Query 031921
Match_columns 150
No_of_seqs 211 out of 1079
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 07:11:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031921.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031921hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3293 Small nuclear ribonucl 100.0 5.9E-35 1.3E-39 220.0 10.8 97 1-97 1-97 (134)
2 cd01723 LSm4 The eukaryotic Sm 99.9 3.6E-27 7.9E-32 164.1 10.0 76 2-77 1-76 (76)
3 cd01724 Sm_D1 The eukaryotic S 99.9 7.9E-27 1.7E-31 167.9 10.8 83 2-85 1-84 (90)
4 cd01721 Sm_D3 The eukaryotic S 99.9 4.9E-26 1.1E-30 156.4 10.0 70 3-73 1-70 (70)
5 cd01725 LSm2 The eukaryotic Sm 99.9 1.9E-25 4.1E-30 157.5 9.7 77 2-78 1-78 (81)
6 cd01733 LSm10 The eukaryotic S 99.9 2.5E-24 5.4E-29 151.2 10.1 70 2-72 9-78 (78)
7 cd01726 LSm6 The eukaryotic Sm 99.9 5.3E-23 1.1E-27 139.8 9.3 67 3-70 1-67 (67)
8 KOG3428 Small nuclear ribonucl 99.9 6E-23 1.3E-27 151.8 9.5 90 1-92 1-91 (109)
9 cd01722 Sm_F The eukaryotic Sm 99.9 3E-22 6.4E-27 136.6 9.2 68 2-70 1-68 (68)
10 PRK00737 small nuclear ribonuc 99.9 9.3E-22 2E-26 135.6 10.0 68 2-70 4-71 (72)
11 KOG3172 Small nuclear ribonucl 99.9 6.5E-22 1.4E-26 146.5 9.6 80 2-82 5-84 (119)
12 cd01732 LSm5 The eukaryotic Sm 99.9 1.3E-21 2.8E-26 136.8 10.1 70 1-70 2-73 (76)
13 cd01731 archaeal_Sm1 The archa 99.9 2.4E-21 5.2E-26 131.8 9.5 67 3-70 1-67 (68)
14 COG1958 LSM1 Small nuclear rib 99.8 3.9E-20 8.4E-25 129.1 9.4 70 2-71 7-79 (79)
15 smart00651 Sm snRNP Sm protein 99.8 5.1E-20 1.1E-24 123.3 9.4 67 5-71 1-67 (67)
16 PF01423 LSM: LSM domain ; In 99.8 5.3E-20 1.1E-24 123.4 8.4 67 5-71 1-67 (67)
17 cd01719 Sm_G The eukaryotic Sm 99.8 1.5E-19 3.2E-24 125.0 9.1 71 3-74 1-71 (72)
18 KOG3448 Predicted snRNP core p 99.8 1.9E-19 4.1E-24 129.4 8.4 88 1-88 1-89 (96)
19 cd01730 LSm3 The eukaryotic Sm 99.8 7.9E-19 1.7E-23 123.7 9.3 69 2-70 1-81 (82)
20 cd00600 Sm_like The eukaryotic 99.8 9E-19 2E-23 115.6 8.8 63 7-70 1-63 (63)
21 cd01720 Sm_D2 The eukaryotic S 99.8 1.4E-18 3E-23 124.6 9.5 70 2-71 2-85 (87)
22 KOG3482 Small nuclear ribonucl 99.8 2.1E-18 4.5E-23 120.1 6.3 68 2-70 8-75 (79)
23 cd01729 LSm7 The eukaryotic Sm 99.7 8.9E-18 1.9E-22 118.5 9.6 70 4-73 4-80 (81)
24 cd01718 Sm_E The eukaryotic Sm 99.7 8.6E-18 1.9E-22 118.7 9.4 69 2-70 6-78 (79)
25 cd01717 Sm_B The eukaryotic Sm 99.7 1E-16 2.2E-21 112.0 8.6 67 5-71 3-78 (79)
26 cd01728 LSm1 The eukaryotic Sm 99.7 2.2E-16 4.8E-21 110.0 9.4 69 3-71 3-73 (74)
27 cd01727 LSm8 The eukaryotic Sm 99.7 2.8E-16 6.1E-21 108.7 8.9 69 5-73 2-73 (74)
28 KOG1783 Small nuclear ribonucl 99.7 9E-18 2E-22 116.8 1.1 70 2-72 6-75 (77)
29 PTZ00138 small nuclear ribonuc 99.7 7.1E-16 1.5E-20 111.2 9.7 70 2-71 14-87 (89)
30 cd06168 LSm9 The eukaryotic Sm 99.6 5.3E-15 1.1E-19 103.3 9.1 67 5-71 3-74 (75)
31 KOG1780 Small Nuclear ribonucl 99.5 2.6E-14 5.7E-19 99.8 6.0 65 6-71 8-72 (77)
32 KOG3460 Small nuclear ribonucl 99.4 2.8E-14 6E-19 101.8 1.7 73 2-74 5-89 (91)
33 KOG1775 U6 snRNA-associated Sm 99.4 1.9E-13 4.2E-18 96.1 3.6 70 1-70 6-77 (84)
34 KOG1774 Small nuclear ribonucl 99.2 1.6E-11 3.5E-16 87.3 4.7 70 2-71 12-85 (88)
35 KOG1781 Small Nuclear ribonucl 98.8 5.8E-10 1.3E-14 81.9 -0.5 71 5-75 20-97 (108)
36 KOG3168 U1 snRNP component [Tr 98.7 1.3E-09 2.9E-14 86.5 -0.3 71 5-75 7-86 (177)
37 KOG1784 Small Nuclear ribonucl 98.7 1.6E-08 3.4E-13 73.4 4.5 81 5-85 3-86 (96)
38 KOG1782 Small Nuclear ribonucl 98.5 1.6E-08 3.4E-13 76.8 0.3 67 7-73 14-82 (129)
39 KOG3459 Small nuclear ribonucl 98.2 2.2E-07 4.8E-12 69.4 -0.4 68 3-70 25-106 (114)
40 PF14438 SM-ATX: Ataxin 2 SM d 98.0 2.7E-05 5.8E-10 53.6 6.2 45 4-48 4-51 (77)
41 cd01739 LSm11_C The eukaryotic 97.6 5.4E-05 1.2E-09 52.0 2.8 38 12-49 8-49 (66)
42 PF12701 LSM14: Scd6-like Sm d 97.1 0.0029 6.3E-08 46.3 7.3 68 8-75 4-80 (96)
43 PF11095 Gemin7: Gem-associate 97.0 0.0039 8.4E-08 44.4 7.0 64 3-72 15-79 (80)
44 KOG3262 H/ACA small nucleolar 96.9 0.0039 8.4E-08 51.0 6.9 10 6-15 59-68 (215)
45 cd01716 Hfq Hfq, an abundant, 96.2 0.014 3.1E-07 39.5 5.3 37 6-42 3-41 (61)
46 KOG3262 H/ACA small nucleolar 96.1 0.066 1.4E-06 44.0 9.5 7 70-76 127-133 (215)
47 TIGR02383 Hfq RNA chaperone Hf 96.1 0.016 3.4E-07 39.4 4.9 38 5-42 6-45 (61)
48 PRK00395 hfq RNA-binding prote 95.7 0.025 5.5E-07 40.2 5.0 38 5-42 10-49 (79)
49 cd01736 LSm14_N LSm14 (also kn 95.4 0.071 1.5E-06 37.5 6.2 61 8-68 2-72 (74)
50 PF02237 BPL_C: Biotin protein 94.8 0.15 3.3E-06 32.1 6.0 31 11-42 2-32 (48)
51 PF06372 Gemin6: Gemin6 protei 94.8 0.15 3.3E-06 40.7 7.2 62 6-75 11-73 (166)
52 KOG1073 Uncharacterized mRNA-a 94.0 0.087 1.9E-06 46.7 4.7 70 6-75 3-82 (361)
53 COG1923 Hfq Uncharacterized ho 94.0 0.11 2.4E-06 36.8 4.3 34 5-38 10-45 (77)
54 PF10842 DUF2642: Protein of u 92.5 1.1 2.4E-05 30.8 7.4 52 4-70 13-65 (66)
55 PRK14091 RNA-binding protein H 91.9 0.38 8.3E-06 38.5 5.2 37 6-42 96-134 (165)
56 PRK14091 RNA-binding protein H 91.1 0.53 1.1E-05 37.7 5.2 38 5-42 15-54 (165)
57 cd01735 LSm12_N LSm12 belongs 89.6 1.8 3.9E-05 29.2 6.1 31 10-40 4-34 (61)
58 PRK14639 hypothetical protein; 87.4 1.4 3E-05 33.9 5.0 35 5-40 81-115 (140)
59 PRK14638 hypothetical protein; 86.9 1.2 2.5E-05 34.7 4.4 35 5-40 93-127 (150)
60 PRK02001 hypothetical protein; 86.6 1.7 3.6E-05 34.1 5.1 34 6-40 84-117 (152)
61 PRK14644 hypothetical protein; 80.8 3.7 8.1E-05 31.5 4.8 35 6-41 79-117 (136)
62 PTZ00034 40S ribosomal protein 80.5 1.2 2.7E-05 34.1 2.0 27 54-80 62-92 (124)
63 KOG0921 Dosage compensation co 80.2 4.2 9.1E-05 40.8 5.9 18 24-41 1073-1091(1282)
64 cd01734 YlxS_C YxlS is a Bacil 79.4 3.9 8.5E-05 28.3 4.2 31 5-35 18-52 (83)
65 COG0779 Uncharacterized protei 79.0 6.2 0.00013 31.1 5.6 33 4-36 91-127 (153)
66 PRK14642 hypothetical protein; 78.8 4.5 9.8E-05 33.1 4.9 67 5-73 93-180 (197)
67 PRK14640 hypothetical protein; 76.8 5.9 0.00013 30.8 4.9 35 5-40 90-128 (152)
68 PRK00092 ribosome maturation p 76.5 10 0.00023 29.2 6.2 30 5-34 91-124 (154)
69 PRK11625 Rho-binding antitermi 75.3 20 0.00042 25.7 6.8 57 7-72 18-74 (84)
70 PRK14632 hypothetical protein; 72.0 6.5 0.00014 31.2 4.1 35 5-40 91-132 (172)
71 PF02576 DUF150: Uncharacteris 71.8 7.1 0.00015 29.5 4.2 30 5-34 80-113 (141)
72 PRK14633 hypothetical protein; 70.5 7.8 0.00017 30.1 4.2 35 5-40 87-125 (150)
73 PRK14643 hypothetical protein; 69.5 9.7 0.00021 30.1 4.6 36 5-40 97-137 (164)
74 PRK14636 hypothetical protein; 69.3 7.6 0.00016 31.1 4.0 30 5-34 91-124 (176)
75 PRK14645 hypothetical protein; 69.2 8 0.00017 30.3 4.0 30 5-35 95-124 (154)
76 PRK14634 hypothetical protein; 68.7 8.5 0.00018 30.0 4.1 35 5-40 93-131 (155)
77 PRK14647 hypothetical protein; 67.8 9.2 0.0002 29.9 4.1 30 5-34 92-130 (159)
78 KOG3973 Uncharacterized conser 67.6 8.6 0.00019 34.7 4.3 12 61-72 304-315 (465)
79 PF07073 ROF: Modulator of Rho 66.6 5.1 0.00011 28.3 2.2 30 6-37 11-40 (80)
80 PRK14637 hypothetical protein; 66.4 14 0.0003 28.8 4.8 35 5-40 91-126 (151)
81 PRK14646 hypothetical protein; 66.3 10 0.00022 29.6 4.1 35 5-40 93-131 (155)
82 PRK09618 flgD flagellar basal 64.4 20 0.00043 28.0 5.3 26 8-33 88-113 (142)
83 PRK06955 biotin--protein ligas 63.1 27 0.00059 29.6 6.4 32 10-41 247-278 (300)
84 PRK14641 hypothetical protein; 59.4 14 0.0003 29.6 3.8 29 5-33 97-129 (173)
85 PRK14631 hypothetical protein; 58.4 16 0.00035 29.2 4.0 29 5-33 110-142 (174)
86 PF11607 DUF3247: Protein of u 57.9 21 0.00045 26.5 4.1 19 12-30 28-46 (101)
87 PRK11634 ATP-dependent RNA hel 57.8 51 0.0011 31.0 7.7 26 55-81 518-543 (629)
88 KOG3293 Small nuclear ribonucl 56.4 18 0.00038 28.0 3.7 19 55-73 39-58 (134)
89 PF10618 Tail_tube: Phage tail 56.3 26 0.00056 26.2 4.6 27 2-28 64-90 (119)
90 PRK11886 bifunctional biotin-- 51.2 58 0.0013 27.5 6.5 31 10-41 270-300 (319)
91 PRK13325 bifunctional biotin-- 51.1 51 0.0011 31.0 6.6 32 10-41 276-307 (592)
92 smart00333 TUDOR Tudor domain. 48.5 61 0.0013 19.9 4.8 25 11-35 5-29 (57)
93 PRK11911 flgD flagellar basal 46.5 75 0.0016 24.8 5.9 26 9-34 90-115 (140)
94 PRK14630 hypothetical protein; 46.1 34 0.00074 26.3 3.9 29 5-34 90-118 (143)
95 PRK14635 hypothetical protein; 45.7 50 0.0011 25.8 4.9 35 5-40 92-131 (162)
96 PRK10898 serine endoprotease; 45.3 39 0.00084 29.4 4.6 59 13-74 102-162 (353)
97 PRK08330 biotin--protein ligas 44.9 85 0.0019 25.4 6.3 33 9-42 185-218 (236)
98 PF07833 Cu_amine_oxidN1: Copp 44.4 64 0.0014 21.4 4.7 23 1-23 6-28 (93)
99 PRK10590 ATP-dependent RNA hel 44.4 94 0.002 27.5 7.0 12 62-73 342-353 (456)
100 TIGR00567 3mg DNA-3-methyladen 40.0 58 0.0012 26.6 4.5 35 3-37 10-44 (192)
101 PF13437 HlyD_3: HlyD family s 39.9 59 0.0013 22.3 4.1 33 2-34 42-78 (105)
102 TIGR00121 birA_ligase birA, bi 38.8 1E+02 0.0022 24.9 5.9 31 10-41 191-221 (237)
103 TIGR02038 protease_degS peripl 37.8 59 0.0013 28.1 4.6 59 13-74 102-162 (351)
104 PRK06789 flagellar motor switc 37.3 61 0.0013 22.6 3.7 36 7-42 36-71 (74)
105 PRK10139 serine endoprotease; 37.2 59 0.0013 29.3 4.6 61 12-74 114-176 (455)
106 PF03614 Flag1_repress: Repres 36.5 55 0.0012 26.2 3.8 34 11-44 28-61 (165)
107 cd01343 PL1_Passenger_AT Perta 35.5 1.2E+02 0.0025 25.1 5.8 52 14-69 74-125 (233)
108 TIGR02037 degP_htrA_DO peripla 34.8 68 0.0015 28.2 4.5 32 13-44 82-113 (428)
109 TIGR02603 CxxCH_TIGR02603 puta 34.6 60 0.0013 24.1 3.6 21 13-33 58-78 (133)
110 COG4568 Rof Transcriptional an 34.2 50 0.0011 23.6 2.9 25 6-30 17-41 (84)
111 PF02245 Pur_DNA_glyco: Methyl 33.6 69 0.0015 25.9 4.0 34 3-37 9-42 (184)
112 PRK10942 serine endoprotease; 33.0 74 0.0016 28.9 4.5 32 12-43 135-166 (473)
113 cd04479 RPA3 RPA3: A subfamily 30.2 99 0.0021 22.1 4.0 16 4-19 7-22 (101)
114 TIGR00999 8a0102 Membrane Fusi 29.9 1.1E+02 0.0024 24.2 4.7 35 3-37 132-167 (265)
115 PF14563 DUF4444: Domain of un 28.1 56 0.0012 20.7 2.0 22 25-46 10-31 (42)
116 PF03614 Flag1_repress: Repres 27.7 67 0.0014 25.7 2.9 25 11-35 119-143 (165)
117 PTZ00275 biotin-acetyl-CoA-car 27.2 1.3E+02 0.0027 25.5 4.8 30 11-41 236-265 (285)
