Query 034180
Match_columns 102
No_of_seqs 142 out of 1056
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 10:39:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034180.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034180hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01729 LSm7 The eukaryotic Sm 99.8 1.9E-18 4.1E-23 114.6 7.8 60 37-96 1-68 (81)
2 cd01719 Sm_G The eukaryotic Sm 99.7 8E-18 1.7E-22 109.5 7.6 57 40-96 2-58 (72)
3 PRK00737 small nuclear ribonuc 99.7 4.2E-17 9.2E-22 105.6 7.4 57 40-96 6-62 (72)
4 cd01732 LSm5 The eukaryotic Sm 99.7 1.1E-16 2.4E-21 105.4 7.9 56 41-96 6-64 (76)
5 cd01731 archaeal_Sm1 The archa 99.7 1.1E-16 2.3E-21 102.2 7.5 56 41-96 3-58 (68)
6 cd01728 LSm1 The eukaryotic Sm 99.7 2.3E-16 4.9E-21 103.5 8.6 58 39-96 3-63 (74)
7 cd01727 LSm8 The eukaryotic Sm 99.7 3.5E-16 7.6E-21 101.7 7.5 56 41-96 2-61 (74)
8 cd01726 LSm6 The eukaryotic Sm 99.7 5.7E-16 1.2E-20 98.8 7.5 56 41-96 3-58 (67)
9 cd01730 LSm3 The eukaryotic Sm 99.6 6.1E-16 1.3E-20 102.4 7.7 55 42-96 5-72 (82)
10 cd01717 Sm_B The eukaryotic Sm 99.6 6.3E-16 1.4E-20 101.4 7.6 56 41-96 3-68 (79)
11 KOG1780 Small Nuclear ribonucl 99.6 1.9E-16 4.2E-21 104.9 4.8 57 40-96 6-62 (77)
12 cd06168 LSm9 The eukaryotic Sm 99.6 9.2E-16 2E-20 100.8 7.8 56 41-96 3-64 (75)
13 cd01722 Sm_F The eukaryotic Sm 99.6 5.6E-16 1.2E-20 99.2 6.5 56 40-95 3-58 (68)
14 PF01423 LSM: LSM domain ; In 99.6 9.2E-15 2E-19 91.7 8.8 55 42-96 2-57 (67)
15 smart00651 Sm snRNP Sm protein 99.6 7E-15 1.5E-19 92.1 7.3 54 42-95 2-56 (67)
16 COG1958 LSM1 Small nuclear rib 99.6 8.4E-15 1.8E-19 95.8 7.7 47 37-83 6-52 (79)
17 KOG1781 Small Nuclear ribonucl 99.6 1E-16 2.2E-21 111.3 -1.5 66 32-97 11-84 (108)
18 cd01718 Sm_E The eukaryotic Sm 99.6 1.7E-14 3.6E-19 96.1 7.5 57 40-96 8-69 (79)
19 cd00600 Sm_like The eukaryotic 99.5 2.2E-14 4.7E-19 88.5 7.1 53 43-95 1-53 (63)
20 KOG3482 Small nuclear ribonucl 99.5 9E-15 1.9E-19 96.9 4.9 58 40-97 10-67 (79)
21 cd01720 Sm_D2 The eukaryotic S 99.5 2.7E-14 5.8E-19 96.4 6.8 43 43-85 7-51 (87)
22 cd01721 Sm_D3 The eukaryotic S 99.4 3.8E-13 8.2E-18 86.8 6.7 53 42-94 4-56 (70)
23 cd01723 LSm4 The eukaryotic Sm 99.4 8.9E-13 1.9E-17 86.1 6.6 45 42-86 5-49 (76)
24 cd01724 Sm_D1 The eukaryotic S 99.4 1.3E-12 2.8E-17 88.4 7.0 55 41-95 4-58 (90)
25 PTZ00138 small nuclear ribonuc 99.4 2.2E-12 4.8E-17 87.7 7.1 54 43-96 19-77 (89)
26 cd01733 LSm10 The eukaryotic S 99.4 2.3E-12 5E-17 85.1 6.5 54 42-95 13-66 (78)
27 cd01725 LSm2 The eukaryotic Sm 99.2 2.9E-11 6.2E-16 80.1 6.7 45 41-85 4-48 (81)
28 KOG1783 Small nuclear ribonucl 99.2 2E-12 4.3E-17 85.7 -1.2 61 33-93 1-61 (77)
29 KOG1775 U6 snRNA-associated Sm 99.0 1.3E-10 2.9E-15 77.8 2.7 50 38-87 6-56 (84)
30 KOG1774 Small nuclear ribonucl 99.0 3E-10 6.5E-15 76.8 2.7 53 43-95 17-74 (88)
31 KOG3460 Small nuclear ribonucl 99.0 1.1E-10 2.4E-15 79.2 0.1 47 38-84 4-51 (91)
32 KOG1784 Small Nuclear ribonucl 98.8 3.4E-09 7.3E-14 72.9 3.6 46 41-86 3-48 (96)
33 KOG3168 U1 snRNP component [Tr 98.7 1.4E-09 3.1E-14 81.6 -1.5 44 40-83 6-49 (177)
34 KOG1782 Small Nuclear ribonucl 98.6 5E-09 1.1E-13 75.3 -0.9 50 39-88 10-60 (129)
35 KOG3448 Predicted snRNP core p 98.6 2E-07 4.2E-12 64.1 6.4 58 41-98 5-62 (96)
36 KOG3293 Small nuclear ribonucl 97.8 2.6E-05 5.7E-10 56.4 3.8 45 43-87 7-51 (134)
37 cd01739 LSm11_C The eukaryotic 97.8 2.4E-05 5.1E-10 51.0 3.2 37 49-85 9-49 (66)
38 PF14438 SM-ATX: Ataxin 2 SM d 97.1 0.0018 4E-08 41.6 5.9 43 43-85 7-52 (77)
39 KOG3428 Small nuclear ribonucl 97.1 0.0012 2.7E-08 46.6 4.9 46 40-85 4-49 (109)
40 KOG3459 Small nuclear ribonucl 96.6 0.0002 4.3E-09 50.9 -1.9 56 29-84 17-72 (114)
41 KOG3172 Small nuclear ribonucl 96.1 0.019 4.2E-07 40.8 5.7 44 43-86 10-53 (119)
42 PF06372 Gemin6: Gemin6 protei 95.7 0.017 3.6E-07 43.3 4.2 43 38-81 7-50 (166)
43 cd01716 Hfq Hfq, an abundant, 95.7 0.027 5.8E-07 36.1 4.4 29 47-75 10-38 (61)
44 TIGR02383 Hfq RNA chaperone Hf 95.5 0.033 7.1E-07 35.7 4.4 28 48-75 15-42 (61)
45 PF02237 BPL_C: Biotin protein 95.3 0.059 1.3E-06 32.0 4.8 33 46-79 1-33 (48)
46 PRK14638 hypothetical protein; 94.8 0.07 1.5E-06 38.9 5.1 39 38-77 90-128 (150)
47 PRK00395 hfq RNA-binding prote 94.8 0.064 1.4E-06 36.0 4.4 30 47-76 18-47 (79)
48 PRK14639 hypothetical protein; 94.3 0.11 2.5E-06 37.4 5.0 38 38-76 78-115 (140)
49 PRK02001 hypothetical protein; 94.0 0.13 2.9E-06 37.8 5.0 37 39-76 81-117 (152)
50 PF12701 LSM14: Scd6-like Sm d 93.9 0.17 3.7E-06 34.7 5.0 39 44-82 4-43 (96)
51 COG1923 Hfq Uncharacterized ho 93.5 0.18 4E-06 33.7 4.5 31 42-72 11-43 (77)
52 cd01735 LSm12_N LSm12 belongs 93.4 0.34 7.4E-06 30.9 5.4 36 46-81 4-39 (61)
53 PRK14091 RNA-binding protein H 92.8 0.23 5E-06 37.4 4.7 44 32-75 4-51 (165)
54 cd01734 YlxS_C YxlS is a Bacil 92.3 0.44 9.5E-06 31.1 5.0 34 38-71 15-52 (83)
55 PRK14644 hypothetical protein; 92.2 0.39 8.3E-06 34.6 5.0 38 39-77 76-117 (136)
56 PRK14640 hypothetical protein; 91.5 0.53 1.2E-05 34.3 5.2 37 39-76 88-128 (152)
57 PRK14633 hypothetical protein; 91.4 0.55 1.2E-05 34.2 5.2 37 39-76 85-125 (150)
58 PRK14642 hypothetical protein; 90.6 0.66 1.4E-05 35.7 5.1 38 38-76 90-140 (197)
59 PRK14645 hypothetical protein; 90.4 0.68 1.5E-05 34.0 4.9 32 39-71 93-124 (154)
60 PF10842 DUF2642: Protein of u 90.3 2.2 4.8E-05 27.6 6.6 50 40-96 13-63 (66)
61 PF02576 DUF150: Uncharacteris 90.2 0.55 1.2E-05 33.2 4.1 36 40-76 79-118 (141)
62 PRK00092 ribosome maturation p 89.9 0.92 2E-05 32.8 5.2 32 39-70 89-124 (154)
63 PRK14636 hypothetical protein; 89.7 0.83 1.8E-05 34.2 5.0 37 39-76 89-129 (176)
64 PRK14643 hypothetical protein; 89.6 0.89 1.9E-05 33.7 5.0 37 39-75 95-136 (164)
65 cd01736 LSm14_N LSm14 (also kn 89.6 1.2 2.6E-05 29.5 5.1 40 44-83 2-42 (74)
66 PRK14634 hypothetical protein; 89.5 0.96 2.1E-05 33.1 5.1 37 39-76 91-131 (155)
67 COG0779 Uncharacterized protei 89.5 0.97 2.1E-05 33.4 5.1 34 39-72 90-127 (153)
68 PRK14646 hypothetical protein; 89.1 1.1 2.3E-05 32.9 5.1 38 38-76 90-131 (155)
69 PRK14632 hypothetical protein; 88.7 1.1 2.5E-05 33.3 5.1 38 39-77 89-133 (172)
70 PRK14091 RNA-binding protein H 88.4 0.91 2E-05 34.3 4.3 33 43-75 97-131 (165)
71 PRK14647 hypothetical protein; 87.5 1.5 3.3E-05 32.1 5.0 32 39-70 90-130 (159)
72 PRK14631 hypothetical protein; 86.8 1.8 3.8E-05 32.4 5.1 32 38-69 107-142 (174)
73 PRK14637 hypothetical protein; 86.5 1.7 3.7E-05 31.8 4.8 38 38-76 88-126 (151)
74 PRK14641 hypothetical protein; 83.5 2.6 5.7E-05 31.6 4.7 31 39-69 95-129 (173)
75 PF11095 Gemin7: Gem-associate 81.5 4.2 9.1E-05 27.3 4.6 39 40-78 16-55 (80)
76 PRK14630 hypothetical protein; 77.9 5.6 0.00012 28.8 4.7 36 39-76 88-123 (143)
77 PRK06955 biotin--protein ligas 75.7 6.1 0.00013 31.3 4.8 32 46-77 247-278 (300)
78 PRK14635 hypothetical protein; 73.1 9.2 0.0002 28.0 4.8 34 38-71 89-127 (162)
79 PF03614 Flag1_repress: Repres 69.8 10 0.00022 28.6 4.4 35 46-80 27-61 (165)
80 PRK10898 serine endoprotease; 66.8 12 0.00026 30.3 4.7 31 49-79 102-132 (353)
81 TIGR02038 protease_degS peripl 65.0 13 0.00029 29.9 4.6 31 49-79 102-132 (351)
82 PRK11886 bifunctional biotin-- 62.9 17 0.00037 28.6 4.8 31 46-77 270-300 (319)
83 TIGR00121 birA_ligase birA, bi 62.8 18 0.00038 27.4 4.7 31 46-77 191-221 (237)
84 PRK13325 bifunctional biotin-- 60.9 17 0.00037 31.8 4.8 32 46-77 276-307 (592)
85 PRK10139 serine endoprotease; 60.6 17 0.00038 30.5 4.7 32 49-80 115-146 (455)
86 PRK10942 serine endoprotease; 59.5 18 0.00039 30.6 4.6 31 49-79 136-166 (473)
87 PRK08330 biotin--protein ligas 59.0 25 0.00053 26.6 4.9 32 46-78 186-218 (236)
88 PTZ00275 biotin-acetyl-CoA-car 57.2 24 0.00053 27.8 4.8 30 47-77 236-265 (285)
89 COG0340 BirA Biotin-(acetyl-Co 56.9 42 0.00092 26.0 6.0 35 45-79 187-221 (238)
90 PF03614 Flag1_repress: Repres 53.8 15 0.00032 27.7 2.9 25 47-71 119-143 (165)
91 TIGR02037 degP_htrA_DO peripla 53.2 27 0.00059 28.6 4.6 32 49-80 82-113 (428)
92 PF11607 DUF3247: Protein of u 48.2 27 0.00058 24.4 3.2 17 49-65 29-45 (101)
93 PRK09618 flgD flagellar basal 47.7 70 0.0015 23.4 5.5 28 42-69 86-113 (142)
94 PF14563 DUF4444: Domain of un 43.9 32 0.00069 20.6 2.7 21 61-81 10-30 (42)
95 PF07073 ROF: Modulator of Rho 40.3 26 0.00057 23.2 2.2 30 42-73 11-40 (80)
96 PF05071 NDUFA12: NADH ubiquin 39.1 13 0.00028 25.4 0.6 17 63-79 1-17 (105)
97 KOG3382 NADH:ubiquinone oxidor 39.0 16 0.00035 27.1 1.1 21 59-79 43-63 (151)
98 TIGR03170 flgA_cterm flagella 36.7 47 0.001 22.3 3.0 23 45-67 93-116 (122)
99 PF06257 DUF1021: Protein of u 35.8 80 0.0017 20.8 3.9 27 42-68 11-41 (76)
