Query 034064
Match_columns 104
No_of_seqs 105 out of 1043
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 09:22:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034064.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034064hhsearch_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 99.9 3.3E-25 7.2E-30 145.6 10.2 82 21-103 4-87 (87)
2 cd01730 LSm3 The eukaryotic Sm 99.9 7.8E-25 1.7E-29 141.9 9.7 80 21-101 3-82 (82)
3 cd01732 LSm5 The eukaryotic Sm 99.9 2.5E-24 5.4E-29 138.2 10.3 74 18-102 2-75 (76)
4 cd01729 LSm7 The eukaryotic Sm 99.9 1.6E-23 3.5E-28 135.7 9.9 75 23-103 6-80 (81)
5 cd01731 archaeal_Sm1 The archa 99.9 5.8E-23 1.3E-27 128.6 9.0 67 21-101 2-68 (68)
6 cd01728 LSm1 The eukaryotic Sm 99.9 9.5E-23 2.1E-27 130.3 10.1 71 20-101 3-73 (74)
7 PRK00737 small nuclear ribonuc 99.9 7.6E-23 1.7E-27 129.7 9.4 69 19-101 4-72 (72)
8 cd01717 Sm_B The eukaryotic Sm 99.9 9.1E-23 2E-27 131.2 9.7 75 23-101 4-78 (79)
9 cd01719 Sm_G The eukaryotic Sm 99.9 2.1E-22 4.6E-27 127.9 9.4 68 22-103 3-70 (72)
10 cd01727 LSm8 The eukaryotic Sm 99.9 3.6E-22 7.8E-27 127.1 9.4 72 22-103 2-73 (74)
11 cd01718 Sm_E The eukaryotic Sm 99.9 1.8E-21 4E-26 125.9 8.9 73 16-101 3-79 (79)
12 cd01726 LSm6 The eukaryotic Sm 99.9 2.5E-21 5.4E-26 121.0 8.9 66 21-100 2-67 (67)
13 KOG3460 Small nuclear ribonucl 99.8 1.5E-22 3.2E-27 131.4 1.4 86 17-103 3-88 (91)
14 cd01722 Sm_F The eukaryotic Sm 99.8 7.7E-21 1.7E-25 119.2 8.9 67 20-100 2-68 (68)
15 cd06168 LSm9 The eukaryotic Sm 99.8 1.5E-20 3.3E-25 120.4 10.2 72 22-101 3-74 (75)
16 PF01423 LSM: LSM domain ; In 99.8 2.9E-20 6.2E-25 115.0 9.5 66 23-101 2-67 (67)
17 smart00651 Sm snRNP Sm protein 99.8 3.4E-20 7.3E-25 114.6 9.4 66 23-101 2-67 (67)
18 COG1958 LSM1 Small nuclear rib 99.8 4.4E-20 9.6E-25 118.5 9.0 74 18-101 6-79 (79)
19 PTZ00138 small nuclear ribonuc 99.8 6.3E-19 1.4E-23 116.3 8.7 79 11-102 6-88 (89)
20 cd00600 Sm_like The eukaryotic 99.8 1.3E-18 2.8E-23 106.0 8.5 63 24-100 1-63 (63)
21 cd01723 LSm4 The eukaryotic Sm 99.8 1.4E-18 3E-23 111.1 9.0 71 20-103 2-72 (76)
22 KOG1780 Small Nuclear ribonucl 99.8 4E-19 8.7E-24 113.0 6.0 67 23-103 8-74 (77)
23 cd01721 Sm_D3 The eukaryotic S 99.8 6.2E-18 1.3E-22 106.7 9.6 68 21-102 2-69 (70)
24 cd01725 LSm2 The eukaryotic Sm 99.7 2.2E-17 4.7E-22 106.9 9.8 73 19-103 1-73 (81)
25 cd01724 Sm_D1 The eukaryotic S 99.7 5.1E-17 1.1E-21 107.2 9.9 69 21-103 3-71 (90)
26 KOG1781 Small Nuclear ribonucl 99.7 6.5E-19 1.4E-23 117.4 0.1 76 22-103 20-95 (108)
27 cd01733 LSm10 The eukaryotic S 99.7 6.5E-17 1.4E-21 104.2 9.3 67 21-101 11-77 (78)
28 KOG1783 Small nuclear ribonucl 99.6 4.2E-16 9.1E-21 99.0 1.0 69 21-103 8-76 (77)
29 KOG1782 Small Nuclear ribonucl 99.6 3.6E-16 7.9E-21 107.8 0.1 71 22-103 12-82 (129)
30 KOG3482 Small nuclear ribonucl 99.5 1.5E-14 3.4E-19 91.8 6.0 70 20-103 9-78 (79)
31 KOG3168 U1 snRNP component [Tr 99.5 1.3E-15 2.7E-20 110.0 0.7 76 23-102 8-83 (177)
32 KOG1784 Small Nuclear ribonucl 99.5 1.1E-14 2.4E-19 96.0 4.1 72 22-103 3-74 (96)
33 KOG3459 Small nuclear ribonucl 99.4 1.4E-14 3.1E-19 98.2 0.1 74 29-103 36-109 (114)
34 KOG1775 U6 snRNA-associated Sm 99.4 1.3E-13 2.7E-18 88.4 3.9 74 18-102 6-79 (84)
35 KOG1774 Small nuclear ribonucl 99.4 8.7E-13 1.9E-17 85.5 5.6 69 22-103 19-87 (88)
36 KOG3448 Predicted snRNP core p 99.2 1.1E-10 2.5E-15 76.7 8.4 73 18-102 1-73 (96)
37 cd01739 LSm11_C The eukaryotic 99.0 2E-10 4.3E-15 71.7 2.9 38 29-66 8-49 (66)
38 KOG3293 Small nuclear ribonucl 98.9 3.9E-09 8.3E-14 73.2 6.1 72 18-102 1-72 (134)
39 KOG3428 Small nuclear ribonucl 98.3 1.1E-05 2.3E-10 54.9 8.6 67 21-102 4-70 (109)
40 KOG3172 Small nuclear ribonucl 98.2 7.1E-06 1.5E-10 55.9 6.4 72 17-102 3-74 (119)
41 PF14438 SM-ATX: Ataxin 2 SM d 97.6 0.00024 5.2E-09 44.8 6.2 70 21-97 4-76 (77)
42 cd01716 Hfq Hfq, an abundant, 96.7 0.0039 8.5E-08 38.5 4.4 29 29-58 11-39 (61)
43 TIGR02383 Hfq RNA chaperone Hf 96.6 0.0055 1.2E-07 37.9 4.4 29 29-58 15-43 (61)
44 PF02237 BPL_C: Biotin protein 96.1 0.032 6.9E-07 32.3 5.8 35 27-62 1-35 (48)
45 COG1923 Hfq Uncharacterized ho 95.4 0.043 9.3E-07 35.4 4.7 31 29-60 19-49 (77)
46 PRK00395 hfq RNA-binding prote 95.1 0.049 1.1E-06 35.3 4.3 31 29-59 19-49 (79)
47 PF12701 LSM14: Scd6-like Sm d 94.9 0.53 1.2E-05 31.3 8.9 71 25-100 4-75 (96)
48 PF11095 Gemin7: Gem-associate 93.5 1 2.2E-05 29.2 7.8 64 20-102 15-79 (80)
49 cd01735 LSm12_N LSm12 belongs 93.4 0.26 5.6E-06 30.4 4.7 36 27-62 4-39 (61)
50 PRK14638 hypothetical protein; 93.1 0.2 4.4E-06 35.6 4.5 36 22-58 93-128 (150)
51 PRK14091 RNA-binding protein H 93.0 0.2 4.3E-06 36.6 4.4 29 29-58 24-52 (165)
52 cd01736 LSm14_N LSm14 (also kn 92.4 1.2 2.5E-05 28.5 6.9 70 25-98 2-72 (74)
53 PRK14639 hypothetical protein; 91.8 0.37 8E-06 33.9 4.5 36 22-58 81-116 (140)
54 PRK02001 hypothetical protein; 91.5 0.4 8.8E-06 34.3 4.5 36 22-58 83-118 (152)
55 PRK14644 hypothetical protein; 91.0 1.1 2.3E-05 31.5 6.1 51 7-58 63-117 (136)
56 PRK14091 RNA-binding protein H 90.2 0.58 1.3E-05 34.2 4.3 31 29-59 104-134 (165)
57 PF06372 Gemin6: Gemin6 protei 88.8 0.88 1.9E-05 33.2 4.4 39 23-62 11-50 (166)
58 cd01734 YlxS_C YxlS is a Bacil 88.0 1.4 3.1E-05 27.9 4.6 36 22-58 18-57 (83)
59 PRK14640 hypothetical protein; 87.6 1.3 2.9E-05 31.4 4.7 49 9-58 76-129 (152)
60 PRK14633 hypothetical protein; 87.2 1.5 3.2E-05 31.2 4.6 36 22-58 87-126 (150)
61 PRK14642 hypothetical protein; 86.3 1.6 3.4E-05 32.7 4.6 47 10-57 80-140 (197)
62 PRK14636 hypothetical protein; 85.7 1.7 3.8E-05 31.7 4.5 36 22-58 91-130 (176)
63 PRK14645 hypothetical protein; 85.1 1.9 4.1E-05 30.9 4.4 35 22-58 95-129 (154)
64 PF10842 DUF2642: Protein of u 85.1 2.7 5.9E-05 26.2 4.5 55 20-101 12-66 (66)
65 PF02576 DUF150: Uncharacteris 84.9 1.5 3.2E-05 30.4 3.7 48 9-57 66-118 (141)
66 PRK14643 hypothetical protein; 84.3 2.3 4.9E-05 30.8 4.5 31 22-52 97-131 (164)
67 COG0779 Uncharacterized protei 84.2 2.5 5.3E-05 30.4 4.6 36 22-58 92-131 (153)
68 PRK00092 ribosome maturation p 83.2 2.9 6.3E-05 29.5 4.6 42 10-51 78-124 (154)
69 PRK14634 hypothetical protein; 83.0 2.9 6.3E-05 29.8 4.6 36 22-58 93-132 (155)
70 PRK14632 hypothetical protein; 82.8 2.9 6.2E-05 30.4 4.6 36 22-58 91-133 (172)
71 PRK14646 hypothetical protein; 82.5 3.1 6.7E-05 29.7 4.6 36 22-58 93-132 (155)
72 PRK14647 hypothetical protein; 81.3 3.6 7.8E-05 29.4 4.6 30 22-51 92-130 (159)
73 PRK14637 hypothetical protein; 80.6 3.4 7.4E-05 29.4 4.2 36 22-58 91-127 (151)
74 PF03614 Flag1_repress: Repres 80.3 5.1 0.00011 29.1 5.0 35 27-61 27-61 (165)
75 PRK14631 hypothetical protein; 78.8 4.8 0.0001 29.3 4.6 29 22-50 110-142 (174)
76 PRK14641 hypothetical protein; 75.4 5.9 0.00013 28.9 4.3 29 22-50 97-129 (173)
77 PRK10898 serine endoprotease; 73.7 7 0.00015 31.1 4.7 32 30-61 102-133 (353)
78 TIGR02038 protease_degS peripl 73.6 6.9 0.00015 31.0 4.6 32 30-61 102-133 (351)
79 PRK06955 biotin--protein ligas 72.9 8.8 0.00019 29.8 4.9 34 26-59 246-279 (300)
80 PRK10942 serine endoprotease; 71.6 7.7 0.00017 32.2 4.6 31 30-60 136-166 (473)
81 PRK10139 serine endoprotease; 67.5 11 0.00024 31.1 4.7 32 30-61 115-146 (455)
82 TIGR02037 degP_htrA_DO peripla 63.5 14 0.00031 29.8 4.6 32 30-61 82-113 (428)
83 PF03614 Flag1_repress: Repres 62.9 8.8 0.00019 27.9 2.9 25 28-52 119-143 (165)
84 PF11607 DUF3247: Protein of u 62.6 12 0.00026 25.1 3.3 19 29-47 28-46 (101)
85 PRK14630 hypothetical protein; 61.6 17 0.00037 25.5 4.1 35 22-58 90-124 (143)
86 TIGR00121 birA_ligase birA, bi 60.2 23 0.0005 26.3 4.9 33 25-58 189-221 (237)
87 PRK11886 bifunctional biotin-- 59.3 23 0.0005 27.4 4.9 32 26-58 269-300 (319)
88 PRK13325 bifunctional biotin-- 58.8 22 0.00047 30.5 5.0 33 27-59 276-308 (592)
89 PF06257 DUF1021: Protein of u 58.1 33 0.00072 21.9 4.6 32 17-48 5-40 (76)
90 PTZ00275 biotin-acetyl-CoA-car 55.6 30 0.00065 26.8 4.9 32 27-59 235-266 (285)
91 PF05071 NDUFA12: NADH ubiquin 54.8 5.4 0.00012 26.6 0.6 17 44-60 1-17 (105)
92 COG0340 BirA Biotin-(acetyl-Co 54.5 41 0.00089 25.5 5.4 37 24-60 185-221 (238)
93 PRK14635 hypothetical protein; 53.8 30 0.00064 24.7 4.4 36 22-58 92-132 (162)
94 PF14563 DUF4444: Domain of un 53.1 15 0.00033 21.0 2.2 22 42-63 10-31 (42)
95 PF06308 ErmC: 23S rRNA methyl 50.7 12 0.00027 19.1 1.4 11 1-11 1-11 (27)
96 PRK08330 biotin--protein ligas 48.4 50 0.0011 24.5 5.0 33 26-59 185-218 (236)
97 KOG3382 NADH:ubiquinone oxidor 46.3 11 0.00024 26.9 1.1 22 39-60 42-63 (151)
98 PRK06646 DNA polymerase III su 46.1 36 0.00077 24.2 3.7 34 5-38 3-38 (154)
99 TIGR03170 flgA_cterm flagella 43.7 31 0.00068 22.7 3.0 24 25-48 92-116 (122)
100 COG4466 Veg Uncharacterized pr 40.6 30 0.00065 22.4 2.4 40 19-58 9-53 (80)
101 TIGR02603 CxxCH_TIGR02603 puta 38.1 68 0.0015 21.7 4.1 29 31-60 59-87 (133)
102 PRK07018 flgA flagellar basal 37.5 39 0.00085 25.3 3.0 24 25-48 203-227 (235)
103 KOG3493 Ubiquitin-like protein 36.6 28 0.0006 22.0 1.7 20 23-42 5-24 (73)
104 PF11743 DUF3301: Protein of u 36.4 38 0.00083 22.2 2.5 21 83-103 76-96 (97)
105 PRK09618 flgD flagellar basal 34.0 1.6E+02 0.0034 20.9 5.5 27 24-50 87-113 (142)
106 PF07073 ROF: Modulator of Rho 31.8 31 0.00068 22.1 1.4 25 28-54 16-40 (80)
107 PRK08477 biotin--protein ligas 31.6 1.2E+02 0.0025 22.6 4.7 34 25-59 171-204 (211)
108 PRK05728 DNA polymerase III su 28.9 90 0.0019 21.6 3.5 35 5-39 3-39 (142)
109 PRK08515 flgA flagellar basal 28.8 85 0.0019 23.4 3.6 24 25-48 192-215 (222)
110 PF09465 LBR_tudor: Lamin-B re 28.5 1.2E+02 0.0027 18.2 3.5 25 27-51 7-32 (55)
111 PRK06005 flgA flagellar basal 28.1 76 0.0017 22.6 3.1 24 25-48 127-151 (160)
112 PRK10708 hypothetical protein; 27.8 72 0.0016 19.5 2.4 26 28-53 3-28 (62)
113 COG5316 Uncharacterized conser 27.6 1.4E+02 0.003 25.0 4.7 45 20-65 73-117 (421)
114 PRK12617 flgA flagellar basal 27.4 74 0.0016 23.8 3.0 24 25-48 182-206 (214)
115 COG2927 HolC DNA polymerase II 27.1 1.2E+02 0.0025 21.7 3.8 34 5-38 3-38 (144)
