Query 033952
Match_columns 107
No_of_seqs 103 out of 1090
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 08:08:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033952.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033952hhsearch_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 1E-28 2.2E-33 161.9 10.8 87 19-106 1-87 (87)
2 cd01730 LSm3 The eukaryotic Sm 99.9 5.4E-26 1.2E-30 147.1 9.8 82 20-104 1-82 (82)
3 cd01732 LSm5 The eukaryotic Sm 99.9 2.1E-24 4.6E-29 138.2 10.2 74 19-105 2-75 (76)
4 PRK00737 small nuclear ribonuc 99.9 3.7E-24 8E-29 135.5 9.3 71 18-104 2-72 (72)
5 cd01731 archaeal_Sm1 The archa 99.9 7.1E-24 1.5E-28 132.6 9.1 68 21-104 1-68 (68)
6 cd01726 LSm6 The eukaryotic Sm 99.9 1.3E-22 2.9E-27 126.6 8.9 67 21-103 1-67 (67)
7 cd01729 LSm7 The eukaryotic Sm 99.9 4.3E-22 9.3E-27 128.8 10.2 74 24-105 6-79 (81)
8 cd01717 Sm_B The eukaryotic Sm 99.9 4.9E-22 1.1E-26 127.6 9.7 75 24-104 4-78 (79)
9 cd01718 Sm_E The eukaryotic Sm 99.9 9.9E-22 2.2E-26 126.8 9.9 75 17-104 3-79 (79)
10 cd01722 Sm_F The eukaryotic Sm 99.9 6.1E-22 1.3E-26 124.0 8.5 68 20-103 1-68 (68)
11 cd01719 Sm_G The eukaryotic Sm 99.9 9.1E-22 2E-26 124.7 9.1 70 21-106 1-70 (72)
12 cd01728 LSm1 The eukaryotic Sm 99.9 2.1E-21 4.6E-26 123.8 10.2 71 21-104 3-73 (74)
13 cd01727 LSm8 The eukaryotic Sm 99.9 2.9E-21 6.3E-26 122.7 9.4 72 23-106 2-73 (74)
14 KOG3460 Small nuclear ribonucl 99.9 7.1E-23 1.5E-27 132.1 1.9 85 18-105 3-87 (91)
15 COG1958 LSM1 Small nuclear rib 99.9 8.2E-21 1.8E-25 121.8 9.9 75 18-104 5-79 (79)
16 PTZ00138 small nuclear ribonuc 99.8 2.5E-20 5.4E-25 122.6 10.0 77 16-105 10-88 (89)
17 PF01423 LSM: LSM domain ; In 99.8 5.7E-20 1.2E-24 113.6 9.4 66 24-104 2-67 (67)
18 cd06168 LSm9 The eukaryotic Sm 99.8 6.9E-20 1.5E-24 117.1 9.9 72 23-104 3-74 (75)
19 cd01723 LSm4 The eukaryotic Sm 99.8 7.7E-20 1.7E-24 116.8 9.1 72 20-106 1-72 (76)
20 cd01721 Sm_D3 The eukaryotic S 99.8 1E-19 2.3E-24 114.6 9.4 69 21-105 1-69 (70)
21 smart00651 Sm snRNP Sm protein 99.8 9E-20 2E-24 112.6 9.0 66 24-104 2-67 (67)
22 KOG3459 Small nuclear ribonucl 99.8 7.9E-21 1.7E-25 128.0 1.5 97 9-106 13-109 (114)
23 cd00600 Sm_like The eukaryotic 99.8 1.1E-18 2.3E-23 106.4 8.4 63 25-103 1-63 (63)
24 cd01733 LSm10 The eukaryotic S 99.8 7.3E-18 1.6E-22 108.4 9.4 76 13-104 2-77 (78)
25 cd01724 Sm_D1 The eukaryotic S 99.8 7.3E-18 1.6E-22 111.0 9.5 70 21-106 2-71 (90)
26 cd01725 LSm2 The eukaryotic Sm 99.7 1.6E-17 3.5E-22 107.3 9.4 73 20-106 1-73 (81)
27 KOG1780 Small Nuclear ribonucl 99.7 1.8E-17 4E-22 104.8 6.5 68 20-105 6-73 (77)
28 KOG3482 Small nuclear ribonucl 99.6 4.8E-16 1E-20 98.2 6.5 73 18-106 6-78 (79)
29 KOG1774 Small nuclear ribonucl 99.6 5.9E-16 1.3E-20 99.6 5.7 77 17-106 9-87 (88)
30 KOG1781 Small Nuclear ribonucl 99.6 3.9E-17 8.4E-22 108.4 0.0 75 24-106 21-95 (108)
31 KOG1775 U6 snRNA-associated Sm 99.6 4.2E-16 9.2E-21 99.3 4.3 76 17-105 4-79 (84)
32 KOG1783 Small nuclear ribonucl 99.5 1.3E-15 2.8E-20 96.2 1.4 72 18-105 4-75 (77)
33 KOG3168 U1 snRNP component [Tr 99.5 1.9E-15 4.1E-20 108.7 0.6 79 20-105 5-83 (177)
34 KOG1782 Small Nuclear ribonucl 99.5 1E-14 2.2E-19 100.2 0.2 69 25-106 14-82 (129)
35 KOG1784 Small Nuclear ribonucl 99.4 1.6E-13 3.4E-18 90.0 4.5 71 23-105 3-73 (96)
36 cd01739 LSm11_C The eukaryotic 99.3 9.9E-13 2.2E-17 81.6 2.5 45 25-69 1-49 (66)
37 KOG3293 Small nuclear ribonucl 99.3 7.7E-12 1.7E-16 86.2 5.7 72 19-105 1-72 (134)
38 KOG3448 Predicted snRNP core p 99.2 3.3E-10 7.2E-15 74.1 8.5 70 22-105 4-73 (96)
39 KOG3172 Small nuclear ribonucl 99.1 5.7E-10 1.2E-14 75.4 6.6 74 17-106 2-75 (119)
40 KOG3428 Small nuclear ribonucl 98.5 1.1E-06 2.4E-11 59.5 8.1 67 22-105 4-70 (109)
41 cd01716 Hfq Hfq, an abundant, 97.3 0.00078 1.7E-08 41.5 5.1 39 24-62 3-41 (61)
42 PF14438 SM-ATX: Ataxin 2 SM d 97.3 0.0014 3E-08 41.3 6.2 69 23-100 5-76 (77)
43 TIGR02383 Hfq RNA chaperone Hf 97.2 0.0011 2.4E-08 40.8 5.2 39 24-62 7-45 (61)
44 PRK00395 hfq RNA-binding prote 97.0 0.0021 4.5E-08 41.5 5.1 40 24-63 11-50 (79)
45 COG1923 Hfq Uncharacterized ho 96.4 0.009 1.9E-07 38.3 4.7 36 24-59 11-46 (77)
46 PF12701 LSM14: Scd6-like Sm d 95.7 0.18 3.9E-06 33.5 8.6 71 26-103 4-75 (96)
47 PRK14091 RNA-binding protein H 95.4 0.038 8.3E-07 40.1 5.1 40 24-63 96-135 (165)
48 PRK14091 RNA-binding protein H 95.4 0.041 8.8E-07 40.0 5.1 40 24-63 16-55 (165)
49 cd01735 LSm12_N LSm12 belongs 95.0 0.069 1.5E-06 32.8 4.5 32 32-63 6-37 (61)
50 PF02237 BPL_C: Biotin protein 93.7 0.24 5.3E-06 28.4 4.8 31 32-63 3-33 (48)
51 PF03614 Flag1_repress: Repres 92.0 0.26 5.7E-06 35.6 3.9 35 20-54 108-142 (165)
52 cd01736 LSm14_N LSm14 (also kn 91.7 2 4.3E-05 27.4 7.2 69 27-101 3-72 (74)
53 PRK14638 hypothetical protein; 91.4 0.4 8.6E-06 34.1 4.4 33 25-60 95-127 (150)
54 PRK14639 hypothetical protein; 89.9 0.67 1.5E-05 32.5 4.3 33 25-60 83-115 (140)
55 PRK02001 hypothetical protein; 89.7 0.68 1.5E-05 33.1 4.3 33 25-60 85-117 (152)
56 PF11095 Gemin7: Gem-associate 89.7 3.9 8.4E-05 26.4 7.5 62 22-104 16-78 (80)
57 PF06372 Gemin6: Gemin6 protei 87.6 1.2 2.6E-05 32.4 4.5 42 18-63 6-48 (166)
58 PRK14644 hypothetical protein; 85.2 2.1 4.4E-05 30.0 4.5 33 25-60 80-116 (136)
59 cd01734 YlxS_C YxlS is a Bacil 83.5 3 6.5E-05 26.4 4.4 33 25-60 20-56 (83)
60 PRK14640 hypothetical protein; 83.5 2.6 5.7E-05 29.9 4.5 33 25-60 92-128 (152)
61 PRK14642 hypothetical protein; 82.6 2.8 6E-05 31.3 4.5 29 25-55 95-136 (197)
62 PRK14636 hypothetical protein; 82.6 2.7 5.9E-05 30.6 4.4 33 25-60 93-129 (176)
63 PRK14633 hypothetical protein; 82.2 3.1 6.8E-05 29.4 4.5 33 25-60 89-125 (150)
64 PF02576 DUF150: Uncharacteris 81.6 2.9 6.2E-05 28.9 4.1 35 23-60 80-118 (141)
65 COG0779 Uncharacterized protei 81.0 3.7 7.9E-05 29.5 4.5 34 24-60 93-130 (153)
66 PRK14645 hypothetical protein; 81.0 3.4 7.3E-05 29.5 4.3 32 25-60 97-128 (154)
67 PRK14643 hypothetical protein; 80.5 3.7 8E-05 29.6 4.4 35 24-60 98-137 (164)
68 PF03614 Flag1_repress: Repres 80.3 3.8 8.2E-05 29.6 4.3 34 30-63 27-60 (165)
69 PF14563 DUF4444: Domain of un 80.2 2 4.3E-05 24.5 2.3 22 45-66 10-31 (42)
70 PRK14632 hypothetical protein; 79.6 4.1 8.8E-05 29.6 4.4 33 25-60 93-132 (172)
71 PRK14646 hypothetical protein; 79.3 4.4 9.6E-05 28.9 4.5 34 24-60 94-131 (155)
72 PRK14634 hypothetical protein; 79.2 4.5 9.8E-05 28.8 4.5 33 25-60 95-131 (155)
73 PRK00092 ribosome maturation p 77.8 5.3 0.00011 28.1 4.5 29 24-54 92-124 (154)
74 PF11607 DUF3247: Protein of u 77.3 6.1 0.00013 26.4 4.3 24 26-49 22-45 (101)
75 PRK14647 hypothetical protein; 76.4 5.9 0.00013 28.2 4.4 28 25-54 94-130 (159)
76 PRK14637 hypothetical protein; 73.4 6.8 0.00015 27.8 4.1 33 25-60 93-126 (151)
77 PRK14631 hypothetical protein; 72.8 7.9 0.00017 28.2 4.4 28 24-53 111-142 (174)
78 PRK10898 serine endoprotease; 71.3 9.4 0.0002 30.3 4.9 35 30-64 99-133 (353)
79 PRK14641 hypothetical protein; 70.6 8.5 0.00018 28.0 4.1 27 25-53 99-129 (173)
80 TIGR02038 protease_degS peripl 70.0 10 0.00022 30.0 4.8 33 32-64 101-133 (351)
81 PRK10139 serine endoprotease; 68.6 13 0.00027 30.8 5.2 34 30-63 112-145 (455)
82 PRK10942 serine endoprotease; 66.7 13 0.00029 30.8 5.0 34 30-63 133-166 (473)
83 PRK06955 biotin--protein ligas 66.2 20 0.00044 27.8 5.7 34 29-62 246-279 (300)
84 PF10842 DUF2642: Protein of u 65.4 20 0.00043 22.2 4.4 57 19-104 8-66 (66)
85 TIGR02037 degP_htrA_DO peripla 60.7 21 0.00046 28.8 5.1 35 30-64 79-113 (428)
86 KOG3382 NADH:ubiquinone oxidor 57.6 5.8 0.00013 28.2 1.1 26 40-65 40-65 (151)
87 KOG1073 Uncharacterized mRNA-a 55.1 37 0.00081 27.7 5.5 75 25-105 4-79 (361)
88 PF07073 ROF: Modulator of Rho 55.0 15 0.00032 23.5 2.6 25 24-48 9-33 (80)
89 PF08863 YolD: YolD-like prote 52.5 54 0.0012 20.3 5.4 37 24-60 34-73 (92)
90 PRK11886 bifunctional biotin-- 52.2 46 0.001 25.7 5.5 32 29-61 269-300 (319)
91 PRK14630 hypothetical protein; 52.1 29 0.00062 24.4 4.0 32 25-60 92-123 (143)
92 PRK14635 hypothetical protein; 49.0 37 0.00081 24.2 4.2 33 25-60 94-131 (162)
93 TIGR00121 birA_ligase birA, bi 49.0 63 0.0014 23.9 5.7 32 29-61 190-221 (237)
94 PTZ00275 biotin-acetyl-CoA-car 48.8 61 0.0013 25.0 5.7 32 30-62 235-266 (285)
95 PF05071 NDUFA12: NADH ubiquin 48.4 11 0.00024 25.1 1.3 17 47-63 1-17 (105)
96 COG0340 BirA Biotin-(acetyl-Co 45.0 79 0.0017 23.9 5.7 33 31-63 189-221 (238)
97 PRK11625 Rho-binding antitermi 44.4 58 0.0013 21.0 4.2 31 23-55 14-44 (84)
98 PRK13325 bifunctional biotin-- 43.1 72 0.0016 27.4 5.7 32 31-62 277-308 (592)
99 PRK08330 biotin--protein ligas 36.6 1.4E+02 0.003 22.1 5.9 32 30-62 186-218 (236)
100 PF06257 DUF1021: Protein of u 32.9 96 0.0021 19.7 3.8 26 24-51 11-40 (76)
101 PF07317 YcgR: Flagellar regul 31.3 1.5E+02 0.0033 19.3 4.9 41 22-62 11-51 (108)
102 PRK08477 biotin--protein ligas 31.1 1.9E+02 0.0041 21.4 5.8 36 26-62 169-204 (211)
103 PF11743 DUF3301: Protein of u 30.6 57 0.0012 21.3 2.6 21 86-106 76-96 (97)
104 TIGR02603 CxxCH_TIGR02603 puta 29.8 79 0.0017 21.4 3.3 27 33-59 58-85 (133)
105 PRK10708 hypothetical protein; 28.8 66 0.0014 19.6 2.4 26 31-56 3-28 (62)
106 PF02751 TFIIA_gamma_C: Transc 28.7 1.1E+02 0.0024 18.0 3.3 27 41-67 4-33 (52)
107 PF10246 MRP-S35: Mitochondria 28.2 38 0.00082 22.9 1.4 36 30-66 62-97 (104)
108 PRK09618 flgD flagellar basal 26.9 2.3E+02 0.0051 20.0 5.5 26 26-53 88-113 (142)
109 TIGR03170 flgA_cterm flagella 26.5 89 0.0019 20.5 3.0 20 32-51 96-116 (122)
110 PRK06630 hypothetical protein; 25.9 36 0.00079 22.8 1.0 19 45-63 11-29 (99)
111 smart00166 UBX Domain present 25.6 74 0.0016 19.5 2.3 24 31-54 3-26 (80)
112 smart00333 TUDOR Tudor domain. 24.6 1.4E+02 0.003 16.6 4.8 24 32-55 6-29 (57)
113 PF14153 Spore_coat_CotO: Spor 23.3 1.1E+02 0.0024 22.5 3.2 32 24-55 125-157 (185)
114 PRK07018 flgA flagellar basal 22.5 99 0.0021 23.1 2.9 20 32-51 207-227 (235)
115 PF10781 DSRB: Dextransucrase 22.2 96 0.0021 18.9 2.2 25 32-56 4-28 (62)
