Query 033904
Match_columns 109
No_of_seqs 114 out of 1075
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 07:36:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033904.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033904hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01720 Sm_D2 The eukaryotic S 100.0 6.9E-28 1.5E-32 158.7 10.7 87 21-108 1-87 (87)
2 cd01730 LSm3 The eukaryotic Sm 99.9 3.6E-25 7.9E-30 143.9 9.7 82 22-106 1-82 (82)
3 cd01732 LSm5 The eukaryotic Sm 99.9 5.9E-24 1.3E-28 136.8 10.1 73 21-106 2-74 (76)
4 PRK00737 small nuclear ribonuc 99.9 7.9E-24 1.7E-28 134.6 9.4 70 21-106 3-72 (72)
5 cd01731 archaeal_Sm1 The archa 99.9 1.4E-23 2.9E-28 131.9 9.2 68 23-106 1-68 (68)
6 cd01726 LSm6 The eukaryotic Sm 99.9 2E-22 4.3E-27 126.4 9.0 67 23-105 1-67 (67)
7 cd01729 LSm7 The eukaryotic Sm 99.9 9.3E-22 2E-26 127.8 10.2 76 23-107 4-79 (81)
8 cd01717 Sm_B The eukaryotic Sm 99.9 7.7E-22 1.7E-26 127.3 9.6 75 26-106 4-78 (79)
9 cd01718 Sm_E The eukaryotic Sm 99.9 8.7E-22 1.9E-26 127.7 9.8 75 19-106 3-79 (79)
10 cd01722 Sm_F The eukaryotic Sm 99.9 6.5E-22 1.4E-26 124.5 8.5 68 22-105 1-68 (68)
11 cd01719 Sm_G The eukaryotic Sm 99.9 1.9E-21 4.1E-26 123.9 8.9 69 23-107 1-69 (72)
12 cd01728 LSm1 The eukaryotic Sm 99.9 6.4E-21 1.4E-25 122.2 10.2 71 23-106 3-73 (74)
13 COG1958 LSM1 Small nuclear rib 99.9 8.6E-21 1.9E-25 122.2 10.0 76 19-106 4-79 (79)
14 cd01727 LSm8 The eukaryotic Sm 99.8 9.6E-21 2.1E-25 120.9 9.4 72 25-108 2-73 (74)
15 PTZ00138 small nuclear ribonuc 99.8 2.4E-20 5.3E-25 123.3 9.9 78 17-107 9-88 (89)
16 cd01721 Sm_D3 The eukaryotic S 99.8 5.1E-20 1.1E-24 116.6 9.7 69 23-107 1-69 (70)
17 PF01423 LSM: LSM domain ; In 99.8 5.3E-20 1.1E-24 114.3 9.4 67 25-106 1-67 (67)
18 cd01723 LSm4 The eukaryotic Sm 99.8 5E-20 1.1E-24 118.2 9.3 72 22-108 1-72 (76)
19 KOG3460 Small nuclear ribonucl 99.8 1.8E-21 3.9E-26 126.2 1.4 85 20-107 3-87 (91)
20 cd06168 LSm9 The eukaryotic Sm 99.8 1.2E-19 2.5E-24 116.6 9.8 72 25-106 3-74 (75)
21 smart00651 Sm snRNP Sm protein 99.8 8.3E-20 1.8E-24 113.3 8.9 66 26-106 2-67 (67)
22 KOG3459 Small nuclear ribonucl 99.8 3.2E-21 6.8E-26 130.6 1.8 106 2-108 4-109 (114)
23 cd00600 Sm_like The eukaryotic 99.8 1.8E-18 3.9E-23 105.9 8.4 63 27-105 1-63 (63)
24 cd01724 Sm_D1 The eukaryotic S 99.8 3.3E-18 7.1E-23 113.2 9.7 71 22-108 1-71 (90)
25 cd01725 LSm2 The eukaryotic Sm 99.8 3.6E-18 7.8E-23 110.9 9.4 73 22-108 1-73 (81)
26 cd01733 LSm10 The eukaryotic S 99.8 4E-18 8.6E-23 110.1 9.6 72 19-106 6-77 (78)
27 KOG3482 Small nuclear ribonucl 99.7 2.5E-17 5.4E-22 104.5 6.6 73 20-108 6-78 (79)
28 KOG1780 Small Nuclear ribonucl 99.7 1.7E-16 3.7E-21 100.9 6.0 68 22-107 6-73 (77)
29 KOG1774 Small nuclear ribonucl 99.6 4.5E-16 9.8E-21 100.7 5.9 76 20-108 10-87 (88)
30 KOG1775 U6 snRNA-associated Sm 99.6 1.3E-15 2.9E-20 97.5 4.3 76 18-106 3-78 (84)
31 KOG1781 Small Nuclear ribonucl 99.6 2.6E-16 5.6E-21 105.0 0.1 74 26-107 21-94 (108)
32 KOG3168 U1 snRNP component [Tr 99.5 1.3E-15 2.8E-20 110.1 0.7 74 27-106 9-82 (177)
33 KOG1783 Small nuclear ribonucl 99.5 2E-15 4.4E-20 95.8 1.3 71 21-107 5-75 (77)
34 KOG1782 Small Nuclear ribonucl 99.4 2E-14 4.4E-19 99.2 0.0 69 27-108 14-82 (129)
35 KOG3293 Small nuclear ribonucl 99.4 1.4E-12 3.1E-17 90.2 6.3 71 21-106 1-71 (134)
36 KOG1784 Small Nuclear ribonucl 99.4 7E-13 1.5E-17 87.4 4.4 70 25-106 3-72 (96)
37 cd01739 LSm11_C The eukaryotic 99.3 8.9E-13 1.9E-17 82.3 2.5 45 27-71 1-49 (66)
38 KOG3448 Predicted snRNP core p 99.2 6.6E-11 1.4E-15 77.8 8.4 70 24-107 4-73 (96)
39 KOG3172 Small nuclear ribonucl 99.2 7.4E-11 1.6E-15 80.1 6.6 72 20-107 3-74 (119)
40 KOG3428 Small nuclear ribonucl 98.6 4.4E-07 9.6E-12 61.7 8.6 66 24-106 4-69 (109)
41 cd01716 Hfq Hfq, an abundant, 97.4 0.00045 9.8E-09 42.8 5.0 39 26-64 3-41 (61)
42 TIGR02383 Hfq RNA chaperone Hf 97.3 0.00066 1.4E-08 42.0 5.1 40 25-64 6-45 (61)
43 PF14438 SM-ATX: Ataxin 2 SM d 97.2 0.0022 4.8E-08 40.5 6.5 69 25-102 5-76 (77)
44 PRK00395 hfq RNA-binding prote 97.1 0.0014 3.1E-08 42.5 5.0 40 25-64 10-49 (79)
45 COG1923 Hfq Uncharacterized ho 96.7 0.0047 1E-07 39.8 4.8 34 26-59 11-44 (77)
46 PF12701 LSM14: Scd6-like Sm d 95.8 0.15 3.2E-06 34.1 8.6 71 28-105 4-75 (96)
47 PRK14091 RNA-binding protein H 95.7 0.026 5.6E-07 41.2 5.0 40 25-64 95-134 (165)
48 PRK14091 RNA-binding protein H 95.6 0.028 6.2E-07 41.0 5.0 40 25-64 15-54 (165)
49 PF02237 BPL_C: Biotin protein 95.3 0.11 2.4E-06 30.0 6.0 33 34-67 3-35 (48)
50 cd01735 LSm12_N LSm12 belongs 95.2 0.054 1.2E-06 33.5 4.5 34 34-67 6-39 (61)
51 PRK14638 hypothetical protein; 92.1 0.3 6.6E-06 34.9 4.3 33 27-62 95-127 (150)
52 PF11095 Gemin7: Gem-associate 91.6 2.2 4.9E-05 27.6 7.6 63 24-107 16-79 (80)
53 cd01736 LSm14_N LSm14 (also kn 91.0 2.4 5.3E-05 27.1 7.2 69 29-103 3-72 (74)
54 PRK02001 hypothetical protein; 90.7 0.49 1.1E-05 34.0 4.3 33 27-62 85-117 (152)
55 PRK14639 hypothetical protein; 90.7 0.51 1.1E-05 33.3 4.3 33 27-62 83-115 (140)
56 PF06372 Gemin6: Gemin6 protei 90.4 0.73 1.6E-05 33.7 5.0 43 21-67 7-50 (166)
57 PF03614 Flag1_repress: Repres 89.2 0.69 1.5E-05 33.6 4.0 35 22-56 108-142 (165)
58 PF11607 DUF3247: Protein of u 88.8 0.44 9.6E-06 32.0 2.6 27 25-51 19-45 (101)
59 PRK14644 hypothetical protein; 86.8 1.5 3.2E-05 30.9 4.5 34 27-63 80-117 (136)
60 cd01734 YlxS_C YxlS is a Bacil 86.0 2 4.4E-05 27.3 4.4 33 27-62 20-56 (83)
61 PRK14640 hypothetical protein; 85.4 1.9 4E-05 30.8 4.5 34 27-63 92-129 (152)
62 PRK14636 hypothetical protein; 84.6 2 4.3E-05 31.5 4.4 35 26-63 92-130 (176)
63 PRK14642 hypothetical protein; 84.1 2.2 4.7E-05 32.0 4.5 34 22-57 87-136 (197)
64 PRK14633 hypothetical protein; 84.1 2.4 5.1E-05 30.2 4.5 34 27-63 89-126 (150)
65 COG0779 Uncharacterized protei 84.0 2.4 5.1E-05 30.6 4.5 38 22-62 86-130 (153)
66 PF02576 DUF150: Uncharacteris 83.3 2.3 4.9E-05 29.6 4.1 35 25-62 80-118 (141)
67 PF03614 Flag1_repress: Repres 83.1 2.7 5.9E-05 30.5 4.4 35 32-66 27-61 (165)
68 PRK14645 hypothetical protein; 82.6 2.6 5.7E-05 30.2 4.3 32 27-62 97-128 (154)
69 PRK14643 hypothetical protein; 82.5 2.8 6E-05 30.4 4.4 30 26-57 98-131 (164)
70 PRK14632 hypothetical protein; 82.2 2.9 6.3E-05 30.5 4.4 34 27-63 93-133 (172)
71 PRK14634 hypothetical protein; 81.4 3.4 7.3E-05 29.6 4.5 33 27-62 95-131 (155)
72 PRK14646 hypothetical protein; 81.3 3.4 7.3E-05 29.6 4.4 34 26-62 94-131 (155)
73 PRK00092 ribosome maturation p 80.7 3.7 8.1E-05 29.1 4.5 29 26-56 92-124 (154)
74 PRK14647 hypothetical protein; 79.0 4.4 9.6E-05 29.0 4.4 28 27-56 94-130 (159)
75 PF10842 DUF2642: Protein of u 77.5 6.9 0.00015 24.4 4.4 34 19-55 6-41 (66)
76 PRK14631 hypothetical protein; 76.1 5.7 0.00012 29.1 4.4 28 26-55 111-142 (174)
77 PRK14637 hypothetical protein; 75.5 5.5 0.00012 28.5 4.1 34 27-63 93-127 (151)
78 PF14563 DUF4444: Domain of un 75.1 3.4 7.4E-05 23.7 2.3 22 47-68 10-31 (42)
79 PRK14641 hypothetical protein; 73.7 6.4 0.00014 28.8 4.1 27 27-55 99-129 (173)
80 PRK10898 serine endoprotease; 67.0 13 0.00028 29.7 4.9 33 34-66 101-133 (353)
81 TIGR02038 protease_degS peripl 65.8 14 0.0003 29.4 4.8 33 34-66 101-133 (351)
82 PRK10139 serine endoprotease; 63.6 18 0.00039 30.0 5.2 34 33-66 113-146 (455)
83 PRK10942 serine endoprotease; 61.8 19 0.00041 30.1 5.0 32 34-65 135-166 (473)
84 PRK06955 biotin--protein ligas 59.9 32 0.00069 26.8 5.8 32 33-64 248-279 (300)
85 PRK14630 hypothetical protein; 55.1 24 0.00051 24.9 4.0 32 27-62 92-123 (143)
86 PF08863 YolD: YolD-like prote 55.0 49 0.0011 20.6 5.7 38 26-63 34-74 (92)
87 TIGR02037 degP_htrA_DO peripla 54.6 25 0.00053 28.6 4.5 33 34-66 81-113 (428)
88 PRK14635 hypothetical protein; 53.7 28 0.0006 25.0 4.2 33 27-62 94-131 (162)
89 PRK11886 bifunctional biotin-- 47.7 61 0.0013 25.2 5.6 30 33-63 271-300 (319)
90 KOG3382 NADH:ubiquinone oxidor 46.0 12 0.00025 26.8 1.2 26 43-68 41-66 (151)
91 PF05071 NDUFA12: NADH ubiquin 45.2 9.9 0.00022 25.4 0.7 17 49-65 1-17 (105)
92 PF14153 Spore_coat_CotO: Spor 44.8 32 0.0007 25.5 3.4 34 24-57 123-157 (185)
93 KOG1073 Uncharacterized mRNA-a 44.6 67 0.0015 26.3 5.5 75 27-107 4-79 (361)
94 PF07073 ROF: Modulator of Rho 44.6 28 0.0006 22.4 2.7 18 33-50 16-33 (80)
95 TIGR00121 birA_ligase birA, bi 44.4 85 0.0018 23.3 5.8 30 33-63 192-221 (237)
96 PTZ00275 biotin-acetyl-CoA-car 43.9 83 0.0018 24.4 5.8 31 33-64 236-266 (285)
97 PRK13325 bifunctional biotin-- 42.6 52 0.0011 28.4 4.8 31 34-64 278-308 (592)
98 COG0340 BirA Biotin-(acetyl-Co 39.3 1.2E+02 0.0025 23.1 5.9 34 33-66 189-222 (238)
99 PRK08330 biotin--protein ligas 38.6 85 0.0018 23.4 5.0 32 33-65 187-219 (236)
100 PF02604 PhdYeFM_antitox: Anti 37.7 26 0.00055 21.1 1.7 43 16-60 6-48 (75)
101 PF06257 DUF1021: Protein of u 37.2 73 0.0016 20.3 3.8 33 26-62 11-47 (76)
102 PF11743 DUF3301: Protein of u 35.8 40 0.00088 22.1 2.5 21 88-108 76-96 (97)
103 TIGR02603 CxxCH_TIGR02603 puta 33.6 57 0.0012 22.2 3.1 20 36-55 59-78 (133)
104 PRK11625 Rho-binding antitermi 30.8 1.3E+02 0.0029 19.5 4.3 26 26-51 15-40 (84)
105 TIGR03170 flgA_cterm flagella 30.7 61 0.0013 21.4 2.8 20 34-53 96-116 (122)
106 COG5316 Uncharacterized conser 30.4 1.7E+02 0.0036 24.5 5.7 64 4-70 52-117 (421)
107 PF09465 LBR_tudor: Lamin-B re 29.9 1.1E+02 0.0024 18.4 3.5 25 33-57 8-33 (55)
108 PRK08477 biotin--protein ligas 25.1 2.8E+02 0.0061 20.6 5.8 31 33-64 174-204 (211)
109 PRK06630 hypothetical protein; 24.9 40 0.00086 22.7 1.0 19 47-65 11-29 (99)
110 PRK09618 flgD flagellar basal 24.8 1.4E+02 0.0031 21.2 3.9 26 28-55 88-113 (142)
111 PF07317 YcgR: Flagellar regul 24.2 2.2E+02 0.0047 18.7 5.2 41 24-64 11-51 (108)
112 PRK07018 flgA flagellar basal 23.7 90 0.002 23.4 2.9 20 34-53 207-227 (235)
113 KOG0971 Microtubule-associated 21.4 61 0.0013 30.1 1.8 68 33-107 8-79 (1243)
114 COG0265 DegQ Trypsin-like seri 21.2 1.8E+02 0.004 22.7 4.3 33 34-66 95-127 (347)
115 KOG4401 Uncharacterized conser 20.3 1.5E+02 0.0032 22.2 3.3 33 34-66 11-43 (184)
No 1
>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=99.95 E-value=6.9e-28 Score=158.75 Aligned_cols=87 Identities=90% Similarity=1.381 Sum_probs=73.3
Q ss_pred CCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCc
Q 033904 21 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 100 (109)
Q Consensus 21 ~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn 100 (109)
.||+++|+.++..+++|.|.|++|+.+.|+|.|||+||||+|+||+|++...++++...+ ..+..++|++|.+|||||+
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~-~~~~~~~r~lg~v~iRGd~ 79 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKK-AKPVNKDRFISKMFLRGDS 79 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeecccccccccc-ccceeeeeEcccEEEeCCE
Confidence 489999999998789999999999999999999999999999999999876544332111 1223456789999999999