100 PRK08477 biotin--protein ligas 35.8 88 0.0019 23.8 4.7 34 46-80 173-206 (211)
101 smart00333 TUDOR Tudor domain. 31.9 1E+02 0.0023 17.6 4.1 24 47-70 5-28 (57)
102 TIGR02603 CxxCH_TIGR02603 puta 30.9 75 0.0016 22.0 3.4 21 50-70 59-79 (133)
103 PF09465 LBR_tudor: Lamin-B re 30.6 1E+02 0.0022 19.4 3.5 24 47-70 8-32 (55)
104 PF05585 DUF1758: Putative pep 30.1 43 0.00094 23.6 2.1 39 58-96 112-153 (164)
105 COG0265 DegQ Trypsin-like seri 29.1 1.1E+02 0.0023 24.2 4.4 30 48-77 95-124 (347)
106 PRK07018 flgA flagellar basal 29.0 65 0.0014 24.6 3.0 24 45-68 204-228 (235)
107 KOG1073 Uncharacterized mRNA-a 27.4 69 0.0015 26.9 3.1 36 44-79 5-41 (361)
108 COG2248 Predicted hydrolase (m 27.4 72 0.0016 26.2 3.1 74 17-99 99-172 (304)
109 PHA02723 hypothetical protein; 26.6 39 0.00085 22.2 1.2 21 8-28 45-65 (77)
110 PRK10708 hypothetical protein; 25.3 80 0.0017 20.3 2.4 25 47-71 3-27 (62)
111 PRK11911 flgD flagellar basal 25.0 1.4E+02 0.003 21.9 4.0 26 44-69 89-114 (140)
112 PF14153 Spore_coat_CotO: Spor 23.9 87 0.0019 23.8 2.9 21 51-71 136-157 (185)
113 cd04479 RPA3 RPA3: A subfamily 23.7 2.3E+02 0.005 18.8 5.2 36 41-78 8-48 (101)
114 PRK06630 hypothetical protein; 23.3 41 0.00089 23.5 0.9 19 61-79 11-29 (99)
115 COG2451 Ribosomal protein L35A 23.0 1.8E+02 0.0038 20.4 4.0 30 39-68 37-67 (100)
116 PF10618 Tail_tube: Phage tail 22.8 1.3E+02 0.0028 21.0 3.4 30 35-64 61-90 (119)
117 PF10781 DSRB: Dextransucrase 22.0 93 0.002 20.0 2.3 25 47-71 3-27 (62)
118 KOG3487 TRAPP 20 K subunit [In 21.5 87 0.0019 23.1 2.3 38 11-48 4-41 (139)
119 KOG3493 Ubiquitin-like protein 20.9 76 0.0017 20.9 1.7 17 42-58 5-21 (73)
No 1
>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=99.77 E-value=1.9e-18 Score=114.61 Aligned_cols=60 Identities=60% Similarity=1.006 Sum_probs=53.7
Q ss_pred cCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc--------eeecEEEEEE
Q 034180 37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN--------LYNGIFVIVC 96 (102)
Q Consensus 37 ~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~--------~~~~iG~iv~ 96 (102)
+.++++|.++++|+|.|+|+|||+++|+|.|||+||||+|++|+|+..++ ..+.+|.++.
T Consensus 1 ~~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~i 68 (81)
T cd01729 1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVC 68 (81)
T ss_pred CcchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEE
Confidence 35688999999999999999999999999999999999999999998652 4577898876
No 2
>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=99.74 E-value=8e-18 Score=109.47 Aligned_cols=57 Identities=44% Similarity=0.721 Sum_probs=52.7
Q ss_pred cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC 96 (102)
Q Consensus 40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~ 96 (102)
.++|+++++|+|.|+|+||++++|+|.|||+||||+|+||+|+.++.+.+.+|.++.
T Consensus 2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~I 58 (72)
T cd01719 2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVI 58 (72)
T ss_pred chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEE
Confidence 468999999999999999999999999999999999999999987777888888764
No 3
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.71 E-value=4.2e-17 Score=105.61 Aligned_cols=57 Identities=37% Similarity=0.550 Sum_probs=51.3
Q ss_pred cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC 96 (102)
Q Consensus 40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~ 96 (102)
...|.++++++|.|+|+||++|+|+|.|||+|||++|+||.|..+++..+.+|.++.
T Consensus 6 ~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~i 62 (72)
T PRK00737 6 LDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVI 62 (72)
T ss_pred HHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEE
Confidence 456899999999999999999999999999999999999999987777778887754
No 4
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.69 E-value=1.1e-16 Score=105.36 Aligned_cols=56 Identities=21% Similarity=0.421 Sum_probs=49.9
Q ss_pred chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEE---eCceeecEEEEEE
Q 034180 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL---RGNLYNGIFVIVC 96 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~---~~~~~~~iG~iv~ 96 (102)
..|+++++++|.|+++|||+++|+|.|||+|||++|+||+|++ +++..+.+|.++.
T Consensus 6 ~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~i 64 (76)
T cd01732 6 ELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILL 64 (76)
T ss_pred HHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEE
Confidence 4478999999999999999999999999999999999999998 4455677888765
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=99.69 E-value=1.1e-16 Score=102.20 Aligned_cols=56 Identities=41% Similarity=0.510 Sum_probs=51.2
Q ss_pred chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC 96 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~ 96 (102)
..|+++++|+|.|+|+||++|+|+|.|||+|||++|+||+|+.+++..+.+|.++-
T Consensus 3 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~i 58 (68)
T cd01731 3 DVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVI 58 (68)
T ss_pred HHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEE
Confidence 45889999999999999999999999999999999999999988877788887754
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=99.68 E-value=2.3e-16 Score=103.50 Aligned_cols=58 Identities=31% Similarity=0.361 Sum_probs=51.1
Q ss_pred CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc---eeecEEEEEE
Q 034180 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN---LYNGIFVIVC 96 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~---~~~~iG~iv~ 96 (102)
+.++|.++++|+|.|+++|||++.|+|.|||+|||++|+||.|+...+ ..+.+|.++-
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~vi 63 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFII 63 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEE
Confidence 567899999999999999999999999999999999999999987542 3467788765
No 7
>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=99.66 E-value=3.5e-16 Score=101.65 Aligned_cols=56 Identities=32% Similarity=0.440 Sum_probs=49.2
Q ss_pred chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC----ceeecEEEEEE
Q 034180 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG----NLYNGIFVIVC 96 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~----~~~~~iG~iv~ 96 (102)
++|++++|++|.|+++|||.+.|+|.|||+|||++|++|+|+... ...+.+|.++.
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~i 61 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYII 61 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEE
Confidence 579999999999999999999999999999999999999999742 24566787764
No 8
>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=99.65 E-value=5.7e-16 Score=98.85 Aligned_cols=56 Identities=27% Similarity=0.351 Sum_probs=50.4
Q ss_pred chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC 96 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~ 96 (102)
..|++++|++|.|+|++|++|+|+|.|||+|||++|+||+|..+++....+|.++-
T Consensus 3 ~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~I 58 (67)
T cd01726 3 EFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFI 58 (67)
T ss_pred HHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEE
Confidence 45789999999999999999999999999999999999999887777777887653
No 9
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.65 E-value=6.1e-16 Score=102.35 Aligned_cols=55 Identities=31% Similarity=0.443 Sum_probs=47.2
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc-------------eeecEEEEEE
Q 034180 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN-------------LYNGIFVIVC 96 (102)
Q Consensus 42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~-------------~~~~iG~iv~ 96 (102)
.|++.++|+|.|+++|||+++|+|.|||+||||+|+||+|++.++ ..+.+|.++.
T Consensus 5 ~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~i 72 (82)
T cd01730 5 LIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFV 72 (82)
T ss_pred HHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEE
Confidence 357789999999999999999999999999999999999998542 3456777654
No 10
>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=99.65 E-value=6.3e-16 Score=101.40 Aligned_cols=56 Identities=23% Similarity=0.433 Sum_probs=49.0
Q ss_pred chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc----------eeecEEEEEE
Q 034180 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN----------LYNGIFVIVC 96 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~----------~~~~iG~iv~ 96 (102)
..|.+|++++|.|+++|||++.|+|.|||+||||+|+||+|++.++ +.+.+|+++.