116 PF09196 DUF1953: Domain of un 21.5 1.1E+02 0.0024 18.6 2.4 14 92-105 13-26 (66)
117 PLN03095 NADH:ubiquinone oxido 21.4 54 0.0012 22.5 1.2 19 46-64 9-27 (115)
118 PF02604 PhdYeFM_antitox: Anti 21.3 91 0.002 18.4 2.1 41 16-58 8-48 (75)
119 PF09465 LBR_tudor: Lamin-B re 20.2 2.1E+02 0.0045 17.1 3.4 26 30-55 7-33 (55)
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=99.96 E-value=1e-28 Score=161.87 Aligned_cols=87 Identities=90% Similarity=1.381 Sum_probs=73.0
Q ss_pred CCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCc
Q 033952 19 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 98 (107)
Q Consensus 19 ~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~ 98 (107)
.||+++|+.+++.+++|.|+|++|+.+.|+|+|||+||||+|+||+|++...++++++.. ..+..+++++|.+|||||+
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 489999999998899999999999999999999999999999999999976443322111 1123456789999999999
Q ss_pred EEEEEeCC
Q 033952 99 VIIVLRNP 106 (107)
Q Consensus 99 Vv~Is~~~ 106 (107)
|++|+++|
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=5.4e-26 Score=147.13 Aligned_cols=82 Identities=33% Similarity=0.579 Sum_probs=66.6
Q ss_pred CcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcE
Q 033952 20 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 99 (107)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~V 99 (107)
.|+++|+.++ +++|.|+|++||.+.|+|+|||+||||+|+||+|++.......+... .......|.+|.+|||||+|
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--DERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYE-EIVKTTKRNIPMLFVRGDSV 77 (82)
T ss_pred CchHHHHHhC--CCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccc-cccceeEEEcCeEEEeCCEE
Confidence 5999999999 99999999999999999999999999999999999865332111100 01112457899999999999
Q ss_pred EEEEe
Q 033952 100 IIVLR 104 (107)
Q Consensus 100 v~Is~ 104 (107)
++|++
T Consensus 78 v~i~~ 82 (82)
T cd01730 78 ILVSP 82 (82)
T ss_pred EEECC
Confidence 99984
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=99.92 E-value=2.1e-24 Score=138.22 Aligned_cols=74 Identities=26% Similarity=0.507 Sum_probs=64.9
Q ss_pred CCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCc
Q 033952 19 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 98 (107)
Q Consensus 19 ~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~ 98 (107)
..|+++|++++ +++|.|++++|+++.|+|+|||+||||+|+||+|++.. + ++. ..+++|.+||||||
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 57999999999 99999999999999999999999999999999999842 1 111 23679999999999
Q ss_pred EEEEEeC
Q 033952 99 VIIVLRN 105 (107)
Q Consensus 99 Vv~Is~~ 105 (107)
|++|+|.
T Consensus 69 V~~i~p~ 75 (76)
T cd01732 69 ICMLVPG 75 (76)
T ss_pred EEEEECC
Confidence 9999974
No 4
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.91 E-value=3.7e-24 Score=135.49 Aligned_cols=71 Identities=32% Similarity=0.586 Sum_probs=63.2
Q ss_pred CCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCC
Q 033952 18 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 97 (107)
Q Consensus 18 ~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd 97 (107)
...|+++|++++ +++|.|+|++|+.+.|+|+|||+||||+|+||.|++. ++ ..+.+|.+||||+
T Consensus 2 ~~~P~~~L~~~~--~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-----~~---------~~~~lg~v~iRG~ 65 (72)
T PRK00737 2 AQRPLDVLNNAL--NSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-----GE---------VVRKLGKVVIRGD 65 (72)
T ss_pred CcchHHHHHHhC--CCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC-----CC---------eEeEcCcEEEeCC
Confidence 368999999999 9999999999999999999999999999999999752 11 1257999999999
Q ss_pred cEEEEEe
Q 033952 98 SVIIVLR 104 (107)
Q Consensus 98 ~Vv~Is~ 104 (107)
+|++|++
T Consensus 66 ~V~~i~~ 72 (72)
T PRK00737 66 NVVYVSP 72 (72)
T ss_pred EEEEEcC
Confidence 9999974
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=99.91 E-value=7.1e-24 Score=132.58 Aligned_cols=68 Identities=34% Similarity=0.599 Sum_probs=61.6
Q ss_pred cHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033952 21 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 100 (107)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv 100 (107)
|+++|+.++ +++|.|+|++|+.+.|+|+|||+||||+|+||+|++.. + ..+.+|.+||||++|+
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 99999999999999999999999999999999998731 1 1357999999999999
Q ss_pred EEEe
Q 033952 101 IVLR 104 (107)
Q Consensus 101 ~Is~ 104 (107)
+|++
T Consensus 65 ~i~~ 68 (68)
T cd01731 65 FISP 68 (68)
T ss_pred EEcC
Confidence 9985
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=99.89 E-value=1.3e-22 Score=126.63 Aligned_cols=67 Identities=21% Similarity=0.366 Sum_probs=59.7
Q ss_pred cHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033952 21 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 100 (107)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv 100 (107)
|+++|++++ +++|.|+|++|++++|+|.|||+||||+|+||+|... +. ..+.+|.+||||++|+
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 9999999999999999999999999999999988642 11 1257999999999999
Q ss_pred EEE
Q 033952 101 IVL 103 (107)
Q Consensus 101 ~Is 103 (107)
+|+
T Consensus 65 ~I~ 67 (67)
T cd01726 65 YIS 67 (67)
T ss_pred EEC
Confidence 986
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=99.88 E-value=4.3e-22 Score=128.78 Aligned_cols=74 Identities=20% Similarity=0.351 Sum_probs=60.7
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 103 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~Is 103 (107)
-|.+++ +++|+|+|++||++.|+|+|||+||||+|+||+|+..... +... .....+.+|.++|||+||++|+
T Consensus 6 ~L~~~i--~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~---~~~~---~~~~~~~lG~v~iRG~nV~~i~ 77 (81)
T cd01729 6 DLSKYV--DKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPD---DPYK---LTDKTRQLGLVVCRGTSVVLIS 77 (81)
T ss_pred hHHHhc--CCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCC---cccc---cccceeEccEEEEcCCEEEEEe
Confidence 478899 9999999999999999999999999999999999975311 1100 0113467999999999999998
Q ss_pred eC
Q 033952 104 RN 105 (107)
Q Consensus 104 ~~ 105 (107)
+.
T Consensus 78 ~~ 79 (81)
T cd01729 78 PV 79 (81)
T ss_pred cC
Confidence 75
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=99.88 E-value=4.9e-22 Score=127.62 Aligned_cols=75 Identities=21% Similarity=0.441 Sum_probs=60.9
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 103 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~Is 103 (107)
-|..++ +++|+|+|++||.+.|+|+|||+||||+|+||+|++...+.+... ......|++|.+||||++|++|+
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 467888 999999999999999999999999999999999998643211000 01124578999999999999997
Q ss_pred e
Q 033952 104 R 104 (107)
Q Consensus 104 ~ 104 (107)
-
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=9.9e-22 Score=126.75 Aligned_cols=75 Identities=19% Similarity=0.420 Sum_probs=64.3
Q ss_pred cCCCcHHHHHhhhcCCcEEEEEec--CCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEE
Q 033952 17 FNTGPLSVLMMSVKNNTQVLINCR--NNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFL 94 (107)
Q Consensus 17 ~~~~Pl~~L~~~~~~~krV~V~lr--~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~I 94 (107)
....|++.|.++++...+|.|+++ +|+.+.|+|+|||+||||+|+||+|+... ++ ..+.+|.++|
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 456899999999966669999998 89999999999999999999999999741 11 1357999999
Q ss_pred eCCcEEEEEe
Q 033952 95 RGDSVIIVLR 104 (107)
Q Consensus 95 RGd~Vv~Is~ 104 (107)
|||||++|+|
T Consensus 70 RGnnV~~I~p 79 (79)
T cd01718 70 KGDNITLIQN 79 (79)
T ss_pred eCCEEEEEcC
Confidence 9999999985
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=6.1e-22 Score=124.03 Aligned_cols=68 Identities=19% Similarity=0.304 Sum_probs=60.0
Q ss_pred CcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcE
Q 033952 20 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 99 (107)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~V 99 (107)
.|+.+|+.++ +++|.|+|++|+++.|+|.|||+|||++|+||+|... +. ....+|.+||||++|
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 4899999998 9999999999999999999999999999999998742 11 124699999999999
Q ss_pred EEEE
Q 033952 100 IIVL 103 (107)
Q Consensus 100 v~Is 103 (107)
++|+
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=99.87 E-value=9.1e-22 Score=124.74 Aligned_cols=70 Identities=23% Similarity=0.401 Sum_probs=60.8
Q ss_pred cHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033952 21 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 100 (107)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv 100 (107)
|-+.|.+++ +++|.|+|++|+.+.|+|+|||+||||+|+||+|+.. +. ..+.+|.++|||++|+
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 345789999 9999999999999999999999999999999999862 11 1257999999999999
Q ss_pred EEEeCC
Q 033952 101 IVLRNP 106 (107)
Q Consensus 101 ~Is~~~ 106 (107)
+|++..
T Consensus 65 ~i~~~~ 70 (72)
T cd01719 65 MLEALE 70 (72)
T ss_pred EEEccc
Confidence 998753
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=99.87 E-value=2.1e-21 Score=123.79 Aligned_cols=71 Identities=24% Similarity=0.384 Sum_probs=61.2
Q ss_pred cHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033952 21 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 100 (107)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv 100 (107)
++..|..++ +++|.|++++||.+.|+|+|||+||||+|+||.|+.... .. ..++.+|.++||||||+
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--DKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVG----DK-------YGDIPRGIFIIRGENVV 69 (74)
T ss_pred chHHHHHhc--CCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecC----Cc-------cceeEeeEEEEECCEEE
Confidence 466789999 999999999999999999999999999999999987531 11 12367999999999999
Q ss_pred EEEe
Q 033952 101 IVLR 104 (107)
Q Consensus 101 ~Is~ 104 (107)
+|+.
