++.|+|.++|
T Consensus 85 SSPGldRpL~~~~-~f~r~~G~~--V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 85 SSPGLGEPIILPR-QYGRHVGRL--LRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred eCCCCCCcCCCHH-HHHHhCCCE--EEEEEecccCCeEEEEEEEEeee
Confidence 4443334444443 456678865 7787765 33468999999995
No 73
>PRK06955 biotin--protein ligase; Provisional
Probab=62.35 E-value=41 Score=24.49 Aligned_cols=46 Identities=20% Similarity=0.151 Sum_probs=29.9
Q ss_pred ceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEec
Q 034947 25 ARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKET 77 (78)
Q Consensus 25 ~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~ 77 (78)
++|.|.. .++..+.|+..|+|+.=.|+++... +...-.-|+|.+|.
T Consensus 250 ~~V~v~~--~~~~~~~G~~~gId~~G~L~v~~~~-----g~~~~~sGeV~~~~ 295 (300)
T PRK06955 250 REVVLLE--DGAELARGVAHGIDETGQLLLDTPA-----GRQAIAAGDVSLRE 295 (300)
T ss_pred CeEEEEE--CCCcEEEEEEeeECCCceEEEEeCC-----CeEEEEEEEEEEec
Confidence 3465532 3456789999999999999986322 21233457776663
No 74
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=61.71 E-value=30 Score=20.16 Aligned_cols=39 Identities=18% Similarity=0.210 Sum_probs=30.2
Q ss_pred HHHHHhhcCcceEEEEEEecCC-eEEEEEEEEecccccee
Q 034947 15 NLIFRFLQSKARIQIWLFEQKD-LRIEGRIIGFDEYMNLV 53 (78)
Q Consensus 15 ~~L~~~~~k~~~V~V~lk~~~~-~~~~G~L~gfD~~mNlv 53 (78)
..|..++..+.+|+|....++. ..+.|++..+|..-+.+
T Consensus 33 ~~l~~a~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l 72 (92)
T PF08863_consen 33 EKLSEAYQENQPVTITYYEDGYYQSVTGTIHKIDEINRTL 72 (92)
T ss_pred HHHHHHhcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEE
Confidence 3567777777899998886533 67999999999988644
No 75
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=61.36 E-value=14 Score=20.05 Aligned_cols=22 Identities=27% Similarity=0.643 Sum_probs=15.0
Q ss_pred EEEEEEEeccccceeEeceEEE
Q 034947 39 IEGRIIGFDEYMNLVLDDAEEV 60 (78)
Q Consensus 39 ~~G~L~gfD~~mNlvL~da~E~ 60 (78)
..|+..|.|+.+.+.|.+....
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6799999999999999987654
No 76
>PRK14630 hypothetical protein; Provisional
Probab=59.17 E-value=22 Score=23.47 Aligned_cols=47 Identities=17% Similarity=0.187 Sum_probs=29.3
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-+| .++++++ |.|++.. ....|+|.++|+- ++.|+
T Consensus 78 SSPGldRpL~~~~df-~r~~G~~--v~V~l~~---~~~~G~L~~~~d~-~i~l~ 124 (143)
T PRK14630 78 STPGINRKIKSDREF-KIFEGKK--IKLMLDN---DFEEGFILEAKAD-SFIFK 124 (143)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCE--EEEEEcC---cceEEEEEEEeCC-EEEEE
Confidence 555444555555555 4788976 6666643 3358999999883 34443
No 77
>PRK14637 hypothetical protein; Provisional
Probab=55.98 E-value=33 Score=22.92 Aligned_cols=48 Identities=23% Similarity=0.426 Sum_probs=29.2
Q ss_pred CccccceeecChHHHHHHhhcCcceEEEEEEecCCeEE-EEEEEEeccccceeEe
Q 034947 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRI-EGRIIGFDEYMNLVLD 55 (78)
Q Consensus 2 s~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~-~G~L~gfD~~mNlvL~ 55 (78)
||+-..++...|-+ +.+++++. |.|++ ++..++ +|+|.++|+- ++.|+
T Consensus 79 SSPGldRpL~~~~~-f~r~~G~~--V~V~l--~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 79 SSPGIERVIKNAAE-FSIFVGET--VKVWF--ECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred eCCCCCCCCCCHHH-HHHhCCCE--EEEEE--CCCCcEEEEEEEEEeCC-EEEEE
Confidence 45444455555544 45677866 66666 323456 7999999885 34443
No 78
>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=55.98 E-value=38 Score=20.62 Aligned_cols=40 Identities=13% Similarity=0.233 Sum_probs=28.1