Q ss_pred EEEEEeCC
Q 033904 101 VIIVLRNP 108 (109)
Q Consensus 101 Vv~I~~~p 108 (109)
|++|+++|
T Consensus 80 Vv~Is~~~ 87 (87)
T cd01720 80 VILVLRNP 87 (87)
T ss_pred EEEEecCC
Confidence 99999987
No 2
>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=99.93 E-value=3.6e-25 Score=143.93 Aligned_cols=82 Identities=33% Similarity=0.579 Sum_probs=66.5
Q ss_pred CcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcE
Q 033904 22 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 101 (109)
Q Consensus 22 ~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV 101 (109)
.|+++|+.++ +++|.|.|++||.+.|+|+|||+||||+|+||+|++...+++.+.. ........|.+|.+|||||||
T Consensus 1 ~pl~~l~~~~--~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~-~~~~~~~~r~lg~~~iRGd~V 77 (82)
T cd01730 1 EPLDLIRLSL--DERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETY-EEIVKTTKRNIPMLFVRGDSV 77 (82)
T ss_pred CchHHHHHhC--CCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeeccccccccc-ccccceeEEEcCeEEEeCCEE
Confidence 5999999999 9999999999999999999999999999999999987543221110 001112457899999999999
Q ss_pred EEEEe
Q 033904 102 IIVLR 106 (109)
Q Consensus 102 v~I~~ 106 (109)
++|++
T Consensus 78 v~i~~ 82 (82)
T cd01730 78 ILVSP 82 (82)
T ss_pred EEECC
Confidence 99974
No 3
>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=5.9e-24 Score=136.81 Aligned_cols=73 Identities=26% Similarity=0.512 Sum_probs=64.4
Q ss_pred CCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCc
Q 033904 21 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 100 (109)
Q Consensus 21 ~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn 100 (109)
..|+++|++++ +++|.|.+++|+.+.|+|+|||+||||+|+||+|++.. + +++ ..+++|.++|||+|
T Consensus 2 ~~P~~~L~~~~--~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~-~-~~~---------~~~~lg~v~iRG~n 68 (76)
T cd01732 2 LLPLELIDKCI--GSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEIT-P-EGR---------KITKLDQILLNGNN 68 (76)
T ss_pred cChHHHHHHhC--CCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEc-C-CCc---------eeeEcCeEEEeCCe
Confidence 47999999999 99999999999999999999999999999999999842 2 121 13679999999999
Q ss_pred EEEEEe
Q 033904 101 VIIVLR 106 (109)
Q Consensus 101 Vv~I~~ 106 (109)
|++|+|
T Consensus 69 V~~i~p 74 (76)
T cd01732 69 ICMLVP 74 (76)
T ss_pred EEEEEC
Confidence 999996
No 4
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.91 E-value=7.9e-24 Score=134.64 Aligned_cols=70 Identities=33% Similarity=0.595 Sum_probs=62.9
Q ss_pred CCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCc
Q 033904 21 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 100 (109)
Q Consensus 21 ~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn 100 (109)
..|+++|++++ +++|.|+|++|+.|.|+|.|||+||||+|+||.|.+. ++ ..+.+|.++|||+|
T Consensus 3 ~~P~~~L~~~~--~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-----~~---------~~~~lg~v~iRG~~ 66 (72)
T PRK00737 3 QRPLDVLNNAL--NSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-----GE---------VVRKLGKVVIRGDN 66 (72)
T ss_pred cchHHHHHHhC--CCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC-----CC---------eEeEcCcEEEeCCE
Confidence 58999999999 9999999999999999999999999999999999753 21 13579999999999
Q ss_pred EEEEEe
Q 033904 101 VIIVLR 106 (109)
Q Consensus 101 Vv~I~~ 106 (109)
|++|++
T Consensus 67 V~~i~~ 72 (72)
T PRK00737 67 VVYVSP 72 (72)
T ss_pred EEEEcC
Confidence 999974
No 5
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.90 E-value=1.4e-23 Score=131.92 Aligned_cols=68 Identities=34% Similarity=0.599 Sum_probs=61.7
Q ss_pred cHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEE
Q 033904 23 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 102 (109)
Q Consensus 23 Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 102 (109)
|+++|++++ +++|.|+|++|+.|.|+|.|||+||||+|+||+|++.. + .++.+|.++|||+||+
T Consensus 1 p~~~L~~~~--~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----~----------~~~~lg~~~iRG~~I~ 64 (68)
T cd01731 1 PLDVLKDSL--NKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG----E----------PVRKYGRVVIRGDNVL 64 (68)
T ss_pred ChHHHHHhc--CCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC----C----------eEeEcCcEEEeCCEEE
Confidence 899999999 99999999999999999999999999999999998642 1 1367999999999999
Q ss_pred EEEe
Q 033904 103 IVLR 106 (109)
Q Consensus 103 ~I~~ 106 (109)
+|++
T Consensus 65 ~i~~ 68 (68)
T cd01731 65 FISP 68 (68)
T ss_pred EEcC
Confidence 9975
No 6
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=2e-22 Score=126.43 Aligned_cols=67 Identities=21% Similarity=0.366 Sum_probs=59.8
Q ss_pred cHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEE
Q 033904 23 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 102 (109)
Q Consensus 23 Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 102 (109)
|+++|++++ +++|.|+|++|++|+|+|.|||+||||+|+||+|... +. ..+.+|.++|||++|+
T Consensus 1 p~~~L~~~~--~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~-----~~---------~~~~~~~v~IRG~~I~ 64 (67)
T cd01726 1 PSEFLKAII--GRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN-----GQ---------LKNKYGDAFIRGNNVL 64 (67)
T ss_pred CHHHHHhhC--CCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC-----Cc---------eeeEeCCEEEECCEEE
Confidence 899999999 9999999999999999999999999999999998642 21 1356899999999999
Q ss_pred EEE
Q 033904 103 IVL 105 (109)
Q Consensus 103 ~I~ 105 (109)
+|+
T Consensus 65 ~I~ 67 (67)
T cd01726 65 YIS 67 (67)
T ss_pred EEC
Confidence 985
No 7
>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=9.3e-22 Score=127.85 Aligned_cols=76 Identities=20% Similarity=0.340 Sum_probs=61.6
Q ss_pred cHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEE
Q 033904 23 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 102 (109)
Q Consensus 23 Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 102 (109)
+++ |.+++ +++|.|.|++||.|.|+|+|||+||||+|+||+|+...... . . ......+.+|.++|||+||+
T Consensus 4 ~~~-L~~~i--~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~-~--~---~~~~~~~~lG~v~iRG~nV~ 74 (81)
T cd01729 4 ILD-LSKYV--DKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDD-P--Y---KLTDKTRQLGLVVCRGTSVV 74 (81)
T ss_pred hhh-HHHhc--CCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCc-c--c---ccccceeEccEEEEcCCEEE
Confidence 344 89999 99999999999999999999999999999999998753211 1 0 00113477999999999999
Q ss_pred EEEeC
Q 033904 103 IVLRN 107 (109)
Q Consensus 103 ~I~~~ 107 (109)
+|++.
T Consensus 75 ~i~~~ 79 (81)
T cd01729 75 LISPV 79 (81)
T ss_pred EEecC
Confidence 99874
No 8
>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=99.87 E-value=7.7e-22 Score=127.31 Aligned_cols=75 Identities=21% Similarity=0.441 Sum_probs=61.2
Q ss_pred HHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEEE
Q 033904 26 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 105 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I~ 105 (109)
-|..++ +++|.|.|++||.+.|+|.|||+||||+|+||+|++...+.+... ....+.|++|.++|||++|++|+
T Consensus 4 ~l~~~l--~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~----~~~~~~r~lG~v~iRG~~Vv~i~ 77 (79)
T cd01717 4 KMLQLI--NYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKN----SEREEKRTLGLVLLRGENIVSMT 77 (79)
T ss_pred hhHHHc--CCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEecccccccc----ccCcceeEeeeEEEcCCEEEEEE
Confidence 478889 999999999999999999999999999999999998643221100 11224588999999999999997
Q ss_pred e
Q 033904 106 R 106 (109)
Q Consensus 106 ~ 106 (109)
-
T Consensus 78 v 78 (79)
T cd01717 78 V 78 (79)
T ss_pred E
Confidence 4
No 9
>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=99.87 E-value=8.7e-22 Score=127.66 Aligned_cols=75 Identities=19% Similarity=0.420 Sum_probs=64.4
Q ss_pred cCCCcHHHHHHhhhCCcEEEEEec--CCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEE
Q 033904 19 FNTGPLSVLMMSVKNNTQVLINCR--NNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFL 96 (109)
Q Consensus 19 ~~~~Pl~~L~~~~~~~krV~V~Lr--~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~I 96 (109)
.-..|++.|+++++...+|.|+++ +|+.+.|+|.|||+||||+|+||+|+... ++ ..+.+|.++|
T Consensus 3 ~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~----~~---------~~~~lG~ili 69 (79)
T cd01718 3 VMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK----TK---------TRKPLGRILL 69 (79)
T ss_pred cccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC----Cc---------eEeEcCcEEE
Confidence 356899999999966669999998 89999999999999999999999998741 11 1357999999
Q ss_pred eCCcEEEEEe
Q 033904 97 RGDSVIIVLR 106 (109)
Q Consensus 97 RGdnVv~I~~ 106 (109)
|||||++|++
T Consensus 70 RGnnV~~I~p 79 (79)
T cd01718 70 KGDNITLIQN 79 (79)
T ss_pred eCCEEEEEcC
Confidence 9999999984
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=99.87 E-value=6.5e-22 Score=124.48 Aligned_cols=68 Identities=19% Similarity=0.304 Sum_probs=60.1
Q ss_pred CcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcE
Q 033904 22 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 101 (109)
Q Consensus 22 ~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV 101 (109)
.|+.+|++++ +++|.|.|++|+.|.|+|.|||+|||++|+||+|... +. ..+.+|.++|||+||
T Consensus 1 ~p~~~L~~~~--g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~-----~~---------~~~~lg~~~IRG~~I 64 (68)
T cd01722 1 NPKPFLNDLT--GKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID-----GK---------STGNLGEVLIRCNNV 64 (68)
T ss_pred CHHHHHHHcC--CCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC-----Cc---------cccCcCcEEEECCEE
Confidence 4899999999 9999999999999999999999999999999998742 21 124689999999999
Q ss_pred EEEE
Q 033904 102 IIVL 105 (109)
Q Consensus 102 v~I~ 105 (109)
++|+
T Consensus 65 ~~i~ 68 (68)
T cd01722 65 LYIR 68 (68)
T ss_pred EEEC
Confidence 9984
No 11
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=1.9e-21 Score=123.90 Aligned_cols=69 Identities=23% Similarity=0.409 Sum_probs=60.5
Q ss_pred cHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEE
Q 033904 23 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 102 (109)
Q Consensus 23 Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 102 (109)
|-+.|++++ +++|.|.|++|+.+.|+|.|||+||||+|+||+|+.. +. ..+.+|.++|||++|+
T Consensus 1 ~~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~-----~~---------~~~~lg~v~IRG~~I~ 64 (72)
T cd01719 1 HPPELKKYM--DKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS-----GG---------EKNNIGMVVIRGNSIV 64 (72)
T ss_pred CchhhHHhC--CCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEcc-----CC---------ceeEeceEEECCCEEE
Confidence 446899999 9999999999999999999999999999999999863 11 1357899999999999
Q ss_pred EEEeC
Q 033904 103 IVLRN 107 (109)
Q Consensus 103 ~I~~~ 107 (109)
+|++.