116 PRK06630 hypothetical protein; 27.0 35 0.00075 23.0 1.1 19 42-60 11-29 (99)
117 COG0265 DegQ Trypsin-like seri 24.8 1.4E+02 0.0031 23.1 4.3 33 29-61 95-127 (347)
118 PF10781 DSRB: Dextransucrase 24.5 82 0.0018 19.3 2.3 26 28-53 3-28 (62)
119 PF04364 DNA_pol3_chi: DNA pol 24.0 1.3E+02 0.0029 20.5 3.6 35 4-38 2-38 (137)
120 PLN03095 NADH:ubiquinone oxido 23.8 45 0.00097 23.0 1.1 20 43-62 9-28 (115)
121 PF14153 Spore_coat_CotO: Spor 22.8 1.2E+02 0.0025 22.4 3.3 17 37-53 142-158 (185)
122 PRK06804 flgA flagellar basal 22.3 1E+02 0.0023 23.8 3.0 24 25-48 229-253 (261)
123 PRK12618 flgA flagellar basal 22.3 1.1E+02 0.0025 21.2 3.0 24 25-48 108-132 (141)
124 smart00166 UBX Domain present 22.3 85 0.0018 19.2 2.2 23 29-51 4-26 (80)
125 PF14485 DUF4431: Domain of un 22.3 1.1E+02 0.0024 17.6 2.5 14 22-35 12-25 (48)
126 PTZ00276 biotin/lipoate protei 21.6 2.7E+02 0.0058 20.9 5.1 23 37-59 209-231 (245)
127 COG3814 Uncharacterized protei 20.9 1.5E+02 0.0032 21.4 3.3 31 6-37 38-68 (157)
128 smart00725 NEAT NEAr Transport 20.4 2.5E+02 0.0054 18.9 4.4 49 6-57 7-56 (123)
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=99.93 E-value=3.3e-25 Score=145.61 Aligned_cols=82 Identities=82% Similarity=1.249 Sum_probs=66.2
Q ss_pred HHHHHhcC--CcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEE
Q 034064 21 CFWALEFI--VLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 98 (104)
Q Consensus 21 ~~~L~~~l--~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~ 98 (104)
+.+|.+.+ +++|.|+|++||++.|+|+|||+||||+|+||+|.+...++++++. +..+..+++++|.+|||||||++
T Consensus 4 l~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~-~~~~~~~~r~lg~v~iRGd~Vv~ 82 (87)
T cd01720 4 LSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGK-KAKPVNKDRFISKMFLRGDSVIL 82 (87)
T ss_pred HHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccc-cccceeeeeEcccEEEeCCEEEE
Confidence 45677776 8999999999999999999999999999999999987644332211 11123456889999999999999
Q ss_pred EEecC
Q 034064 99 VLRNP 103 (104)
Q Consensus 99 Is~~~ 103 (104)
|+++|
T Consensus 83 Is~~~ 87 (87)
T cd01720 83 VLRNP 87 (87)
T ss_pred EecCC
Confidence 99986
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=99.92 E-value=7.8e-25 Score=141.89 Aligned_cols=80 Identities=30% Similarity=0.422 Sum_probs=64.5
Q ss_pred HHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEE
Q 034064 21 CFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 100 (104)
Q Consensus 21 ~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is 100 (104)
..+|+..++++|.|+++|||++.|+|+|||+||||+|+||+|.+....++++.. +......+|.+|.++||||||++|+
T Consensus 3 l~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~-~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 3 LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETY-EEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred hHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeeccccccccc-ccccceeEEEcCeEEEeCCEEEEEC
Confidence 467888999999999999999999999999999999999999987543322110 0111235688999999999999998
Q ss_pred e
Q 034064 101 R 101 (104)
Q Consensus 101 ~ 101 (104)
|
T Consensus 82 ~ 82 (82)
T cd01730 82 P 82 (82)
T ss_pred C
Confidence 6
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=2.5e-24 Score=138.20 Aligned_cols=74 Identities=26% Similarity=0.422 Sum_probs=64.2
Q ss_pred hhHHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEE
Q 034064 18 MLFCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 97 (104)
Q Consensus 18 ~l~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv 97 (104)
+++..+|+++++++|.|++++||++.|+|+|||+||||+|+||+|.+.. ++ ++ +.+++|.++|||+||+
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~-~~-~~---------~~~~lg~v~iRG~nV~ 70 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEIT-PE-GR---------KITKLDQILLNGNNIC 70 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEc-CC-Cc---------eeeEcCeEEEeCCeEE
Confidence 4677889999999999999999999999999999999999999998743 11 11 2367999999999999
Q ss_pred EEEec
Q 034064 98 IVLRN 102 (104)
Q Consensus 98 ~Is~~ 102 (104)
+|+|-
T Consensus 71 ~i~p~ 75 (76)
T cd01732 71 MLVPG 75 (76)
T ss_pred EEECC
Confidence 99973
No 4
>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=99.90 E-value=1.6e-23 Score=135.70 Aligned_cols=75 Identities=16% Similarity=0.292 Sum_probs=62.1
Q ss_pred HHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEec
Q 034064 23 WALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 102 (104)
Q Consensus 23 ~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~~ 102 (104)
-|+++++++|.|+|+|||++.|+|+|||+||||+|+||+|+......+. +....++.+|.++|||+||++|+|.
T Consensus 6 ~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~------~~~~~~~~lG~v~iRG~nV~~i~~~ 79 (81)
T cd01729 6 DLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPY------KLTDKTRQLGLVVCRGTSVVLISPV 79 (81)
T ss_pred hHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCccc------ccccceeEccEEEEcCCEEEEEecC
Confidence 4889999999999999999999999999999999999999876422110 0012347799999999999999986
Q ss_pred C
Q 034064 103 P 103 (104)
Q Consensus 103 ~ 103 (104)
.
T Consensus 80 ~ 80 (81)
T cd01729 80 D 80 (81)
T ss_pred C
Confidence 4
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=99.89 E-value=5.8e-23 Score=128.57 Aligned_cols=67 Identities=25% Similarity=0.436 Sum_probs=59.9
Q ss_pred HHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEE
Q 034064 21 CFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 100 (104)
Q Consensus 21 ~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is 100 (104)
..+|+++++++|.|+|++|+++.|+|.|||+|||++|+||+|.+.. . .++.+|.++|||+||++|+
T Consensus 2 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~-----~---------~~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 2 LDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG-----E---------PVRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred hHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC-----C---------eEeEcCcEEEeCCEEEEEc
Confidence 4578999999999999999999999999999999999999998642 1 2367999999999999998
Q ss_pred e
Q 034064 101 R 101 (104)
Q Consensus 101 ~ 101 (104)
|
T Consensus 68 ~ 68 (68)
T cd01731 68 P 68 (68)
T ss_pred C
Confidence 6
No 6
>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=99.89 E-value=9.5e-23 Score=130.29 Aligned_cols=71 Identities=24% Similarity=0.309 Sum_probs=61.4
Q ss_pred HHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEE
Q 034064 20 FCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 99 (104)
Q Consensus 20 ~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~I 99 (104)
|...|+++++++|.|+++|||++.|+|+|||+|||++|+||+|.....+ + ..++.+|.+++||+||++|
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~---~--------~~~~~lG~~viRG~~V~~i 71 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD---K--------YGDIPRGIFIIRGENVVLL 71 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC---c--------cceeEeeEEEEECCEEEEE
Confidence 3467999999999999999999999999999999999999999875311 1 1246799999999999999
Q ss_pred Ee
Q 034064 100 LR 101 (104)
Q Consensus 100 s~ 101 (104)
+.
T Consensus 72 g~ 73 (74)
T cd01728 72 GE 73 (74)
T ss_pred Ec
Confidence 86
No 7
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.89 E-value=7.6e-23 Score=129.67 Aligned_cols=69 Identities=25% Similarity=0.356 Sum_probs=60.7
Q ss_pred hHHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEE
Q 034064 19 LFCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 98 (104)
Q Consensus 19 l~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~ 98 (104)
.+..+|+++++++|.|+|+||+++.|+|+|||+|||++|+||+|.+.. + ..+.+|.++|||+||++
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-----~---------~~~~lg~v~iRG~~V~~ 69 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG-----E---------VVRKLGKVVIRGDNVVY 69 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC-----C---------eEeEcCcEEEeCCEEEE
Confidence 345789999999999999999999999999999999999999997531 1 23679999999999999
Q ss_pred EEe
Q 034064 99 VLR 101 (104)
Q Consensus 99 Is~ 101 (104)
|+|
T Consensus 70 i~~ 72 (72)
T PRK00737 70 VSP 72 (72)
T ss_pred EcC
Confidence 985
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=99.89 E-value=9.1e-23 Score=131.19 Aligned_cols=75 Identities=23% Similarity=0.439 Sum_probs=61.6
Q ss_pred HHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEe
Q 034064 23 WALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 101 (104)
Q Consensus 23 ~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~ 101 (104)
-|.++++++|.|+++|||++.|+|.|||+||||+|+||+|++...+.+... ....++|++|+++|||++|++|+-
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~----~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKN----SEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEecccccccc----ccCcceeEeeeEEEcCCEEEEEEE
Confidence 478899999999999999999999999999999999999988653321100 012245889999999999999984
No 9
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=2.1e-22 Score=127.91 Aligned_cols=68 Identities=21% Similarity=0.348 Sum_probs=60.4
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEe
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 101 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~ 101 (104)
..|+++++++|.|+|++||++.|+|.|||+||||+|+||+|.... . ..+.+|.++|||+||++|++
T Consensus 3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~-----~---------~~~~lg~v~IRG~~I~~i~~ 68 (72)
T cd01719 3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG-----G---------EKNNIGMVVIRGNSIVMLEA 68 (72)
T ss_pred hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC-----C---------ceeEeceEEECCCEEEEEEc
Confidence 568999999999999999999999999999999999999998631 1 23679999999999999998
Q ss_pred cC
Q 034064 102 NP 103 (104)
Q Consensus 102 ~~ 103 (104)
..