118 COG0340 BirA Biotin-(acetyl-Co 26.6 1.7E+02 0.0036 24.3 5.3 34 10-43 188-221 (238)
119 KOG0116 RasGAP SH3 binding pro 26.6 1.2E+02 0.0026 27.6 4.7 9 55-63 316-324 (419)
120 PF05954 Phage_GPD: Phage late 26.1 69 0.0015 25.6 2.9 27 7-33 23-49 (292)
121 PRK06792 flgD flagellar basal 25.6 96 0.0021 25.5 3.6 26 9-34 115-140 (190)
122 COG5316 Uncharacterized conser 25.2 2.1E+02 0.0045 26.3 5.9 44 2-46 72-115 (421)
123 cd00540 AAG Alkyladenine DNA g 25.1 1.4E+02 0.0031 24.0 4.5 35 3-38 6-40 (179)
124 PF07076 DUF1344: Protein of u 23.6 83 0.0018 21.3 2.4 24 24-47 4-28 (61)
125 PF05037 DUF669: Protein of un 22.9 54 0.0012 24.7 1.6 25 5-29 96-121 (141)
126 PRK07228 N-ethylammeline chlor 22.4 1.5E+02 0.0033 25.8 4.5 35 36-70 1-35 (445)
127 PF11743 DUF3301: Protein of u 21.9 1.2E+02 0.0026 21.7 3.2 28 45-73 69-96 (97)
128 KOG3199 Nicotinamide mononucle 21.0 30 0.00066 29.1 -0.2 68 13-83 156-228 (234)
129 PF11684 DUF3280: Protein of u 20.3 1.6E+02 0.0034 22.7 3.7 39 22-65 82-123 (140)
130 PF01052 SpoA: Surface present 20.2 1.6E+02 0.0034 19.4 3.3 34 11-44 41-74 (77)
131 TIGR00046 RNA methyltransferas 20.2 1.2E+02 0.0026 24.7 3.3 39 5-43 28-67 (240)
No 1
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=100.00 E-value=5.9e-35 Score=220.02 Aligned_cols=97 Identities=77% Similarity=1.318 Sum_probs=89.6
Q ss_pred CChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccccchhH
Q 031921 1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQ 80 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lpd~ild~~~ 80 (150)
|+||+||+.+++++|.||||||++|.|+|++||.||||+|++|+++++|+++|+.+++|||||++|+||.|||++||.++
T Consensus 1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~iid~vk 80 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEIIDKVK 80 (134)
T ss_pred CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhhcCCCCCCCCCC
Q 031921 81 EETKSRSDRKPPGVGRG 97 (150)
Q Consensus 81 ~~~~~~~~~~~~~~~rg 97 (150)
+|..+..+.+...+.++
T Consensus 81 ee~~~~~~~r~~~r~~~ 97 (134)
T KOG3293|consen 81 EECVSNNRNRKQSRDRG 97 (134)
T ss_pred HHHHHhccchhcccccc
Confidence 99888766554333333
No 2
>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=99.95 E-value=3.6e-27 Score=164.12 Aligned_cols=76 Identities=93% Similarity=1.606 Sum_probs=72.9
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccccc
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVID 77 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lpd~ild 77 (150)
+|++||++++|++|+|||||+.+|+|+|.+||.|||++|+||+++..+++++.+++++||||++|+||++||+++|
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~~~ 76 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEIID 76 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHHCC
Confidence 6999999999999999999999999999999999999999999998899887789999999999999999999875
No 3
>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=99.94 E-value=7.9e-27 Score=167.85 Aligned_cols=83 Identities=29% Similarity=0.471 Sum_probs=76.0
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccc-cchhH
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEV-IDKVQ 80 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lpd~i-ld~~~ 80 (150)
.|++||++++|++|+||||||++|+|+|.+||.||||+|+||+++..++.. .+++++||||++|+||+|||++ +|.++
T Consensus 1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~-~~~~~v~IRG~nI~yi~lPd~l~~~~~l 79 (90)
T cd01724 1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNP-VPLDTLSIRGNNIRYFILPDSLNLDTLL 79 (90)
T ss_pred CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCce-eEcceEEEeCCEEEEEEcCCcCCcchhh
Confidence 478999999999999999999999999999999999999999999777654 6899999999999999999999 78777
Q ss_pred HHhhh
Q 031921 81 EETKS 85 (150)
Q Consensus 81 ~~~~~ 85 (150)
++++.
T Consensus 80 ~~~~~ 84 (90)
T cd01724 80 VDSTP 84 (90)
T ss_pred hhcCC
Confidence 77643
No 4
>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=99.93 E-value=4.9e-26 Score=156.37 Aligned_cols=70 Identities=41% Similarity=0.803 Sum_probs=67.2
Q ss_pred hHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCc
Q 031921 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lpd 73 (150)
|+.||++++|++|+||||||.+|+|+|.+||.|||++|+||+++.++++. .+++++||||+||+||+|||
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~-~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRV-SQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcE-eEcCcEEEeCCEEEEEEeCC
Confidence 89999999999999999999999999999999999999999998888875 58999999999999999997
No 5
>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=99.93 E-value=1.9e-25 Score=157.53 Aligned_cols=77 Identities=31% Similarity=0.608 Sum_probs=70.3
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCe-eeecCeEEEecCeEEEEecCccccch
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDR-FWRMPECYIRGNTIKYLRVPDEVIDK 78 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~-~~~l~~v~IRG~nIryI~lpd~ild~ 78 (150)
+|+.||++++|++|+||||||.+|+|+|.+||.|||++|+||+++.+++.. ..+++++||||++|+||++||+++|.
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~ 78 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDT 78 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcCc
Confidence 689999999999999999999999999999999999999999988765532 35789999999999999999999874
No 6
>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=99.91 E-value=2.5e-24 Score=151.17 Aligned_cols=70 Identities=31% Similarity=0.591 Sum_probs=65.9
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecC
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVP 72 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lp 72 (150)
.+++||++++|++|+||||||.+|+|+|.+||.|||++|+||+++.+++++ .+++++||||++|+||+||
T Consensus 9 tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~-~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 9 TLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQ-VQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred hHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCce-eECCcEEEECCEEEEEEcC
Confidence 368999999999999999999999999999999999999999999877765 4899999999999999998
No 7
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.89 E-value=5.3e-23 Score=139.83 Aligned_cols=67 Identities=33% Similarity=0.581 Sum_probs=62.1
Q ss_pred hHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031921 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
|++||+++++++|+|+||||++|+|+|.+||.||||+|+||+++. +++...+++++||||++|+||+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~-~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYV-NGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEe-CCceeeEeCCEEEECCEEEEEC
Confidence 899999999999999999999999999999999999999999875 4444578999999999999984
No 8
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=99.89 E-value=6e-23 Score=151.81 Aligned_cols=90 Identities=32% Similarity=0.498 Sum_probs=80.6
Q ss_pred CChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccc-cchh
Q 031921 1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEV-IDKV 79 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lpd~i-ld~~ 79 (150)
|..+.||+++.+.+|+|||||+++++|+|.++|.+||++|.+|+.+.+ +++ .+++.++|||++|+|+++||++ +|.+
T Consensus 1 mklvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-~~p-v~l~~lsirgnniRy~~lpD~l~ld~L 78 (109)
T KOG3428|consen 1 MKLVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-GEP-VRLDTLSIRGNNIRYYILPDSLNLDTL 78 (109)
T ss_pred ChHHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC-CCc-eeEEEEEeecceEEEEEccCCcCccee
Confidence 678899999999999999999999999999999999999999999966 465 5899999999999999999999 8988
Q ss_pred HHHhhhhcCCCCC
Q 031921 80 QEETKSRSDRKPP 92 (150)
Q Consensus 80 ~~~~~~~~~~~~~ 92 (150)
++++.++.+.+++
T Consensus 79 lvd~~~~~~~~~~ 91 (109)
T KOG3428|consen 79 LVDDAPRLHLRKN 91 (109)
T ss_pred eeehhhhhhhhcc
Confidence 7777766555544
No 9
>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=99.88 E-value=3e-22 Score=136.63 Aligned_cols=68 Identities=35% Similarity=0.582 Sum_probs=62.3
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
.|++||+++++++|+|+|+||.+|+|+|.+||+||||+|+||+++. ++.++.+++++||||++|+||.
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~-~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI-DGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEe-CCccccCcCcEEEECCEEEEEC
Confidence 4999999999999999999999999999999999999999999884 4444468999999999999984
No 10
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.87 E-value=9.3e-22 Score=135.62 Aligned_cols=68 Identities=32% Similarity=0.581 Sum_probs=63.3
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
.|+++|+++++++|+|+|+||++|+|+|.+||+||||+|+||+|+. +++++.+++.+||||++|.||.
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ-DGEVVRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEc-CCCeEeEcCcEEEeCCEEEEEc
Confidence 6999999999999999999999999999999999999999999985 4455578999999999999986
No 11
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.87 E-value=6.5e-22 Score=146.50 Aligned_cols=80 Identities=36% Similarity=0.674 Sum_probs=75.1
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccccchhHH
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQE 81 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lpd~ild~~~~ 81 (150)
+|+.+|.+++|+.|++|+++|++|+|+|+.+|++||++|+|++.|..|+.. .+++.+||||++|+|+.|||.+.++...
T Consensus 5 vpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~v-s~le~V~IRGS~IRFlvlPdmLKnAPmF 83 (119)
T KOG3172|consen 5 VPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRV-SQLEQVFIRGSKIRFLVLPDMLKNAPMF 83 (119)
T ss_pred cceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcc-eeeeeEEEecCeEEEEECchHhhcCccc
Confidence 699999999999999999999999999999999999999999999999975 6999999999999999999999776665
Q ss_pred H
Q 031921 82 E 82 (150)
Q Consensus 82 ~ 82 (150)
.