T Consensus 65 ~i~~~ 69 (72)
T cd01719 65 MLEAL 69 (72)
T ss_pred EEEcc
Confidence 99864
No 12
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=6.4e-21 Score=122.17 Aligned_cols=71 Identities=25% Similarity=0.433 Sum_probs=61.1
Q ss_pred cHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEE
Q 033904 23 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 102 (109)
Q Consensus 23 Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 102 (109)
++..|.+++ +++|.|.|++|+.+.|+|.|||+||||+|+||.|+... +... .++.+|.++|||+||+
T Consensus 3 ~~~~L~~~l--~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~----~~~~-------~~~~lG~~viRG~~V~ 69 (74)
T cd01728 3 GTASLVDDL--DKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYV----GDKY-------GDIPRGIFIIRGENVV 69 (74)
T ss_pred chHHHHHhc--CCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEec----CCcc-------ceeEeeEEEEECCEEE
Confidence 466799999 99999999999999999999999999999999998753 1111 1367999999999999
Q ss_pred EEEe
Q 033904 103 IVLR 106 (109)
Q Consensus 103 ~I~~ 106 (109)
+|+.
T Consensus 70 ~ig~ 73 (74)
T cd01728 70 LLGE 73 (74)
T ss_pred EEEc
Confidence 9974
No 13
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.85 E-value=8.6e-21 Score=122.25 Aligned_cols=76 Identities=28% Similarity=0.545 Sum_probs=63.1
Q ss_pred cCCCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeC
Q 033904 19 FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 98 (109)
Q Consensus 19 ~~~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRG 98 (109)
....|+++|+.++ +++|.|+|++|++|.|+|+|||+||||+|+||+|.... ++... ..+..+.++|||
T Consensus 4 ~~~~~~~~l~~~~--~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~~~-------~~~~~~~~~IRG 71 (79)
T COG1958 4 LGPLPLSFLKKLL--NKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH---DGEKN-------VRRLGGEVLIRG 71 (79)
T ss_pred ccCCcHHHHHHhh--CCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc---CCccc-------cceeccEEEEEC
Confidence 3557899999999 99999999999999999999999999999999998741 12100 124456999999
Q ss_pred CcEEEEEe
Q 033904 99 DSVIIVLR 106 (109)
Q Consensus 99 dnVv~I~~ 106 (109)
+||++|+.
T Consensus 72 ~~I~~I~~ 79 (79)
T COG1958 72 DNIVLISP 79 (79)
T ss_pred CcEEEEeC
Confidence 99999974
No 14
>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=99.85 E-value=9.6e-21 Score=120.92 Aligned_cols=72 Identities=21% Similarity=0.353 Sum_probs=60.8
Q ss_pred HHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEE
Q 033904 25 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 104 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I 104 (109)
+-|.+++ +++|.|.|++|+.+.|+|+|||+||||+|+||+|+....+ .+ ..++.+|.++|||+||++|
T Consensus 2 ~~L~~~l--~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~-~~---------~~~~~lG~~~iRG~~I~~i 69 (74)
T cd01727 2 STLEDYL--NKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSD-EG---------VEQVVLGLYIIRGDNIAVV 69 (74)
T ss_pred hhHHHhc--CCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCC-CC---------ceeeEeceEEECCCEEEEE
Confidence 4688999 9999999999999999999999999999999999864211 11 1246799999999999999
Q ss_pred EeCC
Q 033904 105 LRNP 108 (109)
Q Consensus 105 ~~~p 108 (109)
++..
T Consensus 70 ~~~d 73 (74)
T cd01727 70 GEID 73 (74)
T ss_pred EccC
Confidence 9753
No 15
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.84 E-value=2.4e-20 Score=123.29 Aligned_cols=78 Identities=22% Similarity=0.482 Sum_probs=67.3
Q ss_pred cccCCCcHHHHHHhhhCCcEEEEEecCC--eEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceE
Q 033904 17 EEFNTGPLSVLMMSVKNNTQVLINCRNN--KKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKM 94 (109)
Q Consensus 17 ~~~~~~Pl~~L~~~~~~~krV~V~Lr~g--r~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i 94 (109)
.+....|+.++.+++....+|.|++.++ +.+.|+|+|||+||||+|+||+|++.. ++ ..+.+|.+
T Consensus 9 ~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~----~~---------~~~~lG~i 75 (89)
T PTZ00138 9 QKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK----KN---------TRKDLGRI 75 (89)
T ss_pred ceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC----Cc---------eeeEcCeE
Confidence 3456789999999999999999999885 889999999999999999999998641 11 13679999
Q ss_pred EEeCCcEEEEEeC
Q 033904 95 FLRGDSVIIVLRN 107 (109)
Q Consensus 95 ~IRGdnVv~I~~~ 107 (109)
+||||||++|++.
T Consensus 76 lIRGnnV~~I~~~ 88 (89)
T PTZ00138 76 LLKGDNITLIMAA 88 (89)
T ss_pred EEcCCEEEEEEcC
Confidence 9999999999875
No 16
>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=99.83 E-value=5.1e-20 Score=116.56 Aligned_cols=69 Identities=14% Similarity=0.300 Sum_probs=60.5
Q ss_pred cHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEE
Q 033904 23 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 102 (109)
Q Consensus 23 Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 102 (109)
|+++|+++. |++|.|+|++|.+|+|+|.+||.|||++|+||.+... +++ ...++.+||||+||.
T Consensus 1 P~~~L~~~~--g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~----~g~----------~~~~~~v~IRG~nI~ 64 (70)
T cd01721 1 PIKLLHEAE--GHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTAR----DGR----------VSQLEQVYIRGSKIR 64 (70)
T ss_pred ChHHHhhCC--CCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECC----CCc----------EeEcCcEEEeCCEEE
Confidence 899999999 9999999999999999999999999999999987532 222 135799999999999
Q ss_pred EEEeC
Q 033904 103 IVLRN 107 (109)
Q Consensus 103 ~I~~~ 107 (109)
+|.-+
T Consensus 65 ~v~lP 69 (70)
T cd01721 65 FFILP 69 (70)
T ss_pred EEEeC
Confidence 99754
No 17
>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=99.83 E-value=5.3e-20 Score=114.34 Aligned_cols=67 Identities=24% Similarity=0.457 Sum_probs=59.6
Q ss_pred HHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEE
Q 033904 25 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 104 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I 104 (109)
.+|++++ +++|+|.|++|+.++|+|.+||+||||+|+||.|.... +. ..+++|.+||||++|++|
T Consensus 1 ~~L~~~~--g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~----~~---------~~~~~~~~~irG~~I~~I 65 (67)
T PF01423_consen 1 NFLQKLI--GKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKN----GP---------EKRSLGLVFIRGSNIRYI 65 (67)
T ss_dssp HHHHHTT--TSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETT----ES---------EEEEEEEEEEEGGGEEEE
T ss_pred ChhHHhC--CcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECC----CC---------cEeECcEEEEECCEEEEE
Confidence 3789999 99999999999999999999999999999999998752 10 247899999999999999
Q ss_pred Ee
Q 033904 105 LR 106 (109)
Q Consensus 105 ~~ 106 (109)
++
T Consensus 66 ~~ 67 (67)
T PF01423_consen 66 SL 67 (67)
T ss_dssp EE
T ss_pred EC
Confidence 85
No 18
>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=99.83 E-value=5e-20 Score=118.18 Aligned_cols=72 Identities=21% Similarity=0.286 Sum_probs=61.7
Q ss_pred CcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcE
Q 033904 22 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 101 (109)
Q Consensus 22 ~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV 101 (109)
-|+.+|+++. |++|.|+|++|+.++|+|.+||.|||++|+||+|... +|+. ...++.+||||++|
T Consensus 1 ~Pl~~L~~~~--g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~g~~---------~~~~~~v~IRG~~I 65 (76)
T cd01723 1 LPLSLLKTAQ--NHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSK----DGDK---------FWKMPECYIRGNTI 65 (76)
T ss_pred CchHHHHhcC--CCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC----CCcE---------eeeCCcEEEeCCEE
Confidence 3999999999 9999999999999999999999999999999998632 2321 13478999999999
Q ss_pred EEEEeCC
Q 033904 102 IIVLRNP 108 (109)
Q Consensus 102 v~I~~~p 108 (109)
.+|+.++
T Consensus 66 ~~i~~p~ 72 (76)
T cd01723 66 KYLRVPD 72 (76)
T ss_pred EEEEcCH
Confidence 9998653
No 19
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.82 E-value=1.8e-21 Score=126.25 Aligned_cols=85 Identities=32% Similarity=0.518 Sum_probs=70.1
Q ss_pred CCCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCC
Q 033904 20 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 99 (109)
Q Consensus 20 ~~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd 99 (109)
...|+++|+-++ +.||.|++|++|.++|+|.|||+|+||+|.||+|+++....+...+++. ....+|.+.-+|+|||
T Consensus 3 v~ePldllrlsL--dErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~-~k~~~r~~emlFvRGd 79 (91)
T KOG3460|consen 3 VEEPLDLLRLSL--DERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEI-VKTTKRTVEMLFVRGD 79 (91)
T ss_pred ccccHHHHhhcc--cceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHH-HhhhhcceeEEEEeCC
Confidence 357999999999 8899999999999999999999999999999999998754433222221 1123578899999999
Q ss_pred cEEEEEeC
Q 033904 100 SVIIVLRN 107 (109)
Q Consensus 100 nVv~I~~~ 107 (109)
+|++|++.
T Consensus 80 ~Vilvspp 87 (91)
T KOG3460|consen 80 GVILVSPP 87 (91)
T ss_pred eEEEEcCc
Confidence 99999975
No 20
>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=99.82 E-value=1.2e-19 Score=116.57 Aligned_cols=72 Identities=17% Similarity=0.314 Sum_probs=60.6
Q ss_pred HHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEE
Q 033904 25 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 104 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I 104 (109)
+-|.+++ +++|+|.|+|||.|.|+|.|||+||||+|+||.|+....+... ....|++|.++|||++|++|
T Consensus 3 ~~L~~~l--~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~--------~~~~r~lGlv~IrG~~Iv~i 72 (75)
T cd06168 3 QKLRSLL--GRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFS--------PTEPRVLGLVMIPGHHIVSI 72 (75)
T ss_pred hHHHHhc--CCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccC--------CccEEEeeeEEEeCCeEEEE
Confidence 3588899 9999999999999999999999999999999999986422111 12358999999999999998
Q ss_pred Ee
Q 033904 105 LR 106 (109)
Q Consensus 105 ~~ 106 (109)
+.
T Consensus 73 ~v 74 (75)
T cd06168 73 EV 74 (75)
T ss_pred EE
Confidence 74
No 21
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.82 E-value=8.3e-20 Score=113.32 Aligned_cols=66 Identities=29% Similarity=0.618 Sum_probs=58.5
Q ss_pred HHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEEE
Q 033904 26 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 105 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I~ 105 (109)
+|++++ +++|.|.|++|+.+.|+|.+||+||||+|+||.|+... .. ..+++|.+||||++|++|+
T Consensus 2 ~L~~~~--~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~----~~---------~~~~~~~~~IrG~~I~~i~ 66 (67)
T smart00651 2 FLKKLI--GKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD----GE---------KKRKLGLVFIRGNNIVYII 66 (67)
T ss_pred hhHHhC--CcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecC----Cc---------EEeEeCCEEEcCCEEEEEe
Confidence 688899 99999999999999999999999999999999998742 11 2468999999999999997
Q ss_pred e
Q 033904 106 R 106 (109)
Q Consensus 106 ~ 106 (109)
+
T Consensus 67 ~ 67 (67)
T smart00651 67 L 67 (67)
T ss_pred C
Confidence 4
No 22
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.82 E-value=3.2e-21 Score=130.58 Aligned_cols=106 Identities=80% Similarity=1.196 Sum_probs=96.5
Q ss_pred CccccccccCccccccccCCCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccc
Q 033904 2 SRAMDEDTTGGKTEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKK 81 (109)
Q Consensus 2 ~~~~~~~~~~~~~e~~~~~~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~ 81 (109)
.+-.++||..+..|++++..||++++..++.....|.|.+|+++.+-|.+.|||.|+|++|+++.|.|+..|+.+++.+
T Consensus 4 ~~pk~e~t~~~~~e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk- 82 (114)
T KOG3459|consen 4 EKPKEECTPLEVPEEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK- 82 (114)
T ss_pred cchhhhcCccccccccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-
Confidence 3456789988888999999999999999999999999999999999999999999999999999999999888776655
Q ss_pred cccccceeeeceEEEeCCcEEEEEeCC
Q 033904 82 ALPVNKDRFISKMFLRGDSVIIVLRNP 108 (109)
Q Consensus 82 ~~~~~~~r~lg~i~IRGdnVv~I~~~p 108 (109)
.+++.+.|++|.+|||||+|+++...|
T Consensus 83 ~~~~~~~r~isK~flRGdsvI~v~r~p 109 (114)
T KOG3459|consen 83 AKPVNKDRFISKMFLRGDSVILVLRNP 109 (114)
T ss_pred CCccchhhhhheeeecCCeEEEEEecc
Confidence 567778899999999999999998776
No 23
>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=1.8e-18 Score=105.89 Aligned_cols=63 Identities=35% Similarity=0.549 Sum_probs=55.5
Q ss_pred HHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEEE
Q 033904 27 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 105 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I~ 105 (109)
|++++ +++|.|.|++|+.|.|+|.+||+|||++|+||.|.+.. + ..+.+|.+||||++|.+|+
T Consensus 1 l~~~~--g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~----~----------~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLV--GKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE----G----------KKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHC--CCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC----C----------cEEECCeEEEECCEEEEEC
Confidence 46778 99999999999999999999999999999999998752 1 1367999999999999984
No 24
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.77 E-value=3.3e-18 Score=113.22 Aligned_cols=71 Identities=20% Similarity=0.255 Sum_probs=61.6
Q ss_pred CcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcE
Q 033904 22 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 101 (109)
Q Consensus 22 ~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV 101 (109)
.|+.+|+++. |++|.|+|++|..|+|+|.++|.|||++|+||+|... ++. ...+|.++|||+||
T Consensus 1 ~~~~fL~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~----~~~----------~~~~~~v~IRG~nI 64 (90)
T cd01724 1 KLVRFLMKLT--NETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLK----GRN----------PVPLDTLSIRGNNI 64 (90)
T ss_pred CHhHHHHhCC--CCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcC----CCc----------eeEcceEEEeCCEE
Confidence 3678999999 9999999999999999999999999999999998753 121 24689999999999
Q ss_pred EEEEeCC
Q 033904 102 IIVLRNP 108 (109)
Q Consensus 102 v~I~~~p 108 (109)
.+|+.+.