T Consensus 70 ~ig~ 73 (74)
T cd01728 70 LLGE 73 (74)
T ss_pred EEEc
Confidence 9975
No 13
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=2.9e-21 Score=122.73 Aligned_cols=72 Identities=21% Similarity=0.362 Sum_probs=61.2
Q ss_pred HHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 033952 23 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 102 (107)
Q Consensus 23 ~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~I 102 (107)
+.|..++ +++|+|++++||.+.|+|+|||+||||+|+||+|+..... ++. .++.+|.++|||+||++|
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---EGV-------EQVVLGLYIIRGDNIAVV 69 (74)
T ss_pred hhHHHhc--CCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCC---CCc-------eeeEeceEEECCCEEEEE
Confidence 4688899 9999999999999999999999999999999999864311 111 236799999999999999
Q ss_pred EeCC
Q 033952 103 LRNP 106 (107)
Q Consensus 103 s~~~ 106 (107)
++.+
T Consensus 70 ~~~d 73 (74)
T cd01727 70 GEID 73 (74)
T ss_pred EccC
Confidence 9864
No 14
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.86 E-value=7.1e-23 Score=132.12 Aligned_cols=85 Identities=32% Similarity=0.518 Sum_probs=71.2
Q ss_pred CCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCC
Q 033952 18 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 97 (107)
Q Consensus 18 ~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd 97 (107)
...|+++|+.++ +.||.|++|++|+++|+|.|||+|+||+|.||+|+++....+...++++ ....+|++..+|+|||
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 457999999999 9999999999999999999999999999999999998754332222221 1235688999999999
Q ss_pred cEEEEEeC
Q 033952 98 SVIIVLRN 105 (107)
Q Consensus 98 ~Vv~Is~~ 105 (107)
+|++|+|.
T Consensus 80 ~Vilvspp 87 (91)
T KOG3460|consen 80 GVILVSPP 87 (91)
T ss_pred eEEEEcCc
Confidence 99999985
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.85 E-value=8.2e-21 Score=121.78 Aligned_cols=75 Identities=31% Similarity=0.576 Sum_probs=62.7
Q ss_pred CCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCC
Q 033952 18 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 97 (107)
Q Consensus 18 ~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd 97 (107)
...|+++|+.++ +++|.|+|++|+++.|+|+|||+||||+|+||+|.+.. ++. . ...+..+.++|||+
T Consensus 5 ~~~~~~~l~~~~--~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~--~-----~~~~~~~~~~IRG~ 72 (79)
T COG1958 5 GPLPLSFLKKLL--NKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH---DGE--K-----NVRRLGGEVLIRGD 72 (79)
T ss_pred cCCcHHHHHHhh--CCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc---CCc--c-----ccceeccEEEEECC
Confidence 457899999999 99999999999999999999999999999999999741 111 1 01244569999999
Q ss_pred cEEEEEe
Q 033952 98 SVIIVLR 104 (107)
Q Consensus 98 ~Vv~Is~ 104 (107)
+|++|++
T Consensus 73 ~I~~I~~ 79 (79)
T COG1958 73 NIVLISP 79 (79)
T ss_pred cEEEEeC
Confidence 9999974
No 16
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.84 E-value=2.5e-20 Score=122.61 Aligned_cols=77 Identities=22% Similarity=0.481 Sum_probs=66.9
Q ss_pred ccCCCcHHHHHhhhcCCcEEEEEecCC--eEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEE
Q 033952 16 EFNTGPLSVLMMSVKNNTQVLINCRNN--KKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMF 93 (107)
Q Consensus 16 ~~~~~Pl~~L~~~~~~~krV~V~lr~g--r~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~ 93 (107)
+....|+..+..+++...+|.|++.++ +.+.|+|+|||+||||+|+||+|++.. ++ ..+.+|.++
T Consensus 10 ~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~----~~---------~~~~lG~il 76 (89)
T PTZ00138 10 KIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK----KN---------TRKDLGRIL 76 (89)
T ss_pred eeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC----Cc---------eeeEcCeEE
Confidence 457789999999999999999999885 889999999999999999999998641 11 135799999
Q ss_pred EeCCcEEEEEeC
Q 033952 94 LRGDSVIIVLRN 105 (107)
Q Consensus 94 IRGd~Vv~Is~~ 105 (107)
||||||++|++.
T Consensus 77 IRGnnV~~I~~~ 88 (89)
T PTZ00138 77 LKGDNITLIMAA 88 (89)
T ss_pred EcCCEEEEEEcC
Confidence 999999999874
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=5.7e-20 Score=113.65 Aligned_cols=66 Identities=23% Similarity=0.416 Sum_probs=58.9
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 103 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~Is 103 (107)
+|++++ +++|+|.|++|+.++|+|.+||+||||+|+||.|.+.. .. ..+++|.+||||++|++|+
T Consensus 2 ~L~~~~--g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~-----~~--------~~~~~~~~~irG~~I~~I~ 66 (67)
T PF01423_consen 2 FLQKLI--GKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKN-----GP--------EKRSLGLVFIRGSNIRYIS 66 (67)
T ss_dssp HHHHTT--TSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETT-----ES--------EEEEEEEEEEEGGGEEEEE
T ss_pred hhHHhC--CcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECC-----CC--------cEeECcEEEEECCEEEEEE
Confidence 688999 99999999999999999999999999999999999742 10 2368999999999999997
Q ss_pred e
Q 033952 104 R 104 (107)
Q Consensus 104 ~ 104 (107)
+
T Consensus 67 ~ 67 (67)
T PF01423_consen 67 L 67 (67)
T ss_dssp E
T ss_pred C
Confidence 5
No 18
>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=99.83 E-value=6.9e-20 Score=117.07 Aligned_cols=72 Identities=17% Similarity=0.314 Sum_probs=60.5
Q ss_pred HHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 033952 23 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 102 (107)
Q Consensus 23 ~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~I 102 (107)
+-|..++ +++|+|+|+|||.+.|+|.|||+||||+|+||.|++...+... ....|.+|.++|||++|++|
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 3578888 9999999999999999999999999999999999986422110 12347899999999999998
Q ss_pred Ee
Q 033952 103 LR 104 (107)
Q Consensus 103 s~ 104 (107)
..
T Consensus 73 ~v 74 (75)
T cd06168 73 EV 74 (75)
T ss_pred EE
Confidence 74
No 19
>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=99.82 E-value=7.7e-20 Score=116.75 Aligned_cols=72 Identities=22% Similarity=0.306 Sum_probs=61.5
Q ss_pred CcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcE
Q 033952 20 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 99 (107)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~V 99 (107)
-|+.+|+.+. +++|.|.|++|+.+.|+|.+||+|||++|+||+|... + |.. ...++.+||||++|
T Consensus 1 ~Pl~~L~~~~--g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~--g~~-------~~~~~~v~IRG~~I 65 (76)
T cd01723 1 LPLSLLKTAQ--NHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSK----D--GDK-------FWKMPECYIRGNTI 65 (76)
T ss_pred CchHHHHhcC--CCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC----C--CcE-------eeeCCcEEEeCCEE
Confidence 3999999998 9999999999999999999999999999999988632 1 211 13579999999999
Q ss_pred EEEEeCC
Q 033952 100 IIVLRNP 106 (107)
Q Consensus 100 v~Is~~~ 106 (107)
.+|..++
T Consensus 66 ~~i~~p~ 72 (76)
T cd01723 66 KYLRVPD 72 (76)
T ss_pred EEEEcCH
Confidence 9998654
No 20
>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=99.82 E-value=1e-19 Score=114.56 Aligned_cols=69 Identities=14% Similarity=0.300 Sum_probs=60.2
Q ss_pred cHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033952 21 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 100 (107)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv 100 (107)
|+++|+.+. +++|.|+|++|.+++|+|.+||+|||+.|+||.+... + +. ...++.+||||+||.
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----D--GR--------VSQLEQVYIRGSKIR 64 (70)
T ss_pred ChHHHhhCC--CCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECC----C--Cc--------EeEcCcEEEeCCEEE
Confidence 889999998 9999999999999999999999999999999987532 1 21 135899999999999
Q ss_pred EEEeC
Q 033952 101 IVLRN 105 (107)
Q Consensus 101 ~Is~~ 105 (107)
+|..+
T Consensus 65 ~v~lP 69 (70)
T cd01721 65 FFILP 69 (70)
T ss_pred EEEeC
Confidence 99754
No 21
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.82 E-value=9e-20 Score=112.64 Aligned_cols=66 Identities=27% Similarity=0.569 Sum_probs=58.1
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 103 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~Is 103 (107)
+|..++ +++|.|.|+||+.+.|+|.+||+||||+|+||+|++.. .+ ..+++|.+||||++|++|.
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 678888 99999999999999999999999999999999998742 01 2368999999999999997
Q ss_pred e
Q 033952 104 R 104 (107)
Q Consensus 104 ~ 104 (107)
+
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=99.80 E-value=7.9e-21 Score=128.01 Aligned_cols=97 Identities=86% Similarity=1.279 Sum_probs=88.2
Q ss_pred cccchhcccCCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceee
Q 033952 9 NVKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRF 88 (107)
Q Consensus 9 ~~~~e~~~~~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~ 88 (107)
.+..|+.++..||++++..++.....|.|.+||++.+-|.++|||.|+|++|+++.|.|+..++++++.+ +++..+.|+
T Consensus 13 ~~~~e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~~~~~~~r~ 91 (114)
T KOG3459|consen 13 LEVPEEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-AKPVNKDRF 91 (114)
T ss_pred cccccccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-CCccchhhh
Confidence 3667899999999999999999999999999999999999999999999999999999998887766755 566677899
Q ss_pred eceEEEeCCcEEEEEeCC
Q 033952 89 ISKMFLRGDSVIIVLRNP 106 (107)
Q Consensus 89 lg~v~IRGd~Vv~Is~~~ 106 (107)
+|.+|||||+|+++...|
T Consensus 92 isK~flRGdsvI~v~r~p 109 (114)
T KOG3459|consen 92 ISKMFLRGDSVILVLRNP 109 (114)
T ss_pred hheeeecCCeEEEEEecc
Confidence 999999999999998665
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=1.1e-18 Score=106.37 Aligned_cols=63 Identities=35% Similarity=0.549 Sum_probs=55.3
Q ss_pred HHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033952 25 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 103 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~Is 103 (107)
|+.++ +++|+|.|+||+.+.|+|.|||+|||++|+||.|++.. + ..+.+|.+||||++|++|.
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 45677 99999999999999999999999999999999999742 1 1367999999999999984
No 24
>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=99.76 E-value=7.3e-18 Score=108.36 Aligned_cols=76 Identities=20% Similarity=0.272 Sum_probs=62.9
Q ss_pred hhcccCCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceE
Q 033952 13 EEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKM 92 (107)
Q Consensus 13 e~~~~~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v 92 (107)
|.......+..+|+.+. |+.|.|+||+|..|.|+|.++|+|||+.|+||++... .+. ...+|.+
T Consensus 2 e~~~~~~tl~~~L~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~------~~~--------~~~~~~v 65 (78)
T cd01733 2 ERTLLENTLIILLQGLQ--GKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDR------NGK--------QVQVEEI 65 (78)
T ss_pred ccchhhchHHHHHHHCC--CCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcC------CCc--------eeECCcE
Confidence 34444566788999998 9999999999999999999999999999999986631 111 1369999
Q ss_pred EEeCCcEEEEEe
Q 033952 93 FLRGDSVIIVLR 104 (107)
Q Consensus 93 ~IRGd~Vv~Is~ 104 (107)
||||++|.+|..
T Consensus 66 ~IRG~nI~yI~l 77 (78)
T cd01733 66 MVTGRNIRYVHI 77 (78)
T ss_pred EEECCEEEEEEc
Confidence 999999999974
No 25
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.76 E-value=7.3e-18 Score=111.02 Aligned_cols=70 Identities=21% Similarity=0.300 Sum_probs=60.9
Q ss_pred cHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033952 21 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 100 (107)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv 100 (107)
|+.+|+++. |++|.|+|++|..|+|+|.++|.|||++|+||+++.. + +. ...+|.+||||++|.