Q ss_pred hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEecccc-ceeEec
Q 034947 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYM-NLVLDD 56 (78)
Q Consensus 13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~m-NlvL~d 56 (78)
-+.+|....++ +|.+.+.+ +.++.|+..|+|... |+..++
T Consensus 15 fLr~l~~~~gk--~v~f~l~e--~t~V~a~F~a~d~~~~~f~Vs~ 55 (80)
T PF11095_consen 15 FLRSLLAMVGK--PVEFTLHE--NTTVSARFGACDIDVSNFQVSN 55 (80)
T ss_dssp HHHHHHHCTTS--EEEEEEGG--G-EEEEEEEEE-TTS-EEEEEE
T ss_pred HHHHHHHhcCC--ceEEEEeC--CeEEEEEEEEecCchheEEhhh
Confidence 45667777775 58888876 788999999999865 555443
No 79
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=54.54 E-value=58 Score=26.27 Aligned_cols=49 Identities=18% Similarity=0.173 Sum_probs=31.1
Q ss_pred hhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEec
Q 034947 20 FLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKET 77 (78)
Q Consensus 20 ~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~ 77 (78)
++++ +|.+ ...++..+.|+..|+|+.=.|+|+.. ++...-.-|+|.+|.
T Consensus 276 ~~gk--~V~v--~~~~~~~~~Gi~~GId~~G~L~l~~~-----~g~~~~~sGEVslr~ 324 (592)
T PRK13325 276 DHGK--AVLL--LRDGETVFEGTVKGVDGQGVLHLETA-----EGKQTVVSGEISLRS 324 (592)
T ss_pred cCCC--eEEE--EeCCCcEEEEEEEEECCCCEEEEEEC-----CCeEEEEEEeEEEee
Confidence 3454 4554 32345679999999999999999632 222234456676664
No 80
>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=52.80 E-value=27 Score=23.96 Aligned_cols=36 Identities=17% Similarity=0.301 Sum_probs=27.2
Q ss_pred hHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEecccc
Q 034947 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYM 50 (78)
Q Consensus 13 Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~m 50 (78)
-+++..++.++.+.|.|.+ .+||+++|+=.|.|..-
T Consensus 109 FF~Icrka~qqg~sIrVyM--~DgR~ieG~stGvnacq 144 (165)
T PF03614_consen 109 FFSICRKAHQQGKSIRVYM--ADGREIEGKSTGVNACQ 144 (165)
T ss_pred HHHHHHHHHHCCCeEEEEE--cCCcEEEeeecccceEE
Confidence 3567778887775566665 56999999999998754
No 81
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=52.48 E-value=29 Score=24.13 Aligned_cols=35 Identities=20% Similarity=0.321 Sum_probs=27.0
Q ss_pred HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEeccc
Q 034947 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEY 49 (78)
Q Consensus 14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~ 49 (78)
++||-++-+.-.+|...+..+ +..|+|.|++||+=
T Consensus 123 I~fL~~~P~~lp~i~C~i~t~-~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIETK-DKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEeC-CceEEEEEEeccCC
Confidence 667777766656677777764 68999999999875
No 82
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=51.98 E-value=8.3 Score=26.00 Aligned_cols=21 Identities=19% Similarity=0.428 Sum_probs=17.1
Q ss_pred EEEEEEEeccccceeEeceEE
Q 034947 39 IEGRIIGFDEYMNLVLDDAEE 59 (78)
Q Consensus 39 ~~G~L~gfD~~mNlvL~da~E 59 (78)
=+|+|+|.|.|=|=--+|-.-
T Consensus 45 kiGTLVG~DkfGNkYyen~~~ 65 (151)
T KOG3382|consen 45 KIGTLVGVDKFGNKYYENNDY 65 (151)
T ss_pred cceeeeeecccccchhcccce
Confidence 459999999999988777643
No 83
>PRK10139 serine endoprotease; Provisional
Probab=50.80 E-value=49 Score=25.59 Aligned_cols=32 Identities=22% Similarity=0.398 Sum_probs=25.4
Q ss_pred cceEEEEEEecCCeEEEEEEEEeccccceeEece
Q 034947 24 KARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (78)
Q Consensus 24 ~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da 57 (78)
...|.|++ .+++++.++++|+|....|.+=..