T Consensus 65 ~yi~lPd 71 (90)
T cd01724 65 RYFILPD 71 (90)
T ss_pred EEEEcCC
Confidence 9998653
No 25
>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=99.77 E-value=3.6e-18 Score=110.91 Aligned_cols=73 Identities=19% Similarity=0.195 Sum_probs=60.8
Q ss_pred CcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcE
Q 033904 22 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 101 (109)
Q Consensus 22 ~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV 101 (109)
.|++||+++. |++|.|+|++|..|+|+|.++|.|||++|+||++... ++... ...++.++|||++|
T Consensus 1 l~~~fL~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~----~~~~~--------~~~~~~v~IRG~~I 66 (81)
T cd01725 1 LFFSFFKTLV--GKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDP----EKYPH--------MLSVKNCFIRGSVV 66 (81)
T ss_pred ChhHHHHhCC--CCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcC----CCccc--------ccccCeEEEECCEE
Confidence 3789999998 9999999999999999999999999999999987532 11100 13469999999999
Q ss_pred EEEEeCC
Q 033904 102 IIVLRNP 108 (109)
Q Consensus 102 v~I~~~p 108 (109)
.+|+.++
T Consensus 67 ~~I~lp~ 73 (81)
T cd01725 67 RYVQLPA 73 (81)
T ss_pred EEEEeCh
Confidence 9998654
No 26
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.77 E-value=4e-18 Score=110.13 Aligned_cols=72 Identities=19% Similarity=0.281 Sum_probs=61.2
Q ss_pred cCCCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeC
Q 033904 19 FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 98 (109)
Q Consensus 19 ~~~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRG 98 (109)
....+..||+.+. |++|.|+|++|..|+|+|.++|.|||++|+||++... ++. ...+|.++|||
T Consensus 6 ~~~tl~~~L~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~----~~~----------~~~~~~v~IRG 69 (78)
T cd01733 6 LENTLIILLQGLQ--GKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDR----NGK----------QVQVEEIMVTG 69 (78)
T ss_pred hhchHHHHHHHCC--CCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcC----CCc----------eeECCcEEEEC
Confidence 3446778999998 9999999999999999999999999999999987632 121 23589999999
Q ss_pred CcEEEEEe
Q 033904 99 DSVIIVLR 106 (109)
Q Consensus 99 dnVv~I~~ 106 (109)
+||.+|+.
T Consensus 70 ~nI~yI~l 77 (78)
T cd01733 70 RNIRYVHI 77 (78)
T ss_pred CEEEEEEc
Confidence 99999975
No 27
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.71 E-value=2.5e-17 Score=104.52 Aligned_cols=73 Identities=19% Similarity=0.302 Sum_probs=65.6
Q ss_pred CCCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCC
Q 033904 20 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 99 (109)
Q Consensus 20 ~~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd 99 (109)
..+|-.||+... +++|.|.|+.|.+|.|+|++.|.||||.|.+|+|++. |.. ...+|.++||.+
T Consensus 6 PvNPKpFL~~l~--gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~id-----G~~---------~g~lGEilIRCN 69 (79)
T KOG3482|consen 6 PVNPKPFLNGLT--GKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYID-----GVS---------TGNLGEILIRCN 69 (79)
T ss_pred cCCchHHHhhcc--CCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhc-----ccc---------cccceeEEEEec
Confidence 568999999999 9999999999999999999999999999999999875 321 246999999999
Q ss_pred cEEEEEeCC
Q 033904 100 SVIIVLRNP 108 (109)
Q Consensus 100 nVv~I~~~p 108 (109)
||.+|.-.|
T Consensus 70 Nvlyi~gv~ 78 (79)
T KOG3482|consen 70 NVLYIRGVP 78 (79)
T ss_pred cEEEEecCC
Confidence 999998766
No 28
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.66 E-value=1.7e-16 Score=100.93 Aligned_cols=68 Identities=24% Similarity=0.446 Sum_probs=58.9
Q ss_pred CcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcE
Q 033904 22 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 101 (109)
Q Consensus 22 ~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV 101 (109)
.| -|++++ +|++.+.|.+||.+.|.|+|||.|||+||+|++|.-.. +. +..+|..+|||++|
T Consensus 6 ~P--eLkkym--dKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~----~~----------~~~ig~~vIrgnsi 67 (77)
T KOG1780|consen 6 HP--ELKKYM--DKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD----GD----------KNNIGMVVIRGNSI 67 (77)
T ss_pred Cc--hHHHhh--hheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc----CC----------cceeeeEEEeccEE
Confidence 56 699999 99999999999999999999999999999999996431 21 13589999999999
Q ss_pred EEEEeC
Q 033904 102 IIVLRN 107 (109)
Q Consensus 102 v~I~~~ 107 (109)
+++.+.
T Consensus 68 v~~eaL 73 (77)
T KOG1780|consen 68 VMVEAL 73 (77)
T ss_pred EEEeec
Confidence 998764
No 29
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.64 E-value=4.5e-16 Score=100.69 Aligned_cols=76 Identities=22% Similarity=0.456 Sum_probs=64.9
Q ss_pred CCCcHHHHHHhhhCCcEEEEEecC--CeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEe
Q 033904 20 NTGPLSVLMMSVKNNTQVLINCRN--NKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLR 97 (109)
Q Consensus 20 ~~~Pl~~L~~~~~~~krV~V~Lr~--gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IR 97 (109)
...|+.++.++++...+|.|||.. |-.+.|.++|||+|||+||+||+|.... .+ . .+.+|.++++
T Consensus 10 mv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k----~~--~-------rk~lGRilLK 76 (88)
T KOG1774|consen 10 MVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSK----TK--S-------RKELGRILLK 76 (88)
T ss_pred ecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccc----cc--C-------CCccccEEEc
Confidence 478999999999999999999997 5789999999999999999999997642 11 1 2369999999
Q ss_pred CCcEEEEEeCC
Q 033904 98 GDSVIIVLRNP 108 (109)
Q Consensus 98 GdnVv~I~~~p 108 (109)
||||.+|...-
T Consensus 77 GDnItli~~~~ 87 (88)
T KOG1774|consen 77 GDNITLIQSAG 87 (88)
T ss_pred CCcEEEEeecC
Confidence 99999998753
No 30
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.59 E-value=1.3e-15 Score=97.46 Aligned_cols=76 Identities=24% Similarity=0.491 Sum_probs=65.2
Q ss_pred ccCCCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEe
Q 033904 18 EFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLR 97 (109)
Q Consensus 18 ~~~~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IR 97 (109)
.++..|+.++.+|+ +++|-|.+++++++.|+|+|||.|.|++|+||+|+-.. | +|+ +...++++++.
T Consensus 3 ~~~llPlEliDkcI--gski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~-~-egr---------~~tk~~~iLLn 69 (84)
T KOG1775|consen 3 PSTLLPLELIDKCI--GSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEIT-P-EGR---------RMTKLDQILLN 69 (84)
T ss_pred hhhcccHHHHHHhc--CceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeC-C-Ccc---------eeeeeeeeeec
Confidence 45678999999999 99999999999999999999999999999999998643 1 121 12468999999
Q ss_pred CCcEEEEEe
Q 033904 98 GDSVIIVLR 106 (109)
Q Consensus 98 GdnVv~I~~ 106 (109)
|+||.+..+
T Consensus 70 GNni~mLvP 78 (84)
T KOG1775|consen 70 GNNITMLVP 78 (84)
T ss_pred CCcEEEEec
Confidence 999999876
No 31
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.57 E-value=2.6e-16 Score=104.99 Aligned_cols=74 Identities=15% Similarity=0.328 Sum_probs=61.3
Q ss_pred HHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEEE
Q 033904 26 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 105 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I~ 105 (109)
-|.+++ +++|+|++.+||..+|+|.|||+.|||||+|++|+... |.+. + +.....|.+|++++||..+++|+
T Consensus 21 DLsky~--Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrd-pdd~--~---~~~~~tR~LGLvV~RGTalvlis 92 (108)
T KOG1781|consen 21 DLSKYL--DKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRD-PDDP--Y---KLTDETRKLGLVVCRGTALVLIS 92 (108)
T ss_pred hHHHhh--ccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcC-CCCc--c---chhhhhheeeeEEEcccEEEEEc
Confidence 466777 99999999999999999999999999999999998753 2221 1 12234588999999999999998
Q ss_pred eC
Q 033904 106 RN 107 (109)
Q Consensus 106 ~~ 107 (109)
+.
T Consensus 93 p~ 94 (108)
T KOG1781|consen 93 PA 94 (108)
T ss_pred CC
Confidence 74
No 32
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.53 E-value=1.3e-15 Score=110.10 Aligned_cols=74 Identities=23% Similarity=0.518 Sum_probs=60.5
Q ss_pred HHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEEEe
Q 033904 27 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 106 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I~~ 106 (109)
|-+++ +.+++|.++|||.|.|.+.+||+||||+|.||+|+....++.++..+ .+++|-+|++++||+||++.+.
T Consensus 9 ml~~i--Nyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~----~eEkr~lgLvllRgenIvs~tV 82 (177)
T KOG3168|consen 9 MLQHI--NYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTD----GEEKRVLGLVLLRGENIVSMTV 82 (177)
T ss_pred HHHhh--cceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccc----cceeeEEEEEEecCCcEEEEec
Confidence 44566 88999999999999999999999999999999998765544331111 2356889999999999999874
No 33
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.53 E-value=2e-15 Score=95.82 Aligned_cols=71 Identities=20% Similarity=0.334 Sum_probs=63.6
Q ss_pred CCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCc
Q 033904 21 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 100 (109)
Q Consensus 21 ~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn 100 (109)
..|-+||...+ |++|.|+|.+|-.|+|+|.+.|.|||+.|+.++|... |+ .++..|.+||||+|
T Consensus 5 ~~~~~fl~~ii--Gr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~n-----gq---------l~n~ygdaFirGnn 68 (77)
T KOG1783|consen 5 SMPGEFLKAII--GRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVN-----GQ---------LKNKYGDAFIRGNN 68 (77)
T ss_pred cCcHHHHHHHh--CCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhc-----Cc---------ccccccceeecccc
Confidence 46889999999 9999999999999999999999999999999999763 43 13568999999999
Q ss_pred EEEEEeC
Q 033904 101 VIIVLRN 107 (109)
Q Consensus 101 Vv~I~~~ 107 (109)
|.+|+..
T Consensus 69 VlyIs~~ 75 (77)
T KOG1783|consen 69 VLYISTQ 75 (77)
T ss_pred EEEEEec
Confidence 9999864
No 34
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.42 E-value=2e-14 Score=99.20 Aligned_cols=69 Identities=28% Similarity=0.437 Sum_probs=58.8
Q ss_pred HHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEEEe
Q 033904 27 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 106 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I~~ 106 (109)
|..++ ++++.|.|||||.+.|.|++||||-|++|.+|+|++.. ++.+ +.+..|..+|||+||+++.-
T Consensus 14 l~~~~--dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v----~~~Y-------~di~~glfiIRGENVvllGe 80 (129)
T KOG1782|consen 14 LVEYL--DKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFV----GNKY-------CDIPRGLFIIRGENVVLLGE 80 (129)
T ss_pred HHHHh--cceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheee----ccee-------cccCceEEEEecCcEEEEec
Confidence 66777 89999999999999999999999999999999999875 2222 34567999999999999975
Q ss_pred CC
Q 033904 107 NP 108 (109)
Q Consensus 107 ~p 108 (109)
.+
T Consensus 81 id 82 (129)
T KOG1782|consen 81 ID 82 (129)
T ss_pred CC
Confidence 43
No 35
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.37 E-value=1.4e-12 Score=90.23 Aligned_cols=71 Identities=23% Similarity=0.296 Sum_probs=61.2
Q ss_pred CCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCc
Q 033904 21 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 100 (109)
Q Consensus 21 ~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn 100 (109)
..||++|+.+. +.++.|+|++|.+|.|.|+..|.+|||.|.+|+++.. +|. + -..++.++|||++
T Consensus 1 mlPLsLL~~aq--~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~----Dgd--k-------f~r~pEcYirGtt 65 (134)
T KOG3293|consen 1 MLPLSLLKTAQ--NHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSE----DGD--K-------FFRMPECYIRGTT 65 (134)
T ss_pred CcchhHHHhcC--CCeEEEEecCCCEecceeecchhhhhcchheeEEecc----CCC--c-------eeecceeEEecce
Confidence 36999999999 9999999999999999999999999999999998753 232 1 1347899999999
Q ss_pred EEEEEe
Q 033904 101 VIIVLR 106 (109)
Q Consensus 101 Vv~I~~ 106 (109)
|-++.-
T Consensus 66 Ikylri 71 (134)
T KOG3293|consen 66 IKYLRI 71 (134)
T ss_pred eEEEec
Confidence 999863
No 36
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.37 E-value=7e-13 Score=87.45 Aligned_cols=70 Identities=19% Similarity=0.385 Sum_probs=58.9
Q ss_pred HHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEE
Q 033904 25 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 104 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I 104 (109)
+-|..++ +++|.|.+.|||.+.|.|.|||+-.||+|+|+.|++.... ++ .+.--+|..+|||+||..|
T Consensus 3 s~L~~y~--n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~---~g-------v~q~~lGlyiirgeNva~i 70 (96)
T KOG1784|consen 3 STLEDYM--NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSET---EG-------VEQIVLGLYIIRGENVAVI 70 (96)
T ss_pred hhHHHHh--hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhh---cc-------hhheeeEEEEEecCcccee
Confidence 3588999 9999999999999999999999999999999999876421 11 1234689999999999998
Q ss_pred Ee
Q 033904 105 LR 106 (109)
Q Consensus 105 ~~ 106 (109)
..