T Consensus 2 ~~~fL~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~-----~-~~--------~~~~~~v~IRG~nI~ 65 (90)
T cd01724 2 LVRFLMKLT--NETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLK-----G-RN--------PVPLDTLSIRGNNIR 65 (90)
T ss_pred HhHHHHhCC--CCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcC-----C-Cc--------eeEcceEEEeCCEEE
Confidence 678999998 9999999999999999999999999999999988742 1 11 246999999999999
Q ss_pred EEEeCC
Q 033952 101 IVLRNP 106 (107)
Q Consensus 101 ~Is~~~ 106 (107)
+|..++
T Consensus 66 yi~lPd 71 (90)
T cd01724 66 YFILPD 71 (90)
T ss_pred EEEcCC
Confidence 998654
No 26
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.74 E-value=1.6e-17 Score=107.34 Aligned_cols=73 Identities=19% Similarity=0.200 Sum_probs=60.5
Q ss_pred CcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcE
Q 033952 20 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 99 (107)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~V 99 (107)
.|+.+|++.. |++|.|+|++|..++|+|.++|.|||++|+||++... + +.. ....++.++|||++|
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----E--KYP------HMLSVKNCFIRGSVV 66 (81)
T ss_pred ChhHHHHhCC--CCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcC----C--Ccc------cccccCeEEEECCEE
Confidence 3789999997 9999999999999999999999999999999976631 1 110 113579999999999
Q ss_pred EEEEeCC
Q 033952 100 IIVLRNP 106 (107)
Q Consensus 100 v~Is~~~ 106 (107)
.+|..++
T Consensus 67 ~~I~lp~ 73 (81)
T cd01725 67 RYVQLPA 73 (81)
T ss_pred EEEEeCh
Confidence 9998653
No 27
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.72 E-value=1.8e-17 Score=104.84 Aligned_cols=68 Identities=24% Similarity=0.435 Sum_probs=59.2
Q ss_pred CcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcE
Q 033952 20 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 99 (107)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~V 99 (107)
.| -|++++ +|++.++|.+||.+.|+|+|||.|||++|+|+.|.-. .+. +..+|.++|||++|
T Consensus 6 ~P--eLkkym--dKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~------~~~--------~~~ig~~vIrgnsi 67 (77)
T KOG1780|consen 6 HP--ELKKYM--DKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNG------DGD--------KNNIGMVVIRGNSI 67 (77)
T ss_pred Cc--hHHHhh--hheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecC------cCC--------cceeeeEEEeccEE
Confidence 46 689999 9999999999999999999999999999999999842 121 13699999999999
Q ss_pred EEEEeC
Q 033952 100 IIVLRN 105 (107)
Q Consensus 100 v~Is~~ 105 (107)
+++.+.
T Consensus 68 v~~eaL 73 (77)
T KOG1780|consen 68 VMVEAL 73 (77)
T ss_pred EEEeec
Confidence 998775
No 28
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.65 E-value=4.8e-16 Score=98.15 Aligned_cols=73 Identities=19% Similarity=0.300 Sum_probs=64.5
Q ss_pred CCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCC
Q 033952 18 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 97 (107)
Q Consensus 18 ~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd 97 (107)
...|-.+|+... +++|.|+|+.|.+|.|+|++.|.||||.|.+|+|++. +. . ...+|.++||.+
T Consensus 6 PvNPKpFL~~l~--gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~id-----G~--~-------~g~lGEilIRCN 69 (79)
T KOG3482|consen 6 PVNPKPFLNGLT--GKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYID-----GV--S-------TGNLGEILIRCN 69 (79)
T ss_pred cCCchHHHhhcc--CCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhc-----cc--c-------cccceeEEEEec
Confidence 458889999999 9999999999999999999999999999999999873 22 1 246999999999
Q ss_pred cEEEEEeCC
Q 033952 98 SVIIVLRNP 106 (107)
Q Consensus 98 ~Vv~Is~~~ 106 (107)
||.+|.-.|
T Consensus 70 Nvlyi~gv~ 78 (79)
T KOG3482|consen 70 NVLYIRGVP 78 (79)
T ss_pred cEEEEecCC
Confidence 999997665
No 29
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.63 E-value=5.9e-16 Score=99.64 Aligned_cols=77 Identities=22% Similarity=0.450 Sum_probs=65.5
Q ss_pred cCCCcHHHHHhhhcCCcEEEEEecC--CeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEE
Q 033952 17 FNTGPLSVLMMSVKNNTQVLINCRN--NKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFL 94 (107)
Q Consensus 17 ~~~~Pl~~L~~~~~~~krV~V~lr~--gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~I 94 (107)
....|+.++.+++++..+|.|+|.. +-.+.|.++|||+|||+||+||+|.... .. .++.+|.+++
T Consensus 9 vmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k------~~-------~rk~lGRilL 75 (88)
T KOG1774|consen 9 VMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSK------TK-------SRKELGRILL 75 (88)
T ss_pred eecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccc------cc-------CCCccccEEE
Confidence 4578999999999999999999998 4678999999999999999999998642 11 1136999999
Q ss_pred eCCcEEEEEeCC
Q 033952 95 RGDSVIIVLRNP 106 (107)
Q Consensus 95 RGd~Vv~Is~~~ 106 (107)
+||||.+|...-
T Consensus 76 KGDnItli~~~~ 87 (88)
T KOG1774|consen 76 KGDNITLIQSAG 87 (88)
T ss_pred cCCcEEEEeecC
Confidence 999999998753
No 30
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.63 E-value=3.9e-17 Score=108.38 Aligned_cols=75 Identities=15% Similarity=0.297 Sum_probs=60.9
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 103 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~Is 103 (107)
-|.+++ +++|+|++.+||+.+|+|+|||+.|||||+|+.|+....+ ...+ .....|.+|.+++||..+++|+
T Consensus 21 DLsky~--Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpd---d~~~---~~~~tR~LGLvV~RGTalvlis 92 (108)
T KOG1781|consen 21 DLSKYL--DKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPD---DPYK---LTDETRKLGLVVCRGTALVLIS 92 (108)
T ss_pred hHHHhh--ccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCC---Cccc---hhhhhheeeeEEEcccEEEEEc
Confidence 345555 9999999999999999999999999999999999976432 1211 2223488999999999999999
Q ss_pred eCC
Q 033952 104 RNP 106 (107)
Q Consensus 104 ~~~ 106 (107)
+..
T Consensus 93 p~d 95 (108)
T KOG1781|consen 93 PAD 95 (108)
T ss_pred CCc
Confidence 864
No 31
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.62 E-value=4.2e-16 Score=99.25 Aligned_cols=76 Identities=22% Similarity=0.457 Sum_probs=65.7
Q ss_pred cCCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeC
Q 033952 17 FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 96 (107)
Q Consensus 17 ~~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG 96 (107)
++..|+.++.+|+ +.+|.|.+++++++.|+|+|||.|.|++|+||+|+-... +++ +-.+++++++.|
T Consensus 4 ~~llPlEliDkcI--gski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~----egr-------~~tk~~~iLLnG 70 (84)
T KOG1775|consen 4 STLLPLELIDKCI--GSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITP----EGR-------RMTKLDQILLNG 70 (84)
T ss_pred hhcccHHHHHHhc--CceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCC----Ccc-------eeeeeeeeeecC
Confidence 4678999999999 999999999999999999999999999999999996531 221 124699999999
Q ss_pred CcEEEEEeC
Q 033952 97 DSVIIVLRN 105 (107)
Q Consensus 97 d~Vv~Is~~ 105 (107)
++|.+..|.
T Consensus 71 Nni~mLvPG 79 (84)
T KOG1775|consen 71 NNITMLVPG 79 (84)
T ss_pred CcEEEEecC
Confidence 999988764
No 32
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.55 E-value=1.3e-15 Score=96.20 Aligned_cols=72 Identities=19% Similarity=0.331 Sum_probs=64.0
Q ss_pred CCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCC
Q 033952 18 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 97 (107)
Q Consensus 18 ~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd 97 (107)
...|-++|...+ +++|.|+|.+|-.++|+|.+.|.||||.|+.++|... |+. .+.+|..||||+
T Consensus 4 ~~~~~~fl~~ii--Gr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~n-------gql-------~n~ygdaFirGn 67 (77)
T KOG1783|consen 4 GSMPGEFLKAII--GRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVN-------GQL-------KNKYGDAFIRGN 67 (77)
T ss_pred ccCcHHHHHHHh--CCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhc-------Ccc-------cccccceeeccc
Confidence 457889999999 9999999999999999999999999999999998862 332 367999999999
Q ss_pred cEEEEEeC
Q 033952 98 SVIIVLRN 105 (107)
Q Consensus 98 ~Vv~Is~~ 105 (107)
+|.+|+..
T Consensus 68 nVlyIs~~ 75 (77)
T KOG1783|consen 68 NVLYISTQ 75 (77)
T ss_pred cEEEEEec
Confidence 99999974
No 33
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.52 E-value=1.9e-15 Score=108.68 Aligned_cols=79 Identities=23% Similarity=0.468 Sum_probs=61.4
Q ss_pred CcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcE
Q 033952 20 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 99 (107)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~V 99 (107)
++-.+|+. + |++++|.++|||.+.|.+.+||+||||+|.||+|.....++..+-. ....+|.+|++++||+||
T Consensus 5 ~sskml~~-i--Nyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~----~~eEkr~lgLvllRgenI 77 (177)
T KOG3168|consen 5 KSSKMLQH-I--NYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMT----DGEEKRVLGLVLLRGENI 77 (177)
T ss_pred chhHHHHh-h--cceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhcccccccccc----ccceeeEEEEEEecCCcE
Confidence 34444444 5 8999999999999999999999999999999999876544322100 113468899999999999
Q ss_pred EEEEeC
Q 033952 100 IIVLRN 105 (107)
Q Consensus 100 v~Is~~ 105 (107)
++.+..
T Consensus 78 vs~tVe 83 (177)
T KOG3168|consen 78 VSMTVE 83 (177)
T ss_pred EEEecc
Confidence 998753
No 34
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.45 E-value=1e-14 Score=100.21 Aligned_cols=69 Identities=28% Similarity=0.441 Sum_probs=59.5
Q ss_pred HHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 033952 25 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 104 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~Is~ 104 (107)
|..++ ++++.|.|||||.+.|+|++||||-|++|.+|.|++.. ++. ++.+..|..+|||+||+++..
T Consensus 14 l~~~~--dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v----~~~-------Y~di~~glfiIRGENVvllGe 80 (129)
T KOG1782|consen 14 LVEYL--DKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFV----GNK-------YCDIPRGLFIIRGENVVLLGE 80 (129)
T ss_pred HHHHh--cceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheee----cce-------ecccCceEEEEecCcEEEEec
Confidence 55666 99999999999999999999999999999999999875 221 455679999999999999976
Q ss_pred CC
Q 033952 105 NP 106 (107)
Q Consensus 105 ~~ 106 (107)
.|
T Consensus 81 id 82 (129)
T KOG1782|consen 81 ID 82 (129)
T ss_pred CC
Confidence 54
No 35
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.43 E-value=1.6e-13 Score=90.04 Aligned_cols=71 Identities=18% Similarity=0.363 Sum_probs=59.8
Q ss_pred HHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 033952 23 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 102 (107)
Q Consensus 23 ~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~I 102 (107)
+-|..++ +++|.|.+.|||.+.|.|+|||+-.||+|+|+.|++... .++. ..--+|..+|||+||..|
T Consensus 3 s~L~~y~--n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~---~~gv-------~q~~lGlyiirgeNva~i 70 (96)
T KOG1784|consen 3 STLEDYM--NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSE---TEGV-------EQIVLGLYIIRGENVAVI 70 (96)
T ss_pred hhHHHHh--hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhh---hcch-------hheeeEEEEEecCcccee
Confidence 4578899 999999999999999999999999999999999998642 1221 124599999999999998
Q ss_pred EeC
Q 033952 103 LRN 105 (107)
Q Consensus 103 s~~ 105 (107)
.+.
T Consensus 71 g~i 73 (96)
T KOG1784|consen 71 GEI 73 (96)
T ss_pred eec
Confidence 764
No 36
>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=9.9e-13 Score=81.63 Aligned_cols=45 Identities=31% Similarity=0.409 Sum_probs=39.1
Q ss_pred HHhhhcCCcEEEEEecCCe----EEEEEEEEecCccceEeeceEEEeec
Q 033952 25 LMMSVKNNTQVLINCRNNK----KLLGRVRAFDRHCNMVLENVREMWTE 69 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~gr----~i~G~L~~fD~hmNlvL~d~~E~~~~ 69 (107)
|++|++++.||+|.+|.-+ .+.|.|+|||+||||+|.||+|.|..
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 3567888999999999743 67899999999999999999999864
No 37
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.28 E-value=7.7e-12 Score=86.15 Aligned_cols=72 Identities=22% Similarity=0.293 Sum_probs=61.4
Q ss_pred CCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCc
Q 033952 19 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 98 (107)
Q Consensus 19 ~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~ 98 (107)
+.||++|+.+- +.++.|.|++|.+|.|+|+..|.+|||-|.+|+++.. + +.+. -.+..|+|||++
T Consensus 1 mlPLsLL~~aq--~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~----D--gdkf-------~r~pEcYirGtt 65 (134)
T KOG3293|consen 1 MLPLSLLKTAQ--NHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSE----D--GDKF-------FRMPECYIRGTT 65 (134)
T ss_pred CcchhHHHhcC--CCeEEEEecCCCEecceeecchhhhhcchheeEEecc----C--CCce-------eecceeEEecce
Confidence 46999999997 9999999999999999999999999999999998753 2 2221 248899999999
Q ss_pred EEEEEeC
Q 033952 99 VIIVLRN 105 (107)
Q Consensus 99 Vv~Is~~ 105 (107)
|-++...
