Query 034651
Match_columns 88
No_of_seqs 119 out of 1009
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 05:04:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034651.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034651hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00138 small nuclear ribonuc 100.0 4.7E-29 1E-33 156.5 11.7 87 1-87 3-89 (89)
2 cd01718 Sm_E The eukaryotic Sm 100.0 8.1E-29 1.8E-33 152.4 10.4 79 7-85 1-79 (79)
3 KOG1774 Small nuclear ribonucl 99.9 7.4E-27 1.6E-31 143.2 6.6 87 1-87 1-87 (88)
4 PRK00737 small nuclear ribonuc 99.9 1.3E-24 2.8E-29 131.3 8.8 70 11-85 3-72 (72)
5 cd01732 LSm5 The eukaryotic Sm 99.9 6.2E-24 1.3E-28 129.8 9.9 72 11-86 2-75 (76)
6 cd01731 archaeal_Sm1 The archa 99.9 1E-23 2.3E-28 125.8 9.0 68 13-85 1-68 (68)
7 cd01726 LSm6 The eukaryotic Sm 99.9 1.6E-23 3.5E-28 124.8 8.6 67 13-84 1-67 (67)
8 cd01720 Sm_D2 The eukaryotic S 99.9 2.7E-23 5.9E-28 129.9 9.9 73 12-86 2-86 (87)
9 cd01730 LSm3 The eukaryotic Sm 99.9 2.9E-23 6.3E-28 128.1 8.9 70 12-85 1-82 (82)
10 cd01722 Sm_F The eukaryotic Sm 99.9 1E-22 2.2E-27 121.7 8.0 68 12-84 1-68 (68)
11 cd01721 Sm_D3 The eukaryotic S 99.9 2.9E-22 6.3E-27 120.5 9.2 70 13-87 1-70 (70)
12 cd01719 Sm_G The eukaryotic Sm 99.9 4.4E-22 9.4E-27 120.4 9.1 70 14-88 2-71 (72)
13 cd01723 LSm4 The eukaryotic Sm 99.9 3.5E-22 7.6E-27 121.7 8.7 72 12-87 1-72 (76)
14 cd01729 LSm7 The eukaryotic Sm 99.9 9.7E-22 2.1E-26 121.3 9.5 70 14-87 4-80 (81)
15 COG1958 LSM1 Small nuclear rib 99.9 1.1E-21 2.4E-26 120.0 9.0 73 9-85 4-79 (79)
16 cd01728 LSm1 The eukaryotic Sm 99.8 1.7E-20 3.6E-25 114.1 9.8 70 13-86 3-74 (74)
17 smart00651 Sm snRNP Sm protein 99.8 2E-20 4.4E-25 110.3 8.6 66 16-85 2-67 (67)
18 cd01724 Sm_D1 The eukaryotic S 99.8 2.1E-20 4.5E-25 117.4 9.0 71 12-87 1-71 (90)
19 PF01423 LSM: LSM domain ; In 99.8 2.2E-20 4.7E-25 110.3 8.3 67 15-85 1-67 (67)
20 cd01727 LSm8 The eukaryotic Sm 99.8 3.2E-20 6.9E-25 112.5 9.2 68 16-87 3-73 (74)
21 cd01717 Sm_B The eukaryotic Sm 99.8 4.7E-20 1E-24 112.9 8.7 66 16-85 4-78 (79)
22 KOG1780 Small Nuclear ribonucl 99.8 4.9E-20 1.1E-24 111.3 6.5 69 12-87 6-74 (77)
23 cd01733 LSm10 The eukaryotic S 99.8 2E-19 4.3E-24 110.3 8.8 71 11-86 8-78 (78)
24 cd01725 LSm2 The eukaryotic Sm 99.8 1.9E-19 4.1E-24 111.0 8.6 72 12-87 1-73 (81)
25 cd00600 Sm_like The eukaryotic 99.8 1.6E-18 3.5E-23 100.8 8.4 63 17-84 1-63 (63)
26 cd06168 LSm9 The eukaryotic Sm 99.8 8.3E-18 1.8E-22 102.5 9.5 67 15-85 3-74 (75)
27 KOG3460 Small nuclear ribonucl 99.7 8.6E-19 1.9E-23 108.1 1.4 73 10-86 3-87 (91)
28 KOG3482 Small nuclear ribonucl 99.7 5.1E-17 1.1E-21 98.0 6.1 72 11-87 7-78 (79)
29 KOG1775 U6 snRNA-associated Sm 99.7 3.2E-17 6.9E-22 99.7 4.0 74 10-87 5-80 (84)
30 KOG3293 Small nuclear ribonucl 99.6 1.2E-15 2.5E-20 100.1 5.6 72 12-87 2-73 (134)
31 KOG1783 Small nuclear ribonucl 99.6 2E-16 4.3E-21 95.4 1.4 72 11-87 5-76 (77)
32 KOG1781 Small Nuclear ribonucl 99.6 2E-16 4.3E-21 100.2 -0.1 72 12-87 17-95 (108)
33 KOG1784 Small Nuclear ribonucl 99.4 2.1E-13 4.6E-18 85.4 4.3 68 16-87 4-74 (96)
34 KOG3172 Small nuclear ribonucl 99.3 2.6E-12 5.7E-17 82.7 6.2 73 10-87 3-75 (119)
35 KOG3448 Predicted snRNP core p 99.3 1.7E-11 3.6E-16 76.6 7.5 69 14-86 4-73 (96)
36 KOG1782 Small Nuclear ribonucl 99.2 2.2E-12 4.7E-17 84.6 -0.0 67 17-87 14-82 (129)
37 KOG3459 Small nuclear ribonucl 99.2 3.4E-12 7.5E-17 82.3 -0.0 74 11-86 23-108 (114)
38 KOG3168 U1 snRNP component [Tr 99.2 3.3E-12 7.1E-17 87.7 -0.2 66 18-87 10-84 (177)
39 KOG3428 Small nuclear ribonucl 99.0 2.5E-09 5.5E-14 68.9 8.2 68 14-87 4-71 (109)
40 cd01739 LSm11_C The eukaryotic 98.9 8.8E-10 1.9E-14 65.4 2.6 46 18-63 2-49 (66)
41 cd01716 Hfq Hfq, an abundant, 97.4 0.00054 1.2E-08 40.3 5.2 39 16-56 3-41 (61)
42 TIGR02383 Hfq RNA chaperone Hf 97.4 0.0006 1.3E-08 40.1 5.3 39 16-56 7-45 (61)
43 PRK00395 hfq RNA-binding prote 97.2 0.0012 2.6E-08 40.7 5.2 40 16-57 11-50 (79)
44 COG1923 Hfq Uncharacterized ho 96.9 0.0026 5.7E-08 38.9 4.7 35 16-52 11-45 (77)
45 PF14438 SM-ATX: Ataxin 2 SM d 96.5 0.0061 1.3E-07 36.5 4.5 63 15-81 5-76 (77)
46 PF12701 LSM14: Scd6-like Sm d 96.3 0.033 7.1E-07 35.3 6.9 64 19-86 5-77 (96)
47 PRK14091 RNA-binding protein H 96.2 0.015 3.2E-07 40.3 5.2 41 15-57 95-135 (165)
48 PRK14091 RNA-binding protein H 96.2 0.015 3.3E-07 40.2 5.2 41 15-57 15-55 (165)
49 cd01736 LSm14_N LSm14 (also kn 94.3 0.31 6.7E-06 29.6 6.1 60 19-82 3-72 (74)
50 PF02237 BPL_C: Biotin protein 93.9 0.41 8.8E-06 26.2 5.7 47 21-76 2-48 (48)
51 PRK14633 hypothetical protein; 90.4 0.63 1.4E-05 31.4 4.4 38 15-55 87-126 (150)
52 cd01734 YlxS_C YxlS is a Bacil 90.2 0.75 1.6E-05 27.8 4.2 49 2-54 6-56 (83)
53 PRK14634 hypothetical protein; 88.9 0.91 2E-05 30.8 4.3 50 2-55 81-132 (155)
54 PRK14640 hypothetical protein; 88.8 0.99 2.2E-05 30.5 4.4 45 7-55 83-129 (152)
55 PRK14636 hypothetical protein; 87.7 1.2 2.6E-05 30.9 4.3 49 2-54 79-129 (176)
56 cd01735 LSm12_N LSm12 belongs 86.4 2.1 4.5E-05 25.0 4.2 31 29-59 9-39 (61)
57 PRK14638 hypothetical protein; 86.4 1.6 3.5E-05 29.5 4.3 36 15-55 93-128 (150)
58 PRK14643 hypothetical protein; 86.2 1.7 3.7E-05 29.9 4.4 33 15-49 97-131 (164)
59 COG0779 Uncharacterized protei 85.9 1.9 4.1E-05 29.5 4.4 39 15-54 92-130 (153)
60 PRK14646 hypothetical protein; 85.6 1.9 4.1E-05 29.3 4.3 38 15-55 93-132 (155)
61 PRK14632 hypothetical protein; 84.8 2.6 5.6E-05 29.1 4.8 38 15-55 91-133 (172)
62 PRK02001 hypothetical protein; 84.7 2.2 4.7E-05 29.0 4.3 43 7-55 76-118 (152)
63 PRK14639 hypothetical protein; 84.3 2.3 5.1E-05 28.4 4.3 36 15-55 81-116 (140)
64 PRK00092 ribosome maturation p 84.3 2.5 5.5E-05 28.4 4.4 32 15-48 91-124 (154)
65 PRK14631 hypothetical protein; 84.2 2.3 5E-05 29.5 4.3 31 15-47 110-142 (174)
66 PF14563 DUF4444: Domain of un 84.0 1.5 3.2E-05 23.9 2.6 22 39-60 10-31 (42)
67 PRK14647 hypothetical protein; 83.7 3.3 7.1E-05 28.1 4.8 32 15-48 92-130 (159)
68 PRK14644 hypothetical protein; 80.5 2.9 6.4E-05 27.8 3.6 37 16-55 79-117 (136)
69 PRK14645 hypothetical protein; 80.3 3.9 8.4E-05 27.8 4.2 34 15-54 95-128 (154)
70 PF11095 Gemin7: Gem-associate 80.3 11 0.00024 23.1 6.0 62 14-85 16-78 (80)
71 PRK14642 hypothetical protein; 78.9 4.6 9.9E-05 28.7 4.3 37 15-54 93-140 (197)
72 PRK14637 hypothetical protein; 78.7 5.2 0.00011 27.1 4.4 37 15-55 91-127 (151)
73 PF02576 DUF150: Uncharacteris 77.7 2.3 4.9E-05 28.0 2.4 37 15-54 80-118 (141)
74 PRK14635 hypothetical protein; 76.0 7.4 0.00016 26.5 4.6 49 2-54 80-131 (162)
75 PRK14641 hypothetical protein; 74.1 7 0.00015 27.1 4.1 31 15-47 97-129 (173)
76 KOG1073 Uncharacterized mRNA-a 65.6 20 0.00043 27.8 5.4 64 18-85 5-78 (361)
77 PRK06955 biotin--protein ligas 61.0 41 0.0009 24.8 6.2 29 26-56 251-279 (300)
78 PRK11886 bifunctional biotin-- 58.4 71 0.0015 23.5 7.1 44 26-77 274-317 (319)
79 PF06372 Gemin6: Gemin6 protei 56.6 20 0.00043 24.8 3.7 63 11-86 7-70 (166)
80 PF10842 DUF2642: Protein of u 56.5 39 0.00085 19.9 7.3 54 14-85 13-66 (66)
81 PF08863 YolD: YolD-like prote 56.4 40 0.00086 19.9 6.4 41 15-55 33-74 (92)
82 PF05071 NDUFA12: NADH ubiquin 56.3 7.2 0.00016 24.7 1.4 17 41-57 1-17 (105)
83 PF14153 Spore_coat_CotO: Spor 54.1 24 0.00052 24.8 3.8 35 14-49 123-157 (185)
84 KOG3382 NADH:ubiquinone oxidor 53.9 7.4 0.00016 26.4 1.1 22 39-60 45-66 (151)
85 PRK14630 hypothetical protein; 51.8 27 0.00059 23.3 3.7 34 15-54 90-123 (143)
86 PRK13325 bifunctional biotin-- 48.8 70 0.0015 26.2 6.1 29 26-56 280-308 (592)
87 PF03614 Flag1_repress: Repres 40.3 49 0.0011 22.9 3.5 33 15-49 111-143 (165)
88 TIGR02038 protease_degS peripl 39.5 67 0.0015 24.2 4.5 29 27-57 104-132 (351)
89 PRK08330 biotin--protein ligas 38.4 1.4E+02 0.0029 21.1 5.7 28 26-56 190-218 (236)
90 TIGR00121 birA_ligase birA, bi 37.8 1.4E+02 0.0031 20.9 7.0 27 26-55 195-221 (237)
91 PF03614 Flag1_repress: Repres 37.4 63 0.0014 22.3 3.7 33 24-58 29-61 (165)
92 PRK10898 serine endoprotease; 37.3 79 0.0017 23.9 4.6 30 26-57 103-132 (353)
93 PRK06630 hypothetical protein; 34.1 23 0.0005 22.6 1.1 19 39-57 11-29 (99)
94 PF12869 tRNA_anti-like: tRNA_ 33.6 43 0.00094 21.4 2.4 24 34-57 120-143 (144)
95 PF11607 DUF3247: Protein of u 33.5 79 0.0017 20.2 3.4 29 14-44 18-46 (101)
96 PTZ00275 biotin-acetyl-CoA-car 32.4 1.8E+02 0.0039 21.3 5.7 28 26-56 239-266 (285)
97 TIGR02037 degP_htrA_DO peripla 32.3 98 0.0021 23.7 4.5 31 26-58 83-113 (428)
98 PF11743 DUF3301: Protein of u 32.1 74 0.0016 19.7 3.2 25 63-87 72-96 (97)
99 PRK10942 serine endoprotease; 31.7 1E+02 0.0022 24.4 4.5 30 26-57 137-166 (473)
100 PF10894 DUF2689: Protein of u 28.8 5.6 0.00012 23.0 -2.2 15 47-61 21-35 (61)
101 PLN03095 NADH:ubiquinone oxido 27.4 37 0.00079 22.2 1.2 21 39-59 8-28 (115)
102 PF06507 Auxin_resp: Auxin res 26.7 1.6E+02 0.0034 18.0 4.0 43 7-49 21-69 (83)
103 KOG3865 Arrestin [Signal trans 25.9 1.5E+02 0.0032 23.2 4.3 39 22-60 209-247 (402)
104 PRK10139 serine endoprotease; 25.7 1.5E+02 0.0033 23.2 4.6 31 25-57 115-145 (455)
105 PF09465 LBR_tudor: Lamin-B re 25.2 1.4E+02 0.0031 17.0 3.3 21 27-48 12-32 (55)
106 KOG3535 Adaptor protein Disabl 24.9 46 0.001 26.8 1.5 18 30-48 43-60 (557)
107 PRK07228 N-ethylammeline chlor 23.9 1.8E+02 0.0038 22.2 4.5 36 50-85 1-36 (445)
108 PF11684 DUF3280: Protein of u 23.5 89 0.0019 20.9 2.5 38 37-79 83-123 (140)
109 COG0340 BirA Biotin-(acetyl-Co 23.4 2.9E+02 0.0062 19.9 6.3 33 21-57 189-221 (238)
110 PF06214 SLAM: Signaling lymph 20.7 93 0.002 20.6 2.1 35 15-49 50-84 (126)
111 PRK08183 NADH dehydrogenase; V 20.4 58 0.0012 21.8 1.1 20 39-58 24-43 (133)
No 1
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.96 E-value=4.7e-29 Score=156.47 Aligned_cols=87 Identities=70% Similarity=1.135 Sum_probs=80.2
Q ss_pred CCccccceeeecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcE
Q 034651 1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNI 80 (88)
Q Consensus 1 ~~~~~~~~~~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I 80 (88)
|++++.||.|..|+..+.+++.++.+|.||++++++++++|+|.|||+|||++|+||+|+..+++..+.+|.++||||||
T Consensus 3 ~~~~~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV 82 (89)
T PTZ00138 3 MTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNI 82 (89)
T ss_pred CcccccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEE
Confidence 67778899999999999999999999999999988999999999999999999999999864455678999999999999
Q ss_pred EEEEecC
Q 034651 81 TLMMNTG 87 (88)
Q Consensus 81 ~~I~~~~ 87 (88)
++|++.+
T Consensus 83 ~~I~~~~ 89 (89)
T PTZ00138 83 TLIMAAK 89 (89)
T ss_pred EEEEcCC
Confidence 9998753
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=99.96 E-value=8.1e-29 Score=152.44 Aligned_cols=79 Identities=84% Similarity=1.311 Sum_probs=72.8
Q ss_pred ceeeecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEe