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~i 68 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLL 68 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEE
Confidence 4689999999999999999999999999999999999999987432 3467888764
No 11
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.64 E-value=1.9e-16 Score=104.87 Aligned_cols=57 Identities=46% Similarity=0.690 Sum_probs=53.5
Q ss_pred cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC 96 (102)
Q Consensus 40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~ 96 (102)
.|+|++|++|++.+++++||...|+|.|||.|||+||+++.|...++....+|.++-
T Consensus 6 ~PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vI 62 (77)
T KOG1780|consen 6 HPELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVI 62 (77)
T ss_pred CchHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEE
Confidence 459999999999999999999999999999999999999999998888999998764
No 12
>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=99.64 E-value=9.2e-16 Score=100.82 Aligned_cols=56 Identities=18% Similarity=0.299 Sum_probs=50.9
Q ss_pred chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC------ceeecEEEEEE
Q 034180 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG------NLYNGIFVIVC 96 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~------~~~~~iG~iv~ 96 (102)
..|+++++++|+|+++|||.+.|+|.|||++||++|+||.|+..+ .+.+.+|+++.
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~I 64 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMI 64 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEE
Confidence 468999999999999999999999999999999999999999854 45788998875
No 13
>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=99.64 E-value=5.6e-16 Score=99.24 Aligned_cols=56 Identities=29% Similarity=0.342 Sum_probs=50.5
Q ss_pred cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95 (102)
Q Consensus 40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv 95 (102)
...|+++++++|.|+|+||++|+|+|.|||+|||++|+||+|+.+++....+|.++
T Consensus 3 ~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~ 58 (68)
T cd01722 3 KPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVL 58 (68)
T ss_pred HHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEE
Confidence 45689999999999999999999999999999999999999998777677777765
No 14
>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=99.60 E-value=9.2e-15 Score=91.70 Aligned_cols=55 Identities=33% Similarity=0.525 Sum_probs=50.7
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc-eeecEEEEEE
Q 034180 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN-LYNGIFVIVC 96 (102)
Q Consensus 42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~-~~~~iG~iv~ 96 (102)
.|++++|++|+|.++||++++|+|.+||+|||++|+||.|..+++ ..+.+|.++-
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~i 57 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFI 57 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEE
Confidence 588999999999999999999999999999999999999999887 8888887653
No 15
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.58 E-value=7e-15 Score=92.09 Aligned_cols=54 Identities=37% Similarity=0.592 Sum_probs=48.7
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC-ceeecEEEEE
Q 034180 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG-NLYNGIFVIV 95 (102)
Q Consensus 42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~-~~~~~iG~iv 95 (102)
.|+++++++|.|.|+||+++.|+|.|||+|||++|+||.|+.++ ++.+.+|.++
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~ 56 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVF 56 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEE
Confidence 58899999999999999999999999999999999999999877 5666677654
No 16
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.58 E-value=8.4e-15 Score=95.81 Aligned_cols=47 Identities=45% Similarity=0.660 Sum_probs=43.7
Q ss_pred cCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEE
Q 034180 37 KETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL 83 (102)
Q Consensus 37 ~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~ 83 (102)
+.+...|+++++++|.|+|++|++|.|+|.|||+|||++|+||+|+.
T Consensus 6 ~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~ 52 (79)
T COG1958 6 PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEII 52 (79)
T ss_pred CCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEe
Confidence 34566789999999999999999999999999999999999999998
No 17
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.58 E-value=1e-16 Score=111.33 Aligned_cols=66 Identities=52% Similarity=0.857 Sum_probs=59.9
Q ss_pred ccCCCcCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc--------eeecEEEEEEE
Q 034180 32 KMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN--------LYNGIFVIVCF 97 (102)
Q Consensus 32 ~ms~~~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~--------~~~~iG~iv~~ 97 (102)
.+.+++++.++|.+|++|+|+|++.+||+..|+|.|||+.||+||++++|+..++ +.+.+|++||+
T Consensus 11 ~e~~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~R 84 (108)
T KOG1781|consen 11 FEKPKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCR 84 (108)
T ss_pred ccccchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEc
Confidence 3668889999999999999999999999999999999999999999999987442 34899999996
No 18
>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=99.56 E-value=1.7e-14 Score=96.09 Aligned_cols=57 Identities=26% Similarity=0.374 Sum_probs=48.7
Q ss_pred cchHHhhcCC--eEEEEEc--CCeEEEEEEEEecCccceEEcceEEEEe-CceeecEEEEEE
Q 034180 40 VLDLAKFVDK--GVQVKLT--GGRQVTGTLKGYDQLLNLVLDEAVEFLR-GNLYNGIFVIVC 96 (102)
Q Consensus 40 ~~~L~~~i~K--~V~V~Lk--~Gr~i~G~L~gfD~~mNLVL~da~E~~~-~~~~~~iG~iv~ 96 (102)
...+.+++++ +|.|+++ +|++++|+|.|||+|||++|+||+|+.. ++..+.+|.++.
T Consensus 8 ~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~ili 69 (79)
T cd01718 8 INLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILL 69 (79)
T ss_pred HHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEE
Confidence 4458899998 6777776 8999999999999999999999999986 566778898765
No 19
>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=99.55 E-value=2.2e-14 Score=88.55 Aligned_cols=53 Identities=32% Similarity=0.534 Sum_probs=47.8
Q ss_pred HHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95 (102)
Q Consensus 43 L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv 95 (102)
|++++|++|.|.++||+.+.|+|.|||+|||++|+||.|..++...+.+|.++
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~ 53 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVL 53 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEE
Confidence 56789999999999999999999999999999999999998877667677664
No 20
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.54 E-value=9e-15 Score=96.94 Aligned_cols=58 Identities=31% Similarity=0.318 Sum_probs=54.2
Q ss_pred cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEEE
Q 034180 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCF 97 (102)
Q Consensus 40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~~ 97 (102)
.+.|+.+.+|+|.|+||+|.+|+|+|.+.|.|||+.|.+|+|++++.....+|.|+-+
T Consensus 10 KpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIR 67 (79)
T KOG3482|consen 10 KPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIR 67 (79)
T ss_pred hHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEE
Confidence 4569999999999999999999999999999999999999999999999999998743
No 21
>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=99.53 E-value=2.7e-14 Score=96.40 Aligned_cols=43 Identities=23% Similarity=0.445 Sum_probs=39.6
Q ss_pred HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC
Q 034180 43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG 85 (102)
Q Consensus 43 L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~ 85 (102)
|.+.+ +++|.|+|++|+++.|+|.|||+|||++|+||+|.+.+
T Consensus 7 L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~ 51 (87)
T cd01720 7 LTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTE 51 (87)
T ss_pred HHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeec
Confidence 56666 89999999999999999999999999999999998765
No 22
>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=99.44 E-value=3.8e-13 Score=86.75 Aligned_cols=53 Identities=19% Similarity=0.139 Sum_probs=45.5
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEE
Q 034180 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVI 94 (102)
Q Consensus 42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~i 94 (102)
.|.+..|++|.|+||||.+|+|+|.++|+|||++|+||.+...++....+|.+
T Consensus 4 ~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v 56 (70)
T cd01721 4 LLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQV 56 (70)
T ss_pred HHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcE
Confidence 47788999999999999999999999999999999999987655544555554
No 23
>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=99.40 E-value=8.9e-13 Score=86.11 Aligned_cols=45 Identities=22% Similarity=0.295 Sum_probs=41.3
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc
Q 034180 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86 (102)
Q Consensus 42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~ 86 (102)
.|++..|++|.|.|++|++++|+|.++|+|||++|+||.|...++
T Consensus 5 ~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g 49 (76)
T cd01723 5 LLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDG 49 (76)
T ss_pred HHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCC
Confidence 478899999999999999999999999999999999999985444
No 24
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.39 E-value=1.3e-12 Score=88.40 Aligned_cols=55 Identities=25% Similarity=0.303 Sum_probs=49.2
Q ss_pred chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv 95 (102)
-.|++..|++|.|.|+||.+|+|+|.++|+|||++|+||.|..+++....+|.++
T Consensus 4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~ 58 (90)
T cd01724 4 RFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLS 58 (90)
T ss_pred HHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEE
Confidence 3578899999999999999999999999999999999999998877777777664
No 25
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.37 E-value=2.2e-12 Score=87.67 Aligned_cols=54 Identities=28% Similarity=0.465 Sum_probs=44.5
Q ss_pred HHhhcCC--eEEEEEcC--CeEEEEEEEEecCccceEEcceEEEEeC-ceeecEEEEEE
Q 034180 43 LAKFVDK--GVQVKLTG--GRQVTGTLKGYDQLLNLVLDEAVEFLRG-NLYNGIFVIVC 96 (102)
Q Consensus 43 L~~~i~K--~V~V~Lk~--Gr~i~G~L~gfD~~mNLVL~da~E~~~~-~~~~~iG~iv~ 96 (102)
+.+++++ +|.|.+.+ +++++|+|.|||+|||++|+||+|+..+ +..+.+|.++-
T Consensus 19 ~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilI 77 (89)
T PTZ00138 19 IFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILL 77 (89)
T ss_pred HHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEE
Confidence 6678774 67777766 5999999999999999999999999754 46678888764
No 26
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.36 E-value=2.3e-12 Score=85.09 Aligned_cols=54 Identities=24% Similarity=0.242 Sum_probs=47.2
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEE
Q 034180 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIV 95 (102)
Q Consensus 42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv 95 (102)
.|+...|++|.|.||||.+|+|+|.++|+|||++|+||++..+++....+|.++
T Consensus 13 ~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~ 66 (78)
T cd01733 13 LLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIM 66 (78)
T ss_pred HHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEE
Confidence 367889999999999999999999999999999999999887676665666653
No 27
>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=99.24 E-value=2.9e-11 Score=80.10 Aligned_cols=45 Identities=29% Similarity=0.291 Sum_probs=41.0
Q ss_pred chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC
Q 034180 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG 85 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~ 85 (102)
..|++..|++|.|.||+|.+++|+|.++|+|||++|+||++..++
T Consensus 4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~ 48 (81)
T cd01725 4 SFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE 48 (81)
T ss_pred HHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCC
Confidence 357889999999999999999999999999999999999887543
No 28
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.18 E-value=2e-12 Score=85.69 Aligned_cols=61 Identities=30% Similarity=0.335 Sum_probs=53.4
Q ss_pred cCCCcCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEE
Q 034180 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFV 93 (102)
Q Consensus 33 ms~~~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~ 93 (102)
|+.+..+...|++.+||+|.|+|.+|-.|+|+|.+.|.|||+.|+.|+|+.+++..+..|.