T Consensus 69 ~~ 70 (72)
T cd01719 69 LE 70 (72)
T ss_pred cc
Confidence 64
No 10
>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=99.88 E-value=3.6e-22 Score=127.08 Aligned_cols=72 Identities=17% Similarity=0.318 Sum_probs=61.4
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEe
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 101 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~ 101 (104)
..|+++++++|.|+++|||++.|+|+|||+|||++|+||+|.....+. + ..++.+|.+++||+||++|+|
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~-~---------~~~~~lG~~~iRG~~I~~i~~ 71 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDE-G---------VEQVVLGLYIIRGDNIAVVGE 71 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCC-C---------ceeeEeceEEECCCEEEEEEc
Confidence 358899999999999999999999999999999999999998653211 1 134679999999999999998
Q ss_pred cC
Q 034064 102 NP 103 (104)
Q Consensus 102 ~~ 103 (104)
.+
T Consensus 72 ~d 73 (74)
T cd01727 72 ID 73 (74)
T ss_pred cC
Confidence 75
No 11
>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=99.86 E-value=1.8e-21 Score=125.88 Aligned_cols=73 Identities=19% Similarity=0.373 Sum_probs=59.3
Q ss_pred ehhhHHHHHHhcCCc--EEEEEEc--CCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEE
Q 034064 16 TLMLFCFWALEFIVL--QVLINCR--NNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFL 91 (104)
Q Consensus 16 ~~~l~~~~L~~~l~k--rV~V~l~--~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~I 91 (104)
.+..+...+.+++++ +|.|.++ +||+++|+|+|||+||||+|+||+|.... ++ ..+.+|.++|
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 344556778888888 6666666 89999999999999999999999998642 11 2366999999
Q ss_pred eCCcEEEEEe
Q 034064 92 RGDSVIIVLR 101 (104)
Q Consensus 92 RGdnVv~Is~ 101 (104)
|||||++|+|
T Consensus 70 RGnnV~~I~p 79 (79)
T cd01718 70 KGDNITLIQN 79 (79)
T ss_pred eCCEEEEEcC
Confidence 9999999986
No 12
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=2.5e-21 Score=121.02 Aligned_cols=66 Identities=18% Similarity=0.268 Sum_probs=57.9
Q ss_pred HHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEE
Q 034064 21 CFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 100 (104)
Q Consensus 21 ~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is 100 (104)
..+|+++++++|.|+|++|++++|+|.|||+|||++|+||+|.... + ..+.+|.++|||++|++||
T Consensus 2 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~-----~---------~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 2 SEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG-----Q---------LKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred HHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC-----c---------eeeEeCCEEEECCEEEEEC
Confidence 4678999999999999999999999999999999999999986421 1 2356999999999999986
No 13
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.85 E-value=1.5e-22 Score=131.36 Aligned_cols=86 Identities=27% Similarity=0.320 Sum_probs=69.1
Q ss_pred hhhHHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcE
Q 034064 17 LMLFCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 96 (104)
Q Consensus 17 ~~l~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnV 96 (104)
+.-++-+++-+++.||+|+++++|++.|+|+|||+|+|++|.||+|.....+.+++.+++. ....+|.+..+|+|||+|
T Consensus 3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~-~k~~~r~~emlFvRGd~V 81 (91)
T KOG3460|consen 3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEI-VKTTKRTVEMLFVRGDGV 81 (91)
T ss_pred ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHH-HhhhhcceeEEEEeCCeE
Confidence 3345677899999999999999999999999999999999999999987654433322211 122457899999999999
Q ss_pred EEEEecC
Q 034064 97 IIVLRNP 103 (104)
Q Consensus 97 v~Is~~~ 103 (104)
++|||+-
T Consensus 82 ilvspp~ 88 (91)
T KOG3460|consen 82 ILVSPPL 88 (91)
T ss_pred EEEcCcc
Confidence 9999973
No 14
>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=99.85 E-value=7.7e-21 Score=119.20 Aligned_cols=67 Identities=15% Similarity=0.193 Sum_probs=58.1
Q ss_pred HHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEE
Q 034064 20 FCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 99 (104)
Q Consensus 20 ~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~I 99 (104)
+..+|+++++++|.|+|++|+++.|+|.|||+|||++|+||+|.... . ....+|.++|||+||++|
T Consensus 2 p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~-----~---------~~~~lg~~~IRG~~I~~i 67 (68)
T cd01722 2 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG-----K---------STGNLGEVLIRCNNVLYI 67 (68)
T ss_pred HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC-----c---------cccCcCcEEEECCEEEEE
Confidence 35689999999999999999999999999999999999999987431 1 124589999999999998
Q ss_pred E
Q 034064 100 L 100 (104)
Q Consensus 100 s 100 (104)
+
T Consensus 68 ~ 68 (68)
T cd01722 68 R 68 (68)
T ss_pred C
Confidence 4
No 15
>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=99.85 E-value=1.5e-20 Score=120.39 Aligned_cols=72 Identities=15% Similarity=0.272 Sum_probs=61.4
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEe
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 101 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~ 101 (104)
.-|+++++++|+|+++|||.+.|+|.|||+|||++|+||.|+....+... ....|.+|+++|||++|++|+.
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~--------~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFS--------PTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccC--------CccEEEeeeEEEeCCeEEEEEE
Confidence 45888999999999999999999999999999999999999876433211 1245889999999999999874
No 16
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.84 E-value=2.9e-20 Score=115.03 Aligned_cols=66 Identities=24% Similarity=0.442 Sum_probs=59.5
Q ss_pred HHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEe
Q 034064 23 WALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 101 (104)
Q Consensus 23 ~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~ 101 (104)
+|+++++++|.|.+++|++++|+|.+||+|||++|+||.|.....+ .++++|.++|||++|.+|+|
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-------------~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-------------EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-------------EEEEEEEEEEEGGGEEEEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-------------cEeECcEEEEECCEEEEEEC
Confidence 6899999999999999999999999999999999999999875310 34789999999999999986
No 17
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.84 E-value=3.4e-20 Score=114.58 Aligned_cols=66 Identities=27% Similarity=0.557 Sum_probs=58.9
Q ss_pred HHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEe
Q 034064 23 WALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 101 (104)
Q Consensus 23 ~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~ 101 (104)
+|+++++++|.|.++||+++.|+|.|||+|||++|+||+|..... ...+++|.++|||++|.+|++
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------------~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------------EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC-------------cEEeEeCCEEEcCCEEEEEeC
Confidence 588999999999999999999999999999999999999986521 134779999999999999975
No 18
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.83 E-value=4.4e-20 Score=118.48 Aligned_cols=74 Identities=24% Similarity=0.477 Sum_probs=60.8
Q ss_pred hhHHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEE
Q 034064 18 MLFCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 97 (104)
Q Consensus 18 ~l~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv 97 (104)
+.+..+|+++++++|.|+|++|+++.|+|+|||+|||++|+||+|.... +++. ...+..+.++|||+||+
T Consensus 6 ~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~~-------~~~~~~~~~~IRG~~I~ 75 (79)
T COG1958 6 PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH---DGEK-------NVRRLGGEVLIRGDNIV 75 (79)
T ss_pred CCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc---CCcc-------ccceeccEEEEECCcEE
Confidence 3457889999999999999999999999999999999999999998741 1110 01244559999999999
Q ss_pred EEEe
Q 034064 98 IVLR 101 (104)
Q Consensus 98 ~Is~ 101 (104)
+|++
T Consensus 76 ~I~~ 79 (79)
T COG1958 76 LISP 79 (79)
T ss_pred EEeC
Confidence 9974
No 19
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.79 E-value=6.3e-19 Score=116.31 Aligned_cols=79 Identities=25% Similarity=0.455 Sum_probs=60.3
Q ss_pred ecCceehhhHHHHHHhcCCc--EEEEEEcC--CeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeee
Q 034064 11 RNSQTTLMLFCFWALEFIVL--QVLINCRN--NKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFI 86 (104)
Q Consensus 11 ~~~~~~~~l~~~~L~~~l~k--rV~V~l~~--gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~l 86 (104)
+++|..+..+...+.+++.. +|.|.+.+ +++++|+|+|||+|||++|+||+|.+.. + ..++.+
T Consensus 6 ~~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~-----~--------~~~~~l 72 (89)
T PTZ00138 6 RKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK-----K--------NTRKDL 72 (89)
T ss_pred cccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC-----C--------ceeeEc
Confidence 35555665666666666654 56666656 5899999999999999999999997642 1 123679
Q ss_pred CeEEEeCCcEEEEEec
Q 034064 87 SKMFLRGDSVIIVLRN 102 (104)
Q Consensus 87 g~~~IRGdnVv~Is~~ 102 (104)
|.++||||||++|++.
T Consensus 73 G~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 73 GRILLKGDNITLIMAA 88 (89)
T ss_pred CeEEEcCCEEEEEEcC
Confidence 9999999999999875
No 20
>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=1.3e-18 Score=106.02 Aligned_cols=63 Identities=30% Similarity=0.497 Sum_probs=55.8
Q ss_pred HHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEE
Q 034064 24 ALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 100 (104)
Q Consensus 24 L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is 100 (104)
|+++++++|.|.++||+.+.|+|.|||+|||++|+||.|.+.. . ..+.+|.++|||++|.+|.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~-----~---------~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE-----G---------KKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC-----C---------cEEECCeEEEECCEEEEEC
Confidence 4678999999999999999999999999999999999998753 0 2367999999999999873
No 21
>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=99.78 E-value=1.4e-18 Score=111.10 Aligned_cols=71 Identities=15% Similarity=0.150 Sum_probs=59.7
Q ss_pred HHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEE
Q 034064 20 FCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 99 (104)
Q Consensus 20 ~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~I 99 (104)
+..+|++..+++|.|.|++|++++|+|.+||+|||++|+||+|.... ++ ....+|.++|||++|.+|
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~----g~---------~~~~~~~v~IRG~~I~~i 68 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKD----GD---------KFWKMPECYIRGNTIKYL 68 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCC----Cc---------EeeeCCcEEEeCCEEEEE
Confidence 45789999999999999999999999999999999999999985321 11 113468999999999999
Q ss_pred EecC
Q 034064 100 LRNP 103 (104)
Q Consensus 100 s~~~ 103 (104)
+.++
T Consensus 69 ~~p~ 72 (76)
T cd01723 69 RVPD 72 (76)
T ss_pred EcCH
Confidence 8654
No 22
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.78 E-value=4e-19 Score=112.97 Aligned_cols=67 Identities=21% Similarity=0.394 Sum_probs=58.4
Q ss_pred HHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEec
Q 034064 23 WALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 102 (104)
Q Consensus 23 ~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~~ 102 (104)
-|+++++|++.+++++||.++|.|+|||.|||++|+||.|.-.. + .+..+|..+|||++|+++.+.
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~----~----------~~~~ig~~vIrgnsiv~~eaL 73 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD----G----------DKNNIGMVVIRGNSIVMVEAL 73 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc----C----------CcceeeeEEEeccEEEEEeec
Confidence 58999999999999999999999999999999999999996431 1 124689999999999999875
Q ss_pred C
Q 034064 103 P 103 (104)
Q Consensus 103 ~ 103 (104)
.
T Consensus 74 ~ 74 (77)
T KOG1780|consen 74 E 74 (77)
T ss_pred c
Confidence 3
No 23
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.76 E-value=6.2e-18 Score=106.67 Aligned_cols=68 Identities=13% Similarity=0.185 Sum_probs=58.2
Q ss_pred HHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEE
Q 034064 21 CFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 100 (104)
Q Consensus 21 ~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is 100 (104)
..+|.+..+++|.|.|++|.+++|+|.++|.|||+.|+||+|.... ++ ...+|.++|||+||.+|.
T Consensus 2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~----g~----------~~~~~~v~IRG~nI~~v~ 67 (70)
T cd01721 2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARD----GR----------VSQLEQVYIRGSKIRFFI 67 (70)
T ss_pred hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCC----Cc----------EeEcCcEEEeCCEEEEEE
Confidence 3678999999999999999999999999999999999999875321 11 135799999999999997
Q ss_pred ec
Q 034064 101 RN 102 (104)
Q Consensus 101 ~~ 102 (104)
-+
T Consensus 68 lP 69 (70)
T cd01721 68 LP 69 (70)
T ss_pred eC
Confidence 65
No 24
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.74 E-value=2.2e-17 Score=106.92 Aligned_cols=73 Identities=21% Similarity=0.250 Sum_probs=60.8
Q ss_pred hHHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEE
Q 034064 19 LFCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 98 (104)
Q Consensus 19 l~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~ 98 (104)
||+.+|++..+++|.|.|++|..++|+|.++|.|||+.|+||++.... +.. ....++.++|||++|.+
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~----~~~--------~~~~~~~v~IRG~~I~~ 68 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE----KYP--------HMLSVKNCFIRGSVVRY 68 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCC----Ccc--------cccccCeEEEECCEEEE
Confidence 578899999999999999999999999999999999999999875321 110 11346999999999999
Q ss_pred EEecC
Q 034064 99 VLRNP 103 (104)
Q Consensus 99 Is~~~ 103 (104)
|..++
T Consensus 69 I~lp~ 73 (81)
T cd01725 69 VQLPA 73 (81)
T ss_pred EEeCh
Confidence 98654
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=99.73 E-value=5.1e-17 Score=107.20 Aligned_cols=69 Identities=16% Similarity=0.247 Sum_probs=59.9
Q ss_pred HHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEE
Q 034064 21 CFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 100 (104)
Q Consensus 21 ~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is 100 (104)
..+|++..+++|.|.|++|.+++|+|.++|.|||+.|+||+|.... + ....+|.++|||+||.+|.
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~-----~---------~~~~~~~v~IRG~nI~yi~ 68 (90)
T cd01724 3 VRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG-----R---------NPVPLDTLSIRGNNIRYFI 68 (90)
T ss_pred hHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC-----C---------ceeEcceEEEeCCEEEEEE
Confidence 4679999999999999999999999999999999999999987431 1 1245899999999999998
Q ss_pred ecC
Q 034064 101 RNP 103 (104)
Q Consensus 101 ~~~ 103 (104)
-++
T Consensus 69 lPd 71 (90)
T cd01724 69 LPD 71 (90)
T ss_pred cCC
Confidence 664
No 26
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.72 E-value=6.5e-19 Score=117.42 Aligned_cols=76 Identities=13% Similarity=0.279 Sum_probs=64.9
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEe
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 101 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~ 101 (104)
..|.++++++|+|++.+||+.+|+|.|||+.|||+|+|++|+...+++..+ ...+.|.+|++++||..+++|||
T Consensus 20 lDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~------~~~~tR~LGLvV~RGTalvlisp 93 (108)
T KOG1781|consen 20 LDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYK------LTDETRKLGLVVCRGTALVLISP 93 (108)
T ss_pred hhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccc------hhhhhheeeeEEEcccEEEEEcC
Confidence 568999999999999999999999999999999999999998775443211 12345889999999999999998
Q ss_pred cC
Q 034064 102 NP 103 (104)
Q Consensus 102 ~~ 103 (104)
..
T Consensus 94 ~d 95 (108)
T KOG1781|consen 94 AD 95 (108)
T ss_pred Cc
Confidence 64
No 27
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.72 E-value=6.5e-17 Score=104.16 Aligned_cols=67 Identities=19% Similarity=0.259 Sum_probs=57.8
Q ss_pred HHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEE
Q 034064 21 CFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 100 (104)
Q Consensus 21 ~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is 100 (104)
..+|+...+++|.|.|++|.+++|+|.++|.|||+.|+||++.... + ....+|.++|||+||.+|.