T Consensus 66 Ikylri~ 72 (134)
T KOG3293|consen 66 IKYLRIP 72 (134)
T ss_pred eEEEecc
Confidence 9998643
No 38
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.16 E-value=3.3e-10 Score=74.13 Aligned_cols=70 Identities=19% Similarity=0.235 Sum_probs=56.2
Q ss_pred HHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 033952 22 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 101 (107)
Q Consensus 22 l~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~ 101 (107)
.++++..+ |++|.|.|+++-.+.|+|.+.|+|+||-|.|..-.-. +... + --++..|||||..|.+
T Consensus 4 ysfFkslv--g~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~------~kyP--h----m~Sv~ncfIRGSvvrY 69 (96)
T KOG3448|consen 4 YSFFKSLV--GKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDP------DKYP--H----MLSVKNCFIRGSVVRY 69 (96)
T ss_pred HHHHHHhc--CCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCc------ccCC--C----eeeeeeEEEeccEEEE
Confidence 57888899 9999999999999999999999999999999754321 1111 1 1358899999999999
Q ss_pred EEeC
Q 033952 102 VLRN 105 (107)
Q Consensus 102 Is~~ 105 (107)
|..+
T Consensus 70 v~l~ 73 (96)
T KOG3448|consen 70 VQLP 73 (96)
T ss_pred EEeC
Confidence 8653
No 39
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.06 E-value=5.7e-10 Score=75.39 Aligned_cols=74 Identities=14% Similarity=0.247 Sum_probs=62.5
Q ss_pred cCCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeC
Q 033952 17 FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 96 (107)
Q Consensus 17 ~~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG 96 (107)
+..-|+.+|+.+- +.-|.+.+..|..|+|+|.-.|.+||+.|+|++-+.. + +. ..++.++||||
T Consensus 2 s~gvpiKlLhEaq--GhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~----d--g~--------vs~le~V~IRG 65 (119)
T KOG3172|consen 2 SVGVPIKLLHEAQ--GHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTAR----D--GR--------VSQLEQVFIRG 65 (119)
T ss_pred ccccceeeeeccc--CcEEEEEecCCceeeeeeEEeccccccEEEEEEEEcc----C--Cc--------ceeeeeEEEec
Confidence 3567999999986 9999999999999999999999999999999876652 2 21 24699999999
Q ss_pred CcEEEEEeCC
Q 033952 97 DSVIIVLRNP 106 (107)
Q Consensus 97 d~Vv~Is~~~ 106 (107)
+.|.++...+
T Consensus 66 S~IRFlvlPd 75 (119)
T KOG3172|consen 66 SKIRFLVLPD 75 (119)
T ss_pred CeEEEEECch
Confidence 9999887543
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.49 E-value=1.1e-06 Score=59.51 Aligned_cols=67 Identities=22% Similarity=0.362 Sum_probs=55.4
Q ss_pred HHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 033952 22 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 101 (107)
Q Consensus 22 l~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~ 101 (107)
..+|+++. +.+|.|.|++|..+.|++.+.|-+||..|.++.=+. ++. + -++..++|||++|.+
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--NERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTV-------KGE----P----VRLDTLSIRGNNIRY 66 (109)
T ss_pred HHHHHHhh--CCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEec-------CCC----c----eeEEEEEeecceEEE
Confidence 35788888 999999999999999999999999999999986443 121 1 258899999999998
Q ss_pred EEeC
Q 033952 102 VLRN 105 (107)
Q Consensus 102 Is~~ 105 (107)
+-..
T Consensus 67 ~~lp 70 (109)
T KOG3428|consen 67 YILP 70 (109)
T ss_pred EEcc
Confidence 8643
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=97.30 E-value=0.00078 Score=41.48 Aligned_cols=39 Identities=23% Similarity=0.323 Sum_probs=34.1
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 62 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d 62 (107)
+|+.+..++.+|.|.|.||-.+.|.+.+||+|+=|+-.+
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 677777889999999999999999999999998666544
No 42
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.27 E-value=0.0014 Score=41.28 Aligned_cols=69 Identities=13% Similarity=0.167 Sum_probs=40.3
Q ss_pred HHHHhhhcCCcEEEEEecCCeEEEEEEEEecC---ccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcE
Q 033952 23 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDR---HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 99 (107)
Q Consensus 23 ~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~---hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~V 99 (107)
-++...+ |++|.|.++||..|.|.|.+++. -+-++|+-|...-... .... ..........++|.++.|
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 3556667 99999999999999999999999 8999998876543210 0000 112234566788888776
Q ss_pred E
Q 033952 100 I 100 (107)
Q Consensus 100 v 100 (107)
+
T Consensus 76 v 76 (77)
T PF14438_consen 76 V 76 (77)
T ss_dssp -
T ss_pred C
Confidence 5
No 43
>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=97.23 E-value=0.0011 Score=40.85 Aligned_cols=39 Identities=21% Similarity=0.227 Sum_probs=33.8
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 62 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d 62 (107)
+|..+.+++.+|.|.|.+|-.+.|.++|||+|+=|+-.+
T Consensus 7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 677777779999999999999999999999998666544
No 44
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=97.00 E-value=0.0021 Score=41.48 Aligned_cols=40 Identities=25% Similarity=0.277 Sum_probs=34.5
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 63 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~ 63 (107)
+|.....++..|.|.|.+|-.+.|.++|||+|+=|+-.+.
T Consensus 11 fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 11 FLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred HHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 6667777789999999999999999999999987766553
No 45
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.40 E-value=0.009 Score=38.30 Aligned_cols=36 Identities=31% Similarity=0.321 Sum_probs=31.6
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceE
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMV 59 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlv 59 (107)
+|.....++.+|.|.|.||-.+.|.+.+||+|.=|+
T Consensus 11 fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~VlL 46 (77)
T COG1923 11 FLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVLL 46 (77)
T ss_pred HHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence 677777779999999999999999999999997443
No 46
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=95.67 E-value=0.18 Score=33.50 Aligned_cols=71 Identities=17% Similarity=0.225 Sum_probs=52.0
Q ss_pred HhhhcCCcEEEEEecCCeEEEEEEEEecC-ccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033952 26 MMSVKNNTQVLINCRNNKKLLGRVRAFDR-HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 103 (107)
Q Consensus 26 ~~~~~~~krV~V~lr~gr~i~G~L~~fD~-hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~Is 103 (107)
..++ |++|.+..+.+-.|.|+|...|. ..+|.|.+|.-+.++..+.+ . . -.......+.+.+||..|--+.
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--GSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTD-R--E--IPPSDEVYDYIVFRGSDIKDLK 75 (96)
T ss_dssp CCCT--TCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-S-S-------C-CSSSSEEEEETTTEEEEE
T ss_pred cccc--CCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcC-c--c--cCCCCceeeEEEEEccccceEE
Confidence 3567 99999999999999999999998 78999999987765421111 0 0 1122345889999999886554
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.45 E-value=0.038 Score=40.14 Aligned_cols=40 Identities=23% Similarity=0.282 Sum_probs=35.5
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 63 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~ 63 (107)
+|..+..++.+|.|.|.+|-.+.|.+++||+|+=|+..+.
T Consensus 96 fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 96 FLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 7778888899999999999999999999999987776554
No 48
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.40 E-value=0.041 Score=40.00 Aligned_cols=40 Identities=23% Similarity=0.174 Sum_probs=35.2
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 63 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~ 63 (107)
+|..+..++.+|.|.|-+|-.++|.+++||+|.=|+-.+.
T Consensus 16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 7777778899999999999999999999999987766554
No 49
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=94.98 E-value=0.069 Score=32.81 Aligned_cols=32 Identities=28% Similarity=0.358 Sum_probs=29.1
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033952 32 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 63 (107)
Q Consensus 32 ~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~ 63 (107)
|..|.+++..|.+|.|.+.|||.-.+|+.=.+
T Consensus 6 Gs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~ 37 (61)
T cd01735 6 GSQVSCRTCFEQRLQGEVVAFDYPSKMLILKC 37 (61)
T ss_pred ccEEEEEecCCceEEEEEEEecCCCcEEEEEC
Confidence 89999999999999999999999999886443
No 50
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=93.71 E-value=0.24 Score=28.40 Aligned_cols=31 Identities=10% Similarity=0.256 Sum_probs=27.8
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033952 32 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 63 (107)
Q Consensus 32 ~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~ 63 (107)
|++|+|.+ ++..+.|+..+.|.+-.|+++..
T Consensus 3 G~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~ 33 (48)
T PF02237_consen 3 GQEVRVET-GDGEIEGIAEGIDDDGALLVRTE 33 (48)
T ss_dssp TSEEEEEE-TSCEEEEEEEEEETTSEEEEEET
T ss_pred CCEEEEEE-CCeEEEEEEEEECCCCEEEEEEC
Confidence 89999999 67778999999999999999664
No 51
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=92.00 E-value=0.26 Score=35.55 Aligned_cols=35 Identities=6% Similarity=0.182 Sum_probs=31.4
Q ss_pred CcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecC
Q 033952 20 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDR 54 (107)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~ 54 (107)
.=++..++|.++++-|+|.+.|||.+.|.=.|.|.
T Consensus 108 DFF~Icrka~qqg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 108 DFFSICRKAHQQGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred hHHHHHHHHHHCCCeEEEEEcCCcEEEeeecccce
Confidence 34778899999999999999999999999888775
No 52
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=91.65 E-value=2 Score=27.40 Aligned_cols=69 Identities=17% Similarity=0.255 Sum_probs=48.8
Q ss_pred hhhcCCcEEEEEecCCeEEEEEEEEecCccc-eEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 033952 27 MSVKNNTQVLINCRNNKKLLGRVRAFDRHCN-MVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 101 (107)
Q Consensus 27 ~~~~~~krV~V~lr~gr~i~G~L~~fD~hmN-lvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~ 101 (107)
.++ +++|.+..+.+-.|.|+|...|..=. +.|.||..+.++..+. .+.. -.....-++.++.||+.|--
T Consensus 3 ~~I--G~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~-~~~~---ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYI--GSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPT-DGPE---IPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccc--CceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCC-CCCc---cCCCCcceeEEEEcCCcccc
Confidence 356 99999999999999999999997654 5699988776643211 1110 01223458889999998753
No 53
>PRK14638 hypothetical protein; Provisional
Probab=91.44 E-value=0.4 Score=34.09 Aligned_cols=33 Identities=15% Similarity=0.333 Sum_probs=27.2
Q ss_pred HHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL 60 (107)
+.++. |+.|+|++++++.+.|+|.++|.- ++.|
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 45666 999999999999999999999963 3444
No 54
>PRK14639 hypothetical protein; Provisional
Probab=89.89 E-value=0.67 Score=32.54 Aligned_cols=33 Identities=24% Similarity=0.420 Sum_probs=27.7
Q ss_pred HHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL 60 (107)
+.++. |+.|.|.+++++.+.|+|.++|.- ++.|
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 45666 999999999999999999999983 5555
No 55
>PRK02001 hypothetical protein; Validated
Probab=89.75 E-value=0.68 Score=33.08 Aligned_cols=33 Identities=18% Similarity=0.408 Sum_probs=27.6
Q ss_pred HHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL 60 (107)
+.+++ |+.|+|.+.+++.+.|+|.++|.- ++.|
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 35666 999999999999999999999974 4444
No 56
>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=89.74 E-value=3.9 Score=26.39 Aligned_cols=62 Identities=24% Similarity=0.297 Sum_probs=44.2
Q ss_pred HHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCcc-ceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033952 22 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHC-NMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 100 (107)
Q Consensus 22 l~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hm-NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv 100 (107)
|.+|.... +++|.+.|-++.++.|++.|+|... |+..++- ++ | - ......++|...|+
T Consensus 16 Lr~l~~~~--gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L-~T----P---l-----------Gv~~eAlLR~~DVi 74 (80)
T PF11095_consen 16 LRSLLAMV--GKPVEFTLHENTTVSARFGACDIDVSNFQVSNL-QT----P---L-----------GVQPEALLRCSDVI 74 (80)
T ss_dssp HHHHHHCT--TSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEE-ET----T---T-----------TEEEEEEEEGGGEE
T ss_pred HHHHHHhc--CCceEEEEeCCeEEEEEEEEecCchheEEhhhc-CC----C---c-----------ccChhheeecCCEE
Confidence 45666666 9999999999999999999999754 4444332 11 1 1 13678899999999
Q ss_pred EEEe
Q 033952 101 IVLR 104 (107)
Q Consensus 101 ~Is~ 104 (107)
+++-
T Consensus 75 ~~~f 78 (80)
T PF11095_consen 75 SISF 78 (80)
T ss_dssp EEEE
T ss_pred EEEe
Confidence 9875
No 57
>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=87.57 E-value=1.2 Score=32.38 Aligned_cols=42 Identities=26% Similarity=0.328 Sum_probs=29.6
Q ss_pred CCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCc-cceEeece
Q 033952 18 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRH-CNMVLENV 63 (107)
Q Consensus 18 ~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~h-mNlvL~d~ 63 (107)
..+|+.+ ..++ +|.|+|.+.+ +++.|.|..+|.= -|+||-+-
T Consensus 6 ~~~p~~~-~~yv--~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~ 48 (166)
T PF06372_consen 6 KKSPLEW-QDYV--GKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNF 48 (166)
T ss_dssp HS-HHHH-HCTT--T-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE
T ss_pred hCCHHHH-HHhh--CcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEc
Confidence 3567665 5667 9999999999 9999999999974 46777543
No 58
>PRK14644 hypothetical protein; Provisional
Probab=85.17 E-value=2.1 Score=30.02 Aligned_cols=33 Identities=9% Similarity=0.160 Sum_probs=27.6
Q ss_pred HHhhhcCCcEEEEEecCC----eEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCRNN----KKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~g----r~i~G~L~~fD~hmNlvL 60 (107)
+.+++ |+.|.|.+++. +.+.|+|.++|.. ++.|
T Consensus 80 f~r~~--G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l 116 (136)
T PRK14644 80 LENHI--GEIIDVSLNKEVNKTDFITGELLENNPE-TITL 116 (136)
T ss_pred HHHhC--CCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEE
Confidence 56777 99999999876 8999999999984 4555
No 59
>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=83.54 E-value=3 Score=26.39 Aligned_cols=33 Identities=18% Similarity=0.278 Sum_probs=25.6
Q ss_pred HHhhhcCCcEEEEEec---CC-eEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCR---NN-KKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr---~g-r~i~G~L~~fD~hmNlvL 60 (107)
+.+++ |+.|.|.++ +| +.+.|.|.++|.- ++.|
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 35566 999999998 55 6899999999984 4444
No 60
>PRK14640 hypothetical protein; Provisional
Probab=83.45 E-value=2.6 Score=29.88 Aligned_cols=33 Identities=21% Similarity=0.358 Sum_probs=26.1
Q ss_pred HHhhhcCCcEEEEEec----CCeEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCR----NNKKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr----~gr~i~G~L~~fD~hmNlvL 60 (107)
+.+++ |+.|.|.++ +.+.+.|+|.++|.. ++.|
T Consensus 92 f~r~~--G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 92 FEKYV--GQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred HHHhC--CCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 45666 999999994 568999999999984 4444
No 61
>PRK14642 hypothetical protein; Provisional
Probab=82.63 E-value=2.8 Score=31.32 Aligned_cols=29 Identities=17% Similarity=0.189 Sum_probs=24.5
Q ss_pred HHhhhcCCcEEEEEec-------------CCeEEEEEEEEecCc
Q 033952 25 LMMSVKNNTQVLINCR-------------NNKKLLGRVRAFDRH 55 (107)
Q Consensus 25 L~~~~~~~krV~V~lr-------------~gr~i~G~L~~fD~h 55 (107)
+.+++ |+.|.|+|+ +.+.|.|+|.++|..