T Consensus 84 k 84 (119)
T KOG3172|consen 84 K 84 (119)
T ss_pred c
Confidence 4
No 12
>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=99.87 E-value=1.3e-21 Score=136.85 Aligned_cols=70 Identities=24% Similarity=0.509 Sum_probs=64.6
Q ss_pred CChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEc--cCCCeeeecCeEEEecCeEEEEe
Q 031921 1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTS--KDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~--~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
|+|+++|+++++++|+|+|+++++|.|+|.+||.||||+|+||+|+. +++++..+++.+||||++|.+|+
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLV 73 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEE
Confidence 89999999999999999999999999999999999999999999986 34444468999999999999998
No 13
>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=99.86 E-value=2.4e-21 Score=131.75 Aligned_cols=67 Identities=28% Similarity=0.511 Sum_probs=62.7
Q ss_pred hHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031921 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
|+.+|+++++++|+|+|+||++|.|+|.+||+||||+|+||+++..+.+ ...++.+||||++|.||+
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~-~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEP-VRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCe-EeEcCcEEEeCCEEEEEc
Confidence 8999999999999999999999999999999999999999999876654 368999999999999986
No 14
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.83 E-value=3.9e-20 Score=129.09 Aligned_cols=70 Identities=41% Similarity=0.633 Sum_probs=61.8
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEcc-CCCe-eee-cCeEEEecCeEEEEec
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSK-DGDR-FWR-MPECYIRGNTIKYLRV 71 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~-dg~~-~~~-l~~v~IRG~nIryI~l 71 (150)
.|+++|+++++++|.|+||||++|.|+|.+||.||||+|+||+++.. +++. ... .+++||||++|.||.+
T Consensus 7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 68999999999999999999999999999999999999999999864 4443 223 4599999999999963
No 15
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.83 E-value=5.1e-20 Score=123.30 Aligned_cols=67 Identities=42% Similarity=0.677 Sum_probs=61.4
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEec
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~l 71 (150)
.+|+++++++|+|+|+|+++|.|+|.+||.||||+|+||+++..+.....+++.+||||++|+||++
T Consensus 1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 3799999999999999999999999999999999999999998763445789999999999999974
No 16
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.82 E-value=5.3e-20 Score=123.40 Aligned_cols=67 Identities=39% Similarity=0.649 Sum_probs=61.9
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEec
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~l 71 (150)
.||+++++++|+|+|+||++|+|+|.+||.||||+|+||+++..+......++++||||++|+||++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 4899999999999999999999999999999999999999998776344789999999999999985
No 17
>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=99.81 E-value=1.5e-19 Score=125.02 Aligned_cols=71 Identities=23% Similarity=0.308 Sum_probs=63.4
Q ss_pred hHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCcc
Q 031921 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDE 74 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lpd~ 74 (150)
|-++|+++++|+|.|+|++|++|.|+|.+||.||||+|+||+|+..+. ...+++.++|||++|.+|..-|.
T Consensus 1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~-~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGG-EKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCC-ceeEeceEEECCCEEEEEEcccc
Confidence 557899999999999999999999999999999999999999986443 34689999999999999986543
No 18
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.80 E-value=1.9e-19 Score=129.37 Aligned_cols=88 Identities=28% Similarity=0.576 Sum_probs=78.6
Q ss_pred CChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCe-eeecCeEEEecCeEEEEecCccccchh
Q 031921 1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDR-FWRMPECYIRGNTIKYLRVPDEVIDKV 79 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~-~~~l~~v~IRG~nIryI~lpd~ild~~ 79 (150)
|+.++|+++++++.|+|||||+..+.|+|.++|+|+||.|.|+.+++++.-+ ...+..|||||+.|+||++|.+.+|..
T Consensus 1 mLFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtq 80 (96)
T KOG3448|consen 1 MLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQ 80 (96)
T ss_pred CchHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHH
Confidence 8999999999999999999999999999999999999999999998765433 246788999999999999999999988
Q ss_pred HHHhhhhcC
Q 031921 80 QEETKSRSD 88 (150)
Q Consensus 80 ~~~~~~~~~ 88 (150)
+.++.++++
T Consensus 81 ll~da~R~e 89 (96)
T KOG3448|consen 81 LLQDAARRE 89 (96)
T ss_pred HHHHHHHHH
Confidence 888777653
No 19
>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=99.79 E-value=7.9e-19 Score=123.74 Aligned_cols=69 Identities=22% Similarity=0.380 Sum_probs=61.6
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCC------------CeeeecCeEEEecCeEEEE
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDG------------DRFWRMPECYIRGNTIKYL 69 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg------------~~~~~l~~v~IRG~nIryI 69 (150)
.|++||+.+++++|+|+|++|++|.|+|.+||.||||+|+||+|+.... +....++.+||||++|.+|
T Consensus 1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i 80 (82)
T cd01730 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV 80 (82)
T ss_pred CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence 4999999999999999999999999999999999999999999986321 1235889999999999998
Q ss_pred e
Q 031921 70 R 70 (150)
Q Consensus 70 ~ 70 (150)
+
T Consensus 81 ~ 81 (82)
T cd01730 81 S 81 (82)
T ss_pred C
Confidence 6
No 20
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.78 E-value=9e-19 Score=115.59 Aligned_cols=63 Identities=35% Similarity=0.524 Sum_probs=58.2
Q ss_pred HhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031921 7 LKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 7 L~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
|+++++++|+|+|+|+++|.|+|.+||.||||+|+||+++.++.+ ..+++.+||||++|+||+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~-~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGK-KRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCc-EEECCeEEEECCEEEEEC
Confidence 578999999999999999999999999999999999999977654 478999999999999984
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=99.78 E-value=1.4e-18 Score=124.58 Aligned_cols=70 Identities=21% Similarity=0.294 Sum_probs=61.4
Q ss_pred ChHHHHhhcC--CCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCC------------eeeecCeEEEecCeEE
Q 031921 2 LPLSLLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGD------------RFWRMPECYIRGNTIK 67 (150)
Q Consensus 2 lPl~lL~~l~--gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~------------~~~~l~~v~IRG~nIr 67 (150)
=|+++|++++ +++|.|+|+++.+|.|+|.+||.||||+|+||+|++.... ..+.++.+||||++|.
T Consensus 2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 4999999996 8999999999999999999999999999999999764321 2346899999999999
Q ss_pred EEec
Q 031921 68 YLRV 71 (150)
Q Consensus 68 yI~l 71 (150)
||+.
T Consensus 82 ~Is~ 85 (87)
T cd01720 82 LVLR 85 (87)
T ss_pred EEec
Confidence 9863
No 22
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.75 E-value=2.1e-18 Score=120.06 Aligned_cols=68 Identities=37% Similarity=0.573 Sum_probs=64.2
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
.|-+||+.++|++|.|+||.|.+|.|+|+++|.||||.|.+++|. .+|...-++++++||.|||.||.
T Consensus 8 NPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~-idG~~~g~lGEilIRCNNvlyi~ 75 (79)
T KOG3482|consen 8 NPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEY-IDGVSTGNLGEILIRCNNVLYIR 75 (79)
T ss_pred CchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhh-hcccccccceeEEEEeccEEEEe
Confidence 588999999999999999999999999999999999999999997 57777779999999999999995
No 23
>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=99.75 E-value=8.9e-18 Score=118.51 Aligned_cols=70 Identities=19% Similarity=0.280 Sum_probs=60.8
Q ss_pred HHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCC-------CeeeecCeEEEecCeEEEEecCc
Q 031921 4 LSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDG-------DRFWRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 4 l~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg-------~~~~~l~~v~IRG~nIryI~lpd 73 (150)
..-|+++++++|.|+|++|++|.|+|.+||.||||+|+||+|+..+. +...+++.++|||+||.+|...+
T Consensus 4 ~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 4 ILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred hhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 44589999999999999999999999999999999999999986432 13367999999999999997554
No 24
>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=99.75 E-value=8.6e-18 Score=118.69 Aligned_cols=69 Identities=14% Similarity=0.231 Sum_probs=61.9
Q ss_pred ChHHHHhhcCCC--cEEEEEc--CCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031921 2 LPLSLLKTAQGH--PMLVELK--NGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 2 lPl~lL~~l~gk--~V~VeLK--nG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
+|+.+|.+++.+ +|+|+|+ ++.+|.|+|.+||+||||+|+||+|+...++...+++.++|||+||.+|+
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEc
Confidence 799999999998 7888887 89999999999999999999999998643444468999999999999987
No 25
>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=99.69 E-value=1e-16 Score=112.03 Aligned_cols=67 Identities=21% Similarity=0.280 Sum_probs=58.8
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccC---------CCeeeecCeEEEecCeEEEEec
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD---------GDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~d---------g~~~~~l~~v~IRG~nIryI~l 71 (150)
+-|.++++++|.|.|++|++|.|+|.+||.||||+|+||+|+... .++...++.+||||++|.+|.+
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 458899999999999999999999999999999999999997532 1233579999999999999986
No 26
>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=99.69 E-value=2.2e-16 Score=109.97 Aligned_cols=69 Identities=22% Similarity=0.237 Sum_probs=60.2
Q ss_pred hHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCC--eeeecCeEEEecCeEEEEec
Q 031921 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGD--RFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~--~~~~l~~v~IRG~nIryI~l 71 (150)
++..|.++++++|.|.|+++++|.|+|.+||+||||+|+||+|+..+++ ....++.++|||++|.+|.+
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 4678999999999999999999999999999999999999988754332 22578999999999999864
No 27
>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=99.68 E-value=2.8e-16 Score=108.70 Aligned_cols=69 Identities=22% Similarity=0.172 Sum_probs=60.4
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEcc---CCCeeeecCeEEEecCeEEEEecCc
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSK---DGDRFWRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~---dg~~~~~l~~v~IRG~nIryI~lpd 73 (150)
+.|+++++++|.|.|++++.|.|+|.+||.||||+|++|+|... ++.....++.++|||++|.+|..-|
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 56899999999999999999999999999999999999998743 2333357999999999999998654
No 28
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.67 E-value=9e-18 Score=116.82 Aligned_cols=70 Identities=31% Similarity=0.536 Sum_probs=65.9
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecC
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVP 72 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lp 72 (150)
.|-+||++.+|++|.|+|.++..|+|+|+++|.||||.|+.++|. .|++...+++.+||||++|.||+..
T Consensus 6 ~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~-~ngql~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 6 MPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEY-VNGQLKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred CcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHH-hcCcccccccceeeccccEEEEEec
Confidence 588999999999999999999999999999999999999999987 4888778999999999999999864
No 29
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.66 E-value=7.1e-16 Score=111.17 Aligned_cols=70 Identities=13% Similarity=0.209 Sum_probs=60.3
Q ss_pred ChHHHHhhcCC--CcEEEEEcC--CcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEec
Q 031921 2 LPLSLLKTAQG--HPMLVELKN--GETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 2 lPl~lL~~l~g--k~V~VeLKn--G~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~l 71 (150)
.|+.+|.+++. .+|.|+|++ +.+|.|+|.+||.||||+|+||+|+..+.+...++++++|||+||.||+.
T Consensus 14 ~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~ 87 (89)
T PTZ00138 14 QPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA 87 (89)
T ss_pred CCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence 68999999984 568888877 48999999999999999999999986544444689999999999999974
No 30
>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=99.61 E-value=5.3e-15 Score=103.29 Aligned_cols=67 Identities=21% Similarity=0.206 Sum_probs=60.0
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccC-----CCeeeecCeEEEecCeEEEEec
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD-----GDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~d-----g~~~~~l~~v~IRG~nIryI~l 71 (150)
+.|+++++++|.|.|+||+.|.|+|.+||.+|||+|+||.|+... ..+...++.++|||++|..|++
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 568999999999999999999999999999999999999998643 1234689999999999999985
No 31
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.52 E-value=2.6e-14 Score=99.76 Aligned_cols=65 Identities=31% Similarity=0.466 Sum_probs=60.6
Q ss_pred HHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEec
Q 031921 6 LLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~l 71 (150)
.|+++.+|++.|+|..++.+.|+|.+||.||||+|++++|...++++ ..++.++|||++|..+.-
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~-~~ig~~vIrgnsiv~~ea 72 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDK-NNIGMVVIRGNSIVMVEA 72 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCc-ceeeeEEEeccEEEEEee
Confidence 89999999999999999999999999999999999999999888765 589999999999988753
No 32
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.44 E-value=2.8e-14 Score=101.79 Aligned_cols=73 Identities=23% Similarity=0.345 Sum_probs=63.2
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEcc--CCC----------eeeecCeEEEecCeEEEE
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSK--DGD----------RFWRMPECYIRGNTIKYL 69 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~--dg~----------~~~~l~~v~IRG~nIryI 69 (150)
-|++||+-++..+|.|+|++++++.|+|.+||+|+||+|.||++|.. +.+ ....++.+||||++|.+|
T Consensus 5 ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilv 84 (91)
T KOG3460|consen 5 EPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILV 84 (91)
T ss_pred ccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEE
Confidence 59999999999999999999999999999999999999999987642 221 125788999999999999
Q ss_pred ecCcc
Q 031921 70 RVPDE 74 (150)
Q Consensus 70 ~lpd~ 74 (150)
+.|-.