T Consensus 1 ~s~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygd 61 (77)
T KOG1783|consen 1 MSEGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGD 61 (77)
T ss_pred CCcccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccc
Confidence 4444444556999999999999999999999999999999999999999999988888773
No 29
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.03 E-value=1.3e-10 Score=77.80 Aligned_cols=50 Identities=24% Similarity=0.458 Sum_probs=43.6
Q ss_pred CCcchHH-hhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCce
Q 034180 38 ETVLDLA-KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNL 87 (102)
Q Consensus 38 ~~~~~L~-~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~ 87 (102)
..|++|- +.+++++.|.+|+.|++.|+|.|||.|.|++|+|+.|+..+.+
T Consensus 6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e 56 (84)
T KOG1775|consen 6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE 56 (84)
T ss_pred cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC
Confidence 3456644 7899999999999999999999999999999999999975543
No 30
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=98.98 E-value=3e-10 Score=76.80 Aligned_cols=53 Identities=30% Similarity=0.498 Sum_probs=43.3
Q ss_pred HHhhcCC--eEEEEEc--CCeEEEEEEEEecCccceEEcceEEEE-eCceeecEEEEE
Q 034180 43 LAKFVDK--GVQVKLT--GGRQVTGTLKGYDQLLNLVLDEAVEFL-RGNLYNGIFVIV 95 (102)
Q Consensus 43 L~~~i~K--~V~V~Lk--~Gr~i~G~L~gfD~~mNLVL~da~E~~-~~~~~~~iG~iv 95 (102)
+-+|++. +|.|.|. -|..++|.++|||+|||+||++|+|.. +.+.++++|+|+
T Consensus 17 Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRil 74 (88)
T KOG1774|consen 17 IFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRIL 74 (88)
T ss_pred HHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEE
Confidence 4478775 5666665 488999999999999999999999986 456667999886
No 31
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=98.96 E-value=1.1e-10 Score=79.20 Aligned_cols=47 Identities=40% Similarity=0.619 Sum_probs=41.9
Q ss_pred CCcchHHh-hcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEe
Q 034180 38 ETVLDLAK-FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84 (102)
Q Consensus 38 ~~~~~L~~-~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~ 84 (102)
..|++|.+ +++.+|.|+++++|++.|+|.|||+|+|++|.|++|.+.
T Consensus 4 ~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit 51 (91)
T KOG3460|consen 4 EEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETIT 51 (91)
T ss_pred cccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEE
Confidence 35667665 499999999999999999999999999999999999873
No 32
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.83 E-value=3.4e-09 Score=72.89 Aligned_cols=46 Identities=35% Similarity=0.603 Sum_probs=42.9
Q ss_pred chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc
Q 034180 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~ 86 (102)
+.|..|++++|.|...|||.+.|.|.|||+-.||+|+++.|++...
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~ 48 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSE 48 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhh
Confidence 4689999999999999999999999999999999999999998543
No 33
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=98.70 E-value=1.4e-09 Score=81.58 Aligned_cols=44 Identities=30% Similarity=0.584 Sum_probs=41.0
Q ss_pred cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEE
Q 034180 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFL 83 (102)
Q Consensus 40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~ 83 (102)
+..+.+++|.+++|.++|||.+.|.+.+||.|||++|.||+|..
T Consensus 6 sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r 49 (177)
T KOG3168|consen 6 SSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFR 49 (177)
T ss_pred hhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHh
Confidence 44678899999999999999999999999999999999999975
No 34
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.60 E-value=5e-09 Score=75.29 Aligned_cols=50 Identities=38% Similarity=0.647 Sum_probs=44.4
Q ss_pred CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEe-Ccee
Q 034180 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR-GNLY 88 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~-~~~~ 88 (102)
....+.++++|++.|.|+|||.+.|.|.+||+|-|++|++|+|++. ++.+
T Consensus 10 ~t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y 60 (129)
T KOG1782|consen 10 FTTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKY 60 (129)
T ss_pred chhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeeccee
Confidence 4556899999999999999999999999999999999999999973 4433
No 35
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.58 E-value=2e-07 Score=64.06 Aligned_cols=58 Identities=29% Similarity=0.329 Sum_probs=49.5
Q ss_pred chHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEEEE
Q 034180 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVCFL 98 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~~~ 98 (102)
...+..+|++|.|.||++-.+.|+|.|.|+|+|+-|.|..-...++..+....-+|||
T Consensus 5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfI 62 (96)
T KOG3448|consen 5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFI 62 (96)
T ss_pred HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEE
Confidence 3467789999999999999999999999999999999998877766666666666665
No 36
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=97.79 E-value=2.6e-05 Score=56.40 Aligned_cols=45 Identities=24% Similarity=0.287 Sum_probs=39.9
Q ss_pred HHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCce
Q 034180 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNL 87 (102)
Q Consensus 43 L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~ 87 (102)
|...-+.++.|.||+|.+|.|.|...|.+|||.|.+++++.++..
T Consensus 7 L~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd 51 (134)
T KOG3293|consen 7 LKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGD 51 (134)
T ss_pred HHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCC
Confidence 444567899999999999999999999999999999999986643
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=97.78 E-value=2.4e-05 Score=50.96 Aligned_cols=37 Identities=27% Similarity=0.410 Sum_probs=30.1
Q ss_pred CeEEEEEc--CC--eEEEEEEEEecCccceEEcceEEEEeC
Q 034180 49 KGVQVKLT--GG--RQVTGTLKGYDQLLNLVLDEAVEFLRG 85 (102)
Q Consensus 49 K~V~V~Lk--~G--r~i~G~L~gfD~~mNLVL~da~E~~~~ 85 (102)
++|+|-++ +| -.++|.|.+||+|+|++|.|+.|....
T Consensus 9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 56666664 33 489999999999999999999998754
No 38
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.14 E-value=0.0018 Score=41.61 Aligned_cols=43 Identities=21% Similarity=0.323 Sum_probs=34.1
Q ss_pred HHhhcCCeEEEEEcCCeEEEEEEEEecC---ccceEEcceEEEEeC
Q 034180 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQ---LLNLVLDEAVEFLRG 85 (102)
Q Consensus 43 L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~---~mNLVL~da~E~~~~ 85 (102)
+..++|++|.|+++||..|+|.|.+++. -+.++|..|....++
T Consensus 7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~ 52 (77)
T PF14438_consen 7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKS 52 (77)
T ss_dssp HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-
T ss_pred HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccc
Confidence 5678999999999999999999999997 789999988876543
No 39
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=97.07 E-value=0.0012 Score=46.63 Aligned_cols=46 Identities=28% Similarity=0.409 Sum_probs=41.1
Q ss_pred cchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeC
Q 034180 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRG 85 (102)
Q Consensus 40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~ 85 (102)
.-.|.+..+.+|.|.|++|....|++.+.|.+||..|.++.=..++
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~ 49 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG 49 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC
Confidence 3457888999999999999999999999999999999998877664
No 40
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=96.64 E-value=0.0002 Score=50.86 Aligned_cols=56 Identities=18% Similarity=0.265 Sum_probs=44.8
Q ss_pred cccccCCCcCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEe
Q 034180 29 KSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR 84 (102)
Q Consensus 29 ~~~~ms~~~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~ 84 (102)
+.-.+.++|.+...-+.--..+|.|.++|++.+.|...|||.|.|++|+++.|.+.
T Consensus 17 e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwt 72 (114)
T KOG3459|consen 17 EEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWT 72 (114)
T ss_pred cccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCC
Confidence 34445666655555554556789999999999999999999999999999999763
No 41
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=96.13 E-value=0.019 Score=40.85 Aligned_cols=44 Identities=20% Similarity=0.169 Sum_probs=38.8
Q ss_pred HHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCc
Q 034180 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGN 86 (102)
Q Consensus 43 L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~ 86 (102)
|.+.-+.-|.+.++.|..|+|.|+--|.+||++|+|..-...+.
T Consensus 10 LhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg 53 (119)
T KOG3172|consen 10 LHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDG 53 (119)
T ss_pred eecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCC
Confidence 45566788999999999999999999999999999998877654
No 42
>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=95.70 E-value=0.017 Score=43.35 Aligned_cols=43 Identities=26% Similarity=0.363 Sum_probs=32.9
Q ss_pred CCcchHHhhcCCeEEEEEcCCeEEEEEEEEecC-ccceEEcceEE
Q 034180 38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQ-LLNLVLDEAVE 81 (102)
Q Consensus 38 ~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~-~mNLVL~da~E 81 (102)
.+|++..+|++|+|.|.+.| +++.|.+..+|. .-|+||-+-.|
T Consensus 7 ~~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 7 KSPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp S-HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred CCHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 46888999999999999999 999999999994 47899886554
No 43
>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=95.66 E-value=0.027 Score=36.06 Aligned_cols=29 Identities=24% Similarity=0.446 Sum_probs=25.1
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLV 75 (102)
Q Consensus 47 i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV 75 (102)
-+.+|.|-|.+|-.++|.+.|||+|+=++
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll 38 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDNFTVLL 38 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence 34689999999999999999999998444
No 44
>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=95.50 E-value=0.033 Score=35.71 Aligned_cols=28 Identities=29% Similarity=0.464 Sum_probs=24.8
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180 48 DKGVQVKLTGGRQVTGTLKGYDQLLNLV 75 (102)
Q Consensus 48 ~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV 75 (102)
+.+|.|-|.+|-.++|.+.|||+|+=++
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll 42 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLL 42 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEE
Confidence 4689999999999999999999998444
No 45
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=95.27 E-value=0.059 Score=32.00 Aligned_cols=33 Identities=21% Similarity=0.355 Sum_probs=28.5
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEEcce
Q 034180 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (102)
Q Consensus 46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da 79 (102)
.+||+|++.. ++..++|+..|+|+.-.|+++..
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~ 33 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTE 33 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEET
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEEC
Confidence 3789999999 67777999999999999998654
No 46
>PRK14638 hypothetical protein; Provisional
Probab=94.84 E-value=0.07 Score=38.92 Aligned_cols=39 Identities=13% Similarity=0.306 Sum_probs=31.9
Q ss_pred CCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180 38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (102)
Q Consensus 38 ~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~ 77 (102)
+.+.+..+++|++|.|++++++.++|+|.++|+- ++.|.