T Consensus 71 g~ 72 (96)
T KOG1784|consen 71 GE 72 (96)
T ss_pred ee
Confidence 65
No 37
>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=99.31 E-value=8.9e-13 Score=82.26 Aligned_cols=45 Identities=29% Similarity=0.377 Sum_probs=39.1
Q ss_pred HHHhhhCCcEEEEEecCC----eEEEEEEEEecCccceeeeeeEEeeec
Q 033904 27 LMMSVKNNTQVLINCRNN----KKLLGRVRAFDRHCNMVLENVREMWTE 71 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~g----r~i~G~L~~fD~~mNlvL~d~~E~~~~ 71 (109)
|++++.++.||+|.++.- ..++|.|+|||+||||+|.||+|.|..
T Consensus 1 ~~~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 1 LHRCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CchhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 356777899999999974 468899999999999999999999863
No 38
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.24 E-value=6.6e-11 Score=77.81 Aligned_cols=70 Identities=21% Similarity=0.314 Sum_probs=57.8
Q ss_pred HHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEE
Q 033904 24 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 103 (109)
Q Consensus 24 l~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~ 103 (109)
++|++.++ |++|.|.|+++-.++|+|.+.|+|.||-|.|..-.-.. + .|. --++..+||||+.|.+
T Consensus 4 ysfFkslv--g~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~-----k-----yPh--m~Sv~ncfIRGSvvrY 69 (96)
T KOG3448|consen 4 YSFFKSLV--GKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPD-----K-----YPH--MLSVKNCFIRGSVVRY 69 (96)
T ss_pred HHHHHHhc--CCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcc-----c-----CCC--eeeeeeEEEeccEEEE
Confidence 57899999 99999999999999999999999999999998754321 1 111 2467899999999999
Q ss_pred EEeC
Q 033904 104 VLRN 107 (109)
Q Consensus 104 I~~~ 107 (109)
|..+
T Consensus 70 v~l~ 73 (96)
T KOG3448|consen 70 VQLP 73 (96)
T ss_pred EEeC
Confidence 9754
No 39
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.18 E-value=7.4e-11 Score=80.07 Aligned_cols=72 Identities=14% Similarity=0.270 Sum_probs=62.3
Q ss_pred CCCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCC
Q 033904 20 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 99 (109)
Q Consensus 20 ~~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd 99 (109)
..-|+.+|+++. +.-|.+++..|..|+|+|.-.+.+||++|+|++-+.. +|. -..+.++||||+
T Consensus 3 ~gvpiKlLhEaq--GhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~----dg~----------vs~le~V~IRGS 66 (119)
T KOG3172|consen 3 VGVPIKLLHEAQ--GHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTAR----DGR----------VSQLEQVFIRGS 66 (119)
T ss_pred cccceeeeeccc--CcEEEEEecCCceeeeeeEEeccccccEEEEEEEEcc----CCc----------ceeeeeEEEecC
Confidence 457999999999 9999999999999999999999999999999987653 232 135899999999
Q ss_pred cEEEEEeC
Q 033904 100 SVIIVLRN 107 (109)
Q Consensus 100 nVv~I~~~ 107 (109)
.|.|+..+
T Consensus 67 ~IRFlvlP 74 (119)
T KOG3172|consen 67 KIRFLVLP 74 (119)
T ss_pred eEEEEECc
Confidence 99998754
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.61 E-value=4.4e-07 Score=61.71 Aligned_cols=66 Identities=21% Similarity=0.357 Sum_probs=55.5
Q ss_pred HHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEE
Q 033904 24 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 103 (109)
Q Consensus 24 l~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~ 103 (109)
+.+|+++. +.+|+|.|++|..+.|++.+.|-+||..|.++.=... |+ + ..+..+.|||+||.+
T Consensus 4 vr~L~kl~--~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-----~~------p----v~l~~lsirgnniRy 66 (109)
T KOG3428|consen 4 VRFLKKLL--NERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-----GE------P----VRLDTLSIRGNNIRY 66 (109)
T ss_pred HHHHHHhh--CCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC-----CC------c----eeEEEEEeecceEEE
Confidence 45888998 8999999999999999999999999999999875432 22 1 247889999999999
Q ss_pred EEe
Q 033904 104 VLR 106 (109)
Q Consensus 104 I~~ 106 (109)
+..
T Consensus 67 ~~l 69 (109)
T KOG3428|consen 67 YIL 69 (109)
T ss_pred EEc
Confidence 864
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=97.41 E-value=0.00045 Score=42.76 Aligned_cols=39 Identities=23% Similarity=0.323 Sum_probs=34.1
Q ss_pred HHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeee
Q 033904 26 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 64 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d 64 (109)
+|+.+.+++.+|.|.|.+|-.++|.+.+||+|+=|+-.+
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 688888889999999999999999999999998555443
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=97.34 E-value=0.00066 Score=42.03 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=34.5
Q ss_pred HHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeee
Q 033904 25 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 64 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d 64 (109)
.+|+.+.+++.+|.|.|.+|-.+.|.+.+||+|+=|+-.+
T Consensus 6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 3778888889999999999999999999999998655443
No 43
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.18 E-value=0.0022 Score=40.53 Aligned_cols=69 Identities=13% Similarity=0.167 Sum_probs=40.9
Q ss_pred HHHHHhhhCCcEEEEEecCCeEEEEEEEEecC---ccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcE
Q 033904 25 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDR---HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 101 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~---~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV 101 (109)
-++..++ |++|.|.+++|..|+|.|.+++. -+.++|.-|...-... .... ..........++|.++.|
T Consensus 5 ~l~~~lv--G~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~---~~~~----~~~~~~~~~tlii~~~dv 75 (77)
T PF14438_consen 5 YLLTNLV--GQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSD---QSNS----DPLSSEIVETLIIPAKDV 75 (77)
T ss_dssp HHHHTTT--TSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-------------EEEEEEE-GGGEEE----
T ss_pred HHHHhCc--CCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccc---cccC----CccCCCCCceEEEecccc
Confidence 3566777 99999999999999999999999 8999999888653210 0000 011123457778888776
Q ss_pred E
Q 033904 102 I 102 (109)
Q Consensus 102 v 102 (109)
+
T Consensus 76 v 76 (77)
T PF14438_consen 76 V 76 (77)
T ss_dssp -
T ss_pred C
Confidence 5
No 44
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=97.10 E-value=0.0014 Score=42.49 Aligned_cols=40 Identities=25% Similarity=0.308 Sum_probs=34.6
Q ss_pred HHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeee
Q 033904 25 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 64 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d 64 (109)
.+|..+.+++.+|.|.|.+|-.+.|.+.|||+|+=|+-.+
T Consensus 10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 3777888889999999999999999999999998665544
No 45
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.67 E-value=0.0047 Score=39.80 Aligned_cols=34 Identities=32% Similarity=0.295 Sum_probs=31.4
Q ss_pred HHHHhhhCCcEEEEEecCCeEEEEEEEEecCccc
Q 033904 26 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCN 59 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mN 59 (109)
+|.....++.+|.|.|.+|-.++|.+.+||+|.=
T Consensus 11 fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~V 44 (77)
T COG1923 11 FLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVV 44 (77)
T ss_pred HHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEE
Confidence 7888888899999999999999999999999973
No 46
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=95.80 E-value=0.15 Score=34.09 Aligned_cols=71 Identities=18% Similarity=0.279 Sum_probs=51.7
Q ss_pred HHhhhCCcEEEEEecCCeEEEEEEEEecC-ccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEEE
Q 033904 28 MMSVKNNTQVLINCRNNKKLLGRVRAFDR-HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 105 (109)
Q Consensus 28 ~~~~~~~krV~V~Lr~gr~i~G~L~~fD~-~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I~ 105 (109)
..++ |++|.+..+.+-.|+|+|...|. -..+.|.+|.-+.++.+..+.. ..+ .......+..||..|--+.
T Consensus 4 ~~~I--Gs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~---ipp--~~~v~~~I~Fr~sDIkdL~ 75 (96)
T PF12701_consen 4 DPYI--GSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDRE---IPP--SDEVYDYIVFRGSDIKDLK 75 (96)
T ss_dssp CCCT--TCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS------C---CSSSSEEEEETTTEEEEE
T ss_pred cccc--CCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcc---cCC--CCceeeEEEEEccccceEE
Confidence 3567 99999999999999999999998 6799999999877643211110 001 1124688999999887654
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.71 E-value=0.026 Score=41.24 Aligned_cols=40 Identities=23% Similarity=0.302 Sum_probs=35.0
Q ss_pred HHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeee
Q 033904 25 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 64 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d 64 (109)
.+|..+.+++.+|.|.|.+|-.++|.+.+||+|.=|+..+
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 3788888889999999999999999999999998555544
No 48
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.63 E-value=0.028 Score=41.01 Aligned_cols=40 Identities=23% Similarity=0.187 Sum_probs=34.5
Q ss_pred HHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeee
Q 033904 25 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 64 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d 64 (109)
.+|+.+.+++.+|.|.|.+|-.++|.+.+||+|.=|+-.+
T Consensus 15 ~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~ 54 (165)
T PRK14091 15 IFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRD 54 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 3788888889999999999999999999999998554444
No 49
>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=95.34 E-value=0.11 Score=30.01 Aligned_cols=33 Identities=9% Similarity=0.229 Sum_probs=29.2
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceeeeeeEE
Q 033904 34 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENVRE 67 (109)
Q Consensus 34 ~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E 67 (109)
|++|+|.+ ++..++|+..+.|..-.|+++....
T Consensus 3 G~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 3 GQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 88999999 6777899999999999999987544
No 50
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=95.20 E-value=0.054 Score=33.45 Aligned_cols=34 Identities=26% Similarity=0.330 Sum_probs=30.0
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceeeeeeEE
Q 033904 34 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENVRE 67 (109)
Q Consensus 34 ~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E 67 (109)
|..|.+.+-.|..|+|.+.+||.-.+|++=.+.+
T Consensus 6 Gs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 6 GSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 8999999999999999999999999887655443
No 51
>PRK14638 hypothetical protein; Provisional
Probab=92.06 E-value=0.3 Score=34.85 Aligned_cols=33 Identities=15% Similarity=0.333 Sum_probs=27.1
Q ss_pred HHHhhhCCcEEEEEecCCeEEEEEEEEecCccceee
Q 033904 27 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL 62 (109)
+.++. |+.|+|.+++++.++|+|.++|.- ++.|
T Consensus 95 f~r~~--G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 95 YVRFT--GKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred HHHhC--CCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 45566 999999999999999999999963 3444
No 52
>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=91.62 E-value=2.2 Score=27.63 Aligned_cols=63 Identities=25% Similarity=0.339 Sum_probs=45.5
Q ss_pred HHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCcc-ceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEE
Q 033904 24 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHC-NMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 102 (109)
Q Consensus 24 l~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~m-NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 102 (109)
|.+|.... |++|.+.|.++....|++.|+|... |+..++-. .|- | ..+..++|..-|+
T Consensus 16 Lr~l~~~~--gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-----TPl-G-------------v~~eAlLR~~DVi 74 (80)
T PF11095_consen 16 LRSLLAMV--GKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-----TPL-G-------------VQPEALLRCSDVI 74 (80)
T ss_dssp HHHHHHCT--TSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-----TTT-T-------------EEEEEEEEGGGEE
T ss_pred HHHHHHhc--CCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-----CCc-c-------------cChhheeecCCEE
Confidence 44556666 9999999999999999999999876 55555422 121 1 2578999999999
Q ss_pred EEEeC
Q 033904 103 IVLRN 107 (109)
Q Consensus 103 ~I~~~ 107 (109)
.++..