T Consensus 85 spp~~ 89 (91)
T KOG3460|consen 85 SPPLR 89 (91)
T ss_pred cCccc
Confidence 98743
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.40 E-value=1.9e-13 Score=96.09 Aligned_cols=70 Identities=27% Similarity=0.538 Sum_probs=64.1
Q ss_pred CChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEc--cCCCeeeecCeEEEecCeEEEEe
Q 031921 1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTS--KDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~--~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
.+|++++.+.+|.+|.|.+|+++++.|+|.+||+|.|++|+||+|+. +++....+++.+++.||+|..+.
T Consensus 6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLv 77 (84)
T KOG1775|consen 6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLV 77 (84)
T ss_pred cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEe
Confidence 38999999999999999999999999999999999999999999764 56667789999999999998764
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.21 E-value=1.6e-11 Score=87.35 Aligned_cols=70 Identities=17% Similarity=0.280 Sum_probs=59.1
Q ss_pred ChHHHHhhcC--CCcEEEEEcC--CcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEec
Q 031921 2 LPLSLLKTAQ--GHPMLVELKN--GETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 2 lPl~lL~~l~--gk~V~VeLKn--G~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~l 71 (150)
.|+.++-.++ -.+|.|+|.. +..++|.|++||+|||++|+||++.+.....-..++.++++|+||..|+-
T Consensus 12 ~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~ 85 (88)
T KOG1774|consen 12 QPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQS 85 (88)
T ss_pred CcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEee
Confidence 6888877775 4679999987 78999999999999999999999987544332479999999999999874
No 35
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.81 E-value=5.8e-10 Score=81.88 Aligned_cols=71 Identities=18% Similarity=0.243 Sum_probs=61.3
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCC-------eeeecCeEEEecCeEEEEecCccc
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGD-------RFWRMPECYIRGNTIKYLRVPDEV 75 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~-------~~~~l~~v~IRG~nIryI~lpd~i 75 (150)
--|.+++.+.|.|++..|++++|+|.+||+.|||+|+|++|+..|.+ ..++++.+++||..+..|+..|-.
T Consensus 20 lDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~ 97 (108)
T KOG1781|consen 20 LDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGS 97 (108)
T ss_pred hhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcch
Confidence 45789999999999999999999999999999999999998765432 236899999999999998866543
No 36
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=98.75 E-value=1.3e-09 Score=86.51 Aligned_cols=71 Identities=24% Similarity=0.311 Sum_probs=60.7
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEc---------cCCCeeeecCeEEEecCeEEEEecCccc
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTS---------KDGDRFWRMPECYIRGNTIKYLRVPDEV 75 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~---------~dg~~~~~l~~v~IRG~nIryI~lpd~i 75 (150)
+-|-+++|..+.|.|.|+++|.|++..||.|||++|.||+|.. .++++...|..|++||+||...++.+..
T Consensus 7 skml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegpp 86 (177)
T KOG3168|consen 7 SKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPP 86 (177)
T ss_pred hHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCC
Confidence 3456778999999999999999999999999999999998753 2455557899999999999999876555
No 37
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.72 E-value=1.6e-08 Score=73.39 Aligned_cols=81 Identities=22% Similarity=0.201 Sum_probs=67.4
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEc---cCCCeeeecCeEEEecCeEEEEecCccccchhHH
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTS---KDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQE 81 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~---~dg~~~~~l~~v~IRG~nIryI~lpd~ild~~~~ 81 (150)
+-|..+++++|.|-..||+.+.|.|.+||+..||.|+++-+.. ..+.....++..+|||.||..|-..|+.+|+.++
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~~ld 82 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDSRLD 82 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhhhhh
Confidence 4588999999999999999999999999999999999997643 1233335789999999999999998888886555
Q ss_pred Hhhh
Q 031921 82 ETKS 85 (150)
Q Consensus 82 ~~~~ 85 (150)
-.+-
T Consensus 83 ~tki 86 (96)
T KOG1784|consen 83 LTKI 86 (96)
T ss_pred hhhc
Confidence 4433
No 38
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.54 E-value=1.6e-08 Score=76.80 Aligned_cols=67 Identities=27% Similarity=0.332 Sum_probs=55.8
Q ss_pred HhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCee--eecCeEEEecCeEEEEecCc
Q 031921 7 LKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRF--WRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 7 L~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~--~~l~~v~IRG~nIryI~lpd 73 (150)
|-+.+.++++|-|+||+.+.|.|.+||+|-|++|++|++..--++.+ ...+.++|||.||..|-..|
T Consensus 14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid 82 (129)
T KOG1782|consen 14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEID 82 (129)
T ss_pred HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCC
Confidence 66778999999999999999999999999999999999754323221 35688999999999987433
No 39
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.21 E-value=2.2e-07 Score=69.40 Aligned_cols=68 Identities=21% Similarity=0.341 Sum_probs=56.9
Q ss_pred hHHHHhhcC--CCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEcc------CCCe------eeecCeEEEecCeEEE
Q 031921 3 PLSLLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSK------DGDR------FWRMPECYIRGNTIKY 68 (150)
Q Consensus 3 Pl~lL~~l~--gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~------dg~~------~~~l~~v~IRG~nIry 68 (150)
|+++|..++ ..+|+|-++|...+.|.+.+||.|+|++|+|+.+.+. ++.. .+.++.+||||++|..
T Consensus 25 pls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~ 104 (114)
T KOG3459|consen 25 PLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVIL 104 (114)
T ss_pred chhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEE
Confidence 788887776 7889999999999999999999999999999998652 2222 2457899999999887
Q ss_pred Ee
Q 031921 69 LR 70 (150)
Q Consensus 69 I~ 70 (150)
+.
T Consensus 105 v~ 106 (114)
T KOG3459|consen 105 VL 106 (114)
T ss_pred EE
Confidence 65
No 40
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.96 E-value=2.7e-05 Score=53.63 Aligned_cols=45 Identities=24% Similarity=0.351 Sum_probs=37.3
Q ss_pred HHHHhhcCCCcEEEEEcCCcEEEEEEEEecC---ccceEEccEEEEcc
Q 031921 4 LSLLKTAQGHPMLVELKNGETYNGHLVNCDT---WMNIHLREVICTSK 48 (150)
Q Consensus 4 l~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~---~MNl~L~dv~et~~ 48 (150)
+.++.+++|++|.|.++||..|+|+|.+++. -+.++|+.+.....
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~ 51 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK 51 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence 4678999999999999999999999999998 89999999998753
No 41
>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=97.59 E-value=5.4e-05 Score=52.01 Aligned_cols=38 Identities=24% Similarity=0.304 Sum_probs=31.8
Q ss_pred CCcEEEEEcC----CcEEEEEEEEecCccceEEccEEEEccC
Q 031921 12 GHPMLVELKN----GETYNGHLVNCDTWMNIHLREVICTSKD 49 (150)
Q Consensus 12 gk~V~VeLKn----G~~~~G~L~~vD~~MNl~L~dv~et~~d 49 (150)
.++|.|.++. .-.++|.|++||.||||.|.||+|++..
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 5678887765 3478899999999999999999998754
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.11 E-value=0.0029 Score=46.25 Aligned_cols=68 Identities=25% Similarity=0.225 Sum_probs=55.7
Q ss_pred hhcCCCcEEEEEcCCcEEEEEEEEecC-ccceEEccEEEEccCCCe--------eeecCeEEEecCeEEEEecCccc
Q 031921 8 KTAQGHPMLVELKNGETYNGHLVNCDT-WMNIHLREVICTSKDGDR--------FWRMPECYIRGNTIKYLRVPDEV 75 (150)
Q Consensus 8 ~~l~gk~V~VeLKnG~~~~G~L~~vD~-~MNl~L~dv~et~~dg~~--------~~~l~~v~IRG~nIryI~lpd~i 75 (150)
..++|++|.+..|++..|+|+|..+|. .-.|.|+||...-.++.+ ...++.+..||+.|+-+.+-+.-
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~ 80 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPP 80 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCC
Confidence 467899999999999999999999996 679999999987544321 13578999999999999875544
No 43
>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=97.01 E-value=0.0039 Score=44.39 Aligned_cols=64 Identities=20% Similarity=0.309 Sum_probs=51.4
Q ss_pred hHHHHhhcCCCcEEEEEcCCcEEEEEEEEecC-ccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecC
Q 031921 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDT-WMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVP 72 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~-~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lp 72 (150)
.|.+|.++.+++|.+.|....++.++..+||. ..|+.++|-. ++=| .+++..||.+-|..+++.
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~--TPlG----v~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ--TPLG----VQPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE--TTTT----EEEEEEEEGGGEEEEEE-
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC--CCcc----cChhheeecCCEEEEEec
Confidence 46788999999999999999999999999995 6699988865 2334 468899999999999874
No 44
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=96.88 E-value=0.0039 Score=51.05 Aligned_cols=10 Identities=20% Similarity=0.484 Sum_probs=4.8
Q ss_pred HHhhcCCCcE
Q 031921 6 LLKTAQGHPM 15 (150)
Q Consensus 6 lL~~l~gk~V 15 (150)
||..+++..|
T Consensus 59 flh~Cegd~V 68 (215)
T KOG3262|consen 59 FLHMCEGDLV 68 (215)
T ss_pred hhhhcCCceE
Confidence 4455555444
No 45
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=96.24 E-value=0.014 Score=39.55 Aligned_cols=37 Identities=22% Similarity=0.391 Sum_probs=30.7
Q ss_pred HHhhcC--CCcEEEEEcCCcEEEEEEEEecCccceEEcc
Q 031921 6 LLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 6 lL~~l~--gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~d 42 (150)
||+.+. ..+|+|-|.||..+.|.+.+||.|+=+.-.+
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 565554 6889999999999999999999998665543
No 46
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=96.10 E-value=0.066 Score=43.97 Aligned_cols=7 Identities=29% Similarity=0.610 Sum_probs=3.3
Q ss_pred ecCcccc
Q 031921 70 RVPDEVI 76 (150)
Q Consensus 70 ~lpd~il 76 (150)
+-|+.+|
T Consensus 127 i~p~Kll 133 (215)
T KOG3262|consen 127 IDPDKLL 133 (215)
T ss_pred ecccccC
Confidence 3455553
No 47
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=96.09 E-value=0.016 Score=39.38 Aligned_cols=38 Identities=24% Similarity=0.324 Sum_probs=31.0
Q ss_pred HHHhhcC--CCcEEEEEcCCcEEEEEEEEecCccceEEcc
Q 031921 5 SLLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 5 ~lL~~l~--gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~d 42 (150)
.||+.+. ..+|+|-|.||..+.|.+.+||.|+=+.-.+
T Consensus 6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 3555553 7889999999999999999999998666543
No 48
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.74 E-value=0.025 Score=40.21 Aligned_cols=38 Identities=18% Similarity=0.353 Sum_probs=30.9
Q ss_pred HHHhhcC--CCcEEEEEcCCcEEEEEEEEecCccceEEcc
Q 031921 5 SLLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 5 ~lL~~l~--gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~d 42 (150)
.||+.+. ..+|+|-|.||..+.|.+.+||.|+=|...+
T Consensus 10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 3555553 7899999999999999999999998666544
No 49
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=95.42 E-value=0.071 Score=37.49 Aligned_cols=61 Identities=23% Similarity=0.187 Sum_probs=47.4
Q ss_pred hhcCCCcEEEEEcCCcEEEEEEEEecC-ccceEEccEEEEccCCCe---------eeecCeEEEecCeEEE
Q 031921 8 KTAQGHPMLVELKNGETYNGHLVNCDT-WMNIHLREVICTSKDGDR---------FWRMPECYIRGNTIKY 68 (150)
Q Consensus 8 ~~l~gk~V~VeLKnG~~~~G~L~~vD~-~MNl~L~dv~et~~dg~~---------~~~l~~v~IRG~nIry 68 (150)
.+++|++|.+-.|.+..|+|+|.++|. ---|.|+||.+.-.++.+ ...++.+..||+.|+-
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 367899999999999999999999996 447889999977544321 1246777888887764
No 50
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=94.82 E-value=0.15 Score=32.14 Aligned_cols=31 Identities=19% Similarity=0.155 Sum_probs=27.6
Q ss_pred CCCcEEEEEcCCcEEEEEEEEecCccceEEcc
Q 031921 11 QGHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~d 42 (150)
+|++|+|++ ++..++|+...+|+.=.|.|+.
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~ 32 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRT 32 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEE
Confidence 689999999 7777799999999999998865
No 51
>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=94.76 E-value=0.15 Score=40.74 Aligned_cols=62 Identities=26% Similarity=0.312 Sum_probs=43.3
Q ss_pred HHhhcCCCcEEEEEcCCcEEEEEEEEecC-ccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccc
Q 031921 6 LLKTAQGHPMLVELKNGETYNGHLVNCDT-WMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEV 75 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG~~~~G~L~~vD~-~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lpd~i 75 (150)
.+..+++|.|.|.+.| ++|.|.|..+|+ .-||+|-+-.+ +++. .--+|-|.+|+.|.+-++.