T Consensus 95 f~rfi--G~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 95 FERFA--GEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG 136 (197)
T ss_pred HHHhC--CCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence 35556 999999998 678999999999884
No 62
>PRK14636 hypothetical protein; Provisional
Probab=82.59 E-value=2.7 Score=30.64 Aligned_cols=33 Identities=12% Similarity=0.263 Sum_probs=26.0
Q ss_pred HHhhhcCCcEEEEEec---CC-eEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCR---NN-KKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr---~g-r~i~G~L~~fD~hmNlvL 60 (107)
+.++. |+.|.|+++ +| +.+.|+|.++|.- ++.|
T Consensus 93 f~r~~--G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 93 FADWA--GHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred HHHhC--CCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 45666 999999998 45 6999999999883 4444
No 63
>PRK14633 hypothetical protein; Provisional
Probab=82.21 E-value=3.1 Score=29.44 Aligned_cols=33 Identities=18% Similarity=0.198 Sum_probs=26.0
Q ss_pred HHhhhcCCcEEEEEec----CCeEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCR----NNKKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr----~gr~i~G~L~~fD~hmNlvL 60 (107)
+.+++ |+.|.|+++ +.+.+.|+|.++|+. ++.|
T Consensus 89 f~r~~--G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 89 AQALV--GFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HHHhC--CCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 45666 999999994 558999999999985 4545
No 64
>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=81.64 E-value=2.9 Score=28.92 Aligned_cols=35 Identities=14% Similarity=0.251 Sum_probs=25.3
Q ss_pred HHHHhhhcCCcEEEEEec----CCeEEEEEEEEecCccceEe
Q 033952 23 SVLMMSVKNNTQVLINCR----NNKKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 23 ~~L~~~~~~~krV~V~lr----~gr~i~G~L~~fD~hmNlvL 60 (107)
.-+.+++ |+.|.|.++ +.+.+.|+|.++|. =.++|
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 34444
No 65
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.97 E-value=3.7 Score=29.47 Aligned_cols=34 Identities=21% Similarity=0.317 Sum_probs=28.4
Q ss_pred HHHhhhcCCcEEEEEe----cCCeEEEEEEEEecCccceEe
Q 033952 24 VLMMSVKNNTQVLINC----RNNKKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 24 ~L~~~~~~~krV~V~l----r~gr~i~G~L~~fD~hmNlvL 60 (107)
-+.++. |+.|.|+| .+.+.+.|+|.++|+-. +.+
T Consensus 93 ~f~r~~--G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 93 HFARFI--GEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred HHHHhc--CcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 456667 99999999 67899999999999987 444
No 66
>PRK14645 hypothetical protein; Provisional
Probab=80.96 E-value=3.4 Score=29.52 Aligned_cols=32 Identities=9% Similarity=0.227 Sum_probs=25.0
Q ss_pred HHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL 60 (107)
+.+++ |+.|.|.+ +++.+.|+|.++|.- .+.|
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 45666 99999986 789999999999884 3444
No 67
>PRK14643 hypothetical protein; Provisional
Probab=80.48 E-value=3.7 Score=29.60 Aligned_cols=35 Identities=20% Similarity=0.305 Sum_probs=26.8
Q ss_pred HHHhhhcCCcEEEEEecC----CeEEEEEEEEecCc-cceEe
Q 033952 24 VLMMSVKNNTQVLINCRN----NKKLLGRVRAFDRH-CNMVL 60 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~----gr~i~G~L~~fD~h-mNlvL 60 (107)
-+.+++ |+.|.|.++. .+.+.|+|.++|.- ..+.|
T Consensus 98 df~r~~--G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 98 ELVKAL--NQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred HHHHhc--CCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 345667 9999999975 57899999999864 34433
No 68
>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=80.31 E-value=3.8 Score=29.65 Aligned_cols=34 Identities=21% Similarity=0.144 Sum_probs=31.0
Q ss_pred cCCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033952 30 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 63 (107)
Q Consensus 30 ~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~ 63 (107)
..+-+|+|.+.||..|.|++-+|+.--|++|.-+
T Consensus 27 ~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~ 60 (165)
T PF03614_consen 27 FNDIPVRVVSENGQVFCMYVSGFMSKENKILAPD 60 (165)
T ss_pred hcCCceEEEecCCcEEEEEEeccCcccCEEeccC
Confidence 4479999999999999999999999999999654
No 69
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=80.20 E-value=2 Score=24.49 Aligned_cols=22 Identities=23% Similarity=0.327 Sum_probs=14.9
Q ss_pred EEEEEEEecCccceEeeceEEE
Q 033952 45 LLGRVRAFDRHCNMVLENVREM 66 (107)
Q Consensus 45 i~G~L~~fD~hmNlvL~d~~E~ 66 (107)
..|++.|.|+.+.|.|++....
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 6899999999999999886544
No 70
>PRK14632 hypothetical protein; Provisional
Probab=79.65 E-value=4.1 Score=29.55 Aligned_cols=33 Identities=21% Similarity=0.325 Sum_probs=26.0
Q ss_pred HHhhhcCCcEEEEEecC-------CeEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCRN-------NKKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~-------gr~i~G~L~~fD~hmNlvL 60 (107)
+.+++ |+.|.|++++ .+.+.|+|.++|.- ++.|
T Consensus 93 f~r~i--G~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l 132 (172)
T PRK14632 93 MSPYV--GRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL 132 (172)
T ss_pred HHHhC--CCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence 45666 9999999986 57999999999863 4444
No 71
>PRK14646 hypothetical protein; Provisional
Probab=79.30 E-value=4.4 Score=28.86 Aligned_cols=34 Identities=12% Similarity=0.053 Sum_probs=26.2
Q ss_pred HHHhhhcCCcEEEEEecCC----eEEEEEEEEecCccceEe
Q 033952 24 VLMMSVKNNTQVLINCRNN----KKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~g----r~i~G~L~~fD~hmNlvL 60 (107)
-+.+++ |+.|.|+++.. +.+.|+|.++|.- ++.|
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 346667 99999999753 6889999999984 4555
No 72
>PRK14634 hypothetical protein; Provisional
Probab=79.16 E-value=4.5 Score=28.80 Aligned_cols=33 Identities=12% Similarity=0.209 Sum_probs=25.5
Q ss_pred HHhhhcCCcEEEEEecCC----eEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCRNN----KKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~g----r~i~G~L~~fD~hmNlvL 60 (107)
+.++. |+.|.|++... +.+.|+|.++|.- ++.|
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 45666 99999999742 7899999999984 4444
No 73
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=77.76 E-value=5.3 Score=28.15 Aligned_cols=29 Identities=21% Similarity=0.218 Sum_probs=24.2
Q ss_pred HHHhhhcCCcEEEEEe----cCCeEEEEEEEEecC
Q 033952 24 VLMMSVKNNTQVLINC----RNNKKLLGRVRAFDR 54 (107)
Q Consensus 24 ~L~~~~~~~krV~V~l----r~gr~i~G~L~~fD~ 54 (107)
-+.+++ |+.|.|.+ .+++.+.|+|.++|.
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 346677 99999997 466899999999998
No 74
>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=77.34 E-value=6.1 Score=26.41 Aligned_cols=24 Identities=17% Similarity=0.291 Sum_probs=18.1
Q ss_pred HhhhcCCcEEEEEecCCeEEEEEE
Q 033952 26 MMSVKNNTQVLINCRNNKKLLGRV 49 (107)
Q Consensus 26 ~~~~~~~krV~V~lr~gr~i~G~L 49 (107)
-.-+.-+.+|.+.|+||+.+.|++
T Consensus 22 v~~L~ge~~V~l~L~DGs~l~Gtv 45 (101)
T PF11607_consen 22 VSELDGEERVELELDDGSMLRGTV 45 (101)
T ss_dssp HHCTTTT-EEEEEETTS-EEEEEE
T ss_pred HhhcCCcceEEEEEcCCCeeeeee
Confidence 333456789999999999999997
No 75
>PRK14647 hypothetical protein; Provisional
Probab=76.45 E-value=5.9 Score=28.23 Aligned_cols=28 Identities=14% Similarity=0.188 Sum_probs=23.3
Q ss_pred HHhhhcCCcEEEEEec---------CCeEEEEEEEEecC
Q 033952 25 LMMSVKNNTQVLINCR---------NNKKLLGRVRAFDR 54 (107)
Q Consensus 25 L~~~~~~~krV~V~lr---------~gr~i~G~L~~fD~ 54 (107)
+.+++ |+.|.|+++ +.+.+.|+|.++|.
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 45666 999999996 34799999999997
No 76
>PRK14637 hypothetical protein; Provisional
Probab=73.35 E-value=6.8 Score=27.83 Aligned_cols=33 Identities=18% Similarity=0.248 Sum_probs=24.9
Q ss_pred HHhhhcCCcEEEEEecCCeEE-EEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCRNNKKL-LGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~gr~i-~G~L~~fD~hmNlvL 60 (107)
+.++. |+.|.|++.+.+.+ .|+|.++|.- ++.|
T Consensus 93 f~r~~--G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 93 FSIFV--GETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred HHHhC--CCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 45666 99999999555556 7999999985 4444
No 77
>PRK14631 hypothetical protein; Provisional
Probab=72.77 E-value=7.9 Score=28.18 Aligned_cols=28 Identities=25% Similarity=0.288 Sum_probs=23.3
Q ss_pred HHHhhhcCCcEEEEEec----CCeEEEEEEEEec
Q 033952 24 VLMMSVKNNTQVLINCR----NNKKLLGRVRAFD 53 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr----~gr~i~G~L~~fD 53 (107)
-+.+++ |+.|.|.+. +.+.+.|+|.++|
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 346666 999999996 4589999999998
No 78
>PRK10898 serine endoprotease; Provisional
Probab=71.25 E-value=9.4 Score=30.34 Aligned_cols=35 Identities=6% Similarity=0.222 Sum_probs=29.9
Q ss_pred cCCcEEEEEecCCeEEEEEEEEecCccceEeeceE
Q 033952 30 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 64 (107)
Q Consensus 30 ~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~ 64 (107)
+....+.|.+.+|+.+.++++++|....|.|=.+.