T Consensus 114 a~~i~V~~--~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 114 AQKISIQL--NDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CCEEEEEE--CCCCEEEEEEEEEcCCCCEEEEEe
Confidence 34577777 558999999999999999987443
No 84
>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=50.25 E-value=7.2 Score=24.46 Aligned_cols=17 Identities=29% Similarity=0.636 Sum_probs=15.0
Q ss_pred EEEEEeccccceeEece
Q 034947 41 GRIIGFDEYMNLVLDDA 57 (78)
Q Consensus 41 G~L~gfD~~mNlvL~da 57 (78)
|+|+|.|.|=|---++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999987765
No 85
>PRK10898 serine endoprotease; Provisional
Probab=48.41 E-value=37 Score=25.28 Aligned_cols=30 Identities=23% Similarity=0.300 Sum_probs=23.6
Q ss_pred eEEEEEEecCCeEEEEEEEEeccccceeEece
Q 034947 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (78)
Q Consensus 26 ~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da 57 (78)
.+.|.+ .+|+.+.+.++++|...+|.+=..
T Consensus 103 ~i~V~~--~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 103 QIIVAL--QDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred EEEEEe--CCCCEEEEEEEEEcCCCCEEEEEE
Confidence 466666 558999999999999999976443
No 86
>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=45.61 E-value=48 Score=24.59 Aligned_cols=30 Identities=23% Similarity=0.378 Sum_probs=23.6
Q ss_pred eEEEEEEecCCeEEEEEEEEeccccceeEece
Q 034947 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (78)
Q Consensus 26 ~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da 57 (78)
.+.|.+ .+|+.+.++++++|...+|.+=..
T Consensus 103 ~i~V~~--~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 103 QIVVAL--QDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred EEEEEE--CCCCEEEEEEEEecCCCCEEEEEe
Confidence 355555 558999999999999999987443
No 87
>PRK10942 serine endoprotease; Provisional
Probab=45.51 E-value=60 Score=25.27 Aligned_cols=29 Identities=17% Similarity=0.432 Sum_probs=23.7
Q ss_pred eEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (78)
Q Consensus 26 ~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d 56 (78)
.|.|.+ .+++++.++++++|...+|.|=.
T Consensus 137 ~i~V~~--~dg~~~~a~vv~~D~~~DlAvlk 165 (473)
T PRK10942 137 KIKVQL--SDGRKFDAKVVGKDPRSDIALIQ 165 (473)
T ss_pred EEEEEE--CCCCEEEEEEEEecCCCCEEEEE
Confidence 466666 56899999999999999987653
No 88
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=44.90 E-value=59 Score=19.02 Aligned_cols=39 Identities=10% Similarity=0.344 Sum_probs=26.1
Q ss_pred cCh--HHHHHHhhcCcceEEEEEEecCCeEEEEEEEEec-cccceeEec
Q 034947 11 TQP--INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFD-EYMNLVLDD 56 (78)
Q Consensus 11 ~~P--l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD-~~mNlvL~d 56 (78)
..| .+.|.++++++ |.|.- . .-.+.|+|.+.. .| ++|+.
T Consensus 8 vdpyvyq~lq~liG~~--vvV~T--~-~g~v~G~L~~V~pDh--Ivl~~ 49 (66)
T PF10842_consen 8 VDPYVYQTLQSLIGQR--VVVQT--T-RGSVRGILVDVKPDH--IVLEE 49 (66)
T ss_pred cCHHHHHHHHHhcCCE--EEEEE--c-CCcEEEEEEeecCCE--EEEEe
Confidence 455 67899999987 65654 3 345799999874 33 35543
No 89
>PRK08330 biotin--protein ligase; Provisional
Probab=42.46 E-value=1.1e+02 Score=21.14 Aligned_cols=47 Identities=23% Similarity=0.249 Sum_probs=28.6
Q ss_pred hhcCcceEEEEEEecCCeEE-EEEEEEeccccceeEeceEEEEecCC-eeeeeeEEEEe
Q 034947 20 FLQSKARIQIWLFEQKDLRI-EGRIIGFDEYMNLVLDDAEEVHIKKN-TRKPLGFFSKE 76 (78)
Q Consensus 20 ~~~k~~~V~V~lk~~~~~~~-~G~L~gfD~~mNlvL~da~E~~~~~~-~~~~lG~ilir 76 (78)
++++ +|.+.- + +..+ .|+..|+|+.=.|+++... +. ..-..|+|.+|
T Consensus 186 ~~g~--~v~~~~--~-~~~~~~G~~~gI~~~G~L~v~~~~-----g~~~~~~~gev~~~ 234 (236)
T PRK08330 186 ILGK--RVKIIG--D-GEILVEGIAEDIDEFGALILRLDD-----GTVKKVLYGDVSLR 234 (236)
T ss_pred hcCC--eEEEEE--C-CcEEEEEEEEEECCCCEEEEEECC-----CCEEEEEEEEEEEe
Confidence 3444 465542 3 4454 6999999999999886321 11 12334777665
No 90
>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=41.93 E-value=67 Score=24.25 Aligned_cols=30 Identities=13% Similarity=0.290 Sum_probs=23.8
Q ss_pred eEEEEEEecCCeEEEEEEEEeccccceeEece
Q 034947 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (78)
Q Consensus 26 ~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da 57 (78)
.+.|.+ .+++.+.+++.++|...+|.|=..