Q 034651 7 QRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 7 ~~~~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~ 85 (88)
||.|..|++.+.++++++++|+||+++++|++++|+|.|||+|||++|+||+|+...+.+.+.+|.++||||||++|+|
T Consensus 1 ~~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 1 QKVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred CccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence 5789999999999999999999999987899999999999999999999999995435577889999999999999985
No 3
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.94 E-value=7.4e-27 Score=143.22 Aligned_cols=87 Identities=75% Similarity=1.201 Sum_probs=81.0
Q ss_pred CCccccceeeecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcE
Q 034651 1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNI 80 (88)
Q Consensus 1 ~~~~~~~~~~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I 80 (88)
||+++.||.|++|++++.+|+..+.+|.||+..+-|..++|.++|||+|||+||+||+|.+.+....+.+|.++++||||
T Consensus 1 ms~~kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnI 80 (88)
T KOG1774|consen 1 MSREKVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNI 80 (88)
T ss_pred CCcccccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcE
Confidence 88988999999999999999999999999999988999999999999999999999999976655566999999999999
Q ss_pred EEEEecC
Q 034651 81 TLMMNTG 87 (88)
Q Consensus 81 ~~I~~~~ 87 (88)
.+|...+
T Consensus 81 tli~~~~ 87 (88)
T KOG1774|consen 81 TLIQSAG 87 (88)
T ss_pred EEEeecC
Confidence 9998764
No 4
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.92 E-value=1.3e-24 Score=131.26 Aligned_cols=70 Identities=30% Similarity=0.590 Sum_probs=63.0
Q ss_pred ecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEe
Q 034651 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 11 ~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~ 85 (88)
..|+++|+++++++ |.|++++ |++|+|+|.|||+|||++|+||.|.+ +++..+.+|.++|||+||++|+|
T Consensus 3 ~~P~~~L~~~~~k~--V~V~lk~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 3 QRPLDVLNNALNSP--VLVRLKG--GREFRGELQGYDIHMNLVLDNAEEIQ-DGEVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred cchHHHHHHhCCCE--EEEEECC--CCEEEEEEEEEcccceeEEeeEEEEc-CCCeEeEcCcEEEeCCEEEEEcC
Confidence 47999999999996 8888875 58999999999999999999999984 55677899999999999999974
No 5
>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=99.91 E-value=6.2e-24 Score=129.82 Aligned_cols=72 Identities=35% Similarity=0.616 Sum_probs=62.9
Q ss_pred ecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEe--cCCeeeecCeEEEeCCcEEEEEec
Q 034651 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI--KKNTRKPLGRILLKGDNITLMMNT 86 (88)
Q Consensus 11 ~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~--~~~~~~~~g~v~iRG~~I~~I~~~ 86 (88)
..|+++|.++++++ |.|.+++ |+++.|+|.|||+|||++|+||+|++. ++++.+.+|.++|||+||++|+|.
T Consensus 2 ~~P~~~L~~~~~~~--V~V~l~~--gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 2 LLPLELIDKCIGSR--IWIVMKS--DKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred cChHHHHHHhCCCE--EEEEECC--CeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence 47999999999986 7777764 699999999999999999999999963 234578899999999999999975
No 6
>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=99.91 E-value=1e-23 Score=125.79 Aligned_cols=68 Identities=29% Similarity=0.593 Sum_probs=61.4
Q ss_pred chHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEe
Q 034651 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 13 Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~ 85 (88)
|+++|+++++++ |.|.+++ |+.|+|+|.|||+|||++|+||+|++ .+...+.+|.++|||+||++|+|
T Consensus 1 p~~~L~~~~~~~--V~V~l~~--g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 1 PLDVLKDSLNKP--VLVKLKG--GKEVRGRLKSYDQHMNLVLEDAEEID-DGEPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred ChHHHHHhcCCE--EEEEECC--CCEEEEEEEEECCcceEEEeeEEEEe-cCCeEeEcCcEEEeCCEEEEEcC
Confidence 899999999996 8888875 59999999999999999999999985 44577899999999999999975
No 7
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.90 E-value=1.6e-23 Score=124.82 Aligned_cols=67 Identities=19% Similarity=0.449 Sum_probs=60.9
Q ss_pred chHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEE
Q 034651 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 84 (88)
Q Consensus 13 Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~ 84 (88)
|+++|+++++++ |+|+|++ |++|+|+|.|||+|||++|+||+|. ..+.+...++.++|||++|.+|+
T Consensus 1 p~~~L~~~~~~~--V~V~Lk~--g~~~~G~L~~~D~~mNlvL~~~~~~-~~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRP--VVVKLNS--GVDYRGILACLDGYMNIALEQTEEY-VNGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCe--EEEEECC--CCEEEEEEEEEccceeeEEeeEEEE-eCCceeeEeCCEEEECCEEEEEC
Confidence 899999999996 9999985 5899999999999999999999987 45667889999999999999985
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=99.90 E-value=2.7e-23 Score=129.88 Aligned_cols=73 Identities=22% Similarity=0.507 Sum_probs=62.6
Q ss_pred cchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecC------------CeeeecCeEEEeCCc
Q 034651 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK------------NTRKPLGRILLKGDN 79 (88)
Q Consensus 12 ~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~------------~~~~~~g~v~iRG~~ 79 (88)
+|+++|.+++....+|.|++++ |+++.|+|.|||+|||++|+||+|.+... .+.+.+|.+|||||+
T Consensus 2 gPl~~L~~~~~~~~~V~V~lr~--~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~ 79 (87)
T cd01720 2 GPLSLLTQAVKNNTQVLINCRN--NKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDS 79 (87)
T ss_pred ChHHHHHHHHcCCCEEEEEEcC--CCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCE
Confidence 7999999999554479999876 58999999999999999999999986432 135678999999999
Q ss_pred EEEEEec
Q 034651 80 ITLMMNT 86 (88)
Q Consensus 80 I~~I~~~ 86 (88)
|++|++.
T Consensus 80 Vv~Is~~ 86 (87)
T cd01720 80 VILVLRN 86 (87)
T ss_pred EEEEecC
Confidence 9999875
No 9
>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=99.90 E-value=2.9e-23 Score=128.12 Aligned_cols=70 Identities=26% Similarity=0.521 Sum_probs=61.0
Q ss_pred cchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecC------------CeeeecCeEEEeCCc
Q 034651 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK------------NTRKPLGRILLKGDN 79 (88)
Q Consensus 12 ~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~------------~~~~~~g~v~iRG~~ 79 (88)
.|+++|+.+++++ |.|.+++ |+++.|+|.|||+||||+|+||+|++... ...+.+|.++|||+|
T Consensus 1 ~pl~~l~~~~~k~--V~V~l~~--gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~ 76 (82)
T cd01730 1 EPLDLIRLSLDER--VYVKLRG--DRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDS 76 (82)
T ss_pred CchHHHHHhCCCE--EEEEECC--CCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCE
Confidence 4999999999996 8888765 59999999999999999999999996431 246799999999999
Q ss_pred EEEEEe
Q 034651 80 ITLMMN 85 (88)
Q Consensus 80 I~~I~~ 85 (88)
|++|++
T Consensus 77 Vv~i~~ 82 (82)
T cd01730 77 VILVSP 82 (82)
T ss_pred EEEECC
Confidence 999974
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=99.89 E-value=1e-22 Score=121.70 Aligned_cols=68 Identities=24% Similarity=0.439 Sum_probs=60.9
Q ss_pred cchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEE
Q 034651 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 84 (88)
Q Consensus 12 ~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~ 84 (88)
.|+.+|++++++. |.|+|++ |++|+|+|.|||+|||++|+||+|. ..+.+...+|.++|||+||.+|+
T Consensus 1 ~p~~~L~~~~g~~--V~V~Lk~--g~~~~G~L~~~D~~mNi~L~~~~e~-~~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 1 NPKPFLNDLTGKP--VIVKLKW--GMEYKGTLVSVDSYMNLQLANTEEY-IDGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCE--EEEEECC--CcEEEEEEEEECCCEEEEEeeEEEE-eCCccccCcCcEEEECCEEEEEC
Confidence 4899999999996 8888876 5999999999999999999999998 45556788999999999999984
No 11
>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=99.88 E-value=2.9e-22 Score=120.46 Aligned_cols=70 Identities=19% Similarity=0.320 Sum_probs=62.6
Q ss_pred chHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEecC
Q 034651 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 13 Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
|+++|+++.++. |+|+||+ |.+|+|+|.+||+|||++|+||.+.. .+++...++.+||||+||.+|..+|
T Consensus 1 P~~~L~~~~g~~--V~VeLk~--g~~~~G~L~~~D~~MNl~L~~~~~~~-~~g~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 1 PIKLLHEAEGHI--VTVELKT--GEVYRGKLIEAEDNMNCQLKDVTVTA-RDGRVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCE--EEEEECC--CcEEEEEEEEEcCCceeEEEEEEEEC-CCCcEeEcCcEEEeCCEEEEEEeCC
Confidence 899999999985 9999987 48999999999999999999999873 3445678899999999999999875
No 12
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=4.4e-22 Score=120.42 Aligned_cols=70 Identities=27% Similarity=0.568 Sum_probs=61.1
Q ss_pred hHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEecCC
Q 034651 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK 88 (88)
Q Consensus 14 l~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~~~ 88 (88)
-..|.++++|+ |.|.+++ |++++|+|.|||+|||++|+||+|+. ++...+.+|.++|||++|++|++.++
T Consensus 2 ~~~L~~~i~k~--V~V~L~~--g~~~~G~L~~~D~~mNlvL~~~~E~~-~~~~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 2 PPELKKYMDKK--LSLKLNG--NRKVSGILRGFDPFMNLVLDDAVEVN-SGGEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred chhhHHhCCCe--EEEEECC--CeEEEEEEEEEcccccEEeccEEEEc-cCCceeEeceEEECCCEEEEEEcccc
Confidence 34689999997 7777764 69999999999999999999999984 55678899999999999999998763
No 13
>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=99.88 E-value=3.5e-22 Score=121.73 Aligned_cols=72 Identities=14% Similarity=0.235 Sum_probs=63.6
Q ss_pred cchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEecC
Q 034651 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 12 ~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
.|+++|+++.+++ |+|++|+ |++++|+|.+||+|||++|+||+|...+++....++.++|||++|.+|..++
T Consensus 1 ~Pl~~L~~~~g~~--V~VeLkn--g~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~ 72 (76)
T cd01723 1 LPLSLLKTAQNHP--MLVELKN--GETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPD 72 (76)
T ss_pred CchHHHHhcCCCE--EEEEECC--CCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCH
Confidence 4999999999996 9999986 5899999999999999999999998544555677899999999999998765
No 14
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=9.7e-22 Score=121.26 Aligned_cols=70 Identities=24% Similarity=0.461 Sum_probs=59.5
Q ss_pred hHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecC-------CeeeecCeEEEeCCcEEEEEec
Q 034651 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK-------NTRKPLGRILLKGDNITLMMNT 86 (88)
Q Consensus 14 l~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~-------~~~~~~g~v~iRG~~I~~I~~~ 86 (88)
+.-|.++++++ |.|.++ +|++++|+|.|||+||||+|+||+|+.... ...+.+|.++|||+||++|++.