T Consensus 11 ~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~----~----------~~~~~~~v~IRG~nI~yI~ 76 (78)
T cd01733 11 IILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN----G----------KQVQVEEIMVTGRNIRYVH 76 (78)
T ss_pred HHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC----C----------ceeECCcEEEECCEEEEEE
Confidence 4778999999999999999999999999999999999999876321 1 1235899999999999987
Q ss_pred e
Q 034064 101 R 101 (104)
Q Consensus 101 ~ 101 (104)
-
T Consensus 77 l 77 (78)
T cd01733 77 I 77 (78)
T ss_pred c
Confidence 4
No 28
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.57 E-value=4.2e-16 Score=98.95 Aligned_cols=69 Identities=17% Similarity=0.252 Sum_probs=61.7
Q ss_pred HHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEE
Q 034064 21 CFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 100 (104)
Q Consensus 21 ~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is 100 (104)
..+|++.++++|.|+|.+|-.++|+|.+.|.|||+.|+.++|.... + .+++.|.+||||+||++||
T Consensus 8 ~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ng-----q---------l~n~ygdaFirGnnVlyIs 73 (77)
T KOG1783|consen 8 GEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNG-----Q---------LKNKYGDAFIRGNNVLYIS 73 (77)
T ss_pred HHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcC-----c---------ccccccceeeccccEEEEE
Confidence 4789999999999999999999999999999999999999998642 2 2467899999999999999
Q ss_pred ecC
Q 034064 101 RNP 103 (104)
Q Consensus 101 ~~~ 103 (104)
...
T Consensus 74 ~~~ 76 (77)
T KOG1783|consen 74 TQK 76 (77)
T ss_pred ecc
Confidence 754
No 29
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.56 E-value=3.6e-16 Score=107.76 Aligned_cols=71 Identities=27% Similarity=0.406 Sum_probs=61.8
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEe
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 101 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~ 101 (104)
.-+.+++++++.|.|+|||.+.|.|++||||.|++|++|.|++.- ++ ...++..|.++|||+||++++.
T Consensus 12 ~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v----~~-------~Y~di~~glfiIRGENVvllGe 80 (129)
T KOG1782|consen 12 TSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFV----GN-------KYCDIPRGLFIIRGENVVLLGE 80 (129)
T ss_pred hHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheee----cc-------eecccCceEEEEecCcEEEEec
Confidence 458899999999999999999999999999999999999998764 11 1345678999999999999987
Q ss_pred cC
Q 034064 102 NP 103 (104)
Q Consensus 102 ~~ 103 (104)
.+
T Consensus 81 id 82 (129)
T KOG1782|consen 81 ID 82 (129)
T ss_pred CC
Confidence 65
No 30
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.54 E-value=1.5e-14 Score=91.84 Aligned_cols=70 Identities=16% Similarity=0.192 Sum_probs=61.8
Q ss_pred HHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEE
Q 034064 20 FCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 99 (104)
Q Consensus 20 ~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~I 99 (104)
+..||+...+++|.|+|+-|.++.|+|.+-|.||||-|.+|+|.+.. . ..-.+|.++||.+||++|
T Consensus 9 PKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-----~---------~~g~lGEilIRCNNvlyi 74 (79)
T KOG3482|consen 9 PKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-----V---------STGNLGEILIRCNNVLYI 74 (79)
T ss_pred chHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc-----c---------ccccceeEEEEeccEEEE
Confidence 46899999999999999999999999999999999999999997653 1 224699999999999999
Q ss_pred EecC
Q 034064 100 LRNP 103 (104)
Q Consensus 100 s~~~ 103 (104)
.-.|
T Consensus 75 ~gv~ 78 (79)
T KOG3482|consen 75 RGVP 78 (79)
T ss_pred ecCC
Confidence 7654
No 31
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.53 E-value=1.3e-15 Score=110.01 Aligned_cols=76 Identities=24% Similarity=0.476 Sum_probs=62.5
Q ss_pred HHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEec
Q 034064 23 WALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 102 (104)
Q Consensus 23 ~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~~ 102 (104)
-|-.++|.+.+|.++|||.+.|.+.+||+||||+|.||+|....++..++.. ..+++|-+|++++||+||++.+..
T Consensus 8 kml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~----~~eEkr~lgLvllRgenIvs~tVe 83 (177)
T KOG3168|consen 8 KMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMT----DGEEKRVLGLVLLRGENIVSMTVE 83 (177)
T ss_pred HHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhcccccccccc----ccceeeEEEEEEecCCcEEEEecc
Confidence 3677899999999999999999999999999999999999866544433111 123568899999999999998764
No 32
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.52 E-value=1.1e-14 Score=95.96 Aligned_cols=72 Identities=13% Similarity=0.273 Sum_probs=62.2
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEe
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 101 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~ 101 (104)
.-|+.|++++|.|.+.|||.+.|.|.|||+-.||+|+|+.|+.....+ ..++..+|..+|||+||.+|++
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~----------gv~q~~lGlyiirgeNva~ig~ 72 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETE----------GVEQIVLGLYIIRGENVAVIGE 72 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhc----------chhheeeEEEEEecCccceeee
Confidence 458999999999999999999999999999999999999998774221 1234679999999999999998
Q ss_pred cC
Q 034064 102 NP 103 (104)
Q Consensus 102 ~~ 103 (104)
..
T Consensus 73 iD 74 (96)
T KOG1784|consen 73 ID 74 (96)
T ss_pred cc
Confidence 64
No 33
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.44 E-value=1.4e-14 Score=98.19 Aligned_cols=74 Identities=86% Similarity=1.373 Sum_probs=66.6
Q ss_pred CcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEecC
Q 034064 29 VLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 103 (104)
Q Consensus 29 ~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~~~ 103 (104)
...|.|.+||++.+-|.+.|||.|+|++|+++.|.|.+.+..+++++ .++..++|++|.+|||||+|+.+...|
T Consensus 36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~~~~~~~r~isK~flRGdsvI~v~r~p 109 (114)
T KOG3459|consen 36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-AKPVNKDRFISKMFLRGDSVILVLRNP 109 (114)
T ss_pred CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-CCccchhhhhheeeecCCeEEEEEecc
Confidence 46899999999999999999999999999999999998877777654 667777899999999999999998766
No 34
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.43 E-value=1.3e-13 Score=88.44 Aligned_cols=74 Identities=23% Similarity=0.389 Sum_probs=62.7
Q ss_pred hhHHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEE
Q 034064 18 MLFCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 97 (104)
Q Consensus 18 ~l~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv 97 (104)
.|++.++.+.++.+|.|.++++|++.|+|.|||.|.|++|+|++|+-..+ + ++ .-.+++++++.|+||.
T Consensus 6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~-e-gr---------~~tk~~~iLLnGNni~ 74 (84)
T KOG1775|consen 6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITP-E-GR---------RMTKLDQILLNGNNIT 74 (84)
T ss_pred cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCC-C-cc---------eeeeeeeeeecCCcEE
Confidence 46778899999999999999999999999999999999999999975432 1 11 1245899999999999
Q ss_pred EEEec
Q 034064 98 IVLRN 102 (104)
Q Consensus 98 ~Is~~ 102 (104)
++.|-
T Consensus 75 mLvPG 79 (84)
T KOG1775|consen 75 MLVPG 79 (84)
T ss_pred EEecC
Confidence 98774
No 35
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.38 E-value=8.7e-13 Score=85.48 Aligned_cols=69 Identities=19% Similarity=0.385 Sum_probs=50.1
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEEe
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 101 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is~ 101 (104)
.+|.....-.|...=+-|-.++|.++|||+|||++|+||+|..... + ..+.+|.++++||||.+|..
T Consensus 19 r~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~----~---------~rk~lGRilLKGDnItli~~ 85 (88)
T KOG1774|consen 19 RFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT----K---------SRKELGRILLKGDNITLIQS 85 (88)
T ss_pred HHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc----c---------CCCccccEEEcCCcEEEEee
Confidence 4455554444444444466799999999999999999999975420 1 11369999999999999976
Q ss_pred cC
Q 034064 102 NP 103 (104)
Q Consensus 102 ~~ 103 (104)
..
T Consensus 86 ~~ 87 (88)
T KOG1774|consen 86 AG 87 (88)
T ss_pred cC
Confidence 53
No 36
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.21 E-value=1.1e-10 Score=76.70 Aligned_cols=73 Identities=22% Similarity=0.329 Sum_probs=59.8
Q ss_pred hhHHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEE
Q 034064 18 MLFCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 97 (104)
Q Consensus 18 ~l~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv 97 (104)
|||+.|++..++++|.|.|+++-.+.|+|.|.|+|.|+-|+|..-... ++ .|.. -.+..+||||+.|-
T Consensus 1 mLFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~-----~k-----yPhm--~Sv~ncfIRGSvvr 68 (96)
T KOG3448|consen 1 MLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDP-----DK-----YPHM--LSVKNCFIRGSVVR 68 (96)
T ss_pred CchHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCc-----cc-----CCCe--eeeeeEEEeccEEE
Confidence 689999999999999999999999999999999999999999764321 01 1222 34678999999998
Q ss_pred EEEec
Q 034064 98 IVLRN 102 (104)
Q Consensus 98 ~Is~~ 102 (104)
+|..+
T Consensus 69 Yv~l~ 73 (96)
T KOG3448|consen 69 YVQLP 73 (96)
T ss_pred EEEeC
Confidence 88654
No 37
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.02 E-value=2e-10 Score=71.72 Aligned_cols=38 Identities=29% Similarity=0.426 Sum_probs=32.2
Q ss_pred CcEEEEEEcC----CeEEEEEEEEecCccceEeeceEEeeec
Q 034064 29 VLQVLINCRN----NKKLLGRVRAFDRHCNMVLENVREMWTE 66 (104)
Q Consensus 29 ~krV~V~l~~----gr~i~G~L~~fD~~mNLvL~d~~E~~~~ 66 (104)
..||+|.++. +..++|.|.|||+||||+|.|++|.|..
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 3577777776 3578999999999999999999999864
No 38
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=98.90 E-value=3.9e-09 Score=73.20 Aligned_cols=72 Identities=17% Similarity=0.139 Sum_probs=60.3
Q ss_pred hhHHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEE
Q 034064 18 MLFCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 97 (104)
Q Consensus 18 ~l~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv 97 (104)
||++.+|+..-+.++.|.|++|-++.|.|+.+|.+|||.|.++.+... |++. --..+.+.|||.+|-
T Consensus 1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~----Dgdk---------f~r~pEcYirGttIk 67 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSE----DGDK---------FFRMPECYIRGTTIK 67 (134)
T ss_pred CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEecc----CCCc---------eeecceeEEecceeE
Confidence 577889999999999999999999999999999999999999998643 1221 123688999999999
Q ss_pred EEEec
Q 034064 98 IVLRN 102 (104)
Q Consensus 98 ~Is~~ 102 (104)
++--+
T Consensus 68 ylri~ 72 (134)
T KOG3293|consen 68 YLRIP 72 (134)
T ss_pred EEecc
Confidence 87543
No 39
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.26 E-value=1.1e-05 Score=54.94 Aligned_cols=67 Identities=16% Similarity=0.265 Sum_probs=55.5
Q ss_pred HHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEE
Q 034064 21 CFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 100 (104)
Q Consensus 21 ~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is 100 (104)
..+|.+..+++|.|.|++|..+.|++.+.|.+||..|.++.=... ++ ...+..+.+||+||=++-
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-----~~----------pv~l~~lsirgnniRy~~ 68 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-----GE----------PVRLDTLSIRGNNIRYYI 68 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC-----CC----------ceeEEEEEeecceEEEEE
Confidence 467999999999999999999999999999999999998874332 11 134788999999998875
Q ss_pred ec
Q 034064 101 RN 102 (104)
Q Consensus 101 ~~ 102 (104)
.+
T Consensus 69 lp 70 (109)
T KOG3428|consen 69 LP 70 (109)
T ss_pred cc
Confidence 43
No 40
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=98.18 E-value=7.1e-06 Score=55.90 Aligned_cols=72 Identities=13% Similarity=0.173 Sum_probs=58.5
Q ss_pred hhhHHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcE
Q 034064 17 LMLFCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 96 (104)
Q Consensus 17 ~~l~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnV 96 (104)
+.++..+|.+.-+.-|.+.+..|-.|.|+|+--|..||..|+|..-.... +. -.++.+++|||+.|
T Consensus 3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d----g~----------vs~le~V~IRGS~I 68 (119)
T KOG3172|consen 3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD----GR----------VSQLEQVFIRGSKI 68 (119)
T ss_pred cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC----Cc----------ceeeeeEEEecCeE
Confidence 34555778888999999999999999999999999999999998765331 21 13588999999999
Q ss_pred EEEEec
Q 034064 97 IIVLRN 102 (104)
Q Consensus 97 v~Is~~ 102 (104)
-++-.+
T Consensus 69 RFlvlP 74 (119)
T KOG3172|consen 69 RFLVLP 74 (119)
T ss_pred EEEECc
Confidence 887654
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.64 E-value=0.00024 Score=44.85 Aligned_cols=70 Identities=10% Similarity=0.170 Sum_probs=42.9
Q ss_pred HHHHHhcCCcEEEEEEcCCeEEEEEEEEecC---ccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEE
Q 034064 21 CFWALEFIVLQVLINCRNNKKLLGRVRAFDR---HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 97 (104)
Q Consensus 21 ~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~---~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv 97 (104)
.+++...++.+|.|+++||..|+|.|.+++. =+-++|.-|.........+ . ..........++|.++.|+
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~-~------~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN-S------DPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-------------EEEEEEE-GGGEEE-----
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc-C------CccCCCCCceEEEeccccC
Confidence 4678899999999999999999999999999 8899998887653321110 0 0112234577888887765
No 42
>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=96.71 E-value=0.0039 Score=38.51 Aligned_cols=29 Identities=31% Similarity=0.496 Sum_probs=25.7
Q ss_pred CcEEEEEEcCCeEEEEEEEEecCccceEee
Q 034064 29 VLQVLINCRNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 29 ~krV~V~l~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
+.+|.|.|.+|-.++|.+.|||+|+ +.|+
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD~ft-Vll~ 39 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFDNFT-VLLE 39 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEcceE-EEEE
Confidence 5689999999999999999999999 4444
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=96.57 E-value=0.0055 Score=37.88 Aligned_cols=29 Identities=28% Similarity=0.423 Sum_probs=25.5
Q ss_pred CcEEEEEEcCCeEEEEEEEEecCccceEee
Q 034064 29 VLQVLINCRNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 29 ~krV~V~l~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
+.+|.|.|.+|-.++|.+.|||+|+ +.|+
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ft-Vll~ 43 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFT-VLLE 43 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeE-EEEE
Confidence 5689999999999999999999999 4443
No 44
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.12 E-value=0.032 Score=32.25 Aligned_cols=35 Identities=9% Similarity=0.172 Sum_probs=30.2
Q ss_pred cCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEE
Q 034064 27 FIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVRE 62 (104)
Q Consensus 27 ~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E 62 (104)
+++++|++.. ++..++|+..|.|..-.|+++....