T Consensus 75 ~~~f~ 79 (80)
T PF11095_consen 75 SISFD 79 (80)
T ss_dssp EEEE-
T ss_pred EEEec
Confidence 99864
No 53
>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=90.98 E-value=2.4 Score=27.11 Aligned_cols=69 Identities=19% Similarity=0.300 Sum_probs=48.5
Q ss_pred HhhhCCcEEEEEecCCeEEEEEEEEecCccc-eeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEE
Q 033904 29 MSVKNNTQVLINCRNNKKLLGRVRAFDRHCN-MVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 103 (109)
Q Consensus 29 ~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mN-lvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~ 103 (109)
.++ |++|.+..+.+-.|.|.|.++|..=. +.|.||..+.++.++.+ .. ...+ ...-...++.||+.|--
T Consensus 3 ~~I--G~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~-~~-~ipp--~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYI--GSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTD-GP-EIPP--SDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccc--CceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCC-CC-ccCC--CCcceeEEEEcCCcccc
Confidence 466 99999999999999999999998874 56999888776532211 10 0001 11235789999998753
No 54
>PRK02001 hypothetical protein; Validated
Probab=90.73 E-value=0.49 Score=33.98 Aligned_cols=33 Identities=18% Similarity=0.408 Sum_probs=27.5
Q ss_pred HHHhhhCCcEEEEEecCCeEEEEEEEEecCccceee
Q 033904 27 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL 62 (109)
+.+++ |+.|+|.+.+++.|.|+|.++|.- ++.|
T Consensus 85 f~r~~--G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 85 YKKNI--GRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred HHHhC--CCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 45566 999999999999999999999974 4444
No 55
>PRK14639 hypothetical protein; Provisional
Probab=90.69 E-value=0.51 Score=33.30 Aligned_cols=33 Identities=24% Similarity=0.420 Sum_probs=27.7
Q ss_pred HHHhhhCCcEEEEEecCCeEEEEEEEEecCccceee
Q 033904 27 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL 62 (109)
+.+++ |+.|+|.+.+++.+.|+|.++|.- ++.|
T Consensus 83 f~r~~--G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 83 FAKSI--GELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHhC--CCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 55666 999999999999999999999983 4555
No 56
>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=90.39 E-value=0.73 Score=33.69 Aligned_cols=43 Identities=28% Similarity=0.366 Sum_probs=31.7
Q ss_pred CCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCcc-ceeeeeeEE
Q 033904 21 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHC-NMVLENVRE 67 (109)
Q Consensus 21 ~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~m-NlvL~d~~E 67 (109)
.+|+. +..++ +|.|+|.+.+ +++.|.|..+|.=- |+||-+-.|
T Consensus 7 ~~p~~-~~~yv--~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 7 KSPLE-WQDYV--GKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp S-HHH-HHCTT--T-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred CCHHH-HHHhh--CcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 46766 66778 9999999999 99999999999865 888876554
No 57
>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=89.16 E-value=0.69 Score=33.58 Aligned_cols=35 Identities=6% Similarity=0.182 Sum_probs=30.8
Q ss_pred CcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecC
Q 033904 22 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDR 56 (109)
Q Consensus 22 ~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~ 56 (109)
.=++...++-++|+-|+|++.|||+++|.=.|.|.
T Consensus 108 DFF~Icrka~qqg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 108 DFFSICRKAHQQGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred hHHHHHHHHHHCCCeEEEEEcCCcEEEeeecccce
Confidence 33778888999999999999999999999888774
No 58
>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=88.77 E-value=0.44 Score=31.95 Aligned_cols=27 Identities=19% Similarity=0.286 Sum_probs=19.7
Q ss_pred HHHHHhhhCCcEEEEEecCCeEEEEEE
Q 033904 25 SVLMMSVKNNTQVLINCRNNKKLLGRV 51 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr~gr~i~G~L 51 (109)
.-|...+..+.+|.+.|+||+.+.|++
T Consensus 19 E~lv~~L~ge~~V~l~L~DGs~l~Gtv 45 (101)
T PF11607_consen 19 EHLVSELDGEERVELELDDGSMLRGTV 45 (101)
T ss_dssp HHHHHCTTTT-EEEEEETTS-EEEEEE
T ss_pred HHHHhhcCCcceEEEEEcCCCeeeeee
Confidence 344455556889999999999999987
No 59
>PRK14644 hypothetical protein; Provisional
Probab=86.77 E-value=1.5 Score=30.87 Aligned_cols=34 Identities=9% Similarity=0.167 Sum_probs=27.8
Q ss_pred HHHhhhCCcEEEEEecCC----eEEEEEEEEecCccceeee
Q 033904 27 LMMSVKNNTQVLINCRNN----KKLLGRVRAFDRHCNMVLE 63 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~g----r~i~G~L~~fD~~mNlvL~ 63 (109)
+.+++ |+.|.|.|++. +.+.|+|.++|.. ++.|.
T Consensus 80 f~r~~--G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 80 LENHI--GEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHhC--CCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 66777 99999999876 8999999999983 45454
No 60
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=85.99 E-value=2 Score=27.32 Aligned_cols=33 Identities=18% Similarity=0.278 Sum_probs=25.6
Q ss_pred HHHhhhCCcEEEEEec---CC-eEEEEEEEEecCccceee
Q 033904 27 LMMSVKNNTQVLINCR---NN-KKLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr---~g-r~i~G~L~~fD~~mNlvL 62 (109)
+..++ |+.|.|.++ +| +.+.|.|.++|.- ++.|
T Consensus 20 ~~r~~--G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 20 FERAV--GKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred HHHhC--CCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 45566 999999998 55 6899999999983 4444
No 61
>PRK14640 hypothetical protein; Provisional
Probab=85.44 E-value=1.9 Score=30.79 Aligned_cols=34 Identities=21% Similarity=0.346 Sum_probs=26.6
Q ss_pred HHHhhhCCcEEEEEec----CCeEEEEEEEEecCccceeee
Q 033904 27 LMMSVKNNTQVLINCR----NNKKLLGRVRAFDRHCNMVLE 63 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr----~gr~i~G~L~~fD~~mNlvL~ 63 (109)
+.+++ |+.|.|.++ +.+.++|+|.++|.. ++.|.
T Consensus 92 f~r~~--G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 92 FEKYV--GQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred HHHhC--CCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 45666 999999994 568999999999984 44443
No 62
>PRK14636 hypothetical protein; Provisional
Probab=84.58 E-value=2 Score=31.53 Aligned_cols=35 Identities=11% Similarity=0.221 Sum_probs=26.9
Q ss_pred HHHHhhhCCcEEEEEec---CC-eEEEEEEEEecCccceeee
Q 033904 26 VLMMSVKNNTQVLINCR---NN-KKLLGRVRAFDRHCNMVLE 63 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr---~g-r~i~G~L~~fD~~mNlvL~ 63 (109)
-+.+++ |+.|+|.|+ +| +.|+|+|.++|.- ++.|.
T Consensus 92 df~r~~--G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~ 130 (176)
T PRK14636 92 DFADWA--GHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA 130 (176)
T ss_pred HHHHhC--CCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence 355666 999999998 45 6999999999883 45543
No 63
>PRK14642 hypothetical protein; Provisional
Probab=84.13 E-value=2.2 Score=32.03 Aligned_cols=34 Identities=21% Similarity=0.244 Sum_probs=26.7
Q ss_pred CcHHH---HHHhhhCCcEEEEEec-------------CCeEEEEEEEEecCc
Q 033904 22 GPLSV---LMMSVKNNTQVLINCR-------------NNKKLLGRVRAFDRH 57 (109)
Q Consensus 22 ~Pl~~---L~~~~~~~krV~V~Lr-------------~gr~i~G~L~~fD~~ 57 (109)
.||.- +.+++ |+.|.|.|+ +.+.|+|+|.++|..
T Consensus 87 RPLk~~~df~rfi--G~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 87 RPLRHEQDFERFA--GEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG 136 (197)
T ss_pred CCCCCHHHHHHhC--CCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence 45443 44555 999999998 678999999999984
No 64
>PRK14633 hypothetical protein; Provisional
Probab=84.06 E-value=2.4 Score=30.23 Aligned_cols=34 Identities=18% Similarity=0.201 Sum_probs=26.4
Q ss_pred HHHhhhCCcEEEEEec----CCeEEEEEEEEecCccceeee
Q 033904 27 LMMSVKNNTQVLINCR----NNKKLLGRVRAFDRHCNMVLE 63 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr----~gr~i~G~L~~fD~~mNlvL~ 63 (109)
+.+++ |+.|.|.++ +.+.|+|+|.++|.. ++.|.
T Consensus 89 f~r~~--G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 89 AQALV--GFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHHhC--CCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 45566 999999995 568999999999985 44453
No 65
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.95 E-value=2.4 Score=30.59 Aligned_cols=38 Identities=24% Similarity=0.378 Sum_probs=30.0
Q ss_pred CcHH---HHHHhhhCCcEEEEEe----cCCeEEEEEEEEecCccceee
Q 033904 22 GPLS---VLMMSVKNNTQVLINC----RNNKKLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 22 ~Pl~---~L~~~~~~~krV~V~L----r~gr~i~G~L~~fD~~mNlvL 62 (109)
.||. -+..+. |+.|.|+| .+.+.+.|+|.++|.-. +++
T Consensus 86 RpL~~~~~f~r~~--G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 86 RPLKTAEHFARFI--GEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred CCcCCHHHHHHhc--CcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 4544 455666 99999999 67899999999999987 444
No 66
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=83.28 E-value=2.3 Score=29.59 Aligned_cols=35 Identities=14% Similarity=0.251 Sum_probs=25.2
Q ss_pred HHHHHhhhCCcEEEEEec----CCeEEEEEEEEecCccceee
Q 033904 25 SVLMMSVKNNTQVLINCR----NNKKLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 25 ~~L~~~~~~~krV~V~Lr----~gr~i~G~L~~fD~~mNlvL 62 (109)
.-+.+++ |+.|.|+++ +.+.+.|+|.++|. =.++|
T Consensus 80 ~~~~~~i--G~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 80 RDFERFI--GRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHHH---SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHHhc--CCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 3567788 999999995 45789999999999 33444
No 67
>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=83.09 E-value=2.7 Score=30.55 Aligned_cols=35 Identities=20% Similarity=0.131 Sum_probs=31.4
Q ss_pred hCCcEEEEEecCCeEEEEEEEEecCccceeeeeeE
Q 033904 32 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 66 (109)
Q Consensus 32 ~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~ 66 (109)
..+-+|+|.+-||..|.|++.+|+.-=|++|.-+.
T Consensus 27 ~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 27 FNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred hcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 34789999999999999999999999999997654
No 68
>PRK14645 hypothetical protein; Provisional
Probab=82.62 E-value=2.6 Score=30.21 Aligned_cols=32 Identities=9% Similarity=0.227 Sum_probs=25.0
Q ss_pred HHHhhhCCcEEEEEecCCeEEEEEEEEecCccceee
Q 033904 27 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL 62 (109)
+.+++ |+.|.|.+ +++.+.|+|.++|.- .+.|
T Consensus 97 f~r~~--G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 97 FERFA--GLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred HHHhC--CCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 44556 99999976 789999999999984 3444
No 69
>PRK14643 hypothetical protein; Provisional
Probab=82.53 E-value=2.8 Score=30.40 Aligned_cols=30 Identities=23% Similarity=0.352 Sum_probs=25.0
Q ss_pred HHHHhhhCCcEEEEEecC----CeEEEEEEEEecCc
Q 033904 26 VLMMSVKNNTQVLINCRN----NKKLLGRVRAFDRH 57 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr~----gr~i~G~L~~fD~~ 57 (109)
-+.+++ |+.|.|.|+. .+.+.|+|.++|.-
T Consensus 98 df~r~~--G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 98 ELVKAL--NQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHhc--CCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 355677 9999999975 58899999999875
No 70
>PRK14632 hypothetical protein; Provisional
Probab=82.22 E-value=2.9 Score=30.49 Aligned_cols=34 Identities=21% Similarity=0.319 Sum_probs=26.2
Q ss_pred HHHhhhCCcEEEEEecC-------CeEEEEEEEEecCccceeee
Q 033904 27 LMMSVKNNTQVLINCRN-------NKKLLGRVRAFDRHCNMVLE 63 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~-------gr~i~G~L~~fD~~mNlvL~ 63 (109)
+.+++ |+.|.|.|++ .+.|.|+|.++|.- ++.|.
T Consensus 93 f~r~i--G~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 93 MSPYV--GRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHHhC--CCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 45666 9999999986 57999999999863 44443
No 71
>PRK14634 hypothetical protein; Provisional
Probab=81.42 E-value=3.4 Score=29.61 Aligned_cols=33 Identities=12% Similarity=0.196 Sum_probs=25.6
Q ss_pred HHHhhhCCcEEEEEecC----CeEEEEEEEEecCccceee
Q 033904 27 LMMSVKNNTQVLINCRN----NKKLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~----gr~i~G~L~~fD~~mNlvL 62 (109)
+.+++ |+.|+|.++. .+.|.|+|.++|.- ++.|
T Consensus 95 f~r~~--G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 95 FQTFR--GFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred HHHhC--CCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 55666 9999999974 27899999999984 4444
No 72
>PRK14646 hypothetical protein; Provisional
Probab=81.34 E-value=3.4 Score=29.60 Aligned_cols=34 Identities=12% Similarity=0.053 Sum_probs=26.4
Q ss_pred HHHHhhhCCcEEEEEecCC----eEEEEEEEEecCccceee
Q 033904 26 VLMMSVKNNTQVLINCRNN----KKLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr~g----r~i~G~L~~fD~~mNlvL 62 (109)
=+.+++ |+.|+|.|++. +.+.|+|.++|.- ++.|
T Consensus 94 df~r~~--G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 94 DFKTFK--GFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHHhC--CCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 355666 99999999753 6889999999984 4555
No 73
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=80.65 E-value=3.7 Score=29.07 Aligned_cols=29 Identities=21% Similarity=0.218 Sum_probs=24.3
Q ss_pred HHHHhhhCCcEEEEEe----cCCeEEEEEEEEecC
Q 033904 26 VLMMSVKNNTQVLINC----RNNKKLLGRVRAFDR 56 (109)
Q Consensus 26 ~L~~~~~~~krV~V~L----r~gr~i~G~L~~fD~ 56 (109)
-+.+++ |+.|+|.+ .+++.+.|+|.++|.
T Consensus 92 ~f~r~~--G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 92 DFRRFI--GREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHhC--CCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 356667 99999997 467899999999998
No 74
>PRK14647 hypothetical protein; Provisional
Probab=78.99 E-value=4.4 Score=29.02 Aligned_cols=28 Identities=14% Similarity=0.188 Sum_probs=23.3
Q ss_pred HHHhhhCCcEEEEEec---------CCeEEEEEEEEecC
Q 033904 27 LMMSVKNNTQVLINCR---------NNKKLLGRVRAFDR 56 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr---------~gr~i~G~L~~fD~ 56 (109)
+.+++ |+.|.|.++ +.+.|.|+|.++|.