T Consensus 83 ~i~V~~--~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 83 EITVTL--SDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred eEEEEe--CCCCEEEEEEEEecCCCCEEEEEe
Confidence 455665 558999999999999999887544
No 91
>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=41.18 E-value=50 Score=20.95 Aligned_cols=29 Identities=14% Similarity=0.295 Sum_probs=19.9
Q ss_pred HHHHHHhhcCcceEEEEEEecCCeEEEEEEE
Q 034947 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRII 44 (78)
Q Consensus 14 l~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~ 44 (78)
++.|-..++...+|.+.|++ |+.+.|++.
T Consensus 18 LE~lv~~L~ge~~V~l~L~D--Gs~l~Gtv~ 46 (101)
T PF11607_consen 18 LEHLVSELDGEERVELELDD--GSMLRGTVA 46 (101)
T ss_dssp HHHHHHCTTTT-EEEEEETT--S-EEEEEEC
T ss_pred HHHHHhhcCCcceEEEEEcC--CCeeeeeec
Confidence 45566677777788888855 899999863
No 92
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=40.46 E-value=68 Score=20.08 Aligned_cols=51 Identities=12% Similarity=0.252 Sum_probs=33.0
Q ss_pred cccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEecc-ccceeEeceEEEE
Q 034947 4 TKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDE-YMNLVLDDAEEVH 61 (78)
Q Consensus 4 ~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~-~mNlvL~da~E~~ 61 (78)
|.|+|+++.-.+++++.-.-. .| ...+| +.|++...++ +.=+.+.+.++..
T Consensus 28 RPQrKr~K~~~~ml~sL~kGD-~V----vT~gG--i~G~V~~v~d~~v~I~l~~~~~i~ 79 (97)
T COG1862 28 RPQRKRMKEHQELLNSLKKGD-EV----VTIGG--IVGTVTKVGDDTVEIELGDGTKIK 79 (97)
T ss_pred CHHHHHHHHHHHHHHhccCCC-EE----EEcCC--eEEEEEEEecCcEEEEECCCeEEE
Confidence 336677777777777765443 33 33678 8899999988 4455555555553
No 93
>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=39.48 E-value=70 Score=21.92 Aligned_cols=42 Identities=17% Similarity=0.351 Sum_probs=27.7
Q ss_pred ChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEecccc-ceeEeceEE
Q 034947 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYM-NLVLDDAEE 59 (78)
Q Consensus 12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~m-NlvL~da~E 59 (78)
.|+. +..|++|. |.|.+ .+ +++.|.|..+|.=- |+||-+..|
T Consensus 8 ~p~~-~~~yv~K~--VkV~~--~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 8 SPLE-WQDYVGKE--VKVTL--SD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp -HHH-HHCTTT-E--EEEEE--TT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred CHHH-HHHhhCcE--EEEEE--ec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 4554 45688976 76766 55 99999999999755 888875544
No 94
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=39.35 E-value=58 Score=22.39 Aligned_cols=32 Identities=13% Similarity=0.086 Sum_probs=26.3
Q ss_pred ceEEEEEEecCCeEEEEEEEEeccccceeEeceE
Q 034947 25 ARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAE 58 (78)
Q Consensus 25 ~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~ 58 (78)
-||.|.+ ++|..|.|.+.||+.-=|.+|..+.
T Consensus 30 ~pVrvv~--~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 30 IPVRVVS--ENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred CceEEEe--cCCcEEEEEEeccCcccCEEeccCC
Confidence 4555555 6699999999999999999988665
No 95
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=37.96 E-value=1.5e+02 Score=21.35 Aligned_cols=45 Identities=24% Similarity=0.276 Sum_probs=29.8
Q ss_pred ceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEec
Q 034947 25 ARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKET 77 (78)
Q Consensus 25 ~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir~ 77 (78)
+.|.+.. + +..+.|++.|+|..-.|++++. ++.+.-..|+|.+|.