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 4789999999 6777899999999999999976444
No 45
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=95.40 E-value=0.043 Score=35.35 Aligned_cols=31 Identities=35% Similarity=0.476 Sum_probs=26.9
Q ss_pred CcEEEEEEcCCeEEEEEEEEecCccceEeece
Q 034064 29 VLQVLINCRNNKKLLGRVRAFDRHCNMVLENV 60 (104)
Q Consensus 29 ~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~ 60 (104)
..+|.|-|.+|-.++|.++|||+|. +.|++.
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~~ 49 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFDNFV-VLLKNT 49 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeeeeEE-EEEEcC
Confidence 5689999999999999999999998 666543
No 46
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.12 E-value=0.049 Score=35.28 Aligned_cols=31 Identities=26% Similarity=0.374 Sum_probs=26.2
Q ss_pred CcEEEEEEcCCeEEEEEEEEecCccceEeec
Q 034064 29 VLQVLINCRNNKKLLGRVRAFDRHCNMVLEN 59 (104)
Q Consensus 29 ~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d 59 (104)
+.+|.|.|.+|-.++|.+.|||+|+=|+-.+
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 5689999999999999999999999444334
No 47
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=94.85 E-value=0.53 Score=31.33 Aligned_cols=71 Identities=20% Similarity=0.315 Sum_probs=50.9
Q ss_pred HhcCCcEEEEEEcCCeEEEEEEEEecC-ccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEEE
Q 034064 25 LEFIVLQVLINCRNNKKLLGRVRAFDR-HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 100 (104)
Q Consensus 25 ~~~l~krV~V~l~~gr~i~G~L~~fD~-~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~Is 100 (104)
.++++++|.+..+++-.|+|+|...|. --.+.|.+|.-.-.+-+..+. . -+. .+.....+..||..|--+.
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~---~-ipp-~~~v~~~I~Fr~sDIkdL~ 75 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDR---E-IPP-SDEVYDYIVFRGSDIKDLK 75 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS-------C--CSSSSEEEEETTTEEEEE
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCc---c-cCC-CCceeeEEEEEccccceEE
Confidence 468999999999999999999999998 678999998865443211111 0 011 1234689999999886654
No 48
>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=93.46 E-value=1 Score=29.20 Aligned_cols=64 Identities=23% Similarity=0.256 Sum_probs=45.5
Q ss_pred HHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCcc-ceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEE
Q 034064 20 FCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHC-NMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 98 (104)
Q Consensus 20 ~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~m-NLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~ 98 (104)
|+.+|....+++|.+.|.++.+++|+..|+|... |+..++ -+. | - ...+..++|..-|++
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~-L~T----P---------l-----Gv~~eAlLR~~DVi~ 75 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSN-LQT----P---------L-----GVQPEALLRCSDVIS 75 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEE-EET----T---------T-----TEEEEEEEEGGGEEE
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhh-cCC----C---------c-----ccChhheeecCCEEE
Confidence 3567888889999999999999999999999754 333332 111 1 0 125789999999999
Q ss_pred EEec
Q 034064 99 VLRN 102 (104)
Q Consensus 99 Is~~ 102 (104)
++..
T Consensus 76 ~~f~ 79 (80)
T PF11095_consen 76 ISFD 79 (80)
T ss_dssp EEE-
T ss_pred EEec
Confidence 8754
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=93.36 E-value=0.26 Score=30.36 Aligned_cols=36 Identities=25% Similarity=0.247 Sum_probs=30.6
Q ss_pred cCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEE
Q 034064 27 FIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVRE 62 (104)
Q Consensus 27 ~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E 62 (104)
.++..|.+++-.|.+++|.+.+||.-.+++.=.+.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 468899999999999999999999999887554433
No 50
>PRK14638 hypothetical protein; Provisional
Probab=93.08 E-value=0.2 Score=35.64 Aligned_cols=36 Identities=17% Similarity=0.260 Sum_probs=30.4
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+..+++++|.|++++++.++|+|.++|.- ++.|.
T Consensus 93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 5578999999999999999999999999974 34443
No 51
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.03 E-value=0.2 Score=36.58 Aligned_cols=29 Identities=24% Similarity=0.279 Sum_probs=25.1
Q ss_pred CcEEEEEEcCCeEEEEEEEEecCccceEee
Q 034064 29 VLQVLINCRNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 29 ~krV~V~l~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+|.|.|.+|-.++|.+.|||+|. +.|+
T Consensus 24 k~~VtvfL~nG~rl~G~I~~fD~ft-VlL~ 52 (165)
T PRK14091 24 KTPVTMFLVKGVKLQGIITWFDNFS-ILLR 52 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceE-EEEE
Confidence 4588899999999999999999999 4444
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=92.40 E-value=1.2 Score=28.55 Aligned_cols=70 Identities=20% Similarity=0.321 Sum_probs=47.6
Q ss_pred HhcCCcEEEEEEcCCeEEEEEEEEecCccc-eEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEE
Q 034064 25 LEFIVLQVLINCRNNKKLLGRVRAFDRHCN-MVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 98 (104)
Q Consensus 25 ~~~l~krV~V~l~~gr~i~G~L~~fD~~mN-LvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~ 98 (104)
.++++++|.+..+.+-.|+|.|.+.|..=. +.|.|+...-++-+..+ . ++ -+. ...-...++.||+.|--
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~-~-~~-ipp-~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTD-G-PE-IPP-SDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCC-C-Cc-cCC-CCcceeEEEEcCCcccc
Confidence 468999999999999999999999998765 55888776544321111 0 00 011 12346889999998743
No 53
>PRK14639 hypothetical protein; Provisional
Probab=91.84 E-value=0.37 Score=33.92 Aligned_cols=36 Identities=25% Similarity=0.258 Sum_probs=31.1
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+..+++++|+|++++++.++|+|.++|.- ++.|+
T Consensus 81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 5578999999999999999999999999984 45553
No 54
>PRK02001 hypothetical protein; Validated
Probab=91.53 E-value=0.4 Score=34.31 Aligned_cols=36 Identities=22% Similarity=0.269 Sum_probs=30.7
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+..+++..|.|++.+++.++|+|.++|.- ++.|.
T Consensus 83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence 4578999999999999999999999999985 35553
No 55
>PRK14644 hypothetical protein; Provisional
Probab=90.96 E-value=1.1 Score=31.54 Aligned_cols=51 Identities=6% Similarity=-0.022 Sum_probs=38.3
Q ss_pred EEEEecCceehhhHHHHHHhcCCcEEEEEEcCC----eEEEEEEEEecCccceEee
Q 034064 7 RFSFRNSQTTLMLFCFWALEFIVLQVLINCRNN----KKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 7 ~~~~~~~~~~~~l~~~~L~~~l~krV~V~l~~g----r~i~G~L~~fD~~mNLvL~ 58 (104)
+...++.+..=.|...-+..+++++|.|++++. ++++|+|.++|.. ++.|+
T Consensus 63 ~LEVSSPGldRpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 63 SLDISSPGFDMDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred EEEEECCCCCCCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 344555555545555578999999999999886 8999999999984 35554
No 56
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=90.21 E-value=0.58 Score=34.16 Aligned_cols=31 Identities=26% Similarity=0.326 Sum_probs=26.0
Q ss_pred CcEEEEEEcCCeEEEEEEEEecCccceEeec
Q 034064 29 VLQVLINCRNNKKLLGRVRAFDRHCNMVLEN 59 (104)
Q Consensus 29 ~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d 59 (104)
..+|.|.|.+|-.++|.+.|||+|+=|.-.+
T Consensus 104 k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 104 GEPVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 5589999999999999999999999444334
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=88.83 E-value=0.88 Score=33.18 Aligned_cols=39 Identities=23% Similarity=0.306 Sum_probs=28.6
Q ss_pred HHHhcCCcEEEEEEcCCeEEEEEEEEecC-ccceEeeceEE
Q 034064 23 WALEFIVLQVLINCRNNKKLLGRVRAFDR-HCNMVLENVRE 62 (104)
Q Consensus 23 ~L~~~l~krV~V~l~~gr~i~G~L~~fD~-~mNLvL~d~~E 62 (104)
.+..+++|+|+|.+.| +++.|.|-..|. --|++|-+-.|
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 4678999999999999 999999999997 35677764333
No 58
>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=88.02 E-value=1.4 Score=27.93 Aligned_cols=36 Identities=17% Similarity=0.103 Sum_probs=28.6
Q ss_pred HHHHhcCCcEEEEEEc---CC-eEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCR---NN-KKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~---~g-r~i~G~L~~fD~~mNLvL~ 58 (104)
..+..++++.|.|+++ +| ++++|.|.++|.- ++.|.
T Consensus 18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l~ 57 (83)
T cd01734 18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTLE 57 (83)
T ss_pred HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEEE
Confidence 4578899999999997 45 6899999999984 34443
No 59
>PRK14640 hypothetical protein; Provisional
Probab=87.64 E-value=1.3 Score=31.42 Aligned_cols=49 Identities=14% Similarity=0.216 Sum_probs=34.6
Q ss_pred EEecCceehhhH-HHHHHhcCCcEEEEEE----cCCeEEEEEEEEecCccceEee
Q 034064 9 SFRNSQTTLMLF-CFWALEFIVLQVLINC----RNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 9 ~~~~~~~~~~l~-~~~L~~~l~krV~V~l----~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
..++.+..=.|. -..+..+++++|.|++ .+.++++|+|.++|.-. +.|.
T Consensus 76 EVSSPGl~RpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~-v~l~ 129 (152)
T PRK14640 76 EVSSPGLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDM-ITLT 129 (152)
T ss_pred EEeCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCCE-EEEE
Confidence 334444333333 2557899999999999 56799999999999853 5554
No 60
>PRK14633 hypothetical protein; Provisional
Probab=87.19 E-value=1.5 Score=31.18 Aligned_cols=36 Identities=17% Similarity=0.248 Sum_probs=29.5
Q ss_pred HHHHhcCCcEEEEEEc----CCeEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCR----NNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~----~gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+..+++++|.|+++ +++.++|+|.++|+- ++.|.
T Consensus 87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 5578999999999994 678999999999985 35554
No 61
>PRK14642 hypothetical protein; Provisional
Probab=86.33 E-value=1.6 Score=32.65 Aligned_cols=47 Identities=15% Similarity=0.013 Sum_probs=33.7
Q ss_pred EecCceehhhH-HHHHHhcCCcEEEEEEc-------------CCeEEEEEEEEecCccceEe
Q 034064 10 FRNSQTTLMLF-CFWALEFIVLQVLINCR-------------NNKKLLGRVRAFDRHCNMVL 57 (104)
Q Consensus 10 ~~~~~~~~~l~-~~~L~~~l~krV~V~l~-------------~gr~i~G~L~~fD~~mNLvL 57 (104)
.++.+..=.|- -..+..++++.|.|+++ +.+.++|+|.++|.- ++.|
T Consensus 80 VSSPGldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 80 VSSPGIDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred EeCCCCCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 34444333333 35678899999999998 679999999999984 3444
No 62
>PRK14636 hypothetical protein; Provisional
Probab=85.75 E-value=1.7 Score=31.71 Aligned_cols=36 Identities=11% Similarity=0.178 Sum_probs=29.2
Q ss_pred HHHHhcCCcEEEEEEc---CC-eEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCR---NN-KKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~---~g-r~i~G~L~~fD~~mNLvL~ 58 (104)
..+..+++++|.|+++ +| +.++|+|.++|.- ++.|.
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~ 130 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA 130 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence 5678999999999997 44 6999999999883 45553
No 63
>PRK14645 hypothetical protein; Provisional
Probab=85.14 E-value=1.9 Score=30.89 Aligned_cols=35 Identities=14% Similarity=0.237 Sum_probs=28.5
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+..+++++|.|++ ++++++|+|.++|.-. +.|.