T Consensus 90 ~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 90 RGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred CCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 3455688999999999999999999999999863 34443
No 47
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.80 E-value=0.064 Score=36.00 Aligned_cols=30 Identities=20% Similarity=0.418 Sum_probs=25.6
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecCccceEE
Q 034180 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 47 i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL 76 (102)
-+.+|.|-|.+|-.++|.+.|||+|.=++-
T Consensus 18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~ 47 (79)
T PRK00395 18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLR 47 (79)
T ss_pred cCCCEEEEEeCCcEEEEEEEEEccEEEEEE
Confidence 346899999999999999999999984443
No 48
>PRK14639 hypothetical protein; Provisional
Probab=94.29 E-value=0.11 Score=37.41 Aligned_cols=38 Identities=18% Similarity=0.296 Sum_probs=31.6
Q ss_pred CCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEE
Q 034180 38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 38 ~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL 76 (102)
+.+.+..+++|++|.|++.+++.+.|+|.++|+- ++.|
T Consensus 78 ~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 78 SKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred CCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 3455688999999999999999999999999873 4554
No 49
>PRK02001 hypothetical protein; Validated
Probab=94.03 E-value=0.13 Score=37.75 Aligned_cols=37 Identities=22% Similarity=0.396 Sum_probs=31.0
Q ss_pred CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEE
Q 034180 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL 76 (102)
.+.+..+++|++|.|++.+++.++|.|.++|+- ++.|
T Consensus 81 ~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 81 VPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred CHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 445688999999999999999999999999864 3444
No 50
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=93.86 E-value=0.17 Score=34.73 Aligned_cols=39 Identities=13% Similarity=0.224 Sum_probs=34.7
Q ss_pred HhhcCCeEEEEEcCCeEEEEEEEEecC-ccceEEcceEEE
Q 034180 44 AKFVDKGVQVKLTGGRQVTGTLKGYDQ-LLNLVLDEAVEF 82 (102)
Q Consensus 44 ~~~i~K~V~V~Lk~Gr~i~G~L~gfD~-~mNLVL~da~E~ 82 (102)
.+|+|++|.+..+++-.|+|+|...|. --.|.|.++.-+
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~ 43 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSF 43 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEET
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeec
Confidence 368999999999999999999999995 578999998765
No 51
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=93.51 E-value=0.18 Score=33.74 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=25.7
Q ss_pred hHHhh--cCCeEEEEEcCCeEEEEEEEEecCcc
Q 034180 42 DLAKF--VDKGVQVKLTGGRQVTGTLKGYDQLL 72 (102)
Q Consensus 42 ~L~~~--i~K~V~V~Lk~Gr~i~G~L~gfD~~m 72 (102)
.|+.. -+.+|.|-|.+|-.+.|.+.|||+|.
T Consensus 11 fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~ 43 (77)
T COG1923 11 FLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV 43 (77)
T ss_pred HHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE
Confidence 35543 34688999999999999999999997
No 52
>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=93.39 E-value=0.34 Score=30.90 Aligned_cols=36 Identities=11% Similarity=0.170 Sum_probs=29.8
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEE
Q 034180 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81 (102)
Q Consensus 46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E 81 (102)
.+|..|++++-.|.+++|.+.+||.-.++++-.+.+
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 378999999999999999999999877766554433
No 53
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=92.83 E-value=0.23 Score=37.42 Aligned_cols=44 Identities=20% Similarity=0.352 Sum_probs=31.7
Q ss_pred ccCCCcCCcch--HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180 32 KMSGRKETVLD--LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLV 75 (102)
Q Consensus 32 ~ms~~~~~~~~--L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV 75 (102)
+|++++....+ |+.+. ..+|.|-|.+|-.++|.+.|||+|.=|+
T Consensus 4 ~m~~~~~nlQD~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL 51 (165)
T PRK14091 4 NMAEKVNNLQDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILL 51 (165)
T ss_pred cccccccchHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEE
Confidence 46654444444 55443 3578888999999999999999997443
No 54
>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=92.33 E-value=0.44 Score=31.08 Aligned_cols=34 Identities=38% Similarity=0.496 Sum_probs=28.1
Q ss_pred CCcchHHhhcCCeEEEEEc---CC-eEEEEEEEEecCc
Q 034180 38 ETVLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQL 71 (102)
Q Consensus 38 ~~~~~L~~~i~K~V~V~Lk---~G-r~i~G~L~gfD~~ 71 (102)
..+.+..+++|+.|.|+++ +| +.+.|.|.++|+-
T Consensus 15 ~~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 15 KKEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred CCHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 3455688999999999997 55 6999999999863
No 55
>PRK14644 hypothetical protein; Provisional
Probab=92.17 E-value=0.39 Score=34.64 Aligned_cols=38 Identities=18% Similarity=0.258 Sum_probs=30.7
Q ss_pred CcchHHhhcCCeEEEEEcCC----eEEEEEEEEecCccceEEc
Q 034180 39 TVLDLAKFVDKGVQVKLTGG----RQVTGTLKGYDQLLNLVLD 77 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~G----r~i~G~L~gfD~~mNLVL~ 77 (102)
...++.+++|++|.|++++. ++++|.|.++|+- ++.|.
T Consensus 76 ~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 76 ETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred CHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 33478899999999999876 8999999999873 35553
No 56
>PRK14640 hypothetical protein; Provisional
Probab=91.50 E-value=0.53 Score=34.27 Aligned_cols=37 Identities=24% Similarity=0.397 Sum_probs=29.7
Q ss_pred CcchHHhhcCCeEEEEE----cCCeEEEEEEEEecCccceEE
Q 034180 39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~L----k~Gr~i~G~L~gfD~~mNLVL 76 (102)
.+.+..+++|++|.|++ .++++++|.|.++|+- ++.|
T Consensus 88 ~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 88 KVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred CHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 44568899999999998 5679999999999864 3444
No 57
>PRK14633 hypothetical protein; Provisional
Probab=91.43 E-value=0.55 Score=34.17 Aligned_cols=37 Identities=16% Similarity=0.281 Sum_probs=29.5
Q ss_pred CcchHHhhcCCeEEEEE----cCCeEEEEEEEEecCccceEE
Q 034180 39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~L----k~Gr~i~G~L~gfD~~mNLVL 76 (102)
.+.+..+++|++|.|++ .+++.++|+|.++|+- ++.|
T Consensus 85 ~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 85 NIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred CHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 44568899999999998 4669999999999874 3444
No 58
>PRK14642 hypothetical protein; Provisional
Probab=90.56 E-value=0.66 Score=35.68 Aligned_cols=38 Identities=16% Similarity=0.322 Sum_probs=30.7
Q ss_pred CCcchHHhhcCCeEEEEEc-------------CCeEEEEEEEEecCccceEE
Q 034180 38 ETVLDLAKFVDKGVQVKLT-------------GGRQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 38 ~~~~~L~~~i~K~V~V~Lk-------------~Gr~i~G~L~gfD~~mNLVL 76 (102)
+...+..+++|++|.|+++ +.+.++|+|.++|+- ++.|
T Consensus 90 k~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 90 RHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred CCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 3455688999999999997 679999999999864 3444
No 59
>PRK14645 hypothetical protein; Provisional
Probab=90.36 E-value=0.68 Score=34.00 Aligned_cols=32 Identities=22% Similarity=0.302 Sum_probs=27.1
Q ss_pred CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCc
Q 034180 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQL 71 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~ 71 (102)
.+.+..+++|++|.|++ +++.++|+|.++|+-
T Consensus 93 ~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 93 TARHFERFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred CHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 34468889999999986 789999999999864
No 60
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=90.28 E-value=2.2 Score=27.59 Aligned_cols=50 Identities=26% Similarity=0.325 Sum_probs=35.5
Q ss_pred cchHHhhcCCeEEEEEcCCeEEEEEEEEec-CccceEEcceEEEEeCceeecEEEEEE
Q 034180 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRGNLYNGIFVIVC 96 (102)
Q Consensus 40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD-~~mNLVL~da~E~~~~~~~~~iG~iv~ 96 (102)
...|++++|++|.|.+..|.. +|+|.+.. .|. +|+.. .....-++..|+.
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~~----~~~~~IR~~~IV~ 63 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEEN----GTPFFIRIAQIVW 63 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEeC----CcEEEEEeeeEEE
Confidence 345889999999999976665 99999995 444 55433 3445566666664
No 61
>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=90.17 E-value=0.55 Score=33.23 Aligned_cols=36 Identities=31% Similarity=0.553 Sum_probs=26.3
Q ss_pred cchHHhhcCCeEEEEEc----CCeEEEEEEEEecCccceEE
Q 034180 40 VLDLAKFVDKGVQVKLT----GGRQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 40 ~~~L~~~i~K~V~V~Lk----~Gr~i~G~L~gfD~~mNLVL 76 (102)
+.++.+++|++|.|+++ +.+++.|+|.++|+ -.++|
T Consensus 79 ~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 79 PRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 44688999999999994 45799999999987 23444
No 62
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=89.86 E-value=0.92 Score=32.76 Aligned_cols=32 Identities=31% Similarity=0.577 Sum_probs=27.6
Q ss_pred CcchHHhhcCCeEEEEE----cCCeEEEEEEEEecC
Q 034180 39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQ 70 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~L----k~Gr~i~G~L~gfD~ 70 (102)
.+.++.+++|+.|.|++ .+++.++|.|.++|+
T Consensus 89 ~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 89 KARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred CHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 34568899999999997 567899999999986
No 63
>PRK14636 hypothetical protein; Provisional
Probab=89.74 E-value=0.83 Score=34.22 Aligned_cols=37 Identities=27% Similarity=0.499 Sum_probs=29.2
Q ss_pred CcchHHhhcCCeEEEEEc---CC-eEEEEEEEEecCccceEE
Q 034180 39 TVLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk---~G-r~i~G~L~gfD~~mNLVL 76 (102)
.+.+..+++|++|.|+++ +| +.++|+|.++|+- ++.|
T Consensus 89 ~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 89 RPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred CHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 345688999999999997 55 7999999999863 3444
No 64
>PRK14643 hypothetical protein; Provisional
Probab=89.63 E-value=0.89 Score=33.72 Aligned_cols=37 Identities=19% Similarity=0.249 Sum_probs=29.2
Q ss_pred CcchHHhhcCCeEEEEEcC----CeEEEEEEEEecCc-cceE
Q 034180 39 TVLDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQL-LNLV 75 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~----Gr~i~G~L~gfD~~-mNLV 75 (102)
...+..+++|++|.|+++. .+.++|+|.++|.- ..+.
T Consensus 95 ~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~ 136 (164)
T PRK14643 95 SQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFR 136 (164)
T ss_pred CHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEE
Confidence 3556889999999999864 58999999999853 3443
No 65
>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=89.61 E-value=1.2 Score=29.55 Aligned_cols=40 Identities=10% Similarity=0.167 Sum_probs=33.6
Q ss_pred HhhcCCeEEEEEcCCeEEEEEEEEecCc-cceEEcceEEEE
Q 034180 44 AKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFL 83 (102)
Q Consensus 44 ~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~-mNLVL~da~E~~ 83 (102)
.+|+|+++.+..+.+-.|+|+|..+|.. --+.|.|+..+-
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fG 42 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFG 42 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeec
Confidence 3689999999999999999999999955 457788877653
No 66
>PRK14634 hypothetical protein; Provisional
Probab=89.53 E-value=0.96 Score=33.13 Aligned_cols=37 Identities=19% Similarity=0.224 Sum_probs=28.9
Q ss_pred CcchHHhhcCCeEEEEEcC----CeEEEEEEEEecCccceEE
Q 034180 39 TVLDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~----Gr~i~G~L~gfD~~mNLVL 76 (102)
.+.+..+++|++|.|++++ .+.++|+|.++|+- ++.|
T Consensus 91 ~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 91 SDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred CHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 4556889999999999863 28999999999863 3444
No 67
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.46 E-value=0.97 Score=33.42 Aligned_cols=34 Identities=29% Similarity=0.487 Sum_probs=29.6
Q ss_pred CcchHHhhcCCeEEEEE----cCCeEEEEEEEEecCcc
Q 034180 39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLL 72 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~L----k~Gr~i~G~L~gfD~~m 72 (102)
...+..+++|+.|.|.+ .+++.++|+|.++|+-.