T Consensus 4 ~~~L~~~i~k~--V~V~l~--~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~ 79 (81)
T cd01729 4 ILDLSKYVDKK--IRVKFQ--GGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPV 79 (81)
T ss_pred hhhHHHhcCCe--EEEEEC--CCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecC
Confidence 33489999997 777776 469999999999999999999999985431 2568899999999999999987
Q ss_pred C
Q 034651 87 G 87 (88)
Q Consensus 87 ~ 87 (88)
+
T Consensus 80 ~ 80 (81)
T cd01729 80 D 80 (81)
T ss_pred C
Confidence 6
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.87 E-value=1.1e-21 Score=119.99 Aligned_cols=73 Identities=34% Similarity=0.667 Sum_probs=61.6
Q ss_pred eeecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEe-cCCe-eeecC-eEEEeCCcEEEEEe
Q 034651 9 IMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI-KKNT-RKPLG-RILLKGDNITLMMN 85 (88)
Q Consensus 9 ~~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~~~-~~~~g-~v~iRG~~I~~I~~ 85 (88)
.+..|+++|+++++++ |.|+||+ |++|.|+|.|||+|||++|+||+|+.. ++.. .+.++ .++|||+||++|.+
T Consensus 4 ~~~~~~~~l~~~~~~~--V~V~lk~--g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 4 LGPLPLSFLKKLLNKR--VLVKLKN--GREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred ccCCcHHHHHHhhCCE--EEEEECC--CCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 3567999999999975 9999986 489999999999999999999999964 3333 34445 99999999999964
No 16
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.85 E-value=1.7e-20 Score=114.13 Aligned_cols=70 Identities=24% Similarity=0.398 Sum_probs=59.3
Q ss_pred chHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCC--eeeecCeEEEeCCcEEEEEec
Q 034651 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKN--TRKPLGRILLKGDNITLMMNT 86 (88)
Q Consensus 13 Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~~~g~v~iRG~~I~~I~~~ 86 (88)
++..|.++++++ |.|.++ +|++|.|+|.|||+|||++|+||.|+...+. ..+.+|.+++||+||++|.++
T Consensus 3 ~~~~L~~~l~k~--v~V~l~--~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~~ 74 (74)
T cd01728 3 GTASLVDDLDKK--VVVLLR--DGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGEI 74 (74)
T ss_pred chHHHHHhcCCE--EEEEEc--CCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEcC
Confidence 467789999997 777775 4699999999999999999999999854432 467899999999999999863
No 17
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.84 E-value=2e-20 Score=110.29 Aligned_cols=66 Identities=27% Similarity=0.585 Sum_probs=58.4
Q ss_pred HHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEe
Q 034651 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 16 ~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~ 85 (88)
+|.++++++ |.|.+++ |+.+.|+|.+||+|||++|+||+|++.+..+.+.++.++|||++|.+|.+
T Consensus 2 ~L~~~~~~~--V~V~l~~--g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKR--VLVELKN--GREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcE--EEEEECC--CcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 578899986 8888875 58999999999999999999999996443688999999999999999974
No 18
>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=99.84 E-value=2.1e-20 Score=117.40 Aligned_cols=71 Identities=21% Similarity=0.395 Sum_probs=63.7
Q ss_pred cchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEecC
Q 034651 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 12 ~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
.|+.+|+++.++. |+|+||++ ..|+|+|.++|.|||++|+||+++ .+++....++.++|||+||.||..++
T Consensus 1 ~~~~fL~~l~g~~--V~VeLKng--~~~~G~L~~vD~~MNl~L~~a~~~-~~~~~~~~~~~v~IRG~nI~yi~lPd 71 (90)
T cd01724 1 KLVRFLMKLTNET--VTIELKNG--TIVHGTITGVDPSMNTHLKNVKLT-LKGRNPVPLDTLSIRGNNIRYFILPD 71 (90)
T ss_pred CHhHHHHhCCCCE--EEEEECCC--CEEEEEEEEEcCceeEEEEEEEEE-cCCCceeEcceEEEeCCEEEEEEcCC
Confidence 3788999999985 99999874 799999999999999999999998 45667788999999999999999885
No 19
>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=99.84 E-value=2.2e-20 Score=110.28 Aligned_cols=67 Identities=25% Similarity=0.544 Sum_probs=58.9
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEe
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~ 85 (88)
++|+++++++ |.|.+++ |+.++|+|.+||+|||++|+||.|....+.+.+.++.++|||++|++|.+
T Consensus 1 ~~L~~~~g~~--V~V~l~~--g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKR--VRVELKN--GRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSE--EEEEETT--SEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcE--EEEEEeC--CEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 4789999986 8888765 69999999999999999999999995433389999999999999999985
No 20
>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=99.84 E-value=3.2e-20 Score=112.51 Aligned_cols=68 Identities=26% Similarity=0.437 Sum_probs=58.0
Q ss_pred HHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEec---CCeeeecCeEEEeCCcEEEEEecC
Q 034651 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK---KNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 16 ~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
.|.++++++ |.|.++ +|+.+.|+|.|||+|||++|+||+|+... +...+.+|.+++||+||++|++.+
T Consensus 3 ~L~~~l~~~--V~V~l~--dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 3 TLEDYLNKT--VSVITV--DGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hHHHhcCCE--EEEEEC--CCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 578899997 666664 57999999999999999999999998542 335778999999999999999876
No 21
>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=99.83 E-value=4.7e-20 Score=112.94 Aligned_cols=66 Identities=32% Similarity=0.582 Sum_probs=56.3
Q ss_pred HHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecC---------CeeeecCeEEEeCCcEEEEEe
Q 034651 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK---------NTRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 16 ~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~---------~~~~~~g~v~iRG~~I~~I~~ 85 (88)
-|.++++++ |.|.++ +|+++.|+|.|||+|||++|+||+|++... .+.+.+|.++|||++|++|+.
T Consensus 4 ~l~~~l~~~--V~V~l~--dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYR--LRVTLQ--DGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCE--EEEEEC--CCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 478899996 777776 469999999999999999999999986421 356889999999999999974
No 22
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.81 E-value=4.9e-20 Score=111.28 Aligned_cols=69 Identities=23% Similarity=0.513 Sum_probs=59.9
Q ss_pred cchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEecC
Q 034651 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 12 ~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
.| -|++|++|+ + .++.++||..+|+|.|||.|||+||+++.|. ..++.+..++.++|||++|+.+++.+
T Consensus 6 ~P--eLkkymdKk--i--~lklnG~r~v~GiLrGyD~FmNiVlde~vE~-~~~~~~~~ig~~vIrgnsiv~~eaL~ 74 (77)
T KOG1780|consen 6 HP--ELKKYMDKK--I--VLKLNGGRKVTGILRGYDPFMNIVLDETVEP-NGDGDKNNIGMVVIRGNSIVMVEALE 74 (77)
T ss_pred Cc--hHHHhhhhe--E--EEEeCCCcEEEEEEeccchHHhhhhhhceee-cCcCCcceeeeEEEeccEEEEEeecc
Confidence 57 679999998 4 4445788999999999999999999999998 44567888999999999999998765
No 23
>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=99.81 E-value=2e-19 Score=110.33 Aligned_cols=71 Identities=20% Similarity=0.316 Sum_probs=61.9
Q ss_pred ecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEec
Q 034651 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNT 86 (88)
Q Consensus 11 ~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~ 86 (88)
..+..+|+.+.++. |+|+||++ ..|+|+|.++|.|||++|+||++. ..++....++.++|||++|.||..|
T Consensus 8 ~tl~~~L~~l~g~~--V~VeLKng--~~~~G~L~~vD~~MNl~L~~~~~~-~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 8 NTLIILLQGLQGKV--VTVELRNE--TTVTGRIASVDAFMNIRLAKVTII-DRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred chHHHHHHHCCCCE--EEEEECCC--CEEEEEEEEEcCCceeEEEEEEEE-cCCCceeECCcEEEECCEEEEEEcC
Confidence 45688899998885 99999975 799999999999999999999987 3455666899999999999999864
No 24
>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=99.81 E-value=1.9e-19 Score=110.98 Aligned_cols=72 Identities=15% Similarity=0.282 Sum_probs=61.1
Q ss_pred cchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecC-CeeeecCeEEEeCCcEEEEEecC
Q 034651 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK-NTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 12 ~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~-~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
+|+++|+++.++. |+|+||+ |..|+|+|.++|.|||++|+||++...++ .....++.++|||++|.+|..++
T Consensus 1 l~~~fL~~l~g~~--V~VeLKn--g~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~ 73 (81)
T cd01725 1 LFFSFFKTLVGKE--VTVELKN--DLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPA 73 (81)
T ss_pred ChhHHHHhCCCCE--EEEEECC--CcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeCh
Confidence 4889999999985 9999996 48999999999999999999998874222 23456789999999999999875
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=99.78 E-value=1.6e-18 Score=100.83 Aligned_cols=63 Identities=35% Similarity=0.657 Sum_probs=55.1
Q ss_pred HHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEE
Q 034651 17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 84 (88)
Q Consensus 17 L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~ 84 (88)
|+++++++ |.|.+++ |+.|.|+|.+||+|||++|+||.|.+. +.+.+.++.++|||++|.+|.
T Consensus 1 l~~~~g~~--V~V~l~~--g~~~~G~L~~~D~~~Ni~L~~~~~~~~-~~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKT--VRVELKD--GRVLEGVLVAFDKYMNLVLDDVEETIK-EGKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCE--EEEEECC--CcEEEEEEEEECCCCCEEECCEEEEec-CCcEEECCeEEEECCEEEEEC
Confidence 46778885 8888875 599999999999999999999999954 467899999999999999984
No 26
>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=99.76 E-value=8.3e-18 Score=102.52 Aligned_cols=67 Identities=18% Similarity=0.292 Sum_probs=57.4
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEec-----CCeeeecCeEEEeCCcEEEEEe
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK-----KNTRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-----~~~~~~~g~v~iRG~~I~~I~~ 85 (88)
+.|.++++++ |.|.++ +||.|.|+|.+||+|||++|+||.|+... +.+.+.+|.++|||++|++|+.