T Consensus 273 ~~v~~~~--~-~~~~~G~~~gi~~~G~L~i~~~-----g~~~~~~~gev~~~~ 317 (319)
T PRK11886 273 REVKLII--G-DKEISGIARGIDEQGALLLEDD-----GVEKPFNGGEISLRS 317 (319)
T ss_pred CeEEEEe--C-CcEEEEEEEEECCCceEEEEeC-----CcEEEEEEeEEEEec
Confidence 3466653 3 4568999999999999998521 122234567777764
No 96
>PF03306 AAL_decarboxy: Alpha-acetolactate decarboxylase; InterPro: IPR005128 Alpha-acetolactate decarboxylase plays a dual role in the cell: (i) it catalyzes the second step of the acetoin pathway, (S)-2-hydroxy-2-methyl-3-oxobutanoate = (R)-2-acetoin + CO2 and thus potentially the internal pH of cells and (ii) it controls the pool of alpha-acetolactate during leucine and valine synthesis.; GO: 0047605 acetolactate decarboxylase activity, 0019751 polyol metabolic process, 0005789 endoplasmic reticulum membrane; PDB: 1XV2_B.
Probab=37.11 E-value=62 Score=22.91 Aligned_cols=30 Identities=20% Similarity=0.411 Sum_probs=17.5
Q ss_pred ecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEe
Q 034947 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGF 46 (78)
Q Consensus 10 ~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gf 46 (78)
...|..-|.....++ ....+.+ ++|+|+||
T Consensus 126 qe~Py~~l~e~~~~Q--~~f~~~n-----i~GTlVGf 155 (220)
T PF03306_consen 126 QEKPYPPLAEVAKNQ--PEFTFEN-----IEGTLVGF 155 (220)
T ss_dssp --SS---THHHHTT----EEEEEE-----EEEEEEEE
T ss_pred ccCCCCChhHHhccC--ceEEecC-----cEEEEEEE
Confidence 456777777887764 4455544 88999999
No 97
>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=37.09 E-value=1.4e+02 Score=20.65 Aligned_cols=44 Identities=23% Similarity=0.204 Sum_probs=28.5
Q ss_pred ceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEe
Q 034947 25 ARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKE 76 (78)
Q Consensus 25 ~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir 76 (78)
++|.+.- + +..+.|+..|+|+.=.|++++. ++.+.-..|+|.+|
T Consensus 194 ~~V~v~~--~-~~~~~G~~~gI~~~G~L~v~~~-----~~~~~~~sGev~~~ 237 (237)
T TIGR00121 194 REVSLTT--G-NGEIEGIARGIDKDGALLLEDG-----GGIKKIISGEISLR 237 (237)
T ss_pred CeEEEEe--C-CcEEEEEEEeECCCceEEEEeC-----CeEEEEEEEEEEEC
Confidence 3466543 3 3568999999999999999621 11223455777654
No 98
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=34.25 E-value=48 Score=19.95 Aligned_cols=28 Identities=14% Similarity=0.243 Sum_probs=17.9
Q ss_pred HHHHhhcCcceEEEEEEecCCeEEEEEEEEeccc
Q 034947 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEY 49 (78)
Q Consensus 16 ~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~ 49 (78)
-+.+.+.+...| ...+| +.|++...|+-
T Consensus 33 ~m~~~L~~Gd~V----vT~gG--i~G~V~~i~d~ 60 (84)
T TIGR00739 33 KLIESLKKGDKV----LTIGG--IIGTVTKIAEN 60 (84)
T ss_pred HHHHhCCCCCEE----EECCC--eEEEEEEEeCC
Confidence 344445555333 33678 88999999874
No 99
>KOG3865 consensus Arrestin [Signal transduction mechanisms]
Probab=34.03 E-value=82 Score=24.33 Aligned_cols=41 Identities=5% Similarity=0.141 Sum_probs=34.0
Q ss_pred hhcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEE
Q 034947 20 FLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60 (78)
Q Consensus 20 ~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~ 60 (78)
|.+++..|.|.+.||+++.++-+=...++|-+++|-..-.|
T Consensus 207 yHGE~isvnV~V~NNsnKtVKkIK~~V~Q~adi~Lfs~aqy 247 (402)
T KOG3865|consen 207 YHGEPISVNVHVTNNSNKTVKKIKISVRQVADICLFSTAQY 247 (402)