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~~----sv~~I~ghaVk~vevl~~~ 73 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGKR----SVKVIMGHAVKSVEVLSEG 73 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS-E----EEEEE-GGGEEEEEEEE--
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCce----eEEEEEccceEEEEEccCC
Confidence 4678999999999999 999999999996 66998875543 3432 2478999999999876553
No 52
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.01 E-value=0.087 Score=46.71 Aligned_cols=70 Identities=23% Similarity=0.223 Sum_probs=55.4
Q ss_pred HHhhcCCCcEEEEEcCCcEEEEEEEEec-CccceEEccEEEEccCCCe---------eeecCeEEEecCeEEEEecCccc
Q 031921 6 LLKTAQGHPMLVELKNGETYNGHLVNCD-TWMNIHLREVICTSKDGDR---------FWRMPECYIRGNTIKYLRVPDEV 75 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG~~~~G~L~~vD-~~MNl~L~dv~et~~dg~~---------~~~l~~v~IRG~nIryI~lpd~i 75 (150)
+...++|+.|.+.-|++..|+|+|..+| +-.=|-|++|.++-.++.+ ...++.|+.||+.|+-|.+-+..
T Consensus 3 ~~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p 82 (361)
T KOG1073|consen 3 LVTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETP 82 (361)
T ss_pred cccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCc
Confidence 3467899999999999999999999999 4668999999766443321 02578999999999988765533
No 53
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=93.96 E-value=0.11 Score=36.76 Aligned_cols=34 Identities=21% Similarity=0.398 Sum_probs=28.6
Q ss_pred HHHhhc--CCCcEEEEEcCCcEEEEEEEEecCccce
Q 031921 5 SLLKTA--QGHPMLVELKNGETYNGHLVNCDTWMNI 38 (150)
Q Consensus 5 ~lL~~l--~gk~V~VeLKnG~~~~G~L~~vD~~MNl 38 (150)
.||.++ ...+|+|-|.||..+.|.+.+||.|.=|
T Consensus 10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~Vl 45 (77)
T COG1923 10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVL 45 (77)
T ss_pred HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEE
Confidence 466665 4789999999999999999999998633
No 54
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=92.52 E-value=1.1 Score=30.76 Aligned_cols=52 Identities=25% Similarity=0.448 Sum_probs=38.6
Q ss_pred HHHHhhcCCCcEEEEEcCCcEEEEEEEEecC-ccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031921 4 LSLLKTAQGHPMLVELKNGETYNGHLVNCDT-WMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 4 l~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~-~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
+..|++++|++|.|++..|+. +|+|.++.. |. +|+. ++ ..+|||=.+|.+|.
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~------~~------~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEE------NG------TPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEe------CC------cEEEEEeeeEEEEc
Confidence 567999999999999977776 999999874 33 3222 12 33678888888874
No 55
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=91.92 E-value=0.38 Score=38.50 Aligned_cols=37 Identities=24% Similarity=0.451 Sum_probs=30.4
Q ss_pred HHhhcC--CCcEEEEEcCCcEEEEEEEEecCccceEEcc
Q 031921 6 LLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 6 lL~~l~--gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~d 42 (150)
||+.+. ..+|+|-|.||..+.|++.+||.|+=|...+
T Consensus 96 fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 96 FLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 555553 6889999999999999999999998666544
No 56
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=91.11 E-value=0.53 Score=37.72 Aligned_cols=38 Identities=18% Similarity=0.292 Sum_probs=30.9
Q ss_pred HHHhhcC--CCcEEEEEcCCcEEEEEEEEecCccceEEcc
Q 031921 5 SLLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 5 ~lL~~l~--gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~d 42 (150)
.||+.+. ..+|+|-|.||..+.|++.+||.|.=|...+
T Consensus 15 ~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~ 54 (165)
T PRK14091 15 IFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRD 54 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 3555554 6789999999999999999999998666544
No 57
>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=89.56 E-value=1.8 Score=29.22 Aligned_cols=31 Identities=13% Similarity=0.127 Sum_probs=27.3
Q ss_pred cCCCcEEEEEcCCcEEEEEEEEecCccceEE
Q 031921 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L 40 (150)
.+|..|.+++..|.+++|.|.+||..-++.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lI 34 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLI 34 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEE
Confidence 4789999999999999999999998776553
No 58
>PRK14639 hypothetical protein; Provisional
Probab=87.42 E-value=1.4 Score=33.93 Aligned_cols=35 Identities=23% Similarity=0.397 Sum_probs=29.7
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEE
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L 40 (150)
.-++.++|+.|.|+|++...+.|+|.++|.. ++.|
T Consensus 81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 4567889999999999999999999999973 4444
No 59
>PRK14638 hypothetical protein; Provisional
Probab=86.90 E-value=1.2 Score=34.72 Aligned_cols=35 Identities=17% Similarity=0.194 Sum_probs=29.2
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEE
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L 40 (150)
.-+..++|+.|.|+|++...++|+|.++|.- +++|
T Consensus 93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 3467889999999999999999999999963 3444
No 60
>PRK02001 hypothetical protein; Validated
Probab=86.60 E-value=1.7 Score=34.13 Aligned_cols=34 Identities=32% Similarity=0.415 Sum_probs=28.9
Q ss_pred HHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEE
Q 031921 6 LLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L 40 (150)
-+..++|+.|.|.|.+...+.|+|.++|.. +++|
T Consensus 84 ~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 84 QYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred HHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 467889999999999999999999999974 3444
No 61
>PRK14644 hypothetical protein; Provisional
Probab=80.81 E-value=3.7 Score=31.50 Aligned_cols=35 Identities=23% Similarity=0.312 Sum_probs=29.2
Q ss_pred HHhhcCCCcEEEEEcCC----cEEEEEEEEecCccceEEc
Q 031921 6 LLKTAQGHPMLVELKNG----ETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG----~~~~G~L~~vD~~MNl~L~ 41 (150)
-+..++|+.|.|+|++. ..+.|+|.++|.. ++.|.
T Consensus 79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 47788999999999887 9999999999973 44443
No 62
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=80.53 E-value=1.2 Score=34.13 Aligned_cols=27 Identities=26% Similarity=0.641 Sum_probs=16.1
Q ss_pred eecCeEEEecCeEE----EEecCccccchhH
Q 031921 54 WRMPECYIRGNTIK----YLRVPDEVIDKVQ 80 (150)
Q Consensus 54 ~~l~~v~IRG~nIr----yI~lpd~ild~~~ 80 (150)
|..--.++-=.=|. |++||++++.+..
T Consensus 62 WrhyYw~LT~eGieyLR~yL~LP~eivP~T~ 92 (124)
T PTZ00034 62 WQHYYYYLTDEGIEYLRTYLHLPPDVFPATH 92 (124)
T ss_pred eEEEEEEEchHHHHHHHHHhCCCcccCchhh
Confidence 44444445444443 5789999876554
No 63
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=80.23 E-value=4.2 Score=40.79 Aligned_cols=18 Identities=22% Similarity=0.804 Sum_probs=14.2
Q ss_pred EEEEE-EEEecCccceEEc
Q 031921 24 TYNGH-LVNCDTWMNIHLR 41 (150)
Q Consensus 24 ~~~G~-L~~vD~~MNl~L~ 41 (150)
+.-|. |+-+|+|.+|.++
T Consensus 1073 qsdgq~IV~VDdWIklqIs 1091 (1282)
T KOG0921|consen 1073 QSDGQGIVRVDDWIKLQIS 1091 (1282)
T ss_pred cccCcceEEeeceeeEecc
Confidence 34566 8889999999876
No 64
>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=79.39 E-value=3.9 Score=28.33 Aligned_cols=31 Identities=26% Similarity=0.423 Sum_probs=26.0
Q ss_pred HHHhhcCCCcEEEEEc---CC-cEEEEEEEEecCc
Q 031921 5 SLLKTAQGHPMLVELK---NG-ETYNGHLVNCDTW 35 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK---nG-~~~~G~L~~vD~~ 35 (150)
.-+..++|+.|.|+|+ ++ ..+.|+|.++|..
T Consensus 18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 3467889999999997 55 6899999999973
No 65
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.00 E-value=6.2 Score=31.09 Aligned_cols=33 Identities=18% Similarity=0.290 Sum_probs=29.0
Q ss_pred HHHHhhcCCCcEEEEE----cCCcEEEEEEEEecCcc
Q 031921 4 LSLLKTAQGHPMLVEL----KNGETYNGHLVNCDTWM 36 (150)
Q Consensus 4 l~lL~~l~gk~V~VeL----KnG~~~~G~L~~vD~~M 36 (150)
..-+..++|+.|.|+| .+.+.+.|+|..+|.-+
T Consensus 91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 3457788999999999 77899999999999876
No 66
>PRK14642 hypothetical protein; Provisional
Probab=78.79 E-value=4.5 Score=33.15 Aligned_cols=67 Identities=13% Similarity=0.149 Sum_probs=41.7
Q ss_pred HHHhhcCCCcEEEEEc-------------CCcEEEEEEEEecCccceEE--ccEEEEccCC----C--eeeecCeEEEec
Q 031921 5 SLLKTAQGHPMLVELK-------------NGETYNGHLVNCDTWMNIHL--REVICTSKDG----D--RFWRMPECYIRG 63 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK-------------nG~~~~G~L~~vD~~MNl~L--~dv~et~~dg----~--~~~~l~~v~IRG 63 (150)
.-+..++|+.|.|.|+ +.+.|+|+|.++|.. ++.| ++.-+- +++ + ....+..+-|-=
T Consensus 93 ~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l~~~~~~~~-k~g~~~~k~~~~~~~~~~~~~~ 170 (197)
T PRK14642 93 QDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQIVWSDEPPV-KPGQRVSKKRVPAPLQALGFTL 170 (197)
T ss_pred HHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEEEEeecccC-CCccccccccccccceeEEeeh
Confidence 3467788999999998 779999999999974 4444 322111 112 1 112334555666
Q ss_pred CeEEEEecCc
Q 031921 64 NTIKYLRVPD 73 (150)
Q Consensus 64 ~nIryI~lpd 73 (150)
+.|++..|..
T Consensus 171 ~eik~a~l~p 180 (197)
T PRK14642 171 DELREARLAP 180 (197)
T ss_pred hheeeEEEEE
Confidence 6666666544
No 67
>PRK14640 hypothetical protein; Provisional
Probab=76.78 E-value=5.9 Score=30.75 Aligned_cols=35 Identities=20% Similarity=0.262 Sum_probs=28.1
Q ss_pred HHHhhcCCCcEEEEE----cCCcEEEEEEEEecCccceEE
Q 031921 5 SLLKTAQGHPMLVEL----KNGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeL----KnG~~~~G~L~~vD~~MNl~L 40 (150)
.-++.++|+.|.|.| .+.+.+.|+|.++|.. ++.|
T Consensus 90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 346788999999999 4679999999999974 3444
No 68
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=76.53 E-value=10 Score=29.16 Aligned_cols=30 Identities=20% Similarity=0.350 Sum_probs=26.0
Q ss_pred HHHhhcCCCcEEEEE----cCCcEEEEEEEEecC
Q 031921 5 SLLKTAQGHPMLVEL----KNGETYNGHLVNCDT 34 (150)
Q Consensus 5 ~lL~~l~gk~V~VeL----KnG~~~~G~L~~vD~ 34 (150)
.-+..++|+.|.|+| .+...+.|+|.++|.
T Consensus 91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 456788999999998 467899999999997
No 69
>PRK11625 Rho-binding antiterminator; Provisional
Probab=75.26 E-value=20 Score=25.66 Aligned_cols=57 Identities=19% Similarity=0.198 Sum_probs=35.1
Q ss_pred HhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecC
Q 031921 7 LKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVP 72 (150)
Q Consensus 7 L~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lp 72 (150)
|..+.+.+|.++|+||++++|+. .|-+.+ +.+++...+.+ =....||=++|..|+=|
T Consensus 18 lAC~~~~~l~l~l~dGe~~~g~A--~D~~~~---~k~EyL~l~~~----g~~~~iRLD~I~s~~~~ 74 (84)
T PRK11625 18 LACQHHLMLTLELKDGEVLQAKA--SDLVSR---KNVEYLVVEAA----GETRELRLDKIASFSHP 74 (84)
T ss_pred HHHhcCCeEEEEECCCCEEEEEE--EeeecC---CceEEEEEEcC----CCEEEEEeeeEeeccCc
Confidence 44557899999999999999987 455533 44444322111 12334666666666633
No 70
>PRK14632 hypothetical protein; Provisional
Probab=72.00 E-value=6.5 Score=31.24 Aligned_cols=35 Identities=14% Similarity=0.285 Sum_probs=28.2
Q ss_pred HHHhhcCCCcEEEEEcC-------CcEEEEEEEEecCccceEE
Q 031921 5 SLLKTAQGHPMLVELKN-------GETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKn-------G~~~~G~L~~vD~~MNl~L 40 (150)
.-++.++|+.|.|+|++ ...+.|+|.++|.. +++|
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l 132 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL 132 (172)
T ss_pred HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence 34678899999999986 57999999999863 4444
No 71
>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=71.75 E-value=7.1 Score=29.45 Aligned_cols=30 Identities=23% Similarity=0.418 Sum_probs=23.6
Q ss_pred HHHhhcCCCcEEEEEc----CCcEEEEEEEEecC
Q 031921 5 SLLKTAQGHPMLVELK----NGETYNGHLVNCDT 34 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK----nG~~~~G~L~~vD~ 34 (150)
.-+..++|+.|.|+|+ +...+.|+|.++|.