T Consensus 3 ~~L~~~l~~~--v~V~l~--dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRT--MRIHMT--DGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCe--EEEEEc--CCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 4578999996 666665 57999999999999999999999999643 2468999999999999999874
No 27
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.73 E-value=8.6e-19 Score=108.07 Aligned_cols=73 Identities=26% Similarity=0.501 Sum_probs=62.8
Q ss_pred eecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEec--C----------CeeeecCeEEEeC
Q 034651 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK--K----------NTRKPLGRILLKG 77 (88)
Q Consensus 10 ~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--~----------~~~~~~g~v~iRG 77 (88)
|..|+++|+-+++.+ |.|+++ ++++++|+|.+||+|.|++|.|++|+... + ..++.+..+|+||
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 678999999999996 666665 56999999999999999999999998542 1 2357888999999
Q ss_pred CcEEEEEec
Q 034651 78 DNITLMMNT 86 (88)
Q Consensus 78 ~~I~~I~~~ 86 (88)
++|++|+|+
T Consensus 79 d~Vilvspp 87 (91)
T KOG3460|consen 79 DGVILVSPP 87 (91)
T ss_pred CeEEEEcCc
Confidence 999999986
No 28
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.69 E-value=5.1e-17 Score=97.98 Aligned_cols=72 Identities=25% Similarity=0.384 Sum_probs=65.4
Q ss_pred ecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEecC
Q 034651 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 11 ~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
..|-.+|....++. |.|.||++ .+|+|+|++.|.|||+.|.+|+|+ .++.....+|.++||++||.+|...+
T Consensus 7 vNPKpFL~~l~gk~--V~vkLKwg--~eYkG~LvsvD~YmNlqL~~~eE~-idG~~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 7 VNPKPFLNGLTGKP--VLVKLKWG--QEYKGTLVSVDNYMNLQLANAEEY-IDGVSTGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred CCchHHHhhccCCe--EEEEEecC--cEEEEEEEEecchhheehhhhhhh-hcccccccceeEEEEeccEEEEecCC
Confidence 47888899988885 99999996 899999999999999999999998 57888999999999999999998765
No 29
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.68 E-value=3.2e-17 Score=99.70 Aligned_cols=74 Identities=36% Similarity=0.715 Sum_probs=64.2
Q ss_pred eecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEec--CCeeeecCeEEEeCCcEEEEEecC
Q 034651 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK--KNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 10 ~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
...|++++.++++.+ ||+...+.+++.|+|.|||.|.|++|+|++|+... +....+++++++.|+||.+..|.+
T Consensus 5 ~llPlEliDkcIgsk----i~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 5 TLLPLELIDKCIGSK----IWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred hcccHHHHHHhcCce----EEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence 368999999999998 55555567999999999999999999999999654 447789999999999999988754
No 30
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.61 E-value=1.2e-15 Score=100.11 Aligned_cols=72 Identities=15% Similarity=0.218 Sum_probs=66.4
Q ss_pred cchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEecC
Q 034651 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 12 ~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
.||.+|+.+.+. ++.|+||++ -.|.|.|..+|.||||.|++++++..++.+...++.++|||++|.|+..++
T Consensus 2 lPLsLL~~aq~~--pmlvELKNg--et~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d 73 (134)
T KOG3293|consen 2 LPLSLLKTAQNH--PMLVELKNG--ETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPD 73 (134)
T ss_pred cchhHHHhcCCC--eEEEEecCC--CEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccH
Confidence 699999999998 499999986 589999999999999999999999777788999999999999999998765
No 31
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.60 E-value=2e-16 Score=95.38 Aligned_cols=72 Identities=18% Similarity=0.451 Sum_probs=64.8
Q ss_pred ecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEecC
Q 034651 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 11 ~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
+.|-++|..++++. |.|+| ++|..|+|+|...|.|||+-|+.++|+ .++..+++++..||||++|.+|+...
T Consensus 5 ~~~~~fl~~iiGr~--V~VKl--~sgvdyrG~l~~lDgymNiaLe~tee~-~ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 5 SMPGEFLKAIIGRT--VVVKL--NSGVDYRGTLVCLDGYMNIALESTEEY-VNGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cCcHHHHHHHhCCe--EEEEe--cCCccccceehhhhhHHHHHHHHHHHH-hcCcccccccceeeccccEEEEEecc
Confidence 57899999999996 66666 567999999999999999999999998 57888999999999999999999754
No 32
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.58 E-value=2e-16 Score=100.22 Aligned_cols=72 Identities=25% Similarity=0.449 Sum_probs=60.0
Q ss_pred cchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEec-------CCeeeecCeEEEeCCcEEEEE
Q 034651 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK-------KNTRKPLGRILLKGDNITLMM 84 (88)
Q Consensus 12 ~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------~~~~~~~g~v~iRG~~I~~I~ 84 (88)
..+-.|.+|++++++|. ..+||+.+|+|.|||+.||+||+|+.|+-.+ ..+.|.+|.+++||..+++|+
T Consensus 17 EsilDLsky~Dk~Irvk----f~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlis 92 (108)
T KOG1781|consen 17 ESILDLSKYLDKKIRVK----FTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLIS 92 (108)
T ss_pred hHHhhHHHhhccceEEE----eecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEc
Confidence 34667899999984433 3578999999999999999999999998433 135699999999999999999
Q ss_pred ecC
Q 034651 85 NTG 87 (88)
Q Consensus 85 ~~~ 87 (88)
|.+
T Consensus 93 p~d 95 (108)
T KOG1781|consen 93 PAD 95 (108)
T ss_pred CCc
Confidence 875
No 33
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.42 E-value=2.1e-13 Score=85.37 Aligned_cols=68 Identities=19% Similarity=0.434 Sum_probs=58.8
Q ss_pred HHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEec---CCeeeecCeEEEeCCcEEEEEecC
Q 034651 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK---KNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 16 ~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
-|+.|++++ |.|. .++||.+.|.|.|||+-.||+|+++-|+.++ +.++..+|..+|||+|+.+|.+++
T Consensus 4 ~L~~y~n~~--V~vI--t~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iD 74 (96)
T KOG1784|consen 4 TLEDYMNQR--VSVI--TNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEID 74 (96)
T ss_pred hHHHHhhce--EEEE--ecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecc
Confidence 478999996 5554 4688999999999999999999999998653 557888999999999999999875
No 34
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.35 E-value=2.6e-12 Score=82.69 Aligned_cols=73 Identities=16% Similarity=0.286 Sum_probs=64.4
Q ss_pred eecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEecC
Q 034651 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 10 ~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
+..|+.+|+++-+.- |++++++ |-.|.|+|+..|.+||++|+|.+.+ ..+.....+.++||||+.|.|+..+|
T Consensus 3 ~gvpiKlLhEaqGhI--Vt~Et~t--Ge~YRGkliEaeDnmNcql~di~vT-~~dg~vs~le~V~IRGS~IRFlvlPd 75 (119)
T KOG3172|consen 3 VGVPIKLLHEAQGHI--VTVETKT--GEVYRGKLIEAEDNMNCQLRDITVT-ARDGRVSQLEQVFIRGSKIRFLVLPD 75 (119)
T ss_pred cccceeeeecccCcE--EEEEecC--CceeeeeeEEeccccccEEEEEEEE-ccCCcceeeeeEEEecCeEEEEECch
Confidence 357999999999985 8998876 4699999999999999999999988 45668888999999999999998764
No 35
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.30 E-value=1.7e-11 Score=76.59 Aligned_cols=69 Identities=17% Similarity=0.275 Sum_probs=57.3
Q ss_pred hHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEec-CCeeeecCeEEEeCCcEEEEEec
Q 034651 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK-KNTRKPLGRILLKGDNITLMMNT 86 (88)
Q Consensus 14 l~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~~~~~~~g~v~iRG~~I~~I~~~ 86 (88)
.++++..++++ |+|+||+ +..+.|+|.|.|+|+|+-|.|......+ -+.-.....+||||+.|.||..+
T Consensus 4 ysfFkslvg~~--V~VeLKn--d~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~ 73 (96)
T KOG3448|consen 4 YSFFKSLVGKE--VVVELKN--DLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLP 73 (96)
T ss_pred HHHHHHhcCCe--EEEEEcC--CcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeC
Confidence 46788889986 9999997 4899999999999999999999887432 12345667899999999999875
No 36
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.20 E-value=2.2e-12 Score=84.63 Aligned_cols=67 Identities=25% Similarity=0.492 Sum_probs=56.8
Q ss_pred HHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCC--eeeecCeEEEeCCcEEEEEecC
Q 034651 17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKN--TRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 17 L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~--~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
|.+++.++ +.|-|++ ||.+.|.|.+||||-|++|++|.|...-+. .....|..+|||+||+++..++
T Consensus 14 l~~~~dkK--llVlLRD--GR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid 82 (129)
T KOG1782|consen 14 LVEYLDKK--LLVLLRD--GRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEID 82 (129)
T ss_pred HHHHhcce--EEEEEec--CcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCC
Confidence 68889997 7777765 699999999999999999999999865333 3566789999999999998864
No 37
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.18 E-value=3.4e-12 Score=82.28 Aligned_cols=74 Identities=22% Similarity=0.497 Sum_probs=65.4
Q ss_pred ecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEec------C------CeeeecCeEEEeCC
Q 034651 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIK------K------NTRKPLGRILLKGD 78 (88)
Q Consensus 11 ~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~------~------~~~~~~g~v~iRG~ 78 (88)
.+|++++..++....+|.|-++++ +.+-|.+.|||.|.|++|+|+.|.|.+ + ...+.++.+|||||
T Consensus 23 ~Gpls~~~~~~~~~~~vLi~cRnn--~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGd 100 (114)
T KOG3459|consen 23 TGPLSVLPASVKNNTQVLINCRNN--VKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGD 100 (114)
T ss_pred cCchhhhHHHhhcCceeEEEeccc--HHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCC
Confidence 489999999999999999999875 899999999999999999999999863 1 13688999999999
Q ss_pred cEEEEEec
Q 034651 79 NITLMMNT 86 (88)
Q Consensus 79 ~I~~I~~~ 86 (88)
+|+.+...
T Consensus 101 svI~v~r~ 108 (114)
T KOG3459|consen 101 SVILVLRN 108 (114)
T ss_pred eEEEEEec
Confidence 99988754
No 38
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.18 E-value=3.3e-12 Score=87.74 Aligned_cols=66 Identities=33% Similarity=0.581 Sum_probs=53.3
Q ss_pred HHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEe---------cCCeeeecCeEEEeCCcEEEEEecC
Q 034651 18 FRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHI---------KKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 18 ~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~---------~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
-.+++.+ ..|.+ ++|+.|.|.+.+||.|||++|.||+|+.. ++++.+.++++++||+||++.+..+
T Consensus 10 l~~iNyr--~rv~~--qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg 84 (177)
T KOG3168|consen 10 LQHINYR--MRVRL--QDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG 84 (177)
T ss_pred HHhhcce--EEEEe--ccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence 4457776 44444 56799999999999999999999999842 1357899999999999999987653
No 39
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=99.02 E-value=2.5e-09 Score=68.90 Aligned_cols=68 Identities=21% Similarity=0.321 Sum_probs=58.4
Q ss_pred hHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEecC
Q 034651 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 14 l~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
+.+|.+..+.. |+|+||++ ....|++.+.|.+||..|.++.-. .++ ++..+..+.+||+||.|+..++
T Consensus 4 vr~L~kl~~e~--vtIeLkng--t~v~G~I~~Vd~~Mn~~l~~v~~t-~~~-~pv~l~~lsirgnniRy~~lpD 71 (109)
T KOG3428|consen 4 VRFLKKLLNER--VTIELKNG--TIVHGTIDSVDVQMNTHLKHVKMT-VKG-EPVRLDTLSIRGNNIRYYILPD 71 (109)
T ss_pred HHHHHHhhCCe--EEEEecCC--cEEeeeEEEEEhhheeEEEEEEEe-cCC-CceeEEEEEeecceEEEEEccC
Confidence 56788888875 99999974 799999999999999999998876 334 6778899999999999998875
No 40
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=98.91 E-value=8.8e-10 Score=65.41 Aligned_cols=46 Identities=26% Similarity=0.430 Sum_probs=36.5
Q ss_pred HHhhcCcceEEEEEEeCCC--eEEEEEEEEeccccceEEeceEEEEec
Q 034651 18 FRFLQSKARIQIWLFEQKD--LRIEGRIIGFDEYMNLVLDDAEEVHIK 63 (88)
Q Consensus 18 ~~~l~k~~~V~V~lk~~~g--~~~~G~L~~~D~~mNlvL~d~~e~~~~ 63 (88)
.+++..+.+|.|+++..+| ..++|.|++||+|||++|.|+.|.+..