T Consensus 94 f~r~~--G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 94 YERYA--GRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHhC--CcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 45566 999999996 34899999999997
No 75
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=77.53 E-value=6.9 Score=24.41 Aligned_cols=34 Identities=12% Similarity=0.160 Sum_probs=26.5
Q ss_pred cCCCc--HHHHHHhhhCCcEEEEEecCCeEEEEEEEEec
Q 033904 19 FNTGP--LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFD 55 (109)
Q Consensus 19 ~~~~P--l~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD 55 (109)
+..+| ...|++.+ |++|.|.+-.|.. +|+|.+.-
T Consensus 6 s~vdpyvyq~lq~li--G~~vvV~T~~g~v-~G~L~~V~ 41 (66)
T PF10842_consen 6 SLVDPYVYQTLQSLI--GQRVVVQTTRGSV-RGILVDVK 41 (66)
T ss_pred eccCHHHHHHHHHhc--CCEEEEEEcCCcE-EEEEEeec
Confidence 34566 56789999 9999999976654 99998753
No 76
>PRK14631 hypothetical protein; Provisional
Probab=76.06 E-value=5.7 Score=29.06 Aligned_cols=28 Identities=25% Similarity=0.288 Sum_probs=23.5
Q ss_pred HHHHhhhCCcEEEEEec----CCeEEEEEEEEec
Q 033904 26 VLMMSVKNNTQVLINCR----NNKKLLGRVRAFD 55 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr----~gr~i~G~L~~fD 55 (109)
-+.+++ |+.|.|.|. +.+.|+|+|.++|
T Consensus 111 df~r~~--G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 111 QLQGYI--GQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHhC--CCeEEEEEecccCCceEEEEEEEEee
Confidence 355666 999999996 4589999999998
No 77
>PRK14637 hypothetical protein; Provisional
Probab=75.53 E-value=5.5 Score=28.46 Aligned_cols=34 Identities=18% Similarity=0.240 Sum_probs=25.1
Q ss_pred HHHhhhCCcEEEEEecCCeEE-EEEEEEecCccceeee
Q 033904 27 LMMSVKNNTQVLINCRNNKKL-LGRVRAFDRHCNMVLE 63 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~gr~i-~G~L~~fD~~mNlvL~ 63 (109)
+.+++ |+.|.|.+.+.+.+ +|+|.++|.- ++.|.
T Consensus 93 f~r~~--G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 93 FSIFV--GETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHhC--CCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 45556 99999999555566 7999999985 44443
No 78
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=75.06 E-value=3.4 Score=23.66 Aligned_cols=22 Identities=23% Similarity=0.327 Sum_probs=15.2
Q ss_pred EEEEEEEecCccceeeeeeEEe
Q 033904 47 LLGRVRAFDRHCNMVLENVREM 68 (109)
Q Consensus 47 i~G~L~~fD~~mNlvL~d~~E~ 68 (109)
.+|+.+|.|+.+.|.|++....
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 6899999999999999987654
No 79
>PRK14641 hypothetical protein; Provisional
Probab=73.70 E-value=6.4 Score=28.83 Aligned_cols=27 Identities=11% Similarity=0.255 Sum_probs=22.2
Q ss_pred HHHhhhCCcEEEEEecC----CeEEEEEEEEec
Q 033904 27 LMMSVKNNTQVLINCRN----NKKLLGRVRAFD 55 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~----gr~i~G~L~~fD 55 (109)
+.+++ |+.|.|.|.+ .+.++|+|.++|
T Consensus 99 f~r~~--G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 99 YGRHV--GRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHhC--CCEEEEEEecccCCeEEEEEEEEeee
Confidence 45556 9999999976 468999999995
No 80
>PRK10898 serine endoprotease; Provisional
Probab=66.97 E-value=13 Score=29.69 Aligned_cols=33 Identities=6% Similarity=0.205 Sum_probs=29.3
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceeeeeeE
Q 033904 34 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 66 (109)
Q Consensus 34 ~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~ 66 (109)
...+.|.+.+|+.+.+.++++|...+|.|=.+.
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 467999999999999999999999999886654
No 81
>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=65.76 E-value=14 Score=29.43 Aligned_cols=33 Identities=9% Similarity=0.264 Sum_probs=29.1
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceeeeeeE
Q 033904 34 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 66 (109)
Q Consensus 34 ~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~ 66 (109)
...+.|.+.+|+.+.++++++|...+|.|=.+.
T Consensus 101 ~~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 101 ADQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 457899999999999999999999999986654
No 82
>PRK10139 serine endoprotease; Provisional
Probab=63.65 E-value=18 Score=30.00 Aligned_cols=34 Identities=9% Similarity=0.278 Sum_probs=30.1
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceeeeeeE
Q 033904 33 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 66 (109)
Q Consensus 33 ~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~ 66 (109)
....|.|.+.||+.+.++++++|....|.+=.+.
T Consensus 113 ~a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 113 QAQKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CCCEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 4668999999999999999999999999886654
No 83
>PRK10942 serine endoprotease; Provisional
Probab=61.75 E-value=19 Score=30.06 Aligned_cols=32 Identities=16% Similarity=0.295 Sum_probs=28.8
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceeeeee
Q 033904 34 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 65 (109)
Q Consensus 34 ~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~ 65 (109)
...|.|.+.||+.+.++++++|...+|.|=.+
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 56799999999999999999999999988754
No 84
>PRK06955 biotin--protein ligase; Provisional
Probab=59.91 E-value=32 Score=26.84 Aligned_cols=32 Identities=13% Similarity=0.223 Sum_probs=27.6
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceeeee
Q 033904 33 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 64 (109)
Q Consensus 33 ~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d 64 (109)
.+++|+|...+++.+.|++.++|..-.|++++
T Consensus 248 ~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 248 AGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred CCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 38999997666778999999999999999964
No 85
>PRK14630 hypothetical protein; Provisional
Probab=55.07 E-value=24 Score=24.92 Aligned_cols=32 Identities=6% Similarity=0.077 Sum_probs=23.6
Q ss_pred HHHhhhCCcEEEEEecCCeEEEEEEEEecCccceee
Q 033904 27 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL 62 (109)
+.+++ |+.|+|.+.+. ...|+|.++|.- ++.|
T Consensus 92 f~r~~--G~~v~V~l~~~-~~~G~L~~~~d~-~i~l 123 (143)
T PRK14630 92 FKIFE--GKKIKLMLDND-FEEGFILEAKAD-SFIF 123 (143)
T ss_pred HHHhC--CCEEEEEEcCc-ceEEEEEEEeCC-EEEE
Confidence 45566 99999999654 459999999883 3444
No 86
>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=55.01 E-value=49 Score=20.55 Aligned_cols=38 Identities=16% Similarity=0.202 Sum_probs=29.9
Q ss_pred HHHHhhhCCcEEEEEecCC---eEEEEEEEEecCccceeee
Q 033904 26 VLMMSVKNNTQVLINCRNN---KKLLGRVRAFDRHCNMVLE 63 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr~g---r~i~G~L~~fD~~mNlvL~ 63 (109)
.|..++..+..|+|..-++ ..++|++..+|..-+.+.-
T Consensus 34 ~l~~a~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~ 74 (92)
T PF08863_consen 34 KLSEAYQENQPVTITYYEDGYYQSVTGTIHKIDEINRTLKL 74 (92)
T ss_pred HHHHHhcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEE
Confidence 5777777788898888765 4688999999999876553
No 87
>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=54.56 E-value=25 Score=28.56 Aligned_cols=33 Identities=3% Similarity=0.234 Sum_probs=29.3
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceeeeeeE
Q 033904 34 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 66 (109)
Q Consensus 34 ~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~ 66 (109)
...+.|.+.+|+.+.++++++|.+.+|.|=.+.
T Consensus 81 ~~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 81 ADEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CCeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 457899999999999999999999999887654
No 88
>PRK14635 hypothetical protein; Provisional
Probab=53.72 E-value=28 Score=24.99 Aligned_cols=33 Identities=21% Similarity=0.127 Sum_probs=24.4
Q ss_pred HHHhhhCCcEEEEEec--CCeEEEE---EEEEecCccceee
Q 033904 27 LMMSVKNNTQVLINCR--NNKKLLG---RVRAFDRHCNMVL 62 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr--~gr~i~G---~L~~fD~~mNlvL 62 (109)
+.++. |+.|.|.+. ++..+.| .|.++|.- ++.|
T Consensus 94 ~~r~~--G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 94 LDRFR--GIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHHhC--CCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 45566 999999886 4577887 99999874 4444
No 89
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=47.70 E-value=61 Score=25.16 Aligned_cols=30 Identities=23% Similarity=0.374 Sum_probs=26.1
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceeee
Q 033904 33 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLE 63 (109)
Q Consensus 33 ~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~ 63 (109)
.|++|++.. ++..++|++.+.|..-.|+|.
T Consensus 271 ~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 271 LGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred cCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 389999986 446799999999999999996
No 90
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=45.95 E-value=12 Score=26.80 Aligned_cols=26 Identities=19% Similarity=0.280 Sum_probs=19.4
Q ss_pred CCeEEEEEEEEecCccceeeeeeEEe
Q 033904 43 NNKKLLGRVRAFDRHCNMVLENVREM 68 (109)
Q Consensus 43 ~gr~i~G~L~~fD~~mNlvL~d~~E~ 68 (109)
.+-.=.|+|+|.|+|-|=.-+|-.-+
T Consensus 41 td~~kiGTLVG~DkfGNkYyen~~~f 66 (151)
T KOG3382|consen 41 TDDHKIGTLVGVDKFGNKYYENNDYF 66 (151)
T ss_pred cccccceeeeeecccccchhccccee
Confidence 33445689999999999888776433
No 91
>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=45.16 E-value=9.9 Score=25.40 Aligned_cols=17 Identities=29% Similarity=0.284 Sum_probs=15.3
Q ss_pred EEEEEecCccceeeeee
Q 033904 49 GRVRAFDRHCNMVLENV 65 (109)
Q Consensus 49 G~L~~fD~~mNlvL~d~ 65 (109)
|+|+|.|.|-|..-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 88999999999988775
No 92
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=44.78 E-value=32 Score=25.47 Aligned_cols=34 Identities=12% Similarity=0.215 Sum_probs=23.8
Q ss_pred HHHHHHhhhCCcEEEEEec-CCeEEEEEEEEecCc
Q 033904 24 LSVLMMSVKNNTQVLINCR-NNKKLLGRVRAFDRH 57 (109)
Q Consensus 24 l~~L~~~~~~~krV~V~Lr-~gr~i~G~L~~fD~~ 57 (109)
++||-...-+--+|.+.+. ++..|+|+|+++|.=
T Consensus 123 I~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 3455555544456666665 578999999999975
No 93
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=44.58 E-value=67 Score=26.34 Aligned_cols=75 Identities=17% Similarity=0.244 Sum_probs=50.4
Q ss_pred HHHhhhCCcEEEEEecCCeEEEEEEEEecCc-cceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEEE
Q 033904 27 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRH-CNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 105 (109)
Q Consensus 27 L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~-mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I~ 105 (109)
...++ |+.|-+.-+.+-.|+|+|--.|-. .=|-|.+|.-+.++.+++..... -+. .+ -..-|+.||+.|-.+.
T Consensus 4 ~t~yI--GS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~--p~~-~k-Vy~YIlFRGSDIKDL~ 77 (361)
T KOG1073|consen 4 VTSYI--GSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQV--PPD-DK-VYDYILFRGSDIKDLI 77 (361)
T ss_pred ccccc--cceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcC--CCC-cc-ceeeEEecCcccceee
Confidence 34577 999999999999999999877743 45778888776665333221110 011 11 3578999999998665
Q ss_pred eC
Q 033904 106 RN 107 (109)
Q Consensus 106 ~~ 107 (109)
..
T Consensus 78 V~ 79 (361)
T KOG1073|consen 78 VQ 79 (361)
T ss_pred ec
Confidence 43
No 94
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=44.58 E-value=28 Score=22.37 Aligned_cols=18 Identities=11% Similarity=0.320 Sum_probs=12.5
Q ss_pred CCcEEEEEecCCeEEEEE
Q 033904 33 NNTQVLINCRNNKKLLGR 50 (109)
Q Consensus 33 ~~krV~V~Lr~gr~i~G~ 50 (109)
.+.+|++.|+||..+.|+
T Consensus 16 ~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 16 YRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp TTT-EEEE-TTT--EEES
T ss_pred cCCeEEEEEeCCCEEEEE
Confidence 477899999999999996
No 95
>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=44.41 E-value=85 Score=23.34 Aligned_cols=30 Identities=23% Similarity=0.382 Sum_probs=26.0
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceeee
Q 033904 33 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLE 63 (109)
Q Consensus 33 ~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~ 63 (109)
.+++|+|... +..+.|+..+.|..-.|+|+
T Consensus 192 ~g~~V~v~~~-~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 192 IGREVSLTTG-NGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred cCCeEEEEeC-CcEEEEEEEeECCCceEEEE
Confidence 3899999864 46799999999999999996
No 96
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=43.94 E-value=83 Score=24.41 Aligned_cols=31 Identities=19% Similarity=0.411 Sum_probs=26.8
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceeeee
Q 033904 33 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 64 (109)
Q Consensus 33 ~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d 64 (109)
.+++|+|.. ++..+.|++.+.|..-.|+|..
T Consensus 236 ~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 236 KDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred CCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 389999875 5688999999999999999974
No 97
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=42.63 E-value=52 Score=28.38 Aligned_cols=31 Identities=23% Similarity=0.288 Sum_probs=27.2
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceeeee
Q 033904 34 NTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 64 (109)
Q Consensus 34 ~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d 64 (109)
|++|++...++..+.|+.++.|..-.|+|..