T Consensus 80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 4577889999999994 45799999999998
No 72
>PRK14633 hypothetical protein; Provisional
Probab=70.50 E-value=7.8 Score=30.07 Aligned_cols=35 Identities=14% Similarity=0.137 Sum_probs=28.0
Q ss_pred HHHhhcCCCcEEEEEc----CCcEEEEEEEEecCccceEE
Q 031921 5 SLLKTAQGHPMLVELK----NGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK----nG~~~~G~L~~vD~~MNl~L 40 (150)
.-++.++|+.|.|+|+ +...++|+|.++|.. ++.|
T Consensus 87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 4567889999999994 569999999999974 4444
No 73
>PRK14643 hypothetical protein; Provisional
Probab=69.48 E-value=9.7 Score=30.10 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=28.5
Q ss_pred HHHhhcCCCcEEEEEcC----CcEEEEEEEEecCc-cceEE
Q 031921 5 SLLKTAQGHPMLVELKN----GETYNGHLVNCDTW-MNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKn----G~~~~G~L~~vD~~-MNl~L 40 (150)
.-++.++|+.|.|.|+. ...+.|+|.++|.- ..|.|
T Consensus 97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 35678899999999976 59999999999964 34443
No 74
>PRK14636 hypothetical protein; Provisional
Probab=69.30 E-value=7.6 Score=31.06 Aligned_cols=30 Identities=23% Similarity=0.422 Sum_probs=25.8
Q ss_pred HHHhhcCCCcEEEEEc---CC-cEEEEEEEEecC
Q 031921 5 SLLKTAQGHPMLVELK---NG-ETYNGHLVNCDT 34 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK---nG-~~~~G~L~~vD~ 34 (150)
.-+..++|+.|.|+|+ ++ +.++|+|.++|.
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~ 124 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDG 124 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeC
Confidence 3467889999999997 55 799999999987
No 75
>PRK14645 hypothetical protein; Provisional
Probab=69.16 E-value=8 Score=30.29 Aligned_cols=30 Identities=17% Similarity=0.188 Sum_probs=25.7
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCc
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTW 35 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~ 35 (150)
.-+..++|++|.|.+ ++..+.|+|.++|..
T Consensus 95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 346788999999986 789999999999974
No 76
>PRK14634 hypothetical protein; Provisional
Probab=68.69 E-value=8.5 Score=30.04 Aligned_cols=35 Identities=17% Similarity=0.355 Sum_probs=27.4
Q ss_pred HHHhhcCCCcEEEEEcCC----cEEEEEEEEecCccceEE
Q 031921 5 SLLKTAQGHPMLVELKNG----ETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG----~~~~G~L~~vD~~MNl~L 40 (150)
.-++.++|+.|.|+|++. ..|.|+|.++|.- ++.|
T Consensus 93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 346788999999999743 7999999999973 3444
No 77
>PRK14647 hypothetical protein; Provisional
Probab=67.79 E-value=9.2 Score=29.86 Aligned_cols=30 Identities=17% Similarity=0.142 Sum_probs=25.7
Q ss_pred HHHhhcCCCcEEEEEc---------CCcEEEEEEEEecC
Q 031921 5 SLLKTAQGHPMLVELK---------NGETYNGHLVNCDT 34 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK---------nG~~~~G~L~~vD~ 34 (150)
.-++.++|+.|.|+|+ +.+.+.|+|.++|.
T Consensus 92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 4567889999999996 35899999999996
No 78
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=67.60 E-value=8.6 Score=34.70 Aligned_cols=12 Identities=25% Similarity=0.329 Sum_probs=5.2
Q ss_pred EecCeEEEEecC
Q 031921 61 IRGNTIKYLRVP 72 (150)
Q Consensus 61 IRG~nIryI~lp 72 (150)
=||-.--.+..|
T Consensus 304 DRGGR~nE~~pp 315 (465)
T KOG3973|consen 304 DRGGRTNEMVPP 315 (465)
T ss_pred CCCCCcccCCCC
Confidence 355444444433
No 79
>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=66.62 E-value=5.1 Score=28.30 Aligned_cols=30 Identities=30% Similarity=0.405 Sum_probs=18.2
Q ss_pred HHhhcCCCcEEEEEcCCcEEEEEEEEecCccc
Q 031921 6 LLKTAQGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MN 37 (150)
.|..+...+|.++|+||+++.|+ +.|...|
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 35667899999999999999997 4444444
No 80
>PRK14637 hypothetical protein; Provisional
Probab=66.35 E-value=14 Score=28.82 Aligned_cols=35 Identities=14% Similarity=0.172 Sum_probs=26.1
Q ss_pred HHHhhcCCCcEEEEEcCCcEE-EEEEEEecCccceEE
Q 031921 5 SLLKTAQGHPMLVELKNGETY-NGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~-~G~L~~vD~~MNl~L 40 (150)
.-+..++|+.|.|+|.+...+ +|+|.++|.. ++.|
T Consensus 91 ~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 91 AEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred HHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 456788999999999544455 7999999974 3433
No 81
>PRK14646 hypothetical protein; Provisional
Probab=66.27 E-value=10 Score=29.61 Aligned_cols=35 Identities=29% Similarity=0.326 Sum_probs=27.6
Q ss_pred HHHhhcCCCcEEEEEcCC----cEEEEEEEEecCccceEE
Q 031921 5 SLLKTAQGHPMLVELKNG----ETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG----~~~~G~L~~vD~~MNl~L 40 (150)
.-++.++|+.|.|+|++. ..++|+|.++|.- +|+|
T Consensus 93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 456788999999999652 7889999999974 4444
No 82
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=64.37 E-value=20 Score=28.02 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=23.9
Q ss_pred hhcCCCcEEEEEcCCcEEEEEEEEec
Q 031921 8 KTAQGHPMLVELKNGETYNGHLVNCD 33 (150)
Q Consensus 8 ~~l~gk~V~VeLKnG~~~~G~L~~vD 33 (150)
.+++||.|++++.++..+.|++.++.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 46789999999999999999999987
No 83
>PRK06955 biotin--protein ligase; Provisional
Probab=63.08 E-value=27 Score=29.63 Aligned_cols=32 Identities=16% Similarity=0.099 Sum_probs=27.7
Q ss_pred cCCCcEEEEEcCCcEEEEEEEEecCccceEEc
Q 031921 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~ 41 (150)
.++++|+|...++.++.|++.++|+.=.|+|+
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 56999999766778899999999998888875
No 84
>PRK14641 hypothetical protein; Provisional
Probab=59.44 E-value=14 Score=29.58 Aligned_cols=29 Identities=17% Similarity=0.274 Sum_probs=24.6
Q ss_pred HHHhhcCCCcEEEEEcC----CcEEEEEEEEec
Q 031921 5 SLLKTAQGHPMLVELKN----GETYNGHLVNCD 33 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKn----G~~~~G~L~~vD 33 (150)
.-++.++|+.|.|.|++ ...++|+|.++|
T Consensus 97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 34678899999999976 468999999995
No 85
>PRK14631 hypothetical protein; Provisional
Probab=58.38 E-value=16 Score=29.17 Aligned_cols=29 Identities=21% Similarity=0.362 Sum_probs=25.3
Q ss_pred HHHhhcCCCcEEEEEc----CCcEEEEEEEEec
Q 031921 5 SLLKTAQGHPMLVELK----NGETYNGHLVNCD 33 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK----nG~~~~G~L~~vD 33 (150)
.-++.++|+.|.|+|+ +.+.++|+|.++|
T Consensus 110 ~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 110 EQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 4567889999999996 4599999999998
No 86
>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=57.93 E-value=21 Score=26.46 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=15.4
Q ss_pred CCcEEEEEcCCcEEEEEEE
Q 031921 12 GHPMLVELKNGETYNGHLV 30 (150)
Q Consensus 12 gk~V~VeLKnG~~~~G~L~ 30 (150)
...|.++|+||+.+.||+.
T Consensus 28 e~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 28 EERVELELDDGSMLRGTVA 46 (101)
T ss_dssp T-EEEEEETTS-EEEEEEC
T ss_pred cceEEEEEcCCCeeeeeec
Confidence 5689999999999999984
No 87
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=57.78 E-value=51 Score=31.04 Aligned_cols=26 Identities=8% Similarity=0.137 Sum_probs=15.1
Q ss_pred ecCeEEEecCeEEEEecCccccchhHH
Q 031921 55 RMPECYIRGNTIKYLRVPDEVIDKVQE 81 (150)
Q Consensus 55 ~l~~v~IRG~nIryI~lpd~ild~~~~ 81 (150)
.++.+-|.- +-.||.+|+++.+.+..
T Consensus 518 ~ig~i~i~~-~~s~v~~~~~~~~~~~~ 543 (629)
T PRK11634 518 YIGNIKLFA-SHSTIELPKGMPGEVLQ 543 (629)
T ss_pred hCCcEEEeC-CceEEEcChhhHHHHHH
Confidence 445555543 34678888877554444
No 88
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=56.40 E-value=18 Score=28.00 Aligned_cols=19 Identities=21% Similarity=0.504 Sum_probs=8.4
Q ss_pred ecCeEEEec-CeEEEEecCc
Q 031921 55 RMPECYIRG-NTIKYLRVPD 73 (150)
Q Consensus 55 ~l~~v~IRG-~nIryI~lpd 73 (150)
+|.+|.+-- +.-+|+.+|+
T Consensus 39 ~L~~Vi~ts~Dgdkf~r~pE 58 (134)
T KOG3293|consen 39 HLREVICTSEDGDKFFRMPE 58 (134)
T ss_pred chheeEEeccCCCceeecce
Confidence 344443332 2344555665
No 89
>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=56.29 E-value=26 Score=26.18 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=24.1
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEE
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGH 28 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~ 28 (150)
+|+..|+.+.+-+|+.||.||.+|...
T Consensus 64 ~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 64 TDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CCHHHHhCCcccEEEEEecCCcEEEec
Confidence 578889999999999999999999754
No 90
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=51.21 E-value=58 Score=27.50 Aligned_cols=31 Identities=13% Similarity=0.109 Sum_probs=26.8
Q ss_pred cCCCcEEEEEcCCcEEEEEEEEecCccceEEc
Q 031921 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~ 41 (150)
+.|+.|+|.. ++.+++|++..+|+.-.|+|+
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 4699999987 446799999999999999885
No 91
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=51.12 E-value=51 Score=31.01 Aligned_cols=32 Identities=19% Similarity=0.335 Sum_probs=27.7
Q ss_pred cCCCcEEEEEcCCcEEEEEEEEecCccceEEc
Q 031921 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~ 41 (150)
++|++|.|...+..+++|++..+|+.=.|.|+
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 56999998766677899999999999888885
No 92
>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=48.54 E-value=61 Score=19.90 Aligned_cols=25 Identities=20% Similarity=0.407 Sum_probs=21.7
Q ss_pred CCCcEEEEEcCCcEEEEEEEEecCc
Q 031921 11 QGHPMLVELKNGETYNGHLVNCDTW 35 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~vD~~ 35 (150)
.|+.|.+...++.-|++++++++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5788888887899999999999964
No 93
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=46.51 E-value=75 Score=24.77 Aligned_cols=26 Identities=19% Similarity=0.219 Sum_probs=23.1
Q ss_pred hcCCCcEEEEEcCCcEEEEEEEEecC
Q 031921 9 TAQGHPMLVELKNGETYNGHLVNCDT 34 (150)
Q Consensus 9 ~l~gk~V~VeLKnG~~~~G~L~~vD~ 34 (150)
+++||.|+..+.++..+.|++.++..
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEEE
Confidence 68899999888999999999998864
No 94
>PRK14630 hypothetical protein; Provisional
Probab=46.15 E-value=34 Score=26.34 Aligned_cols=29 Identities=17% Similarity=0.298 Sum_probs=23.8
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecC
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDT 34 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~ 34 (150)
.-++.++|++|.|.|+.. ...|+|.++|.