T Consensus 2 ~~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 2 HRCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred chhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 4566666677777765443 379999999999999999999999743
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=97.43 E-value=0.00054 Score=40.26 Aligned_cols=39 Identities=23% Similarity=0.482 Sum_probs=32.2
Q ss_pred HHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEec
Q 034651 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (88)
Q Consensus 16 ~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d 56 (88)
+|..+..++.+|+|.|.| |..++|.+.|||+|+=+.-.+
T Consensus 3 fln~~r~~~~~Vtv~L~N--G~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 3 FLNAARKEKIPVTIYLVN--GVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred HHHHHHHcCCcEEEEEeC--CcEEEEEEEEEcceEEEEEEC
Confidence 567777788899999987 489999999999998666544
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=97.41 E-value=0.0006 Score=40.06 Aligned_cols=39 Identities=15% Similarity=0.444 Sum_probs=31.9
Q ss_pred HHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEec
Q 034651 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (88)
Q Consensus 16 ~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d 56 (88)
+|..+..++++|+|.|.| |..+.|.+.|||+|+=++-.+
T Consensus 7 fln~~r~~~~~Vti~L~n--G~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 7 FLNTLRKERIPVTVFLVN--GVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred HHHHHHHcCCcEEEEEeC--CcEEEEEEEEEeeeEEEEEEC
Confidence 566677778899999987 489999999999998666544
No 43
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=97.21 E-value=0.0012 Score=40.66 Aligned_cols=40 Identities=18% Similarity=0.534 Sum_probs=32.1
Q ss_pred HHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEece
Q 034651 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 16 ~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~ 57 (88)
+|..+..++.+|+|.|.| |..+.|.+.|||.|+=+.-.+.
T Consensus 11 fLn~lr~~~~~VtifL~N--G~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 11 FLNALRKERVPVTIYLVN--GIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred HHHHHHHcCCCEEEEEeC--CcEEEEEEEEEccEEEEEEECC
Confidence 455666677889999987 4899999999999987666554
No 44
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.92 E-value=0.0026 Score=38.88 Aligned_cols=35 Identities=20% Similarity=0.563 Sum_probs=28.0
Q ss_pred HHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccce
Q 034651 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNL 52 (88)
Q Consensus 16 ~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNl 52 (88)
+|......+++|+|.|.| |..+.|.+.|||+|.=+
T Consensus 11 fLn~~Rk~~i~VtIfLvN--G~~L~G~V~sfD~f~Vl 45 (77)
T COG1923 11 FLNALRKEKIPVTIFLVN--GFKLQGQVESFDNFVVL 45 (77)
T ss_pred HHHHHHhcCCeEEEEEEc--CEEEEEEEEeeeeEEEE
Confidence 445555566899999987 58999999999999733
No 45
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=96.55 E-value=0.0061 Score=36.50 Aligned_cols=63 Identities=11% Similarity=0.170 Sum_probs=37.3
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEecc---ccceEEeceEEEEecC------CeeeecCeEEEeCCcEE
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDE---YMNLVLDDAEEVHIKK------NTRKPLGRILLKGDNIT 81 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~---~mNlvL~d~~e~~~~~------~~~~~~g~v~iRG~~I~ 81 (88)
-++..++|.. |.|.+++ |..|+|.|.+++. -+-++|+-+....... ........+++.++.|+
T Consensus 5 ~l~~~lvG~~--V~V~~~~--G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 5 YLLTNLVGQT--VEVTTKN--GSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHHTTTTSE--EEEEETT--S-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHHhCcCCE--EEEEECC--CCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 4566778885 8888876 5799999999999 8999999888763211 11244456667666654
No 46
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=96.30 E-value=0.033 Score=35.33 Aligned_cols=64 Identities=19% Similarity=0.338 Sum_probs=47.7
Q ss_pred HhhcCcceEEEEEEeCCCeEEEEEEEEecc-ccceEEeceEEEEecC--------CeeeecCeEEEeCCcEEEEEec
Q 034651 19 RFLQSKARIQIWLFEQKDLRIEGRIIGFDE-YMNLVLDDAEEVHIKK--------NTRKPLGRILLKGDNITLMMNT 86 (88)
Q Consensus 19 ~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~--------~~~~~~g~v~iRG~~I~~I~~~ 86 (88)
.|+|++ |.+.. +.+..|+|+|..+|. --.+.|.|+.-+-.++ .....+..+..||..|.-+...
T Consensus 5 ~~IGs~--ISlis--k~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~ 77 (96)
T PF12701_consen 5 PYIGSK--ISLIS--KSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVI 77 (96)
T ss_dssp CCTTCE--EEEEE--TTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEEC
T ss_pred cccCCE--EEEEE--CCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEE
Confidence 468886 55555 456999999999998 7889999988764332 1234678999999999877653
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=96.18 E-value=0.015 Score=40.25 Aligned_cols=41 Identities=20% Similarity=0.380 Sum_probs=33.0
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEece
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~ 57 (88)
.+|..+..++.+|+|.|.| |..++|.+.|||.|.=|.-.+.
T Consensus 95 ~fLn~~rk~k~~VtvfL~N--G~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVN--GVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred HHHHHHHhcCCcEEEEEec--CcEEEEEEEEEcceEEEEEeCC
Confidence 3566666777899999986 5899999999999986666554
No 48
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=96.16 E-value=0.015 Score=40.18 Aligned_cols=41 Identities=20% Similarity=0.428 Sum_probs=32.9
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEece
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~ 57 (88)
.+|..+..++.+|+|.|.+| ..++|.+.+||+|.=|.-.+.
T Consensus 15 ~fLn~~Rk~k~~VtvfL~nG--~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 15 IFLNSLRKTKTPVTMFLVKG--VKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred HHHHHHHhcCCcEEEEEecC--cEEEEEEEEEcceEEEEEeCC
Confidence 35666677788999999874 899999999999986665554
No 49
>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=94.29 E-value=0.31 Score=29.63 Aligned_cols=60 Identities=18% Similarity=0.325 Sum_probs=41.6
Q ss_pred HhhcCcceEEEEEEeCCCeEEEEEEEEeccccce-EEeceEEEEecCC---------eeeecCeEEEeCCcEEE
Q 034651 19 RFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNL-VLDDAEEVHIKKN---------TRKPLGRILLKGDNITL 82 (88)
Q Consensus 19 ~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNl-vL~d~~e~~~~~~---------~~~~~g~v~iRG~~I~~ 82 (88)
.+++++ +.+.. ..+..|+|+|.++|..=.. .|+|+..+-+++. ...-++.++.||+.|.-
T Consensus 3 ~~IG~~--isLIS--k~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYIGSK--ISLIS--KSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred cccCce--EEEEe--cCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 468886 55544 4568999999999987654 4888877644321 23456688999988753
No 50
>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=93.86 E-value=0.41 Score=26.16 Aligned_cols=47 Identities=21% Similarity=0.272 Sum_probs=31.7
Q ss_pred hcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEe
Q 034651 21 LQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLK 76 (88)
Q Consensus 21 l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iR 76 (88)
+++. |++.. + +..++|+..++|+.-.|+++..... -....-|.+++|
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 4664 66665 3 4688999999999999999765441 123344566554
No 51
>PRK14633 hypothetical protein; Provisional
Probab=90.43 E-value=0.63 Score=31.43 Aligned_cols=38 Identities=8% Similarity=0.152 Sum_probs=27.5
Q ss_pred HHHHHhhcCcceEEEEEEe--CCCeEEEEEEEEeccccceEEe
Q 034651 15 NLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~--~~g~~~~G~L~~~D~~mNlvL~ 55 (88)
.-+.+|+|++ |.|.++. ++.++++|+|.++|+- ++.|.
T Consensus 87 ~~f~r~~G~~--v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 87 IQAQALVGFN--VKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHHHHhCCCe--EEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 4457888887 5555543 4678999999999984 45553
No 52
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=90.24 E-value=0.75 Score=27.82 Aligned_cols=49 Identities=18% Similarity=0.355 Sum_probs=30.8
Q ss_pred CccccceeeecchHHHHHhhcCcceEEEEEEe--CCCeEEEEEEEEeccccceEE
Q 034651 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVL 54 (88)
Q Consensus 2 ~~~~~~~~~~~Pl~~L~~~l~k~~~V~V~lk~--~~g~~~~G~L~~~D~~mNlvL 54 (88)
|++-..++...| .-+.+++|+. |.|+++. ++.+.++|.|.++|+- ++.|
T Consensus 6 SSPGl~RpL~~~-~~~~r~~G~~--v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 6 SSPGAERPLKKE-ADFERAVGKY--VHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred cCCCCCCcCCCH-HHHHHhCCCE--EEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 444223443444 3447888886 6776663 3347899999999984 4444
No 53
>PRK14634 hypothetical protein; Provisional
Probab=88.87 E-value=0.91 Score=30.84 Aligned_cols=50 Identities=14% Similarity=0.198 Sum_probs=31.4
Q ss_pred CccccceeeecchHHHHHhhcCcceEEEEEEe--CCCeEEEEEEEEeccccceEEe
Q 034651 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 2 ~~~~~~~~~~~Pl~~L~~~l~k~~~V~V~lk~--~~g~~~~G~L~~~D~~mNlvL~ 55 (88)
|++--.++...|- -+.+++|+. |.|+++. ++.+.++|+|.++|.- ++.|.
T Consensus 81 SSPGldRpL~~~~-~f~r~~G~~--V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14634 81 SSPGIGDQLSSDR-DFQTFRGFP--VEVSHRDDDGSEQRLEGLLLERNED-HLQIN 132 (155)
T ss_pred eCCCCCCcCCCHH-HHHHhCCCe--EEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence 3442234444443 447888987 6676653 3347999999999983 45453
No 54
>PRK14640 hypothetical protein; Provisional
Probab=88.77 E-value=0.99 Score=30.50 Aligned_cols=45 Identities=11% Similarity=0.141 Sum_probs=29.5
Q ss_pred ceeeecchHHHHHhhcCcceEEEEEEe--CCCeEEEEEEEEeccccceEEe
Q 034651 7 QRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 7 ~~~~~~Pl~~L~~~l~k~~~V~V~lk~--~~g~~~~G~L~~~D~~mNlvL~ 55 (88)
.++...| .-+.+++|+. |.|.++. ++.+.++|+|.++|+- ++.|.
T Consensus 83 ~RpL~~~-~~f~r~~G~~--v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 83 DRPLFKV-AQFEKYVGQE--AAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred CCcCCCH-HHHHHhCCCe--EEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 3433333 3457888887 6666543 3568999999999984 45453
No 55
>PRK14636 hypothetical protein; Provisional
Probab=87.67 E-value=1.2 Score=30.92 Aligned_cols=49 Identities=20% Similarity=0.329 Sum_probs=31.2
Q ss_pred CccccceeeecchHHHHHhhcCcceEEEEEEe--CCCeEEEEEEEEeccccceEE
Q 034651 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVL 54 (88)
Q Consensus 2 ~~~~~~~~~~~Pl~~L~~~l~k~~~V~V~lk~--~~g~~~~G~L~~~D~~mNlvL 54 (88)
|++--.++...| .-+.+|+|+. |.|+++. ++.+.++|+|.++|.- ++.|
T Consensus 79 SSPGldRpL~~~-~df~r~~G~~--V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 79 SSPGIDRPLTRP-KDFADWAGHE--ARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred eCCCCCCCCCCH-HHHHHhCCCe--EEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 344334444444 4557889987 6666652 3347999999999883 4554
No 56
>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=86.39 E-value=2.1 Score=25.01 Aligned_cols=31 Identities=13% Similarity=0.246 Sum_probs=23.3
Q ss_pred EEEEeCCCeEEEEEEEEeccccceEEeceEE
Q 034651 29 IWLFEQKDLRIEGRIIGFDEYMNLVLDDAEE 59 (88)
Q Consensus 29 V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e 59 (88)
|++++-.|-+++|.+.+||.-.++++=.|.+
T Consensus 9 V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 9 VSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred EEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 4445555789999999999999987555443
No 57
>PRK14638 hypothetical protein; Provisional
Probab=86.36 E-value=1.6 Score=29.47 Aligned_cols=36 Identities=19% Similarity=0.188 Sum_probs=26.0
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEe
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~ 55 (88)
.-+.+++|+. |.|.++ +++.++|+|.++|.- ++.|.