T ss_pred ecCCceeEEEEEecCCcceeeeeEEEeEeeceEEEEecccc
Confidence 55777889999999999998888888899999999754444
No 100
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=30.97 E-value=55 Score=20.62 Aligned_cols=28 Identities=14% Similarity=0.265 Sum_probs=18.6
Q ss_pred HHHHHhhcCcceEEEEEEecCCeEEEEEEEEecc
Q 034947 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDE 48 (78)
Q Consensus 15 ~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~ 48 (78)
.-+.+.+.+..+| ...+| +.|++.+.|+
T Consensus 47 ~~~~~~Lk~Gd~V----vT~gG--i~G~Vv~i~~ 74 (106)
T PRK05585 47 KKMLSSLAKGDEV----VTNGG--IIGKVTKVSE 74 (106)
T ss_pred HHHHHhcCCCCEE----EECCC--eEEEEEEEeC
Confidence 4445555655343 33678 8899999987
No 101
>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=29.52 E-value=47 Score=20.86 Aligned_cols=25 Identities=24% Similarity=0.438 Sum_probs=10.4
Q ss_pred cCCeEEEEEEEEeccccceeEeceE
Q 034947 34 QKDLRIEGRIIGFDEYMNLVLDDAE 58 (78)
Q Consensus 34 ~~~~~~~G~L~gfD~~mNlvL~da~ 58 (78)
++...+.|+..|||-.-++.|++|.
T Consensus 120 G~~Vti~G~~~g~~~~~~v~l~~c~ 144 (144)
T PF12869_consen 120 GQKVTIKGICTGYSLMGVVMLDDCQ 144 (144)
T ss_dssp TSEEEEEEE-----SSS-EEEE---
T ss_pred CCEEEEEEEEEeeecCCcEEeeccC
Confidence 3445678999999844477777763
No 102
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=28.94 E-value=2.2e+02 Score=20.27 Aligned_cols=48 Identities=21% Similarity=0.133 Sum_probs=30.6
Q ss_pred hcCcceEEEEEEecCCeEEEEEEEEeccccceeEeceEEEEecCCeeeeeeEEEEe
Q 034947 21 LQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGFFSKE 76 (78)
Q Consensus 21 ~~k~~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~da~E~~~~~~~~~~lG~ilir 76 (78)
+++. | ++...++....|+-.|+|..-.|+++..... .....-|+|.+|
T Consensus 189 ~g~~--V--~~~~~~~~~~gg~a~~id~~G~L~l~~~~g~----~~~~~~Gev~~~ 236 (238)
T COG0340 189 LGKE--V--RLTLGGGVIFGGIAKGIDEDGALLLETDDGE----VQTIYSGEVSLR 236 (238)
T ss_pred CCCE--E--EEEeCCCcEeeeEEEEECCCceEEEEeCCCe----EEEEeccEEEee
Confidence 5554 5 4444555566669999999999999876211 123345666655
No 103
>PRK06630 hypothetical protein; Provisional
Probab=27.65 E-value=34 Score=21.72 Aligned_cols=19 Identities=21% Similarity=0.387 Sum_probs=16.4
Q ss_pred EEEEEEEeccccceeEece
Q 034947 39 IEGRIIGFDEYMNLVLDDA 57 (78)
Q Consensus 39 ~~G~L~gfD~~mNlvL~da 57 (78)
..|+|+|-|+|=|---++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4699999999999988774
No 104
>PF10894 DUF2689: Protein of unknown function (DUF2689); InterPro: IPR024396 Members of this protein family are annotated as conjugal transfer protein TrbD; however, currently no function is known.
Probab=25.98 E-value=8.2 Score=22.30 Aligned_cols=15 Identities=27% Similarity=0.512 Sum_probs=13.2
Q ss_pred ccccceeEeceEEEE
Q 034947 47 DEYMNLVLDDAEEVH 61 (78)
Q Consensus 47 D~~mNlvL~da~E~~ 61 (78)
|.||+-||++|.-..
T Consensus 21 DDFmhaVlSNCtTrI 35 (61)
T PF10894_consen 21 DDFMHAVLSNCTTRI 35 (61)
T ss_pred HHHHHHHHhcCceeE
Confidence 999999999998664
No 105
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=23.77 E-value=2.9e+02 Score=19.99 Aligned_cols=29 Identities=21% Similarity=0.135 Sum_probs=22.0
Q ss_pred ceEEEEEEecCCeEEEEEEEEeccccceeEec
Q 034947 25 ARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (78)
Q Consensus 25 ~~V~V~lk~~~~~~~~G~L~gfD~~mNlvL~d 56 (78)
+.|.|.. ++..+.|++.|+|.-=.|+++.