T Consensus 90 ~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 90 TAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred CHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 34468899999999999 78899999999999765
No 68
>PRK14646 hypothetical protein; Provisional
Probab=89.13 E-value=1.1 Score=32.91 Aligned_cols=38 Identities=21% Similarity=0.225 Sum_probs=29.5
Q ss_pred CCcchHHhhcCCeEEEEEcC---C-eEEEEEEEEecCccceEE
Q 034180 38 ETVLDLAKFVDKGVQVKLTG---G-RQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 38 ~~~~~L~~~i~K~V~V~Lk~---G-r~i~G~L~gfD~~mNLVL 76 (102)
+.+.+..+++|++|.|++++ | +.++|.|.++|+- ++.|
T Consensus 90 ~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 90 TSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred CCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 34556889999999999853 3 7899999999864 3555
No 69
>PRK14632 hypothetical protein; Provisional
Probab=88.69 E-value=1.1 Score=33.29 Aligned_cols=38 Identities=18% Similarity=0.368 Sum_probs=29.9
Q ss_pred CcchHHhhcCCeEEEEEcC-------CeEEEEEEEEecCccceEEc
Q 034180 39 TVLDLAKFVDKGVQVKLTG-------GRQVTGTLKGYDQLLNLVLD 77 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~-------Gr~i~G~L~gfD~~mNLVL~ 77 (102)
.+.+..+++|++|.|++++ .+.++|+|.++|+- ++.|+
T Consensus 89 ~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 89 RAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred CHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 3456889999999999975 57999999999863 34443
No 70
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=88.39 E-value=0.91 Score=34.26 Aligned_cols=33 Identities=21% Similarity=0.362 Sum_probs=26.6
Q ss_pred HHhhc--CCeEEEEEcCCeEEEEEEEEecCccceE
Q 034180 43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLV 75 (102)
Q Consensus 43 L~~~i--~K~V~V~Lk~Gr~i~G~L~gfD~~mNLV 75 (102)
|+... ..+|.|-|.+|-.++|.+.|||+|.=|.
T Consensus 97 Ln~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL 131 (165)
T PRK14091 97 LSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLL 131 (165)
T ss_pred HHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEE
Confidence 55443 3588888999999999999999998444
No 71
>PRK14647 hypothetical protein; Provisional
Probab=87.54 E-value=1.5 Score=32.05 Aligned_cols=32 Identities=19% Similarity=0.353 Sum_probs=27.0
Q ss_pred CcchHHhhcCCeEEEEEc---------CCeEEEEEEEEecC
Q 034180 39 TVLDLAKFVDKGVQVKLT---------GGRQVTGTLKGYDQ 70 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk---------~Gr~i~G~L~gfD~ 70 (102)
.+.+..+++|++|.|+++ +.+.++|+|.++|+
T Consensus 90 ~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 90 KEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred CHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 445688999999999995 34899999999986
No 72
>PRK14631 hypothetical protein; Provisional
Probab=86.81 E-value=1.8 Score=32.45 Aligned_cols=32 Identities=19% Similarity=0.323 Sum_probs=27.2
Q ss_pred CCcchHHhhcCCeEEEEEc----CCeEEEEEEEEec
Q 034180 38 ETVLDLAKFVDKGVQVKLT----GGRQVTGTLKGYD 69 (102)
Q Consensus 38 ~~~~~L~~~i~K~V~V~Lk----~Gr~i~G~L~gfD 69 (102)
..+.+..+++|++|.|+++ +.+.++|+|.++|
T Consensus 107 ~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 107 FQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred CCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 3455688999999999995 4599999999998
No 73
>PRK14637 hypothetical protein; Provisional
Probab=86.51 E-value=1.7 Score=31.76 Aligned_cols=38 Identities=29% Similarity=0.359 Sum_probs=28.5
Q ss_pred CCcchHHhhcCCeEEEEEcCCeEE-EEEEEEecCccceEE
Q 034180 38 ETVLDLAKFVDKGVQVKLTGGRQV-TGTLKGYDQLLNLVL 76 (102)
Q Consensus 38 ~~~~~L~~~i~K~V~V~Lk~Gr~i-~G~L~gfD~~mNLVL 76 (102)
..+.+..+++|++|.|++.+.+.+ +|+|.++|+- ++.|
T Consensus 88 ~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 88 KNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred CCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 345568899999999999544556 7999999864 3444
No 74
>PRK14641 hypothetical protein; Provisional
Probab=83.50 E-value=2.6 Score=31.57 Aligned_cols=31 Identities=19% Similarity=0.270 Sum_probs=25.8
Q ss_pred CcchHHhhcCCeEEEEEcC----CeEEEEEEEEec
Q 034180 39 TVLDLAKFVDKGVQVKLTG----GRQVTGTLKGYD 69 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~----Gr~i~G~L~gfD 69 (102)
.+.+..+++|+.|.|++++ .+.++|.|.++|
T Consensus 95 ~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 95 LPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred CHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 3445888999999999865 469999999995
No 75
>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=81.49 E-value=4.2 Score=27.26 Aligned_cols=39 Identities=21% Similarity=0.240 Sum_probs=28.9
Q ss_pred cchHHhhcCCeEEEEEcCCeEEEEEEEEecCc-cceEEcc
Q 034180 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDE 78 (102)
Q Consensus 40 ~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~-mNLVL~d 78 (102)
...|....||+|.+.|.++.+..|.+.|.|.. .|+..++
T Consensus 16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~ 55 (80)
T PF11095_consen 16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSN 55 (80)
T ss_dssp HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEE
T ss_pred HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhh
Confidence 34567778999999999999999999999954 5655443
No 76
>PRK14630 hypothetical protein; Provisional
Probab=77.85 E-value=5.6 Score=28.76 Aligned_cols=36 Identities=11% Similarity=0.161 Sum_probs=27.3
Q ss_pred CcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEE
Q 034180 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL 76 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL 76 (102)
.+.+..+++|++|.|++.+. ..+|+|.++|+- ++.|
T Consensus 88 ~~~df~r~~G~~v~V~l~~~-~~~G~L~~~~d~-~i~l 123 (143)
T PRK14630 88 SDREFKIFEGKKIKLMLDND-FEEGFILEAKAD-SFIF 123 (143)
T ss_pred CHHHHHHhCCCEEEEEEcCc-ceEEEEEEEeCC-EEEE
Confidence 44568899999999999654 359999999863 3444
No 77
>PRK06955 biotin--protein ligase; Provisional
Probab=75.71 E-value=6.1 Score=31.28 Aligned_cols=32 Identities=25% Similarity=0.414 Sum_probs=27.7
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (102)
Q Consensus 46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~ 77 (102)
+++++|.+...+++.++|+..|+|+.-.|+++
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 57899999766778899999999999999885
No 78
>PRK14635 hypothetical protein; Provisional
Probab=73.12 E-value=9.2 Score=28.05 Aligned_cols=34 Identities=18% Similarity=0.123 Sum_probs=27.0
Q ss_pred CCcchHHhhcCCeEEEEEc--CCeEEEE---EEEEecCc
Q 034180 38 ETVLDLAKFVDKGVQVKLT--GGRQVTG---TLKGYDQL 71 (102)
Q Consensus 38 ~~~~~L~~~i~K~V~V~Lk--~Gr~i~G---~L~gfD~~ 71 (102)
+.+.++.++.|++|.|++. +++.+.| .|.++|+-
T Consensus 89 ~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~ 127 (162)
T PRK14635 89 RLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD 127 (162)
T ss_pred CCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC
Confidence 3455688999999999875 4678888 99999863
No 79
>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=69.80 E-value=10 Score=28.63 Aligned_cols=35 Identities=23% Similarity=0.223 Sum_probs=31.0
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEEcceE
Q 034180 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (102)
Q Consensus 46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~ 80 (102)
+-+-+|+|.+.||+.+.|.+.||+.-=|.+|..+.
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 44569999999999999999999999999987665
No 80
>PRK10898 serine endoprotease; Provisional
Probab=66.78 E-value=12 Score=30.32 Aligned_cols=31 Identities=29% Similarity=0.387 Sum_probs=27.0
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEEcce
Q 034180 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (102)
Q Consensus 49 K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da 79 (102)
.++.|++.||+.+.+.+.++|...+|.+=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 5789999999999999999999988866554
No 81
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=65.01 E-value=13 Score=29.91 Aligned_cols=31 Identities=29% Similarity=0.432 Sum_probs=27.1
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEEcce
Q 034180 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (102)
Q Consensus 49 K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da 79 (102)
.++.|++.||+.+.+.+.++|...++.+=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4689999999999999999999988887554
No 82
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=62.89 E-value=17 Score=28.61 Aligned_cols=31 Identities=26% Similarity=0.644 Sum_probs=26.4
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (102)
Q Consensus 46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~ 77 (102)
++|++|.+.. ++..++|++.|+|....|++.
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 4789999986 456799999999999999985
No 83
>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=62.80 E-value=18 Score=27.41 Aligned_cols=31 Identities=19% Similarity=0.384 Sum_probs=26.3
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (102)
Q Consensus 46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~ 77 (102)
.+|++|.+... +.++.|+..|+|+.-.|+++
T Consensus 191 ~~g~~V~v~~~-~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTG-NGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeC-CcEEEEEEEeECCCceEEEE
Confidence 46899999864 46799999999999999985
No 84
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=60.90 E-value=17 Score=31.80 Aligned_cols=32 Identities=31% Similarity=0.257 Sum_probs=27.8
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (102)
Q Consensus 46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~ 77 (102)
++|++|.+...++++++|+..|+|+.-.|+|+
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 56899998766777899999999999999985
No 85
>PRK10139 serine endoprotease; Provisional
Probab=60.60 E-value=17 Score=30.54 Aligned_cols=32 Identities=22% Similarity=0.414 Sum_probs=27.9
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEEcceE
Q 034180 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (102)
Q Consensus 49 K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~ 80 (102)
.++.|++.||+++.+.++|+|....|.+=...
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 58999999999999999999999888775543
No 86
>PRK10942 serine endoprotease; Provisional
Probab=59.53 E-value=18 Score=30.61 Aligned_cols=31 Identities=23% Similarity=0.412 Sum_probs=27.1
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEEcce
Q 034180 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (102)
Q Consensus 49 K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da 79 (102)
.++.|++.||+++.+.+++.|...+|-|=..