T Consensus 93 ~~f~r~~G~~--v~V~~~--~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 93 KDYVRFTGKL--AKIVTK--DGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHHHhCCCE--EEEEEC--CCcEEEEEEEEEeCC-EEEEE
Confidence 3457888886 666665 468999999999973 34443
No 58
>PRK14643 hypothetical protein; Provisional
Probab=86.16 E-value=1.7 Score=29.85 Aligned_cols=33 Identities=15% Similarity=0.217 Sum_probs=24.6
Q ss_pred HHHHHhhcCcceEEEEEEe--CCCeEEEEEEEEeccc
Q 034651 15 NLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEY 49 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~--~~g~~~~G~L~~~D~~ 49 (88)
.-+.+|+|+. |.|.++. ++.+.++|+|.++|.-
T Consensus 97 ~df~r~~G~~--V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 97 EELVKALNQW--VYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHHhcCCe--EEEEEecccCCceEEEEEEEEEeCC
Confidence 4557889987 6666654 3458999999999864
No 59
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.85 E-value=1.9 Score=29.47 Aligned_cols=39 Identities=23% Similarity=0.425 Sum_probs=27.7
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEE
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL 54 (88)
+-+.+|+|+.+.|..+..-.+.+.++|+|.++|.-. +++
T Consensus 92 ~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 92 EHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred HHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 455888999744444334456789999999999987 444
No 60
>PRK14646 hypothetical protein; Provisional
Probab=85.60 E-value=1.9 Score=29.30 Aligned_cols=38 Identities=13% Similarity=0.071 Sum_probs=26.8
Q ss_pred HHHHHhhcCcceEEEEEEeC--CCeEEEEEEEEeccccceEEe
Q 034651 15 NLIFRFLQSKARIQIWLFEQ--KDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~--~g~~~~G~L~~~D~~mNlvL~ 55 (88)
.-+.+|+|+. |.|+++.. +.+.++|+|.++|+- ++.|.
T Consensus 93 ~df~r~~G~~--v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 93 RDFKTFKGFP--VNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred HHHHHhCCCE--EEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 4558889987 66666543 336899999999984 55553
No 61
>PRK14632 hypothetical protein; Provisional
Probab=84.79 E-value=2.6 Score=29.13 Aligned_cols=38 Identities=13% Similarity=0.352 Sum_probs=27.5
Q ss_pred HHHHHhhcCcceEEEEEEeC-----CCeEEEEEEEEeccccceEEe
Q 034651 15 NLIFRFLQSKARIQIWLFEQ-----KDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~-----~g~~~~G~L~~~D~~mNlvL~ 55 (88)
.-+.+|+|+. |.|.++.. +.+.++|+|.++|.- ++.|.
T Consensus 91 ~~f~r~iG~~--V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 91 EQMSPYVGRQ--IELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHHHHhCCCE--EEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 4457888886 77777652 367999999999873 45554
No 62
>PRK02001 hypothetical protein; Validated
Probab=84.74 E-value=2.2 Score=29.03 Aligned_cols=43 Identities=16% Similarity=0.305 Sum_probs=29.0
Q ss_pred ceeeecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEe
Q 034651 7 QRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 7 ~~~~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~ 55 (88)
.++...| .-+.+|+|+. |.|.+. +++.++|+|.++|+- +++|.
T Consensus 76 dRpL~~~-~~f~r~~G~~--v~V~l~--~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 76 TSPLKVP-RQYKKNIGRE--LEVLTK--NGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred CCcCCCH-HHHHHhCCCE--EEEEEC--CCCEEEEEEEEEeCC-EEEEE
Confidence 3333334 3447888986 666664 468999999999985 45553
No 63
>PRK14639 hypothetical protein; Provisional
Probab=84.30 E-value=2.3 Score=28.36 Aligned_cols=36 Identities=19% Similarity=0.372 Sum_probs=26.8
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEe
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~ 55 (88)
.-+.+++|+. |.|++. +++.++|+|.++|+ -++.|.
T Consensus 81 ~~f~r~~G~~--v~v~l~--~~~~~~G~L~~~~~-~~i~l~ 116 (140)
T PRK14639 81 EHFAKSIGEL--VKITTN--EKEKFEGKIVSVDD-ENITLE 116 (140)
T ss_pred HHHHHhCCCE--EEEEEC--CCcEEEEEEEEEeC-CEEEEE
Confidence 4557888886 667664 46899999999998 355553
No 64
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=84.25 E-value=2.5 Score=28.38 Aligned_cols=32 Identities=16% Similarity=0.379 Sum_probs=24.3
Q ss_pred HHHHHhhcCcceEEEEEE--eCCCeEEEEEEEEecc
Q 034651 15 NLIFRFLQSKARIQIWLF--EQKDLRIEGRIIGFDE 48 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk--~~~g~~~~G~L~~~D~ 48 (88)
.-+.+++|+. |.|.++ .++++.++|+|.++|+
T Consensus 91 ~~f~r~~G~~--v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 91 RDFRRFIGRE--VKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHHhCCCe--EEEEEEcccCCceEEEEEEEEeeC
Confidence 4567889987 555553 3457899999999998
No 65
>PRK14631 hypothetical protein; Provisional
Probab=84.19 E-value=2.3 Score=29.49 Aligned_cols=31 Identities=6% Similarity=0.385 Sum_probs=23.5
Q ss_pred HHHHHhhcCcceEEEEEEe--CCCeEEEEEEEEec
Q 034651 15 NLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFD 47 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~--~~g~~~~G~L~~~D 47 (88)
.-+.+|+|+. |.|+++. ++.+.++|+|.++|
T Consensus 110 ~df~r~~G~~--V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 110 EQLQGYIGQQ--VALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHHhCCCe--EEEEEecccCCceEEEEEEEEee
Confidence 4558889987 6666643 34689999999998
No 66
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=83.96 E-value=1.5 Score=23.86 Aligned_cols=22 Identities=27% Similarity=0.643 Sum_probs=15.1
Q ss_pred EEEEEEEeccccceEEeceEEE
Q 034651 39 IEGRIIGFDEYMNLVLDDAEEV 60 (88)
Q Consensus 39 ~~G~L~~~D~~mNlvL~d~~e~ 60 (88)
.+|+..|.|+.+.+.|++....
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 67
>PRK14647 hypothetical protein; Provisional
Probab=83.69 E-value=3.3 Score=28.15 Aligned_cols=32 Identities=19% Similarity=0.308 Sum_probs=24.1
Q ss_pred HHHHHhhcCcceEEEEEEe-------CCCeEEEEEEEEecc
Q 034651 15 NLIFRFLQSKARIQIWLFE-------QKDLRIEGRIIGFDE 48 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~-------~~g~~~~G~L~~~D~ 48 (88)
.-+.+++|+. |.|.++. ++.+.++|+|.++|+
T Consensus 92 ~~f~r~~G~~--v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 92 ADYERYAGRL--VKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHHHhCCcE--EEEEEeccccccccCCceEEEEEEEeecC
Confidence 4557888886 6776653 135899999999997
No 68
>PRK14644 hypothetical protein; Provisional
Probab=80.46 E-value=2.9 Score=27.83 Aligned_cols=37 Identities=16% Similarity=0.183 Sum_probs=27.0
Q ss_pred HHHHhhcCcceEEEEEEeC--CCeEEEEEEEEeccccceEEe
Q 034651 16 LIFRFLQSKARIQIWLFEQ--KDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 16 ~L~~~l~k~~~V~V~lk~~--~g~~~~G~L~~~D~~mNlvL~ 55 (88)
-+.+++|+. |.|+++.. +-+.++|.|.++|.. ++.|.
T Consensus 79 ~f~r~~G~~--v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 79 ELENHIGEI--IDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHHhCCCe--EEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 578999997 66666543 237899999999984 45554
No 69
>PRK14645 hypothetical protein; Provisional
Probab=80.31 E-value=3.9 Score=27.80 Aligned_cols=34 Identities=18% Similarity=0.204 Sum_probs=24.0
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEE
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL 54 (88)
.-+.+++|+. |.|. . +++.++|+|.++|+- .+.|
T Consensus 95 ~df~r~~G~~--v~v~--~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 95 RHFERFAGLK--AKVR--G-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred HHHHHhCCCE--EEEE--c-CCeEEEEEEEEEeCC-EEEE
Confidence 3457788886 5554 3 468999999999984 3444
No 70
>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=80.25 E-value=11 Score=23.12 Aligned_cols=62 Identities=11% Similarity=0.171 Sum_probs=41.4
Q ss_pred hHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEecccc-ceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEe
Q 034651 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYM-NLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 14 l~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~m-NlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~ 85 (88)
|..|....++. |.+.+..+ .+.+|+..++|... |+..+|- ++ . -...+..++|..-|++++-
T Consensus 16 Lr~l~~~~gk~--v~f~l~e~--t~V~a~F~a~d~~~~~f~Vs~L-~T--P---lGv~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 16 LRSLLAMVGKP--VEFTLHEN--TTVSARFGACDIDVSNFQVSNL-QT--P---LGVQPEALLRCSDVISISF 78 (80)
T ss_dssp HHHHHHCTTSE--EEEEEGGG---EEEEEEEEE-TTS-EEEEEEE-ET--T---TTEEEEEEEEGGGEEEEEE
T ss_pred HHHHHHhcCCc--eEEEEeCC--eEEEEEEEEecCchheEEhhhc-CC--C---cccChhheeecCCEEEEEe
Confidence 55566666664 88888754 78999999999754 4544443 21 1 2235689999999999864
No 71
>PRK14642 hypothetical protein; Provisional
Probab=78.89 E-value=4.6 Score=28.72 Aligned_cols=37 Identities=16% Similarity=0.122 Sum_probs=26.4
Q ss_pred HHHHHhhcCcceEEEEEEe-----------CCCeEEEEEEEEeccccceEE
Q 034651 15 NLIFRFLQSKARIQIWLFE-----------QKDLRIEGRIIGFDEYMNLVL 54 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~-----------~~g~~~~G~L~~~D~~mNlvL 54 (88)
.-+.+|+++. |.|.++. ++.+.|+|+|.++|.. ++.|
T Consensus 93 ~df~rfiG~~--V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 93 QDFERFAGEV--IDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred HHHHHhCCCe--EEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 3457788886 6776662 1458999999999984 5545
No 72
>PRK14637 hypothetical protein; Provisional
Probab=78.70 E-value=5.2 Score=27.06 Aligned_cols=37 Identities=27% Similarity=0.376 Sum_probs=24.3
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEe
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~ 55 (88)
.-+.+++|+. |.|++ ++.+..++|+|.++|+- ++.|.
T Consensus 91 ~~f~r~~G~~--V~V~l-~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 91 AEFSIFVGET--VKVWF-ECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHHHhCCCE--EEEEE-CCCCcEEEEEEEEEeCC-EEEEE
Confidence 4457888887 66665 23333448999999985 44443
No 73
>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=77.68 E-value=2.3 Score=28.02 Aligned_cols=37 Identities=24% Similarity=0.415 Sum_probs=24.9
Q ss_pred HHHHHhhcCcceEEEEEEe--CCCeEEEEEEEEeccccceEE
Q 034651 15 NLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVL 54 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~--~~g~~~~G~L~~~D~~mNlvL 54 (88)
+-+.+++|+. |.|+++. ++.++++|+|.++|. =.++|
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 5678999997 7777642 334689999999999 34444
No 74
>PRK14635 hypothetical protein; Provisional
Probab=75.99 E-value=7.4 Score=26.50 Aligned_cols=49 Identities=16% Similarity=0.252 Sum_probs=30.3
Q ss_pred CccccceeeecchHHHHHhhcCcceEEEEEEeCCCeEEEE---EEEEeccccceEE
Q 034651 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEG---RIIGFDEYMNLVL 54 (88)
Q Consensus 2 ~~~~~~~~~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G---~L~~~D~~mNlvL 54 (88)
|++--.++...| .-+.+|.|+. |.|.+..+++..++| +|.++|.- ++.|
T Consensus 80 SSPGldRpL~~~-~~~~r~~G~~--v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 80 SSAGAERKLRLP-EDLDRFRGIP--VRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred cCCCCCCcCCCH-HHHHHhCCCE--EEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 344223443444 3447888887 556665545678888 99999884 4444
No 75
>PRK14641 hypothetical protein; Provisional
Probab=74.07 E-value=7 Score=27.14 Aligned_cols=31 Identities=6% Similarity=0.115 Sum_probs=22.8
Q ss_pred HHHHHhhcCcceEEEEEEe--CCCeEEEEEEEEec
Q 034651 15 NLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFD 47 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~--~~g~~~~G~L~~~D 47 (88)
.-+.+++|+. |.|.++. ++.+.++|+|.++|
T Consensus 97 ~~f~r~~G~~--V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRL--LRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCE--EEEEEecccCCeEEEEEEEEeee
Confidence 4457888887 6666654 33568999999995
No 76
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=65.59 E-value=20 Score=27.82 Aligned_cols=64 Identities=20% Similarity=0.276 Sum_probs=42.6
Q ss_pred HHhhcCcceEEEEEEeCCCeEEEEEEEEecc-ccceEEeceEEEEecCC---------eeeecCeEEEeCCcEEEEEe
Q 034651 18 FRFLQSKARIQIWLFEQKDLRIEGRIIGFDE-YMNLVLDDAEEVHIKKN---------TRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 18 ~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~---------~~~~~g~v~iRG~~I~~I~~ 85 (88)
..|++++ |.+.-| .+..|+|+|--+|- --=|-|.++..+-+++. ....+..++.||+.|.-+..