T Consensus 95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~~-i~l~ 129 (154)
T PRK14645 95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGDQ-VTFD 129 (154)
T ss_pred HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCCE-EEEE
Confidence 557789999999986 7899999999999853 5553
No 64
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=85.11 E-value=2.7 Score=26.22 Aligned_cols=55 Identities=16% Similarity=0.211 Sum_probs=38.5
Q ss_pred HHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeeecCCCCCCCcccccccceeeeeCeEEEeCCcEEEE
Q 034064 20 FCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 99 (104)
Q Consensus 20 ~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~~~IRGdnVv~I 99 (104)
++..|++++|++|.|.+-.|. ++|+|.+-..=. ++|+.. -..++||=..|++|
T Consensus 12 vyq~lq~liG~~vvV~T~~g~-v~G~L~~V~pDh-Ivl~~~-------------------------~~~~~IR~~~IV~v 64 (66)
T PF10842_consen 12 VYQTLQSLIGQRVVVQTTRGS-VRGILVDVKPDH-IVLEEN-------------------------GTPFFIRIAQIVWV 64 (66)
T ss_pred HHHHHHHhcCCEEEEEEcCCc-EEEEEEeecCCE-EEEEeC-------------------------CcEEEEEeeeEEEE
Confidence 478899999999999996555 599998754321 233221 13567888888887
Q ss_pred Ee
Q 034064 100 LR 101 (104)
Q Consensus 100 s~ 101 (104)
.|
T Consensus 65 ~p 66 (66)
T PF10842_consen 65 MP 66 (66)
T ss_pred cC
Confidence 65
No 65
>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=84.94 E-value=1.5 Score=30.41 Aligned_cols=48 Identities=17% Similarity=0.111 Sum_probs=30.0
Q ss_pred EEecCceehhhH-HHHHHhcCCcEEEEEEc----CCeEEEEEEEEecCccceEe
Q 034064 9 SFRNSQTTLMLF-CFWALEFIVLQVLINCR----NNKKLLGRVRAFDRHCNMVL 57 (104)
Q Consensus 9 ~~~~~~~~~~l~-~~~L~~~l~krV~V~l~----~gr~i~G~L~~fD~~mNLvL 57 (104)
..++.+..=.|. ..-+..+++++|.|+++ +.+++.|+|.++|. -.++|
T Consensus 66 EVSSPG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 66 EVSSPGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp EEE--SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred EEeCCCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 344444443343 35688999999999994 55789999999999 33555
No 66
>PRK14643 hypothetical protein; Provisional
Probab=84.27 E-value=2.3 Score=30.76 Aligned_cols=31 Identities=16% Similarity=0.141 Sum_probs=26.8
Q ss_pred HHHHhcCCcEEEEEEcC----CeEEEEEEEEecCc
Q 034064 22 FWALEFIVLQVLINCRN----NKKLLGRVRAFDRH 52 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~----gr~i~G~L~~fD~~ 52 (104)
..+..+++++|.|+++. .+.++|+|.++|.-
T Consensus 97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 55788999999999975 58999999999864
No 67
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.16 E-value=2.5 Score=30.42 Aligned_cols=36 Identities=28% Similarity=0.323 Sum_probs=31.4
Q ss_pred HHHHhcCCcEEEEEE----cCCeEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINC----RNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l----~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+..++++.|.|++ .+.+.++|+|.++|.-. +.+.
T Consensus 92 ~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~~ 131 (153)
T COG0779 92 EHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTLE 131 (153)
T ss_pred HHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEEE
Confidence 567899999999999 78999999999999987 5553
No 68
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=83.20 E-value=2.9 Score=29.52 Aligned_cols=42 Identities=21% Similarity=0.090 Sum_probs=31.2
Q ss_pred EecCceehhhH-HHHHHhcCCcEEEEEE----cCCeEEEEEEEEecC
Q 034064 10 FRNSQTTLMLF-CFWALEFIVLQVLINC----RNNKKLLGRVRAFDR 51 (104)
Q Consensus 10 ~~~~~~~~~l~-~~~L~~~l~krV~V~l----~~gr~i~G~L~~fD~ 51 (104)
.++.+..=.|. ...+..++|+.|.|++ .+++.++|+|.++|.
T Consensus 78 VSSPGi~RpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 78 VSSPGLDRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred EeCCCCCCcCCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 34444333333 2567899999999997 567899999999998
No 69
>PRK14634 hypothetical protein; Provisional
Probab=82.99 E-value=2.9 Score=29.82 Aligned_cols=36 Identities=14% Similarity=0.161 Sum_probs=29.0
Q ss_pred HHHHhcCCcEEEEEEcC----CeEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCRN----NKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~----gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+..+++++|.|++.+ .+.++|+|.++|.- ++.|.
T Consensus 93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14634 93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQIN 132 (155)
T ss_pred HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence 55789999999999974 37999999999984 35554
No 70
>PRK14632 hypothetical protein; Provisional
Probab=82.79 E-value=2.9 Score=30.38 Aligned_cols=36 Identities=17% Similarity=0.229 Sum_probs=29.1
Q ss_pred HHHHhcCCcEEEEEEcC-------CeEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCRN-------NKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~-------gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+..++++.|.|++.+ .++++|+|.++|.- ++.|+
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 55789999999999975 57999999999873 35554
No 71
>PRK14646 hypothetical protein; Provisional
Probab=82.51 E-value=3.1 Score=29.69 Aligned_cols=36 Identities=14% Similarity=0.025 Sum_probs=29.2
Q ss_pred HHHHhcCCcEEEEEEcC----CeEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCRN----NKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~----gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+..+++++|.|++++ .+.++|+|.++|.- ++.|+
T Consensus 93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 56788999999999965 36889999999985 46664
No 72
>PRK14647 hypothetical protein; Provisional
Probab=81.31 E-value=3.6 Score=29.38 Aligned_cols=30 Identities=13% Similarity=0.087 Sum_probs=26.2
Q ss_pred HHHHhcCCcEEEEEEc---------CCeEEEEEEEEecC
Q 034064 22 FWALEFIVLQVLINCR---------NNKKLLGRVRAFDR 51 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~---------~gr~i~G~L~~fD~ 51 (104)
..+..++|+.|.|+++ +.+.++|+|.++|.
T Consensus 92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 5578999999999995 35899999999997
No 73
>PRK14637 hypothetical protein; Provisional
Probab=80.57 E-value=3.4 Score=29.41 Aligned_cols=36 Identities=17% Similarity=0.100 Sum_probs=28.6
Q ss_pred HHHHhcCCcEEEEEEcCCeEE-EEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCRNNKKL-LGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i-~G~L~~fD~~mNLvL~ 58 (104)
..+..+++++|.|++.+.+++ +|+|.++|.- ++.|.
T Consensus 91 ~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 91 AEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 557889999999999655666 7999999985 45554
No 74
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=80.35 E-value=5.1 Score=29.12 Aligned_cols=35 Identities=20% Similarity=0.150 Sum_probs=30.8
Q ss_pred cCCcEEEEEEcCCeEEEEEEEEecCccceEeeceE
Q 034064 27 FIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 61 (104)
Q Consensus 27 ~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~ 61 (104)
.-+-+|+|.+.||..+.|.+.||+.--|.+|.-+.
T Consensus 27 ~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 27 FNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred hcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 34569999999999999999999999999987543
No 75
>PRK14631 hypothetical protein; Provisional
Probab=78.78 E-value=4.8 Score=29.34 Aligned_cols=29 Identities=24% Similarity=0.214 Sum_probs=25.8
Q ss_pred HHHHhcCCcEEEEEEc----CCeEEEEEEEEec
Q 034064 22 FWALEFIVLQVLINCR----NNKKLLGRVRAFD 50 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~----~gr~i~G~L~~fD 50 (104)
..+..++++.|.|++. +.+.++|+|.++|
T Consensus 110 ~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 110 EQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 5678999999999996 4589999999998
No 76
>PRK14641 hypothetical protein; Provisional
Probab=75.41 E-value=5.9 Score=28.93 Aligned_cols=29 Identities=7% Similarity=0.091 Sum_probs=25.1
Q ss_pred HHHHhcCCcEEEEEEcC----CeEEEEEEEEec
Q 034064 22 FWALEFIVLQVLINCRN----NKKLLGRVRAFD 50 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~----gr~i~G~L~~fD 50 (104)
..+..++|+.|.|++.+ .+.++|+|.++|
T Consensus 97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 56789999999999976 568999999995
No 77
>PRK10898 serine endoprotease; Provisional
Probab=73.71 E-value=7 Score=31.07 Aligned_cols=32 Identities=6% Similarity=0.173 Sum_probs=28.7
Q ss_pred cEEEEEEcCCeEEEEEEEEecCccceEeeceE
Q 034064 30 LQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 61 (104)
Q Consensus 30 krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~ 61 (104)
..+.|++.||+.+.+++.++|....|.+=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 58999999999999999999999999886554
No 78
>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=73.61 E-value=6.9 Score=30.99 Aligned_cols=32 Identities=9% Similarity=0.234 Sum_probs=28.5
Q ss_pred cEEEEEEcCCeEEEEEEEEecCccceEeeceE
Q 034064 30 LQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 61 (104)
Q Consensus 30 krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~ 61 (104)
..+.|++.||+.+.+++.++|...+|.|=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 47999999999999999999999999986544
No 79
>PRK06955 biotin--protein ligase; Provisional
Probab=72.89 E-value=8.8 Score=29.83 Aligned_cols=34 Identities=12% Similarity=0.199 Sum_probs=29.3
Q ss_pred hcCCcEEEEEEcCCeEEEEEEEEecCccceEeec
Q 034064 26 EFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLEN 59 (104)
Q Consensus 26 ~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d 59 (104)
-+++++|.+...+++.++|+..|.|....|++++
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 3678999997667788999999999999999863
No 80
>PRK10942 serine endoprotease; Provisional
Probab=71.55 E-value=7.7 Score=32.16 Aligned_cols=31 Identities=13% Similarity=0.267 Sum_probs=28.2
Q ss_pred cEEEEEEcCCeEEEEEEEEecCccceEeece
Q 034064 30 LQVLINCRNNKKLLGRVRAFDRHCNMVLENV 60 (104)
Q Consensus 30 krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~ 60 (104)
..|.|++.||+++.+++.++|...+|.|=..
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 5799999999999999999999999988644
No 81
>PRK10139 serine endoprotease; Provisional
Probab=67.50 E-value=11 Score=31.09 Aligned_cols=32 Identities=9% Similarity=0.274 Sum_probs=28.7
Q ss_pred cEEEEEEcCCeEEEEEEEEecCccceEeeceE
Q 034064 30 LQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 61 (104)
Q Consensus 30 krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~ 61 (104)
.+|.|++.||+++.+++.|+|....|.+=.+.
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 58999999999999999999999999886543
No 82
>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=63.54 E-value=14 Score=29.75 Aligned_cols=32 Identities=3% Similarity=0.203 Sum_probs=28.6
Q ss_pred cEEEEEEcCCeEEEEEEEEecCccceEeeceE
Q 034064 30 LQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 61 (104)
Q Consensus 30 krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~ 61 (104)
..+.|.+.+|+.+.+++.++|...+|.|=...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 47899999999999999999999999986554
No 83
>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=62.90 E-value=8.8 Score=27.89 Aligned_cols=25 Identities=4% Similarity=0.129 Sum_probs=22.0
Q ss_pred CCcEEEEEEcCCeEEEEEEEEecCc
Q 034064 28 IVLQVLINCRNNKKLLGRVRAFDRH 52 (104)
Q Consensus 28 l~krV~V~l~~gr~i~G~L~~fD~~ 52 (104)
-++-|+|.+.|||+++|+=.|-|..
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 4789999999999999999887754
No 84
>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=62.65 E-value=12 Score=25.13 Aligned_cols=19 Identities=21% Similarity=0.205 Sum_probs=15.3
Q ss_pred CcEEEEEEcCCeEEEEEEE
Q 034064 29 VLQVLINCRNNKKLLGRVR 47 (104)
Q Consensus 29 ~krV~V~l~~gr~i~G~L~ 47 (104)
+.+|.+.|+||+.+.|++.
T Consensus 28 e~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 28 EERVELELDDGSMLRGTVA 46 (101)
T ss_dssp T-EEEEEETTS-EEEEEEC
T ss_pred cceEEEEEcCCCeeeeeec
Confidence 4699999999999999973
No 85
>PRK14630 hypothetical protein; Provisional
Probab=61.60 E-value=17 Score=25.55 Aligned_cols=35 Identities=9% Similarity=-0.064 Sum_probs=27.4
Q ss_pred HHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
..+..++|++|.|++.+.. .+|+|.++|.-. +.|+
T Consensus 90 ~df~r~~G~~v~V~l~~~~-~~G~L~~~~d~~-i~l~ 124 (143)
T PRK14630 90 REFKIFEGKKIKLMLDNDF-EEGFILEAKADS-FIFK 124 (143)
T ss_pred HHHHHhCCCEEEEEEcCcc-eEEEEEEEeCCE-EEEE
Confidence 5578999999999996644 599999999843 5553
No 86
>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=60.22 E-value=23 Score=26.30 Aligned_cols=33 Identities=24% Similarity=0.337 Sum_probs=27.8
Q ss_pred HhcCCcEEEEEEcCCeEEEEEEEEecCccceEee
Q 034064 25 LEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 25 ~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
...++++|.+... +.+++|+..|.|....|+++
T Consensus 189 ~~~~g~~V~v~~~-~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 189 SAHIGREVSLTTG-NGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred hhccCCeEEEEeC-CcEEEEEEEeECCCceEEEE
Confidence 3456999999874 46799999999999999996
No 87
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=59.29 E-value=23 Score=27.38 Aligned_cols=32 Identities=25% Similarity=0.380 Sum_probs=27.5
Q ss_pred hcCCcEEEEEEcCCeEEEEEEEEecCccceEee
Q 034064 26 EFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLE 58 (104)
Q Consensus 26 ~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~ 58 (104)
-+++++|.+... +..++|++.|.|....|+++
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 367999999874 46799999999999999996
No 88
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=58.84 E-value=22 Score=30.52 Aligned_cols=33 Identities=21% Similarity=0.143 Sum_probs=29.0
Q ss_pred cCCcEEEEEEcCCeEEEEEEEEecCccceEeec
Q 034064 27 FIVLQVLINCRNNKKLLGRVRAFDRHCNMVLEN 59 (104)
Q Consensus 27 ~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d 59 (104)
.++++|.+...+++.++|+.+|.|+...|+|+.
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 678999987677778999999999999999963
No 89
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=58.12 E-value=33 Score=21.89 Aligned_cols=32 Identities=13% Similarity=0.001 Sum_probs=24.2
Q ss_pred hhhHHHHHHhcCCcEEEEEEcCCeE----EEEEEEE
Q 034064 17 LMLFCFWALEFIVLQVLINCRNNKK----LLGRVRA 48 (104)
Q Consensus 17 ~~l~~~~L~~~l~krV~V~l~~gr~----i~G~L~~ 48 (104)
+.-....|..++|++|.++-+.||. -.|.|..