T Consensus 238 ~~V~v~~---~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 238 KKVLIDQ---DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred CEEEEEe---CCCEEEEEEEEECCCCeEEEEe
Confidence 3465542 3578999999999999998863
No 106
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=23.14 E-value=48 Score=21.49 Aligned_cols=20 Identities=30% Similarity=0.552 Sum_probs=16.8
Q ss_pred EEEEEEeccccceeEeceEE
Q 034947 40 EGRIIGFDEYMNLVLDDAEE 59 (78)
Q Consensus 40 ~G~L~gfD~~mNlvL~da~E 59 (78)
.|.|+|-|+|=|---++..+
T Consensus 9 ~g~lVG~D~~GNkYYE~~~~ 28 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPSY 28 (115)
T ss_pred cceEeEEcCCCCeeeEcCCC
Confidence 49999999999998887543
No 107
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.02 E-value=91 Score=24.01 Aligned_cols=57 Identities=18% Similarity=0.232 Sum_probs=36.1
Q ss_pred HHhhcCcceEEEEEEecCCeEEEEEEEEeccc-cceeEeceEEEEecCC---------eeeeeeEEEEecC
Q 034947 18 FRFLQSKARIQIWLFEQKDLRIEGRIIGFDEY-MNLVLDDAEEVHIKKN---------TRKPLGFFSKETT 78 (78)
Q Consensus 18 ~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~~-mNlvL~da~E~~~~~~---------~~~~lG~ilir~~ 78 (78)
..|+++. |.|.-+.+.+|+|+|--+|-= -=|-|.++.-+-.+++ ..+.+--|+-||.
T Consensus 5 t~yIGS~----ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGS 71 (361)
T KOG1073|consen 5 TSYIGSF----ISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGS 71 (361)
T ss_pred cccccce----eEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCc
Confidence 4588987 666666689999999877632 2366777654421111 1126778888874
No 108
>TIGR01252 acetolac_decarb alpha-acetolactate decarboxylase. Puruvate can be fermented to 2,3-butanediol. It is first converted to alpha-acetolactate by alpha-acetolactate synthase, then decarboxylated to acetoin by this enzyme. Acetoin can be reduced in some species to 2,3-butanediol by acetoin reductase.
Probab=22.40 E-value=87 Score=22.44 Aligned_cols=29 Identities=17% Similarity=0.426 Sum_probs=19.5
Q ss_pred cChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEe
Q 034947 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGF 46 (78)
Q Consensus 11 ~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gf 46 (78)
..|..-|......+ ++ ..+.+ ++|+|+||
T Consensus 129 ~kPy~~l~e~~~~Q-~~-f~~~n-----v~GTlvGF 157 (232)
T TIGR01252 129 EKPYPPFVEVVKGQ-PE-FHFDN-----VTGTIVGF 157 (232)
T ss_pred CCCCcCHHHHhcCC-ce-EEEec-----cEEEEEEE
Confidence 45777777777654 33 45433 78999998
No 109
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.68 E-value=36 Score=24.15 Aligned_cols=45 Identities=22% Similarity=0.234 Sum_probs=27.9
Q ss_pred CCccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEe
Q 034947 1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGF 46 (78)
Q Consensus 1 ms~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gf 46 (78)
||.+ .++....+.+++..-=-....|.|++++.+-.+++|.+.|=
T Consensus 1 m~~~-~~ri~~e~k~v~~~~eisq~~I~ve~vn~~~~~ikG~I~GP 45 (200)
T KOG0418|consen 1 MSNA-FKRINREQKEVLDDPEISQAGIIVEMVNENLKEIKGHIAGP 45 (200)
T ss_pred CccH-HHHHHHHHHHhccChhhhhcceEEEEccCChhhceeEecCC
Confidence 5552 23444455555554421124588999987778999999884
No 110
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=21.61 E-value=26 Score=20.98 Aligned_cols=10 Identities=50% Similarity=0.933 Sum_probs=8.4