T Consensus 90 ~df~r~~G~~v~V~l~~~-~~~G~L~~~~d 118 (143)
T PRK14630 90 REFKIFEGKKIKLMLDND-FEEGFILEAKA 118 (143)
T ss_pred HHHHHhCCCEEEEEEcCc-ceEEEEEEEeC
Confidence 346788999999999664 45999999987
No 95
>PRK14635 hypothetical protein; Provisional
Probab=45.69 E-value=50 Score=25.83 Aligned_cols=35 Identities=26% Similarity=0.391 Sum_probs=26.3
Q ss_pred HHHhhcCCCcEEEEEc--CCcEEEE---EEEEecCccceEE
Q 031921 5 SLLKTAQGHPMLVELK--NGETYNG---HLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK--nG~~~~G---~L~~vD~~MNl~L 40 (150)
.-+..++|+.|.|.+. ++..+.| +|.++|.- ++.|
T Consensus 92 ~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 92 EDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 3467889999999986 4578887 99999864 3444
No 96
>PRK10898 serine endoprotease; Provisional
Probab=45.34 E-value=39 Score=29.36 Aligned_cols=59 Identities=15% Similarity=0.291 Sum_probs=39.4
Q ss_pred CcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecC--eEEEecCeEEEEecCcc
Q 031921 13 HPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMP--ECYIRGNTIKYLRVPDE 74 (150)
Q Consensus 13 k~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~--~v~IRG~nIryI~lpd~ 74 (150)
..+.|.+.|+.+|..+|+.+|..++|-|=.+... + -++..+. ...-.|..|..|-.|-.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~~~--~-l~~~~l~~~~~~~~G~~V~aiG~P~g 162 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKINAT--N-LPVIPINPKRVPHIGDVVLAIGNPYN 162 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEcCC--C-CCeeeccCcCcCCCCCEEEEEeCCCC
Confidence 5789999999999999999999999977655421 1 1111221 12335677777766643
No 97
>PRK08330 biotin--protein ligase; Provisional
Probab=44.89 E-value=85 Score=25.41 Aligned_cols=33 Identities=21% Similarity=0.252 Sum_probs=26.0
Q ss_pred hcCCCcEEEEEcCCcEE-EEEEEEecCccceEEcc
Q 031921 9 TAQGHPMLVELKNGETY-NGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 9 ~l~gk~V~VeLKnG~~~-~G~L~~vD~~MNl~L~d 42 (150)
..+|++|+|.. ++.++ .|++..+|+.=.|.|+.
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 35799999976 45554 79999999988888763
No 98
>PF07833 Cu_amine_oxidN1: Copper amine oxidase N-terminal domain; InterPro: IPR012854 Amine oxidases (AO) are enzymes that catalyse the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (1.4.3.4 from EC) and copper-containing (1.4.3.6 from EC). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor []: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen [, ]. In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling []. The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access. The two N-terminal domains share a common structural fold, its core consisting of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the stalk, of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other [, ]. This entry represents a domain found at the N-terminal of certain copper amine oxidases, as well as in related proteins such as cell wall hydrolase and N-acetylmuramoyl-L-alanine amidase. This domain consists of a five-stranded antiparallel beta-sheet twisted around an alpha helix [, ]. ; PDB: 1SPU_A 2WGQ_A 2WO0_A 1JRQ_A 1QAF_B 1D6U_B 1QAL_A 2WOF_A 1OAC_B 1QAK_A ....
Probab=44.44 E-value=64 Score=21.38 Aligned_cols=23 Identities=22% Similarity=0.326 Sum_probs=17.2
Q ss_pred CChHHHHhhcCCCcEEEEEcCCc
Q 031921 1 MLPLSLLKTAQGHPMLVELKNGE 23 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~ 23 (150)
|+|+.+|.+++|..|...-++.+
T Consensus 6 ~vPl~~i~~~lg~~v~~d~~~~~ 28 (93)
T PF07833_consen 6 YVPLRFIAEALGAKVSWDNKTKT 28 (93)
T ss_dssp EEEHHHHHHHHT-EEEEETTTTE
T ss_pred EEEHHHHHHHcCCEEEEEcCCcE
Confidence 68999999999998877544443
No 99
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=44.36 E-value=94 Score=27.51 Aligned_cols=12 Identities=17% Similarity=0.440 Sum_probs=6.5
Q ss_pred ecCeEEEEecCc
Q 031921 62 RGNTIKYLRVPD 73 (150)
Q Consensus 62 RG~nIryI~lpd 73 (150)
.|..|.+|...|
T Consensus 342 ~G~ai~l~~~~d 353 (456)
T PRK10590 342 TGEALSLVCVDE 353 (456)
T ss_pred CeeEEEEecHHH
Confidence 455666665443
No 100
>TIGR00567 3mg DNA-3-methyladenine glycosylase (3mg). This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine.
Probab=39.95 E-value=58 Score=26.57 Aligned_cols=35 Identities=20% Similarity=0.459 Sum_probs=29.8
Q ss_pred hHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccc
Q 031921 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MN 37 (150)
++.+=+.|+|+.+..++.++..+.|.|+.+..|+-
T Consensus 10 ~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 10 AVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred HHHHHHHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 34556789999999999989888999999999974
No 101
>PF13437 HlyD_3: HlyD family secretion protein
Probab=39.91 E-value=59 Score=22.33 Aligned_cols=33 Identities=21% Similarity=0.382 Sum_probs=26.6
Q ss_pred ChHHHHhhc--CCCcEEEEEcCC--cEEEEEEEEecC
Q 031921 2 LPLSLLKTA--QGHPMLVELKNG--ETYNGHLVNCDT 34 (150)
Q Consensus 2 lPl~lL~~l--~gk~V~VeLKnG--~~~~G~L~~vD~ 34 (150)
+|-..+..+ .|..|+|.+.++ ..+.|+|..++.
T Consensus 42 v~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 42 VPEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred EChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 455666676 699999999854 699999999998
No 102
>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=38.79 E-value=1e+02 Score=24.90 Aligned_cols=31 Identities=16% Similarity=0.083 Sum_probs=26.6
Q ss_pred cCCCcEEEEEcCCcEEEEEEEEecCccceEEc
Q 031921 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~ 41 (150)
.++++|+|...+ .++.|++..+|+.=.|.|+
T Consensus 191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 469999998755 5799999999999999886
No 103
>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=37.85 E-value=59 Score=28.13 Aligned_cols=59 Identities=14% Similarity=0.224 Sum_probs=38.6
Q ss_pred CcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeec--CeEEEecCeEEEEecCcc
Q 031921 13 HPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRM--PECYIRGNTIKYLRVPDE 74 (150)
Q Consensus 13 k~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l--~~v~IRG~nIryI~lpd~ 74 (150)
..+.|.+.|+..|.++|+.+|...+|-|=.+.... -++..+ ..-.-.|..|..|-.|-.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~~~~---~~~~~l~~s~~~~~G~~V~aiG~P~~ 162 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIEGDN---LPTIPVNLDRPPHVGDVVLAIGNPYN 162 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEecCCC---CceEeccCcCccCCCCEEEEEeCCCC
Confidence 46889999999999999999999999876554321 111112 112334666666666643
No 104
>PRK06789 flagellar motor switch protein; Validated
Probab=37.28 E-value=61 Score=22.61 Aligned_cols=36 Identities=19% Similarity=0.296 Sum_probs=27.5
Q ss_pred HhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEcc
Q 031921 7 LKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 7 L~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~d 42 (150)
|.++.+.+|.|.+++-..-+|.|+.+|..+=+.+.+
T Consensus 36 Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 36 LENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred eCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 455678888888888888888888888877665544
No 105
>PRK10139 serine endoprotease; Provisional
Probab=37.17 E-value=59 Score=29.34 Aligned_cols=61 Identities=13% Similarity=0.201 Sum_probs=40.5
Q ss_pred CCcEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecC--eEEEecCeEEEEecCcc
Q 031921 12 GHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMP--ECYIRGNTIKYLRVPDE 74 (150)
Q Consensus 12 gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~--~v~IRG~nIryI~lpd~ 74 (150)
...|.|.|.|+++|..+|+.+|...+|-|=.+... +.-++..+. .-+--|..|.-|-.|..
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~--~~l~~~~lg~s~~~~~G~~V~aiG~P~g 176 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNP--SKLTQIAIADSDKLRVGDFAVAVGNPFG 176 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEecCC--CCCceeEecCccccCCCCEEEEEecCCC
Confidence 35799999999999999999999999877555321 111112222 12334777777777754
No 106
>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=36.54 E-value=55 Score=26.23 Aligned_cols=34 Identities=18% Similarity=0.063 Sum_probs=30.8
Q ss_pred CCCcEEEEEcCCcEEEEEEEEecCccceEEccEE
Q 031921 11 QGHPMLVELKNGETYNGHLVNCDTWMNIHLREVI 44 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~ 44 (150)
-.-+|.|.+.||.++.+.+..|+.--|.+|.-+.
T Consensus 28 ~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 28 NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 3689999999999999999999999999987665
No 107
>cd01343 PL1_Passenger_AT Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases, SPATEs (serine protease autotransporters secreted by Enterobacteriaceae), Bordetella pertacins, and nonprotease autotransporters, TibA and similar AIDA-like proteins.
Probab=35.49 E-value=1.2e+02 Score=25.12 Aligned_cols=52 Identities=13% Similarity=0.222 Sum_probs=36.5
Q ss_pred cEEEEEcCCcEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEE
Q 031921 14 PMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYL 69 (150)
Q Consensus 14 ~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI 69 (150)
.+.+.|.++..+.|.+...+ -+|.|.+-..+...++. .+..+.+.+..|.|-
T Consensus 74 ~~~~~l~~~s~l~G~i~~~~--~~v~l~~~s~W~~tg~S--~v~~L~l~~g~v~f~ 125 (233)
T cd01343 74 LAELLLGGNAAWTGAIQGLN--ATVSLNLNSVWTLTGDS--NVNNLTLNGGTVDFN 125 (233)
T ss_pred eEEEEEcCCCEEEeEEeccc--ceEEEcCCCEEEEeCCc--ccceeEecCCEEEec
Confidence 68899999999999999988 55666633333344443 567777777777654
No 108
>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=34.82 E-value=68 Score=28.24 Aligned_cols=32 Identities=22% Similarity=0.394 Sum_probs=27.9
Q ss_pred CcEEEEEcCCcEEEEEEEEecCccceEEccEE
Q 031921 13 HPMLVELKNGETYNGHLVNCDTWMNIHLREVI 44 (150)
Q Consensus 13 k~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~ 44 (150)
..+.|.+.|+.+|..+|..+|..++|-|=.+.
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 56889999999999999999999998876554
No 109
>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=34.63 E-value=60 Score=24.12 Aligned_cols=21 Identities=24% Similarity=0.358 Sum_probs=18.5
Q ss_pred CcEEEEEcCCcEEEEEEEEec
Q 031921 13 HPMLVELKNGETYNGHLVNCD 33 (150)
Q Consensus 13 k~V~VeLKnG~~~~G~L~~vD 33 (150)
..+.|.|+||+++.|.|..=|
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASET 78 (133)
T ss_pred ccEEEEECCCCEEEEEEEecC
Confidence 458999999999999999855
No 110
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=34.17 E-value=50 Score=23.63 Aligned_cols=25 Identities=28% Similarity=0.410 Sum_probs=20.6
Q ss_pred HHhhcCCCcEEEEEcCCcEEEEEEE
Q 031921 6 LLKTAQGHPMLVELKNGETYNGHLV 30 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG~~~~G~L~ 30 (150)
.|..+..-+++.+||+|..|.++-.
T Consensus 17 ElACl~hl~l~L~lkdGev~~a~A~ 41 (84)
T COG4568 17 ELACLHHLPLTLELKDGEVLQAKAS 41 (84)
T ss_pred HHHHhhhceEEEEEcCCeEEEEEeh
Confidence 3556678899999999999999743
No 111
>PF02245 Pur_DNA_glyco: Methylpurine-DNA glycosylase (MPG); InterPro: IPR003180 Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA []. Its action is induced by alkylating chemotherapeutics, as well as deaminated and lipid peroxidation-induced purine adducts []. MPG without an N-terminal extension excises hypoxanthine with one-third of the efficiency of full-length MPG under similar conditions, suggesting that is function may largely be attributable to the N-terminal extension [].; GO: 0003677 DNA binding, 0003905 alkylbase DNA N-glycosylase activity, 0006284 base-excision repair; PDB: 1BNK_A 1F6O_A 3QI5_A 3UBY_B 1F4R_A 1EWN_A.