T Consensus 99 ~~a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 99 NDADQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CCCCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 34568899999999999999999999999885553
No 79
>PRK14641 hypothetical protein; Provisional
Probab=70.64 E-value=8.5 Score=28.05 Aligned_cols=27 Identities=11% Similarity=0.255 Sum_probs=22.2
Q ss_pred HHhhhcCCcEEEEEecC----CeEEEEEEEEec
Q 033952 25 LMMSVKNNTQVLINCRN----NKKLLGRVRAFD 53 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~----gr~i~G~L~~fD 53 (107)
+.+++ |+.|.|.+.+ .+.+.|+|.++|
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 45666 9999999976 468999999995
No 80
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=69.96 E-value=10 Score=30.04 Aligned_cols=33 Identities=9% Similarity=0.264 Sum_probs=28.8
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceEeeceE
Q 033952 32 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 64 (107)
Q Consensus 32 ~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~ 64 (107)
...+.|.+.+|+.+.++++++|....|.|=.+.
T Consensus 101 ~~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 101 ADQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 457899999999999999999999999985543
No 81
>PRK10139 serine endoprotease; Provisional
Probab=68.62 E-value=13 Score=30.75 Aligned_cols=34 Identities=9% Similarity=0.271 Sum_probs=30.3
Q ss_pred cCCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033952 30 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 63 (107)
Q Consensus 30 ~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~ 63 (107)
+....|.|.+.||+.+.++++++|....|.+=.+
T Consensus 112 ~~a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 112 NQAQKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CCCCEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 5567899999999999999999999999988554
No 82
>PRK10942 serine endoprotease; Provisional
Probab=66.74 E-value=13 Score=30.75 Aligned_cols=34 Identities=18% Similarity=0.320 Sum_probs=29.6
Q ss_pred cCCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033952 30 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 63 (107)
Q Consensus 30 ~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~ 63 (107)
.....|.|.+.||+.+.++++++|...+|.|=.+
T Consensus 133 ~~a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 133 DNATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCCCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 3456899999999999999999999999988644
No 83
>PRK06955 biotin--protein ligase; Provisional
Probab=66.18 E-value=20 Score=27.79 Aligned_cols=34 Identities=12% Similarity=0.190 Sum_probs=28.5
Q ss_pred hcCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033952 29 VKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 62 (107)
Q Consensus 29 ~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d 62 (107)
...+++|+|...+++.+.|+++|.|..-.|+++.
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 4458999997666778999999999999999953
No 84
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=65.42 E-value=20 Score=22.24 Aligned_cols=57 Identities=18% Similarity=0.323 Sum_probs=38.1
Q ss_pred CCc--HHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeC
Q 033952 19 TGP--LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 96 (107)
Q Consensus 19 ~~P--l~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG 96 (107)
..| ...|++.+ |++|.|.+-.| .++|+|++.-.- .++|+. .-..+|||=
T Consensus 8 vdpyvyq~lq~li--G~~vvV~T~~g-~v~G~L~~V~pD-hIvl~~-------------------------~~~~~~IR~ 58 (66)
T PF10842_consen 8 VDPYVYQTLQSLI--GQRVVVQTTRG-SVRGILVDVKPD-HIVLEE-------------------------NGTPFFIRI 58 (66)
T ss_pred cCHHHHHHHHHhc--CCEEEEEEcCC-cEEEEEEeecCC-EEEEEe-------------------------CCcEEEEEe
Confidence 445 45788888 99999999655 459999886421 123311 123678888
Q ss_pred CcEEEEEe
Q 033952 97 DSVIIVLR 104 (107)
Q Consensus 97 d~Vv~Is~ 104 (107)
.+|+.|.|
T Consensus 59 ~~IV~v~p 66 (66)
T PF10842_consen 59 AQIVWVMP 66 (66)
T ss_pred eeEEEEcC
Confidence 88888754
No 85
>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=60.71 E-value=21 Score=28.81 Aligned_cols=35 Identities=3% Similarity=0.229 Sum_probs=29.9
Q ss_pred cCCcEEEEEecCCeEEEEEEEEecCccceEeeceE
Q 033952 30 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 64 (107)
Q Consensus 30 ~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~ 64 (107)
..-..+.|.+.+++.+.+++.++|.+.+|.|=.+.
T Consensus 79 ~~~~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 79 DGADEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CCCCeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 34568899999999999999999999999985553
No 86
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=57.59 E-value=5.8 Score=28.17 Aligned_cols=26 Identities=23% Similarity=0.319 Sum_probs=20.0
Q ss_pred cCCeEEEEEEEEecCccceEeeceEE
Q 033952 40 RNNKKLLGRVRAFDRHCNMVLENVRE 65 (107)
Q Consensus 40 r~gr~i~G~L~~fD~hmNlvL~d~~E 65 (107)
+.+-.=+|+|+|.|+|-|=.-+|-.-
T Consensus 40 rtd~~kiGTLVG~DkfGNkYyen~~~ 65 (151)
T KOG3382|consen 40 RTDDHKIGTLVGVDKFGNKYYENNDY 65 (151)
T ss_pred hcccccceeeeeecccccchhcccce
Confidence 34445579999999999988877543
No 87
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.12 E-value=37 Score=27.66 Aligned_cols=75 Identities=20% Similarity=0.341 Sum_probs=51.9
Q ss_pred HHhhhcCCcEEEEEecCCeEEEEEEEEec-CccceEeeceEEEeeccCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033952 25 LMMSVKNNTQVLINCRNNKKLLGRVRAFD-RHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 103 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~gr~i~G~L~~fD-~hmNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd~Vv~Is 103 (107)
...++ |+.|.+.-+.+-.|.|+|--.| +-.-|-|.+|.-+.++..+++ +... +. .......|+.||..|-.+.
T Consensus 4 ~t~yI--GS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~-~pq~--p~-~~kVy~YIlFRGSDIKDL~ 77 (361)
T KOG1073|consen 4 VTSYI--GSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTD-GPQV--PP-DDKVYDYILFRGSDIKDLI 77 (361)
T ss_pred ccccc--cceeEEeecccceeeeEEEeccccccceehhheeecccccCCCC-CCcC--CC-CccceeeEEecCcccceee
Confidence 34567 9999999999999999998777 456788888866665433221 1111 11 1125889999999998655
Q ss_pred eC
Q 033952 104 RN 105 (107)
Q Consensus 104 ~~ 105 (107)
..
T Consensus 78 V~ 79 (361)
T KOG1073|consen 78 VQ 79 (361)
T ss_pred ec
Confidence 43
No 88
>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=55.02 E-value=15 Score=23.54 Aligned_cols=25 Identities=8% Similarity=0.256 Sum_probs=16.1
Q ss_pred HHHhhhcCCcEEEEEecCCeEEEEE
Q 033952 24 VLMMSVKNNTQVLINCRNNKKLLGR 48 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr~i~G~ 48 (107)
.|.-+-.-+.+|++.|+||..+.|+
T Consensus 9 yiEiAC~~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 9 YIEIACMYRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp HHHHHHTTTT-EEEE-TTT--EEES
T ss_pred HHHHHHhcCCeEEEEEeCCCEEEEE
Confidence 4444444589999999999999997
No 89
>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=52.46 E-value=54 Score=20.26 Aligned_cols=37 Identities=16% Similarity=0.209 Sum_probs=30.3
Q ss_pred HHHhhhcCCcEEEEEecCCe---EEEEEEEEecCccceEe
Q 033952 24 VLMMSVKNNTQVLINCRNNK---KLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr---~i~G~L~~fD~hmNlvL 60 (107)
.|..++..+..|+|..-++. .+.|++..+|..-+.+.
T Consensus 34 ~l~~a~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~ 73 (92)
T PF08863_consen 34 KLSEAYQENQPVTITYYEDGYYQSVTGTIHKIDEINRTLK 73 (92)
T ss_pred HHHHHhcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEE
Confidence 57777778899999887653 67899999999988776
No 90
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=52.21 E-value=46 Score=25.74 Aligned_cols=32 Identities=22% Similarity=0.320 Sum_probs=27.0
Q ss_pred hcCCcEEEEEecCCeEEEEEEEEecCccceEee
Q 033952 29 VKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLE 61 (107)
Q Consensus 29 ~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~ 61 (107)
...+++|.+... +..+.|++.+.|..-.|+++
T Consensus 269 ~~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 269 LFLGREVKLIIG-DKEISGIARGIDEQGALLLE 300 (319)
T ss_pred cccCCeEEEEeC-CcEEEEEEEEECCCceEEEE
Confidence 345899999874 56799999999999999995
No 91
>PRK14630 hypothetical protein; Provisional
Probab=52.07 E-value=29 Score=24.36 Aligned_cols=32 Identities=6% Similarity=0.077 Sum_probs=23.7
Q ss_pred HHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL 60 (107)
+.+++ |++|.|++.+. ...|+|.++|.- ++.|
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 45666 99999999654 459999999883 3434
No 92
>PRK14635 hypothetical protein; Provisional
Probab=49.03 E-value=37 Score=24.20 Aligned_cols=33 Identities=21% Similarity=0.127 Sum_probs=24.1
Q ss_pred HHhhhcCCcEEEEEec--CCeEEEE---EEEEecCccceEe
Q 033952 25 LMMSVKNNTQVLINCR--NNKKLLG---RVRAFDRHCNMVL 60 (107)
Q Consensus 25 L~~~~~~~krV~V~lr--~gr~i~G---~L~~fD~hmNlvL 60 (107)
+.++. |+.|.|.+. ++..+.| +|.++|.- ++.|
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 45666 999999886 4567777 99999884 4444
No 93
>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=48.99 E-value=63 Score=23.91 Aligned_cols=32 Identities=22% Similarity=0.366 Sum_probs=26.9
Q ss_pred hcCCcEEEEEecCCeEEEEEEEEecCccceEee
Q 033952 29 VKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLE 61 (107)
Q Consensus 29 ~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~ 61 (107)
.-.+++|.|... +..+.|+..|.|..-.|+++
T Consensus 190 ~~~g~~V~v~~~-~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 190 AHIGREVSLTTG-NGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred hccCCeEEEEeC-CcEEEEEEEeECCCceEEEE
Confidence 345899999864 46789999999999999995
No 94
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=48.81 E-value=61 Score=25.02 Aligned_cols=32 Identities=19% Similarity=0.376 Sum_probs=27.2
Q ss_pred cCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033952 30 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 62 (107)
Q Consensus 30 ~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d 62 (107)
..+++|.|.. ++..+.|++.+.|..-.|+++.
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 3589999875 5688999999999999999964
No 95
>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=48.45 E-value=11 Score=25.05 Aligned_cols=17 Identities=29% Similarity=0.284 Sum_probs=15.1
Q ss_pred EEEEEecCccceEeece
Q 033952 47 GRVRAFDRHCNMVLENV 63 (107)
Q Consensus 47 G~L~~fD~hmNlvL~d~ 63 (107)
|+|+|.|.|-|..-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999998664
No 96
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=44.95 E-value=79 Score=23.94 Aligned_cols=33 Identities=15% Similarity=0.177 Sum_probs=29.9
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033952 31 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 63 (107)
Q Consensus 31 ~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~ 63 (107)
.+++|++...++..+.|+..+.|..-.|+|+..
T Consensus 189 ~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 189 LGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred CCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 599999999988888899999999999999664
No 97
>PRK11625 Rho-binding antiterminator; Provisional
Probab=44.41 E-value=58 Score=21.04 Aligned_cols=31 Identities=10% Similarity=0.181 Sum_probs=23.5
Q ss_pred HHHHhhhcCCcEEEEEecCCeEEEEEEEEecCc
Q 033952 23 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRH 55 (107)
Q Consensus 23 ~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~h 55 (107)
+.|.-+...+.+|.+.+++|..+.|+. .|=+
T Consensus 14 DyLElAC~~~~~l~l~l~dGe~~~g~A--~D~~ 44 (84)
T PRK11625 14 DNLELACQHHLMLTLELKDGEVLQAKA--SDLV 44 (84)
T ss_pred hHHHHHHhcCCeEEEEECCCCEEEEEE--Eeee
Confidence 355555556899999999999999975 4544
No 98
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=43.06 E-value=72 Score=27.40 Aligned_cols=32 Identities=22% Similarity=0.291 Sum_probs=27.6
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033952 31 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 62 (107)
Q Consensus 31 ~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d 62 (107)
.+++|.+...++..+.|+.+|.|..-.|+|+.
T Consensus 277 ~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 277 HGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred CCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 48999987666778999999999999999963
No 99
>PRK08330 biotin--protein ligase; Provisional
Probab=36.63 E-value=1.4e+02 Score=22.07 Aligned_cols=32 Identities=19% Similarity=0.166 Sum_probs=26.0
Q ss_pred cCCcEEEEEecCCeEE-EEEEEEecCccceEeec
Q 033952 30 KNNTQVLINCRNNKKL-LGRVRAFDRHCNMVLEN 62 (107)
Q Consensus 30 ~~~krV~V~lr~gr~i-~G~L~~fD~hmNlvL~d 62 (107)
-.+++|.+.. ++..+ .|+..+.|..-.|+++.