T Consensus 5 l~~Ik~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~ 40 (76)
T PF06257_consen 5 LADIKKELESHVGKRVKLKANKGRKKIIEREGVLEE 40 (76)
T ss_dssp HHHHHHHHHHTTTSEEEEEE--SSS--S-EEEEEEE
T ss_pred HHHHHHHHHHcCCCEEEEEEcCCceEEEEEEEEEEe
Confidence 3344678999999999999999973 6899864
No 90
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=55.60 E-value=30 Score=26.77 Aligned_cols=32 Identities=19% Similarity=0.345 Sum_probs=27.5
Q ss_pred cCCcEEEEEEcCCeEEEEEEEEecCccceEeec
Q 034064 27 FIVLQVLINCRNNKKLLGRVRAFDRHCNMVLEN 59 (104)
Q Consensus 27 ~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d 59 (104)
.++++|.|.. ++..+.|++.|.|....|+++.
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 4689999875 5688999999999999999864
No 91
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=54.77 E-value=5.4 Score=26.59 Aligned_cols=17 Identities=29% Similarity=0.284 Sum_probs=15.1
Q ss_pred EEEEEecCccceEeece
Q 034064 44 GRVRAFDRHCNMVLENV 60 (104)
Q Consensus 44 G~L~~fD~~mNLvL~d~ 60 (104)
|+|+|.|.|.|---++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 88999999999987765
No 92
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=54.48 E-value=41 Score=25.51 Aligned_cols=37 Identities=14% Similarity=0.082 Sum_probs=32.9
Q ss_pred HHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeece
Q 034064 24 ALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENV 60 (104)
Q Consensus 24 L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~ 60 (104)
....++++|.+...++....|+..+.|....|+++..
T Consensus 185 ~~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 185 RSLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred HhccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 3556899999999998899999999999999999875
No 93
>PRK14635 hypothetical protein; Provisional
Probab=53.79 E-value=30 Score=24.75 Aligned_cols=36 Identities=22% Similarity=0.112 Sum_probs=27.5
Q ss_pred HHHHhcCCcEEEEEEc--CCeEEEE---EEEEecCccceEee
Q 034064 22 FWALEFIVLQVLINCR--NNKKLLG---RVRAFDRHCNMVLE 58 (104)
Q Consensus 22 ~~L~~~l~krV~V~l~--~gr~i~G---~L~~fD~~mNLvL~ 58 (104)
..+..+.+..|.|++. ++..++| +|.++|.- ++.|.
T Consensus 92 ~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~ 132 (162)
T PRK14635 92 EDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE 132 (162)
T ss_pred HHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence 5578899999999886 4678887 99999874 34443
No 94
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=53.10 E-value=15 Score=20.99 Aligned_cols=22 Identities=23% Similarity=0.327 Sum_probs=15.0
Q ss_pred EEEEEEEecCccceEeeceEEe
Q 034064 42 LLGRVRAFDRHCNMVLENVREM 63 (104)
Q Consensus 42 i~G~L~~fD~~mNLvL~d~~E~ 63 (104)
.+|+..|.|+...+.|++..+.
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 7899999999999999886653
No 95
>PF06308 ErmC: 23S rRNA methylase leader peptide (ErmC); InterPro: IPR009391 This family consists of several very short bacterial 23S rRNA methylase leader peptide (ErmC) sequences. ermC confers resistance to macrolide-lincosamide streptogramin B antibiotics by specifying a ribosomal RNA methylase, which results in decreased ribosomal affinity for these antibiotics. ermC expression is induced by exposure to erythromycin [].; GO: 0046677 response to antibiotic
Probab=50.73 E-value=12 Score=19.08 Aligned_cols=11 Identities=45% Similarity=0.507 Sum_probs=8.1
Q ss_pred CeEEEEEEEEe
Q 034064 1 MLVIQIRFSFR 11 (104)
Q Consensus 1 ~~~~~~~~~~~ 11 (104)
|||.|+|+--.
T Consensus 1 mlvfq~r~vdk 11 (27)
T PF06308_consen 1 MLVFQMRNVDK 11 (27)
T ss_pred CeeEEEeeccc
Confidence 78999887533
No 96
>PRK08330 biotin--protein ligase; Provisional
Probab=48.41 E-value=50 Score=24.51 Aligned_cols=33 Identities=18% Similarity=0.171 Sum_probs=27.3
Q ss_pred hcCCcEEEEEEcCCeEE-EEEEEEecCccceEeec
Q 034064 26 EFIVLQVLINCRNNKKL-LGRVRAFDRHCNMVLEN 59 (104)
Q Consensus 26 ~~l~krV~V~l~~gr~i-~G~L~~fD~~mNLvL~d 59 (104)
..++++|.+.. ++..+ .|+..|.|....|+++.
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 46799999875 56665 79999999999999874
No 97
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=46.29 E-value=11 Score=26.88 Aligned_cols=22 Identities=23% Similarity=0.344 Sum_probs=17.4
Q ss_pred CeEEEEEEEEecCccceEeece
Q 034064 39 NKKLLGRVRAFDRHCNMVLENV 60 (104)
Q Consensus 39 gr~i~G~L~~fD~~mNLvL~d~ 60 (104)
+-.=.|+|+|-|+|.|=--+|-
T Consensus 42 d~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 42 DDHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred ccccceeeeeecccccchhccc
Confidence 3345789999999999877765
No 98
>PRK06646 DNA polymerase III subunit chi; Provisional
Probab=46.07 E-value=36 Score=24.25 Aligned_cols=34 Identities=12% Similarity=0.034 Sum_probs=27.9
Q ss_pred EEEEEEecCceehhhHHHHHHhcC--CcEEEEEEcC
Q 034064 5 QIRFSFRNSQTTLMLFCFWALEFI--VLQVLINCRN 38 (104)
Q Consensus 5 ~~~~~~~~~~~~~~l~~~~L~~~l--~krV~V~l~~ 38 (104)
+|.|+|++..+.+-..+.++++.. +.||.|...+
T Consensus 3 ~v~FYhL~~~~~~~~acrL~~Ka~~~G~rv~I~~~d 38 (154)
T PRK06646 3 QFSIYQTSDELLLKSILLLIEKCYYSDLKSVILTAD 38 (154)
T ss_pred eeEEEEeCCChHHHHHHHHHHHHHHcCCEEEEEcCC
Confidence 689999999999888888888776 5677777754
No 99
>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=43.66 E-value=31 Score=22.72 Aligned_cols=24 Identities=17% Similarity=0.072 Sum_probs=20.7
Q ss_pred HhcCCcEEEEE-EcCCeEEEEEEEE
Q 034064 25 LEFIVLQVLIN-CRNNKKLLGRVRA 48 (104)
Q Consensus 25 ~~~l~krV~V~-l~~gr~i~G~L~~ 48 (104)
.-.++..|+|+ +.+|+.+.|++.+
T Consensus 92 ~g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 92 DGAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred ccCCCCEEEEEECCCCCEEEEEEeC
Confidence 55789999999 7899999999875
No 100
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.63 E-value=30 Score=22.40 Aligned_cols=40 Identities=10% Similarity=0.021 Sum_probs=28.0
Q ss_pred hHHHHHHhcCCcEEEEEEcCCeEE----EEEE-EEecCccceEee
Q 034064 19 LFCFWALEFIVLQVLINCRNNKKL----LGRV-RAFDRHCNMVLE 58 (104)
Q Consensus 19 l~~~~L~~~l~krV~V~l~~gr~i----~G~L-~~fD~~mNLvL~ 58 (104)
-...-+..+++++|.++.++||.= .|.| ..|-.++=+-|+
T Consensus 9 ~IK~~i~ah~G~~v~lk~ngGRKk~~~r~G~L~EtYpSvFIiel~ 53 (80)
T COG4466 9 DIKESIDAHLGERVTLKANGGRKKTIERSGILIETYPSVFIIELD 53 (80)
T ss_pred HHHHHHHhccCcEEEEEecCCceeeehhceEEeeecCcEEEEEec
Confidence 345678899999999999999863 5666 355555533343
No 101
>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=38.08 E-value=68 Score=21.74 Aligned_cols=29 Identities=10% Similarity=0.133 Sum_probs=21.3
Q ss_pred EEEEEEcCCeEEEEEEEEecCccceEeece
Q 034064 31 QVLINCRNNKKLLGRVRAFDRHCNMVLENV 60 (104)
Q Consensus 31 rV~V~l~~gr~i~G~L~~fD~~mNLvL~d~ 60 (104)
...|.++||+.++|.+..=|.. .+.|.++
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~~~-~~~l~~~ 87 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASETAD-GVTVKMP 87 (133)
T ss_pred cEEEEECCCCEEEEEEEecCCC-eEEEEcC
Confidence 4789999999999999885433 2444443
No 102
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=37.48 E-value=39 Score=25.28 Aligned_cols=24 Identities=13% Similarity=0.076 Sum_probs=21.0
Q ss_pred HhcCCcEEEEE-EcCCeEEEEEEEE
Q 034064 25 LEFIVLQVLIN-CRNNKKLLGRVRA 48 (104)
Q Consensus 25 ~~~l~krV~V~-l~~gr~i~G~L~~ 48 (104)
+..+|..|+|+ +.+|+.+.|++.+
T Consensus 203 ~G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 203 DGAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCCeEEEEECCCCCEEEEEEeC
Confidence 45789999999 9999999999875
No 103
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=36.61 E-value=28 Score=21.99 Aligned_cols=20 Identities=10% Similarity=0.245 Sum_probs=16.2
Q ss_pred HHHhcCCcEEEEEEcCCeEE
Q 034064 23 WALEFIVLQVLINCRNNKKL 42 (104)
Q Consensus 23 ~L~~~l~krV~V~l~~gr~i 42 (104)
.+++.++|+|+|+++..-++
T Consensus 5 ~~nDrLGKKVRvKCn~dDti 24 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDTI 24 (73)
T ss_pred hhhhhcCceEEEEeCCcccc
Confidence 47889999999999876543
No 104
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=36.39 E-value=38 Score=22.16 Aligned_cols=21 Identities=29% Similarity=0.523 Sum_probs=19.3
Q ss_pred eeeeCeEEEeCCcEEEEEecC
Q 034064 83 DRFISKMFLRGDSVIIVLRNP 103 (104)
Q Consensus 83 ~r~lg~~~IRGdnVv~Is~~~ 103 (104)
+|+-|.+..+|..+..+.-+|
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 488999999999999999887
No 105
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=34.01 E-value=1.6e+02 Score=20.91 Aligned_cols=27 Identities=19% Similarity=0.155 Sum_probs=23.8
Q ss_pred HHhcCCcEEEEEEcCCeEEEEEEEEec
Q 034064 24 ALEFIVLQVLINCRNNKKLLGRVRAFD 50 (104)
Q Consensus 24 L~~~l~krV~V~l~~gr~i~G~L~~fD 50 (104)
...++++.|.+...+|..++|++.+..
T Consensus 87 a~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 87 YSELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 467899999999999999999998774
No 106
>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=31.76 E-value=31 Score=22.08 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=13.7
Q ss_pred CCcEEEEEEcCCeEEEEEEEEecCccc
Q 034064 28 IVLQVLINCRNNKKLLGRVRAFDRHCN 54 (104)
Q Consensus 28 l~krV~V~l~~gr~i~G~L~~fD~~mN 54 (104)
-.-+|.+.|+||..++|+ +.|-..|
T Consensus 16 ~~~~v~L~l~dG~~~~g~--A~dt~~~ 40 (80)
T PF07073_consen 16 YRYPVKLTLKDGEQIEGK--ALDTRTN 40 (80)
T ss_dssp TTT-EEEE-TTT--EEES--S-EEE--
T ss_pred cCCeEEEEEeCCCEEEEE--EEEEEEe
Confidence 345999999999999997 4444443
No 107
>PRK08477 biotin--protein ligase; Provisional
Probab=31.57 E-value=1.2e+02 Score=22.59 Aligned_cols=34 Identities=3% Similarity=-0.129 Sum_probs=28.5
Q ss_pred HhcCCcEEEEEEcCCeEEEEEEEEecCccceEeec
Q 034064 25 LEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLEN 59 (104)
Q Consensus 25 ~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d 59 (104)
.-.+++.|.|. .+++.++|+..+.|+..-|++.-
T Consensus 171 ~~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~ 204 (211)
T PRK08477 171 EFEKSKSFSFH-IDGKLVSLKDAELLEDGSILING 204 (211)
T ss_pred HHHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECC
Confidence 44678899986 57899999999999999998764
No 108
>PRK05728 DNA polymerase III subunit chi; Validated
Probab=28.88 E-value=90 Score=21.58 Aligned_cols=35 Identities=20% Similarity=0.339 Sum_probs=26.5
Q ss_pred EEEEEEecCceehhhHHHHHHhcC--CcEEEEEEcCC
Q 034064 5 QIRFSFRNSQTTLMLFCFWALEFI--VLQVLINCRNN 39 (104)
Q Consensus 5 ~~~~~~~~~~~~~~l~~~~L~~~l--~krV~V~l~~g 39 (104)
++.|++++.+..+-..+.++++.. ++||.|...+.
T Consensus 3 ~v~FY~l~~~~~~~~~c~L~~ka~~~g~rv~I~~~d~ 39 (142)
T PRK05728 3 RADFYHLTLSALEALLCELAEKALRAGWRVLVQCEDE 39 (142)
T ss_pred eEEEEecCchhHHHHHHHHHHHHHHCCCEEEEEcCCH
Confidence 788889877777766777777765 68998888653
No 109
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.85 E-value=85 Score=23.43 Aligned_cols=24 Identities=17% Similarity=0.021 Sum_probs=20.9
Q ss_pred HhcCCcEEEEEEcCCeEEEEEEEE
Q 034064 25 LEFIVLQVLINCRNNKKLLGRVRA 48 (104)
Q Consensus 25 ~~~l~krV~V~l~~gr~i~G~L~~ 48 (104)
...+|..|+|+..+|+.+.|++.|
T Consensus 192 ~G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 192 DGNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred cCCCCCEEEEEeCCCCEEEEEEec
Confidence 457899999999889999999876
No 110
>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=28.48 E-value=1.2e+02 Score=18.20 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=18.2
Q ss_pred cCCcEEEEEEcCCeEE-EEEEEEecC
Q 034064 27 FIVLQVLINCRNNKKL-LGRVRAFDR 51 (104)
Q Consensus 27 ~l~krV~V~l~~gr~i-~G~L~~fD~ 51 (104)
..+++|++.=-+...+ .|++.+||.