T Consensus 5 t~yIGS~--ISLISk--~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V 78 (361)
T KOG1073|consen 5 TSYIGSF--ISLISK--NDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIV 78 (361)
T ss_pred cccccce--eEEeec--ccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeee
Confidence 4678987 565555 45899999987773 33456777655433210 11277899999999986654
No 77
>PRK06955 biotin--protein ligase; Provisional
Probab=61.00 E-value=41 Score=24.80 Aligned_cols=29 Identities=24% Similarity=0.263 Sum_probs=22.3
Q ss_pred eEEEEEEeCCCeEEEEEEEEeccccceEEec
Q 034651 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (88)
Q Consensus 26 ~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d 56 (88)
+|++.. .++..++|+..|+|+.-.|+++.
T Consensus 251 ~V~v~~--~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 251 EVVLLE--DGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred eEEEEE--CCCcEEEEEEeeECCCceEEEEe
Confidence 466642 23567899999999999999964
No 78
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=58.39 E-value=71 Score=23.48 Aligned_cols=44 Identities=27% Similarity=0.367 Sum_probs=28.7
Q ss_pred eEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeC
Q 034651 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKG 77 (88)
Q Consensus 26 ~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG 77 (88)
.|++.. + +..++|++.|+|+.-.|++++.. +.+....|.+.+|.
T Consensus 274 ~v~~~~--~-~~~~~G~~~gi~~~G~L~i~~~g-----~~~~~~~gev~~~~ 317 (319)
T PRK11886 274 EVKLII--G-DKEISGIARGIDEQGALLLEDDG-----VEKPFNGGEISLRS 317 (319)
T ss_pred eEEEEe--C-CcEEEEEEEEECCCceEEEEeCC-----cEEEEEEeEEEEec
Confidence 466653 2 35799999999999999996211 11233446666654
No 79
>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=56.59 E-value=20 Score=24.83 Aligned_cols=63 Identities=13% Similarity=0.273 Sum_probs=37.2
Q ss_pred ecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccc-cceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEec
Q 034651 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEY-MNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNT 86 (88)
Q Consensus 11 ~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~-mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~~ 86 (88)
..|+.+ ..|++|. |.|.+. + +++.|.|-.+|.- -|+||-+-.| ++ .. ..-+|=|..|..|...
T Consensus 7 ~~p~~~-~~yv~K~--VkV~~~--d-~~~~G~v~TiDPVS~siVL~~~~e---~~--~~--sv~~I~ghaVk~vevl 70 (166)
T PF06372_consen 7 KSPLEW-QDYVGKE--VKVTLS--D-KEYKGWVYTIDPVSASIVLVNFQE---DG--KR--SVKVIMGHAVKSVEVL 70 (166)
T ss_dssp S-HHHH-HCTTT-E--EEEEET--T-EEEEEEEEEE-TTT--EEEEEE-T---TS---E--EEEEE-GGGEEEEEEE
T ss_pred CCHHHH-HHhhCcE--EEEEEe--c-cEEEEEEEEeCCCCCeEEEEEccc---CC--ce--eEEEEEccceEEEEEc
Confidence 357665 7899997 666664 5 8999999999974 5777765433 11 12 2356667777766543
No 80
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=56.54 E-value=39 Score=19.90 Aligned_cols=54 Identities=9% Similarity=0.209 Sum_probs=36.9
Q ss_pred hHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEe
Q 034651 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 14 l~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~ 85 (88)
...|.+.+|++ |.|..-. ..++|+|.+...- .++|+.. -...|||=..|++|.|
T Consensus 13 yq~lq~liG~~--vvV~T~~---g~v~G~L~~V~pD-hIvl~~~------------~~~~~IR~~~IV~v~p 66 (66)
T PF10842_consen 13 YQTLQSLIGQR--VVVQTTR---GSVRGILVDVKPD-HIVLEEN------------GTPFFIRIAQIVWVMP 66 (66)
T ss_pred HHHHHHhcCCE--EEEEEcC---CcEEEEEEeecCC-EEEEEeC------------CcEEEEEeeeEEEEcC
Confidence 57789999996 7787633 3689999987531 1233322 2478899888888754
No 81
>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=56.40 E-value=40 Score=19.89 Aligned_cols=41 Identities=17% Similarity=0.150 Sum_probs=29.6
Q ss_pred HHHHHhhcCcceEEEEEEeCC-CeEEEEEEEEeccccceEEe
Q 034651 15 NLIFRFLQSKARIQIWLFEQK-DLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~-g~~~~G~L~~~D~~mNlvL~ 55 (88)
..|..++.....|+|..-.++ -..++|++..+|..-+.+.-
T Consensus 33 ~~l~~a~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~ 74 (92)
T PF08863_consen 33 EKLSEAYQENQPVTITYYEDGYYQSVTGTIHKIDEINRTLKL 74 (92)
T ss_pred HHHHHHhcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEE
Confidence 456677766667777766532 25799999999999886653
No 82
>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=56.31 E-value=7.2 Score=24.71 Aligned_cols=17 Identities=29% Similarity=0.636 Sum_probs=15.6
Q ss_pred EEEEEeccccceEEece
Q 034651 41 GRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 41 G~L~~~D~~mNlvL~d~ 57 (88)
|+|+|.|.|-|..-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999998876
No 83
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=54.09 E-value=24 Score=24.80 Aligned_cols=35 Identities=23% Similarity=0.338 Sum_probs=23.1
Q ss_pred hHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccc
Q 034651 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEY 49 (88)
Q Consensus 14 l~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~ 49 (88)
|++|-.+=+.--+|.-.+.. ++..|+|++.+||.=
T Consensus 123 I~fL~~~P~~lp~i~C~i~t-~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIET-KDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEe-CCceEEEEEEeccCC
Confidence 55665544444345555555 357999999999974
No 84
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=53.93 E-value=7.4 Score=26.35 Aligned_cols=22 Identities=18% Similarity=0.410 Sum_probs=17.9
Q ss_pred EEEEEEEeccccceEEeceEEE
Q 034651 39 IEGRIIGFDEYMNLVLDDAEEV 60 (88)
Q Consensus 39 ~~G~L~~~D~~mNlvL~d~~e~ 60 (88)
=.|+|+|.|+|-|=.-+|-.-.
T Consensus 45 kiGTLVG~DkfGNkYyen~~~f 66 (151)
T KOG3382|consen 45 KIGTLVGVDKFGNKYYENNDYF 66 (151)
T ss_pred cceeeeeecccccchhccccee
Confidence 4599999999999888876433
No 85
>PRK14630 hypothetical protein; Provisional
Probab=51.80 E-value=27 Score=23.30 Aligned_cols=34 Identities=21% Similarity=0.132 Sum_probs=23.3
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEE
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL 54 (88)
.-+.+++|++ |.|.+.. ...+|+|.++|. -++.|
T Consensus 90 ~df~r~~G~~--v~V~l~~---~~~~G~L~~~~d-~~i~l 123 (143)
T PRK14630 90 REFKIFEGKK--IKLMLDN---DFEEGFILEAKA-DSFIF 123 (143)
T ss_pred HHHHHhCCCE--EEEEEcC---cceEEEEEEEeC-CEEEE
Confidence 4457888887 6666643 346899999988 34444
No 86
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=48.76 E-value=70 Score=26.17 Aligned_cols=29 Identities=21% Similarity=0.276 Sum_probs=21.9
Q ss_pred eEEEEEEeCCCeEEEEEEEEeccccceEEec
Q 034651 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (88)
Q Consensus 26 ~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d 56 (88)
+|.+.. .++..++|+..|+|+.-.|+|+.
T Consensus 280 ~V~v~~--~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 280 AVLLLR--DGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred eEEEEe--CCCcEEEEEEEEECCCCEEEEEE
Confidence 355532 23467999999999999999964
No 87
>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=40.32 E-value=49 Score=22.88 Aligned_cols=33 Identities=18% Similarity=0.270 Sum_probs=21.7
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccc
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEY 49 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~ 49 (88)
++..++-+.. +.|++.+.+||+++|+=.|.|..
T Consensus 111 ~Icrka~qqg--~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 111 SICRKAHQQG--KSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred HHHHHHHHCC--CeEEEEEcCCcEEEeeecccceE
Confidence 3344444444 44555557789999999998863
No 88
>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=39.50 E-value=67 Score=24.18 Aligned_cols=29 Identities=24% Similarity=0.374 Sum_probs=23.2
Q ss_pred EEEEEEeCCCeEEEEEEEEeccccceEEece
Q 034651 27 IQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 27 V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~ 57 (88)
+.|.+ .+|+.+.+++.++|...++-|=..
T Consensus 104 i~V~~--~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 104 IVVAL--QDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred EEEEE--CCCCEEEEEEEEecCCCCEEEEEe
Confidence 55554 457899999999999999988544
No 89
>PRK08330 biotin--protein ligase; Provisional
Probab=38.41 E-value=1.4e+02 Score=21.07 Aligned_cols=28 Identities=29% Similarity=0.324 Sum_probs=20.9
Q ss_pred eEEEEEEeCCCeEE-EEEEEEeccccceEEec
Q 034651 26 RIQIWLFEQKDLRI-EGRIIGFDEYMNLVLDD 56 (88)
Q Consensus 26 ~V~V~lk~~~g~~~-~G~L~~~D~~mNlvL~d 56 (88)
+|.+.. ++..+ +|+..|+|+.-.|+++.
T Consensus 190 ~v~~~~---~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 190 RVKIIG---DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred eEEEEE---CCcEEEEEEEEEECCCCEEEEEE
Confidence 466643 23454 79999999999999974
No 90
>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=37.76 E-value=1.4e+02 Score=20.93 Aligned_cols=27 Identities=26% Similarity=0.334 Sum_probs=21.7
Q ss_pred eEEEEEEeCCCeEEEEEEEEeccccceEEe
Q 034651 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLD 55 (88)
Q Consensus 26 ~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~ 55 (88)
+|++.. + +..++|+..|+|+.-.|+++
T Consensus 195 ~V~v~~--~-~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 195 EVSLTT--G-NGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred eEEEEe--C-CcEEEEEEEeECCCceEEEE
Confidence 466653 2 35799999999999999997
No 91
>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=37.35 E-value=63 Score=22.35 Aligned_cols=33 Identities=12% Similarity=0.088 Sum_probs=26.6
Q ss_pred cceEEEEEEeCCCeEEEEEEEEeccccceEEeceE
Q 034651 24 KARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAE 58 (88)
Q Consensus 24 ~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~ 58 (88)
..+|.|.+ .+|..+.|.+.||+.-=|.+|.-+.
T Consensus 29 ~~pVrvv~--~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 29 DIPVRVVS--ENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred CCceEEEe--cCCcEEEEEEeccCcccCEEeccCC
Confidence 35566555 5679999999999999999997654
No 92
>PRK10898 serine endoprotease; Provisional
Probab=37.25 E-value=79 Score=23.89 Aligned_cols=30 Identities=20% Similarity=0.242 Sum_probs=23.5
Q ss_pred eEEEEEEeCCCeEEEEEEEEeccccceEEece
Q 034651 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 26 ~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~ 57 (88)
.+.|.+. +|+.+.+++.++|...+|-|=..
T Consensus 103 ~i~V~~~--dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 103 QIIVALQ--DGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred EEEEEeC--CCCEEEEEEEEEcCCCCEEEEEE
Confidence 3556554 56899999999999999977554
No 93
>PRK06630 hypothetical protein; Provisional
Probab=34.09 E-value=23 Score=22.62 Aligned_cols=19 Identities=21% Similarity=0.387 Sum_probs=16.8
Q ss_pred EEEEEEEeccccceEEece
Q 034651 39 IEGRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 39 ~~G~L~~~D~~mNlvL~d~ 57 (88)
..|+|+|-|+|-|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4699999999999998874
No 94
>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=33.55 E-value=43 Score=21.37 Aligned_cols=24 Identities=25% Similarity=0.433 Sum_probs=10.3
Q ss_pred CCCeEEEEEEEEeccccceEEece
Q 034651 34 QKDLRIEGRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 34 ~~g~~~~G~L~~~D~~mNlvL~d~ 57 (88)
|+-..++|+..|||-.-++.|++|
T Consensus 120 G~~Vti~G~~~g~~~~~~v~l~~c 143 (144)
T PF12869_consen 120 GQKVTIKGICTGYSLMGVVMLDDC 143 (144)
T ss_dssp TSEEEEEEE-----SSS-EEEE--
T ss_pred CCEEEEEEEEEeeecCCcEEeecc
Confidence 344567799999985566777776
No 95
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=33.55 E-value=79 Score=20.16 Aligned_cols=29 Identities=14% Similarity=0.270 Sum_probs=19.5
Q ss_pred hHHHHHhhcCcceEEEEEEeCCCeEEEEEEE
Q 034651 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRII 44 (88)
Q Consensus 14 l~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~ 44 (88)
|+-|-..++...+|.+.|+ +|+.+.|++.