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 5789999999999999999999988876643
No 87
>PRK08330 biotin--protein ligase; Provisional
Probab=58.98 E-value=25 Score=26.63 Aligned_cols=32 Identities=22% Similarity=0.320 Sum_probs=25.8
Q ss_pred hcCCeEEEEEcCCeEE-EEEEEEecCccceEEcc
Q 034180 46 FVDKGVQVKLTGGRQV-TGTLKGYDQLLNLVLDE 78 (102)
Q Consensus 46 ~i~K~V~V~Lk~Gr~i-~G~L~gfD~~mNLVL~d 78 (102)
+++++|.+.. +++.+ .|+..|+|+.-.|+++.
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 5789999875 56665 79999999998888863
No 88
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=57.16 E-value=24 Score=27.82 Aligned_cols=30 Identities=27% Similarity=0.264 Sum_probs=25.8
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (102)
Q Consensus 47 i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~ 77 (102)
+|++|.+.. ++..+.|++.|+|..-.|+++
T Consensus 236 ~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~ 265 (285)
T PTZ00275 236 KDKKVLIDQ-DNELIVGYLQGLLHDGSLLLL 265 (285)
T ss_pred CCCEEEEEe-CCCEEEEEEEEECCCCeEEEE
Confidence 689988864 678999999999998888885
No 89
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=56.85 E-value=42 Score=26.03 Aligned_cols=35 Identities=31% Similarity=0.393 Sum_probs=31.2
Q ss_pred hhcCCeEEEEEcCCeEEEEEEEEecCccceEEcce
Q 034180 45 KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (102)
Q Consensus 45 ~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da 79 (102)
..++++|++...++....|+-.|+|....|+++..
T Consensus 187 ~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 187 LSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred ccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 34889999999998999999999999999998876
No 90
>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=53.80 E-value=15 Score=27.74 Aligned_cols=25 Identities=24% Similarity=0.512 Sum_probs=22.2
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecCc
Q 034180 47 VDKGVQVKLTGGRQVTGTLKGYDQL 71 (102)
Q Consensus 47 i~K~V~V~Lk~Gr~i~G~L~gfD~~ 71 (102)
-|+-|+|-+.|||+++|.=.|.|..
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 4688999999999999999999854
No 91
>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=53.20 E-value=27 Score=28.60 Aligned_cols=32 Identities=22% Similarity=0.355 Sum_probs=27.9
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEEcceE
Q 034180 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (102)
Q Consensus 49 K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~ 80 (102)
.++.|.+.||+++.+.+.+.|...+|.|=...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 57889999999999999999999988776554
No 92
>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=48.20 E-value=27 Score=24.44 Aligned_cols=17 Identities=29% Similarity=0.595 Sum_probs=14.2
Q ss_pred CeEEEEEcCCeEEEEEE
Q 034180 49 KGVQVKLTGGRQVTGTL 65 (102)
Q Consensus 49 K~V~V~Lk~Gr~i~G~L 65 (102)
.+|.+.|+||+.+.|++
T Consensus 29 ~~V~l~L~DGs~l~Gtv 45 (101)
T PF11607_consen 29 ERVELELDDGSMLRGTV 45 (101)
T ss_dssp -EEEEEETTS-EEEEEE
T ss_pred ceEEEEEcCCCeeeeee
Confidence 58999999999999997
No 93
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=47.68 E-value=70 Score=23.45 Aligned_cols=28 Identities=21% Similarity=0.364 Sum_probs=24.7
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEEec
Q 034180 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYD 69 (102)
Q Consensus 42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD 69 (102)
....++||.|.+...+|..+.|+..+..
T Consensus 86 ~a~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 86 KYSELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 3457999999999999999999999985
No 94
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=43.94 E-value=32 Score=20.61 Aligned_cols=21 Identities=29% Similarity=0.498 Sum_probs=14.1
Q ss_pred EEEEEEEecCccceEEcceEE
Q 034180 61 VTGTLKGYDQLLNLVLDEAVE 81 (102)
Q Consensus 61 i~G~L~gfD~~mNLVL~da~E 81 (102)
..|+..|.|+.+.+.|.+..+
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~ 30 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDT 30 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-
T ss_pred cceeEEeeccccceEEEeCCc
Confidence 689999999999999987654
No 95
>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=40.26 E-value=26 Score=23.16 Aligned_cols=30 Identities=27% Similarity=0.418 Sum_probs=17.1
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEEecCccc
Q 034180 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLN 73 (102)
Q Consensus 42 ~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mN 73 (102)
++.=.-+.+|.+.|+||..++|+ +.|--.|
T Consensus 11 EiAC~~~~~v~L~l~dG~~~~g~--A~dt~~~ 40 (80)
T PF07073_consen 11 EIACMYRYPVKLTLKDGEQIEGK--ALDTRTN 40 (80)
T ss_dssp HHHHTTTT-EEEE-TTT--EEES--S-EEE--
T ss_pred HHHHhcCCeEEEEEeCCCEEEEE--EEEEEEe
Confidence 44545678999999999999998 4444444
No 96
>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=39.09 E-value=13 Score=25.41 Aligned_cols=17 Identities=35% Similarity=0.483 Sum_probs=14.4
Q ss_pred EEEEEecCccceEEcce
Q 034180 63 GTLKGYDQLLNLVLDEA 79 (102)
Q Consensus 63 G~L~gfD~~mNLVL~da 79 (102)
|+|+|.|.|.|-=-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999876655
No 97
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=39.01 E-value=16 Score=27.09 Aligned_cols=21 Identities=29% Similarity=0.370 Sum_probs=15.6
Q ss_pred eEEEEEEEEecCccceEEcce
Q 034180 59 RQVTGTLKGYDQLLNLVLDEA 79 (102)
Q Consensus 59 r~i~G~L~gfD~~mNLVL~da 79 (102)
-.=.|+|+|.|+|-|=--+|-
T Consensus 43 ~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 43 DHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred cccceeeeeecccccchhccc
Confidence 344689999999998655543
No 98
>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=36.72 E-value=47 Score=22.30 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=19.9
Q ss_pred hhcCCeEEEE-EcCCeEEEEEEEE
Q 034180 45 KFVDKGVQVK-LTGGRQVTGTLKG 67 (102)
Q Consensus 45 ~~i~K~V~V~-Lk~Gr~i~G~L~g 67 (102)
..+|..|+|+ +..|+.+.|+..|
T Consensus 93 g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 93 GAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred cCCCCEEEEEECCCCCEEEEEEeC
Confidence 4688999999 7899999999876
No 99
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=35.80 E-value=80 Score=20.83 Aligned_cols=27 Identities=33% Similarity=0.501 Sum_probs=20.5
Q ss_pred hHHhhcCCeEEEEEcCCe----EEEEEEEEe
Q 034180 42 DLAKFVDKGVQVKLTGGR----QVTGTLKGY 68 (102)
Q Consensus 42 ~L~~~i~K~V~V~Lk~Gr----~i~G~L~gf 68 (102)
+|..++|++|.++-+.|| +-+|+|..-
T Consensus 11 ~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 11 ELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 578899999999999986 678998764
No 100
>PRK08477 biotin--protein ligase; Provisional
Probab=35.75 E-value=88 Score=23.82 Aligned_cols=34 Identities=9% Similarity=-0.007 Sum_probs=28.2
Q ss_pred hcCCeEEEEEcCCeEEEEEEEEecCccceEEcceE
Q 034180 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (102)
Q Consensus 46 ~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~ 80 (102)
.+++.|.+. .+++.++|+..|.|+...|++.--.
T Consensus 173 ~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~ 206 (211)
T PRK08477 173 EKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKK 206 (211)
T ss_pred HcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEE
Confidence 378999986 5789999999999999988876543
No 101
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=31.87 E-value=1e+02 Score=17.55 Aligned_cols=24 Identities=17% Similarity=0.192 Sum_probs=20.3
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecC
Q 034180 47 VDKGVQVKLTGGRQVTGTLKGYDQ 70 (102)
Q Consensus 47 i~K~V~V~Lk~Gr~i~G~L~gfD~ 70 (102)
.|..+.++..+|+-++|++.+++.
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~ 28 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDG 28 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECC
Confidence 466777777789999999999985
No 102
>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=30.92 E-value=75 Score=22.02 Aligned_cols=21 Identities=24% Similarity=0.417 Sum_probs=18.1
Q ss_pred eEEEEEcCCeEEEEEEEEecC
Q 034180 50 GVQVKLTGGRQVTGTLKGYDQ 70 (102)
Q Consensus 50 ~V~V~Lk~Gr~i~G~L~gfD~ 70 (102)
...|.++||+.+.|.+..=|.
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~~ 79 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASETA 79 (133)
T ss_pred cEEEEECCCCEEEEEEEecCC
Confidence 478899999999999998653
No 103
>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=30.61 E-value=1e+02 Score=19.37 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=17.8
Q ss_pred cCCeEEEEEcCC-eEEEEEEEEecC
Q 034180 47 VDKGVQVKLTGG-RQVTGTLKGYDQ 70 (102)
Q Consensus 47 i~K~V~V~Lk~G-r~i~G~L~gfD~ 70 (102)
.|..|.++--++ .-|+|.+.+||.
T Consensus 8 ~Ge~V~~rWP~s~lYYe~kV~~~d~ 32 (55)
T PF09465_consen 8 IGEVVMVRWPGSSLYYEGKVLSYDS 32 (55)
T ss_dssp SS-EEEEE-TTTS-EEEEEEEEEET
T ss_pred CCCEEEEECCCCCcEEEEEEEEecc
Confidence 688999998765 566999999995
No 104
>PF05585 DUF1758: Putative peptidase (DUF1758); InterPro: IPR008737 This is a family of nematode proteins of unknown function []. However, it seems likely that these proteins act as aspartic peptidases.