Probab=33.57 E-value=69 Score=25.87 Aligned_cols=34 Identities=15% Similarity=0.482 Sum_probs=25.8
Q ss_pred hHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccc
Q 031921 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MN 37 (150)
++.+=+.|+|+.+..++.++. +.|.|+.+..|+-
T Consensus 9 ~~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 9 TVEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp HHHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred HHHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 456668899999999999888 9999999988875
No 112
>PRK10942 serine endoprotease; Provisional
Probab=32.96 E-value=74 Score=28.89 Aligned_cols=32 Identities=22% Similarity=0.439 Sum_probs=27.7
Q ss_pred CCcEEEEEcCCcEEEEEEEEecCccceEEccE
Q 031921 12 GHPMLVELKNGETYNGHLVNCDTWMNIHLREV 43 (150)
Q Consensus 12 gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv 43 (150)
...|.|.|.|+++|..+++..|...+|-|=.+
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 35689999999999999999999999876544
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=30.25 E-value=99 Score=22.08 Aligned_cols=16 Identities=13% Similarity=0.071 Sum_probs=13.0
Q ss_pred HHHHhhcCCCcEEEEE
Q 031921 4 LSLLKTAQGHPMLVEL 19 (150)
Q Consensus 4 l~lL~~l~gk~V~VeL 19 (150)
-++|++++|++|+|--
T Consensus 7 ~~~L~~f~gk~V~ivG 22 (101)
T cd04479 7 GAMLSQFVGKTVRIVG 22 (101)
T ss_pred HHHHHhhCCCEEEEEE
Confidence 3689999999998763
No 114
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=29.91 E-value=1.1e+02 Score=24.25 Aligned_cols=35 Identities=17% Similarity=0.219 Sum_probs=26.9
Q ss_pred hHHHHhhc-CCCcEEEEEcCCcEEEEEEEEecCccc
Q 031921 3 PLSLLKTA-QGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 3 Pl~lL~~l-~gk~V~VeLKnG~~~~G~L~~vD~~MN 37 (150)
|-..+..+ .|.+|.|.+.++..+.|+|..++...+
T Consensus 132 ~~~~~~~i~~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 132 PAKDVSRIRKGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CHHHHhhCCCCCEEEEEECCCCEEEEEEEEEccccC
Confidence 44444444 489999999889999999999997553
No 115
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=28.05 E-value=56 Score=20.67 Aligned_cols=22 Identities=23% Similarity=0.300 Sum_probs=14.7
Q ss_pred EEEEEEEecCccceEEccEEEE
Q 031921 25 YNGHLVNCDTWMNIHLREVICT 46 (150)
Q Consensus 25 ~~G~L~~vD~~MNl~L~dv~et 46 (150)
..|+..++|+.+.+.|++...+
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6899999999999999886543
No 116
>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=27.68 E-value=67 Score=25.74 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=22.9
Q ss_pred CCCcEEEEEcCCcEEEEEEEEecCc
Q 031921 11 QGHPMLVELKNGETYNGHLVNCDTW 35 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~vD~~ 35 (150)
+++-|.|-|.||.+++|+-+++|..
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 5899999999999999999999864
No 117
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=27.25 E-value=1.3e+02 Score=25.51 Aligned_cols=30 Identities=17% Similarity=0.111 Sum_probs=25.8
Q ss_pred CCCcEEEEEcCCcEEEEEEEEecCccceEEc
Q 031921 11 QGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~ 41 (150)
.|+.|+|.. ++.++.|++..+|..=.|+|+
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 699999976 568899999999998888775
No 118
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=26.56 E-value=1.7e+02 Score=24.32 Aligned_cols=34 Identities=18% Similarity=0.187 Sum_probs=30.8
Q ss_pred cCCCcEEEEEcCCcEEEEEEEEecCccceEEccE
Q 031921 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREV 43 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv 43 (150)
.+|++|++++.++.+..|+...+|..-.|+|+..
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 4799999999999999999999999999888765
No 119
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=26.55 E-value=1.2e+02 Score=27.60 Aligned_cols=9 Identities=11% Similarity=0.139 Sum_probs=4.2
Q ss_pred ecCeEEEec
Q 031921 55 RMPECYIRG 63 (150)
Q Consensus 55 ~l~~v~IRG 63 (150)
+...|.+|.
T Consensus 316 k~~~I~vr~ 324 (419)
T KOG0116|consen 316 KEGGIQVRS 324 (419)
T ss_pred cccceEEec
Confidence 344455544
No 120
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=26.13 E-value=69 Score=25.61 Aligned_cols=27 Identities=22% Similarity=0.511 Sum_probs=23.1
Q ss_pred HhhcCCCcEEEEEcCCcEEEEEEEEec
Q 031921 7 LKTAQGHPMLVELKNGETYNGHLVNCD 33 (150)
Q Consensus 7 L~~l~gk~V~VeLKnG~~~~G~L~~vD 33 (150)
+..++|++|.|.|.....++|.+..++
T Consensus 23 ~~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 23 LKDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp CGGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hhHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 355899999999998899999999995
No 121
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=25.62 E-value=96 Score=25.45 Aligned_cols=26 Identities=12% Similarity=0.120 Sum_probs=22.8
Q ss_pred hcCCCcEEEEEcCCcEEEEEEEEecC
Q 031921 9 TAQGHPMLVELKNGETYNGHLVNCDT 34 (150)
Q Consensus 9 ~l~gk~V~VeLKnG~~~~G~L~~vD~ 34 (150)
+++||.|.+.-.++..+.|++.++.-
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~~ 140 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVRL 140 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEEE
Confidence 56899999988899999999998863
No 122
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=25.20 E-value=2.1e+02 Score=26.26 Aligned_cols=44 Identities=16% Similarity=0.183 Sum_probs=36.3
Q ss_pred ChHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccceEEccEEEE
Q 031921 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICT 46 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~et 46 (150)
.|-.++.+++||.|+- =|+|.+++++|.+-|.-.-+.+.|-++.
T Consensus 72 s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v 115 (421)
T COG5316 72 SPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEV 115 (421)
T ss_pred CchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEE
Confidence 5778999999999999 7999999999999997666666555544
No 123
>cd00540 AAG Alkyladenine DNA glycosylase (AAG), also known as 3-methyladenine DNA glycosylase, catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site. AAG bends DNA by intercalating between the base pairs, causing the damaged base to flip out of the double helix and into the enzyme active site for cleavage. Although AAG represents one of six DNA glycosylase classes, it lacks the helix-hairpin-helix active site motif associated with the other BER glycosylases and is structurally quite distinct from them.
Probab=25.12 E-value=1.4e+02 Score=23.96 Aligned_cols=35 Identities=14% Similarity=0.404 Sum_probs=28.6
Q ss_pred hHHHHhhcCCCcEEEEEcCCcEEEEEEEEecCccce
Q 031921 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNI 38 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~MNl 38 (150)
++.+=+.|+||.+..++. +.++.|.|+.+..|+--
T Consensus 6 ~~~vA~~LLGk~Lv~~~~-~~~~~grIvEtEAY~G~ 40 (179)
T cd00540 6 TVEVARDLLGKVLVRRLP-GGILSGRIVETEAYLGP 40 (179)
T ss_pred HHHHHHHhCCCEEEEECC-CCEEEEEEEEEeccCCC
Confidence 456668899999987775 66899999999999743
No 124
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=23.61 E-value=83 Score=21.32 Aligned_cols=24 Identities=21% Similarity=0.225 Sum_probs=19.0
Q ss_pred EEEEEEEEecC-ccceEEccEEEEc
Q 031921 24 TYNGHLVNCDT-WMNIHLREVICTS 47 (150)
Q Consensus 24 ~~~G~L~~vD~-~MNl~L~dv~et~ 47 (150)
..+|+|.++|. .|-|+|+|-+-+.
T Consensus 4 ~veG~I~~id~~~~titLdDGksy~ 28 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSYK 28 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEEE
Confidence 57899999996 6689998876543
No 125
>PF05037 DUF669: Protein of unknown function (DUF669); InterPro: IPR007731 This entry is represented by Streptococcus phage Sfi11, Gp151. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.93 E-value=54 Score=24.69 Aligned_cols=25 Identities=32% Similarity=0.558 Sum_probs=20.5
Q ss_pred HHHhhcCCCcEEEEEcCC-cEEEEEE
Q 031921 5 SLLKTAQGHPMLVELKNG-ETYNGHL 29 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG-~~~~G~L 29 (150)
.++..++|++|.|.++.. ..+.|+.
T Consensus 96 ~~~~~l~gk~l~V~v~~~~~e~nGk~ 121 (141)
T PF05037_consen 96 QFLNQLLGKPLRVTVKWEENEYNGKT 121 (141)
T ss_pred HHHHHHcCCeeEEEecccccCCCCcE
Confidence 467888999999999988 7777754
No 126
>PRK07228 N-ethylammeline chlorohydrolase; Provisional
Probab=22.39 E-value=1.5e+02 Score=25.83 Aligned_cols=35 Identities=14% Similarity=0.144 Sum_probs=21.3
Q ss_pred cceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031921 36 MNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 36 MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~ 70 (150)
|++.|+++..++.+......-..+.|.+..|..|.
T Consensus 1 ~~~~i~~~~vi~~~~~~~~~~g~V~I~dg~I~~vg 35 (445)
T PRK07228 1 MTILIKNAGIVTMNAKREIVDGDVLIEDDRIAAVG 35 (445)
T ss_pred CeEEEEccEEEecCCCcEecccEEEEECCEEEEec
Confidence 56777776655444332234466777777777764
No 127
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=21.86 E-value=1.2e+02 Score=21.70 Aligned_cols=28 Identities=21% Similarity=0.269 Sum_probs=23.1
Q ss_pred EEccCCCeeeecCeEEEecCeEEEEecCc
Q 031921 45 CTSKDGDRFWRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 45 et~~dg~~~~~l~~v~IRG~nIryI~lpd 73 (150)
|.+.+|+. ..-+++.+.|..+.-|.+|+
T Consensus 69 EFS~~G~~-ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 69 EFSSDGED-RYQGELVMLGRRLISVELPP 96 (97)
T ss_pred EEeCCChh-cceEEEEEECCeeeEEEcCC
Confidence 55567765 56799999999999999986
No 128
>KOG3199 consensus Nicotinamide mononucleotide adenylyl transferase [Coenzyme transport and metabolism]
Probab=20.97 E-value=30 Score=29.12 Aligned_cols=68 Identities=22% Similarity=0.408 Sum_probs=43.5
Q ss_pred CcEEEEEcCCcEEEEEEEEec---C--ccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccccchhHHHh
Q 031921 13 HPMLVELKNGETYNGHLVNCD---T--WMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQEET 83 (150)
Q Consensus 13 k~V~VeLKnG~~~~G~L~~vD---~--~MNl~L~dv~et~~dg~~~~~l~~v~IRG~nIryI~lpd~ild~~~~~~ 83 (150)
.-+.+..+.|.-+.=.|.+-| . .-|++++|.++. +.-.-.++..++-||-+|+|. +||.+++.+.+++
T Consensus 156 yGl~cv~r~gsD~~~~i~~~d~i~~~~~~~l~ikn~~~~--N~ISStklr~ai~r~~SVkYl-~PD~Vi~yI~~h~ 228 (234)
T KOG3199|consen 156 YGLVCVTREGSDVENFLSSHDIILEKRRNILHIKNEIVP--NDISSTKLRQAIRRGQSVKYL-TPDSVIEYIREHN 228 (234)
T ss_pred CcEEEEeccCCCHHHHHhccHHHHHhhcceEEEeeeeec--CCcchHHHHHHHHcCCeeEee-CcHHHHHHHHHhh
Confidence 444454555555555555555 2 237788887764 222224778888899999986 6888888776654
No 129
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=20.29 E-value=1.6e+02 Score=22.73 Aligned_cols=39 Identities=31% Similarity=0.340 Sum_probs=28.3
Q ss_pred CcEEEEEEEEec---CccceEEccEEEEccCCCeeeecCeEEEecCe
Q 031921 22 GETYNGHLVNCD---TWMNIHLREVICTSKDGDRFWRMPECYIRGNT 65 (150)
Q Consensus 22 G~~~~G~L~~vD---~~MNl~L~dv~et~~dg~~~~~l~~v~IRG~n 65 (150)
...+.|.+..+- -+||+.|.||. .++. ..-..+-||||+
T Consensus 82 d~~lvG~VqKvS~Lil~~~~~v~Dv~----tg~~-v~~~~~diRgnt 123 (140)
T PF11684_consen 82 DYVLVGEVQKVSNLILNMNVYVRDVE----TGKV-VRGRSVDIRGNT 123 (140)
T ss_pred CEEEEEEEechhhhheeeeEEEEECC----CCCE-EeeeeeeEecCc
Confidence 456778777666 48899999984 4554 456778899886
No 130
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=20.25 E-value=1.6e+02 Score=19.41 Aligned_cols=34 Identities=15% Similarity=0.402 Sum_probs=25.3
Q ss_pred CCCcEEEEEcCCcEEEEEEEEecCccceEEccEE
Q 031921 11 QGHPMLVELKNGETYNGHLVNCDTWMNIHLREVI 44 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~vD~~MNl~L~dv~ 44 (150)
....|.|.+.+-..+.|.|..++..+=+.+.+..
T Consensus 41 ~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~~ 74 (77)
T PF01052_consen 41 ADEPVELRVNGQPIFRGELGRVNGRLAVRITELI 74 (77)
T ss_dssp SSTEEEEEETTEEEEEEEEEEETTEEEEEEEEE-
T ss_pred CCCCEEEEECCEEEEEEEEEEECCEEEEEEEEEc
Confidence 3567888887778888888888887777766654
No 131
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=20.24 E-value=1.2e+02 Score=24.71 Aligned_cols=39 Identities=15% Similarity=0.194 Sum_probs=28.6
Q ss_pred HHHhhcCCCcEEEEEcCCcEEEEEEEEecCc-cceEEccE
Q 031921 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTW-MNIHLREV 43 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~vD~~-MNl~L~dv 43 (150)
.+|..-.|..|.|-.-++..|..+|..++.. ..+.+.+.
T Consensus 28 ~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i~~~ 67 (240)
T TIGR00046 28 RVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCELLEG 67 (240)
T ss_pred HcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEEEec
Confidence 3555667999998877899999999999854 34444433
Done!