T Consensus 18 LE~lv~~L~ge~~V~l~L~--DGs~l~Gtv~ 46 (101)
T PF11607_consen 18 LEHLVSELDGEERVELELD--DGSMLRGTVA 46 (101)
T ss_dssp HHHHHHCTTTT-EEEEEET--TS-EEEEEEC
T ss_pred HHHHHhhcCCcceEEEEEc--CCCeeeeeec
Confidence 4555556666678888886 4689999974
No 96
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=32.39 E-value=1.8e+02 Score=21.35 Aligned_cols=28 Identities=21% Similarity=0.145 Sum_probs=22.2
Q ss_pred eEEEEEEeCCCeEEEEEEEEeccccceEEec
Q 034651 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDD 56 (88)
Q Consensus 26 ~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d 56 (88)
+|.+.. ++..++|++.|+|+.-.|+++.
T Consensus 239 ~V~v~~---~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 239 KVLIDQ---DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred EEEEEe---CCCEEEEEEEEECCCCeEEEEe
Confidence 466643 3468999999999999999974
No 97
>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=32.33 E-value=98 Score=23.75 Aligned_cols=31 Identities=13% Similarity=0.310 Sum_probs=24.2
Q ss_pred eEEEEEEeCCCeEEEEEEEEeccccceEEeceE
Q 034651 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAE 58 (88)
Q Consensus 26 ~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~ 58 (88)
.+.|.+ .+|+.+.+++.++|...++.|=...
T Consensus 83 ~i~V~~--~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 83 EITVTL--SDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred eEEEEe--CCCCEEEEEEEEecCCCCEEEEEec
Confidence 455655 4578999999999999999875543
No 98
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=32.14 E-value=74 Score=19.75 Aligned_cols=25 Identities=8% Similarity=0.171 Sum_probs=21.5
Q ss_pred cCCeeeecCeEEEeCCcEEEEEecC
Q 034651 63 KKNTRKPLGRILLKGDNITLMMNTG 87 (88)
Q Consensus 63 ~~~~~~~~g~v~iRG~~I~~I~~~~ 87 (88)
.++..+.-|.+.++|..+..|..+|
T Consensus 72 ~~G~~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 72 SDGEDRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred CCChhcceEEEEEECCeeeEEEcCC
Confidence 3567888899999999999998876
No 99
>PRK10942 serine endoprotease; Provisional
Probab=31.73 E-value=1e+02 Score=24.41 Aligned_cols=30 Identities=17% Similarity=0.405 Sum_probs=23.8
Q ss_pred eEEEEEEeCCCeEEEEEEEEeccccceEEece
Q 034651 26 RIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 26 ~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~ 57 (88)
.+.|.+ .+|+++.++++++|...+|-|=..
T Consensus 137 ~i~V~~--~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 137 KIKVQL--SDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred EEEEEE--CCCCEEEEEEEEecCCCCEEEEEe
Confidence 455655 467999999999999999977643
No 100
>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=28.79 E-value=5.6 Score=23.02 Aligned_cols=15 Identities=27% Similarity=0.512 Sum_probs=13.5
Q ss_pred ccccceEEeceEEEE
Q 034651 47 DEYMNLVLDDAEEVH 61 (88)
Q Consensus 47 D~~mNlvL~d~~e~~ 61 (88)
|.||+-||+||+-..
T Consensus 21 DDFmhaVlSNCtTrI 35 (61)
T PF10894_consen 21 DDFMHAVLSNCTTRI 35 (61)
T ss_pred HHHHHHHHhcCceeE
Confidence 899999999998764
No 101
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=27.41 E-value=37 Score=22.23 Aligned_cols=21 Identities=29% Similarity=0.488 Sum_probs=17.5
Q ss_pred EEEEEEEeccccceEEeceEE
Q 034651 39 IEGRIIGFDEYMNLVLDDAEE 59 (88)
Q Consensus 39 ~~G~L~~~D~~mNlvL~d~~e 59 (88)
-.|.|+|-|+|-|-.-++..+
T Consensus 8 r~g~lVG~D~~GNkYYE~~~~ 28 (115)
T PLN03095 8 RAGRLVGEDEFGNKYYENPSY 28 (115)
T ss_pred ecceEeEEcCCCCeeeEcCCC
Confidence 359999999999999987543
No 102
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=26.70 E-value=1.6e+02 Score=17.97 Aligned_cols=43 Identities=16% Similarity=0.280 Sum_probs=28.6
Q ss_pred ceeeecchHHHHHhhcCc----ceEEEEEEe--CCCeEEEEEEEEeccc
Q 034651 7 QRIMTQPINLIFRFLQSK----ARIQIWLFE--QKDLRIEGRIIGFDEY 49 (88)
Q Consensus 7 ~~~~~~Pl~~L~~~l~k~----~~V~V~lk~--~~g~~~~G~L~~~D~~ 49 (88)
..+.+-|.+...+++..+ .|+...... ...+.+.|++.|+...
T Consensus 21 ~sEFVV~~~k~~~al~~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~ 69 (83)
T PF06507_consen 21 PSEFVVPASKYDKALNHPWSVGMRFKMRFETEDSSERRWQGTIVGVSDL 69 (83)
T ss_pred CcceEEEHHHHHHHhcCCCCCCcEEEEEeccCCCccceeeeEEeEeecc
Confidence 455778888888888755 345554433 2235689999998764
No 103
>KOG3865 consensus Arrestin [Signal transduction mechanisms]
Probab=25.86 E-value=1.5e+02 Score=23.17 Aligned_cols=39 Identities=5% Similarity=0.121 Sum_probs=32.0
Q ss_pred cCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEE
Q 034651 22 QSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60 (88)
Q Consensus 22 ~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~ 60 (88)
|+++.|.|.+.|+..+.+.-+=..++|+-+++|-....+
T Consensus 209 GE~isvnV~V~NNsnKtVKkIK~~V~Q~adi~Lfs~aqy 247 (402)
T KOG3865|consen 209 GEPISVNVHVTNNSNKTVKKIKISVRQVADICLFSTAQY 247 (402)
T ss_pred CCceeEEEEEecCCcceeeeeEEEeEeeceEEEEecccc
Confidence 456889999999999999988899999999999744333
No 104
>PRK10139 serine endoprotease; Provisional
Probab=25.65 E-value=1.5e+02 Score=23.24 Aligned_cols=31 Identities=23% Similarity=0.374 Sum_probs=24.9
Q ss_pred ceEEEEEEeCCCeEEEEEEEEeccccceEEece
Q 034651 25 ARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 25 ~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~ 57 (88)
..+.|++. +|+++.++++++|....|-+=..
T Consensus 115 ~~i~V~~~--dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 115 QKISIQLN--DGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CEEEEEEC--CCCEEEEEEEEEcCCCCEEEEEe
Confidence 35777764 56899999999999999987544
No 105
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=25.24 E-value=1.4e+02 Score=17.00 Aligned_cols=21 Identities=19% Similarity=0.471 Sum_probs=13.7
Q ss_pred EEEEEEeCCCeEEEEEEEEecc
Q 034651 27 IQIWLFEQKDLRIEGRIIGFDE 48 (88)
Q Consensus 27 V~V~lk~~~g~~~~G~L~~~D~ 48 (88)
|.+|=-+ +...|+|++.+||.
T Consensus 12 V~~rWP~-s~lYYe~kV~~~d~ 32 (55)
T PF09465_consen 12 VMVRWPG-SSLYYEGKVLSYDS 32 (55)
T ss_dssp EEEE-TT-TS-EEEEEEEEEET
T ss_pred EEEECCC-CCcEEEEEEEEecc
Confidence 5555432 34567999999997
No 106
>KOG3535 consensus Adaptor protein Disabled [Signal transduction mechanisms]
Probab=24.93 E-value=46 Score=26.80 Aligned_cols=18 Identities=17% Similarity=0.447 Sum_probs=14.7
Q ss_pred EEEeCCCeEEEEEEEEecc
Q 034651 30 WLFEQKDLRIEGRIIGFDE 48 (88)
Q Consensus 30 ~lk~~~g~~~~G~L~~~D~ 48 (88)
+.| |+|..|.++|+|+|+
T Consensus 43 RFk-g~GV~YKaKLIGidd 60 (557)
T KOG3535|consen 43 RFK-GNGVSYKAKLIGIDD 60 (557)
T ss_pred hhc-CCCeeeeeeeccccc
Confidence 444 468999999999996
No 107
>PRK07228 N-ethylammeline chlorohydrolase; Provisional
Probab=23.91 E-value=1.8e+02 Score=22.16 Aligned_cols=36 Identities=19% Similarity=0.363 Sum_probs=21.1
Q ss_pred cceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEe
Q 034651 50 MNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 85 (88)
Q Consensus 50 mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~ 85 (88)
|.+++.++.-+..++.....-+.++|+++-|..|.+
T Consensus 1 ~~~~i~~~~vi~~~~~~~~~~g~V~I~dg~I~~vg~ 36 (445)
T PRK07228 1 MTILIKNAGIVTMNAKREIVDGDVLIEDDRIAAVGD 36 (445)
T ss_pred CeEEEEccEEEecCCCcEecccEEEEECCEEEEecC
Confidence 556666665543222223445677888888777754
No 108
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=23.48 E-value=89 Score=20.88 Aligned_cols=38 Identities=16% Similarity=0.217 Sum_probs=25.2
Q ss_pred eEEEEEEE---EeccccceEEeceEEEEecCCeeeecCeEEEeCCc
Q 034651 37 LRIEGRII---GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDN 79 (88)
Q Consensus 37 ~~~~G~L~---~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~ 79 (88)
..++|.+. ..=-+||+.+.|+. .++...-+.+=||||+
T Consensus 83 ~~lvG~VqKvS~Lil~~~~~v~Dv~-----tg~~v~~~~~diRgnt 123 (140)
T PF11684_consen 83 YVLVGEVQKVSNLILNMNVYVRDVE-----TGKVVRGRSVDIRGNT 123 (140)
T ss_pred EEEEEEEechhhhheeeeEEEEECC-----CCCEEeeeeeeEecCc
Confidence 44445443 34457888888873 2456666889999986
No 109
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=23.43 E-value=2.9e+02 Score=19.87 Aligned_cols=33 Identities=21% Similarity=0.262 Sum_probs=24.1
Q ss_pred hcCcceEEEEEEeCCCeEEEEEEEEeccccceEEece
Q 034651 21 LQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDA 57 (88)
Q Consensus 21 l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~ 57 (88)
+++. |.+. .+++....|+-.++|..-.|+++..
T Consensus 189 ~g~~--V~~~--~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 189 LGKE--VRLT--LGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred CCCE--EEEE--eCCCcEeeeEEEEECCCceEEEEeC
Confidence 4454 5554 4444566669999999999999876
No 110
>PF06214 SLAM: Signaling lymphocytic activation molecule (SLAM) protein; InterPro: IPR010407 This entry is found in several mammalian signalling lymphocytic activation molecule (SLAM) proteins. Optimal T cell activation and expansion require engagement of the TCR plus co-stimulatory signals delivered through accessory molecules. SLAM, a 70 kDa co-stimulatory molecule belonging to the Ig superfamily, is defined as a human cell surface molecule that mediates CD28-independent proliferation of human T cells and IFN-gamma production by human Th1 and Th2 clones []. SLAM has also been recognised as a receptor for Measles virus [].; GO: 0004872 receptor activity, 0046649 lymphocyte activation, 0009986 cell surface, 0016021 integral to membrane; PDB: 3ALX_D 3ALZ_B 3ALW_A.
Probab=20.71 E-value=93 Score=20.56 Aligned_cols=35 Identities=11% Similarity=0.167 Sum_probs=21.4
Q ss_pred HHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccc
Q 034651 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEY 49 (88)
Q Consensus 15 ~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~ 49 (88)
+-+.++++|.++|.|.....-|-.+.-+++++|-.
T Consensus 50 egI~KSmnkSi~IlVt~a~Sp~~~vkkKIvSldl~ 84 (126)
T PF06214_consen 50 EGINKSMNKSIHILVTMAKSPGSSVKKKIVSLDLS 84 (126)
T ss_dssp TSTSTT----SEEEEEEESSSTT---EEEEEE-TT
T ss_pred hhhhhhhccceEEEEEeccCCccchhheEEEeccc
Confidence 45678889998999888777778899999999853
No 111
>PRK08183 NADH dehydrogenase; Validated
Probab=20.40 E-value=58 Score=21.78 Aligned_cols=20 Identities=25% Similarity=0.370 Sum_probs=16.9
Q ss_pred EEEEEEEeccccceEEeceE
Q 034651 39 IEGRIIGFDEYMNLVLDDAE 58 (88)
Q Consensus 39 ~~G~L~~~D~~mNlvL~d~~ 58 (88)
-.|+|+|-|+|-|-.-++..
T Consensus 24 r~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 24 RKGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred ccCeEeEecCCCCeeeecCC
Confidence 35999999999999987654
Done!