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 4489999875 56665 69999999999999964
No 100
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=32.93 E-value=96 Score=19.67 Aligned_cols=26 Identities=15% Similarity=0.213 Sum_probs=19.0
Q ss_pred HHHhhhcCCcEEEEEecCCe----EEEEEEEE
Q 033952 24 VLMMSVKNNTQVLINCRNNK----KLLGRVRA 51 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr~gr----~i~G~L~~ 51 (107)
-|...+ |++|.+..+.|| +-.|.|..
T Consensus 11 ~l~~~v--G~~V~l~a~~GRkK~~~r~GvL~~ 40 (76)
T PF06257_consen 11 ELESHV--GKRVKLKANKGRKKIIEREGVLEE 40 (76)
T ss_dssp HHHHTT--TSEEEEEE--SSS--S-EEEEEEE
T ss_pred HHHHcC--CCEEEEEEcCCceEEEEEEEEEEe
Confidence 467777 999999999997 46798864
No 101
>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=31.27 E-value=1.5e+02 Score=19.33 Aligned_cols=41 Identities=15% Similarity=0.221 Sum_probs=30.7
Q ss_pred HHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033952 22 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 62 (107)
Q Consensus 22 l~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d 62 (107)
+.+|+...+.+..|+|...+|..+.=+|.+.|.--+.++=|
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 45788888889999999888888999999999988776644
No 102
>PRK08477 biotin--protein ligase; Provisional
Probab=31.05 E-value=1.9e+02 Score=21.44 Aligned_cols=36 Identities=3% Similarity=0.067 Sum_probs=29.1
Q ss_pred HhhhcCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033952 26 MMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 62 (107)
Q Consensus 26 ~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d 62 (107)
+.....++.|+|. .+++.+.|+..+.|..--|++.-
T Consensus 169 ~~~~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~ 204 (211)
T PRK08477 169 KLEFEKSKSFSFH-IDGKLVSLKDAELLEDGSILING 204 (211)
T ss_pred HHHHHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECC
Confidence 3333569999986 57899999999999999998854
No 103
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=30.56 E-value=57 Score=21.28 Aligned_cols=21 Identities=29% Similarity=0.523 Sum_probs=19.1
Q ss_pred eeeeceEEEeCCcEEEEEeCC
Q 033952 86 DRFISKMFLRGDSVIIVLRNP 106 (107)
Q Consensus 86 ~r~lg~v~IRGd~Vv~Is~~~ 106 (107)
.|+-|.+.++|..+..|..+|
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 378999999999999999887
No 104
>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=29.78 E-value=79 Score=21.39 Aligned_cols=27 Identities=11% Similarity=0.116 Sum_probs=19.9
Q ss_pred cEEEEEecCCeEEEEEEEEec-CccceE
Q 033952 33 TQVLINCRNNKKLLGRVRAFD-RHCNMV 59 (107)
Q Consensus 33 krV~V~lr~gr~i~G~L~~fD-~hmNlv 59 (107)
....|.++||+.+.|.++.=| ....|.
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~~~~~~l~ 85 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASETADGVTVK 85 (133)
T ss_pred ccEEEEECCCCEEEEEEEecCCCeEEEE
Confidence 347899999999999998833 333443
No 105
>PRK10708 hypothetical protein; Provisional
Probab=28.80 E-value=66 Score=19.59 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=21.5
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCcc
Q 033952 31 NNTQVLINCRNNKKLLGRVRAFDRHC 56 (107)
Q Consensus 31 ~~krV~V~lr~gr~i~G~L~~fD~hm 56 (107)
-+.+|.|++.++-.=.|++.+...|-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 37899999999988888888877664
No 106
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=28.68 E-value=1.1e+02 Score=18.04 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=20.6
Q ss_pred CCeEEEEEEEEe---cCccceEeeceEEEe
Q 033952 41 NNKKLLGRVRAF---DRHCNMVLENVREMW 67 (107)
Q Consensus 41 ~gr~i~G~L~~f---D~hmNlvL~d~~E~~ 67 (107)
+.-.+.|.|..| |+-|-.+|.|++=..
T Consensus 4 ~k~~fKG~L~tYrfcDnVWTFi~kn~~fk~ 33 (52)
T PF02751_consen 4 NKLSFKGHLDTYRFCDNVWTFILKNVEFKM 33 (52)
T ss_dssp -EEEEEEEEEEEEEETTEEEEEEEEEEEEE
T ss_pred eeEEEEEeeeEEEeeCcEEEEEEcCEEEEE
Confidence 345678998765 999999999987554
No 107
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=28.16 E-value=38 Score=22.91 Aligned_cols=36 Identities=6% Similarity=0.145 Sum_probs=30.7
Q ss_pred cCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEE
Q 033952 30 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREM 66 (107)
Q Consensus 30 ~~~krV~V~lr~gr~i~G~L~~fD~hmNlvL~d~~E~ 66 (107)
+.|.+|++.|+ +-++.+++.|.|+++-|.-.||+=.
T Consensus 62 ~~G~rV~lrLk-dlELs~~FLG~~~d~TllEAd~~Ll 97 (104)
T PF10246_consen 62 VRGSRVRLRLK-DLELSAHFLGASKDTTLLEADATLL 97 (104)
T ss_pred ccCCEEEEEEC-CHhhhhhhccCCCCcEEEEeeeEEE
Confidence 44999999999 5678899999999999999888644
No 108
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=26.89 E-value=2.3e+02 Score=20.01 Aligned_cols=26 Identities=12% Similarity=0.138 Sum_probs=22.2
Q ss_pred HhhhcCCcEEEEEecCCeEEEEEEEEec
Q 033952 26 MMSVKNNTQVLINCRNNKKLLGRVRAFD 53 (107)
Q Consensus 26 ~~~~~~~krV~V~lr~gr~i~G~L~~fD 53 (107)
..++ |+.|.+...+|..+.|++.+..
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 3566 9999999899999999998875
No 109
>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=26.49 E-value=89 Score=20.47 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=13.6
Q ss_pred CcEEEEE-ecCCeEEEEEEEE
Q 033952 32 NTQVLIN-CRNNKKLLGRVRA 51 (107)
Q Consensus 32 ~krV~V~-lr~gr~i~G~L~~ 51 (107)
|..|+|. +.+++.+.|++.+
T Consensus 96 G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 96 GDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred CCEEEEEECCCCCEEEEEEeC
Confidence 6677777 6677777776654
No 110
>PRK06630 hypothetical protein; Provisional
Probab=25.88 E-value=36 Score=22.80 Aligned_cols=19 Identities=16% Similarity=0.106 Sum_probs=16.6
Q ss_pred EEEEEEEecCccceEeece
Q 033952 45 LLGRVRAFDRHCNMVLENV 63 (107)
Q Consensus 45 i~G~L~~fD~hmNlvL~d~ 63 (107)
..|+|+|-|+|-|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4799999999999988774
No 111
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=25.59 E-value=74 Score=19.47 Aligned_cols=24 Identities=17% Similarity=0.320 Sum_probs=19.6
Q ss_pred CCcEEEEEecCCeEEEEEEEEecC
Q 033952 31 NNTQVLINCRNNKKLLGRVRAFDR 54 (107)
Q Consensus 31 ~~krV~V~lr~gr~i~G~L~~fD~ 54 (107)
...+|.|.+-||..+.+++.+-|.
T Consensus 3 ~~~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 3 DQCRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred CeEEEEEEcCCCCEEEEEeCCCCc
Confidence 357899999999999998876554
No 112
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=24.59 E-value=1.4e+02 Score=16.57 Aligned_cols=24 Identities=13% Similarity=0.152 Sum_probs=20.3
Q ss_pred CcEEEEEecCCeEEEEEEEEecCc
Q 033952 32 NTQVLINCRNNKKLLGRVRAFDRH 55 (107)
Q Consensus 32 ~krV~V~lr~gr~i~G~L~~fD~h 55 (107)
|..+.+...+|..++|++.+++.-
T Consensus 6 G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 6 GDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCEEEEEeCCCCEEEEEEEEECCC
Confidence 677777777899999999999964
No 113
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=23.35 E-value=1.1e+02 Score=22.52 Aligned_cols=32 Identities=13% Similarity=0.194 Sum_probs=20.6
Q ss_pred HHHhhhcCCcEEEEEec-CCeEEEEEEEEecCc
Q 033952 24 VLMMSVKNNTQVLINCR-NNKKLLGRVRAFDRH 55 (107)
Q Consensus 24 ~L~~~~~~~krV~V~lr-~gr~i~G~L~~fD~h 55 (107)
||-..--.--+|.+.+. ++..|+|+|.+||+=
T Consensus 125 fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 125 FLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 44443322345555554 468999999999975
No 114
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.52 E-value=99 Score=23.10 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=16.1
Q ss_pred CcEEEEE-ecCCeEEEEEEEE
Q 033952 32 NTQVLIN-CRNNKKLLGRVRA 51 (107)
Q Consensus 32 ~krV~V~-lr~gr~i~G~L~~ 51 (107)
|..|+|. +.+|+.+.|++.+
T Consensus 207 Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 207 GQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCeEEEEECCCCCEEEEEEeC
Confidence 7788888 8888888888765
No 115
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=22.19 E-value=96 Score=18.89 Aligned_cols=25 Identities=16% Similarity=0.219 Sum_probs=20.8
Q ss_pred CcEEEEEecCCeEEEEEEEEecCcc
Q 033952 32 NTQVLINCRNNKKLLGRVRAFDRHC 56 (107)
Q Consensus 32 ~krV~V~lr~gr~i~G~L~~fD~hm 56 (107)
+.+|.|++.++-.=.|++.+...|-
T Consensus 4 nD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 4 NDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred ccEEEEecCCcccccceEEEEeecc
Confidence 7899999999877788888877664
No 116
>PF09196 DUF1953: Domain of unknown function (DUF1953); InterPro: IPR015279 This domain is found in the Archaeal protein maltooligosyl trehalose synthase produced by Sulfolobus spp. Its function has not, as yet, been defined. ; PDB: 3HJE_A 1IV8_A.
Probab=21.54 E-value=1.1e+02 Score=18.64 Aligned_cols=14 Identities=14% Similarity=0.624 Sum_probs=11.1
Q ss_pred EEEeCCcEEEEEeC
Q 033952 92 MFLRGDSVIIVLRN 105 (107)
Q Consensus 92 v~IRGd~Vv~Is~~ 105 (107)
=|+|||.|..|...
T Consensus 13 gf~r~~kilviikt 26 (66)
T PF09196_consen 13 GFIRFNKILVIIKT 26 (66)
T ss_dssp EEEETTTEEEEEES
T ss_pred eEEecCEEEEEEec
Confidence 48999999887653
No 117
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=21.38 E-value=54 Score=22.48 Aligned_cols=19 Identities=32% Similarity=0.286 Sum_probs=16.4
Q ss_pred EEEEEEecCccceEeeceE
Q 033952 46 LGRVRAFDRHCNMVLENVR 64 (107)
Q Consensus 46 ~G~L~~fD~hmNlvL~d~~ 64 (107)
.|.|+|-|+|-|-.-++..
T Consensus 9 ~g~lVG~D~~GNkYYE~~~ 27 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPS 27 (115)
T ss_pred cceEeEEcCCCCeeeEcCC
Confidence 6999999999999887643
No 118
>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=21.25 E-value=91 Score=18.43 Aligned_cols=41 Identities=17% Similarity=0.173 Sum_probs=27.2
Q ss_pred ccCCCcHHHHHhhhcCCcEEEEEecCCeEEEEEEEEecCccce
Q 033952 16 EFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNM 58 (107)
Q Consensus 16 ~~~~~Pl~~L~~~~~~~krV~V~lr~gr~i~G~L~~fD~hmNl 58 (107)
.+...+-.+|+.....+.+| +.+++|+. .+.|..++.|=++
T Consensus 8 e~r~~~~~~l~~v~~~~~pv-~It~~g~~-~~vli~~~~ye~l 48 (75)
T PF02604_consen 8 EFRNNFSELLDEVEEGEEPV-IITKNGKP-VAVLISVEDYERL 48 (75)
T ss_dssp HHHHTHHHHHHHHHHCT-EE-EEEETTEE-EEEEEEHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCeE-EEEECCCC-CeecccHHHHHHH
Confidence 34556777888887544556 66677766 7888888776443
No 119
>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=20.23 E-value=2.1e+02 Score=17.15 Aligned_cols=26 Identities=15% Similarity=0.278 Sum_probs=18.7
Q ss_pred cCCcEEEEEecCCe-EEEEEEEEecCc
Q 033952 30 KNNTQVLINCRNNK-KLLGRVRAFDRH 55 (107)
Q Consensus 30 ~~~krV~V~lr~gr-~i~G~L~~fD~h 55 (107)
..|.+|.+.=-++. .|.|.+.+||.-
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEeccc
Confidence 34889999888775 569999999963
Done!