Probab=30.10 E-value=43 Score=23.63 Aligned_cols=39 Identities=18% Similarity=0.155 Sum_probs=27.6
Q ss_pred CeEEEEEEEEecCccceEEcceEEEEeCc---eeecEEEEEE
Q 034180 58 GRQVTGTLKGYDQLLNLVLDEAVEFLRGN---LYNGIFVIVC 96 (102)
Q Consensus 58 Gr~i~G~L~gfD~~mNLVL~da~E~~~~~---~~~~iG~iv~ 96 (102)
...=...|+|.|-|..++.........++ ....+|+|+|
T Consensus 112 ~~~~iDiLIG~D~~~~ll~~~~i~~~~~~~~a~~T~~GWiis 153 (164)
T PF05585_consen 112 ESSPIDILIGADYFWQLLTGGQIKRLPGGPTAQETKFGWIIS 153 (164)
T ss_pred CCCCCeEEEccchHHHHhCCceEecCCCCCEEEeCCeEeEEe
Confidence 33446789999998888866655544443 5688999986
No 105
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=29.08 E-value=1.1e+02 Score=24.21 Aligned_cols=30 Identities=30% Similarity=0.496 Sum_probs=24.6
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEEc
Q 034180 48 DKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (102)
Q Consensus 48 ~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~ 77 (102)
..++.+.+.||+++.+.++|.|.-.-+.+-
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavl 124 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVL 124 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEE
Confidence 367888899999999999999987655443
No 106
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.03 E-value=65 Score=24.62 Aligned_cols=24 Identities=25% Similarity=0.533 Sum_probs=20.8
Q ss_pred hhcCCeEEEE-EcCCeEEEEEEEEe
Q 034180 45 KFVDKGVQVK-LTGGRQVTGTLKGY 68 (102)
Q Consensus 45 ~~i~K~V~V~-Lk~Gr~i~G~L~gf 68 (102)
..+|..|+|+ +.+|+.+.|+..+=
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~~ 228 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTGD 228 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeCC
Confidence 4689999999 99999999998763
No 107
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.41 E-value=69 Score=26.94 Aligned_cols=36 Identities=14% Similarity=0.144 Sum_probs=29.7
Q ss_pred HhhcCCeEEEEEcCCeEEEEEEEEec-CccceEEcce
Q 034180 44 AKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEA 79 (102)
Q Consensus 44 ~~~i~K~V~V~Lk~Gr~i~G~L~gfD-~~mNLVL~da 79 (102)
..|||++|.++-|..-+|+|+|.-+| +--=|-|.++
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnV 41 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNV 41 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhhe
Confidence 36899999999999999999998888 3345667765
No 108
>COG2248 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]
Probab=27.39 E-value=72 Score=26.24 Aligned_cols=74 Identities=7% Similarity=0.040 Sum_probs=53.0
Q ss_pred cCcceeeecccccccccCCCcCCcchHHhhcCCeEEEEEcCCeEEEEEEEEecCccceEEcceEEEEeCceeecEEEEEE
Q 034180 17 RSARVSFNLGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRGNLYNGIFVIVC 96 (102)
Q Consensus 17 ~~~~~~~~~~~~~~~~ms~~~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~L~gfD~~mNLVL~da~E~~~~~~~~~iG~iv~ 96 (102)
+.++...|+|+..-++-++ ++....|.+.-+....|..-||++++ |-+.+++=+.-.+.|....++|.++.
T Consensus 99 ~gK~lLlKhPte~IN~SQ~-~Ra~~fl~~~~~~~~~ie~ADgk~f~--------fG~t~IefS~pvpHG~eGskLGyVl~ 169 (304)
T COG2248 99 KGKLLLLKHPTENINRSQR-RRAYRFLESLKDIAREIEYADGKTFE--------FGGTVIEFSPPVPHGREGSKLGYVLM 169 (304)
T ss_pred cCcEEEecCchhhhCHHHH-HHHHHHHHHhhhhcceeEecCCceEE--------eCCEEEEecCCCCCCCcccccceEEE
Confidence 4577888888877666554 55677788777777789999999875 45555544444556777788899887
Q ss_pred EEE
Q 034180 97 FLL 99 (102)
Q Consensus 97 ~~~ 99 (102)
+..
T Consensus 170 v~V 172 (304)
T COG2248 170 VAV 172 (304)
T ss_pred EEE
Confidence 654
No 109
>PHA02723 hypothetical protein; Provisional
Probab=26.59 E-value=39 Score=22.22 Aligned_cols=21 Identities=38% Similarity=0.575 Sum_probs=14.6
Q ss_pred eeEEEEEEecCcceeeecccc
Q 034180 8 NAVSFFIVCRSARVSFNLGFL 28 (102)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~ 28 (102)
|..--||.|||.|-+....++
T Consensus 45 n~ivnfimcrsnlnn~~i~~~ 65 (77)
T PHA02723 45 NDIVNFIMCRSNLNNIFIFFL 65 (77)
T ss_pred ccceeeeEecccCCCceeeee
Confidence 344568999999987665443
No 110
>PRK10708 hypothetical protein; Provisional
Probab=25.28 E-value=80 Score=20.25 Aligned_cols=25 Identities=28% Similarity=0.505 Sum_probs=22.0
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecCc
Q 034180 47 VDKGVQVKLTGGRQVTGTLKGYDQL 71 (102)
Q Consensus 47 i~K~V~V~Lk~Gr~i~G~L~gfD~~ 71 (102)
++.+|.|++.+|..=+|++.+...|
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F 27 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEF 27 (62)
T ss_pred cccEEEEecCCCccccceEEEEeec
Confidence 5678999999999999999988876
No 111
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=25.04 E-value=1.4e+02 Score=21.88 Aligned_cols=26 Identities=15% Similarity=0.399 Sum_probs=22.7
Q ss_pred HhhcCCeEEEEEcCCeEEEEEEEEec
Q 034180 44 AKFVDKGVQVKLTGGRQVTGTLKGYD 69 (102)
Q Consensus 44 ~~~i~K~V~V~Lk~Gr~i~G~L~gfD 69 (102)
..++||.|.....+|..+.|++.++.
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~ 114 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQ 114 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEE
Confidence 47899999988889999999998775
No 112
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=23.92 E-value=87 Score=23.76 Aligned_cols=21 Identities=19% Similarity=0.455 Sum_probs=15.3
Q ss_pred EEEEE-cCCeEEEEEEEEecCc
Q 034180 51 VQVKL-TGGRQVTGTLKGYDQL 71 (102)
Q Consensus 51 V~V~L-k~Gr~i~G~L~gfD~~ 71 (102)
+...+ .+++.|+|+++++|+=
T Consensus 136 i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 136 IKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred CceEEEeCCceEEEEEEeccCC
Confidence 43333 3589999999999843
No 113
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=23.71 E-value=2.3e+02 Score=18.84 Aligned_cols=36 Identities=28% Similarity=0.306 Sum_probs=21.3
Q ss_pred chHHhhcCCeEEEEEc----CCeEEEEEEEEecC-ccceEEcc
Q 034180 41 LDLAKFVDKGVQVKLT----GGRQVTGTLKGYDQ-LLNLVLDE 78 (102)
Q Consensus 41 ~~L~~~i~K~V~V~Lk----~Gr~i~G~L~gfD~-~mNLVL~d 78 (102)
..|.+|.+|+|++.-+ +|. .-++.+-|. -.++.|..
T Consensus 8 ~~L~~f~gk~V~ivGkV~~~~~~--~~~~~~~Dg~~v~v~l~~ 48 (101)
T cd04479 8 AMLSQFVGKTVRIVGKVEKVDGD--SLTLISSDGVNVTVELNR 48 (101)
T ss_pred HHHHhhCCCEEEEEEEEEEecCC--eEEEEcCCCCEEEEEeCC
Confidence 3588999999987621 232 345555564 34444443
No 114
>PRK06630 hypothetical protein; Provisional
Probab=23.32 E-value=41 Score=23.50 Aligned_cols=19 Identities=21% Similarity=0.221 Sum_probs=15.9
Q ss_pred EEEEEEEecCccceEEcce
Q 034180 61 VTGTLKGYDQLLNLVLDEA 79 (102)
Q Consensus 61 i~G~L~gfD~~mNLVL~da 79 (102)
..|.|+|-|+|.|---++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3799999999999876654
No 115
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=22.97 E-value=1.8e+02 Score=20.39 Aligned_cols=30 Identities=20% Similarity=0.272 Sum_probs=24.0
Q ss_pred CcchHHhhcCCeEEEEEcC-CeEEEEEEEEe
Q 034180 39 TVLDLAKFVDKGVQVKLTG-GRQVTGTLKGY 68 (102)
Q Consensus 39 ~~~~L~~~i~K~V~V~Lk~-Gr~i~G~L~gf 68 (102)
++.+-+.|++|+|.=+-+. |+.+.|++.-.
T Consensus 37 s~~eA~~y~gk~v~yk~~~~G~Vi~G~V~R~ 67 (100)
T COG2451 37 SPEEAQFYLGKRVCYKYRSSGRVIKGKVVRT 67 (100)
T ss_pred CHHHHHhhhccEEEEEeCCCCcEEEEEEEEe
Confidence 4567788999988777776 99999998543
No 116
>PF10618 Tail_tube: Phage tail tube protein; InterPro: IPR019596 This entry is represented by Bacteriophage Mu, GpM tail tube protein. Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube.
Probab=22.83 E-value=1.3e+02 Score=20.97 Aligned_cols=30 Identities=20% Similarity=0.293 Sum_probs=24.6
Q ss_pred CCcCCcchHHhhcCCeEEEEEcCCeEEEEE
Q 034180 35 GRKETVLDLAKFVDKGVQVKLTGGRQVTGT 64 (102)
Q Consensus 35 ~~~~~~~~L~~~i~K~V~V~Lk~Gr~i~G~ 64 (102)
.+-.+..++...-+-.|...+.+|+.|.+.
T Consensus 61 ~~~~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 61 TKDTDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CCCCCHHHHhCCcccEEEEEecCCcEEEec
Confidence 455567778888889999999999999765
No 117
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=22.01 E-value=93 Score=19.96 Aligned_cols=25 Identities=28% Similarity=0.490 Sum_probs=21.9
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecCc
Q 034180 47 VDKGVQVKLTGGRQVTGTLKGYDQL 71 (102)
Q Consensus 47 i~K~V~V~Lk~Gr~i~G~L~gfD~~ 71 (102)
++.+|.|++.+|..=+|++.+...|
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F 27 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPF 27 (62)
T ss_pred cccEEEEecCCcccccceEEEEeec
Confidence 5678999999999999999988876
No 118
>KOG3487 consensus TRAPP 20 K subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.51 E-value=87 Score=23.08 Aligned_cols=38 Identities=13% Similarity=0.216 Sum_probs=31.7
Q ss_pred EEEEEecCcceeeecccccccccCCCcCCcchHHhhcC
Q 034180 11 SFFIVCRSARVSFNLGFLKSLKMSGRKETVLDLAKFVD 48 (102)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~ms~~~~~~~~L~~~i~ 48 (102)
-|.|+|+-..-.|+.+....-+..+.+....+|++++.
T Consensus 4 yfaIig~~d~Pvye~e~~~~~~~~~~~~~~~~LN~FI~ 41 (139)
T KOG3487|consen 4 YFAIIGHCDNPVYEMEFGCPENSKAARDDNRHLNQFIV 41 (139)
T ss_pred EEEEEecCCCceEEeecCCCCcccccchhhHHHHHHHH
Confidence 58899999999999999877777777888888888764
No 119
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.85 E-value=76 Score=20.94 Aligned_cols=17 Identities=29% Similarity=0.229 Sum_probs=13.5
Q ss_pred hHHhhcCCeEEEEEcCC
Q 034180 42 DLAKFVDKGVQVKLTGG 58 (102)
Q Consensus 42 ~L~~~i~K~V~V~Lk~G 58 (102)
-++..+||+|+|+.+..
T Consensus 5 ~~nDrLGKKVRvKCn~d 21 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTD 21 (73)
T ss_pred hhhhhcCceEEEEeCCc
Confidence 36788999999997644
Done!