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~ 32 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDS 32 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEET
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecc
Confidence 3578899998887765 999999997
No 111
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.11 E-value=76 Score=22.59 Aligned_cols=24 Identities=13% Similarity=-0.049 Sum_probs=19.9
Q ss_pred HhcCCcEEEEE-EcCCeEEEEEEEE
Q 034064 25 LEFIVLQVLIN-CRNNKKLLGRVRA 48 (104)
Q Consensus 25 ~~~l~krV~V~-l~~gr~i~G~L~~ 48 (104)
+-..++.|+|+ +.+|+.++|++.+
T Consensus 127 ~G~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 127 SGAAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred cCCCCCEEEEEECCCCCEEEEEEec
Confidence 45678899999 8899999998764
No 112
>PRK10708 hypothetical protein; Provisional
Probab=27.76 E-value=72 Score=19.54 Aligned_cols=26 Identities=15% Similarity=0.174 Sum_probs=21.9
Q ss_pred CCcEEEEEEcCCeEEEEEEEEecCcc
Q 034064 28 IVLQVLINCRNNKKLLGRVRAFDRHC 53 (104)
Q Consensus 28 l~krV~V~l~~gr~i~G~L~~fD~~m 53 (104)
++.+|.|++.++-.=.|++.+...|-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 57899999999988899988777663
No 113
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=27.55 E-value=1.4e+02 Score=24.98 Aligned_cols=45 Identities=9% Similarity=-0.127 Sum_probs=38.0
Q ss_pred HHHHHHhcCCcEEEEEEcCCeEEEEEEEEecCccceEeeceEEeee
Q 034064 20 FCFWALEFIVLQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWT 65 (104)
Q Consensus 20 ~~~~L~~~l~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~E~~~ 65 (104)
...++++.++|-|+- =++|++.+++|.+-|.-.=+-+.|-.|...
T Consensus 73 ~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~~ 117 (421)
T COG5316 73 PGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVLG 117 (421)
T ss_pred chhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEEe
Confidence 356789999999888 889999999999999888777778777654
No 114
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.37 E-value=74 Score=23.84 Aligned_cols=24 Identities=17% Similarity=0.038 Sum_probs=20.2
Q ss_pred HhcCCcEEEEE-EcCCeEEEEEEEE
Q 034064 25 LEFIVLQVLIN-CRNNKKLLGRVRA 48 (104)
Q Consensus 25 ~~~l~krV~V~-l~~gr~i~G~L~~ 48 (104)
+...+..|+|+ +.+||.++|+..+
T Consensus 182 ~G~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 182 DAGENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCCCEEEEEECCCCCEEEEEEeC
Confidence 45678999999 7999999998865
No 115
>COG2927 HolC DNA polymerase III, chi subunit [DNA replication, recombination, and repair]
Probab=27.12 E-value=1.2e+02 Score=21.68 Aligned_cols=34 Identities=26% Similarity=0.353 Sum_probs=27.4
Q ss_pred EEEEEEecCceehhhHHHHHHhcC--CcEEEEEEcC
Q 034064 5 QIRFSFRNSQTTLMLFCFWALEFI--VLQVLINCRN 38 (104)
Q Consensus 5 ~~~~~~~~~~~~~~l~~~~L~~~l--~krV~V~l~~ 38 (104)
++-|++...+..+-..+.++++.. |.||.|.+.|
T Consensus 3 ~~~FY~l~~~~~~~~~c~L~~k~~~~G~rvlI~~~d 38 (144)
T COG2927 3 EATFYLLSESTLLAAACRLAEKAWRSGWRVLIQCED 38 (144)
T ss_pred eeEEEEecchhHHHHHHHHHHHHHHcCCeEEEEeCC
Confidence 577899999988877788888776 7788888865
No 116
>PRK06630 hypothetical protein; Provisional
Probab=27.05 E-value=35 Score=22.98 Aligned_cols=19 Identities=16% Similarity=0.106 Sum_probs=16.4
Q ss_pred EEEEEEEecCccceEeece
Q 034064 42 LLGRVRAFDRHCNMVLENV 60 (104)
Q Consensus 42 i~G~L~~fD~~mNLvL~d~ 60 (104)
..|+|+|-|+|.|---++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3799999999999988774
No 117
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=24.78 E-value=1.4e+02 Score=23.11 Aligned_cols=33 Identities=3% Similarity=0.183 Sum_probs=27.9
Q ss_pred CcEEEEEEcCCeEEEEEEEEecCccceEeeceE
Q 034064 29 VLQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 61 (104)
Q Consensus 29 ~krV~V~l~~gr~i~G~L~~fD~~mNLvL~d~~ 61 (104)
..++.+.+.||+++.+.+.|+|...=+.+-...
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki~ 127 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKID 127 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEec
Confidence 568899999999999999999999877765443
No 118
>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=24.54 E-value=82 Score=19.29 Aligned_cols=26 Identities=12% Similarity=0.123 Sum_probs=21.8
Q ss_pred CCcEEEEEEcCCeEEEEEEEEecCcc
Q 034064 28 IVLQVLINCRNNKKLLGRVRAFDRHC 53 (104)
Q Consensus 28 l~krV~V~l~~gr~i~G~L~~fD~~m 53 (104)
++.+|.|++.++-.=.|++.+...|-
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 57899999999988899988777663
No 119
>PF04364 DNA_pol3_chi: DNA polymerase III chi subunit, HolC; InterPro: IPR007459 The DNA polymerase III holoenzyme (2.7.7.7 from EC) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either the tau or gamma product of gene dnax, complexed to delta.delta and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3SXU_A 1EM8_C.
Probab=24.05 E-value=1.3e+02 Score=20.53 Aligned_cols=35 Identities=20% Similarity=0.256 Sum_probs=19.7
Q ss_pred EEEEEEEecCceehhhHHHHHHhcC--CcEEEEEEcC
Q 034064 4 IQIRFSFRNSQTTLMLFCFWALEFI--VLQVLINCRN 38 (104)
Q Consensus 4 ~~~~~~~~~~~~~~~l~~~~L~~~l--~krV~V~l~~ 38 (104)
-+|.|+++.+....-..+.++++.. ++||.|...|
T Consensus 2 t~v~Fy~l~~~~~~~~~c~L~~k~~~~g~rv~V~~~d 38 (137)
T PF04364_consen 2 TRVDFYHLSSDDLERFACRLAEKAYRQGQRVLVLCPD 38 (137)
T ss_dssp EEEEEEE-S----HHHHHHHHHHHHHTT--EEEE-SS
T ss_pred CeEEEEEcCCCcHHHHHHHHHHHHHHcCCeEEEEeCC
Confidence 3789999999888656666666655 6788888875
No 120
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=23.75 E-value=45 Score=22.96 Aligned_cols=20 Identities=30% Similarity=0.227 Sum_probs=16.8
Q ss_pred EEEEEEecCccceEeeceEE
Q 034064 43 LGRVRAFDRHCNMVLENVRE 62 (104)
Q Consensus 43 ~G~L~~fD~~mNLvL~d~~E 62 (104)
.|.|+|-|+|.|---++..+
T Consensus 9 ~g~lVG~D~~GNkYYE~~~~ 28 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPSY 28 (115)
T ss_pred cceEeEEcCCCCeeeEcCCC
Confidence 69999999999998876543
No 121
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=22.85 E-value=1.2e+02 Score=22.44 Aligned_cols=17 Identities=18% Similarity=0.313 Sum_probs=14.1
Q ss_pred cCCeEEEEEEEEecCcc
Q 034064 37 RNNKKLLGRVRAFDRHC 53 (104)
Q Consensus 37 ~~gr~i~G~L~~fD~~m 53 (104)
.++..|.|++.+||+=.
T Consensus 142 t~~~~Y~G~I~~~~~~~ 158 (185)
T PF14153_consen 142 TKDKSYRGIILSYDEGE 158 (185)
T ss_pred eCCceEEEEEEeccCCE
Confidence 35789999999999763
No 122
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.35 E-value=1e+02 Score=23.79 Aligned_cols=24 Identities=4% Similarity=-0.093 Sum_probs=20.5
Q ss_pred HhcCCcEEEEE-EcCCeEEEEEEEE
Q 034064 25 LEFIVLQVLIN-CRNNKKLLGRVRA 48 (104)
Q Consensus 25 ~~~l~krV~V~-l~~gr~i~G~L~~ 48 (104)
+...+..|+|+ +.+||.++|++.+
T Consensus 229 ~G~~Gd~IrVrN~~SgkvV~a~V~~ 253 (261)
T PRK06804 229 NGRKGELIKVKNLSSGRVVTATVDG 253 (261)
T ss_pred CCCCCCEEEEEECCCCCEEEEEEec
Confidence 45678999999 8899999999876
No 123
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.34 E-value=1.1e+02 Score=21.25 Aligned_cols=24 Identities=13% Similarity=0.095 Sum_probs=19.6
Q ss_pred HhcCCcEEEEE-EcCCeEEEEEEEE
Q 034064 25 LEFIVLQVLIN-CRNNKKLLGRVRA 48 (104)
Q Consensus 25 ~~~l~krV~V~-l~~gr~i~G~L~~ 48 (104)
.-..+..|+|+ +.+||.++|+..+
T Consensus 108 ~G~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 108 RGGVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred cCCCCCEEEEEECCCCCEEEEEEec
Confidence 45678899996 7889999998875
No 124
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=22.31 E-value=85 Score=19.20 Aligned_cols=23 Identities=17% Similarity=0.255 Sum_probs=19.0
Q ss_pred CcEEEEEEcCCeEEEEEEEEecC
Q 034064 29 VLQVLINCRNNKKLLGRVRAFDR 51 (104)
Q Consensus 29 ~krV~V~l~~gr~i~G~L~~fD~ 51 (104)
..+|.|++-||..+++++..-|.
T Consensus 4 ~~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 4 QCRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred eEEEEEEcCCCCEEEEEeCCCCc
Confidence 35899999999999999876554
No 125
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=22.26 E-value=1.1e+02 Score=17.60 Aligned_cols=14 Identities=7% Similarity=0.097 Sum_probs=11.0
Q ss_pred HHHHhcCCcEEEEE
Q 034064 22 FWALEFIVLQVLIN 35 (104)
Q Consensus 22 ~~L~~~l~krV~V~ 35 (104)
..++.+++|+|.|.
T Consensus 12 ~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 12 SYLKSLLGKRVSVT 25 (48)
T ss_pred HHHHHhcCCeEEEE
Confidence 44777999999875
No 126
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=21.55 E-value=2.7e+02 Score=20.88 Aligned_cols=23 Identities=0% Similarity=0.011 Sum_probs=20.0
Q ss_pred cCCeEEEEEEEEecCccceEeec
Q 034064 37 RNNKKLLGRVRAFDRHCNMVLEN 59 (104)
Q Consensus 37 ~~gr~i~G~L~~fD~~mNLvL~d 59 (104)
.++..++|+..|.|+-..|+++.
T Consensus 209 ~~~~~~~G~~~gId~~G~Lvv~~ 231 (245)
T PTZ00276 209 TGRDPEELTALSLNEWGHLIVRR 231 (245)
T ss_pred cCCcEEEEEEEEECCCCeEEEEE
Confidence 46677899999999999999975
No 127
>COG3814 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.86 E-value=1.5e+02 Score=21.39 Aligned_cols=31 Identities=10% Similarity=0.057 Sum_probs=22.8
Q ss_pred EEEEEecCceehhhHHHHHHhcCCcEEEEEEc
Q 034064 6 IRFSFRNSQTTLMLFCFWALEFIVLQVLINCR 37 (104)
Q Consensus 6 ~~~~~~~~~~~~~l~~~~L~~~l~krV~V~l~ 37 (104)
|+.+|+..-|-+.+...+..++. +.+.|.++
T Consensus 38 ~yItf~T~apgV~~~s~lk~kYP-eqmTIVlQ 68 (157)
T COG3814 38 FYITFLTGAPGVRIPSKLKQKYP-EQMTIVLQ 68 (157)
T ss_pred EEEEEecCCCceeccHHHHhhCc-cceEEEee
Confidence 67788888888877777555554 47777776
No 128
>smart00725 NEAT NEAr Transporter domain.
Probab=20.38 E-value=2.5e+02 Score=18.91 Aligned_cols=49 Identities=8% Similarity=0.021 Sum_probs=30.2
Q ss_pred EEEEEecCceehhhHHHHHHhcCCcEEEEEEcCCeEE-EEEEEEecCccceEe
Q 034064 6 IRFSFRNSQTTLMLFCFWALEFIVLQVLINCRNNKKL-LGRVRAFDRHCNMVL 57 (104)
Q Consensus 6 ~~~~~~~~~~~~~l~~~~L~~~l~krV~V~l~~gr~i-~G~L~~fD~~mNLvL 57 (104)
|-|+.+.+++.= ...+..+++++..+..+||..+ +=+|..-|-.-++-+
T Consensus 7 i~~~vlk~~~~~---~Sma~~Y~~~pa~l~v~nGk~~v~ltl~~s~~~~~f~i 56 (123)
T smart00725 7 INFVVLKDNSNE---ESMMDDYLNKPAKLIVKNGKTYVTLTLNNSSFWKDFEV 56 (123)
T ss_pred EEEEEEeCCCCc---hhhHHHhhcCceEEEEECCEEEEEEEEcCCccEEEEEE
Confidence 344444443332 2448999999999999999754 555666443334444
Done!