T Consensus 278 gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 278 GKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred CCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 8899987666778999999999999999964
No 98
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=39.32 E-value=1.2e+02 Score=23.13 Aligned_cols=34 Identities=15% Similarity=0.169 Sum_probs=30.6
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceeeeeeE
Q 033904 33 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 66 (109)
Q Consensus 33 ~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~ 66 (109)
-+++|++...++..+.|+..+.|..-.|+|+...
T Consensus 189 ~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~~ 222 (238)
T COG0340 189 LGKEVRLTLGGGVIFGGIAKGIDEDGALLLETDD 222 (238)
T ss_pred CCCEEEEEeCCCcEeeeEEEEECCCceEEEEeCC
Confidence 4899999999888999999999999999998763
No 99
>PRK08330 biotin--protein ligase; Provisional
Probab=38.65 E-value=85 Score=23.36 Aligned_cols=32 Identities=19% Similarity=0.157 Sum_probs=26.0
Q ss_pred CCcEEEEEecCCeEE-EEEEEEecCccceeeeee
Q 033904 33 NNTQVLINCRNNKKL-LGRVRAFDRHCNMVLENV 65 (109)
Q Consensus 33 ~~krV~V~Lr~gr~i-~G~L~~fD~~mNlvL~d~ 65 (109)
.+++|.+.. ++..+ .|+..+.|..-.|++...
T Consensus 187 ~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 187 LGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred cCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence 389999875 55565 699999999999999753
No 100
>PF02604 PhdYeFM_antitox: Antitoxin Phd_YefM, type II toxin-antitoxin system; InterPro: IPR006442 This entry is represented by Bacteriophage P1, prevent-host-death protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins is characterised by a region of about 55 amino acids toward the N-terminal end of bacterial proteins which are themselves only 85 amino acids, or thereabouts, in length. The best-characterised member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (IPR006440 from INTERPRO) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. ; PDB: 3DBO_A 2ODK_B 3G5O_D 2A6Q_B 3D55_C 3OEI_E 3CTO_C 3K33_D 3KH2_F 3HS2_C ....
Probab=37.66 E-value=26 Score=21.07 Aligned_cols=43 Identities=16% Similarity=0.143 Sum_probs=29.3
Q ss_pred ccccCCCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccce
Q 033904 16 EEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNM 60 (109)
Q Consensus 16 ~~~~~~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNl 60 (109)
..++...+-.+++.....+.+| +.+++|+. .+.|+++++|=++
T Consensus 6 ~~e~r~~~~~~l~~v~~~~~pv-~It~~g~~-~~vli~~~~ye~l 48 (75)
T PF02604_consen 6 ITEFRNNFSELLDEVEEGEEPV-IITKNGKP-VAVLISVEDYERL 48 (75)
T ss_dssp HHHHHHTHHHHHHHHHHCT-EE-EEEETTEE-EEEEEEHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCCeE-EEEECCCC-CeecccHHHHHHH
Confidence 3445567778888888665667 45677776 7888888776543
No 101
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=37.23 E-value=73 Score=20.32 Aligned_cols=33 Identities=12% Similarity=0.137 Sum_probs=21.5
Q ss_pred HHHHhhhCCcEEEEEecCCe----EEEEEEEEecCccceee
Q 033904 26 VLMMSVKNNTQVLINCRNNK----KLLGRVRAFDRHCNMVL 62 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr~gr----~i~G~L~~fD~~mNlvL 62 (109)
-|..++ |++|.+..+.|| +-.|.|... |=|+..
T Consensus 11 ~l~~~v--G~~V~l~a~~GRkK~~~r~GvL~~t--YPsvFv 47 (76)
T PF06257_consen 11 ELESHV--GKRVKLKANKGRKKIIEREGVLEET--YPSVFV 47 (76)
T ss_dssp HHHHTT--TSEEEEEE--SSS--S-EEEEEEEE---SSEEE
T ss_pred HHHHcC--CCEEEEEEcCCceEEEEEEEEEEee--cCcEEE
Confidence 467778 999999999997 467988643 334443
No 102
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=35.80 E-value=40 Score=22.12 Aligned_cols=21 Identities=29% Similarity=0.523 Sum_probs=19.2
Q ss_pred eeeeceEEEeCCcEEEEEeCC
Q 033904 88 DRFISKMFLRGDSVIIVLRNP 108 (109)
Q Consensus 88 ~r~lg~i~IRGdnVv~I~~~p 108 (109)
.|+-|.+.++|..+..|..+|
T Consensus 76 ~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 76 DRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred hcceEEEEEECCeeeEEEcCC
Confidence 478899999999999999888
No 103
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=33.62 E-value=57 Score=22.23 Aligned_cols=20 Identities=15% Similarity=0.178 Sum_probs=17.4
Q ss_pred EEEEEecCCeEEEEEEEEec
Q 033904 36 QVLINCRNNKKLLGRVRAFD 55 (109)
Q Consensus 36 rV~V~Lr~gr~i~G~L~~fD 55 (109)
...|.++||+.+.|.+++=|
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET 78 (133)
T ss_pred cEEEEECCCCEEEEEEEecC
Confidence 48899999999999998844
No 104
>PRK11625 Rho-binding antiterminator; Provisional
Probab=30.85 E-value=1.3e+02 Score=19.47 Aligned_cols=26 Identities=8% Similarity=0.239 Sum_probs=19.8
Q ss_pred HHHHhhhCCcEEEEEecCCeEEEEEE
Q 033904 26 VLMMSVKNNTQVLINCRNNKKLLGRV 51 (109)
Q Consensus 26 ~L~~~~~~~krV~V~Lr~gr~i~G~L 51 (109)
.|.-+.-.+.+|.+.|++|..+.|+.
T Consensus 15 yLElAC~~~~~l~l~l~dGe~~~g~A 40 (84)
T PRK11625 15 NLELACQHHLMLTLELKDGEVLQAKA 40 (84)
T ss_pred HHHHHHhcCCeEEEEECCCCEEEEEE
Confidence 34444445789999999999999975
No 105
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=30.68 E-value=61 Score=21.38 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=11.6
Q ss_pred CcEEEEE-ecCCeEEEEEEEE
Q 033904 34 NTQVLIN-CRNNKKLLGRVRA 53 (109)
Q Consensus 34 ~krV~V~-Lr~gr~i~G~L~~ 53 (109)
|..|+|. +.+|+.+.|++.+
T Consensus 96 G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 96 GDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred CCEEEEEECCCCCEEEEEEeC
Confidence 5556666 5566666665543
No 106
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=30.42 E-value=1.7e+02 Score=24.55 Aligned_cols=64 Identities=16% Similarity=0.041 Sum_probs=48.0
Q ss_pred cccccccCccccccc--cCCCcHHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeeeeEEeee
Q 033904 4 AMDEDTTGGKTEEEE--FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWT 70 (109)
Q Consensus 4 ~~~~~~~~~~~e~~~--~~~~Pl~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~E~~~ 70 (109)
||.+++.+.-.|++- -...|-.++++++ ||.|+- =++|++.+++|.+-|.-.=+.+.|-.|...
T Consensus 52 a~~~~~~~~~~eqn~~y~l~s~~~l~~~~~--GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~~ 117 (421)
T COG5316 52 AAVEGLPGKALEQNYDYDLLSPGKLVEKSL--GKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVLG 117 (421)
T ss_pred hhhcCCcceeecccccccccCchhHHhhhh--CcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEEe
Confidence 566676654444331 1346888999999 999998 789999999999999888777777766653
No 107
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=29.94 E-value=1.1e+02 Score=18.43 Aligned_cols=25 Identities=16% Similarity=0.295 Sum_probs=18.1
Q ss_pred CCcEEEEEecCCeE-EEEEEEEecCc
Q 033904 33 NNTQVLINCRNNKK-LLGRVRAFDRH 57 (109)
Q Consensus 33 ~~krV~V~Lr~gr~-i~G~L~~fD~~ 57 (109)
.|.+|.++=-++.. |.|.+.+||.-
T Consensus 8 ~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 8 IGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred CCCEEEEECCCCCcEEEEEEEEeccc
Confidence 38899998887765 59999999973
No 108
>PRK08477 biotin--protein ligase; Provisional
Probab=25.12 E-value=2.8e+02 Score=20.61 Aligned_cols=31 Identities=3% Similarity=0.046 Sum_probs=26.3
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceeeee
Q 033904 33 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 64 (109)
Q Consensus 33 ~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d 64 (109)
.++.|+|. .+++.++|+..+.|+.--|++.-
T Consensus 174 ~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~ 204 (211)
T PRK08477 174 KSKSFSFH-IDGKLVSLKDAELLEDGSILING 204 (211)
T ss_pred cCCEEEEE-ECCEEEEEEEeeECCCCeEEECC
Confidence 48899986 57899999999999998888764
No 109
>PRK06630 hypothetical protein; Provisional
Probab=24.95 E-value=40 Score=22.74 Aligned_cols=19 Identities=16% Similarity=0.106 Sum_probs=16.6
Q ss_pred EEEEEEEecCccceeeeee
Q 033904 47 LLGRVRAFDRHCNMVLENV 65 (109)
Q Consensus 47 i~G~L~~fD~~mNlvL~d~ 65 (109)
..|.|+|-|+|-|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4799999999999988874
No 110
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=24.79 E-value=1.4e+02 Score=21.19 Aligned_cols=26 Identities=12% Similarity=0.138 Sum_probs=22.4
Q ss_pred HHhhhCCcEEEEEecCCeEEEEEEEEec
Q 033904 28 MMSVKNNTQVLINCRNNKKLLGRVRAFD 55 (109)
Q Consensus 28 ~~~~~~~krV~V~Lr~gr~i~G~L~~fD 55 (109)
..++ |+.|.+...+|..++|++.+..
T Consensus 88 ~slV--Gk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELI--GKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHh--CCEEEEEeCCCCEEEEEEEEEE
Confidence 4567 9999999899999999998875
No 111
>PF07317 YcgR: Flagellar regulator YcgR; InterPro: IPR009926 This entry represents the N-terminal domain of YcgR proteins. The function of this domain is not known, but it is known to interact with the C-terminal which has cyclic-di-GMP bound []. YcgR is involved in the flagellar motor function and is a member of the flagellar regulon [, ].; PDB: 2GJG_A 3KYF_A.
Probab=24.16 E-value=2.2e+02 Score=18.70 Aligned_cols=41 Identities=15% Similarity=0.221 Sum_probs=30.3
Q ss_pred HHHHHHhhhCCcEEEEEecCCeEEEEEEEEecCccceeeee
Q 033904 24 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 64 (109)
Q Consensus 24 l~~L~~~~~~~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d 64 (109)
..+|....+.+..|+|...+|..|.=.|.+.|.--|.++=|
T Consensus 11 ~~~Lr~L~~~~~~l~v~~~~g~~f~T~iL~VD~~~~~l~lD 51 (108)
T PF07317_consen 11 LAVLRDLAKQRSPLTVRHPRGQSFITSILAVDPDRGTLVLD 51 (108)
T ss_dssp HHHHHHHHHTT--EEEETT-SSEEEE-EEEEETTTTEEEEE
T ss_pred HHHHHHHHhCCCeEEEEeCCCCEEEEEEEEEeCCCCEEEEE
Confidence 35788888888999999888888999999999988776655
No 112
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.68 E-value=90 Score=23.44 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=15.0
Q ss_pred CcEEEEE-ecCCeEEEEEEEE
Q 033904 34 NTQVLIN-CRNNKKLLGRVRA 53 (109)
Q Consensus 34 ~krV~V~-Lr~gr~i~G~L~~ 53 (109)
|..|+|. +.+|+.+.|++.+
T Consensus 207 Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 207 GQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCeEEEEECCCCCEEEEEEeC
Confidence 6777777 7778888887654
No 113
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=21.39 E-value=61 Score=30.11 Aligned_cols=68 Identities=18% Similarity=0.178 Sum_probs=41.6
Q ss_pred CCcEEEEEecC--CeE-EEE-EEEEecCccceeeeeeEEeeeccCCCCCCccccccccceeeeceEEEeCCcEEEEEeC
Q 033904 33 NNTQVLINCRN--NKK-LLG-RVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 107 (109)
Q Consensus 33 ~~krV~V~Lr~--gr~-i~G-~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~I~~~ 107 (109)
-|.||.|.=+| |+. |.| +..+-.+|.-+||+.+..... | +....+.-.+.-..| +|||-.+|+..-.+
T Consensus 8 vG~RVevtgknl~G~VayvG~T~FA~G~WvGVvLDep~GKNn-----G-sVqg~qYF~Cd~ncG-~FVr~sq~r~lEda 79 (1243)
T KOG0971|consen 8 VGTRVEVTGKNLQGTVAYVGQTQFAEGKWVGVVLDEPKGKNN-----G-SVQGVQYFECDENCG-VFVRSSQVRELEDA 79 (1243)
T ss_pred ccceEEeccCCccceEEEecccccccCceEEEEeccccCCCC-----C-cccceeeEecCCCcc-eEeehhhhHHhhcc
Confidence 38899999777 654 667 677888888889988764321 1 111111112333445 88998886655433
No 114
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=21.18 E-value=1.8e+02 Score=22.66 Aligned_cols=33 Identities=3% Similarity=0.206 Sum_probs=28.1
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceeeeeeE
Q 033904 34 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 66 (109)
Q Consensus 34 ~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~ 66 (109)
-.++.|.+.+|+.+.+.++++|...-+.+-...
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki~ 127 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKID 127 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEec
Confidence 568899999999999999999999887765544
No 115
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.32 E-value=1.5e+02 Score=22.18 Aligned_cols=33 Identities=24% Similarity=0.264 Sum_probs=30.2
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceeeeeeE
Q 033904 34 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 66 (109)
Q Consensus 34 ~krV~V~Lr~gr~i~G~L~~fD~~mNlvL~d~~ 66 (109)
+..|.+..-++...+|.+.|||---++..-++.
T Consensus 11 g~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 11 GSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 788999999999999999999999998888777
Done!