Q ss_pred EEEEEecccc
Q 034947 41 GRIIGFDEYM 50 (78)
Q Consensus 41 G~L~gfD~~m 50 (78)
.++.|||.|+
T Consensus 41 NiikGfd~y~ 50 (80)
T PF09340_consen 41 NIIKGFDGYL 50 (80)
T ss_pred CCeeChhhhh
Confidence 5778999995
No 111
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=21.03 E-value=85 Score=21.99 Aligned_cols=44 Identities=16% Similarity=0.163 Sum_probs=32.8
Q ss_pred CCccccceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEecc
Q 034947 1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDE 48 (78)
Q Consensus 1 ms~~~~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~ 48 (78)
|+-.+++-....|++.++.++....-|+|. . +-...|++.-+|-
T Consensus 136 M~e~fP~Vs~~~~l~vI~~LL~~~~AVlV~-e---~G~~vGIITk~DI 179 (187)
T COG3620 136 MGEPFPTVSPDESLNVISQLLEEHPAVLVV-E---NGKVVGIITKADI 179 (187)
T ss_pred hcCCCCcCCCCCCHHHHHHHHhhCCeEEEE-e---CCceEEEEeHHHH
Confidence 677777777788999999999987777775 2 2347788776664
No 112
>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=20.90 E-value=1.3e+02 Score=18.48 Aligned_cols=17 Identities=24% Similarity=0.302 Sum_probs=11.4
Q ss_pred EEEEe-cCCeEEEEEEEE
Q 034947 29 IWLFE-QKDLRIEGRIIG 45 (78)
Q Consensus 29 V~lk~-~~~~~~~G~L~g 45 (78)
|+++| .+++.+.|+..+
T Consensus 99 I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 99 IRVRNLSSGKIISGIVTG 116 (122)
T ss_pred EEEEECCCCCEEEEEEeC
Confidence 55554 567888887765
No 113
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.64 E-value=1.2e+02 Score=21.18 Aligned_cols=22 Identities=9% Similarity=0.135 Sum_probs=15.4
Q ss_pred hhcCcceEEEEEEecCCeEEEEEEEE
Q 034947 20 FLQSKARIQIWLFEQKDLRIEGRIIG 45 (78)
Q Consensus 20 ~~~k~~~V~V~lk~~~~~~~~G~L~g 45 (78)
.++.. |++++.+|+.+.|+..|
T Consensus 194 ~~Gd~----IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 194 NLGDI----IQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCE----EEEEeCCCCEEEEEEec
Confidence 45554 55666788888888776
No 114
>COG4990 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.29 E-value=2.3e+02 Score=20.06 Aligned_cols=46 Identities=22% Similarity=0.353 Sum_probs=31.0
Q ss_pred ChHHHHHHhhcCcceEEEEEEecCCeE-EEEEEEEeccccceeEeceE
Q 034947 12 QPINLIFRFLQSKARIQIWLFEQKDLR-IEGRIIGFDEYMNLVLDDAE 58 (78)
Q Consensus 12 ~Pl~~L~~~~~k~~~V~V~lk~~~~~~-~~G~L~gfD~~mNlvL~da~ 58 (78)
..+.-+...+.|..||.||.-+=.+-. -.=.+.|||++ |+...|-.
T Consensus 121 ksl~~ik~ql~kg~PV~iw~T~~~~~s~H~v~itgyDk~-n~yynDpy 167 (195)
T COG4990 121 KSLSDIKGQLLKGRPVVIWVTNFHSYSIHSVLITGYDKY-NIYYNDPY 167 (195)
T ss_pred CcHHHHHHHHhcCCcEEEEEecccccceeeeEeeccccc-ceEecccc
Confidence 457778888899999999975422222 23356799986 56666654
No 115
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=20.22 E-value=1.2e+02 Score=19.32 Aligned_cols=36 Identities=19% Similarity=0.394 Sum_probs=21.6
Q ss_pred cceeecChHHHHHHhhcCcceEEEEEEecCCeEEEEEEEEecc
Q 034947 6 VQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDE 48 (78)
Q Consensus 6 ~~~~~~~Pl~~L~~~~~k~~~V~V~lk~~~~~~~~G~L~gfD~ 48 (78)
|+|....-.+++.++ .+... +.+.+| +.|++...++
T Consensus 25 QkKr~K~~~~m~~~L-k~GD~----VvT~gG--i~G~V~~I~d 60 (109)
T PRK05886 25 QRKAMQATIDLHESL-QPGDR----VHTTSG--LQATIVGITD 60 (109)
T ss_pred HHHHHHHHHHHHHhc-CCCCE----EEECCC--eEEEEEEEeC
Confidence 445444444555554 54433 333678 8899999875
Done!